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Chen P, Li Z, Cao N, Wu RX, Kuang ZR, Yu F. Comparison of Bacterial Communities in Five Ectomycorrhizal Fungi Mycosphere Soil. Microorganisms 2024; 12:1329. [PMID: 39065098 PMCID: PMC11279354 DOI: 10.3390/microorganisms12071329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Ectomycorrhizal fungi have huge potential value, both nutritionally and economically, but most of them cannot be cultivated artificially. To better understand the influence of abiotic and biotic factors upon the growth of ectomycorrhizal fungi, mycosphere soil and bulk soil of five ectomycorrhizal fungi (Calvatia candida, Russula brevipes, Leucopaxillus laterarius, Leucopaxillus giganteus, and Lepista panaeola) were used as research objects for this study. Illumina MiSeq sequencing technology was used to analyze the community structure of the mycosphere and bulk soil bacteria of the five ectomycorrhizal fungi, and a comprehensive analysis was conducted based on soil physicochemical properties. Our results show that the mycosphere soil bacteria of the five ectomycorrhizal fungi are slightly different. Escherichia, Usitatibacter, and Bradyrhizobium are potential mycorrhizal-helper bacteria of distinct ectomycorrhizal fungi. Soil water content, soil pH, and available potassium are the main factors shaping the soil bacterial community of the studied ectomycorrhizal fungi. Moreover, from the KEGG functional prediction and LEfSe analysis, there are significant functional differences not only between the mycosphere soil and bulk soil. 'Biosynthesis of terpenoidsand steroids', 'alpha-Linolenic acid metabolism', 'Longevity regulating pathway-multiple species', 'D-Arginine and D-ornithine metabolism', 'Nitrotoluene degradation' and other functions were significantly different in mycosphere soil. These findings have pivotal implications for the sustainable utilization of ectomycorrhizal fungi, the expansion of edible fungus cultivation in forest environments, and the enhancement of derived economic benefits.
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Affiliation(s)
| | | | | | | | | | - Fei Yu
- College of Forestry, Shanxi Agricultural University, Jinzhong 030801, China; (P.C.); (Z.L.); (N.C.); (R.-X.W.); (Z.-R.K.)
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Zhou Z, Huang F, Chen L, Liu F, Wang B, Tang J. Effects of antibiotics on microbial nitrogen cycling and N 2O emissions: A review. CHEMOSPHERE 2024; 357:142034. [PMID: 38615962 DOI: 10.1016/j.chemosphere.2024.142034] [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: 01/14/2024] [Revised: 03/31/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Sulfonamides, quinolones, tetracyclines, and macrolides are the most prevalent classes of antibiotics used in both medical treatment and agriculture. The misuse of antibiotics leads to their extensive dissemination in the environment. These antibiotics can modify the structure and functionality of microbial communities, consequently impacting microbial-mediated nitrogen cycling processes including nitrification, denitrification, and anammox. They can change the relative abundance of nirK/norB contributing to the emission of nitrous oxide, a potent greenhouse gas. This review provides a comprehensive examination of the presence of these four antibiotic classes across different environmental matrices and synthesizes current knowledge of their effects on the nitrogen cycle, including the underlying mechanisms. Such an overview is crucial for understanding the ecological impacts of antibiotics and for guiding future research directions. The presence of antibiotics in the environment varies widely, with significant differences in concentration and type across various settings. We conducted a comprehensive review of over 70 research articles that compare various aspects including processes, antibiotics, concentration ranges, microbial sources, experimental methods, and mechanisms of influence. Antibiotics can either inhibit, have no effect, or even stimulate nitrification, denitrification, and anammox, depending on the experimental conditions. The influence of antibiotics on the nitrogen cycle is characterized by dose-dependent responses, primarily inhibiting nitrification, denitrification, and anammox. This is achieved through alterations in microbial community composition and diversity, carbon source utilization, enzyme activities, electron transfer chain function, and the abundance of specific functional enzymes and antibiotic resistance genes. These alterations can lead to diminished removal of reactive nitrogen and heightened nitrous oxide emissions, potentially exacerbating the greenhouse effect and related environmental issues. Future research should consider diverse reaction mechanisms and expand the scope to investigate the combined effects of multiple antibiotics, as well as their interactions with heavy metals and other chemicals or organisms.
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Affiliation(s)
- Zikun Zhou
- MOE Key Laboratory of Solid Waste Treatment and Resource Recycle, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Fuyang Huang
- MOE Key Laboratory of Solid Waste Treatment and Resource Recycle, Southwest University of Science and Technology, Mianyang, Sichuan, PR China.
| | - Linpeng Chen
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing, PR China
| | - Fei Liu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences (Beijing), Beijing, PR China
| | - Bin Wang
- MOE Key Laboratory of Solid Waste Treatment and Resource Recycle, Southwest University of Science and Technology, Mianyang, Sichuan, PR China.
| | - Jie Tang
- College of Environment and Civil Engineering, Chengdu University of Technology, Chengdu, Sichuan, PR China
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Qiu L, Sha A, Li N, Ran Y, Xiang P, Zhou L, Zhang T, Wu Q, Zou L, Chen Z, Li Q, Zhao C. The characteristics of fungal responses to uranium mining activities and analysis of their tolerance to uranium. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 277:116362. [PMID: 38657459 DOI: 10.1016/j.ecoenv.2024.116362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/29/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
The influence of uranium (U) mining on the fungal diversity (FD) and communities (FC) structure was investigated in this work. Our results revealed that soil FC richness and FD indicators obviously decreased due to U, such as Chao1, observed OTUs and Shannon index (P<0.05). Moreover, the abundances of Mortierella, Gibberella, and Tetracladium were notably reduced in soil samples owing to U mining activities (P<0.05). In contrast, the abundances of Cadophora, Pseudogymnoascus, Mucor, and Sporormiella increased in all soil samples after U mining (P<0.05). Furthermore, U mining not only dramatically influenced the Plant_Pathogen guild and Saprotroph and Pathotroph modes (P<0.05), but also induced the differentiation of soil FC and the enrichment of the Animal_Pathogen-Soil_Saprotroph and Endophyte guilds and Symbiotroph and Pathotroph Saprotroph trophic modes. In addition, various fungal populations and guilds were enriched to deal with the external stresses caused by U mining in different U mining areas and soil depths (P<0.05). Finally, nine U-tolerant fungi were isolated and identified with a minimum inhibitory concentration range of 400-600 mg/L, and their adsorption efficiency for U ranged from 11.6% to 37.9%. This study provides insights into the impact of U mining on soil fungal stability and the response of fungi to U mining activities, as well as aids in the screening of fungal strains that can be used to promote remediation of U mining sites on plateaus.
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Affiliation(s)
- Lu Qiu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Ajia Sha
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Na Li
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China
| | - Yanqiong Ran
- Sichuan Ecological and Environmental Monitoring Center, Chengdu, Sichuan, China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Lin Zhou
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhaoqiong Chen
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China.
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
| | - Changsong Zhao
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China.
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Zhu S, Zhao W, Sun S, Yang X, Mao H, Sheng L, Chen Z. Metagenomic analysis revealed N-metabolizing microbial response of Iris tectorum to Cr stress after colonization by arbuscular mycorrhizal fungi. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116157. [PMID: 38430578 DOI: 10.1016/j.ecoenv.2024.116157] [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: 08/10/2023] [Revised: 11/08/2023] [Accepted: 02/25/2024] [Indexed: 03/04/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting bacteria enhance plant tolerance to abiotic stress and promote plant growth in contaminated soil. However, the interaction mechanism between rhizosphere microbial communities under chromium (Cr) stress remains unclear. This study conducted a greenhouse pot experiment and metagenomics analysis to reveal the comprehensive effects of the interaction between AMF (Rhizophagus intraradices) and nitrogen-N metabolizing plant growth promoters on the growth of Iris tectorum. The results showed that AMF significantly increased the biomass and nutrient levels of I. tectorum in contaminated soil and decreased the content of Cr in the soil. Metagenomics analysis revealed that the structure and composition of the rhizosphere microbial community involved in nitrogen metabolism changed significantly after inoculation with AMF under Cr stress. Functional genes related to soil nitrogen mineralization (gltB, gltD, gdhA, ureC, and glnA), nitrate reduction to ammonium (nirB, nrfA, and nasA), and soil nitrogen assimilation (NRT, nrtA, and nrtC) were up-regulated in the N-metabolizing microbial community. In contrast, the abundance of functional genes involved in denitrification (nirK and narI) was down-regulated. In addition, the inoculation of AMF regulates the synergies between the N-metabolic rhizosphere microbial communities and enhances the complexity and stability of the rhizosphere ecological network. This study provides a basis for improving plant tolerance to heavy metal stress by regulating the functional abundance of N-metabolizing plant growth-promoting bacteria through AMF inoculation. It helps to understand the potential mechanism of wetland plant remediation of Cr-contaminated soil.
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Affiliation(s)
- Sixi Zhu
- College of Eco-environment Engineering, Guizhou Minzu University, China; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China.
| | - Wei Zhao
- College of Eco-environment Engineering, Guizhou Minzu University, China; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Suxia Sun
- College of Eco-environment Engineering, Guizhou Minzu University, China; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Xiuqin Yang
- College of Eco-environment Engineering, Guizhou Minzu University, China; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Huan Mao
- College of Eco-environment Engineering, Guizhou Minzu University, China; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Luying Sheng
- College of Eco-environment Engineering, Guizhou Minzu University, China; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Zhongbing Chen
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcka 129, Suchdol, Praha 16500, Czech Republic
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Ye R, Huo W, Shao Y, Wang H, Lu W, Zhang H. Fungal community diversity and their contribution to nitrogen cycling in in-situ aerated landfills: Insights from field and laboratory studies. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 179:1-11. [PMID: 38442433 DOI: 10.1016/j.wasman.2024.02.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
The application of in-situ aeration technology in landfills has been reported to promote fungal growth, but the community diversity and function of fungi in the aerated landfill system remain unknown. This study firstly investigated an in-situ aerated remediation landfill site to characterize the fungal community diversity in refuse. And to further reveal the fungal involvement in the nitrogen cycling system, laboratory-scale simulated aerated landfill reactors were then constructed. The results in the aerated landfill site showed a significant correlation between fungal community structure and ammonia nitrogen content in the refuse. Dominant fungi in the fungal community included commonly found environmental fungi such as Fusarium, Aspergillus, Gibberella, as well as unique fungi in the aerated system like Chaetomium. In the laboratory-scale aerated landfill simulation experiments, the fungal system was constructed using bacterial inhibitor, and nitrogen balance analysis confirmed the significant role of fungal nitrification in the nitrogen cycling process. When ammonia nitrogen was not readily available, fungi converted organic nitrogen to nitrate, serving as the main nitrification mechanism in the system, with a contribution rate ranging from 62.71 % to 100 % of total nitrification. However, when ammonia nitrogen was present in the system, autotrophic nitrification became the main mechanism, and the contribution of fungal nitrification to total nitrification was only 15.96 %. Additionally, fungi were capable of directly utilizing nitrite for nitrate production with a rate of 4.65 mg L-1 d-1. This research article contributes to the understanding of the importance of fungi in the aerated landfill systems, filling a gap in knowledge.
