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Khattar G, Peres-Neto PR. The Geography of Metacommunities: Landscape Characteristics Drive Geographic Variation in the Assembly Process through Selecting Species Pool Attributes. Am Nat 2024; 203:E142-E156. [PMID: 38635361 DOI: 10.1086/729423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
AbstractThe nonrandom association between landscape characteristics and the dominant life history strategies observed in species pools is a typical pattern in nature. Here, we argue that these associations determine predictable changes in the relative importance of assembly mechanisms along broadscale geographic gradients (i.e., the geographic context of metacommunity dynamics). To demonstrate that, we employed simulation models in which groups of species with the same initial distribution of niche breadths and dispersal abilities interacted across a wide range of landscapes with contrasting characteristics. By assessing the traits of dominant species in the species pool in each landscape type, we determined how different landscape characteristics select for different life history strategies at the metacommunity level. We analyzed the simulated data using the same analytical approaches used in the study of empirical metacommunities to derive predictions about the causal relationships between landscape characteristics and dominant life histories in species pools, as well as their reciprocal influence on empirical inferences regarding the assembly process. We provide empirical support for these predictions by contrasting the assembly of moth metacommunities in a tropical versus a temperate mountainous landscape. Together, our model framework and empirical analyses demonstrate how the geographic context of metacommunities influences our understanding of community assembly across broadscale ecological gradients.
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2
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Sebastián M, Giner CR, Balagué V, Gómez-Letona M, Massana R, Logares R, Duarte CM, Gasol JM. The active free-living bathypelagic microbiome is largely dominated by rare surface taxa. ISME COMMUNICATIONS 2024; 4:ycae015. [PMID: 38456147 PMCID: PMC10919342 DOI: 10.1093/ismeco/ycae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 03/09/2024]
Abstract
A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean's surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e. with potential for protein synthesis, RNA) free-living communities in 13 stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (or with potential for protein synthesis) and dominate the bathypelagic active microbiome.
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Affiliation(s)
- Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Caterina R Giner
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Vanessa Balagué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Markel Gómez-Letona
- Instituto de Oceanografía y Cambio Global, Universidad de Las Palmas de Gran Canaria, Parque Científico Tecnológico Marino de Taliarte, s/n, Telde, Las Palmas 35214, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
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3
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Kiemel K, Weithoff G, Tiedemann R. DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity. Mol Ecol 2023; 32:6190-6209. [PMID: 35869804 DOI: 10.1111/mec.16627] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2023]
Abstract
Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (i) spatial and temporal connectivity of the communities, (ii) environmental factors influencing local communities, and (iii) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.
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Affiliation(s)
- Katrin Kiemel
- Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Guntram Weithoff
- Unit of Ecology and Ecosystem Modelling, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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4
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Bundschuh M, Mesquita-Joanes F, Rico A, Camacho A. Understanding Ecological Complexity in a Chemical Stress Context: A Reflection on Recolonization, Recovery, and Adaptation of Aquatic Populations and Communities. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1857-1866. [PMID: 37204216 DOI: 10.1002/etc.5677] [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: 02/18/2023] [Revised: 04/17/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023]
Abstract
