1
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Isaac A, Mohamed AR, Amin SA. Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis. Appl Environ Microbiol 2024; 90:e0057024. [PMID: 38809046 PMCID: PMC11218658 DOI: 10.1128/aem.00570-24] [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: 03/29/2024] [Accepted: 05/05/2024] [Indexed: 05/30/2024] Open
Abstract
The complex interactions between bacterioplankton and phytoplankton have prompted numerous studies that investigate phytoplankton microbiomes with the aim of characterizing beneficial or opportunistic taxa and elucidating core bacterial members. Oftentimes, this knowledge is garnered through 16S rRNA gene profiling of microbiomes from phytoplankton isolated across spatial and temporal scales, yet these studies do not offer insight into microbiome assembly and structuring. In this study, we aimed to identify taxa central to structuring and establishing the microbiome of the ubiquitous diatom Asterionellopsis glacialis. We introduced a diverse environmental bacterial community to A. glacialis in nutrient-rich or nutrient-poor media in a continuous dilution culture setup and profiled the bacterial community over 7 days. 16S rRNA amplicon sequencing showed that cyanobacteria (Coleofasciculaceae) and Rhodobacteraceae dominate the microbiome early on and maintain a persistent association throughout the experiment. Differential abundance, co-abundance networks, and differential association analyses revealed that specific members of the family Rhodobacteraceae, particularly Sulfitobacter amplicon sequence variants, become integral members in microbiome assembly. In the presence of the diatom, Sulfitobacter species and other Rhodobacteraceae developed positive associations with taxa that are typically in high abundance in marine ecosystems (Pelagibacter and Synechococcus), leading to restructuring of the microbiome compared to diatom-free controls. These positive associations developed predominantly under oligotrophic conditions, highlighting the importance of investigating phytoplankton microbiomes in as close to natural conditions as possible to avoid biases that develop under routine laboratory conditions. These findings offer further insight into phytoplankton-bacteria interactions and illustrate the importance of Rhodobacteraceae, not merely as phytoplankton symbionts but as key taxa involved in microbiome assembly. IMPORTANCE Most, if not all, microeukaryotic organisms harbor an associated microbial community, termed the microbiome. The microscale interactions that occur between these partners have global-scale consequences, influencing marine primary productivity, carbon cycling, and harmful algal blooms to name but a few. Over the last decade, there has been a growing interest in the study of phytoplankton microbiomes, particularly within the context of bloom dynamics. However, long-standing questions remain regarding the process of phytoplankton microbiome assembly. The significance of our research is to tease apart the mechanism of microbiome assembly with a particular focus on identifying bacterial taxa, which may not merely be symbionts but architects of the phytoplankton microbiome. Our results strengthen the understanding of the ecological mechanisms that underpin phytoplankton-bacteria interactions in order to accurately predict marine ecosystem responses to environmental perturbations.
