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Selective Bacterial Community Enrichment between the Pitcher Plants Sarracenia minor and Sarracenia flava. Microbiol Spectr 2021; 9:e0069621. [PMID: 34817222 PMCID: PMC8612160 DOI: 10.1128/spectrum.00696-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The interconnected and overlapping habitats present in natural ecosystems remain a challenge in determining the forces driving microbial community composition. The cuplike leaf structures of some carnivorous plants, including those of the family Sarraceniaceae, are self-contained ecological habitats that represent systems for exploring such microbial ecology questions. We investigated whether Sarracenia minor and Sarracenia flava cultivate distinct bacterial communities when sampled at the same geographic location and time. This sampling strategy eliminates many abiotic environmental variables present in other studies that compare samples harvested over time, and it could reveal biotic factors driving the selection of microbes. DNA extracted from the decomposing detritus trapped in each Sarracenia leaf pitcher was profiled using 16S rRNA amplicon sequencing. We identified a surprising amount of bacterial diversity within each pitcher, but we also discovered bacteria whose abundance was specifically enriched in one of the two Sarracenia species. These differences in bacterial community representation suggest some biotic influence of the Sarracenia plant on the bacterial composition of their pitchers. Overall, our results suggest that bacterial selection due to factors other than geographic location, weather, or prey availability is occurring within the pitchers of these two closely related plant species. This indicates that specific characteristics of S. minor and S. flava may play a role in fostering distinct bacterial communities. These confined, naturally occurring microbial ecosystems within Sarracenia pitchers may provide model systems to answer important questions about the drivers of microbial community composition, succession, and response to environmental perturbations. IMPORTANCE This study uses amplicon sequencing to compare the bacterial communities of environmental samples from the detritus of the leaf cavities of Sarracenia minor and Sarracenia flava pitcher plants. We sampled the detritus at the same time and in the same geographic location, eliminating many environmental variables present in other comparative studies. This study revealed that different species of Sarracenia contain distinct bacterial members within their pitchers, suggesting that these communities are not randomly established based on environmental factors and the prey pool but are potentially enriched for by the plants' chemical or physical environment. This study of these naturally occurring, confined microbial ecosystems will help further establish carnivorous pitcher plants as a model system for answering important questions about the development and succession of microbial communities.
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Ishaq SL, Parada FJ, Wolf PG, Bonilla CY, Carney MA, Benezra A, Wissel E, Friedman M, DeAngelis KM, Robinson JM, Fahimipour AK, Manus MB, Grieneisen L, Dietz LG, Pathak A, Chauhan A, Kuthyar S, Stewart JD, Dasari MR, Nonnamaker E, Choudoir M, Horve PF, Zimmerman NB, Kozik AJ, Darling KW, Romero-Olivares AL, Hariharan J, Farmer N, Maki KA, Collier JL, O’Doherty KC, Letourneau J, Kline J, Moses PL, Morar N. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems 2021; 6:e0047121. [PMID: 34313460 PMCID: PMC8407420 DOI: 10.1128/msystems.00471-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems. Yet engagement with beneficial microbiomes is dictated by access to public resources, such as nutritious food, clean water and air, safe shelter, social interactions, and effective medicine. In this way, microbiomes have sociopolitical contexts that must be considered. The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Here, we outline opportunities for integrating microbiology and social equity work through broadening education and training; diversifying research topics, methods, and perspectives; and advocating for evidence-based public policy that supports sustainable, equitable, and microbial wealth for all.
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Affiliation(s)
- Suzanne L. Ishaq
- University of Maine, School of Food and Agriculture, Orono, Maine, USA
| | - Francisco J. Parada
- Centro de Estudios en Neurociencia Humana y Neuropsicología, Facultad de Psicología, Universidad Diego Portales, Santiago, Chile
| | - Patricia G. Wolf
- Institute for Health Research and Policy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Carla Y. Bonilla
- Gonzaga University, Department of Biology, Spokane, Washington, USA
| | - Megan A. Carney
- University of Arizona, School of Anthropology, Tucson, Arizona, USA
| | - Amber Benezra
- Stevens Institute of Technology, Science and Technology Studies, Hoboken, New Jersey, USA
| | | | - Michael Friedman
- American International College of Arts and Sciences of Antigua, Antigua, Antigua and Barbuda, West Indies
| | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jake M. Robinson
- University of Sheffield, Department of Landscape Architecture, Sheffield, United Kingdom
| | - Ashkaan K. Fahimipour
- Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, California, USA
- National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, Santa Cruz, California, USA
| | - Melissa B. Manus
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Laura Grieneisen
- Department of Genetics, Cell, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Leslie G. Dietz
- University of Oregon, Biology and the Built Environment Center, Eugene, Oregon, USA
| | - Ashish Pathak
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, Florida, USA
| | - Ashvini Chauhan
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, Florida, USA
| | - Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Justin D. Stewart
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mauna R. Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Emily Nonnamaker
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Mallory Choudoir
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Patrick F. Horve
- University of Oregon, Biology and the Built Environment Center, Eugene, Oregon, USA
| | - Naupaka B. Zimmerman
- University of San Francisco, Department of Biology, San Francisco, California, USA
| | - Ariangela J. Kozik
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine Weatherford Darling
- Social Science Program, University of Maine at Augusta, Augusta, Maine, USA
- University of Maine, Graduate School of Biomedical Science & Engineering, Bangor, Maine, USA
| | | | - Janani Hariharan
- Field of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Nicole Farmer
- National Institutes of Health, Clinical Center, Bethesda, Maryland, USA
| | - Katherine A. Maki
- National Institutes of Health, Clinical Center, Bethesda, Maryland, USA
| | - Jackie L. Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | | | - Jeffrey Letourneau
- Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | | | - Peter L. Moses
- Robert Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
- Finch Therapeutics, Somerville, Massachusetts, USA
| | - Nicolae Morar
- Environmental Studies Program, University of Oregon, Eugene, Oregon, USA
- Department of Philosophy, University of Oregon, Eugene, Oregon, USA
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Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution. PLoS Biol 2021; 19:e3001322. [PMID: 34411089 PMCID: PMC8376202 DOI: 10.1371/journal.pbio.3001322] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions. This Essay argues that in order to truly understand how marine hosts benefit from the immense diversity of microbes, we need to expand towards long-term, multi-disciplinary research focussing on few areas of the world’s ocean that we refer to as “natural experiments,” where processes can be studied at scales that far exceed those captured in laboratory experiments.
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Kaup M, Trull S, Hom EFY. On the move: sloths and their epibionts as model mobile ecosystems. Biol Rev Camb Philos Soc 2021; 96:2638-2660. [PMID: 34309191 PMCID: PMC9290738 DOI: 10.1111/brv.12773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/20/2022]
Abstract
Sloths are unusual mobile ecosystems, containing a high diversity of epibionts living and growing in their fur as they climb slowly through the canopies of tropical forests. These epibionts include poorly studied algae, arthropods, fungi, and bacteria, making sloths likely reservoirs of unexplored biodiversity. This review aims to identify gaps and eliminate misconceptions in our knowledge of sloths and their epibionts, and to identify key questions to stimulate future research into the functions and roles of sloths within a broader ecological and evolutionary context. This review also seeks to position the sloth fur ecosystem as a model for addressing fundamental questions in metacommunity and movement ecology. The conceptual and evidence-based foundation of this review aims to serve as a guide for future hypothesis-driven research into sloths, their microbiota, sloth health and conservation, and the coevolution of symbioses in general.
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Affiliation(s)
- Maya Kaup
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, 38677-1848, U.S.A
| | - Sam Trull
- The Sloth Institute, Tulemar Gardens, Provincia de Puntarenas, Manuel Antonio, 60601, Costa Rica
| | - Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, 38677-1848, U.S.A
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Huang M, Chai L, Jiang D, Zhang M, Jia W, Huang Y. Spatial Patterns of Soil Fungal Communities Are Driven by Dissolved Organic Matter (DOM) Quality in Semi-Arid Regions. MICROBIAL ECOLOGY 2021; 82:202-214. [PMID: 32322922 DOI: 10.1007/s00248-020-01509-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Soil fungi are ecologically important as decomposers, pathogens, and symbionts in nature. Understanding their biogeographic patterns and driving forces is pivotal to predict alterations arising from environmental changes in ecosystem. Dissolved organic matter (DOM) is an essential resource for soil fungi; however, the role of its quality in structuring fungal community patterns remains elusive. Here using Illumina MiSeq sequencing, we characterized total fungi and their functional groups in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China, which are currently suffering great pressure from climate change. Total fungi and their functional groups were all observed to exhibit significant biogeographic patterns which were primarily driven by environmental variables. DOM quality was the best and consistent predictor of diversity of both total fungi and functional groups. Specifically, plant-derived DOM was associated with greater diversity relative to microbe-dominated origins. In addition, fungal diversity linearly increased with increases in degree of humification in DOM. Similarly, among all measured environmental variables, DOM quality had the strongest effects on the community composition of total fungi and functional groups. Together, our work contributes to the factors underlying fungal biogeographic patterns and adds detail to the importance of DOM quality in structuring fungal communities.
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Affiliation(s)
- Muke Huang
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Liwei Chai
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Dalin Jiang
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Mengjun Zhang
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Weiqian Jia
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Yi Huang
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China.
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56
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Boynton PJ, Wloch‐Salamon D, Landermann D, Stukenbrock EH. Forest Saccharomyces paradoxus are robust to seasonal biotic and abiotic changes. Ecol Evol 2021; 11:6604-6619. [PMID: 34141244 PMCID: PMC8207440 DOI: 10.1002/ece3.7515] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/25/2021] [Accepted: 03/16/2021] [Indexed: 01/02/2023] Open
Abstract
Microorganisms are famous for adapting quickly to new environments. However, most evidence for rapid microbial adaptation comes from laboratory experiments or domesticated environments, and it is unclear how rates of adaptation scale from human-influenced environments to the great diversity of wild microorganisms. We examined potential monthly-scale selective pressures in the model forest yeast Saccharomyces paradoxus. Contrary to expectations of seasonal adaptation, the S. paradoxus population was stable over four seasons in the face of abiotic and biotic environmental changes. While the S. paradoxus population was diverse, including 41 unique genotypes among 192 sampled isolates, there was no correlation between S. paradoxus genotypes and seasonal environments. Consistent with observations from other S. paradoxus populations, the forest population was highly clonal and inbred. This lack of recombination, paired with population stability, implies that selection is not acting on the forest S. paradoxus population on a seasonal timescale. Saccharomyces paradoxus may instead have evolved generalism or phenotypic plasticity with regard to seasonal environmental changes long ago. Similarly, while the forest population included diversity among phenotypes related to intraspecific interference competition, there was no evidence for active coevolution among these phenotypes. At least ten percent of the forest S. paradoxus individuals produced "killer toxins," which kill sensitive Saccharomyces cells, but the presence of a toxin-producing isolate did not predict resistance to the toxin among nearby isolates. How forest yeasts acclimate to changing environments remains an open question, and future studies should investigate the physiological responses that allow microbial cells to cope with environmental fluctuations in their native habitats.
