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Sun P, Fan K, Jiang Y, Chu H, Chen Y, Wu Y. Accumulated temperature dictates the regional structural variation of prokaryotic periphyton at soil-water interface in paddy fields. WATER RESEARCH 2024; 265:122259. [PMID: 39154398 DOI: 10.1016/j.watres.2024.122259] [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: 05/07/2024] [Revised: 07/30/2024] [Accepted: 08/12/2024] [Indexed: 08/20/2024]
Abstract
As a pervasive microbial aggregate found at the water-soil interface in paddy fields, periphyton plays crucial roles in modulating nutrient biogeochemical cycling. Consequently, it effectively mitigates non-point source pollution due to its diverse composition. Despite its significance, the mechanisms governing periphyton diversity across different rice planting regions remain poorly understood. To bridge this gap, we investigated periphyton grown in 200 paddy fields spanning 25° of latitude. Initially, we analyzed local diversity and latitudinal variations in prokaryotic communities within paddy field periphyton, identifying 7 abundant taxa, 42 moderate taxa, and 39 rare taxa as the fundamental prokaryotic framework. Subsequently, to elucidate the mechanisms governing periphyton diversity across large scales, we constructed interaction models illustrating triangular relationships among local richness, assembly, and regional variation of prokaryotic subcommunities. Our findings suggest that accumulated temperature-driven environmental filtering partially influences the assembly process of prokaryotes, thereby impacting local species richness and ultimately governing regional structural variations in periphyton. Furthermore, we determined that a latitude of 39° represents the critical threshold maximizing local species richness of periphyton in paddy fields. This study advances our understanding of the factors shaping periphyton geo-imprints and provides valuable insights into predicting their responses to environmental changes, potentially influencing rice production outcomes.
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Affiliation(s)
- Pengfei Sun
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Kunkun Fan
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Yuji Jiang
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Haiyan Chu
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China
| | - Yin Chen
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK.
| | - Yonghong Wu
- Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing 211135, China; University of Chinese Academy of Sciences, No.188, Tianquan Road, Nanjing 211135, China.
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2
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Larkin AA, Brock ML, Fagan AJ, Moreno AR, Gerace SD, Lees LE, Suarez SA, Eloe-Fadrosh EA, Martiny A. Climate-driven succession in marine microbiome biodiversity and biogeochemical function. RESEARCH SQUARE 2024:rs.3.rs-4682733. [PMID: 39184082 PMCID: PMC11343179 DOI: 10.21203/rs.3.rs-4682733/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Seasonal and El Niño-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. We quantified changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observed seasonal oscillations between large genome lineages during cold, nutrient rich conditions in winter and spring versus small genome lineages, including Prochlorococcus and Pelagibacter , in summer and fall. Parallel interannual changes separated communities depending on ENSO condition. Biodiversity shifts translated into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.
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Pandey P, Chowdhury D, Wang Y. Denaturing Gradient Gel Electrophoresis Approach for Microbial Shift Analysis in Thermophilic and Mesophilic Anaerobic Digestions. Gels 2024; 10:339. [PMID: 38786256 PMCID: PMC11120850 DOI: 10.3390/gels10050339] [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: 04/15/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
To determine the evolution of microbial community and microbial shift under anaerobic processes, this study investigates the use of denaturing gradient gel electrophoresis (DGGE). In the DGGE, short- and medium-sized DNA fragments are separated based on their melting characteristics, and this technique is used in this study to understand the dominant bacterial community in mesophilic and thermophilic anaerobic digestion processes. Dairy manure is known for emitting greenhouse gases (GHGs) such as methane, and GHG emissions from manure is a biological process that is largely dependent on the manure conditions, microbial community presence in manure, and their functions. Additional efforts are needed to understand the GHG emissions from manure and develop control strategies to minimize the biological GHG emissions from manure. To study the microbial shift during anaerobic processes responsible for GHG emission, we conducted a series of manure anaerobic digestion experiments, and these experiments were conducted in lab-scale reactors operated under various temperature conditions (28 °C, 36 °C, 44 °C, and 52 °C). We examined the third variable region (V3) of the 16S rRNA gene fingerprints of bacterial presence in anaerobic environment by PCR amplification and DGGE separation. Results showed that bacterial community was affected by the temperature conditions and anaerobic incubation time of manure. The microbial community structure of the original manure changed over time during anaerobic processes, and the community composition changed substantially with the temperature of the anaerobic process. At Day 0, the sequence similarity confirmed that most of the bacteria were similar (>95%) to Acinetobacter sp. (strain: ATCC 31012), a Gram-negative bacteria, regardless of temperature conditions. At day 7, the sequence similarity of DNA fragments of reactors (28 °C) was similar to Acinetobacter sp.; however, the DNA fragments of effluent of reactors at 44 °C and 52 °C were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 97%) and Tepidimicrobium ferriphilum (strain: DSM 16624) (similarity: 100%), respectively. At day 60, the analysis showed that DNA fragments of effluent of 28 °C reactor were similar to Galbibacter mesophilus (strain: NBRC 10162) (similarity: 87%), and DNA fragments of effluent of 36 °C reactors were similar to Syntrophomonas curvata (strain: GB8-1) (similarity: 91%). In reactors with a relatively higher temperature, the DNA fragments of effluent of 44 °C reactor were similar to Dielma fastidiosa (strain: JC13) (similarity: 86%), and the DNA fragments of effluent of 52 °C reactor were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 99%). To authors' knowledge, this is one of the few studies where DGGE-based approach is utilized to study and compare microbial shifts under mesophilic and thermophilic anaerobic digestions of manure simultaneously. While there were challenges in identifying the bands during gradient gel electrophoresis, the joint use of DGGE and sequencing tool can be potentially useful for illustrating and comparing the change in microbial community structure under complex anaerobic processes and functionality of microbes for understanding the consequential GHG emissions from manure.
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Affiliation(s)
- Pramod Pandey
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA; (D.C.); (Y.W.)
| | - Dhrubajyoti Chowdhury
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA; (D.C.); (Y.W.)
- Department of Life Sciences, School of Science, Gandhi Institute of Technology and Management, Rushikonda, Visakhapatnam 530045, Andhra Pradesh, India
| | - Yi Wang
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA; (D.C.); (Y.W.)
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Zhu G, Luan L, Zhou S, Dini-Andreote F, Bahram M, Yang Y, Geisen S, Zheng J, Wang S, Jiang Y. Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates. Microbiol Res 2024; 282:127669. [PMID: 38442455 DOI: 10.1016/j.micres.2024.127669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower β-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.
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Affiliation(s)
- Guofan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu 51005, Estonia
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen 6700 ES, Netherlands
| | - Jie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shaopeng Wang
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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5
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Arellano AA, Young EB, Coon KL. An inquiline mosquito modulates microbial diversity and function in an aquatic microecosystem. Mol Ecol 2024; 33:e17314. [PMID: 38441172 PMCID: PMC10989397 DOI: 10.1111/mec.17314] [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: 11/02/2023] [Revised: 02/03/2024] [Accepted: 02/21/2024] [Indexed: 03/09/2024]
Abstract
Understanding microbial roles in ecosystem function requires integrating microscopic processes into food webs. The carnivorous pitcher plant, Sarracenia purpurea, offers a tractable study system where diverse food webs of macroinvertebrates and microbes facilitate digestion of captured insect prey, releasing nutrients supporting the food web and host plant. However, how interactions between these macroinvertebrate and microbial communities contribute to ecosystem functions remains unclear. We examined the role of the pitcher plant mosquito, Wyeomyia smithii, in top-down control of the composition and function of pitcher plant microbial communities. Mosquito larval abundance was enriched or depleted across a natural population of S. purpurea pitchers over a 74-day field experiment. Bacterial community composition and microbial community function were characterized by 16S rRNA amplicon sequencing and profiling of carbon substrate use, bulk metabolic rate, hydrolytic enzyme activity, and macronutrient pools. Bacterial communities changed from pitcher opening to maturation, but larvae exerted minor effects on high-level taxonomic composition. Higher larval abundance was associated with lower diversity communities with distinct functions and elevated nitrogen availability. Treatment-independent clustering also supported roles for larvae in curating pitcher microbial communities through shifts in community diversity and function. These results demonstrate top-down control of microbial functions in an aquatic microecosystem.
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Affiliation(s)
- Aldo A. Arellano
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
| | - Erica B. Young
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI USA
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI USA
| | - Kerri L. Coon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
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Connors E, Dutta A, Trinh R, Erazo N, Dasarathy S, Ducklow H, Weissman JL, Yeh YC, Schofield O, Steinberg D, Fuhrman J, Bowman JS. Microbial community composition predicts bacterial production across ocean ecosystems. THE ISME JOURNAL 2024; 18:wrae158. [PMID: 39105280 PMCID: PMC11385589 DOI: 10.1093/ismejo/wrae158] [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: 03/05/2024] [Revised: 06/28/2024] [Accepted: 08/05/2024] [Indexed: 08/07/2024]
Abstract
Microbial ecological functions are an emergent property of community composition. For some ecological functions, this link is strong enough that community composition can be used to estimate the quantity of an ecological function. Here, we apply random forest regression models to compare the predictive performance of community composition and environmental data for bacterial production (BP). Using data from two independent long-term ecological research sites-Palmer LTER in Antarctica and Station SPOT in California-we found that community composition was a strong predictor of BP. The top performing model achieved an R2 of 0.84 and RMSE of 20.2 pmol L-1 hr-1 on independent validation data, outperforming a model based solely on environmental data (R2 = 0.32, RMSE = 51.4 pmol L-1 hr-1). We then operationalized our top performing model, estimating BP for 346 Antarctic samples from 2015 to 2020 for which only community composition data were available. Our predictions resolved spatial trends in BP with significance in the Antarctic (P value = 1 × 10-4) and highlighted important taxa for BP across ocean basins. Our results demonstrate a strong link between microbial community composition and microbial ecosystem function and begin to leverage long-term datasets to construct models of BP based on microbial community composition.
