Microbiology Resource Announcements

Three novel Pseudomonas species associated with healthy plants are described from the United States. They are Pseudomonas arenae sp. nov. from soybean in Missouri and Phragmites sp. in New Jersey; Pseudomonas glycinis sp. nov. from Vaccinium macrocarpon fruit in Massachusetts, groundwater in Tennessee and soybean in Indiana; and Pseudomonas harudinis sp. nov. from Phragmites sp. in New Jersey. No pathogenic strains are known for any of the novel species based on genome comparisons to assemblies in GenBank.

Two novel Pseudomonas species associated with healthy plants and other habitats are described from the United States. They are Pseudomonas zeiradicis strain PI116 from corn in Missouri, compost from Massachusetts, urban soil from Iowa and water of Lake Erie; and Pseudomonas soyae strain JL117 from soybean in Indiana and Wisconsin, and soil in Wyoming. No plant pathogenic strains are known for any of the novel species based on genome comparisons to assemblies in GenBank.

Three new Curtobacterium species from healthy tissues of agricultural crop plants in the United States are reported. They are Curtobacterium glycinis sp. nov. from soybean in Missouri, Curtobacterium gossypii from cotton in Puerto Rico and corn in Missouri, and Curtobacterium oryzae sp. nov. from rice in Texas.

Four novel bacterial species collected from healthy tissues of corn, rice and soybean plants in the United States are described. These include Cellulomonas zeae sp. nov. isolated from corn in Indiana; Lelliottia zeae sp. nov. from corn in Indiana and rice in Arkansas; Paraburkholderia zeae sp. nov. isolated from corn in Iowa; and Sphingomonas zeigerminis sp. nov. from corn in Mississippi and soy in Arkansas. No pathogenic strains are known for any of the novel species based on genome comparisons to assemblies in GenBank.

Five novel species from healthy plants and other substrates are described. These are Paenibacillus glycinicola sp. nov. from Glycine max in Iowa, United States; Paenibacillus triticicola sp. nov. from Triticum aestivum in Australia, Allium cepa in Texas, garden soil in Wisconsin, cows milk in New York state, Panicum virgatum in Michigan, sweet sorghum in Nebraska, and Zea mays in Ohio; Pseudescherichia oryzae sp. nov. from Oryza sativa in Arkansas; Pseudomonas gossypii sp. nov. from a healthy Bos taurus in Kansas, Capsicum annuum from Arizona, Gossypium hirsutum in New Mexico, Oklahoma, and Texas, and Zea mays from Arkansas; and Tardiphaga zeae sp. nov. from Zea mays in Iowa. No pathogenic strains are known for any of the novel species.

A number of bacteria with close resemblance to Vibrio cholerae has been isolated over the years by the Centers for Disease Control and Prevention (CDC), which could not be assigned a proper taxonomic designation based on preliminary identification methods. Nine such isolates have been found to share 16S rRNA gene identity exceeding 99% with V. cholerae, yet DNA-DNA hybridization (60.4-62.1%) and average nucleotide identity values (94.4-95.1%) were below the species cut-off, indicating a potentially novel species. Phylogenetic analysis of core genomes places this group of isolates in a monophyletic clade, within the "Cholerae clade," but distinct from any other species. Extensive phenotypic characterization reveals unique biochemical properties that distinguish this novel species from V. cholerae. Comparative genomic analysis reveals a unique set of siderophore genes, suggesting that iron acquisition strategies could be vital for the divergence of the novel species from a common ancestor with V. cholerae. Based on genetic, phylogenetic, and phenotypic differences observed, we propose these isolates represent a novel species of the genus Vibrio, for which the name Vibrio tarriae sp. nov. is proposed. Strain 2521-89 (= DSM 112461 = CCUG 75318), isolated from lake water, is the type strain. Author NotesThe GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain 2521-89 is MW773202.1. The genome sequences (genome assemblies) of strains 2521-89, 2523-88, 2015V-1076, 2016V-1018, 2016V-1062, 2017V-1038, 2017V-1070 and 2017V-1124 are deposited under the accession number NZ_CP022353.1, QKKG01000001.1, QKKH00000000.1, QKKI00000000.1, QKKJ00000000.1, QKKK00000000.1, QKKM00000000.1, and QKKN00000000.1, respectively. All the whole genome sequences are deposited under bioproject ID: PRJNA391152.

A new Vibrio strain K08M4T was isolated from the broad-nosed pipefish Syngnathus typhle in the Kiel Fjord. Infection experiments revealed that K08M4T is highly virulent for juvenile pipefish. Cells of strain K08M4T are Gram-stain-negative, curved rod-shaped and motile by means of a single polar flagellum. The strain can grow aerobically at 9 to 40{degrees}C, at pH 4 to 10.5 and tolerates up to 12% (w/v) NaCl. The most prevalent (> 10%) cellular fatty acids of K08M4T were C16:1{omega} 7c and C16:0. Whole-genome comparisons revealed that K08M4T represents a separate evolutionary lineage which is distinct from other Vibrio species and falls within the Vibrio Splendidus clade. The genome is 4,886,292 bp in size, consists of two circular chromosomes (3,298,328 bp, 1,587,964 bp), and comprises 4,178 protein-coding genes and 175 RNA genes. In this study, we describe the phenotypic features of the new isolate and present the annotation and analysis of its complete genome sequence. Based on these data, the new isolate represents a new species for which we propose the name Vibrio syngnathi. The type strain is K08M4T (=DSM 109818T). Supplementary materialOne supplementary figure and six supplementary table are available with the online version of the Manuscript.