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Affiliation(s)
- Rong Ye
- School of Environment, Tsinghua University, Beijing 100084, China; Nanjing Institute of Environment Sciences, Ministry of Ecology & Environment, Nanjing 210042, China
| | - Weizhong Huo
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yuchao Shao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hongtao Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wenjing Lu
- School of Environment, Tsinghua University, Beijing 100084, China.
| | - Houhu Zhang
- Nanjing Institute of Environment Sciences, Ministry of Ecology & Environment, Nanjing 210042, China
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Zhao M, Sun Y, Liu S, Li Y, Chen Y. Effects of stand density on the structure of soil microbial functional groups in Robinia pseudoacacia plantations in the hilly and gully region of the Loess Plateau, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169337. [PMID: 38103600 DOI: 10.1016/j.scitotenv.2023.169337] [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: 08/04/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Elucidating the responses of soil microbial functional groups to changes in stand density is crucial for understanding the sustainability of forest development. In this study, we obtained soil samples from Robinia pseudoacacia plantations of three different stand densities (low, middle, and high densities of 750, 1125, and 1550 trees ha-1, respectively) in the hilly and gully region of the Loess Plateau, China. We sought to determine the effects of stand density on the structure of soil microbial functional groups. Stand density had no significant effects on species diversity indices of fungal trophic modes or bacterial functional groups involved in carbon (C) cycling and nitrogen (N) cycling. However, differences in stand density substantially altered the composition of fungal functional groups. In low-density plantations, saprophytic fungi were the main trophic mode, with a high relative abundance of ∼62 %, whereas the fungal communities associated with middle- and high-density plantations were dominated by other fungi with a combined trophic mode, which accounted for ∼43 % and ∼41 % of the fungal trophic modes, respectively. Furthermore, we detected increases in the relative abundance of plant pathogens, nitrifiers, and nitrous oxide-denitrifying bacteria with increasing stand density. Results of the Monte Carlo test showed that soil pH influenced the composition of soil fungal (but not bacterial) groups. These findings suggested that a high density of trees might inhibit the decomposition of recalcitrant organic material and stimulate nitrous oxide emission, consequently decreasing soil nutrient availability and stimulating soil N loss. Moreover, high-density stands might increase the potential risk for plant disease. Overall, the present study suggested that reducing stand density to coverage between 750 and 1125 trees ha-1 would increase soil nutrient availability and prevent N loss from the soil. To verify these suppositions, further research is needed to determine the links between microbial functional groups composition and soil biogeochemistry.
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Affiliation(s)
- Min Zhao
- Institute of Soil and Water Conservation, State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yarong Sun
- Institute of Soil and Water Conservation, State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Shaohua Liu
- Institute of Soil and Water Conservation, State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yichun Li
- Institute of Soil and Water Conservation, State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yunming Chen
- Institute of Soil and Water Conservation, State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Northwest A & F University, Yangling, Shaanxi 712100, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, China.
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Liu M, Xue R, Han N, Yang S, Wang D, Hu Y, Gu K, Su J. The impact of different preceding crops on soil nitrogen structure and nitrogen cycling in tobacco-planting soil. Sci Rep 2024; 14:1767. [PMID: 38243087 PMCID: PMC10799046 DOI: 10.1038/s41598-024-52285-z] [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: 10/07/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024] Open
Abstract
Soil nitrogen content, structure, and nitrogen cycling play a crucial role in tobacco growth quality, with different preceding crops having varying impacts on tobacco cultivation soil. This study conducted using field experiments, employed three treatments with different preceding crops, namely tobacco, barley, and rapeseed, to investigate the effects of different preceding crops on soil nitrogen structure and the expression levels of soil nitrogen cycling-related functional genes in tobacco cultivation soil. The results indicated that different preceding crops had varying effects on the content of different nitrogen forms in tobacco cultivation soil. Ammonium nitrogen and nitrate nitrogen were the two nitrogen forms which were most influenced by preceding crops, with the ammonium nitrogen content in soils following barley and rapeseed preceding crops increasing by 82.88% and 63.56%, respectively, compared to sole tobacco cultivation. The nitrate nitrogen content in tobacco cultivation soil was 26.97% higher following barley preceding crops and 24.39% higher following rapeseed preceding crops compared to sole tobacco cultivation. Simultaneously, different preceding crops also affected the expression levels of nitrogen cycling-related genes in tobacco cultivation soil. In the nitrification process, amoA was significantly impacted, with its expression reduced by 64.39% and 72.24% following barley and rapeseed preceding crops, respectively, compared to sole tobacco cultivation. In the denitrification process, except for the narG gene, all other genes were subjected to varying degrees of inhibition when preceded by barley and rapeseed crops. Correlation analysis between soil nitrogen structure and the expression levels of nitrogen cycling-related genes revealed that increased nitrogen levels suppressed the expression of Arch-amoA. Additionally, ammonium nitrogen strongly influenced the expression levels of most soil nitrogen cycling functional genes. In conclusion, preceding crops alter soil nitrogen structure, possibly due to changes in soil microorganisms, and different preceding crops modified the expression levels of nitrogen cycling-related genes in tobacco cultivation soil, consequently affecting the proportions of various nitrogen forms in the soil.
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Affiliation(s)
- Ming Liu
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Rujun Xue
- Weishan City Branch of Yunnan Tobacco Company, Weishan, 672400, Yunnan, China
| | - Ningbo Han
- Weishan City Branch of Yunnan Tobacco Company, Weishan, 672400, Yunnan, China
| | - Shanqin Yang
- Weishan City Branch of Yunnan Tobacco Company, Weishan, 672400, Yunnan, China
| | - Dexun Wang
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Yanxia Hu
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Kaiyuan Gu
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China
| | - Jiaen Su
- Dali Prefecture Branch of Yunnan Tobacco Company, Dali, 671000, Yunnan, China.
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Le Ho H, Tran-Van L, Quyen PTQ, Kim SG, Jiang LM, Chew KW, Khoo KS, Chan SS, Tran TNT, Nguyen TDP. Bioinformatic Approach to Investigate Larvae Gut Microbiota Cellulosimicrobium protaetiae via Whole-Genome Analysis. Mol Biotechnol 2024:10.1007/s12033-023-00984-9. [PMID: 38231315 DOI: 10.1007/s12033-023-00984-9] [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: 07/25/2023] [Accepted: 11/05/2023] [Indexed: 01/18/2024]
Abstract
The insect larvae Protaetia brevitarsis seulensis have recently been researched as a nutritious food source and concentrated on their environmental impacts. Therefore, their gut microbiota has been studied to elucidate their effects and roles on the environment. Of the abundance of bacterial genus identified based on the 16S rRNA genes from isolates of the gut of insect larva Protaetia brevitarsis seulensis, six of the prominent genus were identified as Bacillus (40.2%), Cellulosimicrobium (33.5%), Microbacterium (2.8%), Streptomyces (3%), Krasilnikoviella (17.5%), and Isoptericola (3%) and their similarity of 16S rRNA blast changed from 99 to 100%. Cellulosimicrobium protaetiae BI34T showed strong denitrification and cellulose degradation activity. The newly complete genome sequence of BI34T and the genomes of five species was published in the genus Cellulosimicrobium with emphasis on the denitrification and secondary metabolite genes. In order to elucidate the relationship between the strain BI34T and the host insect larva, the whole-genome sequence was analyzed and compared with the genomes of five strains in the same genus, Cellulosimicrobium, loaded from GenBank. Our results revealed the composition of the gut microbiota of the insect larvae and analyzed the genomic data for the new strain to predict its characteristics and to understand the nitrogen metabolism pathway.
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Affiliation(s)
- Han Le Ho
- The University of Danang, University of Science and Technology, 54 Nguyen Luong Bang St., Da Nang, 550 000, Vietnam
| | - Luan Tran-Van
- The University of Danang, University of Science and Technology, 54 Nguyen Luong Bang St., Da Nang, 550 000, Vietnam
| | - Phan Thi Quy Quyen
- The University of Danang, University of Technology and Education, 48 Cao Thang St., Danang, 550 000, Vietnam
| | - Song-Gun Kim
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup, 56212, Jeonbuk, Korea
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong, Daejeon, 34113, Korea
| | - Ling Min Jiang
- University of Science and Technology (UST), 217 Gajeong-ro, Yuseong, Daejeon, 34113, Korea
| | - Kit Wayne Chew
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan
| | - Sook Sin Chan
- Institut Sains Biologi, Fakulti Sains, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Thi Ngoc Thu Tran
- The University of Danang, University of Technology and Education, 48 Cao Thang St., Danang, 550 000, Vietnam
| | - Thi Dong Phuong Nguyen
- The University of Danang, University of Technology and Education, 48 Cao Thang St., Danang, 550 000, Vietnam.
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9
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Harrison TL, Parshuram ZA, Frederickson ME, Stinchcombe JR. Is there a latitudinal diversity gradient for symbiotic microbes? A case study with sensitive partridge peas. Mol Ecol 2024; 33:e17191. [PMID: 37941312 DOI: 10.1111/mec.17191] [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: 05/08/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
Mutualism is thought to be more prevalent in the tropics than temperate zones and may therefore play an important role in generating and maintaining high species richness found at lower latitudes. However, results on the impact of mutualism on latitudinal diversity gradients are mixed, and few empirical studies sample both temperate and tropical regions. We investigated whether a latitudinal diversity gradient exists in the symbiotic microbial community associated with the legume Chamaecrista nictitans. We sampled bacteria DNA from nodules and the surrounding soil of plant roots across a latitudinal gradient (38.64-8.68 °N). Using 16S rRNA sequence data, we identified many non-rhizobial species within C. nictitans nodules that cannot form nodules or fix nitrogen. Species richness increased towards lower latitudes in the non-rhizobial portion of the nodule community but not in the rhizobial community. The microbe community in the soil did not effectively predict the non-rhizobia community inside nodules, indicating that host selection is important for structuring non-rhizobia communities in nodules. We next factorially manipulated the presence of three non-rhizobia strains in greenhouse experiments and found that co-inoculations of non-rhizobia strains with rhizobia had a marginal effect on nodule number and no effect on plant growth. Our results suggest that these non-rhizobia bacteria are likely commensals-species that benefit from associating with a host but are neutral for host fitness. Overall, our study suggests that temperate C. nictitans plants are more selective in their associations with the non-rhizobia community, potentially due to differences in soil nitrogen across latitude.
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Affiliation(s)
- Tia L Harrison
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Zoe A Parshuram
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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10
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Li Q, Xiong Z, Xiang P, Zhou L, Zhang T, Wu Q, Zhao C. Effects of uranium mining on soil bacterial communities and functions in the Qinghai-Tibet plateau. CHEMOSPHERE 2024; 347:140715. [PMID: 37979803 DOI: 10.1016/j.chemosphere.2023.140715] [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: 05/10/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023]
Abstract
The microecological effects of plateau uranium mining are still unknown. In this study, we used 16S rRNA high-throughput sequencing to analyze the impact of plateau uranium mining on the microbial diversity and community structure of tailings soil, tunnel soil, and soil at different depths in an open pit. The results showed that uranium mining significantly reduced soil microbial community richness and diversity indicators, including Chao1, Pielou evenness, and Shannon index (P < 0.05). Uranium mining activities significantly reduced the abundance of RB41, Vicinamidactaceae, and Nitrospira (P < 0.05). Interestingly, the abundance of Thiobacillus, Sphingomonas, and Sulfuriferula significantly increased in the soil samples from various environments and depths during uranium mining (P < 0.05). Beta diversity analysis found that uranium mining resulted in the differentiation of soil microbial communities. Functional enrichment analysis found that uranium mining resulted in the functional enrichment of DNA binding response regulator, DNA helicase, methyl-accepting chemotaxis protein, and Helicase conserved C-terminal domain, whereas cell wall synthesis, nonspecific serine/threonine protein kinase, RNA polymerase sigma-70 factor, and ATP binding cassette transporter were significantly affected by uranium mining (P < 0.05). In addition, we also found that different uranium mining environments and soil depths enriched diverse microbial populations and functions to cope with the environmental pressures that were elicited by uranium mining, including Gaiella, Gemmatimonas, Lysobacter, Pseudomonas, signal transformation histidine kinase, DNA-directed DNA polymerase, and iron complex outer membrane receptor protein functions (P < 0.05). The results have enhanced our understanding of the impact of uranium mining on plateau soil microecological stability and the mechanism of microbial response to uranium mining activities for the first time and aided us in screening microbial strains that can promote the environmental remediation of uranium mining in plateaus.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhuang Xiong
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Lin Zhou
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Changsong Zhao
- School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China.
