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van Breugel M, Bongers F, Norden N, Meave JA, Amissah L, Chanthorn W, Chazdon R, Craven D, Farrior C, Hall JS, Hérault B, Jakovac C, Lebrija-Trejos E, Martínez-Ramos M, Muñoz R, Poorter L, Rüger N, van der Sande M, Dent DH. Feedback loops drive ecological succession: towards a unified conceptual framework. Biol Rev Camb Philos Soc 2024; 99:928-949. [PMID: 38226776 DOI: 10.1111/brv.13051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/17/2024]
Abstract
The core principle shared by most theories and models of succession is that, following a major disturbance, plant-environment feedback dynamics drive a directional change in the plant community. The most commonly studied feedback loops are those in which the regrowth of the plant community causes changes to the abiotic (e.g. soil nutrients) or biotic (e.g. dispersers) environment, which differentially affect species availability or performance. This, in turn, leads to shifts in the species composition of the plant community. However, there are many other PE feedback loops that potentially drive succession, each of which can be considered a model of succession. While plant-environment feedback loops in principle generate predictable successional trajectories, succession is generally observed to be highly variable. Factors contributing to this variability are the stochastic processes involved in feedback dynamics, such as individual mortality and seed dispersal, and extrinsic causes of succession, which are not affected by changes in the plant community but do affect species performance or availability. Both can lead to variation in the identity of dominant species within communities. This, in turn, leads to further contingencies if these species differ in their effect on their environment (priority effects). Predictability and variability are thus intrinsically linked features of ecological succession. We present a new conceptual framework of ecological succession that integrates the propositions discussed above. This framework defines seven general causes: landscape context, disturbance and land-use, biotic factors, abiotic factors, species availability, species performance, and the plant community. When involved in a feedback loop, these general causes drive succession and when not, they are extrinsic causes that create variability in successional trajectories and dynamics. The proposed framework provides a guide for linking these general causes into causal pathways that represent specific models of succession. Our framework represents a systematic approach to identifying the main feedback processes and causes of variation at different successional stages. It can be used for systematic comparisons among study sites and along environmental gradients, to conceptualise studies, and to guide the formulation of research questions and design of field studies. Mapping an extensive field study onto our conceptual framework revealed that the pathways representing the study's empirical outcomes and conceptual model had important differences, underlining the need to move beyond the conceptual models that currently dominate in specific fields and to find ways to examine the importance of and interactions among alternative causal pathways of succession. To further this aim, we argue for integrating long-term studies across environmental and anthropogenic gradients, combined with controlled experiments and dynamic modelling.
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Affiliation(s)
- Michiel van Breugel
- Department of Geography, National University of Singapore, Arts Link, #03-01 Block AS2, 117570, Singapore
- Yale-NUS College, 16 College Avenue West, Singapore, 138527, Singapore
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building - 401, Panama City, 0843-03092, Panama
| | - Frans Bongers
- Forest Ecology and Forest Management Group, Wageningen University & Research, PO Box 47, 6700 AA, Wageningen, The Netherlands
| | - Natalia Norden
- Centro de Estudios Socioecológicos y Cambio Global, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Avenida Circunvalar #16-20, Bogotá, Colombia
| | - Jorge A Meave
- Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México. Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, C.P. 04510, Mexico
| | - Lucy Amissah
- CSIR-Forestry Research Institute of Ghana, UPO Box 63, Kumasi, Ghana
| | - Wirong Chanthorn
- Department of Environmental Technology and Management, Faculty of Environment, Kasetsart University, 50 Ngamwongwan Road, Jatujak District, 10900, Thailand
| | - Robin Chazdon
- Forest Research Institute, University of the Sunshine Coast, 90 Sippy Downs Dr, Sippy Downs, Queensland, 4556, Australia
| | - Dylan Craven
- Center for Genomics, Ecology & Environment, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago, 8580745, Chile
| | - Caroline Farrior
- Department of Integrative Biology, University of Texas at Austin, 2415 Speedway, Stop C0930, Austin, Texas, 78705, USA
| | - Jefferson S Hall
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building - 401, Panama City, 0843-03092, Panama
| | - Bruno Hérault
- CIRAD, UPR Forêts et Sociétés, F-34398 Montpellier, France & Forêts et Sociétés, Univ Montpellier, CIRAD, Montpellier, France
| | - Catarina Jakovac
- Departamento de Fitotecnia, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346, 88034-000, Florianópolis, Brazil
| | - Edwin Lebrija-Trejos
- Department of Biology and Environment, University of Haifa-Oranim, Tivon, 36006, Israel
| | - Miguel Martínez-Ramos
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Campus Morelia, Antigua Carretera a Pátzcuaro # 8701, Col. Ex-Hacienda de San José de la Huerta, CP 58190, Morelia, Michoacán, Mexico
| | - Rodrigo Muñoz
- Forest Ecology and Forest Management Group, Wageningen University & Research, PO Box 47, 6700 AA, Wageningen, The Netherlands
| | - Lourens Poorter
- Forest Ecology and Forest Management Group, Wageningen University & Research, PO Box 47, 6700 AA, Wageningen, The Netherlands
| | - Nadja Rüger
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building - 401, Panama City, 0843-03092, Panama
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany
- Department of Economics, Institute of Empirical Economic Research, University of Leipzig, Grimmaische Str. 12, 04109, Leipzig, Germany
| | - Masha van der Sande
- Forest Ecology and Forest Management Group, Wageningen University & Research, PO Box 47, 6700 AA, Wageningen, The Netherlands
| | - Daisy H Dent
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building - 401, Panama City, 0843-03092, Panama
- ETH Zürich, Department of Environmental Systems Science, Institute for Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland
- Max Planck Institute for Animal Behavior, Am Obstberg 1, 78315 Radolfzell, Germany
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Guaschino M, Garello M, Nari L, Zhimo YV, Droby S, Spadaro D. Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease. Front Microbiol 2024; 15:1330865. [PMID: 38577679 PMCID: PMC10991698 DOI: 10.3389/fmicb.2024.1330865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/14/2024] [Indexed: 04/06/2024] Open
Abstract
Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.
