1
|
Batsch M, Guex I, Todorov H, Heiman CM, Vacheron J, Vorholt JA, Keel C, van der Meer JR. Fragmented micro-growth habitats present opportunities for alternative competitive outcomes. Nat Commun 2024; 15:7591. [PMID: 39217178 PMCID: PMC11365936 DOI: 10.1038/s41467-024-51944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Bacteria in nature often thrive in fragmented environments, like soil pores, plant roots or plant leaves, leading to smaller isolated habitats, shared with fewer species. This spatial fragmentation can significantly influence bacterial interactions, affecting overall community diversity. To investigate this, we contrast paired bacterial growth in tiny picoliter droplets (1-3 cells per 35 pL up to 3-8 cells per species in 268 pL) with larger, uniform liquid cultures (about 2 million cells per 140 µl). We test four interaction scenarios using different bacterial strains: substrate competition, substrate independence, growth inhibition, and cell killing. In fragmented environments, interaction outcomes are more variable and sometimes even reverse compared to larger uniform cultures. Both experiments and simulations show that these differences stem mostly from variation in initial cell population growth phenotypes and their sizes. These effects are most significant with the smallest starting cell populations and lessen as population size increases. Simulations suggest that slower-growing species might survive competition by increasing growth variability. Our findings reveal how microhabitat fragmentation promotes diverse bacterial interaction outcomes, contributing to greater species diversity under competitive conditions.
Collapse
Affiliation(s)
- Maxime Batsch
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Isaline Guex
- Department of Mathematics, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Helena Todorov
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara M Heiman
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Julia A Vorholt
- Institute for Microbiology, Swiss Federal Institute of Technology (ETH Zürich), CH-8049, Zürich, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| |
Collapse
|
2
|
Saccò M, Mammola S, Altermatt F, Alther R, Bolpagni R, Brancelj A, Brankovits D, Fišer C, Gerovasileiou V, Griebler C, Guareschi S, Hose GC, Korbel K, Lictevout E, Malard F, Martínez A, Niemiller ML, Robertson A, Tanalgo KC, Bichuette ME, Borko Š, Brad T, Campbell MA, Cardoso P, Celico F, Cooper SJB, Culver D, Di Lorenzo T, Galassi DMP, Guzik MT, Hartland A, Humphreys WF, Ferreira RL, Lunghi E, Nizzoli D, Perina G, Raghavan R, Richards Z, Reboleira ASPS, Rohde MM, Fernández DS, Schmidt SI, van der Heyde M, Weaver L, White NE, Zagmajster M, Hogg I, Ruhi A, Gagnon MM, Allentoft ME, Reinecke R. Groundwater is a hidden global keystone ecosystem. GLOBAL CHANGE BIOLOGY 2024; 30:e17066. [PMID: 38273563 DOI: 10.1111/gcb.17066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 01/27/2024]
Abstract
Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.
Collapse
Affiliation(s)
- Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stefano Mammola
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research Council, Verbania Pallanza, Italy
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Helsinki, Finland
- National Biodiversity Future Center, Palermo, Italy
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Roman Alther
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Rossano Bolpagni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Anton Brancelj
- Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
- Department for Environmental Science, University of Nova Gorica, Nova Gorica, Slovenia
| | - David Brankovits
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research Council, Verbania Pallanza, Italy
| | - Cene Fišer
- SubBio Lab, Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Vasilis Gerovasileiou
- Faculty of Environment, Department of Environment, Ionian University, Zakynthos, Greece
- Biotechnology and Aquaculture (IMBBC), Thalassocosmos, Institute of Marine Biology, Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Christian Griebler
- Department of Functional & Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Simone Guareschi
- Estación Biologica de Doñana (EBD-CSIC), Seville, Spain
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Grant C Hose
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kathryn Korbel
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Elisabeth Lictevout
- International Groundwater Resources Assessment Center (IGRAC), Delft, The Netherlands
| | - Florian Malard
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Univ Lyon, Villeurbanne, France
| | - Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research Council, Verbania Pallanza, Italy
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama, USA
| | - Anne Robertson
- School of Life and Health Sciences, Roehampton University, London, UK
| | - Krizler C Tanalgo
- Ecology and Conservation Research Laboratory (Eco/Con Lab), Department of Biological Sciences, College of Science and Mathematics, University of Southern Mindanao, Kabacan, Cotabato, Philippines
| | - Maria Elina Bichuette
- Laboratory of Subterranean Studies (LES), Department of Ecology and Evolutionary Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Špela Borko
- SubBio Lab, Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Traian Brad
- Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Matthew A Campbell
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Helsinki, Finland