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 Gram-positive and obligately anaerobic bacterium was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. The microorganism grew at 37-45{degrees} C and pH 6-7.5. This strain produced acetic acid as the primary metabolic end product. Major fatty acids were C12:0, C14:0, C14:0 DMA and summed feature 1 (C13:1 at 12-13 and C14:0 aldehyde). Phylogenetic analyses based on 16S rRNA gene sequence suggested that strain SW165 belongs to the family Atopobiaceae with the closest relatives being Olsenella profusa DSM 13989T (96.33% similarity), Olsenella umbonate DSM 26220T (96.18%) and Olsenella uli DSM 7084T (96.03%). Genome sequencing revealed a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the highest G+C content among members of the genus Olsenella. Phylogenetic and phenotypic comparison indicated that strain SW165 represents a novel species of the genus Olsenella, for which the name Olsenella lakotia sp. nov. is proposed. The type strain is SW165 (=DSM 107283T).

Stenotrophomonas goyi sp. nov. has been isolated from a contaminated algal culture (Chlamydomonas reinhardtii). Its genome has been fully sequenced (4,487,389 base pairs) and a tentative annotation is provided (4,147 genes). The genome information suggests that S. goyi sp. nov. is unable to use sulfate and nitrate as sulfur and nitrogen sources, respectively. Growth tests have confirmed the dependence of the sulfur-containing amino acids methionine and cysteine. The potential biotechnological interest of this bacteria is discussed here and in a related research paper (Fakhimi et al., 2023b).

A novel chemoheterotrophic psychrophilic bacterium, designated as strain I4T was isolated form a permanent snowfield in Washington State, USA. Growth is extremely slow, regardless of temperate (tested between 4{degrees}-25{degrees} C) but was had marginal optimal growth at 8.5{degrees} C. I4T was determined to be able to utilize 102 of the 190 tested carbon sources, 70 or the 95 tested nitrogen sources, 34 or the 59 tested phosphorous sources, and 10 of the 35 tested sulfur sources. I4T was seen to grow from pH 5.0-5.5 but could grow as low as 4.5 pH and as high as 9.5 pH with specific amendments. The genome of I4T was sequenced and it is approximate 4.0 Mb and has a G + C content of 66.2 mol%. Phylogenomic analyses using two independent methods places I4T within the genus Sphingomonas with S. sanguinis being its closest relative. On the basis of its genomic, physiological, and morphological properties, I4T (=ATCC TSD-357T= NCIMB 15472T) is proposed as the type strain of a novel species, Sphingomonas nivalis sp. nov.

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.

The first completed, circular mitochondrial genome and the first draft chloroplastic genome of Northern Atlantic blue diatom Haslea ostrearia (Naviculaceae, Bacillariophyceae) are described. The mitochondrial genome is composed of 38,696 bases and contains 64 genes, including 31 protein-coding genes (CDS), 2 ribosomal RNA (rRNA) genes and 23 transfer RNA (tRNA) genes. For the chloroplast, the genome is composed of 130,200 bases with 169 genes (131 CDS, 6 rRNA genes, 31 tRNA genes, and 1 transfermessenger RNA (tmRNA) gene). Phylogenetic trees suggest the proximity of all H. ostrearia strains yet available and the possibility to use these genomes as future references.

Chlamydomonas reinhardtii (Chlamydomonas hereafter) is a powerful model organism for studies of photosynthesis, ciliary motility, and other cellular processes [1-4]. The CLiP library of mapped nuclear random insertion mutants [5,6] has accelerated progress for hundreds of laboratories in these fields by providing mutants in genes of interest. However, its value was limited by its modest coverage of the genome with high-confidence disruption alleles (46% of nuclear protein-coding genes with 1+ high-confidence allele in exons/introns; 12% of genes with 3+ alleles in exons/introns). Here we introduce the CLiP2 (Chlamydomonas Library Project 2) library, which greatly expands the number of available mapped high-confidence insertional mutants. The CLiP2 library includes 71,700 strains, covering 79% of nuclear protein-coding genes with 1+ high-confidence allele in exons/introns and 49% of genes with 3+ alleles in exons/introns. The mutants are available to the community via the Chlamydomonas Resource Center.

