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%, C18:1 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).

Isolation and Characterization of Paracoccus maritimus sp. nov., from Intertidal Sediment

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).

Paracoccus onchidii sp. nov., a moderately halophilic bacterium isolated from a marine invertebrate from the South China Sea

A novel moderately halophilic bacterial strain, designated Z330^T, was isolated from the egg of a marine invertebrate of the genus Onchidium collected in the South China Sea. The 16S rRNA gene sequence of strain Z330^T exhibited the highest similarity value to that of the type strain Paracoccus fistulariae KCTC 22803^T (97.6%), Paracoccus seriniphilus NBRC 100798^T (97.6%) and Paracoccus aestuarii DSM 19484^T (97.6%). Phylogenomic and 16S rRNA phylogenetic analysis showed that strain Z330^T was most closely related to P. seriniphilus NBRC 100798^T and P. fistulariae KCTC 22803^T. Strain Z330^T grew optimally at 28-30 °C, pH 7.0-8.0 with the presence of 5.0-7.0% (w/v) NaCl. In addition, growth of strain Z330^T occurred at 0.5-16% NaCl, indicated strain Z330^T was a moderately halophilic and halotolerant bacterium of genus Paracoccus. The predominant respiratory quinone in strain Z330^T was identified as ubiquinone-10. The major polar lipids of strain Z330^T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, glycolipid and six unidentified polar lipids. The major fatty acids of strain Z330^T was summed feature 8 (C_18:1 ω6c and/or C_18:1 ω7c). The draft genome sequence of strain Z330^T includes 4,084,570 bp in total (N50 = 174,985 bp) with a medium read coverage of 463.6 × and 83 scaffolds. The DNA G + C content of strain Z330^T was 60.5%. In silico DNA-DNA hybridization with the four type strains showed 20.5, 22.3, 20.1 and 20.1% relatedness to Paracoccus fistulariae KCTC 22803^T, Paracoccus seriniphilus NBRC 100798^T, Paracoccus aestuarii DSM 19484^T and Paracoccus denitrificans 1A10901^T, respectively. And the average nucleotide identity (ANIb) values between strain Z330^T and these four type strains were 76.2, 80.0, 75.8 and 73.8%, respectively, lower than the 95-96% threshold value for dividing prokaryotic species. On the basis of the phenotypic, phylogenetic, phylogenomic and chemotaxonomic properties, a novel species of the genus Paracoccus, Paracoccus onchidii sp. nov. is proposed with the type strain Z330^T (= KCTC 92727^T = MCCC 1K08325^T).

Paracoccus binzhouensis sp. nov., isolated from activated sludge

A gram-stain-negative, non-motile and rod-shaped strain, designated wg1^T, was isolated from activated sludge obtained from wastewater treatment plant in Binzhou (Shandong province, PR China). Growth of strain wg1^T 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 wg1^T belonged to the genus Paracoccus. The species with highest similarity to strain wg1^T was Paracoccus communis VKM B-2787^T (98.27%), followed by Paracoccus kondratievae VKM B-2222^T (98.25%). The isoprenoid quinone was Q-10. Major cellular fatty acids were summed feature 8, C_16:0 and C_18:0. 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 wg1^T contained 12 clusters, and the gene involved in primary metabolism showed differences in the comparison between wg1^T and reference strains. The dDDH values of strain wg1^T with P. communis VKM B-2787^T, P. kondratievae VKM B-2222^T and P. denitrificans DSM 413^T were 45.30, 30.60 and 39.50%, respectively. Based on its physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain wg1^T is considered to represent a novel species for which the name Paracoccus binzhouensis sp. nov., is proposed. The type strain is wg1^T (= KCTC 72861^T = CCTCC AB 2019400^T).

