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Pearman WS, Duffy GA, Liu XP, Gemmell NJ, Morales SE, Fraser CI. Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographical distance. ANNALS OF BOTANY 2024; 133:169-182. [PMID: 37804485 PMCID: PMC10921836 DOI: 10.1093/aob/mcad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/06/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND AND AIMS Contrasting patterns of host and microbiome biogeography can provide insight into the drivers of microbial community assembly. Distance-decay relationships are a classic biogeographical pattern shaped by interactions between selective and non-selective processes. Joint biogeography of microbiomes and their hosts is of increasing interest owing to the potential for microbiome-facilitated adaptation. METHODS In this study, we examine the coupled biogeography of the model macroalga Durvillaea and its microbiome using a combination of genotyping by sequencing (host) and 16S rRNA amplicon sequencing (microbiome). Alongside these approaches, we use environmental data to characterize the relationship between the microbiome, the host, and the environment. KEY RESULTS We show that although the host and microbiome exhibit shared biogeographical structure, these arise from different processes, with host biogeography showing classic signs of geographical distance decay, but with the microbiome showing environmental distance decay. Examination of microbial subcommunities, defined by abundance, revealed that the abundance of microbes is linked to environmental selection. As microbes become less common, the dominant ecological processes shift away from selective processes and towards neutral processes. Contrary to expectations, we found that ecological drift does not promote structuring of the microbiome. CONCLUSIONS Our results suggest that although host macroalgae exhibit a relatively 'typical' biogeographical pattern of declining similarity with increasing geographical distance, the microbiome is more variable and is shaped primarily by environmental conditions. Our findings suggest that the Baas Becking hypothesis of 'everything is everywhere, the environment selects' might be a useful hypothesis to understand the biogeography of macroalgal microbiomes. As environmental conditions change in response to anthropogenic influences, the processes structuring the microbiome of macroalgae might shift, whereas those governing the host biogeography are less likely to change. As a result, increasingly decoupled host-microbe biogeography might be observed in response to such human influences.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, New Zealand
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, New Zealand
| | - Xiaoyue P Liu
- Department of Marine Science, University of Otago, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, New Zealand
| | - Sergio E Morales
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, New Zealand
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2
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Pearman WS, Morales SE, Vaux F, Gemmell NJ, Fraser CI. Host population crashes disrupt the diversity of associated marine microbiomes. Environ Microbiol 2024; 26:e16611. [PMID: 38519875 DOI: 10.1111/1462-2920.16611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 03/01/2024] [Indexed: 03/25/2024]
Abstract
Host-associated microbial communities are shaped by myriad factors ranging from host conditions, environmental conditions and other microbes. Disentangling the ecological impact of each of these factors can be particularly difficult as many variables are correlated. Here, we leveraged earthquake-induced changes in host population structure to assess the influence of population crashes on marine microbial ecosystems. A large (7.8 magnitude) earthquake in New Zealand in 2016 led to widespread coastal uplift of up to ~6 m, sufficient to locally extirpate some intertidal southern bull kelp populations. These uplifted populations are slowly recovering, but remain at much lower densities than at nearby, less-uplifted sites. By comparing the microbial communities of the hosts from disturbed and relatively undisturbed populations using 16S rRNA gene amplicon sequencing, we observed that disturbed host populations supported higher functional, taxonomic and phylogenetic microbial beta diversity than non-disturbed host populations. Our findings shed light on microbiome ecological assembly processes, particularly highlighting that large-scale disturbances that affect host populations can dramatically influence microbiome structure. We suggest that disturbance-induced changes in host density limit the dispersal opportunities of microbes, with host community connectivity declining with the density of host populations.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, Dunedin, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- National Institute of Water and Atmospheric Research Ltd, Auckland, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Felix Vaux
- National Institute of Water and Atmospheric Research Ltd, Auckland, New Zealand
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, Dunedin, New Zealand
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3
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Zhang YS, Zhang YQ, Zhao XM, Liu XL, Qin QL, Liu NH, Xu F, Chen XL, Zhang YZ, Li PY. Metagenomic insights into the dynamic degradation of brown algal polysaccharides by kelp-associated microbiota. Appl Environ Microbiol 2024; 90:e0202523. [PMID: 38259074 PMCID: PMC10880675 DOI: 10.1128/aem.02025-23] [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: 11/12/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Marine bacteria play important roles in the degradation and cycling of algal polysaccharides. However, the dynamics of epiphytic bacterial communities and their roles in algal polysaccharide degradation during kelp decay are still unclear. Here, we performed metagenomic analyses to investigate the identities and predicted metabolic abilities of epiphytic bacterial communities during the early and late decay stages of the kelp Saccharina japonica. During kelp decay, the dominant epiphytic bacterial communities shifted from Gammaproteobacteria to Verrucomicrobia and Bacteroidetes. In the early decay stage of S. japonica, epiphytic bacteria primarily targeted kelp-derived labile alginate for degradation, among which the gammaproteobacterial Vibrionaceae (particularly Vibrio) and Psychromonadaceae (particularly Psychromonas), abundant in alginate lyases belonging to the polysaccharide lyase (PL) families PL6, PL7, and PL17, were key alginate degraders. More complex fucoidan was preferred to be degraded in the late decay stage of S. japonica by epiphytic bacteria, predominantly from Verrucomicrobia (particularly Lentimonas), Pirellulaceae of Planctomycetes (particularly Rhodopirellula), Pontiellaceae of Kiritimatiellota, and Flavobacteriaceae of Bacteroidetes, which depended on using glycoside hydrolases (GHs) from the GH29, GH95, and GH141 families and sulfatases from the S1_15, S1_16, S1_17, and S1_25 families to depolymerize fucoidan. The pathways for algal polysaccharide degradation in dominant epiphytic bacterial groups were reconstructed based on analyses of metagenome-assembled genomes. This study sheds light on the roles of different epiphytic bacteria in the degradation of brown algal polysaccharides.IMPORTANCEKelps are important primary producers in coastal marine ecosystems. Polysaccharides, as major components of brown algal biomass, constitute a large fraction of organic carbon in the ocean. However, knowledge of the identities and pathways of epiphytic bacteria involved in the degradation process of brown algal polysaccharides during kelp decay is still elusive. Here, based on metagenomic analyses, the succession of epiphytic bacterial communities and their metabolic potential were investigated during the early and late decay stages of Saccharina japonica. Our study revealed a transition in algal polysaccharide-degrading bacteria during kelp decay, shifting from alginate-degrading Gammaproteobacteria to fucoidan-degrading Verrucomicrobia, Planctomycetes, Kiritimatiellota, and Bacteroidetes. A model for the dynamic degradation of algal cell wall polysaccharides, a complex organic carbon, by epiphytic microbiota during kelp decay was proposed. This study deepens our understanding of the role of epiphytic bacteria in marine algal carbon cycling as well as pathogen control in algal culture.
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Affiliation(s)
- Yi-Shuo Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Qi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiang-Ming Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Lei Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Fei Xu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Joint Research Center for Marine Microbiol Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Joint Research Center for Marine Microbiol Science and Technology, Shandong University and Ocean University of China, Qingdao, China
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4
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Khan T, Song W, Nappi J, Marzinelli EM, Egan S, Thomas T. Functional guilds and drivers of diversity in seaweed-associated bacteria. FEMS MICROBES 2023; 5:xtad023. [PMID: 38213395 PMCID: PMC10781435 DOI: 10.1093/femsmc/xtad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.
