Weidong Mu, Haoran Liu, Bai Guo, Kaiyue Wang, Jinhua Hu, Jianjun Song, Xiuyun Li, Shuzhen Wei, Aijv Liu, Hongliang Liu
{"title":"从湿地分离出的抗苯甲酸盐和亚硒酸盐还原细菌 Paracoccus benzoatiresistens sp.","authors":"Weidong Mu, Haoran Liu, Bai Guo, Kaiyue Wang, Jinhua Hu, Jianjun Song, Xiuyun Li, Shuzhen Wei, Aijv Liu, Hongliang Liu","doi":"10.1007/s10482-024-01969-7","DOIUrl":null,"url":null,"abstract":"<div><p>A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6<sup>T</sup>, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25–37 °C (optimum, 30 °C), pH 5–9 (optimum, pH 7), and in the presence of 1.0–4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6<sup>T</sup> belongs to the genus <i>Paracoccus</i>, and the closest members were <i>Paracoccus shandongensis</i> wg2<sup>T</sup> with 98.1% similarity, <i>Paracoccus fontiphilus</i> MVW-1<sup> T</sup> (97.9%), <i>Paracoccus everestensis</i> S8-55<sup> T</sup> (97.7%), <i>Paracoccus subflavus</i> GY0581<sup>T</sup> (97.6%), <i>Paracoccus sediminis</i> CMB17<sup>T</sup> (97.3%), <i>Paracoccus caeni</i> MJ17<sup>T</sup> (97.0%), and <i>Paracoccus angustae</i> E6<sup>T</sup> (97.0%). The genome size of strain EF6<sup>T</sup> was 4.88 Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6<sup>T</sup> and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C<sub>18:1</sub> <i>ω</i>6<i>c</i> and/or C<sub>18:1</sub> <i>ω</i>7<i>c</i>) and C<sub>18:1</sub> (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6<sup>T</sup> displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (<i>acdA</i>, <i>pcaF</i>, <i>fadA</i>, <i>pcaC</i>, <i>purB</i>, and <i>catA</i>) and twenty selenite resistance and reduction-related genes (<i>iscR</i>, <i>ssuB</i>, <i>ssuD</i>, <i>selA</i>, <i>selD</i> and so on). Additionally, EF6<sup>T</sup> possesses unique genes (<i>catA</i>, <i>ssuB</i>, and <i>ssuC</i>) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6<sup>T</sup> a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in <i>Paracoccus</i>. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6<sup>T</sup> is considered to represent a novel species of the genus <i>Paracoccus</i> within the family <i>Rhodobacteraceae</i>, for which the name <i>Paracoccus benzoatiresistens</i> sp. nov. is proposed. The type strain is EF6<sup>T</sup> (= GDMCC 1.3400<sup> T</sup> = JCM 35642<sup> T</sup> = MCCC 1K08702<sup>T</sup>).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8000,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Paracoccus benzoatiresistens sp. nov., a benzoate resistance and selenite reduction bacterium isolated from wetland\",\"authors\":\"Weidong Mu, Haoran Liu, Bai Guo, Kaiyue Wang, Jinhua Hu, Jianjun Song, Xiuyun Li, Shuzhen Wei, Aijv Liu, Hongliang Liu\",\"doi\":\"10.1007/s10482-024-01969-7\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6<sup>T</sup>, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25–37 °C (optimum, 30 °C), pH 5–9 (optimum, pH 7), and in the presence of 1.0–4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6<sup>T</sup> belongs to the genus <i>Paracoccus</i>, and the closest members were <i>Paracoccus shandongensis</i> wg2<sup>T</sup> with 98.1% similarity, <i>Paracoccus fontiphilus</i> MVW-1<sup> T</sup> (97.9%), <i>Paracoccus everestensis</i> S8-55<sup> T</sup> (97.7%), <i>Paracoccus subflavus</i> GY0581<sup>T</sup> (97.6%), <i>Paracoccus sediminis</i> CMB17<sup>T</sup> (97.3%), <i>Paracoccus caeni</i> MJ17<sup>T</sup> (97.0%), and <i>Paracoccus angustae</i> E6<sup>T</sup> (97.0%). The genome size of strain EF6<sup>T</sup> was 4.88 Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6<sup>T</sup> and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C<sub>18:1</sub> <i>ω</i>6<i>c</i> and/or C<sub>18:1</sub> <i>ω</i>7<i>c</i>) and C<sub>18:1</sub> (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6<sup>T</sup> displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (<i>acdA</i>, <i>pcaF</i>, <i>fadA</i>, <i>pcaC</i>, <i>purB</i>, and <i>catA</i>) and twenty selenite resistance and reduction-related genes (<i>iscR</i>, <i>ssuB</i>, <i>ssuD</i>, <i>selA</i>, <i>selD</i> and so on). Additionally, EF6<sup>T</sup> possesses unique genes (<i>catA</i>, <i>ssuB</i>, and <i>ssuC</i>) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6<sup>T</sup> a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in <i>Paracoccus</i>. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6<sup>T</sup> is considered to represent a novel species of the genus <i>Paracoccus</i> within the family <i>Rhodobacteraceae</i>, for which the name <i>Paracoccus benzoatiresistens</i> sp. nov. is proposed. The type strain is EF6<sup>T</sup> (= GDMCC 1.3400<sup> T</sup> = JCM 35642<sup> T</sup> = MCCC 1K08702<sup>T</sup>).</p></div>\",\"PeriodicalId\":50746,\"journal\":{\"name\":\"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology\",\"volume\":\"117 1\",\"pages\":\"\"},\"PeriodicalIF\":1.8000,\"publicationDate\":\"2024-05-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s10482-024-01969-7\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","FirstCategoryId":"99","ListUrlMain":"https://link.springer.com/article/10.1007/s10482-024-01969-7","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
Paracoccus benzoatiresistens sp. nov., a benzoate resistance and selenite reduction bacterium isolated from wetland
A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6T, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25–37 °C (optimum, 30 °C), pH 5–9 (optimum, pH 7), and in the presence of 1.0–4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6T belongs to the genus Paracoccus, and the closest members were Paracoccus shandongensis wg2T with 98.1% similarity, Paracoccus fontiphilus MVW-1 T (97.9%), Paracoccus everestensis S8-55 T (97.7%), Paracoccus subflavus GY0581T (97.6%), Paracoccus sediminis CMB17T (97.3%), Paracoccus caeni MJ17T (97.0%), and Paracoccus angustae E6T (97.0%). The genome size of strain EF6T was 4.88 Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6T and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C18:1ω6c and/or C18:1ω7c) and C18:1 (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6T displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (acdA, pcaF, fadA, pcaC, purB, and catA) and twenty selenite resistance and reduction-related genes (iscR, ssuB, ssuD, selA, selD and so on). Additionally, EF6T possesses unique genes (catA, ssuB, and ssuC) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6T a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in Paracoccus. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6T is considered to represent a novel species of the genus Paracoccus within the family Rhodobacteraceae, for which the name Paracoccus benzoatiresistens sp. nov. is proposed. The type strain is EF6T (= GDMCC 1.3400 T = JCM 35642 T = MCCC 1K08702T).
期刊介绍:
Antonie van Leeuwenhoek publishes papers on fundamental and applied aspects of microbiology. Topics of particular interest include: taxonomy, structure & development; biochemistry & molecular biology; physiology & metabolic studies; genetics; ecological studies; especially molecular ecology; marine microbiology; medical microbiology; molecular biological aspects of microbial pathogenesis and bioinformatics.