Recovery, recolonization, and adaptation in a chemical stress context are processes that regenerate local populations and communities as well as the functions these communities perform. Recolonization, either by species previously present or by new species able to occupy the niches left empty, refers to a metacommunity process with stressed ecosystems benefiting from the dispersal of organisms from other areas. A potential consequence of recolonization is a limited capacity of local populations to adapt to potentially repeating events of chemical stress exposure when their niches have been effectively occupied by the new colonizers or by new genetic lineages of the taxa previously present. Recovery, instead, is an internal process occurring within stressed ecosystems. More specifically, the impact of a stressor on a community benefits less sensitive individuals of a local population as well as less sensitive taxa within a community. Finally, adaptation refers to phenotypic and, sometimes, genetic changes at the individual and population levels, allowing the permanence of individuals of previously existing taxa without necessarily changing the community taxonomic composition (i.e., not replacing sensitive species). Because these processes are usually operating in parallel in nature, though at different degrees, it seems relevant to try to understand their relative importance for the regeneration of community structure and ecosystem functioning after chemical exposure. In the present critical perspective, we employed case studies supporting our understanding of the underlying processes with the hope to provide a theoretical framework to disentangle the relevance of the three processes for the regeneration of a biological community after chemical exposure. Finally, we provide some recommendations to experimentally compare their relative importance so that the net effects of these processes can be used to parameterize risk-assessment models and inform ecosystem management. Environ Toxicol Chem 2023;42:1857-1866. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Francesc Mesquita-Joanes
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, València, Spain
| | - Andreu Rico
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, València, Spain
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Madrid, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, València, Spain
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5
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Eskelinen A, Jessen MT, Bahamonde HA, Bakker JD, Borer ET, Caldeira MC, Harpole WS, Jia M, Lannes LS, Nogueira C, Olde Venterink H, Peri PL, Porath-Krause AJ, Seabloom EW, Schroeder K, Tognetti PM, Yasui SLE, Virtanen R, Sullivan LL. Herbivory and nutrients shape grassland soil seed banks. Nat Commun 2023; 14:3949. [PMID: 37402739 DOI: 10.1038/s41467-023-39677-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
Anthropogenic nutrient enrichment and shifts in herbivory can lead to dramatic changes in the composition and diversity of aboveground plant communities. In turn, this can alter seed banks in the soil, which are cryptic reservoirs of plant diversity. Here, we use data from seven Nutrient Network grassland sites on four continents, encompassing a range of climatic and environmental conditions, to test the joint effects of fertilization and aboveground mammalian herbivory on seed banks and on the similarity between aboveground plant communities and seed banks. We find that fertilization decreases plant species richness and diversity in seed banks, and homogenizes composition between aboveground and seed bank communities. Fertilization increases seed bank abundance especially in the presence of herbivores, while this effect is smaller in the absence of herbivores. Our findings highlight that nutrient enrichment can weaken a diversity maintaining mechanism in grasslands, and that herbivory needs to be considered when assessing nutrient enrichment effects on seed bank abundance.
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Affiliation(s)
- Anu Eskelinen
- Ecology and Genetics Unit, University of Oulu, P.O. Box 3000, Oulu, Finland.
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, Puschstraße 4, 04103, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103, Leipzig, Germany.
| | - Maria-Theresa Jessen
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, Puschstraße 4, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103, Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Theodor-Lieser-Str. 4, 06120, Halle, Germany
| | - Hector A Bahamonde
- Faculty of Agricultural and Forestry Sciences, National University of La Plata, Av. 60 y 119, La Plata, 1900, Buenos Aires, Argentina
| | - Jonathan D Bakker
- School of Environmental and Forest Sciences, University of Washington, Box 354115, Seattle, WA, 98195-4115, USA
| | - Elizabeth T Borer
- University of Minnesota, Department of Ecology, Evolution and Behavior, 140 Gortner Laboratory, 1479 Gortner Ave, St Paul, MN, 55108, USA
| | - Maria C Caldeira
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - W Stanley Harpole
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, Puschstraße 4, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103, Leipzig, Germany
- Martin Luther University Halle-Wittenberg, am Kirchtor 1, 06108, Halle (Saale), Germany
