Systematic and applied microbiology最新文献

{"title":"Phenylobacterium ferrooxidans sp. nov., isolated from a sub-surface geothermal aquifer in Iceland","authors":"Eva Pouder,&nbsp;Erwann Vince,&nbsp;Karen Jacquot,&nbsp;Maimouna batoma Traoré,&nbsp;Ashley Grosche,&nbsp;Maria Ludwig,&nbsp;Mohamed Jebbar,&nbsp;Loïs Maignien,&nbsp;Karine Alain,&nbsp;Sophie Mieszkin","doi":"10.1016/j.syapm.2024.126578","DOIUrl":"10.1016/j.syapm.2024.126578","url":null,"abstract":"<div><div>A novel bacterial strain, HK31-G^T, was isolated from a subsurface geothermal aquifer (Hellisheidi, SW-Iceland) and was characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene along with phylogenomic position indicated that the novel strain belongs to the genus <em>Phenylobacterium</em>. Cells are motile Gram-negative thin rods. Physiological characterization showed that strain HK31-G^T is a mesophilic bacterium able to grow from 10 to 30 °C, at pH values between 6 and 8 and at NaCl concentrations between 0 and 0.5 %. Optimal growth was observed without sodium chloride at 25 °C and pH 6. Strain HK31-G^T is chemoorganoheterotroph and its major saturated fatty acids are C_18:1<em>ω7c</em>, C₁₆_:1<em>ω6c</em> and C_16:0, the predominant quinone is Q-10 and the major polar lipid is phosphatidylglycerol. The new strain also possesses the capacity to use ferrous iron (Fe(II)) as the sole energy source and can also be considered as a chemolithoautotrophic microorganism. The overall genome of strain HK31-G^T was estimated to be 4.46 Mbp in size with a DNA G + C content of 67.95 %. Genes involved in iron metabolism were identified, but no genes typically involved in Fe(II)-oxidation were found. According to the overall genome relatedness indices (OGRI) values, six MAGs from groundwater have been assigned to the same species as the new strain HK31-G^T. Furthermore, OGRI values between the genome of strain HK31-G^T and the genomes of its closest relatives are below the species delineation threshold. Therefore, given the polyphasic approach used, strain HK31-G^T represents a novel species of the genus <em>Phenylobacterium</em>, for which the name <em>Phenylobacterium ferrooxidans</em> sp. nov. is proposed. The type strain is HK31-G^T (DSM 116432^T = UBOCC-M-3429^T = LMG 33376^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126578"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems","authors":"Jette F. Petersen ,&nbsp;Laura C. Valk ,&nbsp;Maarten D. Verhoeven,&nbsp;Marta A. Nierychlo,&nbsp;Caitlin M. Singleton,&nbsp;Morten K.D. Dueholm,&nbsp;Per H. Nielsen","doi":"10.1016/j.syapm.2024.126574","DOIUrl":"10.1016/j.syapm.2024.126574","url":null,"abstract":"<div><div>Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is <em>Rhodoferax,</em> an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of <em>Rhodoferax</em> species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of “<em>Rhodoferax</em>” revealed that species previously assigned to <em>Rhodoferax</em> in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the <em>Rhodoferax</em> genus.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126574"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans","authors":"Isabella Wilkie,&nbsp;Luis H. Orellana","doi":"10.1016/j.syapm.2024.126562","DOIUrl":"10.1016/j.syapm.2024.126562","url":null,"abstract":"<div><div>Members of the phylum <em>Verrucomicrobiota</em> play a significant role in various ecosystems, yet they are underrepresented in databases due to their comparatively lower abundance and isolation challenges. The use of cultivation-independent approaches has unveiled their hidden diversity and specialized metabolic capabilities, yet many of these populations remain uncharacterized. In