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Affiliation(s)
- Primrose J. Boynton
- Biology DepartmentWheaton CollegeNortonMAUSA
- Environmental Genomics Research GroupMax‐Planck Institute for Evolutionary BiologyPlönGermany
| | - Dominika Wloch‐Salamon
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Doreen Landermann
- Environmental Genomics Research GroupMax‐Planck Institute for Evolutionary BiologyPlönGermany
| | - Eva H. Stukenbrock
- Environmental Genomics Research GroupMax‐Planck Institute for Evolutionary BiologyPlönGermany
- Botanical InstituteChristian‐Albrechts UniversitätKielGermany
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57
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Diego D, Hannisdal B, Dahle H. On how the power supply shapes microbial survival. Math Biosci 2021; 338:108615. [PMID: 33857526 DOI: 10.1016/j.mbs.2021.108615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/29/2021] [Accepted: 04/04/2021] [Indexed: 10/21/2022]
Abstract
Understanding how environmental factors affect microbial survival is an important open problem in microbial ecology. Patterns of microbial community structure have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and patterns of microbial survival. We reveal a complex set of interdependences between power supply and distributions of survival probability across microbial habitats, in a case without interspecific resource competition. We also find that different properties determining power supply, such as substrate fluxes and Gibbs energies of reactions, affect microbial survival in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of microbial survival across physicochemical gradients, such as pH gradients. Our findings show the importance of taking energy fluxes into account in order to reveal fundamental connections between microbial survival and environmental conditions, and to obtain a better understanding of microbial population dynamics in natural environments.
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Affiliation(s)
- David Diego
- Department of Earth Science, University of Bergen, Allégaten, NO-5007 Bergen, Norway; K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway.
| | - Bjarte Hannisdal
- Department of Earth Science, University of Bergen, Allégaten, NO-5007 Bergen, Norway; K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway
| | - Håkon Dahle
- K.G. Jebsen Centre for Deep Sea Research, Allégaten, NO-5007 Bergen, Norway; Department of Biological Sciences, University of Bergen, Thormøhlens gate 53A, NO-5006 Bergen, Norway; Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway
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58
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Ammitzboll H, Jordan GJ, Baker SC, Freeman J, Bissett A. Diversity and abundance of soil microbial communities decline, and community compositions change with severity of post-logging fire. Mol Ecol 2021; 30:2434-2448. [PMID: 33772907 DOI: 10.1111/mec.15900] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 03/11/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022]
Abstract
Understanding the effects of logging and fire on forest soil communities is integral to our knowledge of forest ecology and effective resource management. The resulting changes in soil biota have substantial impacts on forest succession and associated ecosystem processes. We quantified bacterial and fungal abundance, diversity and community composition across a logging and burn severity gradient, approximately one month after fire, in temperate wet eucalypt forests in Tasmania, Australia. Using amplicon sequencing and real-time quantitative PCR of the bacterial 16S rRNA gene and fungal ITS1 region, we demonstrate that (i) burn severity is a strong driver of soil microbial community composition, (ii) logging and high severity burning substantially reduce the biomass and diversity of soil bacteria and fungi, and (iii) the impacts of logging and burning on soil microbial communities are largely restricted to the top 10 cm of soil, with weak impacts on the subsoil. The impacts of disturbance on microbial community composition are greater than the effects of site-to-site edaphic differences. Fire also drives more divergence in community composition than logging alone. Key microbial taxa driving differences in severely burnt soils include bacterial genera implicated in plant-growth promotion and producing antifungal compounds as well as saprotrophic fungi that are also capable of forming ectomycorrhizal associations. Our research suggests that low-moderate severity burns are important for maintaining diversity and biomass in soil microbial communities but having a range of burn severities across a site contributes to the overall diversity of habitat conditions providing for both microbial and plant diversity.
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Affiliation(s)
- Hans Ammitzboll
- Biological Sciences, University of Tasmania, Hobart, Australia.,ARC Industrial Training Centre for Forest Value, University of Tasmania, Hobart, Australia
| | | | - Susan C Baker
- Biological Sciences, University of Tasmania, Hobart, Australia.,ARC Industrial Training Centre for Forest Value, University of Tasmania, Hobart, Australia
| | - Jules Freeman
- Biological Sciences, University of Tasmania, Hobart, Australia.,Forest Genetics, Scion, Rotorua, New Zealand
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McGinn J, Lamason RL. The enigmatic biology of rickettsiae: recent advances, open questions and outlook. Pathog Dis 2021; 79:ftab019. [PMID: 33784388 PMCID: PMC8035066 DOI: 10.1093/femspd/ftab019] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/26/2021] [Indexed: 02/05/2023] Open
Abstract
Rickettsiae are obligate intracellular bacteria that can cause life-threatening illnesses and are among the oldest known vector-borne pathogens. Members of this genus are extraordinarily diverse and exhibit a broad host range. To establish intracellular infection, Rickettsia species undergo complex, multistep life cycles that are encoded by heavily streamlined genomes. As a result of reductive genome evolution, rickettsiae are exquisitely tailored to their host cell environment but cannot survive extracellularly. This host-cell dependence makes for a compelling system to uncover novel host-pathogen biology, but it has also hindered experimental progress. Consequently, the molecular details of rickettsial biology and pathogenesis remain poorly understood. With recent advances in molecular biology and genetics, the field is poised to start unraveling the molecular mechanisms of these host-pathogen interactions. Here, we review recent discoveries that have shed light on key aspects of rickettsial biology. These studies have revealed that rickettsiae subvert host cells using mechanisms that are distinct from other better-studied pathogens, underscoring the great potential of the Rickettsia genus for revealing novel biology. We also highlight several open questions as promising areas for future study and discuss the path toward solving the fundamental mysteries of this neglected and emerging human pathogen.
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Affiliation(s)
- Jon McGinn
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Rebecca L Lamason
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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60
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Kleerebezem R, Stouten G, Koehorst J, Langenhoff A, Schaap P, Smidt H. Experimental infrastructure requirements for quantitative research on microbial communities. Curr Opin Biotechnol 2021; 67:158-165. [PMID: 33596519 DOI: 10.1016/j.copbio.2021.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/27/2023]
Abstract
Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of genomic data, main attention of microbial ecology research shifted from cultivation-oriented studies towards metagenomic studies. Despite these efforts, the direct link between the molecular properties and the measurable changes in the functional performance of the ecosystem is often poorly documented. A quantitative understanding of functional properties in relation to the molecular changes requires effective integration, standardization, and parallelization of experiments. High-resolution functional characterization is a prerequisite for interpretation of changes in metagenomic properties, and will improve our understanding of microbial communities and facilitate their exploration for health and circular economy related objectives.
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Affiliation(s)
- Robbert Kleerebezem
- Delft University of Technology, Department of Biotechnology, Delft, The Netherlands.
| | - Gerben Stouten
- Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Jasper Koehorst
- Wageningen University and Research, Laboratory of Systems and Synthetic Biology, Wageningen, The Netherlands
| | - Alette Langenhoff
- Wageningen University and Research, Department of Environmental Technology, Wageningen, The Netherlands
| | - Peter Schaap
- Wageningen University and Research, Laboratory of Systems and Synthetic Biology, Wageningen, The Netherlands
| | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
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61
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Juvigny-Khenafou NPD, Piggott JJ, Atkinson D, Zhang Y, Wu N, Matthaei CD. Fine sediment and flow velocity impact bacterial community and functional profile more than nutrient enrichment. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02212. [PMID: 32754996 DOI: 10.1002/eap.2212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Freshwater ecosystems face many simultaneous pressures due to human activities. Consequently, there has been a rapid loss of freshwater biodiversity and an increase in biomonitoring programs. Our study assessed the potential of benthic stream bacterial communities as indicators of multiple-stressor impacts associated with urbanization and agricultural intensification. We conducted a fully crossed four-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21 d of colonization, 21 d of manipulations) and investigated the effects of nutrient enrichment, flow-velocity reduction and added fine sediment after 2 and 3 weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S rRNA genes), as well as curated biological databases (METAGENassit, MetaCyc), to identify changes in bacterial relative abundances and predicted metabolic functional profile. Sediment addition and flow-velocity reduction were the most pervasive stressors. They both increased α-diversity and had strong taxon-specific effects on community composition and predicted functions. Sediment and flow velocity also interacted frequently, with 88% of all bacterial response variables showing two-way interactions and 33% showing three-way interactions including nutrient enrichment. Changes in relative abundances of common taxa were associated with shifts in dominant predicted functions, which can be extrapolated to underlaying stream-wide mechanisms such as carbon use and bacterial energy production pathways. Observed changes were largely stable over time and occurred after just 2 weeks of exposure, demonstrating that bacterial communities can be well-suited for early detection of multiple stressors. Overall, added sediment and reduced flow velocity impacted both bacterial community structure and predicted function more than nutrient enrichment. In future research and stream management, a holistic approach to studying multiple-stressor impacts should include multiple trophic levels with their functional responses, to enhance our mechanistic understanding of complex stressor effects and promote establishment of more efficient biomonitoring programs.
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Affiliation(s)
- Noël P D Juvigny-Khenafou
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
- Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road Suzhou, Jiangsu, 215123, China
| | - Jeremy J Piggott
- Trinity Centre for the Environment & Department of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - David Atkinson
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Yixin Zhang
- Department of Landscape Architecture, Soochow University, Suzhou, 215123, China
| | - Naicheng Wu
- Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road Suzhou, Jiangsu, 215123, China
| | - Christoph D Matthaei
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
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Djemiel C, Dequiedt S, Karimi B, Cottin A, Girier T, El Djoudi Y, Wincker P, Lelièvre M, Mondy S, Chemidlin Prévost-Bouré N, Maron PA, Ranjard L, Terrat S. BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons. BMC Bioinformatics 2020; 21:492. [PMID: 33129268 PMCID: PMC7603665 DOI: 10.1186/s12859-020-03829-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 10/21/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool. RESULTS BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups. CONCLUSIONS The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Battle Karimi
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Aurélien Cottin
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Thibault Girier
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Yassin El Djoudi
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Patrick Wincker
- CEA/Institut de Biologie François Jacob/Génoscope, 2, Rue Gaston Crémieux, CP5706, 91057, Evry Cedex, France
| | - Mélanie Lelièvre
- Agroécologie - Plateforme GenoSol, BP 86510, 21000, Dijon, France
| | - Samuel Mondy
- Agroécologie - Plateforme GenoSol, BP 86510, 21000, Dijon, France
| | | | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France.
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Egorova DA, Voronina OL, Solovyev AI, Kunda MS, Aksenova EI, Ryzhova NN, Danilova KV, Rykova VS, Scherbakova AA, Semenov AN, Polyakov NB, Grumov DA, Shevlyagina NV, Dolzhikova IV, Romanova YM, Gintsburg AL. Integrated into Environmental Biofilm Chromobacterium vaccinii Survives Winter with Support of Bacterial Community. Microorganisms 2020; 8:E1696. [PMID: 33143246 PMCID: PMC7716238 DOI: 10.3390/microorganisms8111696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/30/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022] Open
Abstract
Chromobacterium species are common in tropical and subtropical zones in environmental samples according to numerous studies. Here, we describe an environmental case of resident Chromobacterium vaccinii in biofilms associated with Carex spp. roots in Moscow region, Russia (warm-summer humid continental climate zone). We performed broad characterization of individual properties as well as surrounding context for better understanding of the premise of C. vaccinii survival during the winter season. Genome properties of isolated strains propose some insights into adaptation to habit and biofilm mode of life, including social cheaters carrying ΔluxR mutation. Isolated C. vaccinii differs from previously described strains in some biochemical properties and some basic characteristics like fatty acid composition as well as unique genome features. Despite potential to modulate membrane fluidity and presence of several genes responsible for cold shock response, isolated C. vaccinii did not survive during exposure to 4 °C, while in the complex biofilm sample, it was safely preserved for at least half a year in vitro at 4 °C. The surrounding bacterial community within the same biofilm with C. vaccinii represented a series of psychrophilic bacterial species, which may share resistance to low temperatures with other species within biofilm and provide C. vaccinii an opportunity to survive during the cold winter season.