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11
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Rashad YM, Hafez M, Rashad M. Diazotrophic Azotobacter salinestris YRNF3: a probable calcite-solubilizing bio-agent for improving the calcareous soil properties. Sci Rep 2023; 13:20621. [PMID: 37996572 PMCID: PMC10667278 DOI: 10.1038/s41598-023-47924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
Calcareous soils are characterized by a high calcium carbonate content (calcite), which plays a crucial role in the soil structure, plant growth, and nutrient availability. The high content of CaCO3 leads to the increment of the soil alkalinity, which results in a lowering of the nutrient availability causing a challenge for the agriculture in these soils. In this study, the calcite-solubilizing potential of the diazotrophic Azotobacter salinestris YRNF3 was investigated in vitro as a probable bio-agent for enhancing the calcareous soils properties such as soil pH and nutrient availability. Twelve diazotrophic bacterial strains were isolated from wheat rhizosphere collected from different wheat-cultivated fields in five Egyptian governorates. Using Nessler's reagent, all isolated bacterial strains were found to have the ability to produce ammonia. By amplification of nifH gene, a PCR product of 450 bp was obtained for all isolated bacterial strains. For each isolate, three biological and three technical replicates were applied. All isolated diazotrophic bacteria were qualitatively screened for their calcite-solubilizing ability. To quantitatively investigate the calcite-solubilizing potential of A. salinestris YRNF3 in vitro, changes in the contents of soluble calcium (Ca2+), bicarbonate (HCO3-), total nitrogen (TN), total protein (TP), and pH were daily measured in its culture filtrate along 10 days of incubation. The results showed that the pH values in the culture filtrate ranged from 5.73 to 7.32. Concentration of Ca2+ and HCO3- in the culture filtrate significantly decreased with the increment in the incubation time, while concentration of TN increased along the time. The highest TN concentration (0.0807 gL-1) was observed on days 4 and 5, compared to that of the day 0 (0.0014 gL-1). Content of TP in the culture filtrate also significantly increased along the incubation period. The highest TP content was recorded in day 4 (0.0505%), while no TP content was recorded on day 0. Furthermore, data obtained revealed that A. salinestris YRNF3 produced acid phosphatase at low activity (5.4 U mL-1). HPLC analysis of the culture filtrate indicated production of different organic acids, namely lactic acid (82.57 mg mL-1), formic acid (46.8 mg mL-1), while acetic acid was detected in a low quantity (3.11 mg mL-1). For each analysis, three replicates of each treatment were analyzed. Means of the tested treatments were compared using Tukey's HSD test at p ≤ 0.05. In conclusion, findings of this work suggested that A. salinestris YRNF3 has the potential to be a probable bioagent to be used for the reclamation of the calcareous soils by solubilizing CaCO3, improving soil fertility, and promoting plant growth. However, further studies are needed to investigate its field application and their long-term effects on the soil properties and plant productivity. To the best of the author's knowledge, this is the first study reporting the calcite-solubilizing ability of a nitrogen-fixing bacteria. Having these two abilities by one microorganism is a unique feature, which qualifies it as a promising bioagent for reclamation of the calcareous soils.
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Affiliation(s)
- Younes M Rashad
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, 21934, Egypt.
| | - Mohamed Hafez
- Land and Water Technologies Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, 21934, Egypt.
| | - Mohamed Rashad
- Land and Water Technologies Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, 21934, Egypt
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12
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Lartey I, Benucci GMN, Marsh TL, Bonito GM, Melakeberhan H. Characterizing microbial communities associated with northern root-knot nematode ( Meloidogyne hapla) occurrence and soil health. Front Microbiol 2023; 14:1267008. [PMID: 38029134 PMCID: PMC10667709 DOI: 10.3389/fmicb.2023.1267008] [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: 07/25/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.
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Affiliation(s)
- Isaac Lartey
- Agricultural Nematology Laboratory, Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Gian M. N. Benucci
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Terence L. Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Gregory M. Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Haddish Melakeberhan
- Agricultural Nematology Laboratory, Department of Horticulture, Michigan State University, East Lansing, MI, United States
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13
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Li Y, Xiong L, Yu H, Zeng K, Wei Y, Li H, Zeng W, Ji X. Function and distribution of nitrogen-cycling microbial communities in the Napahai plateau wetland. Arch Microbiol 2023; 205:357. [PMID: 37872393 DOI: 10.1007/s00203-023-03695-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
Nitrogen is an essential component of living organisms and a major nutrient that limits life on Earth. Until now, freely available nitrogen mainly comes from atmospheric nitrogen, but most organisms rely on bioavailable forms of nitrogen, which depends on the complex network of microorganisms with a wide variety of metabolic functions. Microbial-mediated nitrogen cycling contributes to the biogeochemical cycling of wetlands, but its specific microbial abundance, composition, and distribution need to be studied. Based on the metagenomic data, we described the composition and functional characteristics of microbial nitrogen cycle-related genes in the Napahai plateau wetland. Six nitrogen cycling pathways existed, such as dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification, anammox, and nitrate assimilation. Most genes related to the nitrogen cycling in this region come from bacteria, mainly from Proteobacteria and Acidobacteria. Habitat types and nitrogen cycle-related genes largely explained the relative abundance of total nitrogen pathways. Phylogenetic trees were constructed based on nitrogen cycle-related genes from different habitats and sources, combined with PCoA analysis, most of them clustered separately, indicating richness and uniqueness. Some microbial groups seemed to be special or general in the nitrogen cycling. In conclusion, it suggested that microorganisms regulated the N cycling process, and may lead to N loss throughout the wetland, thus providing a basis for further elucidation of the microbial regulation of N cycling processes and the Earth's elemental cycles.
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Affiliation(s)
- Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Kun Zeng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Weikun Zeng
- School of Medicine, Kunming University, Kunming, 650214, China
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
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14
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Zaman T, Asad SA, Irshad M, Faridullah, Shahzad M, Nazir R, Arefeen A, Iqbal A, Hafeez F. Unraveling the impact of human perturbation on nitrogen cycling in terrestrial ecosystems of lower Himalaya, Pakistan. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1324. [PMID: 37845391 DOI: 10.1007/s10661-023-11964-6] [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: 07/10/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023]
Abstract
Terrestrial ecosystems are under the enormous pressure of land use management regimes through human disturbances, resulting in the disruption of biogeochemical cycles and associated ecosystem services. Nitrogen (N) in soil ecosystems is of vital importance for primary productivity, hence estimating the extent of these human interventions on N-cycling processes becomes imperative from economic and environmental perspectives. This work investigated the impacts of variable anthropogenic activities on N cycling in three different terrestrial ecosystems (arable, grassland, and forest) in three regions of lower Himalaya, Pakistan. Potential nitrification (PNA) and denitrification (DEA) enzyme activities, relative distribution of inorganic N species (NH4, NO3), and the role of inherent edaphic factors were assessed. Results revealed high nitrification potentials and increased nitrous oxide (N2O) emissions in the incubated soil microcosms, in the order as arable > grassland > forest ecosystems. Notably, higher rates of both studied processes (~ 30-50%) and elevated soil mineral nitrogen pool were observed in arable ecosystems. Forest soils, assumed as pristine ecosystems relying mainly on natural N fixation, produced (de)nitrification rates relatively lower than grasslands, followed by arable soils which were moderately disturbed through long-term fertilization and intensive land-use regimes. Linear regression modeling revealed that the inorganic N species (particularly NO3), and inherent edaphic factors were the key determinants of high (de)nitrification rates, hence warn of accelerated N losses in these ecosystems. The study highlights that elevated PNA and DEA being proxies for the altered N cycling in the studied terrestrial ecosystems are of great ecological relevance in view of predicted N2O budget in the lower Himalaya.
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Affiliation(s)
- Tahir Zaman
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Saeed Ahmad Asad
- Department of Bio Sciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Muhammad Irshad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Faridullah
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Muhammad Shahzad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Rashid Nazir
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Awais Arefeen
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Akhtar Iqbal
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan.
| | - Farhan Hafeez
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan.
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15
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You A, Hua L, Hu J, Tian J, Ding T, Cheng N, Hu L. Patters of reactive nitrogen removal at the waters in the semi-constructed wetland. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118733. [PMID: 37562250 DOI: 10.1016/j.jenvman.2023.118733] [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: 05/02/2023] [Revised: 07/12/2023] [Accepted: 07/29/2023] [Indexed: 08/12/2023]
Abstract
Protection and rectification patters of urban wetlands have been considered in strategies to balance services to society and negative consequences of excess reactive nitrogen (Nr) loading. However, the knowledge about strategies of semi-constructed wetlands on nitrogen (N) cycling pathways and removal Nr from the overlying water is limited. This study aimed to reveal considerable differences among rectification patterns of the typical semi-constructed wetland (Xixi wetland), comprising rational exploitation area (REA), rehabilitation and reconstruction area (RRA), and conservation area (CA) by analyzing the N distribution and N protentional pathways among them. Results pointed out that both NH4+ and NO3- concentration were prominently higher in REA, as opposed to CA and RRA. Sediments in RRA had relatively higher NH4+ content, indicating the efficiency of dissimilatory nitrate reduction (DNRA) in RRA. Moreover, there was a significant shift in the microbial community structure across different sites and sediments. Metagenomic analysis distinguished the N cycling pathways, with nitrification (M00804), denitrification (M00529), and DNRA (M00530) being the crucial pathways in the semi-constructed wetland. The relative abundance of N metabolic pathways (ko00910) varied among different types of sediments, being more abundant in shore and rhizosphere areas and less abundant in bottom sediments. Methylobacter and Nitrospira were the predominant nitrifiers in shore sediments, while Methylocystis was enriched in the bottom sediments and rhizosphere soils. Furthermore, Anaeromyxobacter, Anaerolinea, Dechloromonas, Nocardioides, and Methylocystis were identified as the primary denitrifiers with N reductase genes (nirK, nirS, or nosZ). Among these, Anaeromyxobacter, Dechloromonas, and Methylocystis were the primary contributors containing the nosZ gene in semi-constructed wetlands, driving the conversion of N2O to N2. This study provides important insights into rectification-dependent Nr removal from the overlying water in terms of N distribution and N metabolic functional microbial communities in the semi-constructed wetlands.
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Affiliation(s)
- Aiju You
- Zhejiang Institute of Hydraulics & Estuary, Zhejiang Institute of Marine Planning & Design, Hangzhou, 310020, China
| | - Lei Hua
- Zhejiang Institute of Hydraulics & Estuary, Zhejiang Institute of Marine Planning & Design, Hangzhou, 310020, China
| | - Jingwen Hu
- Zhejiang Institute of Hydraulics & Estuary, Zhejiang Institute of Marine Planning & Design, Hangzhou, 310020, China
| | - Junsong Tian
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Tao Ding
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Na Cheng
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Lifang Hu
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China.
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16
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Sun N, Fan B, Yang F, Zhao L, Wang M. Effects of adding corn steep liquor on bacterial community composition and carbon and nitrogen transformation during spent mushroom substrate composting. BMC Microbiol 2023; 23:156. [PMID: 37237262 DOI: 10.1186/s12866-023-02894-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Carbon and nitrogen are essential energy and nutrient substances in the composting process. Corn steep liquor (CSL) is rich in soluble carbon and nitrogen nutrients and active substances and is widely used in the biological industry. Nonetheless, limited research has been done on the effect of CSL on composting. This work firstly reveals the effect of adding CSL to bacterial community composition and carbon and nitrogen conversion during composting. This study provides the choice of auxiliary materials for the spent mushroom substrate compost (SMS) and some novel knowledge about the effect of bacterial community on C and N cycling during composting of SMS and CSL. Two treatments were set up in the experiment: 100% spent mushroom substrate (SMS) as CK and SMS + 0.5% CSL (v/v) as CP. RESULTS The results showed that the addition of CSL enhanced the initial carbon and nitrogen content of the compost, altered the bacterial community structure, and increased the bacterial diversity and relative abundance, which might be beneficial to the conversion and retention of carbon and nitrogen in the composting process. In this paper, network analysis was used to screen the core bacteria involved in carbon and nitrogen conversion. In the CP network, the core bacteria were divided into two categories, synthesizing and degrading bacteria, and there were more synthesizing bacteria than degrading bacteria, so the degradation and synthesis of organic matter were carried out simultaneously, while only degrading bacteria were found in the CK network. Functional prediction by Faprotax identified 53 groups of functional bacteria, among which 20 (76.68% abundance) and 14 (13.15% abundance) groups of functional bacteria were related to carbon and nitrogen conversion, respectively. Adding CSL stimulated the compensatory effect of core and functional bacteria, enhanced the carbon and nitrogen transformation ability, stimulated the activity of low-abundance bacteria, and reduced the competitive relationship between the bacterial groups. This may be why the addition of CSL accelerated the organic matter degradation and increased carbon and nitrogen preservation. CONCLUSIONS These findings indicate that the addition of CSL promoted the cycling and preservation of carbon and nitrogen in the SMS composts, and the addition of CSL to the compost may be an effective way to dispose of agricultural waste.