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Affiliation(s)
- Micol Guaschino
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | - Marco Garello
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | | | - Yeka V. Zhimo
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Samir Droby
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
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3
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Schauberger C, Seki D, Cutts EM, Glud RN, Thamdrup B. Uniform selective pressures within redox zones drive gradual changes in microbial community composition in hadal sediments. Environ Microbiol 2023; 25:1594-1604. [PMID: 36999247 DOI: 10.1111/1462-2920.16377] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/19/2023] [Indexed: 04/01/2023]
Abstract
Microbial communities in marine sediments are highly diverse, yet the processes that give rise to this complexity are unclear. It has been proposed that benthic microbial communities must be continuously re-seeded from the water column because dispersal within the sediment is severely limited. Previous studies consistently report that the composition of the microbial community gradually changes with sediment depth. However, the relative contributions of the processes that underlie these compositional gradients have not been determined, and it is unknown whether microbial dispersal is indeed too slow to outpace burial. Here, we applied ecological statistical frameworks to 16S rRNA gene amplicon-based community composition data from Atacama Trench sediments to investigate the links between biogeochemistry, burial, and microbial community assembly processes. We confirm that dispersal limitation affects microbial communities and find that gradual changes in community composition are driven by selective pressures that change abruptly across the discrete boundaries between redox zones rather than along continuous biogeochemical gradients, while selective pressures are uniform within each zone. The gradual changes in community composition over centimetres of depth within a zone hence reflects a decades-long response to the abruptly changing selective pressures.
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Affiliation(s)
- Clemens Schauberger
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - David Seki
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Elise M Cutts
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ronnie N Glud
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Ocean and Environmental Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Bo Thamdrup
- Hadal & Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
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Han D, Richter-Heitmann T, Kim JH, Friedrich MW, Yin X, Elvert M, Ryu JS, Jang K, Nam SI. Influence of sedimentary deposition on the microbial assembly process in Arctic Holocene marine sediments. Front Microbiol 2023; 14:1231839. [PMID: 37700860 PMCID: PMC10493304 DOI: 10.3389/fmicb.2023.1231839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/15/2023] [Indexed: 09/14/2023] Open
Abstract
The sea-level rise during the Holocene (11-0 ky BP) and its resulting sedimentation and biogeochemical processes may control microbial life in Arctic sediments. To gain further insight into this interaction, we investigated a sediment core (up to 10.7 m below the seafloor) from the Chuckchi Shelf of the western Arctic Ocean using metabarcoding-based sequencing and qPCR to characterize archaeal and bacterial 16S rRNA gene composition and abundance, respectively. We found that Arctic Holocene sediments harbor local microbial communities, reflecting geochemical and paleoclimate separations. The composition of bacterial communities was more diverse than that of archaeal communities, and specifically distinct at the boundary layer of the sulfate-methane transition zone. Enriched cyanobacterial sequences in the Arctic middle Holocene (8-7 ky BP) methanogenic sediments remarkably suggest past cyanobacterial blooms. Bacterial communities were phylogenetically influenced by interactions between dispersal limitation and environmental selection governing community assembly under past oceanographic changes. The relative influence of stochastic and deterministic processes on the bacterial assemblage was primarily determined by dispersal limitation. We have summarized our findings in a conceptual model that revealed how changes in paleoclimate phases cause shifts in ecological succession and the assembly process. In this ecological model, dispersal limitation is an important driving force for progressive succession for bacterial community assembly processes on a geological timescale in the western Arctic Ocean. This enabled a better understanding of the ecological processes that drive the assembly of communities in Holocene sedimentary habitats affected by sea-level rise, such as in the shallow western Arctic shelves.