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Affiliation(s)
- Elizabeth Connors
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, United States
- Scripps Polar Center, UC San Diego, La Jolla, CA 92037, United States
| | - Avishek Dutta
- Department of Geology, University of Georgia, Athens, GA 30602, United States
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, United States
| | - Rebecca Trinh
- Lamont-Doherty Earth Observatory, Columbia University, New York, NY 10964, United States
| | - Natalia Erazo
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, United States
| | - Srishti Dasarathy
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, United States
| | - Hugh Ducklow
- Lamont-Doherty Earth Observatory, Columbia University, New York, NY 10964, United States
| | - J L Weissman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
- Department of Biology, The City College of New York, New York, NY 10003, United States
| | - Yi-Chun Yeh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Oscar Schofield
- Coastal Ocean Observation Laboratory, Institute of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8520, United States
| | - Deborah Steinberg
- Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA 23062, United States
| | - Jed Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States
| | - Jeff S Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA 92037, United States
- Scripps Polar Center, UC San Diego, La Jolla, CA 92037, United States
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Schnyder E, Bodelier PLE, Hartmann M, Henneberger R, Niklaus PA. Experimental erosion of microbial diversity decreases soil CH 4 consumption rates. Ecology 2023; 104:e4178. [PMID: 37782571 DOI: 10.1002/ecy.4178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/11/2023] [Accepted: 08/25/2023] [Indexed: 10/04/2023]
Abstract
Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4 ) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 101 -107 -fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.
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Affiliation(s)
- Elvira Schnyder
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Martin Hartmann
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ruth Henneberger
- Institute of Molecular Health Science, ETH Zürich, Zürich, Switzerland
| | - Pascal A Niklaus
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
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Wang A, He M, Liu H, Ouyang W, Liu X, Li Q, Lin C, Liu X. Distribution heterogeneity of sediment bacterial community in the river-lake system impacted by nonferrous metal mines: Diversity, composition and co-occurrence patterns. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122715. [PMID: 37821043 DOI: 10.1016/j.envpol.2023.122715] [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: 07/26/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023]
Abstract
Metal(loid) pollution caused by mining activities can affect microbial communities. However, knowledge of the diversity, composition, and co-occurrence patterns of bacterial communities in aquatic systems impacted by nonferrous metal mines. Here, the metal(loid) contents and bacterial communities in sediments from the Zijiang River (tributary to mainstream) to Dongting Lake were investigated by geochemical and molecular biology methods. The results indicated that the river sediments had lower pH and higher ecological risk of metal(loid)s than the lake sediment. The diversity and composition of bacterial communities in river sediments significantly (p < 0.05) differed from those in lake sediments, showing distributional heterogeneity. The biomarkers of tributary, mainstream, and lake sediments were mainly members of Deltaproteobacteria, Firmicutes, and Nitrospirae, respectively, reflecting species sorting in different habitats. Multivariate statistical analysis demonstrated that total and bioavailable Sb, As, and Zn were positively correlated with bacterial community richness. pH, TOC, TN, and Zn were crucial factors in shaping the distribution difference of bacterial communities. Environment-bacteria network analysis indicated that pH, SO42-, and total and bioavailable As and Sb greatly influenced the bacterial composition at the genus level. Bacteria-bacteria network analysis manifested that the co-occurrence network in mainstream sediments with a higher risk of metal(loid) pollution exhibited higher modularity and connectivity, which might be the survival mechanism for bacterial communities adapted to metal(loid) pollution. This study can provide a theoretical basis for understanding the ecological status of aquatic systems.
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Affiliation(s)
- Aihua Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Huiji Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Wei Ouyang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China; Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai, 519087, China.
| | - Xinyi Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Qin Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Chunye Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xitao Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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9
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Morin S, Artigas J. Twenty Years of Research in Ecosystem Functions in Aquatic Microbial Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1867-1888. [PMID: 37401851 DOI: 10.1002/etc.5708] [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: 11/29/2022] [Revised: 12/20/2022] [Accepted: 06/27/2023] [Indexed: 07/05/2023]
Abstract
One of the major threats to freshwater biodiversity is water pollution including excessive loads of nutrients, pesticides, industrial chemicals, and/or emerging contaminants. The widespread use of organic pesticides for agricultural and nonagricultural (industry, gardening, etc.) purposes has resulted in the presence of their residues in various environments, including surface waters. However, the contribution of pesticides to the deterioration of freshwater ecosystems (i.e., biodiversity decline and ecosystem functions impairment) remains uncertain. Once in the aquatic environment, pesticides and their metabolites can interact with microbial communities, causing undesirable effects. The existing legislation on ecological quality assessment of water bodies in Europe is based on water chemical quality and biological indicator species (Water Framework Directive, Pesticides Directive), while biological functions are not yet included in monitoring programs. In the present literature review, we analyze 20 years (2000-2020) of research on ecological functions provided by microorganisms in aquatic ecosystems. We describe the set of ecosystem functions investigated in these studies and the range of endpoints used to establish causal relationships between pesticide exposure and microbial responses. We focus on studies addressing the effects of pesticides at environmentally realistic concentrations and at the microbial community level to inform the ecological relevance of the ecotoxicological assessment. Our literature review highlights that most studies were performed using benthic freshwater organisms and that autotrophic and heterotrophic communities are most often studied separately, usually testing the pesticides that target the main microbial component (i.e., herbicides for autotrophs and fungicides for heterotrophs). Overall, most studies demonstrate deleterious impacts on the functions studied, but our review points to the following shortcomings: (1) the nonsystematic analysis of microbial functions supporting aquatic ecosystems functioning, (2) the study of ecosystem functions (i.e., nutrient cycling) via proxies (i.e., potential extracellular enzymatic activity measurements) which are sometimes disconnected from the current ecosystem functions, and (3) the lack of consideration of chronic exposures to assess the impact of, adaptations to, or recovery of aquatic microbial communities from pesticides. Environ Toxicol Chem 2023;42:1867-1888. © 2023 SETAC.
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Affiliation(s)
| | - Joan Artigas
- Laboratoire Microorganismes: Génome et Environnement, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
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10
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Martiny JBH, Martiny AC, Brodie E, Chase AB, Rodríguez-Verdugo A, Treseder KK, Allison SD. Investigating the eco-evolutionary response of microbiomes to environmental change. Ecol Lett 2023; 26 Suppl 1:S81-S90. [PMID: 36965002 DOI: 10.1111/ele.14209] [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: 11/08/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/27/2023]
Abstract
Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.
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Affiliation(s)
- Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
| | - Eoin Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, Texas, USA
| | | | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
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11
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Wang Y, Gu W, Liu X, Liu H, Tang G, Yang C. Combined impacts of algae-induced variations in water soluble organic matter and heavy metals on bacterial community structure in sediment from Chaohu Lake, a eutrophic shallow lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162481. [PMID: 36858233 DOI: 10.1016/j.scitotenv.2023.162481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Many lakes are suffering from eutrophication and heavy metals-contamination. However, the combined impacts of algae bloom and its induced variations in heavy metals on microbial community in sediment from eutrophic lakes remain unclear. In this study, we performed field experiments to investigate how algae bloom impacted water soluble organic matter (WSOM) and heavy metals in sediment from Chaohu Lake, a eutrophic shallow lake, and probed their combined impacts on sediment bacterial community structure. The results showed that algae bloom increased WSOM quantity, in particular, the soluble microbial by-product-like (SMP) and fulvic acid-like (Fa-L) components markedly enhanced by 203.70 % and 70.17 %, respectively. We also found that algae bloom redistributed the spatial patterns of heavy metals and altered their chemical species in sediment, then promoted contamination degree and potential ecological risk of heavy metals in sediment. Moreover, sediment bacterial community richness and diversity obviously decreased after algae bloom, and the variance partitioning analysis (VPA) results showed that combined impacts of algae-induced changes in WSOM and heavy metals explained 66.56 % of the variations in bacterial community structure. These findings depicted how algae bloom influence sediment WSOM and heavy metals, and revealed the combined impacts of algae-induced variations on microbial community structure in shallow eutrophic lake.
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Affiliation(s)
- Yulai Wang
- School of Energy and Environment, Anhui University of Technology, Maanshan City 243002, China
| | - Wanqing Gu
- School of Energy and Environment, Anhui University of Technology, Maanshan City 243002, China
| | - Xin Liu
- School of Energy and Environment, Anhui University of Technology, Maanshan City 243002, China
| | - Hui Liu
- School of Energy and Environment, Anhui University of Technology, Maanshan City 243002, China
| | - Gui Tang
- School of Energy and Environment, Anhui University of Technology, Maanshan City 243002, China
| | - Changming Yang
- Key Laboratory of Yangtze River Water Environment of the Ministry of Education, Tongji University, Shanghai 200092, China.
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12
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Aqueous Geochemical Controls on the Sestonic Microbial Community in Lakes Michigan and Superior. Microorganisms 2023; 11:microorganisms11020504. [PMID: 36838469 PMCID: PMC9963676 DOI: 10.3390/microorganisms11020504] [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: 12/13/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 02/19/2023] Open
Abstract
Despite being the largest freshwater lake system in the world, relatively little is known about the sestonic microbial community structure in the Laurentian Great Lakes. The goal of this research was to better understand this ecosystem using high-throughput sequencing of microbial communities as a function of water depth at six locations in the westernmost Great Lakes of Superior and Michigan. The water column was characterized by gradients in temperature, dissolved oxygen (DO), pH, and other physicochemical parameters with depth. Mean nitrate concentrations were 32 μmol/L, with only slight variation within and between the lakes, and with depth. Mean available phosphorus was 0.07 μmol/L, resulting in relatively large N:P ratios (97:1) indicative of P limitation. Abundances of the phyla Actinobacteria, Bacteroidetes, Cyanobacteria, Thaumarchaeota, and Verrucomicrobia differed significantly among the Lakes. Candidatus Nitrosopumilus was present in greater abundance in Lake Superior compared to Lake Michigan, suggesting the importance of ammonia-oxidating archaea in water column N cycling in Lake Superior. The Shannon diversity index was negatively correlated with pH, temperature, and salinity, and positively correlated with DO, latitude, and N2 saturation. Results of this study suggest that DO, pH, temperature, and salinity were major drivers shaping the community composition in the Great Lakes.