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Affiliation(s)
- Tahsin Khan
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Jadranka Nappi
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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5
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King NG, Uribe R, Moore PJ, Earp HS, Gouraguine A, Hinostroza D, Perez-Matus A, Smith K, Smale DA. Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru. MICROBIAL ECOLOGY 2023; 86:2574-2582. [PMID: 37415044 DOI: 10.1007/s00248-023-02262-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.
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Affiliation(s)
- Nathan G King
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, PL1 2PB, UK.
| | - Roberto Uribe
- Área de Macroalgas y Biodiversidad, Instituto del Mar del Perú - IMARPE, av. La Ribera # 805, Huanchaco, La Libertad, Perú
| | - Pippa J Moore
- Dove Marine Laboratory, Newcastle University, Newcastle-Upon-Tyne, NE1 7RU, UK
| | - Hannah S Earp
- Dove Marine Laboratory, Newcastle University, Newcastle-Upon-Tyne, NE1 7RU, UK
- Department of Life Science, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Adam Gouraguine
- Dove Marine Laboratory, Newcastle University, Newcastle-Upon-Tyne, NE1 7RU, UK
| | - Diego Hinostroza
- Programa de Maestría en Ciencias del Mar, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Perez-Matus
- Subtidal Ecology Laboratory (Subelab), Estación Costera de Investigaciones Marinas (ECIM), Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114, -D, Santiago, Chile
| | - Kathryn Smith
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Dan A Smale
- Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, PL1 2PB, UK
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6
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Davis KM, Zeinert L, Byrne A, Davis J, Roemer C, Wright M, Parfrey LW. Successional dynamics of the cultivated kelp microbiome. JOURNAL OF PHYCOLOGY 2023; 59:538-551. [PMID: 37005360 DOI: 10.1111/jpy.13329] [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: 04/22/2022] [Revised: 01/29/2023] [Accepted: 02/26/2023] [Indexed: 06/15/2023]
Abstract
Kelp are important primary producers that are colonized by diverse microbes that can have both positive and negative effects on their hosts. The kelp microbiome could support the burgeoning kelp cultivation sector by improving host growth, stress tolerance, and resistance to disease. Fundamental questions about the cultivated kelp microbiome still need to be addressed before microbiome-based approaches can be developed. A critical knowledge gap is how cultivated kelp microbiomes change as hosts grow, particularly following outplanting to sites that vary in abiotic conditions and microbial source pools. In this study we assessed if microbes that colonize kelp in the nursery stage persist after outplanting. We characterized microbiome succession over time on two species of kelp, Alaria marginata and Saccharina latissima, outplanted to open ocean cultivation sites in multiple geographic locations. We tested for host-species specificity of the microbiome and the effect of different abiotic conditions and microbial source pools on kelp microbiome stability during the cultivation process. We found the microbiome of kelp in the nursery is distinct from that of outplanted kelp. Few bacteria persisted on kelp following outplanting. Instead, we identified significant microbiome differences correlated with host species and microbial source pools at each cultivation site. Microbiome variation related to sampling month also indicates that seasonality in host and/or abiotic factors may influence temporal succession and microbiome turnover in cultivated kelps. This study provides a baseline understanding of microbiome dynamics during kelp cultivation and highlights research needs for applying microbiome manipulation to kelp cultivation.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Center and Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Logan Zeinert
- Centre for Applied Research, Technology and Innovation, North Island College, 1685 S Dogwood St, Campbell River, British Columbia, V9W 8C1, Canada
| | - Allison Byrne
- Centre for Applied Research, Technology and Innovation, North Island College, 1685 S Dogwood St, Campbell River, British Columbia, V9W 8C1, Canada
| | - Jonathan Davis
- School of Aquatic & Fishery Sciences, College of the Environment, University of Washington, 1122 NE Boat St, Box 355020, Seattle, Washington, 98195-5020, USA
| | - Cosmo Roemer
- M. C. Wright and Associates Ltd., 2231 Neil Drive, Nanaimo, British Columbia, V9R 6T5, Canada
| | - Michael Wright
- M. C. Wright and Associates Ltd., 2231 Neil Drive, Nanaimo, British Columbia, V9R 6T5, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Center, Department of Botany, and Department of Zoology University of British Columbia, 6270 University Blvd, Vancouver, British Columbia, V6T 1Z4, Canada
- Hakai Institute, PO Box 25039, Campbell River, British Columbia, V9W 0B7, Canada
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7
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King NG, Moore PJ, Thorpe JM, Smale DA. Consistency and Variation in the Kelp Microbiota: Patterns of Bacterial Community Structure Across Spatial Scales. MICROBIAL ECOLOGY 2023; 85:1265-1275. [PMID: 35589992 DOI: 10.1007/s00248-022-02038-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/09/2022] [Indexed: 05/10/2023]
Abstract
Kelp species are distributed along ~ 25% of the world's coastlines and the forests they form represent some of the world's most productive and diverse ecosystems. Like other marine habitat-formers, the associated microbial community is fundamental for host and, in turn, wider ecosystem functioning. Given there are thousands of bacteria-host associations, determining which relationships are important remains a major challenge. We characterised the associated bacteria of two habitat-forming kelp species, Laminaria hyperborea and Saccharina latissima, from eight sites across a range of spatial scales (10 s of metres to 100 s of km) in the northeast Atlantic. We found no difference in diversity or community structure between the two kelps, but there was evidence of regional structuring (across 100 s km) and considerable variation between individuals (10 s of metres). Within sites, individuals shared few amplicon sequence variants (ASVs) and supported a very small proportion of diversity found across the wider study area. However, consistent characteristics between individuals were observed with individual host communities containing a small conserved "core" (8-11 ASVs comprising 25 and 32% of sample abundances for L. hyperborea and S. latissima, respectively). At a coarser taxonomic resolution, communities were dominated by four classes (Planctomycetes, Gammaproteobacteria, Alphaproteobacteria and Bacteroidia) that made up ~ 84% of sample abundances. Remaining taxa (47 classes) made up very little contribution to overall abundance but the majority of taxonomic diversity. Overall, our study demonstrates the consistent features of kelp bacterial communities across large spatial scales and environmental gradients and provides an ecologically meaningful baseline to track environmental change.
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Affiliation(s)
- Nathan G King
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK.
| | - Pippa J Moore
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jamie M Thorpe
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK
| | - Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK
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8
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Loudon AH, Park J, Parfrey LW. Identifying the core microbiome of the sea star Pisaster ochraceus in the context of sea star wasting disease. FEMS Microbiol Ecol 2023; 99:6998556. [PMID: 36690340 DOI: 10.1093/femsec/fiad005] [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: 07/21/2022] [Revised: 11/08/2022] [Accepted: 01/21/2023] [Indexed: 01/25/2023] Open
Abstract
Sea stars are keystone species and their mass die-offs due to sea star wasting disease (SSWD) impact marine communities and have fueled recent interest in the microbiome of sea stars. We assessed the host specificity of the microbiome associated with three body regions of the sea star Pisaster ochraceus using 16S rRNA gene amplicon surveys of the bacterial communities living on and in Pisaster, their environment, and sympatric marine hosts across three populations in British Columbia, Canada. Overall, the bacterial communities on Pisaster are distinct from their environment and differ by both body region and geography. We identified core bacteria specifically associated with Pisaster across populations and nearly absent in other hosts and the environment. We then investigated the distribution of these core bacteria on SSWD-affected Pisaster from one BC site and by reanalyzing a study of SSWD on Pisaster from California. We find no differences in the distribution of core bacteria in early disease at either site and two core taxa differ in relative abundance in advanced disease in California. Using phylogenetic analyses, we find that most core bacteria have close relatives on other sea stars and marine animals, suggesting these clades have evolutionary adaptions to an animal-associated lifestyle.
