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Kim JS, Lee M, Ki DW, Kwon SW, Ko YJ, Kim JS, Yun BS, Kim SJ. Production of a New Biosurfactant by a New Yeast Species Isolated from Prunus mume Sieb. et Zucc. J Microbiol Biotechnol 2023; 33:1023-1029. [PMID: 37280777 PMCID: PMC10468678 DOI: 10.4014/jmb.2205.05052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 03/21/2023] [Accepted: 04/21/2023] [Indexed: 06/08/2023]
Abstract
Biosurfactants reduce surface and interfacial tension due to their amphiphilic properties and are an eco-friendly alternative for chemical surfactants. In this study, a new yeast strain JAF-11 that produces a biosurfactant was selected using drop collapse method, and the properties of the extracts were investigated. The nucleotide sequences of the strain were compared with closely related strains and identified based on the D1/D2 domain of the large subunit ribosomal DNA (LSU) and internal transcribed spacer (ITS) regions. Neodothiora populina CPC 39399T, the closest species with strain JAF-11, showed a sequence similarity of 97.75% for LSU and 94.27% for ITS, respectively. The result suggests that the strain JAF-11 represents a distinct species that cannot be assigned to any existing genus or species in the family Dothideaceae. Strain JAF-11 produced a biosurfactant reducing the surface tension of water from 72 mN/m to 34.5 mN/m on the sixth day of culture and the result of measuring the critical micelle concentration (CMC) by extracting the crude biosurfactant was found to be 24 mg/l. The molecular weight 502 of the purified biosurfactant was confirmed by measuring the fast atom bombardment mass spectrum. The chemical structure was analyzed by measuring 1H nuclear magnetic resonance (NMR), 13C NMR, and two-dimensional NMRs of the compound. The molecular formula was C26H46O9, and it was composed of one octanoyl group and two hexanoyl groups to myo-inositol moiety. The new biosurfactant is the first report of a compound produced by a new yeast strain, JAF-11.
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Chen X, Chen XM, He JB, Yuan Q, Jiang MX, Wang JA, Jiang Y. Corynebacterium hylobatis sp. nov. and Corynebacterium lemuris sp. nov., two novel species of the genus Corynebacterium isolated from faeces of primates. Int J Syst Evol Microbiol 2023; 73. [PMID: 37534982 DOI: 10.1099/ijsem.0.005985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023] Open
Abstract
Two Gram-stain positive, aerobic, short-rod-shaped, catalase-positive, oxidase-negative and non-motile strains, designated YIM 101343T and YIM 101645T, were isolated from faeces of Hylobates hoolock and Lemur catta, respectively. The results of 16S rRNA gene analysis indicated that both represented members of the genus Corynebacterium, and they shared a similarity of 98.0 % with each other. Corynebacterium marinum DSM 44953T showed the highest similarity with both strains YIM 101343T (99.0 %) and YIM 101645T (97.3 %). The results of phylogenetic analysis based on 16S rRNA gene indicated that strain YIM 101343T formed a cluster with C. marinum DSM 44953T and Corynebacterium comes 2019T, strain YIM 101645T formed a cluster with Corynebacterium halotolerans YIM 70093T, and the two clusters were neighbours. The genomic size of strain YIM 101343T was 3068751 bp and that of strain YIM 101645T was 3169714 bp. The dDDH, ANI and AAI values among strains YIM 101343T, YIM 101645T and the closely related species indicated that the two isolates represented two different novel species. Both strains contained meso-diaminopimelic acid and short-chain mycolic acids, and the major menaquinones were MK-9(H2) and MK-8(H2). The major polar lipids of the two strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids (>10 %) of both strains were C16 : 0, summed feature 4 and C18 : 1ω9c, but C17 : 1 ω8c was only present as a major component in YIM 101645T . In addition, phenotypic and some chemotaxonomic characteristics of strains YIM 101343T, YIM 101645T and the closely related species were different. Thus, strains YIM 101343T and YIM 101645T should represent two novel species of the genus Corynebacterium, for which the names Corynebacterium hylobatis sp. nov. and Corynebacterium lemuris sp. nov. are proposed, respectively. The type strains are YIM 101343T (=DSM 45970T=CCTCC AB 2013221T) and YIM 101645T (=BCRC 16963T=CCTCC AB 2013281T=KCTC 39868T).
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Trinh NH, Kim J. Chitinophaga nivalis sp. nov., isolated from forest soil in Pyeongchang, Republic of Korea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37589171 DOI: 10.1099/ijsem.0.005981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Rod-shaped Gram-stain-negative, aerobic bacterial strains, designated PC14 and PC15T, were isolated from a forest soil sample collected in Pyeongchang county, Gangwon-do, Republic of Korea. Strains PC14 and PC15T grew at 15-37 °C (optimum, 28-30 °C in tryptone soya agar and Mueller-Hinton agar), hydrolysed chitin and casein, and tolerated pH 8.5 and 2 % (w/v) NaCl. The strains were most closely related to members of the genus Chitinophaga, namely Chitinophaga arvensicola DSM 3695T (98.4 %), Chitinophaga longshanensis Z29T (98.3 %), Chitinophaga ginsengisegetis Gsoil 040T (97.8 %), Chitinophaga polysaccharea MRP-15T (97.8 %) and Chitinophaga niastensis JS16-4T (97.7 %). The type strain grew well on conventional commercial media in the laboratory, including tryptone soya agar, Mueller-Hinton agar, Reasoner's 2A agar, nutrient agar and Luria-Bertani agar. The major polar lipid profile comprised phosphatidylethanolamine, an unidentified aminolipid and unidentified polar lipids. The major respiratory quinone was menaquinone-7. The main fatty acids were iso-C15:0, C16:1 ω5c, C16:0 3-OH, iso-C15:0 3-OH and iso-C17:0 3-OH. The DNA G+C content of the isolated strain based on the whole genome sequence was 46.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strains PC14 and PC15T and the reference type strains ranged from 71.0 to 76.5 %, and from 20.3 to 20.7 %, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain PC15T could be differentiated phylogenetically and phenotypically from the recognized species of the genus Chitinophaga. Therefore, strain PC15T is considered to represent a novel species, for which the name Chitinophaga nivalis sp. nov. is proposed. The type strain is PC15T (=KACC 22893T=JCM 35788T).
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Sharma A, Kaur E, Joshi R, Kumari P, Khatri A, Swarnkar MK, Kumar D, Acharya V, Nadda G. Systematic analyses with genomic and metabolomic insights reveal a new species, Ophiocordyceps indica sp. nov. from treeline area of Indian Western Himalayan region. Front Microbiol 2023; 14:1188649. [PMID: 37547690 PMCID: PMC10399244 DOI: 10.3389/fmicb.2023.1188649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Ophiocordyceps is a species-rich genus in the order Hypocreales (Sordariomycetes, Ascomycota) depicting a fascinating relationship between microbes and insects. In the present study, a new species, Ophiocordyceps indica sp. nov., is discovered infecting lepidopteran larvae from tree line locations (2,202-2,653 m AMSL) of the Kullu District, Himachal Pradesh, Indian Western Himalayan region, using combinations of morphological and molecular phylogenetic analyses. A phylogeny for Ophiocordyceps based on a combined multigene (nrSSU, nrLSU, tef-1α, and RPB1) dataset is provided, and its taxonomic status within Ophiocordycipitaceae is briefly discussed. Its genome size (~59 Mb) revealed 94% genetic similarity with O. sinensis; however, it differs from other extant Ophiocordyceps species based on morphological characteristics, molecular phylogenetic relationships, and genetic distance. O. indica is identified as the second homothallic species in the family Ophiocordycipitaceae, after O. sinensis. The presence of targeted marker components, viz. nucleosides (2,303.25 μg/g), amino acids (6.15%), mannitol (10.13%), and biological activity data, suggests it to be a new potential source of nutraceutical importance. Data generated around this economically important species will expand our understanding regarding the diversity of Ophiocordyceps-like taxa from new locations, thus providing new research avenues.
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Wang Z, Liu L, Hu D, Wang ET, Gu C, Wang H. Diversity of common bean rhizobia in blackland of northeastern China and their symbiotic compatibility with two host varieties. Front Microbiol 2023; 14:1195307. [PMID: 37485523 PMCID: PMC10362387 DOI: 10.3389/fmicb.2023.1195307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
The common bean (Phaseolus vulgaris L.) is an important crop in the world that forms root nodules with diverse rhizobia. Aiming to learn the rhizobial communities associated with the common bean in the black soil of Northeast China, 79 rhizobia were isolated from root nodules of two host varieties (Cuican and Jiadouwang) grown in two sites of blackland and were characterized by comparative sequence analyses of 16S rRNA, recA, atpD, nodC, and nifH genes, and whole genome. As a result, Rhizobium indigoferae, R. anhuiense, and R. croatiense as minor groups and three dominant novel Rhizobium species were identified based on their average nucleotide identity and DNA-DNA hybridization values to the type strains of relative species. This community composition of rhizobia associated with the common bean in the tested black soils was unique. Despite their different species affiliations, all of them were identified into the symbiovar phaseoli according to the phylogenies of symbiotic genes, nodC and nifH. While the phylogenetic discrepancies found in nodC, nifH evidenced that the evolutions of nodulation (nod) and nitrogen fixation (nif ) genes were partially independent. In addition, only one dominant rhizobial species was shared by the two common bean varieties grown in the two soil samples, implying that both the plant variety and the soil characteristics affected the compatibility between rhizobia and their hosts. These findings further enlarged the spectrum of common bean-nodulating rhizobia and added more information about the interactions among the soil factors, rhizobial species, and host plants in the symbiosis.
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Jung Y, Chhetri G, Kim I, So Y, Park S, Woo H, Lee KH, Seo T. Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37490399 DOI: 10.1099/ijsem.0.005989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4T and GMJ5T, were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4T and GMJ5T were both positive for catalase and oxidase. Strain PBS4-4T grew at 15-37 °C and pH 5.0-12.0. Strain GMJ5T grew at 15-37 °C and pH 5.0-11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4T and GMJ5T form a closely related cluster with the genus Chryseobacterium. The average nucleotide identity and digital DNA-DNA hybridization values between strain PBS4-4T and its closely related strains were 79.4-84.5% and 23.2-28.7 %, respectively. For GMJ5T, the values were 78.3-79.3% and 22.0-22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Strain GMJ5T had one other major fatty acid: iso-C17 : 0 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4T and GMJ5T represent novel species within the genus Chryseobacterium, and the names Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov. are proposed, respectively. The type strain of C. edaphi is PBS4-4T (=KACC 22882T=TBRC 17052T) and the type strain of C. gilvum is GMJ5T (=KACC 22883T=TBRC 17053T).