this study, we focus on members of the family MB11C04 associated with North Sea spring blooms. Our analyses revealed recurrent MB11C04 populations with increased abundance in the late stages of spring blooms over ten-years. By examining their genomic content, we identified specialized genetic features for the degradation of complex polysaccharides, particularly sulfated and fucose-rich compounds, suggesting their role in utilizing organic matter during the collapse of the bloom. Furthermore, we describe two novel genera each with a novel species (<em>Seribacter</em> gen. Nov., <em>Chordibacter</em> gen. Nov.) in accordance with the SeqCode initiative based on high quality metagenome-assembled genomes. We also propose a new name for the family MB11C04, <em>Seribacteraceae</em>. Our findings shed light on the ecological significance and metabolic potential of <em>Verrucomicrobiota</em> populations in spring bloom events.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126562"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Natronorarus salvus gen. nov., sp. nov., Halalkalicoccus ordinarius sp. nov., and Halalkalicoccus salilacus sp. nov., halophilic archaea from a soda lake and two saline lakes, and proposal to classify the genera Halalkalicoccus and Natronorarus into Halalkalicoccaceae fam. nov. in the order Halobacteriales within the class Halobacteria","authors":"Ya-Ling Mao ,&nbsp;Xin-Yue Dong ,&nbsp;Cong-Qi Tao,&nbsp;Zhang-Ping Wu,&nbsp;Xiao-Wei Shi,&nbsp;Jing Hou,&nbsp;Heng-Lin Cui","doi":"10.1016/j.syapm.2024.126577","DOIUrl":"10.1016/j.syapm.2024.126577","url":null,"abstract":"<div><div>Four novel halophilic archaeal strains CGA53^T, CG83^T, FCH27^T, and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53^T showed the highest 16S rRNA gene similarity (92.6%) to <em>Salinilacihabitans rarus</em> AD-4^T, and the other three strains were found to be related to <em>Halalkalicoccus</em> species with similarities of 97.6–98.3%. Metagenomic studies indicated that these four strains are low abundant inhabitants detected in these hypersaline environments, and only one MAG of Chagannuoer Soda Lake (CG) could be assigned to the genus <em>Halalkalicoccus</em>. Their growth occurred at 20–60 °C (optima, 42, 37, 37–42, and 35 °C), 0.9–5.1 M NaCl (optima, 3.9, 2.6, 3.5, and 3 M), and 0–1.0 M MgCl₂ (optima, 0.5, 0.7, and 0.1) and pH 5.5–10.5 (optima, 9.0, 7.5, 7.0, and 7.0), respectively. Phylogenetic and phylogenomic analyses revealed that strains CG83^T, FCH27^T, and SEDH24 cluster with the current species of the genus <em>Halalkalicoccus</em>, and strain CGA53^T forms an independent branch separated from this genus. The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), and average amino acid identity (AAI) values among strains CGA53^T, CG83^T, FCH27^T, SEDH24, and the type species of the current genera within the class <em>Halobacteria</em> were 67.4–81.6%, 16.5–28.6% and 49.7–74.1%, respectively, clearly lower than the cutoff values for species demarcation. Strain CGA53^T may represent a novel species of a new genus according to the cutoff value for genus demarcation of 65% AAI. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, antibiotic sensitivity, and H₂S formation, were found among these four strains and <em>Halalkalicoccus</em> species. Genome-based classification supported that strains CGA53^T, CG83^T, FCH27^T, SEDH24, and the current species of <em>Halalkalicoccus</em> represent a novel family of the order <em>Halobacteriales</em> within the class <em>Halobacteria</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126577"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic characterization of Bifidobacterium kimbladii sp. nov., a