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Affiliation(s)
- Daria A. Egorova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Olga L. Voronina
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Andrey I. Solovyev
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Marina S. Kunda
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Ekaterina I. Aksenova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Natalia N. Ryzhova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Ksenya V. Danilova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Valentina S. Rykova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Anastasya A. Scherbakova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Andrey N. Semenov
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Nikita B. Polyakov
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
- Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Daniil A. Grumov
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Natalia V. Shevlyagina
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Inna V. Dolzhikova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
| | - Yulia M. Romanova
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119991 Moscow, Russia
| | - Alexander L. Gintsburg
- N.F. Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health, 123098 Moscow, Russia; (A.I.S.); (M.S.K.); (E.I.A.); (N.N.R.); (K.V.D.); (V.S.R.); (A.A.S.); (A.N.S.); (N.B.P.); (D.A.G.); (N.V.S.); (I.V.D.); (Y.M.R.); (A.L.G.)
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119991 Moscow, Russia
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64
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Jiao C, Zhao D, Zeng J, Guo L, Yu Z. Disentangling the seasonal co-occurrence patterns and ecological stochasticity of planktonic and benthic bacterial communities within multiple lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140010. [PMID: 32563874 DOI: 10.1016/j.scitotenv.2020.140010] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Both the planktonic bacterial community (PBC) and benthic bacterial community (BBC) are important for biogeochemical processes in freshwater lakes. Despite their ecological significance, little is known about their seasonal co-occurrence patterns and the ecological processes that drive them. In this study, we aimed to investigate the ecological associations among bacterial taxa and assembly processes of PBC and BBC in different seasons. We used 16S rRNA gene high-throughput sequencing of a total of 150 water and sediment samples collected from multiple lakes distributed in an urban region of China during winter and summer. Our results revealed that PBC showed stronger seasonal variations in co-occurrence patterns than BBC, suggesting that BBC had greater temporal stability than PBC. Winter PBC network was characterized by higher connectivity and complexity, and thereby the formation of a highly stable community structure; whereas lower connectivity arising from the presence of fewer predicted keystone taxa (hubs and connectors in a network) was destabilizing to summer PBC network. In addition, the phylum Firmicutes identified as a putative keystone taxon of PBC in both seasons played a non-negligible role in maintaining network structure which may result from strong functional associations with other bacterioplankton. Temperature and pH were the best explanatory factors predicting the seasonal co-occurrence patterns of PBC and BBC, respectively. Normalized stochasticity ratio based on null-model analysis indicated that deterministic processes overwhelmed stochastic processes in governing the assembly of PBC and BBC in both seasons. However, we observed a greater influence of ecological stochasticity on BBC assembly than PBC assembly in both seasons. Taken together, these findings provide insights into understanding the impacts of habitat heterogeneity and seasonal variability on microbial assemblage patterns in lake ecosystems.
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Affiliation(s)
- Congcong Jiao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Lin Guo
- Department of Biological and Environmental Sciences, Texas A&M University, Commerce, TX 76129, USA
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China
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65
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Cooke J, Araya Y, Bacon KL, Bagniewska JM, Batty LC, Bishop TR, Burns M, Charalambous M, Daversa DR, Dougherty LR, Dyson M, Fisher AM, Forman D, Garcia C, Harney E, Hesselberg T, John EA, Knell RJ, Maseyk K, Mauchline AL, Peacock J, Pernetta AP, Pritchard J, Sutherland WJ, Thomas RL, Tigar B, Wheeler P, White RL, Worsfold NT, Lewis Z. Teaching and learning in ecology: a horizon scan of emerging challenges and solutions. OIKOS 2020. [DOI: 10.1111/oik.07847] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Julia Cooke
- School of Environment, Earth and Ecosystem Sciences, The Open Univ. UK
| | - Yoseph Araya
- School of Environment, Earth and Ecosystem Sciences, The Open Univ. UK
| | - Karen L. Bacon
- School of Geography, Univ. of Leeds UK
- Botany and Plant Sciences, Martin Ryan Inst., National Univ. of Ireland Galway Ireland
| | | | - Lesley C. Batty
- School of Geography, Earth and Environmental Sciences, Univ. of Birmingham Birmingham UK
| | - Tom R. Bishop
- Dept of Earth, Ocean and Ecological Sciences, Univ. of Liverpool Liverpool UK
- Dept of Zoology and Entomology, Univ. of Pretoria Pretoria South Africa
| | - Moya Burns
- School of Biological Sciences, College of Life Sciences, Univ. of Leicester UK
| | | | | | | | - Miranda Dyson
- School of Environment, Earth and Ecosystem Sciences, The Open Univ. UK
| | - Adam M. Fisher
- Inst. of Integrative Biology, Univ. of Liverpool Liverpool UK
| | - Dan Forman
- Dept of Biosciences, Swansea Univ. Swansea UK
| | - Cristina Garcia
- Inst. of Integrative Biology, Univ. of Liverpool Liverpool UK
| | - Ewan Harney
- Inst. of Integrative Biology, Univ. of Liverpool Liverpool UK
| | | | | | - Robert J. Knell
- School of Biological and Chemical Sciences, Queen Mary Univ. of London UK
| | - Kadmiel Maseyk
- School of Environment, Earth and Ecosystem Sciences, The Open Univ. UK
| | - Alice L. Mauchline
- School of Agriculture, Policy and Development, Univ. of Reading Reading UK
| | | | - Angelo P. Pernetta
- Ecology, Conservation and Zoonosis Research and Enterprise Group, School of Pharmacy and Biomolecular Sciences, Univ. of Brighton UK
| | | | | | - Rebecca L. Thomas
- Dept of Biological Sciences, Royal Holloway Univ. of London Egham UK
| | - Barbara Tigar
- School of Forensic and Applied Sciences, Univ. of Central Lancashire Preston UK
| | - Philip Wheeler
- School of Environment, Earth and Ecosystem Sciences, The Open Univ. UK
| | - Rachel L. White
- Ecology, Conservation and Zoonosis Research and Enterprise Group, School of Pharmacy and Biomolecular Sciences, Univ. of Brighton UK
| | - Nicholas T. Worsfold
- School of Geography, Earth and Environmental Sciences, Univ. of Birmingham Birmingham UK
| | - Zenobia Lewis
- School of Life Sciences, Univ. of Liverpool Liverpool L69 7ZB UK
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66
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Zhu YX, Song ZR, Song YL, Zhao DS, Hong XY. The microbiota in spider mite feces potentially reflects intestinal bacterial communities in the host. INSECT SCIENCE 2020; 27:859-868. [PMID: 31411007 DOI: 10.1111/1744-7917.12716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/30/2019] [Accepted: 08/10/2019] [Indexed: 05/25/2023]
Abstract
Microorganisms provide many physiological functions to herbivorous hosts. Spider mites (genus Tetranychus) are important agricultural pests throughout the world; however, the composition of the spider mite microbial community, especially gut microbiome, remains unclear. Here, we investigated the bacterial community in five spider mite species and their associated feces by deep sequencing of the 16S rRNA gene. The composition of the bacterial community was significantly different among the five prevalent spider mite species, and some bacterial symbionts showed host-species specificity. Moreover, the abundance of the bacterial community in spider mite feces was significantly higher than that in the corresponding spider mite samples. However, Flavobacterium was detected in all samples, and represent a "core microbiome". Remarkably, the maternally inherited endosymbiont Wolbachia was detected in both spider mite and feces. Overall, these results offer insight into the complex community of symbionts in spider mites, and give a new direction for future studies.
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Affiliation(s)
- Yu-Xi Zhu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Zhang-Rong Song
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Yue-Ling Song
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Dian-Shu Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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67
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Doane M, Haggerty JM, da Silva Lopes CR, Yates P, Edwards R, Dinsdale E, Lopes FAC, Bruce T. Latitude and chlorophyll a density drive the distribution of carbohydrate-active enzymes in the planktonic microbial fraction of the epipelagic zone. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:473-485. [PMID: 32608067 DOI: 10.1111/1758-2229.12865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/08/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Microbes drive the majority of the global carbon cycle. The effect of environmental conditions on selecting microbial functional diversity is well established, and recent studies have revealed the effects of geographic distances on selecting the functional components of marine microbial communities. Our study is the first attempt at establishing the effects of environmental factors on driving the marine carbohydrate-active enzyme (CAZyme) distribution. We characterized the diversity of CAZyme genes and investigated the correlations between their distributions and biogeographic parameters (latitude, longitude, distance from the equator, site depth, water depth, chlorophyll density, salinity and temperature). Therefore, we accessed a subset of surface water samples (38 metagenomes) from the Global Ocean Sampling project. Only chlorophyll and latitude altered the distribution patterns of CAZymes, revealing the existence of two latitudinal gradients (positive and negative) of marine CAZyme abundance. Considering the importance of carbohydrates in microbial life, characterization of the spatial patterns of the genetic repertoire involved in carbohydrate metabolism represents an important step in improving our understanding of the metabolic strategies associated with the microbial marine carbon cycle and their effects on the productivity of marine ecosystems.