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Jung Y, Chhetri G, Kim I, So Y, Park S, Seo T. Ideonella oryzae sp. nov., isolated from soil, and Spirosoma liriopis sp. nov., isolated from fruits of Liriope platyphylla. Int J Syst Evol Microbiol 2023; 73. [PMID: 37409567 DOI: 10.1099/ijsem.0.005943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
Gram-negative, aerobic, motile by means of two or more polar or subpolar flagella, rod-shaped strain NS12-5T and Gram-negative, facultatively anaerobic, yellow-coloured, rod-shaped strain RP8T were isolated from rice rhizosphere soil and fermented fruits of Liriope platyphylla in the Republic of Korea, respectively. The result of phylogenetic analyses based on 16S rRNA gene sequences showed that strain NS12-5T was most closely related to Ideonella aquatica 4Y11T with 99.79 % sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain NS12-5T and species of the genus Ideonella were 75.6-91.7 % and 20.3-43.9 %, respectively. Growth occurred at 15-40 °C and pH 5-11, and NaCl was not needed for growth. The major fatty acids of strain NS12-5T were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0, and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain NS12-5T was 69.03 mol%. The result of phylogenetic analyses based on 16S rRNA gene sequences revealed that strain RP8T was most closely related to Spirosoma aureum BT328T with 96.01 % sequence similarity. The ANI and dDDH values between strain RP8T and reference strains of the genus Spirosoma were 72.9-76.4 % and 18.6-20.0 %, respectively. Growth occurred at 15-37 °C and pH 5-11, and NaCl was not needed for growth. The major fatty acids of strain RP8T were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 1 ω5c and iso-C15 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C contents of strain RP8T were 54.9 mol%. Based on phenotypic, genomic and phylogenetic results, strains NS12-5T and RP8T represent novel species in the genus Ideonella and Spirosoma, respectively, and the names Ideonella oryzae sp. nov. and Spirosoma liriopis sp. nov. are proposed. The type strain of I. oryzae sp. nov. is NS12-5T (=KACC 22691T=TBRC 16346T) and the type strain of S. liriopis is RP8T (=KACC 22688T=TBRC 16345T).
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Eilers T, Dillen J, Van de Vliet N, Wittouck S, Lebeer S. Lactiplantibacillus carotarum AMBF275 T sp. nov. isolated from carrot juice fermentation. Int J Syst Evol Microbiol 2023; 73. [PMID: 37505084 DOI: 10.1099/ijsem.0.005976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
A novel strain of the genus Lactiplantibacillus, named AMBF275T, was isolated from fermented carrot juice, a salted fermented beverage dominated by lactic acid bacteria. The results of phylogenetic analysis indicated that the 16S rRNA gene of AMBF275T is most similar to the 16S rRNA gene of Lactiplantibacillus garii FI11369T with a sequence similarity of 99.4 %. However, a genome-wide comparison using average nucleotide identity (ANI) revealed that AMBF275T and L. garii FI11369T have an ANI of only 82.35 %. ANI values between AMBF275T and other representative strains of species of the genus Lactiplantibacillus from the Genome Taxonomy Database (GTDB) were even lower than this 82.35 %, indicating that AMBF275T represents a distinct species. We thus propose the name Lactiplantibacillus carotarum sp. nov. for this novel species, with AMBF275T (=LMG 32885T, =CECT 30757T) as the type strain.
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Khanal M, Bhatta BP, Malla S. Isolation and Characterization of Bacteria Associated with Onion and First Report of Onion Diseases Caused by Five Bacterial Pathogens in Texas, U.S.A. PLANT DISEASE 2023:PDIS09222206SR. [PMID: 36451309 DOI: 10.1094/pdis-09-22-2206-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial diseases pose a severe challenge to growers and cause significant loss to the billion-dollar onion industry in the United States. Texas is the sixth largest onion producing state, yet the bacterial communities associated with short-day onion crops grown in Texas have not been studied. This study was conducted to identify, characterize, and understand the diversity of bacteria associated with onion production in Texas. In 2020, 190 foliar and 210 bulb samples were collected from onion crops in the Rio Grande Valley and Winter Garden regions of Texas. Sequencing of the 16s rRNA gene was used to identify each bacterial strains to a genus. The pathogenicity to onion of each bacterial strain was tested using three assays: a red onion scale assay, a yellow onion bulb assay, and a foliar assay. Whole genome sequencing was done to identify the onion-pathogenic strains to species. Collectively, isolates of 24 genera belonging to three phyla were detected, including 19 genera from foliar samples and nine genera from bulb samples. Isolates in the Phylum Proteobacteria, including 15 genera of Gram-negative bacteria, were the most abundant of the taxa, comprising 90.0% of the strains isolated. The diversity of foliar isolates was evenly distributed between Gram-positive and Gram-negative bacteria, while Gram-negative bacteria dominated the isolates from bulb samples. In total, 83.9% of the bacterial isolates were not pathogenic on onion, with only isolates of Pantoea, Pseudomonas, Burkholderia, Erwinia, Enterobacter, and Curtobacterium proving pathogenic. Strains of Burkholderia gladioli, Pseudomonas alliivorans, Pantoea agglomerans, P. ananatis, and P. allii are the first documented cases of these pathogens of onion in Texas. Identifying and characterizing the nature of onion microflora, including pathogens of onion, is vital to developing rapid disease detection techniques via pathogenomics and minimizing losses through the application of effective disease management measures.
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Li G, Leal-Dutra C, Cuesta-Maté A, Conlon B, Peereboom N, Beemelmanns C, Aanen D, Rosendahl S, de Beer Z, Poulsen M. Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution. PERSOONIA 2023; 51:257-279. [PMID: 38665980 PMCID: PMC11041896 DOI: 10.3767/persoonia.2023.51.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/14/2023] [Indexed: 04/28/2024]
Abstract
The genus Podaxis was first described from India by Linnaeus in 1771, but several revisions of the genus have left the taxonomy unclear. Forty-four Podaxis species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled Podaxis pistillaris. Recent molecular analyses based on barcoding genes suggest that the genus comprises several species, but their status is largely unresolved. Here we obtained basidiospores and photographs from 166 fungarium specimens from around the world and generated a phylogeny based on rDNA internal transcribed spacer ITS1,5.8S and ITS2 (ITS), and a phylogenomic analysis of 3 839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we propose that the genus includes at least 16 unambiguous species. Based on 10 type specimens (holotype, paratype, and syntype), four recorded species were confirmed, P. carcinomalis, P. deflersii, P. emerici, and P. farlowii. Comparing phylogenetic analysis with described species, including morphology, ecology, and distribution, we resurrected P. termitophilus and designated neotypes, epitypes, or lectotypes for five previously described species, P. aegyptiacus, P. africana, P. beringamensis, P. calyptratus, and P. perraldieri. Lastly, based on phylogenies and morphology of type material, we synonymized three reported species, P. algericus, P. arabicus, and P. rugospora with P. pistillaris, and described five new species that we named P. desolatus, P. inyoensis, P. mareebaensis, P. namaquensis, and P. namibensis. Citation: Li GS, Leal-Dutra CA, Cuesta-Maté A, et al. 2023. Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution. Persoonia 51: 257-279. doi: 10.3767/persoonia.2023.51.07.
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Kim W, Jang S, Chae N, Kim M, Yeh JY, Kim S, Lee YM. Hymenobacter canadensis sp. nov., isolated from freshwater of the pond in Cambridge Bay, Canada. Int J Syst Evol Microbiol 2023; 73. [PMID: 37326606 DOI: 10.1099/ijsem.0.005913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
A Gram-stain-negative, aerobic, reddish-coloured, rod-shaped and non-motile strain PAMC 29467T, was isolated from freshwater of the pond in Cambridge Bay, Canada. Strain PAMC 29467T was closely related to Hymenobacter yonginensis (98.1 % 16S rRNA gene similarity). Genomic relatedness analyses showed that strain PAMC 29467T is distinguishable from H. yonginensis based on average nucleotide identity (91.3 %) and digital DNA-DNA hybridization values (39.3 %). The major fatty acids (>10 %) of strain PAMC 29467T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0 iso, C16 : 1 ω5c and summed feature 4 (C17 : 1 iso l and/or anteiso B). The major respiratory quinone was menaquinone-7. The genomic DNA G+C content was 61.5 mol%. Strain PAMC 29467T was separated from the type species in the genus Hymenobacter by its distinct phylogenetic position and some physiological characteristics. As a result, a novel species is proposed, with the name Hymenobacter canadensis sp. nov. (type strain, PAMC 29467T=KCTC 92787T=JCM 35843T).
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Yao B, Huang R, Zhang Z, Shi S. Diverse Virulence Attributes of Pantoea alfalfae sp. nov. CQ10 Responsible for Bacterial Leaf Blight in Alfalfa Revealed by Genomic Analysis. Int J Mol Sci 2023; 24:ijms24098138. [PMID: 37175847 PMCID: PMC10179099 DOI: 10.3390/ijms24098138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Alfalfa is widely grown worldwide for its excellent nutritional value. Pantoea species living in alfalfa seeds can easily spread over great distances with frequent trade. However, the pathogenic properties of this dangerous hitchhiker on alfalfa have not been evaluated. Here, we identified the taxonomic status of Pantoea strain CQ10 isolated from the interior of alfalfa seeds based on the whole genome sequence. The diverse virulence attributes of strain CQ10 during host infection were characterized through pathogenicity assays and functional and genomic analyses. We report that strain CQ10 belongs to a novel species in the genus Pantoea, which was phylogenetically close to Pantoea vagans and Pantoea agglomerans. Strain CQ10 caused bacterial leaf blight of alfalfa after inoculation from the roots. We found that strain CQ10 possesses a large number of pathogenic genes involved in shaping the virulence properties during bacteria-host interactions, including motility, biofilm, type VI secretion system, and nutrient acquisition. Compared with P. vagans and P. agglomerans, the unique virulence factors of strain CQ10 were mainly involved in motility and biofilm, which were confirmed by in vitro experiments. Taken together, our results suggest that strain CQ10 is the first Pantoea species to infect alfalfa, and it possesses diverse virulence attributes among which motility and biofilm may be the best weapons.
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Liu SW, Luo KK, Li FN, Zhang BY, Zhang DJ, Sun CH. Georgenia halotolerans sp. nov., a halotolerant actinobacterium isolated from Taklamakan desert soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37227258 DOI: 10.1099/ijsem.0.005906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
A Gram-stain-positive, aerobic, non-motile, non-spore-forming and rod-shaped actinobacterium, designated strain 10Sc9-8T, was isolated from Taklamakan desert soil sampled in the Xinjiang Uygur Autonomous Region, China. Strain 10Sc9-8T grew at 8‒37 °C (optimum, 28‒30 °C), pH 6.0‒10.0 (optimum, pH 7.0-8.0) and in the presence of 0‒15 % (w/v) NaCl (optimum, 0-3 %). Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 10Sc9-8T was affiliated with members of the genus Georgenia and showed the highest 16S rRNA gene sequence similarity to Georgenia yuyongxinii Z443T (97.4 %). Phylogenomic analysis based on the whole genome sequences indicated that strain 10Sc9-8T should be assigned into the genus Georgenia. The average nucleotide identity and digital DNA-DNA hybridization values calculated from the whole genome sequences indicated that strain 10Sc9-8T was clearly separated from other closely related species of the genus Georgenia with values below the thresholds for species delineation. Chemotaxonomic analyses showed that the cell-wall peptidoglycan was in a variant of A4α type with an interpeptide bridge comprising l-Lys-l-Ala-Gly-l-Asp. The predominant menaquinone was MK-8(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, several unidentified phospholipids, glycolipids and one unidentified lipid. The major fatty acids were anteiso-C15 : 0, anteiso-C15 : 1 A and C16 : 0. The genomic DNA G+C content was 72.7 mol%. On the basis of phenotypic, phylogenetic and phylogenomic data, strain 10Sc9-8T represents a novel species of the genus Georgenia, for which the name Georgenia halotolerans sp. nov. is proposed. The type strain is 10Sc9-8T (=JCM 33946T=CPCC 206219T).
