Qing-Lei Sun

Deep-sea chemosynthetic ecosystems, including cold seeps and hydrothermal vents, are widely spread in global oceans. Campylobacterota are important primary producers in deep-sea hydrothermal vents and serve as a vital food source for local invertebrates. However, the nutrients that these bacteria can provide to their hosts are unclear. To date, research on Campylobacterota in cold seeps is very limited. Consequently, little is known about the biological features and ecological potential of Campylobacterota in cold seeps. In the present work, we examined the diversity, growth, metabolic characteristics, and nutrient production of Campylobacterota in a deep-sea cold seep. Over 1000 Campylobacterota ASVs, especially autotrophic Sulfurovum and Sulfurimonas, were identified. By optimizing the culture medium, 9 Sulfurovum and Sulfurimonas strains were isolated, including three potentially novel species. Two novel species were characterized and found to exhibit unique morphological features. These two novel strains possessed complete reverse tricarboxylic acid pathways. One novel strain, FCS5, was a psychrotolerant autotroph with denitrification and phosphorus-removing capacity. FCS5 could grow in the absence of vitamins. Consistently, metabolomics and transcriptome analyses indicated that FCS5 produced multiple vitamins, which regulated the expressions of a large number of genes associated with carbon fixation and multiple-nutrient synthesis. Besides vitamins, autotrophic Campylobacterota also produced abundant free amino acids, fatty acids (short-chain, medium, and long-chain), and proteins. This study indicates that the cold seep abounds with Campylobacterota, which are capable of providing various nutrients for the chemosynthetic ecosystem. In addition, these bacteria may have wide applications, such as in wastewater treatment and carbon emission reduction.

Chemoautotrophs within Campylobacterota, especially Sulfurovum and Sulfurimonas , are abundant in the seawater–sediment interface of the Formosa cold seep in the South China Sea. However, the in situ activity and function of Campylobacterota are unknown. In this study, the geochemical role of Campylobacterota in the Formosa cold seep was investigated with multiple means. Two members of Sulfurovum and Sulfurimonas were isolated for the first time from deep-sea cold seep. These isolates are new chemoautotrophic species that can use molecular hydrogen as an energy source and CO ₂ as a sole carbon source. Comparative genomics identified an important hydrogen-oxidizing cluster in Sulfurovum and Sulfurimonas . Metatranscriptomic analysis detected high expression of hydrogen-oxidizing gene in the RS, suggesting that H ₂ was likely an energy source in the cold seep. Genomic analysis indicated that the Sulfurovum and Sulfurimonas isolates possess a truncated sulfur-oxidizing system, and metatranscriptomic analysis revealed that Sulfurovum and Sulfurimonas with this genotype were active in the surface of RS and likely contributed to thiosulfate production. Furthermore, geochemical and in situ analyses revealed sharply decreased nitrate concentration in the sediment–water interface due to microbial consumption. Consistently, the denitrification genes of Sulfurimonas and Sulfurovum were highly expressed, suggesting an important contribution of these bacteria to nitrogen cycling. Overall, this study demonstrated that Campylobacterota played a significant role in the cycling of nitrogen and sulfur in a deep-sea cold seep. IMPORTANCE: Chemoautotrophs within Campylobacterota, in particular Sulfurovum and Sulfurimonas , are ubiquitous in deep-sea cold seeps and hydrothermal vents. However, to date, no Sulfurovum or Sulfurimonas has been isolated from cold seeps, and the ecological roles of these bacteria in cold seeps remain to be investigated. In this study, we obtained two isolates of Sulfurovum and Sulfurimonas from Formosa cold seep, South China Sea. Comparative genomics, metatranscriptomics, geochemical analysis, and in situ experimental study indicated collectively that Campylobacterota played a significant part in nitrogen and sulfur cycling in cold seep and was the cause of thiosulfate accumulation and sharp reduction of nitrate level in the sediment–water interface. The findings of this study promoted our understanding of the in situ function and ecological role of deep-sea Campylobacterota.

