1
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Zhao Z, Wang Y, Wei Y, Peng G, Wei T, He J, Li R, Wang Y. Distinctive patterns of bacterial community succession in the riverine micro-plastisphere in view of biofilm development and ecological niches. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135974. [PMID: 39341189 DOI: 10.1016/j.jhazmat.2024.135974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 09/20/2024] [Accepted: 09/25/2024] [Indexed: 09/30/2024]
Abstract
Exploring plastic bacterial community succession is a crucial step in analyzing and predicting the ecological assembly processes of the plastisphere and its associated environmental impacts. However, microbial biofilm development and niche differentiation during plastic bacterial community succession have rarely scarcely considered. Here, we assessed the differences between three microplastics (MPs) and two natural polymers in terms of biofilm development and niche properties during bacterial community succession, and identified a genus of MPs-degrading bacteria with strong competitive potential in the plastisphere. MPs biofilm development exhibits secondary succession characteristics, whereas natural polymer biofilms persist during the primary succession stage. During succession in plastic bacterial communities, the relationship between nutrient resources and microbial competition was reflected in a positive correlation between species competition and niche breadth, which contradicted the common belief that increased nutrient availability leads to reduced competition. Furthermore, the co-occurrence network revealed that specialists were species with greater competitive potential within the plastisphere. Additionally, the MPs-degrading Exiguobacterium genus represented a key taxon in the plastisphere. Our study provides a reliable pathway for revealing the specificity of plastic bacterial community succession from multiple perspectives and enhances the understanding of ecological assembly processes in the plastisphere.
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Affiliation(s)
- Zhen Zhao
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Yijin Wang
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Yihua Wei
- School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Gen Peng
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Tingyu Wei
- School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Jianqiao He
- Institute of Green and Low Carbon Technology, Guangxi Institute of Industrial Technology, Nanning 530004, China
| | - Ruilong Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China.
| | - Yinghui Wang
- Institute of Green and Low Carbon Technology, Guangxi Institute of Industrial Technology, Nanning 530004, China.
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2
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Loos D, Filho APDC, Dutilh BE, Barber AE, Panagiotou G. A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists. Cell Rep 2024; 43:114046. [PMID: 38581683 DOI: 10.1016/j.celrep.2024.114046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/22/2023] [Accepted: 03/19/2024] [Indexed: 04/08/2024] Open
Abstract
Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.
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Affiliation(s)
- Daniel Loos
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Ailton Pereira da Costa Filho
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Bas E Dutilh
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Institute of Biodiversity, Friedrich Schiller University, Jena, Germany; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Amelia E Barber
- Junior Research Group Fungal Informatics, Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany; Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
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3
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Wang Y, Jiao M, Zhao Z, Wang Y, Li T, Wei Y, Li R, Yang F. Insight into the role of niche concept in deciphering the ecological drivers of MPs-associated bacterial communities in mangrove forest. WATER RESEARCH 2024; 249:120995. [PMID: 38071907 DOI: 10.1016/j.watres.2023.120995] [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: 05/12/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
Myriad inherent and variable environmental features are controlling the assembly and succession of bacterial communities colonizing on mangrove microplastics (MPs). However, the mechanisms governing mangrove MPs-associated bacterial responses to environmental changes still remain unknown. Here, we assessed the dissimilarities of MPs-associated bacterial composition, diversity and functionality as well as quantified the niche variations of each taxon on plastispheres along river-mangrove-ocean and mangrove landward-to-seaward gradients in the Beibu Gulf, China, respectively. The bacterial richness and diversity as well as the niche breadth on mangrove sedimentary MPs dramatically decreased from landward to seaward regions. Characterizing the niche variations linked the difference of ecological drivers of MPs-associated bacterial populations and functions between river-mangrove-ocean (microplastic properties) and mangrove landward-to-seaward plastispheres (sediment physicochemical properties) to the trade-offs between selective stress exerted by inherent plastic substrates and microbial competitive stress imposed by environmental conditions. Notably, Rhodococcus erythropolis was predicted to be the generalist species and closely associated to biogeochemical cycles of mangrove plastispheres. Our work provides a reliable pathway for tackling the hidden mechanisms of environmental factors driving MPs-associated microbe from perspectives of niches and highlights the spatial dynamic variations of mangrove MPs-associated bacteria.
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Affiliation(s)
- Yijin Wang
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China; School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Meng Jiao
- School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Zhen Zhao
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Yinghui Wang
- Institute of Green and Low Carbon Technology, Guangxi Institute of Industrial Technology 16 Songxiang Road, Nanning 530004, China
| | - Tiezhu Li
- School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Yihua Wei
- School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Ruilong Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China.
| | - Fei Yang
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research of Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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4
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Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics. Front Microbiol 2023; 14:1261137. [PMID: 38033594 PMCID: PMC10684785 DOI: 10.3389/fmicb.2023.1261137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).