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Affiliation(s)
- Michael Doane
- Biology Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
- Sydney Institute of Marine Science, 19 Chowder Bay, Mosman, New South Wales, 2088, Australia
| | - John Matthew Haggerty
- Biology Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
| | | | - Peter Yates
- Sydney Institute of Marine Science, 19 Chowder Bay, Mosman, New South Wales, 2088, Australia
| | - Rob Edwards
- Computational Science Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
| | - Elizabeth Dinsdale
- Biology Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
| | | | - Thiago Bruce
- Biology Department, San Diego State University, 550 Campanile Drive, San Diego, CA, 92182, USA
- Departamento de Biologia Celular, Laboratório de Enzimologia, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
- Departamento de Microbiologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Ondina, Salvador, BA, Brazil
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68
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Mammola S, Amorim IR, Bichuette ME, Borges PAV, Cheeptham N, Cooper SJB, Culver DC, Deharveng L, Eme D, Ferreira RL, Fišer C, Fišer Ž, Fong DW, Griebler C, Jeffery WR, Jugovic J, Kowalko JE, Lilley TM, Malard F, Manenti R, Martínez A, Meierhofer MB, Niemiller ML, Northup DE, Pellegrini TG, Pipan T, Protas M, Reboleira ASPS, Venarsky MP, Wynne JJ, Zagmajster M, Cardoso P. Fundamental research questions in subterranean biology. Biol Rev Camb Philos Soc 2020; 95:1855-1872. [DOI: 10.1111/brv.12642] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS) University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
- Molecular Ecology Group (MEG) Water Research Institute (IRSA), National Research Council (CNR) Corso Tonolli, 50 Pallanza 28922 Italy
| | - Isabel R. Amorim
- cE3c – Centre for Ecology Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Faculty of Agrarian and Environmental Sciences, Rua Capitão João d'Àvila Pico da Urze Angra do Heroísmo Azores 9700‐042 Portugal
| | - Maria E. Bichuette
- Laboratory of Subterranean Studies Federal University of São Carlos Rodovia Washington Luís km 235 São Carlos São Paulo 13565‐905 Brazil
| | - Paulo A. V. Borges
- cE3c – Centre for Ecology Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Faculty of Agrarian and Environmental Sciences, Rua Capitão João d'Àvila Pico da Urze Angra do Heroísmo Azores 9700‐042 Portugal
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science Thompson Rivers University 805 TRU Way Kamloops British Columbia Canada
| | - Steven J. B. Cooper
- Evolutionary Biology Unit South Australian Museum North Terrace Adelaide South Australia 5000 Australia
- Australian Centre for Evolutionary Biology and Biodiversity, and Environment Institute, School of Biological Sciences University of Adelaide Adelaide South Australia 5005 Australia
| | - David C. Culver
- Department of Environmental Science American University 4400 Massachusetts Avenue, N.W. Washington DC 20016 U.S.A
| | - Louis Deharveng
- UMR7205 – ISYEB Museum national d'Histoire naturelle 45 rue Buffon (CP50) Paris 75005 France
| | - David Eme
- IFREMER Centre Atlantique Unité Ecologie et Modèles pour l'Halieutique Rue de l'Île d'Yeu Nantes 44980 France
| | - Rodrigo Lopes Ferreira
- Center of Studies in Subterranean Biology, Biology Department Federal University of Lavras Campus Universitário Lavras Minas Gerais CEP 37202‐553 Brazil
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty University of Ljubljana Jamnikarjeva 101, PO BOX 2995 Ljubljana SI‐1000 Slovenia
| | - Žiga Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty University of Ljubljana Jamnikarjeva 101, PO BOX 2995 Ljubljana SI‐1000 Slovenia
| | - Daniel W. Fong
- Department of Biology American University 4400 Massachusetts Avenue, N.W. Washington DC 20016 U.S.A
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, Division of Limnology University of Vienna Althanstrasse 14 Vienna 1090 Austria
| | - William R. Jeffery
- Department of Biology University of Maryland College Park MD 20742 U.S.A
| | - Jure Jugovic
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies University of Primorska Glagoljaška 8 Koper SI‐6000 Slovenia
| | - Johanna E. Kowalko
- Harriet L. Wilkes Honors College Florida Atlantic University 5353 Parkside Dr Jupiter FL 33458 U.S.A
| | - Thomas M. Lilley
- BatLab Finland, Finnish Museum of Natural History University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
| | - Florian Malard
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés Univ. Lyon 1, ENTPE, CNRS, Université de Lyon, Bat. Forel 6 rue Raphaël Dubois Villeurbanne cedex 69622 France
| | - Raoul Manenti
- Department of Environmental Science and Policy Università degli Studi di Milano Via Celoria 26 Milan 20113 Italy
| | - Alejandro Martínez
- Molecular Ecology Group (MEG) Water Research Institute (IRSA), National Research Council (CNR) Corso Tonolli, 50 Pallanza 28922 Italy
| | - Melissa B. Meierhofer
- BatLab Finland, Finnish Museum of Natural History University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
- Department of Rangeland, Wildlife and Fisheries Management Texas A&M University 534 John Kimbrough Blvd. College Station TX 77843 U.S.A
| | - Matthew L. Niemiller
- Department of Biological Sciences The University of Alabama in Huntsville 301 Sparkman Drive NW Huntsville AL 35899 U.S.A
| | - Diana E. Northup
- Department of Biology University of New Mexico Albuquerque NM 87131‐0001 U.S.A
| | - Thais G. Pellegrini
- Center of Studies in Subterranean Biology, Biology Department Federal University of Lavras Campus Universitário Lavras Minas Gerais CEP 37202‐553 Brazil
| | - Tanja Pipan
- ZRC SAZU Karst Research Institute Novi trg 2 Ljubljana SI‐1000 Slovenia
- UNESCO Chair on Karst Education University of Nova Gorica Vipavska cesta Nova Gorica 5000 Slovenia
| | - Meredith Protas
- Department of Natural Sciences and Mathematics Domenicas University of California 50 Acacia Avenue San Rafael CA 94901 U.S.A
| | - Ana Sofia P. S. Reboleira
- Natural History Museum of Denmark University of Copenhagen Universitetsparken 15 Copenhagen 2100 Denmark
| | - Michael P. Venarsky
- Australian Rivers Institute Griffith University 170 Kessels Road Nathan Queensland 4111 Australia
| | - J. Judson Wynne
- Department of Biological Sciences, Center for Adaptable Western Landscapes Northern Arizona University Box 5640 Flagstaff AZ 86011 U.S.A
| | - Maja Zagmajster
- SubBio Lab, Department of Biology, Biotechnical Faculty University of Ljubljana Jamnikarjeva 101, PO BOX 2995 Ljubljana SI‐1000 Slovenia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS) University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
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69
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François S, Pybus OG. Towards an understanding of the avian virome. J Gen Virol 2020; 101:785-790. [PMID: 32519942 PMCID: PMC7641393 DOI: 10.1099/jgv.0.001447] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/21/2020] [Indexed: 02/06/2023] Open
Abstract
The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.
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Affiliation(s)
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, UK
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70
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Marinkovic ZS, Vulin C, Acman M, Song X, Di Meglio JM, Lindner AB, Hersen P. Observing Nutrient Gradients, Gene Expression and Growth Variation Using the "Yeast Machine" Microfluidic Device. Bio Protoc 2020; 10:e3668. [PMID: 33659338 DOI: 10.21769/bioprotoc.3668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/26/2020] [Accepted: 05/18/2020] [Indexed: 11/02/2022] Open
Abstract
The natural environment of microbial cells like bacteria and yeast is often a complex community in which growth and internal organization reflect morphogenetic processes and interactions that are dependent on spatial position and time. While most of research is performed in simple homogeneous environments (e.g., bulk liquid cultures), which cannot capture full spatiotemporal community dynamics, studying biofilms or colonies is complex and usually does not give access to the spatiotemporal dynamics at single cell level. Here, we detail a protocol for generation of a microfluidic device, the "yeast machine", with arrays of long monolayers of yeast colonies to advance the global understanding of how intercellular metabolic interactions affect the internal structure of colonies within defined and customizable spatial dimensions. With Saccharomyces cerevisiae as a model yeast system we used the "yeast machine" to demonstrate the emergence of glucose gradients by following expression of fluorescently labelled hexose transporters. We further quantified the expression spatial patterns with intra-colony growth rates and expression of other genes regulated by glucose availability. In addition to this, we showed that gradients of amino acids also form within a colony, potentially opening similar approaches to study spatiotemporal formation of gradients of many other nutrients and metabolic waste products. This approach could be used in the future to decipher the interplay between long-range metabolic interactions, cellular development, and morphogenesis in other same species or more complex multi-species systems at single-cell resolution and timescales relevant to ecology and evolution.
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Affiliation(s)
- Zoran S Marinkovic
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France.,U1284 INSERM and.,CRI, Université de Paris, 8-10 Rue Charles V, 75004, Paris, France
| | - Clément Vulin
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France.,Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland.,Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
| | - Mislav Acman
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France.,CRI, Université de Paris, 8-10 Rue Charles V, 75004, Paris, France
| | - Xiaohu Song
- U1284 INSERM and.,CRI, Université de Paris, 8-10 Rue Charles V, 75004, Paris, France
| | - Jean Marc Di Meglio
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France
| | - Ariel B Lindner
- U1284 INSERM and.,CRI, Université de Paris, 8-10 Rue Charles V, 75004, Paris, France
| | - Pascal Hersen
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France.,Institut Curie, PSL Research University, CNRS, Physico Chimie Curie, UMR 168, 75005, Paris, France.,Sorbonne Université, CNRS, Physico Chimie Curie, UMR 168, 75005, Paris, France
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71
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Macey MC, Fox-Powell M, Ramkissoon NK, Stephens BP, Barton T, Schwenzer SP, Pearson VK, Cousins CR, Olsson-Francis K. The identification of sulfide oxidation as a potential metabolism driving primary production on late Noachian Mars. Sci Rep 2020; 10:10941. [PMID: 32616785 PMCID: PMC7331718 DOI: 10.1038/s41598-020-67815-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/15/2020] [Indexed: 01/11/2023] Open
Abstract
The transition of the martian climate from the wet Noachian era to the dry Hesperian (4.1-3.0 Gya) likely resulted in saline surface waters that were rich in sulfur species. Terrestrial analogue environments that possess a similar chemistry to these proposed waters can be used to develop an understanding of the diversity of microorganisms that could have persisted on Mars under such conditions. Here, we report on the chemistry and microbial community of the highly reducing sediment of Colour Peak springs, a sulfidic and saline spring system located within the Canadian High Arctic. DNA and cDNA 16S rRNA gene profiling demonstrated that the microbial community was dominated by sulfur oxidising bacteria, suggesting that primary production in the sediment was driven by chemolithoautotrophic sulfur oxidation. It is possible that the sulfur oxidising bacteria also supported the persistence of the additional taxa. Gibbs energy values calculated for the brines, based on the chemistry of Gale crater, suggested that the oxidation of reduced sulfur species was an energetically viable metabolism for life on early Mars.
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Affiliation(s)
- M C Macey
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK.
| | - M Fox-Powell
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
- School of Earth and Environmental Sciences, University of St Andrews, Irvine Building, St Andrews, UK
| | - N K Ramkissoon
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - B P Stephens
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - T Barton
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - S P Schwenzer
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - V K Pearson
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - C R Cousins
- School of Earth and Environmental Sciences, University of St Andrews, Irvine Building, St Andrews, UK
| | - K Olsson-Francis
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
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72
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Liu K, Hou J, Liu Y, Hu A, Wang M, Wang F, Chen Y, Gu Z. Biogeography of the free-living and particle-attached bacteria in Tibetan lakes. FEMS Microbiol Ecol 2020; 95:5513440. [PMID: 31183497 DOI: 10.1093/femsec/fiz088] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 06/08/2019] [Indexed: 12/16/2022] Open
Abstract
The free-living (FL) and particle-attached (PA) bacteria have different dispersal potentials and ecological roles in aquatic ecosystems. However, our knowledge of their diversity and regional biogeographic patterns in high-altitude alpine lakes is limited. In this study, to investigate the diversity and geographic patterns of the FL and PA bacterial communities and to quantify the relative influence of environmental filtering and dispersal limitation in shaping the FL and PA bacterial communities, we collected surface water samples from 26 lakes over 1000 kilometers on the Tibetan Plateau. The majority of sequences exclusively in the FL bacteria were Actinobacteria (29.4%), Proteobacteria (27.7%) and Bacteroidetes (21.6%), while sequences exclusively in the PA bacteria were dominated by Proteobacteria (57.9%). The α-diversity indices, including Shannon index and Pielou's evenness, were significantly lower in the FL bacteria than that in PA bacteria. The surrounding soils as an important potential source contributed more to the diversity of the PA bacteria than the FL bacteria. Both of the FL and PA bacterial communities exhibited a significant regional distance-decay pattern. Environmental filtering and dispersal limitation were significantly related to the spatial variation of the FL and PA bacterial communities, whereas the environmental filtering/dispersal limitation effect ratio was higher in the FL bacterial communities. Our study is the first to describe the regional-scale spatial variability and to identify the factors that drive regional variability of the FL and PA bacterial communities in Tibetan lakes.