In this study, we report a novel Gram-positive bacterium, designated as strain CS13^T, isolated from deep-sea sediment collected in the cold seep area of the South China Sea. Growth of strain CS13^T occurred at 16–37 °C (optimum 25–28 °C), pH 7.0–9.0 (optimum, 7.0), and 0–8% (w/v) NaCl (optimum, 2–3%). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CS13^T belonged to the genus Bacillus. The closest phylogenetic neighbors of strain CS13^T are Bacillus carboniphilus JCM 9731^T (96.0%), Bacillus pakistanensis NCCP-168^T (95.7%) and Bacillus acidicola 105-2^T (95.6%). The genomic DNA G + C content of strain CS13^T is 43.7 mol%. The principal respiratory quinone was menaquinone 7 (MK—7). The polar lipids of CS13^T contained diphosphatidylglycerol, phosphatidylglycerol, phospholipid, and glycolipid. The major fatty acids of CS13^T contained anteiso-C_15:0, anteiso-C_17:0, C_16:0 and C_18:0. Strain CS13^T harboured meso-diaminopimelic acid as the diagnostic diamino acid. Phylogenetic, physiological, biochemical, and morphological analyses suggested that strain CS13^T represents a novel species of genus Bacillus, and the name Bacillus fonticola sp. nov. is proposed for the type species CS13^T (= CCTCC AB 2019194^T = JCM 33663^T).

In the Formosa cold seep of the South China Sea (SCS), large amounts of methane and sulfide hydrogen are released from the subseafloor. In this study, we systematically investigated the microbial communities in the seawater–sediment interface of Formosa cold seep using high-throughput sequencing techniques including amplicon sequencing based on next-generation sequencing and Pacbio amplicon sequencing platforms, and metagenomics. We found that Sulfurovum dominated the microbial communities in the sediment–seawater interface, including the seawater close to the seepage, the surface sediments, and the gills of the dominant animal inhabitant (Shinkaia crosnieri). A nearly complete 16S rRNA gene sequence of the dominant operational taxonomic units (OTUs) was obtained from the Pacbio sequencing platforms and classified as OTU-L1, which belonged to Sulfurovum. This OTU was potentially novel as it shared relatively low similarity percentages (Sulfurovum was assembled using the binning technique based on metagenomic data. Genome analysis suggested that Sulfurovum sp. in this region may fix carbon by the reductive tricarboxylic acid (rTCA) pathway, obtain energy by oxidizing reduced sulfur through sulfur oxidizing (Sox) pathway, and utilize nitrate as electron acceptors. These results demonstrated that Sulfurovum probably plays an important role in the carbon, sulfur, and nitrogen cycles of the Formosa cold seep of the SCS. This study improves our understanding of the diversity, distribution, and function of sulfur-oxidizing bacteria in deep-sea cold seep.

In this study, we reported a novel yellow-pigmented, Gram-stain-negative bacterium with appendages, designated as strain L2T, isolated from the South China Sea. Growth of strain L2T occurred at 22–40 °C (optimum, 37 °C), pH 6.0–10.0 (pH 7.0) and with 0–8 % (w/v) NaCl (2 %). Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain L2T belonged to the genus Muricauda . The close phylogenetic neighbours of strain L2T were Muricauda marina H19-56T, Muricauda ruestringensis B1T, Muricauda antarctica Ar-22T, Muricauda taeanensis 105T and Muricauda flavescens SW-62T (96.4 %, 95.9 %, 95.9 %, 95.8 % and 94.5 % identities, respectively). The genomic DNA G+C content of strain L2T was 51.3±4.6 mol%. Theg major isoprenoid quinone was MK-6 (100.0 %). The polar lipids contained phosphatidylethanolamine and two unidentified lipids. The major fatty acids (>10 % of total fatty acids) were iso-C17 : 0 3-OH (30.3 %), iso-C15 : 1 G (20.6 %) and iso-C15 : 0 (17.6 %). Phylogenetic, physiological, biochemical and morphological analysis suggested that this strain represents a novel species of genus Muricauda , and the name Muricauda iocasae sp. nov. is proposed with the type species L2T (=CCTCC AB 2017193 T=KCTC 62196T).