Four novel halophilic archaeal strains CGA53T, CG83T, FCH27T, and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53T showed the highest 16S rRNA gene similarity (92.6%) to Salinilacihabitans rarus AD-4T, and the other three strains were found to be related to Halalkalicoccus 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 Halalkalicoccus. 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 CG83T, FCH27T, and SEDH24 cluster with the current species of the genus Halalkalicoccus, and strain CGA53T 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 CGA53T, CG83T, FCH27T, SEDH24, and the type species of the current genera within the class Halobacteria 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 CGA53T 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 Halalkalicoccus species. Genome-based classification supported that strains CGA53T, CG83T, FCH27T, SEDH24, and the current species of Halalkalicoccus represent a novel family of the order Halobacteriales within the class Halobacteria.
{"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, Xin-Yue Dong, Cong-Qi Tao, Zhang-Ping Wu, Xiao-Wei Shi, Jing Hou, Heng-Lin Cui","doi":"10.1016/j.syapm.2024.126577","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126577","url":null,"abstract":"<p><p>Four novel halophilic archaeal strains CGA53<sup>T</sup>, CG83<sup>T</sup>, FCH27<sup>T</sup>, and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53<sup>T</sup> showed the highest 16S rRNA gene similarity (92.6%) to Salinilacihabitans rarus AD-4<sup>T</sup>, and the other three strains were found to be related to Halalkalicoccus 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 Halalkalicoccus. 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 MgCl<sub>2</sub> (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<sup>T</sup>, FCH27<sup>T</sup>, and SEDH24 cluster with the current species of the genus Halalkalicoccus, and strain CGA53<sup>T</sup> 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<sup>T</sup>, CG83<sup>T</sup>, FCH27<sup>T</sup>, SEDH24, and the type species of the current genera within the class Halobacteria 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<sup>T</sup> 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 H<sub>2</sub>S formation, were found among these four strains and Halalkalicoccus species. Genome-based classification supported that strains CGA53<sup>T</sup>, CG83<sup>T</sup>, FCH27<sup>T</sup>, SEDH24, and the current species of Halalkalicoccus represent a novel family of the order Halobacteriales within the class Halobacteria.</p>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"126577"},"PeriodicalIF":3.3,"publicationDate":"2024-12-15","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}
Four Gram-stain-negative, aerobic, rod-shaped bacteria, designated WL0002T, WL0024T, WL0050T, and WL0075T, 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 U test: p < 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 Defluviimonas. Additionally, Albidovulum inexpectatum DSM 12048T formed a distinct branch within Defluviimonas. The evolutionary distance (ED) and percentage of conserved proteins (POCP) analysis indicated that the four strains and the genus strains of Albidovulum and Defluviimonas should be recognized as a single genus. Genomic relatedness analysis among the four strains and type strains of the genera Albidovulum and Defluviimonas was below species delimitation thresholds, except for strains WL0024T and "D. salinarum" CAU 1641T, which should belong to the same species. Based on phenotypic and genotypic characterization, the four strains should be recognized as novel species in Albidovulum, and it is reasonable to reclassify the genus Defluviimonas as a later heterotypic synonym of Albidovulum, consistent with the classification of the Genome Taxonomy Database (GTDB). Four names are proposed as follows: Albidovulum marisflavi sp. nov. (type strain WL0002T = MCCC 1K06013T = JCM 34653T = GDMCC 1.2437T), Albidovulum salinarum sp. nov. (WL0024T = MCCC 1K06062T = JCM 34656T = GDMCC 1.2438T), Albidovulum litorale sp. nov. (WL0050T = MCCC 1K07524T = JCM 35566T = GDMCC 1.3084T), and Albidovulum sediminicola sp. nov. (WL0075T = MCCC 1K06064T = JCM 34660T = GDMCC 1.2419T).