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13
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Barrón-Sandoval A, Martiny JBH, Pérez-Carbajal T, Bullock SH, Leija A, Hernández G, Escalante AE. Functional significance of microbial diversity in arid soils: biological soil crusts and nitrogen fixation as a model system. FEMS Microbiol Ecol 2023; 99:6998555. [PMID: 36690342 PMCID: PMC9923382 DOI: 10.1093/femsec/fiad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
Microbial communities respond to changes in environmental conditions; however, how compositional shifts affect ecosystem processes is still not well-understood and it is often assumed that different microbial communities will function equally under similar environmental conditions. We evaluated this assumption of functional redundancy using biological soil crusts (BSCs) from two arid ecosystems in Mexico with contrasting climate conditions (hot and cold deserts) following an experimental approach both in the field (reciprocal transplants) and in laboratory conditions (common garden), focusing on the community's composition and potential for nitrogen fixation. Potential of nitrogen fixation was assessed through the acetylene reduction assay. Community composition and diversity was determined with T-RFLPs of nifH gene, high throughput sequencing of 16S rRNA gene amplicons and metagenomic libraries. BSCs tended to show higher potential nitrogen fixation rates when experiencing temperatures more similar to their native environment. Moreover, changes in potential nitrogen fixation, taxonomic and functional community composition, and diversity often depended on an interactive effect of origin of the communities and the environment they experienced. We interpret our results as legacy effects that result from ecological specialization of the BSC communities to their native environment. Overall, we present evidence of nonfunctional redundancy of BSCs in terms of nitrogen fixation.
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Affiliation(s)
- Alberto Barrón-Sandoval
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, UNAM. Circuito Exterior s/n, junto al Jardín Botánico, Coyacán, Mexico City, 014510, Mexico,Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92627, United States
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA 92627, United States
| | - Teresa Pérez-Carbajal
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, UNAM. Circuito Exterior s/n, junto al Jardín Botánico, Coyacán, Mexico City, 014510, Mexico
| | - Stephen H Bullock
- Department of Conservation Biology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ctra. Ensenada-Tijuana No. 3918, Ensenada, 22860 Baja CA, Mexico
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av, Universidad 1001, 62210 Cuernavaca, Morelos, Mexico
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av, Universidad 1001, 62210 Cuernavaca, Morelos, Mexico
| | - Ana E Escalante
- Corresponding author: Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecología, UNAM. Circuito Exterior s/n, junto al Jardín Botánico, Coyacán, Mexico City, 04510. Mexico. Tel: +52(55)5623-7714; E-mail:
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14
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Poppeliers SWM, Hefting M, Dorrepaal E, Weedon JT. Functional microbial ecology in arctic soils: the need for a year-round perspective. FEMS Microbiol Ecol 2022; 98:6824434. [PMID: 36368693 PMCID: PMC9701097 DOI: 10.1093/femsec/fiac134] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.
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Affiliation(s)
- Sanne W M Poppeliers
- Corresponding author: Department of Biology, Utrecht University, 3584 CH, The Netherlands. E-mail:
| | - Mariet Hefting
- Department of Biology, Utrecht University, 3584 CH, The Netherlands
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Umea University, SE-981 07, Abisko, Sweden
| | - James T Weedon
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
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15
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Marais TS, Huddy RJ, Harrison STL. Elemental sulphur recovery from a sulphate-rich aqueous stream in a single hybrid linear flow channel reactor is mediated through microbial community dynamics and adaptation to reactor zones. FEMS Microbiol Ecol 2022; 98:6763417. [PMID: 36259757 DOI: 10.1093/femsec/fiac059] [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: 11/03/2021] [Revised: 04/20/2022] [Accepted: 10/03/2022] [Indexed: 01/21/2023] Open
Abstract
The coupled application of biological sulphate reduction (BSR) and partial sulphide oxidation to treat sulphate-rich wastewater is an effective strategy to mitigate pollution and recover elemental sulphur for repurposing. The recent development of the hybrid linear flow channel reactor (LFCR) achieves simultaneous BSR and partial sulphide oxidation with biosulphur recovery via a floating sulphur biofilm (FSB). Here, we explore the microbial community zoning and dynamics facilitating the process. A total of three continuous LFCRs were used to evaluate the effect of reactor zones, hydraulic residence time (HRT), carbon source, namely lactate and acetate, as well as reactor geometry and scale on process performance and microbial community dynamics. Community composition of sessile and planktonic microbial consortia were resolved at a 5- and 2-day HRT through 16S rRNA amplicon sequencing. Preferential attachment and prevalence of specific phylotypes within the sessile and planktonic communities revealed clear adaptation of key microorganisms to different microenvironments. Key microbial taxa affiliated with sulphate reduction and sulphide oxidation as well as those implicated in fermentation and syntrophic metabolism, fluctuated in response to changes in HRT and process performance. Through understanding the relationship between microbial community dynamics and process performance, this research will inform better process design and optimization of the hybrid LFCR.
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Affiliation(s)
- T S Marais
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town, Private Bag X1, Rondebosch 7701, South Africa.,Future Water Institute, 1 Madiba Circle, University of Cape Town, 7700, South Africa
| | - R J Huddy
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town, Private Bag X1, Rondebosch 7701, South Africa.,Future Water Institute, 1 Madiba Circle, University of Cape Town, 7700, South Africa
| | - S T L Harrison
- Centre for Bioprocess Engineering Research, Department of Chemical Engineering, University of Cape Town, Private Bag X1, Rondebosch 7701, South Africa.,Future Water Institute, 1 Madiba Circle, University of Cape Town, 7700, South Africa
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16
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Chen W, Wei J, Su Z, Wu L, Liu M, Huang X, Yao P, Wen D. Deterministic mechanisms drive bacterial communities assembly in industrial wastewater treatment system. ENVIRONMENT INTERNATIONAL 2022; 168:107486. [PMID: 36030743 DOI: 10.1016/j.envint.2022.107486] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Microbial communities are responsible for biological treatment of many industrial wastewater, but our knowledge of their diversity, assembly patterns, and function is still poor. Here, we analyzed the bacterial communities of wastewater and activated sludge samples taken from 11 full-scale industrial wastewater treatment plants (IWWTPs) characterized by the same process design but different wastewater types and WWTP compartments. We found significantly different diversity and compositions of bacterial assemblages among distinct wastewater types and IWWTPs compartments. IWWTPs bacterial communities exhibited a clear species abundance distribution. The dispersal-driven process was weak in shaping IWWTP communities. Meanwhile, environmental and operating conditions were important factors in regulating the structure of the activated sludge community and pollutants removal, indicating that bacterial community was largely driven by deterministic mechanisms. The core microbial community in IWWTPs was different from that in municipal wastewater treatment plants (MWWTPs), and many taxa (e.g. the genus Citreitalea) rarely were detected before, indicating IWWTPs harbored unique core bacterial communities. Furthermore, we found that bacterial community compositions were strongly linked to activated sludge function. These findings are important to both microbial ecologists and environmental engineers, who may optimize the operation strategies jointly for maintaining biodiversity, which in turn may promote a more stable performance of the IWWTP. Overall, our study enhances the mechanistic understanding of the IWWTP microbial community diversity, assembly patterns, and function, and provides important implications for microbial ecology and wastewater treatment processes.
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Affiliation(s)
- Weidong Chen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jie Wei
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Environment, Tsinghua University, Beijing 100084, China
| | - Linwei Wu
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing China
| | - Min Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xiaoxuan Huang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Pengcheng Yao
- Zhejiang Institute of Hydraulics and Estuary, Hangzhou 310017, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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17
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Costa-Roura S, Villalba D, Balcells J, De la Fuente G. First Steps into Ruminal Microbiota Robustness. Animals (Basel) 2022; 12:2366. [PMID: 36139226 PMCID: PMC9495070 DOI: 10.3390/ani12182366] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/01/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.
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18
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Sridhar B, Wilhelm RC, Debenport SJ, Fahey TJ, Buckley DH, Goodale CL. Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils. GLOBAL CHANGE BIOLOGY 2022; 28:5399-5415. [PMID: 35770362 DOI: 10.1111/gcb.16321] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Microbial community structure and function regularly covary with soil pH, yet effects of these interactions on soil carbon are rarely tested experimentally within natural ecosystems. We investigated the enduring (25 year) impacts of liming on microbial community structure and decomposition at an acidic northern hardwood forest, where experimental liming increased pH one unit and surprisingly doubled the organic carbon stocks of the forest floor. We show that this increase in carbon storage corresponded with restructuring of the bacterial and fungal communities that drive decomposition. In the Oe horizon, liming reduced the activities of five extracellular enzymes that mediate decomposition, while the Oa horizon showed an especially large (64%) reduction in the activity of a sixth, peroxidase, which is an oxidative enzyme central to lignocellulose degradation. Decreased enzyme activities corresponded with loss of microbial taxa important for lignocellulose decay, including large reductions in the dominant ectomycorrhizal genera Russula and Cenococcum, saprotrophic and wood decaying fungi, and Actinobacteria (Thermomonosporaceae). These results demonstrate the importance of pH as a dominant regulator of microbial community structure and illustrate how changes to this structure can produce large, otherwise unexpected increases in carbon storage in forest soils.
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Affiliation(s)
- Bhavya Sridhar
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Spencer J Debenport
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Timothy J Fahey
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Christine L Goodale
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, USA
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19
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Karaoz U, Brodie EL. microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes. FRONTIERS IN BIOINFORMATICS 2022; 2:918853. [PMID: 36304272 PMCID: PMC9580909 DOI: 10.3389/fbinf.2022.918853] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2023] Open
Abstract
Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.