- Departamento de Biologia Animal, and Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Fulvio Celico
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Steven J B Cooper
- South Australian Museum, North Terrace, Adelaide, South Australia, Australia
- Department of Ecology and Evolutionary Biology, School of Biological Sciences and Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - David Culver
- Department of Environmental Science, American University, Washington, DC, USA
| | - Tiziana Di Lorenzo
- National Biodiversity Future Center, Palermo, Italy
- Research Institute on Terrestrial Ecosystems of the National Research Council of Italy (IRET CNR), Florence, Italy
| | - Diana M P Galassi
- Department of Life, Health and Environmental Sciences (MESVA), University of L'Aquila, L'Aquila, Italy
| | - Michelle T Guzik
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Adam Hartland
- Lincoln Agritech Ltd, Ruakura, Kirikiriroa, Aotearoa, New Zealand
| | - William F Humphreys
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Western Australian Museum, Welshpool, Western Australia, Australia
| | - Rodrigo Lopes Ferreira
- Centro de Estudos em Biologia Subterrânea, Departamento de Ecologia e Conservação, Instituto de Ciências Naturais, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Enrico Lunghi
- Department of Life, Health and Environmental Sciences (MESVA), University of L'Aquila, L'Aquila, Italy
| | - Daniele Nizzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Perina
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Zoe Richards
- Coral Conservation and Research Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Ana Sofia P S Reboleira
- Departamento de Biologia Animal, and Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Melissa M Rohde
- Rohde Environmental Consulting, LLC, Seattle, Washington, USA
- Graduate Program in Environmental Science, State University of New York College of Environmental Science and Forestry, Syracuse, New York, USA
| | | | - Susanne I Schmidt
- Department of Lake Research, Helmholtz Centre for Environmental Research, Magdeburg, Germany
| | - Mieke van der Heyde
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Louise Weaver
- Water & Environment Group, Institute of Environmental Science & Research Ltd., Christchurch, New Zealand
| | - Nicole E White
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Maja Zagmajster
- SubBio Lab, Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Ian Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Nunavut, Canada
| | - Albert Ruhi
- Department of Environmental Science, Policy & Management, University of California, Berkeley, California, USA
| | - Marthe M Gagnon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert Reinecke
- Institute of Geography, Johannes Gutenberg-University Mainz, Mainz, Germany
| |
Collapse
|
3
|
Danielsen ACS, Nielsen PH, Hermansen C, Weber PL, de Jonge LW, Jørgensen VR, Greve MH, Corcoran D, Dueholm MKD, Bruhn D. Improved description of terrestrial habitat types by including microbial communities as indicators. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118677. [PMID: 37556895 DOI: 10.1016/j.jenvman.2023.118677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/11/2023]
Abstract
Soils host diverse communities of microorganisms essential for ecosystem functions and soil health. Despite their importance, microorganisms are not covered by legislation protecting biodiversity or habitats, such as the Habitats Directive. Advances in molecular methods have caused breakthroughs in microbial community analysis, and recent studies have shown that parts of the communities are habitat-specific. If distinct microbial communities are present in the habitat types defined in the Habitats Directive, the Directive may be improved by including these communities. Thus, monitoring and reporting of biodiversity and conservation status of habitat types could be based not only on plant communities but also on microbial communities. In the present study, bacterial and plant communities were examined in six habitat types defined in the Habitats Directive by conducting botanical surveys and collecting soil samples for amplicon sequencing across 19 sites in Denmark. Furthermore, selected physico-chemical properties expected to differ between habitat types and explain variations in community composition of bacteria and vegetation were analysed (pH, electrical conductivity (EC), soil texture, soil water repellency, soil organic carbon content (OC), inorganic nitrogen, and in-situ water content (SWC)). Despite some variations within the same habitat type and overlaps between habitat types, habitat-specific communities were observed for both bacterial and plant communities, but no correlation was observed between the alpha diversity of vegetation and bacteria. PERMANOVA analysis was used to evaluate the variables best able to explain variation in the community composition of vegetation and bacteria. Habitat type alone could explain 46% and 47% of the variation in bacterial and plant communities, respectively. Excluding habitat type as a variable, the best model (pH, SWC, OC, fine silt, and Shannon's diversity index for vegetation) could explain 37% of the variation for bacteria. For vegetation, the best model (pH, EC, ammonium content and Shannon's diversity index for bacteria) could explain 25% of the variation. Based on these results, bacterial communities could be included in the Habitats Directive to improve the monitoring, as microorganisms are more sensitive to changes in the environment compared to vegetation, which the current monitoring is based on.