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Affiliation(s)
- Ashley Isaac
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Amin R. Mohamed
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Shady A. Amin
- Marine Microbiomics Lab, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Mubadala ACCESS Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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2
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Qiao Z, Barnes E, Tringe S, Schachtman DP, Liu P. Poisson hurdle model-based method for clustering microbiome features. Bioinformatics 2022; 39:6873739. [PMID: 36469352 PMCID: PMC9825753 DOI: 10.1093/bioinformatics/btac782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 10/13/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. RESULTS We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation-maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. AVAILABILITY AND IMPLEMENTATION R package is freely available for download at https://cran.r-project.org/package=PHclust. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhili Qiao
- To whom correspondence should be addressed. or
| | - Elle Barnes
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720, USA
| | - Susannah Tringe
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720, USA,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Peng Liu
- To whom correspondence should be addressed. or
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3
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Capistrant-Fossa KA, Morrison HG, Engelen AH, Quigley CTC, Morozov A, Serrão EA, Brodie J, Gachon CMM, Badis Y, Johnson LE, Hoarau G, Abreu MH, Tester PA, Stearns LA, Brawley SH. The microbiome of the habitat-forming brown alga Fucus vesiculosus (Phaeophyceae) has similar cross-Atlantic structure that reflects past and present drivers 1. JOURNAL OF PHYCOLOGY 2021; 57:1681-1698. [PMID: 34176151 DOI: 10.1111/jpy.13194] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/23/2021] [Accepted: 06/04/2021] [Indexed: 05/25/2023]
Abstract
Latitudinal diversity gradients have provided many insights into species differentiation and community processes. In the well-studied intertidal zone, however, little is known about latitudinal diversity in microbiomes associated with habitat-forming hosts. We investigated microbiomes of Fucus vesiculosus because of deep understanding of this model system and its latitudinally large, cross-Atlantic range. Given multiple effects of photoperiod, we predicted that cross-Atlantic microbiomes of the Fucus microbiome would be similar at similar latitudes and correlate with environmental factors. We found that community structure and individual amplicon sequencing variants (ASVs) showed distinctive latitudinal distributions, but alpha diversity did not. Latitudinal differentiation was mostly driven by ASVs that were more abundant in cold temperate to subarctic (e.g., Granulosicoccus_t3260, Burkholderia/Caballeronia/Paraburkholderia_t8371) or warm temperate (Pleurocapsa_t10392) latitudes. Their latitudinal distributions correlated with different humidity, tidal heights, and air/sea temperatures, but rarely with irradiance or photoperiod. Many ASVs in potentially symbiotic genera displayed novel phylogenetic biodiversity with differential distributions among tissues and regions, including closely related ASVs with differing north-south distributions that correlated with Fucus phylogeography. An apparent southern range contraction of F. vesiculosus in the NW Atlantic on the North Carolina coast mimics that recently observed in the NE Atlantic. We suggest cross-Atlantic microbial structure of F. vesiculosus is related to a combination of past (glacial-cycle) and contemporary environmental drivers.
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Affiliation(s)
| | - Hilary G Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Massachusetts, 02543, USA
| | - Aschwin H Engelen
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-139, Portugal
| | | | - Aleksey Morozov
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Massachusetts, 02543, USA
| | - Ester A Serrão
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-139, Portugal
| | - Juliet Brodie
- Natural History Museum, Department of Life Sciences, London, SW7 5BD, UK
| | | | - Yacine Badis
- Scottish Association for Marine Science, Oban, PA37 1QA, UK
| | - Ladd E Johnson
- Département de Biologie, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway
| | | | | | - Leigh A Stearns
- Department of Geology, University of Kansas, Lawrence, Kansas, 66045, USA
| | - Susan H Brawley
- School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA
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4
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Nikolova C, Ijaz UZ, Gutierrez T. Exploration of marine bacterioplankton community assembly mechanisms during chemical dispersant and surfactant-assisted oil biodegradation. Ecol Evol 2021; 11:13862-13874. [PMID: 34707823 PMCID: PMC8525123 DOI: 10.1002/ece3.8091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 11/07/2022] Open
Abstract
Assembly processes in marine microbial communities amended with crude oil and chemical dispersant are poorly understood and even more so when biosurfactants are used. We set up a microcosm experiment in which microbiome structure was analyzed using 16S rRNA gene amplicon sequencing and six null models to better understand and quantify the mechanisms and patterns controlling the assembly of a marine crude oil degrading microbial community in the presence of chemical dispersant or rhamnolipid biosurfactant. Although each null model quantifies different aspects of the community assembly, there was a general agreement that neither purely stochastic nor purely deterministic processes dominated the microbial communities, and their influence was variable over time. Determinism was dominant in the early phase of incubation, while stochasticity was prevalent in the middle and late stages. There was faster recruitment of phylogenetically distant species in the dispersant-amended community compared to oil-only or rhamnolipid-amended communities. This analysis provides important insights of how chemical dispersants and rhamnolipid influence microbial communities' dynamics and identified which groups may be excluded-an important consideration for biodegradation process and oil spill response.