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Affiliation(s)
- Keshao Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juzhi Hou
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Anyi Hu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Mingda Wang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Wang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuying Chen
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengquan Gu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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73
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Juvigny-Khenafou NPD, Zhang Y, Piggott JJ, Atkinson D, Matthaei CD, Van Bael SA, Wu N. Anthropogenic stressors affect fungal more than bacterial communities in decaying leaf litter: A stream mesocosm experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:135053. [PMID: 31859062 DOI: 10.1016/j.scitotenv.2019.135053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Despite the progress made in environmental microbiology techniques and knowledge, the succession and functional changes of the microbial community under multiple stressors are still poorly understood. This is a substantial knowledge gap as microbial communities regulate the biogeochemistry of stream ecosystems. Our study assessed the structural and temporal changes in stream fungal and bacterial communities associated with decomposing leaf litter under a multiple-stressor scenario. We conducted a fully crossed 4-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21 days of colonisation, 21 days of manipulations) and investigated the effects of nutrient enrichment, flow velocity reduction and sedimentation after 2 and 3 weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S and 18S rRNA genes) to identify changes in microbial community composition. Our results indicate that (1) shifts in relative abundances of the pre-existing terrestrial microbial community, rather than changes in community identity, drove the observed responses to stressors; (2) changes in relative abundances within the microbial community paralleled decomposition rate patterns with time; (3) both fungal and bacterial communities had a certain resistance to stressors, as indicated by relatively minor changes in alpha diversity or multivariate community structure; (4) overall, stressor interactions were more common than stressor main effects when affecting microbial diversity metrics or abundant individual genera; and (5) stressor effects on microbes often changed from 2 weeks to 3 weeks of stressor exposure, with several response patterns being reversed. Our study suggests that future research should focus more on understanding the temporal dynamics of fungal and bacterial communities and how they relate to ecosystem processes to advance our understanding of the mechanisms associated with multiple-stressor interactions.
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Affiliation(s)
- Noël P D Juvigny-Khenafou
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK; Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Yixin Zhang
- Department of Landscape Architecture, Gold Mantis School of Architecture, Soochow University, Suzhou, China.
| | - Jeremy J Piggott
- Trinity Centre for the Environment & Department of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - David Atkinson
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Christoph D Matthaei
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Sunshine A Van Bael
- Department of Ecology and Evolutionary Biology, Tulane University, 6823 St. Charles Avenue, Boggs 400, New Orleans, LA 70118, USA
| | - Naicheng Wu
- Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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74
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Kambe J, Sasaki Y, Inoue R, Tomonaga S, Kinjo T, Watanabe G, Jin W, Nagaoka K. Analysis of infant microbiota composition and the relationship with breast milk components in the Asian elephant (Elephas maximus) at the zoo. J Vet Med Sci 2020; 82:983-989. [PMID: 32350162 PMCID: PMC7399312 DOI: 10.1292/jvms.20-0190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The prevention of diseases through health control is essential at zoos. Here, we investigated the gut microbiota formation during infancy in an Asian elephant and compared the
composition between infant and mother. Besides, we analyzed the components of breast milk and examined the correlation with the infant gut microbiota. Analysis revealed the gut
microbiota of the infant contained high amount of Lactobacillales and its diversity was relatively low compared to that of the mother. We found several milk
components, showed a positive correlation with the change of Lactobacillales. The present study revealed the mechanism of gut microbiota formation during infancy
in an Asian elephant and provides important insights into the health control of Asian elephants in zoos.
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Affiliation(s)
- Jun Kambe
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Yu Sasaki
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Department of Applied Biological Sciences, Setsunan University, Osaka 573-0101, Japan
| | - Shozo Tomonaga
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Teruo Kinjo
- Okinawa Zoo Animal Hospital, Okinawa Zoo and Museum, Okinawa 904-0021, Japan
| | - Gen Watanabe
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Wanzhu Jin
- Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen West Road, Chaoyang, Beijing, China
| | - Kentaro Nagaoka
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
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75
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Liu K, Liu Y, Hu A, Wang F, Chen Y, Gu Z, Anslan S, Hou J. Different community assembly mechanisms underlie similar biogeography of bacteria and microeukaryotes in Tibetan lakes. FEMS Microbiol Ecol 2020; 96:5822764. [DOI: 10.1093/femsec/fiaa071] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/18/2020] [Indexed: 01/05/2023] Open
Abstract
ABSTRACTGeographic patterns of bacteria and microeukaryotes have attracted increasing attention. However, mechanisms underlying geographic patterns in the community composition of both microbial groups are still poorly resolved. In particular, knowledge of whether bacterial communities and microeukaryotic communities are subject to the same or different assembly mechanisms is still limited. In this study, we investigated the biogeographic patterns of bacterial and microeukaryotic communities of 23 lakes on the Tibetan Plateau and quantified the relative influence of assembly mechanisms in shaping both microbial communities. Results showed that water salinity was the major driving force in controlling the community structures of bacteria and microeukaryotes. Although bacterial and microeukaryotic communities exhibited similar distance-decay patterns, the bacterial communities were mainly governed by environmental filtering (a niche-related process), whereas microeukaryotic communities were strongly driven by dispersal limitation (a neutral-related process). Furthermore, we found that bacteria exhibited wider niche breadths and higher dispersal ability but lower community stabilities than microeukaryotes. The similar distribution patterns but contrasting assembly mechanisms effecting bacteria and microeukaryotes resulted from the differences in dispersal ability and community stability. Our results highlight the importance of considering organism types in studies of the assembly mechanisms that shape microbial communities in microbial ecology.
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Affiliation(s)
- Keshao Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101, China
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Feng Wang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuying Chen
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengquan Gu
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sten Anslan
- Technische Universität Braunschweig, Zoological Institute, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Juzhi Hou
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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76
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Rojas CA, Holekamp KE, Winters AD, Theis KR. Body site-specific microbiota reflect sex and age-class among wild spotted hyenas. FEMS Microbiol Ecol 2020; 96:5700710. [PMID: 31926016 DOI: 10.1093/femsec/fiaa007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
Host-associated microbial communities, henceforth 'microbiota', can affect the physiology and behavior of their hosts. In mammals, host ecological, social and environmental variables are associated with variation in microbial communities. Within individuals in a given mammalian species, the microbiota also partitions by body site. Here, we build on this work and sequence the bacterial 16S rRNA gene to profile the microbiota at six distinct body sites (ear, nasal and oral cavities, prepuce, rectum and anal scent gland) in a population of wild spotted hyenas (Crocuta crocuta), which are highly social, large African carnivores. We inquired whether microbiota at these body sites vary with host sex or social rank among juvenile hyenas, and whether they differ between juvenile females and adult females. We found that the scent gland microbiota differed between juvenile males and juvenile females, whereas the prepuce and rectal microbiota differed between adult females and juvenile females. Social rank, however, was not a significant predictor of microbiota profiles. Additionally, the microbiota varied considerably among the six sampled body sites and exhibited strong specificity among individual hyenas. Thus, our findings suggest that site-specific niche selection is a primary driver of microbiota structure in mammals, but endogenous host factors may also be influential.
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Affiliation(s)
- Connie A Rojas
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Andrew D Winters
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
| | - Kevin R Theis
- BEACON Center for the Study of Evolution in Action, Michigan State University, 567 Wilson Rd, East Lansing, MI, 48824, USA.,Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, 540 E Canfield St, Detroit, MI, 48201, USA
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77
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Dey CJ, Rego AI, Midwood JD, Koops MA. A review and meta-analysis of collaborative research prioritization studies in ecology, biodiversity conservation and environmental science. Proc Biol Sci 2020; 287:20200012. [PMID: 32183628 PMCID: PMC7126043 DOI: 10.1098/rspb.2020.0012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/17/2020] [Indexed: 11/12/2022] Open
Abstract
Collaborative research prioritization (CRP) studies have become increasingly popular during the last decade. By bringing together a diverse group of stakeholders, and using a democratic process to create a list of research priorities, these methods purport to identify research topics that will better meet the needs of science users. Here, we review 41 CRP studies in the fields of ecology, biodiversity conservation and environmental science that collectively identify 2031 research priorities. We demonstrate that climate change, ecosystem services and protected areas are common terms found in the research priorities of many CRP studies, and that identified research priorities have become less unique over time. In addition, we show that there is a considerable variation in the size and composition of the groups involved in CRP studies, and that at least one aspect of the identified research priorities (lexical diversity) is related to the size of the CRP group. Although some CRP studies have been highly cited, the evidence that CRP studies have directly motivated research is weak, perhaps because most CRP studies have not directly involved organizations that fund science. We suggest that the most important impact of CRP studies may lie in their ability to connect individuals across sectors and help to build diverse communities of practice around important issues at the science-policy interface.
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Affiliation(s)
- Cody J. Dey
- Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, Ontario, CanadaL7S 1A1
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78
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Fountain-Jones NM, Clark NJ, Kinsley AC, Carstensen M, Forester J, Johnson TJ, Miller EA, Moore S, Wolf TM, Craft ME. Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition. J Anim Ecol 2020; 89:817-828. [PMID: 31782152 DOI: 10.1111/1365-2656.13154] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 11/04/2019] [Indexed: 01/04/2023]
Abstract
Microbial communities are increasingly recognized as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free-living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison with other factors such as host characteristics or spatial proximity of hosts. Here, we ask how gut microbial communities are structured in a population of North American moose Alces alces. We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition. We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information. We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy. Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non-model hosts.
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Affiliation(s)
| | - Nicholas J Clark
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, The University of Queensland, Gatton, Qld, Australia
| | - Amy C Kinsley
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA.,Center for Animal Health and Food Safety, University of Minnesota, St Paul, MN, USA
| | - Michelle Carstensen
- Minnesota Department of Natural Resources, Wildlife Health Program, Forest Lake, MN, USA
| | - James Forester
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St Paul, MN, USA
| | - Timothy J Johnson
- Center for Animal Health and Food Safety, University of Minnesota, St Paul, MN, USA
| | - Elizabeth A Miller
- Center for Animal Health and Food Safety, University of Minnesota, St Paul, MN, USA
| | - Seth Moore
- Department of Biology and Environment, Grand Portage Band of Chippewa, Grand Portage, MN, USA
| | - Tiffany M Wolf
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, USA
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79
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Le Page G, Gunnarsson L, Trznadel M, Wedgwood KCA, Baudrot V, Snape J, Tyler CR. Variability in cyanobacteria sensitivity to antibiotics and implications for environmental risk assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133804. [PMID: 31419690 DOI: 10.1016/j.scitotenv.2019.133804] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/05/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Once released into the environment antibiotics can kill or inhibit the growth of bacteria, and in turn potentially have effects on bacterial community structure and ecosystem function. Environmental risk assessment (ERA) seeks to establish protection limits to minimise chemical impacts on the environment, but recent evidence suggests that the current regulatory approaches for ERA for antibiotics may not be adequate for protecting bacteria that have fundamental roles in ecosystem function. In this study we assess the differences in interspecies sensitivity of eight species of cyanobacteria to seven antibiotics (cefazolin, cefotaxime, ampicillin, sufamethazine, sulfadiazine, azithromycin and erythromycin) with three different modes of action. We found that variability in the sensitivity to these antibiotics between species was dependent on the mode of action and varied by up to 70 times for β-lactams. Probabilistic analysis using species sensitivity distributions suggest that the current predicted no effect concentration PNEC for the antibiotics may be either over or under protective of cyanobacteria dependent on the species on which it is based and the mode of action of the antibiotic; the PNECs derived for the macrolide antibiotics were over protective but PNECs for β-lactams were generally under protective. For some geographical locations we identify a significant risk to cyanobacteria populations based upon measured environmental concentrations of selected antibiotics. We conclude that protection limits, as determined according to current regulatory guidance, may not always be protective and might be better derived using SSDs and that including toxicity data for a wider range of (cyano-) bacteria would improve confidence for the ERA of antibiotics.