Collapse
Affiliation(s)
- Anne-Cathrine Storgaard Danielsen
- Section of Soil Physics and Hydropedology, Department of Agroecology, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark; SustainScapes - Center for Sustainable Landscapes Under Global Change, Department of Biology, Aarhus University, Nordre Ringgade 1, 8000, Aarhus C, Denmark.
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, Aalborg, DK 9220, Denmark
| | - Cecilie Hermansen
- Section of Soil Physics and Hydropedology, Department of Agroecology, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark; SustainScapes - Center for Sustainable Landscapes Under Global Change, Department of Biology, Aarhus University, Nordre Ringgade 1, 8000, Aarhus C, Denmark
| | - Peter Lystbæk Weber
- Section of Soil Physics and Hydropedology, Department of Agroecology, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark
| | - Lis Wollesen de Jonge
- Section of Soil Physics and Hydropedology, Department of Agroecology, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark; SustainScapes - Center for Sustainable Landscapes Under Global Change, Department of Biology, Aarhus University, Nordre Ringgade 1, 8000, Aarhus C, Denmark
| | - Vibeke Rudkjøbing Jørgensen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, Aalborg, DK 9220, Denmark
| | - Mogens Humlekrog Greve
- Section of Soil Physics and Hydropedology, Department of Agroecology, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark; SustainScapes - Center for Sustainable Landscapes Under Global Change, Department of Biology, Aarhus University, Nordre Ringgade 1, 8000, Aarhus C, Denmark
| | - Derek Corcoran
- SustainScapes - Center for Sustainable Landscapes Under Global Change, Department of Biology, Aarhus University, Nordre Ringgade 1, 8000, Aarhus C, Denmark
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, Aalborg, DK 9220, Denmark
| | - Dan Bruhn
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, Aalborg, DK 9220, Denmark
| |
Collapse
|
4
|
The chosen few-variations in common and rare soil bacteria across biomes. THE ISME JOURNAL 2021; 15:3315-3325. [PMID: 34035442 PMCID: PMC8528968 DOI: 10.1038/s41396-021-00981-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 02/05/2023]
Abstract
Soil bacterial communities are dominated by a few abundant species, while their richness is associated with rare species with largely unknown ecological roles and biogeography. Analyses of previously published soil bacterial community data using a novel classification of common and rare bacteria indicate that only 0.4% of bacterial species can be considered common and are prevalent across biomes. The remaining bacterial species designated as rare are endemic with low relative abundances. Observations coupled with mechanistic models highlight the central role of soil wetness in shaping bacterial rarity. An individual-based model reveals systematic shifts in community composition induced by low carbon inputs in drier soils that deprive common species of exhibiting physiological advantages relative to other species. We find that only a "chosen few" common species shape bacterial communities across biomes; however, their contributions are curtailed in resource-limited environments where a larger number of rare species constitutes the soil microbiome.
Collapse
|
5
|
Jones B, Goodall T, George PBL, Gweon HS, Puissant J, Read DS, Emmett BA, Robinson DA, Jones DL, Griffiths RI. Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database. Front Microbiol 2021; 12:682886. [PMID: 34349739 PMCID: PMC8326369 DOI: 10.3389/fmicb.2021.682886] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER/), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios.
