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Yang Z, Cui X, Fan X, Ruan Y, Xiang Z, Ji L, Gao H, Zhang M, Shan S, Liu W. "Active carbon" is more advantageous to the bacterial community in the rice rhizosphere than "stable carbon". Comput Struct Biotechnol J 2024; 23:1288-1297. [PMID: 38560279 PMCID: PMC10978811 DOI: 10.1016/j.csbj.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Carbon materials are commonly used for soil carbon sequestration and fertilization, which can also affect crop growth by manipulating the rhizosphere bacterial community. However, the comparison of the differences between active carbon (e.g., organic fertilizers) and stable carbon (e.g., biochar) on rhizosphere microdomains is still unclear. Hence, a trial was implemented to explore the influence of control (CK, no fertilizer; NPK, chemical fertilizer), organic fertilizer (CF-O, organic fertilizer; CF-BO, biochar-based organic fertilizer) and biochar material (CF-B, perishable garbage biochar; CF-PMB, pig manure biochar) on the diversity, composition, and interaction of rice rhizosphere bacterial community through 16 S rRNA gene high-throughput sequencing. Our results demonstrate that organic fertilizer increases bacterial alpha-diversity compared to no-carbon supply treatment to the extend, whereas biochar has the opposite effect. The rhizosphere bacterial community composition showed pronounced variations among the various fertilization treatments. The relative abundance in Firmicutes decreased with organic fertilizer application, whereas that in Chloroflexi and Actinobacteria decreased with biochar application. Bacterial network analysis demonstrate that organic fertilizer enhances the complexity and key taxa of bacterial interactions, while biochar exhibits an opposing trend. The findings of our study indicate that organic fertilizer may contribute to a positive and advantageous impact on bacterial diversity and interaction in rice rhizosphere, whereas the influence of biochar is not as favorable and constructive. This study lays the foundation for elucidating the fate of the rhizosphere bacterial community following different carbon material inputs in the context of sustainable agricultural development.
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Affiliation(s)
- Zongkun Yang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xin Cui
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xiaoge Fan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yefeng Ruan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Zhennan Xiang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Lingfei Ji
- Department of Biology, University of York, York, UK
| | - Han Gao
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Min Zhang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Wenbo Liu
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
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Shu D, Banerjee S, Mao X, Zhang J, Cui W, Zhang W, Zhang B, Chen S, Jiao S, Wei G. Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174953. [PMID: 39069174 DOI: 10.1016/j.scitotenv.2024.174953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/07/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.
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Affiliation(s)
- Duntao Shu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo 58102, ND, USA
| | - Xinyi Mao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Jiaqi Zhang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Weili Cui
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Wu Zhang
- Heihe Branch, Heilongjiang Academy of Agricultural Sciences, Heihe, Heilongjiang 150086, China
| | - Baogang Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Sanfeng Chen
- College of Biological Sciences, China Agricultural University, Beijing 100091, China
| | - Shuo Jiao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
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Lu Q, An Z, Zhang B, Lu X, Mao X, Li J, Chang SX, Liu Y, Fu X. Optimizing tradeoff strategies of soil microbial community between metabolic efficiency and resource acquisition along a natural regeneration chronosequence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174337. [PMID: 38964388 DOI: 10.1016/j.scitotenv.2024.174337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/09/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
The tradeoff between community-level soil microbial metabolic efficiency and resource acquisition strategies during natural regeneration remains unclear. Herein, we examined variations in soil extracellular enzyme activity, microbial metabolic quotient (qCO2), and microbial carbon use efficiency (CUE) along a chronosequence of natural regeneration by sampling secondary forests at 1, 10, 20, 30, 40, and 100 years after rubber plantation (RP) clearance. The results showed that the natural logarithms of carbon (C)-, nitrogen (N)-, and phosphorus (P)-acquiring enzyme activities were 1:1.68:1.37 and 1:1.54:1.38 in the RP and secondary forests, respectively, thus demonstrating that microbial metabolism was co-limited by N and P. Moreover, the soil microbial C limitation initially increased (1-40 years) and later decreased (100 years). Overall, the qCO2 increased, decreased, and then increased again in the initial (< 10 years), middle (10-40 years), and late (100 years) successional stages, respectively. Except for specific P-acquiring enzyme activities, the changes in other indicators with natural regeneration were consistent in the dry and wet seasons. Both qCO2 and CUE were mainly predicted by microbial community composition and physiological traits. These results indicate that soil microbial communities could employ tradeoff strategies between metabolic efficiency and resource acquisition to cope with variations in resources. Our findings provide new information on tradeoff strategies between metabolic efficiency and resource acquisition during natural regeneration.
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Affiliation(s)
- Qiang Lu
- State Environmental Protection Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Zhengfeng An
- Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Beibei Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaoqiang Lu
- State Environmental Protection Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Xia Mao
- Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China
| | - Jiaqi Li
- State Environmental Protection Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Scott X Chang
- Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Yan Liu
- State Environmental Protection Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China.
| | - Xiangxiang Fu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
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Reif J, Gamero A, Hološková A, Aunins A, Chodkiewicz T, Hristov I, Kurlavičius P, Leivits M, Szép T, Voříšek P. Accelerated farmland bird population declines in European countries after their recent EU accession. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174281. [PMID: 38936735 DOI: 10.1016/j.scitotenv.2024.174281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/20/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Agricultural intensification is a major driver of global biodiversity loss. In Europe, intensification progressed over the 20th century and was accelerated by instruments of the EU's Common Agricultural Policy. Central and Eastern European (CEE) countries standing outside the EU until the beginning of the 21st century employed less intensive farming and are considered one of the continent's farmland biodiversity strongholds. Their recent EU accession might be either viewed as a threat to farmland biodiversity due to the availability of funds to increase agricultural production or as an opportunity to implement conservation measures aimed to preserve biodiversity. Here we assessed these possibilities using long-term monitoring data on farmland bird populations in seven CEE countries. We tested whether mean relative abundance and population trends changed after countries' EU accession, and whether such changes also occurred in agricultural management and conservation measures. Both agricultural intensity and spending for agri-environmental and climatic schemes increased when the CEE countries joined the EU. At the same time, farmland bird populations started to decline and their relative abundance was lower after than before EU accession. In addition, increases in fertilizer application were negatively associated with annual changes in relative farmland bird population sizes, indicating a negative impact of intensive agriculture. Taken together, these results indicate that despite the great power of the EU's environmental legislation to improve the population status of species at risk, this does not apply to farmland birds. In their case, the adverse impacts of agricultural intensification most likely overrode the possible benefits of conservation measures. To secure this region as one of the continent's farmland biodiversity strongholds, policy and management actions are urgently needed.
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Affiliation(s)
- Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czechia; Department of Zoology, Faculty of Science, Palacký University, Olomouc, Czechia.
| | - Anna Gamero
- Czech Society for Ornithology/Pan-European Common Bird Monitoring Scheme, Prague, Czechia
| | - Adriana Hološková
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czechia
| | - Ainars Aunins
- Department of Zoology and Animal Ecology, Faculty of Biology, University of Latvia, Jelgavas iela 1, Riga LV-1004, Latvia; Latvian Ornithological Society, Skolas iela 3, Riga LV-1010, Latvia
| | - Tomasz Chodkiewicz
- Museum & Institute of Zoology, Polish Academy of Sciences, Warszawa, Poland; Polish Society for the Protection of Birds (OTOP), Marki, Poland
| | - Iordan Hristov
- Bulgarian Society for the Protection of Birds/BirdLife Bulgaria, Sofia, Bulgaria
| | - Petras Kurlavičius
- Vytautas Magnus University, Kaunas, Lithuania; Lithuanian Ornithological Society (LOD), Vilnius, Lithuania
| | - Meelis Leivits
- Estonian Environment Agency, Nigula Nature Centre, 86107 Reinu village, Estonia
| | - Tibor Szép
- University of Nyíregyháza, Nyíregyháza, Hungary
| | - Petr Voříšek
- Czech Society for Ornithology/European Bird Census Council, Prague, Czechia
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Xu H, Zou Z, Jin Y, Kuzyakov Y, Huang X, Wu X, Zhu F. Assembly processes and co-occurrence of bacterial communities in tree rhizosphere under Pb-Zn contamination. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135135. [PMID: 38986409 DOI: 10.1016/j.jhazmat.2024.135135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Rhizosphere bacteria are critical for supporting plant performance in stressful environments. Understanding the assembly and co-occurrence of rhizosphere bacterial communities contributes significantly to both plant growth and heavy metal accumulation. In this study, Ligustrum lucidum and Melia azedarach were planted in soils with simulated varying levels of Pb-Zn contamination. The Rhizosphere bacterial communities were investigated by using 16S rRNA gene sequencing. The impacts of Pb-Zn contamination on the diversity and structure of the rhizosphere bacterial community were found to be greater than those of both tree species. The variation in bacterial community structure in both trees was mainly driven by the combinations of Pb-Zn and soil properties. Deterministic processes (non-planted, 82 %; L. lucidum, 73 %; M. azedarach, 55 %) proved to be the most important assembly processes for soil bacterial communities, but both trees increased the importance of stochastic processes (18 %, 27 %, 45 %). The rhizosphere co-occurrence networks exhibited greater stability compared to the non-planted soil networks. Rare taxa played a dominant role in maintaining the stability of rhizosphere networks, as most of the keystone taxa within rhizosphere networks belonged to rare taxa. Dissimilarities in the structure and network complexity of rhizosphere bacterial communities were significantly associated with differences in tree biomass and metal accumulation. These variations in response varied between both trees, with L. lucidum exhibiting greater potential for phytoremediation in its rhizosphere compared to M. azedarach. Our results offer valuable insights for designing effective microbe-assisted phytoremediation systems.
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Affiliation(s)
- Hongyang Xu
- College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Ziying Zou
- School of Geographical Sciences, Hunan Normal University, Changsha 410081, China
| | - Yuke Jin
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha 410125, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen 37077, Germany; Peoples Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Xinhao Huang
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha 410125, China
| | - Xiaohong Wu
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
| | - Fan Zhu
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha 410125, China.
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Lu Y, Xu J, Feng Y, Jiang J, Wu C, Chen Y. How can the microbial community in watershed sediment maintain its resistance in the presence of shifting antibiotic residuals? JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122242. [PMID: 39163669 DOI: 10.1016/j.jenvman.2024.122242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/04/2024] [Accepted: 08/16/2024] [Indexed: 08/22/2024]
Abstract
The widespread presence of antibiotics in global watershed environments poses a serious threat to public health and ecosystems. It is essential to examine the resistance of microbial communities in watershed environments in response to shifting antibiotic residues. Sediment samples were collected from seven sites across a watershed, encompassing surface sediment (0-10 cm) and bottom sediment (30-40 cm) depths. The aim was to replicate exposure scenarios to different antibiotics (oxytetracycline (OTC) and sulfadiazine (SD)) at varying concentrations (0, 10, and 100 μg/L) in sediment overlying water, within controlled laboratory settings. The study findings revealed significant variations in the microbial community structure of sediments between different treatments, with distinct differences observed in the upper stream and top sediment layers compared to the sediments located downstream and in the bottom layers. After the introduction of antibiotics, a significant decrease in microbial nodes was observed in the genus-level co-occurrence network analysis of the bottom sediment layer, particularly in the OTC treatment groups. In contrast, the downstream region displayed more robust correlations among the top 20 genera than the upstream area. There was no significant variance observed in the expression of Antibiotic resistance genes (ARGs), consisting of tetracycline resistance genes (tetC, tetG, tetM, tetW, and tetX) and sulfonamide resistance genes (sul1, sul2, and sul3), between sediments in the top and bottom layers. Nevertheless, downstream samples exhibited significantly higher levels of ARGs when compared to upstream samples. Network correlation analysis indicated notably lower correlations between ARGs and bacterial genera in sediments from upstream or surface layers compared to those in downstream or deeper layers. Moreover, correlations in the sediments from surface layers and upstream regions showed a decreasing trend with increasing SD exposure concentrations, while those in deeper layers and downstream areas remained relatively stable. The presence of antibiotics notably enhanced the correlation between sediment properties and ARGs, particularly emphasizing associations with total carbon, nitrogen, and sulfur content. However, the introduction of SD and OTC resulted in a decrease in the influence of these sediment factors on microbial community functions related to sulfur and nitrogen metabolism, as indicated by KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation. The research provided empirical evidence on how microbial resistance responds to changes in antibiotics in sediment samples taken from various depths and locations within a watershed. It emphasized the urgent need for heightened awareness of the movement and alteration of antibiotic resistance patterns in watershed ecosystems.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Rural Environmental Remediation and Waste Recycling (Quanzhou Normal University), Fujian Province University, Quanzhou, 362000, China; Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541000, China
| | - Jinghua Xu
- Key Laboratory of Rural Environmental Remediation and Waste Recycling (Quanzhou Normal University), Fujian Province University, Quanzhou, 362000, China; School of Resources and Environmental Science, Quanzhou Normal University, Quanzhou, 362000, China
| | - Ying Feng
- Key Laboratory of Rural Environmental Remediation and Waste Recycling (Quanzhou Normal University), Fujian Province University, Quanzhou, 362000, China; School of Resources and Environmental Science, Quanzhou Normal University, Quanzhou, 362000, China
| | - Jinping Jiang
- Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541000, China
| | - Chunfa Wu
- School of Ecology and Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Yongshan Chen
- Key Laboratory of Rural Environmental Remediation and Waste Recycling (Quanzhou Normal University), Fujian Province University, Quanzhou, 362000, China; School of Resources and Environmental Science, Quanzhou Normal University, Quanzhou, 362000, China.
