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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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Fountain-Jones NM, Giraud T, Zinger L, Bik H, Creer S, Videvall E. Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions. Mol Ecol 2024; 33:e17223. [PMID: 38014746 DOI: 10.1111/mec.17223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.
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Affiliation(s)
| | - Tatiana Giraud
- Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, Université Paris-Saclay, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, CNRS, Institut de Recherche pour le Développement (IRD), Université Toulouse 3 Paul Sabatier, Toulouse, France
| | - Holly Bik
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Simon Creer
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Elin Videvall
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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3
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Wei N, Tan J. Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure. MICROBIAL ECOLOGY 2023; 86:2858-2868. [PMID: 37610498 DOI: 10.1007/s00248-023-02288-6] [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: 05/24/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
To understand how microbiota influence plant populations in nature, it is important to examine the biogeographic distribution of plant-associated microbiomes and the underlying mechanisms. However, we currently lack a fundamental understanding of the biogeography of plant microbiomes across populations and the environmental and host genetic factors that shape their distribution. Leveraging the broad distribution and extensive genetic variation in duckweeds (the Lemna species complex), we identified key factors that governed plant microbiome diversity and compositional variation geographically. In line with the microbial biogeography of free-living microbiomes, we observed higher bacterial richness in temperate regions relative to lower latitudes in duckweed microbiomes (with 10% higher in temperate populations). Our analyses revealed that higher temperature and sodium concentration in aquatic environments showed a negative impact on duckweed bacterial richness, whereas temperature, precipitation, pH, and concentrations of phosphorus and calcium, along with duckweed genetic variation, influenced the biogeographic variation of duckweed bacterial community composition. Analyses of plant microbiome assembly processes further revealed that niche-based selection played an important role (26%) in driving the biogeographic variation of duckweed bacterial communities, alongside the contributions of dispersal limitation (33%) and drift (39%). These findings add significantly to our understanding of host-associated microbial biogeography and provide important insights for predicting plant microbiome vulnerability and resilience under changing climates and intensifying anthropogenic activities.
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Affiliation(s)
- Na Wei
- The Holden Arboretum, Kirtland, OH, 44094, USA.
| | - Jiaqi Tan
- Department of Biological Sciences, Louisianan State University, Baton Rouge, LA, 70803, USA.
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4
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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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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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6
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Vadillo Gonzalez S, Vranken S, Coleman MA, Wernberg T, Steinberg PD, Marzinelli EM. Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata. Mol Ecol 2023; 32:4584-4598. [PMID: 37332135 DOI: 10.1111/mec.17056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/21/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.
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Affiliation(s)
- Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
| | - Sofie Vranken
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
| | - Melinda A Coleman
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- New South Wales Fisheries, Department of Primary Industries, National Marine Science Centre, Coffs Harbour, New South Wales, Australia
| | - Thomas Wernberg
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- Institute of Marine Research, Floedevigen Research Station, His, Norway
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
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7
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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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8
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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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Li H, Li JJ, Gao TH, Bi YX, Liu ZY. The Influence of Host Specificity and Temperature on Bacterial Communities Associated with Sargassum (Phaeophyceae) Species. JOURNAL OF PHYCOLOGY 2022; 58:815-828. [PMID: 36308470 DOI: 10.1111/jpy.13293] [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: 05/22/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Host-related microbiota are critically important for the adaptation/acclimation of hosts to changing environments, but how environmental factors and host characteristics shape the microbial communities remains largely unknown. We investigated the effects of temperature on habitat-forming macroalgae and their associated bacterial communities. Three Sargassum species (S. horneri, S. fusiforme, and S. thunbergii) and seawater samples were sampled in Gouqi Island, China, and these macroalgal samples were incubated at different temperatures (10, 20, and 27°C) for 7 d. Bacterial communities were identified from the 16S rRNA gene V3-V4 regions. The algae-associated bacterial communities of the field samples were significantly different from seawater, implying host specificity. During laboratory incubation, decreased physiological status (photosynthetic rate and oxidative stress response) was detected for all the species at 10°C, especially with regard to S. horneri and S. fusiforme. For each host, associated bacterial communities at 20 and 27°C clustered closely, and these were separated from samples at 10°C based on constrained PCoA analyses. Permutational multivariate analysis of variance revealed that algae-associated bacterial communities were more affected by host species (23.3%) than by temperature (2.48%) during laboratory incubation. The changes in bacterial community composition may be influenced by algae metabolites, which should be tested in a future study. These results further contribute to our understanding of algal microbiome changes in response to environmental changes.