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Ye L, Zhang G, Pu J, Yang C, Liu Y, Xu M, Jin D, Lu S, Liu L, Yang J, Xu J. Cellulomonas xiejunii sp. nov., Cellulomonas chengniuliangii sp. nov. and Cellulomonas wangsupingiae sp. nov., three cellulolytic bacteria isolated from intestinal contents of Marmota himalayana. Int J Syst Evol Microbiol 2023; 73. [PMID: 37227268 DOI: 10.1099/ijsem.0.005909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Six facultative anaerobic, Gram-stain-positive, oxidase-negative, rod-shaped bacteria (strains zg-B89T, zg-B12, zg-Y338T, zg-Y138, zg-Y908T and zg-Y766), were isolated from the intestinal contents of Marmota himalayana in Qinghai Province, PR China. The 16S rRNA gene sequence analysis showed that zg-B89T showed highest similarity to Cellulomonas iranensis NBRC 101100T (99.5 %), zg-Y338T to Cellulomonas cellasea DSM 20118T (98.7 %), and zg-Y908T to Cellulomonas flavigena DSM 20109T (99.0 %). Phylogenetic and phylogenomic analysis based on 16S rRNA gene and 881 core genes revealed that these six strains formed three separate clades in the genus Cellulomonas. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between these three novel species and all members of the genus Cellulomonas were below species thresholds (95-96 % for ANI and 70 % for dDDH). The DNA G+C contents of zg-B89T, zg-Y338T and zg-Y908T were 73.6, 72.9 and 74.5 %, respectively. Strains zg-B89T and zg-Y908T had anteiso-C15 : 0, C16 : 0 and anteiso-C15 : 1 A, and zg-Y338T had anteiso-C15 : 0, C16 : 0 and iso-C16 : 0 as the main fatty acids. All novel type strains had MK-9 (H4) as the predominant respiratory quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside as the major polar lipids, and rhamnose, ribose and glucose as the cell-wall sugars. The peptidoglycan amino acids of zg-B89T, zg-Y338T and zg-Y908T contained ornithine, alanine, glutamic acid and aspartic acid (except for zg-Y338T). Based on genotypic, phenotypic, phylogenetic and biochemical properties, the six uncharacterized strains represent three novel species in the genus Cellulomonas, for which the names Cellulomonas xiejunii sp. nov. (type strain zg-B89T=GDMCC 1.2821T=KCTC 49756T), Cellulomonas chengniuliangii sp. nov. (type strain zg-Y338T=GDMCC 1.2829T=KCTC 49754T) and Cellulomonas wangsupingiae sp. nov. (type strain zg-Y908T=GDMCC 1.2820T=KCTC 49755T) are proposed, respectively.
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Gao R, Dong H, Liu Y, Yao Q, Li H, Zhu H. Sphingomonas lycopersici sp. nov., isolated from tomato rhizosphere soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37256772 DOI: 10.1099/ijsem.0.005920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
Two aerobic, Gram-stain-negative, non-motile and non-spore-forming rods bacterial strains, designated MMSM20T and MMSM24, were isolated from tomato rhizosphere soil and could produce indole-3-acetic acid and siderophore. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that strains MMSM20T and MMSM24 belonged to the genus Sphingomonas and were most closely related to three validly published species Sphingomonas jeddahensis G39T, Sphingomonas mucosissima DSM 17494T and Sphingomonas dokdonensis DSM 21029T. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains MMSM20T and MMSM24 were 97.6 and 81.0 %, respectively, demonstrating that they were conspecific. The ANI and dDDH values between the two strains and the three type strains above were below the threshold values for species delimitation. The genomic DNA G+C contents of strains MMSM20T and MMSM24 were 66.6 and 66.4 mol%, respectively. The major fatty acids of the two strains were identified as C14 : 0 2OH, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c); the predominant quinone was ubiquinone 10; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and unidentified lipids. Results of phenotypic and genotypic analyses supported that strains MMSM20T and MMSM24 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lycopersici sp. nov. is proposed. The type strain is MMSM20T (=GDMCC 1.3401T=JCM 35647T).
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Zhang G, Liu Y, Cheng Y, Yang J, Jin D, Lu S, Pu J, Li W, Ge Y, Ma C, Luo W, Xu J. Identification of Nocardioides marmotae sp. nov. and Nocardioides faecalis sp. nov., two new members of the genus Nocardioides. Int J Syst Evol Microbiol 2023; 73. [PMID: 37232277 DOI: 10.1099/ijsem.0.005875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
A polyphasic taxonomic characterization of two novel strain pairs (designated zg-579T/zg-578 and zg-536T/zg-ZUI104) isolated from the faeces of Marmota himalayana was conducted based on phylogenetic analysis of the nearly full-length 16S rRNA gene and genome, digital DNA-DNA hybridization, ortho-average nucleotide identity (Ortho-ANI), and phenotypic and chemotaxonomic traits. Comparative analysis of the nearly full-length 16S rRNA gene sequences showed that strain zg-579T was most closely related to Nocardioides dokdonensis FR1436T (97.57 %) and Nocardioides deserti SC8A-24T (97.36 %), whereas strain zg-536T had the highest similarity to Nocardioides caeni MN8T (98.33 %), Nocardioides convexus W2-2-3T (98.26 %) and Nocardioides daeguensis 2C1-5T (98.19 %). Low levels of DNA-DNA relatedness and Ortho-ANI values (19.8-31.0 %/78.6-88.2 %, zg-579T; 19.9-31.3 %/78.8-86.2 %, zg-536T) between the two new type strains and previously known species within the genus Nocardioides support the hypothesis that the four newly characterized strains could be considered to represent two novel species within this genus. The dominant cellular fatty acids found in strain pair zg-536T/zg-ZUI104 were iso-C16 : 0 and C18 : 1 ω9c, whereas C17 : 1 ω8c was major component in zg-579T/zg-578. Galactose and ribose were the main cell-wall sugars in these two new strain pairs. Diphosphatidylglycerol (DPG), phosphatidylcholine, phosphatidylglycerol (PG) and phosphatidylinositol (PI) were the major polar lipids in zg-579T, whereas DPG, PG and PI predominated in zg-536T. Both strain pairs had MK8(H4) as the major respiratory quinone and ll-diaminopimelic acid as the major cell-wall peptidoglycan. The optimal growth conditions for the two novel strain pairs were 30 °C, pH 7.0 and 0.5 % NaCl (w/v). Based on these polyphasic characterizations, two novel species within the genus Nocardioides are proposed, i.e. Nocardioides marmotae sp. nov. and Nocardioides faecalis sp. nov., with zg-579T (=CGMCC 4.7663T=JCM 33892T) and zg-536T (=CGMCC 4.7662T=JCM 33891T) as the type strains.
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Huang Q, Qian Z, Peng T, Li J, Ye X, Huang T, Hu Z. Novosphingobium mangrovi sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37204827 DOI: 10.1099/ijsem.0.005896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, designated as HK4-1T, was isolated from mangrove sediments in Hong Kong, PR China. Based on 16S rRNA gene sequence data, strain HK4-1T was found to belong to the genus Novosphingobium, family Erythrobacteraceae, and showed high similarity to Novosphingobium chloroacetimidivorans BUT-14T (96.88 %) and Novosphingobium indicum H25T (96.88 %). The G+C content of the whole genome of strain HK4-1T was 64.05 mol%. The major fatty acids were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and two unknown lipids. The predominant respiratory quinone was Q-10. Based on genomic, phylogenetic, phenotypic, physiological and chemotaxonomic data, strain HK4-1T should be classified as representing a novel species of the genus Novosphingobium, for which the name Novosphingobium mangrovi sp. nov. is proposed. The type strain of Novosphingobium mangrovi sp. nov. is HK4-1T (=MCCC 1K08252T=JCM 35764T).
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Wang H, Li Y, Gu Y, Zhou G, Chen X, Zhang X, Shao Z, Zhang J, Zhang M. Isolation and Genomic Characteristics of Cat-Borne Campylobacter felis sp. nov. and Sheep-Borne Campylobacter ovis sp. nov. Microorganisms 2023; 11:microorganisms11040971. [PMID: 37110394 PMCID: PMC10145079 DOI: 10.3390/microorganisms11040971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Nine novel bacterial strains were isolated from the feces of cats and sheep in 2019 and 2020 in Beijing, China. Cells were 1-3 μm long and ≤0.5 μm wide, Gram-stain negative, microaerobic, motile, oxidase positive, and urease negative. Phylogenetic analyses based on 16S rRNA gene sequences indicated that these nine isolates belong to the genus Campylobacter but formed two robust clades that were clearly separate from the currently recognized species and, respectively, isolated from the cat and sheep. Both these strains shared low 16S rRNA gene sequence similarity, dDDH relatedness, and ANI values with their closest species C. upsaliensis CCUG 14913T and C. lanienae NCTC 13004T, and against each other, which are below the cut-off values generally recognized for isolates of the same species. The genomic DNA G + C contents of type strains XJK22-1T and SYS25-1T were 34.99 mol% and 32.43 mol%, respectively. Electron microscopy showed that these cells were spiral shaped, with bipolar single flagella. Based on results from genotypic, phenotypic, phylogenetic, and phylogenomic analyses, these nine strains represent two novel species within the genus Campylobacter, for which the names Campylobacter felis sp. nov. (Type strain XJK22-1T = GDMCC 1.3684T = JCM 35847T) and Campylobacter ovis sp. nov. (Type strain SYS25-1T = GDMCC 1.3685T) are proposed.
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Wang W, Mu H, Ren X, Ouyang Q, Li J. Genome-based classification of Pedobacter polysacchareus sp. nov., isolated from Antarctic soil producing exopolysaccharide. FEMS Microbiol Lett 2023; 370:7110977. [PMID: 37028936 DOI: 10.1093/femsle/fnad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/28/2023] [Accepted: 04/06/2023] [Indexed: 04/09/2023] Open
Abstract
A psychrotolerant bacterial strain, designated ZS13-49T, with strong extracellular polysaccharide synthesis ability was isolated from soil collected in Antarctica and subjected to polyphasic taxonomic and comparative genomics. Chemotaxonomic features, including fatty acids, and polar lipid profiles, support the assignment of strain ZS13-49T to the genus Pedobacter. 16S rRNA gene phylogeny demonstrates that strain ZS13-49T forms a well-supported separate branch as a sister clade to Pedobacter gandavensis LMG 31462T and is clearly separated from Pedobacter steynii DSM 19110T and Pedobacter caeni DSM 16990T. Phylogenetic analysis showed strain ZS13-49T shared the highest 16S rRNA gene sequence similarity (99.9%) with P. gandavensis LMG 31462T. However, the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) value and average amino identity (AAI) value between strain ZS13-49T and P. gandavensis LMG 31462T were 26.5, 83.3 and 87.5%, respectively. Phylogenomic tree and a comparative genomic analysis indicated distinct characteristics to distinguish strain ZS13-49T from the closely related species. The complete genome sequence of strain ZS13-49T consists of 5 830,353 bp with 40.61% G + C content. Genomic features of strain ZS13-49T adapted to Antarctic environment were also revealed. Based on the phenotypic, chemotaxonomic and genomic data, strain ZS13-49T could be assigned to a novel species within the genus Pedobacter for which the name Pedobacter polysacchareus sp. nov. is proposed. The type strain is ZS13-49T ( = CCTCC AB 2019394T = KCTC 72824T).