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Affiliation(s)
- Christina Nikolova
- Institute of Mechanical, Process and Energy EngineeringSchool of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
| | | | - Tony Gutierrez
- Institute of Mechanical, Process and Energy EngineeringSchool of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
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5
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Karimi E, Geslain E, Belcour A, Frioux C, Aïte M, Siegel A, Corre E, Dittami SM. Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines. PeerJ 2021; 9:e11344. [PMID: 33996285 PMCID: PMC8106915 DOI: 10.7717/peerj.11344] [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: 10/08/2020] [Accepted: 04/03/2021] [Indexed: 01/29/2023] Open
Abstract
Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.
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Affiliation(s)
- Elham Karimi
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Enora Geslain
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France.,FR2424, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Arnaud Belcour
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | | | - Méziane Aïte
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Anne Siegel
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Erwan Corre
- FR2424, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Simon M Dittami
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
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6
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Ellner SP, Snyder RE, Adler PB, Hooker G. An expanded modern coexistence theory for empirical applications. Ecol Lett 2018; 22:3-18. [DOI: 10.1111/ele.13159] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/11/2018] [Accepted: 08/14/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Stephen P. Ellner
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Robin E. Snyder
- Department of Biology Case Western Reserve University Cleveland OH USA
| | - Peter B. Adler
- Department of Wildland Resources and the Ecology Center Utah State University Logan UT USA
| | - Giles Hooker
- Department of Biological Statistics and Computational Biology Cornell University Ithaca NY USA
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7
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Eurich JG, McCormick MI, Jones GP. Direct and indirect effects of interspecific competition in a highly partitioned guild of reef fishes. Ecosphere 2018. [DOI: 10.1002/ecs2.2389] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Jacob G. Eurich
- ARC Centre of Excellence for Coral Reef Studies, and Department of Marine Biology and Aquaculture College of Science and Engineering James Cook University Townsville Queensland 4811 Australia
| | - Mark I. McCormick
- ARC Centre of Excellence for Coral Reef Studies, and Department of Marine Biology and Aquaculture College of Science and Engineering James Cook University Townsville Queensland 4811 Australia
| | - Geoffrey P. Jones
- ARC Centre of Excellence for Coral Reef Studies, and Department of Marine Biology and Aquaculture College of Science and Engineering James Cook University Townsville Queensland 4811 Australia
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8
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Pirog A, Gélin P, Bédier A, Bianchetti G, Georget S, Frouin P, Magalon H. Clonal structure through space and time: High stability in the holothurian Stichopus chloronotus (Echinodermata). Ecol Evol 2017; 7:7534-7547. [PMID: 28944037 PMCID: PMC5606904 DOI: 10.1002/ece3.3285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/24/2017] [Accepted: 06/30/2017] [Indexed: 11/24/2022] Open
Abstract
Sea cucumbers are increasingly exploited for human consumption and for their curative properties, and many wild populations are now depleted or in danger of extinction. While aquaculture is seen as an alternative to fisheries and as a mean to restore wild populations, more knowledge is needed on their reproductive strategies to render this practice efficient, notably for fissiparous holothurians, which are some of the mobile animals able of asexual reproduction by transverse fission. Little information is available on their population genetic diversity and structure. Here, the clonal structure of populations of the fissiparous sea cucumber Stichopus chloronotus has been investigated using nine microsatellite loci and a random sampling, at different spatial (intra‐reef and inter‐reef) and temporal (inter‐season and inter‐year) scales. Our findings highlight the importance of asexual reproduction in maintaining these populations, and the prevalence of the “initial seedling recruitment” strategy (ISR), leading to a high stability of clonal composition over seasons and years. It also seemed that clonal propagation was limited to the reef scale (<10 km) while reefs were connected by sexual dispersal. This is the first time that clonal structure in sea cucumbers has been studied at such a fine scale, with a specific sampling strategy. It provides key findings on the genetic diversity and structure of fissiparous sea cucumbers, which will be useful for the management of wild populations and aquaculture.
