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Yuan X, Ma S, Geng H, Cao M, Chen H, Zhou B, Yuan R, Luo S, Sun K, Wang F. Joint effect of black carbon deriving from wheat straw burning and plastic mulch film debris on the soil biochemical properties, bacterial and fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174522. [PMID: 38981545 DOI: 10.1016/j.scitotenv.2024.174522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024]
Abstract
Black carbon (BC) formed after straw burning remains in farmland soil and coexists with plastic mulch film (PMF) debris. It is unclear how BC influences soil multifunctionality in the presence of PMF debris. In this study, we determined the joint effects of BC and PMF debris on soil biochemical properties and microbial communities. We conducted a soil microcosm experiment by adding BC formed by direct burning of wheat straw and PMF debris (polyethylene (PE) and biodegradable PMF (BP)) into soil at the dosages of 1 %, and soils were sampled on the 15th, 30th, and 100th day of soil incubation for high-throughput sequencing. The results showed that the degradation of PMF debris was accompanied by the release of microplastics (MPs). BC decreased NH4+-N (PE: 68.63 %; BP: 58.97 %) and NO3--N (PE: 12.83 %; BP: 51.37 %) and increased available phosphorus (AP) (PE: 79.12 %; BP: 26.09 %) in soil containing PMF debris. There were significant differences in enzyme activity among all the treatments. High-throughput sequencing indicated that BC reduced bacterial and fungal richness and fungal diversity in PMF debris-exposed soil, whereas PMF debris and BC resulted in significant changes in the proportion of dominant phyla and genera of bacteria and fungi, which were affected by incubation time. Furthermore, BC affected microorganisms by influencing soil properties, and pH and N content were the main influencing factors. In addition, FAPRPTAX analysis indicated that BC and PMF debris affected soil C and N cycling. These findings provide new insights into the response of soil multifunctionality to BC and PMF debris.
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Affiliation(s)
- Xiaoyan Yuan
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China; School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing, 100875, PR China
| | - Shuai Ma
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing, 100875, PR China.
| | - Huanhuan Geng
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Manman Cao
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing, 100875, PR China
| | - Huilun Chen
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Beihai Zhou
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Rongfang Yuan
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Shuai Luo
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Ke Sun
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing, 100875, PR China
| | - Fei Wang
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing, 100875, PR China.
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Meng XR, Gan Y, Liao LJ, Li CN, Wang R, Liu M, Deng JY, Chen Y. How the root bacterial community of Ficus tikoua responds to nematode infection: enrichments of nitrogen-fixing and nematode-antagonistic bacteria in the parasitized organs. FRONTIERS IN PLANT SCIENCE 2024; 15:1374431. [PMID: 39006956 PMCID: PMC11239514 DOI: 10.3389/fpls.2024.1374431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/06/2024] [Indexed: 07/16/2024]
Abstract
Plant-parasitic nematodes (PPNs) are among the most damaging pathogens to host plants. Plants can modulate their associated bacteria to cope with nematode infections. The tritrophic plant-nematode-microbe interactions are highly taxa-dependent, resulting in the effectiveness of nematode agents being variable among different host plants. Ficus tikoua is a versatile plant with high application potential for fruits or medicines. In recent years, a few farmers have attempted to cultivate this species in Sichuan, China, where parasitic nematodes are present. We used 16S rRNA genes to explore the effects of nematode parasitism on root-associated bacteria in this species. Our results revealed that nematode infection had effects on both endophytic bacterial communities and rhizosphere communities in F. tikoua roots, but on different levels. The species richness increased in the rhizosphere bacterial communities of infected individuals, but the community composition remained similar as compared with that of healthy individuals. Nematode infection induces a deterministic assembly process in the endophytic bacterial communities of parasitized organs. Significant taxonomic and functional changes were observed in the endophytic communities of root knots. These changes were characterized by the enrichment of nitrogen-fixing bacteria, including Bradyrhizobium, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and nematode-antagonistic bacteria, such as Pseudonocardia, Pseudomonas, Steroidobacter, Rhizobacter, and Ferrovibrio. Our results would help the understanding of the tritrophic plant-nematode-bacterium interactions in host plants other than dominant crops and vegetables and would provide essential information for successful nematode management when F. tikoua were cultivated on large scales.
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Affiliation(s)
- Xiang-Rui Meng
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Yu Gan
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Li-Jun Liao
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Chao-Nan Li
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Rong Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Mei Liu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Jun-Yin Deng
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yan Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
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Zhang X, Li H, Li B, Song K, Sha Y, Liu Y, Dong S, Wang D, Yang L. Microbial Community Shifts in Tea Plant Rhizosphere under Seawater Stress: Enrichment of Beneficial Taxa. Microorganisms 2024; 12:1287. [PMID: 39065056 PMCID: PMC11279268 DOI: 10.3390/microorganisms12071287] [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: 05/15/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Seawater intrusion has a significant impact on the irrigation quality of agricultural water, thereby posing a threat to plant growth and development. We hypothesized that the rhizosphere of tea plants harbors beneficial microorganisms, which may improve the tolerance of tea plants to seawater stress. This study utilized 16s and ITS techniques to analyze microbial community shifts in the tea plant rhizosphere and non-rhizosphere under seawater stress conditions. The findings suggest that seawater stress leads to a reduction in microbial diversity, although the rhizosphere microbial diversity in stressed soils showed a relatively higher level. Moreover, the rhizosphere of the tea plant under seawater stress exhibited an enrichment of plant growth-promoting rhizobacteria alongside a higher presence of pathogenic fungi. Network analysis revealed that seawater stress resulted in the construction of a more complex and stable rhizosphere microbial network compared to normal conditions. Predictions of bacterial potential functions highlighted a greater diversity of functional groups, enhancing resource utilization efficiency. In general, the rhizosphere microorganisms of tea plants are jointly selected by seawater and the host. The microorganisms closely related to the rhizosphere of tea plants are retained and, at the same time, attract beneficial microorganisms that may alleviate stress. These findings provide new insights into plant responses to saline stress and have significant implications for leveraging vegetation to enhance the resilience of coastal saline soils and contribute to economic progress.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China (K.S.); (Y.L.)
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Zhang B, Mao W, Chen S, Wang X. Characteristics and key driving factors of nitrous oxide emissions from a full-scale landfill leachate treatment system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172821. [PMID: 38688376 DOI: 10.1016/j.scitotenv.2024.172821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/01/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
The characteristics of N2O emission from a full-scale landfill leachate treatment system were investigated by in-situ monitoring over 1.4 years and driving factors responsible for these emissions were identified by statistical analysis of multidimensional environmental variables. The results showed that the maximum N2O emission flux of 2.21 × 107 mg N·h-1 occurred in the nitrification tanks, where 98.5 % of the total N2O was released, with only 1.5 % of the total N2O emitted from the denitrification tanks. Limited oxygen in nitrification tank was responsible for N2O hotspot. The N2O emissions from the parallel lines A and B (both comprising the primary biochemical system) accounted for 52.6 % and 46.6 %, respectively, while the secondary biochemical system contributed only 0.8 % to the total emissions. Higher nitrite concentration in line A and lower nitrogen loading in the secondary biochemical system caused these discrepancies. We found that during the steady state of leachate treatment, intensive N2O emissions of 253.4-1270.5 kg N·d-1 were measured. The corresponding N2O emission factor (EF) ranged from 8.86 to 49.6 %, much higher than those of municipal wastewater treatment. But N2O EF was inconceivably as low as 0.42 % averagely after system maintenance. Influent with low salinity was the key reason, followed by the high MLSS and varying microbial community after maintenance. The dominant genus shifted from Lentimicrobium and Thauera to Norank-F-Anaerolineaceae and Unclassified-F-Rhodocyclaceae. This study underscores the significance of landfill leachate treatment in urban nitrogen management and provides valuable insights into the characteristics and driving factors of N2O emissions from such systems. The findings offer important references for greenhouse gas emission inventories and strategies for N2O control in full-scale wastewater treatment plants.
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Affiliation(s)
- Bo Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wenlong Mao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Shaohua Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Xiaojun Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Asif A, Chen JS, Hsu GJ, Hussain B, Nagarajan V, Koner S, Huang SW, Hsu BM. Influence of Geothermal Fumaroles in Driving the Microbial Community Dynamics and Functions of Adjacent Ecosystems. J Basic Microbiol 2024:e2400157. [PMID: 38859671 DOI: 10.1002/jobm.202400157] [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: 03/19/2024] [Revised: 05/07/2024] [Accepted: 05/19/2024] [Indexed: 06/12/2024]
Abstract
Growing evidence suggests that the hydrochemical properties of geothermal fumaroles may play a crucial role in shaping the diversity and functions of microbial communities in various environments. In the present study, the impact of geothermal furaneols on the microbial communities and their metabolic functions across the rock-soil-plant continuum was explored considering varying distances from the fumarole source. The results revealed that bacterial phylum Proteobacteria was predominant in all sample types, except in the 10 m rock sample, irrespective of the sampling distance. Archaeal phyla, such as Euryarchaeota and Crenarchaeota, were more prevalent in rock and soil samples, whereas bacterial phyla were more prevalent in plant samples. Thermoacidophilic archaeons, including Picrophilus, Ferroplasma, and Thermogymnomonas were dominant in rocks and soil samples of 1 and 5 m distances; acidophilic mesophiles, including Ferrimicrobium and Granulicella were abundant in the rhizoplane samples, whereas rhizosphere-associated microbes including Pseudomonas, Pedobacter, Rhizobium, and Novosphingobium were found dominant in the rhizosphere samples. The functional analysis highlighted the higher expression of sulfur oxidative pathways in the rock and soil samples; dark iron oxidation and nitrate/nitrogen respiratory functions in the rhizosphere samples. The findings underscore microbial adaptations across the rock-soil-plant continuum, emphasizing the intricate relationship between geothermal fumaroles and microbial communities in adjacent ecosystems. These insights offer a crucial understanding of the evolution of microbial life and highlight their pivotal roles in shaping ecosystem dynamics and functions.
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Affiliation(s)
- Aslia Asif
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
- Doctoral Program in Science, Technology, Environment and Mathematics (STEM), National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Gwo-Jong Hsu
- Division of Infectious Disease, Department of Internal Medicine, Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Shih-Wei Huang
- Center for Environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung, Taiwan
- Super Micro Research and Technology Center, Cheng Shiu University, Kaohsiung, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
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Xu J, Ming H, Ren K, Li D, Huang H, Li J, Shao K, Li H, Fan J. Spatial heterogeneity plays a vital role in shaping the structure and function of estuarine carbon-fixing bacterial communities. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106544. [PMID: 38795574 DOI: 10.1016/j.marenvres.2024.106544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/18/2024] [Accepted: 05/05/2024] [Indexed: 05/28/2024]
Abstract
Carbon-fixing bacterial communities are essential drivers of carbon fixation in estuarine ecosystems that critically affect the global carbon cycle. This study compared the abundances of the Calvin cycle functional genes cbbL and cbbM and Reductive tricarboxylic acid cycle gene aclB, as well as compared carbon-fixing bacterial community features in the two estuaries, predicted potential ecological functions of carbon-fixation bacteria, and analyzed their symbiosis strategies in two estuaries having different geographical distributions. Gammaproteobacteria was the dominant carbon-fixing bacterial community in the two estuaries. However, a higher number of Alphaproteobacteria were noted in the Liaohe Estuary, and a higher number of Betaproteobacteria were found in the Yalujiang Estuary. The carbon-fixing functional gene levels exhibited the order of aclB > cbbL > cbbM, and significant effects of Cu, Pb, and petroleum were observed (p < 0.05). Nitrogen-associated nutrient levels are major environmental factors that affect carbon-fixing bacterial community distribution patterns. Spatial factors significantly affected cbbL carbon-fixing functional bacterial community structure more than environmental factors. With the increase in offshore distance, the microbial-led processes of methylotrophy and nitrogen fixation gradually weakened, but a gradual strengthening of methanotrophy and nitrification was observed. Symbiotic network analysis of the microorganisms mediating these ecological processes revealed that the carbon-fixing bacterial community in these two estuaries had a non-random symbiotic pattern, and microbial communities from the same module were strongly linked among the carbon, nitrogen, and sulfur cycle. These findings could advance the understanding of carbon fixation in estuarine ecosystems.
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Affiliation(s)
- Jianrong Xu
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Hongxia Ming
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Kaijia Ren
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Dongwei Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; College of Environmental Sciences and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Huiling Huang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Jiajie Li
- Faculty of Science, The University of Sydney, Sydney, 2007, Australia
| | - Kuishuang Shao
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Jingfeng Fan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China.
