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Lumpi T, Guo X, Lindström ES. Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence. Environ Microbiol 2023; 25:2289-2302. [PMID: 37381117 DOI: 10.1111/1462-2920.16450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/31/2023] [Indexed: 06/30/2023]
Abstract
When bacterial communities mix, immigration history can fundamentally affect the community composition as a result of priority effects. Priority effects arise when an early immigrant exhausts resources and/or alters habitat conditions, thereby influencing the establishment success of the late arriver. The strength of priority effects is context-dependent and expected to be stronger if environmental conditions favour the growth of the first arriver. In this study, we conducted a two-factorial experiment testing the importance of nutrient availability and grazing on the strength of priority effects in complex aquatic bacterial communities. We did so by mixing two dissimilar communities, simultaneously, and with a 38 h time-delay. Priority effects were measured as the invasion resistance of the first community to the invading second community. We found stronger priority effects in treatments with high nutrient availability and absence of grazing, but in general, the arrival timing was less important than the selection by nutrients and grazing. At the population level, the results were complex, but priority effects may have been driven by bacteria belonging to for example, the genera Rhodoferax and Herbaspirillum. Our study highlights the importance of arrival timing in complex bacterial communities, especially if environmental conditions favour rapid community growth.
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Affiliation(s)
- Theresa Lumpi
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Xin Guo
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
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2
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Hanashiro FTT, De Meester L, Vanhamel M, Mukherjee S, Gianuca AT, Verbeek L, van den Berg E, Souffreau C. Bacterioplankton Assembly Along a Eutrophication Gradient Is Mainly Structured by Environmental Filtering, Including Indirect Effects of Phytoplankton Composition. MICROBIAL ECOLOGY 2023; 85:400-410. [PMID: 35306576 DOI: 10.1007/s00248-022-01994-x] [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: 08/21/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Biotic interactions are suggested to be key factors structuring bacterioplankton community assembly but are rarely included in metacommunity studies. Eutrophication of ponds and lakes provides a useful opportunity to evaluate how bacterioplankton assembly is affected by specific environmental conditions, especially also by biotic interactions with other trophic levels such as phytoplankton and zooplankton. Here, we evaluated the importance of deterministic and stochastic processes on bacterioplankton community assembly in 35 shallow ponds along a eutrophication gradient in Belgium and assessed the direct and indirect effects of phytoplankton and zooplankton community variation on bacterioplankton assembly through a path analysis and network analysis. Environmental filtering by abiotic factors (suspended matter concentration and pH) explained the largest part of the bacterioplankton community variation. Phytoplankton community structure affected bacterioplankton structure through its effect on variation in chlorophyll-a and suspended matter concentration. Bacterioplankton communities were also spatially structured through pH. Overall, our results indicate that environmental variation is a key component driving bacterioplankton assembly along a eutrophication gradient and that indirect biotic interactions can also be important in explaining bacterioplankton community composition. Furthermore, eutrophication led to divergence in community structure and more eutrophic ponds had a higher diversity of bacteria.
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Affiliation(s)
- Fabio Toshiro T Hanashiro
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium.
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
- Leibniz Institut für Gewässerökologie und Binnenfischerei (IGB), Müggelseedamm 310, 12587, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195, Berlin, Germany
| | - Matthias Vanhamel
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
- Laboratory of Reproductive Genomics, KU Leuven, ON I Herestraat 49, 3000, Leuven, Belgium
| | - Andros T Gianuca
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, 59078-900, Brazil
| | - Laura Verbeek
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Edwin van den Berg
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution & Conservation, KU Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
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3
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Cao X, Zhao D, Li C, Röttjers L, Faust K, Zhang H. Regime transition Shapes the Composition, Assembly Processes, and Co-occurrence Pattern of Bacterioplankton Community in a Large Eutrophic Freshwater Lake. MICROBIAL ECOLOGY 2022; 84:336-350. [PMID: 34585289 DOI: 10.1007/s00248-021-01878-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
At certain nutrient concentrations, shallow freshwater lakes are generally characterized by two contrasting ecological regimes with disparate patterns of biodiversity and biogeochemical cycles: a macrophyte-dominated regime (MDR) and a phytoplankton-dominated regime (PDR). To reveal ecological mechanisms that affect bacterioplankton along the regime shift, Illumina MiSeq sequencing of the 16S rRNA gene combined with a novel network clustering tool (Manta) were used to identify patterns of bacterioplankton community composition across the regime shift in Taihu Lake, China. Marked divergence in the composition and ecological assembly processes of bacterioplankton community was observed under the regime shift. The alpha diversity of the bacterioplankton community consistently and continuously decreased with the regime shift from MDR to PDR, while the beta diversity presents differently. Moreover, as the regime shifted from MDR to PDR, the contribution of deterministic processes (such as environmental selection) to the assembly of bacterioplankton community initially decreased and then increased again as regime shift from MDR to PDR, most likely as a consequence of differences in nutrient concentration. The topological properties, including modularity, transitivity and network diameter, of the bacterioplankton co-occurrence networks changed along the regime shift, and the co-occurrences among species changed in structure and were significantly shaped by the environmental variables along the regime transition from MDR to PDR. The divergent environmental state of the regimes with diverse nutritional status may be the most important factor that contributes to the dissimilarity of bacterioplankton community composition along the regime shift.