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Affiliation(s)
- Andrew H Loudon
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jungsoo Park
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Hakai Institute, PO Box 25039, Campbell River, BC V9W 0B7, Canada
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9
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Lajoie G, Parfrey LW. Beyond specialization: re-examining routes of host influence on symbiont evolution. Trends Ecol Evol 2022; 37:590-598. [PMID: 35466020 DOI: 10.1016/j.tree.2022.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/15/2022] [Accepted: 03/20/2022] [Indexed: 11/17/2022]
Abstract
Our understanding of host influence on microbial evolution has focused on symbiont specialization and the genomic streamlining that often accompanies it. However, a vast diversity of symbiotic lineages facultatively interact with hosts or associate with multiple hosts. Yet, there are no clear expectations for how host association influences the niche of these symbionts or their evolution. Here, we discuss how weak or variable selection on microbial symbiotic associations, horizontal transmission, and low costs of adaptation to novel host habitats are predicted to promote the expansion or maintenance of microbial niches. This broad perspective will aid in developing better and more general predictions for evolution in microbial symbioses.
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Affiliation(s)
- Geneviève Lajoie
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4.
| | - Laura Wegener Parfrey
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4
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10
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Weigel BL, Miranda KK, Fogarty EC, Watson AR, Pfister CA. Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes. mSystems 2022; 7:e0142221. [PMID: 35642511 PMCID: PMC9238374 DOI: 10.1128/msystems.01422-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/13/2022] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic organisms evolved in a microbial world and often have intimate associations with diverse bacterial groups. Kelp, brown macroalgae in the order Laminariales, play a vital role in coastal ecosystems, yet we know little about the functional role of the microbial symbionts that cover their photosynthetic surfaces. Here, we reconstructed 79 bacterial metagenome-assembled genomes (MAGs) from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine their metabolic potential and functional roles. Despite the annual life history of bull kelp, nearly half of the bacterial MAGs were detected across multiple years. Diverse members of the kelp microbiome, spanning 6 bacterial phyla, contained genes for transporting and assimilating dissolved organic matter (DOM), which is secreted by kelp in large quantities and likely fuels the metabolism of these heterotrophic bacteria. Bacterial genomes also contained alginate lyase and biosynthesis genes, involved in polysaccharide degradation and biofilm formation, respectively. Kelp-associated bacterial genomes contained genes for dissimilatory nitrate reduction and urea hydrolysis, likely providing a reduced source of nitrogen to the host kelp. The genome of the most abundant member of the kelp microbiome and common macroalgal symbiont, Granulosicoccus, contained a full suite of genes for synthesizing cobalamin (vitamin B12), suggesting that kelp-associated bacteria have the potential to provide their host kelp with vitamins. Finally, kelp-associated Granulosicoccus contained genes that typify the aerobic anoxygenic phototrophic bacteria, including genes for bacteriochlorophyll synthesis and photosystem II reaction center proteins, making them the first known photoheterotrophic representatives of this genus. IMPORTANCE Kelp (brown algae in the order Laminariales) are foundational species that create essential habitat in temperate and arctic coastal marine ecosystems. These photosynthetic giants host millions of microbial taxa whose functions are relatively unknown, despite their potential importance for host-microbe interactions and nutrient cycling in kelp forest ecosystems. We reconstructed bacterial genomes from metagenomic samples collected from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine the functional gene content of specific members of the kelp microbiome. These bacterial genomes spanned 6 phyla and 19 families and included common alga-associated microbial symbionts such as Granulosicoccus. Key functions encoded in kelp-associated bacterial genomes included dissolved organic matter assimilation, alginate metabolism, vitamin B12 biosynthesis, and nitrogen reduction from nitrate and urea to ammonium, potentially providing the host kelp with vitamins and reduced nitrogen.
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Affiliation(s)
- Brooke L. Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
| | | | - Emily C. Fogarty
- Committee on Microbiology, University of Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Andrea R. Watson
- Committee on Microbiology, University of Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Catherine A. Pfister
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, USA
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11
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Ramírez-Puebla ST, Weigel BL, Jack L, Schlundt C, Pfister CA, Mark Welch JL. Spatial organization of the kelp microbiome at micron scales. MICROBIOME 2022; 10:52. [PMID: 35331334 PMCID: PMC8944128 DOI: 10.1186/s40168-022-01235-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/21/2022] [Indexed: 05/15/2023]
Abstract
BACKGROUND Elucidating the spatial structure of host-associated microbial communities is essential for understanding taxon-taxon interactions within the microbiota and between microbiota and host. Macroalgae are colonized by complex microbial communities, suggesting intimate symbioses that likely play key roles in both macroalgal and bacterial biology, yet little is known about the spatial organization of microbes associated with macroalgae. Canopy-forming kelp are ecologically significant, fixing teragrams of carbon per year in coastal kelp forest ecosystems. We characterized the micron-scale spatial organization of bacterial communities on blades of the kelp Nereocystis luetkeana using fluorescence in situ hybridization and spectral imaging with a probe set combining phylum-, class-, and genus-level probes to localize and identify > 90% of the microbial community. RESULTS We show that kelp blades host a dense microbial biofilm composed of disparate microbial taxa in close contact with one another. The biofilm is spatially differentiated, with clustered cells of the dominant symbiont Granulosicoccus sp. (Gammaproteobacteria) close to the kelp surface and filamentous Bacteroidetes and Alphaproteobacteria relatively more abundant near the biofilm-seawater interface. A community rich in Bacteroidetes colonized the interior of kelp tissues. Microbial cell density increased markedly along the length of the kelp blade, from sparse microbial colonization of newly produced tissues at the meristematic base of the blade to an abundant microbial biofilm on older tissues at the blade tip. Kelp from a declining population hosted fewer microbial cells compared to kelp from a stable population. CONCLUSIONS Imaging revealed close association, at micrometer scales, of different microbial taxa with one another and with the host. This spatial organization creates the conditions necessary for metabolic exchange among microbes and between host and microbiota, such as provisioning of organic carbon to the microbiota and impacts of microbial nitrogen metabolisms on host kelp. The biofilm coating the surface of the kelp blade is well-positioned to mediate interactions between the host and surrounding organisms and to modulate the chemistry of the surrounding water column. The high density of microbial cells on kelp blades (105-107 cells/cm2), combined with the immense surface area of kelp forests, indicates that biogeochemical functions of the kelp microbiome may play an important role in coastal ecosystems. Video abstract.
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Affiliation(s)
- S. Tabita Ramírez-Puebla
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
- Present Address: The Forsyth Institute, Cambridge, MA USA
| | - Brooke L. Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL USA
- Present Address: Friday Harbor Laboratories, University of Washington, Friday Harbor, WA USA
| | - Loretha Jack
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
- Present Address: Wisconsin’s Green Fire, Rhinelander, WI USA
| | - Cathleen Schlundt
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
- Present Address: GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
| | | | - Jessica L. Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
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Guo Z, Wang L, Jiang Z, Liang Z. Comparison studies of epiphytic microbial communities on four macroalgae and their rocky substrates. MARINE POLLUTION BULLETIN 2022; 176:113435. [PMID: 35183021 DOI: 10.1016/j.marpolbul.2022.113435] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/09/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Macroalgae and their rocky substrates both support diverse and abundant microbiota, performing essential ecological functions in marine ecosystem. However, the differences in the epiphytic microbial communities on macroalgae and rocky substrate are still poorly understood. In this study, the epiphytic microbial communities on four macroalgae (Corallina officinalis, Rhodomela confervoides, Sargassum thunbergii, and Ulva linza) and their rocky substrates from Weihai coast zone were characterized using high-throughput sequencing technology. The results showed that the alpha diversity indices were greater in rocky substrates than that in macroalgae. The microbial similarities among macroalgae and rocky substrate groups tended to decrease from the high taxonomic ranks to lower ranks, only 22.69% of the total amplicon sequence variants (ASVs) were shared between them. The functional analysis revealed that the microbiotas were mainly involved in metabolic activities. This study would provide the theoretical foundation for macroalgal cultivation and algal reef applications.