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Blakney AJC, Morvan S, Lucotte M, Moingt M, Charbonneau A, Bipfubusa M, Gonzalez E, Pitre FE. Site properties, environmental factors, and crop identify influence soil bacterial communities more than municipal biosolid application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171854. [PMID: 38522550 DOI: 10.1016/j.scitotenv.2024.171854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Reducing the environmental impact of Canadian field crop agriculture, including the reliance on conventional synthesised fertilisers, are key societal targets for establishing long-term sustainable practices. Municipal biosolids (MSB) are an abundant, residual organic material, rich in phosphate, nitrogen and other oligo-nutrients, that could be used in conjunction with conventional fertilisers to decrease their use. Though MBS have previously been shown to be an effective fertiliser substitute for different crops, including corn and soybean, there remain key knowledge gaps concerning the impact of MBS on the resident soil bacterial communities in agro-ecosystems. We hypothesised that the MBS fertiliser amendment would not significantly impact the structure or function of the soil bacterial communities, nor contribute to the spread of human pathogenic bacteria, in corn or soybean agricultural systems. In field experiments, fertiliser regimes for both crops were amended with MBS, and compared to corn and soybean plots with standard fertiliser treatments. We repeated this across four different agricultural sites in Quebec, over 2021 and 2022. We sampled MBS-treated, and untreated soils, and identified the composition of the soil bacterial communities via 16S rRNA metabarcoding. We found no indication that the MBS fertiliser amendment altered the structure of the soil bacterial communities, but rather that the soil type and crop identities were the most significant factors in structuring the bacterial communities. Moreover, there was no evidence that the MBS-treated soils were enriched in potential human bacterial pathogens over the two years of our study. Our analysis indicates that not only can MBS function as substitutes for conventional, synthesised fertilisers, but that they also do not disrupt the structure of the resident soil bacterial communities in the short term. Finally, we suggest that the use of MBS in agro-ecosystems poses no greater concern to the public than existing soil bacterial communities. This highlights the significant role MBS could potentially have in reducing the use of conventional industrial fertilisers and improving agricultural production, without risking environmental contamination.
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Affiliation(s)
- Andrew J C Blakney
- Institut de Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke East, Montréal, QC H1X 2B2, Canada.
| | - Simon Morvan
- Institut de Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke East, Montréal, QC H1X 2B2, Canada
| | - Marc Lucotte
- GEOTOP & Institut des Sciences de l'environnement, Université du Québec à Montréal, 201, Avenue du Président-Kennedy, Montréal, QC H2X3Y7, Canada.
| | - Matthieu Moingt
- GEOTOP & Institut des Sciences de l'environnement, Université du Québec à Montréal, 201, Avenue du Président-Kennedy, Montréal, QC H2X3Y7, Canada
| | - Ariane Charbonneau
- GEOTOP & Institut des Sciences de l'environnement, Université du Québec à Montréal, 201, Avenue du Président-Kennedy, Montréal, QC H2X3Y7, Canada
| | - Marie Bipfubusa
- Centre de Recherche sur les Grains, Inc. (CÉROM), Saint-Mathieu-de-Beloeil, QC J3G 0E2, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill Genome Centre, McGill University, Montréal, Québec, Canada
| | - Frédéric E Pitre
- Institut de Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke East, Montréal, QC H1X 2B2, Canada
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Meng X, Liu M, Meng Z, Wu C, Bao C, Xu B, Wang G, Ma H, Liu Z, Zheng X, Xie X, Cui X. Effects of different restoration stages on soil microbial community composition and diversity in Naolihe Wetland, China. Front Microbiol 2024; 15:1403849. [PMID: 38808276 PMCID: PMC11132264 DOI: 10.3389/fmicb.2024.1403849] [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: 03/20/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
Soil microorganisms can be used as one of the important indicators of wetland ecosystem restoration. To study the effects of different restoration stages on soil microbial community composition and diversity in Naolihe Wetland, we employed a "time and space parallel" method. Four restoration stages, namely corn field (Corn), short-term restoration wetland (2 years, ST), long-term restoration wetland (8 years, LT) and natural wetland (>25 years, NW), were selected to represent the restoration time and geographical location in Naolihe Nature Wetland. We investigated the composition and diversity of soil microbial communities in different restoration wetland (from corn fields to natural wetlands) by using 16S rRNA and ITS rRNA gene sequencing. We also performed chemical experiments to measure soil enzyme activity and physicochemical properties at each sampling site. The results showed that soil physicochemical properties and enzyme activities significantly differed with the extension of wetland restoration years (p < 0.05). Proteobacteria, Acidobacteria, and Actinobacteria are the most dominant phyla in bacterial. The alpha diversity of soil bacteria was the highest in the corn field (Corn), and ST-LT-NW first decreased and then increased with the extension of wetland restoration years. There are two most dominant phyla (Ascomycota and Mucoromycota) in fungal. However, the alpha diversity of soil fungi was the lowest in the Corn and LT stage, and ST-LT-NW first decreased and then increased with the extension of wetland restoration years. The research findings indicated that the changes in soil physicochemical properties with the extension of wetland restoration years play a significant role in shaping the structure and diversity changes of soil microbial communities. Through the analyses of bacterial and fungal functions using the FUNGuild and FAPROTAX databases, the results showed that the abundance of aerobic bacteria in the soil increased more than that of anaerobic bacteria as the wetland restoration years prolonged, while the abundance of saprotrophic, symbiotic, and pathogenic fungi in the soil significantly decreased with the prolonged wetland restoration years. This study will help us better understand the process of restoration after farmland abandonment, providing valuable reference information for the implementation of a series of wetland ecological restoration projects in the future.
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Affiliation(s)
- Xiangzheng Meng
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Manhong Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Zhaojun Meng
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Chengdan Wu
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Chonglin Bao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Bin Xu
- Discipline Inspection Commission and Supervision Commission of Qiqihar, Qiqihar, China
| | - Guangxin Wang
- Hongxinglong Branch, Heilongjiang Naolihe National Nature Reserve Administration, Shuangyashan, China
| | - Huan Ma
- Hongxinglong Branch, Heilongjiang Naolihe National Nature Reserve Administration, Shuangyashan, China
| | - Ze Liu
- Hongxinglong Branch, Heilongjiang Naolihe National Nature Reserve Administration, Shuangyashan, China
| | - Xu Zheng
- Hongxinglong Branch, Heilongjiang Naolihe National Nature Reserve Administration, Shuangyashan, China
| | - Xingyu Xie
- Hongxinglong Branch, Heilongjiang Naolihe National Nature Reserve Administration, Shuangyashan, China
| | - Xingbo Cui
- Hongxinglong Branch, Heilongjiang Naolihe National Nature Reserve Administration, Shuangyashan, China
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Huang SW, Hussain B, Chen JS, Asif A, Hsu BM. Evaluating groundwater ecosystem dynamics in response to post in-situ remediation of mixed chlorinated volatile organic compounds (CVOCs): An insight into microbial community resilience, adaptability, and metabolic functionality for sustainable remediation and ecosystem restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170874. [PMID: 38350560 DOI: 10.1016/j.scitotenv.2024.170874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/15/2024]
Abstract
The in-situ remediation of groundwater contaminated with mixed chlorinated volatile organic compounds (CVOCs) has become a significant global research interest. However, limited attention has been given in understanding the effects of these remediation efforts on the groundwater microbial communities, which are vital for maintaining ecosystem health through their involvement in biogeochemical cycles. Hence, this study aimed to provide valuable insights into the impacts of in-situ remediation methods on groundwater microbial communities and ecosystem functionality, employing high-throughput sequencing coupled with functional and physiological assays. The results showed that both bioremediation and chemical remediation methods adversely affected microbial diversity and abundance compared to non-polluted sites. Certain taxa such as Pseudomonas, Acinetobacter, and Vogesella were sensitive to these remediation methods, while Aquabacterium exhibited greater adaptability. Functional annotation unveiled the beneficial impact of bioremediation on the sulfur cycle and specific taxa such as Cellvibrio, Massilia, Algoriphagus, and Flavobacterium which showed a significant positive relationship with dark oxidation of sulfur compounds. In contrast, chemical remediation showed adverse impacts on the nitrogen cycle with a reduced abundance of nitrogen and nitrate respiration along with a reduced utilization of amines (nitrogen rich substrate). The findings of this study offer valuable insights into the potential impacts of in-situ remediation methods on groundwater microbial communities and ecosystem functionality, emphasizing the need for meticulous consideration to ensure the implementation of effective and sustainable remediation strategies that safeguard ecosystem health and function.
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Affiliation(s)
- Shih-Wei Huang
- Center for environmental Toxin and Emerging Contaminant, Cheng Shiu University, Kaohsiung, Taiwan; Institute of Environmental Toxin and Emerging Contaminant, Cheng Shiu University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Aslia Asif
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Doctoral Program in Science, Technology, Environment and Mathematics, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan.
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10
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Qiang W, Gunina A, Kuzyakov Y, Liu Q, Pang X. Decoupled response of microbial taxa and functions to nutrients: The role of stoichiometry in plantations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120574. [PMID: 38520862 DOI: 10.1016/j.jenvman.2024.120574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 03/25/2024]
Abstract
The resource quantity and elemental stoichiometry play pivotal roles in shaping belowground biodiversity. However, a significant knowledge gap remains regarding the influence of different plant communities established through monoculture plantations on soil fungi and bacteria's taxonomic and functional dynamics. This study aimed to elucidate the mechanisms underlying the regulation and adaptation of microbial communities at the taxonomic and functional levels in response to communities formed over 34 years through monoculture plantations of coniferous species (Japanese larch, Armand pine, and Chinese pine), deciduous forest species (Katsura), and natural shrubland species (Asian hazel and Liaotung oak) in the temperate climate. The taxonomic and functional classifications of fungi and bacteria were examined for the mineral topsoil (0-10 cm) using MiSeq-sequencing and annotation tools of microorganisms (FAPROTAX and Funguild). Soil bacterial (6.52 ± 0.15) and fungal (4.46 ± 0.12) OTUs' diversity and richness (5.83*103±100 and 1.12*103±46.4, respectively) were higher in the Katsura plantation compared to Armand pine and Chinese pine. This difference was attributed to low soil DOC/OP (24) and DON/OP (11) ratios in the Katsura, indicating that phosphorus availability increased microbial community diversity. The Chinese pine plantation exhibited low functional diversity (3.34 ± 0.04) and richness (45.2 ± 0.41) in bacterial and fungal communities (diversity 3.16 ± 0.15 and richness 56.8 ± 3.13), which could be attributed to the high C/N ratio (25) of litter. These findings suggested that ecological stoichiometry, such as of enzyme, litter C/N, soil DOC/DOP, and DON/DOP ratios, was a sign of the decoupling of soil microorganisms at the genetic and functional levels to land restoration by plantations. It was found that the stoichiometric ratios of plant biomass served as indicators of microbial functions, whereas the stoichiometric ratios of available nutrients in soil regulated microbial genetic diversity. Therefore, nutrient stoichiometry could serve as a strong predictor of microbial diversity and composition during forest restoration.
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Affiliation(s)
- Wei Qiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany
| | - Anna Gunina
- Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany; Tyumen State University, 625003, Tyumen, Russia; Peoples Friendship University of Russia (RUDN) University, 117198, Moscow, Russia
| | - Yakov Kuzyakov
- Peoples Friendship University of Russia (RUDN) University, 117198, Moscow, Russia; Institute of Environmental Sciences, Kazan Federal University, 420049, Kazan, Russia; Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Göttingen, Germany
| | - Qinghua Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China.
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11
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Li F, Lu S, Sun W. Comparison of Rhizosphere Bacterial Communities of Pinus squamata, a Plant Species with Extremely Small Populations (PSESP) in Different Conservation Sites. Microorganisms 2024; 12:638. [PMID: 38674583 PMCID: PMC11051972 DOI: 10.3390/microorganisms12040638] [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: 01/31/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Pinus squamata is one of the most threatened conifer species in the world. It is endemic to northeastern Yunnan Province, China, and has been prioritized as a Plant Species with Extremely Small Populations (PSESP). The integrated study of soil properties and rhizosphere bacteria can assist conservation to understand the required conditions for the protection and survival of rare and endangered species. However, differences between the rhizospheric bacterial communities found in the soil surrounding P. squamata at different conservation sites remain unclear. In this study, Samples were collected from wild, ex situ, and reintroduced sites. Bacterial communities in different conservation sites of P. squamata rhizosphere soils were compared using Illumina sequencing. The soil physicochemical properties were determined, the relationships between the bacterial communities and soil physicochemical factors were analyzed, and the potential bacterial ecological functions were predicted. The reintroduced site Qiaojia (RQ) had the highest richness and diversity of bacterial community. Actinobacteria, Proteobacteria, and Acidobacteriota were the dominant phyla, and Bradyrhizobium, Mycobacterium, Acidothermus were the most abundant genera. Samples were scattered (R = 0.93, p = 0.001), indicating significant difference between the different conservation sites. The abundance of Mycobacterium differed between sites (0.01 < p ≤ 0.05), and the relative abundances of Bradyrhizobium and Acidothermus differed significantly among different sites (0.001 < p ≤ 0.01). Soil total potassium (TK) and available nitrogen (AN) were the main factors driving bacterial community at the phylum level (0.01 < p ≤ 0.05). This study generated the first insights into the diversity, compositions, and potential functions of bacterial communities associated with the rhizosphere soils of P. squamata in different conservation sites and provides a foundation to assess the effect of conservation based on bacterial diversity and plant growth-promoting rhizobacteria (PGPR) to guide future research into the conservation of P. squamata.
