Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia

Microbial community diversity from nearshore to offshore in the East China Sea

The Pollution Nagasaki (PN) section of the East China Sea (ECS) is a typical area for studying the complex hydrographic dynamics between Changjiang River discharge and Kuroshio, displaying intense variations of environmental gradients from nearshore to offshore. However, the temporal and spatial changes of microbial communities along the PN section have long been overlooked. In this study, we performed a comprehensive investigation into the abundance, diversity and ecology of free-living (FL) and particle-associated (PA) microbial communities in seawater samples along the PN section during both summer and winter. Distinct hydrological conditions and resulting environmental gradients were observed between summer and winter, with clear features of intrusive Kuroshio subsurface water in summer and strong vertical mixing of seawater in winter. Bacterial abundance along the PN section was higher in summer (1.11 × 108 copies·L-1 - 7.37 × 108 copies·L-1) than in winter (1.83 × 106 copies·L-1 - 1.34 × 108 copies·L-1). Microbial diversity, as indicated by α-diversity indices, remained at relatively stable levels in summer, while a clear decreasing trend was observed in winter along the PN section. Additionally, the winter communities exhibited a more evident spatial shift along the PN section compared to the summer communities. 16S rRNA gene amplicon sequencing showed that microbial community composition varied considerably between different seasons (summer and winter) and lifestyles (FL and PA), with a notable dominance of Ralstonia species. in winter. Regarding the assembly of microbial communities, the stochastic process represented by dispersal limitation was the dominant process in summer, while the deterministic homogeneous selection was the most important process in winter. Correspondingly, distinct topological properties of the microbial co-occurrence networks were shown between different seasons and along the PN section. These results enhance our understanding of how hydrological conditions influence dynamic changes of microbial communities along the PN section, providing new insights for the microbial community assembly and interactions in such a complex environment.

Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs

Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health.

Interaction and Assembly of Bacterial Communities in High-Latitude Coral Habitat Associated Seawater

Threatened by climate change and ocean warming, coral reef ecosystems have been shifting in geographic ranges toward a higher latitude area. The water-associated microbial communities and their potential role in primary production contribution are well studied in tropical coral reefs, but poorly defined in high-latitude coral habitats to date. In this study, amplicon sequencing of 16S rRNA and cbbL gene, co-occurrence network, and βNTI were used. The community structure of bacterial and carbon-fixation bacterial communities showed a significant difference between the center of coral, transitional, and non-coral area. Nitrite, DOC, pH, and coral coverage ratio significantly impacted the β-diversity of bacterial and carbon-fixation communities. The interaction of heterotrophs and autotrophic carbon-fixers was more complex in the bottom than in surface water. Carbon-fixers correlated with diverse heterotrophs in surface water but fewer lineages of heterotrophic taxa in the bottom. Bacterial community assembly showed an increase by deterministic process with decrease of coral coverage in bottom water, which may correlate with the gradient of nitrite and pH in the habitat. A deterministic process dominated the assembly of carbon-fixation bacterial community in surface water, while stochastic process dominated t the bottom. In conclusion, the structure and assembly of bacterial and carbon-fixer community were affected by multi-environmental variables in high-latitude coral habitat-associated seawater.

Temporal dynamic of biofilms enhances the settlement of the central-Mediterranean reef-builder Dendropoma cristatum (Biondi, 1859)

Research on marine invertebrate settlement provides baseline knowledge for restoration technique implementation, especially for biogenic engineers with limited dispersion ability. Previously, we determined that the maturity of a biofilm strongly enhances the settlement of the vermetid reef-builder Dendropoma cristatum. To elucidate settlement-related biofilm features, here we analyse the structure and composition of marine biofilms over time, through microscopic observations, eukaryotic and prokaryotic fingerprinting analyses and 16S rDNA Illumina sequencing. The vermetid settlement temporal increase matched with the higher biofilm coverage on the substratum and the reduction of the eukaryotic abundance and diversity. The prokaryotic assemblage become, over time, more similar to that found on the reef-associated biofilm. Vermetids may detect these differences and selectively settle on those biofilms which show an advantageous structure and composition. These outcomes may support the production of ideal substrates for vermetid colonization and their further translocation to repopulate degraded reefs.

Anthropogenic impact on Indonesian coastal water and ecosystems: Current status and future opportunities

Indonesia, the world's largest archipelagic country and the fourth most populated nation, has struggled with coastal water pollution in the last decades. With the increasing population in coastal urban cities, more land-based pollutants are transported to the coastal water and adversely affected the tropical ecosystems. This paper provides an overview of anthropogenic pollutant studies in Indonesian coastal water and ecosystems from 1986 to 2021. Nutrients, heavy metals, organic pollutants, and plastic debris are the most-studied contaminants. We found that 82%, 54% and 50% of the studies exceeding nutrients, heavy metals, and organic pollutants standard limit, respectively; thus, indicating poor water quality status in part of Indonesian coastal water. The coral reef ecosystems is found to be the most sensitive to anthropogenic disturbance. The potential effect of climate change, new coastal pollution hotspots in eastern Indonesia, marine anthropogenic sources, legacy/emerging pollutants, and the need for research related to the biological contamination, are discussed for future opportunities.

