Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands

Phylogenomic analysis expands the known repertoire of single-stranded DNA viruses in benthic zones of the South Indian Ocean

Single-stranded (ss) DNA viruses are ubiquitous and constitute some of the most diverse entities on Earth. Most studies have focused on ssDNA viruses from terrestrial environments resulting in a significant deficit in benthic ecosystems including aphotic zones of the South Indian Ocean (SIO). Here, we assess the diversity and phylogeny of ssDNA in deep waters of the SIO using a combination of established viral taxonomy tools and a Hidden Markov Model based approach. Replication initiator protein-associated (Rep) phylogenetic reconstruction and sequence similarity networks were used to show that the SIO hosts divergent and as yet unknown circular Rep-encoding ssDNA viruses. Several sequences appear to represent entirely novel families, expanding the repertoire of known ssDNA viruses. Results suggest that a small proportion of these viruses may be circular genetic elements, which may strongly influence the diversity of both eukaryotes and prokaryotes in the SIO. Taken together, our data show that the SIO harbours a diverse assortment of previously unknown ssDNA viruses. Due to their potential to infect a variety of hosts, these viruses may be crucial for marine nutrient recycling through their influence of the biological carbon pump.

Environmental gradients shape microbiome assembly and stability in the East China sea

Microbiomes play a key role in marine ecosystem functioning and sustainability. Their organization and stability in coastal areas, particularly in anthropogenic-influenced regions, however, remains unclear compared with an understanding of how microbial community shifts respond to marine environmental gradients. Here, the assembly and community associations across vertical and horizontal gradients in the East China Sea are systematically researched. The seawater microbial communities possessed higher robustness and lower fragmentation and vulnerability compared to the sediment microbiomes. Spatial gradients act as a deterministic filtering factor for microbiome organization. Microbial communities had lower phylogenetic distance and higher niche breadth in the nearshore and offshore areas compared to intermediate areas. The phylogenetic distance of microbiomes decreased from the surface to the bottom but the niche breadth was enhanced in surface and bottom environments. Vertical gradients destabilized microbial associations, while the community diversity was enhanced. Multivariate regression tree analysis and canonical correspondence analysis indicated that depth, distance from shore, nutrient availability, temperature, salinity, and chlorophyll a, affected the distribution and co-occurrence of microbial groups. Our results highlight the crucial roles of environmental gradients in determining microbiome association and stability. These results improve our understanding of the survival strategies/adaptive mechanisms of microbial communities in response to environmental variation and provide new insights for protecting the ecosystems and maintaining the sustainability of ecological functions.

Microbial ecology of the Southern Ocean

The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.

Four Lentisphaerae Family Metagenome-Assembled Genomes from the South Atlantic Ocean

We present four Lentisphaerae metagenome-assembled genomes (MAGs) from the South Atlantic Ocean. The medium-quality genomes, affiliated with the family of Lentisphaeraceae, ranged from 4.86 to 5.46 Mbp and harbored the genetic capacity to produce secondary metabolites. This resource provides a basis for investigating the functional attributes of this phylum.

Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region

The ecological and oceanographic processes that drive the response of pelagic ocean microbiomes to environmental changes remain poorly understood, particularly in coastal upwelling ecosystems. Here we show that seasonal and interannual variability in coastal upwelling predicts pelagic ocean microbiome diversity and community structure in the Southern California Current region. Ribosomal RNA gene sequencing, targeting prokaryotic and eukaryotic microbes, from samples collected seasonally during 2014-2020 indicate that nitracline depth is the most robust predictor of spatial microbial community structure and biodiversity in this region. Striking ecological changes occurred due to the transition from a warm anomaly during 2014-2016, characterized by intense stratification, to cooler conditions in 2017-2018, representative of more typical upwelling conditions, with photosynthetic eukaryotes, especially diatoms, changing most strongly. The regional slope of nitracline depth exerts strong control on the relative proportion of highly diverse offshore communities and low biodiversity, but highly productive nearshore communities.