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Wang M, Zhang W, Dong Z, Yang Z, Zhao J, Guo X. Distinct mediating patterns between metal filtering and species coexistence of rare and abundant subcommunities in heavily polluted river sediments. ENVIRONMENT INTERNATIONAL 2023; 172:107747. [PMID: 36693298 DOI: 10.1016/j.envint.2023.107747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/21/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
It is unknown how anthropogenic pollutants released into freshwater ecosystems affect the assembly processes of microbial communities in river sediment. We used high-throughput sequencing to examine the assembly of rare and abundant subcommunities in a heavily polluted urban river: the Beiyun River in Beijing, China. Although deterministic processes overrode stochastic processes in shaping local rare and abundant subcommunities, there were distinctly different assembly mechanisms of rare and abundant subcommunities. Rare subcommunity assembly was governed more by interspecificinteractions, and environmental selection and dispersal limitation explained only a small fraction of the variation. However, both factors seemed to govern the assembly of abundant subcommunities. Our results implied that microbial co-occurrence associations tended to be higher when rare subcommunities were less driven by community assembly, and that these associations tended to be lower when abundant subcommunities were more driven by community assembly. A balance between the community assembly and species coexistence was exhibited atthesubcommunitylevel. Importantly, we tried to disentangle the assembly process of abundant subcommunities into introduction and colonization processes characterized by the presence/absence and relative abundance datasets. Interestingly, metals explained the highest percentage of spatial variation in the species introduction process. By affecting nutrient availability, metals also shaped the abundant subcommunity in the species colonization process, but this did not surpass nutrient availability. Therefore, disentangling the introduction and colonization processes enhances our understanding of the assembly mechanisms of microbial communities in heavily polluted running water ecosystems at fine geographical scales.
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Affiliation(s)
- Min Wang
- College of Resources Environment and Tourism, Capital Normal University, Beijing 100048, PR China
| | - Wei Zhang
- College of Resources Environment and Tourism, Capital Normal University, Beijing 100048, PR China
| | - Zhi Dong
- School of Life Sciences, Peking University, Beijing 100871, PR China
| | - Zirou Yang
- College of Resources Environment and Tourism, Capital Normal University, Beijing 100048, PR China
| | - Junying Zhao
- College of Resources Environment and Tourism, Capital Normal University, Beijing 100048, PR China
| | - Xiaoyu Guo
- College of Resources Environment and Tourism, Capital Normal University, Beijing 100048, PR China.
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2
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Alkatheri AH, Yap PSX, Abushelaibi A, Lai KS, Cheng WH, Erin Lim SH. Microbial Genomics: Innovative Targets and Mechanisms. Antibiotics (Basel) 2023; 12:antibiotics12020190. [PMID: 36830101 PMCID: PMC9951906 DOI: 10.3390/antibiotics12020190] [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: 10/18/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Multidrug resistance (MDR) has become an increasing threat to global health because bacteria can develop resistance to antibiotics over time. Scientists worldwide are searching for new approaches that go beyond traditional antibiotic discovery and development pipelines. Advances in genomics, however, opened up an unexplored therapeutic opportunity for the discovery of new antibacterial agents. Genomic approaches have been used to discover several novel antibiotics that target critical processes for bacterial growth and survival, including histidine kinases (HKs), LpxC, FabI, peptide deformylase (PDF), and aminoacyl-tRNA synthetases (AaRS). In this review, we will discuss the use of microbial genomics in the search for innovative and promising drug targets as well as the mechanisms of action for novel antimicrobial agents. We will also discuss future directions on how the utilization of the microbial genomics approach could improve the odds of antibiotic development having a more successful outcome.