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Affiliation(s)
- Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
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20
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Phytoplankton and Bacterial Communities’ Patterns in a Highly Dynamic Ecosystem (Central Mediterranean Sea). WATER 2022. [DOI: 10.3390/w14132057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Straits of Messina (Southern Italy, Mediterranean Sea) are a very complex area: they connect two basins (Tyrrhenian and Ionian) with different hydrographic features and is characterised by upwelling and mixing phenomena. The aim of the study was to evaluate if and how the physical and chemical water conditions and hydrodynamics influenced the phytoplankton and bacterial patterns and the functioning of this ecosystem. During a late winter survey, size-fractionated phytoplankton (from 0.2 to 200 μm) biomass (chlorophyll a), cell densities and species composition as well as total picoplankton abundances, morphotype composition, and activity levels of the enzymes leucine aminopeptidase, β-glucosidase, and alkaline phosphatase were investigated. The obtained results showed a marked diversification among the water masses identified within the Straits area. The analyses of the phytoplankton diversity indices, particularly those based on phylogenetic relationships between species (indices of taxonomic diversity and distinctness), confirmed our findings. In conclusion, the patterns of phytoplankton and bacterial communities provide a suitable approach to evaluate how microbial communities respond to changing environmental scenarios. This tool could be applied to other temperate Mediterranean ecosystems.
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21
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Ren Z, Zhang C, Li X, Ma K, Cui B. Abundant and Rare Bacterial Taxa Structuring Differently in Sediment and Water in Thermokarst Lakes in the Yellow River Source Area, Qinghai-Tibet Plateau. Front Microbiol 2022; 13:774514. [PMID: 35422785 PMCID: PMC9002311 DOI: 10.3389/fmicb.2022.774514] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/02/2022] [Indexed: 01/28/2023] Open
Abstract
Thermokarst lakes are forming from permafrost thaw and are severely affected by accelerating climate change. Sediment and water in these lakes are distinct habitats but closely connected. However, our understanding of the differences and linkages between sediment and water in thermokarst lakes remains largely unknown, especially from the perspective of community assembly mechanisms. Here, we examined bacterial communities in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau. Bacterial taxa were divided into abundant and rare according to their relative abundance, and the Sorensen dissimilarity (βsor) was partitioned into turnover (βturn) and nestedness (βnest). The whole bacterial communities and the abundant and rare subcommunities differed substantially between sediment and water in taxonomical composition, α-diversity, and β-diversity. Sediment had significantly lower α-diversity indexes but higher β-diversity than water. In general, bacterial communities are predominantly governed by strong turnover processes (βturn/βsor ratio of 0.925). Bacterial communities in sediment had a significantly higher βturn/βsor ratio than in water. Abundant subcommunities were significantly lower in the βturn/βsor ratio compared with rare subcommunities. The results suggest that the bacterial communities of thermokarst lakes, especially rare subcommunities or particularly in sediment, might be strongly structured by heterogeneity in the source material, environmental filtering, and geographical isolation, leading to compositionally distinct communities. This integral study increased our current knowledge of thermokarst lakes, enhancing our understanding of the community assembly rules and ecosystem structures and processes of these rapidly changing and vulnerable ecosystems.
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Affiliation(s)
- Ze Ren
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China.,School of Environment, Beijing Normal University, Beijing, China
| | - Cheng Zhang
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China.,School of Engineering Technology, Beijing Normal University, Zhuhai, China
| | - Xia Li
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China.,School of Environment, Beijing Normal University, Beijing, China
| | - Kang Ma
- School of Environment, Beijing Normal University, Beijing, China
| | - Baoshan Cui
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China.,School of Environment, Beijing Normal University, Beijing, China
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22
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Wang D, Zhou H, Zuo J, Chen P, She Y, Yao B, Dong S, Wu J, Li F, Njoroge DM, Shi G, Mao X, Ma L, Zhang Z, Mao Z. Responses of Soil Microbial Metabolic Activity and Community Structure to Different Degraded and Restored Grassland Gradients of the Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:770315. [PMID: 35463442 PMCID: PMC9024238 DOI: 10.3389/fpls.2022.770315] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/22/2022] [Indexed: 05/31/2023]
Abstract
Climate change and land-use disturbances are supposed to have severely affected the degraded alpine grasslands on the Tibetan Plateau. Artificial grassland establishment has been implemented as a restoration tool against grassland degradation. However, the impact of such degradation and restoration processes on soil microbial communities and soil quality is not clearly understood. Here, we aim to investigate how the dynamics of microbial community and soil quality of alpine grasslands respond to a gradient of degradation and that of restoration, respectively. We conducted a randomised experiment with four degradation stages (light, moderate, heavy, and extreme degradation) and three restoration stages (artificial restoration for 1, 5, and 10 years). We analysed the abundance and diversity of soil bacteria and fungi, and measured soil nutrients, enzymatic activity and microbial biomass. The concentration of soil nitrogen (TN), soil organic matter (OM) in heavy degraded grassland decreased significantly by 37.4 and 45.08% compared with that in light degraded grassland. TN and OM in 10-years restored grassland also increased significantly by 33.10 and 30.42% compared to that in 1-year restored grassland. Four soil enzymatic activity indicators related to microbial biomass decreased with degradation gradient and increased with recovery time (i.e., restoration gradient). Both bacterial and fungal community structure was significantly different among grassland degradation or restoration successional stages. The LEfSe analysis revealed that 29 fungal clades and 9 bacterial clades were susceptible to degraded succession, while16 fungal clades and 5 bacterial clades were susceptible to restoration succession. We conclude that soil quality (TN, OM, and enzymatic activity) deteriorated significantly in heavy degraded alpine grassland. Soil microbial community structure of alpine is profoundly impacted by both degradation and restoration processes, fungal communities are more sensitive to grassland succession than bacterial communities. Artificial grasslands can be used as an effective method of restoring degraded grassland, but the soil functions of artificial grassland, even after 10 years of recovery, cannot be restored to the original state of alpine grassland.
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Affiliation(s)
- Dangjun Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huakun Zhou
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Juan Zuo
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Peng Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yandi She
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Buqing Yao
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Shikui Dong
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Jianshuang Wu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Denis Mburu Njoroge
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guoxi Shi
- Key Laboratory of Utilization of Agriculture Solid Waste Resources, College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, China
| | - Xufeng Mao
- School of Geographical Sciences, Qinghai Normal University, Xining, China
| | - Li Ma
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhonghua Zhang
- Key Laboratory of Cold Regions Restoration Ecology, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhun Mao
- AMAP, Univ. Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
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23
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Variations and Mutual Relations of Vegetation–Soil–Microbes of Alpine Meadow in the Qinghai-Tibet Plateau under Degradation and Cultivation. LAND 2022. [DOI: 10.3390/land11030396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Artificial cultivation had been applied to recover the meadow suffering from serious degradation in the Qinghai–Tibet Plateau. Studies focusing only on the changes in vegetation, soil and microbes along the meadow degradation were insufficient, and artificial cultivation as an important part of succession was always neglected. Here, the variables of vegetation, soil, and soil bacteria are surveyed in four types of alpine meadow in the protected lands of the Qinghai–Tibet Plateau: intact alpine meadow (IAM), moderate degradation alpine meadow (MDAM), extreme degradation alpine meadow (black soil beach (BSB)), and artificial alpine grassland (AAG). The results indicated that degradation and cultivation significantly changed the characteristics of the vegetation community, physicochemical features of the soil, and soil bacterial community diversity. Soil bacteria took a considerably longer time to adapt to degradation and cultivation than vegetation and soil. Compared to IAM and BSB, ADAM and AAG had more specific bacteria identified by ANOVA and LEfSe analysis, implying an unstable state. Combined with vegetation and soil variables, it was speculated that the unstable AAG was not significantly improved from the degraded meadow, and also lagged significantly compared to IAM. Correlation analysis revealed that aboveground biomass, species richness, vegetation coverage, SOC, C/N, BD, WC, and pH were significantly associated with bacterial diversity under community level. Aboveground biomass was an effective indicator for soil bacterial gene copies. Redundancy analysis demonstrated that the soil bacterial community is mainly regulated by the vegetation coverage, Gleason index, Simpson index, TN, TP, and pH under phylum and genus level. Partial mantel test analysis indicated that the physicochemical features of the soil were the most important factor correlating with the soil bacterial community along the degradation and cultivation, compared to other environmental factors.
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24
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Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
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Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
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25
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Li W, Chen X, Li M, Cai Z, Gong H, Yan M. Microplastics as an aquatic pollutant affect gut microbiota within aquatic animals. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127094. [PMID: 34530278 DOI: 10.1016/j.jhazmat.2021.127094] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/18/2021] [Accepted: 08/29/2021] [Indexed: 05/27/2023]
Abstract
The adverse impact of microplastics (MPs) on gut microbiota within aquatic animals depends on the overall effect of chemicals and biofilm of MPs. Thus, it is ideal to fully understand the influences that arise from each or even all of these characteristics, which should give us a whole picture of consequences that are brought by MPs. Harmful effects of MPs on gut microbiota within aquatic organisms start from the ingestion of MPs by aquatic organisms. According to this, the present review will discuss the ingestion of MPs and its following results on gut microbial communities within aquatic animals, in which chemical components, such as plastic polymers, heavy metals and POPs, and the biofilm of MPs would be involved. This review firstly analyzed the impacts of MPs on aquatic organisms in detail about its chemical components and biofilm based on previous relevant studies. At last, the significance of field studies, functional studies and complex dynamics of gut microbial ecology in the future research of MPs affecting gut microbiota is discussed.