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Affiliation(s)
- Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Department of Ocean Science (OCES), The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Masato S. Abe
- Faculty of Culture and Information Science, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Masato Yamamichi
- Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yusuke Okazaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Alberto Canarini
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Keitaro Fukushima
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - E. Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
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5
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Vila JC, Goldford J, Estrela S, Bajic D, Sanchez-Gorostiaga A, Damian-Serrano A, Lu N, Marsland R, Rebolleda-Gomez M, Mehta P, Sanchez A. Metabolic similarity and the predictability of microbial community assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564019. [PMID: 37961608 PMCID: PMC10634833 DOI: 10.1101/2023.10.25.564019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
When microbial communities form, their composition is shaped by selective pressures imposed by the environment. Can we predict which communities will assemble under different environmental conditions? Here, we hypothesize that quantitative similarities in metabolic traits across metabolically similar environments lead to predictable similarities in community composition. To that end, we measured the growth rate and by-product profile of a library of proteobacterial strains in a large number of single nutrient environments. We found that growth rates and secretion profiles were positively correlated across environments when the supplied substrate was metabolically similar. By analyzing hundreds of in-vitro communities experimentally assembled in an array of different synthetic environments, we then show that metabolically similar substrates select for taxonomically similar communities. These findings lead us to propose and then validate a comparative approach for quantitatively predicting the effects of novel substrates on the composition of complex microbial consortia.
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Affiliation(s)
- Jean C.C. Vila
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joshua Goldford
- Division of Geophysical and Planetary sciences,California Institute of Technology, Pasadena, CA, USA
| | - Sylvie Estrela
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Djordje Bajic
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Section of Industrial Microbiology, Department of Biotechnology, Technical University Delft, Delft, The Netherlands
| | - Alicia Sanchez-Gorostiaga
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Alcalá de Henares, Spain
| | - Alejandro Damian-Serrano
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Department of Biology, University of Oregon, Eugene, OR, USA
| | - Nanxi Lu
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Robert Marsland
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Maria Rebolleda-Gomez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
| | - Pankaj Mehta
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Alvaro Sanchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbial Biotechnology, National Center for Biotechnology CNB-CSIC; Madrid, Spain
- New address: Institute of Functional Biology & Genomics IBFG, CSIC & University of Salamanca; Salamanca, Spain
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6
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Malard LA, Guisan A. Into the microbial niche. Trends Ecol Evol 2023; 38:936-945. [PMID: 37236880 DOI: 10.1016/j.tree.2023.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.
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Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
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7
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Hellal J, Barthelmebs L, Bérard A, Cébron A, Cheloni G, Colas S, Cravo-Laureau C, De Clerck C, Gallois N, Hery M, Martin-Laurent F, Martins J, Morin S, Palacios C, Pesce S, Richaume A, Vuilleumier S. Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges. FEMS Microbiol Ecol 2023; 99:fiad102. [PMID: 37669892 PMCID: PMC10516372 DOI: 10.1093/femsec/fiad102] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023] Open
Abstract
Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.
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Affiliation(s)
| | - Lise Barthelmebs
- Université de Perpignan Via Domitia, Biocapteurs – Analyse-Environnement, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Annette Bérard
- UMR EMMAH INRAE/AU – équipe SWIFT, 228, route de l'Aérodrome, 84914 Avignon Cedex 9, France
| | | | - Giulia Cheloni
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Simon Colas
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro-Bio Tech (Liege University), Passage des Déportés 2, 5030 Gembloux, Belgium
| | | | - Marina Hery
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Fabrice Martin-Laurent
- Institut Agro Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie, 21065 Dijon, France
| | - Jean Martins
- IGE, UMR 5001, Université Grenoble Alpes, CNRS, G-INP, INRAE, IRD Grenoble, France
| | | | - Carmen Palacios
- Université de Perpignan Via Domitia, CEFREM, F-66860 Perpignan, France
- CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | | | - Agnès Richaume
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France
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8
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Hernandez DJ, Kiesewetter KN, Almeida BK, Revillini D, Afkhami ME. Multidimensional specialization and generalization are pervasive in soil prokaryotes. Nat Ecol Evol 2023; 7:1408-1418. [PMID: 37550510 DOI: 10.1038/s41559-023-02149-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 07/04/2023] [Indexed: 08/09/2023]
Abstract
Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analysed 236 environmental soil microbiomes across the United States and demonstrate that 90% of >1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had many ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with ~220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities, probably stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance and community roles.
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Affiliation(s)
| | | | | | - Daniel Revillini
- Department of Biology, University of Miami, Coral Gables, FL, USA
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9
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Tapio M, Fischer D, Mäntysaari P, Tapio I. Rumen Microbiota Predicts Feed Efficiency of Primiparous Nordic Red Dairy Cows. Microorganisms 2023; 11:1116. [PMID: 37317090 DOI: 10.3390/microorganisms11051116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 06/16/2023] Open
Abstract
Efficient feed utilization in dairy cows is crucial for economic and environmental reasons. The rumen microbiota plays a significant role in feed efficiency, but studies utilizing microbial data to predict host phenotype are limited. In this study, 87 primiparous Nordic Red dairy cows were ranked for feed efficiency during their early lactation based on residual energy intake, and the rumen liquid microbial ecosystem was subsequently evaluated using 16S rRNA amplicon and metagenome sequencing. The study used amplicon data to build an extreme gradient boosting model, demonstrating that taxonomic microbial variation can predict efficiency (rtest = 0.55). Prediction interpreters and microbial network revealed that predictions were based on microbial consortia and the efficient animals had more of the highly interacting microbes and consortia. Rumen metagenome data was used to evaluate carbohydrate-active enzymes and metabolic pathway differences between efficiency phenotypes. The study showed that an efficient rumen had a higher abundance of glycoside hydrolases, while an inefficient rumen had more glycosyl transferases. Enrichment of metabolic pathways was observed in the inefficient group, while efficient animals emphasized bacterial environmental sensing and motility over microbial growth. The results suggest that inter-kingdom interactions should be further analyzed to understand their association with the feed efficiency of animals.