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Affiliation(s)
- Asma Hussain Alkatheri
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Polly Soo-Xi Yap
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor 47500, Malaysia
| | - Aisha Abushelaibi
- Office of Campus Director, Abu Dhabi Colleges, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Wan-Hee Cheng
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana BBN, Nilai 71800, Malaysia
| | - Swee-Hua Erin Lim
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
- Correspondence:
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3
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DePoy AN, King GM. Distribution and diversity of anaerobic thermophiles and putative anaerobic nickel-dependent carbon monoxide-oxidizing thermophiles in mesothermal soils and sediments. Front Microbiol 2023; 13:1096186. [PMID: 36699584 PMCID: PMC9868602 DOI: 10.3389/fmicb.2022.1096186] [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: 11/11/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Even though thermophiles are best known from geothermal and other heated systems, numerous studies have demonstrated that they occur ubiquitously in mesothermal and permanently cold soils and sediments. Cultivation based studies of the latter have revealed that the thermophiles within them are mostly spore-forming members of the Firmicutes. Since the geographic distribution of spores is presumably unconstrained by transport through the atmosphere, similar communities (composition and diversity) of thermophiles might be expected to emerge in mesothermal habitats after they are heated. Alternatively, thermophiles might experience environmental selection before or after heating leading to divergent communities. After demonstrating the ubiquity of anaerobic thermophiles and CO uptake in a variety of mesothermal habitats and two hot springs, we used high throughput sequencing of 16S rRNA genes to assess the composition and diversity of populations that emerged after incubation at 60°C with or without headspace CO concentrations of 25%. Anaerobic Firmicutes dominated relative abundances at most sites but anaerobic thermophilic members of the Acidobacteria and Proteobacteria were also common. Nonetheless, compositions at the amplicon sequence variant (ASV) level varied among the sites with no convergence resulting from heating or CO addition as indicated by beta diversity analyses. The distinctions among thermophilic communities paralleled patterns observed for unheated "time zero" mesothermal soils and sediments. Occupancy analyses showed that the number of ASVs occupying each of n sites decreased unimodally with increasing n; no ASV occupied all 14 sites and only one each occupied 11 and 12 sites, while 69.3% of 1873 ASVs occupied just one site. Nonetheless, considerations of distances among the sites occupied by individual ASVs along with details of their distributions indicated that taxa were not dispersal limited but rather were constrained by environmental selection. This conclusion was supported by βMNTD and βNTI analyses, which showed dispersal limitation was only a minor contributor to taxon distributions.
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4
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Châtillon E, Duran R, Rigal F, Cagnon C, Cébron A, Cravo-Laureau C. New insights into microbial community coalescence in the land-sea continuum. Microbiol Res 2022; 267:127259. [PMID: 36436444 DOI: 10.1016/j.micres.2022.127259] [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: 05/13/2022] [Revised: 10/30/2022] [Accepted: 11/13/2022] [Indexed: 11/23/2022]
Abstract
The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment.
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Affiliation(s)
- Elise Châtillon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - François Rigal
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France
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5
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Macroecological distributions of gene variants highlight the functional organization of soil microbial systems. THE ISME JOURNAL 2022; 16:726-737. [PMID: 34580430 PMCID: PMC8857198 DOI: 10.1038/s41396-021-01120-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.
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6
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Wang X, Reilly K, Heathcott R, Biswas A, Johnson LJ, Teasdale S, Grelet GA, Podolyan A, Gregorini P, Attwood GT, Palevich N, Morales SE. Soil Nitrogen Treatment Alters Microbiome Networks Across Farm Niches. Front Microbiol 2022; 12:786156. [PMID: 35237240 PMCID: PMC8882991 DOI: 10.3389/fmicb.2021.786156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/27/2021] [Indexed: 12/05/2022] Open
Abstract
Agriculture is fundamental for food production, and microbiomes support agriculture through multiple essential ecosystem services. Despite the importance of individual (i.e., niche specific) agricultural microbiomes, microbiome interactions across niches are not well-understood. To observe the linkages between nearby agricultural microbiomes, multiple approaches (16S, 18S, and ITS) were used to inspect a broad coverage of niche microbiomes. Here we examined agricultural microbiome responses to 3 different nitrogen treatments (0, 150, and 300 kg/ha/yr) in soil and tracked linked responses in other neighbouring farm niches (rumen, faecal, white clover leaf, white clover root, rye grass leaf, and rye grass root). Nitrogen treatment had little impact on microbiome structure or composition across niches, but drastically reduced the microbiome network connectivity in soil. Networks of 16S microbiomes were the most sensitive to nitrogen treatment across amplicons, where ITS microbiome networks were the least responsive. Nitrogen enrichment in soil altered soil and the neighbouring microbiome networks, supporting our hypotheses that nitrogen treatment in soil altered microbiomes in soil and in nearby niches. This suggested that agricultural microbiomes across farm niches are ecologically interactive. Therefore, knock-on effects on neighbouring niches should be considered when management is applied to a single agricultural niche.
