Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building coralsPorites luteaandIsopora palifera

GigaScience, Journal Year: 2022, Volume and Issue: 12

Published: Dec. 28, 2022

Abstract At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward millimeter-thin tissue, leaving diverse skeleton microbiome underexplored. Here, we present a genome-centric view reef-building corals Porites lutea and Isopora palifera, through compendium ∼400 high-quality bacterial archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla 57 classes. Skeletal harbored array stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average 22 ± 15 genes in P. 28 23 I. palifera with eukaryotic-like motifs thought to be involved maintaining host association. We provide comprehensive insights into putative functional role key metabolic processes such as nitrogen fixation, dissimilatory assimilatory nitrate, sulfate reduction. Our study provides critical genomic resources for better understanding its functioning.

Language: Английский

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Fine‐scale mapping of physicochemical and microbial landscapes of the coral skeleton

Environmental Microbiology, Journal Year: 2023, Volume and Issue: 25(8), P. 1505 - 1521

Published: March 23, 2023

The coral skeleton harbours a diverse community of bacteria and microeukaryotes exposed to light, O2 pH gradients, but how such physicochemical gradients affect the microbiome remains unclear. In this study, we employed chemical imaging pH, hyperspectral reflectance spatially resolved taxonomic inferred functional characterization explore links between microenvironment in reef-building corals Porites lutea Paragoniastrea benhami. environment was more stable deep skeleton, diversity evenness bacterial increased with skeletal depth, suggesting that stratified along gradients. bulk low habitat, whereas varied from 6-9 depth. Physicochemical explained β-diversity communities, layers showed peaks had higher relative abundance endolithic algae, reflecting link abiotic composition. Our study physicochemical, microbial landscapes provides new insights into involvement microbes holobiont metabolism.

Language: Английский

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Coral growth anomalies, neoplasms, and tumors in the Anthropocene

Trends in Microbiology, Journal Year: 2022, Volume and Issue: 30(12), P. 1160 - 1173

Published: June 17, 2022

Language: Английский

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Assessing the coral microbiome at the scale of tissue-specific habitats within the coral meta-organism

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: Sept. 23, 2022

As sequencing techniques have advanced and become cheaper in recent years, there has been a rapid increase the number of studies conducted into role microbiome coral health, physiology, response to environmental change. However, is substantial variation methodological approaches applied. For example, DNA extraction protocols types tissues sampled from meta-organism are known influence downstream analyses amplified microbial communities subsequently interpretation diversity, stability role. Studies generally focused on whole organisms, which sampling steps homogenize microhabitats, however other targeting specific microhabitats identified sources distinct compartments coral’s landscape. Here we present comparative analysis methodologies optimized for generation data fragments two commonly studied branching genera with tissue structure. We investigate imperforate Pocillopora , where does not penetrate through calcium carbonate matrix, perforate Acropora skeleton interwoven throughout branch. Through comparing generated different using fixed isolated skeletal structure fragments, identify inherent sample types, species, protocols.

Language: Английский

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Bacterial Microbiota of Ostreobium, the Coral-Isolated Chlorophyte Ectosymbiont, at Contrasted Salinities

Microorganisms, Journal Year: 2023, Volume and Issue: 11(5), P. 1318 - 1318

Published: May 17, 2023

Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve calcium carbonate skeletons coral colonies in reefs contrasted salinities. Here, we analyzed their bacterial community's composition plasticity response to salinity. Multiple cultures Pocillopora coral-isolated strains from two distinct rbcL lineages representative IndoPacific environmental phylotypes were pre-acclimatized (>9 months) three ecologically relevant reef salinities: 32.9, 35.1, 40.2 psu. Bacterial visualized for first time at filament scale by CARD-FISH algal tissue sections, within siphons, surface or mucilage. Ostreobium-associated microbiota, characterized 16S rDNA metabarcoding cultured thalli corresponding supernatants, structured host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on lineage, shifted Rhizobiales' abundances salinity increase. A small core microbiota composed seven ASVs (~1.5% ASVs, 19-36% cumulated proportions) was persistent across salinities both genotypes, putative intracellular Amoebophilaceae Rickettsiales_AB1, as well Hyphomonadaceae also detected (Ostreobium-colonized) skeletons. This novel knowledge taxonomic diversity bacteria paves way functional interaction studies holobiont.