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Affiliation(s)
- Xinyi Cao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.
| | - Chaoran Li
- Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK
| | - Lisa Röttjers
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Hongjie Zhang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
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4
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Zhang B, Yang T, Sun C, Wen X. Drivers of microbial beta-diversity in wastewater treatment plants in China. J Environ Sci (China) 2022; 115:341-349. [PMID: 34969461 DOI: 10.1016/j.jes.2021.07.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 06/14/2023]
Abstract
As one of the most well-documented biogeographic patterns, the distance-decay relationship provides insights into the underlying mechanisms driving biodiversity distribution. Although wastewater treatment plants (WWTPs) are well-controlled engineered ecosystems, this pattern has been seen among microbial communities in activated sludge (AS). However, little is known about the relative importance of environmental heterogeneity and dispersal limitation in shaping AS microbial community across China; especially they are related to spatial scale and organism types. Here, we assessed the distance-decay relationship based on different spatial scales and microbial phylogenetic groups by analyzing 132 activated sludge (AS) samples across China comprising 3,379,200 16S rRNA sequences. Our results indicated that the drivers of distance-decay pattern in China were scale-dependent. Microbial biogeographic patterns in WWTPs were mainly driven by dispersal limitation at both local and national scales. In contrast, conductivity, SRT, and pH played dominant roles in shaping AS microbial community compositions at the regional scale. Turnover rates and the drivers of beta-diversity also varied with microorganism populations. Moreover, a quantitative relationship between dispersal limitation ratio and AS microbial turnover rate was generated. Collectively, these results highlighted the importance of considering multiple spatial scales and micro-organism types for understanding microbial biogeography in WWTPs and provided new insights into predicting variations in AS community structure in response to environmental disturbance.
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Affiliation(s)
- Bing Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ting Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Chenxiang Sun
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China.
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5
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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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6
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Li L, Pujari L, Wu C, Huang D, Wei Y, Guo C, Zhang G, Xu W, Liu H, Wang X, Wang M, Sun J. Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean. Front Microbiol 2021; 12:616956. [PMID: 34456881 PMCID: PMC8385211 DOI: 10.3389/fmicb.2021.616956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial communities are composed of many rare species and a few abundant species. Considering the disproportionate importance of rare species for ecosystem functioning, it is important to understand the mechanisms structuring the rare and abundant components of a diverse community in response to environmental changes. Here, we used a 16S ribosomal RNA gene sequencing approach to investigate the bacterial community diversity in the Eastern Indian Ocean (EIO) during the monsoon and intermonsoon. We employed a phylogenetic null model and network analysis to evaluate the assembly processes and co-occurrence pattern of the microbial community. We found that higher bacterial diversity was detected in the intermonsoon with high temperature and low Chlorophyll a concentrations and N/P ratios. The balance between ecological deterministic processes and stochastic processes varied with seasons in the EIO. Meanwhile, conditionally rare taxa (CRT) were more likely modulated by variable selection processes than always rare taxa (ART) and abundant taxa (AT) (CRT > ART > AT). By linking assembly process and species co-occurrence, we demonstrated that the microbial co-occurrence associations tended to be higher when deterministic processes (mainly variable selection) were weaker. This negative trend was observed in rare species rather than abundant species. The linkage could enhance our understanding of the underlying mechanisms underpinning the generation and maintenance of microbial community diversity.
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Affiliation(s)
- Liuyang Li
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Laxman Pujari
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Chao Wu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Danyue Huang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqiu Wei
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Congcong Guo
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Wenzhe Xu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Xingzhou Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
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7
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Gorokhova E, Motiei A, El-Shehawy R. Understanding Biofilm Formation in Ecotoxicological Assays With Natural and Anthropogenic Particulates. Front Microbiol 2021; 12:632947. [PMID: 34276580 PMCID: PMC8281255 DOI: 10.3389/fmicb.2021.632947] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Fossil-made polymers harbor unique bacterial assemblages, and concerns have been raised that ingested microplastic may affect the consumer gut microbiota and spread pathogens in animal populations. We hypothesized that in an ecotoxicity assay with a mixture of polystyrene (PS) and clay: (1) microbiome of the test animals inoculates the system with bacteria; (2) relative contribution of PS and the total amount of suspended solids (SS) select for specific bacterial communities; and (3) particle aggregation is affected by biofilm community composition, with concomitant effects on the animal survival. Mixtures of PS and clay at different concentrations of SS (10, 100, and 1000 mg/L) with a varying microplastics contribution (%PS; 0-80%) were incubated with Daphnia magna, whose microbiome served as an inoculum for the biofilms during the exposure. After 4-days of exposure, we examined the biofilm communities by 16S rRNA gene sequencing, particle size distribution, and animal survival. The biofilm communities were significantly different from the Daphnia microbiota used to inoculate the system, with an overrepresentation of predatory, rare, and potentially pathogenic taxa in the biofilms. The biofilm diversity was stimulated by %PS and decreased by predatory bacteria. Particle aggregate size and the biofilm composition were the primary drivers of animal survival, with small particles and predatory bacteria associated with a higher death rate. Thus, in effect studies with solid waste materials, ecological interactions in the biofilm can affect particle aggregation and support potentially harmful microorganisms with concomitant effects on the test animals.
