Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula

Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria

BACKGROUND

The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line.

RESULTS

We found significant differences in microbial community structure on either side of this boundary (R2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community.

CONCLUSION

Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.

Meta-analysis reveals variations in microbial communities from diverse stony coral taxa at different geographical distances

Coral-associated microbial communities play a vital role in underpinning the health and resilience of reef ecosystems. Previous studies have demonstrated that the microbial communities of corals are affected by multiple factors, mainly focusing on host species and geolocation. However, up-to-date, insight into how the coral microbiota is structured by vast geographic distance with rich taxa is deficient. In the present study, the coral microbiota in six stony coral species collected from the coastal area of three countries, including United States of America (USA), Australia and Fiji, was used for analysis. It was found that the geographic influence on the coral microbiota was stronger than the coral host influence, even though both were significant. Interestingly, the contribution of the deterministic process to bacterial community composition increased as geographical distance grew. A total of 65 differentially abundant features of functions in coral microbial communities were identified to be associated with three geolocations. While in the same coastal area of USA, the similar relationship of coral microbiota was consistent with the phylogenetic relationship of coral hosts. In contrast to the phylum Proteobacteria, which was most abundant in other coral species in USA, Cyanobacteria was the most abundant phylum in Orbicella faveolata. The above findings may help to better understand the multiple natural driving forces shaping the coral microbial community to contribute to defining the healthy baseline of the coral microbiome.

Bacterial Communities Vary from Different Scleractinian Coral Species and between Bleached and Non-Bleached Corals

Bleaching is one of the most relevant factors implicated in the integrity of coral reef ecosystems, with the increasing frequency and intensity of damaging events representing a serious threat to reef biodiversity. Here, we analyzed changes in coral-associated bacteria from three types of non-bleached and bleached scleractinian corals (Acropora digitifera, Galaxea fascicularis, and Porites pukoensis) in Hainan Luhuitou peninsula coastal areas. The community structure of symbiotic bacteria differed significantly among the three apparently healthy corals. The bleached corals had higher bacterial alpha diversity and some specific bacteria genera, including Ruegeria, Methyloceanibacter, Filomicrobium, Halioglobus, Rubripirellula, Rhodopirellula, Silicimonas, Blastopirellula, Sva0996 marine group, Woeseia, and unclassified_c_Gammaproteobacteria, were consistently increased in bleached groups. Network analysis revealed significantly different degrees of modularity between bleached and non-bleached groups at the bacterial genus level, and a higher proportion of links was dominated by positive co-occurrences. Functional prediction analysis illustrated that coral-associated bacteria remained relatively consistent in the bleached and non-bleached groups. Structure equation modeling revealed that the bacterial community diversity and function were directly influenced by host and environment factors. These findings suggested that coral-associated bacterial responses to bleaching occur in a host-dependent manner, informing novel strategies for restoring coral and aiding adaption to bleaching stress. IMPORTANCE Accumulating evidence indicates that coral-associated bacteria play an important role in the health of holobionts. However, the variability of the symbiotic bacterial community structure among coral species with different coral health statuses remains largely unknown. Here, we investigated three apparent non-bleached (healthy) and bleached coral species (sampled in situ), involving related symbiotic bacterial profiles, including composition, alpha diversity, network relationship, and potential function. Structural equation modeling analysis was used to analyze the relationship between coral status and abiotic and biotic factors. The bacterial community structure of different groups was shown to exhibit host-specific traits. Both host and environmental impacts had primary effects on coral-associated microbial communities. Future studies are needed to identify the mechanisms that mediate divergent microbial consortia.

The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival

BACKGROUND

Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.

CONCLUSION

The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.

Bacterial and Fungal Co-Occurrence in the Nudibranch, Pteraeolidia semperi

Despite the increasing recognition and importance surrounding bacterial and fungal interactions, and their critical contributions to ecosystem functioning and host fitness, studies examining their co-occurrence remain in their infancy. Similarly, studies have yet to characterise the bacterial and fungal communities associated with nudibranchs or their core microbial members. Doing this can advance our understanding of how the microbiome helps a host adapt and persist in its environment. In this study, we characterised the bacterial and fungal communities associated with 46 Pteraeolidia semperi nudibranch individuals collected from four offshore islands in Singapore. We found no distinct spatial structuring of microbial community, richness, or diversity across sampling locations. The bacterial genera Mycoplasma and Endozoicomonas were found across all samples and islands. The fungal genus Leucoagaricus was found with the highest occurrence, but was not found everywhere, and this is the first record of its reported presence in marine environments. The co-occurrence network suggests that bacterial and fungal interactions are limited, but we identified the bacterial family Colwelliaceae as a potential keystone taxon with its disproportionately high number of edges. Furthermore, Colwelliaceae clusters together with other bacterial families such as Pseudoalteromonadaceae and Alteromonadaceae, all of which have possible roles in the digestion of food.