Summary
Coral‐associated microorganisms are thought to play a fundamental role in the health and ecology of corals, but understanding of specific coral–microbial interactions are lacking. In order to ...create a framework to examine coral–microbial specificity, we integrated and phylogenetically compared 21,100 SSU rRNA gene Sanger‐produced sequences from bacteria and archaea associated with corals from previous studies, and accompanying host, location and publication metadata, to produce the Coral Microbiome Database. From this database, we identified 39 described and candidate phyla of Bacteria and two Archaea phyla associated with corals, demonstrating that corals are one of the most phylogenetically diverse animal microbiomes. Secondly, this new phylogenetic resource shows that certain microorganisms are indeed specific to corals, including evolutionary distinct hosts. Specifically, we identified 2–37 putative monophyletic, coral‐specific sequence clusters within bacterial genera associated with the greatest number of coral species (Vibrio, Endozoicomonas and Ruegeria) as well as functionally relevant microbial taxa (“Candidatus Amoebophilus”, “Candidatus Nitrosopumilus” and under recognized cyanobacteria). This phylogenetic resource provides a framework for more targeted studies of corals and their specific microbial associates, which is timely given the escalated need to understand the role of the coral microbiome and its adaptability to changing ocean and reef conditions.
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BFBNIB, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. ...Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Summary
Coralline algae are a crucial component of reef systems, stabilising reef substrate, providing habitat and contributing to accretion. Coralline algae and their surface microbial biofilms are ...also important as settlement cues for marine invertebrates, yet few studies address the impact of future environmental conditions on interactions between coralline algae, reef microbes and settlement by larvae of marine invertebrates. We exposed the temperate coralline algal species Amphiroa gracilis to warming and/or acidification scenarios for 21 days. Algae became bleached but photosystem II function was not measurably impacted. Settlement by larvae of the sea urchin Heliocidaris erythrogramma was reduced and the structure of the prokaryotic community associated with A. gracilis was altered. Coralline algae in ambient conditions were dominated by Alphaproteobacteria from the Rhodobacteraceae including Loktonella; those under warming were dominated by Bacteroidetes and Verrucomicrobia; acidification resulted in less Loktonella and more Planctomycetes and a combination of warming and acidification caused increases in Bacteroidetes, Verrucomicrobia and the Alphaproteobacteria family Hyphomonadaceae. These experiments indicate that predicted future environmental change may reduce the ability of some temperate reef coralline algae and associated reef microbes to facilitate settlement of invertebrate larvae as well as having a direct impact to algae via bleaching.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the ...co-occurrence of multiple partners within the coral ‘holobiont’ and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus
Symbiodinium
and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and
Symbiodinium
with 13 coral genera across six water basins. The majority of the bacteria-
Symbiodinium
co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and
Symbiodinium
that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.
In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a ...subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
SAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world's oceans, where they play a major role in the ocean carbon cycle. Correlations between the ...phylogenetic branching order and spatiotemporal patterns in cell distributions from planktonic ocean environments indicate that SAR11 has evolved into perhaps a dozen or more specialized ecotypes that span evolutionary distances equivalent to a bacterial order. We isolated and sequenced genomes from diverse SAR11 cultures that represent three major lineages and encompass the full breadth of the clade. The new data expand observations about genome evolution and gene content that previously had been restricted to the SAR11 Ia subclade, providing a much broader perspective on the clade's origins, evolution, and ecology. We found small genomes throughout the clade and a very high proportion of core genome genes (48 to 56%), indicating that small genome size is probably an ancestral characteristic. In their level of core genome conservation, the members of SAR11 are outliers, the most conserved free-living bacteria known. Shared features of the clade include low GC content, high gene synteny, a large hypervariable region bounded by rRNA genes, and low numbers of paralogs. Variation among the genomes included genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important to niche partitioning and ecotype divergence within the clade. These data provide support for the conclusion that streamlining selection for efficient cell replication in the planktonic habitat has occurred throughout the evolution and diversification of this clade. IMPORTANCE The SAR11 clade is the most abundant group of marine microorganisms worldwide, making them key players in the global carbon cycle. Growing knowledge about their biochemistry and metabolism is leading to a more mechanistic understanding of organic carbon oxidation and sequestration in the oceans. The discovery of small genomes in SAR11 provided crucial support for the theory that streamlining selection can drive genome reduction in low-nutrient environments. Study of isolates in culture revealed atypical organic nutrient requirements that can be attributed to genome reduction, such as conditional auxotrophy for glycine and its precursors, a requirement for reduced sulfur compounds, and evidence for widespread cycling of C1 compounds in marine environments. However, understanding the genetic variation and distribution of such pathways and characteristics like streamlining throughout the group has required the isolation and genome sequencing of diverse SAR11 representatives, an analysis of which we provide here.