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Affiliation(s)
- Miika Tapio
- Genomics and Breeding, Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Daniel Fischer
- Applied Statistical Methods, Natural Resources, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Päivi Mäntysaari
- Animal Nutrition, Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Ilma Tapio
- Genomics and Breeding, Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
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10
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von Meijenfeldt FAB, Hogeweg P, Dutilh BE. A social niche breadth score reveals niche range strategies of generalists and specialists. Nat Ecol Evol 2023; 7:768-781. [PMID: 37012375 PMCID: PMC10172124 DOI: 10.1038/s41559-023-02027-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/27/2023] [Indexed: 04/05/2023]
Abstract
Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microorganisms because it depends on an objective definition of the environment. Here, by defining the environment of a microorganism as the community it resides in, we integrated information from over 22,000 environmental sequencing samples to derive a quantitative measure of the niche, which we call social niche breadth. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, whereas social specialists are stable but low in abundance. Social generalists have a more diverse and open pan-genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, whereby specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies.
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Affiliation(s)
- F A Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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11
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Muller EEL. The social dimension of microbial niches. Nat Ecol Evol 2023; 7:649-650. [PMID: 37012376 DOI: 10.1038/s41559-023-02020-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Emilie E L Muller
- Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 Université de Strasbourg-CNRS, Strasbourg, France.
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12
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Lin Q, De Vrieze J, Li L, Fang X, Li X. Interconnected versus unconnected microorganisms: Does it matter in anaerobic digestion functioning. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 331:117307. [PMID: 36652878 DOI: 10.1016/j.jenvman.2023.117307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
Microorganisms in anaerobic digestion (AD) are essential for wastes/pollutants treatment and energy recovery. Due to microbial enormous diversity, developing effective perspectives to understand microbial roles therein is urgent. This study conducted AD of swine manure, used an ensemble-based network analysis to distinguish interconnected, unconnected, copresence (positively interconnected) and mutual-exclusion (negatively interconnected) microorganisms within microbial communities, and explored their importance towards AD performances, using amplicon sequencing of 16S rRNA and 16S rRNA gene. Our analyses revealed greater importance of interconnected than unconnected microorganisms towards CH4 production and AD multifunctionality, which was attributed to higher niche breadth, deterministic community assembly, community stability and phylogenetic conservatism. The diversity was higher in unconnected than interconnected microorganisms, but was not linked to AD performances. Compared to copresence microorganisms, mutual-exclusion microorganisms showed greater and equal importance towards CH4 production and AD multifunctionality, which was attributed to their roles in stabilizing microbial communities. The increased feedstock biodegradability, by replacing part of manure with fructose or apple waste, hardly affected the relative importance of interconnected versus unconnected microorganisms towards CH4 production or AD multifunctionality. Our findings develop a new framework to understand microbial roles, and have important implications in targeted manipulation of critical microorganisms in waste-treatment systems.
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Affiliation(s)
- Qiang Lin
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent 9000, Belgium
| | - Lingjuan Li
- Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Xiaoyu Fang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiangzhen Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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13
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Kuang J, Deng D, Han S, Bates CT, Ning D, Shu W, Zhou J. Resistance potential of soil bacterial communities along a biodiversity gradient in forest ecosystems. MLIFE 2022; 1:399-411. [PMID: 38818486 PMCID: PMC10989803 DOI: 10.1002/mlf2.12042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/01/2024]
Abstract
Higher biodiversity is often assumed to be a more desirable scenario for maintaining the functioning of ecosystems, but whether species-richer communities are also more disturbance-tolerant remains controversial. In this study, we investigated the bacterial communities based on 472 soil samples from 28 forests across China with associated edaphic and climatic properties. We developed two indexes (i.e., community mean tolerance breadth [CMTB] and community mean response asynchrony [CMRA]) to explore the relationship between diversity and community resistance potential. Moreover, we examined this resistance potential along the climatic and latitudinal gradients. We revealed that CMTB was significantly and negatively related to species richness, resulting from the changes in balance between relative abundances of putative specialists and generalists. In comparison, we found a unimodal relationship between CMRA and richness, suggesting that higher biodiversity might not always lead to higher community resistance. Moreover, our results showed differential local patterns along latitude. In particular, local patterns in the northern region mainly followed general relationships rather than those for the southern forests, which may be attributed to the differences in annual means and annual variations of climate conditions. Our findings highlight that the community resistance potential depends on the composition of diverse species with differential environmental tolerance and responses. This study provides a new, testable evaluation by considering tolerance breadth and response asynchrony at the community level, which will be helpful in assessing the influence of disturbance under rapid shifts in biodiversity and species composition as a result of global environmental change.