Full-length 16S rRNA gene sequencing reveals spatiotemporal dynamics of bacterial community in a heavily polluted estuary, China

Understanding the bacterial community structure of the river estuary could provide insights into the resident microorganisms in response to environmental pollution. In this study, the bacterial community structure of Liaohe Estuary was investigated using single-molecule real-time sequencing (SMRT). A total of 57 samples were collected and grouped according to habitat, space, season, and lifestyle. In seawater, regardless of whether it is particle-attached (PA) or free-living (FL) bacteria, the area with higher alpha diversity is the nearshore area in the dry season, while it is the midstream area in the wet season. The bacterial communities in sediment and seawater samples were different at the genus level in the nearshore area, and habitat type was the main factor. A marked difference in the bacterial community was observed in the dry season between different lifestyles but not in the wet season, which resulted from lifestyle transitions of bacterioplankton. Bacterial community varied spatially but not seasonally in sediment samples. In seawater, both FL and PA bacterial communities varied spatially during the wet season. Seasonal differences were only observed in FL bacterial community. Zn and sand were the principal determining factors of the bacterial community in the sediment, Cu and salinity were the main environmental factors for FL bacteria, and Cu, salinity, Zn and temperature were the main environmental factors for PA bacteria. Besides, the tide and nutrients were also the main drivers of the bacterial community in seawater. The indicative taxa, related to Cyanobium_PCC-6307, Pseudomonas and Vibrio, further evidenced the presence of possible bloom, crude oil and pathogen contamination. Overall, our results can contribute to the knowledge of the bacterial community and anthropogenic impacts on the Liaohe Estuary.

Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers

The highly populated coasts of the Bay of Bengal are particularly vulnerable to water-borne diseases, pollution and climatic extremes. The environmental factors behind bacterial community composition and Vibrio distribution were investigated in an estuarine system of a cholera-endemic region in the coastline of Bangladesh. Higher temperatures and sewage pollution were important drivers of the abundance of toxigenic Vibrio cholerae. A closer relation between non-culturable Vibrio and particulate organic matter (POM) was inferred during the post-monsoon. The distribution of operational taxonomic units (OTUs) of Vibrio genus was likely driven by salinity and temperature. The resuspension of sediments increased Vibrio abundance and organic nutrient concentrations. The δ¹³C dynamic in POM followed an increasing gradient from freshwater to marine stations; nevertheless, it was not a marker of sewage pollution. Bacteroidales and culturable coliforms were reliable indicators of untreated wastewater during pre and post-monsoon seasons. The presumptive incorporation of depleted-ammonium derived from ammonification processes under the hypoxic conditions, by some microorganisms such as Cloacibacterium and particularly by Arcobacter nearby the sewage discharge, contributed to the drastic ¹⁵N depletion in the POM. The likely capacity of extracellular polymeric substances production of these taxa may facilitate the colonization of POM from anthropogenic origin and may signify important properties for wastewater bioremediation. Genera of potential pathogens other than Vibrio associated with sewage pollution were Acinetobacter, Aeromonas, Arcobacter, and Bergeyella. The changing environmental conditions of the estuary favored the abundance of early colonizers and the island biogeography theory explained the distribution of some bacterial groups. This multidisciplinary study evidenced clearly the eutrophic conditions of the Karnaphuli estuary and assessed comprehensively its current bacterial baseline and potential risks. The prevailing conditions together with human overpopulation and frequent natural disasters, transform the region in one of the most vulnerable to climate change. Adaptive management strategies are urgently needed to enhance ecosystem health.

Sea anemone and clownfish microbiota diversity and variation during the initial steps of symbiosis

Clownfishes and sea anemones form an intriguing long-term association, but the mechanism underlying this symbiosis is not well understood. Since clownfishes seem to cover themselves with sea anemone mucus, we investigated the microbiomes of the two partners to search for possible shifts in their compositions. We used a 16S rRNA gene sequencing strategy to study the dynamics of the microbiota during the association between the clownfish Amphiprion ocellaris and its host Heteractis magnifica under laboratory conditions. The experiment conducted in aquaria revealed that both clownfish and sea anemone mucus had specific signatures compared to artificial sea water. The microbiomes of both species were highly dynamic during the initiation of the symbiosis and for up to seven days after contact. Three families of bacteria (Haliangiaceae, Pseudoalteromonadacae, Saprospiracae) were shared between the two organisms after symbiosis. Once the symbiosis had been formed, the clownfishes and sea anemone then shared some communities of their mucus microbiota. This study paves the way for further investigations to determine if similar microbial signatures exist in natural environments, whether such microbial sharing can be beneficial for both organisms, and whether the microbiota is implicated in the mechanisms that protect the clownfish from sea anemone stinging.

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System

Saharan dust input and seasonal upwelling along North–West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2–3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.

Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities

Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these anthropogenic inputs. The present study is the first to investigate how bacterial community composition responds to small-scale changes in water quality in several coral reef habitats of the Spermonde Archipelago including the water column, particles, and back-reef sediments, on a densely populated and an uninhabited island. The main aims were to elucidate if (a) water quality indicators and organic matter concentrations differ between the uninhabited and the densely populated island of the archipelago, and (b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which are associated with differences in water quality. Several key water quality parameters, such as inorganic nitrate and phosphate, chlorophyll a, and transparent exopolymer particles (TEP) were significantly higher at the inhabited than at the uninhabited island. Bacterial communities in sediments and particle-attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter-rich conditions occurring in higher proportions at the inhabited island. Within the individual reef habitats, variations in bacterial community composition between the islands were associated with differences in water quality. We also observed that copiotrophic, opportunistic bacterial taxa were enriched at the inhabited island with its higher chlorophyll a, dissolved organic carbon and TEP concentrations. Given the increasing strain on tropical coastal ecosystems, this study suggests that effluents from densely populated islands lacking sewage treatment can alter bacterial communities that may be important for coral reef ecosystem function.