Structure and stability of the coral microbiome in space and time

Dunphy, Courtney M.; Gouhier, Tarik C.; Chu, Nathaniel D.; Vollmer, Steven V.

doi:10.1038/s41598-019-43268-6

Cited by 84 publications

(78 citation statements)

References 71 publications

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“…The host, environment, and time can influence the microbiome composition [26]. However, in general, the host is the most significant factor influencing the microbial community.…”

Section: Discussionmentioning

confidence: 99%

“…Purported to enhance the hosts' fitness and functioning [17], the coral microbiome is the central part of a widespread hypothesis of co-evolutive processes known as holobiont [18,19]. Taking into account factors such as location, environmental changes, depth, bleaching, and diseases, the microbiome of more than 30 coral species has already been studied [20][21][22][23][24][25][26]. Focusing on Bacteria, it is suggested that Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Cyanobacteria are predominant [20] and that their diversity and abundance are linked to biotic and abiotic factors such as seasonality, anthropic impacts, temperature changes, diseases, etc.…”

Section: Introductionmentioning

confidence: 99%

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Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis

et al. 2020

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Background: Commonly known as sun-coral, Tubastraea tagusensis is an azooxanthellate scleractinian coral that successfully invaded the Southwestern Atlantic causing significant seascape changes. Today it is reported to over 3500 km along the Brazilian coast, with several rocky shores displaying high substrate coverage. Apart from its singular invasiveness capacity, the documentation and, therefore, understanding of the role of symbiotic microorganisms in the sun-coral invasion is still scarce. However, in general, the broad and constant relationship between corals and microorganisms led to the development of co-evolution hypotheses. As such, it has been shown that the microbial community responds to environmental factors, adjustment of the holobiont, adapting its microbiome, and improving the hosts' fitness in a short space of time. Here we describe the microbial community (i.e. Bacteria) associated with suncoral larvae and adult colonies from a locality displaying a high invasion development. Results: The usage of high throughput sequencing indicates a great diversity of Bacteria associated with T. tagusensis, with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, and Firmicutes corresponding to the majority of the microbiome in all samples. However, T. tagusensis' microbial core consists of only eight genera for colonies, and, within them, three are also present in the sequenced larvae. Overall, the microbiome from colonies sampled at different depths did not show significant differences. The microbiome of the larvae suggests a partial vertical transfer of the microbial core in this species. Conclusion: Although diverse, the microbiome core of adult Tubastraea tagusensis is composed of only eight genera, of which three are transferred from the mother colony to their larvae. The remaining bacteria genera are acquired from the seawater, indicating that they might play a role in the host fitness and, therefore, facilitate the sun-coral invasion in the Southwestern Atlantic.

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“…The host, environment, and time can influence the microbiome composition [26]. However, in general, the host is the most significant factor influencing the microbial community.…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis

et al. 2020

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“…The mucus was strongly influenced by environmental factors, while the skeleton microbiome was the most diverse and most likely to show phylogenetic structure, reflecting the influence of host traits. The influence of phylosymbiosis, defined as "microbial community relationships that recapitulate the phylogeny of their host" (Brucker and Bordenstein, 2013), was higher than regional dispersal or environmental heterogeneity and differed across anatomy, being stronger in the skeleton than in tissue or mucus (Pollock et al, 2018;Dunphy et al, 2019). Regarding the prevalence of spatial structure, Pollock et al (2018) showed that the external mucus microbiome is 1.15-fold more influenced by collection site than coral tissue and 1.28-fold more than skeleton communities (Pollock et al, 2018).…”

Section: Coralsmentioning

confidence: 99%

“…The spatial structure of coral microbiomes could be influenced by regional processes including dispersal limitation and spatiotemporal environmental heterogeneity even at small spatial distances (Dunphy et al, 2019). Nevertheless, these spatial differences are limited in comparison to differences between coral genera or species (Dunphy et al, 2019).…”

Section: Coralsmentioning

confidence: 99%

Spatial Structure of Marine Host-Associated Microbiomes: Effect of Taxonomy, Species Traits, and Study Design

Schellenberg

Clarke

2020

Front. Mar. Sci.