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Affiliation(s)
- Elena Gorokhova
- Department of Environmental Science (ACES), Stockholm University, Stockholm, Sweden
| | - Asa Motiei
- Department of Environmental Science (ACES), Stockholm University, Stockholm, Sweden
| | - Rehab El-Shehawy
- Department of Environmental Science (ACES), Stockholm University, Stockholm, Sweden
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8
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Liao J, Bergholz P, Wiedmann M. Adjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and Dispersal. Appl Environ Microbiol 2021; 87:e02516-20. [PMID: 33452036 PMCID: PMC8105029 DOI: 10.1128/aem.02516-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 11/20/2022] Open
Abstract
High-quality habitats for wildlife (e.g., forest) provide essential ecosystem services while increasing species diversity and habitat connectivity. Unfortunately, the presence of such habitats adjacent to produce fields may increase risk for contamination of fruits and vegetables by enteric bacteria, including Escherichia coliE. coli survives in extrahost environments (e.g., soil) and could be dispersed across landscapes by wildlife. Understanding how terrestrial landscapes impact the distribution of soil E. coli strains is of importance in assessing the contamination risk of agricultural products. Here, using multilocus sequence typing, we characterized 938 E. coli soil isolates collected from two watersheds with different landscape patterns in New York State, USA, and compared the distribution of E. coli and the influence that environmental selection and dispersal have on the distribution between these two watersheds. Results showed that for the watershed with widespread produce fields, sparse forests, and limited interaction between the two land use types, E. coli composition was significantly different between produce field sites and forest sites; this distribution appears to be shaped by relatively strong environmental selection, likely from soil phosphorus, and slight dispersal limitation. For the watershed with more forested areas and stronger interaction between produce field sites and forest sites, E. coli composition between these two land use types was relatively homogeneous; this distribution appeared to be a consequence of wildlife-driven dispersal, inferred by competing models. Collectively, our results suggest that terrestrial landscape attributes could impact the biogeographic pattern of enteric bacteria by adjusting the importance of environmental selection and dispersal.IMPORTANCE Understanding the ecology of enteric bacteria in extrahost environments is important for the development and implementation of strategies to minimize preharvest contamination of produce with enteric pathogens. Our findings suggest that watershed landscape is an important factor influencing the importance of ecological drivers and dispersal patterns of E. coli Agricultural areas in such watersheds may have a higher risk of produce contamination due to fewer environmental constraints and higher potential of dispersal of enteric bacteria between locations. Thus, there is a perceived trade-off between priorities of environmental conservation and public health in on-farm food safety, with limited ecological data supporting or refuting the role of wildlife in dispersing pathogens under normal operating conditions. By combining field sampling and spatial modeling, we explored ecological principles underlying the biogeographic pattern of enteric bacteria at the regional level, which can benefit agricultural, environmental, and public health scientists who aim to reduce the risk of food contamination by enteric bacteria while minimizing negative impacts on wildlife habitats.
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Affiliation(s)
- Jingqiu Liao
- Department of Food Science, Cornell University, Ithaca, New York, USA
- Graduate Field of Microbiology, Cornell University, Ithaca, New York, USA
| | - Peter Bergholz
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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9
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Vass M, Székely AJ, Lindström ES, Osman OA, Langenheder S. Warming mediates the resistance of aquatic bacteria to invasion during community coalescence. Mol Ecol 2021; 30:1345-1356. [PMID: 33448073 DOI: 10.1111/mec.15800] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 01/04/2023]
Abstract
The immigration history of communities can profoundly affect community composition. For instance, early-arriving species can have a lasting effect on community structure by reducing the invasion success of late-arriving ones through priority effects. This can be particularly important when early-arriving communities coalesce with another community during dispersal (mixing) events. However, the outcome of such community coalescence is unknown as we lack knowledge on how different factors influence the persistence of early-arriving communities and the invasion success of late-arriving taxa. Therefore, we implemented a full-factorial experiment with aquatic bacteria where temperature and dispersal rate of a better adapted community were manipulated to test their joint effects on the resistance of early-arriving communities to invasion, both at community and population level. Our 16S rRNA gene sequencing-based results showed that invasion success of better adapted late-arriving bacteria equaled or even exceeded what we expected based on the dispersal ratios of the recipient and invading communities suggesting limited priority effects on the community level. Patterns detected at the population level, however, showed that resistance of aquatic bacteria to invasion might be strengthened by warming as higher temperatures (a) increased the sum of relative abundances of persistent bacteria in the recipient communities, and (b) restricted the total relative abundance of successfully established late-arriving bacteria. Warming-enhanced resistance, however, was not always found and its strengths differed between recipient communities and dispersal rates. Nevertheless, our findings highlight the potential role of warming in mitigating the effects of invasion at the population level.