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Affiliation(s)
- Agathe Pirog
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS) Saint Denis, La Réunion France
| | - Pauline Gélin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS) Saint Denis, La Réunion France.,Laboratory of Excellence CORAIL Perpignan France
| | - Alexandre Bédier
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS) Saint Denis, La Réunion France
| | - Grégoire Bianchetti
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS) Saint Denis, La Réunion France
| | - Stéphane Georget
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS) Saint Denis, La Réunion France
| | - Patrick Frouin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS) Saint Denis, La Réunion France.,Laboratory of Excellence CORAIL Perpignan France
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS) Saint Denis, La Réunion France.,Laboratory of Excellence CORAIL Perpignan France
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9
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Zozaya-Valdés E, Roth-Schulze AJ, Egan S, Thomas T. Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra. Environ Microbiol 2017; 19:3012-3024. [PMID: 28419766 DOI: 10.1111/1462-2920.13758] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 04/07/2017] [Indexed: 01/10/2023]
Abstract
Disease is increasingly viewed as a major factor impacting the health of both natural and cultured populations of marine organisms, including macroalgae. The red macroalga Delisea pulchra suffers from a bleaching disease resulting from host stress and infection by opportunistic bacterial pathogens. However, how pathogens cause the disease and how the entire macro algal-associated community is involved in the process is unclear. Here, we perform a metagenomic analysis of microbial communities associated with diseased and healthy D. pulchra across multiple bleaching events. Analysis of reconstructed 16S rRNA gene sequences showed that bacteria belonging to the families Rhodobacteraceae, Saprospiraceae and Flavobacteriaceae, including bacteria previously implicated in algal bleaching, to be enriched in diseased D. pulchra. Genes with predicted functions related to chemotaxis, motility, oxidative stress response, vitamin biosynthesis and nutrient acquisition were also prevalent in microbiomes of bleached algae, which may have a role in pathogenicity. Reconstruction of genomes that were abundant on bleached samples revealed that no single organism contains all bleaching-enriched functional genes. This observation indicates that potential virulence traits are distributed across multiple bacteria and that the disease in D. pulchra may result from a consortium of opportunistic pathogens, analogous to dysbiotic or polymicrobial diseases.
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Affiliation(s)
- Enrique Zozaya-Valdés
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Alexandra J Roth-Schulze
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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10
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Turgeon K, Kramer DL. Immigration Rates during Population Density Reduction in a Coral Reef Fish. PLoS One 2016; 11:e0156417. [PMID: 27271081 PMCID: PMC4896503 DOI: 10.1371/journal.pone.0156417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/14/2016] [Indexed: 12/04/2022] Open
Abstract
Although the importance of density-dependent dispersal has been recognized in theory, few empirical studies have examined how immigration changes over a wide range of densities. In a replicated experiment using a novel approach allowing within-site comparison, we examined changes in immigration rate following the gradual removal of territorial damselfish from a limited area within a much larger patch of continuous habitat. In all sites, immigration occurred at intermediate densities but did not occur before the start of removals and only rarely as density approached zero. In the combined data and in 5 of 7 sites, the number of immigrants was a hump-shaped function of density. This is the first experimental evidence for hump-shaped, density-dependent immigration. This pattern may be more widespread than previously recognized because studies over more limited density ranges have identified positive density dependence at low densities and negative density dependence at high densities. Positive density dependence at low density can arise from limits to the number of potential immigrants and from behavioral preferences for settling near conspecifics. Negative density dependence at high density can arise from competition for resources, especially high quality territories. The potential for non-linear effects of local density on immigration needs to be recognized for robust predictions of conservation reserve function, harvest impacts, pest control, and the dynamics of fragmented populations.