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Affiliation(s)
- Fengrong Li
- School of Life Sciences, Yunnan University, Kunming 650091, China;
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shugang Lu
- School of Life Sciences, Yunnan University, Kunming 650091, China;
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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12
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Casado M, Sanz C, Cáceres R, Rufat J, Vallverdú X, Casadesús J, Matamoros V, Piña B. Evolution of microbiome composition, antibiotic resistance gene loads, and nitrification during the on-farm composting of the solid fraction of pig slurry using two bulking agents. ENVIRONMENTAL RESEARCH 2024; 245:117944. [PMID: 38109952 DOI: 10.1016/j.envres.2023.117944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023]
Abstract
Composting is a nature-based method used to stabilize organic matter and to transform nitrogen from animal farm manure or solid fraction of slurry (SFS). The use of composted material as source of nutrients for agriculture is limited by its potential to facilitate the propagation of biological hazards like pathogens and antibiotic-resistant bacteria and their associated antibiotic-resistance genes (ARG). We show here an experimental on-farm composting (one single batch) of pig SFS, performed under realistic conditions (under dry continental Mediterranean climate) for 280 days, and using two different bulking agents (maize straw and tree pruning residues) for the initial mixtures. The observed reduction in potentially pathogenic bacteria (80-90%) and of ARG loads (60-100%) appeared to be linked to variations in the microbiome composition occurring during the first 4 months of composting, and concurrent with the reduction of water-soluble ammonium and organic matter loads. Nitrification during the composting has also been observed for both composting piles. Similar patterns have been demonstrated at small scale and the present study stresses the fact that the removal can also occur at full scale. The results suggest that adequate composition of the starting material may accelerate the composting process and improve its global performance. While the results confirm the sanitization potential of composting, they also issue a warning to limit ARG loads in soils and in animal and human gut microbiomes, as the only way to limit their presence in foodstuffs and, therefore, to reduce consumers' exposure.
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Affiliation(s)
- Marta Casado
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain
| | - Claudia Sanz
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain
| | - Rafaela Cáceres
- IRTA. Torre Marimon, 08140, Caldes de Montbui, Catalunya, Spain.
| | - Josep Rufat
- IRTA. Fruit Centre, Building of the Parc Gardeny, 25003, Lleida, Catalunya, Spain
| | - Xavier Vallverdú
- IRTA. Fruit Centre, Building of the Parc Gardeny, 25003, Lleida, Catalunya, Spain
| | - Jaume Casadesús
- IRTA. Fruit Centre, Building of the Parc Gardeny, 25003, Lleida, Catalunya, Spain
| | - Víctor Matamoros
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain
| | - Benjamin Piña
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain
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13
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Li Z, Feng C, Lei J, He X, Wang Q, Zhao Y, Qian Y, Zhan X, Shen Z. Farmland Microhabitat Mediated by a Residual Microplastic Film: Microbial Communities and Function. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:3654-3664. [PMID: 38318812 DOI: 10.1021/acs.est.3c07717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
How the plastisphere mediated by the residual microplastic film in farmlands affects microhabitat systems is unclear. Here, microbial structure, assembly, and biogeochemical cycling in the plastisphere and soil in 33 typical farmland sites were analyzed by amplicon sequencing of 16S rRNA genes and ITS and metagenome analysis. The results indicated that residual microplastic film was colonized by microbes, forming a unique niche called the plastisphere. Notable differences in the microbial community structure and function were observed between soil and plastisphere. Residual microplastic film altered the microbial symbiosis and assembly processes. Stochastic processes significantly dominated the assembly of the bacterial community in the plastisphere and soil but only in the plastisphere for the fungal community. Deterministic processes significantly dominated the assembly of fungal communities only in soil. Moreover, the plastisphere mediated by the residual microplastic film acted as a preferred vector for pathogens and microorganisms associated with plastic degradation and the nitrogen and sulfur cycle. The abundance of genes associated with denitrification and sulfate reduction activity in the plastisphere was pronouncedly higher than that of soil, which increase the potential risk of nitrogen and sulfur loss. The results will offer a scientific understanding of the harm caused by the residual microplastic film in farmlands.
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Affiliation(s)
- Zhenling Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Chenghong Feng
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Jinming Lei
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiaokang He
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Qixuan Wang
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Yue Zhao
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
| | - Yibin Qian
- National Plot Zone for Ecological Conservation (Hainan) Research Center, Hainan Research Academy of Environmental Sciences, Haikou 571127, P. R. China
| | - Xinmin Zhan
- Civil Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Zhenyao Shen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, School of Environment, Beijing Normal University, Beijing 100875, P. R. China
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14
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Reiß F, Kiefer N, Purahong W, Borken W, Kalkhof S, Noll M. Active soil microbial composition and proliferation are directly affected by the presence of biocides from building materials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168689. [PMID: 38000743 DOI: 10.1016/j.scitotenv.2023.168689] [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: 08/19/2022] [Revised: 09/20/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
Abstract
Combinations of biocides are commonly added to building materials to prevent microbial growth and thereby cause degradation of the façades. These biocides reach the environment by leaching from façades posing an environmental risk. Although ecotoxicity to the aquatic habitat is well established, there is hardly any data on the ecotoxicological effects of biocides on the soil habitat. This study aimed to characterize the effect of the biocides terbutryn, isoproturon, octhilinone, and combinations thereof on the total and metabolically active soil microbial community composition and functions. Total soil microbial community was retrieved directly from the nucleic acid extracts, while the DNA of the active soil microbial community was separated after bromodeoxyuridine labeling. Bacterial 16S rRNA gene and fungal internal transcribed spacer region gene-based amplicon sequencing was carried out for both active and total, while gene copy numbers were quantified only for the total soil microbial community. Additionally, soil respiration and physico-chemical parameters were analyzed to investigate overall soil microbial activity. The bacterial and fungal gene copy numbers were significantly affected by single biocides and combined biocide soil treatment but not soil respiration and physico-chemical parameters. While the total soil microbiome experienced only minor effects from single and combined biocide treatment, the active soil microbiome was significantly impacted in its diversity, richness, composition, and functional patterns. The active bacterial richness was more sensitive than fungal richness. However, the adverse effects of the biocide combination treatments on soil bacterial richness were highly dependent on the identities of the biocide combination. Our results demonstrate that the presence of biocides frequently used in building materials affects the active soil microbiome. Thereby, the approach described herein can be used as an ecotoxicological measure for the effect on complex soil environments in future studies.
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Affiliation(s)
- Fabienne Reiß
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Nadine Kiefer
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Werner Borken
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Stefan Kalkhof
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany; Proteomics Unit, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany; Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
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15
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Shen Z, Xie G, Yu B, Zhang Y, Shao K, Gong Y, Gao G, Tang X. Eutrophication diminishes bacterioplankton functional dissimilarity and network complexity while enhancing stability: Implications for the management of eutrophic lakes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120119. [PMID: 38244411 DOI: 10.1016/j.jenvman.2024.120119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/13/2024] [Accepted: 01/13/2024] [Indexed: 01/22/2024]
Abstract
Eutrophication is a growing environmental concern in lake ecosystems globally, significantly impacting the structures and ecological functions of bacterioplankton communities and posing a substantial threat to the stability of lake ecosystems. However, the patterns of functional dissimilarity, network complexity, and stability within bacterioplankton communities across different trophic states, along with the underlying mechanisms through which eutrophication influences these aspects, are not well-understood. To bridge this knowledge gap, we collected 88 samples from 34 lakes spanning trophic gradients and investigated bacterioplankton communities using network analysis and multiple statistical methods. Our results reveal that eutrophication, progressing from mesotrophic to hyper-eutrophic states, reduces the putative functional dissimilarity of bacterioplankton, particularly affecting the relative proportions of functional groups such as oxygenic photoautotrophy, phototrophy, and photoautotrophy. Network complexity exhibited a unimodal pattern across increasing trophic states, peaking at mesotrophic states and then decreasing towards hyper-eutrophic conditions, while stability exhibited the opposite pattern (U-shaped), indicating a variation in response to trophic state changes. In essence, eutrophication diminishes network complexity but enhances network stability. Collectively, these findings shed light on the ecological impact of eutrophication on bacterioplankton communities and elucidate the potential mechanisms by which eutrophication drives functional dissimilarity, network complexity and stability within bacterioplankton communities. These insights carry significant implications for the ecological management of eutrophic lakes.
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Affiliation(s)
- Zhen Shen
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guijuan Xie
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Biology and Pharmaceutical Engineering, West Anhui University, Lu'an 237012, China
| | - Bobing Yu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuqing Zhang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yi Gong
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Zheng H, Chen T, Li W, Hong J, Xu J, Yu Z. Endosymbiotic bacteria within the nematode-trapping fungus Arthrobotrys musiformis and their potential roles in nitrogen cycling. Front Microbiol 2024; 15:1349447. [PMID: 38348183 PMCID: PMC10860758 DOI: 10.3389/fmicb.2024.1349447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024] Open
Abstract
Endosymbiotic bacteria (ESB) have important effects on their hosts, contributing to its growth, reproduction and biological functions. Although the effects of exogenous bacteria on the trap formation of nematode-trapping fungi (NTF) have been revealed, the effects of ESB on NTF remain unknown. In this study, we investigated the species diversity of ESB in the NTF Arthrobotrys musiformis using high-throughput sequencing and culture-dependent approaches, and compared bacterial profiles to assess the effects of strain source and culture media on A. musiformis. PICRUSt2 and FAPROTAX were used to predict bacterial function. Our study revealed that bacterial communities in A. musiformis displayed high diversity and heterogeneity, with Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as the dominant phyla. The ESB between A. musiformis groups isolated from different habitats and cultured in the same medium were more similar to each other than the other groups isolated from the same habitat but cultured in different media. Function analysis predicted a broad and diverse functional repertoire of ESB in A. musiformis, and unveiled that ESB have the potential to function in five modules of the nitrogen metabolism. We isolated nitrogen-fixing and denitrifying bacteria from the ESB and demonstrated their effects on trap formation of A. musiformis. Among seven bacteria that we tested, three bacterial species Bacillus licheniformis, Achromobacter xylosoxidans and Stenotrophomonas maltophilia were found to be efficient in inducing trap formation. In conclusion, this study revealed extensive ESB diversity within NTF and demonstrated that these bacteria likely play important roles in nitrogen cycling, including nematode trap formation.
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Affiliation(s)
- Hua Zheng
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Tong Chen
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Wenjie Li
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jianan Hong
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Zefen Yu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
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17
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Liu S, Imad S, Hussain S, Xiao S, Yu X, Cao H. Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs. BMC Microbiol 2024; 24:34. [PMID: 38262927 PMCID: PMC10804495 DOI: 10.1186/s12866-023-03150-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Frogs are critical economic animals essential to agricultural ecosystem equilibrium. However, Meningitis-like Infectious Disease (MID) often affects them in agricultural settings. While frog-associated microbiota contribute to elemental cycling and immunity, the effects of frog sex and health on gut bacteria remain understudied, and the relationship between frog habitat and soil microbes is unclear. We aimed to determine how frog sex, health status and habitat influence symbiotic bacteria and community assembly mechanism to provide guidance for sustainable frog farming and conservation. RESULTS We employed 16S rRNA sequencing to investigate gut microbiota differences in relation to frog sex and health status. We also compared symbiotic communities in frog-aggregation, native and soybean soil on the farm. Results showed that gut bacterial β-diversity and taxonomy were markedly influenced by frog sex and health. Healthy frogs had more robust gut bacterial metabolism than frogs infected with MID. Cooccurrence network analysis revealed that healthy female frogs had more complex microbial network structure than males; however, diseased males showed the greatest network complexity. The assembly mechanism of gut bacteria in male frogs was dominated by deterministic processes, whereas in female frogs it was dominated by stochastic processes. Among symbiotic bacteria in frog habitat soils, deterministic processes predominantly shaped the community assembly of soybean soil. In particular, soybean soil was enriched in pathogens and nitrogen functions, whereas frog-aggregation soil was markedly increased in sulphur respiration and hydrocarbon degradation. CONCLUSION Our study reveals that sex mainly alters the interaction network and assembly mechanism of frog intestinal bacteria; MID infection significantly inhibits the metabolic functions of intestinal bacteria. Furthermore, diverse frog habitat soils could shape more symbiotic bacteria to benefit frog farming. Our findings provide new horizons for symbiotic bacteria among frogs, which could contribute to sustainable agriculture and ecological balance.
