Weak Influence of Paleoenvironmental Conditions on the Subsurface Biosphere of Lake Ohrid over the Last 515 ka

Sediment bacterial biogeography across reservoirs in the Hanjiang river basin, southern China: the predominant influence of eutrophication-induced carbon enrichment

A fundamental goal of reservoir ecosystem management is to understand bacterial biogeographic patterns and the mechanisms shaping them at a regional scale. However, little is known about how eutrophication, a major water quality challenge in reservoirs, influences sediment bacterial biogeographic patterns in subtropical regions. In this study, sediment bacterial communities were sampled from 21 subtropical reservoirs in the Hanjiang river basin, southern China, and spanning trophic states from oligotrophic to eutrophic. Our findings demonstrated that eutrophication-driven changes in total carbon (TC) significantly shaped the regional biogeographic patterns of sediment bacterial communities, weakening the "distance-decay" relationships that typically link bacterial community similarity to geographical distance. TC content exceeding a threshold of 13.2 g·kg-1 resulted in substantial shifts in bacterial community structure. Specifically, high TC levels promoted the dominance of copiotrophic bacteria such as Syntrophales (Deltaproteobacteria), Clostridiaceae (Firmicutes), and VadinHA17 (Bacteroidetes), while oligotrophic taxa like Anaerolineaceae (Chloroflexi) and Nitrospirota were prevalent in low TC sediments. Additionally, higher TC content was associated with increased regional heterogeneity in bacterial community composition. Reservoirs with elevated TC levels exhibited more complex bacterial interaction networks, characterized by stronger niche segregation and higher competition compared to low TC networks. Overall, these findings underscore the pivotal role of sediment TC in shaping bacterial biogeography at a regional scale. They provide valuable insights for predicting ecosystem responses to eutrophication and offer guidance for mitigating the impacts of anthropogenic activities on freshwater ecosystems.

Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere

Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth's carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445-8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with in situ methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.IMPORTANCEThe Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.

Metabolic features that select for Bathyarchaeia in modern ferruginous lacustrine subsurface sediments

Ferruginous conditions prevailed through Earth's early oceans history, yet our understanding of biogeochemical cycles in anoxic iron-rich, sulfate-poor sediments remains elusive in terms of redox processes and organic matter remineralization. Using comprehensive geochemistry, cell counts, and metagenomic data, we investigated the taxonomic and functional distribution of the microbial subsurface biosphere in Lake Towuti, a stratified ferruginous analogue. Below the zone in which pore water becomes depleted in electron acceptors, cell densities exponentially decreased while microbial assemblages shifted from iron- and sulfate-reducing bacterial populations to fermentative anaerobes and methanogens, mostly selecting Bathyarchaeia below the sulfate reduction zone. Bathyarchaeia encode metabolic machinery to cycle and assimilate polysulfides via sulfhydrogenase, sulfide dehydrogenase, and heterodisulfide reductase, using dissimilatory sulfite reductase subunit E and rubredoxin as carriers. Their metagenome-assembled genomes showed that carbon fixation could proceed through the complete methyl-branch Wood-Ljungdahl pathway, conducting (homo)acetogenesis in the absence of methyl coenzyme M reductase. Further, their partial carbonyl-branch, assumed to act in tetrahydrofolate interconversions of C1 and C2 compounds, could support close interactions with methylotrophic methanogens in the fermentation zone. Thus, Bathyarchaeia appeared capable of coupling sulfur-redox reactions with fermentative processes, using electron bifurcation in a redox-conserving (homo)acetogenic Wood-Ljungdahl pathway, and revealing geochemical ferruginous conditions at the transition between the sulfate reduction and fermentation zone as their preferential niche.

Succession and environmental response of sediment bacterial communities in the Liao River Estuary at the centenary scale

Microbial community succession in turbulent estuarine environments is key to the understanding of microbial community development in estuaries. Centennial-scale sediment core samples collected from the Liao River Estuary (LRE) channel bar and side beaches were studied for geochemistry and 16S rRNA gene-based bacterial analyses. The results showed that bacterial community composition significantly differed between the sediments of the two sides of the channel bar, with Campilobacterota and Bacteroidota being dominant bacterial phyla in the tributary (T1, T2) and mainstream (MS1, MS2) sediment, respectively. Co-occurrence network of the bacterial community at the genus level showed more centralized and compacted topological features in tributary with weaker hydrodynamic, and the keystone taxas were Halioglobus, Luteolibacter, and Lutibacter in the bacterial community. The bacterial network structure had more edges and larger average degree in LRE sediments from the stage of the year 2016-2009 and the stage before 1939, which was possibly related to hydrodynamic conditions and nutrients. Stochastic processes (dispersal limitation) were the key factors driving bacterial community assembly in the LRE sediments. In addition, total organic carbon (TOC), total sulfur (TS), and grain size were the main deterministic factors affecting the change of bacterial community structure. Relative microbial abundance has the potential to indicate geologically historical environmental changes. This study provided a new perspective to reveal the succession and response of bacterial communities under frequent fluctuation environments.

Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari)

Background

Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a ‘natural’ host microbiome. Focusing on an endangered elasmobranch species—the whitespotted eagle ray Aetobatus narinari—we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.

Results

Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.

Conclusion

For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00187-8.

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000-6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.