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Affiliation(s)
- Weixin Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Xiaofeng Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Minqian Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Zeming Cai
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Han Gong
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China.
| | - Muting Yan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China; Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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26
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Wang Y, Lu G, Yu H, Du X, He Q, Yao S, Zhao L, Huang C, Wen X, Deng Y. Meadow degradation increases spatial turnover rates of the fungal community through both niche selection and dispersal limitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149362. [PMID: 34375268 DOI: 10.1016/j.scitotenv.2021.149362] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/08/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
The alpine meadow ecosystem, as the main ecosystem of the Qinghai-Tibet Plateau, has been heavily degraded over the past several decades due to overgrazing and climate change. Although soil microorganisms play key roles in the stability and succession of grassland ecosystems, their response to grassland degradation has not been investigated at spatial scale. Here, we systematically analyzed the spatial turnover rates of soil prokaryotic and fungal communities in degraded and undegraded meadows through distance-decay relationship (DDR) and species area relationship (SAR), as well as the community assembly mechanisms behind them. Although the composition and structure of both fungal and prokaryotic communities showed significant changes between undegraded and degraded meadows, steeper spatial turnover rates were only observed in fungi (Degraded Alpine Meadow β = 0.0142, Undegraded Alpine Meadow β = 0.0077, P < 0.05). Mantel tests indicated that edaphic variables and vegetation factors showed significant correlations to the β diversity of fungal community only in degraded meadow, suggesting soil and vegetation heterogeneity both contributed to the variation of fungal community in that system. Correspondingly, a novel phylogenetic null model analysis demonstrated that environmental selection was enhanced in the fungal community assembly process during meadow degradation. Interestingly, dispersal limitation was also enhanced for the fungal community in the degraded meadow, and its relative contribution to other assembly process (i.e. selection and drift) showed a significant linear increase with spatial distance, suggesting that dispersal limitation played a greater role as distance increased. Our findings indicated the spatial scaling of the fungal community is altered during meadow degradation by both niche selection and dispersal limitation. This study provides a new perspective for the assessment of soil microbial responses to vegetation changes in alpine areas.
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Affiliation(s)
- Yingcheng Wang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China
| | - Guangxin Lu
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Hao Yu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Shiting Yao
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Lirong Zhao
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Caixia Huang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Xiaocheng Wen
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
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27
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Hicks LC, Frey B, Kjøller R, Lukac M, Moora M, Weedon JT, Rousk J. Toward a function-first framework to make soil microbial ecology predictive. Ecology 2021; 103:e03594. [PMID: 34807459 DOI: 10.1002/ecy.3594] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/27/2021] [Accepted: 09/10/2021] [Indexed: 01/21/2023]
Abstract
Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions. We first view the microbial community associated with a specific function as a whole and describe the dependence of microbial functions on environmental factors (e.g., the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of "biomarker" taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition. In this paper, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH, and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.
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Affiliation(s)
- Lettice C Hicks
- Section of Microbial Ecology, Department of Biology, Lund University, Ecology Building, Lund, 22362, Sweden
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Rasmus Kjøller
- Department of Biology, Terrestrial Ecology Section, University of Copenhagen, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Martin Lukac
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, United Kingdom.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, 16500, Czech Republic
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - James T Weedon
- Systems Ecology, Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, The Netherlands
| | - Johannes Rousk
- Section of Microbial Ecology, Department of Biology, Lund University, Ecology Building, Lund, 22362, Sweden
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28
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Distinct methane-dependent biogeochemical states in Arctic seafloor gas hydrate mounds. Nat Commun 2021; 12:6296. [PMID: 34728618 PMCID: PMC8563959 DOI: 10.1038/s41467-021-26549-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 09/27/2021] [Indexed: 01/04/2023] Open
Abstract
Archaea mediating anaerobic methane oxidation are key in preventing methane produced in marine sediments from reaching the hydrosphere; however, a complete understanding of how microbial communities in natural settings respond to changes in the flux of methane remains largely uncharacterized. We investigate microbial communities in gas hydrate-bearing seafloor mounds at Storfjordrenna, offshore Svalbard in the high Arctic, where we identify distinct methane concentration profiles that include steady-state, recently-increasing subsurface diffusive flux, and active gas seepage. Populations of anaerobic methanotrophs and sulfate-reducing bacteria were highest at the seep site, while decreased community diversity was associated with a recent increase in methane influx. Despite high methane fluxes and methanotroph doubling times estimated at 5-9 months, microbial community responses were largely synchronous with the advancement of methane into shallower sediment horizons. Together, these provide a framework for interpreting subseafloor microbial responses to methane escape in a warming Arctic Ocean.
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29
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Osburn ED, Badgley BD, Strahm BD, Aylward FO, Barrett JE. Emergent properties of microbial communities drive accelerated biogeochemical cycling in disturbed temperate forests. Ecology 2021; 102:e03553. [PMID: 34622940 DOI: 10.1002/ecy.3553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/31/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023]
Abstract
Despite ever-increasing availability of detailed information about microbial community structure, relationships of microbial diversity with ecosystem functioning remain unclear. We investigated these relationships at the Coweeta Hydrologic Laboratory, where past forest disturbances (e.g., clear-cut) have altered both ecosystem processes (e.g., increased N export) and microbial communities (e.g., increased bacterial diversity). We sampled soils from disturbed and adjacent reference forests, characterized resident microbial communities, and measured several microbial C-cycle and N-cycle process rates. Microbial communities from historically disturbed soils exhibited altered ecosystem functioning, including generally higher rates of C- and N-cycle processes. Disturbed soil microbial communities also exhibited altered ecosystem multifunctionality, a composite variable consisting of all measured process rates as well as extracellular enzyme activities. Although we found few relationships between ecosystem functions and microbial alpha diversity, all functions were correlated with microbial community composition metrics, particularly r:K strategist ratios of bacterial phyla. Additionally, for both ecosystem multifunctionality and specific processes (i.e., C- and N-mineralization), microbial metrics significantly improved models seeking to explain variation in process rates. Our work sheds light on the links between microbial communities and ecosystem functioning and identifies specific microbial metrics important for modeling ecosystem responses to environmental change.
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Affiliation(s)
- Ernest D Osburn
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Brian D Badgley
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Brian D Strahm
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - J E Barrett
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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30
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Luan J, Li S, Dong W, Liu Y, Wang Y, Liu S. Litter decomposition affected by bamboo expansion is modulated by litter‐mixing and microbial composition. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junwei Luan
- Institute of Resources and EnvironmentKey Laboratory of Bamboo and Rattan Science and Technology of State Forestry and Grassland Administration, International Centre for Bamboo and Rattan Beijing PR China
| | - Siyu Li
- Institute of Resources and EnvironmentKey Laboratory of Bamboo and Rattan Science and Technology of State Forestry and Grassland Administration, International Centre for Bamboo and Rattan Beijing PR China
| | - Wei Dong
- School of Resources and Environmental Engineering Jiangxi University of Science and Technology Ganzhou PR China
| | - Yanchun Liu
- School of Life Sciences Henan University Kaifeng PR China
| | - Yi Wang
- Institute of Resources and EnvironmentKey Laboratory of Bamboo and Rattan Science and Technology of State Forestry and Grassland Administration, International Centre for Bamboo and Rattan Beijing PR China
| | - Shirong Liu
- The Research Institute of Forest Ecology, Environment and Protection Chinese Academy of Forestry Beijing PR China
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31
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Sun YQ, Ge Y. Temporal Changes in the Function of Bacterial Assemblages Associated With Decomposing Earthworms. Front Microbiol 2021; 12:682224. [PMID: 34456883 PMCID: PMC8386022 DOI: 10.3389/fmicb.2021.682224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022] Open
Abstract
Soil invertebrate corpse decomposition is an ecologically significant, yet poorly understood, process affecting nutrient biogeochemical cycling in terrestrial ecosystems. Here, we attempted to answer how the substrate chemistry and microbial community change during soil invertebrate (earthworm) decomposition and what roles microbes play in this process. Specifically, the dead earthworms (Amynthas corticis) were buried in two soils where the earthworms inhabited, or not, until more than 50% of the earthworm mass was lost. For both soils, earthworms decomposed faster during the early stage (between 0 and 3 days), as reflected by the higher rate of decomposition and increased accumulation of dissolved organic matter (DOM). This decomposition pattern was paralleled by bacterial community dynamics, where bacterial richness and diversity were significantly higher during early decomposition (p < 0.05) with the relative abundances of many genera decreasing as decomposition progressed. The succession of the bacterial community composition was significantly correlated with time-course changes in DOM composition (p < 0.05). Particularly, more functional groups (e.g., microbes associated with carbon, nitrogen, and sulfur cycling) were identified to be linked with the change of a specific DOM type during the early decomposition phase. By exploring the ecologically important process of soil invertebrate decomposition and its associated bacterial communities, this study provides evidence, e.g., a statistically significant positive correlation between bacterial community and DOM compositions, which supports the widely recognized yet less-tested microbial community structure–function relationship hypothesis in invertebrate decomposition.
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Affiliation(s)
- Yao-Qin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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32
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Saifuddin M, Bhatnagar JM, Phillips RP, Finzi AC. Ectomycorrhizal fungi are associated with reduced nitrogen cycling rates in temperate forest soils without corresponding trends in bacterial functional groups. Oecologia 2021; 196:863-875. [PMID: 34170396 DOI: 10.1007/s00442-021-04966-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/09/2021] [Indexed: 11/30/2022]
Abstract
Microbial processes play a central role in controlling the availability of N in temperate forests. While bacteria, archaea, and fungi account for major inputs, transformations, and exports of N in soil, relationships between microbial community structure and N cycle fluxes have been difficult to detect and characterize. Several studies have reported differences in N cycling based on mycorrhizal type in temperate forests, but associated differences in N cycling genes underlying these fluxes are not well-understood. We explored how rates of soil N cycle fluxes vary across gradients of mycorrhizal abundance (hereafter "mycorrhizal gradients") at four temperate forest sites in Massachusetts and Indiana, USA. We paired measurements of N-fixation, net nitrification, and denitrification rates with gene abundance data for specific bacterial functional groups associated with each process. We find that the availability of NO3 and rates of N-fixation, net nitrification, and denitrification are reduced in stands dominated by trees associated with ECM fungi. On average, rates of N-fixation and denitrification in stands dominated by trees associated with arbuscular mycorrhizal fungi were more than double the corresponding rates in stands dominated by trees associated with ectomycorrhizal fungi. Despite the structuring of flux rates across the mycorrhizal gradients, we did not find concomitant shifts in the abundances of N-cycling bacterial genes, and gene abundances were not correlated with process rates. Given that AM-associating trees are replacing ECM-associating trees throughout much of the eastern US, our results suggest that shifts in mycorrhizal dominance may accelerate N cycling independent of changes in the relative abundance of N cycling bacteria, with consequences for forest productivity and N retention.
