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 yHMH446T(=NRRL Y‐64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.
more »
« less
Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility
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 148926T) 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 148926T) 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.
more »
« less
- Award ID(s):
- 2215705
- PAR ID:
- 10656450
- Publisher / Repository:
- Nature Portfolio
- Date Published:
- Journal Name:
- Scientific Reports
- Volume:
- 14
- Issue:
- 1
- ISSN:
- 2045-2322
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
An endosymbiotic bacterium of the genusSodalis, designated as strain HZT, was cultured from the parasitoid waspSpalangia cameroni, which develops on the pupae of various host flies. The bacterium was detected inS. cameronideveloped on houseflies,Musca domestica, in a poultry facility in Hazon, northern Israel. After culturing, this bacterium displayed no surface motility on Luria–Bertani agar and was rod-shaped and irregular in size, ~10–30 nm in diameter and 5–20 µm in length. Phylogenetic analyses revealed that strain HZTis closely related toSodalis praecaptivusstrain HST, a free-living species of the genusSodalisthat includes many insect endosymbionts. Although these bacteria maintain >98% sequence identity in shared genes, genomic characterization revealed that strain HZThas undergone substantial reductive evolution, such that it lacks many gene functions that are maintained inS. praecaptivusstrain HST. Based on the results of phylogenetic, genomic and chemotaxonomic analyses, we propose that this endosymbiont should be classified in a new subspecies asS. praecaptivussubsp. spalangiaesubsp. nov. The type strain for this new subspecies is HZT(=ATCC TSD-398T=NCIMB 15482T). The subspeciesSodalis praecaptivussubsp.praecaptivusstrain HSTis created automatically with the type strain ATCC BAA-2554T(=DSMZ 27494T).more » « less
-
Glass, Jennifer B (Ed.)ABSTRACT Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of thePlanctomycetes-Verrucomicrobia-Chlamydia(PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2Tfrom microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2Trepresents a novel species within thePontiellagenus in theKiritimatiellotaphylum (within the PVC superphylum). Strain NLcol2Tis able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T(= DSM 113125T= MCCC 1K08672T) is proposed to be the type strain of a novel species in thePontiellagenus, and the namePontiella agarivoranssp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of theKiritimatiellotaphylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2Texpands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.more » « less
-
Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genusSaccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containingSaccharomycopsis lassenensis,Saccharomycopsis fermentans,Saccharomycopsis javanensis,Saccharomycopsis babjevae,Saccharomycopsis schoeniiandSaccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains withSaccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set ofSaccharomycopsisspecies whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer toSaccharomycopsis fodiensandSaccharomycopsissp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The nameSaccharomycopsis praedatoriasp. nov. is proposed to accommodate the novel species. The holotype ofSaccharomycopsis praedatoriais CBS 16589T. The MycoBank number is MB849369.S. praedatoriawas able to kill cells ofSaccharomyces cerevisiaeby means of penetration with infection pegs, a trait common to most species ofSaccharomycopsis.more » « less
-
Abstract The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all roseobacters in surface oceans and have 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 nameThalassovivens spotae, gen nov., sp. nov. for the type strain US3C007T.more » « less
An official website of the United States government