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Affiliation(s)
- Zhansheng Guo
- Marine College, Shandong University, Weihai 264209, China
| | - Lu Wang
- Marine College, Shandong University, Weihai 264209, China
| | - Zhaoyang Jiang
- Marine College, Shandong University, Weihai 264209, China.
| | - Zhenlin Liang
- Marine College, Shandong University, Weihai 264209, China.
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Florez JZ, Camus C, Hengst MB, Buschmann AH. A mesocosm study on bacteria-kelp interactions: Importance of nitrogen availability and kelp genetics. JOURNAL OF PHYCOLOGY 2021; 57:1777-1791. [PMID: 34570392 DOI: 10.1111/jpy.13213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 06/12/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Macroalgal holobiont studies involve understanding interactions between the host, its microbiota, and the environment. We analyzed the effect of bacteria-kelp interactions on phenotypic responses of two genetically distinct populations of giant kelp, Macrocystis pyrifera (north and south), exposed to different nitrogen (N) concentrations. In co-culture experiments with different N concentration treatments, we evaluated kelp growth responses and changes in three specific molecular markers associated with the N cycle, both in epiphytic bacteria (relative abundance of nrfA-gene: cytochrome c nitrite reductase) and macroalgae (expression of NR-gene: nitrate reductase; GluSyn-gene: glutamate synthase). Both kelp populations responded differently to N limitation, with M. pyrifera-south sporophytes having a lower specific growth rate (SGR) under N-limiting conditions than the northern population; M. pyrifera-north sporophytes showed no significant differences in SGR when exposed to low-N and high-N concentrations. This corresponded to a higher GluSyn-gene expression in the M. pyrifera-north sporophytes and the co-occurrence of specific nrfA bacterial taxa. These bacteria may increase ammonium availability under low-N concentrations, allowing M. pyrifera-north to optimize nutrient assimilation by increasing the expression of GluSyn. We conclude that bacteria-kelp interactions are important in enhancing kelp growth rates under low N availability, although this effect may be regulated by the genetic background of kelp populations.
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Affiliation(s)
- July Z Florez
- Programa de Doctorado en Ciencias mención Conservación y Manejo de Recursos Naturales, Universidad de Los Lagos, Puerto Montt, Chile
- Centro i˜mar and CeBiB, Universidad de Los Lagos, Puerto Montt, Chile
- Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile
| | - Carolina Camus
- Centro i˜mar and CeBiB, Universidad de Los Lagos, Puerto Montt, Chile
| | - Martha B Hengst
- Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Biotecnología y Bioingeniería (CeBiB), Santiago, Chile
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14
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Paix B, Layglon N, Le Poupon C, D'Onofrio S, Misson B, Garnier C, Culioli G, Briand JF. Integration of spatio-temporal variations of surface metabolomes and epibacterial communities highlights the importance of copper stress as a major factor shaping host-microbiota interactions within a Mediterranean seaweed holobiont. MICROBIOME 2021; 9:201. [PMID: 34641951 PMCID: PMC8507236 DOI: 10.1186/s40168-021-01124-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Although considered as holobionts, macroalgae and their surface microbiota share intimate interactions that are still poorly understood. Little is known on the effect of environmental parameters on the close relationships between the host and its surface-associated microbiota, and even more in a context of coastal pollutions. Therefore, the main objective of this study was to decipher the impact of local environmental parameters, especially trace metal concentrations, on an algal holobiont dynamics using the Phaeophyta Taonia atomaria as a model. Through a multidisciplinary multi-omics approach combining metabarcoding and untargeted LC-MS-based metabolomics, the epibacterial communities and the surface metabolome of T. atomaria were monitored along a spatio-temporal gradient in the bay of Toulon (Northwestern Mediterranean coast) and its surrounding. Indeed, this geographical area displays a well-described trace metal gradient particularly relevant to investigate the effect of such pollutants on marine organisms. RESULTS Epibacterial communities of T. atomaria exhibited a high specificity whatever the five environmentally contrasted collecting sites investigated on the NW Mediterranean coast. By integrating metabarcoding and metabolomics analyses, the holobiont dynamics varied as a whole. During the occurrence period of T. atomaria, epibacterial densities and α-diversity increased while the relative proportion of core communities decreased. Pioneer bacterial colonizers constituted a large part of the specific and core taxa, and their decrease might be linked to biofilm maturation through time. Then, the temporal increase of the Roseobacter was proposed to result from the higher temperature conditions, but also the increased production of dimethylsulfoniopropionate (DMSP) at the algal surface which could constitute of the source of carbon and sulfur for the catabolism pathways of these taxa. Finally, as a major result of this study, copper concentration constituted a key factor shaping the holobiont system. Thus, the higher expression of carotenoids suggested an oxidative stress which might result from an adaptation of the algal surface metabolome to high copper levels. In turn, this change in the surface metabolome composition could result in the selection of particular epibacterial taxa. CONCLUSION We showed that associated epibacterial communities were highly specific to the algal host and that the holobiont dynamics varied as a whole. While temperature increase was confirmed to be one of the main parameters associated to Taonia dynamics, the originality of this study was highlighting copper-stress as a major driver of seaweed-epibacterial interactions. In a context of global change, this study brought new insights on the dynamics of a Mediterranean algal holobiont submitted to heavy anthropic pressures. Video abstract.
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Affiliation(s)
- Benoît Paix
- Université de Toulon, Laboratoire MAPIEM, EA, 4323, Toulon, France
- Present adress: Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Nicolas Layglon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Christophe Le Poupon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Sébastien D'Onofrio
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Benjamin Misson
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Cédric Garnier
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM, 110, Toulon, France
| | - Gérald Culioli
- Université de Toulon, Laboratoire MAPIEM, EA, 4323, Toulon, France.
- Present address: Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), UMR CNRS-IRD-Avignon Université-Aix-Marseille Université, Avignon, France.
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15
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Phelps CM, McMahon K, Bissett A, Bernasconi R, Steinberg PD, Thomas T, Marzinelli EM, Huggett MJ. The surface bacterial community of an Australian kelp shows cross-continental variation and relative stability within regions. FEMS Microbiol Ecol 2021; 97:fiab089. [PMID: 34156064 DOI: 10.1093/femsec/fiab089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/18/2021] [Indexed: 11/12/2022] Open
Abstract
Epiphytic microbial communities often have a close relationship with their eukaryotic host, assisting with defence, health, disease prevention and nutrient transfer. Shifts in the structure of microbial communities could therefore have negative effects on the individual host and indirectly impact the surrounding ecosystem, particularly for major habitat-forming hosts, such as kelps in temperate rocky shores. Thus, an understanding of the structure and dynamics of host-associated microbial communities is essential for monitoring and assessing ecosystem changes. Here, samples were taken from the ecologically important kelp, Ecklonia radiata, over a 17-month period, from six different sites in two distinct geographic regions (East and West coasts of Australia), separated by ∼3,300 kms, to understand variation in the kelp bacterial community and its potential environmental drivers. Differences were observed between kelp bacterial communities between the largely disconnected geographical regions. In contrast, within each region and over time the bacterial communities were considerably more stable, despite substantial seasonal changes in environmental conditions.