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33
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Wang C, Morrissey EM, Mau RL, Hayer M, Piñeiro J, Mack MC, Marks JC, Bell SL, Miller SN, Schwartz E, Dijkstra P, Koch BJ, Stone BW, Purcell AM, Blazewicz SJ, Hofmockel KS, Pett-Ridge J, Hungate BA. The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization. ISME JOURNAL 2021; 15:2738-2747. [PMID: 33782569 DOI: 10.1038/s41396-021-00959-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/19/2021] [Accepted: 03/04/2021] [Indexed: 11/09/2022]
Abstract
Microorganisms drive soil carbon mineralization and changes in their activity with increased temperature could feedback to climate change. Variation in microbial biodiversity and the temperature sensitivities (Q10) of individual taxa may explain differences in the Q10 of soil respiration, a possibility not previously examined due to methodological limitations. Here, we show phylogenetic and taxonomic variation in the Q10 of growth (5-35 °C) among soil bacteria from four sites, one from each of Arctic, boreal, temperate, and tropical biomes. Differences in the temperature sensitivities of taxa and the taxonomic composition of communities determined community-assembled bacterial growth Q10, which was strongly predictive of soil respiration Q10 within and across biomes. Our results suggest community-assembled traits of microbial taxa may enable enhanced prediction of carbon cycling feedbacks to climate change in ecosystems across the globe.
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Affiliation(s)
- Chao Wang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.,CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA.
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Juan Piñeiro
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Michelle C Mack
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Sheryl L Bell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Samantha N Miller
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Steven J Blazewicz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S Hofmockel
- Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, USA.,Ecology, Evolution and Organismal Biology Department, Iowa State University, Ames, IA, USA
| | - Jennifer Pett-Ridge
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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34
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Metals Alter Membership but Not Diversity of a Headwater Stream Microbiome. Appl Environ Microbiol 2021; 87:AEM.02635-20. [PMID: 33452033 DOI: 10.1128/aem.02635-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/25/2020] [Indexed: 11/20/2022] Open
Abstract
Metal contamination from mining or natural weathering is a common feature of surface waters in the American west. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination and identify candidate microbial taxa to be used to indicate metal stress in stream ecosystems. We evaluated microbiome membership from sediments at multiple sites within the principal drainage of an EPA superfund site near the headwaters of the Upper Arkansas River, Leadville, CO. From each sample, we extracted DNA and sequenced the 16S rRNA gene amplicon on the Illumina MiSeq platform. We used the remaining sediments to simultaneously evaluate environmental metal concentrations. We also conducted an artificial stream mesocosm experiment using sediments collected from two of the observational study sites. The mesocosm experiment had a two-by-two factorial design: (i) location (upstream or downstream of contaminating tributary), and (ii) treatment (metal exposure or control). We found no difference in diversity between upstream and downstream sites in the field. Similarly, diversity changed very little following experimental metal exposure. However, microbiome membership differed between upstream and downstream locations and experimental metal exposure changed microbiome membership in a manner that depended on origin of the sediments used in each mesocosm.IMPORTANCE Our results suggest that microbiomes can be reliable indicators of ecosystem metal stress even when surface water chemistry and other metrics used to assess ecosystem health do not indicate ecosystem stress. Results presented in this study, in combination with previously published work on this same ecosystem, are consistent with the idea that a microbial response to metals at the base of the food web may be affecting primary consumers. If effects of metals are mediated through shifts in the microbiome, then microbial metrics, as presented here, may aid in the assessment of stream ecosystem health, which currently does not include assessments of the microbiome.
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Saia SM, Carrick HJ, Buda AR, Regan JM, Walter MT. Critical Review of Polyphosphate and Polyphosphate Accumulating Organisms for Agricultural Water Quality Management. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2722-2742. [PMID: 33559467 DOI: 10.1021/acs.est.0c03566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Despite ongoing management efforts, phosphorus (P) loading from agricultural landscapes continues to impair water quality. Wastewater treatment research has enhanced our knowledge of microbial mechanisms influencing P cycling, especially regarding microbes known as polyphosphate accumulating organisms (PAOs) that store P as polyphosphate (polyP) under oxic conditions and release P under anoxic conditions. However, there is limited application of PAO research to reduce agricultural P loading and improve water quality. Herein, we conducted a meta-analysis to identify articles in Web of Science on polyP and its use by PAOs across five disciplines (i.e., wastewater treatment, terrestrial, freshwater, marine, and agriculture). We also summarized research that provides preliminary support for PAO-mediated P cycling in natural habitats. Terrestrial, freshwater, marine, and agriculture disciplines had fewer polyP and PAO articles compared to wastewater treatment, with agriculture consistently having the least. Most meta-analysis articles did not overlap disciplines. We found preliminary support for PAOs in natural habitats and identified several knowledge gaps and research opportunities. There is an urgent need for interdisciplinary research linking PAOs, polyP, and oxygen availability with existing knowledge of P forms and cycling mechanisms in natural and agricultural environments to improve agricultural P management strategies and achieve water quality goals.
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Affiliation(s)
- Sheila M Saia
- Depatment of Biological and Agricultural Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Hunter J Carrick
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Anthony R Buda
- Pasture Systems and Watershed Management Research Unit, Agricultural Research Service, United States Department of Agriculture, University Park, Pennsylvania 16802, United States
| | - John M Regan
- Department of Civil and Environmental Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - M Todd Walter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
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Walker AM, Leigh MB, Mincks SL. Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope. Front Microbiol 2021; 12:581124. [PMID: 33584606 PMCID: PMC7876419 DOI: 10.3389/fmicb.2021.581124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.
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Affiliation(s)
- Alexis M Walker
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Sarah L Mincks
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
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Meyer KM, Morris AH, Webster K, Klein AM, Kroeger ME, Meredith LK, Brændholt A, Nakamura F, Venturini A, Fonseca de Souza L, Shek KL, Danielson R, van Haren J, Barbosa de Camargo P, Tsai SM, Dini-Andreote F, de Mauro JMS, Barlow J, Berenguer E, Nüsslein K, Saleska S, Rodrigues JLM, Bohannan BJM. Belowground changes to community structure alter methane-cycling dynamics in Amazonia. ENVIRONMENT INTERNATIONAL 2020; 145:106131. [PMID: 32979812 DOI: 10.1016/j.envint.2020.106131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6 ± 9482.3 μg CH4 m-2 d-1), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8 ± 120.5 μg CH4 m-2 d-1), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2 ± 35.7 μg CH4 m-2 d-1), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.
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Affiliation(s)
- Kyle M Meyer
- Department of Integrative Biology, University of California - Berkeley, Berkeley, CA, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
| | - Andrew H Morris
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | | | - Ann M Klein
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA; College of the Siskiyous, Weed, CA, USA
| | - Marie E Kroeger
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Laura K Meredith
- School of Natural Resources and the Environment, Tucson, AZ, USA; Biosphere 2, University of Arizona, Tucson, AZ, USA
| | - Andreas Brændholt
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Fernanda Nakamura
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Andressa Venturini
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Leandro Fonseca de Souza
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Katherine L Shek
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Rachel Danielson
- Department of Land, Air, and Water Resources, University of California - Davis, Davis, CA, USA
| | - Joost van Haren
- Biosphere 2, University of Arizona, Tucson, AZ, USA; Honors College, University of Arizona, Tucson, AZ, USA
| | | | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Fernando Dini-Andreote
- Department of Soil Science, 'Luiz de Queiroz' College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - José M S de Mauro
- Universidade Federal do Oeste do Pará, Santarém-Tapajós, Pará, Brazil
| | - Jos Barlow
- Lancaster Environmental Centre, Lancaster University, Lancaster, UK
| | - Erika Berenguer
- Lancaster Environmental Centre, Lancaster University, Lancaster, UK; Environmental Change Institute, University of Oxford, Oxford, UK
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Scott Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Jorge L M Rodrigues
- Department of Land, Air, and Water Resources, University of California - Davis, Davis, CA, USA
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38
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Adkins J, Docherty KM, Gutknecht JLM, Miesel JR. How do soil microbial communities respond to fire in the intermediate term? Investigating direct and indirect effects associated with fire occurrence and burn severity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140957. [PMID: 32736103 DOI: 10.1016/j.scitotenv.2020.140957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/11/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
Abstract
Fires transform soil microbial communities directly via heat-induced mortality and indirectly by altering plant and soil characteristics. Emerging evidence suggests the magnitude of changes to some plant and soil properties increases with burn severity, but the persistence of changes varies among plant and soil characteristics, ranging from months to years post-fire. Thus, which environmental attributes shape microbial communities at intermediate time points during ecosystem recovery, and how these characteristics vary with severity, remains poorly understood. We identified the network of properties that influence microbial communities three years after fire, along a burn severity gradient in Sierra Nevada mixed-conifer forest. We used phospholipid fatty acid (PLFA) analysis and bacterial 16S-rDNA amplicon sequencing to characterize the microbial community in mineral soil. Using structural equation modelling, we applied a systems approach to identifying the interconnected relationships among severity, vegetation, soil, and microbial communities. Dead tree basal area, soil pH, and extractable phosphorus increased with severity, whereas live tree basal area, forest floor mass, and the proportion of the ≥53 μm soil fraction decreased. Forest floor loss was associated with decreased soil moisture across the severity gradient, decreased live tree basal area was associated with increased shrub coverage, and increased dead tree basal area was associated with increases in total and inorganic soil nitrogen. Soil fungal abundance decreased across the severity gradient, despite a slightly positive response of fungi to lower soil moisture in high severity areas. Bacterial phylogenetic diversity was negatively related to severity and was driven by differences in nutrients and soil texture. The abundance of Bacteroidetes increased and the abundance of Acidobacteria decreased across the severity gradient due to differences in soil pH. Overall, we found that the effects of burn severity on vegetation and soil physicochemical characteristics interact to shape microbial communities at an intermediate time point in ecosystem recovery.