novel species from the honey stomach of the honeybee Apis mellifera","authors":"M. Modesto ,&nbsp;D. Scarafile ,&nbsp;A. Vásquez ,&nbsp;R. Pukall ,&nbsp;M. Neumann-Schaal ,&nbsp;S. Pascarelli ,&nbsp;B. Sgorbati ,&nbsp;M. Ancora ,&nbsp;C. Cammà ,&nbsp;P. Mattarelli ,&nbsp;T.C. Olofsson","doi":"10.1016/j.syapm.2025.126579","DOIUrl":"10.1016/j.syapm.2025.126579","url":null,"abstract":"<div><div>Six novel <em>Bifidobacterium</em> strains H1HS16N^T, Bin2N, Hma3N, H6bp22N, H1HS10N, and H6bp9N, were isolated from the honey stomach of <em>Apis mellifera</em>. Cells are Gram-positive, non-motile, non-sporulating, facultatively anaerobic, and fructose 6-phosphate phosphoketolase-positive. Optimal growth conditions occur at 37 °C in anaerobiosis in MRS medium added with 2 % fructose and 0.1 % L-cysteine. The 16S rRNA gene sequences analysis revealed clustering with <em>Bifidobacterium</em> species found in honeybees. Strains Hma3N, H6bp22N, and H1HS16N^T showed significant similarity to <em>Bifidobacterium polysaccharolyticum</em> JCM 34588^T, with an average similarity of 99.63 %. In contrast, strains Bin2N, H1HS10N, and H6bp9N were closely related to <em>Bifidobacterium apousia</em> JCM 34587^T, with an average similarity of 99.22 %. Moreover, strains Hma3N and H6bp22N exhibited ANI values of 96.65 % and 96.53 % when compared to <em>Bifidobacterium polysaccharolyticum</em> JCM 34588^T, while strains H1HS16N^T, Bin2N, H6bp9N, and H1HS10N revealed ANI values of 94.18 %, 94.33 %, 94.22 %, and 95.50 % respectively when compared to <em>B. apousia</em> JCM 34587^T. dDDH analysis confirmed that strains Hma3N and H6bp22N belong to <em>B. polysaccharolyticum</em>, whereas strains H1HS16N^T, Bin2N, H6bp9N, and H1HS10N represent a novel species. The peptidoglycan of the novel species is of the A4α type (L-Lys-D-Asp). The main cellular fatty acids of the type strain H1HS16N^T are C_16:0, C_14:0, C_19:0 cyclo ω9c, and C_18:1 ω9c. The DNA G + C content of the type strain is 60.8 mol%.</div><div>Genome analyses of the strains were also conducted to determine their biosynthesis-related gene clusters, probiotic features, and ecological distribution patterns.</div><div>Phenotypic and genotypic characterization show that strain H1HS16N^T is distinct from the type strains of other recognized <em>Bifidobacterium</em> species. Thus, <em>Bifidobacterium kimbladii</em> sp. nov. (H1HS16N^T = DSM 115187^T = CCUG 76695^T) is proposed as a novel <em>Bifidobacterium</em> species.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126579"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Description of Albidovulum litorale sp. nov., Albidovulum marisflavi sp. nov., Albidovulum salinarum sp. nov., and Albidovulum sediminicola sp. nov., and proposal for reclassification of the genus Defluviimonas as a later heterotypic synonym of Albidovulum","authors":"Wei He ,&nbsp;Dao-Feng Zhang ,&nbsp;Xing-Jie Li ,&nbsp;Hong-Chuan Wang ,&nbsp;Lin-Qiong Wang ,&nbsp;Yang Yuan","doi":"10.1016/j.syapm.2024.126576","DOIUrl":"10.1016/j.syapm.2024.126576","url":null,"abstract":"<div><div>Four Gram-stain-negative, aerobic, rod-shaped bacteria, designated WL0002^T, WL0024^T, WL0050^T, and WL0075^T, were isolated from sediment in the coastal areas of Nantong City, China. Metagenomic analysis revealed higher relative abundance of taxa closely related to the four strains in sediment (0.79–2.0 %) than in water (0.34–1.3 %) (Mann-Whitney <em>U</em> test: <em>p</em> &lt; 0.001). Phylogenetic analysis based on 16S rRNA gene and the bac120 gene set both suggested that the four strains are closely related to the genus <em>Defluviimonas</em>. Additionally, <em>Albidovulum inexpectatum</em> DSM 12048^T formed a distinct