Publications

4877

Abstract Sandy sediments of the coastal ocean are generally not considered a habitat for highly active sulfate-reducing microorganisms (SRM) due to fluctuations in oxygen concentrations and carbon availability. This study investigated the taxonomic composition and gene expression patterns of sulfate-reducing communities in both sandy, organic-poor sediments and muddy, organic-rich sediments in the mesohaline southern Baltic Sea. Our results revealed that a novel order-level lineage within the class Thermodesulfovibrionia (phylum Nitrospirota), named Arenidesulfomonadales, contributed significantly to sulfate reduction in the sandy sediments and supported sulfate reduction rates similar to those in the organic-rich, muddy sediments. In the sands, Thermodesulfovibrionia effectively competed with Desulfobacterales, which strongly dominated the sulfate-reducing communities in the organic-rich sediments. Metatranscriptomic data revealed that Desulfobacterales functioned as typical secondary fermenters in both sediment types and expressed nearly complete sets of genes for the catabolism of fermentation products such as lactate, propionate, and butyrate. In contrast, the gene expression profile of Thermodesulfovibrionia suggests that hydrogenotrophic sulfate reduction, coupled with carbon fixation via the Wood–Ljungdahl pathway and a reduced capacity to oxidize organic compounds, was a competitive metabolic strategy enabling sulfate reduction to proceed independently of fermentation-derived carbon. Overall, our results suggest that overlooked lineages of SRM may contribute to higher levels of sulfate reduction than previously assumed in the extensive areas of permeable sediments of coastal and shelf seas.

Abstract The candidate phylum Cloacimonadota is frequently detected in anoxic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood. Metagenomic evidence suggests capacities for amino acid fermentation, carbohydrate degradation, as well as a potential role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from an acidified lab-scale anaerobic baffled reactor fed with sugar beet pulp, where an increase in the relative abundance of Cloacimonadota correlated with recovery of methanogenesis, resulting in increased methane content in the produced biogas. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of the dominant Cloacimonadota operational taxonomic unit (OTU). Furthermore, using a curated database of 204 genome-resolved Cloacimonadota species, we characterized the phylum-level metabolic potential. Comparative genomics revealed alternative proteins, including 2-oxoglutarate:ferredoxin oxidoreductase and aspartate aminotransferase, likely to substitute for missing enzymes in the classical mmc pathway. These proteins were widely distributed and highly conserved across the analyzed Cloacimonadota genomes, suggesting that this variant of the SPO pathway could represent a phylum-specific trait. Moreover, we hypothesize that these alternative pathway steps may link propionate metabolism to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a potential syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.

Abstract Dermatophilaceae polyphosphate-accumulating organisms (PAOs), formerly classified as Tetrasphaera PAOs, play pivotal roles in enhanced biological phosphorus removal (EBPR). However, their phylogenetic diversity, ecological preferences, and metabolic traits remain poorly characterized, and a robust marker gene for their classification is lacking. Here, we performed an extensive phylogenomic and metabolic analysis of Dermatophilaceae PAOs utilizing 46 newly recovered metagenome-assembled genomes from a laboratory-scale EBPR reactor treating high-strength wastewater and full-scale wastewater treatment plants. These analyses revealed a previously uncharacterized PAO genus, named here as Candidatus Dermatophostum, which shows specific preference for high-phosphorus environments. Its representative species, Ca. Dermatophostum ammonifactor, was enriched in the EBPR reactor and its PAO phenotype was confirmed by polyphosphate staining and fluorescence in situ hybridization. Integrative meta-omics combining genomic, transcriptomic, and protein structure analyses revealed its specialized metabolic capabilities for phosphate metabolism, glycogen synthesis, and dissimilatory nitrate reduction to ammonium. Moreover, Ca. Dermatophostum was found to be widely distributed across wastewater treatment plants worldwide, underscoring both its diverse metabolic capabilities and potential engineering implications for mitigating nitrous oxide (N2O) emissions for EBPR system. Finally, we propose a ppk1-based classification framework that resolves Dermatophilaceae PAOs into six distinct clades, consistent with whole-genome phylogeny, and demonstrates that ppk1 can serve as a reliable marker gene for tracking these populations. Together, these findings expand the ecological and functional understanding of Dermatophilaceae PAOs and highlight their promise for advancing sustainable wastewater treatment and resource recovery.

An anaerobic, salt-tolerant, rod-shaped bacterium, strain JL216-2 T , was isolated from the shell of the hydrothermal gastropod Alviniconcha marisindica in the Tianxiu hydrothermal field on the Carlsberg Ridge, Indian Ocean. Cells of strain JL216-2 T were motile and 0.5×3–6 µm in size. Strain JL216-2 T grew at 10–32 °C (optimal 28 °C), pH 6.0–9.0 (optimal pH 7.0) and 0.5–12.0% (w/v) sodium chloride(NaCl, optimal 2.5%). Strain JL216-2 T exhibited metabolic versatility, being capable of heterotrophic growth on complex organic compounds. It also performed autotrophic growth by utilizing carbon dioxide (CO₂) fixation or sodium bicarbonate (NaHCO 3 ) as the sole carbon source, driven by hydrogen oxidation coupled with Fe(III) reduction. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to Helicovermis profundi S502 T (90.43% sequence similarity). The genome size of strain JL216-2 T was 4.91 Mb, with a G+C content of 39.54 mol%. Phylogenomic analysis and overall genome relatedness indices values indicated a close relatedness of strain JL216-2 T to H. profundi S502 T and Fusibacter spp. The combined genotypic and phenotypic data showed that strain JL216-2 T represents a novel genus within the order Eubacteriales . The type strain is JL216-2 T (=MCCC M30262 T =KACC 23553 T ).

Abstract The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB release 10 (R10-RS226) spans 715 230 bacterial and 17 245 archaeal genomes organized into 136 646 bacterial and 6968 archaeal species clusters. Fewer new major branches of prokaryotic life are being discovered with each release of GTDB, suggesting that we are beginning to saturate readily discoverable microbial diversity through culture-independent analyses. However, species discovery continues unabated as >95% of bacterial and archaeal species remain to be genomically elucidated based on conservative projections. We present additions to the GTDB website, methodological improvements, policy changes, notable nomenclatural updates, and user applications. We conclude with a summary of future plans for the resource including a fungal taxonomy and a nomenclatural extension to classify pathogens.