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Paracoccus benzoatiresistens sp. nov., a benzoate resistance and selenite reduction bacterium isolated from wetland. Antonie Van Leeuwenhoek 2024; 117:81. [PMID: 38777900 DOI: 10.1007/s10482-024-01969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/13/2024] [Indexed: 05/25/2024]
Abstract
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%, C18:1 ω6c and/or C18:1 ω7c) 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).
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Isolation and Characterization of Paracoccus maritimus sp. nov., from Intertidal Sediment. Curr Microbiol 2024; 81:134. [PMID: 38592513 DOI: 10.1007/s00284-024-03637-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/05/2024] [Indexed: 04/10/2024]
Abstract
A novel Paracoccus-related strain, designated YLB-12T, was isolated from a sediment sample from the tidal zone of Shapowei Port, Xiamen, Fujian Province, PR China. The novel strain is a Gram-stain-negative, short, rod-shaped, nonmotile, catalase- and oxidase-positive strain that grows at 10-37 °C and pH 5.0-9.0 in the presence of 0-12.0% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain belongs to the genus Paracoccus and that its highest sequence similarity was to Paracoccus homiensis DD-R11T (98.5%), followed by Paracoccus zeaxanthinifaciens ATCC 21588T (97.4%), Paracoccus rhizosphaerae LMG 26205T (97.2%), Paracoccus beibuensis CGMCC 1.7295T (97.1%) and Paracoccus halotolerans CFH 90064T (97.0%). The DNA‒DNA hybridization values between strain YLB-12T and the five closely related type strains ranged from 20.4 to 22.4%. The genomic G+C content of strain YLB-12T was 63.7%. In addition to diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol, the polar lipids of the strain YLB-12T also consisted of an unidentified glycolipid and four unidentified polar lipids. The cells contained summed feature 8 (C18: 1ω6c /C18: 1ω7c, 62.7%) as the major cellular fatty acid and ubiquinone-10 as the predominant menaquinone. On the basis of its phenotypic and genotypic characteristics, strain YLB-12T represents a novel species within the genus Paracoccus, for which the name Paracoccus maritimus sp. nov. is proposed. The type strain was YLB-12T (= MCCC 1A17213T = KCTC 82197T).
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Abyssibius alkaniclasticus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae, isolated from the Mariana Trench. Int J Syst Evol Microbiol 2023; 73. [PMID: 36790414 DOI: 10.1099/ijsem.0.005715] [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
A Gram-stain-negative bacterium with rod-shaped or irregular cells approximately 0.5-0.9×2.0-3.8 µm in size, designated as 960558T, was isolated from sediment sampled in the Mariana Trench. Strain 960558T grows at 4-37 °C (optimum, 28 °C), pH 6-7 (optimum, pH 7) and in the presence of 1-5 % (w/v) NaCl (optimum, 3 %). Strain 960558T utilizes tetradecane or hexadecane as a sole carbon and energy source, respectively. Phylogenetic trees based on 16S rRNA gene sequences and phylogenomic reconstruction revealed a close phylogenetic relationship between strain 960558T and members of the family Rhodobacteraceae by forming a separate branch within the type species of closely related genera. The validly published species that is most closely related to strain 960558T is Planktotalea lamellibrachiae JAM 119T, which has the highest 16S rRNA gene sequence similarity (93.47 %). Ubiquinone 10 is the predominant ubiquinone, while C16 : 0, 11-methyl C18 : 1 ω7c and C18 : 1 ω7c and/or C18 : 1 ω6c are the predominant fatty acids (>10 %). Additionally, phosphatidylglycerol, glycolipids, diphosphatidylglycerol, unidentified polar lipids and unidentified aminolipids are the major polar lipids. The DNA G+C content of strain 960558T is 61 %. Average nucleotide identity and digital DNA-DNA hybridization results of strain 960558T with other type strains are <70.2 and 22.1 %, respectively. Based on its phylogenetic, chemotaxonomic and other phenotypic properties, strain 960558T is considered to represent a novel genus and species within the family Rhodobacteraceae, for which the name Abyssibius alkaniclasticus gen. nov., sp. nov. is proposed. The type strain of Abyssibius alkaniclasticus is 960558T (=KCTC 82619T=MCCC 1K04727T).
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Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36861375 DOI: 10.1099/ijsem.0.005581] [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: 03/03/2023] Open
Abstract
Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.