{"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, Dao-Feng Zhang, Xing-Jie Li, Hong-Chuan Wang, Lin-Qiong Wang, Yang Yuan","doi":"10.1016/j.syapm.2024.126576","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126576","url":null,"abstract":"<p><p>Four Gram-stain-negative, aerobic, rod-shaped bacteria, designated WL0002<sup>T</sup>, WL0024<sup>T</sup>, WL0050<sup>T</sup>, and WL0075<sup>T</sup>, 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 U test: p < 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 Defluviimonas. Additionally, Albidovulum inexpectatum DSM 12048<sup>T</sup> formed a distinct branch within Defluviimonas. The evolutionary distance (ED) and percentage of conserved proteins (POCP) analysis indicated that the four strains and the genus strains of Albidovulum and Defluviimonas should be recognized as a single genus. Genomic relatedness analysis among the four strains and type strains of the genera Albidovulum and Defluviimonas was below species delimitation thresholds, except for strains WL0024<sup>T</sup> and \"D. salinarum\" CAU 1641<sup>T</sup>, which should belong to the same species. Based on phenotypic and genotypic characterization, the four strains should be recognized as novel species in Albidovulum, and it is reasonable to reclassify the genus Defluviimonas as a later heterotypic synonym of Albidovulum, consistent with the classification of the Genome Taxonomy Database (GTDB). Four names are proposed as follows: Albidovulum marisflavi sp. nov. (type strain WL0002<sup>T</sup> = MCCC 1K06013<sup>T</sup> = JCM 34653<sup>T</sup> = GDMCC 1.2437<sup>T</sup>), Albidovulum salinarum sp. nov. (WL0024<sup>T</sup> = MCCC 1K06062<sup>T</sup> = JCM 34656<sup>T</sup> = GDMCC 1.2438<sup>T</sup>), Albidovulum litorale sp. nov. (WL0050<sup>T</sup> = MCCC 1K07524<sup>T</sup> = JCM 35566<sup>T</sup> = GDMCC 1.3084<sup>T</sup>), and Albidovulum sediminicola sp. nov. (WL0075<sup>T</sup> = MCCC 1K06064<sup>T</sup> = JCM 34660<sup>T</sup> = GDMCC 1.2419<sup>T</sup>).</p>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"126576"},"PeriodicalIF":3.3,"publicationDate":"2024-12-09","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}
Pub Date : 2024-12-06DOI: 10.1016/j.syapm.2024.126574
Jette F Petersen, Laura C Valk, Maarten D Verhoeven, Marta A Nierychlo, Caitlin M Singleton, Morten K D Dueholm, Per H Nielsen
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 Rhodoferax, 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 Rhodoferax 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 "Rhodoferax" revealed that species previously assigned to Rhodoferax 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 Rhodoferax genus.
{"title":"Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems.","authors":"Jette F Petersen, Laura C Valk, Maarten D Verhoeven, Marta A Nierychlo, Caitlin M Singleton, Morten K D Dueholm, Per H Nielsen","doi":"10.1016/j.syapm.2024.126574","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126574","url":null,"abstract":"<p><p>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 Rhodoferax, 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 Rhodoferax 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 \"Rhodoferax\" revealed that species previously assigned to Rhodoferax 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 Rhodoferax genus.</p>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"126574"},"PeriodicalIF":3.3,"publicationDate":"2024-12-06","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-05DOI: 10.1016/j.syapm.2024.126575
Yu-Qi Ye, Xin-Yue Zhang, Hong-Nan Gong, Meng-Qi Ye, Zong-Jun Du
During a study on sediment bacterial diversity in coastal China, three bacterial strains, DH-69T, EH-24, and ECK-19T, were isolated from coastal sediments off Xiaoshi Island, Weihai. These strains were Gram-staining-negative, aerobic, and coccoid to rod-shaped with prosthecae and flagella. Comparison of the 16S rRNA gene showed that they shared the highest identity values with Hyphococcus flavus MCCC 1K03223T (96.2-97.6 %), followed by Marinicaulis flavus SY-3-19T (95.2-96.8 %) and Marinicaulis aureus HHTR114T (95.2-96.2 %). Genome comparisons using average nucleotide identity (ANI) and average amino acid identity (AAI) suggested that the three novel strains and the three related strains belonged to the same genus, with strains DH-69T, EH-24, and ECK-19T identified as two distinct novel species. Pan-genome analysis revealed that 995 core genes were shared among 23 Hyphococcus genomes/MAGs. Secondary metabolites analysis identified a biosynthesis gene cluster for microsclerodermin, a potent antifungal peptide, in the novel strains. Moreover, these newly isolated strains were detected in various ecosystems, with a particular prevalence in marine environments, based on analysis of 500,048 amplicon datasets, underscoring their ecological preference. Based on polyphasic characterizations, strains DH-69T and EH-24 represent a novel species of the genus Hyphococcus, for which the name Hyphococcus formosus sp. nov. is proposed with the type strain DH-69T (= MCCC 1H00436T = KCTC 8010T). Strain ECK-19T represents another novel Hyphococcus species, for which the name Hyphococcus lacteus sp. nov. is proposed with the type strain ECK-19T (= MCCC 1H00435T = KCTC 8009T). Furthermore, Marinicaulis flavus and Marinicaulis aureus are proposed to be reclassified as Hyphococcus luteus nom. nov. and Hyphococcus aureus comb. nov., respectively, accompanied by an emended description of the genus Hyphococcus.