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Affiliation(s)
- Jialiang Kuang
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of EducationSchool of Environment and Energy, South China University of TechnologyGuangzhouChina
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education InstitutesCollege of Ecology and Evolution, Sun Yat‐sen UniversityGuangzhouChina
| | - Dongmei Deng
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- Guangxi Key Laboratory of Green Processing of Sugar ResourcesCollege of Biological and Chemical Engineering, Guangxi University of Science and TechnologyLiuzhouChina
| | - Shun Han
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Colin T. Bates
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Daliang Ning
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Wensheng Shu
- School of Life SciencesSouth China Normal UniversityGuangzhouChina
| | - Jizhong Zhou
- Institute for Environmental Genomics, and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- School of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOklahomaUSA
- School of Computer SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental SciencesLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
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14
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Qi H, Huang D, Wang F, Ye M, Jiang X. Spatial dynamics of prokaryotic microbial communities in sediments of the Yellow Sea: Assembly process, co-occurrence relationships, and environmental implications. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115645. [PMID: 35797911 DOI: 10.1016/j.jenvman.2022.115645] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Marine sediment microorganisms play an important role in the biogeochemical cycle of elements and the transformation of exogenous pollutants; therefore, it is important to study the microbial assembly process and inter taxa associations. In this study, we investigated the profiles and assembly processes of microbial communities of sediments collected from 19 points in the Yellow Sea. As revealed by 16S rRNA sequencing, Proteobacteria (43.11%-65.54%) was the dominant phylum in marine sediment. Further, the physicochemical properties of sediments were significantly influenced by depth (P < 0.05), and the effects of homogeneous selection became greater with increasing depth. The microbial species located in marine sediment at 35°N had a significantly higher co-occurrence relationship (82.76%) than those at 34°N (57.99%) and 36°N (54.07%). Additionally, the microbial community structure of the sediments changed significantly at the genus level with strong fluctuations in the physicochemical properties. By contrast, the carbon, nitrogen, and sulfur associated functional gene diversity and abundance showed no clear variation among different locations, indicating the probable functional redundancy and a potential functional gene pool of the microbes in marine sediments. This study could provide new insights into the composition of microorganisms in sediments in the Yellow Sea, the driving force of microbial diversity, the assembly process, the modes of species' co-occurrence, and their ecological functions.
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Affiliation(s)
- Huiyuan Qi
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Fenghe Wang
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China.
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
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15
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Hu R, Liu S, Saleem M, Xiong Z, Zhou Z, Luo Z, Shu L, He Z, Wang C. Environmentally‐induced reconstruction of microbial communities alters particulate carbon flux of deep chlorophyll maxima in the South China sea. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruiwen Hu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Songfeng Liu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Muhammad Saleem
- Department of Biological Sciences Alabama State University Montgomery AL USA
| | - Zhiyao Xiong
- School of Marine Sciences Sun Yat‐sen University Zhuhai
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
- College of Agronomy Hunan Agricultural University Changsha China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
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16
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Rodriguez V, Moskwa LM, Oses R, Kühn P, Riveras-Muñoz N, Seguel O, Scholten T, Wagner D. Impact of Climate and Slope Aspects on the Composition of Soil Bacterial Communities Involved in Pedogenetic Processes along the Chilean Coastal Cordillera. Microorganisms 2022; 10:847. [PMID: 35630293 PMCID: PMC9143490 DOI: 10.3390/microorganisms10050847] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 02/04/2023] Open
Abstract
Soil bacteria play a fundamental role in pedogenesis. However, knowledge about both the impact of climate and slope aspects on microbial communities and the consequences of these items in pedogenesis is lacking. Therefore, soil-bacterial communities from four sites and two different aspects along the climate gradient of the Chilean Coastal Cordillera were investigated. Using a combination of microbiological and physicochemical methods, soils that developed in arid, semi-arid, mediterranean, and humid climates were analyzed. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and Planctomycetes were found to increase in abundance from arid to humid climates, while Actinobacteria and Gemmatimonadetes decreased along the transect. Bacterial-community structure varied with climate and aspect and was influenced by pH, bulk density, plant-available phosphorus, clay, and total organic-matter content. Higher bacterial specialization was found in arid and humid climates and on the south-facing slope and was likely promoted by stable microclimatic conditions. The presence of specialists was associated with ecosystem-functional traits, which shifted from pioneers that accumulated organic matter in arid climates to organic decomposers in humid climates. These findings provide new perspectives on how climate and slope aspects influence the composition and functional capabilities of bacteria, with most of these capabilities being involved in pedogenetic processes.