Language: Английский

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Characteristics of The Bleached Microbiome of The Generalist CoralPocillopora damicornisfrom Two Distinct Reef Habitats

Integrative Organismal Biology, Journal Year: 2023, Volume and Issue: 5(1)

Published: Jan. 1, 2023

Synopsis Generalist coral species may play an important role in predicting, managing, and responding to the growing reef crisis as sea surface temperatures are rising wide bleaching events becoming more common. Pocilloporids amongst most widely distributed studied of generalist corals, characterized by a broad geographic distribution, phenotypic plasticity, tolerance sub-optimal conditions for recruitment survival. Emerging research indicates that microbial communities associated with Pocilloporid corals be contributing their persistence on reefs impacted thermal stress; however, we lack detailed information shifts coral–bacterial symbiosis during across many habitats these found. Here, bacterial healthy bleached Pocillopora damicornis occurred austral summer 2020 Heron Island, southern Great Barrier Reef, 2019 Lord Howe southerly Australia. Regardless location, significant differences α β diversities, core community, inferred functional profile microbiome P. were not detected. Consistent previous reports, patterns microbiome, including no increase pathogenic taxa or evidence dysbiosis, conserved responses. We hypothesize resilience holobiont interactions aid survive Symbiodiniaceae loss contribute success Pocilloporids.

Language: Английский

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Intestinal Microbiome Richness of Coral Reef Damselfishes (Actinopterygii: Pomacentridae)

Integrative Organismal Biology, Journal Year: 2022, Volume and Issue: 4(1)

Published: Jan. 1, 2022

Fish gastro-intestinal system harbors diverse microbiomes that affect the host's digestion, nutrition, and immunity. Despite great taxonomic diversity of fish, little is understood about fish microbiome factors determine its structure composition. Damselfish are important coral reef species play pivotal roles in determining algae population structures reefs. Broadly, damselfish belong to either two trophic guilds based on whether they planktivorous or algae-farming. In this study, we used 16S rRNA gene sequencing investigate intestinal 5 algae-farming (Pomacentridae) from Great Barrier Reef. We detected Gammaproteobacteria ASVs belonging genus Actinobacillus 80% sampled individuals across 2 guilds, thus, bacteria can be considered possible core members pomacentrid microbiomes. Algae-farming had greater bacterial alpha-diversity, a more shared 35 ± 22 ASVs, whereas 7 3 ASVs. Our data also highlight differences associated with both guilds. For instance, were enriched Pasteurellaceae, whilst Vibrionaceae. Finally, show shifts community composition along intestines. classes Bacteroidia, Clostridia, Mollicutes predominant anterior regions while abundance was higher stomach. results suggest richness communities reflects host diet guild.O sistema de peixes abriga microbiomas diversos que afetam digestão, nutrição e imunidade do hospedeiro. Apesar da grande diversidade taxonômica dos peixes, entende-se pouco sobre o microbioma fatores determinam sua estrutura composição. Peixes-donzela são espécies importantes em recifes exercem papéis pivotais na determinação algas corais recifes. De forma geral, peixes-donzela pertencem à uma duas guildas tróficas dependendo se planctívoros ou algívoros. Nesse estudo, usamos sequenciamento para investigar cinco planctívoras algívoras Grande Barreira Corais. Detectamos pertencendo ao gênero indivíduos amostrados nas tróficas, logo, bactérias desse podem ser consideradas como possíveis membros essenciais pomacentrídeos. algívoros apresentaram maior alpha-diversidade bacteriana, um essencial mais diverso compartilharam Nossos dados também ilustram diferenças nos associados com ambas tróficas. Por exemplo, estavam enriquecidos enquanto planctívoros, Finalmente, demonstramos mudanças composição comunidade bacteriana associada as Clostridia foram predominantes regiões intestinais anteriores abundância foi no estômago. resultados sugerem riqueza das comunidades bacterianas refletem dieta espécie hospedeiro, bem guilda trófica.鱼类肠道中种类丰富的微生物菌群对于鱼类的消化、营养和免疫都有影响。尽管鱼类的分类多样性很高, 但我们对于鱼类体内的微生物菌群及能够影响其结构和组成的因素却知之甚少。雀鲷科鱼类是一种重要的珊瑚礁鱼类, 并且对珊瑚礁中的藻类和珊瑚种群结构起到关键性作用。概括来说, 基于食性的不同(以浮游生物为食或以藻类为食), 雀鲷科鱼类分属于两种摄食类群。在本研究中, 我们利用16S rRNA基因序列对于大堡礁的五种以浮游生物为食的雀鲷和五种以藻类为食的雀鲷分别进行了研究。在这两种类群80%的样本中, 我们都发现了属于放线杆菌属Actinobacillus的Gammaproteobacteria的扩增子序列变体。因此, 此属细菌很可能是雀鲷肠道微生物菌群的主要组成。食藻类雀鲷具有更高的细菌α多样性, 它们的核心微生物菌群的多样性更高, 共享了35 22个扩增子序列变体, 而食浮游生物类雀鲷的核心微生物菌群则只共享了7 3个扩增子序列变体。我们的数据还突出了两种营养类群肠道微生物的区别。例如, 食藻类雀鲷有更多的Pasteurellaceae, 而食浮游生物类雀鲷则有更多的Vibrionaceae。最后, 我们还展示了肠道中细菌群落的更替。在肠道前部, Clostridia和Mollicutes占据主导地位;而在胃中, Gammaproteobacteria则丰度更高。我们的结果意味着肠道菌群的丰富性反映了鱼类宿主的食性和摄食类群。.Il gastro intestinale dei pesci ospita un microbiota che influenza la digestione, nutrizione immunitario dell'ospite. Nonostante l'enorme diversità taxonomica pesci, nostra comprensione del di questi animali ed i fattori determinano struttura composizione è ancora scarsa. I damigella includono specie importanti per le barriere coralline forniscono servizi grado influenzare delle popolazioni alghe coralli. generale, appartengono due gruppi funzionali basati sul loro tipo dieta, vengono divisi consumatori plankton alghe. questo studio abbiamo sequenziato il investigare cinque consumano provenienti dalla Barriera Corallina. Abbiamo rilevato l’80% degli individui analizzati entrambi avevano appartenenti al phylum Gammaproteobatteri, così, suggeriamo batteri genere possono essere considerati membri essenziali Pomacentridi. una maggiore (alpha), essenziale più vasto condividevano mentre nostri dati evidenziano differenze nel associato con ai funzionali. Per esempio, avevo maggior numero fine, riportiamo variazioni nella comunità batteriche lungo l'intestino. alle classi erano abbondanti nell'intestino anteriore nello stomaco. resultati suggeriscono dell'intestino riflette gruppo funzionale

