Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation

BACKGROUND

The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur oxidation in genomes of the type strains of this genus have been poorly studied. Furthermore, taxonomic errors have been identified in this genus, potentially leading to significant confusion in ecological and evolutionary interpretations in subsequent studies of the genus Sulfitobacter. This study aims to investigate the taxonomic status of this genus and explore the metabolism associated with sulfur oxidation.

RESULTS

This study suggests that Sulfitobacter algicola does not belong to Sulfitobacter and should be reclassified into a novel genus, for which we propose the name Parasulfitobacter gen. nov., with Parasulfitobacter algicola comb. nov. as the type species. Additionally, enzymes involved in the sulfur oxidation process, such as the sulfur oxidization (Sox) system, the disulfide reductase protein family, and the sulfite dehydrogenase (SoeABC), were identified in almost all Sulfitobacter species. This finding implies that the majority of Sulfitobacter species can oxidize reduced sulfur compounds. Differences in the modular organization of sox gene clusters among Sulfitobacter species were identified, along with the presence of five genes with unknown function located in some of the sox gene clusters. Lastly, this study revealed the presence of the demethylation pathway and the cleavage pathway used by many Sulfitobacter species to degrade dimethylsulfoniopropionate (DMSP). These pathways enable these bacteria to utilize DMSP as important source of sulfur and carbon or as a defence strategy.

CONCLUSIONS

Our findings contribute to interpreting the mechanism by which Sulfitobacter species participate in the global sulfur cycle. The taxonomic rearrangement of S. algicola into the novel genus Parasulfitobacter will prevent confusion in ecological and evolutionary interpretations in future studies of the genus Sulfitobacter.

Recent advancements in coral health, microbiome interactions and climate change

Corals are the visible indicators of the disasters induced by global climate change and anthropogenic activities and have become a highly vulnerable ecosystem on the verge of extinction. Multiple stressors could act individually or synergistically which results in small to large scale tissue degradation, reduced coral covers, and makes the corals vulnerable to various diseases. The coralline diseases are like the Chicken pox in humans because they spread hastily throughout the coral ecosystem and can devastate the coral cover formed over centuries in an abbreviated time. The extinction of the entire reef ecosystem will alter the ocean and earth's amalgam of biogeochemical cycles causing a threat to the entire planet. The current manuscript provides an overview of the recent advancement in coral health, microbiome interactions and climate change. Culture dependent and independent approaches in studying the microbiome of corals, the diseases caused by microorganisms, and the reservoirs of coral pathogens are also discussed. Finally, we discuss the possibilities of protecting the coral reefs from diseases through microbiome transplantation and the capabilities of remote sensing in monitoring their health status.

Comparative Genomic Analysis of Cold-Water Coral-Derived Sulfitobacter faviae: Insights into Their Habitat Adaptation and Metabolism

Sulfitobacter is one of the major sulfite-oxidizing alphaproteobacterial groups and is often associated with marine algae and corals. Their association with the eukaryotic host cell may have important ecological contexts due to their complex lifestyle and metabolism. However, the role of Sulfitobacter in cold-water corals remains largely unexplored. In this study, we explored the metabolism and mobile genetic elements (MGEs) in two closely related Sulfitobacter faviae strains isolated from cold-water black corals at a depth of ~1000 m by comparative genomic analysis. The two strains shared high sequence similarity in chromosomes, including two megaplasmids and two prophages, while both contained several distinct MGEs, including prophages and megaplasmids. Additionally, several toxin-antitoxin systems and other types of antiphage elements were also identified in both strains, potentially helping Sulfitobacter faviae overcome the threat of diverse lytic phages. Furthermore, the two strains shared similar secondary metabolite biosynthetic gene clusters and genes involved in dimethylsulfoniopropionate (DMSP) degradation pathways. Our results provide insight into the adaptive strategy of Sulfitobacter strains to thrive in ecological niches such as cold-water corals at the genomic level.

Microbial Associations of Abyssal Gorgonians and Anemones (>4,000 m Depth) at the Clarion-Clipperton Fracture Zone