Collapse
Affiliation(s)
- Briony Jones
- UK Centre for Ecology and Hydrology, Bangor, United Kingdom.,School of Environment, Natural Resources and Geography, Bangor University, Bangor, United Kingdom
| | - Tim Goodall
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Paul B L George
- UK Centre for Ecology and Hydrology, Bangor, United Kingdom.,School of Environment, Natural Resources and Geography, Bangor University, Bangor, United Kingdom
| | - Hyun S Gweon
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Jeremy Puissant
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Daniel S Read
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | | | | | - Davey L Jones
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | | |
Collapse
|
6
|
Hahn MW, Huemer A, Pitt A, Hoetzinger M. Opening a next-generation black box: Ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit. Mol Ecol Resour 2021; 21:2471-2485. [PMID: 34101998 DOI: 10.1111/1755-0998.13444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/10/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. The faster evolving protein-encoding gene priB was used to reveal ecological patterns hidden within a single operational taxonomic unit (OTU) defined by >99% 16S rRNA sequence similarity. The studied subcluster PnecC of the genus Polynucleobacter represents a ubiquitous group of abundant freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3,400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. In addition to the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. An unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca2+ -rich and Ca2+ -poor habitats. This compositional pattern strongly resembled the vicariance of plant species on silicate and limestone soils. The new cultivation-independent approach presented opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.
Collapse
Affiliation(s)
- Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Andrea Huemer
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Matthias Hoetzinger
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| |
Collapse
|
7
|
Dickey JR, Swenie RA, Turner SC, Winfrey CC, Yaffar D, Padukone A, Beals KK, Sheldon KS, Kivlin SN. The Utility of Macroecological Rules for Microbial Biogeography. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.633155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroecological rules have been developed for plants and animals that describe large-scale distributional patterns and attempt to explain the underlying physiological and ecological processes behind them. Similarly, microorganisms exhibit patterns in relative abundance, distribution, diversity, and traits across space and time, yet it remains unclear the extent to which microorganisms follow macroecological rules initially developed for macroorganisms. Additionally, the usefulness of these rules as a null hypothesis when surveying microorganisms has yet to be fully evaluated. With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. Here, we review and synthesize these macroecological microbial studies with two main objectives: (1) to determine to what extent macroecological rules explain the distribution of host-associated and free-living microorganisms, and (2) to understand which environmental factors and stochastic processes may explain these patterns among microbial clades (archaea, bacteria, fungi, and protists) and habitats (host-associated and free living; terrestrial and aquatic). Overall, 78% of microbial macroecology studies focused on free living, aquatic organisms. In addition, most studies examined macroecological rules at the community level with only 35% of studies surveying organismal patterns across space. At the community level microorganisms often tracked patterns of macroorganisms for island biogeography (74% confirm) but rarely followed Latitudinal Diversity Gradients (LDGs) of macroorganisms (only 32% confirm). However, when microorganisms and macroorganisms shared the same macroecological patterns, underlying environmental drivers (e.g., temperature) were the same. Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology.
Collapse
|
8
|
Diversity of Dominant Soil Bacteria Increases with Warming Velocity at the Global Scale. DIVERSITY 2021. [DOI: 10.3390/d13030120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding global soil bacterial diversity is important because of its role in maintaining a healthy global ecosystem. Given the effects of environmental changes (e.g., warming and human impact) on the diversity of animals and plants, effects on soil bacterial diversity are expected; however, they have been poorly evaluated at the global scale to date. Thus, in this study, we focused on the dominant soil bacteria, which are likely critical drivers of key soil processes worldwide, and investigated the effects of warming velocity and human activities on their diversity. Using a global dataset of bacteria, we performed spatial analysis to evaluate the effects of warming velocity and human activities, while statistically controlling for the potentially confounding effects of current climate and geographic parameters with global climate and geographic data. We demonstrated that the diversity of the dominant soil bacteria was influenced globally, not only by the aridity index (dryness) and pH but also by warming velocity from the Last Glacial Maximum (21,000 years ago) to the present, showing significant increases. The increase in bacterial diversity with warming velocity was particularly significant in forests and grasslands. An effect of human activity was also observed, but it was secondary to warming velocity. These findings provide robust evidence and advance our understanding of the effects of environmental changes (particularly global warming) on soil bacterial diversity at the global scale.
