Coral microbiome dynamics, functions and design in a changing world

Oppen, Madeleine J. H. van; Blackall, Linda L.

doi:10.1038/s41579-019-0223-4

Cited by 287 publications

(253 citation statements)

References 116 publications

(136 reference statements)

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“…Bacterial communities of the adult parents A. tenuis and A. loripes differed from those of A. sarmentosa and A. florida . Species‐specific bacterial communities are commonly observed in adult corals (van Oppen & Blackall, ). However, Littman, Willis, Pfeffer, et al () found closely related Acropora species from the same reef shared similar bacterial communities, yet these communities were distinct from conspecifics from a different reef.…”

Section: Discussionmentioning

confidence: 99%

“…Multiple Symbiodiniaceae and bacterial taxa can co‐exist within a coral host, with up to 10 2 –10 3 bacterial strains and ~15 Symbiodiniaceae operational taxonomic units (OTUs based on 97% ITS2 sequence similarity cut‐off) found within a coral host (Blackall et al, ). Temporal changes and spatial differences in bacterial communities associated with adult coral colonies are thought to be driven by a variety of factors, including temperature, pH/ p CO 2 , coral health status, light intensity, water depth and nutrient level (Morrow, Muller, & Lesser, ; van Oppen & Blackall, ). Conversely, bacterial communities of conspecific corals may remain stable despite seasonal environmental variations (Littman, Willis, Pfeffer, & Bourne, ) or exposure to different pH conditions (Meron et al, ; Webster et al, ; Zhou et al, ).…”

Section: Introductionmentioning

confidence: 99%

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The roles of age, parentage and environment on bacterial and algal endosymbiont communities in Acropora corals

et al. 2019

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The bacterial and microalgal endosymbiont (Symbiodiniaceae spp.) communities associated with corals have important roles in their health and resilience, yet little is known about the factors driving their succession during early coral life stages. Using 16S rRNA gene and ITS2 metabarcoding, we compared these communities in four Acropora coral species and their hybrids obtained from two laboratory crosses (Acropora tenuis × Acropora loripes and Acropora sarmentosa × Acropora florida) across the parental, recruit (7 months old) and juvenile (2 years old) life stages. We tested whether microbiomes differed between (a) life stages, (b) hybrids and purebreds, and (c) treatment conditions (ambient/elevated temperature and pCO2). Microbial communities of early life stage corals were highly diverse, lacked host specificity and were primarily determined by treatment conditions. Over time, a winnowing process occurred, and distinct microbial communities developed between the two species pair crosses by 2 years of age, irrespective of hybrid or purebred status. These findings suggest that the microbial communities of corals have a period of flexibility prior to adulthood, which can be valuable to future research aimed at the manipulation of coral microbial communities.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The roles of age, parentage and environment on bacterial and algal endosymbiont communities in Acropora corals

et al. 2019

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“…Coral microbiomes gained a lot of interest over the last few years in regard to their influence on host fitness and survival in the face of ongoing environmental changes [e.g., ocean warming, reviewed by van Oppen and Blackall (2019)]. Coral microbiomes consist of three essential elements (1) a conserved core microbiome, (2) regional bacteria specific to the geographic area, and (3) a set of environmentally variable bacteria (Hernandez-Agreda et al, 2016;Kellogg et al, 2017;van de Water et al, 2017). The coral microbial community changes across anatomy and therefore the coral tissue sampled affects the likelihood of detecting a spatially structured microbiome (Pollock et al, 2018).…”

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 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). For example, coral dominant dinoflagellate Symbiodinium can fix carbon dioxide and provide corals with organic compounds (5).…”

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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Coral microbiome dynamics, functions and design in a changing world

Cited by 287 publications

References 116 publications

The roles of age, parentage and environment on bacterial and algal endosymbiont communities in Acropora corals

The roles of age, parentage and environment on bacterial and algal endosymbiont communities in Acropora corals

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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