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Marine host-associated microbiomes can strongly influence their host's function and are shaped by selection, dispersal, diversification, and drift. These processes can lead to spatially structured microbiomes, with potential implications for host fitness in different locations. We review the literature on marine host-associated microbiomes to identify if spatially structured microbiomes are more prevalent in certain taxonomic groups, are linked to species traits, or sampling design and methodology. The 28 papers analyzed represented 38 host species, with spatial structure detected in 75% of species, increasing to 83% when restricted to studies using high-throughput DNA sequencing. Spatial structure was detected in all coral and marine mammal microbiomes, but was less common in fish (69%) and sponges (46%). Mobile species and external tissues were more likely to show spatially structured microbiomes than sessile species and internal tissues. We found no relationship between spatial structuring and maximum distance between sampling sites, with studies on large (>1000 km) and small spatial scales (<100 km) almost as likely to show spatial structure (87% vs. 79%). Our results support using high-throughput sequencing for studying marine host-associated microbiomes due to better taxonomic resolution compared to other methods. Given the observed generality of spatially structured microbiomes, future studies should test whether microbiome variation between locations affects host fitness. Researchers should include sufficient environmental microbiome sampling and host data to distinguish host and environmental effects. This will help resolve the relative importance of selection, dispersal, diversification and drift in shaping marine host-associated microbiomes.

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“…Microbial symbionts in reef-building corals, which support a variety of marine life, reside in the mucus, tissue, and skeleton of diverse corals, influencing health of its host coral (1, 2). Microbial symbionts comprise bacteria, archaea, algae, fungi, and viruses, and their composition is influenced by their host corals’ genetic factors and dynamic environmental conditions (3). They can help corals prevent or mitigate diseases and benefit corals by involving them in carbon, nitrogen, and sulfur cycles (4).…”

Section: Introductionmentioning

confidence: 99%

A genomic view of coral-associatedProsthecochlorisand a companion sulfate-reducing bacterium

Chen

Yang

Tandon

et al. 2019

Preprint

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19Endolithic microbial symbionts in the coral skeleton may play a pivotal role in 20 maintaining coral health. However, compared to aerobic microorganisms, research on the 21 roles of endolithic anaerobic microorganisms and microbe-microbe interactions in the coral 22 skeleton are still in their infancy. In our previous study, we showed that a group of coral-23 associated Prosthecochloris (CAP), a genus of anaerobic green sulfur bacteria, was 24 dominant in the skeleton of the coral Isopora palifera. Though CAP is diverse, the 16S 25 rRNA phylogeny presents it as a distinct clade separate from other free-living 26Prosthecochloris. In this study, we build on previous research and further characterize the 27 genomic and metabolic traits of CAP by recovering two new near-complete CAP 28 genomes-Candidatus Prosthecochloris isoporaea and Candidatus Prosthecochloris sp. 29 N1-from coral Isopora palifera endolithic cultures. Genomic analysis revealed that these 30 two CAP genomes have high genomic similarities compared with other Prosthecochloris 31 and harbor several CAP-unique genes. Interestingly, different CAP species harbor various 32 pigment synthesis and sulfur metabolism genes, indicating that individual CAPs can adapt 33 to a diversity of coral microenvironments. A novel near-complete SRB genome-34Candidatus Halodesulfovibrio lyudaonia-was also recovered from the same culture. The 35 fact that CAP and various sulfate-reducing bacteria (SRB) co-exist in coral endolithic 36 cultures and coral skeleton highlights the importance of SRB in the coral endolithic 37 community. Based on functional genomic analysis of Ca. P. sp. N1 and Ca. H. lyudaonia, 38 we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton. 39 40 Importance 41Little is known about the ecological roles of endolithic microbes in the coral skeleton; 42 one potential role is as a nutrient source for their coral hosts. Here, we identified a close 43 ecological relationship between CAP and SRB. Recovering novel near-complete CAP and 44 SRB genomes from endolithic cultures in this study enabled us to understand the genomic 45 and metabolic features of anaerobic endolithic bacteria in coral skeletons. These results 46 demonstrate that CAP members with similar functions in carbon, sulfur, and nitrogen 47 metabolisms harbor different light-harvesting components, suggesting that CAP in the 48 skeleton adapts to niches with different light intensities. Our study highlights the potential 49 ecological roles of CAP and SRB in coral skeletons and paves the way for future 50 investigations into how coral endolithic communities will respond to environmental 51 changes. 52 53 54 55

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Structure and stability of the coral microbiome in space and time

Cited by 84 publications

References 71 publications

Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis

Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis

Spatial Structure of Marine Host-Associated Microbiomes: Effect of Taxonomy, Species Traits, and Study Design

A genomic view of coral-associatedProsthecochlorisand a companion sulfate-reducing bacterium

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