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Affiliation(s)
- Senlin Liu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Sewar Imad
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | | | - Xiaowei Yu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China.
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18
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Zhang Z, Wang W, Liu J, Wu H. Discrepant responses of bacterial community and enzyme activities to conventional and biodegradable microplastics in paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168513. [PMID: 37977392 DOI: 10.1016/j.scitotenv.2023.168513] [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: 10/07/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The prevalence of microplastics in soil ecosystems has raised concerns about their potential effects on soil properties. As promising alternatives to conventional plastics, biodegradable plastics have been increasingly applied in agricultural activities, which may release microplastics into the soil due to incomplete degradation. Compared to conventional microplastics, biodegradable microplastics in soil may induce different impacts on soil microbial properties, which have yet to be well studied. Through a 41-day microcosm experiment, we evaluated the differential effects of conventional (polypropylene, PP) and biodegradable (polylactic acid, PLA) microplastics on the geochemical properties, enzyme activities, and microbial community structure in paddy soil. Adding PLA or PP microplastics into soil significantly increased pH values and altered the contents of carbon and nitrogen nutrients. Exposure to microplastics significantly increased the activity of fluorescein diacetate hydrolase, but had varying effects on the activities of urease, sucrase, and alkaline phosphatase depending on microplastic types and doses. The addition of microplastics also influenced the structure of soil bacterial community, with Proteobacteria, Actinobacteriota, and Acidobacteriota being the dominant phyla. Significant differences in the genera of Pseudarthrobacter, Acidothermus, Bacillus, Aquisphaera, and Massilia were observed between treatments. Results of structural equation modeling (SEM) demonstrated that changes in soil carbon and nitrogen nutrients and pH values positively affected the bacterial community, while soil bacterial community as a whole exerted a negative impact on enzyme activities. FAPRPTAX analysis showed that the addition of microplastics altered the relative abundances of functional genes related to the metabolism of cellulose decomposition and ureolysis in paddy soil. Findings of this study clearly suggest that microplastic impacts on soil geochemical and microbial properties should be an integral part of future risk assessment and that to evaluate microplastic impacts, both the concentration and polymer type must be taken into account.
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Affiliation(s)
- Zhiyu Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun 130012, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun 130012, China; Jilin Normal University, 1301 Haifeng Street, Siping 136000, China
| | - Wenfeng Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun 130012, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun 130012, China.
| | - Jiping Liu
- Jilin Normal University, 1301 Haifeng Street, Siping 136000, China
| | - Haitao Wu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun 130012, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 4888 Shengbei Street, Changchun 130012, China.
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19
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Chen JS, Hussain B, Tsai HC, Nagarajan V, Kumar RS, Lin IC, Hsu BM. Deciphering microbial communities and their unique metabolic repertoire across rock-soil-plant continuum in the Dayoukeng fumarolic geothermal field of the Tatun Volcano Group. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7330-7344. [PMID: 38158533 DOI: 10.1007/s11356-023-31313-x] [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: 05/08/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
High temperature and sulfur concentrations in geothermal sulfur fumaroles host unique microbial ecosystems with niche-specific metabolic diversity and physiological functions. In this study, the microbial communities and their functionalities associated with the Dayoukeng geothermal field and the rock-soil-plant continuum were investigated to underpin the microbial modulation at different distances from the fumaroles source. At the phylum level, Bacteroidota, Planctomycetota, Armatimonadota, and Patescibacteria were abundant in plant samples; Elusimicrobiota and Desulfobacterota were in the rock samples while Nitrospirota, Micrarchaeota, and Deinococcota were dominant in the soil samples. Acidophilic thermophiles were enriched in samples within close proximity to the fumaroles, primarily at a distance of 1 m. The sulfur and iron-oxidizing acidophilic bacterial genera such as Acidothiobacillus and Sulfobacillus were abundant in the rock samples. The thermoacidophilic archaeon Acidianus and acidophilic bacteria Acidiphilium were abundant in the soil samples. Additionally, Thermosporothrix and Acidothermus were found abundant in the plant samples. The results of the functional annotation indicated that dark sulfur oxidation, iron oxidation, and hydrogen oxidation pathways were abundant in the soil samples up to 1 m from the fumaroles, while methanogenic and fermentation pathways were more prevalent in the soil samples located 10 m from the fumaroles. Interestingly, the results of this study indicated a higher microbial richness and abundance of acidophilic communities in the soils and plants compared to the rocks of the DYK fumarolic geothermal field.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
- Department of Biomedical Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Rajendran Senthil Kumar
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - I-Ching Lin
- Department of Family Medicine, Asia University Hospital, Taichung, Taiwan
- Department of Kinesiology, Health and Leisure, Chienkuo Technology University, Chenghua, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan.
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20
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Hanišáková N, Vítězová M, Vítěz T, Kushkevych I, Kotrlová E, Novák D, Lochman J, Zavada R. Microbiological insight into various underground gas storages in Vienna Basin focusing on methanogenic Archaea. Front Microbiol 2023; 14:1293506. [PMID: 38188570 PMCID: PMC10771303 DOI: 10.3389/fmicb.2023.1293506] [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: 09/13/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive understanding of the microbial communities within any UGS facilities designated for hydrogen storage. In this study, underground water samples and water samples from surface technologies from 7 different UGS objects located in the Vienna Basin were studied using both molecular biology methods and cultivation methods. Results from 16S rRNA sequencing revealed that the proportion of archaea in the groundwater samples ranged from 20 to 58%, with methanogens being the predominant. Some water samples collected from surface technologies contained up to 87% of methanogens. Various species of methanogens were isolated from individual wells, including Methanobacterium sp., Methanocalculus sp., Methanolobus sp. or Methanosarcina sp. We also examined water samples for the presence of sulfate-reducing bacteria known to be involved in microbially induced corrosion and identified species of the genus Desulfovibrio in the samples. In the second part of our study, we contextualized our data by comparing it to available sequencing data from terrestrial subsurface environments worldwide. This allowed us to discern patterns and correlations between different types of underground samples based on environmental conditions. Our findings reveal presence of methanogens in all analyzed groups of underground samples, which suggests the possibility of unintended microbial hydrogen-to-methane conversion and the associated financial losses. Nevertheless, the prevalence of methanogens in our results also highlights the potential of the UGS environment, which can be effectively leveraged as a bioreactor for the conversion of hydrogen into methane, particularly in the context of Power-to-Methane technology.
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Affiliation(s)
- Nikola Hanišáková
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Monika Vítězová
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tomáš Vítěz
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
- Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Ivan Kushkevych
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Eva Kotrlová
- Section of Microbiology, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Novák
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Lochman
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Roman Zavada
- Innovation Unit, NAFTA a.s., Bratislava, Slovakia
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21
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Zhang M, Kong Z, Fu H, Shu X, Xue Q, Lai H, Guo Q. Rhizosphere microbial ecological characteristics of strawberry root rot. Front Microbiol 2023; 14:1286740. [PMID: 38033596 PMCID: PMC10687216 DOI: 10.3389/fmicb.2023.1286740] [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: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Strawberry (Fragaria × ananassa Duch.) holds a preeminent position among small fruits globally due to its delectable fruits and significant economic value. However, strawberry cultivation is hampered by various plant diseases, hindering the sustainable development of the strawberry industry. The occurrence of plant diseases is closely linked to imbalance in rhizosphere microbial community structure. Methods In the present study, a systematic analysis of the differences and correlations among non-culturable microorganisms, cultivable microbial communities, and soil nutrients in rhizosphere soil, root surface soil, and non-rhizosphere soil of healthy and diseased strawberry plants affected by root rot was conducted. The goal was to explore the relationship between strawberry root rot occurrence and rhizosphere microbial community structure. Results According to the results, strawberry root rot altered microbial community diversity, influenced fungal community composition in strawberry roots, reduced microbial interaction network stability, and enriched more endophytic-phytopathogenic bacteria and saprophytic bacteria. In addition, the number of bacteria isolated from the root surface soil of diseased plants was significantly higher than that of healthy plants. Discussion In summary, the diseased strawberry plants changed microbial community diversity, fungal species composition, and enriched functional microorganisms significantly, in addition to reshaping the microbial co-occurrence network. The results provide a theoretical basis for revealing the microecological mechanism of strawberry root rot and the ecological prevention and control of strawberry root rot from a microbial ecology perspective.
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Affiliation(s)
| | | | | | | | | | | | - Qiao Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
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22
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Acuña JJ, Hu J, Inostroza NG, Valenzuela T, Perez P, Epstein S, Sessitsch A, Zhang Q, Jorquera MA. Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables. Sci Rep 2023; 13:19829. [PMID: 37963999 PMCID: PMC10645892 DOI: 10.1038/s41598-023-47099-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal-Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.
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Affiliation(s)
- Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Millennium Institute Center for Genome Regulation (MI-CGR), Valenzuela Puelma 10207, 7800003, Santiago, La Reina, Chile
| | - Jingming Hu
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Tamara Valenzuela
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Pablo Perez
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Slava Epstein
- College of Science, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Angela Sessitsch
- Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Qian Zhang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China.
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
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23
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Xing X, Yuan X, Zhang Y, Men C, Zhang Z, Zheng X, Ni D, Xi H, Zuo J. Enhanced denitrification of the AO-MBBR system used for expressway service area sewage treatment: A new perspective on decentralized wastewater treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118763. [PMID: 37683385 DOI: 10.1016/j.jenvman.2023.118763] [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: 05/20/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Decentralized wastewater treatment warrants considerable development in numerous countries and regions. Owing to the unique characteristics of high ammonia nitrogen concentrations and low carbon/nitrogen ratio, nitrogen removal is a key challenge in treating expressway service area sewage. In this study, an anoxic/oxic-moving bed biofilm reactor (A/O-MBBR) and a traditional A/O bioreactor were continuously operated for 115 days and their outcomes were compared to investigate the enhancement effect of carriers on the total nitrogen removal (TN) for expressway service area sewage. Results revealed that A/O-MBBR required lower dissolved oxygen, exhibited higher tolerance toward harsh conditions, and demonstrated better shock load resistance than traditional A/O bioreactor. The TN removal load of A/O-MBBR reached 181.5 g‧N/(m3‧d), which was 15.24% higher than that of the A/O bioreactor. Furthermore, under load shock resistance, the TN removal load of A/O-MBBR still reached 327.0 g‧N/(m3‧d), with a TN removal efficiency of above 80%. Moreover, kinetics demonstrated that the denitrification rate of the A/O-MBBR was 121.9% higher than that of the A/O bioreactor, with the anoxic tank biofilm contributing 60.9% of the total denitrification rate. Community analysis results revealed that the genera OLB8, uncultured_f_Saprospiraceae and OLB12 were the dominant in biofilm loaded on carriers, and OLB8 was the key for enhanced denitrification. FAPROTAX and PICRUSt2 analyses confirmed that more bacteria associated with nitrogen metabolism were enriched by the A/O-MBBR carriers through full denitrification metabolic pathway and dissimilatory nitrate reduction pathway. This study offers a perspective into the development of cost-effective and high-efficiency treatment solutions for expressway service area sewage.
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Affiliation(s)
- Xin Xing
- Research Institute of Highway Ministry of Transport, Beijing, 100088, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Xin Yuan
- Research Institute of Highway Ministry of Transport, Beijing, 100088, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Yu Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Cong Men
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Zhuowei Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Xiaoying Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Dong Ni
- Research Institute of Highway Ministry of Transport, Beijing, 100088, China.
| | - Huatian Xi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Jiane Zuo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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Wang S, Heal KV, Zhang Q, Yu Y, Tigabu M, Huang S, Zhou C. Soil microbial community, dissolved organic matter and nutrient cycling interactions change along an elevation gradient in subtropical China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118793. [PMID: 37619380 DOI: 10.1016/j.jenvman.2023.118793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/27/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
To identify possible dominating processes involved in soil microbial community assembly, dissolved organic matter (DOM) and multi-nutrient cycling (MNC) interactions and contribute to understanding of climate change effects on these important cycles, we investigated the interaction of soil chemistry, DOM components and microbial communities in five vegetation zones - ranging from evergreen broad-leaved forest to alpine meadow - along an elevation gradient of 290-1960 m in the Wuyi Mountains, Fujian Province, China. Soil DOM composition and microbial community assembly were characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and Illumina MiSeq high-throughput sequencing, respectively. Sloan's neutral model and the modified stochasticity ratio were used to infer community assembly processes. Key microbial drivers of the soil MNC index were identified from partial least squares path models. Our results showed that soil DOM composition is closely related to the vegetation types along an elevation gradient, the structure and composition of the microbial community, and soil nutrient status. Overall, values of the double bond equivalent (DBE), modified aromaticity index (AImod) increased, and H/C ratio and molecular lability boundary (MLBL) percentage decreased with elevation. Lignins/CRAM-like structures compounds dominated soil DOM in each vegetation type and its relative abundance decreased with elevation. Aliphatic/protein and lipids components also decreased, but the relative abundance of aromatic structures and tannin increased with elevation. The alpha diversity index of soil bacteria gradually decreased with elevation, with deterministic processes dominating the microbial community assembly in the highest elevation zone. Bacterial communities were conducive to the decomposition of labile degradable DOM compounds (H/C ≥ 1.5) at low elevation. In the cooler and wetter conditions at higher-elevation sites the relative abundance of potentially resistant soil DOM components (H/C < 1.5) gradually increased. Microbial community diversity and composition were important predictors of potential soil nutrient cycling. Although higher elevation sites have higher nutrient cycling potential, soil DOM was assessed to be a more stable carbon store, with apparent lower lability and bioavailability than at lower elevation sites. Overall, this study increases understanding of the potential linkage between soil microbial community, multiple nutrient cycling and DOM fate in subtropical mountain ecosystems that can help predict the effect of climate change on soil carbon sequestration and thus inform ecosystem management.