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Affiliation(s)
- XinYue Wang
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Kerri Reilly
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Rosemary Heathcott
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Ambarish Biswas
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Linda J. Johnson
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Suliana Teasdale
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | | | | | - Pablo Gregorini
- Department of Agricultural Science, Lincoln University, Lincoln, New Zealand
| | - Graeme T. Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Nikola Palevich
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Sergio E. Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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7
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Westmeijer G, Mehrshad M, Turner S, Alakangas L, Sachpazidou V, Bunse C, Pinhassi J, Ketzer M, Åström M, Bertilsson S, Dopson M. Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities. Commun Biol 2022; 5:37. [PMID: 35017653 PMCID: PMC8752596 DOI: 10.1038/s42003-021-02980-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/15/2021] [Indexed: 12/20/2022] Open
Abstract
The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the Äspö Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions. Westmeijer et al. employ high-throughput sequencing to investigate the connection between deep biosphere groundwaters and surface microbial communities. They suggest that the microbial communities of deep biosphere groundwaters in the Fennoscandian Shield are mostly comprised of autochthonous species, rather than migratory surface representatives.
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Affiliation(s)
- George Westmeijer
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden.
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75 007, Uppsala, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
| | - Linda Alakangas
- Swedish Nuclear Fuel and Waste Management Co (SKB), 57 229, Oskarshamn, Sweden
| | - Varvara Sachpazidou
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden.,Helmholtz-Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
| | - Marcelo Ketzer
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Mats Åström
- Department of Biology and Environmental Sciences, Linnaeus University, 39 231, Kalmar, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75 007, Uppsala, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39 231, Kalmar, Sweden
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8
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Abstract
The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.
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9
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Yan Q, Deng J, Wang F, Liu Y, Liu K. Community Assembly and Co-occurrence Patterns Underlying the Core and Satellite Bacterial Sub-communities in the Tibetan Lakes. Front Microbiol 2021; 12:695465. [PMID: 34745022 PMCID: PMC8567192 DOI: 10.3389/fmicb.2021.695465] [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: 04/15/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial communities normally comprise a few core species and large numbers of satellite species. These two sub-communities have different ecological and functional roles in natural environments, but knowledge on the assembly processes and co-occurrence patterns of the core and satellite species in Tibetan lakes is still sparse. Here, we investigated the ecological processes and co-occurrence relationships of the core and satellite bacterial sub-communities in the Tibetan lakes via 454 sequencing of 16S rRNA gene. Our studies indicated that the core and satellite bacterial sub-communities have similar dominant phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). But the core sub-communities were less diverse and exhibited a stronger distance-decay relationship than the satellite sub-communities. In addition, topological properties of nodes in the network demonstrated that the core sub-communities had more complex and stable co-occurrence associations and were primarily driven by stochastic processes (58.19%). By contrast, the satellite sub-communities were mainly governed by deterministic processes (62.17%). Overall, this study demonstrated the differences in the core and satellite sub-community assembly and network stability, suggesting the importance of considering species traits to understand the biogeographic distribution of bacterial communities in high-altitude lakes.
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Affiliation(s)
- Qi Yan
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Jianming Deng
- School of Life Sciences, Lanzhou University, Lanzhou, China.,State Key Laboratory of Grassland and Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Feng Wang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China.,State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
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10
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Hugoni M, Nunan N, Thioulouse J, Dubost A, Abrouk D, Martins JMF, Goffner D, Prigent-Combaret C, Grundmann G. Small-Scale Variability in Bacterial Community Structure in Different Soil Types. MICROBIAL ECOLOGY 2021; 82:470-483. [PMID: 33443587 DOI: 10.1007/s00248-020-01660-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.
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Affiliation(s)
- Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France.