| | - Meiyu Jia
- School of Environmental and Forest Sciences, University of Washington, Box 354115, Seattle, WA, 98195-4115, USA
- School of Water Resources & Environmental Engineering, East China University of Technology, Nanchang, 330013, China
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekou Wai Street, Beijing City, 100875, China
| | - Luciola S Lannes
- Department of Biology and Animal Sciences, São Paulo State University-UNESP, Ilha Solteira, 01049-010, Brazil
| | - Carla Nogueira
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Harry Olde Venterink
- Department of Biology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Brussels, Belgium
| | - Pablo L Peri
- National Institute of Agricultural Research (INTA), Southern Patagonia National University (UNPA), CONICET, Río Gallegos, (CP 9400), Santa Cruz, Argentina
| | - Anita J Porath-Krause
- University of Minnesota, Department of Ecology, Evolution and Behavior, 140 Gortner Laboratory, 1479 Gortner Ave, St Paul, MN, 55108, USA
| | - Eric W Seabloom
- University of Minnesota, Department of Ecology, Evolution and Behavior, 140 Gortner Laboratory, 1479 Gortner Ave, St Paul, MN, 55108, USA
| | - Katie Schroeder
- University of Minnesota, Department of Ecology, Evolution and Behavior, 140 Gortner Laboratory, 1479 Gortner Ave, St Paul, MN, 55108, USA
- Odum School of Ecology, University of Georgia, Athens, GA, 30603, USA
| | - Pedro M Tognetti
- IFEVA, University of Buenos Aires, CONICET, Facultad de Agronomía, Av. San Martin, 4453 C1417DSE, Buenos Aires, Argentina
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Simone-Louise E Yasui
- Queensland University of Technology, School of Biological and Environmental Sciences, Brisbane, QLD 4072, Australia
| | - Risto Virtanen
- Ecology and Genetics Unit, University of Oulu, P.O. Box 3000, Oulu, Finland
| | - Lauren L Sullivan
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060, USA
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
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6
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Schwartz DA, Shoemaker WR, Măgălie A, Weitz JS, Lennon JT. Bacteria-phage coevolution with a seed bank. THE ISME JOURNAL 2023:10.1038/s41396-023-01449-2. [PMID: 37286738 DOI: 10.1038/s41396-023-01449-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
Dormancy is an adaptation to living in fluctuating environments. It allows individuals to enter a reversible state of reduced metabolic activity when challenged by unfavorable conditions. Dormancy can also influence species interactions by providing organisms with a refuge from predators and parasites. Here we test the hypothesis that, by generating a seed bank of protected individuals, dormancy can modify the patterns and processes of antagonistic coevolution. We conducted a factorially designed experiment where we passaged a bacterial host (Bacillus subtilis) and its phage (SPO1) in the presence versus absence of a seed bank consisting of dormant endospores. Owing in part to the inability of phages to attach to spores, seed banks stabilized population dynamics and resulted in minimum host densities that were 30-fold higher compared to bacteria that were unable to engage in dormancy. By supplying a refuge to phage-sensitive strains, we show that seed banks retained phenotypic diversity that was otherwise lost to selection. Dormancy also stored genetic diversity. After characterizing allelic variation with pooled population sequencing, we found that seed banks retained twice as many host genes with mutations, whether phages were present or not. Based on mutational trajectories over the course of the experiment, we demonstrate that seed banks can dampen bacteria-phage coevolution. Not only does dormancy create structure and memory that buffers populations against environmental fluctuations, it also modifies species interactions in ways that can feed back onto the eco-evolutionary dynamics of microbial communities.
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Affiliation(s)
- Daniel A Schwartz
- Department of Biology, Indiana University, Bloomington, Indiana, IN, USA
| | - William R Shoemaker
- The Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy
| | - Andreea Măgălie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Institut de Biologie, École Normale Supérieure, Paris, France
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, IN, USA.
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7
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Factors affecting functional diversity of grassland vegetations. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.110078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Bergmann GE, Leveau JHJ. A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds. Front Microbiol 2022; 13:877519. [PMID: 35935241 PMCID: PMC9355165 DOI: 10.3389/fmicb.2022.877519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.