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Affiliation(s)
- Máté Vass
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Anna J Székely
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Omneya A Osman
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
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10
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Mony C, Vandenkoornhuyse P, Bohannan BJM, Peay K, Leibold MA. A Landscape of Opportunities for Microbial Ecology Research. Front Microbiol 2020; 11:561427. [PMID: 33329422 PMCID: PMC7718007 DOI: 10.3389/fmicb.2020.561427] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/30/2020] [Indexed: 11/13/2022] Open
Abstract
Microbes encompass tremendous biodiversity, provide support to all living forms, including humans, and play an important role in many ecosystem services. The rules that govern microorganism community assembly are increasingly revealed due to key advances in molecular and analytical methods but their understanding remain a key challenge in microbial ecology. The existence of biogeographic patterns within microbial communities has been established and explained in relation to landscape-scale processes, including selection, drift, dispersal and mutation. The effect of habitat patchiness on microorganisms' assembly rules remains though incompletely understood. Here, we review how landscape ecology principles can be adapted to explore new perspectives on the mechanisms that determine microbial community structure. To provide a general overview, we characterize microbial landscapes, the spatial and temporal scales of the mechanisms that drive microbial assembly and the feedback between microorganisms and landscape structure. We provide evidence for the effects of landscape heterogeneity, landscape fragmentation and landscape dynamics on microbial community structure, and show that predictions made for macro-organisms at least partly also apply to microorganisms. We explain why emerging metacommunity approaches in microbial ecology should include explicit characterization of landscape structure in their development and interpretation. We also explain how biotic interactions, such as competition, prey-predator or mutualist relations may influence the microbial landscape and may be involved in the above-mentioned feedback process. However, we argue that the application of landscape ecology to the microbial world cannot simply involve transposing existing theoretical frameworks. This is due to the particularity of these organisms, in terms of size, generation time, and for some of them, tight interaction with hosts. These characteristics imply dealing with unusual and dependent space and time scales of effect. Evolutionary processes have also a strong importance in microorganisms' response to their landscapes. Lastly, microorganisms' activity and distribution induce feedback effects on the landscape that have to be taken into account. The transposition of the landscape ecology framework to microorganisms provides many challenging research directions for microbial ecology.
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Affiliation(s)
- Cendrine Mony
- UMR CNRS ECOBIO, Université de Rennes, Rennes, France
| | | | | | - Kabir Peay
- Department of Biology, University of Stanford, Stanford, CA, United States
| | - Mathew A Leibold
- Department of Biology, University of Florida, Gainesville, FL, United States
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11
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Szabó A, Korponai K, Somogyi B, Vajna B, Vörös L, Horváth Z, Boros E, Szabó-Tugyi N, Márialigeti K, Felföldi T. Grazing pressure-induced shift in planktonic bacterial communities with the dominance of acIII-A1 actinobacterial lineage in soda pans. Sci Rep 2020; 10:19871. [PMID: 33199773 PMCID: PMC7669872 DOI: 10.1038/s41598-020-76822-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
Astatic soda pans of the Pannonian Steppe are unique environments with respect to their multiple extreme physical and chemical characteristics (high daily water temperature fluctuation, high turbidity, alkaline pH, salinity, polyhumic organic carbon concentration, hypertrophic state and special ionic composition). However, little is known about the seasonal dynamics of the bacterial communities inhabiting these lakes and the role of environmental factors that have the main impact on their structure. Therefore, two soda pans were sampled monthly between April 2013 and July 2014 to reveal changes in the planktonic community. By late spring in both years, a sudden shift in the community structure was observed, the previous algae-associated bacterial communities had collapsed, resulting the highest ratio of Actinobacteria within the bacterioplankton (89%, with the dominance of acIII-A1 lineage) ever reported in the literature. Before these peaks, an extremely high abundance (> 10,000 individuum l-1) of microcrustaceans (Moina brachiata and Arctodiaptomus spinosus) was observed. OTU-based statistical approaches showed that in addition to algal blooms and water-level fluctuations, zooplankton densities had the strongest effect on the composition of bacterial communities. In these extreme environments, this implies a surprisingly strong, community-shaping top-down role of microcrustacean grazers.
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Affiliation(s)
- Attila Szabó
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary.
| | - Kristóf Korponai
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary
| | - Boglárka Somogyi
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg Kunó u. 3, Tihany, 8237, Hungary
| | - Balázs Vajna
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary
| | - Lajos Vörös
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg Kunó u. 3, Tihany, 8237, Hungary
| | - Zsófia Horváth
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg Kunó u. 3, Tihany, 8237, Hungary
| | - Emil Boros
- Centre for Ecological Research, Danube Research Institute, Karolina út 29, Budapest, 1113, Hungary
| | - Nóra Szabó-Tugyi
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg Kunó u. 3, Tihany, 8237, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/C, Budapest, 1117, Hungary
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12
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Liu J, Zhu S, Liu X, Yao P, Ge T, Zhang XH. Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship. THE ISME JOURNAL 2020; 14:1463-1478. [PMID: 32132664 PMCID: PMC7242467 DOI: 10.1038/s41396-020-0621-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 12/30/2022]
Abstract
Studies of marine benthic archaeal communities are updating our view of their taxonomic composition and metabolic versatility. However, large knowledge gaps remain with regard to community assembly processes and inter taxa associations. Here, using 16S rRNA gene amplicon sequencing and qPCR, we investigated the spatiotemporal dynamics, assembly processes, and co-occurrence relationships of the archaeal community in 58 surface sediment samples collected in both summer and winter from across ~1500 km of the eastern Chinese marginal seas. Clear patterns in spatiotemporal dynamics in the archaeal community structure were observed, with a more pronounced spatial rather than seasonal variation. Accompanying the geographic variation was a significant distance-decay pattern with varying contributions from different archaeal clades, determined by their relative abundance. In both seasons, dispersal limitation was the most important process, explaining ~40% of the community variation, followed by homogeneous selection and ecological drift, that made an approximately equal contribution (~30%). This meant that stochasticity rather than determinism had a greater impact on the archaeal community assembly. Furthermore, we observed seasonality in archaeal co-occurrence patterns: closer inter-taxa connections in winter than in summer, and unmatched geographic patterns between community composition and co-occurrence relationship. These results demonstrate that the benthic archaeal community was assembled under a seasonal-consistent mechanism but the co-occurrence relationships changed over the seasons, indicating complex archaeal dynamic patterns in coastal sediments of the eastern Chinese marginal seas.