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Cao J, Yang X, Guo M, Wu Y, Wang C. Reclamation of abandoned cropland switches fungal community assembly from deterministic to stochastic processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175494. [PMID: 39153623 DOI: 10.1016/j.scitotenv.2024.175494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/28/2024] [Accepted: 08/11/2024] [Indexed: 08/19/2024]
Abstract
Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of abandoned agricultural land reclamation on the soil microbe is still poorly understood, especially for the microbial community assembly mechanisms. Here, we investigated the influence of reclamation on the relative importance of stochastic and deterministic processes in shaping microbial community assembly. After reclaiming abandoned cropland for corn and soybean cultivation, the fungal community assembly was shifted to stochastic processes, while bacterial communities remained predominantly influenced by stochastic processes. Our study revealed that reclamation did not significantly affect bacterial diversity, community niche breadth, and community similarity. In contrast, fungal communities exhibited lower alpha diversity, narrower niche breadths, greater niche overlap and higher community similarity in corn and soybean cultivation treatment in response to reclamation. Moreover, soil pH and soil available phosphorus were the most important environmental factors influencing fungal richness, niche breadths, community assembly processes, and community similarity. Together, the reclamation of abandoned cropland promoted the transformation of the fungal community assembly from deterministic process to a stochastic process, leading to decreased fungal diversity and broader ecological niche width, ultimately resulting in greater similarity among fungal communities. This finding provides insight into the varied responses of microbial diversity and ecological process to abandoned cropland reclamation, offering valuable guidance for the conservation and sustainable management of abandoned cropland in future land-use practices.
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Affiliation(s)
- Jia Cao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Xi Yang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Mengyao Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Yafen Wu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Chong Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China.
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Mu X, Shi S, Hu X, Gan X, Han Q, Yu Q, Qu J, Li H. Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135472. [PMID: 39137548 DOI: 10.1016/j.jhazmat.2024.135472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/07/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika's intestine, and cold had no significant effect on the composition and structure of pika's intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.
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Affiliation(s)
- Xianxian Mu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Shunqin Shi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xueqian Hu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xueying Gan
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
| | - Jiapeng Qu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China.
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China.
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Jiao Y, Sun X, Dong X, Yin J, Li Z, Zhang K, Altaf MM, Li D, Zhu Z. Enhancing mango yield and soil health with organic and slow-release fertilizers: A multifaceted evaluation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175297. [PMID: 39127209 DOI: 10.1016/j.scitotenv.2024.175297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/04/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
Excessive utilization of chemical fertilizers in mango orchards not only hampers the attainment of sustainable harvests but also poses significant ecological detriments. This investigation proposes a promising solution by advocating the judicious replacement of chemical fertilizers with organic fertilizer (OF) and slow-release fertilizer (SRF), with potential to bolster soil health and augment crop productivity. In light of the promise held by these alternatives, it is imperative to establish detailed fertilization protocols for enhanced sustainable practices in mango farming. This two-year field study employed a comprehensive suite of seven fertilization strategies, unveiling that a 25 % chemical fertilizers substitution with OF and SRF improved mango yields by 12.5 % and 11.3 %, respectively, over standard practices. Additionally, these approaches substantially augmented the nutritional quality of mangoes, evident from Vitamin C enhancements of 53.9 % to 56.9 %, and improvements in sugar-to-acid ratio (19.2 %-30.3 %) and solid-to-acid ratio (12.1 %-25.3 %). Notably, the application of OF and SRF led to increased leaf nitrogen and phosphorus concentrations, while simultaneously reducing soil phosphorus and potassium levels. Furthermore, these fertilizers fostered the growth of beneficial soil microorganisms, namely Actinobacteria and Proteobacteria, and strengthened the synergy within the soil bacterial community, hence optimizing bacterial competition and nutrient cycling. The study proposes that the adoption of OF or SRF can effectively regulate soil nutrient balance, promote resilient and functional soil bacterial ecosystems, and ultimately improve mango yield and fruit quality. It recommends a fertilization scheme incorporating 25 % organic or slow-release nitrogen to align with ecological sustainability goals, promoting a more vigorous and resilient soil and crop system.
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Affiliation(s)
- Yangqiu Jiao
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China; Jincheng Association for Science and Technology, Jincheng 048000, Shanxi Province, China
| | - Xiaoyan Sun
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Xuezhi Dong
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Jing Yin
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China; Shandong Vicome Greenland Chemical Co., Ltd, Jinan 250204, Shandong Province, China
| | - Zhidong Li
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Kailu Zhang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Shenzhen 518000, Guangdong Province, China
| | - Muhammad Mohsin Altaf
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Dong Li
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China.
| | - Zhiqiang Zhu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China.
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10
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Xia X, Wang L, Pei H, Dong C, Zhang Y, Ding J. Nanoplastics exposure simplifies the network structure of sea cucumber (Apostichopus japonicus) gut microbiota and improves cluster randomness. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124663. [PMID: 39097257 DOI: 10.1016/j.envpol.2024.124663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 07/26/2024] [Accepted: 08/01/2024] [Indexed: 08/05/2024]
Abstract
Nanoplastics (NPs) are abundant in ocean environments, leading to environmental pollution and notable disruptions to the physiological functions of marine animals. To investigate the toxic effects of NPs on echinoderms, specifically sea cucumbers (Apostichopus japonicus), they were exposed to varying concentrations of NPs (0, 102, 104 particles/L) for 14 d. Subsequently, the 102 particles/L exposure group was purified for 35 d to elucidate the impact of both NPs exposure and purification on the intestinal bacteria structure and function. The results showed that the richness and variety of intestinal bacteria in sea cucumbers significantly reduced under NPs exposure, and then they could be restored to the pre-exposure treatment state after 35 d of purification. With the increase of NPs exposure concentration in the environment, the intestinal core bacteria gradually changed from Firmicutes and Proteobacteria to Pseudoalteromonas and Vibrio. The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database annotated that the gut microbiota of sea cucumbers was significantly downregulated in the glycosylation, carbohydratic and amino acid metabolic pathways (P < 0. 05), exogenous substance biodegradation and metabolism, DNA replication and repair pathways were significantly up-regulated (P < 0.05) under the exposure of NPs. In addition, nanoplastics exposure simplified the symbiotic network relationships of the gut bacteria, reduced the selective effect of host on the intestinal bacteria, and increased stochasticity. In conclusion, waterborne NPs can adversely affect the structure and function of sea cucumber intestinal bacteria, with these effects persisting for a duration. However, as the purification time lengthens, these adverse effects gradually diminish. This study aims to provide some theoretical basis for the biotoxic effects of NPs.
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Affiliation(s)
- Xinglong Xia
- Dalian Ocean University, Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian, 116023, China; Dalian Ocean University, Liaoning Province Aquatic Germplasm Resources Protection and Utilization Engineering Research Center, Dalian, 116023, China
| | - Luo Wang
- Dalian Ocean University, Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian, 116023, China; Dalian Ocean University, Liaoning Province Aquatic Germplasm Resources Protection and Utilization Engineering Research Center, Dalian, 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
| | - Honglin Pei
- Dalian Ocean University, Liaoning Province Aquatic Germplasm Resources Protection and Utilization Engineering Research Center, Dalian, 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Changkun Dong
- Dalian Ocean University, Liaoning Province Aquatic Germplasm Resources Protection and Utilization Engineering Research Center, Dalian, 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Yanmin Zhang
- Dalian Ocean University, Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian, 116023, China; Dalian Ocean University, Liaoning Province Aquatic Germplasm Resources Protection and Utilization Engineering Research Center, Dalian, 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jun Ding
- Dalian Ocean University, Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian, 116023, China; Dalian Ocean University, Liaoning Province Aquatic Germplasm Resources Protection and Utilization Engineering Research Center, Dalian, 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
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11
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Niu Y, Kang E, Li Y, Zhang X, Yan Z, Li M, Yan L, Zhang K, Wang X, Yang A, Yu X, Kang X, Cui X. Non-flooding conditions caused by water table drawdown alter microbial network complexity and decrease multifunctionality in alpine wetland soils. ENVIRONMENTAL RESEARCH 2024; 254:119152. [PMID: 38754612 DOI: 10.1016/j.envres.2024.119152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Several soil functions of alpine wetland depend on microbial communities, including carbon storage and nutrient cycling, and soil microbes are highly sensitive to hydrological conditions. Wetland degradation is often accompanied by a decline in water table. With the water table drawdown, the effects of microbial network complexity on various soil functions remain insufficiently understood. In this research, we quantified soil multifunctionality of flooded and non-flooded sites in the Lalu Wetland on the Tibetan Plateau. We employed high-throughput sequencing to investigate the microbial community responses to water table depth changes, as well as the relationships between microbial network properties and soil multifunctionality. Our findings revealed a substantial reduction in soil multifunctionality at both surface and subsurface soil layers (0-20 cm and 20-40 cm) in non-flooded sites compared to flooded sites. The α-diversity of bacteria in the surface soil of non-flooded sites was significantly lower than that in flooded sites. Microbial network properties (including the number of nodes, number of edges, average degree, density, and modularity of co-occurrence networks) exhibited significant correlations with soil multifunctionality. This study underscores the adverse impact of non-flooded conditions resulting from water table drawdown on soil multifunctionality in alpine wetland soils, driven by alterations in microbial community structure. Additionally, we identified soil pH and moisture content as pivotal abiotic factors influencing soil multifunctionality, with microbial network complexity emerging as a valuable predictor of multifunctionality.
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Affiliation(s)
- Yuechuan Niu
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Enze Kang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yong Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaodong Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Zhongqing Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Meng Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Liang Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Kerou Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaodong Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ao Yang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaoshun Yu
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaoming Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China.
| | - Xiaoyong Cui
- University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Tang J, Lin B, Shan Y, Ruan S, Jiang W, Li Q, Zhu L, Li R, Yang Q, Du H, Yang S, Sun Q, Chen S. Effects of sorghum varieties on microbial communities and volatile compounds in the fermentation of light-flavor Baijiu. Front Microbiol 2024; 15:1421928. [PMID: 39144211 PMCID: PMC11322492 DOI: 10.3389/fmicb.2024.1421928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/08/2024] [Indexed: 08/16/2024] Open
Abstract
Light-flavor Baijiu (LFB) fermentation is a representative spontaneous mixed-culture solid-state fermentation process in which sorghum is used as the raw material. Raw materials and microorganisms are crucial to the flavor formation and quality of LFB. However, the microbial and physicochemical dynamics of different sorghum varieties during LFB fermentation, as well as their impact on flavor compounds are still largely unknown. Herein, PacBio single-molecule real-time (SMRT) sequencing and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) were applied to investigate microbial community succession and volatile flavor formation in glutinous/non-glutinous sorghum-based fermented grains during LFB fermentation. Fermented grains made of glutinous sorghum Liangnuo No. 1 (GLN) had higher bacterial α-diversity and lower fungal α-diversity than those with fermented grains prepared with non-glutinous red sorghum (NRS) (p < 0.05). The dominant microbial species were Saccharomyces cerevisiae, Acetobacter pasteurinus, and Lactobacillus helveticus, the latter two of which were the predominant bacteria observed at the end of fermentation in GLN and NRS, respectively. Moisture content and reducing sugar had a more significant impact on the microorganisms in GLN, while amino acid nitrogen, total free amino acids, and residual starch were the main driving factors driving the microbial community in NRS. The correlation network and discriminant analysis indicated that a relatively high content of 4-vinylguaiacol showed a significant positive association with significant differential microbial species in GLN. These results provided valuable insights for improving the quality of LFB.