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Paracoccus binzhouensis sp. nov., isolated from activated sludge. Arch Microbiol 2021; 203:3007-3013. [PMID: 33774710 DOI: 10.1007/s00203-021-02286-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/23/2021] [Accepted: 03/16/2021] [Indexed: 11/29/2022]
Abstract
A gram-stain-negative, non-motile and rod-shaped strain, designated wg1T, was isolated from activated sludge obtained from wastewater treatment plant in Binzhou (Shandong province, PR China). Growth of strain wg1T occurred at 25-45 °C (optimum, 37 °C), at pH 7.0-9.0 (optimum growth at pH 8.0) and at a salinity range of 0-4% (optimum, 1%). The chemotaxonomic, phenotypic and genomic traits were investigated. The 16S rRNA gene sequence analysis showed that strain wg1T belonged to the genus Paracoccus. The species with highest similarity to strain wg1T was Paracoccus communis VKM B-2787T (98.27%), followed by Paracoccus kondratievae VKM B-2222T (98.25%). The isoprenoid quinone was Q-10. Major cellular fatty acids were summed feature 8, C16:0 and C18:0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), aminoglycolipid (AGL), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), one unidentified lipid (L) and one unidentified phospholipid (PL). The genome size was 4,834,448 bp with a G+C content of 67.67 mol%. The prediction result of secondary metabolites based on genome has shown that the strain wg1T contained 12 clusters, and the gene involved in primary metabolism showed differences in the comparison between wg1T and reference strains. The dDDH values of strain wg1T with P. communis VKM B-2787T, P. kondratievae VKM B-2222T and P. denitrificans DSM 413T were 45.30, 30.60 and 39.50%, respectively. Based on its physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain wg1T is considered to represent a novel species for which the name Paracoccus binzhouensis sp. nov., is proposed. The type strain is wg1T (= KCTC 72861T = CCTCC AB 2019400T).
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Paracoccus amoyensis sp. nov., isolated from the surface seawater along the coast of Xiamen Island, China. Int J Syst Evol Microbiol 2021; 71. [PMID: 33528347 DOI: 10.1099/ijsem.0.004685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 11-3T was isolated from the surface seawater along the coast of Xiamen Island, China. Cells were Gram-stain-negative, oxidase- and catalase-positive, short and rod-shaped, nonmotile, 0.5-1.0 μm in width and 1.0-2.0 μm in length. Growth of strain 11-3T was at temperature of 15-37°C (optimum 28-35°C), at pH of 5.0-11.0 (optimum 7.0-9.0) and at salinity range of 0-10 (optimum 0.5-1). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 11-3T belonged to the genus Paracoccus and had the highest similarity with Paracoccus caeni MJ17T (98.1 %), followed by Paracoccus xiamenensis 12-3T (97.1 %), Paracoccus zeaxanthinifaciens ATCC 21588T (97.1 %), Paracoccus aestuarii DSM 19484T (97.0 %), Paracoccus liaowanqingii 2251T (97.0 %), Paracoccus fistulariae KCTC 22803T (97.0 %) and other species of the genus Paracoccus (95.2-96.8 %). The DNA-DNA hybridization values between strain 11-3T and the selected strains (P. caeni MJ17T, P. xiamenensis 12-3T, P. zeaxanthinifaciens ATCC 21588T, P. aestuarii DSM 19484T and P. liaowanqingii 2251T) were 19.4, 19.5, 21.6, 19.3 and 19.8 %, respectively. Corresponding, their ANI values were 77.53, 75.61, 75.36, 75.73 and 75.33 %, respectively. The major fatty acid was summed feature 8 (C18:1 ω6c/ω7c). The major respiratory quinone was Q10. The polar lipids included phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), unidentified glycolipid (GL) and unidentified aminolipid (AL). The DNA G+C content of strain 11-3T was 60.1 %. Based on results of the phylogenetic analysis, phenotypic and chemotaxonomic characteristics, strain 11-3T represents a novel species of the genus Paracoccus, for which the name Paracoccus amoyensis sp. nov. is proposed. The type strain is 11-3T (=MCCC 1A16380T=KCTC 72689T).