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Affiliation(s)
- Ning Sun
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Bowen Fan
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Fengjun Yang
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| | - Liqin Zhao
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Mengmeng Wang
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
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17
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Hastuti YP, Siregar A, Fatma YS, Supriyono E. Application of a nitrifying bacterium Pseudomonas sp . HIB_D to reduce nitrogen waste in the Litopenaeus vannamei cultivation environment. AQUACULTURE INTERNATIONAL : JOURNAL OF THE EUROPEAN AQUACULTURE SOCIETY 2023:1-17. [PMID: 37361879 PMCID: PMC10183693 DOI: 10.1007/s10499-023-01123-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/09/2023] [Indexed: 06/28/2023]
Abstract
Pseudomonas sp. HIB_D has been observed to have nitrification activity that can oxidize ammonia/ammonium to nitrite and nitrate. This bacterium was isolated from the aquaculture environment with Ancol Indonesian marine water sources. Pseudomonas sp. HIB_D was applied in the rearing water of Litopenaeus vannamei to decrease nitrogen pollution levels and support a sustainable cultivation environment. This present study was set up using a completely randomized design with four treatments and three replications, i.e., control (without bacterial application) and bacterial application with a cell density of 107, 108, and 109 CFU mL-1 in a volume of 100 mL for 90 L seawater treatment. Thirty-six individuals of 15-day-old postlarvae L. vannamei (PL 15) (a density of 120 PL m-2) were used in this study for an 8-week rearing period. Based on the water quality analysis, the ammonia level under the bacterial applications was lower than in the control after 8-week cultivation. Nitrate levels increased at week 6 and decreased at week 8, specifically in 109 CFU mL-1 treatment. L. vannamei with 109 CFU mL-1 bacterial application had the best production performance with a survival rate of 94.33 ± 2.78%, an absolute length gain of 10.59 ± 0.22 cm, an absolute weight gain of 8.16 ± 0.33 g, a specific growth rate of 14.12% ± 0.01% day-1, and a feed conversion ratio of 1.26 ± 0.03. The blood glucose level and total hemocyte count of shrimp under the bacterial application with a density of 109 CFU mL-1 showed the highest level (30.71 ± 13.9 mg dL-1) and the lowest level (15 × 106 cells mL-1), respectively. The results showed that all treatments performed better than the control, in which the 109 CFU mL-1 bacterial application was the best treatment.
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Affiliation(s)
- Yuni Puji Hastuti
- Department of Aquaculture, Faculty of Fisheries and Marine Science, IPB University, Jl. Raya Dramaga, Bogor, 16680 West Java Indonesia
| | - Anggi Siregar
- Department of Aquaculture, Faculty of Fisheries and Marine Science, IPB University, Jl. Raya Dramaga, Bogor, 16680 West Java Indonesia
| | - Yuli Siti Fatma
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta-Bogor Km. 46, Cibinong, West Java 16911 Bogor, Indonesia
| | - Eddy Supriyono
- Department of Water Resource Management, Faculty of Fisheries and Marine Science, IPB University, Jl. Raya Dramaga, Bogor, 16680 West Java Indonesia
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18
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Avila Clasen L, Permin A, Horwath AB, Metcalfe DB, Rousk K. Do Nitrogen and Phosphorus Additions Affect Nitrogen Fixation Associated with Tropical Mosses? PLANTS (BASEL, SWITZERLAND) 2023; 12:1443. [PMID: 37050067 PMCID: PMC10097241 DOI: 10.3390/plants12071443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Tropical cloud forests are characterized by abundant and biodiverse mosses which grow epiphytically as well as on the ground. Nitrogen (N)-fixing cyanobacteria live in association with most mosses, and contribute greatly to the N pool via biological nitrogen fixation (BNF). However, the availability of nutrients, especially N and phosphorus (P), can influence BNF rates drastically. To evaluate the effects of increased N and P availability on BNF in mosses, we conducted a laboratory experiment where we added N and P, in isolation and combined, to three mosses (Campylopus sp., Dicranum sp. and Thuidium peruvianum) collected from a cloud forest in Peru. Our results show that N addition almost completely inhibited BNF within a day, whereas P addition caused variable results across moss species. Low N2 fixation rates were observed in Campylopus sp. across the experiment. BNF in Dicranum sp. was decreased by all nutrients, while P additions seemed to promote BNF in T. peruvianum. Hence, each of the three mosses contributes distinctively to the ecosystem N pool depending on nutrient availability. Moreover, increased N input will likely significantly decrease BNF associated with mosses also in tropical cloud forests, thereby limiting N input to these ecosystems via the moss-cyanobacteria pathway.
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Affiliation(s)
- Lina Avila Clasen
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark (K.R.)
| | - Aya Permin
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark (K.R.)
| | - Aline B. Horwath
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Daniel B. Metcalfe
- Department of Physical Geography and Ecosystem Science, Lund University, 221 00 Lund, Sweden
- Department of Ecology and Environmental Science, University of Umeå, 907 36 Umeå, Sweden
| | - Kathrin Rousk
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark (K.R.)
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19
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Cao J, Zhang Y, Dai G, Cui K, Wu X, Qin F, Xu J, Dong F, Pan X, Zheng Y. The long-acting herbicide mesosulfuron-methyl inhibits soil microbial community assembly mediating nitrogen cycling. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130293. [PMID: 36444049 DOI: 10.1016/j.jhazmat.2022.130293] [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: 08/09/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Mesosulfuron-methyl is a widely used herbicide in wheat fields. We previously reported that mesosulfuron-methyl alters the bacterial/fungal community structure in experimental indoor microcosms, ultimately affecting NO3--N and NH4+-N contents in soil nitrogen (N) cycling. However, how mesosulfuron-methyl application alter soil N cycling by changing microbial community assembly is unknown. Here, we designed an outdoor experiment comprising 2-month periods to investigate changes in soil N-cycle functional genes and structural shifts in the microbial community assembly in response to mesosulfuron-methyl applied at 11.25 and 112.5 g a.i. hm-2. Results showed that high mesosulfuron-methyl input significantly decreased AOA amoA and nirK abundances within the initial 15 days, but increased AOB amoA on day 60. The nifH abundance displayed a stimulation-inhibition trend. Moreover, high mesosulfuron-methyl input decreased the network's complexity, and newly formed multiple network modules exhibited strong negative associations with nifH, AOB amoA, nirK and nirS. Further structural equation model demonstrated that mesosulfuron-methyl did reveal strong direct inhibition of nirK, and it indirectly affected nirK by changing nifH abundance and Planomicrobium. Thus mesosulfuron-methyl perturbs N-cycling processes by reshaping bacterial community assembly. Taken together, our study provides theoretical support for determining the microbiological mechanism by which mesosulfuron-methyl affects soil N cycling.
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Affiliation(s)
- Junli Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100193, People's Republic of China; Shanxi Center for Testing of Functional Agro-Products, Shanxi Agricultural University, Taiyuan 030031, People's Republic of China
| | - Ying Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100193, People's Republic of China; Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550006, People's Republic of China
| | - Gaochen Dai
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100193, People's Republic of China; Key Laboratory of Mountain Environment, Guizhou normal University, Guiyang 550025, People's Republic of China
| | - Kai Cui
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100193, People's Republic of China
| | - Xiaohu Wu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100193, People's Republic of China.
| | - Fanxin Qin
- Key Laboratory of Mountain Environment, Guizhou normal University, Guiyang 550025, People's Republic of China
| | - Jun Xu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100193, People's Republic of China
| | - Fengshou Dong
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100193, People's Republic of China
| | - Xinglu Pan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100193, People's Republic of China
| | - Yongquan Zheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100193, People's Republic of China
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20
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Mishra A, Singh L, Singh D. Unboxing the black box-one step forward to understand the soil microbiome: A systematic review. MICROBIAL ECOLOGY 2023; 85:669-683. [PMID: 35112151 PMCID: PMC9957845 DOI: 10.1007/s00248-022-01962-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.
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Affiliation(s)
- Apurva Mishra
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, 201002, India
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Lal Singh
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Dharmesh Singh
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstrasse 30, 81675, Munich, Bavaria, Germany.
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21
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Sepp SK, Vasar M, Davison J, Oja J, Anslan S, Al-Quraishy S, Bahram M, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Drenkhan R, Fraser L, Garibay Oriel R, Hiiesalu I, Koorem K, Kõljalg U, Moora M, Mucina L, Öpik M, Põlme S, Pärtel M, Phosri C, Semchenko M, Vahter T, Vasco Palacios AM, Tedersoo L, Zobel M. Global diversity and distribution of nitrogen-fixing bacteria in the soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1100235. [PMID: 36743494 PMCID: PMC9895822 DOI: 10.3389/fpls.2023.1100235] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria.
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Affiliation(s)
- Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C. Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Juan José Cantero
- Universidad Nacional de Córdoba, Instituto Multidisciplinario de Biología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Universidad Nacional de Río Cuarto, Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne University of Picardie, Amiens, France
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Roberto Garibay Oriel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Perth, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Aida M. Vasco Palacios
- Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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22
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Gou Z, Zheng H, He Z, Su Y, Chen S, Chen H, Chen G, Ma NL, Sun Y. The combined action of biochar and nitrogen-fixing bacteria on microbial and enzymatic activities of soil N cycling. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120790. [PMID: 36460190 DOI: 10.1016/j.envpol.2022.120790] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
This study aims to investigate the positive effects of the combined use of Enterobacter cloacae and biochar on improving nitrogen (N) utilization. The greenhouse pots experimental results showed the synergy of biochar and E. cloacae increased soil total N content and plant N uptake by 33.54% and 15.1%, respectively. Soil nitrogenase (NIT) activity increased by 253.02%. Ammonia monooxygenase (AMO) and nitrate reductase (NR) activity associated with nitrification and denitrification decreased by 10.94% and 29.09%, respectively. The relative abundance of N fixing microorganisms like Burkholderia and Bradyrhizobium significantly increased. Sphingomonas and Ottowia, two bacteria involved in the nitrification and denitrification processes, were found to be in lower numbers. The E. cloacae's ability to fix N2 and promote the growth of plants allow the retention of N in soil and make more N available for plant development. Biochar served as a reservoir of N for plants by adsorbing N from the soil and providing a shelter for E. cloacae. Thus, biochar and E. cloacae form a synergy for the management of agricultural N and the mitigation of negative impacts of pollution caused by excessive use of N fertilizer.