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Affiliation(s)
- Charlie M Phelps
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
| | - Kathryn McMahon
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
| | - Andrew Bissett
- CSIRO Oceans and Atmosphere, Castray Esp, Battery Point, Tas, 7004, Australia
| | - Rachele Bernasconi
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
| | - Peter D Steinberg
- Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, High St, Kensington, NSW, 2052, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, High St, Kensington, NSW, 2052, Australia
| | - Ezequiel M Marzinelli
- Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551
- The University of Sydney, School of Life and Environmental Sciences, Coastal and Marine Ecosystems, City Rd, Camperdown, NSW, 2006, Australia
| | - Megan J Huggett
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
- School of Environmental and Life Sciences, University of Newcastle, 10 Chittaway Rd, Ourimbah, NSW, 2258, Australia
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16
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Ahmed A, Khurshid A, Tang X, Wang J, Khan TU, Mao Y. Structural and Functional Impacts of Microbiota on Pyropia yezoensis and Surrounding Seawater in Cultivation Farms along Coastal Areas of the Yellow Sea. Microorganisms 2021; 9:microorganisms9061291. [PMID: 34204837 PMCID: PMC8231614 DOI: 10.3390/microorganisms9061291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022] Open
Abstract
Pyropia yezoensis is the most important commercial edible red algae in China, carrying a variety of resident microbes at its surface. To understand microbiome diversity, community structure, interactions and functions with hosts in this regard, thalli and seawater sampleswere collected from Yantai and Rizhao cultivation farms in the Yellow Sea. The thalli and seawater samples (n = 12) were collected and studied using an Illumina NovaSeq 6000 platform and 16S ribosomal RNA (rRNA) gene sequencing, along with the consideration of environmental factors. Bacterial communities in association with P. yezoensis and surrounding seawater were predominated by Cyanobacteria, Proteobacteria, and Bacteroidetes. The variability of bacterial communities related to P. yezoensis and seawater were predominantly shaped by nitrate (NO3), ammonium (NH4), and temperature. Cluster analysis revealed a close relationship between thalli (RTH and YTH) and seawater (RSW and YSW) in terms of the residing bacterial communities, respectively. PICRUSt analysis revealed the presence of genes associated with amino acid transportation and metabolism, which explained the bacterial dependence on algal-provided nutrients. This study reveals that the diversity of microbiota for P. yezoensis is greatly influenced by abiotic factors and algal organic exudates which trigger chemical signaling and transportation responses from the bacterial community, which in turn activates genes to metabolize subsequent substrates.
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Affiliation(s)
- Arsalan Ahmed
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (A.A.); (A.K.); (X.T.); (J.W.); (T.U.K.)
| | - Anam Khurshid
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (A.A.); (A.K.); (X.T.); (J.W.); (T.U.K.)
| | - Xianghai Tang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (A.A.); (A.K.); (X.T.); (J.W.); (T.U.K.)
| | - Junhao Wang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (A.A.); (A.K.); (X.T.); (J.W.); (T.U.K.)
| | - Tehsin Ullah Khan
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (A.A.); (A.K.); (X.T.); (J.W.); (T.U.K.)
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (A.A.); (A.K.); (X.T.); (J.W.); (T.U.K.)
- Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Ministry of Education), College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
- Correspondence:
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Davis KM, Mazel F, Parfrey LW. The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant. Environ Microbiol 2021; 23:2617-2631. [PMID: 33817918 DOI: 10.1111/1462-2920.15496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023]
Abstract
It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Hakai Institute, PO Box 309, Heriot Bay, BC, V0P 1H0, Canada
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18
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Weigel BL, Pfister CA. Oxygen metabolism shapes microbial settlement on photosynthetic kelp blades compared to artificial kelp substrates. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:176-184. [PMID: 33372322 DOI: 10.1111/1758-2229.12923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
We examined factors shaping community assembly of the bull kelp (Nereocystis luetkeana) microbiome by comparing microbial biofilm formation on photosynthetic kelp blade tissues and artificial kelp substrates ('agar substrates') deployed into a kelp forest. New kelp blade tissues were colonized by markedly distinct microbial taxa relative to agar substrates during the same time interval, even when agar substrates were infused with N. luetkeana blades, suggesting that microbial settlement onto kelp surfaces is more than just attraction to a polysaccharide-rich surface. Further, common seawater taxa such as Colwellia sp. and Psychromonas sp. became abundant on agar substrates but avoided new kelp blade tissues, indicating that host-specific factors may deter certain surface-associated marine microbial taxa. Over two-thirds of the bacterial taxa in the kelp microbiome were associated with strictly aerobic metabolisms; thus, photosynthetic production of O2 may favour aerobic microbial metabolisms. While living kelp blades primarily recruited aerobic microbes, including the obligate aerobe Granulosicoccus sp., microbes that colonized agar substrates were predominantly facultative anaerobes. We also found that infusion of kelp tissues into agar substrates altered microbial community composition and lowered taxonomic diversity relative to control agar substrates, suggesting that non-living components of the kelp blade also impact microbial community assembly.
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Affiliation(s)
- Brooke L Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA
| | - Catherine A Pfister
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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Brunet M, de Bettignies F, Le Duff N, Tanguy G, Davoult D, Leblanc C, Gobet A, Thomas F. Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities. Environ Microbiol 2021; 23:1638-1655. [PMID: 33400326 PMCID: PMC8248336 DOI: 10.1111/1462-2920.15389] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/14/2020] [Accepted: 01/02/2021] [Indexed: 12/30/2022]
Abstract
Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6-month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide-degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.
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Affiliation(s)
- Maéva Brunet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Florian de Bettignies
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Nolwen Le Duff
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Gwenn Tanguy
- Sorbonne Université, CNRS, FR2424, Genomer, Station Biologique de RoscoffRoscoff29680France
| | - Dominique Davoult
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
| | - Angélique Gobet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRDSèteFrance
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)Roscoff29680France
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Sanders-Smith R, Segovia BT, Forbes C, Hessing-Lewis M, Morien E, Lemay MA, O'Connor MI, Parfrey LW. Host-Specificity and Core Taxa of Seagrass Leaf Microbiome Identified Across Tissue Age and Geographical Regions. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.605304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The seagrass Zostera marina is a widespread foundational species in temperate coastal ecosystems that supports diverse communities of epiphytes and grazers. Bacteria link the production of seagrass to higher trophic levels and are thought to influence seagrass biology and health. Yet, we lack a clear understanding of the factors that structure the seagrass microbiome, or whether there is a consistent microbial community associated with seagrass that underpins functional roles. We sampled surface microbiome (epibiota) from new and old growth seagrass leaves and the surrounding seawater in eight meadows among four regions along the Central Coast of British Columbia, Canada to assess microbiome variability across space and as leaves age. We found that the seagrass leaf microbiome differs strongly from seawater. Microbial communities in new and old growth leaves are different from each other and from artificial seagrass leaves we deployed in one meadow. The microbiome on new leaves is less diverse and there is a small suite of core OTUs (operational taxonomic units) consistently present across regions. The overall microbial community for new leaves is more dispersed but with little regional differentiation, while the epiphytes on old leaves are regionally distinct. Many core OTUs on old leaves are commonly associated with marine biofilms. Together these observations suggest a stronger role for host filtering in new compared to old leaves, and a stronger influence of the environment and environmental colonization in old leaves. We found 11 core microbial taxa consistently present on old and new leaves and at very low relative abundance on artificial leaves and in the water column. These 11 taxa appear to be strongly associated with Z. marina. These core taxa may perform key functions important for the host such as detoxifying seagrass waste products, enhancing plant growth, and controlling epiphyte cover.