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Affiliation(s)
- Dukki Han
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung-si, Gangwon-do, Republic of Korea
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ji-Hoon Kim
- Marine Geology & Energy Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, Republic of Korea
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Organic Geochemistry Group, Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jong-Sik Ryu
- Department of Earth and Environmental Sciences, Pukyong National University, Busan, Republic of Korea
| | - Kwangchul Jang
- Division of Glacial Environment Research, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Seung-Il Nam
- Division of Glacial Environment Research, Korea Polar Research Institute, Incheon, Republic of Korea
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5
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Du X, Gu S, Zhang Z, Li S, Zhou Y, Zhang Z, Zhang Q, Wang L, Ju Z, Yan C, Li T, Wang D, Yang X, Peng X, Deng Y. Spatial distribution patterns across multiple microbial taxonomic groups. ENVIRONMENTAL RESEARCH 2023; 223:115470. [PMID: 36775088 DOI: 10.1016/j.envres.2023.115470] [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: 12/06/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Even in the vertical dimension, soil bacterial communities are spatially distributed in a distance-decay relationship (DDR). However, whether this pattern is universal among all soil microbial taxonomic groups, and how body size influences this distribution, remains elusive. Our study consisted of obtaining 140 soil samples from two adjacent ecosystems in the Yellow River Delta (YRD), both nontidal and tidal, and measuring the DDR between topsoil and subsoil for bacteria, archaea, fungi and protists (rhizaria). Our results showed that the entire community generally fitted the DDR patterns (P < 0.001), this was also true at the kingdom level (P < 0.001, with the exception of the fungal community), and for most individual phyla (47/75) in both ecosystems and with soil depth. Meanwhile, these results presented a general trend that the community turnover rate of nontidal soils was higher than tidal soils (P < 0.05), and that the rate of topsoil was also higher than that of subsoil (P < 0.05). Additionally, microbial spatial turnover rates displayed a negative relationship with body sizes in nontidal topsoil (R2 = 0.29, P = 0.009), suggesting that the smaller the body size of microorganisms, the stronger the spatial limitation was in this environment. However, in tidal soils, the body size effect was negligible, probably owing to the water's fluidity. Moreover, community assembly was judged to be deterministic, and heterogeneous selection played a dominant role in the different environments. Specifically, the spatial distance was much more influential, while the soil salinity in these ecosystems was the major environmental factor in selecting the distributions of microbial communities. Overall, this study revealed that microbial community compositions at different taxonomic levels followed relatively consistent distribution patterns and mechanisms in this coastal area.
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Affiliation(s)
- Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Zheng Zhang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Shuzhen Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Yuqi Zhou
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Zhaojing Zhang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Qi Zhang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Linlin Wang
- Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Zhicheng Ju
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengliang Yan
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tong Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Institute for Marine Science and Technology, Shandong University, Qingdao, 266237, China.
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6
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Edwards JA, Saran UB, Bonnette J, MacQueen A, Yin J, Nguyen TU, Schmutz J, Grimwood J, Pennacchio LA, Daum C, Glavina Del Rio T, Fritschi FB, Lowry DB, Juenger TE. Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range. Curr Biol 2023; 33:1926-1938.e6. [PMID: 37080198 DOI: 10.1016/j.cub.2023.03.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.
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Affiliation(s)
- Joseph A Edwards
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
| | - Usha Bishnoi Saran
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jun Yin
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Tu Uyen Nguyen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Len A Pennacchio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Tijana Glavina Del Rio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Felix B Fritschi
- Department of Plant Science and Technology, University of Missouri, Agriculture Bldg, 52, Columbia, MO 65201, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Rm 166, East Lansing, MI 48824, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
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7
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Wu Q, Wan W. Insight into application of phosphate-solubilizing bacteria promoting phosphorus availability during chicken manure composting. BIORESOURCE TECHNOLOGY 2023; 373:128707. [PMID: 36746213 DOI: 10.1016/j.biortech.2023.128707] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Understanding ecological roles of phosphate-solubilizing bacteria (PSB) is important to optimize composting systems. Illumina MiSeq sequencing, gene quantitation, and statistical analyses were employed to explore ecological mechanisms underlying available phosphorus (AP) facilitation during composting with the inoculation of PSB Pseudomonas sp. WWJ-22. Results displayed that the inoculation of PSB significantly increased AP from 0.83 to 1.23 g kg-1, and notably increased abundances of phosphorus-cycling genes as well as numbers of PSB mineralizing phytate and lecithin. The PSB addition significantly affected compost bacterial community composition, and phosphorus factions and phosphorus-cycling genes independently explained 25.4 % and 25.0 % bacterial compositional dissimilarity. Stochastic and homogenizing processes affected more on bacterial community assembly, and rare bacteria potentially mediated organic phosphorus mineralization. These results emphasized that phosphorus fractions, PSB number, phosphorus-cycling gene abundance, and bacterial community composition contributed differently to phosphorus availability. Findings highlight ecological roles of exogenous PSB during chicken manure composting.
