Vertical shifts of particle-attached and free-living prokaryotes in the water column above the cold seeps of the South China Sea

Organic matter composition fluctuations disrupt free-living bacterial communities more than particle-associated bacterial communities in coastal waters

Marine organic matter fuels the growth of microbial communities, shaping the composition of bacteria that specialize in its breakdown. However, responses of free-living (FL) and particle-associated (PA) bacterial communities to the changing pools of dissolved organic matter (DOM) and particulate organic matter (POM) remained unclear. This study investigates the composition of size-fractionated bacterial communities, DOM and POM in coastal waters over a 22-day period that includes a diatom bloom. Co-occurrence analysis showed that the FL bacterial communities were significantly less stable than PA communities. During the diatom bloom, we observed a significant increase in DOM molecules, particularly those derived from amino acids and peptides. In contrast, the relative intensities of major POM molecule classes remained stable despite the algal bloom's influence. Our study revealed a strong negative correlation between bacterial alpha-diversity and the amount of molecules in the organic matter pool. Similarly, bacterial community beta-diversity was found to be related to the composition of organic matter pool. However, the composition of organic matter was more strongly related to the composition of FL bacterial communities compared to PA communities. This suggests that FL bacteria exhibit greater variations in temporal dynamics and higher sensitivity to the specific structure of organic matter molecules.

Distinct diversity patterns and assembly mechanisms of prokaryotic microbial sub-community in the water column of deep-sea cold seeps

Methane leakage from deep-sea cold seeps has a major impact on marine ecosystems. Microbes sequester methane in the water column of cold seeps and can be divided into abundant and rare groups. Both abundant and rare groups play an important role in cold seep ecosystems, and the environmental heterogeneity in cold seeps may enhance conversion between taxa with different abundances. Yet, the environmental stratification and assembly mechanisms of these microbial sub-communities remain unclear. We investigated the diversities and assembly mechanisms in microbial sub-communities with distinct abundance in the deep-sea cold seep water column, from 400 m to 1400 m. We found that bacterial β-diversity, as measured by Sørensen dissimilarities, exhibited a significant species turnover pattern that was influenced by several environmental factors including depth, temperature, SiO32-, and salinity. In contrast, archaeal β-diversity showed a relatively high percentage of nestedness pattern, which was driven by the levels of soluble reactive phosphate and SiO32-. During the abundance dependency test, abundant taxa of both bacteria and archaea showed a significant species turnover, while the rare taxa possessed a higher percentage of nestedness. Stochastic processes were prominent in shaping the prokaryotic community, but deterministic processes were more pronounced for the abundant taxa than rare ones. Furthermore, the metagenomics results revealed that the abundances of methane oxidation, sulfur oxidation, and nitrogen fixation-related genes and related microbial groups were significantly higher in the bottom water. Our results implied that the carbon, sulfur, and nitrogen cycles were potentially strongly coupled in the bottom water. Overall, the results obtained in this study highlight taxonomic and abundance-dependent microbial community diversity patterns and assembly mechanisms in the water column of cold seeps, which will help understand the impacts of fluid seepage from the sea floor on the microbial community in the water column and further provide guidance for the management of cold seep ecosystem under future environmental pressures.

Impact of dust deposition on the growth of marine autotrophic and heterotrophic microorganisms: Evidence from the South China Sea

Aeolian dust can provide nutrients for the ocean and affect the growth of phytoplankton. However, the impacts of dust deposition on autotrophic and heterotrophic microorganisms have rarely been studied. In this study, we conducted two microcosm experiments in the low-nutrient and low-chlorophyll environment of the South China Sea and found that dust did not stimulate the abundance of autotrophic and heterotrophic microorganisms. Our results show that dust contains most of the unreacted iron-bearing minerals, and thus provides limited bioavailable iron and nitrogen for bacterioplankton and phytoplankton growth. These results elucidate the overlooked impacts of the properties of the iron-bearing minerals in aeolian dust on microbial communities, which may play an important role in marine ecosystems and climate change.

Biodiversity exploration of Formosa Ridge cold seep in the South China Sea using an eDNA metabarcoding approach

The Formosa Ridge, also named Site F, is an active cold seep marine ecosystem site that has been studied since it was discovered on the continental slope of the northeast South China Sea (SCS). However, few studies have focused on the eukaryotic diversity at Site F. Environmental DNA (eDNA) technology is a non-invasive method applied in biodiversity surveys with a high species detection probability. In the present study, we identified multi-trophic biodiversity using eDNA metabarcoding combined with multiple ribosomal RNA gene (rDNA) markers. We detected 142 phytoplankton, 90 invertebrates, and 64 fish species by amplifying the 18S rRNA gene V4 region, the 18S rRNA gene V9 region, and the 12S rRNA gene. The results elucidated dissimilar trends of different assemblages with depth. The diversity of phytoplankton and invertebrate assemblages markedly decreased with depth, whereas little change was observed within the fish assemblage. We comprehensively assessed the relationship between the three assemblages and environmental factors (temperature, salinity, depth, dissolved oxygen, and chlorophyll a). These factors strongly impacted on phytoplankton and invertebrates, but only slightly on fish. We inferred the finding might be due to fish having a strong migration capacity and wide distribution. This study indicates that eDNA metabarcoding with multiple markers is a powerful tool for marine biodiversity research that is able to provide technical support and knowledge for resource management and biodiversity protection efforts.