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Hu Y, Li H, Chen Y, Zhang Q, Zheng S, Rao D, Chun Z, Zhao R. Paenibacillus dendrobii sp. nov., an indole-3-acetic acid-producing endophytic bacterium isolated from Dendrobium nobile. Int J Syst Evol Microbiol 2023; 73. [PMID: 37040428 DOI: 10.1099/ijsem.0.005824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
A novel rod-shaped, Gram-stain-positive, spore-forming and motile by peritrichous flagella strain, designated HJL G12T, was isolated from the root of Chinese herb Dendrobium nobile. Strain HJL G12T grew optimally at pH 7.0, 30 °C and in the presence of 1.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene and genomic sequences showed that HJL G12T clustered with Paenibacillus chibensis NBRC 15958T and Paenibacillus dokdonensis YH-JAE5T with 98.3 and 98.2 % sequence similarity. The DNA-DNA hybridization values between strain HJL G12T and the two reference strains were 23.6 % and 24.9 %, respectively. Menaquinone-7 was the only respiratory quinone and meso-diaminopimelic acid was present in the cell-wall peptidoglycan. Antesio-C15 : 0 and iso-C16 : 0 were detected to be the major cellular fatty acids. The cellular polar lipid profile contained diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysyl-phospatidylglycerol and three unidentified aminophospholipids. Based on these results, strain HJL G12T is considered to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus dendrobii sp. nov. is proposed, with HJL G12T (=NBRC 115617T=CGMCC 1.18520T) as the type strain.
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Liu Y, Zhang G, Yang J, Cheng Y, Ye L, Lai XH, Yang C, Ma C, Tao Y, Jin D, Lu S, Liu L, Xu J. Arthrobacter caoxuetaonis sp. nov., Arthrobacter zhangbolii sp. nov. and Arthrobacter gengyunqii sp. nov., isolated from Marmota himalayana faeces from Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2023; 73. [PMID: 37042839 DOI: 10.1099/ijsem.0.005742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
Six aerobic or facultative anaerobic, motile, Gram-stain-positive, catalase-positive and oxidase-negative strains (zg-Y453T, zg-Y324, zg-Y462T, zg-Y411, zg-Y809T and zg-Y786) were isolated from different faecal samples of Marmota himalayana from the Qinghai-Tibet Plateau. Pale yellow, round, raised and moist colonies appeared 48 h after incubation at 28 °C on brain-heart infusion plates supplemented with 5 % defibrinated sheep blood. According to the 16S rRNA gene sequence alignment, two strain pairs (zg-Y453T/zg-Y324 and zg-Y462T/zg-Y411) shared the highest similarities to Arthrobacter luteolus (99.5 and 99.2 %), and the other one (zg-Y809T/zg-Y786) to Arthrobacter citreus (99.5 %). Results of phylogenetic analysis based on the 16S rRNA gene and genome sequences showed that these six strains represented three separate species within the genus Arthrobacter. The average nucleotide identity and digital DNA-DNA hybridization values between the three novel type strains (zg-Y453T/zg-Y462T/zg-Y809T) and other known species in this genus were all below respective thresholds (70.2-81.5/19.6-24.2 %, 70.6-81.8/19.8-25.0 %, and 70.4-88.2/19.9-35.3 %). Although phylogenetically related, there were obvious chemotaxonomic and phenotypic differences: strain pair zg-Y462T/zg-Y411 had anteiso-C15 : 0 as the only major fatty acid; the three novel species had different dominant quinones, MK-8(H2) in strains zg-Y462T/zg-Y809T (74.8/81.1 %) and MK-8(H2)/MK-9(H2) (43.1/53.0 %) in zg-Y453T; similarly, the ability to reduce nitrate in strains zg-Y453T and zg-Y462T could differentiate them from zg-Y809T. All strains had diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, but differed slightly in the types of unidentified glycolipids, phospholipids and lipids. Based on the results of these polyphasic taxonomic analyses, three novel species within the genus Arthrobacter are proposed, namely Arthrobacter caoxuetaonis sp. nov. (type strain, zg-Y453T=GDMCC 1.2809T=JCM 35173T), Arthrobacter zhangbolii sp. nov. (type strain, zg-Y462T=GDMCC 1.2880T=JCM 35170T) and Arthrobacter gengyunqii sp. nov. (type strain, zg-Y809T=GDMCC 1.2808T=JCM 35168T).
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Dong K, Pu J, Yang J, Zhou G, Gao Y, Kang Z, Lei W, Ji X, Min G, Li H, Li J, Sun B, Xu J. Whole-genome sequencing of Paracoccus species isolated from the healthy human eye and description of Paracoccus shanxieyensis sp. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37068015 DOI: 10.1099/ijsem.0.005838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Currently, the genus Paracoccus comprises 76 recognized species. Members of Paracoccus are mostly isolated from environmental, animal, and plant sources. This report describes and proposes a novel species of Paracoccus isolated from clinical specimens of the human ocular surface. We isolated two aerobic, Gram-stain-negative, non-spore-forming, coccoid or short rod-shaped, and non-motile strains (designated DK398T and DK608) from conjunctival sac swabs of two healthy volunteers. The results showed that the strains grew best under the conditions of 28°C, pH 7.0, and 1.0 % (w/v) NaCl. Sequence analysis based on the 16S rRNA gene showed that strains DK398T and DK608 were members of Paracoccus, most similar to Paracoccus laeviglucosivorans 43PT (98.54 and 98.62 %), Paracoccus litorisediminis GHD-05T (98.34 and 98.41 %), and Paracoccus limmosus NB88T (98.21 and 98.29 %). Phenotypic analysis showed that DK398T and DK608 were positive for catalase and oxidase, negative for producing N-acetyl-β-glucosaminic acid, arginine dihydrolase, and β-glucuronidase but positive for leucine arylamidase. The predominant isoprenoid quinone was Q-10, and the major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and an unidentified glycolipid. The major fatty acids (>10%) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The meso-diaminopimelic acid was found in the cell wall peptidoglycan of DK398T. The major cell wall sugars were ribose and galactose. Based on the results of phylogenetic analyses, low (<83.22 %) average nucleotide identity, digital DNA-DNA hybridization (<26.0%), chemotaxonomic analysis, and physiological properties, strain DK398T represents a novel species of the genus Paracoccus, for which the name Paracoccus shanxieyensis sp. nov. is proposed. The type strain is DK398T (=CGMCC 1.17227T=JCM 33719T).
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Martín-Rodríguez AJ, Thorell K, Joffré E, Jensie-Markopoulos S, Moore ERB, Sjöling Å. Shewanella septentrionalis sp. nov. and Shewanella holmiensis sp. nov., isolated from Baltic Sea water and sediments. Int J Syst Evol Microbiol 2023; 73. [PMID: 37083582 DOI: 10.1099/ijsem.0.005767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Two bacterial strains, SP1W3T and SP1S2-7T, were isolated from samples of water and sediments collected in Vaxholm, a town located on the Stockholm archipelago in the Baltic Sea, in November 2021. The strains were identified as novel genomic species within the genus Shewanella, based upon comparative analysis of whole genome sequence data. Strain SP1W3T (genome size, 5.20 Mbp; G+C content, 46.0 mol%), isolated from water, was determined to be most closely related to S. hafniensis ATCC-BAA 1207T and S. baltica NCTC 10735T, with digital DNA-DNA hybridization (dDDH) values of 61.7% and 60.4 %, respectively. Strain SP1S2-7T (genome size, 4.26 Mbp; G+C content, 41.5 mol%), isolated from sediments, was observed to be most closely related to S. aestuarii JCM17801T, with a pairwise dDDH value of 33.8 %. Polyphasic analyses of physiological and phenotypic characteristics, in addition to genomic analyses, confirmed that each of these two strains represent distinct, novel species within the genus Shewanella, for which the names Shewanella septentrionalis sp. nov. (type strain SP1W3T=CCUG 76164T=CECT 30651T) and Shewanella holmiensis sp. nov. (type strain SP1S2-7T=CCUG 76165T=CECT 30652T) are proposed.
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Shao X, Meng D, Lei JX, Ding YY, Su JY, Wang YN, Li Y. Limimaricola litoreus sp. nov., isolated from intertidal sand of the Yellow Sea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37022765 DOI: 10.1099/ijsem.0.005772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
A novel species of the genus Limimaricola, designated ASW11-118T, was isolated from an intertidal sand sample of the Yellow Sea, PR China. Growth of strain ASW11-118T occurred at 10-40 °C (optimum, 28 °C), pH 5.5-8.5 (optimum, pH 7.5) and with 0.5-8.0 % (w/v) NaCl (optimum, 1.5%). Strain ASW11-118T has the highest 16S rRNA gene sequence similarity to Limimaricola cinnabarinus LL-001T (98.8%) and 98.6 % to Limimaricola hongkongensis DSM 17492T. Phylogenetic analysis based on genomic sequences indicated that strain ASW11-118T belongs to the genus Limimaricola. The genome size of strain ASW11-118T was 3.8 Mb and DNA G+C content was 67.8 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain ASW11-118T and other members of the genus Limimaricola were below 86.6 and 31.3 %, respectively. The predominant respiratory quinone was ubiquinone-10. The predominant cellular fatty acid was C18 : 1 ω7c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and one unknown aminolipid. On the basis of the data presented, strain ASW11-118T is considered to represent a novel species of the genus Limimaricola, for which the name Limimaricola litoreus sp. nov. is proposed. The type strain is ASW11-118T (=MCCC 1K05581T=KCTC 82494T).
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Li F, Xu S, Li Z, Yue Y, Song J, Du B, Che Y, Han L, Qiu X, Kang Y, Liu X, Chen S, Li Z. Nocardia pulmonis sp. nov., an actinomycete isolated from a patient with pulmonary infection. Int J Syst Evol Microbiol 2023; 73. [PMID: 37022776 DOI: 10.1099/ijsem.0.005728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
A novel bacterial strain, CDC141T, was isolated from sputum samples of a patient with pulmonary infection in Hainan Province, PR China. We performed a polyphasic study to assess the taxonomic position of the new species. Based on the results of 16S rRNA gene sequence analyses, strain CDC141T belonged to the genus Nocardia with the highest sequence similarity to Nocardia nova NBRC 15556T (98.84 %) and Nocardia macrotermitis RB20T (98.54 %). The dapb1 gene sequence-based phylogenetic and phylogenomic trees further showed that the novel strain was clustered in a distinct clade adjacent to Nocardia pseudobrasiliensis DSM 44290T. The DNA G+C content of strain CDC141T was 68.57 mol%. The genomic diversity analysis revealed low average nucleotide identity and in silico DNA‒DNA hybridization values (<84.7 and <28.9 %, respectively) with its closest relative. Growth occurred at 20-40 °C, pH 6.0-9.0 and with NaCl concentrations of 0.5-2.5 % (w/v). The main fatty acids of strain CDC141T were C16 : 0, C18 : 0 10-methyl, TBSA, C16 : 1 ω6c/C16 : 1 ω7c, C18 : 1 ω9c, C18 : 0, C17 : 1 iso I/anteiso B and C17 : 0. The polar lipid profile was dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, unidentified glycolipids, unidentified phospholipids and unidentified lipids. MK8 (H4ω-cycl) and MK8 (H4) were the major respiratory quinones. These characteristics were consistent with the typical chemotaxonomic properties of members of the genus Nocardia. Based on the results of phenotypic and genetic analyses, strain CDC141T was identified as representing a new species of the genus Nocardia, with the proposed name Nocardia pulmonis sp. nov. (CDC141T=JCM 34955T=GDMCC 4.207T).