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Affiliation(s)
- Victoria Rodriguez
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
| | - Lisa-Marie Moskwa
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
| | - Rómulo Oses
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama, Universidad de Atacama (CRIDESAT UDA), Copayapu 484, Copiapó 1530000, Chile;
| | - Peter Kühn
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Nicolás Riveras-Muñoz
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Oscar Seguel
- Facultad de Ciencias Agronómicas, Universidad de Chile, Av. Santa Rosa #11315, La Pintana, Santiago 8820808, Chile;
| | - Thomas Scholten
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
- Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany
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17
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Guo H, Dong P, Gao F, Huang L, Wang S, Wang R, Yan M, Zhang D. Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system. NPJ Biofilms Microbiomes 2022; 8:22. [PMID: 35410335 PMCID: PMC9001642 DOI: 10.1038/s41522-022-00288-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
Sucrose is an effective carbon source for creating more reliable and environmentally friendly conditions for shrimp growth by regulating bacteria in biofloc-based culture systems. However, the influence of sucrose addition on the interaction, co-occurrence networks, and assembly mechanisms of bacterial communities in biofloc-based culture systems remains largely unknown. Here, we comprehensively investigated the effects of sucrose addition on bacterial communities in three habitats (water, bioflocs, and gut). The bacterial community structures and compositions of these three habitats became more similar in groups with sucrose addition, compared with those in controls. More than 50% gut bacterial communities were mainly derived from water and biofloc communities in the sucrose addition groups, but only about 33% bacterial communities migrated from water and biofloc to the gut in the control culture system. Sucrose addition accordantly enriched core taxa belonging to the phylum Actinobacteria and the families Rhodobacteraceae and Flavobacteriaceae in water, biofloc, and gut habitats. These core taxa were important for maintaining bacterial network stability in the sucrose addition culture systems and some were identified as keystone taxa for improving shrimp growth. Furthermore, after sucrose addition, gut bacterial community assembly from water and biofloc was dominated by the heterogeneous select with the ratios of 55-91% and 67-83%, respectively, indicating that sucrose addition can directionally shape the bacterial assembly of the shrimp culture system. These results provide a basis for selectively regulating certain beneficial taxa to improve shrimp growth in culture systems.
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Affiliation(s)
- Haipeng Guo
- State key laboratory for managing biotic and chemical threats to the quality and safety of agro-products, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Pengsheng Dong
- State key laboratory for managing biotic and chemical threats to the quality and safety of agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Fan Gao
- State key laboratory for managing biotic and chemical threats to the quality and safety of agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Lei Huang
- State key laboratory for managing biotic and chemical threats to the quality and safety of agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Sipeng Wang
- State key laboratory for managing biotic and chemical threats to the quality and safety of agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Ruoyu Wang
- State key laboratory for managing biotic and chemical threats to the quality and safety of agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Mengchen Yan
- State key laboratory for managing biotic and chemical threats to the quality and safety of agro-products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Demin Zhang
- State key laboratory for managing biotic and chemical threats to the quality and safety of agro-products, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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18
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Vanni C, Schechter MS, Acinas SG, Barberán A, Buttigieg PL, Casamayor EO, Delmont TO, Duarte CM, Eren AM, Finn RD, Kottmann R, Mitchell A, Sánchez P, Siren K, Steinegger M, Gloeckner FO, Fernàndez-Guerra A. Unifying the known and unknown microbial coding sequence space. eLife 2022; 11:e67667. [PMID: 35356891 PMCID: PMC9132574 DOI: 10.7554/elife.67667] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40-60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data.
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Affiliation(s)
- Chiara Vanni
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine MicrobiologyBremenGermany
- Jacobs University BremenBremenGermany
| | - Matthew S Schechter
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine MicrobiologyBremenGermany
- Department of Medicine, University of ChicagoChicagoUnited States
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Albert Barberán
- Department of Environmental Science, University of ArizonaTucsonUnited States
| | - Pier Luigi Buttigieg
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Alfred Wegener InstituteBremerhavenGermany
| | - Emilio O Casamayor
- Center for Advanced Studies of Blanes CEAB-CSIC, Spanish Council for ResearchBlanesSpain
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-SaclayEvryFrance
| | - Carlos M Duarte
- Red Sea Research Centre and Computational Bioscience Research Center, King Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - A Murat Eren
- Department of Medicine, University of ChicagoChicagoUnited States
- Josephine Bay Paul Center, Marine Biological LaboratoryWoods HoleUnited States
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusHinxtonUnited Kingdom
| | - Renzo Kottmann
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Alex Mitchell
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusHinxtonUnited Kingdom
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Kimmo Siren
- Section for Evolutionary Genomics, The GLOBE Institute, University of CopenhagenCopenhagenDenmark
| | - Martin Steinegger
- School of Biological Sciences, Seoul National UniversitySeoulRepublic of Korea
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoulRepublic of Korea
| | - Frank Oliver Gloeckner
- Jacobs University BremenBremenGermany
- University of Bremen and Life Sciences and ChemistryBremenGermany
- Computing Center, Helmholtz Center for Polar and Marine ResearchBremerhavenGermany
| | - Antonio Fernàndez-Guerra
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine MicrobiologyBremenGermany
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of CopenhagenCopenhagenDenmark
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19
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Metagenomic Sequencing Reveals that the Assembly of Functional Genes and Taxa Varied Highly and Lacked Redundancy in the Earthworm Gut Compared with Soil under Vanadium Stress. mSystems 2022; 7:e0125321. [PMID: 35089099 PMCID: PMC8725585 DOI: 10.1128/msystems.01253-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Exploring the ecological mechanism of microbial community assembly in soil and the earthworm gut in a vanadium polluted environment could help us understand the effects of vanadium stress on microbial diversity maintenance and function, as well as the mechanism of microbial mitigation of vanadium stress. Combining metagenomic sequencing and abundance distribution models, we explored the assembly of earthworm intestinal bacteria and native soil bacteria after 21 days of earthworm exposure to a gradient level of vanadate (0 to 300 mg kg−1) in soil. Stochastic processes dominated the assembly of both genes and taxa in earthworm gut and soil. Both the composition of taxa and functional genes in earthworm gut varied highly with the vanadium concentration, while in soil, only the taxa changed significantly, whereas the functional genes were relatively stable. The functional redundancy in soil, but not in the earthworm gut, was confirmed by a Mantel test and analysis of similarities (ANOSIM) test. In addition, vanadium detoxifying gene (VDG)-carrying taxa were more diverse but less abundant in soil than in the worm gut; and VDGs were more abundant in soil than in the worm gut. Their wider niche breadth indicated that VDG-carrying taxa were generalists in soil, in contrast to their role in the worm gut. These results suggested that earthworm intestinal and soil microbes adopted different strategies to counteract vanadium stress. The results provide new insights into the effects of soil vanadium stress on the assembly of earthworm gut and soil microbiota from both bacterial taxa and genetic function perspectives. IMPORTANCE Metagenomic sequencing revealed the variation of functional genes in the microbial community in soil and earthworm gut with increasing vanadium concentrations, which provided a new insight to explore the effect of vanadium stress on microbial community assembly from the perspective of functional genes. Our results reinforced the view that functional genes and taxa do not appear to have a simple corresponding relationship. Taxa are more sensitive compared with functional genes, suggesting the existence of bacterial functional redundancy in soil, but not in the earthworm gut. These observations indicate different assembly patterns of earthworm intestinal and soil bacteria under vanadium stress. Thus, it is important and necessary to include genetic functions to comprehensively understand microbial community assembly.