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9
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Custer GF, Bresciani L, Dini-Andreote F. Ecological and Evolutionary Implications of Microbial Dispersal. Front Microbiol 2022; 13:855859. [PMID: 35464980 PMCID: PMC9019484 DOI: 10.3389/fmicb.2022.855859] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Dispersal is simply defined as the movement of species across space and time. Despite this terse definition, dispersal is an essential process with direct ecological and evolutionary implications that modulate community assembly and turnover. Seminal ecological studies have shown that environmental context (e.g., local edaphic properties, resident community), dispersal timing and frequency, and species traits, collectively account for patterns of species distribution resulting in either their persistence or unsuccessful establishment within local communities. Despite the key importance of this process, relatively little is known about how dispersal operates in microbiomes across divergent systems and community types. Here, we discuss parallels of macro- and micro-organismal ecology with a focus on idiosyncrasies that may lead to novel mechanisms by which dispersal affects the structure and function of microbiomes. Within the context of ecological implications, we revise the importance of short- and long-distance microbial dispersal through active and passive mechanisms, species traits, and community coalescence, and how these align with recent advances in metacommunity theory. Conversely, we enumerate how microbial dispersal can affect diversification rates of species by promoting gene influxes within local communities and/or shifting genes and allele frequencies via migration or de novo changes (e.g., horizontal gene transfer). Finally, we synthesize how observed microbial assemblages are the dynamic outcome of both successful and unsuccessful dispersal events of taxa and discuss these concepts in line with the literature, thus enabling a richer appreciation of this process in microbiome research.
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Affiliation(s)
- Gordon F Custer
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Luana Bresciani
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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10
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Choudoir MJ, DeAngelis KM. A framework for integrating microbial dispersal modes into soil ecosystem ecology. iScience 2022; 25:103887. [PMID: 35243247 PMCID: PMC8866892 DOI: 10.1016/j.isci.2022.103887] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Dispersal is a fundamental community assembly process that maintains soil microbial biodiversity across spatial and temporal scales, yet the impact of dispersal on ecosystem function is largely unpredictable. Dispersal is unique in that it contributes to both ecological and evolutionary processes and is shaped by both deterministic and stochastic forces. The ecosystem-level ramifications of dispersal outcomes are further compounded by microbial dormancy dynamics and environmental selection. Here we review the knowledge gaps and challenges that remain in defining how dispersal, environmental filtering, and microbial dormancy interact to influence the relationship between microbial community structure and function in soils. We propose the classification of microbial dispersal into three categories, through vegetative or active cells, through dormant cells, and through acellular dispersal, each with unique spatiotemporal dynamics and microbial trait associations. This conceptual framework should improve the integration of dispersal in defining soil microbial community structure-function relationships.
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11
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Hao YQ, Zhao XF, Ai HX, Gao SM, Teng WK, Zheng J, Shu WS. Microbial biogeography of acid mine drainage sediments at a regional scale across Southern China. FEMS Microbiol Ecol 2022; 98:6520435. [PMID: 35108388 DOI: 10.1093/femsec/fiac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/03/2022] [Accepted: 01/30/2022] [Indexed: 11/14/2022] Open
Abstract
Investigations of microbial biogeography in extreme environments provide unique opportunities to disentangle the roles of environment and space in microbial community assembly. Here, we reported a comprehensive microbial biogeographic survey of 90 acid mine drainage (AMD) sediment samples from 18 mining sites of various mineral types across southern China. We found that environmental selection was strong in determining the AMD habitat species pool. However, microbial alpha diversity was primarily explained by mining sites rather than environmental factors, and microbial beta diversity correlated more strongly with geographic than environmental distance at both large and small spatial scales. Particularly, the presence/absence of widespread AMD habitat generalists was only correlated with geographic distance and independent of environmental variation. These distance-decay patterns suggested that spatial processes played a more important role in determining microbial compositional variation across space; which could be explained by the reinforced impacts of dispersal limitation in less fluid, spatially structured sediment habitat with diverse pre-existing communities. In summary, our findings suggested that the deterministic assembling and spatial constraints interact to shape microbial biogeography in AMD sediments; and provided implications that spatial processes should be considered when predicting microbial dynamics in response to severe environmental change across large spatial scales.