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Affiliation(s)
- Jie Tang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Bin Lin
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Yimin Shan
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Song Ruan
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Wei Jiang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Qun Li
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Liping Zhu
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Rui Li
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Qiang Yang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Hai Du
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shengzhi Yang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Qi Sun
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
| | - Shenxi Chen
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine Health Food, Jing Brand Research Institute, Jing Brand Co., Ltd., Daye, China
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13
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Yang Y, Chen C, Yao K, Grossart HP. Seasonal dynamics of free-living (FL) and particle-attached (PA) bacterial communities in a plateau reservoir. Front Microbiol 2024; 15:1428701. [PMID: 39101032 PMCID: PMC11295932 DOI: 10.3389/fmicb.2024.1428701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 06/26/2024] [Indexed: 08/06/2024] Open
Abstract
In terms of lifestyle, bacterioplankton can be classified as free-living (FL) and particle-attached (PA) forms, and both play essential roles in biogeochemical cycling in aquatic ecosystems. Structure, distribution, and community assembly of FL and PA bacteria in plateau riverine waterbodies are largely unknown. Therefore, we explored the seasonal dynamics of FLand PA bacterial communities in the Wujiangdu reservoir, Yungui Plateau using 16S rRNA gene high-throughput sequencing. Results revealed there was a significant environmental heterogeneity in Wujiangdu reservoir seasonally. The dominant phylum was Actinomycetota for FL and Pseudomonadota for PA bacteria. Species richness and diversity was higher in autumn and winter compared to spring and summer. In general, PA diversity was greater than FL, but with some temporal variations. Species turnover was the major contributor to β-diversity of both FL and PA lifestyles, and significant differences were noticed between FL and PA bacterial community composition. Distinct co-occurrence network patterns implied that more connections exist between FL bacteria, while more complex PA networks were in parallel to their greater diversity and stronger interactions in biofilms on particles. Dispersal limitation was the major driving force for both FL and PA bacterial community assembly. Deterministic processes were of relatively low importance, with homogeneous selection for FL and heterogeneous selection for PA bacteria. Temperature was the most important environmental driver of seasonal bacterial dynamics, followed by nitrate for FL and Secchi depth for PA bacteria. This study allows for a better understanding of the temporal variability of different bacteria lifestyles in reservoirs in the vulnerable and rapidly changing plateau environment, facilitating further microbial research related to global warming and eutrophication.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Chen Chen
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Kai Yao
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Potsdam University, Potsdam, Germany
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14
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Gong J, Wang C, Wang J, Yang Y, Kong X, Liu J, Tang M, Lou H, Wen Z, Yang S, Yi Y. Integrative study of transcriptome and microbiome to reveal the response of Rhododendron decorum to cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116536. [PMID: 38833983 DOI: 10.1016/j.ecoenv.2024.116536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/06/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
The anomalies of cadmium (Cd) in karst region pose a severe threat to plant growth and development. In this study, the responses of Rhododendron decorum to Cd stress were investigated at physiological, molecular, and endophytic microbial levels, and the potential correlation among these responses was assessed. The Cd stress impeded R. decorum growth and led to an increase in malondialdehyde (MDA) and hydrogen peroxide (H2O2) levels, as well as enhanced superoxide dismutase (SOD) and catalase (CAT) activities. Meanwhile, Cd stress increased the Cd (up to 80 times compared to the control), sodium (Na), aluminum (Al), and zinc (Zn) contents, while decreased the magnesium (Mg) and manganese (Mn) contents in R. decorum leaves. Transcriptome suggested that Cd significantly regulated the pathways including "protein repair", "hormone-mediated signaling pathway", and "ATP-binding cassette (ABC) transporters". Additionally, q-PCR analysis showed that Cd stress significantly up-regulated the expressions of ABCB19-like and pleiotropic drug resistance, while down-regulated the expressions of indole-3-acetic acid-amido synthetase and cytokinin dehydrogenase. The Cd stress influenced the composition of endophytic microbial communities in R. decorum leaves and enhanced the interspecific bacterial associations. Furthermore, the bacterial genera Achromobacter, Aureimonas and fungal genus Vishniacozyma exhibited a high degree of connectivity with other nodes in networks constructed by the metal element contents, differentially expressed genes (DEGs), and microbial communities, respectively. These findings provide a comprehensive insight into the response of R. decorum to Cd-induced stress, which might facilitate the breeding of the Cd-tolerant R. decorum.
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Affiliation(s)
- Jiyi Gong
- College of Water Sciences, Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, Beijing Normal University, Beijing 100875, China; Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Chao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Jianfeng Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Yang Yang
- Gansu Yasheng Agricultural Research Institute Co., Ltd., Lanzhou 730010, China
| | - Xin Kong
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Jie Liu
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Ming Tang
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Hezhen Lou
- College of Water Sciences, Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, Beijing Normal University, Beijing 100875, China
| | - Zhirui Wen
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Shengtian Yang
- College of Water Sciences, Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, Beijing Normal University, Beijing 100875, China.
| | - Yin Yi
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, Guizhou 550025, China.
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15
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Martins BR, Radl V, Treder K, Michałowska D, Pritsch K, Schloter M. The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics. FEMS Microbiol Ecol 2024; 100:fiae088. [PMID: 38839598 PMCID: PMC11242454 DOI: 10.1093/femsec/fiae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/22/2024] [Accepted: 06/04/2024] [Indexed: 06/07/2024] Open
Abstract
Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We showed that plant growth characteristics were related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce indole acetic acid and siderophores) exhibited greater relative abundance in high- and medium-performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus, and Azohydromonas. Conversely, the network within low-performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness, and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices.
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Affiliation(s)
- Benoit Renaud Martins
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Krzysztof Treder
- Plant Breeding and Acclimatization Institute – National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, Bonin Str 3, 76-009 Bonin, Poland
| | - Dorota Michałowska
- Plant Breeding and Acclimatization Institute – National Research Institute in Radzików, Bonin Division, Department of Potato Protection and Seed Science at Bonin, Bonin Str 3, 76-009 Bonin, Poland
| | - Karin Pritsch
- Research Unit for Environmental Simulation (EUS), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Chair for Environmental Microbiology, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Alte Akademie 8, 85354 Freising, Germany
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16
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Wang W, Portal-Gonzalez N, Wang X, Li J, Li H, Portieles R, Borras-Hidalgo O, He W, Santos-Bermudez R. Insights into the microbial assembly and metabolites associated with ginger (Zingiber officinale L. Roscoe) microbial niches and agricultural environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174395. [PMID: 38992353 DOI: 10.1016/j.scitotenv.2024.174395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Ginger, a vegetable export from China, is well-known for its spicy flavour and use in traditional Chinese medicine. By examining the interactions of ginger plants' microbiome and metabolome, we can gain insights to advance agriculture, the environment, and other fields. Our study used metataxonomic analysis to investigate ginger plants' prokaryotic and fungal microbiomes in open fields and greenhouses. We also conducted untargeted metabolomic analysis to identify specific metabolites closely associated with ginger microbiome assembly under both agricultural conditions. Various bacteria and fungi were classified as generalists or specialists based on their ability to thrive in different environments and microbial niches. Our results indicate that ginger plants grown in greenhouses have a greater prokaryotic diversity, while those grown in open fields exhibit a greater fungal diversity. We have identified specific co-occurring prokaryotic and fungal genera associated with ginger plant agroecosystems that can enhance the health and growth of ginger plants while maintaining a healthy environment. In the open field these genera include Sphingomonas, Methylobacterium-Methylorubrum, Bacillus, Acidovorax, Rhizobium, Microbacterium, unclassified_f_Comamonadaceae, Herbaspirillum, Klebsiella, Enterobacter, Chryseobacterium, Nocardioides, Subgroup_10, Enterococcus, Pseudomonas, Devosia, g_unclassified_f_Chaetomiaceae, Pseudaleuria, Mortierella, Cheilymenia, and Pseudogymnoascus. In the greenhouse, the enriched genera were Rhizobium, Stenotrophomonas, Aureimonas, Bacillus, Nocardioides, Pseudomonas, Enterobacter, Delftia, Trichoderma, Mortierella, Cheilymenia, Schizothecium, and Actinomucor. Our research has identified several previously unknown microbial genera for ginger plant agroecosystems. Furthermore, our study has important implications for understanding the correlation between ginger's microbiome and metabolome profiles in diverse environments and may pave the way for future research. Specific microbial genera in crop production environments are associated with essential metabolites, including Safingol, Docosatrienoic acid, P-acetaminophen, and Hypoglycin B.
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Affiliation(s)
- Wenbo Wang
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Nayanci Portal-Gonzalez
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China
| | - Xia Wang
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China
| | - Jialin Li
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Roxana Portieles
- Joint R&D Center of Biotechnology, RETDA, Yota Bio-Engineering Co., Ltd., 99 Shenzhen Road, Rizhao 276826, Shandong, People's Republic of China.
| | - Orlando Borras-Hidalgo
- Joint R&D Center of Biotechnology, RETDA, Yota Bio-Engineering Co., Ltd., 99 Shenzhen Road, Rizhao 276826, Shandong, People's Republic of China.
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
| | - Ramon Santos-Bermudez
- School of Biological Science and Technology, University of Jinan, No. 336, West Road of Nan Xinzhuang, Jinan 250022, Shandong, People's Republic of China.
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17
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Zhong J, Li Z, Tang H, Dong W, Wei C, He T. The application of varying amount of green manure combined with nitrogen fertilizer altered the soil bacterial community and rice yield in karst paddy areas. BMC PLANT BIOLOGY 2024; 24:646. [PMID: 38977970 PMCID: PMC11229212 DOI: 10.1186/s12870-024-05351-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/27/2024] [Indexed: 07/10/2024]
Abstract
Long-term application of green manure (GM) and nitrogen (N) fertilizers markedly improved soil fertility and boosted rice yield in ecologically fragile karst paddy fields. However, the precise response mechanisms of the soil bacterial community to varying amounts of green manure alone and in combination with N fertilizer in such environments remain poorly elucidated. In this study, we investigated the soil bacterial communities, keystone taxa, and their relationship with soil environmental variables across eight fertilization treatments. These treatments included group without N addition (N0M0, no N fertilizer and no GM; N0M22.5, 22.5 t/ha GM; N0M45, 45 t/ha GM, N0M67.5, 67.5 t/ha GM) and group with N addition (NM0, N fertilizer and no GM; NM22.5, N fertilizer and 22.5 t/ha GM; NM45, N fertilizer and 45 t/ha GM; NM67.5, N fertilizer and 67.5 t/ha GM). The results revealed that increasing green manure input significantly boosted rice yield by 15.51-22.08% and 21.84-35% in both the group without and with N addition, respectively, compared to N0M0 treatment. Moreover, with escalating green manure input, soil TN, AN, AK, and AP showed an increasing trend in the group without N addition. However, following the addition of N fertilizer, TN and AN content initially rose, followed by a decline due to the enhanced nutrient availability for rice. Furthermore, the application of a large amount of N fertilizer decreased the C: N ratio in the soil, resulting in significant changes in both the soil microbial community and its function. Particularly noteworthy was the transition of keystone taxa from their original roles as N-fixing and carbon-degrading groups (oligotrophs) to roles in carbon degradation (copiotrophs), nitrification, and denitrification. This shift in soil community and function might serve as a primary factor contributing to enhanced nutrient utilization efficiency in rice, thus significantly promoting rice yield.
