Complete genome sequence of Cellulomonas sp. strain ATA003.

The Gram-positive, rod-shaped endophytic bacterium Cellulomonas sp. strain ATA003 was isolated from the endemic cactus Maihueniopsis domeykoensis seeds collected in the Coastal Atacama Desert, Chile. Here, we present a circular genome with a size of 4,084,881 bp and a GC content of 73.8% obtained by Nanopore sequencing.

Clay-associated microbial communities and their relevance for a nuclear waste repository in the Opalinus Clay rock formation.

Microorganisms are known to be natural agents of biocorrosion and mineral transformation, thereby potentially affecting the safety of deep geological repositories used for high-level nuclear waste storage. To better understand how resident microbial communities of the deep terrestrial biosphere may act on mineralogical and geochemical characteristics of insulating clays, we analyzed their structure and potential metabolic functions, as well as site-specific mineralogy and element composition from the dedicated Mont Terri underground research laboratory, Switzerland. We found that the Opalinus Clay formation is mainly colonized by Alphaproteobacteria, Firmicutes, and Bacteroidota, which are known for corrosive biofilm formation. Potential iron-reducing bacteria were predominant in comparison to methanogenic archaea and sulfate-reducing bacteria. Despite microbial communities in Opalinus Clay being in majority homogenous, site-specific mineralogy and geochemistry conditions have selected for subcommunities that display metabolic potential for mineral dissolution and transformation. Our findings indicate that the presence of a potentially low-active mineral-associated microbial community must be further studied to prevent effects on the repository's integrity over the long term.

Genome Sequence of Arthrobacter sp. Strain ATA002, a Seed Endophytic Bacterium from the Atacama Desert.

The Gram-positive diazotrophic seed endophytic bacterium Arthrobacter sp. strain ATA002 was isolated from seeds of the endemic cactus Maihueniopsis domeykoensis collected in the Atacama Desert, Chile. Here, we present a circular genome sequence, obtained by Nanopore sequencing, with a size of 3,904,590 bp and a GC content of 65.9%.

Draft Genome Sequence of Paenalcaligenes niemegkensis NGK35T, Isolated from Plastic-Polluted Soil of an Abandoned Landfill.

The Gram-negative bacterium Paenalcaligenes niemegkensis NGK35T was isolated from plastic debris in an abandoned landfill. It has the ability to grow on polyethylene and hexadecane as the sole carbon sources. Here, we report the corresponding draft genome, which contains 3.66 Mbp and is characterized by a G+C content of 52.1%.

Draft Genome Sequence of Nocardioides alcanivorans NGK65T, a Hexadecane-Degrading Bacterium.

The Gram-positive bacterium Nocardioides alcanivorans NGK65T was isolated from plastic-polluted soil and cultivated on medium with polyethylene as the single carbon source. Nanopore sequencing revealed the presence of candidate enzymes for the biodegradation of polyethylene. Here, we report the draft genome of this newly described member of the terrestrial plastisphere.

Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste.

Strain NGK65T, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65T hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0-1% NaCl and at pH 7.5-8.0. Glycerol, d-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate, sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C16:0 followed by iso-C17:0 and C18:1 ω9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65T belongs to the genus Nocardioides (phylum Actinobacteria), appearing most closely related to Nocardioides daejeonensis MJ31T (98.6%) and Nocardioides dubius KSL-104T (98.3%). The genomic DNA G+C content of strain NGK65T was 68.2%. Strain NGK65T and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9% as well as digital DNA-DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides. Based on phenotypic and molecular characterization, strain NGK65T can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65T (=DSM 113112T=NCCB 100846T).

Paenalcaligenes niemegkensis sp. nov., a novel species of the family Alcaligenaceae isolated from plastic waste.

Strain NGK35T is a motile, Gram-stain-negative, rod-shaped (1.0-2.1 µm long and 0.6-0.8 µm wide), aerobic bacterium that was isolated from plastic-polluted landfill soil. The strain grew at temperatures between 6 and 37 °C (optimum, 28 °C), in 0-10 % NaCl (optimum, 1 %) and at pH 6.0-9.5 (optimum, pH 7.5-8.5). It was positive for cytochrome c oxidase, catalase as well as H2S production, and hydrolysed casein and urea. It used a variety of different carbon sources including citrate, lactate and pyruvate. The predominant membrane fatty acids were C16 : 1 cis9 and C16 : 0, followed by C17 : 0 cyclo and C18 : 1 cis11. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, followed by diphosphatidyglycerol. The only quinone was ubiquinone Q-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK35T belongs to the genus Paenalcaligenes (family Alcaligenaceae), appearing most closely related to Paenalcaligenes hominis CCUG 53761AT (96.90 %) and Paenalcaligenes suwonensis ABC02-12T (96.94 %). The genomic DNA G+C content of strain NGK35T was 52.1 mol %. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Paenalcaligenes. Based on phenotypic and molecular characterization, strain NGK35T can clearly be differentiated from its phylogenetic neighbours establishing a novel species, for which the name Paenalcaligenes niemegkensis sp. nov. is proposed. The type strain is NGK35T (=DSM 113270T=NCCB 100854T).

Anaerobic methanotrophic communities thrive in deep submarine permafrost.

Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ13C-methane signatures distinguish horizons of potential AOM coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate potential activity of AOM communities in submarine permafrost sediments at low temperatures. Modeled potential AOM consumes 72-100% of submarine permafrost methane and up to 1.2 Tg of carbon per year for the total expected area of submarine permafrost. This is comparable with AOM habitats such as cold seeps. We thus propose that AOM is active where submarine permafrost thaws, which should be included in global methane budgets.