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Affiliation(s)
- Yi-Qi Hao
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xin-Feng Zhao
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hong-Xia Ai
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Kai Teng
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jin Zheng
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
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12
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Gao P, Dong J, Wang S, Zhang W, Yang T, Zhang J, Che D. Cool-Warm Temperature Stratification and Simulated Bird Digestion Optimize Removal of Dormancy in Rosa rugosa Seeds. FRONTIERS IN PLANT SCIENCE 2022; 12:808206. [PMID: 35111183 PMCID: PMC8801612 DOI: 10.3389/fpls.2021.808206] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Rosa rugosa Thunb. has been explored multi-function in medicinal, edible, cosmetic, ornamental and ecological etc. However, R. rugosa natural populations have recently declined substantially in China, besides of global climate change, this species also has the defect of limiting the reproduction of itself such as the hard-to-release seed dormancy. In this study, only 30% of R. rugosa seeds were viable, and the others were incompletely developed or diseased seeds. Without stratification, morphologically complete viable seeds imbibed water but those seeds could not germinate even after seed husk removal under suitable condition to exhibit a physiological dormancy. After cold (4°C) and warm (18 ± 2°C) stratification, macromolecular substances containing carbon or nitrogen accumulated, and respiration, antioxidant enzyme activity, and gibberellin (GA3) /abscisic acid (ABA) and auxin (IAA)/ABA ratios increased significantly in seeds. Water absorption also increased as endocarps softened. Thus, physiological dormancy of seed was broken. Although warm and cold stratification increased separation between endocarp and embryo, the endocarp binding force was removed insufficiently, because only 10.20% of seeds germinated. Therefore, stratified seeds were treated with simulated bird digestion. Then, folds and cracks in loosened endocarps increased permeability, and water absorption rate increased to 64.43% compare to 21.14% in cold and warm stratification treatment. With simulated digestion, 24.20% of radicles broke through the endocarp with plumules and cambiums to develop into seedlings. Thus, the seed dormancy type of R. rugosa is physiological as seeds imbibed water and possessed fully developed embryos with a low growth potential in combination with a mechanical constraint from the endocarp. Cold stratification helped remove physiological dormancy, and additional warm stratification accelerated the process. The optimal stratification treatment was 4°C for 45 days followed by 18 ± 2°C for 15 days. After warm and cold stratification, simulated bird digestion broke the mechanical constraint from the seed covering layers. Based on this research, production of R. rugosa seedlings can be greatly increased to help protect the species from further declines.
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Affiliation(s)
- Peng Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Jie Dong
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Sihan Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
- Aerospace Shenzhou Biotechnology Group Corporation Limited, Beijing, China
| | - Wuhua Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Tao Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Jinzhu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
| | - Daidi Che
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Region Landscape Plants and Applications, Harbin, China
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13
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Picoche C, Barraquand F. Seed banks can help to maintain the diversity of interacting phytoplankton species. J Theor Biol 2022; 538:111020. [PMID: 35032473 DOI: 10.1016/j.jtbi.2022.111020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/01/2022] [Accepted: 01/06/2022] [Indexed: 10/19/2022]
Abstract
Seed formation is part of the reproductive cycle, leading to the accumulation of resistance stages that can withstand harsh environmental conditions for long periods of time. At the community level, multiple species with such long-lasting life stages can be more likely to coexist. While the implications of this process for biodiversity have been studied in terrestrial plants, seed banks are usually neglected in phytoplankton multispecies dynamic models, in spite of widespread empirical evidence for such seed banks. In this study, we build a metacommunity model of interacting phytoplankton species, including a resting stage supplying the seed bank. The model is parameterized with empirically-driven growth rate functions and field-based interaction estimates, which include both facilitative and competitive interactions. Exchanges between compartments (coastal pelagic cells, coastal resting cells on the seabed, and open ocean pelagic cells) are controlled by hydrodynamical parameters to which the sensitivity of the model is assessed. We consider two models, i.e., with and without a saturating effect of the interactions on the growth rates. Our results are consistent between models, and show that a seed bank allows to maintain all species in the community over 30 years. Indeed, a fraction of the species are vulnerable to extinction at specific times within the year, but this process is buffered by their survival in their resting stage. We thus highlight the potential role of the seed bank in the recurrent re-invasion of the coastal community, and of coastal environments in re-seeding oceanic regions. Moreover, the seed bank enables populations to tolerate stronger interactions within the community as well as more severe changes in the environment, such as those predicted within a climate change context. Our study therefore shows how a resting stage may help phytoplanktonic diversity maintenance.