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Affiliation(s)
- Juxin Zhong
- Key Laboratory of Karst Dynamics, Ministry of Natural Resources & Guangxi, Institute of Karst Geology, Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, Ministry of Natural Resources, Chinese Academy of Geological Sciences, Guilin, Guangxi, 541004, China
- Agricultural Resource and Environment Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Arable Land Conservation, Nanning, Guangxi, 530007, China
| | - Zhongyi Li
- Agricultural Resource and Environment Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Arable Land Conservation, Nanning, Guangxi, 530007, China.
| | - Hongqin Tang
- Agricultural Resource and Environment Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Arable Land Conservation, Nanning, Guangxi, 530007, China.
| | - Wenbin Dong
- Agricultural Resource and Environment Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Arable Land Conservation, Nanning, Guangxi, 530007, China
| | - Caihui Wei
- Agricultural Resource and Environment Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Arable Land Conservation, Nanning, Guangxi, 530007, China
| | - Tieguang He
- Agricultural Resource and Environment Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Arable Land Conservation, Nanning, Guangxi, 530007, China
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18
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Xu Z, Zheng B, Yang Y, Yang Y, Jiang G, Tian Y. Effects of biodegradable (PBAT/PLA) and conventional (LDPE) mulch film residues on bacterial communities and metabolic functions in different agricultural soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134425. [PMID: 38691998 DOI: 10.1016/j.jhazmat.2024.134425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Soil health is a crucial aspect of sustainable agriculture and food production, necessitating attention to the ecological risks associated with substantial amounts of mulch film residues. Biodegradable mulch films (BDMs) carry the same risk of mulch film residues formation as low-density polyethylene (LDPE) mulch films during actual use. More information is needed to elucidate the specific impacts of mulch film residues on the soil environment. Integrated 16S rRNA gene sequencing and non-targeted metabolomics, this study revealed the response patterns of bacterial communities, metabolites, and metabolic functions in the soil from three different agricultural regions to the presence of mulch film residues. LDPE mulch film residues negatively impacted the bacterial communities in the soils of Heilongjiang (HLJ) and Yunnan (YN) and had a lesser impact on the metabolic spectrum in the soils of HLJ, YN, and Xinjiang (XJ). BDM residues had a greater negative impact on all three soils in terms of both the bacterial communities and metabolites. The impact of BDM treatment on the soils of HLJ, YN, and XJ increased sequentially in that order. It is recommended that, when promoting the use of biodegradable mulch films, a fuller assessment should be made, accounting for local soil properties.
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Affiliation(s)
- Zhe Xu
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Bijun Zheng
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Yichen Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Yi Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Guangyang Jiang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Yongqiang Tian
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China.
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19
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Che J, Wu Y, Yang H, Chang Y, Wu W, Lyu L, Wang X, Cao F, Li W. Metabolites of blueberry roots at different developmental stages strongly shape microbial community structure and intra-kingdom interactions at the root-soil interface. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174333. [PMID: 38945231 DOI: 10.1016/j.scitotenv.2024.174333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
The rhizosphere microorganisms of blueberry plants have long coexisted with their hosts under distinctively acidic soil conditions, exerting a profound influence on host performance through mutualistic symbiotic interactions. Meanwhile, plants can regulate rhizosphere microorganisms by exerting host effects to meet the functional requirements of plant growth and development. However, it remains unknown how the developmental stages of blueberry plants affect the structure, function, and interactions of the rhizosphere microbial communities. Here, we examined bacterial communities and root metabolites at three developmental stages (flower and leaf bud development stage, fruit growth and development stage, and fruit maturation stage) of blueberry plants. The results revealed that the Shannon and Chao 1 indices as well as community composition varied significantly across all three developmental stages. The relative abundance of Actinobacteria significantly increased by 10 % (p < 0.05) from stage 1 to stage 2, whereas that of Proteobacteria decreased significantly. The co-occurrence network analysis revealed a relatively complex network with 1179 edges and 365 nodes in the stage 2. Niche breadth was highest at stage 2, while niche overlap tended to increase as the plant developed. Furthermore, the untargeted metabolome analysis revealed that the number of differential metabolites of vitamins, nucleic acids, steroids, and lipids increased between stage 1 to stage2 and stage 2 to stage 3, while those for differential metabolites of carbohydrates and peptides decreased. Significant changes in expression levels of levan, L-glutamic acid, indoleacrylic acid, oleoside 11-methyl ester, threo-syringoylglycerol, gingerglycolipid B, and bovinic acid were highly correlated with the bacterial community structure. Collectively, our study reveals that significant alterations in dominant bacterial taxa are strongly correlated with the dynamics of root metabolites. These findings lay the groundwork for developing prebiotic products to enhance the beneficial effects of root microorganisms and boosting blueberry productivity via a sustainable approach.
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Affiliation(s)
- Jilu Che
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China; Department of Biological Sciences, Faculty of Science, National University of Singapore, 117543, Singapore.
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China.
| | - Hao Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Ying Chang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 117543, Singapore; Science Division, Yale-NUS College, 138527, Singapore.
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Xiaomin Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Fuliang Cao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China
| | - Weilin Li
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China.
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20
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Wang J, Jia M, Zhang L, Li X, Zhang X, Wang Z. Biodegradable microplastics pose greater risks than conventional microplastics to soil properties, microbial community and plant growth, especially under flooded conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172949. [PMID: 38703848 DOI: 10.1016/j.scitotenv.2024.172949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/10/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Biodegradable plastics (bio-plastics) are often viewed as viable option for mitigating plastic pollution. Nevertheless, the information regarding the potential risks of microplastics (MPs) released from bio-plastics in soil, particularly in flooded soils, is lacking. Here, our objective was to investigate the effect of polylactic acid MPs (PLA-MPs) and polyethylene MPs (PE-MPs) on soil properties, microbial community and plant growth under both non-flooded and flooded conditions. Our results demonstrated that PLA-MPs dramatically increased soil labile carbon (C) content and altered its composition and chemodiversity. The enrichment of labile C stimulated microbial N immobilization, resulting in a depletion of soil mineral nitrogen (N). This specialized environment created by PLA-MPs further filtered out specific microbial species, resulting in a low diversity and simplified microbial community. PLA-MPs caused an increase in denitrifiers (Noviherbaspirillum and Clostridium sensu stricto) and a decrease in nitrifiers (Nitrospira, MND1, and Ellin6067), potentially exacerbating the mineral N deficiency. The mineral N deficit caused by PLA-MPs inhibited wheatgrass growth. Conversely, PE-MPs had less effect on soil ecosystems, including soil properties, microbial community and wheatgrass growth. Overall, our study emphasizes that PLA-MPs cause more adverse effect on the ecosystem than PE-MPs in the short term, and that flooded conditions exacerbate and prolong these adverse effects. These results offer valuable insights for evaluating the potential threats of bio-MPs in both uplands and wetlands.
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Affiliation(s)
- Jie Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Minghao Jia
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China
| | - Long Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaona Li
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China
| | - Xiaokai Zhang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environmental and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
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21
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Li K, Chen A, Sheng R, Hou H, Zhu B, Wei W, Zhang W. Long-term chemical and organic fertilization induces distinct variations of microbial associations but unanimous elevation of soil multifunctionality. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172862. [PMID: 38705286 DOI: 10.1016/j.scitotenv.2024.172862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024]
Abstract
Intricate microbial associations contribute greatly to the multiple functions (multifunctionality) of natural ecosystems. However, the relationship between microbial associations and soil multifunctionality (SMF) in artificial ecosystems, particularly in agricultural ecosystem with frequent fertilization, remains unclear. In this study, based on a 28-year paddy field experiment, high-throughput sequencing and networks analysis was performed to investigate changes in soil microbial (archaea, bacteria, fungi, and protists) associations and how these changes correlate with SMF under long-term fertilization. Compared to no fertilization (CK), both chemical fertilization with N, P, and K (CF) and chemical fertilization plus rice straw retention (CFR) treatments showed significantly higher soil nutrient content, grain yield, microbial abundance, and SMF. With the exception of archaeal diversity, the CF treatment exhibited the lowest bacterial, fungal, and protist diversity, and the simplest microbial co-occurrence network. In contrast, the CFR treatment had the lowest archaeal diversity, but the highest bacterial, fungal, and protist diversity. Moreover, the CFR treatment exhibited the most complex microbial co-occurrence network with the highest number of nodes, edges, and interkingdom edges. These results highlight that both chemical fertilization with and without straw retention caused high ecosystem multifunctionality while changing microbial association oppositely. Furthermore, these results indicate that rice straw retention contributes to the development of the soil microbiome and ensures the sustainability of high-level ecosystem multifunctionality.
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Affiliation(s)
- Ke Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; College of Resource and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anlei Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Rong Sheng
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Haijun Hou
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Baoli Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wenxue Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wenzhao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
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22
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Gao C, Bezemer TM, de Vries FT, van Bodegom PM. Trade-offs in soil microbial functions and soil health in agroecosystems. Trends Ecol Evol 2024:S0169-5347(24)00138-1. [PMID: 38910081 DOI: 10.1016/j.tree.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 06/25/2024]
Abstract
Soil microbial communities play pivotal roles in maintaining soil health in agroecosystems. However, how the delivery of multiple microbial functions in agroecosystems is maintained remains poorly understood. This may put us at risk of incurring unexpected trade-offs between soil functions. We elucidate how interactions between soil microbes can lead to trade-offs in the functioning of agricultural soils. Interactions within soil microbial communities can result in not only positive but also neutral and negative relationships among soil functions. Altering soil conditions through soil health-improving agricultural management can alleviate these functional trade-offs by promoting the diversity and interrelationships of soil microbes, which can help to achieve more productive and sustainable agroecosystems.
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Affiliation(s)
- Chenguang Gao
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands.
| | - Thiemo Martijn Bezemer
- Institute of Biology, Above-Belowground Interactions Group, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1090 GE Amsterdam, The Netherlands
| | - Peter M van Bodegom
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
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23
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Li D, Wu C, Wu J. Soil fungal community has higher network stability than bacterial community in response to warming and nitrogen addition in a subtropical primary forest. Appl Environ Microbiol 2024; 90:e0000124. [PMID: 38771056 PMCID: PMC11218647 DOI: 10.1128/aem.00001-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Global change factors are known to strongly affect soil microbial community function and composition. However, as of yet, the effects of warming and increased anthropogenic nitrogen deposition on soil microbial network complexity and stability are still unclear. Here, we examined the effects of experimental warming (3°C above ambient soil temperature) and nitrogen addition (5 g N m-2 year-1) on the complexity and stability of the soil microbial network in a subtropical primary forest. Compared to the control, warming increased |negative cohesion|:positive cohesion by 7% and decreased network vulnerability by 5%; nitrogen addition decreased |negative cohesion|:positive cohesion by 10% and increased network vulnerability by 11%. Warming and decreased soil moisture acted as strong filtering factors that led to higher bacterial network stability. Nitrogen addition reduced bacterial network stability by inhibiting soil respiration and increasing resource availability. Neither warming nor nitrogen addition changed fungal network complexity and stability. These findings suggest that the fungal community is more tolerant than the bacterial community to climate warming and nitrogen addition. The link between bacterial network stability and microbial community functional potential was significantly impacted by nitrogen addition and warming, while the response of soil microbial network stability to climate warming and nitrogen deposition may be independent of its complexity. Our findings demonstrate that changes in microbial network structure are crucial to ecosystem management and to predict the ecological consequences of global change in the future. IMPORTANCE Soil microbes play a very important role in maintaining the function and health of forest ecosystems. Unfortunately, global change factors are profoundly affecting soil microbial structure and function. In this study, we found that climate warming promoted bacterial network stability and nitrogen deposition decreased bacterial network stability. Changes in bacterial network stability had strong effects on bacterial community functional potentials linked to metabolism, nitrogen cycling, and carbon cycling, which would change the biogeochemical cycle in primary forests.
