Microbiology Resource Announcements

Here we report the complete organellar genome sequences of Medakamo hakoo, a green alga identified in freshwater in Japan. It has 90.8-kb plastid and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein coding genes, respectively, representing the smallest organellar genome among currently known core Trebouxiophyceae.

The draft genome sequence of the soil bacterium Pedococcus sp. 5OH_020, isolated on a natural vitamin B12 analog, contains 4.4 Mbp with 4,108 protein-coding genes. Its genome encodes B12-dependent enzymes including methionine synthase and class II ribonucleotide reductase. Taxonomic analysis suggests it is a novel species within the genus Pedococcus.

A hybrid sequencing approach, using short and long reads sequencing, was employed for characterizing the genomes of the free-living amoeba host Vermamoeba vermiformis, along with its Dependentiae endosymbiont Vermiphilus pyriformis. The amoeba host reconstructed nuclear genome is 39.5 Mb, and its full mitochondrial genome is 61.7 kb. The closed, circular genome of the Dependentiae endosymbiont Vermiphilus pyriformis, naturally infecting V. vermiformis is 1.1 Mb.

Here we report the discovery of a novel Sediminibacterium sequenced from laboratory cultures of freshwater stream cyanobacteria from sites in Southern California, grown in BG11 media.

We present the complete genome sequences of two strains of Teredinibacter turnerae, SR01903 and SR02026, shipworm endosymbionts isolated from the gills of Lyrodus pedicellatus and Teredo bartschi, respectively, and derived from Oxford Nanopore sequencing. These sequences will aid in the comparative genomics of shipworm endosymbionts and understanding of host-symbiont selection.

The genus Sinorhizobium comprises rhizobia that fix nitrogen in symbiosis with legumes. To support taxonomic studies of this genus and of rhizobia more broadly, we report complete genome sequences and annotations for the species type strains Sinorhizobium garamanticum LMG 24692T and Sinorhizobium numidicum LMG 27395T and CIP 109850T. Average nucleotide identity and core-genome phylogenetic analyses confirm that S. garamanticum and S. numidicum represent distinct species.

We report the complete genome sequences of eight Fusobacterium watanabei clinical isolates, ranging from 1.95 to 2.09 Mbp. Analysis against the Genome Taxonomy Database (GTDB) indicates that Fusobacterium watanabei genomes are part of the "Fusobacterium nucleatum_J" group, which also encompasses the previously published FNU strain and Fna C1 isolates.

We report the draft genomes of four Kluyveromyces marxianus isolates obtained from the elaboration process of henequen (Agave fourcroydes) mezcal, a Mexican alcoholic beverage. The average nucleotide identity (ANI) analysis revealed that isolates derived from agave plants are distinct from those from other environments, including agave fermentations.

Janthinobacterium is a genus of Gram-negative environmental bacteria that survive extreme conditions by forming biofilms and producing pigments. Janthinobacterium sp. LS2A, an extremophile isolated from soil in the Chilean Patagonia, contains seven known biosynthetic gene clusters, including the purple pigment violacein, which may aid in its survival in harsh environments.

We report the complete CDS of five viruses: an iflavirus, a protoambidensovirus and three microviruses),which were detected by viromics surveillance of mosquitoes (Aedes albopictus and Culex quinquefasciatus) from the Reunion Island. We detected the protoambidensovirus, which belongs to aclade previously reported only in C. pipiens, in A. albopictus.

We isolated a gammaproteobacterial methanotrophic strain FWC3, from canal sediment from Western India. The strain oxidizes methane and can also grow on methanol. The draft genome of the same was sequenced which showed a size of [~]3.4 Mbp and 63% GC content. FWC3 is a coccoid, pale pink pigmented methanotroph and is seen in the form of diplococci, triplets, tetrads or small aggregates. After comparison of the complete 16S rRNA gene sequence, average amino-acid similarities and digital DNA-DNA hybridization values with that of the neighboring type species, we propose that the strain belongs to a novel genus and species, Ca. Methylolobus aquaticus FWC3Ts.

Enterococcus mundtii is a Gram-positive bacterium found in the environment and mammalian gastrointestinal tracts. It is also an infrequent cause of infections in humans. Here, we describe isolation, sequencing, and genomic analysis of four isolates of E. mundtii obtained from soil. These strains will be valuable tools for future work on understuded species of Enterococcus.