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Affiliation(s)
- Coralie Picoche
- Institute of Mathematics of Bordeaux, University of Bordeaux and CNRS, Talence, France; Integrative and Theoretical Ecology, LabEx COTE, University of Bordeaux, Pessac, France.
| | - Frédéric Barraquand
- Institute of Mathematics of Bordeaux, University of Bordeaux and CNRS, Talence, France; Integrative and Theoretical Ecology, LabEx COTE, University of Bordeaux, Pessac, France
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14
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Wisnoski NI, Shoemaker LG. Seed banks alter metacommunity diversity: The interactive effects of competition, dispersal and dormancy. Ecol Lett 2021; 25:740-753. [PMID: 34965013 DOI: 10.1111/ele.13944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/10/2021] [Accepted: 11/24/2021] [Indexed: 01/12/2023]
Abstract
Dispersal and dormancy are two common strategies allowing for species persistence and the maintenance of biodiversity in variable environments. However, theory and empirical tests of spatial diversity patterns tend to examine either mechanism in isolation. Here, we developed a stochastic, spatially explicit metacommunity model incorporating seed banks with varying germination and survival rates. We found that dormancy and dispersal had interactive, nonlinear effects on the maintenance and distribution of metacommunity diversity. Seed banks promoted local diversity when seed survival was high and maintained regional diversity through interactions with dispersal. The benefits of seed banks for regional diversity were largest when dispersal was high or intermediate, depending on whether local competition was equal or stabilising. Our study shows that classic predictions for how dispersal affects metacommunity diversity can be strongly influenced by dormancy. Together, these results emphasise the need to consider both temporal and spatial processes when predicting multi-scale patterns of diversity.
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Affiliation(s)
- Nathan I Wisnoski
- Wyoming Geographic Information Science Center, University of Wyoming, Laramie, Wyoming, USA
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15
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Leibold MA, Rudolph FJ, Blanchet FG, De Meester L, Gravel D, Hartig F, Peres‐Neto P, Shoemaker L, Chase JM. The internal structure of metacommunities. OIKOS 2021. [DOI: 10.1111/oik.08618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - F. Guillaume Blanchet
- Dépt de Biologie, Univ. de Sherbrooke, Boulevard Univ. Sherbrooke QC Canada
- Dépt de Mathématiques, Univ. de Sherbrooke Sherbrooke QC Canada
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, Univ. of Leuven Leuven Belgium
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Inst. of Biology, Freie Univ. Berlin Berlin Germany
- Berlin‐Brandenburg Inst. of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - Dominique Gravel
- Dépt de Biologie, Univ. de Sherbrooke, Boulevard Univ. Sherbrooke QC Canada
| | - Florian Hartig
- Theoretical Ecology, Univ. of Regensburg Regensburg Germany
| | | | | | - Jonathan M. Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena Leipzig, Dept of Computer Sciences, Martin Luther Univ. Halle‐Wittenberg Halle Germany
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16
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Lennon JT, den Hollander F, Wilke-Berenguer M, Blath J. Principles of seed banks and the emergence of complexity from dormancy. Nat Commun 2021; 12:4807. [PMID: 34376641 PMCID: PMC8355185 DOI: 10.1038/s41467-021-24733-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/02/2021] [Indexed: 02/07/2023] Open
Abstract
Across the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise to multi-scale structures and networks spanning collections of cells to entire ecosystems. We outline the fundamental attributes and emergent phenomena associated with dormancy and seed banks, with the vision for a unifying and mathematically based framework that can address problems in the life sciences, ranging from global change to cancer biology.