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Affiliation(s)
- Jaron Adkins
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
| | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Jessica L M Gutknecht
- Department of Soil, Water, and Climate, University of Minnesota, Twin Cities St. Paul, MN, USA
| | - Jessica R Miesel
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
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Van Nuland ME, Smith DP, Bhatnagar JM, Stefanski A, Hobbie SE, Reich PB, Peay KG. Warming and disturbance alter soil microbiome diversity and function in a northern forest ecotone. FEMS Microbiol Ecol 2020; 96:5849001. [PMID: 32472932 DOI: 10.1093/femsec/fiaa108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
The response to global change by soil microbes is set to affect important ecosystem processes. These impacts could be most immediate in transitional zones, such as the temperate-boreal forest ecotone, yet previous work in these forests has primarily focused on specific subsets of microbial taxa. Here, we examined how bacterial and fungal communities respond to simulated above- and below-ground warming under realistic field conditions in closed and open canopy treatments in Minnesota, USA. Our results show that warming and canopy disturbance shifted bacterial and fungal community structure as dominant bacterial and fungal groups differed in the direction and intensity of their responses. Ectomycorrhizal and saprotrophic fungal communities with greater connectivity (higher prevalence of strongly interconnected taxa based on pairwise co-occurrence relationships) were more resistant to compositional change. Warming effects on soil enzymes involved in the hydrolytic and oxidative liberation of carbon from plant cell walls and nutrients from organic matter were most strongly linked to fungal community responses, although community structure-function relationships differed between fungal guilds. Collectively, these findings indicate that warming and disturbance will influence the composition and function of microbial communities in the temperate-boreal ecotone, and fungal responses are particularly important to understand for predicting future ecosystem functioning.
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Affiliation(s)
| | - Dylan P Smith
- University of California, California Institute for Quantitative Biosciences, Berkeley, CA 94720 USA
| | | | - Artur Stefanski
- Department of Forest Resources, University of Minnesota, St. Paul, MN 55108 USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108 USA
| | - Peter B Reich
- Department of Forest Resources, University of Minnesota, St. Paul, MN 55108 USA.,Hawkesbury Institute for the Environment, Western Sydney University, Richmond, 2753, NSW Australia
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA 94305 USA
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40
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Coll C, Bier R, Li Z, Langenheder S, Gorokhova E, Sobek A. Association between Aquatic Micropollutant Dissipation and River Sediment Bacterial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14380-14392. [PMID: 33104348 PMCID: PMC7676288 DOI: 10.1021/acs.est.0c04393] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Assessment of micropollutant biodegradation is essential to determine the persistence of potentially hazardous chemicals in aquatic ecosystems. We studied the dissipation half-lives of 10 micropollutants in sediment-water incubations (based on the OECD 308 standard) with sediment from two European rivers sampled upstream and downstream of wastewater treatment plant (WWTP) discharge. Dissipation half-lives (DT50s) were highly variable between the tested compounds, ranging from 1.5 to 772 days. Sediment from one river sampled downstream from the WWTP showed the fastest dissipation of all micropollutants after sediment RNA normalization. By characterizing sediment bacteria using 16S rRNA sequences, bacterial community composition of a sediment was associated with its capacity for dissipating micropollutants. Bacterial amplicon sequence variants of the genera Ralstonia, Pseudomonas, Hyphomicrobium, and Novosphingobium, which are known degraders of contaminants, were significantly more abundant in the sediment incubations where fast dissipation was observed. Our study illuminates the limitations of the OECD 308 standard to account for variation of dissipation rates of micropollutants due to differences in bacterial community composition. This limitation is problematic particularly for those compounds with DT50s close to regulatory persistence criteria. Thus, it is essential to consider bacterial community composition as a source of variability in regulatory biodegradation and persistence assessments.
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Affiliation(s)
- Claudia Coll
- Department
of Environmental Science (ACES), Stockholm
University, 10691 Stockholm, Sweden
- Eawag, Swiss Federal Institute of Aquatic
Science and Technology, 8600 Dübendorf, Switzerland
| | - Raven Bier
- Department
of Ecology and Genetics/Limnology, Uppsala
University, Norbyvägen 18D, 752 36 Uppsala, Sweden
- Stroud Water Research Center, AvondalePennsylvania, 19311, United States
| | - Zhe Li
- Department
of Environmental Science (ACES), Stockholm
University, 10691 Stockholm, Sweden
| | - Silke Langenheder
- Department
of Ecology and Genetics/Limnology, Uppsala
University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Elena Gorokhova
- Department
of Environmental Science (ACES), Stockholm
University, 10691 Stockholm, Sweden
| | - Anna Sobek
- Department
of Environmental Science (ACES), Stockholm
University, 10691 Stockholm, Sweden
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41
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Liang D, Ouyang Y, Tiemann L, Robertson GP. Niche Differentiation of Bacterial Versus Archaeal Soil Nitrifiers Induced by Ammonium Inhibition Along a Management Gradient. Front Microbiol 2020; 11:568588. [PMID: 33281763 PMCID: PMC7689314 DOI: 10.3389/fmicb.2020.568588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/12/2020] [Indexed: 01/08/2023] Open
Abstract
Soil nitrification, mediated mainly by ammonia oxidizing archaea (AOA) and bacteria (AOB), converts ammonium (NH4+) to nitrite (NO2−) and thence nitrate (NO3−). To better understand ecological differences between AOA and AOB, we investigated the nitrification kinetics of AOA and AOB under eight replicated cropped and unmanaged ecosystems (including two fertilized natural systems) along a long-term management intensity gradient in the upper U.S. Midwest. For five of eight ecosystems, AOB but not AOA exhibited Haldane kinetics (inhibited by high NH4+ additions), especially in perennial and successional systems. In contrast, AOA predominantly exhibited Michaelis-Menten kinetics, suggesting greater resistance to high nitrogen inputs than AOB. These responses suggest the potential for NH4+-induced niche differentiation between AOA and AOB. Additionally, long-term fertilization significantly enhanced maximum nitrification rates (Vmax) in the early successional systems for both AOA and AOB, but not in the deciduous forest systems. This was likely due to pH suppression of nitrification in the acidic forest soils, corroborated by a positive correlation of Vmax with soil pH but not with amoA gene abundance. Results also demonstrated that soil nitrification potentials were relatively stable, as there were no seasonal differences. Overall, results suggest that (1) NH4+ inhibition of AOB but not AOA could be another factor contributing to niche differentiation between AOA and AOB in soil, and (2) nitrification by both AOA and AOB can be significantly promoted by long-term nitrogen inputs.
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Affiliation(s)
- Di Liang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States.,W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
| | - Yang Ouyang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - Lisa Tiemann
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - G Philip Robertson
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States.,W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
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Albright MBN, Johansen R, Thompson J, Lopez D, Gallegos-Graves LV, Kroeger ME, Runde A, Mueller RC, Washburne A, Munsky B, Yoshida T, Dunbar J. Soil Bacterial and Fungal Richness Forecast Patterns of Early Pine Litter Decomposition. Front Microbiol 2020; 11:542220. [PMID: 33240225 PMCID: PMC7677502 DOI: 10.3389/fmicb.2020.542220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022] Open
Abstract
Discovering widespread microbial processes that drive unexpected variation in carbon cycling may improve modeling and management of soil carbon (Prescott, 2010; Wieder et al., 2015a, 2018). A first step is to identify community features linked to carbon cycle variation. We addressed this challenge using an epidemiological approach with 206 soil communities decomposing Ponderosa pine litter in 618 microcosms. Carbon flow from litter decomposition was measured over a 6-week incubation. Cumulative CO2 from microbial respiration varied two-fold among microcosms and dissolved organic carbon (DOC) from litter decomposition varied five-fold, demonstrating large functional variation despite constant environmental conditions where strong selection is expected. To investigate microbial features driving DOC concentration, two microbial community cohorts were delineated as "high" and "low" DOC. For each cohort, communities from the original soils and from the final microcosm communities after the 6-week incubation with litter were taxonomically profiled. A logistic model including total biomass, fungal richness, and bacterial richness measured in the original soils or in the final microcosm communities predicted the DOC cohort with 72 (P < 0.05) and 80 (P < 0.001) percent accuracy, respectively. The strongest predictors of the DOC cohort were biomass and either fungal richness (in the original soils) or bacterial richness (in the final microcosm communities). Successful forecasting of functional patterns after lengthy community succession in a new environment reveals strong historical contingencies. Forecasting future community function is a key advance beyond correlation of functional variance with end-state community features. The importance of taxon richness-the same feature linked to carbon fate in gut microbiome studies-underscores the need for increased understanding of biotic mechanisms that can shape richness in microbial communities independent of physicochemical conditions.
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Affiliation(s)
| | - Renee Johansen
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Deanna Lopez
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Marie E. Kroeger
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Andreas Runde
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Rebecca C. Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Alex Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Thomas Yoshida
- Chemical Diagnostics and Engineering, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - John Dunbar
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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Biological invasions alter environmental microbiomes: A meta-analysis. PLoS One 2020; 15:e0240996. [PMID: 33091062 PMCID: PMC7580985 DOI: 10.1371/journal.pone.0240996] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Biological invasions impact both agricultural and natural systems. The damage can be quantified in terms of both economic loss and reduction of biodiversity. Although the literature is quite rich about the impact of invasive species on plant and animal communities, their impact on environmental microbiomes is underexplored. Here, we re-analyze publicly available data using a common framework to create a global synthesis of the effects of biological invasions on environmental microbial communities. Our findings suggest that non-native species are responsible for the loss of microbial diversity and shifts in the structure of microbial populations. Therefore, the impact of biological invasions on native ecosystems might be more pervasive than previously thought, influencing both macro- and micro-biomes. We also identified gaps in the literature which encourage research on a wider variety of environments and invaders, and the influence of invaders across seasons and geographical ranges.