Bacterial communities are fundamental symbionts of corals. However, the process by which bacterial communities are acquired across the life history of corals, particularly in larval and early ...juvenile stages, is still poorly characterized. Here, transfer of bacteria of the Scleractinian coral
from adults to spawned egg-sperm bundles was analyzed, as well as acquisition across early developmental stages (larvae and newly settled spat), and 6-month-old juveniles. Larvae were reared under manipulated environmental conditions to determine the source (maternal, seawater, or sediment) of bacteria likely to establish symbiotic relationships with the host using amplicon sequencing of the 16S rRNA gene. Maternal colonies directly transferred bacteria from the families Rhodobacteraceae, Cryomorphaceae, and Endozoicimonaceae to egg-sperm bundles. Furthermore, significant differences in the microbial community structure were identified across generations, yet the structure of the coral bacterial community across early life history stages was not impacted by different environmental rearing conditions. These data indicate that the uptake and structure of bacterial communities is developmentally, rather than environmentally, regulated. Both maternal coral colonies and ubiquitous bacteria found across environmental substrates represent a potential source of symbionts important in establishing the coral microbiome. Uniquely, we report the presence of variation with ontogeny of both the core and resident bacterial communities, supporting the hypothesis that microbial communities are likely to play specific roles within the distinct life history stages of the coral host.
Globally, marine species' distributions are being modified due to rising ocean temperatures. Increasing evidence suggests a circum-global pattern of poleward extensions in the distributions of many ...tropical herbivorous species, including the ecologically important rabbitfish
. Adaptability of a species to such new environments may be heavily influenced by the composition of their gastrointestinal microbe fauna, which is fundamentally important to animal health.
thus provides an opportunity to assess the stability of gastrointestinal microbes under varying environmental conditions. The gastrointestinal microbial communities of
were characterized over 2,000 km of Australia's western coast, from tropical to temperate waters, including near its current southern distributional limit. Sequencing of the 16S rRNA gene demonstrated that each population had a distinct hindgut microbial community, and yet, 20 OTUs occurred consistently in all samples. These OTUs were considered the 'core microbiome' and were highly abundant, composing between 31 and 54% of each population. Furthermore, levels of short chain fatty acids, an indicator of microbial fermentation activity, were similar among tropical and temperate locations. These data suggest that flexibility in the hindgut microbiome may play a role in enabling such herbivores to colonize new environments beyond their existing range.
Abstract
A major goal of microbial ecology is to establish the importance of spatial and environmental factors in driving community variation. Their relative importance likely varies across spatial ...scales, but focus has primarily been on free-living communities within well-connected aquatic environments rather than less connected island-like habitats such as estuaries, and key host-associated communities within these systems. Here we sampled both free-living (seawater and sediment) and host-associated (estuarine fish hindgut microbiome, Pelates sexlineatus) communities across six temperate Australian estuaries spanning ∼500 km. We find that spatial and environmental factors have different influences on these communities, with seawater demonstrating strong distance-decay relationships (R = −0.69) and significant associations with a range of environmental variables. Distance-decay relationships were weak for sediment communities but became stronger over smaller spatial scales (within estuaries, R = −0.5), potentially reflecting environmental filtering across biogeochemical gradients or stochastic processes within estuary sediments. Finally, P. sexlineatus hindgut microbiome communities displayed weak distance-decay relationships (R = −0.36), and limited variation explained by environmental variables, indicating the significance of host-related factors in driving community variation. Our findings provide important ecological insights into the spatial distributions and driving forces of both free-living and host-associated bacterial patterns across temperate estuarine systems.
Environmental and spatial factors have greater influence on estuarine free-living bacterial communities in comparison to host-associated communities across six temperate estuaries spanning 500km.
Sea urchins are important herbivores that can graze macroalgae, creating ‘barren’ areas. These barrens are believed to offer little food for urchins due to the absence of attached macroalgae, leading ...to malnourishment as indicated by a low urchin gonad index. To investigate the diet and resultant gonad index of the long-spined sea urchin Centrostephanus rodgersii in New South Wales, Australia, we dissected 100 C. rodgersii individuals collected in macroalgae and barrens habitats along >470 km of SE NSW coastline. Diverse items were present in the digestive tracts of urchins from all habitats. These items included brown (42% barrens, 46% macroalgae), green (28% barrens, 42% macroalgae) and red algae (15% barrens, 12% macroalgae) and corallines (29% barrens, 37% macroalgae), molluscs (28% barrens, 29% macroalgae) and crustaceans (26% barrens, 22% macroalgae). There was no difference in urchin gut fullness between habitats (85% barrens, 90% macroalgae). Importantly, the gonad index only differed in macroalgae compared to barrens habitats at one location, with no differences detected at the other 4 locations. These results suggest that C. rodgersii has a diverse diet that is similar in both habitats, which could explain the similarities in gut fullness and gonad index. Our results suggest that C. rodgersii eat a broad diet including invertebrates and drift algae, and hence may not be malnourished in barrens. The finding of comparable gonad index between barrens and macroalgal areas further supports this conclusion. These findings challenge the prevailing perspective, indicating that sea urchins have sufficient food to survive and reproduce in different habitats.
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