Paracoccus amoyensis sp. nov., isolated from the surface seawater along the coast of Xiamen Island, China

Strain 11-3^T 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 11-3^T 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 11-3^T belonged to the genus Paracoccus and had the highest similarity with Paracoccus caeni MJ17^T (98.1 %), followed by Paracoccus xiamenensis 12-3^T (97.1 %), Paracoccus zeaxanthinifaciens ATCC 21588^T (97.1 %), Paracoccus aestuarii DSM 19484^T (97.0 %), Paracoccus liaowanqingii 2251^T (97.0 %), Paracoccus fistulariae KCTC 22803^T (97.0 %) and other species of the genus Paracoccus (95.2-96.8 %). The DNA-DNA hybridization values between strain 11-3^T and the selected strains (P. caeni MJ17^T, P. xiamenensis 12-3^T, P. zeaxanthinifaciens ATCC 21588^T, P. aestuarii DSM 19484^T and P. liaowanqingii 2251^T) 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 (C_18:1 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 11-3^T was 60.1 %. Based on results of the phylogenetic analysis, phenotypic and chemotaxonomic characteristics, strain 11-3^T represents a novel species of the genus Paracoccus, for which the name Paracoccus amoyensis sp. nov. is proposed. The type strain is 11-3^T (=MCCC 1A16380^T=KCTC 72689^T).

Paracoccus xiamenensis sp. nov., isolated from seawater on the Xiamen

Strain 12-3T was isolated from seawater of the Guanyinshan Coast, Xiamen, Fujian Province, PR China. The bacterium was Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-negative. Growth of strain 12-3T occurred at 10–37 °C (optimum, 20–30 °C), at pH 5.0–11.0 (optimum, pH 7.0–8.0) and at a salinity range of 0–10 % (optimum, 3–5 %). The results of phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain 12-3T belonged to the genus Paracoccus and had the highest sequence similarity to Paracoccus lutimaris HDM-25T (97.4 %), followed by Paracoccus isoporae SW-3T (96.9 %), Paracoccus caeni MJ17T (96.9 %), Paracoccus pacificus F14T (96.8 %) and other species in the genus Paracoccus (95.3–96.5 %). The average nucleotide identity (ANI) and DNA–DNA hybridization (DDH) values between strain 12-3T and P. lutimaris HDM-25T were 76.1 and 17.0 %, respectively. ANI and DDH values between strain 12-3T and P. isoporae SW-3T were 78.9 and 18.2 %, respectively. The principal fatty acid of strain 12-3T was summed feature 8 (C18 : 1  ω6c/ω7c) and C18 : 0. The respiratory quinone of strain 12-3T was Q10. The polar lipids included phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The G+C content of the chromosomal DNA was 63.9 mol%. The combination of the results of the phylogenetic, phenotypic and chemotaxonomic analyses, and its low ANI and DDH values indicate that strain 12-3T represents a novel species of the genus Paracoccus , for which the name Paracoccus xiamenensis sp. nov. is proposed. The type strain is 12-3T (=MCCC 1A16381T=KCTC 72687T).

Paracoccus aeridis sp. nov., an indole-producing bacterium isolated from the rhizosphere of an orchid, Aerides maculosa

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).

Paracoccus aurantiacus sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island

An orange-pigmented, short-rod-shaped, aerobic and non-motile bacterial strain, designated TK008^T, 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 TK008^T exhibited highest 16S rRNA gene sequence similarity of 97.1 % to Paracoccus pacificus F14^T. The phylogenetic trees based on 16S rRNA gene sequences showed that strain TK008^T was a member of the genus Paracoccus. Digital DNA-DNA hybridization values between strain TK008^T and two closely related species (Paracoccus zhejiangensis and Paracoccus tegillarcae) were 20.6 and 20.9 %. The average nucleotide identity values of strain TK008^T 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 (C_18 : 1ω6c and/or C_18 : 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 TK008^T from genomic sequence data was 62.54 mol%. On the basis of polyphasic analysis, strain TK008^T represents a novel species, for which the name Paracoccus aurantiacus sp. nov. is proposed. The type strain is TK008^T (=CGMCC 1.13898^T=JCM 33630^T).