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Affiliation(s)
- Katrine Turgeon
- Department of Biology, McGill University, 1205 Docteur Penfield Avenue, Montreal, QC, H3A 1B1, Canada
- * E-mail:
| | - Donald L. Kramer
- Department of Biology, McGill University, 1205 Docteur Penfield Avenue, Montreal, QC, H3A 1B1, Canada
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11
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Milici M, Deng ZL, Tomasch J, Decelle J, Wos-Oxley ML, Wang H, Jáuregui R, Plumeier I, Giebel HA, Badewien TH, Wurst M, Pieper DH, Simon M, Wagner-Döbler I. Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton. Front Microbiol 2016; 7:649. [PMID: 27199970 PMCID: PMC4858663 DOI: 10.3389/fmicb.2016.00649] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/18/2016] [Indexed: 12/04/2022] Open
Abstract
We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S–47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone.
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Affiliation(s)
- Mathias Milici
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Zhi-Luo Deng
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Jürgen Tomasch
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Johan Decelle
- UMR 7144 - Sorbonne Universités, UPMC Univ Paris 06Roscoff, France; Centre National de la Recherche Scientifique, UMR 7144Roscoff, France
| | - Melissa L Wos-Oxley
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Hui Wang
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Ruy Jáuregui
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Iris Plumeier
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Helge-Ansgar Giebel
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Thomas H Badewien
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Mascha Wurst
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Dietmar H Pieper
- Group Microbial Interactions and Processes, Helmholtz-Center for Infection Research Braunschweig, Germany
| | - Meinhard Simon
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg Oldenburg, Germany
| | - Irene Wagner-Döbler
- Group Microbial Communication, Helmholtz-Center for Infection Research Braunschweig, Germany
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12
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Dittami SM, Duboscq-Bidot L, Perennou M, Gobet A, Corre E, Boyen C, Tonon T. Host-microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures. THE ISME JOURNAL 2016; 10:51-63. [PMID: 26114888 PMCID: PMC4681850 DOI: 10.1038/ismej.2015.104] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 05/05/2015] [Accepted: 05/19/2015] [Indexed: 01/16/2023]
Abstract
Like most eukaryotes, brown algae live in association with bacterial communities that frequently have beneficial effects on their development. Ectocarpus is a genus of small filamentous brown algae, which comprises a strain that has recently colonized freshwater, a rare transition in this lineage. We generated an inventory of bacteria in Ectocarpus cultures and examined the effect they have on acclimation to an environmental change, that is, the transition from seawater to freshwater medium. Our results demonstrate that Ectocarpus depends on bacteria for this transition: cultures that have been deprived of their associated microbiome do not survive a transfer to freshwater, but restoring their microflora also restores the capacity to acclimate to this change. Furthermore, the transition between the two culture media strongly affects the bacterial community composition. Examining a range of other closely related algal strains, we observed that the presence of two bacterial operational taxonomic units correlated significantly with an increase in low salinity tolerance of the algal culture. Despite differences in the community composition, no indications were found for functional differences in the bacterial metagenomes predicted to be associated with algae in the salinities tested, suggesting functional redundancy in the associated bacterial community. Our study provides an example of how microbial communities may impact the acclimation and physiological response of algae to different environments, and thus possibly act as facilitators of speciation. It paves the way for functional examinations of the underlying host-microbe interactions, both in controlled laboratory and natural conditions.