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Affiliation(s)
- Debao Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Laboratory of Soil Ecology and Health in Universities of Yunnan Province, Yunnan University, Kunming, China
| | - Chuansheng Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, China
| | - Jianping Wu
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Laboratory of Soil Ecology and Health in Universities of Yunnan Province, Yunnan University, Kunming, China
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24
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Li J, Zhao J, Liao X, Hu P, Wang W, Ling Q, Xie L, Xiao J, Zhang W, Wang K. Pathways of soil organic carbon accumulation are related to microbial life history strategies in fertilized agroecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172191. [PMID: 38588738 DOI: 10.1016/j.scitotenv.2024.172191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/10/2024]
Abstract
Although the formation, turnover, and accumulation of soil organic carbon (SOC) are driven by different fertilizer inputs and their subsequent microbial-mediated transformation, the relationship between changes in plant-derived and microbial-derived components and soil microbial life history strategies under different fertilization regimes has not been well explored. In this study, the changes in microbial necromass carbon (MNC), lignin phenols, and glomalin-related soil protein (GRSP), as well as soil microbial life history strategy were determined in a 16-year field experiment in response to different fertilization regimes, including a no-fertilizer control (C), conventional chemical NPK fertilization (NPK), and partial substitutions of the NPK in chemical fertilizers with a low (30 %) or high (60 %) level of straw (0.3S and 0.6S) or cattle manure (0.3M and 0.6M). The results showed that total lignin phenol content and its contribution to SOC were significantly increased by 88.7 % and 74.2 %, respectively, in high-level straw substitution treatment as compared to chemical fertilization. Both high-level straw and cattle manure substitution increased MNC and total GRSP contents, but did not alter their contributions to SOC compared to chemical fertilization. In fertilized treatments, the high-level cattle manure substitution had the lowest and highest bacterial and fungal K/r ratio, respectively. Bacterial K/r ratio was an important factor in predicting bacterial necromass carbon content and there was a significant negative correlation between them. The ratio of ectomycorrhizal to saprotrophic fungi and fungal diversity were important factors for predicting lignin phenol and GRSP contents, respectively. In addition, the SEMs modeling indicated that straw substitution directly affected lignin phenol and MNC accumulation, whereas cattle manure substitution indirectly affected MNC accumulation by affecting microbial life history strategies. In conclusions, agricultural residues inputs support the formation of a multiple carbon pool of SOC compared to chemical fertilization; and microbial life history strategy is an important driver of SOC formation and affects SOC accumulation and stability in agroecosystems.
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Affiliation(s)
- Jiangnan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; College of Environment and Ecology, Hunan Agricultural University, Changsha 410128, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Jie Zhao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Industrial Technology Research Institute for Karst Rocky Desertification Control, Nanning 530012, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China.
| | - Xionghui Liao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Peilei Hu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Wenyu Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Qiumei Ling
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Lei Xie
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Jun Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Wei Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Industrial Technology Research Institute for Karst Rocky Desertification Control, Nanning 530012, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Kelin Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China.
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Gholizadeh S, Nemati I, Vestergård M, Barnes CJ, Kudjordjie EN, Nicolaisen M. Harnessing root-soil-microbiota interactions for drought-resilient cereals. Microbiol Res 2024; 283:127698. [PMID: 38537330 DOI: 10.1016/j.micres.2024.127698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.
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Affiliation(s)
- Somayeh Gholizadeh
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mette Vestergård
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Christopher James Barnes
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Enoch Narh Kudjordjie
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Mogens Nicolaisen
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark.
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26
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Ju H, Zhang J, Zou Y, Xie F, Tang X, Zhang S, Li J. Bacteria undergo significant shifts while archaea maintain stability in Pocillopora damicornis under sustained heat stress. ENVIRONMENTAL RESEARCH 2024; 250:118469. [PMID: 38354884 DOI: 10.1016/j.envres.2024.118469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Global warming reportedly poses a critical risk to coral reef ecosystems. Bacteria and archaea are crucial components of the coral holobiont. The response of archaea associated with warming is less well understood than that of the bacterial community in corals. Also, there have been few studies on the dynamics of the microbial community in the coral holobiont under long-term heat stress. In order to track the dynamic alternations in the microbial communities within the heat-stressed coral holobiont, three-week heat-stress monitoring was carried out on the coral Pocillopora damicornis. The findings demonstrate that the corals were stressed at 32 °C, and showed a gradual decrease in Symbiodiniaceae density with increasing duration of heat stress. The archaeal community in the coral holobiont remained relatively unaltered by the increasing temperature, whereas the bacterial community was considerably altered. Sustained heat stress exacerbated the dissimilarities among parallel samples of the bacterial community, confirming the Anna Karenina Principle in animal microbiomes. Heat stress leads to more complex and unstable microbial networks, characterized by an increased average degree and decreased modularity, respectively. With the extension of heat stress duration, the relative abundances of the gene (nifH) and genus (Tistlia) associated with nitrogen fixation increased in coral samples, as well as the potential pathogenic bacteria (Flavobacteriales) and opportunistic bacteria (Bacteroides). Hence, our findings suggest that coral hosts might recruit nitrogen-fixing bacteria during the initial stages of suffering heat stress. An environment that is conducive to the colonization and development of opportunistic and pathogenic bacteria when the coral host becomes more susceptible as heat stress duration increases.
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Affiliation(s)
- Huimin Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Sanya National Marine Ecosystem Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yiyang Zou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Feiyang Xie
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xiaoyu Tang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Sanya National Marine Ecosystem Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Sanya National Marine Ecosystem Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
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Sun Z, Sun C, Zhang T, Liu J, Wang X, Feng J, Li S, Tang S, Jin K. Soil microbial community variation among different land use types in the agro-pastoral ecotone of northern China is likely to be caused by anthropogenic activities. Front Microbiol 2024; 15:1390286. [PMID: 38841072 PMCID: PMC11150776 DOI: 10.3389/fmicb.2024.1390286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024] Open
Abstract
There are various types of land use in the agricultural and pastoral areas of northern China, including natural grassland and artificial grassland, scrub land, forest land and farmland, may change the soil microbial community However, the soil microbial communities in these different land use types remain poorly understood. In this study, we compared soil microbial communities in these five land use types within the agro-pastoral ecotone of northern China. Our results showed that land use has had a considerable impact on soil bacterial and fungal community structures. Bacterial diversity was highest in shrubland and lowest in natural grassland; fungal diversity was highest in woodland. Microbial network structural complexity also differed significantly among land use types. The lower complexity of artificial grassland and farmland may be a result of the high intensity of anthropogenic activities in these two land-use types, while the higher structural complexity of the shrubland and woodland networks characterised by low-intensity management may be a result of low anthropogenic disturbance. Correlation analysis of soil properties (e.g., soil physicochemical properties, soil nutrients, and microbiomass carbon and nitrogen levels) and soil microbial communities demonstrated that although microbial taxa were correlated to some extent with soil environmental factors, these factors did not sufficiently explain the microbial community differences among land use types. Understanding variability among soil microbial communities within agro-pastoral areas of northern China is critical for determining the most effective land management strategies and conserving microbial diversity at the regional level.
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Affiliation(s)
- Zhaokai Sun
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Chongzhi Sun
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Tongrui Zhang
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jia Liu
- School of Grass Academy, Qingdao Agriculture University, Qingdao, China
| | - Xinning Wang
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jing Feng
- School of Grass Academy, Qingdao Agriculture University, Qingdao, China
| | - Shucheng Li
- Anhui Science and Technology University, College of Agriculture, Huainan, China
| | - Shiming Tang
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Ke Jin
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
- Department of International Cooperation, Chinese Academy of Agricultural Sciences, Beijing, China
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28
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Wang B, Hu K, Li C, Zhang Y, Hu C, Liu Z, Ding J, Chen L, Zhang W, Fang J, Zhang H. Geographic distribution of bacterial communities of inland waters in China. ENVIRONMENTAL RESEARCH 2024; 249:118337. [PMID: 38325783 DOI: 10.1016/j.envres.2024.118337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 02/09/2024]
Abstract
Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.
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Affiliation(s)
- Binhao Wang
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Kaiming Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chuqiao Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yinan Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chao Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zhiquan Liu
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Jiafeng Ding
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Lin Chen
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Wei Zhang
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Jing Fang
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Hangjun Zhang
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China; Hangzhou International Urbanology Research Center and Center for Zhejiang Urban Governance Studies, Hangzhou, 311121, China.
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29
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Zhu L, Wang X, Liu L, Le B, Tan C, Dong C, Yao X, Hu B. Fungi play a crucial role in sustaining microbial networks and accelerating organic matter mineralization and humification during thermophilic phase of composting. ENVIRONMENTAL RESEARCH 2024; 254:119155. [PMID: 38754614 DOI: 10.1016/j.envres.2024.119155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Fungi play an important role in the mineralization and humification of refractory organic matter such as lignocellulose during composting. However, limited research on the ecological role of fungi in composting system hindered the development of efficient microbial agents. In this study, six groups of lab-scale composting experiments were conducted to reveal the role of fungal community in composting ecosystems by comparing them with bacterial community. The findings showed that the thermophilic phase was crucial for organic matter degradation and humic acid formation. The Richness index of the fungal community peaked at 1165 during this phase. PCoA analysis revealed a robust thermal stability in the fungal community. Despite temperature fluctuations, the community structure, predominantly governed by Pichia and Candida, remained largely unaltered. The stability of fungal community and the complexity of ecological networks were 1.26 times and 5.15 times higher than those observed in bacterial community, respectively. Fungi-bacteria interdomain interaction markedly enhanced network complexity, contributing to maintain microbial ecological functions. The core fungal species belonging to the family Saccharomycetaceae drove interdomain interaction during thermophilic phase. This study demonstrated the key role of fungi in the composting system, which would provide theoretical guidance for the development of high efficiency composting agents to strengthen the mineralization and humification of organic matter.
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Affiliation(s)
- Lin Zhu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China; College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaohan Wang
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Liyuan Liu
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Boyi Le
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chunxu Tan
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chifei Dong
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiangwu Yao
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China; College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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30
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Mu L, Dong R, Wang J, Yue J, Pan L, Song C, Wei Z. The positive effect of the enzyme inducer (MnSO 4) on the formation of humic substance in rice straw composting by stimulating key microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171460. [PMID: 38442764 DOI: 10.1016/j.scitotenv.2024.171460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/07/2024]
Abstract
This study investigated the impact of adding enzyme inducer (MnSO4) on humic substance (HS) formation during straw composting. The results demonstrated that both enzyme inducer treatment group (Mn) and functional microorganism treatment group (F) led to an increase in the content of HS compared to the treatment group without enzyme inducer and functional microorganism (CK). Interestingly, the enzyme inducer exhibited a higher promoting effect on HS (57.80 % ~ 58.58 %) than functional microbial (46.54 %). This was because enzyme inducer stimulated the growth of key microorganisms and changed the interaction relationship between microorganisms. The structural equation model suggested that the enzyme inducer promoted the utilization of amino acids by the fungus and facilitated the conversion of precursors to humic substance components. These findings provided a direction for improving the quality of composting products from agricultural straw waste. It also provided theoretical support for adding MnSO4 to compost.
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Affiliation(s)
- Linying Mu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Runshi Dong
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jiaqi Wang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jieyu Yue
- College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Lina Pan
- College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Caihong Song
- School of Life Science, Liaocheng University, Liaocheng 252000, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; College of Life Sciences, Tianjin Normal University, Tianjin 300387, China.
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31
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Iannotti L, Kleban E, Fracassi P, Oenema S, Lutter C. Evidence for Policies and Practices to Address Global Food Insecurity. Annu Rev Public Health 2024; 45:375-400. [PMID: 38166503 DOI: 10.1146/annurev-publhealth-060922-041451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Food insecurity affects an estimated 691-783 million people globally and is disproportionately high in Africa and Asia. It arises from poverty, armed conflict, and climate change, among other demographic and globalization forces. This review summarizes evidence for policies and practices across five elements of the agrifood system framework and identifies gaps that inform an agenda for future research. Under availability, imbalanced agriculture policies protect primarily staple food producers, and there is limited evidence on food security impacts for smallholder and women food producers. Evidence supports the use of cash transfers and food aid for affordability and school feeding for multiple benefits. Food-based dietary guidelines can improve the nutritional quality of dietary patterns, yet they may not reflect the latest evidence or food supplies. Evidence from the newer food environment elements, promotion and sustainability, while relatively minimal, provides insight into achieving long-term impacts. To eliminate hunger, our global community should embrace integrated approaches and bring evidence-based policies and practices to scale.