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Affiliation(s)
- Jiwen Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shangqing Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiaoyue Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Studies, Ocean University of China, Qingdao, 266100, China
| | - Tiantian Ge
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, China
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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13
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Zha Y, Lindström ES, Eiler A, Svanbäck R. Different Roles of Environmental Selection, Dispersal, and Drift in the Assembly of Intestinal Microbial Communities of Freshwater Fish With and Without a Stomach. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00152] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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14
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Langenheder S, Lindström ES. Factors influencing aquatic and terrestrial bacterial community assembly. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:306-315. [PMID: 30618071 DOI: 10.1111/1758-2229.12731] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/26/2018] [Indexed: 05/12/2023]
Abstract
During recent years, many studies have shown that different processes including drift, environmental selection and dispersal can be important for the assembly of bacterial communities in aquatic and terrestrial ecosystems. However, we lack a conceptual overview about the ecological context and factors that influence the relative importance of the different assembly mechanisms and determine their dynamics in time and space. Focusing on free-living, i.e., nonhost associated, bacterial communities, this minireview, therefore, summarizes and conceptualizes findings from empirical studies about how (i) environmental factors, such as environmental heterogeneity, disturbances, productivity and trophic interactions; (ii) connectivity and dispersal rates (iii) spatial scale, (iv) community properties and traits and (v) the use of taxonomic/phylogenetic or functional metrics influence the relative importance of different community assembly processes. We find that there is to-date little consistency among studies and suggest that future studies should now address how (i)-(v) differ between habitats and organisms and how this, in turn, influences the temporal and spatial-scale dependency of community assembly processes in microorganisms.
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Affiliation(s)
- Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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15
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Hanashiro FTT, Mukherjee S, Souffreau C, Engelen J, Brans KI, Busschaert P, De Meester L. Freshwater Bacterioplankton Metacommunity Structure Along Urbanization Gradients in Belgium. Front Microbiol 2019; 10:743. [PMID: 31031725 PMCID: PMC6473040 DOI: 10.3389/fmicb.2019.00743] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/25/2019] [Indexed: 12/29/2022] Open
Abstract
Urbanization is transforming and fragmenting natural environments worldwide, driving changes in biological communities through alterations in local environmental conditions as well as by changing the capacity of species to reach specific habitats. While the majority of earlier studies have been performed on higher plants and animals, it is crucial to increase our insight on microbial responses to urbanization across different spatial scales. Here, using a metacommunity approach, we evaluated the effects of urbanization on bacterioplankton communities in 50 shallow ponds in Belgium (Flanders region), one of the most urbanized areas in Northwest Europe. We estimated the relative importance of local environmental factors (35 abiotic and biotic variables), regional spatial factors and urbanization (built-up area) quantified at two spatial scales (200 m × 200 m and 3 km × 3 km). We show that urbanization at local or regional scales did not lead to strong changes in community composition and taxon diversity of bacterioplankton. Urbanization at regional scale (3 km × 3 km) explained only 2% of community composition variation while at local scale (200 m × 200 m), no effect was detected. Local environmental factors explained 13% (OTUs with relative abundance ≥ 0.1%) to 24% (12 dominant OTUs -≥ 1%) of community variation. Six local environmental variables significantly explained variation in bacterioplankton community composition: pH, alkalinity, conductivity, total phosphorus, abundance of Daphnia and concentration of copper (Cu), of which pH was partly mediated by urbanization. Our results indicate that environmental rather than spatial factors accounted for the variation in bacterioplankton community structure, suggesting that species sorting is the main process explaining bacterioplankton community assembly. Apparently, urbanization does not have a direct and strong effect on bacterioplankton metacommunity structure, probably due to the capacity of these organisms to adapt toward and colonize habitats with different environmental conditions and due to their fast adaptation and metabolic versatility. Thus, bacterioplankton communities inhabiting shallow ponds may be less affected by environmental conditions resulting from urbanization as compared to the impacts previously described for other taxa.
