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Heterotrophic bacteria play a vital role in the marine carbon cycle and viruses are an important regulator of bacterial metabolism and community composition. It remains unclear about how bacteria-virus interactions vary with environmental conditions in oceans. In this study, bacterial metabolic activity and community composition were examined in three treatments with different viral pressure (control, virus-rich and virus-reduced) through bioassay experiments at three stations with different environmental conditions in the shelf of the northern South China Sea. Our results showed that bacteria-virus interactions varied with environmental conditions. Viral lysis mediated bacterial growth rate (BGR) and production by shaping bacterial community composition. Furthermore, the effect of viral lysis on bacterial growth rate and production was reduced in substrate-rich waters compared to substrate-low waters. However, the opposite pattern occurred for viral regulation on bacterial respiration and carbon demand, likely since viral lysis dramatically mitigated the maintenance respiration of bacteria. Consequently, viral lysis to greater extent mitigated bacterial carbon processing in substrate-rich environments than in substrate-low environments. Our findings provided new insights into bacteria-virus interactions, and improved our understanding of the role microbial processes in carbon cycling in oceans. © 2023. American Geophysical Union. All Rights Reserved.

Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can affect the extraction yields for complicated sediment samples. In this work, sub-seafloor sediment samples from the Baltic Sea with high organic carbon content were used to evaluate the influence of different grinding beads on DNA extraction. We found that the grinding beads can affect the DNA extraction from the organic-matter- and biosiliceous-clay-rich samples. A mixture of 0.5-mm and 0.1-mm grinding beads exhibited higher DNA yields and recovered more unique taxa than other bead combinations, such as Stenotrophomonas from Gammaproteobacteria and Leptotrichia from Fusobacteria; therefore, these beads are more suitable than the others for DNA extraction from the samples used in this study. This advantage might be magnified in samples with high biomass. On the contrary, the use of only small beads might lead to underestimation for certain Gram-positive strains. Overall, the discovery of abundant widespread deep biosphere clades in our samples indicated that our optimized DNA extraction method successfully recovered the in situ microbial community. © 2022 by the authors.

The transport of planktonic microbes from the upper ocean to sediments plays an important role in marine ecology and biogeochemistry (e.g., the downward transport of organic matter). In order to have a better understanding of this important process, we investigated the diversity of allochthonous cyanophages, cyanobacteria, and eukaryotic algae in the sediments from the Pearl River Estuary and South China Sea based on psbA, the gene encoding the D1 protein involved in photosynthesis. The psbA is prevalent and diverse in sediments regardless of water depth, revealing that the vertical export of psbA gene-containing planktonic microbes provide an important source of sedimental microbes. Phylogenetic analysis showed the presence of Synechococcus, Synechococcus myovirus, Synechococcus podovirus, Prochlorococcus, Prochlorococcus myovirus, Prochlorococcus podovirus, and eukaryotic algae groups in the sediments. More than 80% of psbA amplicons belong to cyanophages, suggesting the potential prevalent downward transport of cyanophages from the photic zone to the seafloor. Diatoms Pseudosolenia calcar-avis and Opephora were dominant in some sediment samples, different from planktonic community in the photic zones, indicating a potentially different vertical export efficiency among phytoplankton. The principal coordinate analysis indicated that psbA gene-containing microbial community varied in estuarine, continental shelf and deep sea sediments. This study investigated the diversity of psbA gene-containing microorganisms in marine sediments and could facilitate the evaluation of the output of photosynthetic organic carbon.

As the most abundant and genetically diverse biological entities, viruses significantly influence ecological, biogeographical and evolutionary processes in the ocean. However, the biogeography of marine viruses and the drivers shaping viral community are unclear. Here, the biogeographic patterns of T4-like viruses and the relative impacts of deterministic (environmental selection) and dispersal (spatial distance) processes were investigated in the northern South China Sea. The dominant viral operational taxonomic units were affiliated with previously defined Marine, Estuary, Lake and Paddy Groups. A clear viral biogeographic pattern was observed along the environmental gradient from the estuary to open sea. Marine Groups I and IV had a wide geographical distribution, whereas Marine Groups II, III and V were abundant in lower-salinity continental or eutrophic environments. A significant distance-decay pattern was noted for the T4-like viral community, especially for those infecting cyanobacteria. Both deterministic and dispersal processes influenced viral community assembly, although environmental selection (e.g. temperature, salinity, bacterial abundance and community, etc.) had a greater impact than spatial distance. Network analysis confirmed the strong association between viral and bacterial community composition, and suggested a diverse ecological relationship (e.g. lysis, co-infection or mutualistic) between and within viruses and their potential bacterial hosts.

Viruses are an abundant and active component of marine sediments and play a significant role in microbial ecology and biogeochemical cycling at local and global scales. To obtain a better understanding of the ecological characteristics of the viriobenthos, the abundance and morphology of viruses and the diversity and community structure of T4-type phages were systematically investigated in the surface sediments of the subtropical Pearl River Estuary (PRE). Viral abundances ranged from 4.49 × 10(8) to 11.7 × 10(8) viruses/g and prokaryotic abundances ranged from 2.63 × 10(8) to 9.55 × 10(8) cells/g, and both decreased from freshwater to saltwater. Diverse viral morphotypes, including tailed, spherical, filamentous, and rod-shaped viruses, were observed using transmission electron microscopy. Analysis of the major capsid gene (g23) indicated that the sediment T4-type phages were highly diverse and, similar to the trend in viral abundances, their diversity decreased as the salinity increased. Phylogenetic analysis suggested that most of the g23 operational taxonomic units were affiliated with marine, paddy soil, and lake groups. The T4-type phage communities in freshwater and saltwater sediments showed obvious differences, which were related to changes in the Pearl River discharge. The results of this study demonstrated both allochthonous and autochthonous sources of the viral community in the PRE sediments and the movement of certain T4-type viral groups between the freshwater and saline water biomes.