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Affiliation(s)
- Shuzhen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China; Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Kate V Heal
- School of GeoSciences, The University of Edinburgh, Crew Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Qin Zhang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Yuanchun Yu
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
| | - Mulualem Tigabu
- Swedish University of Agricultural Sciences, Faculty of Forest Science, Southern Swedish Forest Research Centre, P.O. Box 190, SE-234 22, Lomma, Sweden
| | - Shide Huang
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354315, Fujian Province, China
| | - Chuifan Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China of Jiangsu Province, Key Laboratory of Soil and Water Conservation and Ecological Restoration of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China; Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.
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25
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Colautti A, Civilini M, Contin M, Celotti E, Iacumin L. Organic vs. conventional: impact of cultivation treatments on the soil microbiota in the vineyard. Front Microbiol 2023; 14:1242267. [PMID: 37901804 PMCID: PMC10602642 DOI: 10.3389/fmicb.2023.1242267] [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: 06/18/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023] Open
Abstract
The aim of this study was to compare the effects of two vineyard management practices on the soil and its associated microbiota. The experiments were conducted in two adjacent plots, one completely organically managed and the other conventionally managed in terms of phytosanitary treatments but fertilized with organic amendments. The chemical soil analyses were correlated to the prokaryotic and fungal communities, which were studied using the metabarcoding technique. The main difference between the two treatments was a significantly higher amount of Cu in the organic managed vineyard soil, while conventional managed soil presented higher concentration of Na and Mg and was also associated with higher pH values. Despite these differences, no significant diversities were observed on soil biodiversity and microbial composition considering alpha and beta diversity metrics. However, the percentages of some phyla analyzed individually differed significantly between the two managements. Analyzing the metabolisms of these phyla, it was discovered an increment of species correlated to soils with higher organic matter content or land not used for agricultural purposes in the organic treated soil. The findings indicate that, despite the use of copper-based phytosanitary products, there was no degradation and loss of biodiversity in the organic soil microbial population compared to conventional management with the same type of fertilization, and the observed microbial population was more similar to that of natural soils.
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Affiliation(s)
| | | | | | | | - Lucilla Iacumin
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
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26
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Colette M, Guentas L, Della Patrona L, Ansquer D, Callac N. Suaeda australis and its associated rhizosphere microbiota: a comparison of the nutrient removal potential between different shrimp farm sediments in New Caledonia. Front Microbiol 2023; 14:1260585. [PMID: 37876780 PMCID: PMC10591223 DOI: 10.3389/fmicb.2023.1260585] [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: 07/18/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Shrimp rearing generate organic waste that is trapped in the pond sediment. In excess, these wastes may impair aquaculture ecosystem and shrimps' health. To promote the biological oxidation of accumulated organic waste, the pond is drained and dried at the end of each production cycle. However, this practice is not always conducive to maintaining microbial decomposition activities in sediments. Shrimp production in New Caledonia is no exception to this problem of pollution of pond bottoms. One promising way of treating this waste would be bioremediation, using a native halophyte plant and its microbiota. Thus, this study explored the nutrient removal potential of Suaeda australis and its microbiota on sediments from four shrimp farms. Suaeda australis was grown in an experimental greenhouse for 6 months. In order to mimic the drying out of the sediments, pots containing only sediments were left to dry in the open air without halophytes. An analysis of the chemical composition and active microbiota was carried out initially and after 6 months in the sediments of the halophyte cultures and in the dry sediments for each farm, respectively. In the initial state, the chemical parameters and the microbial diversity of the sediment varied considerably from one farm to another. Growing Suaeda australis reduced the nitrogen, phosphorus and sulfur content in all type of sediment. However, this reduction varied significantly from one sediment to another. The rhizosphere of Suaeda australis is mainly composed of micro-organisms belonging to the Alphaproteobacteria class. However, the families recruited from this class vary depending on the farm in question. Depending on the sediment, the variation in microbiota leads to different putative biochemical functions. For two of the farms, a similar reduction in nitrogen concentration was observed in both dry and cultivated sediments. This suggests that certain initial chemical characteristics of the sediments influence the nutrient removal efficiency of Suaeda australis. Our study therefore highlights the need to control the pH of sediments before cultivation or in dry sediments in order to ensure optimal microbial decomposition of organic waste and nutrient cycling.
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Affiliation(s)
- Marie Colette
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
- Institute of Exact and Applied Sciences (ISEA), University of New Caledonia, Nouméa, New Caledonia
| | - Linda Guentas
- Institute of Exact and Applied Sciences (ISEA), University of New Caledonia, Nouméa, New Caledonia
| | - Luc Della Patrona
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Dominique Ansquer
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
| | - Nolwenn Callac
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Nouméa, New Caledonia
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27
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Luo X, Gong Y, Xu F, Wang S, Tao Y, Yang M. Soil horizons regulate bacterial community structure and functions in Dabie Mountain of the East China. Sci Rep 2023; 13:15866. [PMID: 37739984 PMCID: PMC10517015 DOI: 10.1038/s41598-023-42981-7] [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: 11/01/2022] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Soil bacterial communities regulate nutrient cycling and plant growth in forests. Although these bacterial communities vary with soil nutrients and plant traits, the variation and degree with soil horizons in different forest types remain unclear. Here, bacterial communities of 44 soil samples from organic horizon (O horizon) and mineral horizon (M horizon) of three forest types (Cunninghamia, broad-leaved and Pinus forests) in subtropical forests of Dabie Mountain, China were analyzed based on amplicon sequencing. We assessed the effects of soil horizons and forest types on bacterial communities. The results showed that the bacterial richness and diversity were significantly higher in the O horizon than in the M horizon. Furthermore, the bacterial community composition and functions were also remarkably different between the two soil horizons. Furthermore, forest types could affect bacterial community composition but not for diversity and functions. Moreover, soil organic matter, including the total organic carbon, available phosphorus, total organic nitrogen, available potassium, ammonium nitrogen, and pH were main drivers for bacterial community composition. The results propose robust evidence that soil horizons strongly driven bacterial community composition and diversity, and suggest that microhabitat of soil bacterial communities is important to maintain the stability of forest ecosystem.
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Affiliation(s)
- Xia Luo
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China.
| | - Yinping Gong
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Feiyan Xu
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Shuai Wang
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Yingying Tao
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Mengmeng Yang
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
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Rodríguez R, Barra PJ, Larama G, Carrion VJ, de la Luz Mora M, Hale L, Durán P. Microbiome engineering optimized by Antarctic microbiota to support a plant host under water deficit. FRONTIERS IN PLANT SCIENCE 2023; 14:1241612. [PMID: 37780522 PMCID: PMC10541027 DOI: 10.3389/fpls.2023.1241612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Climate change challenges modern agriculture to develop alternative and eco-friendly solutions to alleviate abiotic and/or biotic stresses. The use of soil microbiomes from extreme environments opens new avenues to discover novel microorganisms and microbial functions to protect plants. In this study we confirm the ability of a bioinoculant, generated by natural engineering, to promote host development under water stress. Microbiome engineering was mediated through three factors i) Antarctic soil donation, ii) water deficit and iii) multigenerational tomato host selection. We revealed that tomato plants growing in soils supplemented with Antarctic microbiota were tolerant to water deficit stress after 10 generations. A clear increase in tomato seedling tolerance against water deficit stress was observed in all soils over generations of Host Mediated Microbiome Engineering, being Fildes mixture the most representatives, which was evidenced by an increased survival time, plant stress index, biomass accumulation, and decreased leaf proline content. Microbial community analysis using 16s rRNA gene amplicon sequencing data suggested a microbiome restructuring that could be associated with increased tolerance of water deficit. Additionally, the results showed a significant increase in the relative abundance of Candidatus Nitrosocosmicus and Bacillus spp. which could be key taxa associated with the observed tolerance improvement. We proposed that in situ microbiota engineering through the evolution of three factors (long-standing extreme climate adaption and host and stress selection) could represent a promising strategy for novel generation of microbial inoculants.
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Affiliation(s)
- Rodrigo Rodríguez
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Agroscientific SpA, Temuco, Chile
| | - Patricio J. Barra
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Giovanni Larama
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
| | | | - María de la Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Lauren Hale
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Paola Durán
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
- Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco, Chile
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Shao Y, Liu M, Ma X, Wang S, Guo J, Liu D, Zheng X. Investigation on the microbial community of an accelerating stabilization landfill by aeration engineering. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:94878-94889. [PMID: 37542688 DOI: 10.1007/s11356-023-29039-x] [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: 05/15/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023]
Abstract
The microbial community of the landfill undergoing aerobic stabilization process by aeration engineering was investigated. The municipal solid wastes (MSWs) were sampled from two aeration well sites with different landfill temperatures (65.5°C and 41.7°C) under higher and lower stabilization level. The physical component, chemical property, and microbial population of MSWs were analyzed and compared. The result showed that the phylum Firmicutes was dominant in the aerobic landfill; and the genus Weissella and Syntrophaceticus were more abundant in high, and low temperature site, respectively. The bacterial distribution showed difference on two temperature sites and four landfill depths, mainly affected by the ammonia-nitrogen and moisture content of MSWs. The ecological profiles of the microorganisms responded the aeration engineering were predicted. The anaerobic hydrolytic and acetogenic microorganisms were decreased in abundance, while the facultative Lactobacillus increased when the landfill under a higher stabilization level. The function abundances of methane oxidation, sulfide oxidation, and aerobic chemoheterotrophy were enriched by aeration engineering, which was the microbial mechanism for accelerating the stabilization process of landfill.
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Affiliation(s)
- Yan Shao
- Institute of Resources and Environment, Beijing Academy of Science and Technology, No. 27, Xisanhuanbei Road, Haidian District, Beijing, 100095, China
| | - Minghui Liu
- Institute of Resources and Environment, Beijing Academy of Science and Technology, No. 27, Xisanhuanbei Road, Haidian District, Beijing, 100095, China
| | - Xiaochun Ma
- Beijing No. 4 Municipal Construction Engineering Co., Ltd., Beijing Municipal Construction Group Co., Ltd., No. 2, Baianzhuang Street, Xicheng District, Beijing, 100176, China
| | - Senjie Wang
- Beijing No. 4 Municipal Construction Engineering Co., Ltd., Beijing Municipal Construction Group Co., Ltd., No. 2, Baianzhuang Street, Xicheng District, Beijing, 100176, China
| | - Jingxin Guo
- Beijing No. 4 Municipal Construction Engineering Co., Ltd., Beijing Municipal Construction Group Co., Ltd., No. 2, Baianzhuang Street, Xicheng District, Beijing, 100176, China
| | - Dan Liu
- Institute of Resources and Environment, Beijing Academy of Science and Technology, No. 27, Xisanhuanbei Road, Haidian District, Beijing, 100095, China
| | - Xiaowei Zheng
- Institute of Resources and Environment, Beijing Academy of Science and Technology, No. 27, Xisanhuanbei Road, Haidian District, Beijing, 100095, China.