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Affiliation(s)
- Fabio Toshiro T Hanashiro
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KU Leuven, Leuven, Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KU Leuven, Leuven, Belgium
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jessie Engelen
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KU Leuven, Leuven, Belgium
| | - Kristien I Brans
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KU Leuven, Leuven, Belgium
| | - Pieter Busschaert
- Department of Gynaecology and Obstetrics, UZ Leuven, Leuven, Belgium.,Division of Gynaecological Oncology, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KU Leuven, Leuven, Belgium
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16
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Xiao F, Bi Y, Li X, Huang J, Yu Y, Xie Z, Fang T, Cao X, He Z, Juneau P, Yan Q. The Impact of Anthropogenic Disturbance on Bacterioplankton Communities During the Construction of Donghu Tunnel (Wuhan, China). MICROBIAL ECOLOGY 2019; 77:277-287. [PMID: 29951743 DOI: 10.1007/s00248-018-1222-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
Bacterioplankton are both primary producers and primary consumers in aquatic ecosystems, which were commonly investigated to reflect environmental changes, evaluate primary productivity, and assess biogeochemical cycles. However, there is relatively less understanding of their responses to anthropogenic disturbances such as constructions of dams/tunnels/roads that may significantly affect the aquatic ecosystem. To fill such gap, this study focused on the bacterioplankton communities' diversity and turnover during a tunnel construction across an urban lake (Lake Donghu, Wuhan, China), and five batches of samples were collected within 2 months according to the tunnel construction progress. Results indicated that both resources and predator factors contributed significant to the variations of bacterioplankton communities, but the closed area and open areas showed different diversity patterns due to the impacts of tunnel construction. Briefly, the phytoplankton, TN, and TP in water were still significantly correlated with the bacterioplankton composition and diversity like that in normal conditions. Additionally, the organic matter, TN, and NH4-N in sediments also showed clear effects on the bacterioplankton. However, the predator effects on the bacterioplankton in the closed-off construction area mainly derived from large zooplankton (i.e., cladocerans), while small zooplankton such as protozoa and rotifers are only responsible for weak predator effects on the bacterioplankton in the open areas. Further analysis about the ecological driving forces indicated that the bacterioplankton communities' turnover during the tunnel construction was mainly governed by the homogeneous selection due to similar environments within the closed area or the open areas at two different stages. This finding suggests that bacterioplankton communities can quickly adapt to the environmental modifications resulting from tunnel construction activities. This study can also give references to enhance our understanding on bacterioplankton communities' response to ecological and environmental changes due to intensification of construction and urbanization in and around lake ecosystems.
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Affiliation(s)
- Fanshu Xiao
- Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, and the School of Environmental Science and Engineering, Sun Yat-sen University, 132 East Circle, University Town, Guangzhou, 510006, China
| | - Yonghong Bi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xinghao Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jie Huang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yuhe Yu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhicai Xie
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Tao Fang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiuyun Cao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhili He
- Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, and the School of Environmental Science and Engineering, Sun Yat-sen University, 132 East Circle, University Town, Guangzhou, 510006, China
| | - Philippe Juneau
- Département des Sciences biologiques - GRIL - TOXEN, Laboratory of Aquatic Microorganism Ecotoxicology, Université du Québec à Montréal, Succ. Centre-Ville, C.P. 8888, Montréal, Québec, H3C 3P8, Canada
| | - Qingyun Yan
- Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, and the School of Environmental Science and Engineering, Sun Yat-sen University, 132 East Circle, University Town, Guangzhou, 510006, China.
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17
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Shen D, Langenheder S, Jürgens K. Dispersal Modifies the Diversity and Composition of Active Bacterial Communities in Response to a Salinity Disturbance. Front Microbiol 2018; 9:2188. [PMID: 30294307 PMCID: PMC6159742 DOI: 10.3389/fmicb.2018.02188] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 08/27/2018] [Indexed: 11/21/2022] Open
Abstract
Dispersal can influence the response of bacterial communities to environmental changes and disturbances. However, the extent to which dispersal contributes to the community response in dependence of the character and strength of the disturbance remains unclear. Here, we conducted a transplant experiment using dialysis bags in which bacterioplankton originating from brackish and marine regions of the Saint Lawrence Estuary were reciprocally incubated in the two environments for 5 days. Dispersal treatments were set-up by subjecting half of the microcosms in each environment to an exchange of cells between the marine and brackish assemblages at a daily exchange rate of 6% (v/v), and the other half of microcosms were kept as the non-dispersal treatments. Bacterial 16S rRNA sequencing was then used to examine the diversity and composition of the active communities. Alpha diversity of the marine communities that were exposed to the brackish environment was elevated greatly by dispersal, but declined in the absence of dispersal. This indicates that dispersal compensated the loss of diversity in the marine communities after a disturbance by introducing bacterial taxa that were able to thrive and coexist with the remaining community members under brackish conditions. On the contrary, alpha diversity of the brackish communities was not affected by dispersal in either environment. Furthermore, dispersal led to an increase in similarity between marine and brackish communities in both of the environments, with a greater similarity when the communities were incubated in the brackish environment. These results suggest that the higher initial diversity in the brackish than in the marine starting community made the resident community less susceptible to dispersing bacteria. Altogether, this study shows that dispersal modifies the diversity and composition of the active communities in response to a salinity disturbance, and enables the local adjustment of specific bacteria under brackish environmental conditions.
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Affiliation(s)
- Dandan Shen
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Silke Langenheder
- Department of Ecology and Genetic/Limnology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Klaus Jürgens
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
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18
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Wu W, Lu HP, Sastri A, Yeh YC, Gong GC, Chou WC, Hsieh CH. Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities. ISME JOURNAL 2017; 12:485-494. [PMID: 29125596 PMCID: PMC5776463 DOI: 10.1038/ismej.2017.183] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/23/2017] [Accepted: 09/24/2017] [Indexed: 01/21/2023]
Abstract
A central challenge in microbial ecology is to understand the underlying mechanisms driving community assembly, particularly in the continuum of species sorting and dispersal limitation. However, little is known about the relative importance of species sorting and dispersal limitation in shaping marine microbial communities; especially, how they are related to organism types/traits and water depth. Here, we used variation partitioning and null model analysis to compare mechanisms driving bacterial and protist metacommunity dynamics at the basin scale in the East China Sea, based on MiSeq paired-end sequencing of 16S ribosomal DNA (rDNA) and 18S rDNA, respectively, in surface, deep chlorophyll maximum and bottom layers. Our analyses indicated that protist communities were governed more strongly by species sorting relative to dispersal limitation than were bacterial communities; this pattern was consistent across the three-depth layers, albeit to different degrees. Furthermore, we detected that bacteria exhibited wider habitat niche breadths than protists, whereas, passive dispersal abilities were not appreciably different between them. Our findings support the 'size-plasticity' hypothesis: smaller organisms (bacteria) are less environment filtered than larger organisms (protists), as smaller organisms are more likely to be plastic in metabolic abilities and have greater environmental tolerance.