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Affiliation(s)
- Zechang Gou
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Haoyu Zheng
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Ziqi He
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yingjie Su
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Siji Chen
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Huan Chen
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Guang Chen
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Nyuk Ling Ma
- Faculty of Science and Marine Environment, University Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Yang Sun
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
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23
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Potential Roles of Soil Microorganisms in Regulating the Effect of Soil Nutrient Heterogeneity on Plant Performance. Microorganisms 2022; 10:microorganisms10122399. [PMID: 36557652 PMCID: PMC9786772 DOI: 10.3390/microorganisms10122399] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The spatially heterogeneous distribution of soil nutrients is ubiquitous in terrestrial ecosystems and has been shown to promote the performance of plant communities, influence species coexistence, and alter ecosystem nutrient dynamics. Plants interact with diverse soil microbial communities that lead to an interdependent relationship (e.g., symbioses), driving plant community productivity, belowground biodiversity, and soil functioning. However, the potential role of the soil microbial communities in regulating the effect of soil nutrient heterogeneity on plant growth has been little studied. Here, we highlight the ecological importance of soil nutrient heterogeneity and microorganisms and discuss plant nutrient acquisition mechanisms in heterogeneous soil. We also examine the evolutionary advantages of nutrient acquisition via the soil microorganisms in a heterogeneous environment. Lastly, we highlight a three-way interaction among the plants, soil nutrient heterogeneity, and soil microorganisms and propose areas for future research priorities. By clarifying the role of soil microorganisms in shaping the effect of soil nutrient heterogeneity on plant performance, the present study enhances the current understanding of ecosystem nutrient dynamics in the context of patchily distributed soil nutrients.
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Liao J, Luo Q, Hu A, Wan W, Tian D, Ma J, Ma T, Luo H, Lu S. Soil moisture-atmosphere feedback dominates land N 2 O nitrification emissions and denitrification reduction. GLOBAL CHANGE BIOLOGY 2022; 28:6404-6418. [PMID: 35971257 DOI: 10.1111/gcb.16365] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Soil moisture (SM) is essential to microbial nitrogen (N)-cycling networks in terrestrial ecosystems. Studies have found that SM-atmosphere feedbacks dominate the changes in land carbon fluxes. However, the influence of SM-atmosphere feedbacks on the N fluxes changes, and the underlying mechanisms remain highly unsure, leading to uncertainties in climate projections. To fill this gap, we used in situ observation coupled with gridded and remote sensing data to analyze N2 O fluxes emissions globally. Here, we investigated the synergistic effects of temperature, hydroclimate on global N2 O fluxes, as the result of SM-atmosphere feedback impact on N fluxes. We found that SM-temperature feedback dominates land N2 O emissions by controlling the balance between nitrifier and denitrifier genes. The mechanism is that atmospheric water demand increases with temperature and thereby reduces SM, which increases the dominant N2 O production nitrifier (containing amoA AOB gene) and decreases the N2 O consumption denitrifier (containing the nosZ gene), consequently will potential increasing N2 O emissions. However, we find that the spatial variations of soil-water availability as a result of the nonlinear response of SM to vapor pressure deficit caused by temperature are some of the greatest challenges in predicting future N2 O emissions. Our data-driven assessment deepens the understanding of the impact of SM-atmosphere interactions on the soil N cycle, which remains uncertain in earth system models. We suggest that the model needs to account for feedback between SM and atmospheric temperature when estimating the response of the N2 O emissions to climatic change globally, as well as when conducting field-scale investigations of the response of the ecosystem to warming.
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Affiliation(s)
- Jiayuan Liao
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
- School of Atmospheric Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Qiqi Luo
- School of Atmospheric Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Ang Hu
- College of Resources and Environment, Hunan Agricultural University, Changsha, China
| | - Wenkai Wan
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Dian Tian
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Jingwei Ma
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Tian Ma
- School of Atmospheric Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Hao Luo
- School of Atmospheric Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Sheng Lu
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
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25
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Li J, Chen L, Wang H, Ouyang S, Liu X, Lu J. Pattern and drivers of soil fungal community along elevation gradient in the Abies georgei forests of Segila mountains, Southeast Tibet. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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26
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Mishra S, Wang W, Xia S, Lin L, Yang X. Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156863. [PMID: 35750182 DOI: 10.1016/j.scitotenv.2022.156863] [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: 02/14/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The concept of microbial functional genes has added a new dimension to microbial ecology research by improving the model of microbial community-ecosystem functions relationship. However, our knowledge vis-à-vis fine-scale spatial distribution pattern of functional genes and their probable impact on plant community in the hyper-diverse tropical forest ecosystem is very limited. Here, we investigated the spatial pattern of functional genes abundance (NirK, AOA, AOB, and PhoD), identified key influencing factors, and distinguished the key functional group supporting the plant community in a tropical rainforest located in Xishuangbanna. In total, 200 soil samples and vegetation data of ~4800 individuals of plants across a 1 ha study area were collected. Our results detected higher spatial variability with a maximum magnitude of abundance for PhoD gene (4.53 × 107 copies) followed by NirK (2.71 × 106 copies), AOA (1.97 × 106 copies), and AOB (7.38 × 104 copies). A strong spatial dependence was observed for PhoD and NirK over the distance of 17 and 18 m, respectively. Interestingly, the N:P stoichiometry played a critical role in structuring the spatial pattern of the most abundant PhoD gene. The significant positive and negative relationship of PhoD with N:P ratio and available phosphorus, respectively, indicated that the P-limiting environment was a driving factor for recruitment of PhoD gene community. The structural equation modeling ascertained the direct positive impact of PhoD on plant biomass and high demand of available P by plants suggesting that the organic phosphorus mineralization process is essential to maintain plant productivity by re-establishing the availability of the most limiting P nutrient. Our preliminary study improves our understanding of how microbial functional genes-environment associations could be used for monitoring soil health and its overall impact on ecosystem multifunctionality. Finally, we intend to conduct the study at a large spatial scale for achieving a holistic view.
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Affiliation(s)
- Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Wenting Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Shangwen Xia
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Luxiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan 665000, China.
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27
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Li Z, Chen Y, Ling A, Li H, Lin Z, Wang Y. Effects of Biocontrol Agents Application on Soil Bacterial Community and the Quality of Tobacco. Curr Microbiol 2022; 79:320. [PMID: 36121540 DOI: 10.1007/s00284-022-02937-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/13/2022] [Indexed: 11/30/2022]
Abstract
In this study, to evaluate the effect of different biocontrol agents (BCAs) on the soil bacterial community, we investigated the effects of Bacillus amyloliquefaciens, synthetic bacterial community (Aspergillus niger:Bacillus subtilis:Bacillus licheniformis:Streptomyces microflavus = 3:3:3:1, SynCom), and BCAs combined with lime-nitrogen on soil bacterial community by utilizing 16S rRNA sequencing technology. The sequencing shows that BCAs application can improve the value of Shannon and Sobs index of bacterial community during tobacco rosette and vigorous growing period. With the growth of tobacco, the effect of BCAs on the composition and difference of soil bacterial community structure becomes more and more obvious. In terms of average relative richness, the top six phyla of soil bacterial community are Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Gemmatimonadetes, and Bacteroidetes. Bacillus amyloliquefaciens application can increase the relative richness of Proteobacteria and Bacteroidetes. And the combination between BCAs and lime-nitrogen can increase the relative richness of Gemmatimonadetes and Bacteroidetes. The SynCom also can increase the relative richness of Bacteroidetes, whereas it decreases the relative richness of Acidobacteria. Proteobacteria, Acidobacteria, Gemmatimonadetes, and Bacteroidetes showing an extremely significant correlation with pH and exchangeable magnesium (EMg). BCAs application can improve the tobacco yield, effective leaves, and reducing sugar content that also has extremely significant positive correlation with pH and EMg. In conclusion, the results of our field experiments clearly show that BCAs application can significantly affect the soil pH and EMg by changing most of the dominant soil bacterial species. The richness of Bacteroidetes can serve as an indicator of the changes in soil pH and EMg caused by BCAs application.
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Affiliation(s)
- Zhongkui Li
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Yulan Chen
- Liangshan Company of Sichuan Tobacco Company, Xichang, 615000, China
| | - Aifen Ling
- Liangshan Company of Sichuan Tobacco Company, Xichang, 615000, China
| | - Hongli Li
- School of Ecology and Environment, Zhengzhou University, Zhengzhou, 450001, China.
| | - Zhengquan Lin
- Liangshan Prefecture Tobacco Company Ningnan Branch, Dechang, 615400, China
| | - Yan Wang
- School of Ecology and Environment, Zhengzhou University, Zhengzhou, 450001, China
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28
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Chen Z, Dolfing J, Zhuang S, Wu Y. Periphytic biofilms-mediated microbial interactions and their impact on the nitrogen cycle in rice paddies. ECO-ENVIRONMENT & HEALTH (ONLINE) 2022; 1:172-180. [PMID: 38075597 PMCID: PMC10702904 DOI: 10.1016/j.eehl.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 09/13/2022] [Accepted: 09/29/2022] [Indexed: 01/03/2024]
Abstract
Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production. Periphytic biofilms (PBs) at the soil-water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency. PBs are composed of microbial aggregates, including a wide variety of microorganisms (algae, bacteria, fungi, protozoa, and metazoa), extracellular polymeric substances and minerals (iron, aluminum, and calcium), which form an integrated food web and energy flux within a relatively stable micro-ecosystem. PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization. Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated. We summarize the key functional importance of PBs, including the intricate and delicate community structure, microbial interactions among individual phylotypes, a wide diversity of self-produced organics, the active adaptation of PBs to constantly changing environments, and the intricate mechanisms by which PBs regulate the nitrogen cycle. We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability, optimizing nitrogen utilization and crop yields in rice paddies.
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Affiliation(s)
- Zhihao Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle Upon Tyne NE1 8QH, UK
| | - Shunyao Zhuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China
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Lin Y, Ye G, Hu HW, Fan J, He JZ. Manure applications alter the abundance, community structure and assembly process of diazotrophs in an acidic Ultisol. Front Microbiol 2022; 13:965293. [PMID: 36033880 PMCID: PMC9412762 DOI: 10.3389/fmicb.2022.965293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
The excessive usage of nitrogen (N) fertilizers can accelerate the tendency of global climate change. Biological N fixation by diazotrophs contributes substantially to N input and is a viable solution to sustainable agriculture via reducing inorganic N fertilization. However, how manure application influences the abundance, community structure and assembly process of diazotrophs in soil aggregates is not fully understood. Here, we investigated the effect of manure amendment on diazotrophic communities in soil aggregates of an arable soil. Manure application increased soil aggregation, crop yield and the abundance of nifH genes. The abundance of nifH genes increased with aggregate sizes, indicating that diazotrophs prefer to live in larger aggregates. The abundance of nifH genes in large macroaggregates, rather than in microaggregates and silt and clay, was positively associated with plant biomass and crop yield. Both manure application and aggregate size did not alter the Shannon diversity of diazotrophs but significantly changed the diazotrophic community structure. The variation of diazotrophic community structure explained by manure application was greater than that by aggregate size. Manure application promoted the relative abundance of Firmicutes but reduced that of α-Proteobacteria. Stochastic processes played a dominant role in the assembly of diazotrophs in the control treatment. Low-rate manure (9 Mg ha−1) application, rather than medium-rate (18 Mg ha−1) and high-rate (27 Mg ha−1) manure, significantly increased the relative importance of deterministic processes in diazotrophic community assembly. Taken together, our findings demonstrated that long-term manure application increased nifH gene abundance and altered the community structure and assembly process of diazotrophs in soil aggregates, which advanced our understanding of the ecophysiology and functionality of diazotrophs in acidic Ultisols.