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Affiliation(s)
- Jay T. Lennon
- grid.411377.70000 0001 0790 959XIndiana University, Department of Biology, Bloomington, USA
| | - Frank den Hollander
- grid.5132.50000 0001 2312 1970Universiteit Leiden, Mathematical Institute, Leiden, Netherlands
| | - Maite Wilke-Berenguer
- grid.7468.d0000 0001 2248 7639Humboldt-Universität zu Berlin, Institute of Mathematics, Berlin, Germany
| | - Jochen Blath
- grid.6734.60000 0001 2292 8254Technische Universität Berlin, Institute of Mathematics, Berlin, Germany
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17
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Arroyo-Esquivel J, Marculis NG, Hastings A. The effect of colonization dynamics in competition for space in metacommunities. THEOR ECOL-NETH 2021. [DOI: 10.1007/s12080-021-00515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractOne of the main factors that determines habitat suitability for sessile and territorial organisms is the presence or absence of another competing individual in that habitat. This type of competition arises in populations occupying patches in a metacommunity. Previous studies have looked at this process using a continuous-time modeling framework, where colonizations and extinctions occur simultaneously. However, different colonization processes may be performed by different species, which may affect the metacommunity dynamics. We address this issue by developing a discrete-time framework that describes these kinds of metacommunity interactions, and we consider different colonization dynamics. To understand potential dynamics, we consider specific functional forms that characterize the colonization and extinction processes of metapopulations competing for space as their limiting factor. We then provide a mathematical analysis of the models generated by this framework, and we compare these results to what is seen in nature and in previous models.
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18
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Mestre M, Höfer J. The Microbial Conveyor Belt: Connecting the Globe through Dispersion and Dormancy. Trends Microbiol 2020; 29:482-492. [PMID: 33281016 DOI: 10.1016/j.tim.2020.10.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022]
Abstract
Despite the recent increase in knowledge concerning microorganisms, the processes determining their global distribution and functioning have not been disentangled. Microbial dormant stages are adapted to endure specific adverse conditions related to their dispersion path, suggesting that dispersion is not entirely a stochastic process. Long-term dormancy enhances microbial dispersion, promoting the ubiquity of microorganisms. The evidence leads us to propose that there is a global, recurrent, and spatially cyclical dispersion of microorganisms that we have called the Microbial Conveyor Belt. These dispersion cycles directly influence the distribution of microorganisms, the global cycling of inorganic and organic matter, and thus the Earth system's functioning.
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Affiliation(s)
- Mireia Mestre
- Centro de Investigación Oceanográfica COPAS Sur-Austral, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile; Centro FONDAP de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile.
| | - Juan Höfer
- Centro FONDAP de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile; Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile; Centro de Investigación y Formación San Ignacio de Huinay, Huinay, Chile.