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Chai C, Zhu L, Liu J, Han X, Nutaratat P, Khuuamwong P, Hui F. Spencerozyma pingqiaoensis sp. nov., a yeast species isolated from the external surface of rice leaves in China. Int J Syst Evol Microbiol 2023; 73. [PMID: 37022743 DOI: 10.1099/ijsem.0.005820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Four strains (NYNU 178247, NYNU 178251, DMKU-PAL160 and DMKU-PAL137) representing a novel yeast species were isolated from the external surfaces of rice and pineapple leaves collected in China and Thailand. Phylogenetic analysis based on the concatenated sequences of the internal transcribed spacer (ITS) regions and the D1/D2 domains of the large subunit rRNA gene revealed that the novel species belonged to the genus Spencerozyma. The D1/D2 sequence of the novel species differed from its closest relative, Spencerozyma acididurans SYSU-17T, by 3.2 % sequence divergence. The species also differed from Spencerozyma crocea CBS 2029T and Spencerozyma siamensis DMKU13-2T, by 3.0-6.9 % sequence divergence in the D1/D2 sequences out of 592 bp. In the ITS regions, the novel species displayed 19.8-29.2% sequence divergence from S. acididurans SYSU-17T, S. crocea CBS 2029T and S. siamensis DMKU13-2T out of 655 bp. Furthermore, the novel species could also be differentiated from the closely related species by some physiological characteristics. The species name of Spencerozyma pingqiaoensis sp. nov. (Holotype CBS 15238, Mycobank MB 844734) is proposed to accommodate these four strains.
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Kondo R. Pseudodesulfovibrio nedwellii sp. nov., a mesophilic sulphate-reducing bacterium isolated from a xenic culture of an anaerobic heterolobosean protist. Int J Syst Evol Microbiol 2023; 73. [PMID: 37115616 DOI: 10.1099/ijsem.0.005826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
A novel sulphate-reducing bacterium, strain SYKT, was isolated from a xenic culture of an anaerobic protist obtained from a sulphidogenic sediment of the saline Lake Hiruga in Fukui, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SYKT clustered with the members of the genus Pseudodesulfovibrio. The closest relative of strain SYKT was Pseudodesulfovibrio sediminis SF6T, with 16S rRNA gene sequence identity of 97.43 %. Digital DNA-DNA hybridisation and average nucleotide identity values between SYKT and species of the genus Pseudodesulfovibrio fell below the respective thresholds for species delineation, indicating that SYKT represents a novel species of the genus Pseudodesulfovibrio. Cells measured 1.7-3.7×0.2-0.5 µm in size and were Gram-stain-negative, obligately anaerobic, motile by means of a single polar flagellum and had a curved rod or sigmoid shape. Cell growth was observed under saline conditions from pH 6.0 to 9.5 (optimum pH 8.0-9.0) and at a temperature of 10-30 °C (optimum 25 °C). SYKT used lactate, pyruvate, fumarate, formate and H2 as electron donors. It used sulphate, sulphite, thiosulphate and sulphur as terminal electron acceptors. Pyruvate and fumarate were fermented. Major cellular fatty acids were anteiso-C15 : 0, C16 : 0, anteiso-C17 : 1ω9c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of SYKT was 49.4 mol%. On the basis of the the genetic and phenotypic features, SYKT was determined to represent a novel species of the genus Pseudodesulfovibrio for which the name Pseudodesulfovibrio nedwellii sp. nov. is proposed with type strain SYKT (=DSM 114958T=JCM 35746T).
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Guan Y, Li Z, Kang YH, Lee MK. Isolation, Characterization and WholeGenome Analysis of Paenibacillus andongensis sp.nov. from Korean Soil. J Microbiol Biotechnol 2023; 33:1-7. [PMID: 37072682 DOI: 10.4014/jmb.2211.11033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 04/20/2023]
Abstract
The genus Paenibacillus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4T (KCTC 43402T = GDMCC 1.3498T ), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4T . 16S rRNA sequence analysis showed that strain SS4T most closely resembled Paenibacillus marchantiophytorum DSM 29850T (98.22%), Paenibacillus nebraskensis JJ-59T (98.19%), and Paenibacillus aceris KCTC 13870T (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4T belongs to the genus Paenibacillus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4T was determined to belong to the genus Paenibacillus. Comparing P. marchantiophytorum DSM 29850T with average nucleotide identity (ANI 78.97%) and digital DNADNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4T can be classified as a Paenibacillus andongensis species and is a novel member of the genus Paenibacillus.
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Li J, Liang Y, He Z, An L, Liu Y, Zhong M, Hu Z. Tamlana laminarinivorans sp. nov. and Tamlana sargassicola sp. nov., two novel species isolated from Sargassum, show genomic and physiological adaptations for a Sargassum-associated lifestyle. Int J Syst Evol Microbiol 2023; 73. [PMID: 36884369 DOI: 10.1099/ijsem.0.005706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
The genus Tamlana from the Bacteroidota currently includes six validated species. Two strains designated PT2-4T and 62-3T were isolated from Sargassum abundant at the Pingtan island coast in the Fujian Province of China. 16S rRNA gene sequence analysis showed that the closest described relative of strains PT2-4T and 62-3T is Tamlana sedimentorum JCM 19808T with 98.40 and 97.98% sequence similarity, respectively. The 16S rRNA gene sequence similarity between strain PT2-4T and strain 62-3T was 98.68 %. Furthermore, the highest average nucleotide identity values were 87.34 and 88.97 % for strains PT2-4T and 62-3T, respectively. The highest DNA-DNA hybridization (DDH) value of strain PT2-4T was 35.2 % with strain 62-3T, while the DDH value of strain 62-3T was 37.7 % with T. sedimentorum JCM 19808T. Growth of strains PT2-4T and 62-3T occurs at 15-40 °C (optimum, 30 °C) with 0-4 % (w/v) NaCl (optimum 0-1 %). Strains PT2-4T and 62-3T can grow from pH 5.0 to 10.0 (optimum, pH 7.0). The major fatty acids of strains PT2-4T and 62-3T are iso-C15 : 0 and iso G-C15 : 1. MK-6 is the sole respiratory quinone. Genomic and physiological analyses of strains PT2-4T and 62-3T showed corresponding adaptive features. Significant adaptation to the growth environment of macroalgae includes the degradation of brown algae-derived diverse polysaccharides (alginate, laminarin and fucoidan). Notably, strain PT2-4T can utilize laminarin, fucoidan and alginate via specific carbohydrate-active enzymes encoded in polysaccharide utilization loci, rarely described for the genus Tamlana to date. Based on their distinct physiological characteristics and the traits of utilizing polysaccharides from Sargassum, strains PT2-4T and 62-3T are suggested to be classified into two novel species, Tamlana laminarinivorans sp. nov. and Tamlana sargassicola sp. nov. (type strain PT2-4T=MCCC 1K04427T=KCTC 92183T and type strain 62-3T=MCCC 1K04421T=KCTC 92182T).
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Huang ZH, Yang HL, Chen F, Li FN, Meng LJ, Chen XH, Chen MS, Ma X, Zheng ZQ, Tuo L. Paenibacillus mangrovi sp. nov., a novel endophytic bacterium isolated from bark of Kandelia candel. Int J Syst Evol Microbiol 2023; 73. [PMID: 36884384 DOI: 10.1099/ijsem.0.005780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
A endospore-forming bacterium, designated strain KQZ6P-2T, was isolated from surface-sterilized bark of the mangrove plant Kandelia candel, collected from Maowei Sea Mangrove Nature Reserve in Guangxi Zhuang Autonomous Region, China. Strain KQZ6P-2T was able to grow at NaCl concentrations in the range of 0-3 % (w/v) with optimum growth at 0-1 % (w/v) NaCl. Growth occurred at 20-42 °C (optimal growth at 30-37 °C) and pH 5.5-6.5 (optimal growth at pH 6.5). The 16S rRNA gene sequence similarity between strain KQZ6P-2T and its closest phylogenetic neighbour Paenibacillus chibensis JCM 9905T was 98.2 %. Phylogenetic analyses using 16S rRNA gene sequences showed that strain KQZ6P-2T formed a distinct lineage with Paenibacillus chibensis JCM 9905T. The draft genome of strain KQZ6P-2T was 5 937 633 bp in size and its DNA G+C content was 47.2mol%. Comparative genome analysis revealed that the average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values among strain KQZ6P-2T and its related species were below the cut-off levels of 95, 70 and 95.5%, respec-tively. The cell-wall peptidoglycan of strain KQZ6P-2T contained meso-diaminopimelic acid as the diagnostic diamino acid. Major cellular fatty acids were anteiso-C15:0 and C16:0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, four unidentified phospholipids, an unidentified aminolipid and five unidentified lipids. Based on phylogenetic, phenotypic and chemotaxonomic data, strain KQZ6P-2T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus mangrovi sp. nov. is proposed. The type strain is KQZ6P-2T (=MCCC 1K07172T =JCM 34931T).
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He Y, Liu Y, Pei T, Duan J, Du J, Deng X, Zhu H. Tsuneonella litorea sp. nov., a novel carotenoid-producing bacterium isolated from coastal sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37009855 DOI: 10.1099/ijsem.0.005785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and pleomorphic bacterium designated as YG55T was isolated from a coastal sediment sample. Growth was found to occur at 10-37 °C (optimum, 28 °C), at pH 6-9 (optimum, pH 8) and in 0-6 % NaCl (optimum, 1 %). The results of 16S rRNA gene-based analysis showed that strain YG55T was related to the members of the genus Tsuneonella and shared the highest identity of 99.4 % with Tsuneonella dongtanensis GDMCC 1.2307T, followed by Tsuneonella troitsensis JCM 17037T (98.4 %). The phylogenomic results indicated that strain YG55T formed an independent branch distinct from the reference type strains. The 22.7 and 21.8 % digital DNA-DNA hybridization (dDDH) values and 83.0 and 81.8 % average nucleotide identity (ANI) values between strain YG55T and the two relatives were below the species definition thresholds of 70 % (dDDH) and 95-96 % (ANI), indicating that the strain represents a novel genospecies. The results of chemotaxonomic characterization indicated that the major cellular fatty acids of strain YG55T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), C14 : 0 2OH and C16 : 0; the main polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid; the respiratory quinone was ubiquinone-10. The genomic size and DNA G+C contents were 3.03 Mbp and 66.98 %. The strain contained carotenoid biosynthesis genes and could produce carotenoids. Based on its genotypic and phenotypic characteristics, strain YG55T is concluded to represent a novel species of the genus Tsuneonella, for which the name Tsuneonella litorea sp. nov. is proposed. The type strain is YG55T (=GDMCC 1.2590 T=KCTC 82812T).
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Park Y, Liu Q, Maeng S, Oh H, Yun CS, Choe H, Lee HB, Im WT. Sphingomonas cremea sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37000168 DOI: 10.1099/ijsem.0.005796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
A novel Gram-stain-negative, aerobic, rod-shaped, non-motile, cream-coloured strain (G124T) was isolated from ginseng soil collected in Yeongju, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G124T belongs to a distinct lineage within the genus Sphingomonas (family Sphingomonadaceae, order Sphingomonadales and class Alphaproteobacteria). Strain G124T was closely related to Sphingomonas rhizophila THG-T61T (98.5 % 16S rRNA gene sequence similarity), Sphingomonas mesophila SYSUP0001T (98.3 %), Sphingomonas edaphi DAC4T (97.6 %) and Sphingomonas jaspsi TDMA-16T (97.6 %). The strain contained ubiquinone 10 as the major respiratory quinone. The major polar lipid profile of strain G124T comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipids. The predominant cellular fatty acids of strain G124T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 33.4 %), summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c; 27.2 %) and C16 : 0 (18.3 %). The genome size of strain G124T was 2 549 305 bp. The genomic DNA G+C content is 62.0 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain G124T and other Sphingomonas species were in the range of 71.2-75.9 % and 18.7-19.9 %, respectively. Based on the polyphasic analysis such as biochemical, phylogenetic and chemotaxonomic characteristics, strain G124T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas cremea sp. nov. is proposed. The type strain is G124T (=KACC 21691T=LMG 31729T).