| | - Naoise Nunan
- Institute of Ecology and Environmental Sciences - Paris, CNRS - Sorbonne Université, 4 place Jussieu, 75005, Paris, France
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Jean Thioulouse
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Jean M F Martins
- Université Grenoble Alpes, CNRS, IRD, IGE UMR 5001, 38000, Grenoble, France
| | - Deborah Goffner
- Unité Mixte Internationale CNRS 3189 « Environment, Health and Societies », Faculté de Médecine, 51 Bd Pierre Dramard, 13344, Marseille, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Geneviève Grundmann
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
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11
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Jeong SY, Kim TG. Spatial Variance of Species Distribution Predicts the Interspecies Interactions within a Microbial Metacommunity. MICROBIAL ECOLOGY 2021; 81:549-552. [PMID: 32948906 DOI: 10.1007/s00248-020-01603-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Interspecies interactions have a profound influence on spatial distribution of coexisting microbial species. We explored whether spatial variance of species distribution (SVSD) predicts the degree of interspecies interactions within a microbial metacommunity. Simulations were used to determine the relationships from random, lake, soil, and biofilm metacommunity datasets (1,000 times). All of the bacterial datasets showed a negative correlation between the habitat breadth (inverse to SVSD) and the numbers of total, positive, and negative interspecies interactions (P < 0.05); the only exception was the relationship between habitat breadth and negative interactions in the biofilm dataset. The random dataset had no significant relationships (P > 0.05). We repeated the simulations to determine the degree of correlation and reproducibility (100 times). Habitat breadth was negatively correlated with the total and positive interactions in all of the real datasets (P < 0.05), and the negative relationships persisted across repetitions. Despite variability in the slope of total interactions, the slope values of positive interactions were similar for the real datasets (- 19.9, - 19.2, and - 25.8 for lake, soil, and biofilm, respectively). In conclusion, our results demonstrate the patterns of species interaction-distribution and show that interspecies interactions are positively correlated with the SVSD.
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Affiliation(s)
- So-Yeon Jeong
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea
| | - Tae Gwan Kim
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea.
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12
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Mateus-Barros E, de Melo ML, Bagatini IL, Caliman A, Sarmento H. Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria. MICROBIAL ECOLOGY 2021; 81:26-35. [PMID: 32705311 DOI: 10.1007/s00248-020-01560-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Species prevalence across the landscape is related to their local abundance, which is a result of deterministic and stochastic processes that select organisms capable of recolonizing sites where they were once extinct, a process known as the rescue effect. The occupancy-frequency distribution (OFD) describes these patterns and has been extensively used to understand organism's distribution but has been poorly tested on microorganisms. In order to test OFD on freshwater bacteria, we collected data from 60 shallow lakes distributed across a wide area in southeastern Brazil, to determine the bacterial operational taxonomic units (OTUs) that were present in all sites (core) and at only one site (satellite). Then, we analyzed the spatial abundance distributions of individual OTUs to understand the influence of local abundances on regional occupancy patterns. Finally, we tested the environmental factors that influenced occupancy and abundance. We found a significant bimodal OFD for freshwater bacteria using both OTUs (97% clustering) and amplicon sequence variants (ASVs, unique sequences), with 13 core OTUs and 1169 satellite OTUs, but only three core ASVs. Core organisms had a bimodal or gamma abundance distribution. The main driver of the core community was pH, while nutrients were key when the core community was excluded and the rest of the community (mild and satellite taxa) was considered. This study demonstrates the close relationship between local environmental conditions and the abundance and dispersion of microorganisms, which shapes their distribution across the landscape.
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Affiliation(s)
- Erick Mateus-Barros
- Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil.
- Post Graduate Program in Ecology and Natural Resources (PPG-ERN), UFSCar, São Carlos, SP, 13565-905, Brazil.
| | - Michaela L de Melo
- Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
- Département Des Sciences Biologiques, Université du Québec à Montréal, Montreal, Canada
| | - Inessa L Bagatini
- Department of Botany, Laboratory of Phycology, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Adriano Caliman
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-900, Brazil
| | - Hugo Sarmento
- Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, Federal University of São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
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13
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Jeong SY, Choi JY, Kim TG. Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake. MICROBIAL ECOLOGY 2020; 79:801-814. [PMID: 31705158 DOI: 10.1007/s00248-019-01453-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Freshwater planktonic communities comprise a tremendous diversity of microorganisms. This study investigated the distribution patterns of microbial kingdoms (bacteria, fungi, protists, and microbial metazoans) within a lake ecosystem. Water samples were collected from 50 sites along the shoreline in a lake during an early eutrophication period, and MiSeq sequencing was performed with different marker genes. Metacommunity analyses revealed a bimodal occupancy-frequency distribution and a Clementsian gradient persisting throughout all microbial kingdoms, suggesting similar regional processes in all kingdoms. Variation partitioning revealed that environmental characteristics, macrophyte/macroinvertebrate composition, space coordinates, and distance-based Moran's eigenvector maps (dbMEM) together could explain up to 29% of the community variances in microbial kingdoms. Kingdom synchrony results showed strong couplings between kingdoms (R2 ≥ 0.31), except between Fungi and Metazoa (R2 = 0.09). Another variation partitioning revealed that microbial kingdoms could well explain their community variances up to 73%. Interestingly, the kingdom Protista was best synchronized with the other kingdoms. A correlation network showed that positive associations between kingdoms outnumbered the negative ones and that the kingdom Protista acted as a hub among kingdoms. Module analysis showed that network modules included multi-kingdom associations that were prevalent. Our findings suggest that protists coordinate community assembly and distribution of other kingdoms, and inter-kingdom interactions are a key determinant in shaping their community structures in a freshwater lake.