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19
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Castillo-Escrivà A, Mesquita-Joanes F, Rueda J. Effects of the Temporal Scale of Observation on the Analysis of Aquatic Invertebrate Metacommunities. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.561838] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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20
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Gálvez Á, Aguilar-Alberola JA, Armengol X, Bonilla F, Iepure S, Monrós JS, Olmo C, Rojo C, Rueda J, Rueda R, Sasa M, Mesquita-Joanes F. Environment and Space Rule, but Time Also Matters for the Organization of Tropical Pond Metacommunities. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.558833] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Holyoak M, Caspi T, Redosh LW. Integrating Disturbance, Seasonality, Multi-Year Temporal Dynamics, and Dormancy Into the Dynamics and Conservation of Metacommunities. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.571130] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Cid N, Bonada N, Heino J, Cañedo-Argüelles M, Crabot J, Sarremejane R, Soininen J, Stubbington R, Datry T. A Metacommunity Approach to Improve Biological Assessments in Highly Dynamic Freshwater Ecosystems. Bioscience 2020; 70:427-438. [PMID: 32440024 PMCID: PMC7231578 DOI: 10.1093/biosci/biaa033] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Rapid shifts in biotic communities due to environmental variability challenge the detection of anthropogenic impacts by current biomonitoring programs. Metacommunity ecology has the potential to inform such programs, because it combines dispersal processes with niche-based approaches and recognizes variability in community composition. Using intermittent rivers-prevalent and highly dynamic ecosystems that sometimes dry-we develop a conceptual model to illustrate how dispersal limitation and flow intermittence influence the performance of biological indices. We produce a methodological framework integrating physical- and organismal-based dispersal measurements into predictive modeling, to inform development of dynamic ecological quality assessments. Such metacommunity-based approaches could be extended to other ecosystems and are required to underpin our capacity to monitor and protect ecosystems threatened under future environmental changes.
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Affiliation(s)
| | - Núria Bonada
- Freshwater Ecology, Hydrology, and Management research group, University of Barcelona, Barcelona, Catalonia, Spain
| | - Jani Heino
- Finnish Environment Institute, Freshwater Centre, Oulu, Finland
| | - Miguel Cañedo-Argüelles
- Freshwater Ecology, Hydrology, and Management research group, University of Barcelona, Barcelona, Catalonia, Spain
| | | | | | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
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23
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Locey KJ, Muscarella ME, Larsen ML, Bray SR, Jones SE, Lennon JT. Dormancy dampens the microbial distance-decay relationship. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190243. [PMID: 32200741 DOI: 10.1098/rstb.2019.0243] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Much of Earth's biodiversity has the capacity to engage in dormancy, a reversible state of reduced metabolic activity. By increasing resilience to unfavourable conditions, dormancy leads to the accumulation of 'seed banks'. These reservoirs of genetic and phenotypic diversity should diminish the strength of environmental filtering and increase rates of dispersal. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biogeography is lacking. We constructed geographical and environmental distance-decay relationships (DDRs) for the total (DNA) and active (RNA) portions of bacterial communities in a regional-scale 16S rRNA survey of forested ponds in Indiana, USA. As predicted, total communities harboured greater diversity and exhibited weaker DDRs than active communities. These observations were robust to random resampling and different community metrics. To evaluate the processes underlying the biogeographic patterns, we developed a platform of mechanistic models that used the geographical coordinates and environmental characteristics of our study system. Based on more than 106 simulations, our models approximated the empirical DDRs when there was strong environmental filtering along with the presence of long-lived seed banks. By contrast, the inclusion of dispersal generally decreased model performance. Together, our findings support recent theoretical predictions that seed banks can influence the biogeographic patterns of microbial communities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- K J Locey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - M E Muscarella
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - M L Larsen
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - S R Bray
- Department of Biology, Transylvania University, Lexington, Kentucky, USA
| | - S E Jones
- Department of Biological Sciences, University of Notre Dame, South Bend, Indiana, USA
| | - J T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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24
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Wisnoski NI, Muscarella ME, Larsen ML, Peralta AL, Lennon JT. Metabolic insight into bacterial community assembly across ecosystem boundaries. Ecology 2020; 101:e02968. [DOI: 10.1002/ecy.2968] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/14/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - Megan L. Larsen
- Department of Biology Indiana University Bloomington Indiana47405USA
| | - Ariane L. Peralta
- Department of Biology Indiana University Bloomington Indiana47405USA
| | - Jay T. Lennon
- Department of Biology Indiana University Bloomington Indiana47405USA
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25
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Miller ET, Bohannan BJM. Life Between Patches: Incorporating Microbiome Biology Alters the Predictions of Metacommunity Models. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00276] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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