Qian Liu

The obligate mixotroph Mesodinium rubrum significantly impacts coastal ecosystems, yet its population control in oligotrophic waters remains unclear. Integrating field observations from Coast of Sanya (South China Sea) with laboratory nutrient manipulation, we investigated how dissolved inorganic nutrients and prey availability regulate cell cycle progression, using biovolume as a proxy for cycle transitions. Nutrient starvation arrested cells at the small (newly divided) stage. Inorganic replenishment triggered rapid somatic growth and consistent diel biovolume oscillations, expanding in light and shrinking in darkness. However, without cryptophyte prey, cells failed to progress beyond the medium (actively growing) stage and could not accumulate into the large (pre-division) size class, revealing a decoupled regulatory mechanism. Dissolved inorganic nutrients drive cell size expansion (somatic growth), whereas prey-derived organelles serve as a critical prerequisite for division. Field data confirmed that the virtual absence of cryptophytes in Sanya waters restricts M. rubrum to consistently low levels. Our findings demonstrate that population dynamics of this specialist mixotroph transcend traditional nutrient-driven paradigms, underscoring the irreplaceable role of prey in sustaining photosynthetic metabolism and triggering population expansion in oligotrophic systems.

Most studies on the genesis of polymetallic nodules suggested that nodules in the South China Sea (SCS) are hydrogenetic; however, the complexity and the heterogeneity in hydrology and geochemistry of the SCS might cause different processes of nodule formation, impacting their application and economic value. Microbial-mediated ferromanganese deposition is an important process in nodule formation, but the related microbial potentials are still unclear in the SCS. In this study, we sampled in three typical regions (A, B, and C) of the SCS enriched with polymetallic nodules. Firstly, we investigated environmental and microbial characteristics of the water columns to determine the heterogeneity of upper seawater that directly influenced deep-sea environments. Then, microbial compositions and structures in sediment cores, overlying waters, and nodules (inside and outside) collected within the same region were analyzed for inferring features of nodule environments. Microbial interactions between nodules and surrounding environments were estimated with collinear network analysis. The microbial evidence indicated that geochemical characteristics in deep sea of the SCS that were key to the polymetallic nodule formation were severely affected by organic matter flux from upper water column. The sediment in region A was sub-oxic due to the large input of terrigenous and phytoplankton-derived organic matter, potentially enhancing the overflow of reduced metals from the porewater. The intense microbial interaction between nodules and surface sediment reinforced the origin of metals for the ferromanganese deposition from the sediment (diagenetic type). Contrarily, the sediments in regions B and C were relatively rich in oxygen, and metal ions could be majorly supplied from seawater (hydrogenetic type). The large discrepancy in microbial communities between nodule inside and remaining samples suggested that nodules experienced a long-term formation process, consistent with the feature of hydrogenetic nodules. Overall, distributions and interactions of microbial communities in nodules and surrounding environments significantly contributed to the nodule formation in the SCS by manipulating biogeochemical processes that eventually determined the source and the fate of metal ions.

Viruses are the most abundant life forms in the sea, influencing the community structure and metabolism of host cells as well as biogeochemical cycles. However, the diversity and ecological roles of viruses within seamount ecosystems, natural microbiota havens characterized by high biodiversity, remain unknown. Here, the first seamount viral genome (SMVG) dataset, based on a metagenomic analysis of twelve seamount sediment samples collected from the seamount regions of the Northwest Pacific Ocean, is established. A total of 78,069 viral operational taxonomic units (vOTUs) were found, spanning 18 viral classes and 63 viral families. The detection of sixteen viral auxiliary metabolic genes (vAMGs) suggests that viruses may participate in both the complex metabolic dynamics associated with sediment microbial communities and also biogeochemical cycles, including carbon, sulfur, metal, heme, and cobalamin cycling. vAMGs involved in the metabolism of heme, cobalamin and metals, in particular, are more often detected in seamount sediments than in trenches, cool seeps, and hydrothermal vents. This investigation of the viral communities in these seamount sediments provides new insights into the high diversity and ecological potential of the viruses and establishes a foundation for the future study of benthic viruses from deep-sea seamounts.

A gram-stain-negative, aerobic, rod-shaped bacterium strain CJK-A8-3^T was isolated from a polyamine-enriched seawater sample collected from the Changjiang River estuary of China. The colonies were white and circular. Strain CJK-A8-3^T grew optimally at 35 °C, pH 7.0 and 1.5% NaCl. Its polar lipids contained phosphatidylglycerol, phosphatidic acid, unidentified glycolipids, and a combination of phospholipids and glycolipids. The respiratory quinone was ubiquinone-10, and its main fatty acids were C_16:0, 11-methyl C_18:1ω7c and Summed Feature 8 (including C_18:1ω7c/C_18:1ω6c). The phylogenetic tree based on 16S rRNA genes placed strain CJK-A8-3^T in a new linage within the genus Devosia. 16S rRNA gene sequence of strain CJK-A8-3^T showed identities of 98.50% with Devosia beringensis S02^T, 98.15% with D. oryziradicis, and 98.01% with D. submarina JCM 18935^T. The genome size of strain CJK-A8-3^T was 3.81 Mb with the DNA G + C content 63.9%, higher than those of the reference strains (60.4–63.8%). The genome contained genes functional in the metabolism of terrigenous aromatic compounds, alkylphosphonate and organic nitrogen, potentially beneficial for nutrient acquirement and environmental remediation. It also harbored genes functional in antibiotics resistance and balance of osmotic pressure, enhancing their adaptation to estuarine environments. Both genomic investigation and experimental verification showed that strain CJK-A8-3^T could be versatile and efficient to use diverse organic nitrogen compounds as carbon and nitrogen sources. Based on phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain CJK-A8-3^T was identified as a novel Devosia species, named as Devosia aquimaris sp. nov. The type strain is CJK-A8-3^T (= MCCC 1K06953^T = KCTC 92162^T).

Viruses are the most abundant life forms in the sea, influencing the community structure and metabolism of host cells and biogeochemical cycles. However, the diversity of viruses and their ecological roles within seamount sediments ecosystems, natural microbiota havens characterized by high biodiversity, remain largely unknown. Here, the seamount viral genome (SMVG) dataset, based on a metagenomic analysis of twelve seamount sediment samples collected from the seamount regions of the Northwest Pacific Ocean, was established. A total of 78,069 viral operational taxonomic units (vOTUs) were found, spanning 18 viral classes and 63 viral families. The detection of sixteen viral auxiliary metabolic genes (AMGs) suggests that viruses may participate in the metabolic processes associated with sediment microbial communities and biogeochemical cycles, including carbon, sulfur, metal, heme, and cobalamin cycling. AMGs involved in the metabolism of heme, cobalamin, and metals were more often detected in seamount sediments than in trenches, cool seeps, and hydrothermal vents. This investigation of the viral communities in these seamount sediments provides new insights into the high diversity and ecological potential of the viruses and establishes a foundation for the future study of benthic viruses from deep-sea seamounts.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.