{"title":"Description of Hyphococcus formosus sp. nov. and Hyphococcus lacteus sp. nov., isolated from coastal sediment, and reclassification of Marinicaulis flavus as Hyphococcus luteus nom. nov. and Marinicaulis aureus as Hyphococcus aureus comb. nov.","authors":"Yu-Qi Ye, Xin-Yue Zhang, Hong-Nan Gong, Meng-Qi Ye, Zong-Jun Du","doi":"10.1016/j.syapm.2024.126575","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126575","url":null,"abstract":"<p><p>During a study on sediment bacterial diversity in coastal China, three bacterial strains, DH-69<sup>T</sup>, EH-24, and ECK-19<sup>T</sup>, were isolated from coastal sediments off Xiaoshi Island, Weihai. These strains were Gram-staining-negative, aerobic, and coccoid to rod-shaped with prosthecae and flagella. Comparison of the 16S rRNA gene showed that they shared the highest identity values with Hyphococcus flavus MCCC 1K03223<sup>T</sup> (96.2-97.6 %), followed by Marinicaulis flavus SY-3-19<sup>T</sup> (95.2-96.8 %) and Marinicaulis aureus HHTR114<sup>T</sup> (95.2-96.2 %). Genome comparisons using average nucleotide identity (ANI) and average amino acid identity (AAI) suggested that the three novel strains and the three related strains belonged to the same genus, with strains DH-69<sup>T</sup>, EH-24, and ECK-19<sup>T</sup> identified as two distinct novel species. Pan-genome analysis revealed that 995 core genes were shared among 23 Hyphococcus genomes/MAGs. Secondary metabolites analysis identified a biosynthesis gene cluster for microsclerodermin, a potent antifungal peptide, in the novel strains. Moreover, these newly isolated strains were detected in various ecosystems, with a particular prevalence in marine environments, based on analysis of 500,048 amplicon datasets, underscoring their ecological preference. Based on polyphasic characterizations, strains DH-69<sup>T</sup> and EH-24 represent a novel species of the genus Hyphococcus, for which the name Hyphococcus formosus sp. nov. is proposed with the type strain DH-69<sup>T</sup> (= MCCC 1H00436<sup>T</sup> = KCTC 8010<sup>T</sup>). Strain ECK-19<sup>T</sup> represents another novel Hyphococcus species, for which the name Hyphococcus lacteus sp. nov. is proposed with the type strain ECK-19<sup>T</sup> (= MCCC 1H00435<sup>T</sup> = KCTC 8009<sup>T</sup>). Furthermore, Marinicaulis flavus and Marinicaulis aureus are proposed to be reclassified as Hyphococcus luteus nom. nov. and Hyphococcus aureus comb. nov., respectively, accompanied by an emended description of the genus Hyphococcus.</p>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"126575"},"PeriodicalIF":3.3,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814030","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}
Pub Date : 2024-11-22DOI: 10.1016/j.syapm.2024.126565
Victoria A. Saltykova , Olga V. Danilova , Igor Y. Oshkin , Svetlana E. Belova , Natalia E. Suzina , Nikolai V. Pimenov , Svetlana N. Dedysh
A morphologically conspicuous microbial association was detected in a bioreactor running in a continuous mode with methanotrophic bacteria of the genus Methylococcus and natural gas as a growth substrate. The association consisted of spherical Methylococcus cells colonized by elongated rods, which produced rosette-like aggregates and inhibited the cultivation process. An isolate of these bacteria, strain S20T, was obtained and identified as belonging to the alphaproteobacterial family Ancalomicrobiaceae but displaying only a distant relationship (93.9–95.1 % 16S rRNA gene sequence similarity) to characterized members of this family. Strain S20T 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 Methylococcus cells and breaking the integrity of methanotroph cell walls, presumably to feed on methanol. The same interaction was observed with Methylomonas species. The finished genome sequence of strain S20T 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 Ancalomicrobiaceae species. We propose to classify these bacteria as representing a novel genus and species, Methyloraptor flagellatus gen. Nov., sp. nov., with the type strain S20T (=KCTC 8649T = VKM B-3853T).