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Affiliation(s)
- Gareth Le Page
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Lina Gunnarsson
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Maciej Trznadel
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Kyle C A Wedgwood
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Living Systems Institute, Stocker Road, Exeter, Devon, EX4 4QD, UK
| | | | - Jason Snape
- AstraZeneca, Global Safety, Health and Environment, Alderley Park, Macclesfield, Cheshire SK10 4TF, UK; School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry CV4 7AL, UK
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK.
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80
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Deb R, Nair A, Agashe D. Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies. PeerJ 2019; 7:e8058. [PMID: 31763071 PMCID: PMC6870522 DOI: 10.7717/peerj.8058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/18/2019] [Indexed: 02/01/2023] Open
Abstract
Host-associated gut microbiota can have significant impacts on host ecology and evolution and are often host-specific. Multiple factors can contribute to such host-specificity: (1) host dietary specialization passively determining microbial colonization, (2) hosts selecting for specific diet-acquired microbiota, or (3) a combination of both. The latter possibilities indicate a functional association and should produce stable microbiota. We tested these alternatives by analyzing the gut bacterial communities of six species of wild adult dragonfly populations collected across several geographic locations. The bacterial community composition was predominantly explained by sampling location, and only secondarily by host identity. To distinguish the role of host dietary specialization and host-imposed selection, we identified prey in the guts of three dragonfly species. Surprisingly, the dragonflies–considered to be generalist predators–consumed distinct prey; and the prey diversity was strongly correlated with the gut bacterial profile. Such host dietary specialization and spatial variation in bacterial communities suggested passive rather than selective underlying processes. Indeed, the abundance and distribution of 72% of bacterial taxa were consistent with neutral community assembly; and fluorescent in situ hybridization revealed that bacteria only rarely colonized the gut lining. Our results contradict the expectation that host-imposed selection shapes the gut microbiota of most insects, and highlight the importance of joint analyses of diet and gut microbiota of natural host populations.
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Affiliation(s)
- Rittik Deb
- National Centre for Biological Sciences, TIFR, Bangalore, Karnataka, India
| | - Ashwin Nair
- National Centre for Biological Sciences, TIFR, Bangalore, Karnataka, India.,Shanmugha Arts, Science, Technology & Research Academy (SASTRA University), Thanjavur, Tamil Nadu, India
| | - Deepa Agashe
- National Centre for Biological Sciences, TIFR, Bangalore, Karnataka, India
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81
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Falk N, Reid T, Skoyles A, Grgicak-Mannion A, Drouillard K, Weisener CG. Microbial metatranscriptomic investigations across contaminant gradients of the Detroit River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:121-131. [PMID: 31284186 DOI: 10.1016/j.scitotenv.2019.06.451] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 06/09/2023]
Abstract
Microbial community function in freshwater sediments is influenced by the presence and persistence of anthropogenic pollutants, yet simultaneously imposes significant control on their transformation. Thus, microbes provide valuable ecosystem services in terms of biodegradation and bioindicators of compromised habitats. From a remediation perspective it is valuable to leverage the suite of microbial genes at the transcriptional level that are active in either natural versus stressed environments to provide insight into the cycling and fate of contaminants. Metatranscriptomic analysis of total bacterial and archaeal messenger RNA (mRNA) is a useful tool in this facet and was applied to sediments sampled from the Detroit River; a binational Area of Concern (AOC) in the Great Lakes. Previously established sediment surveys and modelling delineated the river into contaminant gradients based on concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and metals. Differential expression analysis through DESeq2 revealed that microbial transcripts associated with nitrate reduction, methanogenesis, and beta-oxidation were significant in legacy polluted sediments and linked with energetic pathways key in the generation of cellular currencies (acetyl-CoA, succinyl-CoA). Gluconeogenesis and polyester synthesis also showed high abundance in contaminated regions, along with increased expression of stress response genes and transposons, despite decreases in community α-diversity. Aromatic cleavage genes were detected, but in low abundance across the contaminant gradient. These results suggest that microbial communities within the Detroit River exploit unique anabolic and catabolic pathways to derive and store energy from legacy organic contaminants while simultaneously recruiting stress-response and gene transfer mechanisms to cope with xenobiotic pressures. By coupling well-resolved chemical datasets with metatranscriptomics, this study adds to the spatial understanding of in-situ microbial activities in pristine and perturbed freshwater sediments.
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Affiliation(s)
- N Falk
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada.
| | - T Reid
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
| | - A Skoyles
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
| | - A Grgicak-Mannion
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
| | - K Drouillard
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
| | - C G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, 2990 Riverside Dr W, Windsor, ON N9C 1A2, Canada
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82
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Griffiths SM, Antwis RE, Lenzi L, Lucaci A, Behringer DC, Butler MJ, Preziosi RF. Host genetics and geography influence microbiome composition in the sponge Ircinia campana. J Anim Ecol 2019; 88:1684-1695. [PMID: 31325164 PMCID: PMC6899969 DOI: 10.1111/1365-2656.13065] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022]
Abstract
Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome. Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome. We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing. We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location. Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco-evolutionary dynamics of host-associated microbiomes.
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Affiliation(s)
- Sarah M. Griffiths
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
| | - Rachael E. Antwis
- School of Environment and Life SciencesUniversity of SalfordSalfordUK
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Anita Lucaci
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Donald C. Behringer
- Fisheries and Aquatic SciencesUniversity of FloridaGainesvilleFLUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFLUSA
| | - Mark J. Butler
- Department of Biological SciencesOld Dominion UniversityNorfolkVAUSA
| | - Richard F. Preziosi
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
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83
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Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nat Commun 2019; 10:4841. [PMID: 31649246 PMCID: PMC6813331 DOI: 10.1038/s41467-019-12798-y] [Citation(s) in RCA: 485] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/01/2019] [Indexed: 12/03/2022] Open
Abstract
The soil microbiome is highly diverse and comprises up to one quarter of Earth’s diversity. Yet, how such a diverse and functionally complex microbiome influences ecosystem functioning remains unclear. Here we manipulated the soil microbiome in experimental grassland ecosystems and observed that microbiome diversity and microbial network complexity positively influenced multiple ecosystem functions related to nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed microbial networks and reduced microbial richness had the lowest multifunctionality due to fewer taxa present that support the same function (redundancy) and lower diversity of taxa that support different functions (reduced functional uniqueness). Moreover, different microbial taxa explained different ecosystem functions pointing to the significance of functional diversity in microbial communities. These findings indicate the importance of microbial interactions within and among fungal and bacterial communities for enhancing ecosystem performance and demonstrate that the extinction of complex ecological associations belowground can impair ecosystem functioning. There is ongoing interest in linking soil microbial diversity to ecosystem function. Here the authors manipulate the diversity and composition of microbial communities and show that complex microbial networks contribute more to ecosystem multifunctionality than simpler or low-diversity networks.
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84
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Marinkovic ZS, Vulin C, Acman M, Song X, Di Meglio JM, Lindner AB, Hersen P. A microfluidic device for inferring metabolic landscapes in yeast monolayer colonies. eLife 2019; 8:e47951. [PMID: 31259688 PMCID: PMC6624017 DOI: 10.7554/elife.47951] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/30/2019] [Indexed: 01/15/2023] Open
Abstract
Microbial colonies are fascinating structures in which growth and internal organization reflect complex morphogenetic processes. Here, we generated a microfluidics device with arrays of long monolayer yeast colonies to further global understanding of how intercellular metabolic interactions affect the internal structure of colonies within defined boundary conditions. We observed the emergence of stable glucose gradients using fluorescently labeled hexose transporters and quantified the spatial correlations with intra-colony growth rates and expression of other genes regulated by glucose availability. These landscapes depended on the external glucose concentration as well as secondary gradients, for example amino acid availability. This work demonstrates the regulatory genetic networks governing cellular physiological adaptation are the key to internal structuration of cellular assemblies. This approach could be used in the future to decipher the interplay between long-range metabolic interactions, cellular development and morphogenesis in more complex systems.
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Affiliation(s)
- Zoran S Marinkovic
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
- U1001 INSERMParisFrance
- CRIUniversité de ParisParisFrance
| | - Clément Vulin
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
- Institute of Biogeochemistry and Pollutant DynamicsETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyEawagDübendorfSwitzerland
| | - Mislav Acman
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
- CRIUniversité de ParisParisFrance
| | | | - Jean-Marc Di Meglio
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
| | | | - Pascal Hersen
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
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85
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Estrada A, Hughey MC, Medina D, Rebollar EA, Walke JB, Harris RN, Belden LK. Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling. PeerJ 2019; 7:e7044. [PMID: 31275740 PMCID: PMC6590418 DOI: 10.7717/peerj.7044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/27/2019] [Indexed: 12/28/2022] Open
Abstract
The amphibian skin microbiome has been the focus of recent studies aiming to better understand the role of these microbial symbionts in host defense against disease. However, host-associated microbial communities are complex and dynamic, and changes in their composition and structure can influence their function. Understanding temporal variation of bacterial communities on amphibian skin is critical for establishing baselines from which to improve the development of mitigation techniques based on probiotic therapy and provides long-term host protection in a changing environment. Here, we investigated whether microbial communities on amphibian skin change over time at a single site. To examine this, we collected skin swabs from two pond-breeding species of treefrogs, Agalychnis callidryas and Dendropsophus ebraccatus, over 4 years at a single lowland tropical pond in Panamá. Relative abundance of operational taxonomic units (OTUs) based on 16S rRNA gene amplicon sequencing was used to determine bacterial community diversity on the skin of both treefrog species. We found significant variation in bacterial community structure across long and short-term time scales. Skin bacterial communities differed across years on both species and between seasons and sampling days only in D. ebraccatus. Importantly, bacterial community structures across days were as variable as year level comparisons. The differences in bacterial community were driven primarily by differences in relative abundance of key OTUs and explained by rainfall at the time of sampling. These findings suggest that skin-associated microbiomes are highly variable across time, and that for tropical lowland sites, rainfall is a good predictor of variability. However, more research is necessary to elucidate the significance of temporal variation in bacterial skin communities and their maintenance for amphibian conservation efforts.
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Affiliation(s)
- Angie Estrada
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Myra C Hughey
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jenifer B Walke
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Smithsonian Tropical Research Institute, Balboa, Ancón, Panamá, Panamá
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86
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Rath KM, Fierer N, Murphy DV, Rousk J. Linking bacterial community composition to soil salinity along environmental gradients. THE ISME JOURNAL 2019; 13:836-846. [PMID: 30446737 PMCID: PMC6461869 DOI: 10.1038/s41396-018-0313-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/30/2018] [Accepted: 10/19/2018] [Indexed: 11/09/2022]
Abstract
Salinization is recognized as a threat to soil fertility worldwide. A challenge in understanding the effects of salinity on soil microbial communities is the fact that it can be difficult to disentangle the effects of salinity from those of other variables that may co-vary with salinity. Here we use a trait-based approach to identify direct effects of salinity on soil bacterial communities across two salinity gradients. Through dose-response relationships between salinity and bacterial growth, we quantified distributions of the trait salt tolerance within the communities. Community salt tolerance was closely correlated with soil salinity, indicating a strong filtering effect of salinity on the bacterial communities. Accompanying the increases in salt tolerance were consistent shifts in bacterial community composition. We identified specific bacterial taxa that increased in relative abundances with community salt tolerance, which could be used as bioindicators for high community salt tolerance. A strong filtering effect was also observed for pH across the gradients, with pH tolerance of bacterial communities correlated to soil pH. We propose phenotypic trait distributions aggregated at the community level as a useful approach to study the role of environmental factors as filters of microbial community composition.