Community assemblages and species coexistence of prokaryotes controlled by local environmental heterogeneity in a cold seep water column

The distribution and heterogeneity characteristics of microbial communities in cold seep water columns are significant factors governing the efficiency of methane filtering and carbon turnover. However, this process is poorly understood. The diversity of vertically stratified microbial communities and the factors controlling the community assemblage process in the water column above the Haima cold seep were investigated in this study. The prokaryotic community diversities varied distinctly with vertical changes in hydrochemistry. Cyanobacteria dominated the light-transmitting layers and Proteobacteria dominated the deeper layers. With respect to microbial community assemblages and co-occurrence networks, stochastic processes were particularly important in shaping prokaryotic communities. In the shallow (≥85 m) and mesopelagic water columns (600-800 m), microbial community characteristics were affected by deterministic processes, reduced network connectivity, and modularity. Microbial community diversities and assemblage processes along a vertical profile were influenced by the vertical variations in pH, temperature, DIC, and nutrients. Stochastic processes may have facilitated the formation of complex co-occurrence networks. Briefly, the distribution of local environmental heterogeneity along the vertical dimension could drive unique microbial community assemblage and species coexistence patterns. This study provides new perspectives on how microorganisms adapt to the environment and build communities, and how species coexist in shared habitats.

Metabolic activity and community structure of prokaryotes associated with particles in the twilight zone of the South China Sea

The twilight zone is an important depth of the ocean where particulate organic matter (POM) remineralization takes place, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity associated with different particles in the twilight zone. The composition and distribution of particle-attached prokaryotes in the twilight zone of the South China Sea (SCS) were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog Ecoplate™ microplates culture to analyze the microbial metabolic activity. We found that α- and γ-Proteobacteria dominating at the lower and upper boundary of the twilight zone, respectively; Methanosarcinales and Halobacteriales of the Euyarchaeota occupied in the larger particles at the upper boundary. Similar microbial community existed between euphotic layer and the upper boundary. Higher amount of shared Operational Taxonomic Units (OTUs) in the larger particles along the water depths, might be due to the fast sinking and major contribution of carbon flux of the larger particles from the euphotic layer. In addition to polymers as the major carbon source, carbohydrates and amino acids were preferentially used by microbial community at the upper and lower boundary, respectively. This could potentially be attributed to the metabolic capabilities of attached microbial groups in different particles, and reflected the initial preference of the carbon source by the natural microbes in the twilight zone as well. The microbial structure and carbon metabolic profiles could be complemented with metatranscriptomic analysis in future studies to augment the understanding of the complex carbon cycling pathways in the twilight zone.

The Ecological Differentiation of Particle-Attached and Free-Living Bacterial Communities in a Seasonal Flooding Lake-the Poyang Lake

Particle-attached (PA) and free-living (FL) bacterial communities play essential roles in the biogeochemical cycling of essential nutrients in aquatic environments. However, little is known about the factors that drive the differentiation of bacterial lifestyles, especially in flooding lake systems. Here we assessed the compositional and functional similarities between the FL and PA bacterial fractions in a typical flooding lake-the Poyang Lake (PYL) of China. The results revealed that PA communities had significantly different compositions and functions from FL communities in every hydrological period, and the diversity of both PA and FL communities was affected mainly by the water regime rather than bacterial lifestyles. PA communities were more diverse and enriched with Proteobacteria and Bacteroidetes, while FL communities had more Actinobacteria. There was a higher abundance of photosynthetic and nitrogen-cycling bacterial groups in PA communities, but a higher abundance of members involved in hydrocarbon degradation, aromatic hydrocarbon degradation, and methylotrophy in FL communities. Water properties (e.g., temperature, pH, total phosphorus) significantly regulated the lifestyle variations of PA and FL bacteria in PYL. Collectively, our results have demonstrated a clear ecological differentiation of PA and FL bacterial communities in flooding lakes, suggesting that the connectivity between FL and PA bacterial fractions is water property-related rather than water regime-related.

Population structure, activity potential and ecotype partitioning of Pseudoalteromonas along the vertical water column of the New Britain Trench

Microbial degradation of organic matter along the vertical profile of the water column is a major process driving the carbon cycle in the ocean. Pseudoalteromonas has been identified as a dominant genus in pelagic marine environments worldwide, playing important roles in the remineralization of organic carbon. However, the current understanding of Pseudoalteromonas was mainly based on shallow water populations or cultivated species. This study analyzed for the first time the structure, activity potential and ecotypes differentiation of Pseudoalteromonas in the water column of the New Britain Trench (NBT) down to 6000 m. Analysis on diversities of the 16S rRNA gene and their transcripts showed that Pseudoalteromonas was greatly enriched in deep-sea waters and showed high activity potentials. The deep-sea Pseudoalteromonas were significantly different from their shallow-water counterparts, suggesting an obvious ecotype division along with the vertical profile. Phylogenetic analysis on the 16S rRNA gene and hsp60 gene of 219 Pseudoalteromonas strains isolated from different depths further showed that the vertical ecotype division could even occur at the strain level, which might be a result of long-term adaptation to environmental conditions at different depths. The discovered depth-specific strains provide valuable models for further studies on adaptation, evolution and functions of the deep-sea Pseudoalteromonas.