branch within <em>Defluviimonas</em>. The evolutionary distance (ED) and percentage of conserved proteins (POCP) analysis indicated that the four strains and the genus strains of <em>Albidovulum</em> and <em>Defluviimonas</em> should be recognized as a single genus. Genomic relatedness analysis among the four strains and type strains of the genera <em>Albidovulum</em> and <em>Defluviimonas</em> was below species delimitation thresholds, except for strains WL0024^T and “<em>D. salinarum</em>” CAU 1641^T, which should belong to the same species. Based on phenotypic and genotypic characterization, the four strains should be recognized as novel species in <em>Albidovulum</em>, and it is reasonable to reclassify the genus <em>Defluviimonas</em> as a later heterotypic synonym of <em>Albidovulum</em>, consistent with the classification of the Genome Taxonomy Database (GTDB). Four names are proposed as follows: <em>Albidovulum marisflavi</em> sp. nov. (type strain WL0002^T = MCCC 1K06013^T = JCM 34653^T = GDMCC 1.2437^T), <em>Albidovulum salinarum</em> sp. nov. (WL0024^T = MCCC 1K06062^T = JCM 34656^T = GDMCC 1.2438^T), <em>Albidovulum litorale</em> sp. nov. (WL0050^T = MCCC 1K07524^T = JCM 35566^T = GDMCC 1.3084^T), and <em>Albidovulum sediminicola</em> sp. nov. (WL0075^T = MCCC 1K06064^T = JCM 34660^T = GDMCC 1.2419^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126576"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142819250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Methyloraptor flagellatus gen. Nov., sp. nov., novel Ancalomicrobiaceae-affiliated facultatively methylotrophic bacteria that feed on methanotrophs of the genus Methylococcus","authors":"Victoria A. Saltykova ,&nbsp;Olga V. Danilova ,&nbsp;Igor Y. Oshkin ,&nbsp;Svetlana E. Belova ,&nbsp;Natalia E. Suzina ,&nbsp;Nikolai V. Pimenov ,&nbsp;Svetlana N. Dedysh","doi":"10.1016/j.syapm.2024.126565","DOIUrl":"10.1016/j.syapm.2024.126565","url":null,"abstract":"<div><div>A morphologically conspicuous microbial association was detected in a bioreactor running in a continuous mode with methanotrophic bacteria of the genus <em>Methylococcus</em> and natural gas as a growth substrate. The association consisted of spherical <em>Methylococcus</em> cells colonized by elongated rods, which produced rosette-like aggregates and inhibited the cultivation process. An isolate of these bacteria, strain S20^T, was obtained and identified as belonging to the alphaproteobacterial family <em>Ancalomicrobiaceae</em> but displaying only a distant relationship (93.9–95.1 % 16S rRNA gene sequence similarity) to characterized members of this family. Strain S20^T was represented by aerobic, motile, facultatively methylotrophic bacteria, which grew between 10 and 45 °C (optimum 30–35 °C) in a pH range of 4.5–8.5 (optimum pH 6.0). These bacteria were capable of attaching to <em>Methylococcus</em> cells and breaking the integrity of methanotroph cell walls, presumably to feed on methanol. The same interaction was observed with <em>Methylomonas</em> species. The finished genome sequence of strain S20^T consisted of a 5.0 Mb chromosome and one plasmid, 0.26 Mb in size; the DNA G + C content was 68.4 %. The genome encoded 3 rRNA operons and ~ 4400 proteins including MxaFI- and XoxF-like methanol dehydrogenases, all enzymes of the serine pathway as well as a complete chemotaxis pathway, a unipolar polysaccharide adhesin, and a wide range of peptidases. The genome sequence displayed 67.20–69.56 % average amino acid identity to those of earlier described <em>Ancalomicrobiaceae</em> species. We propose to classify these bacteria as representing a novel genus and species, <em>Methyloraptor flagellatus</em> gen. Nov., sp. nov., with