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Affiliation(s)
- So-Yeon Jeong
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea
| | - Jong-Yun Choi
- Division of Ecological Assessment, National Institute of Ecology, Seocheon, Choongnam, 33657, South Korea
| | - Tae Gwan Kim
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea.
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14
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Metagenomics Uncovers a Core SAR11 Population in Brackish Surface Waters of the Baltic Sea. WATER 2020. [DOI: 10.3390/w12020501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Baltic Sea represents one of the largest brackish ecosystems where various environmental factors control dynamic seasonal shifts in the structure, diversity, and function of the planktonic microbial communities. In this study, despite seasonal fluctuations, several bacterial populations (<2% of the total OTUs) that are highly dominant (25% of relative abundance) and highly frequently occurring (>85% of occurrence) over four seasons were identified. Mathematical models using occurrence frequency and relative abundance data were able to describe community assembly persisting over time. Further, this work uncovered one of the core bacterial populations phylogenetically affiliated to SAR11 subclade IIIa. The analysis of the hypervariable region of 16S rRNA gene and single copy housekeeping genes recovered from metagenomic datasets suggested that the population was unexpectedly evolutionarily closely related to those inhabiting a mesosaline lacustrine ecosystem rather than other marine/coastal members. Our metagenomic results further revealed that the newly-identified population was the major driver facilitating the seasonal shifts in the overall community structure over the brackish waters of the Baltic Sea. The core community uncovered in this study supports the presence of a brackish water microbiome distinguishable from other marine and freshwater counterparts and will be a useful sentinel for monitoring local/global environmental changes posed on brackish surface waters.
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15
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Carvalho S, Aylagas E, Villalobos R, Kattan Y, Berumen M, Pearman JK. Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome. Proc Biol Sci 2020; 286:20182697. [PMID: 30963940 PMCID: PMC6408595 DOI: 10.1098/rspb.2018.2697] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In an era of coral reef degradation, our knowledge of ecological patterns in reefs is biased towards large conspicuous organisms. The majority of biodiversity, however, inhabits small cryptic spaces within the framework of the reef. To assess this biodiverse community, which we term the ‘reef cryptobiome’, we deployed 87 autonomous reef monitoring structures (ARMS), on 22 reefs across 16 degrees latitude of the Red Sea. Combining ARMS with metabarcoding of the mitochondrial cytochrome oxidase I gene, we reveal a rich community, including the identification of 14 metazoan phyla within 10 416 operational taxonomic units (OTUs). While mobile and sessile subsets were similarly structured along the basin, the main environmental driver was different (particulate organic matter and sea surface temperature, respectively). Distribution patterns of OTUs showed that only 1.5% were present in all reefs, while over half were present in a single reef. On both local and regional scales, the majority of OTUs were rare. The high heterogeneity in community patterns of the reef cryptobiome has implications for reef conservation. Understanding the biodiversity patterns of this critical component of reef functioning will enable a sound knowledge of how coral reefs will respond to future anthropogenic impacts.
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Affiliation(s)
- Susana Carvalho
- 1 Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Eva Aylagas
- 1 Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Rodrigo Villalobos
- 1 Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Yasser Kattan
- 2 Environmental Protection Department , Saudi Aramco, Dhahran 31311 , Saudi Arabia
| | - Michael Berumen
- 1 Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - John K Pearman
- 1 Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
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16
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Hou L, Hu A, Chen S, Zhang K, Orlić S, Rashid A, Yu CP. Deciphering the Assembly Processes of the Key Ecological Assemblages of Microbial Communities in Thirteen Full-Scale Wastewater Treatment Plants. Microbes Environ 2019; 34:169-179. [PMID: 30996148 PMCID: PMC6594736 DOI: 10.1264/jsme2.me18107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Limited information is currently available on the assembly processes (deterministic vs. stochastic) shaping the compositions of key microbial communities in activated sludge (AS). The relative importance of deterministic and stochastic processes for key bacterial and archaeal assemblages (i.e., core-satellite and habitat generalist-specialist) in AS from 13 wastewater treatment plants in China was investigated using 16S rDNA amplicon sequencing. The results obtained indicated 1,388 and 369 core operational taxonomic units (OTUs), 1,038 and 1,683 satellite OTUs, 255 and 48 habitat generalist OTUs, and 192 and 111 habitat specialist OTUs for Bacteria and Archaea, respectively. The proportions of shared OTUs between core and habitat specialist communities were similar to or higher than those between core and habitat generalist communities, suggesting a stronger inter-linkage between the former two groups. Deterministic processes, indicated by abundance-based β-null models, were responsible for shaping core communities, in which NH4-N, OrgC/OrgN, Cr, and Ni were the main controlling factors. In contrast, satellite communities were predominantly influenced by stochastic processes. Moreover, we found that deterministic and stochastic processes were mainly responsible for shaping the assembly of habitat specialists and generalists, respectively. However, the influence of deterministic factors on habitat specialists remains unclear. The present study provides novel insights into the assembly mechanisms of AS microbial communities.