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Affiliation(s)
- Simon M Dittami
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Laëtitia Duboscq-Bidot
- Institut de Recherche Thérapeutique de l'Université de Nantes, UMR 1087, Plateforme Génomique, Nantes, France
| | - Morgan Perennou
- Plateforme de Séquençage-Génotypage, FR 2424 CNRS UPMC, Station Biologique, CS 90074, Roscoff, France
| | - Angélique Gobet
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Erwan Corre
- ABiMS platform, FR 2424 CNRS UPMC, Station Biologique, Roscoff, France
| | - Catherine Boyen
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Thierry Tonon
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
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13
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Shah MA, Callaway RM, Shah T, Houseman GR, Pal RW, Xiao S, Luo W, Rosche C, Reshi ZA, Khasa DP, Chen S. Conyza canadensis suppresses plant diversity in its nonnative ranges but not at home: a transcontinental comparison. THE NEW PHYTOLOGIST 2014; 202:1286-1296. [PMID: 24548283 DOI: 10.1111/nph.12733] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 01/21/2014] [Indexed: 05/28/2023]
Abstract
The impact of invasive species across their native and nonnative ranges is poorly quantified and this impedes a complete understanding of biological invasions. We compared the impact of the native North American plant, Conyza canadensis, which is invasive to Eurasia, on species richness at home and in a number of introduced regions through well replicated transcontinental field studies, glasshouse experiments and individual-based models. Our results demonstrated mostly negative relationships between C. canadensis abundance and native species richness in nonnative ranges, but either positive or no relationships in its native North American range. In glasshouse experiments, the total biomass of Conyza was suppressed more by species from its native range than by species from regions where it is nonnative, but the effects of Conyza on other species did not show a consistent biogeographical pattern. Finally, individual-based models led to the exclusion of Conyza from North American scenarios but to high abundances in scenarios with species from the nonnative ranges of Conyza. We illustrate biogeographical differences in the impact of an invader across regional scales and suggest that inherent differences in one specific aspect of competitive ability, tolerance to the effects of other species, may play some role in these differences.
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Affiliation(s)
- Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar, 190 006, Jammu & Kashmir, India
| | - Ragan M Callaway
- Division of Biological Sciences and the Institute on Ecosystems, The University of Montana, Missoula, MT, 59812, USA
| | - Tabasum Shah
- Department of Botany, University of Kashmir, Srinagar, 190 006, Jammu & Kashmir, India
| | - Gregory R Houseman
- Department of Biological Sciences, Wichita State University, Wichita, KS, USA
| | - Robert W Pal
- Division of Biological Sciences and the Institute on Ecosystems, The University of Montana, Missoula, MT, 59812, USA
- Faculty of Sciences, University of Pecs, Ifjusagu, 6, H-7624, Pecs, Hungary
| | - Sa Xiao
- Division of Biological Sciences and the Institute on Ecosystems, The University of Montana, Missoula, MT, 59812, USA
- Key Laboratory of Cell Activities and Stress Adaptations (Ministry of Education), School of Life Science, Lanzhou University, Lanzhou, Gansu People's Republic of China
| | - Wenbo Luo
- Key Laboratory for Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun, 130024, China
| | - Christoph Rosche
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University of Halle-Wittenberg, D-06108, Halle/Saale, Germany
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190 006, Jammu & Kashmir, India
| | - Damase P Khasa
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec City, QC, GIV0A6, Canada
| | - Shuyan Chen
- Division of Biological Sciences and the Institute on Ecosystems, The University of Montana, Missoula, MT, 59812, USA
- Key Laboratory of Cell Activities and Stress Adaptations (Ministry of Education), School of Life Science, Lanzhou University, Lanzhou, Gansu People's Republic of China
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14
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Xiao S, Ni G, Callaway RM. Models of experimentally derived competitive effects predict biogeographical differences in the abundance of invasive and native plant species. PLoS One 2013; 8:e78625. [PMID: 24265701 PMCID: PMC3827048 DOI: 10.1371/journal.pone.0078625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/13/2013] [Indexed: 11/18/2022] Open
Abstract
Mono-dominance by invasive species provides opportunities to explore determinants of plant distributions and abundance; however, linking mechanistic results from small scale experiments to patterns in nature is difficult. We used experimentally derived competitive effects of an invader in North America, Acroptilon repens, on species with which it co-occurs in its native range of Uzbekistan and on species with which it occurs in its non-native ranges in North America, in individual-based models. We found that competitive effects yielded relative abundances of Acroptilon and other species in models that were qualitatively similar to those observed in the field in the two ranges. In its non-native range, Acroptilon can occur in nearly pure monocultures at local scales, whereas such nearly pure stands of Acroptilon appear to be much less common in its native range. Experimentally derived competitive effects of Acroptilon on other species predicted Acroptilon to be 4-9 times more proportionally abundant than natives in the North American models, but proportionally equal to or less than the abundance of natives in the Eurasian models. Our results suggest a novel way to integrate complex combinations of interactions simultaneously, and that biogeographical differences in the competitive effects of an invader correspond well with biogeographical differences in abundance and impact.