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Affiliation(s)
- Qiusheng Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China.
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8
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Fox A, Widmer F, Lüscher A. Soil microbial community structures are shaped by agricultural systems revealing little temporal variation. ENVIRONMENTAL RESEARCH 2022; 214:113915. [PMID: 35940233 PMCID: PMC9492858 DOI: 10.1016/j.envres.2022.113915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Many studies in soil microbial ecology are undertaken with a single sampling event, with the influence of temporal progression rarely being considered. Under field conditions, soil samples were taken from different agricultural systems; a sown grassland to maize rotation (MC), an intensively managed permanent grassland (INT), as well as extensively managed permanent grasslands with high (EXT_HP), low to sufficient (EXT_LP) and deficient available P (EXT_DP), six times throughout the 2017 growing season. Thus, this study aimed to determine if any differences in soil microbiome structures between both sharply contrasting (MC - INT - EXT), slightly differing (EXT_HP - EXT_DP) and quite similar (EXT_HP - EXT_LP and EXT_LP - EXT_DP) agricultural systems persist through changing growth conditions within the growing season. For both fungal and bacterial community structure, the influence of agricultural system (CV = 0.256, P < 0.001 and CV = 0.145, P < 0.01, respectively) was much greater than that of temporal progression (√CV = 0.065 and 0.042, respectively, both P < 0.001). Importantly, nearly all agricultural systems persistently harbored significantly distinct fungal community structures across each of the six sampling events (all at least P < 0.05). There were not as many pairwise differences in bacterial community structure between the agricultural systems, but some did persist (MC and EXT_HP ∼ EXT_DP, all P < 0.001). Additionally, persistent indicator fungal OTUs (IndVal >0.7, P ≤ 0.05) associated to each agricultural system (except EXT_LP) were found in each of the six sampling events. These results highlight the temporal stability of pairwise differences in soil microbiome structures between established agricultural systems through changing plant growth conditions, even between those with a comparable management regime. This is a highly relevant finding in informing the sampling strategy of studies in soil microbial ecology as well as for designing efficient soil biodiversity monitoring systems.
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Affiliation(s)
- A Fox
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland; Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - F Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - A Lüscher
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland.
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9
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Jia X, Dini-Andreote F, Salles JF. Unravelling the interplay of ecological processes structuring the bacterial rare biosphere. ISME COMMUNICATIONS 2022; 2:96. [PMID: 37938751 PMCID: PMC9723687 DOI: 10.1038/s43705-022-00177-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 06/17/2023]
Abstract
Most ecological communities harbor many rare species (i.e., the rare biosphere), however, relatively little is known about how distinct ecological processes structure their existence. Here, we used spatiotemporal data on soil bacterial communities along a natural ecosystem gradient to model the relative influences of assembly processes structuring the rare and common biospheres. We found a greater influence of homogeneous selection (i.e., imposed by spatiotemporally constant variables) mediating the assembly of the rare biosphere, whereas the common biosphere was mostly governed by variable selection (i.e., imposed by spatial and/or temporal fluctuating variables). By partitioning the different types of rarity, we found homogeneous selection to explain the prevalence of permanently rare taxa, thus suggesting their persistence at low abundances to be restrained by physiological traits. Conversely, the dynamics of conditionally rare taxa were mostly structured by variable selection, which aligns with the ability of these taxa to switch between rarity and commonness as responses to environmental spatiotemporal variations. Taken together, our study contributes to the establishment of a link between conceptual and empirical developments in the ecology of the soil microbial rare biosphere. Besides, this study provides a framework to better understand, model, and predict the existence and dynamics of microbial rare biospheres across divergent systems and scales.
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Affiliation(s)
- Xiu Jia
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, 9747AG, The Netherlands.
| | - Francisco Dini-Andreote
- Department of Plant Science, The Pennsylvania State University, Pennsylvania, University Park, PA, 16801, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16801, USA
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, 9747AG, The Netherlands.