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Affiliation(s)
- Wenxue Wu
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Pei Lu
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Akash Sastri
- Biology Department and Ocean Networks Canada, University of Victoria, Victoria, British Columbia, Canada
| | - Yi-Chun Yeh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Wen-Chen Chou
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Department of Life Science, Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.,Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.,National Center for Theoretical Sciences, Taipei, Taiwan
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19
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The Limnohabitans Genus Harbors Generalistic and Opportunistic Subtypes: Evidence from Spatiotemporal Succession in a Canyon-Shaped Reservoir. Appl Environ Microbiol 2017; 83:AEM.01530-17. [PMID: 28842542 DOI: 10.1128/aem.01530-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/22/2017] [Indexed: 11/20/2022] Open
Abstract
We studied the diversity of Limnohabitans using reverse line blot hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov reservoir (Czech Republic). To examine the succession of distinct lineages, we performed (i) a study of an intensive spring sampling program at the lacustrine part of the Římov reservoir (from ice melt through a phytoplankton peak to the clear-water phase), and (ii) a seasonal study (April to November) when the occurrence of distinct Limnohabitans lineages was related to the inherent longitudinal heterogeneity of the reservoir. Significant spatiotemporal changes in the compositions of distinct Limnohabitans lineages allowed for the identification of "generalists" that were always present throughout the whole season as well as "specialists" that appeared in the reservoir only for limited periods of time or irregularly. Our results indicate that some phytoplankton groups, such as cryptophytes or cyanobacteria, and zooplankton composition were the major factors modulating the distribution and dynamics of distinct Limnohabitans lineages. The highest Limnohabitans diversity was observed during the spring algal bloom, whereas the lowest was during the summer cyanobacterial bloom. The microdiversity also markedly increased upstream in the reservoir, being highest at the inflow, and thus likely reflecting strong influences of the watershed.IMPORTANCE The genus Limnohabitans is a typical freshwater bacterioplankton and is believed to play a significant role in inland freshwater habitats. This work is unique in detecting and tracing different closely related lineages of this bacterial genus in its natural conditions using the semiquantitative reverse line blot hybridization method and in discovering the factors influencing the microdiversity, subtype alternations, and seasonality.
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20
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Segovia BT, Dias JD, Cabral AF, Meira BR, Lansac-Tôha FM, Lansac-Tôha FA, Bini LM, Velho LFM. Common and Rare Taxa of Planktonic Ciliates: Influence of Flood Events and Biogeographic Patterns in Neotropical Floodplains. MICROBIAL ECOLOGY 2017; 74:522-533. [PMID: 28386768 DOI: 10.1007/s00248-017-0974-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
After much discussion about the cosmopolitan nature of microbes, the great issue nowadays is to identify at which spatial extent microorganisms may display biogeographic patterns and if temporal variation is important in altering those patterns. Here, planktonic ciliates were sampled from shallow lakes of four Neotropical floodplains, distributed over a spatial extent of ca. 3000 km, during high and low water periods, along with several abiotic and biotic variables potentially affecting the ciliate community. We found that common ciliate species were more associated with environmental gradients and rare species were more related to spatial variables; however, this pattern seemed to change depending on the temporal and spatial scales considered. Environmental gradients were more important in the high waters for both common and rare species. In low waters, common species continued to be mainly driven by environmental conditions, but rare species were more associated with the spatial component, suggesting dispersal limitation likely due to differences in dispersal ability and ecological tolerance of species. We also found that common and rare species were related to different environmental variables, suggesting different ecological niches. At the largest spatial extents, rare species showed clear biogeographic patterns.
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Affiliation(s)
- Bianca Trevizan Segovia
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil.
| | - Juliana Déo Dias
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Adalgisa Fernanda Cabral
- Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Bianca Ramos Meira
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Fernando Miranda Lansac-Tôha
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Fabio Amodêo Lansac-Tôha
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Luis Mauricio Bini
- Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Luiz Felipe Machado Velho
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
- Programa de Pós-Graduação em Tecnologias Limpas, Centro Universitário Cesumar - UniCesumar/Instituto Cesumar de Ciência, Tecnologia e Inovação (ICETI), Maringá, Paraná, Brazil
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21
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Berga M, Zha Y, Székely AJ, Langenheder S. Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes. Front Microbiol 2017. [PMID: 28642735 PMCID: PMC5463035 DOI: 10.3389/fmicb.2017.00948] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Disturbances and environmental change are important factors determining the diversity, composition, and functioning of communities. However, knowledge about how natural bacterial communities are affected by such perturbations is still sparse. We performed a whole ecosystem manipulation experiment with freshwater rock pools where we applied salinity disturbances of different intensities. The aim was to test how the compositional and functional resistance and resilience of bacterial communities, alpha- and beta-diversity and the relative importance of stochastic and deterministic community assembly processes changed along a disturbance intensity gradient. We found that bacterial communities were functionally resistant to all salinity levels (3, 6, and 12 psu) and compositionally resistant to a salinity increase to 3 psu and resilient to increases of 6 and 12 psu. Increasing salinities had no effect on local richness and evenness, beta-diversity and the proportion of deterministically vs. stochastically assembled communities. Our results show a high functional and compositional stability of bacterial communities to salinity changes of different intensities both at local and regional scales, which possibly reflects long-term adaptation to environmental conditions in the study system.