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Morphological complexity affects the diversity of marine microbiomes. ISME JOURNAL 2020; 15:1372-1386. [PMID: 33349654 DOI: 10.1038/s41396-020-00856-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Large eukaryotes support diverse communities of microbes on their surface-epibiota-that profoundly influence their biology. Alternate factors known to structure complex patterns of microbial diversity-host evolutionary history and ecology, environmental conditions and stochasticity-do not act independently and it is challenging to disentangle their relative effects. Here, we surveyed the epibiota from 38 sympatric seaweed species that span diverse clades and have convergent morphology, which strongly influences seaweed ecology. Host identity explains most of the variation in epibiont communities and deeper host phylogenetic relationships (e.g., genus level) explain a small but significant portion of epibiont community variation. Strikingly, epibiota community composition is significantly influenced by host morphology and epibiota richness increases with morphological complexity of the seaweed host. This effect is robust after controlling for phylogenetic non-independence and is strongest for crustose seaweeds. We experimentally validated the effect of host morphology by quantifying bacterial community assembly on latex sheets cut to resemble three seaweed morphologies. The patterns match those observed in our field survey. Thus, biodiversity increases with habitat complexity in host-associated microbial communities, mirroring patterns observed in animal communities. We suggest that host morphology and structural complexity are underexplored mechanisms structuring microbial communities.
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22
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Menaa F, Wijesinghe PAUI, Thiripuranathar G, Uzair B, Iqbal H, Khan BA, Menaa B. Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions. Mar Drugs 2020; 18:md18120641. [PMID: 33327517 PMCID: PMC7764995 DOI: 10.3390/md18120641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023] Open
Abstract
Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)–microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.
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Affiliation(s)
- Farid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
- Correspondence: or
| | - P. A. U. I. Wijesinghe
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Gobika Thiripuranathar
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan;
| | - Haroon Iqbal
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China;
| | - Barkat Ali Khan
- Department of Pharmacy, Gomal University, Dera Ismail Khan 29050, Pakistan;
| | - Bouzid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
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23
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Paix B, Carriot N, Barry-Martinet R, Greff S, Misson B, Briand JF, Culioli G. A Multi-Omics Analysis Suggests Links Between the Differentiated Surface Metabolome and Epiphytic Microbiota Along the Thallus of a Mediterranean Seaweed Holobiont. Front Microbiol 2020; 11:494. [PMID: 32269559 PMCID: PMC7111306 DOI: 10.3389/fmicb.2020.00494] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/06/2020] [Indexed: 11/13/2022] Open
Abstract
Marine macroalgae constitute an important living resource in marine ecosystems and complex ecological interactions occur at their surfaces with microbial communities. In this context, the present study aimed to investigate how the surface metabolome of the algal holobiont Taonia atomaria could drive epiphytic microbiota variations at the thallus scale. First, a clear discrimination was observed between algal surface, planktonic and rocky prokaryotic communities. These data strengthened the hypothesis of an active role of the algal host in the selection of epiphytic communities. Moreover, significant higher epibacterial density and α-diversity were found at the basal algal parts compared to the apical ones, suggesting a maturation gradient of the community along the thallus. In parallel, a multiplatform mass spectrometry-based metabolomics study, using molecular networking to annotate relevant metabolites, highlighted a clear chemical differentiation at the algal surface along the thallus with similar clustering as for microbial communities. In that respect, higher amounts of sesquiterpenes, phosphatidylcholines (PCs), and diacylglycerylhydroxymethyl-N,N,N-trimethyl-β-alanines (DGTAs) were observed at the apical regions while dimethylsulfoniopropionate (DMSP) and carotenoids were predominantly found at the basal parts of the thalli. A weighted UniFrac distance-based redundancy analysis linking the metabolomics and metabarcoding datasets indicated that these surface compounds, presumably of algal origin, may drive the zonal variability of the epibacterial communities. As only few studies were focused on microbiota and metabolome variation along a single algal thallus, these results improved our understanding about seaweed holobionts. Through this multi-omics approach at the thallus scale, we suggested a plausible scenario where the chemical production at the surface of T. atomaria, mainly induced by the algal physiology, could explain the specificity and the variations of the surface microbiota along the thallus.
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Affiliation(s)
- Benoît Paix
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
| | - Nathan Carriot
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
| | - Raphaëlle Barry-Martinet
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
| | - Stéphane Greff
- UMR 7263, Aix Marseille Université, CNRS, IRD, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Station Marine d'Endoume, Marseille, France
| | - Benjamin Misson
- UMR 7294, Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, Marseille, France
| | - Jean-François Briand
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
| | - Gérald Culioli
- EA 4323, Matériaux Polymères Interfaces Environnement Marin, Université de Toulon, Toulon, France
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24
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Abstract
Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as 'microbial community relationships that recapitulate the phylogeny of their host', we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modelling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigation from a diversity of disciplines.
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Affiliation(s)
- Shen Jean Lim
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
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25
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Thomas F, Dittami SM, Brunet M, Le Duff N, Tanguy G, Leblanc C, Gobet A. Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga-associated bacterial communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:30-37. [PMID: 31692275 DOI: 10.1111/1758-2229.12806] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 05/21/2023]
Abstract
Plant- and alga-associated bacterial communities are generally described via 16S rDNA metabarcoding using universal primers. As plastid genomes encode 16S rDNA related to cyanobacteria, these data sets frequently contain >90% plastidial sequences, and the bacterial diversity may be under-sampled. To overcome this limitation we evaluated in silico the taxonomic coverage for four primer combinations targeting the 16S rDNA V3-V4 region. They included a forward primer universal to Bacteria (S-D-Bact-0341-b-S-17) and four reverse primers designed to avoid plastid DNA amplification. The best primer combination (NOCHL) was compared to the universal primer set in the wet lab using a synthetic community and samples from three macroalgal species. The proportion of plastid sequences was reduced by 99%-100% with the NOCHL primers compared to the universal primers, irrespective of algal hosts, sample collection and extraction protocols. Additionally, the NOCHL primers yielded a higher richness while maintaining the community structure. As Planctomycetes, Verrucomicrobia and Cyanobacteria were underrepresented (70%-90%) compared to universal primers, combining the NOCHL set with taxon-specific primers may be useful for a complete description of the alga-associated bacterial diversity. The NOCHL primers represent an innovation to study algal holobionts without amplifying host plastid sequences and may further be applied to other photosynthetic hosts.
