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Pozas-Schacre C, Bischoff H, Clerissi C, Nugues MM. Negative parental and offspring environmental effects of macroalgae on coral recruitment are linked with alterations in the coral larval microbiome. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240187. [PMID: 39050726 PMCID: PMC11267239 DOI: 10.1098/rsos.240187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 07/27/2024]
Abstract
The persistence of reef-building corals is threatened by macroalgal competitors leading to a major demographic bottleneck in coral recruitment. Whether parental effects exist under coral-algal competition and whether they influence offspring performance via microbiome alterations represent major gaps in our understanding of the mechanisms by which macroalgae may hinder coral recovery. We investigated the diversity, variability and composition of the microbiome of adults and larvae of the coral Pocillopora acuta and surrounding benthic substrate on algal-removed and algal-dominated bommies. We then assessed the relative influence of parental and offspring environmental effects on coral recruitment processes by reciprocally exposing coral larvae from two parental origins (algal-removed and algal-dominated bommies) to algal-removed and algal-dominated environmental conditions. Dense macroalgal assemblages impacted the microbiome composition of coral larvae. Larvae produced by parents from algal-dominated bommies were depleted in putative beneficial bacteria and enriched in opportunistic taxa. These larvae had a significantly lower survival compared to larvae from algal-removed bommies regardless of environmental conditions. In contrast, algal-induced parental and offspring environmental effects interacted to reduce the survival of coral recruits. Together our results demonstrate negative algal-induced parental and offspring environmental effects on coral recruitment that could be mediated by alterations in the offspring microbiome.
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Affiliation(s)
- Chloé Pozas-Schacre
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan, France
| | - Hugo Bischoff
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE BP 1013, 98729 Papetoai, Mo'orea, French Polynesia
| | - Camille Clerissi
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan, France
- Laboratoire d'Excellence CORAIL, Perpignan, France
| | - Maggy M. Nugues
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, 66860 Perpignan, France
- Laboratoire d'Excellence CORAIL, Perpignan, France
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Cyphert EL, Nand S, Franco G, Hajkowski M, Soto L, Lee DM, Ferner M, Zabin C, Blumenthal J, Deck A, Boyer K, Burrus K, Hernandez CJ, Anand A. Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster reefs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594453. [PMID: 38798377 PMCID: PMC11118425 DOI: 10.1101/2024.05.15.594453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Oyster reefs are invaluable ecosystems that provide a wide array of critical ecosystem services, including water filtration, coastal protection, and habitat provision for various marine species. However, these essential habitats face escalating threats from climate change and anthropogenic stressors. To combat these challenges, numerous oyster restoration initiatives have been undertaken, representing a global effort to preserve and restore these vital ecosystems. A significant, yet poorly understood, component of oyster reefs is the microbial communities. These communities account for a substantial proportion of marine reefs and are pivotal in driving key biogeochemical processes. Particularly, the environmental microbiome plays a crucial role in supporting the health and resilience of oyster populations. In our study, we sought to shed light on the microbiome within oyster reef ecosystems by characterizing the abundance, and diversity of microorganisms in the soil, biofilm, and oysters in 4 sites using a combinatorial approach to identify differentially abundant microbes by sample type and by sampling location. Our investigation revealed distinct microbial taxa in oysters, sediment and biofilm. The maximum Shannon Index indicated a slightly increased diversity in Heron's Head (5.47), followed by Brickyard park (5.35), Dunphy Park (5.17) and Point Pinole (4.85). This is likely to be driven by significantly higher oyster mortality observed at Point Pinole during routine monitoring and restoration efforts. Interestingly Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with the biofilm. Yet we have limited understanding of their beneficial and/or detrimental implications to oyster growth and survival. By unraveling the intricate relationships in microbial composition across an oyster reef, our study contributes to advancing the knowledge needed to support effective oyster reef conservation and restoration efforts.
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Affiliation(s)
| | | | | | | | | | | | - Matt Ferner
- San Francisco Bay National Estuarine Research Reserve
| | | | | | - Anna Deck
- San Francisco Bay National Estuarine Research Reserve
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Sun Y, Wu M, Xie S, Zang J, Wang X, Yang Y, Li C, Wang J. Homogenization of bacterial plastisphere community in soil: a continental-scale microcosm study. ISME COMMUNICATIONS 2024; 4:ycad012. [PMID: 38328447 PMCID: PMC10848224 DOI: 10.1093/ismeco/ycad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 02/09/2024]
Abstract
Microplastics alter niches of soil microbiota by providing trillions of artificial microhabitats, termed the "plastisphere." Because of the ever-increasing accumulation of microplastics in ecosystems, it is urgent to understand the ecology of microbes associated with the plastisphere. Here, we present a continental-scale study of the bacterial plastisphere on polyethylene microplastics compared with adjacent soil communities across 99 sites collected from across China through microcosm experiments. In comparison with the soil bacterial communities, we found that plastispheres had a greater proportion of Actinomycetota and Bacillota, but lower proportions of Pseudomonadota, Acidobacteriota, Gemmatimonadota, and Bacteroidota. The spatial dispersion and the dissimilarity among plastisphere communities were less variable than those among the soil bacterial communities, suggesting highly homogenized bacterial communities on microplastics. The relative importance of homogeneous selection in plastispheres was greater than that in soil samples, possibly because of the more uniform properties of polyethylene microplastics compared with the surrounding soil. Importantly, we found that the degree to which plastisphere and soil bacterial communities differed was negatively correlated with the soil pH and carbon content and positively related to the mean annual temperature of sampling sites. Our work provides a more comprehensive continental-scale perspective on the microbial communities that form in the plastisphere and highlights the potential impacts of microplastics on the maintenance of microbial biodiversity and ecosystem functioning.