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Affiliation(s)
- Yongxin Lin
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Guiping Ye
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jianbo Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Jianbo Fan
| | - Ji-Zheng He
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
- Ji-Zheng He
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30
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Ku Y, Lei Y, Han X, Peng J, Zhu Y, Zhao Z. Spatial Patterns and Composition Traits of Soil Microbial Nitrogen-Metabolism Genes in the Robinia pseudoacacia Forests at a Regional Scale. Front Microbiol 2022; 13:918134. [PMID: 35814641 PMCID: PMC9263705 DOI: 10.3389/fmicb.2022.918134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Microbial-driven processes related to the nitrogen-metabolism (N-metabolism) in soil are critical for ecosystem functioning and stability. There are spatial patterns of microbial-mediated nitrogen processes, but we still lack an overview of the soil N-metabolism genes of single nitrogen-fixing tree species pure forests at a regional scale. Here, we investigated the spatial variation and drivers of microbial N-metabolism genes in the rhizosphere soil of Robinia pseudoacacia on the Loess Plateau by metagenomic technology. We found that the distance-decay of soil N functional gene similarities in Robinia pseudoacacia forests on the Loess Plateau spanning a geographic distance of 230 km was significant (p < 0.001). The gene composition and co-occurrence patterns in the process of soil microbial N-metabolism were very different, and they were mainly driven by soil pH and MAP (mean annual precipitation). The proportion of positive links and edges co-occurrence networks between N functional genes increased with increasing pH, suggesting that increasing pH promoted connections between functional genes. The relative frequencies of N-metabolism pathways were consistent on the Loess Plateau, the abundance of ammonia assimilation pathway was highest, and the abundance of the nitrogen fixation pathway was the lowest; only the abundance of the nitrogen fixation pathway was not significantly different. The bacterial and archaeal communities involved in soil nitrogen metabolism were significantly different. Structural equation modeling showed that decreases in soil pH and MAP mainly affected the increase in nitrogen functional gene abundance through an increase in the diversity of N-metabolism microorganisms. In conclusion, this study provides a baseline for biogeographic studies of soil microbe functional genes.
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Affiliation(s)
- Yongli Ku
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Yuting Lei
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Xiaoting Han
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Jieying Peng
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Ying Zhu
- Key Laboratory of Soil and Water Conservation and Ecological Restoration of State Forestry and Grassland Administration, Shaanxi Academy of Forestry, Xi’an, China
| | - Zhong Zhao
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
- Key Laboratory of Silviculture on the Loess Plateau State Forestry Administration, Northwest A&F University, Yangling, China
- *Correspondence: Zhong Zhao, ;
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Meena M, Yadav G, Sonigra P, Nagda A, Mehta T, Swapnil P, Marwal A, Kumar S. Multifarious Responses of Forest Soil Microbial Community Toward Climate Change. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02051-3. [PMID: 35657425 DOI: 10.1007/s00248-022-02051-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.
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Affiliation(s)
- Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India.
| | - Garima Yadav
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Priyankaraj Sonigra
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Adhishree Nagda
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Tushar Mehta
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Prashant Swapnil
- Department of Botany, School of Biological Science, Central University of Punjab, Bhatinda, Punjab, 151401, India
| | - Avinash Marwal
- Department of Biotechnology, Vigyan Bhawan - Block B, New Campus, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
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Zhou Q, Sun H, Jia L, Wu W, Wang J. Simultaneous biological removal of nitrogen and phosphorus from secondary effluent of wastewater treatment plants by advanced treatment: A review. CHEMOSPHERE 2022; 296:134054. [PMID: 35202664 DOI: 10.1016/j.chemosphere.2022.134054] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/04/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
With the advancement of water ecological protection and water control standard, it is the general trend to upgrade the wastewater treatment plants (WWTPs). The simultaneous removal of nitrogen and phosphorus is the key to improve the water quality of secondary effluent of WWTPs to prevent the eutrophication. Therefore, it is urgent to develop the applicable technologies for simultaneous biological removal of nitrogen and phosphorus from secondary effluent. In this review, the composition of secondary effluent from municipal WWTPs were briefly introduced firstly, then the three main treatment processes for simultaneous nitrogen and phosphorus removal, i.e., the enhanced denitrifying phosphorus removal filter, the pyrite-based autotrophic denitrification and the microalgae biological treatment system were summarized, their performances and mechanisms were analyzed. The influencing factors and microbial community structure were discussed. The advanced removal of nitrogen and phosphorus by different technologies were also compared and summarized in terms of performance, operational characteristics, disadvantage and cost. Finally, the challenges and future prospects of simultaneous removal of nitrogen and phosphorus technologies for secondary effluent were proposed. This review will deepen to understand the principles and applications of the advanced removal of nitrogen and phosphorus and provide some valuable information for upgrading the treatment process of WWTPs.
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Affiliation(s)
- Qi Zhou
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China.
| | - Haimeng Sun
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China.
| | - Lixia Jia
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China.
| | - Weizhong Wu
- Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China.
| | - Jianlong Wang
- Laboratory of Environmental Technology, INET, Tsinghua University, Beijing, 100084, PR China.
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Zhong C, Nesbø CL, von Gunten K, Zhang Y, Shao X, Jin R, Konhauser KO, Goss GG, Martin JW, He Y, Qian PY, Lanoil BD, Alessi DS. Complex impacts of hydraulic fracturing return fluids on soil microbial community respiration, structure, and functional potentials. Environ Microbiol 2022; 24:4108-4123. [PMID: 35416402 DOI: 10.1111/1462-2920.16009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022]
Abstract
The consequences of soils exposed to hydraulic fracturing (HF) return fluid, often collectively termed flowback and produced water (FPW), are poorly understood, even though soils are a common receptor of FPW spills. Here, we investigate the impacts on soil microbiota exposed to FPW collected from the Montney Formation of western Canada. We measured soil respiration, microbial community structure, and functional potentials under FPW exposure across a range of concentrations, exposure time, and soil types (luvisol and chernozem). We find that soil type governs microbial community response upon FPW exposure. Within each soil, FPW exposure led to reduced biotic soil respiration, and shifted microbial community structure and functional potentials. We detect substantially higher species richness and more unique functional genes in FPW-exposed soils than in FPW-unexposed soils, with metagenome-assembled genomes (e.g., Marinobacter persicus) from luvisol soil exposed to concentrated FPW being most similar to genomes from HF/FPW sites. Our data demonstrate the complex impacts of microbial communities following FPW exposure, and highlight the site-specific effects in evaluation of spills and agricultural reuse of FPW on the normal soil functions. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Cheng Zhong
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada.,Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangzhou, China
| | - Camilla L Nesbø
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Konstantin von Gunten
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Yifeng Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xiaoqing Shao
- Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, M1C 1A4, Canada
| | - Rong Jin
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Greg G Goss
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Jonathan W Martin
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yuhe He
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangzhou, China
| | - Brian D Lanoil
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
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Duan N, Li L, Liang X, Fine A, Zhuang J, Radosevich M, Schaeffer SM. Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production. Front Microbiol 2022; 13:847005. [PMID: 35444635 PMCID: PMC9015707 DOI: 10.3389/fmicb.2022.847005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.
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Affiliation(s)
- Ning Duan
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lidong Li
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Xiaolong Liang
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Aubrey Fine
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jie Zhuang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sean M. Schaeffer
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Liu X, Le Roux X, Salles JF. The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges. iScience 2022; 25:103821. [PMID: 35243218 PMCID: PMC8867051 DOI: 10.1016/j.isci.2022.103821] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microbial inoculations contribute to reducing agricultural systems' environmental footprint by supporting sustainable production and regulating climate change. However, the indirect and cascading effects of microbial inoculants through the reshaping of soil microbiome are largely overlooked. By discussing the underlying mechanisms of plant- and soil-based microbial inoculants, we suggest that a key challenge in microbial inoculation is to understand their legacy on indigenous microbial communities and the corresponding impacts on agroecosystem functions and services relevant to climate change. We explain how these legacy effects on the soil microbiome can be understood by building on the mechanisms driving microbial invasions and placing inoculation into the context of ecological succession and community assembly. Overall, we advocate that generalizing field trials to systematically test inoculants' effectiveness and developing knowledge anchored in the scientific field of biological/microbial invasion are two essential requirements for applying microbial inoculants in agricultural ecosystems to tackle climate change challenges.
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Affiliation(s)
- Xipeng Liu
- Microbial Ecology cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747 AG Groningen, the Netherlands
| | - Xavier Le Roux
- Microbial Ecology Centre LEM, INRAE, CNRS, VetAgroSup, Université Lyon 1, Université de Lyon, UMR 1418 INRAE, UMR 5557 CNRS, 69622 Villeurbanne, France
| | - Joana Falcão Salles
- Microbial Ecology cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747 AG Groningen, the Netherlands
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Nitrate Water Contamination from Industrial Activities and Complete Denitrification as a Remediation Option. WATER 2022. [DOI: 10.3390/w14050799] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Freshwater is a scarce resource that continues to be at high risk of pollution from anthropogenic activities, requiring remediation in such cases for its continuous use. The agricultural and mining industries extensively use water and nitrogen (N)-dependent products, mainly in fertilizers and explosives, respectively, with their excess accumulating in different water bodies. Although removal of NO3 from water and soil through the application of chemical, physical, and biological methods has been studied globally, these methods seldom yield N2 gas as a desired byproduct for nitrogen cycling. These methods predominantly cause secondary contamination with deposits of chemical waste such as slurry brine, nitrite (NO2), ammonia (NH3), and nitrous oxide (N2O), which are also harmful and fastidious to remove. This review focuses on complete denitrification facilitated by bacteria as a remedial option aimed at producing nitrogen gas as a terminal byproduct. Synergistic interaction of different nitrogen metabolisms from different bacteria is highlighted, with detailed attention to the optimization of their enzymatic activities. A biotechnological approach to mitigating industrial NO3 contamination using indigenous bacteria from wastewater is proposed, holding the prospect of optimizing to the point of complete denitrification. The approach was reviewed and found to be durable, sustainable, cost effective, and environmentally friendly, as opposed to current chemical and physical water remediation technologies.
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Impacts of corn stover management and fertilizer application on soil nutrient availability and enzymatic activity. Sci Rep 2022; 12:1985. [PMID: 35132132 PMCID: PMC8821671 DOI: 10.1038/s41598-022-06042-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/24/2022] [Indexed: 11/08/2022] Open
Abstract
Corn stover is a global resource used in many industrial sectors including bioenergy, fuel, and livestock operations. However, stover removal can negatively impact soil nutrient availability, especially nitrogen (N) and phosphorus (P), biological activity, and soil health. We evaluated the effects of corn stover management combined with N and P fertilization on soil quality, using soil chemical (nitrate, ammonium and Bray-1 P) and biological parameters (β-glucosidase, alkaline phosphatase, arylsulfatase activities and fluorescein diacetate hydrolysis—FDA). The experiment was performed on a Mollisol (Typic Endoaquoll) in a continuous corn system from 2013 to 2015 in Minnesota, USA. The treatments tested included six N rates (0 to 200 kg N ha−1), five P rates (0 to 100 kg P2O5 ha−1), and two residue management strategies (residue removed or incorporated) totalling 60 treatments. Corn stover management significantly impacted soil mineral-N forms and enzyme activity. In general, plots where residue was incorporated were found to have high NH4+ and enzyme activity compared to plots where residue was removed. In contrast, fields where residue was removed showed higher NO3− than plots where residue was incorporated. Residue management had little effect on soil available P. Soil enzyme activity was affected by both nutrient and residue management. In most cases, activity of the enzymes measured in plots where residue was removed frequently showed a positive response to added N and P. In contrast, soil enzyme responses to applied N and P in plots where residue was incorporated were less evident. Soil available nutrients tended to decrease in plots where residue was removed compared with plots where residue was incorporated. In conclusion, stover removal was found to have significant potential to change soil chemical and biological properties and caution should be taken when significant amounts of stover are removed from continuous corn fields. The residue removal could decrease different enzymes related to C-cycle (β-glucosidase) and soil microbial activity (FDA) over continuous cropping seasons, impairing soil health.