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Chi Y, Song S, Xiong K. Effects of different grassland use patterns on soil bacterial communities in the karst desertification areas. Front Microbiol 2023; 14:1208971. [PMID: 37720153 PMCID: PMC10500843 DOI: 10.3389/fmicb.2023.1208971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/07/2023] [Indexed: 09/19/2023] Open
Abstract
Soil bacteria are closely related to soil environmental factors, and their community structure is an important indicator of ecosystem health and sustainability. A large number of artificial grasslands have been established to control rocky desertification in the karst areas of southern China, but the influence of different use patterns on the soil bacterial community in artificial grasslands is not clear. In this study, three grassland use patterns [i.e., grazing (GG), mowing (MG), and enclosure (EG)] were used to investigate the effects of different use patterns on the soil bacterial community in artificial grassland by using 16S rDNA Illumina sequencing and 12 soil environmental indicators. It was found that, compared with EG, GG significantly changed soil pH, increased alkaline hydrolyzable nitrogen (AN) content (P < 0.05), and decreased soil total phosphorus (TP) content (P < 0.05). However, MG significantly decreased the contents of soil organic carbon (SOC), total phosphorus (TP), available nitrogen (AN), ammonium nitrogen (NH4+-N), β-1,4-glucosidase (BG), and N-acetyl-β-D-glucamosonidase (NAG) (P < 0.05). The relative abundance of chemoheterotrophy was significantly decreased by GG and MG (P < 0.05). GG significantly increased the relative abundance of Acidobacteria and Gemmatimonadota (P < 0.05) and significantly decreased the relative abundance of Proteobacteria (P < 0.05), but the richness index (Chao 1) and diversity index (Shannon) of the bacterial community in GG, MG, and EG were not significantly different (P > 0.05). The pH (R2 = 0.79, P = 0.029) was the main factor affecting the bacterial community structure. This finding can provide a scientific reference for ecological restoration and sustainable utilization of grasslands in the karst desertification areas.
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Affiliation(s)
- Yongkuan Chi
- School of Karst Science, Guizhou Normal University, Guiyang, China
- Guizhou Engineering Laboratory for Karst Desertification Control and Eco-Industry, Guiyang, China
| | - Shuzhen Song
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Kangning Xiong
- School of Karst Science, Guizhou Normal University, Guiyang, China
- Guizhou Engineering Laboratory for Karst Desertification Control and Eco-Industry, Guiyang, China
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Su HY, Hussain B, Hsu BM, Lee KH, Mao YC, Chiang LC, Chen JS. Bacterial community analysis identifies Klebsiella pneumoniae as a native symbiotic bacterium in the newborn Protobothrops mucrosquamatus. BMC Microbiol 2023; 23:213. [PMID: 37553640 PMCID: PMC10408043 DOI: 10.1186/s12866-023-02936-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND The study of the native microbiome of organisms is crucial. The connection between the native microbiome and the host affects the formation of the innate immune system and the organism's growth. However, the native microbiome of newborn venomous snakes has not been reported. Therefore, we aimed to determine the oral and skin microbiomes of newborn Protobothrops mucrosquamatus. RESULTS We performed 16 S full-length sequencing on 14 samples collected from 7 newborn P. mucrosquamatus individuals, specifically targeting their oral and skin microbiomes. In terms of the oral and skin microbiome, the main species were Klebsiella pneumoniae lineages. According to subspecies/species analysis, the proportion from highest to lowest was K. quasipneumoniae subsp. similipneumoniae, K. pneumoniae subsp. pneumoniae, and K. pneumoniae subsp. rhinoscleromatis. These three bacteria accounted for 62.5% and 85% of the skin and oral activity, respectively. The oral microbiome of newborn P. mucrosquamatus did not comprise common bacteria found in snakebite wounds or oral cultures in adult snakes. Therefore, the source of other microbiomes in the oral cavities of adult snakes may be the environment or prey. Functional Annotation of the Prokaryotic Taxa analysis showed that the skin/oral native microbiome metabolism was related to fermentation and human infection owing to the dominance of K. pneumoniae lineages. The characteristics of K. pneumoniae may impact the development of venom in venomous snakes. CONCLUSION The results of the native microbiome in the oral cavity and skin of newborn P. mucrosquamatus demonstrated that the habitat environment and prey capture may affect the composition of bacteria in adult snakes. We hypothesized that the native microbiome influences newborn venomous snakes and that K. pneumoniae lineages related to citrate fermentation may play a role in venom growth. However, further verification of this is required.
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Affiliation(s)
- Hung-Yuan Su
- Department of Emergency Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Kuo-Hsin Lee
- Department of Emergency Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
- Department of Emergency Medicine, E-Da Dachang Hospital, I-Shou University, Kaohsiung City, Taiwan
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Centre, Taipei, Taiwan
| | - Liao-Chun Chiang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.
- Department of Biology and Anatomy, National Defense Medical Centre, Taipei, Taiwan.
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan.
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Kuźniar A, Włodarczyk K, Jurczyk S, Maciejewski R, Wolińska A. Ecological Diversity of Bacterial Rhizomicrobiome Core during the Growth of Selected Wheat Cultivars. BIOLOGY 2023; 12:1067. [PMID: 37626953 PMCID: PMC10451756 DOI: 10.3390/biology12081067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023]
Abstract
One of the latest ecological concepts is the occurrence of a biased rhizosphere of microorganisms recruited mostly through interactions among various components of the rhizosphere, including plant roots and the bulk soil microbiome. We compared the diverse attributes of the core microbiome of wheat rhizosphere communities with wheat (W) and legume (L) forecrops determined by three different methods in this study (membership, composition, and functionality). The conclusions of the three methods of microbiome core definition suggest the presence of generalists, i.e., some representative microorganisms from Proteobacteria, Actinobacteria, Hypomicrobiaceae, Bradyrhizobiaceae, Sphingomonas sp., in the wheat rhizomicrobiome. The relative abundance of the core microbiome accounted for 0.1976% (W) and 0.334% (L)-membership method and 6.425% (W) and 4.253% (L)-composition method. Additionally, bacteria of the specialist group, such as Rhodoplanes sp., are functionally important in the rhizomicrobiome core. This small community is strongly connected with other microbes and is essential for maintenance of the sustainability of certain metabolic pathways.
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Affiliation(s)
- Agnieszka Kuźniar
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland; (K.W.); (A.W.)
| | - Kinga Włodarczyk
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland; (K.W.); (A.W.)
| | - Sara Jurczyk
- Department of Artificial Intelligence, The John Paul II Catholic University of Lublin, Konstantynów St. 1 H, 20-708 Lublin, Poland;
| | - Ryszard Maciejewski
- Department of Human Anatomy, Medical University of Lublin, Jaczewskiego 4 St., 20-950 Lublin, Poland;
- Institute of Health Sciences, The John Paul II Catholic University of Lublin, Konstantynów St. 1 H, 20-708 Lublin, Poland
| | - Agnieszka Wolińska
- Department of Biology and Biotechnology of Microorganisms, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland; (K.W.); (A.W.)
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Li H, Zhou H, Yang S, Dai X. Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities. Appl Environ Microbiol 2023; 89:e0070123. [PMID: 37404136 PMCID: PMC10370332 DOI: 10.1128/aem.00701-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 07/06/2023] Open
Abstract
Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.
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Affiliation(s)
- Haizhou Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Huaiyang Zhou
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Shanshan Yang
- College of Marine Science and Technology, China University of Geosciences, Wuhan, Hubei, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institutes of Microbiology, Chinese Academy of Sciences, Beijing, China
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Zhong S, Hou B, Zhang J, Wang Y, Xu X, Li B, Ni J. Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater. Front Microbiol 2023; 14:1111383. [PMID: 37560528 PMCID: PMC10407230 DOI: 10.3389/fmicb.2023.1111383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
The ecological health of karst groundwater has been of global concern due to increasing anthropogenic activities. Bacteria comprising a few abundant taxa (AT) and plentiful rare taxa (RT) play essential roles in maintaining ecosystem stability, yet limited information is known about their ecological differentiation and assembly processes in karst groundwater. Based on a metabarcoding analysis of 64 groundwater samples from typical karst regions in southwest China, we revealed the environmental drivers, ecological roles, and assembly mechanisms of abundant and rare bacterial communities. We found a relatively high abundance of potential functional groups associated with parasites and pathogens in karst groundwater, which might be linked to the frequent regional anthropogenic activities. Our study confirmed that AT was dominated by Proteobacteria and Campilobacterota, while Patescibacteria and Chloroflexi flourished more in the RT subcommunity. The node-level topological features of the co-occurrence network indicated that AT might share similar niches and play more important roles in maintaining bacterial community stability. RT in karst groundwater was less environmentally constrained and showed a wider environmental threshold response to various environmental factors than AT. Deterministic processes, especially homogeneous selection, tended to be more important in the community assembly of AT, whereas the community assembly of RT was mainly controlled by stochastic processes. This study expanded our knowledge of the karst groundwater microbiome and was of great significance to the assessment of ecological stability and drinking water safety in karst regions.
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Affiliation(s)
- Sining Zhong
- Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Bowen Hou
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Jinzheng Zhang
- Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yichu Wang
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Xuming Xu
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Bin Li
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
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Colette M, Guentas L, Patrona LD, Ansquer D, Callac N. Dynamic of active microbial diversity in rhizosphere sediments of halophytes used for bioremediation of earthen shrimp ponds. ENVIRONMENTAL MICROBIOME 2023; 18:58. [PMID: 37438848 DOI: 10.1186/s40793-023-00512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/02/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND In New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, excessive ponds drying may not be suitable for the decomposition activities of microorganisms. Halophytes, salt tolerant plants, naturally grow at vicinity of shrimp ponds; due to their specificity, we explored whether halophytes cultivation during the pond drying period may be suitable for pond bioremediation. In addition, plants are closely associated with microorganisms, which may play a significant role in organic matter decomposition and therefore in bioremediation. Thus, in this study we aimed to determine the impact of 3 halophyte species (Suaeda australis, Sarcocornia quinqueflora and Atriplex jubata) on active sediment microbial communities and their implications on organic matter degradation. RESULTS Drying significantly decreased the microbial diversity index compared to those of wet sediment or sediment with halophytes. Microbial profiles varied significantly over time and according to the experimental conditions (wet, dry sediment or sediment with halophyte species). Halophytes species seemed to promote putative microbial metabolism activities in the sediment. Taxa related to nitrogen removal, carbon mineralisation, sulphur reduction and sulphide oxidation were significant biomarkers in sediment harbouring halophytes and may be relevant for bioremediation. Whereas microbial communities of dry sediment were marked by soil limited-moisture taxa with no identification of microbial metabolic functions. Nitrogen reduction in sediments was evidenced in wet sediment and in sediments with halophytes cultures, along with putative microbial denitrification activities. The greatest nitrogen reduction was observed in halophytes culture. CONCLUSION The efficiency of sediment bioremediation by halophytes appears to be the result of both rhizosphere microbial communities and plant nutrition. Their cultures during the pond drying period may be used as aquaculture diversification by being a sustainable system.
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Affiliation(s)
- Marie Colette
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia.
- Institute of Exact and Applied Sciences (ISEA), EA 7484, University of New Caledonia, Noumea, 98851, New Caledonia.
| | - Linda Guentas
- Institute of Exact and Applied Sciences (ISEA), EA 7484, University of New Caledonia, Noumea, 98851, New Caledonia
| | - Luc Della Patrona
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Dominique Ansquer
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Nolwenn Callac
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
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Abdullah K, Wilkins D, Ferrari BC. Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach. Front Microbiol 2023; 14:1113102. [PMID: 37396353 PMCID: PMC10313077 DOI: 10.3389/fmicb.2023.1113102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/02/2023] [Indexed: 07/04/2023] Open
Abstract
Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.
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Affiliation(s)
- Kristopher Abdullah
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Wilkins
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, TAS, Australia
| | - Belinda C. Ferrari
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Labouyrie M, Ballabio C, Romero F, Panagos P, Jones A, Schmid MW, Mikryukov V, Dulya O, Tedersoo L, Bahram M, Lugato E, van der Heijden MGA, Orgiazzi A. Patterns in soil microbial diversity across Europe. Nat Commun 2023; 14:3311. [PMID: 37291086 PMCID: PMC10250377 DOI: 10.1038/s41467-023-37937-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/06/2023] [Indexed: 06/10/2023] Open
Abstract
Factors driving microbial community composition and diversity are well established but the relationship with microbial functioning is poorly understood, especially at large scales. We analysed microbial biodiversity metrics and distribution of potential functional groups along a gradient of increasing land-use perturbation, detecting over 79,000 bacterial and 25,000 fungal OTUs in 715 sites across 24 European countries. We found the lowest bacterial and fungal diversity in less-disturbed environments (woodlands) compared to grasslands and highly-disturbed environments (croplands). Highly-disturbed environments contain significantly more bacterial chemoheterotrophs, harbour a higher proportion of fungal plant pathogens and saprotrophs, and have less beneficial fungal plant symbionts compared to woodlands and extensively-managed grasslands. Spatial patterns of microbial communities and predicted functions are best explained when interactions among the major determinants (vegetation cover, climate, soil properties) are considered. We propose guidelines for environmental policy actions and argue that taxonomical and functional diversity should be considered simultaneously for monitoring purposes.
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Affiliation(s)
- Maëva Labouyrie
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | | | - Ferran Romero
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Panos Panagos
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Arwyn Jones
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | | | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Olesya Dulya
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emanuele Lugato
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland.
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland.
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy.