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20
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Masasa M, Kushmaro A, Kramarsky-Winter E, Shpigel M, Barkan R, Golberg A, Kribus A, Shashar N, Guttman L. Mono-specific algal diets shape microbial networking in the gut of the sea urchin Tripneustes gratilla elatensis. Anim Microbiome 2021; 3:79. [PMID: 34782025 PMCID: PMC8594234 DOI: 10.1186/s42523-021-00140-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Algivorous sea urchins can obtain energy from a diet of a single algal species, which may result in consequent changes in their gut microbe assemblies and association networks. METHODS To ascertain whether such changes are led by specific microbes or limited to a specific region in the gut, we compared the microbial assembly in the three major gut regions of the sea urchin Tripneustes gratilla elatensis when fed a mono-specific algal diet of either Ulva fasciata or Gracilaria conferta, or an algal-free diet. DNA extracts from 5 to 7 individuals from each diet treatment were used for Illumina MiSeq based 16S rRNA gene sequencing (V3-V4 region). Niche breadth of each microbe in the assembly was calculated for identification of core, generalist, specialist, or unique microbes. Network analyzers were used to measure the connectivity of the entire assembly and of each of the microbes within it and whether it altered with a given diet or gut region. Lastly, the predicted metabolic functions of key microbes in the gut were analyzed to evaluate their potential contribution to decomposition of dietary algal polysaccharides. RESULTS Sea urchins fed with U. fasciata grew faster and their gut microbiome network was rich in bacterial associations (edges) and networking clusters. Bacteroidetes was the keystone microbe phylum in the gut, with core, generalist, and specialist representatives. A few microbes of this phylum were central hub nodes that maintained community connectivity, while others were driver microbes that led the rewiring of the assembly network based on diet type through changes in their associations and centrality. Niche breadth agreed with microbes' richness in genes for carbohydrate active enzymes and correlated Bacteroidetes specialists to decomposition of specific polysaccharides in the algal diets. CONCLUSIONS The dense and well-connected microbial network in the gut of Ulva-fed sea urchins, together with animal's rapid growth, may suggest that this alga was most nutritious among the experimental diets. Our findings expand the knowledge on the gut microbial assembly in T. gratilla elatensis and strengthen the correlation between microbes' generalism or specialism in terms of occurrence in different niches and their metabolic arsenal which may aid host nutrition.
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Affiliation(s)
- Matan Masasa
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev, Eilat Campus, Eilat, Israel.,Israel Oceanographic and Limnological Research, The National Center for Mariculture, P.O. Box 1212, 8811201, Eilat, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, 8410501, Beer-Sheva, Israel
| | - Esti Kramarsky-Winter
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, 8410501, Beer-Sheva, Israel
| | - Muki Shpigel
- Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, 3498838, Haifa, Israel
| | - Roy Barkan
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev, Eilat Campus, Eilat, Israel.,Israel Oceanographic and Limnological Research, The National Center for Mariculture, P.O. Box 1212, 8811201, Eilat, Israel
| | - Alex Golberg
- Department of Environmental Studies, Tel Aviv University, P.O. Box 39040, 6997801, Tel Aviv, Israel
| | - Abraham Kribus
- School of Mechanical Engineering, Tel Aviv University, P.O. Box 39040, 6997801, Tel Aviv, Israel
| | - Nadav Shashar
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev, Eilat Campus, Eilat, Israel
| | - Lior Guttman
- Israel Oceanographic and Limnological Research, The National Center for Mariculture, P.O. Box 1212, 8811201, Eilat, Israel.
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21
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Chen YJ, Leung PM, Wood JL, Bay SK, Hugenholtz P, Kessler AJ, Shelley G, Waite DW, Franks AE, Cook PLM, Greening C. Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem. THE ISME JOURNAL 2021; 15:2986-3004. [PMID: 33941890 PMCID: PMC8443593 DOI: 10.1038/s41396-021-00988-w] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/25/2021] [Accepted: 04/09/2021] [Indexed: 02/03/2023]
Abstract
Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and sampling date. Several taxa were highly abundant and prevalent in all samples, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists; genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments; whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.
