Paracoccus broussonetiae subsp. drimophilus subsp. nov., a Novel Subspecies Salt-Tolerant Endophytic Bacterium from Maize Root in Hunan

In an investigation exploring endophytic microbiota from agricultural crops, an aerobic, non-motile, Gram-negative, coccobacillus-shaped bacterial isolate, designated as strain NGMCC 1.201697T, was isolated from maize roots in Hunan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NGMCC 1.201697T belonged to the genus Paracoccus, showing the highest sequence similarity to Paracoccus broussonetiae CPCC 101403T (99.86%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 98.57% and 87.90% between the novel isolate and its closest phylogenetic relative. However, phenotypic characterization further differentiated the isolate from P. broussonetiae CPCC 101403T. The isolate showed enhanced environmental tolerance adaptability (growth in 0-8% NaCl and 4-37 °C), unique enzymatic activities (esterase C4, β-glucosidase, L-proline arylamidase, and β-galactosidase), and expanded metabolic capabilities (D-mannitol, D-cellobiose, saccharose, and so on). The major polar lipids consisted of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), two unidentified glycolipids (GLs) and four unidentified phospholipids (PLs). The predominant respiratory quinone was ubiquinone-10, and the major fatty acid was summed feature 8 (C18:1 ω7c, 69.42%). The DNA G + C content was 64.49 mol%. Based on results of these analyses, strain NGMCC 1.201697T represents a novel subspecies of Paracoccus broussonetiae, for which the name Paracoccus broussonetiae subsp. drimophilus subsp. nov. is proposed. The type-strain is NGMCC 1.201697T (=CGMCC 1.61958T =JCM 37104T).

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).

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).

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021

Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.

Paracoccus marinaquae sp. nov., isolated from coastal water of the Yellow Sea

A Gram-stain-negative, non-motile and coccoid bacterial strain, designated XHP0099^T, was isolated from the coastal water of the Yellow Sea, China. Growth occurred at 20-37 ℃ (optimum, 28 ℃), pH 5.0-9.0 (optimum, pH 7.0-8.0), and with 0-7.0% NaCl (optimum, 2.0-3.0%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XHP0099^T was related to members of the genus Paracoccus and shared the highest sequence similarity with "P. siganidrum" M26 (98.2%), followed by P. alkanivorans 4-2 ^T (97.6%) and P. alkenifer DSM 11593 ^T (97.4%). The average nucleotide identity, amino acid identity, and digital DNA-DNA hybridization values of strain XHP0099^T against related members in the genus Paracoccus were below the cut-off points proposed for the delineation of a novel species. The major cellular fatty acids (> 10%) were summed feature 8 (C_18:1 ω7c/C_18:1 ω6c), and C_18:0. The major isoprenoid quinone was Q-10 and the polar lipids contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), aminolipid (AL) and unidentified polar lipids (L). The G + C content of the genomic DNA of strain XHP0099^T was 66.0%. Genomic analysis suggested that strain XHP0099^T harbored gene clusters for formaldehyde and the XoxF-type methanol oxidation and type 1 Calvin cycle, which could confer the methylotrophy pathway. Based on the phenotypic, phylogenetic, biochemical and chemotaxonomic analysis, strain XHP0099^T represents a novel species of the genus Paracoccus, for which the name Paracoccus marinaquae sp. nov. is proposed. The type strain is XHP0099^T (= JCM 34661 ^T = GDMCC 1.2414 ^T = MCCC 1K05846^T).