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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Qiang W, Gunina A, Kuzyakov Y, Luo R, Zhang Y, Liu B, Pang X. Shifts of understory vegetation induced by thinning drive the expansion of soil rare fungi. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118119. [PMID: 37207458 DOI: 10.1016/j.jenvman.2023.118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/21/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023]
Abstract
The gap formation due to forest thinning regulates the understorey microclimate, ground vegetation, and soil biodiversity. However, little is known about abundant and rare taxa's various patterns and assemblage mechanisms under thinning gaps. Thinning gaps with increasing sizes (0, 74, 109, and 196 m2) were established 12 years ago in a 36-year-old spruce plantation in a temperate mountain climate. Soil fungal and bacterial communities were analyzed by MiSeq sequencing and related to soil physicochemical properties and aboveground vegetation. The functional microbial taxa were sorted by FAPROTAX and Fungi Functional Guild database. The bacterial community stabilized under varied thinning intensities and was not different from the control plots, whereas the richness of the rare fungal taxa was at least 1.5-fold higher in the large gaps than in the small ones. Total phosphorus and dissolved organic carbon were the main factors influencing microbial communities in soil under various thinning gaps. The diversity and richness of the entire fungal community and rare fungal taxa increased with the understorey vegetation coverage and shrub biomass after thinning. Gap formation by thinning stimulated the understorey vegetation, the rare saprotroph (Undefined Saprotroph), and mycorrhizal fungi (Ectomycorrhizal-Endophyte-Ericoid Mycorrhizal-Litter Saprotroph-Orchid Mycorrhizal and Bryophyte Parasite-Lichen Parasite-Ectomycorrhizal-Ericoid Mycorrhizal-Undefined Saprotroph), which may accelerate nutrient cycling in forest ecosystems. However, the abundance of Endophyte-Plant Pathogens increased by eight times, which showed the potential risk for the artificial spruce forests. Thus, fungi may be the driving force of forest restoration and nutrient cycling under the increasing intensity of thinning and may induce plant diseases. Therefore, vegetation coverage and microbial functional diversity should be considered to evaluate the sustainability of the artificial forest ecosystem and forest restoration.
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Affiliation(s)
- Wei Qiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany
| | - Anna Gunina
- Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany; Department of Soil Biology and Biochemistry, Dokuchaev Soil Science Institute, Russian Federation; Tyumen State University, 625003, Tyumen, Russia
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Göttingen, Germany; Peoples Friendship University of Russia (RUDN University), 117198, Moscow, Russia; Institute of Environmental Sciences, Kazan Federal University, 420049, Kazan, Russia
| | - Ruyi Luo
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China
| | - Yan Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China; Department of Environment and Geography, University of York, Heslington, York, North Yorkshire, UK
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, China.
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40
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Porter TM, Smenderovac E, Morris D, Venier L. All boreal forest successional stages needed to maintain the full suite of soil biodiversity, community composition, and function following wildfire. Sci Rep 2023; 13:7978. [PMID: 37198223 DOI: 10.1038/s41598-023-30732-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 05/19/2023] Open
Abstract
Wildfire is a natural disturbance in boreal forest systems that has been predicted to increase in frequency, intensity, and extent due to climate change. Most studies tend to assess the recovery of one component of the community at a time but here we use DNA metabarcoding to simultaneously monitor soil bacteria, fungi, and arthropods along an 85-year chronosequence following wildfire in jack pine-dominated ecosites. We describe soil successional and community assembly processes to better inform sustainable forest management practices. Soil taxa showed different recovery trajectories following wildfire. Bacteria shared a large core community across stand development stages (~ 95-97% of their unique sequences) and appeared to recover relatively quickly by crown closure. By comparison fungi and arthropods shared smaller core communities (64-77% and 68-69%, respectively) and each stage appeared to support unique biodiversity. We show the importance of maintaining a mosaic ecosystem that represents each stand development stage to maintain the full suite of biodiversity in soils following wildfire, especially for fungi and arthropods. These results will provide a useful baseline for comparison when assessing the effects of human disturbance such as harvest or for assessing the effects of more frequent wildfire events due to climate change.
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Affiliation(s)
- Teresita M Porter
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Canada.
- University of Guelph, Centre for Biodiversity Genomics, Guelph, ON, Canada.
| | - Emily Smenderovac
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Canada
| | - Dave Morris
- Ministry of Natural Resources and Forestry, Thunder Bay, ON, Canada
| | - Lisa Venier
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Canada
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41
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Lin X, Yin H, Wang L, Chen Y, Zhao F, Pu Y, Tang X. Study of a three-dimensional biofilm-electrode reactor (3D-BER) that combined heterotrophic and autotrophic denitrification (HAD) to remove nitrate from water. RSC Adv 2023; 13:14675-14684. [PMID: 37197683 PMCID: PMC10183716 DOI: 10.1039/d3ra01403g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
A three-dimensional biofilm-electrode reactor (3D-BER) that combined heterotrophic and autotrophic denitrification (HAD) was developed to remove nitrate. The denitrification performance of the 3D-BER was evaluated under different experimental conditions, including current intensities (0-80 mA), COD/N ratios (0.5-5), and hydraulic retention times (2-12 h). The results showed that excessive current limited the nitrate removal efficiency. However, a longer hydraulic retention time was not required to achieve a better denitrification effect in the 3D-BER. Moreover, the nitrate could be effectively reduced over a broad range of COD/Ns (1-2.5), and its removal rate peaked at 89% at I = 40 mA, HRT = 8 h, and COD/N = 2. Although the current reduced the diversity of microorganisms in the system, it promoted the growth of dominant species. Nitrification microorganisms were enriched in the reactor, especially Thauera and Hydrogenophaga, which were crucial to the denitrification process. Thus, the combination of autotrophic denitrification and heterotrophic denitrification was promoted by the 3D-BER system to increase the efficiency of nitrogen removal.
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Affiliation(s)
- Xiangyu Lin
- School of Civil Engineering and Architecture, Wuhan University of Technology Wuhan 430070 China
| | - Haoran Yin
- School of Civil Engineering and Architecture, Wuhan University of Technology Wuhan 430070 China
| | - Lixin Wang
- College of Engineering, Pennsylvania State University 201 Old Main, University Park PA 16802-15 USA
| | - Yini Chen
- School of Civil Engineering and Architecture, Wuhan University of Technology Wuhan 430070 China
| | - Fan Zhao
- School of Civil Engineering and Architecture, Wuhan University of Technology Wuhan 430070 China
| | - Yu Pu
- School of Civil Engineering and Architecture, Wuhan University of Technology Wuhan 430070 China
| | - Xinhua Tang
- School of Civil Engineering and Architecture, Wuhan University of Technology Wuhan 430070 China
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42
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Multi-factor correlation analysis of the effect of root-promoting practices on tobacco rhizosphere microecology in growth stages. Microbiol Res 2023; 270:127349. [PMID: 36870194 DOI: 10.1016/j.micres.2023.127349] [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: 11/22/2022] [Revised: 02/18/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023]
Abstract
Some agronomic practices not only promote the development of crop roots and increase overall plant performance but also affect colonisation by rhizosphere microorganisms. However, the composition and temporal dynamics of the tobacco rhizosphere microbiota under different root-promoting practices are poorly understood. Here, we characterised the tobacco rhizosphere microbiota at the knee-high, vigorous growing, and maturity stages under the application of potassium fulvic acid (PFA), γ-Polyglutamic acid (PGA), soymilk root irrigation (SRI), and conventional fertilization (CK) and its correlation with root characteristics and soil nutrients. The results showed that three root-promoting practices notably improved the dry and fresh root weights. Total nitrogen and phosphorus, available phosphorus and potassium, and organic matter contents in the rhizosphere markedly increased at the vigorous growing stage. The rhizosphere microbiota was changed through root-promoting practices. However, with tobacco growth, the change of rhizosphere microbiota showed a pattern of slow first and then fast and the microbiota of different treatments gradually approached. SRI reduced plant-pathogenic fungi but increased chemoheterotrophic and phototrophic bacteria, and arbuscular mycorrhizal fungi. PFA and PGA markedly increased arbuscular mycorrhizal and ectomycorrhizal fungi at the knee-high stage, which benefitted tobacco nutrient absorption. The correlation between rhizosphere microorganisms and environmental factors varied at different growth stages. Notably, the rhizosphere microbiota was more sensitive to environmental factors at the vigorous growing stage, and the interactions were more complex than in other stages. Furthermore, a variance partitioning analysis showed that the influence of root-soil interaction on the rhizosphere microbiota increased with tobacco growth. Overall, all three root-promoting practices could improve root characteristics, rhizosphere nutrient, and rhizosphere microbiota to varying degrees and increase the tobacco biomass, among which PGA had the most obvious effect and most suitable for tobacco cultivation. Our findings revealed the role of root-promoting practices in shaping the rhizosphere microbiota during plant growth and elucidated the assembly patterns and environmental drivers of crop rhizosphere microbiota driven by the application of root-promoting practices in agricultural production.
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43
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Adhikari NP, Adhikari S. First report on the bacterial community composition, diversity, and functions in Ramsar site of Central Himalayas, Nepal. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:573. [PMID: 37060391 DOI: 10.1007/s10661-023-11158-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Wetland bacterial communities are highly sensitive to altered hydrology and the associated change in water physicochemical and biological properties leading to shifts in community composition and diversity, hence affecting the ecological roles. However, relevant studies are lacking in the wetlands of central Himalayas Nepal. Thus, we aimed to explore the variation of bacterial communities, diversity, and ecologic functions in the wet and dry periods of a wetland (designed as Ramsar site, Ramsar no 2257) by using 16S rRNA gene-based Illumina MiSeq sequencing. We reported a pronounced variation in water physicochemical and biological properties (temperature, pH, Chla, DOC, and TN), bacterial diversity, and community composition. Bacterial communities in the dry season harbored significantly higher alpha diversity, while significantly higher richness and abundance were reflected in the wet season. Our results uncovered the effect of nutrients on bacterial abundance, richness, and community composition. Fourteen percent of the total OTUs were shared in two hydrological periods, and the largest portion of unique OTUs (58%) was observed in the dry season. Planctomycetes and Bacteroidetes dominated the wet season exclusive OTUs; meanwhile, Actinobacteria dominated the dry season exclusive OTUs. Bacteria in these wetlands exhibited divergent ecological functions during the dry and wet seasons. By disclosing the variation of water bacterial communities in different hydrologic periods and their relationship with environmental factors, this first-hand work in the Ramsar site of Nepal will develop a baseline dataset for the scientific community that will assist in understanding the wetland's microbial ecology and biogeography.
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Affiliation(s)
- Namita Paudel Adhikari
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- Institute of Tibetan Plateau Research Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Subash Adhikari
- Policy and Planning Commission, Government of Gandaki Province, Pokhara, 33700, Nepal.
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Zhong MH, Yang L, Xiong K, Yang HL, Wang XL. Exploring the mechanism of Self-Consistent balance between microbiota and high efficiency in wastewater treatment. BIORESOURCE TECHNOLOGY 2023; 374:128785. [PMID: 36822553 DOI: 10.1016/j.biortech.2023.128785] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/15/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Sewage treatment mediated by microbial organisms is a promising green trend. However, the complex balance between microbiota stability and highly efficient wastewater treatment requires investigation. This study successfully improved the effectiveness of sewage treatment by resetting the microbial community structure in the activated sludge. Truepera, Methylophaga, unclassified_Fodinicurvataceae, and unclassified_Actinomanarales were the dominant genera, while salinity and NH3-N content were identified as the key environmental factors governing the microbial structure. By optimizing the microflora structure driven by environmental factors, the key minor genera were activated and coordinated with the aforementioned genera, thereby promoting wastewater treatment. Finally, the chemical oxygen demand, NH3-N, and total phosphorus removal rates were improved to 86.8 ± 1.9%, 82.4 ± 4.1%, and 94.8 ± 3.8%, respectively. It provides a new insight to improve the wastewater treatment through setting microbiota by environmental factor driven.
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Affiliation(s)
- Ming-Hui Zhong
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Lin Yang
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Kai Xiong
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Hui-Lin Yang
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Xiao-Lan Wang
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China.