{"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 , Olga V. Danilova , Igor Y. Oshkin , Svetlana E. Belova , Natalia E. Suzina , Nikolai V. Pimenov , 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<sup>T</sup>, 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<sup>T</sup> 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<sup>T</sup> 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<sup>T</sup> (=KCTC 8649<sup>T</sup> = VKM B-3853<sup>T</sup>).</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}
Pub Date : 2024-11-21DOI: 10.1016/j.syapm.2024.126564
Yu-Ting OuYang , Le-Bin Chen , Jian-Yu Jiao , Zi-Xuan Hu , Jiong-Shan Wang , Tian-Hang Yang , Jun Xiao , Ting-Ting She , Pin-Jiao Jin , Shuang Wang , Lan Liu , Wen-Jun Li
Two siderophore-synthesizing species SYSU BS000078T and SYSU BS000231T 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 Parafrigoribacterium mesophilum KCTC 19311T (98.61 % and 98.68 %, respectively). The average nucleotide identity (ANI) values between the two strains and other members of the genus Parafrigoribacterium were lower than 95 %, recommended for distinguishing novel prokaryotic species. Cells of strains SYSU BS000078T and SYSU BS000231T 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 (>10 %) were iso-C16:0, anteiso-C15:0, and anteiso-C17:0. The genome size and G + C content of strain SYSU BS000078T were determined to be 2.89 Mbp and 66.5 %, respectively. Meanwhile, SYSU BS000231T 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 Parafrigoribacterium, which are proposed as Parafrigoribacterium soli sp. nov. SYSU BS000078T (=GDMCC 1.4599T = KCTC 59245T), and Parafrigoribacterium humi sp. nov. SYSU BS000231T (=GDMCC 1.3816T = KCTC 59001T).
{"title":"Parafrigoribacterium soli sp. nov. and Parafrigoribacterium humi sp. nov., two novel siderophore-synthesizing species isolated from black soil","authors":"Yu-Ting OuYang , Le-Bin Chen , Jian-Yu Jiao , Zi-Xuan Hu , Jiong-Shan Wang , Tian-Hang Yang , Jun Xiao , Ting-Ting She , Pin-Jiao Jin , Shuang Wang , Lan Liu , 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<sup>T</sup> and SYSU BS000231<sup>T</sup> 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<sup>T</sup> (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<sup>T</sup> and SYSU BS000231<sup>T</sup> 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 (>10 %) were iso-C<sub>16:0</sub>, anteiso-C<sub>15:0</sub>, and anteiso-C<sub>17:0</sub>. The genome size and G + C content of strain SYSU BS000078<sup>T</sup> were determined to be 2.89 Mbp and 66.5 %, respectively. Meanwhile, SYSU BS000231<sup>T</sup> 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<sup>T</sup> (=GDMCC 1.4599<sup>T</sup> = KCTC 59245<sup>T</sup>), and <em>Parafrigoribacterium humi</em> sp. nov. SYSU BS000231<sup>T</sup> (=GDMCC 1.3816<sup>T</sup> = KCTC 59001<sup>T</sup>).</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}
Pub Date : 2024-11-20DOI: 10.1016/j.syapm.2024.126563
Feng-Bai Lian , Bing-Jun Zhou , Zi-Yang Zhou , Alejandro P. Rooney , Zhen-Xing Xu , Zong-Jun Du
The family Woeseiaceae, 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 Woeseiaceae 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 Woeseiaceae 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 Lentisalinibacter gen. nov. and three species Lentisalinibacter sediminis sp. nov., Lentisalinibacter salinarum sp. nov. and Lentisalinibacter orientalis sp. nov. are proposed. Moreover, phylogenetic analysis based on the 16S rRNA genes and genome sequences revealed that Woeseiaceae is most closely related to Steroidobacterales. Further comparative genomics analysis indicated the separate evolution of Woeseiaceae and Steroidobacterales, supporting the emended description of the order Woeseiales. Woeseiales 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 Woeseiales and their environmental adaptation mechanisms in marine environments.