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Affiliation(s)
- François Thomas
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Simon M Dittami
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Maéva Brunet
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Nolwen Le Duff
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Gwenn Tanguy
- Station Biologique de Roscoff, CNRS, Sorbonne Université, FR2424, Genomer, 29680, Roscoff, France
| | - Catherine Leblanc
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
| | - Angélique Gobet
- Station Biologique de Roscoff (SBR), Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), 29680, Roscoff, France
- MARBEC, Ifremer, IRD, Université de Montpellier, CNRS, 34203, Sète, France
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26
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Cleary DFR, Polónia ARM, Huang YM, Swierts T. Compositional variation between high and low prokaryotic diversity coral reef biotopes translates to different predicted metagenomic gene content. Antonie van Leeuwenhoek 2019; 113:563-587. [PMID: 31802337 DOI: 10.1007/s10482-019-01364-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
Abstract
In a previous study, we identified host species that housed high and low diversity prokaryotic communities. In the present study, we expand on this and assessed the prokaryotic communities associated with seawater, sediment and 11 host species from 7 different phyla in a Taiwanese coral reef setting. The host taxa sampled included hard, octo- and black corals, molluscs, bryozoans, flatworms, fish and sea urchins. There were highly significant differences in composition among host species and all host species housed distinct communities from those found in seawater and sediment. In a hierarchical clustering analysis, samples from all host species, with the exception of the coral Galaxea astreata, formed significantly supported clusters. In addition to this, the coral G. astreata and the bryozoan Triphyllozoon inornatum on the one hand and the coral Tubastraea coccinea, the hermit crab Calcinus laevimanus and the flatworm Thysanozoon nigropapillosum on the other formed significantly supported clusters. In addition to composition, there were highly pronounced differences in richness and evenness among host species from the most diverse species, the bryozoan T. inornatum at 2518 ± 240 OTUs per 10,000 sequences to the least diverse species, the octocoral Cladiella sp. at 142 ± 14 OTUs per 10,000 sequences. In line with the differences in composition, there were significant differences in predicted metagenomic gene counts among host species. Furthermore, there were pronounced compositional and predicted functional differences between high diversity hosts (Liolophura japonica, G. astreata, T. coccinea, C. laevimanus, T. inornatum) and low diversity hosts (Antipathes sp., Pomacentrus coelestis, Modiolus auriculatus, T. nigropapillosum, Cladiella sp. and Diadema savigny). In particular, we found that all tested low diversity hosts were predicted to be enriched for the phosphotransferase system compared to high diversity hosts.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Ana Rita M Polónia
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Yusheng M Huang
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, Penghu, Taiwan.,Department of Marine Recreation, University of Science and Technology, Penghu, Taiwan
| | - Thomas Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands
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27
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Florez JZ, Camus C, Hengst MB, Marchant F, Buschmann AH. Structure of the epiphytic bacterial communities of Macrocystis pyrifera in localities with contrasting nitrogen concentrations and temperature. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101706] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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28
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Pfister CA, Altabet MA, Weigel BL. Kelp beds and their local effects on seawater chemistry, productivity, and microbial communities. Ecology 2019; 100:e02798. [PMID: 31233610 DOI: 10.1002/ecy.2798] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/11/2019] [Accepted: 05/28/2019] [Indexed: 11/10/2022]
Abstract
Kelp forests are known as key habitats for species diversity and macroalgal productivity; however, we know little about how these biogenic habitats interact with seawater chemistry and phototroph productivity in the water column. We examined kelp forest functions at three locales along the Olympic Peninsula of Washington state by quantifying carbonate chemistry, nutrient concentrations, phytoplankton productivity, and seawater microbial communities inside and outside of kelp beds dominated by the canopy kelp species Nereocystis luetkeana and Macrocystis pyrifera. Kelp beds locally increased the pH, oxygen, and aragonite saturation state of the seawater, but lowered seawater inorganic carbon content and total alkalinity. Although kelp beds depleted nitrate and phosphorus concentrations, ammonium and dissolved organic carbon (DOC) concentrations were enhanced. Kelp beds also decreased chlorophyll concentrations and carbon fixed by phytoplankton, although kelp carbon fixation more than compensated for any difference in phytoplankton production. Kelp beds entrained distinct microbial communities, with higher taxonomic and phylogenetic diversity compared to seawater outside of the kelp bed. Kelp forests thus had significant effects on seawater chemistry, productivity and the microbial assemblages in their proximity. Thereby, the diversity of pathways for carbon and nitrogen cycling was also enhanced. Overall, these observations suggest that the contribution of kelp forests to nearshore carbon and nitrogen cycling is greater than previously documented.
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Affiliation(s)
- Catherine A Pfister
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, 60637, USA
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, 60637, USA
| | - Mark A Altabet
- School of Marine Sciences, University of Massachusetts, Dartmouth, Massachusetts, 02744, USA
| | - Brooke L Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, 60637, USA
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29
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Paix B, Othmani A, Debroas D, Culioli G, Briand JF. Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria. Environ Microbiol 2019; 21:3346-3363. [PMID: 30945796 DOI: 10.1111/1462-2920.14617] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/31/2019] [Indexed: 11/30/2022]
Abstract
An integrative multi-omics approach allowed monthly variations for a year of the surface metabolome and the epibacterial community of the Mediterranean Phaeophyceae Taonia atomaria to be investigated. The LC-MS-based metabolomics and 16S rDNA metabarcoding data sets were integrated in a multivariate meta-omics analysis (multi-block PLS-DA from the MixOmic DIABLO analysis) showing a strong seasonal covariation (Mantel test: p < 0.01). A network based on positive and negative correlations between the two data sets revealed two clusters of variables, one relative to the 'spring period' and a second to the 'summer period'. The 'spring period' cluster was mainly characterized by dipeptides positively correlated with a single bacterial taxon of the Alteromonadaceae family (BD1-7 clade). Moreover, 'summer' dominant epibacterial taxa from the second cluster (including Erythrobacteraceae, Rhodospirillaceae, Oceanospirillaceae and Flammeovirgaceae) showed positive correlations with few metabolites known as macroalgal antifouling defences [e.g. dimethylsulphoniopropionate (DMSP) and proline] which exhibited a key role within the correlation network. Despite a core community that represents a significant part of the total epibacteria, changes in the microbiota structure associated with surface metabolome variations suggested that both environment and algal host shape the bacterial surface microbiota.
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Affiliation(s)
- Benoît Paix
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
| | - Ahlem Othmani
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, UMR 6023, Clermont-Ferrand, France
| | - Gérald Culioli
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
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30
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The Macroalgal Holobiont in a Changing Sea. Trends Microbiol 2019; 27:635-650. [DOI: 10.1016/j.tim.2019.03.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 03/01/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
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31
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Weigel BL, Pfister CA. Successional Dynamics and Seascape-Level Patterns of Microbial Communities on the Canopy-Forming Kelps Nereocystis luetkeana and Macrocystis pyrifera. Front Microbiol 2019; 10:346. [PMID: 30863387 PMCID: PMC6399156 DOI: 10.3389/fmicb.2019.00346] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/08/2019] [Indexed: 11/23/2022] Open
Abstract
Canopy-forming kelps create underwater forests that are among the most productive marine ecosystems. On the Pacific coast of North America, two canopy-forming kelps with contrasting life histories co-occur; Macrocystis pyrifera, a perennial species, and Nereocystis luetkeana, an annual species. Kelp blade-associated microbes were sampled from 12 locations across a spatial gradient in Washington, United States, from the outer Pacific Coast to Puget Sound. Microbial communities were characterized using next-generation Illumina sequencing of 16S rRNA genes. At higher taxonomic levels (bacterial phylum and class), canopy-forming kelps hosted remarkably similar microbial communities, but at the amplicon sequence variant level, microbial communities on M. pyrifera and N. luetkeana were host-specific and distinct from free-living bacteria in the surrounding seawater. Microbial communities associated with blades of each kelp species displayed significant geographic variation. The microbiome of N. luetkeana changed along the spatial gradient and was significantly correlated to salinity, with outer Pacific coast sites enriched in Bacteroidetes (family Saprospiraceae) and Gammaproteobacteria (Granulosicoccus sp.), and southern Puget Sound sites enriched in Alphaproteobacteria (family Hyphomonadaceae). We also examined microbial community development and succession on meristematic and apical N. luetkeana blade tissues throughout the summer growing season on Tatoosh Island, WA. Across all dates, microbial communities were less diverse on younger, meristematic blade tissue compared to the older, apical tissues. In addition, phylogenetic relatedness among microbial taxa increased from meristematic to apical blade tissues, suggesting that the addition of microbial taxa to the community was a non-random process that selected for certain phylogenetic groups of microbes. Microbial communities on older, apical tissues displayed significant temporal variation throughout the summer and microbial taxa that were differentially abundant over time displayed clear patterns of community succession. Overall, we report that host species identity, geographic location, and blade tissue age shape the microbial communities on canopy-forming kelps.