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Affiliation(s)
- Lora Iannotti
- E3 Nutrition Lab, Brown School, Washington University in St. Louis, St. Louis, Missouri, USA;
| | - Eliza Kleban
- E3 Nutrition Lab, Brown School, Washington University in St. Louis, St. Louis, Missouri, USA;
| | - Patrizia Fracassi
- Food and Nutrition Division, Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Stineke Oenema
- UN-Nutrition Secretariat, Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Chessa Lutter
- Division of Food Security and Agriculture, RTI International, Washington, DC, USA
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32
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Liu Z, Gu H, Yao Q, Jiao F, Hu X, Liu J, Jin J, Liu X, Wang G. Soil pH and carbon quality index regulate the biogeochemical cycle couplings of carbon, nitrogen and phosphorus in the profiles of Isohumosols. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171269. [PMID: 38423323 DOI: 10.1016/j.scitotenv.2024.171269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
Soil biogeochemical cycles are essential for regulating ecosystem functions and services. However, little knowledge has been revealed on microbe-driven biogeochemical processes and their coupling mechanisms in soil profiles. This study investigated the vertical distribution of soil functional composition and their contribution to carbon (C), nitrogen (N) and phosphorus (P) cycling in the humus horizons (A-horizons) and parent material horizons (C-horizons) in Udic and Ustic Isohumosols using shotgun sequencing. Results showed that the diversity and relative abundance of microbial functional genes was influenced by soil horizons and soil types. In A-horizons, the relative abundances of N mineralization and liable C decomposition genes were significantly greater, but the P cycle-related genes, recalcitrant C decomposition and denitrification genes were lower compared to C-horizons. While, Ustic Isohumosols had lower relative abundances of C decomposition genes but higher relative abundances of N mineralization and P cycling-related pathways compared to Udic Isohumosols. The network analysis revealed that C-horizons had more interactions and stronger stability of functional gene networks than in A-horizons. Importantly, our results provide new insights into the potential mechanisms for the coupling processes of soil biogeochemical cycles among C, N and P, which is mediated by specific microbial taxa. Soil pH and carbon quality index (CQI) were two sensitive indicators for regulating the relative abundances and the relationships of functional genes in biogeochemical cycles. This study contributes to a deeper understanding of the ecological functions of soil microorganisms, thus providing a theoretical basis for the exploration and utilization of soil microbial resources and the development of soil ecological control strategies.
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Affiliation(s)
- Zhuxiu Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Yao
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Feng Jiao
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xiaobing Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
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33
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Wang X, Riaz M, Xia X, Babar S, El-Desouki Z, Li Y, Wang J, Jiang C. Alleviation of cotton growth suppression caused by salinity through biochar is strongly linked to the microbial metabolic potential in saline-alkali soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171407. [PMID: 38432366 DOI: 10.1016/j.scitotenv.2024.171407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/08/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Biochar is a typical soil organic amendment; however, there is limited understanding of its impact on the metabolic characteristics of microorganisms in saline-alkaline soil microenvironment, as well as the advantages and disadvantages of plant-microorganism interactions. To elucidate the mechanisms underlying the impact of saline-alkali stress on cotton, a 6-month pot experiment was conducted, involving the sowing of cotton seedlings in saline-alkali soil. Three different biochar application levels were established: 0 % (C0), 1 % (C1), and 2 % (C2). Results indicated that biochar addition improved the biomass of cotton plants, especially under C2 treatment; the dry weight of cotton bolls were 8.15 times that of C0. Biochar application led to a rise in the accumulation of photosynthetic pigments by 8.30-51.89 % and carbohydrates by 7.4-10.7 times, respectively. Moreover, peroxidase (POD) activity, the content of glutathione (GSH), and ascorbic acid (ASA) were elevated by 23.97 %, 118.39 %, and 48.30 % under C2 treatment, respectively. Biochar caused a reduction in Na+ uptake by 8.21-39.47 %, relative electrical conductivity (REC) of plants, and improved K+/Na+ and Ca2+/Na+ ratio indicating that biochar alleviated salinity-caused growth reduction. Additionally, the application of biochar enhanced the absorption intensity of polysaccharide fingerprints in cotton leaves and roots. Two-factor co-occurrence analysis indicated that the key differential metabolites connected to several metabolic pathways were L-phenylalanine, piperidine, L-tryptophan, and allysine. Interestingly, biochar altered the metabolic characteristics of saline-alkali soil, especially related to the biosynthesis and metabolism of amino acids and purine metabolism. In conclusion, this study demonstrates that biochar may be advantageous in saline soil microenvironment; it has a favorable impact on how plants and soil microbial metabolism interact.
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Affiliation(s)
- Xiangling Wang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Muhammad Riaz
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, PR China
| | - Xiaoyang Xia
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Saba Babar
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zeinab El-Desouki
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yuxuan Li
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jiyuan Wang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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34
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Feng G, Wu Y, Yang C, Zhang Q, Wang S, Dong M, Wang Y, Qi H, Guo L. Effects of coastal saline-alkali soil on rhizosphere microbial community and crop yield of cotton at different growth stages. Front Microbiol 2024; 15:1359698. [PMID: 38706969 PMCID: PMC11066693 DOI: 10.3389/fmicb.2024.1359698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/21/2024] [Indexed: 05/07/2024] Open
Abstract
Soil salinization is a global constraint that significantly hampers agricultural production, with cotton being an important cash crop that is not immune to its detrimental effects. The rhizosphere microbiome plays a critical role in plant health and growth, which assists plants in resisting adverse abiotic stresses including soil salinization. This study explores the impact of soil salinization on cotton, including its effects on growth, yield, soil physical and chemical properties, as well as soil bacterial community structures. The results of β-diversity analysis showed that there were significant differences in bacterial communities in saline-alkali soil at different growth stages of cotton. Besides, the more severity of soil salinization, the more abundance of Proteobacteria, Bacteroidota enriched in rhizosphere bacterial composition where the abundance of Acidobacteriota exhibited the opposite trend. And the co-occurrence network analysis showed that soil salinization affected the complexity of soil bacterial co-occurrence network. These findings provide valuable insights into the mechanisms by which soil salinization affects soil microorganisms in cotton rhizosphere soil and offer guidance for improving soil salinization using beneficial microorganisms.
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Affiliation(s)
- Guoyi Feng
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Yajie Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang, China
| | - Chuanzhen Yang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang, China
| | - Qian Zhang
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Shulin Wang
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Ming Dong
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Yan Wang
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Hong Qi
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Lixue Guo
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang, China
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Darriaut R, Marzari T, Lailheugue V, Tran J, Martins G, Marguerit E, Masneuf-Pomarède I, Lauvergeat V. Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions. FRONTIERS IN PLANT SCIENCE 2024; 15:1358213. [PMID: 38628369 PMCID: PMC11018932 DOI: 10.3389/fpls.2024.1358213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.
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Affiliation(s)
- Romain Darriaut
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Tania Marzari
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Vincent Lailheugue
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Joseph Tran
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Guilherme Martins
- Université de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR Œnologie 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, 1 cours du Général de Gaulle, Gradignan, France
| | - Elisa Marguerit
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Isabelle Masneuf-Pomarède
- Université de Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR Œnologie 1366, ISVV, Villenave d’Ornon, France
- Bordeaux Sciences Agro, 1 cours du Général de Gaulle, Gradignan, France
| | - Virginie Lauvergeat
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
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Liu M, Lv X, Zhang W, Jiang M, Tian L, Qin L, Zou Y. Biological interactions control bacterial but not fungal β diversity during vegetation degradation in saline-alkaline soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170826. [PMID: 38340840 DOI: 10.1016/j.scitotenv.2024.170826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/19/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
The patterns and mechanisms by which soil bacterial and fungal community β-diversity respond to vegetation degradation in saline-alkaline soils are currently not clear, and in particular, the role of biotic interactions is relatively unknown. To investigate the assembly of bacterial and fungal communities in topsoil (0-10 cm) in saline-alkaline soils at different stages of vegetation degradation, the β-Mean Nearest Classification Unit Distance, the β-Nearest Taxon Index, and the Raup-Crick index were calculated. The relative importance of biotic and environmental factors in controlling β diversity under deterministic processes was also quantified by using relative importance analyses. The β diversity of soil bacterial and fungal communities responded differently in different stages of vegetation degradation in saline-alkaline soils, with bacterial β diversity increasing with increasing vegetation degradation but fungal β diversity showing few differences. Deterministic processes regulated soil bacterial community assembly, and biotic factors were important in driving changes in β diversity, whereas both deterministic and stochastic processes were essential in soil fungal community assembly, and environmental factors were important in affecting fungal β diversity. Furthermore, fungal β diversity is far more affected by interactions between fungus and bacteria than bacteria. Our study demonstrates the different effects of vegetation degradation on bacterial and fungal communities in saline soils to provide the overall implications for saline soils microorganisms in deteriorating ecosystems.
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Affiliation(s)
- Miao Liu
- State Key Laboratory of Black Soils Conservation and Utilization & Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station & Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianguo Lv
- State Key Laboratory of Black Soils Conservation and Utilization & Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station & Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Wenguang Zhang
- State Key Laboratory of Black Soils Conservation and Utilization & Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station & Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Ming Jiang
- State Key Laboratory of Black Soils Conservation and Utilization & Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station & Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lei Tian
- State Key Laboratory of Black Soils Conservation and Utilization & Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station & Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lei Qin
- State Key Laboratory of Black Soils Conservation and Utilization & Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station & Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Yuanchun Zou
- State Key Laboratory of Black Soils Conservation and Utilization & Heilongjiang Xingkai Lake Wetland Ecosystem National Observation and Research Station & Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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Castellano-Hinojosa A, Karlsen-Ayala E, Boyd NS, Strauss SL. Impact of repeated fumigant applications on soil properties, crop yield, and microbial communities in a plastic-mulched tomato production system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170659. [PMID: 38325480 DOI: 10.1016/j.scitotenv.2024.170659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
Pre-plant soil fumigation is widely applied to control nematodes, soil-borne fungal pathogens, and weeds in vegetable crops. However, most of the research evaluating the effect of fumigants on crop yield and soil microbial communities has been done on single compounds despite growers mainly applying fumigant combinations. We studied the effect of different fumigant combinations (chloropicrin, 1,3-dichloropropene, and metam potassium) on soil properties, crop yield, and the soil bacterial and fungal microbiome for two consecutive years in a plastic-mulched tomato production system in Florida (United States). While combinations of fumigants did not improve plant productivity more than the individual application of these products, application of fumigants with >60 % chloropicrin did significantly increase yield. Fumigant combinations had no significant effect on bacterial diversity, but fumigants with >35 % chloropicrin reduced soil fungal diversity and induced temporary changes in the soil bacterial and fungal community composition. These changes included short-term increases in the relative abundance of Firmicutes and Ascomycota, as well as decreases in other bacterial and fungal taxa. Repeated fumigation reduced network complexity and the relative abundance of several predicted bacterial functions and fungal guilds, particularly after fumigation and at end of harvest (3-months post fumigation). A structural equation model (SEM) showed fumigants not only directly impact crop yield, but they can also indirectly determine variations in plant productivity through effects on the soil microbiome. Overall, this study increases our understanding of the environmental and agricultural impacts of fumigants in a plastic-mulched tomato production system.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA
| | - Elena Karlsen-Ayala
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA; Northern Research Station, United States Department of Agriculture, Forest Service, 51 Millpond Road, Hamden, CT 06517, USA
| | - Nathan S Boyd
- Gulf Coast Research and Education Center, Department of Horticulture, Institute of Food and Agricultural Sciences, University of Florida, 14625 C.R. 672, Wimauma, FL 33598, USA
| | - Sarah L Strauss
- Southwest Florida Research and Education Center, Department of Soil, Water, and Ecosystem Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA.
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Chao H, Cai A, Heimburger B, Wu Y, Zhao D, Sun M, Hu F. Keystone taxa enhance the stability of soil bacterial communities and multifunctionality under steelworks disturbance. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120664. [PMID: 38508006 DOI: 10.1016/j.jenvman.2024.120664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Continuous discharge of wastewater, emissions, and solid wastes from steelworks poses environmental risks to ecosystems. However, the role of keystone taxa in maintaining multifunctional stability during environmental disturbances remains poorly understood. To address this, we investigated the community diversity, assembly mechanisms, and soil multifunctionality of soils collected from within the steelworks (I), within 2.5 km radius from the steelworks (E), and from an undisturbed area (CK) in Jiangsu Province, China, via 16 S rRNA sequencing. Significant differences were found in the Chao1 and the richness indexes of the total taxa (p < 0.05), while the diversity of keystone taxa was not significant at each site (p > 0.05). The deterministic processes for total taxa were 42.9%, 61.9% and 47.7% in CK, E, and I, respectively. Steelworks stress increased the deterministicity of keystone taxa from 52.3% in CK to 61.9% in E and I soils. The average multifunctionality indices were 0.518, 0.506 and 0.513 for CK, E and I, respectively. Although the soil multifunctionality was positive correlated with α diversity of both the total and keystone taxa, the average degree of keystone taxa in functional network increased significantly (79.96 and 65.58, respectively), while the average degree of total taxa decreased (44.59 and 51.25, respectively) in the E and I. This suggests keystone taxa contribute to promoting the stability of ecosystems. With increasing disturbance, keystone taxa shift their function from basic metabolism (ribosome biogenesis) to detoxification (xenobiotics biodegradation, metabolism, and benzoate degradation). Here we show that keystone taxa are the most important factor in maintaining stable microbial communities and functions, providing new insights for mitigating pollution stress and soil health protection.