A bacterial strain designated NG3T was isolated from a drinking water samples collected from Nagar Kurnool, Telangana State, India (16{degrees} 29 14.5356 N ; 78{degrees} 18 33.966) and characterized using a polyphasic taxonomic approach, Strain NG3T was Gram-negative, aerobic, non pigmented and motile by means of a single polar flagellum. Growth occurred at 18 - 37{degrees} C (optimum 27 - 32{degrees} C), pH at 6.5 - 8.0 (Optimum 7.0 - 7.5) and in the presence of 0-2% NaCl (Optimum 0.7-1.0%), Phylogenetic analyses based on 16S rRNA gene sequence showed that strain NG3T belonged to the genus Rheincheimera and its most closely related neighbor was Rheinheimera aquatica GR5T (GQ168584) with sequence similarity of 99 %. The cellular fatty acid composition of strain NG3T showed a spectrum of 11 fatty acids with a pronounced dominance of saturated fatty acids (82.7 %), including a high abundance of C16 : 0, C18 : 1{omega}7c, and C12 : 0 3-OH. The major respiratory quinone was MK-7 and Q-8. The DNA G+C content of the genomic DNA was 48.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, aminolipid and two uncharacterized phospholipids. The DNA-DNA relatedness of strain NG3T with respect to recognized members of the genus Rheinheimera was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain NG3T represents a novel species in the genus Rheinheimera, for which the name Rheinheimera palamurensis sp. nov. was proposed. The type strain is NG3T (=GU566360=JCM16716=KCTC23111).

We describe sequencing and assembly of complete Halococcus dombrowskii H4T (=ATCC BAA-364T) genome using short- and long-read sequencing technologies. The first closed genome within its genus is composed of a 2,767,537 bp chromosome and five additional plasmids totalling 3,965,466 bp, with GC content of 62.18%. The genome contains 4,029 genes, 3,963 coding sequences and two CRISPR arrays. Unusually, this Euryarchaeote carries multiple rRNA operons with divergent ITS identities across both its chromosome and plasmids.

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).

Strain LLG6346-3.1T, isolated from the thallus of the brown alga Ericaria zosteroides collected in Mediterranean Sea near Bastia in Corsica, France, was characterized using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, motile by gliding, rod-shaped and grew optimally at 30-33 {degrees}C, at pH 8-8.5 and with 4-5 % NaCl. Strain LLG6346-3.1T used the seaweed polysaccharide alginic acid as sole carbon source which was vigorously liquefied. Phylogenetic analyses showed that the bacterium is affiliated to the genus Zobellia (family Flavobacteriaceae, class Flavobacteriia). Strain LLG6346-3.1T exhibited 16S rRNA gene sequence similarity values of 98.5 and 98.3 % to the type strains of Zobellia russellii and Zobellia roscoffensis respectively, and of 97.4-98.2 % to other species of the genus Zobellia. The DNA G+C content of strain LLG6346-3.1T was determined to be 38.28 mol%. Digital DNA-DNA hybridization predictions by the ANI and GGDC methods between strain LLG6346-3.1T and other members of the genus Zobellia showed values of 76-88 %, and below 37 %, respectively. The phenotypic, phylogenetic and genomic analyses show that strain LLG6346-3.1T is distinct from species of the genus Zobellia with validly published names and that it represents a novel species of the genus Zobellia, for which the name Zobellia alginoliquefaciens sp. nov. is proposed. The type strain is LLG6346-3.1T (RCC 7657T = LLG 32918T).

A hydrogenotrophic methanogen, designated strain ACI-7T, was isolated from an alkaline, saline wetland located in eastern Nebraska, USA. Cells were identified as non-motile rods (0.9-4.2 m in length and 0.2-0.4 {micro}m in diameter) that occurred singly, in chains, and as long filaments and twisted aggregates. Strain ACI-7T utilized H2 + CO2 or formate as methanogenic substrates and required growth factors present in yeast extract for continuous cultivation. The strain grew at 20-45{degrees}C (optimum, 40{degrees}C), at pH 6.5-8.5 (optimum, pH 7.3) and with 0-2.5% NaCl (optimum, 0-1%). The genomic G+C content of ACI-7T was 31.79 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated strain ACI-7T was affiliated with the genus Methanobacterium, most closely related to Methanobacterium oryzae FPiT (97.1% sequence similarity) and Methanobacterium veterum MK4T (96.9% sequence similarity). Overall genome relatedness indices for strain ACI-7T compared to other Methanobacterium species ranged from 68.45-78.17% for average nucleotide identity and 18.9-25.7% for digital DNA-DNA hybridization. Morphological, physiological, and genomic characteristics indicate that strain ACI-7T represents a novel species, for which the name Methanobacterium nebraskense sp. nov. is proposed. The type strain is ACI-7T (=DSM 118696T=ATCC TSD-487T).

Recent rumen microbiome metagenomics papers1,2 have published hundreds of metagenome-assembled genomes (MAGs), comparing them to 4,941 MAGs published by Stewart et al3 in order to define novelty. However, there are many more publicly available MAGs from ruminants. In this paper, for the first time, all available resources are combined, catalogued and de-replicated to define putative species-level bins. As well as providing new insights into the constitution of the rumen microbiome, including an updated estimate of the number of microbial species in the rumen, this work demonstrates that a lack of community-adopted standards for the release and annotation of MAGs hinders progress in microbial ecology and metagenomics.