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Affiliation(s)
- Mercè Berga
- Department of Ecology and Genetics/Limnology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden.,Biological Oceanography, Leibniz Institute for Baltic Sea Research WarnemündeRostock, Germany
| | - Yinghua Zha
- Department of Ecology and Genetics/Limnology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
| | - Anna J Székely
- Department of Ecology and Genetics/Limnology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics/Limnology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
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22
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Limberger R, Birtel J, Farias DDS, Matthews B. Ecosystem flux and biotic modification as drivers of metaecosystem dynamics. Ecology 2017; 98:1082-1092. [PMID: 28112404 DOI: 10.1002/ecy.1742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 12/11/2016] [Accepted: 01/04/2017] [Indexed: 11/07/2022]
Abstract
The fluxes of energy, matter, and organisms are important structuring forces of metaecosystems. Such ecosystem fluxes likely interact with environmental heterogeneity and differentially affect the diversity of multiple communities. In an aquatic mesocosm experiment, we tested how ecosystem flux and patch heterogeneity affected the diversity of bacteria, phytoplankton, and zooplankton metacommunities, and the structure and functioning of metaecosystems. We built metaecosystems consisting of three mesocosms that were either connected by flux of living organisms, organic material, and nutrients (alive ecosystem flux) or only by flux of organic material and nutrients (dead ecosystem flux). The three patches of each metaecosystem were either homogeneous or heterogeneous in nutrient loading. We found that the three groups of organisms responded differently to our treatments: flux of living organisms increased bacterial diversity irrespective of nutrient heterogeneity, while flux effects on phytoplankton diversity depended on nutrient heterogeneity, potentially indicating source-sink effects. Although zooplankton diversity was largely unaffected by our manipulations, subtle changes of community composition in response to ecosystem flux had strong effects on lower trophic levels, highlighting the importance of indirect flux effects via alterations in trophic interactions. Furthermore, differential effects of communities on the mean and spatial variability of local abiotic environments influenced the development of metaecosystem heterogeneity through time. Despite identical nutrient loading at the scale of the metaecosystem, abiotic conditions diverged between homogeneous and heterogeneous metaecosystems. For example, concentrations in dissolved organic carbon (DOC) were higher in homogeneous than heterogeneous metaecosystems, possibly because of differential responses of the algal community to local environmental conditions. Similarly, we found that flux effects on organisms translated into effects on DOC concentrations at the patch level, suggesting that flux-mediated changes in abundances of species can alter abiotic conditions. Our study shows that the dynamics of biotic and abiotic compartments of spatially structured ecosystems are intricately linked, highlighting the importance of integrating metacommunity and metaecosystem perspectives.
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Affiliation(s)
- Romana Limberger
- Department of Aquatic Ecology, Eawag, Kastanienbaum, 6047 Switzerland
| | - Julia Birtel
- Department of Aquatic Ecology, Eawag, Kastanienbaum, 6047 Switzerland
| | - Daniel D S Farias
- Programa de Pós-Graduação em Ciências Biológicas (Biodiversidade Neotropical), Universidade Federal do Estado Rio de Janeiro, Rio de Janeiro, RJ, 22290-240 Brazil
| | - Blake Matthews
- Department of Aquatic Ecology, Eawag, Kastanienbaum, 6047 Switzerland
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23
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Comte J, Langenheder S, Berga M, Lindström ES. Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change. Environ Microbiol 2017; 19:251-260. [DOI: 10.1111/1462-2920.13593] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 11/16/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Jérôme Comte
- Department of Ecology and Genetics/LimnologyEvolutionary Biology Centre, Uppsala UniversityNorbyvägen 18 D, 75236Uppsala Sweden
- Environment and Climate Change Canada ‐ Canada Centre for Inland WatersWatershed Hydrology and Ecology Research Division‐Water Science and TechnologyBurlingtonON L7S 1A1Canada
| | - Silke Langenheder
- Department of Ecology and Genetics/LimnologyEvolutionary Biology Centre, Uppsala UniversityNorbyvägen 18 D, 75236Uppsala Sweden
| | - Mercè Berga
- Department of Ecology and Genetics/LimnologyEvolutionary Biology Centre, Uppsala UniversityNorbyvägen 18 D, 75236Uppsala Sweden
- Biological Oceanography, Leibniz Institute for Baltic Sea Research18119 Rostock Warnemünde (IOW), Seestraße 15 Germany
| | - Eva S. Lindström
- Department of Ecology and Genetics/LimnologyEvolutionary Biology Centre, Uppsala UniversityNorbyvägen 18 D, 75236Uppsala Sweden
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24
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Grainger TN, Gilbert B. Dispersal and diversity in experimental metacommunities: linking theory and practice. OIKOS 2016. [DOI: 10.1111/oik.03018] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tess Nahanni Grainger
- Dept of Ecology and Evolutionary Biology; Univ. of Toronto; 25 Willcocks Street Toronto ON, M5S 3B2 Canada
| | - Benjamin Gilbert
- Dept of Ecology and Evolutionary Biology; Univ. of Toronto; 25 Willcocks Street Toronto ON, M5S 3B2 Canada
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