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Li J, Lai Q, Hu A, Liu H, Qin D, Yang X, Tian Y, Yu CP. Salipiger pentaromativorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from mangrove sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 36790415 DOI: 10.1099/ijsem.0.005716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) have been recognized as a potential health risk and are widespread in nature due to their intrinsic chemical stability and high recalcitrance to degradation. A taxonomic study was carried out on strain P9T, which was isolated from a PAH-degrading consortium, enriched from the mangrove sediment from Zhangzhou, PR China. The isolate was chemoheterotrophic, aerobic, Gram-stain-negative, short-rod shaped, and motile by one polar flagellum. Growth was observed at salinities from 0.5-6.0 % (optimum, 3 %), at pH 4-9 (optimum, pH 7) and at 10-41 °C (optimum, 25-30 °C). It did not synthesize bacteriochlorophyll a. Catalase and oxidase activities were positive. Acid was produced from starch, amygdalin, arbutin, cellobiose, d-fructose, maltose, d-mannitol, melezitose, melibiose, raffinose, d-ribose, sucrose, trehalose, d-xylose, aesculin ferric citrate, gentiobiose, glycogen, l-arabinose, l-rhamnose, methyl α-d-glucopyranoside, methyl β-d-xylopyranoside, N-acetylglucosamine and salicin, and weakly positive for d-arabitol, d-galactose, lactose, turanose and glycerol. Phylogenetic analysis revealed that strain P9T fell within the clade comprising the type strains of Salipiger species and formed an independent cluster with Salipiger profundus, which was distinct from other members of the family Rhodobacteraceae. The 16S rRNA gene sequence comparisons showed that strain P9T was most closely related to Salipiger bermudensis HTCC 260T (96.7 %), and other species of the genus Salipiger (95.7-94.2 %). Strain P9T had the highest digital DNA-DNA hybridization value with S. profundus CGMCC 1.12377T (25.0 %) and the highest average nucleotide identity (ANIb and ANIm) values with S. profundus CGMCC 1.12377T(80.3 and 85.8 %, respectively). The sole respiratory quinone was quinone 10. The dominant fatty acids were C18 : 1 ω7c (61.4 %), C16 : 0 (17.5 %) and C19 : 0 ω8c cyclo (7.6 %). The G+C content of the chromosomal DNA was 65.8 mol%. In the polar lipid profile, phospholipid, phosphatidylglycerol, aminolipid, glycolipid and phosphatidylethanolamine were the major compounds. Based on the phenotypic and phylogenetic data, strain P9T represents a novel species of the genus Salipiger, for which the name Salipiger pentaromativorans sp. nov. is proposed. The type strain is P9T (=CCTCC AB 209290T=LMG 25701T=MCCC 1F01055T).
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Crespi S, Drašar V, Salvà-Serra F, Jaén-Luchoro D, Piñeiro-Iglesias B, Lindemann PC, Aliaga-Lozano F, Fernández-Juárez V, Coll-García G, Moore ERB, Bennasar-Figueras A. Legionella maioricensis sp. nov., a new species isolated from the hot water distribution systems of a hospital and a shopping center during routine sampling. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748493 DOI: 10.1099/ijsem.0.005686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Two Legionella-like strains isolated from hot water distribution systems in 2012 have been characterized phenotypically, biochemically and genomically in terms of DNA relatedness. Both strains, HCPI-6T and EUR-108, exhibited biochemical phenotypic profiles typical of Legionella species. Cells were Gram-negative motile rods which grew on BCYEα agar but not on blood agar and displayed phenotypic characteristics typical of the family Legionellaceae, including a requirement for l-cysteine and testing catalase positive. Both strains were negative for oxidase, urease, nitrate reduction and hippurate negative, and non-fermentative. The major ubiquinone was Q12 (59.4 % HCPI-6T) and the dominant fatty acids were C16 : 1 ω7c (28.4 % HCPI-6T, ≈16 % EUR-108), C16 : 0 iso (≈22.5 % and ≈13 %) and C15 : 0 anteiso (19.5 % and ≈23.5 %, respectively). The percent G+C content of genomic DNA was determined to be 39.3 mol %. The 16S rRNA gene, mip sequence and comparative genome sequence-based analyses (average nucleotide identity, ANI; digital DNA-DNA hybridization, dDDH; and phylogenomic treeing) demonstrated that the strains represent a new species of the genus Legionella. The analysis based on the 16S rRNA gene sequences showed that the sequence similarities for both strains ranged from 98.8-90.1 % to other members of the genus. The core genome-based phylogenomic tree (protein-concatemer tree based on concatenation of 418 proteins present in single copy) revealed that these two strains clearly form a separate cluster within the genus Legionella. ANI and dDDH values confirmed the distinctiveness of the strains. Based on the genomic, genotypic and phenotypic findings from a polyphasic study, the isolates are considered to represent a single novel species, for which the name Legionella maioricensis sp. nov. is proposed. The type strain is HCPI-6T (=CCUG 75071T=CECT 30569T).
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Vidal-Verdú À, Molina-Menor E, Satari L, Pascual J, Peretó J, Porcar M. Maritalea mediterranea sp. nov., isolated from marine plastic residues. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748519 DOI: 10.1099/ijsem.0.005677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A novel Gram-reaction-negative, aerobic, motile, rod-shaped, grey bacterium, strain P4.10XT, was isolated from plastic debris sampled from shallow waters in the Mediterranean Sea (Valencia, Spain). P4.10XT was catalase- and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA gene sequences revealed that P4.10XT was closely related to Maritalea myrionectae DSM 19524T and Maritalea mobilis E6T (98.25 and 98.03 % sequence similarity, respectively). The DNA G+C content of the genome sequence of P4.10XT was 53.66 %. The genomic indexes average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) confirmed its classification as representing a novel species of the genus Maritalea. The predominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and C18 : 1 ω7c 11-methyl. The results of this polyphasic study confirm that P4.10XT represents a novel species of the genus Maritalea, for which the name Maritalea mediterranea sp. nov. is proposed (type strain P4.10XT=CECT 30306T = DSM 112386T).
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Nouioui I, Saunderson SC, Midwinter AC, Young MJ, McInnes KM, Watts J, Sangal V. Corynebacterium megadyptis sp. nov. with two subspecies, Corynebacterium megadyptis subsp. megadyptis subsp. nov. and Corynebacterium megadyptis subsp. dunedinense subsp. nov. isolated from yellow-eyed penguins. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749700 DOI: 10.1099/ijsem.0.005713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Novel Corynebacterium strains, 3BT and 7BT, were isolated from the oral cavities of young chicks of yellow-eyed penguins (hoiho), Megadyptes antipodes. A polyphasic taxonomic characterization of these strains revealed chemotaxonomic, biochemical and morphological features that are consistent with those of the genus Corynebacterium. The 16S rRNA gene sequence similarity values between the strains and their closest phylogenetic neighbour, Corynebacterium ciconiae CCUG 47525T were 99.07 %, values that are in line with their phylogenomic positions within the evolutionary radiation of the genus Corynebacterium. Digital DNA-DNA hybridization values and average nucleotide identities between the genome sequences of the two strains and related Corynebacterium species were well below the defined threshold values (70 and 95-96 %, respectively) for prokaryotic species delineation. The genome size of these strains varied between 2.45-2.46 Mb with G+C content 62.7-62.9 mol%. Strains 3BT and 7BT were Gram-stain positive bacilli that were able to grow in presence of 0-10 % (w/v) NaCl and at temperature ranging between 20-37 °C. The major fatty acids (>15 %) were C16 : 0 and C18 : 1 ω9c, and the mycolic acid profile included 32-36 carbon atoms. We propose that these strains represent a novel species, Corynebacterium megadyptis sp. nov. with 3BT (=DSM 111184T=NZRM 4755T) as the type strain. Phylogenomically, strains 3BT and 7BT belong to two lineages with subtle differences in MALDI-TOF spectra, chemotaxonomic profiles and phenotypic properties. The fatty acid profile of strain 3BT contains C18 : 0 as a predominant type (>15 %), which is a minor component in strain 7BT. Strain 7BT can oxidize N-acetyl-d-glucosamine, l-serine, α-hydroxy-butyric acid, l-malic acid, l-glutamic acid, bromo-succinic acid and l-lactic acid, characteristics not observed in strain 3BT. Therefore, we propose that these strains represent two subspecies, namely Corynebacterium megadyptis subsp. megadyptis subsp. nov. (type strain, 3BT=DSM 111184T=NZRM 4755T) and Corynebacterium megadyptis subsp. dunedinense subsp. nov. (type strain, 7BT=DSM 111183T=NZRM 4756T).
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Svetlicic E, Jaén-Luchoro D, Klobucar RS, Jers C, Kazazic S, Franjevic D, Klobucar G, Shelton BG, Mijakovic I. Genomic characterization and assessment of pathogenic potential of Legionella spp. isolates from environmental monitoring. Front Microbiol 2023; 13:1091964. [PMID: 36713227 PMCID: PMC9879626 DOI: 10.3389/fmicb.2022.1091964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Several species in the genus Legionella are known to cause an acute pneumonia when the aerosols containing the bacteria from man-made water systems are inhaled. The disease is usually caused by Legionella pneumophila, but other species have been implicated in the infection. The disease is frequently manifested as an outbreak, which means several people are affected when exposed to the common source of Legionella contamination. Therefor environmental surveillance which includes isolation and identification of Legionella is performed routinely. However, usually no molecular or genome-based methods are employed in further characterization of the isolates during routine environmental monitoring. During several years of such monitoring, isolates from different geographical locations were collected and 39 of them were sequenced by hybrid de novo approach utilizing short and long sequencing reads. In addition, the isolates were typed by standard culture and MALDI-TOF method. The sequencing reads were assembled and annotated to produce high-quality genomes. By employing discriminatory genome typing, four potential new species in the Legionella genus were identified, which are yet to be biochemically and morphologically characterized. Moreover, functional annotations concerning virulence and antimicrobial resistance were performed on the sequenced genomes. The study contributes to the knowledge on little-known non-pneumophila species present in man-made water systems and establishes support for future genetic relatedness studies as well as understanding of their pathogenic potential.
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Le VV, Ko SR, Kang M, Oh HM, Ahn CY. Mucilaginibacter aquariorum sp. nov., Isolated from Fresh Water. J Microbiol Biotechnol 2022; 32:1553-1560. [PMID: 36377201 PMCID: PMC9843747 DOI: 10.4014/jmb.2208.08021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/09/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
A Gram-stain-negative, rod-shaped bacterial strain, JC4T, was isolated from a freshwater sample and determined the taxonomic position. Initial identification based on 16S rRNA gene sequences revealed that strain JC4T is affiliated to the genus Mucilaginibacter with a sequence similarity of 97.97% to Mucilaginibacter rigui WPCB133T. The average nucleotide identity and digital DNA-DNA hybridization values between strain JC4T and Mucilaginibacter species were estimated below 80.92% and 23.9%, respectively. Strain JC4T contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and iso-C15:0 as predominant cellular fatty acids. The dominant polar lipids were identified as phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, and two unidentified lipids. The respiratory quinone was MK-7. The genomic DNA G+C content of strain JC4T was determined to be 42.44%. The above polyphasic evidences support that strain JC4T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter aquariorum sp. nov. is proposed. The type strain is JC4T (= KCTC 92230T = LMG 32715T).