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Affiliation(s)
- Sa Xiao
- Key Laboratory of Cell Activities and Stress Adaptations (Ministry of Education), School of Life Science, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Guangyan Ni
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Ragan M. Callaway
- Division of Biological Sciences and the Institute on Ecosystems, The University of Montana, Missoula, Montana, United States of America
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15
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Suwanvecho U, Brockelman WY. Interspecific territoriality in gibbons (Hylobates lar and H. pileatus) and its effects on the dynamics of interspecies contact zones. Primates 2011; 53:97-108. [PMID: 22127502 DOI: 10.1007/s10329-011-0284-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 10/20/2011] [Indexed: 11/29/2022]
Abstract
We investigated the ecology and interspecific interactions of the two gibbon species (Hylobates lar and H. pileatus) that overlap in distribution within a narrow zone of contact in the headwaters of the Takhong River at Khao Yai National Park in central Thailand. The zone is about 10-km wide, with phenotypic hybrids comprising 6.5% of the adult population. We compared species with respect to diet, territory size, intra- and interspecific group encounters, and territory quality. The two gibbon species exploited the same types of resources within their territories despite variation in the relative abundance of food-plant species between territories. The gibbons were interspecifically territorial, and males of both species displayed aggressive behaviors at both intraspecific and interspecific territorial boundaries. There was no marked difference in the amount of overlap between territories of conspecific and heterospecific pairs of groups. Although the habitat was not homogeneous, territory quality did not vary significantly between species. The species have not diverged in habitat preference or in diet. Neither species dominated in interspecific encounters, and both were reproducing well in the contact zone. We analyzed the potential consequences of several types of interspecific interactions on individual dispersal options and on the structure of the contact zone. Interference competition through interspecific territoriality affects the dispersal of individuals into the range of the other species. In general, territorial competition coupled with limited hybridization leads to predictions of a narrow contact zone or parapatry between species; thus, behavioral and ecological interactions between species need to be considered as potential factors in explaining range borders of primate species.
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Affiliation(s)
- Udomlux Suwanvecho
- Ecology Laboratory, Biotec Central Research Unit, National Science and Technology Development Agency, Klongluang, Pathum Thani 12120, Thailand.
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16
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Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T. Bacterial community assembly based on functional genes rather than species. Proc Natl Acad Sci U S A 2011; 108:14288-93. [PMID: 21825123 PMCID: PMC3161577 DOI: 10.1073/pnas.1101591108] [Citation(s) in RCA: 472] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be "species" (by means of rRNA taxonomy), but rather the more functional level of genes.
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Affiliation(s)
- Catherine Burke
- School of Biotechnology and Biomolecular Sciences
- The iThree Institute, University of Technology, Ultimo, New South Wales 2007, Australia
| | - Peter Steinberg
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales 2088, Australia
| | - Doug Rusch
- The J. Craig Venter Institute, Rockville, MD 20850; and
| | - Staffan Kjelleberg
- School of Biotechnology and Biomolecular Sciences
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
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17
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Robertson DR. Competitive ability and the potential for lotteries among territorial reef fishes. Oecologia 1995; 103:180-190. [DOI: 10.1007/bf00329078] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/1994] [Accepted: 03/13/1995] [Indexed: 11/30/2022]
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18
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Grosberg RK, Levitan DR. For adults only? Supply-side ecology and the history of larval biology. Trends Ecol Evol 1992; 7:130-3. [DOI: 10.1016/0169-5347(92)90148-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Mapstone B, Fowler A. Recruitment and the structure of assemblages of fish on coral reefs. Trends Ecol Evol 1988; 3:72-7. [DOI: 10.1016/0169-5347(88)90020-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Coexistence in a sea urchin guild and its implications to coral reef diversity and degradation. Oecologia 1988; 77:210-218. [DOI: 10.1007/bf00379188] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/1988] [Indexed: 10/26/2022]
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