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Affiliation(s)
- Ya-Jou Chen
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Natural Resources Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Jennifer L Wood
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Adam J Kessler
- Water Studies Centre, School of Chemistry, Monash University, Clayton, VIC, Australia
- School of Earth, Atmosphere and Environment, Monash University, Clayton, VIC, Australia
| | - Guy Shelley
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - David W Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Perran L M Cook
- Water Studies Centre, School of Chemistry, Monash University, Clayton, VIC, Australia.
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
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22
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Martínez Arbas S, Busi SB, Queirós P, de Nies L, Herold M, May P, Wilmes P, Muller EEL, Narayanasamy S. Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies. Front Genet 2021; 12:666244. [PMID: 34194470 PMCID: PMC8236828 DOI: 10.3389/fgene.2021.666244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/30/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, multi-omic studies have enabled resolving community structure and interrogating community function of microbial communities. Simultaneous generation of metagenomic, metatranscriptomic, metaproteomic, and (meta) metabolomic data is more feasible than ever before, thus enabling in-depth assessment of community structure, function, and phenotype, thus resulting in a multitude of multi-omic microbiome datasets and the development of innovative methods to integrate and interrogate those multi-omic datasets. Specifically, the application of reference-independent approaches provides opportunities in identifying novel organisms and functions. At present, most of these large-scale multi-omic datasets stem from spatial sampling (e.g., water/soil microbiomes at several depths, microbiomes in/on different parts of the human anatomy) or case-control studies (e.g., cohorts of human microbiomes). We believe that longitudinal multi-omic microbiome datasets are the logical next step in microbiome studies due to their characteristic advantages in providing a better understanding of community dynamics, including: observation of trends, inference of causality, and ultimately, prediction of community behavior. Furthermore, the acquisition of complementary host-derived omics, environmental measurements, and suitable metadata will further enhance the aforementioned advantages of longitudinal data, which will serve as the basis to resolve drivers of community structure and function to understand the biotic and abiotic factors governing communities and specific populations. Carefully setup future experiments hold great potential to further unveil ecological mechanisms to evolution, microbe-microbe interactions, or microbe-host interactions. In this article, we discuss the challenges, emerging strategies, and best-practices applicable to longitudinal microbiome studies ranging from sampling, biomolecular extraction, systematic multi-omic measurements, reference-independent data integration, modeling, and validation.
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Affiliation(s)
- Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pedro Queirós
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Malte Herold
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emilie E. L. Muller
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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23
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Hardoim CCP, Lôbo-Hajdu G, Custódio MR, Hardoim PR. Prokaryotic, Fungal, and Unicellular Eukaryotic Core Communities Across Three Sympatric Marine Sponges From the Southwestern Atlantic Coast Are Dominated Largely by Deterministic Assemblage Processes. Front Microbiol 2021; 12:674004. [PMID: 34168631 PMCID: PMC8217869 DOI: 10.3389/fmicb.2021.674004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Marine sponges are known to harbor a diverse and complex microbiota; however, a vast majority of surveys have been investigating the prokaryotic communities in the north hemisphere and Australia. In addition, the mechanisms of microbial community assembly are poorly understood in this pivotal player of the ecosystem. Thus, this survey addressed the holobiome of the sponge species in the São Paulo region (Brazil) for the first time and investigated the contribution of neutral and niche processes of prokaryotic, fungal, and unicellular eukaryotic assemblage in three sympatric species Aplysina caissara, Aplysina fulva, and Tedania ignis along with environmental samples. The compositions of the holobiome associated with the sponges and detected in environmental samples were strikingly different. Remarkably, between 47 and 88% of the assigned operational taxonomic units (OTUs) were specifically associated with sponge species. Moreover, around 77, 69, and 53% of the unclassified OTUs from prokaryotic, fungal, and unicellular eukaryotic communities, respectively, showed less than 97% similarity with well-known databases, suggesting that sponges from the southwestern Atlantic coast are an important source of microbial novelty. These values are even higher, around 80 and 61% of the unclassified OTUs, when excluding low abundance samples from fungal and unicellular eukaryotic datasets, respectively. Host species were the major driver shaping the sponge-associated microbial community. Deterministic processes were primarily responsible for the assembly of microbial communities in all sponge species, while neutral processes of prokaryotic and fungal community assembly were also detected in the sympatric A. caissara and T. ignis replicates, respectively. Most of the species-rich sponge-associated lineages from this region are also found in the Northern seas and many of them might play essential roles in the symbioses, such as biosynthesis of secondary metabolites that exhibit antimicrobial and antiviral activities, as well as provide protection against host predation. Overall, in this study the microbiota was assembled by interactions with the host sponge in a deterministic-based manner; closely related sponge species shared a strong phylogenetic signal in their associated prokaryotic and fungal community traits and Brazilian sponges were a reservoir of novel microbial species.