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Affiliation(s)
- Brooke L Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, United States
| | - Catherine A Pfister
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
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32
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Mazel F, Davis KM, Loudon A, Kwong WK, Groussin M, Parfrey LW. Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life? mSystems 2018; 3:e00097-18. [PMID: 30417109 PMCID: PMC6208643 DOI: 10.1128/msystems.00097-18] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.
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Affiliation(s)
- Florent Mazel
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Katherine M. Davis
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Loudon
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Waldan K. Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mathieu Groussin
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Laura Wegener Parfrey
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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33
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Lin JD, Lemay MA, Parfrey LW. Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera. Front Microbiol 2018; 9:1914. [PMID: 30177919 PMCID: PMC6110156 DOI: 10.3389/fmicb.2018.01914] [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: 03/10/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
Bacteria are integral to marine carbon cycling. They transfer organic carbon to higher trophic levels and remineralise it into inorganic forms. Kelp forests are among the most productive ecosystems within the global oceans, yet the diversity and metabolic capacity of bacteria that transform kelp carbon is poorly understood. Here, we use 16S amplicon and metagenomic shotgun sequencing to survey bacterial communities associated with the surfaces of the giant kelp Macrocystis pyrifera and assess the capacity of these bacteria for carbohydrate metabolism. We find that Macrocystis-associated communities are distinct from the water column, and that they become more diverse and shift in composition with blade depth, which is a proxy for tissue age. These patterns are also observed in metagenomic functional profiles, though the broader functional groups—carbohydrate active enzyme families—are largely consistent across samples and depths. Additionally, we assayed more than 250 isolates cultured from Macrocystis blades and the surrounding water column for the ability to utilize alginate, the primary polysaccharide in Macrocystis tissue. The majority of cultured bacteria (66%) demonstrated this capacity; we find that alginate utilization is patchily distributed across diverse genera in the Bacteroidetes and Proteobacteria, yet can also vary between isolates with identical 16S rRNA sequences. The genes encoding enzymes involved in alginate metabolism were detected in metagenomic data across taxonomically diverse bacterial communities, further indicating this capacity is likely widespread amongst bacteria in kelp forests. Overall, the M. pyrifera epibiota shifts across a depth gradient, demonstrating a connection between bacterial assemblage and host tissue state.
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Affiliation(s)
- Jordan D Lin
- Department of Botany, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada
| | - Matthew A Lemay
- Department of Botany, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada
| | - Laura W Parfrey
- Department of Botany, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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Lemay MA, Martone PT, Hind KR, Lindstrom SC, Wegener Parfrey L. Alternate life history phases of a common seaweed have distinct microbial surface communities. Mol Ecol 2018; 27:3555-3568. [PMID: 30055017 DOI: 10.1111/mec.14815] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/26/2022]
Abstract
Macroalgal life histories are complex, often involving the alternation of distinct free-living life history phases that differ in morphology, longevity and ploidy. The surfaces of marine macroalgae support diverse microbial biofilms, yet the degree of microbial variation between alternate phases is unknown. We quantified bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities on the surface of the common intertidal seaweed, Mastocarpus spp., which alternates between gametophyte (foliose, haploid) and sporophyte (encrusting, diploid) life history phases. A large portion (97%) of bacterial taxa on the surface Mastocarpus was also present in samples from the environment, indicating that macroalgal surface communities are largely assembled from the surrounding seawater. Still, changes in the relative abundance of bacterial taxa result in significantly different communities on alternate Mastocarpus life history phases, rocky substrate and seawater at all intertidal elevations. For microeukaryote assemblages, only high intertidal samples had significant differences between life history phases although sporophytes were not different from the rocky substrate at this elevation; gametophytes and sporophytes did not differ in microeukaryote communities in the mid and low zones. By sequencing three host genes, we identified three cryptic species of Mastocarpus in our data set, which co-occur in the mid-to-low intertidal zone. In these samples, M. alaskensis sporophytes harboured distinct bacterial communities compared to M. agardhii and M. intermedius sporophytes, which were not distinguishable. Conversely, microeukaryote communities did not differ among species.
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Affiliation(s)
- Matthew A Lemay
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Patrick T Martone
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Katharine R Hind
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Sandra C Lindstrom
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Laura Wegener Parfrey
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada.,Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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Parfrey LW, Moreau CS, Russell JA. Introduction: The host-associated microbiome: Pattern, process and function. Mol Ecol 2018; 27:1749-1765. [DOI: 10.1111/mec.14706] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Laura Wegener Parfrey
- Department of Botany; Biodiversity Research Centre; University of British Columbia; Vancouver British Columbia Canada
- Department of Zoology; University of British Columbia; Vancouver British Columbia Canada
| | - Corrie S. Moreau
- Department of Science and Education; Field Museum of Natural History; Chicago IL USA
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Chen MY, Parfrey LW. Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co-occurring macroalgae. Mol Ecol 2018; 27:1966-1979. [PMID: 29524281 DOI: 10.1111/mec.14548] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 11/29/2022]
Abstract
Macroalgae variably promote and deter microbial growth through release of organic carbon and antimicrobial compounds into the water column. Consequently, macroalgae influence the microbial composition of the surrounding water column and biofilms on nearby surfaces. Here, we use manipulative experiments to test the hypotheses that (i) Nereocystis luetkeana and Mastocarpus sp. macroalgae alter the water column microbiota in species-specific manner, that (ii) neighbouring macroalgae alter the bacterial communities on the surface (epibiota) of actively growing Nereocystis luetkeana meristem fragments (NMFs), and that (iii) neighbours alter NMF growth rate. We also assess the impact of laboratory incubation on macroalgal epibiota by comparing each species to wild counterparts. We find strong differences between the Nereocystis and Mastocarpus epibiota that are maintained in the laboratory. Nereocystis and Mastocarpus alter water column bacterial community composition and richness in a species specific manner, but cause only small compositional shifts on NMF surfaces that do not differ by species, and do not change richness. Co-incubation with macroalgae results in significant change in abundance of fivefold more genera in the water column compared to NMF surfaces, although the direction (i.e., enrichment or reduction) of shift is generally consistent between the water and NMF surfaces. Finally, NMFs grew during the experiment, but growth did not depend on the presence or identity of neighbouring macroalgae. Thus, macroalgae exhibit a strong and species-specific influence on the water column microbiota, but a much weaker influence on the epibiota of neighbouring macroalgae. Overall, these results support the idea that macroalgae surfaces are highly selective and demonstrate that modulations of macroalgal microbiota operate within an overarching paradigm of host species specificity.
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Affiliation(s)
- Melissa Y Chen
- Botany Department and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Laura Wegener Parfrey
- Botany and Zoology Departments and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Hakai Institute, Hariot Bay, BC, Canada
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