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45
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Kim RH, Tagele SB, Jeong M, Jung DR, Lee D, Park T, Tino BF, Lim K, Kim MA, Park YJ, Shin JH. Spinach (Spinacia oleracea) as green manure modifies the soil nutrients and microbiota structure for enhanced pepper productivity. Sci Rep 2023; 13:4140. [PMID: 36914667 PMCID: PMC10011398 DOI: 10.1038/s41598-023-31204-8] [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: 07/25/2022] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Spinach has been suggested as a potential rotation crop for increasing crop yield by enhancing beneficial fungal microbes in continuous monocropping. However, no research on the use of spinach as a green manure has been reported. Thus, we tested the effects of spinach and Korean mustard cultivars (green and red mustards) (10 g pot -1) as green manure on soil chemical properties, pepper productivity, and soil microbiome of long-year pepper-monocropped soil. Spinach improved the soil nutrition (e.g., pH, SOM, TN, NH4+, and K), weed suppression, and pepper growth. Spinach had by far the highest fruit yield, over 100% pepper fruit yield increment over the mustard green manures and control. Our study showed that the major influencing factors to cause a shift in both bacterial and fungal community assemblies were soil pH, TC TN, and K. Following green manure amendment Bacillota, especially Clostridium, Bacillus and Sedimentibacter, were enriched, whereas Chloroflexi and Acidobacteriota were reduced. In addition, spinach highly reduced the abundance of Leotiomycetes and Fusarium but enriched Papiliotrema. FAPROTAX and FUNGuild analysis revealed that predicted functional profiles of bacterial and fungal communities in spinach-amended soil were changed. Spinach-treated soil was differentially abundant in function related to hydrocarbon degradation and functional guilds of symbiotrophs and ectomycorrhizal. This study contributes significantly to our understanding of how the soil fertility and soil microbiome alteration via spinach green manure application as a pre-plant soil treatment might help alleviate continuous cropping obstacles.
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Affiliation(s)
- Ryeong-Hui Kim
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.,NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Da-Ryung Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dokyung Lee
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - TaeHyung Park
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Bashizi Flory Tino
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyeongmo Lim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Min A Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yeong-Jun Park
- NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea. .,NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Grierson J, Flies EJ, Bissett A, Ammitzboll H, Jones P. Which soil microbiome? Bacteria, fungi, and protozoa communities show different relationships with urban green space type and use-intensity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160468. [PMID: 36464041 DOI: 10.1016/j.scitotenv.2022.160468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/20/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Exposure to diverse microbial communities early in life can help support healthy human immune function. Soil microbiomes in public and private urban green spaces are potentially important sources of contact with diverse microbiomes for much of the global population. However, we lack understanding of how soil microbial communities vary across and within urban green spaces, and whether these patterns vary across microbial kingdoms; closing this knowledge gap may help us optimise green spaces' capacities to provide this ecosystem service. Here we explore the diversity and community compositions of soil microbiomes across urban green space types in Tasmania, Australia. Specifically, we analysed soil bacterial, fungal, and protozoan diversity and composition across private backyards and public parks. Within parks, we conducted separate sampling for areas of high and low intensity use. We found that: (i) bacteria, fungi, and protozoa showed different patterns of variation, (ii) bacterial alpha-diversity was lowest in low-intensity use areas of parks, (iii) there was relatively little variation in the community composition across backyards, and high and low intensity-use park areas and (iv) neither human-associated bacteria, nor potential microbial community function of bacteria and fungi differed significantly across green space types. To our knowledge, this is the first urban soil microbiome analysis which analyses these three soil microbial kingdoms simultaneously across public and private green space types and within public spaces according to intensity of use. These findings demonstrate how green space type and use intensity may impact on soil microbial diversity and composition, and thus may influence our opportunity to gain healthy exposure to diverse environmental microbiomes.
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Affiliation(s)
- Jessica Grierson
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7001, Australia; School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia.
| | - Emily J Flies
- School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO, Hobart, TAS 7000, Australia
| | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart 7001, Australia
| | - Penelope Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7001, Australia; School of Natural Sciences, University of Tasmania, Hobart 7001, Australia; Healthy Landscapes Research Group, University of Tasmania, Hobart 7001, Australia
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47
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Chen Y, Chen X, Chen P, Chen X, Pan L, Han L, Zhu T. Alteration of the Gut Microbiota in Missed Abortion. Indian J Microbiol 2023; 63:106-119. [PMID: 37179577 PMCID: PMC10172435 DOI: 10.1007/s12088-023-01063-y] [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: 11/28/2022] [Accepted: 02/09/2023] [Indexed: 03/03/2023] Open
Abstract
There is a symbiotic relationship between gut microbiota and human beings. Imbalance of the gut microbiota will cause pathological damages to humans. Although many risk factors are associated with missed abortion (MA), the pathological mechanism of it is still unclear. Here, we analyzed gut flora of the patients with MA by S16 high-throughput sequencing. The possible pathogenic mechanisms of the MA were explored. Fecal samples from 14 healthy controls and 16 MA patients were collected to do 16S rRNA gene high-throughput sequencing analysis. The abundance of the Bacteroidetes, Proteobacteria, Actinobacteria, Escherichia, Streptococcus_ Salivarius, and Lactobacillus was significantly reduced in the MA group, while, the abundance of the Klebsiella was significantly increased in the MA patients. The Ruminococcaceae and [Eubacterium]_coprostanoligenes_group were found only in the specimens of the MA patients. The Fabrotax function prediction analysis showed that four photosynthesis function bacteria (cyanobateria, oxygenic_photoautotrophy, photoautotrophy, and phototrophy) only existed in the MA group. In the analysis of the BugBase microbiome function prediction, the Escherichia of the MA group is significantly reduced compared to that of the healthy controls in the items of that Contains_Mobile_Elements, Facultatively_Anaerobic, Forms_Biofilms, Potentially_Pathogenic.png, Gram_Nagative, and Stress_Tolerant_relabundance. These alterations may affect the stability of the host's immune, neural, metabolic and other systems by interfering with the balance of the gut microbiota or by the metabolites of those bacteria, causing the MA. This study explored the possible pathogenic factors of the gut microbiota of the MA. The results provide evidence to figure out the pathogenesis of the MA.
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Affiliation(s)
- Yi Chen
- Gynaecology Department, The First Hospital of Putian, Putian, 351100 Fujian China
| | - Xianqian Chen
- Gynaecology Department, The First Hospital of Putian, Putian, 351100 Fujian China
| | - Pingyu Chen
- Gynaecology Department, The First Hospital of Putian, Putian, 351100 Fujian China
| | - Xiuxia Chen
- Gynaecology Department, The First Hospital of Putian, Putian, 351100 Fujian China
| | - Lin Pan
- Gynaecology Department, The First Hospital of Putian, Putian, 351100 Fujian China
| | - Lihong Han
- Key Laboratory of Translational Tumor Medicine in Fujian Province, School of Basic Medical Science, Putian University, 450 Dongzhen Road West, Putian, 351100 Fujian China
| | - Tang Zhu
- Key Laboratory of Translational Tumor Medicine in Fujian Province, School of Basic Medical Science, Putian University, 450 Dongzhen Road West, Putian, 351100 Fujian China
- Yujia Biotech., D-201, 3 Juquan Road, Guangzhou, 510700 Guangdong China
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Tanunchai B, Ji L, Schroeter SA, Wahdan SFM, Hossen S, Delelegn Y, Buscot F, Lehnert AS, Alves EG, Hilke I, Gleixner G, Schulze ED, Noll M, Purahong W. FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species. MICROBIAL ECOLOGY 2023; 85:411-428. [PMID: 35124727 PMCID: PMC9958157 DOI: 10.1007/s00248-022-01973-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/16/2023]
Abstract
Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.
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Affiliation(s)
- Benjawan Tanunchai
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Li Ji
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, 150040 Harbin, People’s Republic of China
| | - Simon Andreas Schroeter
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Botany Department, Faculty of Science, Suez Canal University, Ismailia, 41522 Egypt
| | - Shakhawat Hossen
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Yoseph Delelegn
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ann-Sophie Lehnert
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Eliane Gomes Alves
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ines Hilke
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Gerd Gleixner
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Biogeochemical Processes Department, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
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49
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Liu K, Wang Q, Sun M, Gao S, Liu Q, Shan L, Guo J, Bian J. Soil bacterial communities of paddy are dependent on root compartment niches but independent of growth stages from Mollisols of Northeast China. Front Microbiol 2023; 14:1170611. [PMID: 37125155 PMCID: PMC10140518 DOI: 10.3389/fmicb.2023.1170611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Deep insights into adhering soil of root zones (rhizosphere and rhizoplane) microbial community could provide a better understanding of the plant-microbe relationship. To better understand the dynamics of these microbial assemblies over the plant life cycle in rhizodeposition along rice roots. Methods Here, we investigated bacterial distribution in bulk, rhizosphere, and rhizoplane soils at tillering, heading, and mature stage, from rice (Oryza sativa) fields of the Northeast China. Results and Discussion Our results revealed that soil bacterial α-diversity and community composition were significantly affected by root compartment niches but not by temporal change. Compared to rhizoplane soils in the same period, bulk in the heading and rhizosphere in the mature had the largest increase in Shannon's index, with 11.02 and 14.49% increases, respectively. Proteobacteria, Chloroflexi, Bacteroidetes, and Acidobacteria are predominant across all soil samples, bulk soil had more phyla increased across the growing season than that of root related-compartments. Deterministic mechanisms had a stronger impact on the bacterial community in the compartments connected to the roots, with the relative importance of the bulk soil, rhizoplane and rhizosphere at 83, 100, and 56%, respectively. Because of ecological niche drivers, the bacterial networks in bulk soils exhibit more complex networks than rhizosphere and rhizoplane soils, reflected by more nodes, edges, and connections. More module hub and connector were observed in bulk (6) and rhizoplane (5) networks than in rhizosphere (2). We also detected shifts from bulk to rhizoplane soils in some functional guilds of bacteria, which changed from sulfur and nitrogen utilization to more carbon and iron cycling processes. Taken together, our results suggest distinct bacterial network structure and distribution patterns among rhizosphere, rhizoplane, and bulk soils, which could possibly result in potential functional differentiation. And the potential functional differentiation may be influenced by plant root secretions, which still needs to be further explored.
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Affiliation(s)
- Kai Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qiuju Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, China
| | - Minglong Sun
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Shiwei Gao
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua, China
| | - Qing Liu
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua, China
| | - Lili Shan
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Junxiang Guo
- Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Jingyang Bian
- Daqing Branches of Heilongjiang Academy of Agricultural Sciences, Daqing, China
- *Correspondence: Jingyang Bian,
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50
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Dai W, Zhang P, Yang F, Wang M, Yang H, Li Z, Wang M, Liu R, Huang Y, Wu S, He G, Zhou J, Wei C. Effects of composite materials and revegetation on soil nutrients, chemical and microbial properties in rare earth tailings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157854. [PMID: 35940274 DOI: 10.1016/j.scitotenv.2022.157854] [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: 04/08/2022] [Revised: 08/01/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The mining of ionic rare earth elements in Ganzhou left large area of barren tailings with severe vegetation destruction in pressing needs of remediation. However, the remediating effects of soil additives combined with revegetation on the preservation of nutrients in the tailings and microbial communities were rarely studied. For this purpose, pilot experiments were implemented in a field, with the control group (CK) only cultivating plants without adding materials, and three treatments including peanut straw biochar composite (T1), phosphorus‑magnesium composite (T2) and modified zeolite composite (T3) along with the cultivation of Medicago sativa L., Paspalum vaginatum Sw. and Lolium perenne L. Soil pH and organic matter in CK significantly decreased from 4.90 to 4.17 and from 6.62 g/kg to 3.87 g/kg after six months, respectively (p ≤ 0.05), while all the treatments could effectively buffer soil acidification (over 5.74) and delay the loss of soil organic matter. Soil cation exchange capacity was still below the detection limit in all the groups except T2. The results of rainfall runoff monitoring indicated that compared with CK, only T2 could significantly reduce the runoff loss of soil NO3- and SO42- by 45.61 %-75.78 % and 64.03 %-76.12 %, respectively (p ≤ 0.05). Compared with CK, the bacterial diversity in T2 and T3 significantly increased 21.18 % and 28.15 %, respectively (p ≤ 0.05), while T1 didn't change the bacterial or fungal diversity (p > 0.05). Co-occurrence network analysis showed that compared with CK, the whole microbial communities interacted more closely in the three treatments. Functional prediction of the microbial communities revealed all the treatments were dominated by carbon transforming bacteria and saprotrophic fungi except T2. This study demonstrated that the composite materials combined with revegetation couldn't retain soil nitrogen compounds and sulfate in rare earth tailings in the long term.
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Affiliation(s)
- Weijie Dai
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fen Yang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Huixian Yang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhiying Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Renlu Liu
- School of Life Sciences, Key Laboratory of Agricultural Environmental Pollution Prevention and Control in Red Soil Hilly Region of Jiangxi Province, Jinggangshan University, Jian 343009, China
| | - Yuanying Huang
- National Research Center for Geoanalysis, Beijing 100037, China; Key Laboratory of Ministry of Natural Resources for Eco-geochemistry, Beijing 100037, China
| | - Song Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Genhe He
- School of Life Sciences, Key Laboratory of Agricultural Environmental Pollution Prevention and Control in Red Soil Hilly Region of Jiangxi Province, Jinggangshan University, Jian 343009, China
| | - Jing Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chaoyang Wei
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
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