A Gram-positive, obligately anaerobic coccobacillus, with the white raised circular colony was isolated from the cecum of feral chickens in Brookings, South Dakota, USA. The 16S rRNA gene sequence analysis suggested that the closest species to strain SW178 was Ruminococcus torques ATCC 27756T (96.94% similarity) that belongs to the family Lachnospiraceae. The genome of strain SW178 is 3.18 Mbp with G+C content of 46.9 mol%. Based on the phylogenetic and phenotypic comparison, we propose that strain SW178 be assigned to the genus Ruminococcus as a novel species, for which the name Ruminococcus catenae is proposed. The type strain is SW178 (= CCOS 1886 T, =DSM 109242T).

The emergence of the mobile resistance-nodulation-division (RND)-type efflux pump tmexCD-toprJ gene cluster that confers multidrug resistance (MDR), including tigecycline resistance, in gram-negative bacteria poses a global public health threat. However, the spread of such clinically important antimicrobial resistance genes (ARGs) in the natural environment has not yet been well investigated. In this study, we investigated MDR aquatic bacteria in Vietnam. A carbapenem- and tigecycline-resistant Shewanella xiamenensis isolate NUITM-VS2 was obtained from urban drainage in Hanoi, Vietnam, in October 2021. S. xiamenensis NUITM-VS2 showed resistance to most antimicrobials tested, including tigecycline, tetracyclines, carbapenems, cephalosporins, fluoroquinolone, and aminoglycosides. Whole-genome analysis was performed by long- and short-read sequencing, resulting in the complete genome sequence consisting of one chromosome and five plasmid sequences. ARGs and plasmid replicons in the genome were detected using ResFinder with the custom ARG database, including all known tigecycline resistance genes, and PlasmidFinder, respectively. A 152.2-kb IncC plasmid, pNUITM-VS2_2, co-carried two mobile tigecycline resistance genes, tet(X4) and tmexC3.2D3.2-toprJ1. In addition, a 24.8-kb untypeable plasmid, pNUITM-VS2_4, carried the carbapenemase gene blaNDM-1. pNUITM-VS2_2 was transferred to Escherichia coli by conjugation, which simultaneously conferred high-level resistance against many antimicrobials, including tigecycline. To the best of our knowledge, this is the first report of the detection of the mobile RND-type efflux pump gene cluster tmexCD-toprJ in Shewanella species. Our results provide genetic evidence of the complexity of the dynamics of clinically important ARGs among aquatic bacteria, which could be important reservoirs for ARGs in the natural environment.

Compared with bacterial and archaeal extremophiles, single-celled eukaryotes living in extreme habitats are understudied and underrepresented in genomic databases. An exception is the obligately halophilic stramenopile Halocafeteria seosinensis strain EHF34. A transcriptome-focused analysis of this extremophilic protists revealed the importance of organic osmolyte regulation and transport in its adaptation to hypersaline environments. However, genomic resources for H. seosinensis are currently limited to a highly fragmented assembly generated by short-read sequencing, which has hindered further investigation of the genome biology and evolution of this fascinating organism. Here, we used long-read Oxford Nanopore sequencing to generate a highly contiguous, chromosome-scale genome assembly for H. seosinensis. The assembly is 38.8 megabase pairs (Mbp) in size and contains 60 nuclear contigs, making it the most contiguous genome for a member of the order Bicosoecida. Approximately 19% of the genome is comprised of transposable elements. Of the 11,684 predicted protein-coding genes, many appear to be associated with DNA mobility-related functions, and several may be linked to adaptation to a hypersaline environment. Analysis of the H. seosinensis long-read genome assembly presented herein will facilitate our understanding of the ways in which protists have adapted to extreme environments. SignificanceHalocafeteria seosinensis is an extremophilic protist adapted to hypersaline environments. Previous analyses of a transcriptome and short-read draft genome assembly for this organism provided insights into the molecular mechanisms underlying osmotic regulation, which facilitate its adaptation to high-salt conditions. However, the lack of contiguity and quality of the draft assembly prevented the characterization of complex genomic regions, including transposable elements and viral insertions, as well as genomic comparisons with related species. Here we present a highly contiguous, chromosome-scale genome assembly for H. seosinensis that enables accurate gene prediction, detailed analysis of repeat content, and comparative genomic analysis. This long-read genome assembly will serve as a valuable resource for studying one of the few tractable halophilic protists sequenced to date.