{"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 , Bing-Jun Zhou , Zi-Yang Zhou , Alejandro P. Rooney , Zhen-Xing Xu , 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}
Pub Date : 2024-11-19DOI: 10.1016/j.syapm.2024.126562
Isabella Wilkie, Luis H Orellana
Members of the phylum Verrucomicrobiota 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 (Seribacter gen. Nov., Chordibacter 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, Seribacteraceae. Our findings shed light on the ecological significance and metabolic potential of Verrucomicrobiota populations in spring bloom events.
{"title":"Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans.","authors":"Isabella Wilkie, Luis H Orellana","doi":"10.1016/j.syapm.2024.126562","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126562","url":null,"abstract":"<p><p>Members of the phylum Verrucomicrobiota 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 (Seribacter gen. Nov., Chordibacter 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, Seribacteraceae. Our findings shed light on the ecological significance and metabolic potential of Verrucomicrobiota populations in spring bloom events.</p>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"126562"},"PeriodicalIF":3.3,"publicationDate":"2024-11-19","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01DOI: 10.1016/j.syapm.2024.126561
Anastasia I. Maltseva , Alexander G. Elcheninov , Alexandra A. Klyukina , Nikolay V. Pimenov , Andrei A. Novikov , Alexander V. Lebedinsky , Evgenii N. Frolov
Representatives of the genus Thermodesulfovibrio are widespread thermophilic sulfate-reducing bacteria. The genus currently includes five species with validly published names. Two new Thermodesulfovibrio strains, 3907-1M T and 3462-1T, 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 Thermodesulfovibrio 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 3907-1MT proved to be capable of autotrophic growth as well. Up to now, the genus Thermodesulfovibrio 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 3462-1T contained internal stop codons in their sequences. On the basis of phylogenomic analysis, as well as distinct phenotypic and genomic properties, strain 3907-1MT (=DSM 112797T =JCM 39445T =VKM B-3594T =UQM 41601T) is proposed to be classified as Thermodesulfovibrio autotrophicus sp. nov., and strain 3462-1T (=JCM 39444T =VKM B-3714T =UQM 41602T) – as Thermodesulfovibrio obliviosus sp. nov. Our results demonstrate a chemolithoautotrophic lifestyle in Thermodesulfovibrio representatives, suggesting greater ecological flexibility of this genus than previously assumed.