the type strain S20^T (=KCTC 8649^T = VKM B-3853^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126565"},"PeriodicalIF":3.3,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142700550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parafrigoribacterium soli sp. nov. and Parafrigoribacterium humi sp. nov., two novel siderophore-synthesizing species isolated from black soil","authors":"Yu-Ting OuYang ,&nbsp;Le-Bin Chen ,&nbsp;Jian-Yu Jiao ,&nbsp;Zi-Xuan Hu ,&nbsp;Jiong-Shan Wang ,&nbsp;Tian-Hang Yang ,&nbsp;Jun Xiao ,&nbsp;Ting-Ting She ,&nbsp;Pin-Jiao Jin ,&nbsp;Shuang Wang ,&nbsp;Lan Liu ,&nbsp;Wen-Jun Li","doi":"10.1016/j.syapm.2024.126564","DOIUrl":"10.1016/j.syapm.2024.126564","url":null,"abstract":"<div><div>Two siderophore-synthesizing species SYSU BS000078^T and SYSU BS000231^T were isolated from the black soil collected from fields located in Heilongjiang province, China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that these two strains showed the highest sequence similarity to <em>Parafrigoribacterium mesophilum</em> KCTC 19311^T (98.61 % and 98.68 %, respectively). The average nucleotide identity (ANI) values between the two strains and other members of the genus <em>Parafrigoribacterium</em> were lower than 95 %, recommended for distinguishing novel prokaryotic species. Cells of strains SYSU BS000078^T and SYSU BS000231^T were aerobic, motile, Gram-stain-positive and non-spore-forming rods. The colonies of these two strains exhibited a cream pigment, with tidy edges and smooth surfaces. Growth was observed within the temperature range of 4–37 °C (optimal growth at 28 °C) and pH range of 6.0–8.0 (optimal growth at pH 7.0). The predominant polar lipids detected in these two strains included diphosphatidylglycerol and phosphatidylglycerol. The predominant respiratory quinones was MK-9. The major cellular fatty acids (&gt;10 %) were iso-C_16:0, anteiso-C_15:0, and anteiso-C_17:0. The genome size and G + C content of strain SYSU BS000078^T were determined to be 2.89 Mbp and 66.5 %, respectively. Meanwhile, SYSU BS000231^T exhibited a genome size of 2.81 Mbp, accompanied by a G + C content of 65.8 %. Based on the phenotypic, physiological, genotypic, and phylogenetic data, these two strains represent two novel species of the genus <em>Parafrigoribacterium</em>, which are proposed as <em>Parafrigoribacterium soli</em> sp. nov. SYSU BS000078^T (=GDMCC 1.4599^T = KCTC 59245^T), and <em>Parafrigoribacterium humi</em> sp. nov. SYSU BS000231^T (=GDMCC 1.3816^T = KCTC 59001^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126564"},"PeriodicalIF":3.3,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142744184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Describing five new strains in the family Woeseiaceae and emended description of the order Woeseiales with genomic features related to environmental adaptation","authors":"Feng-Bai Lian ,&nbsp;Bing-Jun Zhou ,&nbsp;Zi-Yang Zhou ,&nbsp;Alejandro P. Rooney ,&nbsp;Zhen-Xing Xu ,&nbsp;Zong-Jun Du","doi":"10.1016/j.syapm.2024.126563","DOIUrl":"10.1016/j.syapm.2024.126563","url":null,"abstract":"<div><div>The family <em>Woeseiaceae</em>, also known as the JTB255 bacterial group, are ubiquitous and abundant core members of microbial communities in marine surface sediments. However, to date, only one <em>Woeseiaceae</em> strain isolated from marine sediments has been described, and the phylogeny and environmental adaptation mechanisms of this group have been little explored. Here, we isolated five novel <em>Woeseiaceae</em> strains from the marine solar saltern in Weihai, China. Multiple genomic, physiological, and chemotaxonomic characteristics supported that these five isolates