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Lv X, Li Y, Cheng Y, Lai XH, Yang J, Lu S, Zhang G, Yang C, Jin D, Liu L, Xu J. Canibacter zhuwentaonis sp. nov. and Canibacter zhoujuaniae sp. nov. , isolated from Marmota himalayana. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748412 DOI: 10.1099/ijsem.0.005633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Four Gram-stain-positive, facultatively anaerobic, non-motile, non-spore-forming and rod-shaped bacteria (lx-72T, lx-45, ZJ784T and ZJ955) were isolated from the respiratory tract or faeces of marmot (Marmota himalayana) from the Qinghai-Tibet Plateau in China. Analysis of the 16S rRNA gene sequences showed that all strains belong to the genus Canibacter and are more related to Canibacter oris CCUG 64069T (95.1-97.4 % similarity) than to the genus Leucobacter. Both strain pairs grew well at pH 6-9 and 15-42°C, and ZJ784T/ZJ955 could tolerate slightly higher NaCl (0.5-4.5 %, w/v) than lx-72T/lx-45(0.5-3.5 %). Based on whole-genome sequences, the average nucleotide identity and digital DNA-DNA hybridization values between our four isolates and their closest relative were below the species delineation thresholds of 70 % and 95-96 %. The common major fatty acids (>10 %) of our four strains were anteiso-C15 : 0 and anteiso-C17 : 0. For both new type strains, MK-8(H4) and MK-9(H4) were the major isoprenoid quinones, and diphosphatidylglycerol and phosphatidylglycerol were the main polar lipids. The genomic DNA G+C content of all strains was 53.9 mol%. Based on results from the genomic comparison, phylogenetic analysis, and physiological and biochemical characteristics, the four isolates represent two novel species in the genus Canibacter, for which the names Canibacter zhuwentaonis sp. nov. (type strain lx-72T=KCTC 49658T=GDMCC 1.2569T) and Canibacter zhoujuaniae sp. nov. (type strain ZJ784T=KCTC 49507T=GDMCC 1.1997T) are proposed.
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Kim J, Chhetri G, Kim I, So Y, Seo T. Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748605 DOI: 10.1099/ijsem.0.005640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of the genus Paenibacillus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated N4T, JC52T and PR3T, were isolated from rhizosphere soils and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that the three strains belonged to the genus Paenibacillus and formed three independent branches distinct from all reference strains. The results of DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) analyses between the three strains and their relatives further demonstrated that the three strains represented different novel genospecies. Strain N4T exhibited the highest similarity, ANI and digital DDH values with Paenibacillus assamensis DSM 18201T (99.0/87.5/33.9 %) and Paenibacillus insulae DS80T (97.2/-/18.2±1.2 %). Values for JC52T with Paenibacillus validus NBRC 15382T were 96.9, 73.3 and 19.6 %, and with Paenibacillus rigui JCM 16352T were 96.1, 72.1 and 19.3 %. Values for PR3T with Paenibacillus ginsengiterrae DCY89T were 98.2, - and 31.8±1.5 %, with Paenibacillus cellulosilyticus ASM318225v1T were 97.8, 83.3 and 26.7 %, and with Paenibacillus kobensis NBRC 15729T were 97.6, 75.7 and 20.4 %. Cells of the three novel bacterial strains were Gram-positive, spore-forming, motile and rod-shaped. The novel species contained anteiso-C15 : 0 and MK-7 as the predominant fatty acid and menaquinone, respectively. The novel strains have numerous similar known clusters of non-ribosomal peptide synthetases, siderophores, lanthipeptide, lassopeptide-like bacillibactin, paeninodin and polyketide-like chejuenolide A/B lankacidin C. Based on the distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains N4T, JC52T and PR3T represent novel species of the genus Paenibacillus, with the names Paenibacillus agilis sp. nov. (=KACC 19717T=JCM 32775T), Paenibacillus cremeus sp. nov. (=KACC 21221T=NBRC 113867T) and Paenibacillus terricola sp. nov. (=KACC 21455T=NBRC 114385T), respectively.
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Kim YO, Park IS, Kim DG, Park S, Han SH, Yoon JH. Enterovibrio paralichthyis sp. nov., isolated from the gut of an olive flounder Paralichthys olivaceus. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748413 DOI: 10.1099/ijsem.0.005593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
A Gram-stain-negative, facultatively anaerobic, flagellated and coccoid, ovoid or rod-shaped bacterial strain, NIFS-20-8T, was isolated from the intestine of an olive flounder (Paralichthys olivaceus) from the East Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain NIFS-20-8T fell within the clade comprising the type strains of Enterovibrio species. Strain NIFS-20-8T exhibited 16S rRNA gene sequence similarities of 97.2 and 97.1 % to the type strains of Enterovibrio nigricans and Enterovibrio norvegicus, respectively, and of 96.6-97.0 % to the type strains of the other Enterovibrio species. The average nucleotide identity and digital DNA-DNA hybridization values between the genomic sequence of strain NIFS-20-8T and those of the type strains of four Enterovibrio species were 73.8-75.0 and 19.8-21.1 %, respectively. The DNA G+C content of strain NIFS-20-8T from genomic sequence data was 50.55 mol%. Strain NIFS-20-8T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C18 : 1 ω7c as the major fatty acids. The major polar lipids detected in stain NIFS-20-8T were phosphatidylethanolamine and phosphatidylglycerol. Distinguishing phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain NIFS-20-8T is separated from recognized Enterovibrio species. On the basis of the data presented here, strain NIFS-20-8T is considered to represent a novel species of the genus Enterovibrio, for which the name Enterovibrio paralichthyis sp. nov. is proposed. The type strain is NIFS-20-8T (= KCTC 82873T=NBRC 115237T).
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Kim DY, Jeong IC, Lee SY, Jeong YS, Han JE, Tak EJ, Lee JY, Kim PS, Hyun DW, Bae JW. Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748471 DOI: 10.1099/ijsem.0.005643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Two novel Gram-stain-positive, non-motile and non-spore-forming bacterial strains, designated J2M5T and J1M15T, were isolated from the gastrointestinal tract of a lake prawn Palaemon paucidens. Strain J2M5T was an obligately aerobic bacterium that formed milky-coloured colonies and showed a rod-coccus cell cycle, while strain J1M15T was a facultatively aerobic bacterium that formed orangish-yellow-coloured colonies and showed rod-shaped cells. Strains J2M5T and J1M15T showed the highest 16S rRNA gene sequence similarity to Nocardioides ganghwensis JC2055T (98.63 %) and Tessaracoccus flavescens SST-39T (98.08 %), respectively. The whole-genome sequence of strain J2M5T was 4.52 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J2M5T was 72.5 mol%. The whole-genome sequence of strain J1M15T was 3.20 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J1M15T was 69.6mol %. Strains J2M5T and J1M15T showed high OrthoANI similarity to N. ganghwensis JC2055T (83.6 %) and T. flavescens (77.2 %), respectively. We analysed the genome sequences of strains J2M5T and J1M15T in terms of carbohydrate-active enzymes, antibiotic resistance genes and virulence factor genes. Strains J2M5T and J1M15T contained MK-8 (H4) and MK-9 (H4) as the predominant respiratory quinones, respectively. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Additionally, strain J2M5T possessed phosphatidylcholine, phosphatidylserine and phosphatidylethanolamine. The cellular sugar components of strain J2M5T were ribose, mannose, glucose and galactose, and its cellular amino acid components were l-alanine and l-lysine. The cellular sugar components of strain J1M15T were rhamnose, ribose, mannose and glucose, and its cellular amino acid component was l-alanine. The major cellular fatty acids of strains J2M5T and J1M15T were iso-C16 : 0 and anteiso-C15 : 0, respectively. The multiple taxonomic analyses indicated that strains J2M5T and J1M15T represent novel species of the genus Nocardioides and Tessaracoccus, respectively. We propose the names Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov. for strain J2M5T (=KCTC 49461T=CCUG 74767T) and strain J1M15T (=KCTC 49462T=CCUG 74766T), respectively.
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Kim CS, Liu Z, Peng X, Qin K, Huang J, Niu J, Liu Y, Liu J, Sun M, Peng F. Paraconexibacter antarcticus sp. nov., a novel actinobacterium isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748421 DOI: 10.1099/ijsem.0.005647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A Gram-negative, non-motile, aerobic bacterium, named 02-257T, was isolated from Antarctic soil. The cells are surrounded by relatively thin capsules and were catalase-positive and oxidase-negative cocci. Growth of strain 02-257T was observed at 4-35 °C (optimum, 28-30 °C), pH 6.0-8.0 (optimum, pH 6.0) and with 0-1.5% NaCl (optimum, 0 %). Strain 02-257 showed the highest 16S rRNA gene sequence similarity to Paraconexibacter algicola Seoho-28T (95.06 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 02-257T is a member of a novel species belonging to the clade formed by members of the genus Paraconexibacter in the family Paraconexibacteraceae. The DNA G+C content was 72.9 mol%. Strain 02-257T contained C16 : 0-iso (23.0 %), C18 : 1 ω9c (13.8 %), C16 : 0 (12.5 %) and C17 : 1 ω9c-iso (10.8 %) as major cellular fatty acids and menaquinone MK-7(H4) was detected as the only isoprenoid quinone. Diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositole mannoside, phosphatidylinositole dimannoside, unidentified phosphoglycolipid, unidentified aminophospholipid, two unidentified phospholipids, three unidentified aminolipids and six unidentified lipids were the major polar lipids. meso-Diaminopimelic acids were the diagnostic diamino acids in the cell-wall peptidoglycan. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain 02-257T is considered to represent a novel species of the genus Paraconexibacter, for which the name Paraconexibacter antarcticus sp. nov. is proposed. The type strain is 02-257T (=CCTCC AB 2021030T=KCTC 49619T).
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Li Z, Li Y, Li S, Li Z, Mai Y, Cheng J, Su D, Zhan Y, Zhong N, Ye F. Identification of a novel drug-resistant community-acquired Nocardia spp. in a patient with bronchiectasis. Emerg Microbes Infect 2022; 11:1346-1355. [PMID: 35450515 PMCID: PMC9132467 DOI: 10.1080/22221751.2022.2069514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A previously unknown Nocardia species was isolated from the lung tissue and bronchoalveolar lavage fluid (BALF) of a 58-year-old woman with bronchiectasis and recurrent pneumonia. This Nocardia (GZ2020T), which grew readily in Columbia blood agar and could induce pneumonia in a mouse model, represents a novel Nocardia species, and its closest known relatives are Nocardia anaemiae NBRC 100462T, Nocardia pseudovaccinii NBRC 100343T and Nocardia vinacea NBRC 16497T. However, unlike all previously known species, GZ2020T is the first genus of Nocardia spp. that is not susceptible to multiple drugs but does show susceptibility to linezolid and moxifloxacin, and thus, GZ2020T potentially represents a substantial health threat to patients with bronchiectasis and immunocompromised individuals. Although the original pathogen source and method of spreading remain uncertain, a mode of transmission from the environment to humans could exist. Vigilance with respect to its spread in the population and the transmission of antibiotic resistance genes in the environment should be maintained.