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44
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Avila-Jimenez ML, Burns G, He Z, Zhou J, Hodson A, Avila-Jimenez JL, Pearce D. Functional Associations and Resilience in Microbial Communities. Microorganisms 2020; 8:microorganisms8060951. [PMID: 32599781 PMCID: PMC7357002 DOI: 10.3390/microorganisms8060951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022] Open
Abstract
Microbial communities have inherently high levels of metabolic flexibility and functional redundancy, yet the structure of microbial communities can change rapidly with environmental perturbation. To understand whether such changes observed at the taxonomic level translate into differences at the functional level, we analyzed the structure of taxonomic and functional gene distribution across Arctic and Antarctic locations. Taxonomic diversity (in terms of alpha diversity and species richness) differed significantly with location. However, we found that functional genes distributed evenly across bacterial networks and that this functional distribution was also even across different geographic locations. For example, on average 15% of the functional genes were related to carbon cycling across all bacterial networks, slightly over 21% of the genes were stress-related and only 0.5% of the genes were linked to carbon degradation functions. In such a distribution, each bacterial network includes all of the functional groups distributed following the same proportions. However, the total number of functional genes that is included in each bacterial network differs, with some clusters including many more genes than others. We found that the proportion of times a specific gene must occur to be linked to a specific cluster is 8%, meaning the relationship between the total number of genes in the cluster and the number of genes per function follows a linear pattern: smaller clusters require a gene to appear less frequently to get fixed within the cluster, while larger clusters require higher gene frequencies. We suggest that this mechanism of functional association between equally rare or equally abundant genes could have implications for ecological resilience, as non-dominant genes also associate in fully functioning ecological networks, potentially suggesting that there are always pre-existing functional networks available to exploit new ecological niches (where they can become dominant) as they emerge; for example, in the case of rapid or sudden environmental change. Furthermore, this pattern did not correlate with taxonomic distribution, suggesting that bacteria associate based on functionality and this is independent of its taxonomic position. Our analyses based on ecological networks also showed no clear evidence of recent environmental impact on polar marine microbial communities at the functional level, unless all communities analyzed have changed exactly in the same direction and intensity, which is unlikely given we are comparing areas changing at different rates.
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Affiliation(s)
| | - Gavin Burns
- British Antarctic Survey, Cambridge CB3 0ET, UK;
| | - Zhili He
- Department of Microbiology and Plant Science, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA; (Z.H.); (J.Z.)
- Environmental Microbiomics Research Center and School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Science, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA; (Z.H.); (J.Z.)
| | - Andrew Hodson
- Geology Department, University Centre in Svalbard, 9171 Longyearbyen, Norway;
- Department of Environmental Sciences, Western Norway University of Applied Sciences, Røyrgata 6, N-6856 Sogndal, Norway
| | - Jose-Luis Avila-Jimenez
- Department of Informatics and Numerical Analysis, University of Cordoba, Campus Universitario de Rabanales, Carretera Nacional IV, Km. 396. C.P. 14014 Cordoba, Spain;
| | - David Pearce
- British Antarctic Survey, Cambridge CB3 0ET, UK;
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle (UK), Ellison Building, Northumberland Road, Newcastle-upon-Tyne NE1 8ST, UK
- Correspondence:
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45
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Meyer KM, Hopple AM, Klein AM, Morris AH, Bridgham SD, Bohannan BJM. Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function. Mol Ecol 2020; 29:1806-1819. [PMID: 32285532 DOI: 10.1111/mec.15442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 02/28/2020] [Accepted: 04/02/2020] [Indexed: 11/30/2022]
Abstract
Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4 )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4 oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.
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Affiliation(s)
- Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Anya M Hopple
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ann M Klein
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Andrew H Morris
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Scott D Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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46
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Mayr MJ, Besemer K, Sieczko A, Demeter K, Peduzzi P. Bacterial community composition and function along spatiotemporal connectivity gradients in the Danube floodplain (Vienna, Austria). AQUATIC SCIENCES 2020; 82:28. [PMID: 32165802 PMCID: PMC7045780 DOI: 10.1007/s00027-020-0700-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 01/02/2020] [Indexed: 05/25/2023]
Abstract
It is well recognized that river-floodplain systems contribute significantly to riverine ecosystem metabolism, and that bacteria are key players in the aquatic organic carbon cycle, but surprisingly few studies have linked bacterial community composition (BCC), function and carbon quality in these hydrologically highly dynamic habitats. We investigated aquatic BCC and extracellular enzymatic activity (EEA) related to dissolved organic carbon quality and algae composition, including the impact of a major flood event in one of the last remaining European semi-natural floodplain-systems. We found that surface connectivity of floodplain pools homogenizes BCC and EEA, whereas low connectivity led to increased BCC and EEA heterogeneity, supported by their relationship to electrical conductivity, an excellent indicator for surface connection strength. Hydrogeochemical parameters best explained variation of both BCC and EEA, while the algal community and chromophoric DOM properties explained only minor fractions of BCC variation. We conclude that intermittent surface connectivity and especially permanent isolation of floodplain pools from the main river channel may severely alter BCC and EEA, with potential consequences for nutrient cycling, ecological services and greenhouse gas emissions. Disentangling microbial structure-function coupling is therefore crucial, if we are to understand and predict the consequences of human alterations on these dynamic systems.
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Affiliation(s)
- Magdalena J. Mayr
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
| | - Katharina Besemer
- WasserCluster Lunz, Dr. Carl Kupelwieser Promenade 5, 3293 Lunz Am See, Austria
| | - Anna Sieczko
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
- Department of Thematic Studies–Environmental Change, Linköping University, Tema M, Campus Valla, 581 83 Linköping, Sweden
| | - Katalin Demeter
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
| | - Peter Peduzzi
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
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47
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Isobe K, Ise Y, Kato H, Oda T, Vincenot CE, Koba K, Tateno R, Senoo K, Ohte N. Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers. THE ISME JOURNAL 2020; 14:12-25. [PMID: 31481743 PMCID: PMC6908637 DOI: 10.1038/s41396-019-0500-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/06/2019] [Accepted: 08/14/2019] [Indexed: 11/09/2022]
Abstract
We tested the ecosystem functions of microbial diversity with a focus on ammonification (involving diverse microbial taxa) and nitrification (involving only specialized microbial taxa) in forest nitrogen cycling. This study was conducted on a forest slope, in which the soil environment and plant growth gradually changed. We measured the gross and net rates of ammonification and nitrification, the abundance of predicted ammonifiers and nitrifiers, and their community compositions in the soils. The abundance of predicted ammonifiers did not change along the soil environmental gradient, leading to no significant change in the gross ammonification rate. On the other hand, the abundance of nitrifiers and the gross nitrification rate gradually changed. These accordingly determined the spatial distribution of net accumulation of ammonium and nitrate available to plants. The community composition of predicted ammonifiers gradually changed along the slope, implying that diverse ammonifiers were more likely to include taxa that were acclimated to the soil environment and performed ammonification at different slope locations than specialized nitrifiers. Our findings suggest that the abundance of ammonifiers and nitrifiers directly affects the corresponding nitrogen transformation rates, and that their diversity affects the stability of the rates against environmental changes. This study highlights the role of microbial diversity in biogeochemical processes under changing environments and plant growth.
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Affiliation(s)
- Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Yuta Ise
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyu Kato
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomoki Oda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Keisuke Koba
- Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Ryunosuke Tateno
- Field Science Education and Research Center, Kyoto University, Kyoto, Japan
| | - Keishi Senoo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Ohte
- Graduate School of Informatics, Kyoto University, Kyoto, Japan
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48
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Ansari AF, Acharya NIS, Kumaran S, Ravindra K, Reddy YBS, Dixit NM, Raut J. 110th Anniversary: High-Order Interactions Can Eclipse Pairwise Interactions in Shaping the Structure of Microbial Communities. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b03190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aamir Faisal Ansari
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | | | | | | | | | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Janhavi Raut
- Unilever R&D India Pvt, Ltd., Bangalore 560066, India
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49
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Reis PCJ, Thottathil SD, Ruiz-González C, Prairie YT. Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates. Environ Microbiol 2019; 22:738-751. [PMID: 31769176 DOI: 10.1111/1462-2920.14877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/23/2019] [Accepted: 11/22/2019] [Indexed: 11/30/2022]
Abstract
Lake methane (CH4 ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha- and Gammaproteobacteria (Alpha- and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH4 oxidation rates. We found a clear niche separation of Alpha- and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH4 oxidation rates in lakes and that information on the MOB community can help predict CH4 oxidation rates and thus emissions from lakes.
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Affiliation(s)
- Paula C J Reis
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Shoji D Thottathil
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), Barcelona, E-08003, Spain
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
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50
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Predicting Microbial Species in a River Based on Physicochemical Properties by Bio-Inspired Metaheuristic Optimized Machine Learning. SUSTAINABILITY 2019. [DOI: 10.3390/su11246889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The main goal of the analysis of microbial ecology is to understand the relationship between Earth’s microbial community and their functions in the environment. This paper presents a proof-of-concept research to develop a bioclimatic modeling approach that leverages artificial intelligence techniques to identify the microbial species in a river as a function of physicochemical parameters. Feature reduction and selection are both utilized in the data preprocessing owing to the scarce of available data points collected and missing values of physicochemical attributes from a river in Southeast China. A bio-inspired metaheuristic optimized machine learner, which supports the adjustment to the multiple-output prediction form, is used in bioclimatic modeling. The accuracy of prediction and applicability of the model can help microbiologists and ecologists in quantifying the predicted microbial species for further experimental planning with minimal expenditure, which is become one of the most serious issues when facing dramatic changes of environmental conditions caused by global warming. This work demonstrates a neoteric approach for potential use in predicting preliminary microbial structures in the environment.
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