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Farooq MS, Uzair M, Maqbool Z, Fiaz S, Yousuf M, Yang SH, Khan MR. Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers. FRONTIERS IN PLANT SCIENCE 2022; 13:913204. [PMID: 35769304 PMCID: PMC9234532 DOI: 10.3389/fpls.2022.913204] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 05/22/2023]
Abstract
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4 +-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4 +, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
- *Correspondence: Seung Hwan Yang,
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
- Muhammad Ramzan Khan,
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Halbert-Howard A, Häfner F, Karlowsky S, Schwarz D, Krause A. Evaluating recycling fertilizers for tomato cultivation in hydroponics, and their impact on greenhouse gas emissions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:59284-59303. [PMID: 32851526 PMCID: PMC8541969 DOI: 10.1007/s11356-020-10461-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Soilless culture systems offer an environmentally friendly and resource-efficient alternative to traditional cultivation systems fitting within the scheme of a circular economy. The objective of this research was to examine the sustainable integration of recycling fertilizers in hydroponic cultivation-creating a nutrient cycling concept for horticultural cultivation. Using the nutrient film technique (NFT), three recycling-based fertilizer variants were tested against standard synthetic mineral fertilization as the control, with 11 tomato plants (Solanum lycopersicum L. cv. Pannovy) per replicate (n = 4) and treatment: two nitrified urine-based fertilizers differing in ammonium/nitrate ratio (NH4+:NO3-), namely (1) "Aurin" (AUR) and (2) "Crop" (CRO); as well as (3) an organo-mineral mixture of struvite and vinasse (S+V); and (4) a control (NPK). The closed chamber method was adapted for gas fluxes (N2O, CH4, and CO2) from the root zone. There was no indication in differences of the total shoot biomass fresh matter and uptake of N, P and K between recycling fertilizers and the control. Marketable fruit yield was comparable between NPK, CRO and S+V, whereas lower yields occurred in AUR. The higher NH4+:NO3- of AUR was associated with an increased susceptibility of blossom-end-rot, likely due to reduced uptake and translocation of Ca. Highest sugar concentration was found in S+V, which may have been influenced by the presence of organic acids in vinasse. N2O emissions were highest in S+V, which corresponded to our hypothesis that N2O emissions positively correlate with organic-C input by the fertilizer amendments. Remaining treatments showed barely detectable GHG emissions. A nitrified urine with a low NH4+:NO3- (e.g., CRO) has a high potential as recycling fertilizer in NFT systems for tomato cultivation, and S+V proved to supply sufficient P and K for adequate growth and yield. Alternative cultivation strategies may complement the composition of AUR.
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Affiliation(s)
- Aladdin Halbert-Howard
- "Next-generation horticultural systems" (HORTSYS), Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
| | - Franziska Häfner
- "Next-generation horticultural systems" (HORTSYS), Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
| | - Stefan Karlowsky
- "Functional Plant Biology" (FUNCT), Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
| | - Dietmar Schwarz
- "Functional Plant Biology" (FUNCT), Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
| | - Ariane Krause
- "Next-generation horticultural systems" (HORTSYS), Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany.
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Chen Q, Long C, Chen J, Cheng X. Differential response of soil CO 2 , CH 4 , and N 2 O emissions to edaphic properties and microbial attributes following afforestation in central China. GLOBAL CHANGE BIOLOGY 2021; 27:5657-5669. [PMID: 34363712 DOI: 10.1111/gcb.15826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Land use change specially affects greenhouse gas (GHG) emissions, and it can act as a sink/source of GHGs. Alterations in edaphic properties and microbial attributes induced by land use change can individually/interactively contribute to GHG emissions, but how they predictably affect soil CO2 , CH4 , and N2 O emissions remain unclear. Here, we investigated the direct and indirect controls of edaphic properties (i.e., dissolved organic carbon [DOC], soil organic C, total nitrogen, C:N ratio, NH4+ -N, NO3- -N, soil temperature [ST], soil moisture [SM], pH, and bulk density [BD]) and microbial attributes (i.e., total phospholipid fatty acids [PLFAs], 18:1ω7c, nitrifying genes [ammonia-oxidizing archaea, ammonia-oxidizing bacteria], and denitrifying genes [nirS, nirK, and nosZ]) over the annual soil CO2 , CH4 , and N2 O emissions from the woodland, shrubland, and abandoned land in subtropical China. Soil CO2 and N2 O emissions were higher in the afforested lands (woodland and shrubland) than in the abandoned land, but the annual cumulative CH4 uptake did not significantly differ among all land use types. The CO2 emission was positively associated with microbial activities (e.g., total PLFAs), while the CH4 uptake was tightly correlated with soil environments (i.e., ST and SM) and chemical properties (i.e., DOC, C:N ratio, and NH4+ -N concentration), but not significantly related to the methanotrophic bacteria (i.e., 18:1ω7c). Whereas, soil N2 O emission was positively associated with nitrifying genes, but negatively correlated with denitrifying genes especially nosZ. Overall, our results suggested that soil CO2 and N2 O emissions were directly dependent on microbial attributes, and soil CH4 uptake was more directly related to edaphic properties rather than microbial attributes. Thus, different patterns of soil CO2 , CH4 , and N2 O emissions and associated controls following land use change provided novel insights into predicting the effects of afforestation on climate change mitigation outcomes.
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Affiliation(s)
- Qiong Chen
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming, P.R. China
| | - Chunyan Long
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming, P.R. China
| | - Jingwen Chen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Cheng
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming, P.R. China
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Aloo BN, Mbega ER, Makumba BA, Tumuhairwe JB. Effects of agrochemicals on the beneficial plant rhizobacteria in agricultural systems. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:60406-60424. [PMID: 34535866 DOI: 10.1007/s11356-021-16191-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Conventional agriculture relies heavily on chemical pesticides and fertilizers to control plant pests and diseases and improve production. Nevertheless, the intensive and prolonged use of agrochemicals may have undesirable consequences on the structure, diversity, and activities of soil microbiomes, including the beneficial plant rhizobacteria in agricultural systems. Although literature continues to mount regarding the effects of these chemicals on the beneficial plant rhizobacteria in agricultural systems, our understanding of them is still limited, and a proper account is required. With the renewed efforts and focus on agricultural and environmental sustainability, understanding the effects of different agrochemicals on the beneficial plant rhizobacteria in agricultural systems is both urgent and important to deduce practical solutions towards agricultural sustainability. This review critically evaluates the effects of various agrochemicals on the structure, diversity, and functions of the beneficial plant rhizobacteria in agricultural systems and propounds on the prospects and general solutions that can be considered to realize sustainable agricultural systems. This can be useful in understanding the anthropogenic effects of common and constantly applied agrochemicals on symbiotic systems in agricultural soils and shed light on the need for more environmentally friendly and sustainable agricultural practices.
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Affiliation(s)
- Becky Nancy Aloo
- Department of Biological Sciences, University of Eldoret, P.O. Box 1125-30100, Eldoret, Kenya.
| | - Ernest Rashid Mbega
- Department of Sustainable Agriculture and Biodiversity Conservation, Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania
| | - Billy Amendi Makumba
- Department of Biological Sciences, Moi University, P.O. Box 3900-30100, Eldoret, Kenya
| | - John Baptist Tumuhairwe
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, P.O. Box, 7062, Kampala, Uganda
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Cao JH, Qi R, Liu T, Li B, Gao BQ, Chen XL, Zhao Y, Zhao ZG. Patterns of species and phylogenetic diversity in Picea purpurea forests under different levels of disturbance on the northeastern Qinghai-Tibetan Plateau. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Influence of Trichoderma asperellum and Bacillus subtilis as biocontrol and plant growth promoting agents on soil microbiota. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01647-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
The manipulation of soil microbiota can involve changes in microbial diversity and microbial activities, and it is carried out for practical purposes. The microbial diversity can be modified by the inoculation of beneficial microorganisms into soil or by agricultural management practices. This study provides information on the influence of introducing beneficial soil microorganisms on soil indigenous microbiota. The aim of this study was to determine how biocontrol and plant growth promoting agents Trichoderma asperellum and Bacillus subtilis and their consortium affect indigenous soil microbiota without placing emphasis on the plant as a determinant of change.
Methods
Experimental soil samples were treated with B. subtilis and T. asperellum and their consortium. The shift of number of bacterial and fungal CFUs in soil was determined. Biolog EcoPlate assay demonstrated the metabolic activity of microorganisms in soil. The concentration of Trichoderma genus, Firmicutes, Gammaproteobacteria and Acidobacteria DNA in soil samples was determined by molecular methods. A correlation analysis was performed between microbiological and molecular data.
Results
Soil treatment with T. asperellum, B. subtilis and the plant pathogenic fungus Botrytis cinerea changed the number of CFUs and amplified DNA fragments of certain taxa. The study showed that added microorganisms did not significantly affect the metabolic diversity of the community and Shannon-Wiener biodiversity index but change the utilization of carbohydrates, complex carbon compounds and organic phosphorus compounds.
Conclusion
Introduced biocontrol and plant growth promoting agents T. asperellum and B. subtilis survive in soil during a 60-day experiment and influence composition and functionality of indigenous populations. Whereas B. subtilis and T. asperellum and their consortium are inhibitors of the pathogenic fungus B. cinerea, this could further positively affect specific crops.
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Hestrin R, Weber PK, Pett-Ridge J, Lehmann J. Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport. THE NEW PHYTOLOGIST 2021; 231:1746-1757. [PMID: 34077566 DOI: 10.1111/nph.17527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen (N) is an essential nutrient that limits plant growth in many ecosystems. Here we investigate an overlooked component of the terrestrial N cycle - subsurface ammonia (NH3 ) gas transport and its contribution to plant and mycorrhizal N acquisition. We used controlled mesocosms, soil incubations, stable isotopes, and imaging to investigate edaphic drivers of NH3 gas efflux, track lateral subsurface N transport originating from 15 NH3 gas or 15 N-enriched organic matter, and assess plant and mycorrhizal N assimilation from this gaseous transport pathway. NH3 is released from soil organic matter, travels belowground, and contributes to root and fungal N content. Abiotic soil properties (pH and texture) influence the quantity of NH3 available for subsurface transport. Mutualisms with arbuscular mycorrhizal (AM) fungi can substantially increase plant NH3 -N uptake. The grass Brachypodium distachyon acquired 6-9% of total plant N from organic matter-N that traveled as a gas belowground. Colonization by the AM fungus Rhizophagus irregularis was associated with a two-fold increase in total plant N acquisition from subsurface NH3 gas. NH3 gas transport and uptake pathways may be fundamentally different from those of more commonly studied soil N species and warrant further research.
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Affiliation(s)
- Rachel Hestrin
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, 94550, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, 94550, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, 94550, USA
| | - Johannes Lehmann
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY, 14853, USA
- Institute for Advanced Study, TU München, Garching, 85748, Germany
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Huaraca Huasco W, Riutta T, Girardin CAJ, Hancco Pacha F, Puma Vilca BL, Moore S, Rifai SW, Del Aguila-Pasquel J, Araujo Murakami A, Freitag R, Morel AC, Demissie S, Doughty CE, Oliveras I, Galiano Cabrera DF, Durand Baca L, Farfán Amézquita F, Silva Espejo JE, da Costa ACL, Oblitas Mendoza E, Quesada CA, Evouna Ondo F, Edzang Ndong J, Jeffery KJ, Mihindou V, White LJT, N'ssi Bengone N, Ibrahim F, Addo-Danso SD, Duah-Gyamfi A, Djaney Djagbletey G, Owusu-Afriyie K, Amissah L, Mbou AT, Marthews TR, Metcalfe DB, Aragão LEO, Marimon-Junior BH, Marimon BS, Majalap N, Adu-Bredu S, Abernethy KA, Silman M, Ewers RM, Meir P, Malhi Y. Fine root dynamics across pantropical rainforest ecosystems. GLOBAL CHANGE BIOLOGY 2021; 27:3657-3680. [PMID: 33982340 DOI: 10.1111/gcb.15677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/27/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Fine roots constitute a significant component of the net primary productivity (NPP) of forest ecosystems but are much less studied than aboveground NPP. Comparisons across sites and regions are also hampered by inconsistent methodologies, especially in tropical areas. Here, we present a novel dataset of fine root biomass, productivity, residence time, and allocation in tropical old-growth rainforest sites worldwide, measured using consistent methods, and examine how these variables are related to consistently determined soil and climatic characteristics. Our pantropical dataset spans intensive monitoring plots in lowland (wet, semi-deciduous, and deciduous) and montane tropical forests in South America, Africa, and Southeast Asia (n = 47). Large spatial variation in fine root dynamics was observed across montane and lowland forest types. In lowland forests, we found a strong positive linear relationship between fine root productivity and sand content, this relationship was even stronger when we considered the fractional allocation of total NPP to fine roots, demonstrating that understanding allocation adds explanatory power to understanding fine root productivity and total NPP. Fine root residence time was a function of multiple factors: soil sand content, soil pH, and maximum water deficit, with longest residence times in acidic, sandy, and water-stressed soils. In tropical montane forests, on the other hand, a different set of relationships prevailed, highlighting the very different nature of montane and lowland forest biomes. Root productivity was a strong positive linear function of mean annual temperature, root residence time was a strong positive function of soil nitrogen content in montane forests, and lastly decreasing soil P content increased allocation of productivity to fine roots. In contrast to the lowlands, environmental conditions were a better predictor for fine root productivity than for fractional allocation of total NPP to fine roots, suggesting that root productivity is a particularly strong driver of NPP allocation in tropical mountain regions.