SARS-CoV-2 (SC2) variants of concern (VOC) continue to emerge and spread globally, threatening the use of monoclonal antibody therapies and vaccine effectiveness. Several mutations in the SC2 spike glycoprotein have been associated with reduction in antibody neutralization. Genomic surveillance of SC2 variants has been imperative to inform the public health response regarding the use of clinical therapies in specific jurisdictions based on the proportion of particular variants (e.g., Gamma (P.1)) in a region. Florida Department of Health Bureau of Public Health Laboratories (BPHL) performs tiled-amplicon whole genome sequencing for baseline and targeted surveillance of SC2 isolates in Florida from clinical specimens collected from county health departments and hospitals throughout the state. Here, we describe the introduction of SC2 lineage A.2.5 in Florida, which contains S:L452R (a substitution of therapeutic concern) and two novel Spike INDELS, the deletion of 141-143 and ins215AGY, with unknown implications on immune response. The A.2.5 lineage was first detected in Florida among an outbreak at a healthcare facility in January 2021, and subsequent A.2.5 isolates were detected across all geographical regions throughout the state. A time-scaled maximum clade credibility phylogeny determined there were at least eight separate introductions of A.2.5 in the state. The time of introduction of a monophyletic Florida clade was established to be December 2020. The Spike INDELS were determined to reside in the N-terminal domain, a region associated with antibody neutralization. As community transmission of SARS-CoV-2 in Florida continues, genomic surveillance of circulating variants in Florida and the detection of emerging variants are critical for informing public health response to COVID-19.

Full genome sequences of seven mycobacteriophages isolated from environmental soil samples are presented. These bacteriophages, with their respective cluster or subclusters, are Duplo (A2), Dynamo (P1), Gilberta (A11), MaCh (A11), Nikao (K1), Phloss (N), and Skinny (M1). All were temperate Siphoviridae, with genome sizes ranging from 43,107-82,071 bp.

The Atacama Desert is home to bacteria that use biofilms as a means of protecting themselves against the harsh environment. We cultured and sequenced the genomes of three Bacillus sp. isolates from the soil of the Atacama Desert. This information will inform research in survival mechanisms of eubacteria in the Atacama Desert.

Cutaneotrichosporon oleaginosus is an oleaginous yeast with a high content of fatty acids and can accumulate more than 40% of its weight in lipids. It can grow on a wide range of carbon sources and side streams such as crude glycerol. The genome sequence of C. oleaginosus ATCC 20509 is reported here to contribute to its development as a biotechnological platform for producing microbial oils.

Using an isolation chip (iChip), two bacterial strains, MME1T and MME2, exhibiting ovoid to curved rod cell morphologies and white-cream colony pigmentation were isolated from the surface of estuarine sediment at Niv[a] Bugt Strandenge Bird Sanctuary, Denmark (55{degrees}5542.6N 12{degrees}3123.6E). Analysis of the 16S rRNA gene sequence of these isolates suggested them to be members of the genus Psychromonas, as both had above 97.5 % 16S rRNA gene similarity with Psychromonas aquimarina strain JAMM 0404T. Further genomic comparisons suggested MME strains to be representatives of a novel species, having an average nucleotide identity (ANI) < 85 % relative to all other genome sequenced species of the Psychromonas genus. The G+C content was 39.5 mol %. The species was facultative anaerobic, growing optimally at 15 - 20 {degrees}C and pH 7.0. The optimal salinity was lower than for other described species of the genus with 1 - 2 % NaCl, reflecting the estuarine source of isolation. GC-MS analyses identified C16:0, C16:1{omega}7c/ C16:1{omega}7t/ and C14:03OH as the predominant cellular fatty acids. Based on molecular, phenotypic, and chemotaxonomic analyses, we propose that MME1 and MME2 represent a novel species of the genus Psychromonas with the name Psychromonas aestuarii sp. nov. with the MME1T (= DSM 118464T =LMG 33722T) as the type strain.