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10
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Guajardo-Leiva S, Alarcón J, Gutzwiller F, Gallardo-Cerda J, Acuña-Rodríguez IS, Molina-Montenegro M, Crandall KA, Pérez-Losada M, Castro-Nallar E. Source and acquisition of rhizosphere microbes in Antarctic vascular plants. Front Microbiol 2022; 13:916210. [PMID: 36160194 PMCID: PMC9493328 DOI: 10.3389/fmicb.2022.916210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
| | - Jaime Alarcón
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Florence Gutzwiller
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jorge Gallardo-Cerda
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | | | - Marco Molina-Montenegro
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Centro de Investigación en Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | - Keith A. Crandall
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC, United States
| | - Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC, United States
- Division of Emergency Medicine, Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Children’s National Hospital, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
- *Correspondence: Eduardo Castro-Nallar,
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11
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Zhang G, Bai J, Tebbe CC, Huang L, Jia J, Wang W, Wang X, Yu L, Zhao Q. Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes. Mol Ecol 2022; 31:4478-4494. [PMID: 35789059 DOI: 10.1111/mec.16600] [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: 12/16/2021] [Revised: 06/25/2022] [Accepted: 06/30/2022] [Indexed: 11/27/2022]
Abstract
Microbiologically driven ecosystem processes can be profoundly altered by alien plant invasions. The understanding of ecological mechanisms orchestrating different microbial constituents and their roles in emerging functional properties under plant invasions is limited. Here, we investigated soil microbial communities and functions using high-throughput amplicon sequencing and GeoChip technology, respectively, along a chronological gradient of smooth cordgrass invasion in salt marshes located in the Yellow River Estuary, China. We found a positive correlation between microbial diversity and the duration age of invasion, and both bacterial and fungal communities exerted orderly changes with invasion. Soil microbial metabolic potential, as indicated by the abundance of microbial functional genes involved in biogeochemical cycling, decreased in response to invasion. As a consequence, declined soil microbial metabolisms by plant invasion facilitated the carbon accumulation in invaded salt marshes. Bacteria and fungi exhibited distinct contributions to assembly processes along the invasion gradient: bacterial communities were mainly driven by selection and dispersal limitation, while fungi were dramatically shaped by stochastic processes. Soil microbial-mediated functions were taxon-specific, as indicated by community-function relationships. This study demonstrates the distinct contributions of microbial constituents to microbial community assembly and functions and sheds light on the implications of plant invasion on microbiologically driven ecosystem processes in coastal wetlands.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, Braunschweig, Germany
| | - Laibin Huang
- Department of Land, Air, and Water Resources, University of California-, Davis, USA
| | - Jia Jia
- Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, Yellow River Institute of Hydraulic Research, Zhengzhou, P.R. China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Lu Yu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Ji' nan, P.R. China.,Ecology Institute of Shandong Academy of Sciences, Ji' nan, P.R. China
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12
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Song J, Beule L, Jongmans-Hochschulz E, Wichels A, Gerdts G. The travelling particles: community dynamics of biofilms on microplastics transferred along a salinity gradient. ISME COMMUNICATIONS 2022; 2:35. [PMID: 37938248 PMCID: PMC9723596 DOI: 10.1038/s43705-022-00117-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 05/28/2023]
Abstract
Microplastics (MP), as novel substrata for microbial colonization within aquatic ecosystems, are a matter of growing concern due to their potential to propagate foreign or invasive species across different environments. MP are known to harbour a diversity of microorganisms, yet little is understood of the dynamics of their biofilms and their capacity to successfully displace these microorganisms across different aquatic ecosystems typically marked by steep salinity gradients. To address this, we performed an in situ sequential incubation experiment to simulate MP transport from riverine to coastal seawaters using synthetic (high-density polyethylene, HDPE and tyre wear, TW) and natural (Wood) substrata. Bacterial communities on incubated particles were compared to each other as well as to those in surrounding waters, and their dynamics along the gradient investigated. All communities differed significantly from each other in their overall structure along the salinity gradient and were shaped by different ecological processes. While HDPE communities were governed by environmental selection, those on TW and Wood were dominated by stochastic events of dispersal and drift. Upon transfer into coastal seawaters, an almost complete turnover was observed among HDPE and TW communities. While synthetic particles displaced a minor proportion of communities across the salinity gradient, some of these comprised putatively pathogenic and resistant taxa. Our findings present an extensive assessment of MP biofilms and their dynamics upon displacement across different aquatic systems, presenting new insights into the role of MP as transport vectors.