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Lynch C, Peeters C, Walsh N, McCarthy C, Coffey A, Lucey B, Vandamme P. Campylobacter majalis sp. nov. and Campylobacter suis sp. nov., novel Campylobacter species isolated from porcine gastrointestinal mucosa. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748456 DOI: 10.1099/ijsem.0.005510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Strains LMG 7974T and LMG 8286T represent single, novel Campylobacter lineages with Campylobacter pinnipediorum and Campylobacter mucosalis as nearest phylogenomic neighbours, respectively. The results of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses of LMG 7974T, LMG 8286T and type strains of species of the genus Campylobacter confirmed that these strains represent novel species of the genus Campylobacter. The 16S rRNA gene sequences of both strains showed highest identity towards C. mucosalis (97.84 and 98.74 %, respectively). Strains LMG 7974T and LMG 8286T shared 72.5 and 73.7% ANI, respectively, with their nearest phylogenomic neighbours and less than 21 % dDDH. The draft genome sizes of LMG 7974T and LMG 8286T are 1 945429 bp and 1 708214 bp in length with percentage DNA G+C contents of 33.8 and 37.2 %, respectively. Anomalous biochemical characteristics and low MALDI-TOF mass spectrometry log scores supported their designation as representing novel species of the genus Campylobacte. We therefore propose to classify strain LMG 7974T (=CCUG 20705T) as the type strain of the novel species Campylobacter majalis sp. nov. and strain LMG 8286T (=CCUG 24193T, NCTC 11879T) as the type strain of the novel species Campylobacter suis sp. nov.
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Wu ZP, Zheng XW, Sun YP, Wang BB, Hou J, Cui HL. Halocatena salina sp. nov., a filamentous halophilic archaeon isolated from Aiding Salt Lake. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748619 DOI: 10.1099/ijsem.0.005637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A filamentous cell-shaped halophilic archaeon (strain AD-1T) was isolated from Aiding Salt Lake, PR China. Its colonies on HCM7 agar plates were pinkish white, 1-4 mm (diameter), elevated and round. The optimum conditions for growth were observed at 42 °C, 4.3 M NaCl, 0.01 M MgCl2 and pH 7. Strain AD-1T could hydrolyse Tween 60, Tween 80, starch and gelatin. Phylogenetic analysis based on 16S rRNA gene, rpoB' and the concatenated 484 single-copy orthologous proteins revealed that strain AD-1T formed a clade with Halocatena pleomorpha SPP-AMP-1T. The average nucleotide identity and in silico DNA-DNA hybridization values between strain AD-1T and Halocatena pleomorpha SPP-AMP-1T were both below the species delineation thresholds (95~96 and 70 %, respectively). The major phospholipids of strain AD-1T were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, while the major glycolipids were sulphated galactosyl mannosyl glucosyl diether, galactosyl mannosyl glucosyl diether and glucosyl mannosyl glucosyl diether. The phenotypic, phylogenetic and genome-based analyses suggested that strain AD-1T (=CGMCC 1.13724T=JCM 32960T) represents a novel species, for which the name Halocatena salina sp. nov. is proposed.
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Wang C, Lv Y, Zhou L, Zhang Y, Yao Q, Zhu H. Comparative genomics of Myxococcus and Pyxidicoccus, including the description of four novel species: Myxococcus guangdongensis sp. nov., Myxococcus qinghaiensis sp. nov., Myxococcus dinghuensis sp. nov., and Pyxidicoccus xibeiensis sp. nov. Front Microbiol 2022; 13:995049. [PMID: 36439860 PMCID: PMC9684338 DOI: 10.3389/fmicb.2022.995049] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/18/2022] [Indexed: 08/22/2023] Open
Abstract
Myxobacteria are recognized for fascinating social behaviors and producing diverse extracellular active substances. Isolating novel myxobacteria is of great interest in the exploitation of new antibiotics and extracellular enzymes. Herein, four novel strains were isolated from Dinghu Mountain Biosphere Reserve, Guangdong province, and Qinghai virgin forest soils, Qinghai province, China. The phylogenetic analysis based on 16S rRNA gene and genomic sequences indicated that the four strains belong to the genera Myxococcus and Pyxidicoccus, sharing the highly similarities of 16S rRNA gene with the genera Myxococcus and Pyxidicoccus (99.3-99.6%, respectively). The four strains had average nucleotide identity (ANI) values of 82.8-94.5%, digital DNA-DNA hybridization (dDDH) values of 22.2-56.6%, average amino acid identity (AAI) values of 75.8-79.1% and percentage of conserved protein (POCP) values of 66.4-74.9% to members of the genera Myxococcus and Pyxidicoccus. Based on phylogenetic analyses, physiological and biochemical characteristics, and comparative genomic analyses, we propose four novel species of the genera Myxococcus and Pyxidicoccus and further supported the two genera above represented the same genus. Description of the four novel species is Myxococcus guangdongensis sp. nov. (K38C18041901T = GDMCC 1.2320T = JCM 39260T), Myxococcus qinghaiensis sp. nov. (QH3KD-4-1T = GDMCC 1.2316T = JCM 39262T), Myxococcus dinghuensis sp. nov. (K15C18031901T = GDMCC 1.2319T = JCM 39259T), and Pyxidicoccus xibeiensis sp. nov. (QH1ED-7-1T = GDMCC 1.2315T = JCM 39261T), respectively. Furthermore, comparative genomics of all 15 species of the genera Myxococcus and Pyxidicoccus revealed extensive genetic diversity. Core genomes enriched more genes associated with housekeeping functional classes while accessory genomes enriched more genes related to environmental interactions, indicating the former is relatively indispensable compared to signaling pathway genes. The 15 species of Myxococcus and Pyxidicoccus also exhibited great gene diversity of carbohydrate-active enzymes (CAZymes) and secondary metabolite biosynthesis gene clusters (BGCs), especially related to glycosyl transferases (GT2 and GT4), glycoside hydrolases (GH13 and GH23), non-ribosomal peptide synthetases (NRPS), and Type I polyketide synthase (PKS)/NRPS hybrids.
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Zheng K, Hong Y, Guo Z, Debnath SC, Yan C, Li K, Chen G, Xu J, Wu F, Zheng D, Wang P. Acinetobacter sedimenti sp. nov., isolated from beach sediment. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748468 DOI: 10.1099/ijsem.0.005609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, non-haemolytic, oxidase-negative, catalase-positive bacillus strain (A3.8T) was isolated from beach sediment from Zhairuo Island, PR China. The strain grew at pH 6.0-9.0 (optimum, 7.0), with 0-4.5 % NaCl (optimum, 2 %) and at 10-35 °C (optimum, 30 °C). Its whole-genome sequence was 2.5 Mb in size, with a DNA G+C content of 41.6 mol%. On the basis of the results of core genome phylogenetic analysis, A3.8T represents a separate branch within the clade formed by five species of the genus Acinetobacter with 'Acinetobacter marinus' as the most closely related species. The average nucleotide identity compared with the closely related species of the genus Acinetobacter was below 83.66 % and digital DNA-DNA hybridization values were less than 28.80 %. The predominant fatty acids included C18 : 1ω9c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). Q-9 was the major respiratory quinone. The polar lipids are mainly composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two phospholipids, an aminolipid and four unknown lipids. A3.8T cannot assimilate dl-lactate and weakly utilizes l-glutamate, l-leucine, l-phenylalanine and l-tartrate, which distinguishes it from other species of the genus Acinetobacter. On the basis of the genotype, phenotype and biochemical data, strain A3.8T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter sedimenti sp. nov. is proposed. The type strain is A3.8T (=MCCC 1K07161T=LMG 32568T).
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Kwon SL, Cho M, Lee YM, Lee H, Kim C, Kim GH, Kim JJ. Diversity of the Bambusicolous Fungus Apiospora in Korea: Discovery of New Apiospora Species. MYCOBIOLOGY 2022; 50:302-316. [PMID: 36404898 PMCID: PMC9645279 DOI: 10.1080/12298093.2022.2133808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/22/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Many Apiospora species have been isolated from bamboo plants - to date, 34 bambusicolous Apiospora species have been recorded. They are known as saprophytes, endophytes, and plant pathogens. In this study, 242 bambusicolous Apiospora were isolated from various bamboo materials (branches, culms, leaves, roots, and shoots) and examined using DNA sequence similarity based on the internal transcribed spacer, 28S large subunit ribosomal RNA gene, translation elongation factor 1-alpha, and beta-tubulin regions. Nine Apiospora species (Ap. arundinis, Ap. camelliae-sinensis, Ap. hysterina, Ap. lageniformis sp. nov., Ap. paraphaeosperma, Ap. pseudohyphopodii sp. nov., Ap. rasikravindrae, Ap. saccharicola, and Ap. sargassi) were identified via molecular analysis. Moreover, the highest diversity of Apiospora was found in culms, and the most abundant species was Ap. arundinis. Among the nine Apiospora species, two (Ap. hysterina and Ap. paraphaeosperma) were unrecorded in Korea, and the other two species (Ap. lageniformis sp. nov. and Ap. pseudohyphopodii sp. nov.) were potentially novel species. Here, we describe the diversity of bambusicolous Apiospora species in bamboo organs, construct a multi-locus phylogenetic tree, and delineate morphological features of new bambusicolous Apiospora in Korea.
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Jeon D, Jiang L, Peng Y, Seo J, Li Z, Park SH, Jeong RD, Park SJ, Jeong JC, Lee J. Sphingomonas cannabina sp. nov., isolated from Cannabis sativa L. 'Cheungsam'. Int J Syst Evol Microbiol 2022; 72. [PMID: 36260506 DOI: 10.1099/ijsem.0.005566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
A Gram-negative, aerobic, rod-shaped bacterium, designated DM2-R-LB4T was isolated from Cannabis sativa L. 'Cheungsam' in Andong, Republic of Korea. The strain DM2-R-LB4T grew at temperatures of 15-45 °C (optimum, 30-37 °C), pH of 5.5-9 (optimum, 8.0), and 0-2 % (w/v) NaCl concentration (optimum, 0%). Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strain DM2-R-LB4T is related to species of the genus Sphingomonas, and shared 97.8 and 97.5% similarity to Sphingomonas kyenggiensis KCTC 42244T and Sphingomonas leidyi DSM 4733T, respectively. The DNA G+C content was 67.9 mol% and genome analysis of the strain DM2-R-LB4T revealed that the genome size was 4 386 171 bp and contained 4 009 predicted protein-coding genes. The average nucleotide identity (ANI) values between strain DM2-R-LB4T and S. kyenggiensis KCTC 42244T, and S. leidyi DSM 4733T was 76.8 and 76.7 %, respectively, while the values of digital DNA-DNA hybridization (dDDH) were 20.7 and 20.6 %, respectively. C14 : 0 2-OH, C16 : 0, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) were the major fatty acids (>10 %) in the strain DM2-R-LB4T. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), sphingoglycolipid (SGL), glycolipid (GL), phospholipid (PL), and two unidentified polar lipids (L1 and L2). Ubiquinone-10 (Q-10) was the only respiratory quinone. The polyamine pattern was found to contain homospermidine, putrescine, and spermidine. The results of phylogenetic anlayses, polyphasic studies, revealed that strain DM2-R-LB4T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas cannabina sp. nov., is proposed. The type strain is DM2-R-LB4T (=KCTC 92075T = GDMCC 1.3018T).
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