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Affiliation(s)
- Walter Huaraca Huasco
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Terhi Riutta
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Cécile A J Girardin
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | | | | | - Sam Moore
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Sami W Rifai
- ARC Centre of Excellence for Climate Extremes, University of New South Wales, Sydney, NSW, Australia
| | | | - Alejandro Araujo Murakami
- Museo de Historia Natural Noel Kempff Mercado Universidad Autónoma Gabriel Rene Moreno, Santa Cruz, Bolivia
| | - Renata Freitag
- Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil
| | - Alexandra C Morel
- Department of Geography and Environmental Science, University of Dundee, Dundee, UK
| | | | - Christopher E Doughty
- School of Informatics, Computing and Cyber systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Imma Oliveras
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | | | - Vianet Mihindou
- Ministère de la Foret, de la Mer, de l'Environnement, Chargé Du Plan Climat, Libreville, Gabon
| | - Lee J T White
- Ministère de la Foret, de la Mer, de l'Environnement, Chargé Du Plan Climat, Libreville, Gabon
| | - Natacha N'ssi Bengone
- Ministère de la Foret, de la Mer, de l'Environnement, Chargé Du Plan Climat, Libreville, Gabon
| | - Forzia Ibrahim
- Forestry Research Institute of Ghana, Council for Scientific and Industrial Research, University, Kumasi, Ghana
| | - Shalom D Addo-Danso
- Forestry Research Institute of Ghana, Council for Scientific and Industrial Research, University, Kumasi, Ghana
| | - Akwasi Duah-Gyamfi
- Forestry Research Institute of Ghana, Council for Scientific and Industrial Research, University, Kumasi, Ghana
| | - Gloria Djaney Djagbletey
- Forestry Research Institute of Ghana, Council for Scientific and Industrial Research, University, Kumasi, Ghana
| | - Kennedy Owusu-Afriyie
- Forestry Research Institute of Ghana, Council for Scientific and Industrial Research, University, Kumasi, Ghana
| | - Lucy Amissah
- Forestry Research Institute of Ghana, Council for Scientific and Industrial Research, University, Kumasi, Ghana
| | - Armel T Mbou
- Centro Euro-Mediterraneo sui Cambiamenti Climatici, Leece, Italy
| | | | - Daniel B Metcalfe
- Department of Ecology and Environment Science, Umeå University, Umeå, Sweden
| | - Luiz E O Aragão
- Divisão de Sensoriamento Remoto-DIDSR, Instituto Nacional de Pesquisas Espaciais, São Jose dos Campos, SP, Brazil
| | - Ben H Marimon-Junior
- Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil
| | - Beatriz S Marimon
- Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil
| | - Noreen Majalap
- Sabah Forestry Department, Forest Research Centre, Sabah, Malaysia
| | - Stephen Adu-Bredu
- Forestry Research Institute of Ghana, Council for Scientific and Industrial Research, University, Kumasi, Ghana
| | | | - Miles Silman
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA
| | - Robert M Ewers
- Department of Life Science, Imperial College London, Ascot, UK
| | - Patrick Meir
- Research School of Biology, Australian National University, Canberra, ACT, Australia
- School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
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Lab-scale autothermal thermophilic aerobic digestion can maintain and remove nitrogen by controlling shear stress and oxygen supply system. J Biosci Bioeng 2021; 132:293-301. [PMID: 34167861 DOI: 10.1016/j.jbiosc.2021.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 01/12/2023]
Abstract
Autothermal thermophilic aerobic digestion (ATAD) is used to treat human excreta hygienically. We previously reported a unique full-scale ATAD, showing distinctive bacterial community transitions and producing high-nitrogen-content liquid fertilizer; nevertheless, the mechanism remains unclear. One hypothesis involves using a gas-inducing (GI) agitator. We designed a lab-scale GI system and compared it with a disk-turbine (DT) agitator system by mimicking the temperature shift of full-scale ATAD. The agitation system and its agitation speed greatly affected physicochemical properties and bacterial community structure. GI system at 1000 rpm (GI1000; high total carbon removal efficiency, 88.3%), with few nitrifying and denitrifying bacteria, maintained a high ammoniacal nitrogen concentration and had more shared operational taxonomic units related to Acinetobacter sp., Arcobacter sp., and Longimicrobium sp. with the full-scale ATAD compared with the GI system at 490 rpm and DT system at 1000 rpm (DT1000). Furthermore, DT1000, with a high abundance of nitrifying and denitrifying bacteria such as Alcaligenes aquatilis and Pseudomonas caeni, removed 94.7% total nitrogen with 71.9% total carbon removal efficiency. These results suggested that shear stress and oxygen supply system would change the bacterial community structure, thus affected ATAD performances. Consequently, it is possible that ATAD can be applied for not only production of highly nitrogen-containing liquid fertilizer but also extremely nitrogen removal of wastewater.
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Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures. BIOLOGY 2021; 10:biology10070569. [PMID: 34206701 PMCID: PMC8301126 DOI: 10.3390/biology10070569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 11/26/2022]
Abstract
Simple Summary The study of a microbial community nowadays mostly relies on environmental DNA (eDNA)-based amplicon sequencing. However, some studies report that this method is not able to capture all bacterial taxa in the community. This study presents an enrichment culture-based amplicon sequencing method to estimate the proportion of culturable bacteria in soil. A bacterial community derived from this method was compared with those derived from culture-independent methods (eDNA-based amplicon sequencing). This study revealed that the majority of cultured bacteria were rare or completely absent in the community detected by the culture-independent method. Nevertheless, the dominant bacterial Operational Taxonomic Units (OTUs) were also observed, as 8 out of the 30 most frequently detected bacteria from eDNA were found in the enrichment cultures. The method proposed in this study could extend bacterial community’s information derived from the culture-independent method. Furthermore, the enrichment culture-based amplicon sequencing method could be a promising tool for quick screening of a culturable bacterial community and its associated function for various applications. Abstract This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.
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Yuan Z, Ali A, Loreau M, Ding F, Liu S, Sanaei A, Zhou W, Ye J, Lin F, Fang S, Hao Z, Wang X, Le Bagousse-Pinguet Y. Divergent above- and below-ground biodiversity pathways mediate disturbance impacts on temperate forest multifunctionality. GLOBAL CHANGE BIOLOGY 2021; 27:2883-2894. [PMID: 33742479 DOI: 10.1111/gcb.15606] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Biodiversity plays a fundamental role in provisioning and regulating forest ecosystem functions and services. Above-ground (plants) and below-ground (soil microbes) biodiversity could have asynchronous change paces to human-driven land-use impacts. Yet, we know very little how they affect the provision of multiple forest functions related to carbon accumulation, water retention capacity and nutrient cycling simultaneously (i.e. ecosystem multifunctionality; EMF). We used a dataset of 22,000 temperate forest trees from 260 plots within 11 permanent forest sites in Northeastern China, which are recovering from three post-logging disturbances. We assessed the direct and mediating effects of multiple attributes of plant biodiversity (taxonomic, phylogenetic, functional and stand structure) and soil biodiversity (bacteria and fungi) on EMF under the three disturbance levels. We found the highest EMF in highly disturbed rather than undisturbed mature forests. Plant taxonomic, phylogenetic, functional and stand structural diversity had both positive and negative effects on EMF, depending on how the EMF index was quantified, whereas soil microbial diversity exhibited a consistent positive impact. Biodiversity indices explained on average 45% (26%-58%) of the variation in EMF, whereas climate and disturbance together explained on average 7% (0.4%-15%). Our result highlighted that the tremendous effect of biodiversity on EMF, largely overpassing those of both climate and disturbance. While above- (β = 0.02-0.19) and below-ground (β = 0.16-0.26) biodiversity had direct positive effects on EMF, their opposite mediating effects (β = -0.22 vs. β = 0.35 respectively) played as divergent pathways to human disturbance impacts on EMF. Our study sheds light on the need for integrative frameworks simultaneously considering above- and below-ground attributes to grasp the global picture of biodiversity effects on ecosystem functioning and services. Suitable management interventions could maintain both plant and soil microbial biodiversity, and thus guarantee a long-term functioning and provisioning of ecosystem services in an increasing disturbance frequency world.
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Affiliation(s)
- Zuoqiang Yuan
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Arshad Ali
- Department of Forest Resources Management, College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Michel Loreau
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France
| | - Fang Ding
- College of Land and Environment, Shenyang Agriculture University, Shenyang, China
| | - Shufang Liu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Anvar Sanaei
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Wangming Zhou
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ji Ye
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Fei Lin
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Shuai Fang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhanqing Hao
- School of Ecology and Environment, Northernwest Polytechnical University, Xi'an, China
| | - Xugao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yoann Le Bagousse-Pinguet
- Aix Marseille Univ, CNRS, Avignon Université, IRD, IMBE, Technopôle Arbois-Méditerranée Bât. Villemin - BP 80, Aix-en-Provence cedex 04, France
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Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling. Appl Environ Microbiol 2021; 87:e0054621. [PMID: 33837013 DOI: 10.1128/aem.00546-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Toward closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N2O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N2O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ∼45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems. IMPORTANCE Tropical rainforests are the largest terrestrial sinks of atmospheric CO2 and the largest natural source of N2O emissions, two greenhouse gases that are critical for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from three distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.
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Lamichhane P, Veerana M, Lim JS, Mumtaz S, Shrestha B, Kaushik NK, Park G, Choi EH. Low-Temperature Plasma-Assisted Nitrogen Fixation for Corn Plant Growth and Development. Int J Mol Sci 2021; 22:5360. [PMID: 34069725 PMCID: PMC8161386 DOI: 10.3390/ijms22105360] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 12/14/2022] Open
Abstract
Nitrogen fixation is crucial for plants as it is utilized for the biosynthesis of almost all biomolecules. Most of our atmosphere consists of nitrogen, but plants cannot straightforwardly assimilate this from the air, and natural nitrogen fixation is inadequate to meet the extreme necessities of global nutrition. In this study, nitrogen fixation in water was achieved by an AC-driven non-thermal atmospheric pressure nitrogen plasma jet. In addition, Mg, Al, or Zn was immersed in the water, which neutralized the plasma-treated water and increased the rate of nitrogen reduction to ammonia due to the additional hydrogen generated by the reaction between the plasma-generated acid and metal. The effect of the plasma-activated water, with and without metal ions, on germination and growth in corn plants (Zea Mays) was investigated. The germination rate was found to be higher with plasma-treated water and more efficient in the presence of metal ions. Stem lengths and germination rates were significantly increased with respect to those produced by DI water irrigation. The plants responded to the abundance of nitrogen by producing intensely green leaves because of their increased chlorophyll and protein contents. Based on this report, non-thermal plasma reactors could be used to substantially enhance seed germination and seedling growth.
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Affiliation(s)
- Pradeep Lamichhane
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Mayura Veerana
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Jun Sup Lim
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Sohail Mumtaz
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Bhanu Shrestha
- Department of Electronic Engineering, Kwangwoon University, Seoul 01897, Korea;
| | - Nagendra Kumar Kaushik
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Gyungsoon Park
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
| | - Eun Ha Choi
- Plasma Bio-Science Research Center, Applied Plasma Medicine Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Korea; (P.L.); (M.V.); (J.S.L.); (S.M.); (N.K.K.); (G.P.)
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