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Paracoccus lichenicola sp. nov., Isolated from Lichen. Curr Microbiol 2021; 78:816-821. [PMID: 33388938 DOI: 10.1007/s00284-020-02321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
Strain YIM 132242T, isolated from lichen collected from Pu'er, Yunnan Province, China, was short-rod-shaped, Gram-reaction-negative, aerobic, catalase- and oxidase-positive. Growth of the strain was occurred at 10-39 °C (optimum, 28-35 °C), at pH 4.0-10.0 (optimum, pH 7.0-8.0) and at salinities of 0-8% (w/v) NaCl (optimum, 0-2%). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM 132242T belonged to the genus Paracoccus and had the highest levels of sequence similarity to Paracoccus aerius KCTC 42845T (97.0% similarity), Paracoccus sediminis CMB17T (96.8% similarity), and Paracoccus fontiphilus MVW-1T (96.4% similarity). The major fatty acid was identified as C18:1 ω7c (77.6%). The predominant respiratory quinone was ubiquinone-10 (Q-10). Polar lipid analysis indicated the presence of phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), diphosphatidylglycerol (DPG), an unidentified lipid (L), and three unidentified phospholipids (PL1-PL3). Based on the draft genome sequence, the DNA G + C content of the strain was 67.1 mol%, and the values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) of strain YIM 132242T with Paracoccus aerius KCTC 42845T were 85.4% and 29.1%, respectively. On the basis of the data from this polyphasic characterization, strain YIM 132242T represents a novel species of the genus Paracoccus, for which the name Paracoccus lichenicola sp. nov. is proposed. The type strain is YIM 132242T (= KCTC 72463T = CGMCC1.17191T).
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Pectin Degradation is an Important Determinant for Alfalfa Silage Fermentation through the Rescheduling of the Bacterial Community. Microorganisms 2020; 8:E488. [PMID: 32235428 PMCID: PMC7232347 DOI: 10.3390/microorganisms8040488] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/28/2020] [Accepted: 03/28/2020] [Indexed: 11/30/2022] Open
Abstract
This study aimed to evaluate the effects of the four kinds of additives on the silage quality and the relevant bacterial community diversity by Illumina HiSeq 16S rRNA sequencing. The four kinds of additives were Lactobacillus plantarum (LP), organic acids including gallic acid (GA) and phenyllactic acid (PA), pectin (PEC), and enzymes including pectinase (PEE) and cellulase (CE). After 30 d of fermentation, the pH value was shown to have the lowest value in the PEE and PEC groups, followed by the PA group, and then in CE and GA groups; the highest value of pH was found in both LP and control groups. The ammonia nitrogen concentration was lower in the PEE group compared to the other groups except for the PA group. In the comparisons among the seven groups, Lactobacillus was higher in the LP group, Paracoccus was higher in the GA group, Weissella was higher in the PA group, Leuconostoc was higher in the PEC group, Bacillus, Aeromonas, and Curvibacter were higher in the PEE group, and Coriobacteriaceae_UCG_002 was higher in the CE group compared to the other groups. This study proposed that the addition of PEC and PEE improved the fermentation quality of alfalfa silage compared to other additives by improving the bacterial community of Leuconostoc, and Bacillus and Aeromonas, respectively. Moreover, the enhanced fermentation quality of alfalfa silage by the supplementation of PEC and PEE might be attributed to other unclassified genera. This study provides an implication that pectin degradation is an important determinant for alfalfa silage fermentation through the rescheduling of bacterial community diversity.
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Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa. Int J Syst Evol Microbiol 2020; 70:1720-1728. [DOI: 10.1099/ijsem.0.003962] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, coccoid-shaped, catalase- and oxidase-positive, non-denitrifying, neutrophilic bacterium designated as strain JC501T was isolated from an epiphytic rhizosphere of an orchid, Aerides maculosa, growing in the Western Ghats of India. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain JC501T belonged to the genus
Paracoccus
and had the highest levels of sequence identity with
Paracoccus marinus
KKL-A5T (98.9 %),
Paracoccus contaminans
WPAn02T (97.3 %) and other members of the genus
Paracoccus
(<97.3 %). Strain JC501T produced indole-3 acetic acid and other indole derivatives from tryptophan. The dominant respiratory quinone was Q-10 and the major fatty acid was C18 : 1ω7c/C18 : 1ω6c, with significant quantities of C18 : 1ω9c, C17 : 0 and C16 : 0. The polar lipids of strain JC501T comprised phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified glycolipid, two unidentified aminolipids, two unidentified lipids and four unidentified phospholipids. The genome of strain JC501T was 3.3 Mbp with G+C content of 69.4 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of eight housekeeping genes. Based on the results of phylogenetic analyses, low (<85.9 %) average nucleotide identity, digital DNA–DNA hybridization (<29.8 %), chemotaxonomic analysis and physiological properties, strain JC501T could not be classified into any of the recognized species of the genus
Paracoccus
. Strain JC501T represents a novel species, for which the name Paracoccus aeridis sp. nov. is proposed. The type strain is JC501T (=LMG 30532T=NBRC 113644T).