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Affiliation(s)
- Jessica Song
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27498, Helgoland, Germany.
| | - Lukas Beule
- Julius Kühn Institute-Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Königin-Luise-Strasse 19, 14195, Berlin, Germany
| | - Elanor Jongmans-Hochschulz
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27498, Helgoland, Germany
| | - Antje Wichels
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27498, Helgoland, Germany
| | - Gunnar Gerdts
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27498, Helgoland, Germany
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13
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Okamoto N, Keeling PJ, Leander BS, Tai V. Microbial communities in sandy beaches from the three domains of life differ by microhabitat and intertidal location. Mol Ecol 2022; 31:3210-3227. [PMID: 35364623 DOI: 10.1111/mec.16453] [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: 10/09/2020] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022]
Abstract
The microbial communities of sandy beaches are poorly described despite the biogeochemical importance and ubiquity of these ecosystems. Using metabarcoding of the 16S and 18S rRNA genes, we investigated the diversity, microhabitats (with or between sand grains), and intertidal distributions of microorganisms (including meiofauna) from pristine sandy beaches in British Columbia, Canada, and hypothesized that abiotic variations due to microhabitat or intertidal gradients influences the distribution of microorganisms on local scales. Bacterial, archaeal, and protistan communities of the sand were clearly distinct from interstitial communities, and from planktonic communities of the overlying seawater, which correlated with differences in function and lifestyle, e.g., sulfur reduction and gliding motility. In contrast, meiofaunal communities could not be distinguished by sample type, suggesting that they are more frequently mobilized between these microhabitats. Across intertidal zones, high intertidal, mid intertidal, and low intertidal/swash communities were distinct and correlated with moisture, organic carbon and phosphate content, implying that the distribution of microorganisms is influenced by intertidal abiotic gradients. However, few taxa at the genus or species level individually contributed to this zonation pattern; rather, a unique combination of multiple microbial taxa was more likely responsible. Although significant differences in microbial community composition on sandy beaches can be attributed to microhabitat and intertidal gradients, further investigations are needed to assess community assembly processes, the consistency of these distributions, and the functions of the majority of the microorganisms observed in the sand and their effects on the biogeochemistry and ecology of sandy beaches.
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Affiliation(s)
- Noriko Okamoto
- University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Quadra Island, British Columbia, Canada
| | | | - Brian S Leander
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Vera Tai
- University of British Columbia, Vancouver, British Columbia, Canada.,University of Western Ontario, London, Ontario, Canada
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14
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Hawkins JH, Zeglin LH. Microbial Dispersal, Including Bison Dung Vectored Dispersal, Increases Soil Microbial Diversity in a Grassland Ecosystem. Front Microbiol 2022; 13:825193. [PMID: 35432281 PMCID: PMC9009311 DOI: 10.3389/fmicb.2022.825193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial communities display biogeographical patterns that are driven by local environmental conditions and dispersal limitation, but the relative importance of underlying dispersal mechanisms and their consequences on community structure are not well described. High dispersal rates can cause soil microbial communities to become more homogenous across space and therefore it is important to identify factors that promote dispersal. This study experimentally manipulated microbial dispersal within different land management treatments at a native tallgrass prairie site, by changing the relative openness of soil to dispersal and by simulating vector dispersal via bison dung addition. We deployed experimental soil bags with mesh open or closed to dispersal, and placed bison dung over a subset of these bags, to areas with three different land managements: active bison grazing and annual fire, annual fire but no bison grazing, and no bison grazing with infrequent fire. We expected microbial dispersal to be highest in grazed and burned environments, and that the addition of dung would consistently increase overall microbial richness and lead to homogenization of communities over time. Results show that dispersal rates, as the accumulation of taxa over the course of the 3-month experiment, increase taxonomic richness similarly in all land management treatments. Additionally, bison dung seems to be serving as a dispersal and homogenization vector, based on the consistently higher taxon richness and increased community similarity across contrasting grazing and fire treatments when dung is added. This finding also points to microbial dispersal as an important function that herbivores perform in grassland ecosystems, and in turn, as a function that was lost at a continental scale following bison extermination across the Great Plains of North America in the nineteenth century. This study is the first to detect that dispersal and vector dispersal by grazing mammals promote grassland soil microbial diversity and affect microbial community composition.
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Affiliation(s)
| | - Lydia H. Zeglin
- Division of Biology, Kansas State University, Manhattan, KS, United States
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15
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Sikorski J, Baumgartner V, Birkhofer K, Boeddinghaus RS, Bunk B, Fischer M, Fösel BU, Friedrich MW, Göker M, Hölzel N, Huang S, Huber KJ, Kandeler E, Klaus VH, Kleinebecker T, Marhan S, von Mering C, Oelmann Y, Prati D, Regan KM, Richter-Heitmann T, Rodrigues JFM, Schmitt B, Schöning I, Schrumpf M, Schurig E, Solly EF, Wolters V, Overmann J. The Evolution of Ecological Diversity in Acidobacteria. Front Microbiol 2022; 13:715637. [PMID: 35185839 PMCID: PMC8847707 DOI: 10.3389/fmicb.2022.715637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.
