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Here, we report the complete genome sequence of Sphingobacterium sp. PAMC25397, isolated from Ny-Ålesund, Spitsbergen, Norway. The genome is 5.2 Mb in length with a GC content of 37%. This genome harbors biodegradation-related genes involved in benzoate degradation.
Solar radiation impacts most life forms on Earth as an energy source or a regulatory signal. Still, relatively little is known about phototrophic potential and strategies of environmental bacteria beyond cyanobacteria. This study explores the phototrophy related genomic diversity of Sphingomonas faeni strains from boreal, sub-arctic and arctic regions. We analyzed the genomes of 25 plant-associated S. faeni strains isolated from Vaccinium myrtillus, Oxyria digyna, V. vitis-idaea, and Bistorta vivipara, along with a reference S. faeni genome MA-Olki. The strains showed diversity both in overall genome level but also in phototrophic capabilities: Seven strains were identified as aerobic anoxygenic phototrophic bacteria with a complete photosynthesis gene cluster, 16 strains contained xanthorhodopsin genes, and three strains were non-phototrophic, possessing no aerobic anoxygenic phototrophic or xanthorhodopsin genes. Aerobic anoxygenic phototrophic strains were found exclusively in Vaccinium hosts. O. digyna contained only xanthorhodopsin containing strains and B. vivipara showed xanthorhodopsin genes and one non-phototrophic strain. V. vitis-idaea hosted strains for all three different phototrophy categories. Phylogenetic analyses showed aerobic anoxygenic phototrophic positive strains forming a tight phylogenetic group. Xanthorhodopsin strains and non-phototrophic strains clustered into three different subgroups. Phototrophic strains had more photoreceptors. Aerobic anoxygenic phototrophic strains encoded two 5-aminolevulinic acid synthase isoenzymes, one from a hemT-like gene within the photosynthesis gene cluster and one from a hemA-like gene elsewhere in the genome. Our genomic analysis reveals substantial diversity in phototrophic potential among strains of a single bacterial species isolated from different host plants, possibly reflecting the distinct environmental cues each strain encountered.
Polyethylene is increasingly accumulating in nature, including remote places like the Arctic. While abiotic processes fragment polyethylene in situ, biotic transformation by microorganisms is assumed to occur. However, the enzymes and pathways involved remain poorly characterized. In this study, we used an in-house biobank from cold environments to screen for potential bacteria capable of degrading polyethylene by screening the strains in silico using the database PlasticDB and in vivo using a fluorescence-based assay. Using transcriptomic and proteomic analyses to identify genes in promising candidate strains that encode extracellular enzymes potentially capable of degrading PE, we selected a Rhodococcus erythropolis strain and two of its enzymes: a hypothetical protein (Hypr1) and a lipase family protein (Lip2). Expressing the candidate genes heterologously in Escherichia coli resulted in positive results in the fluorescence-based assay for polyethylene transformation. Applying 13C-labelled polyethylene for assessing and estimating polyethylene transformation and carbon assimilation, we found that R. erythropolis and both untransformed and recombinant E. coli extracellularly transformed the initially added polyethylene after 70 days. In addition, untransformed E. coli and R. erythropolis converted small, but significant amounts of polyethylene-derived carbon to carbon dioxide. The 13C-label was also traced into the bacterial biomass of R. erythropolis. Overall, our results provide evidence for biotic transformation of untreated polyethylene and suggests a hypothetical protein and a lipase family protein as two novel enzyme candidates associated with PE transformation.
Glutathione is a key intracellular antioxidant, playing a crucial role in resisting oxidative stress and maintaining cellular redox homeostasis. However, the glutathione metabolic capacity of Tenacibaculum remains poorly characterized. In this study, a Gram-stain-negative bacterium, Tenacibaculum sp. SM2510, was isolated from seawater collected from Kongsfjorden, Svalbard, Norway. Genome sequencing revealed that the strain possesses a single circular chromosome of 2,904,982 bp with a G + C content of 31.44%, encoding 2564 protein-coding genes. Genomic analysis indicates that Tenacibaculum sp. SM2510 may directly take up extracellular oxidized glutathione (GSSG) and reduce it to reduced glutathione (GSH) through a reductive pathway, which potentially allows the strain to alleviate the accumulation of reactive oxygen species (ROS) caused by strong ultraviolet radiation and low temperature in polar environments. Furthermore, genomic analysis predicts that the strain degrades GSH to produce essential life-sustaining substances. In conclusion, these results suggest that Tenacibaculum sp. SM2510 may potentially utilize exogenous glutathione for both antioxidant defense and nutrient acquisition through direct GSH degradation, providing new insights into the environmental adaptive evolution of polar marine bacteria.
Genome-resolved phylogenomics reveals widespread misclassification of metal-reducing bacteria historically assigned to Geobacter based on 16S rRNA gene phylogeny, and highlights species that persist only as 16S rRNA entries without genomes for robust taxonomic resolution. Here, we resolve two such lineages by integrating whole-genome phylogeny with average amino acid identity (AAI) and percentage of conserved proteins (POCP) across 418 dereplicated genomes of Desulfuromonadia. We report a draft genome of the psychrophilic iron-reducing bacterium Geobacter psychrophilus (100% completeness). Phylogenomic analyses place both Geobacter psychrophilus and the GTDB placeholder genus g__JACRCG01 within the family 'Pseudopelobacteraceae', outside Geobacteraceae sensu stricto. Within this framework, G. psychrophilus forms a distinct, well-supported lineage separated from neighbouring genera by discontinuities in AAI and POCP, supporting its reclassification as Irobacter psychrophilus comb. nov. Additionally, we show that Geosyntrophus acetoxidans, a non-axenic syntrophic bacterium, forms a coherent genus with 51 other environmental genomes (placeholder genus g__JACRCG01), for which we propose the replacement name Geosyntrophus gen. nov. Comparative genome analysis revealed conserved family-level metabolic traits together with genus-specific differences in respiratory metabolism, while ANI-based clustering identified substantial species-level diversity within both proposed genera. Metagenome and 16S rRNA-gene survey data further show that Geosyntrophus and Irobacter occur in broadly similar aquatic and subsurface habitats spanning from the Arctic to the Antarctic. Together, these results resolve the taxonomy of two previously ambiguous Desulfuromonadales lineages and shed light on their environmental distribution.