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Paracoccus aurantiacus sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island. Int J Syst Evol Microbiol 2020; 70:2554-2559. [PMID: 32101515 DOI: 10.1099/ijsem.0.004068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An orange-pigmented, short-rod-shaped, aerobic and non-motile bacterial strain, designated TK008T, was isolated from the shallow-sea hydrothermal systems off Kueishantao Island in Taiwan, China, and it was studied by using a polyphasic taxonomic approach. Cells were Gram-stain-negative, and catalase- and oxidase-positive. Strain TK008T exhibited highest 16S rRNA gene sequence similarity of 97.1 % to Paracoccus pacificus F14T. The phylogenetic trees based on 16S rRNA gene sequences showed that strain TK008T was a member of the genus Paracoccus. Digital DNA-DNA hybridization values between strain TK008T and two closely related species (Paracoccus zhejiangensis and Paracoccus tegillarcae) were 20.6 and 20.9 %. The average nucleotide identity values of strain TK008T compared with P. zhejiangensis and P. tegillarcae were 75.2 and 74.6 % respectively. The major isoprenoid quinone was ubiquinone-10. The predominant fatty acids (>10 %) were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids, two unidentified lipids and an unidentified glycolipid. The DNA G+C content of strain TK008T from genomic sequence data was 62.54 mol%. On the basis of polyphasic analysis, strain TK008T represents a novel species, for which the name Paracoccus aurantiacus sp. nov. is proposed. The type strain is TK008T (=CGMCC 1.13898T=JCM 33630T).
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Paracoccus luteus sp. nov., isolated from the intestine of grass carp. Int J Syst Evol Microbiol 2020; 70:543-549. [DOI: 10.1099/ijsem.0.003790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Polyphasic taxonomic analysis of Paracoccus ravus sp. nov., an alphaproteobacterium isolated from marine sediment. FEMS Microbiol Lett 2019; 366:5565046. [DOI: 10.1093/femsle/fnz184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/04/2019] [Indexed: 01/20/2023] Open
Abstract
ABSTRACTPolyphasic taxonomic analysis was performed on a novel marine bacterium, designated as strain YJ057T, isolated from marine sediment collected in the Republic of Korea. The strain was Gram-negative, beige-colored, facultatively anaerobic, coccoid or ovoid-shaped and nonmotile. Preliminary 16S rRNA gene sequence-based phylogenetic analysis indicated that this novel marine isolate belongs to the family Rhodobacteraceae of the class Alphaproteobacteria, and has the greatest (96.2%) sequence similarity to Paracoccus aestuariivivens GHD-30T. Major (>10%) fatty acids of strain YJ057T were C16:0 and C18:1 ω7c, G+C content in the genomic DNA of the strain was 63.6 mol% and the sole respiratory quinone was ubiquinone Q-10. It had phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and some unidentified components (three aminolipids, a glycolipid, a phospholipid and two lipids). As per the distinct phylogenetic position and combination of phenotypic and genotypic traits, the strain is considered a novel species of the genus Paracoccus, and the name Paracoccus ravus sp. nov. is proposed.
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Draft Genome Sequence of Paracoccus sp. Strain 228, Isolated from Surface Water of the Gulf of Gdańsk in the Baltic Sea. Microbiol Resour Announc 2019; 8:8/29/e00347-19. [PMID: 31320427 PMCID: PMC6639606 DOI: 10.1128/mra.00347-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present here the draft genome sequence of Paracoccus sp. strain 228, isolated from the Gulf of Gdańsk in the southern part of the Baltic Sea. The assembly contains 4,131,609 bp in 32 scaffolds. We present here the draft genome sequence of Paracoccus sp. strain 228, isolated from the Gulf of Gdańsk in the southern part of the Baltic Sea. The assembly contains 4,131,609 bp in 32 scaffolds.
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Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp. J Microbiol 2019; 57:444-449. [PMID: 31054135 DOI: 10.1007/s12275-019-8704-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/01/2019] [Accepted: 02/07/2019] [Indexed: 01/14/2023]
Abstract
A Gram-stain-negative and facultatively aerobic bacterium, designated as strain CBA4604T, was isolated from a traditional Korean salted and fermented shrimp food (saeu-jeot). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA4604T formed a clearly distinct phyletic lineage from closely related species within the genus Paracoccus. Strain CBA4604T was the most closely related to P. koreensis Ch05T (97.5% 16S rRNA gene sequence similarity) and other type strains (≤ 97.0%). The genome comprised a chromosome and two plasmids of 3,299,166 bp with 66.5% G+C content. The DNA-DNA relatedness values between strain CBA4604T and P. koreensis Ch05T, P. alcaliphilus DSM 8512T, and P. stylophorae KTW-16T were 30.5%, 22.9%, and 16.7%, respectively. Cells of the strain were short rod-shaped and oxidase- and catalase-positive. The growth of strain CBA-4604T was observed at 10-40°C (optimum, 37°C), pH 6.0-10.0 (optimum, pH 7.0), and in the presence of 0-8.0% (w/v) NaCl (optimum, 0-2.0%). Strain CBA4604T contained ubiquinone 10 as the sole isoprenoid quinone and summed feature 8 (C18:1ω7c/C18:1ω6c) and C18:0 as the major cellular fatty acids. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phospholipid, an unidentified aminolipid, an unidentified glycolipid, and three unidentified lipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, we concluded that strain CBA-4604T represents a novel species in the genus Paracoccus and we propose the name Paracoccus jeotgali sp. nov. The type strain is CBA4604T (= KACC 19579T = JCM 32510T).