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Affiliation(s)
- Johannes Sikorski
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vanessa Baumgartner
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Runa S. Boeddinghaus
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Boyke Bunk
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Bärbel U. Fösel
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Markus Göker
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Norbert Hölzel
- Biodiversity and Ecosystem Research Group, Institute of Landscape Ecology, University Münster, Münster, Germany
| | - Sixing Huang
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Katharina J. Huber
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ellen Kandeler
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | | | - Till Kleinebecker
- Institute of Landscape Ecology and Resources Management, University of GieBen, GieBen, Germany
| | - Sven Marhan
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Daniel Prati
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Kathleen M. Regan
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - João F. Matias Rodrigues
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Barbara Schmitt
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ingo Schöning
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | - Marion Schrumpf
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Emily F. Solly
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Microbiology, Faculty of Life Sciences, Technische Universität Braunschweig, Braunschweig, Germany
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16
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Ma X, Chao L, Li J, Ding Z, Wang S, Li F, Bao Y. The Distribution and Turnover of Bacterial Communities in the Root Zone of Seven Stipa Species Across an Arid and Semi-arid Steppe. Front Microbiol 2022; 12:782621. [PMID: 35003012 PMCID: PMC8741278 DOI: 10.3389/fmicb.2021.782621] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
The bacterial communities of the root-zone soil are capable of regulating vital biogeochemical cycles and the succession of plant growth. Stipa as grassland constructive species is restricted by the difference features of east–west humidity and north–south heat, which shows the population substituting distribution. The distribution, turnover, and potential driving factors and ecological significance of the root-zone bacterial community along broad spatial gradients of Stipa taxa transition remain unclear. This paper investigated seven Stipa species root-zone soils based on high-throughput sequencing combined with the measurements of multiple environmental parameters in arid and semi-arid steppe. The communities of soil bacteria in root zone had considerable turnover, and some regular variations in structure along the Stipa taxa transition are largely determined by climatic factors, vegetation coverage, and pH at a regional scale. Bacterial communities had a clear Stipa population specificity, but they were more strongly affected by the main annual precipitation, which resulted in a biogeographical distribution pattern along precipitation gradient, among which Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi were the phyla that were most abundant. During the transformation of Stipa taxa from east to west, the trend of diversity shown by bacterial community in the root zone decreased first, and then increased sharply at S. breviflora, which was followed by continuous decreasing toward northwest afterwards. However, the richness and evenness showed an opposite trend, and α diversity had close association with altitude and pH. There would be specific and different bacterial taxa interactions in different Stipa species, in which S. krylovii had the simplest and most stable interaction network with the strongest resistance to the environment and S. breviflora had most complex and erratic. Moreover, the bacterial community was mainly affected by dispersal limitation at a certain period. These results are conducive to the prediction of sustainable ecosystem services and protection of microbial resources in a semi-arid grassland ecosystem.
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Affiliation(s)
- Xiaodan Ma
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Lumeng Chao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Jingpeng Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Zhiying Ding
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Siyu Wang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Fansheng Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Yuying Bao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.,State Key Laboratory of Reproductive Regulatory and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
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17
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Sengupta A, Volkmann THM, Danczak RE, Stegen JC, Dontsova K, Abramson N, Bugaj AS, Volk MJ, Matos KA, Meira-Neto AA, Barberán A, Neilson JW, Maier RM, Chorover J, Troch PA, Meredith LK. Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System. Front Microbiol 2021; 12:754698. [PMID: 34887842 PMCID: PMC8650109 DOI: 10.3389/fmicb.2021.754698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.
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Affiliation(s)
- Aditi Sengupta
- Department of Biology, California Lutheran University, Thousand Oaks, CA, United States.,Biosphere 2, University of Arizona, Tucson, AZ, United States
| | | | - Robert E Danczak
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - James C Stegen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Katerina Dontsova
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Nate Abramson
- Department of Geosciences, University of Arizona, Tucson, AZ, United States
| | - Aaron S Bugaj
- Biosphere 2, University of Arizona, Tucson, AZ, United States
| | - Michael J Volk
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | | | - Antonio A Meira-Neto
- Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ, United States
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Julia W Neilson
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Raina M Maier
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Jon Chorover
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Peter A Troch
- Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ, United States
| | - Laura K Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
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18
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Lammel DR, Nüsslein K, Cerri CEP, Veresoglou SD, Rillig MC. Soil biota shift with land use change from pristine rainforest and Savannah (Cerrado) to agriculture in southern Amazonia. Mol Ecol 2021; 30:4899-4912. [PMID: 34297871 DOI: 10.1111/mec.16090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Southern Amazonia is currently experiencing extensive land use change from forests to agriculture caused by increased local and global demand for agricultural products. However, little is known about the impacts of deforestation and land use change on soil biota. We investigated two regions in southern Amazonia (rainforest and Savannah/Cerrado biomes), analysing soil biota community turnover based on 16S (Archaea and Bacteria) and 18S rRNA genes (Eukaryotes, including Fungi, Protists and Animalia) and correlating them with soil chemistry and land use intensity. We found that soil biota community structure is driven by land use change in both Cerrado and rainforest. Crop fields approximatively doubled the richness of soil Archaea, Bacteria and Protists. We propose that crop systems not only increase soil pH and fertility, but also create continued disturbance (crop seasons) that stimulates soil diversity, as predicted by the dynamic equilibrium model (DEM) and the intermediate disturbance hypothesis (IDH). Even though agricultural fields had higher soil biota richness, some taxa were suppressed by agriculture (6/31 operational taxonomic units of Archaea, 245/1790 of Bacteria, 12/74 of Animalia, 20/144 of Fungi and 25/310 of Protists). Consequently, land use change in this region should proceed with caution. In the southern Amazonia region of Brazil, current laws require farmers to keep 20%-80% pristine vegetation areas on their property. Our data support the relevance of this law: since there are unique soil taxa under native vegetation, keeping these pristine areas adjacent to the agricultural fields should maximize soil biodiversity protection in these regions.