Collapse
|
9
|
Walters KE, Martiny JBH. Alpha-, beta-, and gamma-diversity of bacteria varies across habitats. PLoS One 2020; 15:e0233872. [PMID: 32966309 PMCID: PMC7510982 DOI: 10.1371/journal.pone.0233872] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/08/2020] [Indexed: 11/18/2022] Open
Abstract
Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages displayed the highest gamma-diversity. Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta- diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.
Collapse
Affiliation(s)
- Kendra E. Walters
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
| |
Collapse
|
10
|
Ruiz SA, McKay Fletcher DM, Boghi A, Williams KA, Duncan SJ, Scotson CP, Petroselli C, Dias TGS, Chadwick DR, Jones DL, Roose T. Image-based quantification of soil microbial dead zones induced by nitrogen fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138197. [PMID: 32498200 DOI: 10.1016/j.scitotenv.2020.138197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities in agricultural soils underpin many ecosystem services including the maintenance of soil structure, food production, water purification and carbon storage. However, the impact of fertilization on the health of microbial communities is not well understood. This study investigates the spatial and temporal dynamics of nitrogen (N) transport away from a fertilizer granule with pore scale resolution. Specifically, we examined how soil structure and moisture content influence fertilizer derived N movement through the soil pore network and the subsequent impact of on soil microbial communities. We develop a mathematical model to describe N transport and reactions in soil at the pore-scale. Using X-ray Computed Tomography scans, we reconstructed a microscale description of a soil-pore geometry as a computational mesh. Solving two-phase water/air model produced pore-scale water distributions at 15, 30 and 70% water-filled pore volume. The N-speciation model considered ammonium (NH4+), nitrate (NO3-) and dissolved organic N (DON), and included N immobilization, ammonification and nitrification processes, as well as diffusion in soil solution. We simulated the dissolution of a fertilizer pellet and a pore scale N cycle at three different water saturations. To aid interpretation of the model results, microbial activity at a range of N concentrations was measured. The model showed that the diffusion and concentration of N in water films is critically dependent upon soil moisture and N species. We predict that the maximum NH4+ and NO3- concentrations in soil solution around the pellet under dry conditions are in the order of 1 × 103 and 1 × 104 mol m-3 respectively, and under wet conditions 2 × 102 and 1 × 103 mol m-3, respectively. Supporting experimental evidence suggests that these concentrations would be sufficient to reduce microbial activity in the short-term in the zone immediately around the fertilizer pellet (ranging from 0.9 to 3.8 mm), causing a major loss of soil biological functioning. This model demonstrates the importance of pore-scale processes in regulating N movement and their interactions with the soil microbiome.
Collapse
Affiliation(s)
- S A Ruiz
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - D M McKay Fletcher
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - A Boghi
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK; Computational Science Ltd, 30a Bedford Place, Southampton SO15 2DG, UK
| | - K A Williams
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - S J Duncan
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - C P Scotson
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - C Petroselli
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - T G S Dias
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - D R Chadwick
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK; Interdisciplinary Research Centre for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - D L Jones
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK; SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - T Roose
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK.
| |
Collapse
|
11
|
Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes. Nat Commun 2020; 11:116. [PMID: 31913270 PMCID: PMC6949233 DOI: 10.1038/s41467-019-13966-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 12/10/2019] [Indexed: 01/01/2023] Open
Abstract
Soil bacterial diversity varies across biomes with potential impacts on soil ecological functioning. Here, we incorporate key factors that affect soil bacterial abundance and diversity across spatial scales into a mechanistic modeling framework considering soil type, carbon inputs and climate towards predicting soil bacterial diversity. The soil aqueous-phase content and connectivity exert strong influence on bacterial diversity for each soil type and rainfall pattern. Biome-specific carbon inputs deduced from net primary productivity provide constraints on soil bacterial abundance independent from diversity. The proposed heuristic model captures observed global trends of bacterial diversity in good agreement with predictions by an individual-based mechanistic model. Bacterial diversity is highest at intermediate water contents where the aqueous phase forms numerous disconnected habitats and soil carrying capacity determines level of occupancy. The framework delineates global soil bacterial diversity hotspots; located mainly in climatic transition zones that are sensitive to potential climate and land use changes.
Collapse
|