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Affiliation(s)
| | - Gisele Lôbo-Hajdu
- Department of Genetic, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Márcio R. Custódio
- Department of Physiology, Biosciences Institute and NP-Biomar, Center for Marine Biology, University of São Paulo, São Paulo, Brazil
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24
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Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater. Nat Microbiol 2021; 6:524-532. [PMID: 33495621 DOI: 10.1038/s41564-020-00851-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Niche theory is a foundational ecological concept that explains the distribution of species in natural environments. Identifying the dimensions of any organism's niche is challenging because numerous environmental factors can affect organism viability. We used serial invasion experiments to introduce Ruegeria pomeroyi DSS-3, a heterotrophic marine bacterium, into a coastal phytoplankton bloom on 14 dates. RNA-sequencing analysis of R. pomeroyi was conducted after 90 min to assess its niche dimensions in this dynamic ecosystem. We identified ~100 external conditions eliciting transcriptional responses, which included substrates, nutrients, metals and biotic interactions such as antagonism, resistance and cofactor synthesis. The peak bloom was characterized by favourable states for most of the substrate dimensions, but low inferred growth rates of R. pomeroyi at this stage indicated that its niche was narrowed by factors other than substrate availability, most probably negative biotic interactions with the bloom dinoflagellate. Our findings indicate chemical and biological features of the ocean environment that can constrain where heterotrophic bacteria survive.
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25
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Maucourt B, Vuilleumier S, Bringel F. Transcriptional regulation of organohalide pollutant utilisation in bacteria. FEMS Microbiol Rev 2020; 44:189-207. [PMID: 32011697 DOI: 10.1093/femsre/fuaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.
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Affiliation(s)
- Bruno Maucourt
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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26
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Herold M, Martínez Arbas S, Narayanasamy S, Sheik AR, Kleine-Borgmann LAK, Lebrun LA, Kunath BJ, Roume H, Bessarab I, Williams RBH, Gillece JD, Schupp JM, Keim PS, Jäger C, Hoopmann MR, Moritz RL, Ye Y, Li S, Tang H, Heintz-Buschart A, May P, Muller EEL, Laczny CC, Wilmes P. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance. Nat Commun 2020; 11:5281. [PMID: 33077707 PMCID: PMC7572474 DOI: 10.1038/s41467-020-19006-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/16/2020] [Indexed: 12/31/2022] Open
Abstract
The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts. Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.
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Affiliation(s)
- Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,Epidemiology and Microbial Genomics, Laboratoire National de Santé, 1 rue Louis Rech, 3555, Dudelange, Luxembourg
| | - Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,Megeno S.A., 6A Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Abdul R Sheik
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Luise A K Kleine-Borgmann
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Laura A Lebrun
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Benoît J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Hugo Roume
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,MetaGenoPolis, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université Paris-Saclay, Domaine de Vilvert, Bâtiment 325, 78350, Jouy-en-Josas, France
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Dr, Singapore, 637551, Singapore
| | - John D Gillece
- The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ, 86001, USA
| | - James M Schupp
- The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ, 86001, USA
| | - Paul S Keim
- The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ, 86001, USA
| | - Christian Jäger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Yuzhen Ye
- School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - Sujun Li
- School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - Haixu Tang
- School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany.,Helmholtz Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Str. 4, 06120, Halle, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Emilie E L Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,Equipe Adaptations et Interactions Microbiennes, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg. .,Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg.
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27
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Hu A, Wang H, Cao M, Rashid A, Li M, Yu CP. Environmental Filtering Drives the Assembly of Habitat Generalists and Specialists in the Coastal Sand Microbial Communities of Southern China. Microorganisms 2019; 7:microorganisms7120598. [PMID: 31766562 PMCID: PMC6955893 DOI: 10.3390/microorganisms7120598] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 11/16/2022] Open
Abstract
Coastal sands harbor diverse microbial assemblages that play a critical role in the biogeochemical cycling of beach ecosystems. However, little is known about the relative importance of the different ecological processes underlying the assembly of communities of sand microbiota. Here, we employed 16S rDNA amplicon sequencing to investigate the sand microbiota of two coastal beaches, in southern China. The results showed that sand microbial assemblages at intertidal and supratidal zones exhibited contrasting compositions that can be attributed to environmental filtering by electric conductivity. A consistent pattern of habitat generalists and specialists of sand microbiota was observed among different beach zones. Null and neutral model analyses indicated that the environmental filtering was mainly responsible for supratidal microbial communities, while the neutral processes could partially influence the assembly of intertidal communities. Moreover, environmental filtering was found to shape the habitat specialists, while random dispersal played a major role in shaping generalists. The neutral model analysis revealed that the habitat generalists exceeding the neutral prediction harbored a relatively higher proportion of microbial taxa than the specialist counterparts. An opposite pattern was observed for taxa falling below the neutral prediction. Collectively, these findings offer a novel insight into the assembly mechanisms of coastal sand microbiota.
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Affiliation(s)
- Anyi Hu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- Correspondence: (A.H.); (M.L.); Tel.: +86-592-6190582 (A.H.); +86-596-2591356 (M.L.)
| | - Hongjie Wang
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meixian Cao
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Azhar Rashid
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- Nuclear Institute for Food and Agriculture, Tarnab, Peshawar 446, Pakistan
| | - Mingfeng Li
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
- Correspondence: (A.H.); (M.L.); Tel.: +86-592-6190582 (A.H.); +86-596-2591356 (M.L.)
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
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28
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Core gut microbial communities are maintained by beneficial interactions and strain variability in fish. Nat Microbiol 2019; 4:2456-2465. [DOI: 10.1038/s41564-019-0560-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 08/12/2019] [Indexed: 01/22/2023]
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