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Affiliation(s)
- Yuanze Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, Department of Environmental Science and Engineering, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Mochen Wu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, Department of Environmental Science and Engineering, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Siyuan Xie
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, Department of Environmental Science and Engineering, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Jingxi Zang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, Department of Environmental Science and Engineering, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xiang Wang
- Key Laboratory of Arable Land Conservation (North China), Department of Soil and Water Science, College of Land Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China
| | - Changchao Li
- State Key Laboratory of Marine Pollution, Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Yuk Choi Road, Kowloon, Hong Kong 999077, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, Department of Environmental Science and Engineering, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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Cleary DFR, de Voogd NJ, Stuij TM, Swierts T, Oliveira V, Polónia ARM, Louvado A, Gomes NCM, Coelho FJRC. A Study of Sponge Symbionts from Different Light Habitats. MICROBIAL ECOLOGY 2023; 86:2819-2837. [PMID: 37597041 PMCID: PMC10640470 DOI: 10.1007/s00248-023-02267-x] [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: 01/29/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023]
Abstract
The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.
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Affiliation(s)
- D F R Cleary
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands.
| | - T M Stuij
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - T Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - V Oliveira
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Polónia
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A Louvado
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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Elsherbini J, Corzett C, Ravaglioli C, Tamburello L, Polz M, Bulleri F. Epilithic Bacterial Assemblages on Subtidal Rocky Reefs: Variation Among Alternative Habitats at Ambient and Enhanced Nutrient Levels. MICROBIAL ECOLOGY 2023; 86:1552-1564. [PMID: 36790500 PMCID: PMC10497455 DOI: 10.1007/s00248-023-02174-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Temperate rocky reefs often support mosaics of alternative habitats such as macroalgal forests, algal turfs and sea urchin barrens. Although the composition of epilithic microbial biofilms (EMBs) is recognized as a major determinant of macroalgal recruitment, their role in regulating the stability of alternative habitats on temperate rocky reefs remains unexplored. On shallow rocky reefs of the Island of Capraia (NW Mediterranean), we compared EMB structure among canopy stands formed by the fucoid Ericaria brachycarpa, algal turfs, and urchin barrens under ambient versus experimentally enhanced nutrient levels. The three habitats shared a core microbial community consisting of 21.6 and 25.3% of total ASVs under ambient and enhanced nutrient conditions, respectively. Although Gammaproteobacteria, Alphaproteobacteria and Flavobacteriia were the most abundant classes across habitats, multivariate analyses at the ASV level showed marked differences in EMB composition among habitats. Enhancing nutrient level had no significant effect on EMBs, although it increased their similarity between macroalgal canopy and turf habitats. At both ambient and enriched nutrient levels, ASVs mostly belonging to Proteobacteria and Bacteroidetes were more abundant in EMBs from macroalgal canopies than barrens. In contrast, ASVs belonging to the phylum of Proteobacteria and, in particular, to the families of Rhodobacteraceae and Flavobacteriaceae at ambient nutrient levels and of Rhodobacteraceae and Bacteriovoracaceae at enhanced nutrient levels were more abundant in turf than canopy habitats. Our results show that primary surfaces from alternative habitats that form mosaics on shallow rocky reefs in oligotrophic areas host distinct microbial communities that are, to some extent, resistant to moderate nutrient enhancement. Understanding the role of EMBs in generating reinforcing feedback under different nutrient loading regimes appears crucial to advance our understanding of the mechanisms underpinning the stability of habitats alternative to macroalgal forests as well as their role in regulating reverse shifts.
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Affiliation(s)
- Joseph Elsherbini
- MIT Microbiology Graduate Program, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02138, USA
| | - Christopher Corzett
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Chiara Ravaglioli
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy
| | - Laura Tamburello
- Department of Integrative Marine Ecology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, 80077, Punta San Pietro, Ischia, (Naples), Italy
| | - Martin Polz
- MIT Microbiology Graduate Program, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02138, USA
- Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1130, Vienna, Austria
| | - Fabio Bulleri
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy.
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Nelson CE, Wegley Kelly L, Haas AF. Microbial Interactions with Dissolved Organic Matter Are Central to Coral Reef Ecosystem Function and Resilience. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:431-460. [PMID: 36100218 DOI: 10.1146/annurev-marine-042121-080917] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To thrive in nutrient-poor waters, coral reefs must retain and recycle materials efficiently. This review centers microbial processes in facilitating the persistence and stability of coral reefs, specifically the role of these processes in transforming and recycling the dissolved organic matter (DOM) that acts as an invisible currency in reef production, nutrient exchange, and organismal interactions. The defining characteristics of coral reefs, including high productivity, balanced metabolism, high biodiversity, nutrient retention, and structural complexity, are inextricably linked to microbial processing of DOM. The composition of microbes and DOM in reefs is summarized, and the spatial and temporal dynamics of biogeochemical processes carried out by microorganisms in diverse reef habitats are explored in a variety of key reef processes, including decomposition, accretion, trophictransfer, and macronutrient recycling. Finally, we examine how widespread habitat degradation of reefs is altering these important microbe-DOM interactions, creating feedbacks that reduce reef resilience to global change.
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Affiliation(s)
- Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, and Sea Grant College Program, School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA;
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA;
| | - Andreas F Haas
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands;
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