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Affiliation(s)
- Kristin M Rath
- Department of Biology, Section of Microbial Ecology, Lund University, Lund, Sweden
- Centre for Environmental and Climate Research (CEC), Lund University, Lund, Sweden
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Daniel V Murphy
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Johannes Rousk
- Department of Biology, Section of Microbial Ecology, Lund University, Lund, Sweden.
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87
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Mansfeldt C, Achermann S, Men Y, Walser JC, Villez K, Joss A, Johnson DR, Fenner K. Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities. ISME JOURNAL 2019; 13:1589-1601. [PMID: 30787397 DOI: 10.1038/s41396-019-0371-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 12/22/2022]
Abstract
A remaining challenge within microbial ecology is to understand the determinants of richness and diversity observed in environmental microbial communities. In a range of systems, including activated sludge bioreactors, the microbial residence time (MRT) has been previously shown to shape the microbial community composition. However, the physiological and ecological mechanisms driving this influence have remained unclear. Here, this relationship is explored by analyzing an activated sludge system fed with municipal wastewater. Using a model designed in this study based on Monod-growth kinetics, longer MRTs were shown to increase the range of growth parameters that enable persistence, resulting in increased richness and diversity in the modeled community. In laboratory experiments, six sequencing batch reactors treating domestic wastewater were operated in parallel at MRTs between 1 and 15 days. The communities were characterized using both 16S ribosomal RNA and non-target messenger RNA sequencing (metatranscriptomic analysis), and model-predicted monotonic increases in richness were confirmed in both profiles. Accordingly, taxonomic Shannon diversity also increased with MRT. In contrast, the diversity in enzyme class annotations resulting from the metatranscriptomic analysis displayed a non-monotonic trend over the MRT gradient. Disproportionately high abundances of transcripts encoding for rarer enzymes occur at longer MRTs and lead to the disconnect between taxonomic and functional diversity profiles.
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Affiliation(s)
- Cresten Mansfeldt
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland.
| | - Stefan Achermann
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092, Zürich, Switzerland
| | - Yujie Men
- Department of Civil and Environmental Engineering, University of Illinois, 205N. Mathews Ave., Urbana, IL, 61801, USA
| | - Jean-Claude Walser
- Department of Environmental Systems Science, Genetic Diversity Centre, ETH Zürich, Universitätstrasse 16, 8006, Zürich, Switzerland
| | - Kris Villez
- Department of Process Engineering, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Adriano Joss
- Department of Process Engineering, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Kathrin Fenner
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092, Zürich, Switzerland.,Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
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88
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Friberg IM, Taylor JD, Jackson JA. Diet in the Driving Seat: Natural Diet-Immunity-Microbiome Interactions in Wild Fish. Front Immunol 2019; 10:243. [PMID: 30837993 PMCID: PMC6389695 DOI: 10.3389/fimmu.2019.00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/28/2019] [Indexed: 12/18/2022] Open
Abstract
Natural interactions between the diet, microbiome, and immunity are largely unstudied. Here we employ wild three-spined sticklebacks as a model, combining field observations with complementary experimental manipulations of diet designed to mimic seasonal variation in the wild. We clearly demonstrate that season-specific diets are a powerful causal driver of major systemic immunophenotypic variation. This effect occurred largely independently of the bulk composition of the bacterial microbiome (which was also driven by season and diet) and of host condition, demonstrating neither of these, per se, constrain immune allocation in healthy individuals. Nonetheless, through observations in multiple anatomical compartments, differentially exposed to the direct effects of food and immunity, we found evidence of immune-driven control of bacterial community composition in mucus layers. This points to the interactive nature of the host-microbiome relationship, and is the first time, to our knowledge, that this causal chain (diet → immunity → microbiome) has been demonstrated in wild vertebrates. Microbiome effects on immunity were not excluded and, importantly, we identified outgrowth of potentially pathogenic bacteria (especially mycolic-acid producing corynebacteria) as a consequence of the more animal-protein-rich summertime diet. This may provide part of the ultimate explanation (and possibly a proximal cue) for the dramatic immune re-adjustments that we saw in response to diet change.
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Affiliation(s)
- Ida M Friberg
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Joe D Taylor
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Joseph A Jackson
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
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89
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Antwis RE, Edwards KL, Unwin B, Walker SL, Shultz S. Rare gut microbiota associated with breeding success, hormone metabolites and ovarian cycle phase in the critically endangered eastern black rhino. MICROBIOME 2019; 7:27. [PMID: 30770764 PMCID: PMC6377766 DOI: 10.1186/s40168-019-0639-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/29/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Host microbiomes play a role in hormone production and subsequent fertility in humans, but this is less well understood in non-model organisms. This is of particular relevance to species in zoo-based conservation breeding programmes, as relationships between host microbiome composition and reproductive output may allow for the development of microbial augmentation strategies to improve success. Here, we characterise faecal bacterial communities of breeding and non-breeding eastern black rhino (Diceros bicornis michaeli) using 16S rRNA gene amplicon sequencing and quantify progestagen and glucocorticoid metabolite concentrations through enzyme immunoassays to identify such relationships. RESULTS We identified significant differences in black rhino gut microbiome composition according to ID, institution, breeding success and ovarian cycle phase. In particular, the gut microbiome during pregnancy and post-parturition was significantly altered. Around a third of bacterial genera showed more than ± 10% correlation with either progestagen and/or glucocorticoid concentration, and in general, microbial genera correlated with both hormones in the same direction. Through a combination of analyses, we identified four genera (Aerococcaceae, Atopostipes, Carnobacteriaceae and Solobacterium) that were significantly associated with breeding success, pregnancy and/or post-parturition, and higher faecal progestagen metabolite concentrations. These genera had a lower-than-average relative abundance in the gut microbiome. CONCLUSION Our results indicate that many members of the gut microbiome of black rhino are associated with hormone production and breeding success, and some members of the rare microbiota appear to be particularly important. Although the directionality of the relationship is unclear, the variation in gut microbiome communities represents a potential biomarker of reproductive health. We identified four genera that were associated with multiple indicators of reproductive output; these could be candidate probiotics to improve the breeding success of black rhino in zoo-based conservation breeding programmes. Further work is required to understand the efficacy and feasibility of this, either directly through microbial augmentation (e.g. probiotics) or indirectly via dietary manipulation or prebiotics.
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Affiliation(s)
- Rachael E Antwis
- School of Environment and Life Sciences, University of Salford, Salford, UK.
| | - Katie L Edwards
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Bryony Unwin
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Susan L Walker
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Susanne Shultz
- School of Earth and Environmental Sciences, University of Manchester, Manchester, UK
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90
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Marco DE, Abram F. Editorial: Using Genomics, Metagenomics and Other "Omics" to Assess Valuable Microbial Ecosystem Services and Novel Biotechnological Applications. Front Microbiol 2019; 10:151. [PMID: 30809205 PMCID: PMC6379446 DOI: 10.3389/fmicb.2019.00151] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/22/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Diana E. Marco
- Faculty of Exact, Physical and Biological Sciences, CONICET, Córdoba National University, Córdoba, Argentina
| | - Florence Abram
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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91
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Trevelline BK, Fontaine SS, Hartup BK, Kohl KD. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc Biol Sci 2019; 286:20182448. [PMID: 30963956 PMCID: PMC6364583 DOI: 10.1098/rspb.2018.2448] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022] Open
Abstract
The central aim of conservation biology is to understand and mitigate the effects of human activities on biodiversity. To successfully achieve this objective, researchers must take an interdisciplinary approach that fully considers the effects, both direct and indirect, of anthropogenic disturbances on wildlife physiology and health. A recent surge in research has revealed that host-associated microbiota-the archaeal, bacterial, fungal and viral communities residing on and inside organisms-profoundly influence animal health, and that these microbial communities can be drastically altered by anthropogenic activities. Therefore, conservation practitioners should consider the disruption of host-associated microbial diversity as a serious threat to wildlife populations. Despite the tremendous potential for microbiome research to improve conservation outcomes, few efforts have been made to truly integrate these fields. In this review, we call for the microbial renaissance of conservation biology, where biodiversity of host-associated microbiota is recognized as an essential component of wildlife management practices. Using evidence from the existing literature, we will examine the known effects of anthropogenic activities on the diversity of host-associated microbial communities and integrate approaches for maintaining microbial diversity to successfully achieve conservation objectives.
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Affiliation(s)
- Brian K. Trevelline
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samantha S. Fontaine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Barry K. Hartup
- Department of Conservation Medicine, International Crane Foundation, Baraboo, WI, USA
- School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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92
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Jacquiod S, Nunes I, Brejnrod A, Hansen MA, Holm PE, Johansen A, Brandt KK, Priemé A, Sørensen SJ. Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages. MICROBIOME 2018; 6:223. [PMID: 30545417 PMCID: PMC6292020 DOI: 10.1186/s40168-018-0606-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/25/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches (16S rRNA gene transcript amplicon coupled to shotgun mRNA sequencing) to study the legacy effects of a century-long soil copper (Cu) pollution on microbial activity and composition, as well as its effect on the capacity of the microbial community to react to temporal fluctuations. RESULTS Despite evidence of microbial adaptation (e.g., iron homeostasis and avoidance/resistance strategies), increased heterogeneity and richness loss in transcribed gene pools were observed with increasing soil Cu, together with an unexpected predominance of phage mRNA signatures. Apparently, phage activation was either triggered directly by Cu, or indirectly via enhanced expression of DNA repair/SOS response systems in Cu-exposed bacteria. Even though total soil carbon and nitrogen had accumulated with increasing Cu, a reduction in temporally induced mRNA functions was observed. Microbial temporal response groups (TRGs, groups of microbes with a specific temporal response) were heavily affected by Cu, both in abundance and phylogenetic composition. CONCLUSION Altogether, results point toward a Cu-mediated "decoupling" between environmental fluctuations and microbial activity, where Cu-exposed microbes stopped fulfilling their expected contributions to soil functioning relative to the control. Nevertheless, some functions remained active in February despite Cu, concomitant with an increase in phage mRNA signatures, highlighting that somehow, microbial activity is still happening under these adverse conditions.