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Affiliation(s)
- Huizhen Chao
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China; J.F. Blumenbach Institute of Zoology and Anthropology, University of Gottingen, Untere Karspule 2, 37073, Gottingen, Germany
| | - Anjuan Cai
- Jiangsu Provincial Academy of Environmental Science, 210019, China
| | - Bastian Heimburger
- J.F. Blumenbach Institute of Zoology and Anthropology, University of Gottingen, Untere Karspule 2, 37073, Gottingen, Germany
| | - Yunling Wu
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Duokai Zhao
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingming Sun
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Feng Hu
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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Fan Q, Liu K, Wang Z, Liu D, Li T, Hou H, Zhang Z, Chen D, Zhang S, Yu A, Deng Y, Cui X, Che R. Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits. Mol Ecol 2024; 33:e17302. [PMID: 38421102 DOI: 10.1111/mec.17302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024]
Abstract
Revealing the mechanisms underlying soil microbial community assembly is a fundamental objective in molecular ecology. However, despite increasing body of research on overall microbial community assembly mechanisms, our understanding of subcommunity assembly mechanisms for different prokaryotic and fungal taxa remains limited. Here, soils were collected from more than 100 sites across southwestern China. Based on amplicon high-throughput sequencing and iCAMP analysis, we determined the subcommunity assembly mechanisms for various microbial taxa. The results showed that dispersal limitation and homogenous selection were the primary drivers of soil microbial community assembly in this region. However, the subcommunity assembly mechanisms of different soil microbial taxa were highly variable. For instance, the contribution of homogenous selection to Crenarchaeota subcommunity assembly was 70%, but it was only around 10% for the subcommunity assembly of Actinomycetes, Gemmatimonadetes and Planctomycetes. The assembly of subcommunities including microbial taxa with higher occurrence frequencies, average relative abundance and network degrees, as well as wider niches tended to be more influenced by homogenizing dispersal and drift, but less affected by heterogeneous selection and dispersal limitation. The subcommunity assembly mechanisms also varied substantially among different functional guilds. Notably, the subcommunity assembly of diazotrophs, nitrifiers, saprotrophs and some pathogens were predominantly controlled by homogenous selection, while that of denitrifiers and fungal pathogens were mainly affected by stochastic processes such as drift. These findings provide novel insights into understanding soil microbial diversity maintenance mechanisms, and the analysis pipeline holds significant value for future research.
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Affiliation(s)
- Qiuping Fan
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Kaifang Liu
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Zelin Wang
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Dong Liu
- School of Life Sciences, Yunnan University, Kunming, China
| | - Ting Li
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Hou
- School of Ecology and Environment Science, Yunnan University, Kunming, China
| | - Zejin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Danhong Chen
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Song Zhang
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Anlan Yu
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Yongcui Deng
- School of Geography Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rongxiao Che
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
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Lopez-Moreno A, Cerk K, Rodrigo L, Suarez A, Aguilera M, Ruiz-Rodriguez A. Bisphenol A exposure affects specific gut taxa and drives microbiota dynamics in childhood obesity. mSystems 2024; 9:e0095723. [PMID: 38426791 PMCID: PMC10949422 DOI: 10.1128/msystems.00957-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/15/2024] [Indexed: 03/02/2024] Open
Abstract
Cumulative xenobiotic exposure has an environmental and human health impact which is currently assessed under the One Health approach. Bisphenol A (BPA) exposure and its potential link with childhood obesity that has parallelly increased during the last decades deserve special attention. It stands during prenatal or early life and could trigger comorbidities and non-communicable diseases along life. Accumulation in the nature of synthetic chemicals supports the "environmental obesogen" hypothesis, such as BPA. This estrogen-mimicking xenobiotic has shown endocrine disruptive and obesogenic effects accompanied by gut microbiota misbalance that is not yet well elucidated. This study aimed to investigate specific microbiota taxa isolated and selected by direct BPA exposure and reveal its role on the overall children microbiota community and dynamics, driving toward specific obesity dysbiosis. A total of 333 BPA-resistant isolated species obtained through culturing after several exposure conditions were evaluated for their role and interplay with the global microbial community. The selected BPA-cultured taxa biomarkers showed a significant impact on alpha diversity. Specifically, Clostridium and Romboutsia were positively associated promoting the richness of microbiota communities, while Intestinibacter, Escherichia-Shigella, Bifidobacterium, and Lactobacillus were negatively associated. Microbial community dynamics and networks analyses showed differences according to the study groups. The normal-weight children group exhibited a more enriched, structured, and connected taxa network compared to overweight and obese groups, which could represent a more resilient community to xenobiotic substances. In this sense, subnetwork analysis generated with the BPA-cultured genera showed a correlation between taxa connectivity and more diverse potential enzymatic BPA degradation capacities.IMPORTANCEOur findings indicate how gut microbiota taxa with the capacity to grow in BPA were differentially represented within differential body mass index children study groups and how these taxa affected the overall dynamics toward patterns of diversity generally recognized in dysbiosis. Community network and subnetwork analyses corroborated the better connectedness and stability profiles for normal-weight group compared to the overweight and obese groups.
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Affiliation(s)
- Ana Lopez-Moreno
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- />Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Klara Cerk
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, United Kingdom
| | - Lourdes Rodrigo
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
| | - Antonio Suarez
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Campus of Cartuja, University of Granada, Granada, Spain
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- />Instituto de Investigación Biosanitaria ibs, Granada, Spain
| | - Alicia Ruiz-Rodriguez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus of Cartuja, Granada, Spain
- Institute of Nutrition and Food Technology "José Mataix" (INYTA), Centre of Biomedical Research, University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Campus of Cartuja, University of Granada, Granada, Spain
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Song B, Xue Y, Yu Z, He Y, Liu Z, Fang J, Wang Y, Adams JM, Hu Y, Razavi BS. Toxic metal contamination effects mediated by hotspot intensity of soil enzymes and microbial community structure. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133556. [PMID: 38262314 DOI: 10.1016/j.jhazmat.2024.133556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Metal contamination from mine waste is a widespread threat to soil health. Understanding of the effects of toxic metals from mine waste on the spatial patterning of rhizosphere enzymes and the rhizosphere microbiome remains elusive. Using zymography and high-throughput sequencing, we conducted a mesocosm experiment with mine-contaminated soil, to compare the effects of different concentrations of toxic metals on exoenzyme kinetics, microbial communities, and maize growth. The negative effects of toxic metals exerted their effects largely on enzymatic hotspots in the rhizosphere zone, affecting both resistance and the area of hotspots. This study thus revealed the key importance of such hotspots in overall changes in soil enzymatic activity under metal toxicity. Statistical and functional guild analysis suggested that these enzymatic changes and associated microbial community changes were involved in the inhibition of maize growth. Keystone species of bacteria displayed negative correlations with toxic metals and positive correlations with the activity of enzymatic hotspots, suggesting a potential role. This study contributes to an emerging paradigm, that changes both in the activity of soil enzymes and soil biota - whether due to substrate addition or in this case toxicity - are largely confined to enzymatic hotspot areas.
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Affiliation(s)
- Bin Song
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China; University of Helsinki, Department of Forest Sciences, Helsinki, Finland
| | - Yue Xue
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, China
| | - Yucheng He
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Zihao Liu
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Jie Fang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Yuchao Wang
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, China
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China.
| | - Youning Hu
- School of Biological and Environmental Engineering, Xi'an University, Xi'an 710065, China.
| | - Bahar S Razavi
- Department of Soil and Plant Microbiome, Institute of Phytopathology, Christian-Albrechts-University of Kiel, Kiel 24118, Germany
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Huang YH, Yang YJ, Li JY, Lü H, Zhao HM, Xiang L, Li H, Mo CH, Li YW, Cai QY, Li QX. Root-associated bacteria strengthen their community stability against disturbance of antibiotics on structure and functions. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133317. [PMID: 38218031 DOI: 10.1016/j.jhazmat.2023.133317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/04/2023] [Accepted: 12/17/2023] [Indexed: 01/15/2024]
Abstract
Antibiotics affect bacterial community structure and functions in soil. However, the response and adaptation of root-associated bacterial communities to antibiotic stress remains poorly understood. Here, rhizobox experiments were conducted with maize (Zea mays L.) upon exposure to antibiotics ciprofloxacin or tetracycline. High-throughput sequencing analysis of bacterial community and quantitative PCR analysis of nitrogen cycling genes show that ciprofloxacin and tetracycline significantly shift bacterial community structure in bulk soil, whereas plant host may mitigate the disturbances of antibiotics on bacterial communities in root-associated niches (i.e., rhizosphere and rhizoplane) through the community stabilization. Deterministic assembly, microbial interaction, and keystone species (e.g., Rhizobium and Massilia) of root-associated bacterial communities benefit the community stability compared with those in bulk soil. Meanwhile, the rhizosphere increases antibiotic dissipation, potentially reducing the impacts of antibiotics on root-associated bacterial communities. Furthermore, rhizospheric effects deriving from root exudates alleviate the impacts of antibiotics on the nitrogen cycle (i.e., nitrification, organic nitrogen conversion and denitrification) as confirmed by functional gene quantification, which is largely attributed to the bacterial community stability in rhizosphere. The present study enhances the understanding on the response and adaptation of root-associated bacterial community to antibiotic pollution.
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Affiliation(s)
- Yu-Hong Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yu-Jie Yang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jie-Yu Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huixiong Lü
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Qing X Li
- Department of Molecular Bioscience and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
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Matteoli FP, Silva AMM, de Araújo VLVP, Feiler HP, Cardoso EJBN. Organic farming promotes the abundance of fungi keystone taxa in bacteria-fungi interkingdom networks. World J Microbiol Biotechnol 2024; 40:119. [PMID: 38429532 DOI: 10.1007/s11274-024-03926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Soil bacteria-fungi interactions are essential in the biogeochemical cycles of several nutrients, making these microbes major players in agroecosystems. While the impact of the farming system on microbial community composition has been extensively reported in the literature, whether sustainable farming approaches can promote associations between bacteria and fungi is still unclear. To study this, we employed 16S, ITS, and 18S DNA sequencing to uncover how microbial interactions were affected by conventional and organic farming systems on maize crops. The Bray-Curtis index revealed that bacterial, fungal, and arbuscular mycorrhizal fungi communities were significantly different between the two farming systems. Several taxa known to thrive in healthy soils, such as Nitrosophaerales, Orbiliales, and Glomus were more abundant in the organic farming system. Constrained ordination revealed that the organic farming system microbial community was significantly correlated with the β-glucosidase activity, whereas the conventional farming system microbial community significantly correlated with soil pH. Both conventional and organic co-occurrence interkingdom networks exhibited a parallel node count, however, the former had a higher number of edges, thus being denser than the latter. Despite the similar amount of fungal nodes in the co-occurrence networks, the organic farming system co-occurrence network exhibited more than 3-fold the proportion of fungal taxa as keystone nodes than the conventional co-occurrence network. The genera Bionectria, Cercophora, Geastrum, Penicillium, Preussia, Metarhizium, Myceliophthora, and Rhizophlyctis were among the fungal keystone nodes of the organic farming system network. Altogether, our results uncover that beyond differences in microbial community composition between the two farming systems, fungal keystone nodes are far more relevant in the organic farming system, thus suggesting that bacteria-fungi interactions are more frequent in organic farming systems, promoting a more functional microbial community.