represent three novel species within a novel genus, for which <em>Lentisalinibacter</em> gen. nov. and three species <em>Lentisalinibacter sediminis</em> sp. nov., <em>Lentisalinibacter salinarum</em> sp. nov. and <em>Lentisalinibacter orientalis</em> sp. nov. are proposed. Moreover, phylogenetic analysis based on the 16S rRNA genes and genome sequences revealed that <em>Woeseiaceae</em> is most closely related to <em>Steroidobacterales</em>. Further comparative genomics analysis indicated the separate evolution of <em>Woeseiaceae</em> and <em>Steroidobacterales</em>, supporting the emended description of the order <em>Woeseiales</em>. <em>Woeseiales</em> representitives showed facultatively anaerobic characteristics and small genome sizes in contrast to their phylogenetic relatives. They primarily inhabit surface marine sediment environments using multiple metabolic and ecological strategies to adapt to the changing microenvironments. Our results demonstrate the novel representatives of <em>Woeseiales</em> and their environmental adaptation mechanisms in marine environments.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126563"},"PeriodicalIF":3.3,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142700552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thermodesulfovibrio autotrophicus sp. nov., the first autotrophic representative of the widespread sulfate-reducing genus Thermodesulfovibrio, and Thermodesulfovibrio obliviosus sp. nov. that has lost this ability","authors":"Anastasia I. Maltseva ,&nbsp;Alexander G. Elcheninov ,&nbsp;Alexandra A. Klyukina ,&nbsp;Nikolay V. Pimenov ,&nbsp;Andrei A. Novikov ,&nbsp;Alexander V. Lebedinsky ,&nbsp;Evgenii N. Frolov","doi":"10.1016/j.syapm.2024.126561","DOIUrl":"10.1016/j.syapm.2024.126561","url":null,"abstract":"<div><div>Representatives of the genus <em>Thermodesulfovibrio</em> are widespread thermophilic sulfate-reducing bacteria. The genus currently includes five species with validly published names. Two new <em>Thermodesulfovibrio</em> strains, 3907-1M ^T and 3462-1^T, were isolated with molecular hydrogen as an electron donor, sulfate as an electron acceptor and acetate as the carbon source from hot springs of Kunashir Island and Kamchatka Peninsula. Similar to other <em>Thermodesulfovibrio</em> species, the new isolates grew by reduction of sulfate, thiosulfate or Fe (III) with a limited range of electron donors, such as hydrogen (in the presence of acetate), formate (in the presence of acetate), pyruvate and lactate. Surprisingly, strain 3907-1M^T proved to be capable of autotrophic growth as well. Up to now, the genus <em>Thermodesulfovibrio</em> was represented by heterotrophic species only. Genome analysis revealed the presence of a gene cluster encoding enzymes of form III RubisCO-mediated transaldolase variant of the Calvin cycle in both strains, but genes encoding ribulose-1,5-bisphosphate carboxylase and phosphoribulokinase in the genome of the strain 3462-1^T contained internal stop codons in their sequences. On the basis of phylogenomic analysis, as well as distinct phenotypic and genomic properties, strain 3907-1M^T (=DSM 112797^T =JCM 39445^T =VKM B-3594^T =UQM 41601^T) is proposed to be classified as <em>Thermodesulfovibrio autotrophicus</em> sp. nov., and strain 3462-1^T (=JCM 39444^T =VKM B-3714^T =UQM 41602^T) – as <em>Thermodesulfovibrio obliviosus</em> sp. nov. Our results demonstrate a chemolithoautotrophic lifestyle in <em>Thermodesulfovibrio</em> representatives, suggesting greater ecological flexibility of this genus than previously assumed.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126561"},"PeriodicalIF":3.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}