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Affiliation(s)
- Liyuan Hou
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences.,Department of Civil and Environmental Engineering, University of Missouri
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences
| | - Shaohua Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences
| | - Kaisong Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences
| | - Sandi Orlić
- Ruđer Bošković Institute.,Center of Excellence for Science and Technology-integration of Mediterranean region- STIM
| | - Azhar Rashid
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences.,Nuclear Institute for Food and Agriculture
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences.,Graduate Institute of Environmental Engineering, National Taiwan University
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17
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Bunse C, Israelsson S, Baltar F, Bertos-Fortis M, Fridolfsson E, Legrand C, Lindehoff E, Lindh MV, Martínez-García S, Pinhassi J. High Frequency Multi-Year Variability in Baltic Sea Microbial Plankton Stocks and Activities. Front Microbiol 2019; 9:3296. [PMID: 30705671 PMCID: PMC6345115 DOI: 10.3389/fmicb.2018.03296] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/18/2018] [Indexed: 11/17/2022] Open
Abstract
Marine bacterioplankton are essential in global nutrient cycling and organic matter turnover. Time-series analyses, often at monthly sampling frequencies, have established the paramount role of abiotic and biotic variables in structuring bacterioplankton communities and productivities. However, fine-scale seasonal microbial activities, and underlying biological principles, are not fully understood. We report results from four consecutive years of high-frequency time-series sampling in the Baltic Proper. Pronounced temporal dynamics in most investigated microbial variables were observed, including bacterial heterotrophic production, plankton biomass, extracellular enzyme activities, substrate uptake rate constants of glucose, pyruvate, acetate, amino acids, and leucine, as well as nutrient limitation bioassays. Spring blooms consisting of diatoms and dinoflagellates were followed by elevated bacterial heterotrophic production and abundances. During summer, bacterial productivity estimates increased even further, coinciding with an initial cyanobacterial bloom in early July. However, bacterial abundances only increased following a second cyanobacterial bloom, peaking in August. Uptake rate constants for the different measured carbon compounds varied seasonally and inter-annually and were highly correlated to bacterial productivity estimates, temperature, and cyanobacterial abundances. Further, we detected nutrient limitation in response to environmental conditions in a multitude of microbial variables, such as elevated productivities in nutrient bioassays, changes in enzymatic activities, or substrate preferences. Variations among biotic variables often occurred on time scales of days to a few weeks, yet often spanning several sampling occasions. Such dynamics might not have been captured by sampling at monthly intervals, as compared to more predictable transitions in abiotic variables such as temperature or nutrient concentrations. Our study indicates that high resolution analyses of microbial biomass and productivity parameters can help out in the development of biogeochemical and food web models disentangling the microbial black box.
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Affiliation(s)
- Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Stina Israelsson
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Mireia Bertos-Fortis
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Emil Fridolfsson
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Elin Lindehoff
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Markus V Lindh
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Sandra Martínez-García
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
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18
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Hu A, Wang H, Yang X, Hou L, Li J, Li S, Yu CP. Seasonal and spatial variations of prokaryoplankton communities in a salinity-influenced watershed, China. FEMS Microbiol Ecol 2017; 93:3966710. [DOI: 10.1093/femsec/fix093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/11/2017] [Indexed: 12/17/2022] Open
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19
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Gibbons SM. Metapopulation theory provides new insight into microbial biogeography. Environ Microbiol 2017; 19:849-850. [PMID: 28217960 DOI: 10.1111/1462-2920.13702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sean M Gibbons
- Department of Biological Engineering, MIT, Cambridge, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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