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Affiliation(s)
- Samuel Jacquiod
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Agroécologie, AgroSup Dijon, INRA, Univ Bourgogne Franche-Comté, 17 rue Sully, 21000, Dijon, France
| | - Inês Nunes
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Present address: Microbe Technology Department, Novozymes A/S, Krogshoejvej 36, 2880, Bagsværd, Denmark
| | - Asker Brejnrod
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Present address: Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3A, 2200, Copenhagen, Denmark
| | - Martin A Hansen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Peter E Holm
- Present address: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Anders Johansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Kristian K Brandt
- Present address: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Anders Priemé
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
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93
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Alster CJ, Weller ZD, von Fischer JC. A meta-analysis of temperature sensitivity as a microbial trait. GLOBAL CHANGE BIOLOGY 2018; 24:4211-4224. [PMID: 29888841 DOI: 10.1111/gcb.14342] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/12/2018] [Accepted: 05/15/2018] [Indexed: 05/14/2023]
Abstract
Traits-based approaches in microbial ecology provide a valuable way to abstract organismal interaction with the environment and to generate hypotheses about community function. Using macromolecular rate theory (MMRT), we recently identified that temperature sensitivity can be characterized as a distinct microbial trait. As temperature is fundamental in controlling biological reactions, variation in temperature sensitivity across communities, organisms, and processes has the potential to vastly improve understanding of microbial response to climate change. These microbial temperature sensitivity traits include the heat capacity ( ΔCP‡ ), temperature optimum (Topt ), and point of maximum temperature sensitivity (TSmax ), each of which provide unique insights about organismal response to changes in temperature. In this meta-analysis, we analyzed the distribution of these temperature sensitivity traits from bacteria, fungi, and mixed communities across a variety of biological systems (e.g., soils, oceans, foods, wastewater treatment plants) in order to identify commonalities in temperature responses across these diverse organisms and reaction rates. Our analysis of temperature sensitivity traits from over 350 temperature response curves reveals a wide distribution of temperature sensitivity traits, with Topt and TSmax well within biological relevant temperatures. We find that traits vary significantly depending on organism type, microbial diversity, source environment, and biological process, with higher temperature sensitivity found in fungi than bacteria and in less diverse systems. Carbon dioxide production was found to be less temperature sensitive than denitrification, suggesting that changes in temperature will have a potentially larger impact on nitrogen-related processes. As climate changes, these results have important implications for basic understanding of the temperature sensitivity of biological reactions and for ecological understanding of species' trait distributions, as well as for improved treatment of temperature sensitivity in models.
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Affiliation(s)
- Charlotte J Alster
- Department of Biology, Colorado State University, Fort Collins, Colorado
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado
| | - Zachary D Weller
- Department of Biology, Colorado State University, Fort Collins, Colorado
- Department of Statistics, Colorado State University, Fort Collins, Colorado
| | - Joseph C von Fischer
- Department of Biology, Colorado State University, Fort Collins, Colorado
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado
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94
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Le Page G, Gunnarsson L, Snape J, Tyler CR. Antibiotic risk assessment needs to protect both environmental and human health. ENVIRONMENT INTERNATIONAL 2018; 115:397-399. [PMID: 29650232 DOI: 10.1016/j.envint.2018.03.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/20/2018] [Accepted: 03/20/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Gareth Le Page
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK.
| | - Lina Gunnarsson
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Jason Snape
- AstraZeneca, Global Environment, Alderley Park, Macclesfield, Cheshire SK10 4TF, UK; School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, UK
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter, Devon EX4 4QD, UK.
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95
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Aleklett K, Kiers ET, Ohlsson P, Shimizu TS, Caldas VE, Hammer EC. Build your own soil: exploring microfluidics to create microbial habitat structures. ISME JOURNAL 2017; 12:312-319. [PMID: 29135971 PMCID: PMC5776464 DOI: 10.1038/ismej.2017.184] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/25/2017] [Accepted: 09/15/2017] [Indexed: 11/23/2022]
Abstract
Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.
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Affiliation(s)
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | | | - Victor Ea Caldas
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,AMOLF Institute, Amsterdam, The Netherlands
| | - Edith C Hammer
- Department of Microbial Ecology, Lund University, Lund, Sweden
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96
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Forbes KM, Sironen T, Plyusnin A. Hantavirus maintenance and transmission in reservoir host populations. Curr Opin Virol 2017; 28:1-6. [PMID: 29024905 DOI: 10.1016/j.coviro.2017.09.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 12/24/2022]
Abstract
Hantaviruses are primarily hosted by mammalian species of the orders Rodentia, Eulipotyphla and Chiroptera. Spillover to humans is common, and understanding hantavirus maintenance and transmission in reservoir host populations is important for efforts to curtail human disease. Recent field research challenges traditional phases of virus shedding kinetics derived from laboratory rodent infection experiments. Organ infection sites in non-rodent hosts suggest similar transmission routes to rodents, but require direct assessment. Further advances have also been made in understanding virus persistence (and fadeouts) in fluctuating host populations, as well as occupational, recreational and environmental risk factors associated with spillover to humans. However, despite relevance for both intra-species and inter-species transmission, our understanding of the longevity of hantaviruses in natural environments remains limited.
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Affiliation(s)
- Kristian M Forbes
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki FI-00290, Finland; Centre for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University, Millennium Science Complex, State College, PA 16802, United States.
| | - Tarja Sironen
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki FI-00290, Finland; Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland
| | - Alexander Plyusnin
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki FI-00290, Finland
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97
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Bletz MC, Archer H, Harris RN, McKenzie VJ, Rabemananjara FCE, Rakotoarison A, Vences M. Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar. Front Microbiol 2017; 8:1530. [PMID: 28861051 PMCID: PMC5563069 DOI: 10.3389/fmicb.2017.01530] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/28/2017] [Indexed: 12/30/2022] Open
Abstract
Host-associated microbiotas of vertebrates are diverse and complex communities that contribute to host health. In particular, for amphibians, cutaneous microbial communities likely play a significant role in pathogen defense; however, our ecological understanding of these communities is still in its infancy. Here, we take advantage of the fully endemic and locally species-rich amphibian fauna of Madagascar to investigate the factors structuring amphibian skin microbiota on a large scale. Using amplicon-based sequencing, we evaluate how multiple host species traits and site factors affect host bacterial diversity and community structure. Madagascar is home to over 400 native frog species, all of which are endemic to the island; more than 100 different species are known to occur in sympatry within multiple rainforest sites. We intensively sampled frog skin bacterial communities, from over 800 amphibians from 89 species across 30 sites in Madagascar during three field visits, and found that skin bacterial communities differed strongly from those of the surrounding environment. Richness of bacterial operational taxonomic units (OTUs) and phylogenetic diversity differed among host ecomorphs, with arboreal frogs exhibiting lower richness and diversity than terrestrial and aquatic frogs. Host ecomorphology was the strongest factor influencing microbial community structure, with host phylogeny and site parameters (latitude and elevation) explaining less but significant portions of the observed variation. Correlation analysis and topological congruency analyses revealed little to no phylosymbiosis for amphibian skin microbiota. Despite the observed geographic variation and low phylosymbiosis, we found particular OTUs that were differentially abundant between particular ecomorphs. For example, the genus Pigmentiphaga (Alcaligenaceae) was significantly enriched on arboreal frogs, Methylotenera (Methylophilaceae) was enriched on aquatic frogs, and Agrobacterium (Rhizobiaceae) was enriched on terrestrial frogs. The presence of shared bacterial OTUs across geographic regions for selected host genera suggests the presence of core microbial communities which in Madagascar, might be driven more strongly by a species’ preference for specific microhabitats than by the physical, physiological or biochemical properties of their skin. These results corroborate that both host and environmental factors are driving community assembly of amphibian cutaneous microbial communities, and provide an improved foundation for elucidating their role in disease resistance.
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Affiliation(s)
- Molly C Bletz
- Zoological Institute, Technical University of BraunschweigBraunschweig, Germany.,Department of Biology, James Madison University, HarrisonburgVA, United States
| | - Holly Archer
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, United States
| | - Reid N Harris
- Department of Biology, James Madison University, HarrisonburgVA, United States
| | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, United States
| | | | - Andolalao Rakotoarison
- Zoological Institute, Technical University of BraunschweigBraunschweig, Germany.,Mention Biologie et Biodiversité Animale, University of AntananarivoAntananarivo, Madagascar
| | - Miguel Vences
- Zoological Institute, Technical University of BraunschweigBraunschweig, Germany
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98
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Eisenhauer N, Antunes PM, Bennett AE, Birkhofer K, Bissett A, Bowker MA, Caruso T, Chen B, Coleman DC, de Boer W, de Ruiter P, DeLuca TH, Frati F, Griffiths BS, Hart MM, Hättenschwiler S, Haimi J, Heethoff M, Kaneko N, Kelly LC, Leinaas HP, Lindo Z, Macdonald C, Rillig MC, Ruess L, Scheu S, Schmidt O, Seastedt TR, van Straalen NM, Tiunov AV, Zimmer M, Powell JR. Priorities for research in soil ecology. PEDOBIOLOGIA 2017; 63:1-7. [PMID: 29129942 PMCID: PMC5675051 DOI: 10.1016/j.pedobi.2017.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.
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Affiliation(s)
- Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
- Corresponding author:
| | - Pedro M. Antunes
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste. Marie, ON, P6A 2G4 Canada
| | - Alison E. Bennett
- Ecological Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA United Kingdom
| | - Klaus Birkhofer
- Chair of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Konrad-Wachsmann-Allee 6, 03046 Cottbus, Germany
| | - Andrew Bissett
- CSIRO Oceans and Atmosphere, Hobart, TAS 7000, Australia
| | - Matthew A. Bowker
- School of Forestry, Northern Arizona University, 200 East Pine Knoll Drive, Flagstaff, Arizona 86011, USA
| | - Tancredi Caruso
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqinglu, Haidian District, Beijing 100085, China
- University of Chinese Academy of Sciences, 19 Yuquanlu, Shijingshan District, Beijing 100049, China
| | - David C. Coleman
- Odum School of Ecology, University of Georgia, Athens, Georgia 30602, USA
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands
- Department of Soil Quality, Wageningen University, Wageningen, 6708 PB, the Netherlands
| | - Peter de Ruiter
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Faculty of Science, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Thomas H. DeLuca
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA 98195-2100, USA
| | - Francesco Frati
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Bryan S. Griffiths
- Crop and Soil Systems Research Group, Scotland’s Rural College, West Mains Road, Edinburgh, EH9 3JG, United Kingdom
| | - Miranda M. Hart
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna, BC, Canada
| | - Stephan Hättenschwiler
- Centre d’Ecologie Fonctionnelle et Evolutive (CEFE) UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, 1919 Route de Mende, 34293 Montpellier, France
| | - Jari Haimi
- Department of Biological and Environmental Science, University of Jyväskylä, P.O.Box 35, FI-40014, Finland
| | - Michael Heethoff
- Ecological Networks, TU Darmstadt, Schnittspahnstr. 3, 64287 Darmstadt
| | - Nobuhiro Kaneko
- Soil Ecology Research Group, Yokohama National University ,79-7 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Laura C. Kelly
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Oxford Road, M1 5GD, United Kingdom
| | - Hans Petter Leinaas
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Zoë Lindo
- Department of Biology, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Catriona Macdonald
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Matthias C. Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Liliane Ruess
- Institute of Biology, Ecology Group, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Stefan Scheu
- JFB Institute of Zoology and Anthropology, University of Göttingen, Berliner Str. 28, 37073 Göttingen, Germany
| | - Olaf Schmidt
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Timothy R. Seastedt
- Department of Ecology and Evolutionary Biology, Institute of Arctic and Alpine Research, University of Colorado, Boulder, UCB 450, CO 80309, USA
| | - Nico M. van Straalen
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Alexei V. Tiunov
- A.N. Severtsov Institute of Ecology and Evolution RAS, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Martin Zimmer
- Leibniz-Centre for Tropical Marine Research, Fahrenheitstr. 6, 28359 Bremen
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
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