{"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 , Alexander G. Elcheninov , Alexandra A. Klyukina , Nikolay V. Pimenov , Andrei A. Novikov , Alexander V. Lebedinsky , 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 <sup>T</sup> and 3462-1<sup>T</sup>, 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<sup>T</sup> 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<sup>T</sup> contained internal stop codons in their sequences. On the basis of phylogenomic analysis, as well as distinct phenotypic and genomic properties, strain 3907-1M<sup>T</sup> (=DSM 112797<sup>T</sup> =JCM 39445<sup>T</sup> =VKM B-3594<sup>T</sup> =UQM 41601<sup>T</sup>) is proposed to be classified as <em>Thermodesulfovibrio autotrophicus</em> sp. nov., and strain 3462-1<sup>T</sup> (=JCM 39444<sup>T</sup> =VKM B-3714<sup>T</sup> =UQM 41602<sup>T</sup>) – 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}
Pub Date : 2024-11-01DOI: 10.1016/j.syapm.2024.126560
Violetta Shestivska , Petra Španělová , Marcela Krůtová , Martina Maixnerová , Priscila Thiago Dobbler , Tomáš Větrovský , Alexandr Nemec , Martina Kyselková
This study aimed to determine the taxonomic status of a new group of bovine strains of the genus Acinetobacter characterized by the rare ability to grow at temperatures above 44 °C. Initially, 24 strains were isolated from cattle feces collected at 11 farms in Czechia in 2022, representing a tentative new species based on preliminary whole-cell MALDI-TOF MS identification and rpoB gene sequencing. Twelve strains encompassing the within-group diversity were studied in detail, including whole genome de novo sequencing. Core genome-based phylogenetic analysis revealed that the 12 strains form a distinct clade within the genus. The genomic average nucleotide identity based on BLAST (ANIb) values within the clade were ≥ 98.2%, whereas the ANIb values between the clade and the known Acinetobacter species were < 83%. Each of the 12 genomes consisted of a circular chromosome (3.05−3.28 Mb) and 1−6 extrachromosomal elements (1.43−122.5 kb). All strains were non-glucose oxidizing, non-hemolytic, non-proteolytic, and prototrophic, and used acetate, ethanol, and DL-lactate as sole carbon and energy sources. Unrestricted growth at 47 °C was their unique diagnostic characteristic in a genus-wide comparative analysis and their growth kinetics at 37–46 °C differed from that of Acinetobacter baumannii. The studied strains were susceptible to 18 antibiotics except for sporadic resistance to streptomycin, tetracycline, and sulfonamides associated with the presence of strA/strB, tet(Y), and sul2 genes, respectively. We conclude that the studied strains represent a new species, for which we propose the name Acinetobacter thermotolerans sp. nov. The type strain is ANC 7454T (= CCM 9356T = CCUG 77195T = CNCTC 8200T).
{"title":"Proposal of Acinetobacter thermotolerans sp. nov. to accommodate bovine feces-dwelling bacteria growing at 47 °C","authors":"Violetta Shestivska , Petra Španělová , Marcela Krůtová , Martina Maixnerová , Priscila Thiago Dobbler , Tomáš Větrovský , Alexandr Nemec , Martina Kyselková","doi":"10.1016/j.syapm.2024.126560","DOIUrl":"10.1016/j.syapm.2024.126560","url":null,"abstract":"<div><div>This study aimed to determine the taxonomic status of a new group of bovine strains of the genus <em>Acinetobacter</em> characterized by the rare ability to grow at temperatures above 44 °C. Initially, 24 strains were isolated from cattle feces collected at 11 farms in Czechia in 2022, representing a tentative new species based on preliminary whole-cell MALDI-TOF MS identification and <em>rpoB</em> gene sequencing. Twelve strains encompassing the within-group diversity were studied in detail, including whole genome <em>de novo</em> sequencing. Core genome-based phylogenetic analysis revealed that the 12 strains form a distinct clade within the genus. The genomic average nucleotide identity based on BLAST (ANIb) values within the clade were ≥ 98.2%, whereas the ANIb values between the clade and the known <em>Acinetobacter</em> species were < 83%. Each of the 12 genomes consisted of a circular chromosome (3.05−3.28 Mb) and 1−6 extrachromosomal elements (1.43−122.5 kb). All strains were non-glucose oxidizing, non-hemolytic, non-proteolytic, and prototrophic, and used acetate, ethanol, and DL-lactate as sole carbon and energy sources. Unrestricted growth at 47 °C was their unique diagnostic characteristic in a genus-wide comparative analysis and their growth kinetics at 37–46 °C differed from that of <em>Acinetobacter baumannii</em>. The studied strains were susceptible to 18 antibiotics except for sporadic resistance to streptomycin, tetracycline, and sulfonamides associated with the presence of <em>strA</em>/<em>strB</em>, <em>tet</em>(Y), and <em>sul2</em> genes, respectively. We conclude that the studied strains represent a new species, for which we propose the name <em>Acinetobacter thermotolerans</em> sp. nov. The type strain is ANC 7454<sup>T</sup> (= CCM 9356<sup>T</sup> = CCUG 77195<sup>T</sup> = CNCTC 8200<sup>T</sup>).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126560"},"PeriodicalIF":3.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676834","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}
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