Deep coral-dominated communities play paramount roles in benthic environments by increasing their complexity and biodiversity. Coral-associated microbes are crucial to maintain fitness and homeostasis at the holobiont level. However, deep-sea coral biology and their associated microbiomes remain largely understudied, and less from remote and abyssal environments such as those in the Clarion-Clipperton Fracture Zone (CCZ) in the tropical Northeast (NE) Pacific Ocean. Here, we study microbial-associated communities of abyssal gorgonian corals and anemones (>4,000 m depth) in the CCZ; an area harboring the largest known global reserve of polymetallic nodules that are commercially interesting for the deep-sea nodule mining. Coral samples (n = 25) belonged to Isididae and Primnoidae families, while anemones (n = 4) to Actinostolidae family. Significant differences in bacterial community compositions were obtained between these three families, despite sharing similar habitats. Anemones harbored bacterial microbiomes composed mainly of Hyphomicrobiaceae, Parvibaculales, and Pelagibius members. Core microbiomes of corals were mainly dominated by different Spongiibacteraceae and Terasakiellaceae bacterial members, depending on corals' taxonomy. Moreover, the predicted functional profiling suggests that deep-sea corals harbor bacterial communities that allow obtaining additional energy due to the scarce availability of nutrients. This study presents the first report of microbiomes associated with abyssal gorgonians and anemones and will serve as baseline data and crucial insights to evaluate and provide guidance on the impacts of deep-sea mining on these key abyssal communities.

Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation

Gammaproteobacteria from the family Endozoicomonadaceae have emerged as widespread associates of dense marine animal communities. Their abundance in coral reefs involves symbiotic relationships and possibly host nutrition. We explored functions encoded in the genome of an uncultured Endozoicomonadaceae 'Candidatus Acestibacter aggregatus' that lives inside gill cells of large Acesta excavata clams in deep-water coral reefs off mid-Norway. The dominance and deep branching lineage of this symbiont was confirmed using 16S rRNA gene sequencing and phylogenomic analysis from shotgun sequencing data. The 4.5 Mb genome binned in this study has a low GC content of 35% and is enriched in transposon and chaperone gene annotations indicating ongoing adaptation. Genes encoding functions potentially involved with the symbiosis include ankyrins, repeat in toxins, secretion and nutritional systems. Complete pathways were identified for the synthesis of eleven amino acids and six B-vitamins. A minimal chitinolytic machinery was indicated from a glycosyl hydrolase GH18 and a lytic polysaccharide monooxygenase LPMO10. Expression of the latter was confirmed using proteomics. Signal peptides for secretion were identified for six polysaccharide degrading enzymes, ten proteases and three lipases. Our results suggest a nutritional symbiosis fuelled by enzymatic products from extracellular degradation processes.

Correlations Between Prokaryotic Microbes and Stress-Resistant Algae in Different Corals Subjected to Environmental Stress in Hong Kong

Coral reefs are extremely vulnerable to global climate change, as evidenced by increasing bleaching events. Previous studies suggest that both algal and microbial partners benefit coral hosts, but the nature of interactions between Symbiodiniaceae and prokaryotic microbes and their effects on coral hosts remains unclear. In the present study, we examined correlations between Symbiodiniaceae and prokaryotic microbes in Montipora spp. and Porites lutea sampled from two sites in Hong Kong with contrasting environmental conditions in March and October 2014. The results showed that the prokaryotic microbial communities had adaptable structures in both Montipora spp. and P. lutea, and environmental conditions had greater effects on the algal/microbial communities in Montipora spp. than in P. lutea. Further network analysis revealed a greater number of prokaryotic microbes were significantly correlated with potentially stress-resistant Symbiodiniaceae in P. lutea than in Montipora spp. Stress-resistant Symbiodiniaceae played more important roles in the community and in the algal–microbial correlations in P. lutea than in Montipora spp. Since P. lutea is faring better in Hong Kong as the seawater temperature gradually increases, the results suggest that the correlations between stress-resistant algae and prokaryotic microbes could provide a compensation mechanism allowing coral hosts to adapt to higher temperatures, particularly as the prokaryotic microbes correlated with Symbiodiniaceae provide the ecological functions of photosynthesis and nitrogen fixation.

Local Variability in Microbiome Composition and Growth Suggests Habitat Preferences for Two Reef-Building Cold-Water Coral Species

Cold-water coral (CWC) ecosystems provide niches and nurseries for many deep-sea species. Lophelia pertusa and Madrepora oculata, two cosmopolitan species forming three dimensional structures, are found in cold waters under specific hydrological regimes that provide food and reoxygenation. There is now more information about their feeding, their growth and their associated microbiome, however, little is known about the influence of their habitat on their physiology, or on the composition of their bacterial community. The goal of this study was to test if the habitat of L. pertusa and M. oculata influenced the hosts associated bacterial communities, the corals’ survival and their skeletal growth along the slope of a submarine canyon. A transplant experiment was used, based on sampling and cross-redeployment of coral fragments at two contrasted sites, one deeper and one shallower. Our results show that M. oculata had significantly higher skeletal growth rates in the shallower site and that it had a specific microbiome that did not change between sites. Inversely, L. pertusa had the same growth rates at both sites, but its bacterial community compositions differed between locations. Additionally, transplanted L. pertusa acquired the microbial signature of the local corals. Thus, our results suggest that M. oculata prefer the shallower habitat.