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Affiliation(s)
- Huan Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing, 210024, China
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Jing-Jing Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing, 210024, China
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Tian-Heng Gao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, Hohai University, Nanjing, 210024, China
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Yuan-Xin Bi
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Marine Fisheries Research Institute of Zhejiang Province, Zhoushan, 316021, China
| | - Zheng-Yi Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, 264003, China
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10
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Xu N, Wang W, Xu K, Xu Y, Ji D, Chen C, Xie C. Cultivation of different seaweed species and seasonal changes cause divergence of the microbial community in coastal seawaters. Front Microbiol 2022; 13:988743. [PMID: 36160253 PMCID: PMC9490310 DOI: 10.3389/fmicb.2022.988743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Although the effects of certain species of seaweed on the microbial community structure have long been a research focus in marine ecology, the response of the microbial community to seasons and different seaweed species is poorly understood. In the present study, a total of 39 seawater samples were collected during 3 months from three zones: Neoporphyra haitanensis cultivation zones (P), Gracilaria lemaneiformis-Saccharina japonica mixed cultivation zones (G), and control zones (C). These samples were then analyzed using 18S and 16S rRNA gene sequencing to ascertain the fungal and bacterial communities, respectively, along with the determination of environmental factors. Our results showed that increased dissolved oxygen (DO), decreased inorganic nutrients, and released dissolved organic matter (DOM) in seaweed cultivation zone predominantly altered the variability of eukaryotic and prokaryotic microbial communities. Certain microbial groups such as Aurantivirga, Pseudomonas, and Woeseia were stimulated and enriched in response to seaweed cultivation, and the enriched microorganisms varied across seaweed cultivation zones due to differences in the composition of released DOM. In addition, seasonal changes in salinity and temperature were strongly correlated with microbial community composition and structure. Our study provides new insights into the interactions between seaweed and microbial communities.
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Affiliation(s)
- Ningning Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Wenlei Wang
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Kai Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Changsheng Chen
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
- *Correspondence: Chaotian Xie,
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Wood G, Steinberg PD, Campbell AH, Vergés A, Coleman MA, Marzinelli EM. Host genetics, phenotype and geography structure the microbiome of a foundational seaweed. Mol Ecol 2022; 31:2189-2206. [PMID: 35104026 PMCID: PMC9540321 DOI: 10.1111/mec.16378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/18/2022] [Indexed: 12/01/2022]
Abstract
Interactions between hosts and their microbiota are vital to the functioning and resilience of macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives host-microbiota interactions is essential for informing ecosystem restoration and conservation. We investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We quantified 16 morphological and functional phenotypic traits, including host genetics (using 354 single nucleotide polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1,300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e., present on all Phyllospora individuals sampled) exhibited slightly higher associations with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defence, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of how "holobionts" (hosts plus their microbiota) are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.
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Affiliation(s)
- Georgina Wood
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Peter D. Steinberg
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
| | - Alexandra H. Campbell
- USC Seaweed Research GroupUniversity of the Sunshine CoastSunshine CoastQueenslandAustralia
| | - Adriana Vergés
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Melinda A. Coleman
- Department of Primary IndustriesNational Marine Science CentreCoffs HarbourNew South WalesAustralia
| | - Ezequiel M. Marzinelli
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
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