Language: Английский

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Environmental and geographical factors structure cauliflower coral's algal symbioses across the Indo‐Pacific

Journal of Biogeography, Journal Year: 2023, Volume and Issue: 50(4), P. 669 - 684

Published: Jan. 9, 2023

Abstract Aim The symbioses between corals and endosymbiotic dinoflagellates have been described as a flexible relationship whose dynamics could serve source of resilience for coral reef ecosystems. However, the factors that drive establishment maintenance this co‐evolutionary remain unclear. We examined environmental geographical structuring dinoflagellate communities in wide‐ranging Indo‐Pacific to begin address gap. Location Djibouti, Oman, Taiwan French Polynesia. Taxon Cauliflower ( Pocillopora spp.), (family Symbiodiniaceae). Methods analysed publicly available amplicon sequence data from nuclear ribosomal DNA internal transcribed spacer 2, originating spp. also compiled such sea surface temperature (SST) time since last local mass bleaching event. ran generalized least squares models, PERMANOVAs indicator species analyses, understand how thermal regimes distances impacted spp.'s Symbiodiniaceae community composition. Results Sea was most important factor driving differences, with largest effect size statistically significant factors. When focusing on individual genera, SST likewise factor. Our analyses revealed specimens had recently bleached were characterized by roughly equal proportions Cladocopium Durusdinium spp., while not similar proportion those bleached, but showed reduction deficiency made up presence Symbiodinium Main Conclusions provide further support hypothesis coral's facilitate host stress. work is direct conversation larger body biogeography literature highlights can impact contemporary population structure, even marine taxa widespread distributions.

Language: Английский

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Reciprocal transplant experiment reveals multiple factors influencing changes in coral microbial communities across climate zones

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 907, P. 167929 - 167929

Published: Oct. 18, 2023

Previous studies have demonstrated the influence of external factors (environmental and coral host factors) on community structure coral-associated bacteria. However, internal factors, e.g. interaction within bacterial or bacteria itself, often been overlooked in microbiome. Hence, we performed a reciprocal transplant corals between two different climate zones to examine resultant alterations communities. The findings highlight significance environmental selection, highly resilient shaping microbial composition. results support that species consistently harbor specific predominant groups influenced by while locations display unique taxa due variations. transplantation into new environments leads gradual shift community, from initially resembling native location eventually transplanted location, emphasizing crucial role composition for survival under changing ambient conditions. Furthermore, persisted throughout experiment their adaptability changes, suggesting presence robust adaptation resistance mechanisms Genetic adaptations prevalent group, Endozoicomonas, were also observed, variations resilience capabilities among phylotypes. This study highlights need conduct further investigations themselves, as they may hold some key insights understanding dynamics These data which could benefit response environment.

Language: Английский

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Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera

Research Square (Research Square), Journal Year: 2022, Volume and Issue: unknown

Published: July 26, 2022

Abstract At present our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed towards millimetre-thin tissue, leaving diverse skeleton microbiome underexplored. Here, we a genome-centric view reef-building corals' Porites lutea and Isopora palifera , through compendium ~ 400 high-quality bacterial archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla 57 microbial classes. Skeletal harboured array stress response genes, including dimethylsulfoniopropionate synthesis ( dsy B) metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average 22 ± 15 genes in P. 28 23 I. with eukaryotic-like motifs thought to be involved maintaining host association. We provide comprehensive insights into putative functional role key metabolic processes such as nitrogen fixation, dissimilatory assimilatory nitrate, sulphate reduction. Our study provides critical genomic resources for better understanding its functioning.

Language: Английский

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