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Affiliation(s)
- Daniel R Lammel
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Department of Microbiology, University of Massachusetts, Amherst, MA, USA.,ESALQ&CENA, University of São Paulo, Piracicaba, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | | | - Stavros D Veresoglou
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C Rillig
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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19
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Schwob G, Segovia NI, González-Wevar C, Cabrol L, Orlando J, Poulin E. Exploring the Microdiversity Within Marine Bacterial Taxa: Toward an Integrated Biogeography in the Southern Ocean. Front Microbiol 2021; 12:703792. [PMID: 34335536 PMCID: PMC8317501 DOI: 10.3389/fmicb.2021.703792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new approach to unravel the bacterial phylogeographic patterns combining community-wide survey by 16S rRNA gene metabarcoding and intra-species resolution through the oligotyping method, allowing robust estimations of genetic and phylogeographic indices, and migration parameters. As a proof-of-concept, we focused on the bacterial genus Spirochaeta across three distant biogeographic provinces of the Southern Ocean; maritime Antarctica, sub-Antarctic Islands, and Patagonia. Each targeted Spirochaeta operational taxonomic units were characterized by a substantial intrapopulation microdiversity, and significant genetic differentiation and phylogeographic structure among the three provinces. Gene flow estimations among Spirochaeta populations support the role of the Antarctic Polar Front as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current appears as the main driver of gene flow, connecting sub-Antarctic Islands with Patagonia and maritime Antarctica. Additionally, historical processes (drift and dispersal limitation) govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach bridges the gap between microbial and macrobial ecology by revealing strong congruency with macroorganisms distribution patterns at the populational level, shaped by the same oceanographic structures and ecological processes.
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Affiliation(s)
- Guillaume Schwob
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
| | - Nicolás I. Segovia
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Universidad Católica del Norte, Coquimbo, Chile
| | - Claudio González-Wevar
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Facultad de Ciencias, Centro Fondap IDEAL, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Léa Cabrol
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Julieta Orlando
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
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20
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Pascoal F, Costa R, Magalhães C. The microbial rare biosphere: current concepts, methods and ecological principles. FEMS Microbiol Ecol 2021; 97:5974270. [PMID: 33175111 DOI: 10.1093/femsec/fiaa227] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1049-001, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, CA 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, CA 94720 Berkeley, USA
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,School of Science, University of Waikato, Gate 1, Knighton Road 3240, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Steele Ocean Sciences Building, Dalhousie University 1355 Oxford St., B3H4R2 Halifax, NS, Canada
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21
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Stothart MR, Greuel RJ, Gavriliuc S, Henry A, Wilson AJ, McLoughlin PD, Poissant J. Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters. Mol Ecol 2020; 30:555-571. [PMID: 33231332 DOI: 10.1111/mec.15747] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022]
Abstract
Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.
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Affiliation(s)
- Mason R Stothart
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Ruth J Greuel
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Stefan Gavriliuc
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Astrid Henry
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Jocelyn Poissant
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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22
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Hermans SM, Buckley HL, Curran-Cournane F, Taylor M, Lear G. Temporal variation in soil bacterial communities can be confounded with spatial variation. FEMS Microbiol Ecol 2020; 96:5909033. [PMID: 32949457 DOI: 10.1093/femsec/fiaa192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/17/2020] [Indexed: 11/12/2022] Open
Abstract
Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13-24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.
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Affiliation(s)
- Syrie M Hermans
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
| | - Fiona Curran-Cournane
- Ministry for the Environment-Manatū Mō Te Taiao, 45 Queen Street, Auckland 1010, New Zealand
| | - Matthew Taylor
- Waikato Regional Council, 401 Grey Street, Hamilton 3216, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
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