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Affiliation(s)
- Filipe Pereira Matteoli
- Laboratory of Microbial Bioinformatics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru, Brazil.
| | - Antonio M M Silva
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Victor L V P de Araújo
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Henrique P Feiler
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Elke J B N Cardoso
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
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Yang J, Du Z, Huang C, Li W, Xi B, Zhu L, Wu X. Dynamics of microbial functional guilds involved in the humification process during aerobic composting of chicken manure on an industrial scale. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:21044-21056. [PMID: 38381293 DOI: 10.1007/s11356-024-32390-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
Proper composting treatment of poultry manure waste is recommended before its use as a fertilizer. This involves many bioprocesses driven by microorganisms. Therefore, it is important to understand microbial mechanisms behind these bioprocesses in manure composting systems. Many efforts have been made to study the microbial community structure and diversity in these systems using high-throughput sequencing techniques. However, the dynamics of microbial interaction and functionality, especially for key microbial functional guilds, are not yet fully understood. To address these knowledge gaps, we collected samples from a 150-day industrial chicken manure composting system and performed the microbial network analysis based on the sequencing data. We found that the family Bacillaceae and genus Bacillus might play important roles in organic matter biodegradation at the mesophilic/thermophilic phases. Genera Virgibacillus, Gracilibacillus, Nocardiopsis, Novibacillus, and Bacillaceae_BM62 were identified as the key ones for humic acid synthesis at the mature phases. These findings improve our understanding about the fundamental mechanisms behind manure composting and can aid the development of microbial agents to promote manure composting performance.
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Affiliation(s)
- Jie Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Zhe Du
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Caihong Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China.
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Wei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Lin Zhu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xinxin Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, No. 8 Dayangfang, Beiyuan Road, Chaoyang District, Beijing, 100012, China
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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45
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Ren K, Yang X, Li J, Jin H, Gu K, Chen Y, Liu M, Luo Y, Jiang Y. Alleviating the adverse effects of Cd-Pb contamination through the application of silicon fertilizer: Enhancing soil microbial diversity and mitigating heavy metal contamination. CHEMOSPHERE 2024; 352:141414. [PMID: 38336042 DOI: 10.1016/j.chemosphere.2024.141414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
The use of silicon fertilizer (SF) as a means of remediating cadmium (Cd) and lead (Pb) pollution has proven to be beneficial. However, the mechanism via which SF enhances soil quality and crop productivity under Cd- and Pb-contaminated soil (S) remains unclear. This study investigated the impacts of chemical fertilizer, mineral SF (MSF), and organic SF (OSF) on microbial community structure, activity of nutrient acquisition enzymes, and growth of tobacco in the presence of S condition. SF significantly reduced the contents of Cd and Pb in soil under S condition by 6.92-42.43% and increased plant height and leaf area by 15.27-81.77%. Moreover, the use of SF was observed to increase the efficiency of soil carbon and phosphorus cycling under S condition by 6.88-23.08%. Concurrently, SF was found to play a crucial role in facilitating the establishment of a complex, efficient, and interdependent molecular ecological network among soil microorganisms. In this context, Actinobacteriota, Bacteroidota, Ascomycota, and Basidiomycota were observed to be integral components of this network. SF was found to have a substantial positive impact on the metabolic functions and organismal systems of soil microorganisms. Moreover, the combined utilization of the Mantel test and partial least squares path model provided empirical evidence supporting the assertion that the administration of SF had a positive impact on both soil nutrient acquisition enzyme activity and tobacco growth, which was attributed to the enhancement of soil microbial diversity resulting from the application of SF. Furthermore, compared with MSF, OSF has advantages in reducing soil Pb and Cd content, promoting tobacco agronomic traits, increasing the number of key microbial communities, and maintaining the structural stability of microbial networks. The aforementioned findings, therefore, suggest that the OSF played a pivotal role in alleviating the adverse impacts of S, thereby demonstrating its efficacy in this particular process.
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Affiliation(s)
- Ke Ren
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China; College of Agronomy and Biotechnology, Southwest University / Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Xiongwei Yang
- College of Landscape Architecture, Southwest Forestry University, Kunming, 650224, China
| | - Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Hongyan Jin
- College of Landscape Architecture, Southwest Forestry University, Kunming, 650224, China
| | - Kaiyuan Gu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China; College of Agronomy and Biotechnology, Southwest University / Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Yi Chen
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Ming Liu
- College of Agronomy and Biotechnology, Southwest University / Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China
| | - Yigui Luo
- College of Tobacco Science, Yunnan Agricultural University, Kunming, 650031, China.
| | - Yonglei Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China.
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Tang M, Chen Q, Zhong H, Liu S, Sun W. CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater. WATER RESEARCH 2024; 251:121137. [PMID: 38246077 DOI: 10.1016/j.watres.2024.121137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/06/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 metagenome-assembled genomes (MAGs) from 66 groundwater samples, we explored the effect of antibiotics on bacterial, archaeal, and fungal communities, and revealed the pivotal microbes and their mechanisms in coping with antibiotic stress. The results indicated that antibiotics had the most significant influence on bacterial and archaeal communities, while the impact on the fungal community was minimal. Analysis of co-occurrence networks between antibiotics and microbes revealed the critical roles of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea, two representative microbial groups in groundwater ecosystem, in coping with antibiotic resistance and enhancing network connectivity and complexity. Further genomic analysis demonstrated that CPR bacteria carried approximately 6 % of the identified antibiotic resistance genes (ARGs), indicating their potential to withstand antibiotics on their own. Meanwhile, the genomes of CPR bacteria and DPANN archaea were found to encode diverse biosynthetic gene clusters (BGCs) responsible for producing antimicrobial metabolites, which could not only assist CPR and DPANN organisms but also benefit the surrounding microbes in combating antibiotic stress. These findings underscore the significant impact of antibiotics on prokaryotic microbial communities in groundwater, and highlight the importance of CPR bacteria and DPANN archaea in enhancing the overall resilience and functionality of the microbial community in the face of antibiotic stress.
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Affiliation(s)
- Moran Tang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Qian Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China.
| | - Haohui Zhong
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Shufeng Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Weiling Sun
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China.
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47
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Liu J, Pei S, Zheng Q, Li J, Liu X, Ruan Y, Luo B, Ma L, Chen R, Hu W, Niu J, Tian T. Heavy metal contamination impacts the structure and co-occurrence patterns of bacterial communities in agricultural soils. J Basic Microbiol 2024; 64:e2300435. [PMID: 38150647 DOI: 10.1002/jobm.202300435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/12/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023]
Abstract
Heavy metal (HM) contamination caused by mining and smelting activities can be harmful to soil microbiota, which are highly sensitive to HM stress. Here, we explore the effects of HM contamination on the taxonomic composition, predicted function, and co-occurrence patterns of soil bacterial communities in two agricultural fields with contrasting levels of soil HMs (i.e., contaminated and uncontaminated natural areas). Our results indicate that HM contamination does not significantly influence soil bacterial α diversity but changes the bacterial community composition by enriching the phyla Gemmatimonadetes, Planctomycetes, and Parcubacteria and reducing the relative abundance of Actinobacteria. Our results further demonstrate that HM contamination can strengthen the complexity and modularity of the bacterial co-occurrence network but weaken positive interactions between keystone taxa, leading to the gradual disappearance of some taxa that originally played an important role in healthy soil, thereby possibly reducing the resistance of bacterial communities to HM toxicity. The predicted functions of bacterial communities are related to membrane transport, amino acid metabolism, energy metabolism, and carbohydrate metabolism. Among these, functions related to HM detoxification and antioxidation are enriched in uncontaminated soils, while HM contamination enriches functions related to metal resistance. This study demonstrated that microorganisms adapt to the stress of HM pollution by adjusting their composition and enhancing their network complexity and potential ecological functions.
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Affiliation(s)
- Jiangyun Liu
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Shuwei Pei
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Qiwen Zheng
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Jia Li
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Xingrong Liu
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Ye Ruan
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Bin Luo
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Li Ma
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Rentong Chen
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Weigang Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, The People's Republic of China
| | - Jingping Niu
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
| | - Tian Tian
- School of Public Health, Lanzhou University, Lanzhou, Gansu, The People's Republic of China
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48
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Zhao P, Gao G, Ding G, Zhang Y, Ren Y. Fungal complexity and stability across afforestation areas in changing desert environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169398. [PMID: 38114026 DOI: 10.1016/j.scitotenv.2023.169398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
The great achievements in combating desertification are attributed to large-scale afforestation, yet we lack verification of how the stability of the fungal community changes in afforestation areas in desert environments. Here, we present the fungal network structure from different niches (root and bulk soil) of plantations of Mongolian pine, a crucial species for afforestation introduced widely in desertification regions. We assessed changes in community complexity and stability of root-associated fungi (RAF) and soil fungi (SF) among different introduction sites: the Hulunbuir Desert (HB), the Horqin Desert (HQ) and the Mu Us Desert (MU). To illuminate the complexity and stability of the fungal network, the differences in topological properties, fungal function, and vegetation and environmental factors between introduction sites were fully considered. We showed that (1) the SF networks had more nodes and edges than the RAF networks. There was a lower ratio of negative:positive cohesion of RAF networks in HB and MU. For SF but not for RAF, across the three introduction sites, a higher modularity and ratio of negative:positive cohesion indicated higher stability. (2) Ectomycorrhizal (EcM) fungi were the dominant functional group in the RAF network (especially in HQ), and were only significantly correlated with vegetation factor. There was a higher relative abundance and number of OTUs of saprophytic fungi in the SF network and they showed positive correlations with soil nutrients. (3) RAF and SF network complexity and stability showed different responses to environmental and vegetation variables. The key determinant of the complexity and stability of the SF networks in Mongolian pine plantations was soil nutrients, followed by climate conditions. The composition and structure of the RAF community was closely related to host plants. Therefore, clarifying the complexity and stability of fungal communities in afforestation areas in changing desert environments is helpful for understanding the interactions between the environment, plants and fungi.
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Affiliation(s)
- Peishan Zhao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Guanglei Gao
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China.
| | - Guodong Ding
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Ying Zhang
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yue Ren
- Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China; Engineering Research Centre of Forestry Ecological Engineering, Ministry of Education, Beijing Forestry University, Beijing 100083, China; Key Laboratory of State Forestry and Grassland Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
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49
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Khatri-Chhetri U, Banerjee S, Thompson KA, Quideau SA, Boyce MS, Bork EW, Carlyle CN. Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169353. [PMID: 38104847 DOI: 10.1016/j.scitotenv.2023.169353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.
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Affiliation(s)
- Upama Khatri-Chhetri
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Karen A Thompson
- Trent School of Environment, Trent University, Peterborough, ON K9L 0G2, Canada
| | - Sylvie A Quideau
- Department of Renewable Resources, Earth Science Building University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Mark S Boyce
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Edward W Bork
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Cameron N Carlyle
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
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50
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Zhang J, Na M, Wang Y, Ge W, Zhou J, Zhou S. Cadmium levels and soil pH drive structure and function differentiation of endophytic bacterial communities in Sedum plumbizincicola: A field study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168828. [PMID: 38029975 DOI: 10.1016/j.scitotenv.2023.168828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/01/2023]
Abstract
Sedum plumbizincicola is a promising hyperaccumulator for heavy metal phytoremediation. It grows in heavy metal polluted soil and stores specific endophyte resources with heavy metal tolerance or growth promotion characteristics. In this study, the endophyte communities of S. plumbizincicola, growing naturally in the field (two former mining locations and one natural location) were investigated, and their structure and function were comparatively studied. The bioaccumulation and translocation characteristics of cadmium (Cd) and selenium (Se) in S. plumbizincicola were also evaluated. The results showed that the heavy metal pollution reduced the richness and diversity of endophyte communities. Soil pH and Cd concentration could be the key factors affecting the composition of the endophyte community. Co-occurrence network analysis identified that 22 keystone taxa belonging to Actinobacteriota, Firmicutes, Myxococcota and Proteobacteria were positively correlated with Cd bioaccumulation and translocation. The predicted endophyte metabolic pathways were enriched in physiological metabolism, immune system, and genetic Information processing. These findings may help to understand how endophytes assist host plants to enhance their adaptability to harsh environments, and provide a basis for further exploration of plant-endophyte interactions and improvement in phytoremediation efficiency.
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Affiliation(s)
- Jinming Zhang
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241002, China
| | - Meng Na
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241002, China; Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Anhui Normal University, Wuhu, Anhui 241002, China
| | - Yukun Wang
- College of Resources & Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wen Ge
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241002, China
| | - Jihai Zhou
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241002, China; Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Anhui Normal University, Wuhu, Anhui 241002, China
| | - Shoubiao Zhou
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241002, China; Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Anhui Normal University, Wuhu, Anhui 241002, China.
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