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1. New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage

   https://doi.org/10.1093/ismeco/ycaf068  

   Lanclos, Victoria Celeste; Feng, Xiaoyuan; Cheng, Chuankai; Yang, Mingyu; Hider, Cole J; Coelho, Jordan T; Kojima, Conner Y; Barnes, Shelby J; Cleveland, Catie S; Xie, Mei; et al (January 2025, ISME Communications)

   Abstract The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all Roseobacters in surface oceans and has predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best-known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name Candidatus Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007T (= ATCC TSD-433T = NCMA B160T). 

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2. Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov.

   https://doi.org/10.1002/yea.3905  

   Opulente, Dana A; Langdon, Quinn K; Jarzyna, Martin; Buh, Kelly V; Haase, Max_A B; Groenewald, Marizeth; Hittinger, Chris Todd (December 2023, Yeast)

   Abstract A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genusPichia. Strain yHMH446 falls within a clade that includesPichia norvegensis,Pichia pseudocactophila,Candida inconspicua, andPichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to allPichiaspecies with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results,Pichia galeolatasp. nov. is proposed to accommodate yHMH446^T(=NRRL Y‐64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions. 

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3. Draft genome sequences of two Pseudomonas strains isolated from ¹²⁹ I plumes at the Hanford Site

   https://doi.org/10.1128/MRA.00526-23  

   Robinson, Courtney J.; Oliver, Jerome J.; Anike, Alexis; Howard, M. Hope; Saunders, Danielle L.; Lee, Brady D. (November 2023, Microbiology Resource Announcements)

   Putonti, Catherine (Ed.)

   ABSTRACT Pseudomonasstrains DVZ6 and DVZ24 were isolated from a sediment trap incubated in an¹²⁹I plume at the Hanford Site (Washington State, USA). Whole-genome sequencing of the strains revealed that both genomes are 5.77 Mb in size, with a G + C content of 64.75%. 

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4. Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility

   https://doi.org/10.1038/s41598-024-61115-1  

   Chander, Atul Munish; de_Melo_Teixeira, Marcus; Singh, Nitin K; Williams, Michael P; Parker, Ceth W; Leo, Patrick; Stajich, Jason E; Torok, Tamas; Tighe, Scott; Mason, Christopher E; et al (December 2024, Scientific Reports)

   Abstract Members of the familyTrichomeriaceae,belonging to theChaetothyrialesorder and theAscomycotaphylum, are known for their capability to inhabit hostile environments characterized by extreme temperatures, oligotrophic conditions, drought, or presence of toxic compounds. The genusKnufiaencompasses many polyextremophilic species. In this report, the genomic and morphological features of the strain FJI-L2-BK-P2 presented, which was isolated from the Mars 2020 mission spacecraft assembly facility located at the Jet Propulsion Laboratory in Pasadena, California. The identification is based on sequence alignment for marker genes, multi-locus sequence analysis, and whole genome sequence phylogeny. The morphological features were studied using a diverse range of microscopic techniques (bright field, phase contrast, differential interference contrast and scanning electron microscopy). The phylogenetic marker genes of the strain FJI-L2-BK-P2 exhibited highest similarities with type strain ofKnufia obscura(CBS 148926^T) that was isolated from the gas tank of a car in Italy. To validate the species identity, whole genomes of both strains (FJI-L2-BK-P2 and CBS 148926^T) were sequenced, annotated, and strain FJI-L2-BK-P2 was confirmed asK. obscura.The morphological analysis and description of the genomic characteristics ofK. obscuraFJI-L2-BK-P2 may contribute to refining the taxonomy ofKnufiaspecies. Key morphological features are reported in thisK. obscurastrain, resembling microsclerotia and chlamydospore-like propagules. These features known to be characteristic features in black fungi which could potentially facilitate their adaptation to harsh environments. 

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5. Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation

   https://doi.org/10.7717/peerj.14211  

   Heng, Sobroney; Sutheeworapong, Sawannee; Champreda, Verawat; Uke, Ayaka; Kosugi, Akihiko; Pason, Patthra; Waeonukul, Rattiya; Ceballos, Ruben Michael; Ratanakhanokchai, Khanok; Tachaapaikoon, Chakrit (January 2022, PeerJ)

   Background Cellulolytic, hemicellulolytic, and amylolytic (CHA) enzyme-producing halophiles are understudied. The recently defined taxon Iocasia fonsfrigidae consists of one well-described anaerobic bacterial strain: NS-1 T . Prior to characterization of strain NS-1 T , an isolate designated Halocella sp. SP3-1 was isolated and its genome was published. Based on physiological and genetic comparisons, it was suggested that Halocella sp. SP3-1 may be another isolate of I. fronsfrigidae . Despite being geographic variants of the same species, data indicate that strain SP3-1 exhibits genetic, genomic, and physiological characteristics that distinguish it from strain NS-1 T . In this study, we examine the halophilic and alkaliphilic nature of strain SP3-1 and the genetic substrates underlying phenotypic differences between strains SP3-1 and NS-1 T with focus on sugar metabolism and CHA enzyme expression. Methods Standard methods in anaerobic cell culture were used to grow strains SP3-1 as well as other comparator species. Morphological characterization was done via electron microscopy and Schaeffer-Fulton staining. Data for sequence comparisons ( e.g. , 16S rRNA) were retrieved via BLAST and EzBioCloud. Alignments and phylogenetic trees were generated via CLUTAL_X and neighbor joining functions in MEGA (version 11). Genomes were assembled/annotated via the Prokka annotation pipeline. Clusters of Orthologous Groups (COGs) were defined by eegNOG 4.5. DNA-DNA hybridization calculations were performed by the ANI Calculator web service. Results Cells of strain SP3-1 are rods. SP3-1 cells grow at NaCl concentrations of 5-30% (w/v). Optimal growth occurs at 37 °C, pH 8.0, and 20% NaCl (w/v). Although phylogenetic analysis based on 16S rRNA gene indicates that strain SP3-1 belongs to the genus Iocasia with 99.58% average nucleotide sequence identity to Iocasia fonsfrigida NS-1 T , strain SP3-1 is uniquely an extreme haloalkaliphile. Moreover, strain SP3-1 ferments D-glucose to acetate, butyrate, carbon dioxide, hydrogen, ethanol, and butanol and will grow on L-arabinose, D-fructose, D-galactose, D-glucose, D-mannose, D-raffinose, D-xylose, cellobiose, lactose, maltose, sucrose, starch, xylan and phosphoric acid swollen cellulose (PASC). D-rhamnose, alginate, and lignin do not serve as suitable culture substrates for strain SP3-1. Thus, the carbon utilization profile of strain SP3-1 differs from that of I. fronsfrigidae strain NS-1 T . Differences between these two strains are also noted in their lipid composition. Genomic data reveal key differences between the genetic profiles of strain SP3-1 and NS-1 T that likely account for differences in morphology, sugar metabolism, and CHA-enzyme potential. Important to this study, I. fonsfrigidae SP3-1 produces and extracellularly secretes CHA enzymes at different levels and composition than type strain NS-1 T . The high salt tolerance and pH range of SP3-1 makes it an ideal candidate for salt and pH tolerant enzyme discovery. 

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