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Paracoccus subflavus sp. nov., isolated from Pacific Ocean sediment. Int J Syst Evol Microbiol 2019; 69:1472-1476. [DOI: 10.1099/ijsem.0.003344] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Paracoccus suum sp. nov., isolated from a pig farm dust collector. Int J Syst Evol Microbiol 2019; 69:970-974. [DOI: 10.1099/ijsem.0.003226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, coccoid- or short rod-shaped bacterial strain, designated SC2-6T, was isolated from a dust collector of a pig farm located in Wanju-gun, Jeollabuk-do, Republic of Korea. Strain SC2-6T grew within the ranges of 10–37 °C (28–30 °C, optimally), pH 6.0–10.0 (pH 7.0–8.0, optimally) and 0–3% NaCl (w/v). The 16S rRNA gene sequence similarity of strain SC2-6T showed the highest values to
Paracoccus kondratievae
GBT (96.3%),
Paracoccus denitrificans
DSM 413T (96.3%) and
Paracoccus sanguinis
5503T (96.1%). The phylogenetic tree based on the 16S rRNA gene sequences revealed that strain SC2-6T belonged to the genus
Paracoccus
and clustered with
Paracoccus pacificus
F14T. The phylogenetic tree based on the rpoD gene sequences also demonstrated that strain SC2-6T fell into the clade of the genus
Paracoccus
. The DNA G+C content was 66.9 mol%. The major respiratory quinone was ubiquinone-10 and the major fatty acids (> 10% of the total fatty acids) were summed feature 8 (comprising C18 : 1 ω6c and/or C18 : 1 ω7c). The polar lipids were composed of diphosphatidylglycerol, phosphatidylcholine, an unidentified glycolipid, two unidentified aminolipids and two unidentified lipids. On the basis of phenotypic, phylogenetic and genomic data, strain SC2-6T was classified in the genus
Paracoccus
as a member of a novel species, for which the name Paracoccus suum sp. nov. is proposed. The type strain is SC2-6T (=KACC 19328T=NBRC 113110T).
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Paracoccus indicus sp. nov., isolated from surface seawater in the Indian Ocean. Antonie van Leeuwenhoek 2019; 112:927-933. [PMID: 30737708 DOI: 10.1007/s10482-019-01226-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
Abstract
Strain IO390502T, isolated from surface seawater in the Indian Ocean, was characterised using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain IO390502T belongs to the genus Paracoccus and is closely related to Paracoccus seriniphilus DSM 14827T (97.6%), followed by P. zeaxanthinifaciens JCM 21774T (97.5%), P. homiensis DSM 17862T (97.3%), P. marcusii DSM 11574T (97.2%), P. haeundaensis BC 74171T (97.0%) and P. carotinifaciens E-396T (97.0%). Cells are Gram-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile, rod-shaped, and forms creamy-white colonies. Optimal growth occurred at 25-30 °C, pH 5-8, and in the presence of 3-8% NaCl. The genome of strain IO390502T has a G+C content of 64.9 mol% and a 3.5 Mb chromosome. The in silico DNA-DNA hybridisation and average nucleotide identity values between strain IO390502T and the three closely related taxa, P. seriniphilus DSM 14827T, P. zeaxanthinifaciens JCM 21774T and P. homiensis DSM 17862T, are 19.6%, 21.9% and 20.6%, and 76.0%, 79.9% and 77.8%, respectively. Phosphatidylglycerol is the major lipid present, ubiquinone-10 (Q-10) is the sole isoprenoid quinone, and the major cellular fatty acid is C18:1ω7c. Based on data from phenotypic tests and genotypic differences between strain IO390502T and its close phylogenetic relatives, strain IO390502T represents a new species belonging to the genus Paracoccus, for which the name Paracoccus indicus sp. nov. is proposed. The type strain is IO390502T (= JCM 32637T = CCTCC AB 2018071T).
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