Ectobacillus ponti sp. nov., a novel bacterium isolated from Pearl River Estuary.

A Gram-staining-positive, aerobic, motile, and rod-shaped strain, designated SYSU M60031T, was isolated from a Pearl River Estuary sediment sample, Guangzhou, Guangdong, China. The isolate could grow at pH 5.0-8.0 (optimum, pH 7.0), 25-37 °C (optimum, 28 °C) and in the presence of 0-1 % (w/v) NaCl (optimum, 0 %). The predominant respiratory menaquinone of SYSU M60031T was MK-7. The cellular polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, and one unidentified aminolipid. The major fatty acids (>10 % of total) were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and C16 : 0. The genomic DNA G+C content was 51.2 %. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M60031T belonged to the genus Ectobacillus and showed the highest sequence similarity to Ectobacillus funiculus NAF001T (96.16%), followed by Ectobacillus antri SYSU K30001T (95.08 %). Based on the phenotypic, genotypic, and phylogenetic data, strain SYSU M60031T should be considered to represent a novel species of the genus Ectobacillus, for which the name Ectobacillus ponti sp. nov. is proposed. The type strain of the proposed novel isolate is SYSU M60031T (=CGMCC 1.19243T =NBRC 115614T).

Alsobacter ponti sp. nov., a novel denitrification and sulfate reduction bacterium isolated from Pearl River sediment.

A Gram-staining negative, aerobic, motile, and short rods strain, designated SYSU M60028T, was isolated from a Pearl River sediment sample in Guangzhou, Guangdong, China. The isolate could be able to grow at pH 6.0-8.0 (optimum, pH 7.0), 25-37 °C (optimum, 28 °C) and in the presence of 0-2% (w/v) NaCl (optimum, 0% NaCl). The cellular polar lipids of this strain were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and three unidentified lipids. The respiratory quinone of SYSU M60028T was found to be Q-10. The major fatty acids (> 5% of total) were summed feature 8, C16:0, and C18:1 ω7c 11-methy1. The genomic DNA G + C content was 69.9%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M60028T belonged to the genus Alsobacter and had the highest sequences similarities to Alsobacter metallidurans SK200a-9T (96.87%) and Alsobacter soli SH9T (96.87%). Based on the phenotypic, genotypic, and phylogenetic data, strain SYSU M0028T should be considered to represent a novel species of the genus Alsobacter, for which the name Alsobacter ponti sp. nov. is proposed. The type strain is SYSU M60028T (= CGMCC 1.19341T = KCTC 92046T).

Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary.

Microbes (e.g., bacteria and archaea) are indispensable components for the key biological processes of estuarine ecosystems and three main habitats (sediment, particle, and water) are harboring diverse estuarine microbes. However, we still know little about how the microbial community structures, potential keystone species, and network properties change among these three habitats in estuarine ecosystems. In this study, we collected size-fractioned water and sediment samples from the Pearl River Estuary to reveal their microbial diversity, community structures, network properties, and potential keystone taxa. We found that the sediment microbial community was remarkably more diverse than particle-attached (PA) and free-living (FL) communities, whereas its ecological network was less complex in terms of node distance and connectivity. TOC was determined as the main driver of sediment community, while the PA and FL communities were predominantly shaped by NO2-, non-ionic ammonia (NH) and pH. Among the bulk water, there were no significant differences between PA and FL communities in diversity, community structure, and network complexity. However, the PA community was more susceptible to metal elements, suggesting their higher level of involvement in physiological metabolism. Potential keystone taxa among community networks were taxonomically divergent in three habitats. Specifically, Synechococcales (Cyanobacteria) and Actinomarinales (Actinobacteria) exclusively served as the module-hubs in FL network, while members from phylum Proteobacteria and Bacteroidetes were the module-hubs and connectors in PA network. Potential keystone taxa in sediment network were more diverse and covered 9 phyla, including the only archaeal lineage Bathyarchaeia (Crenarchaeota). Overall, our study provided more detailed information about estuarine microbial communities in three habitats, especially the potential keystone species, which provided new perspectives on evaluating further effects of anthropogenic disturbances on estuarine microbes and facilitated the environment monitoring based on microbial community.

Deinococcus aestuarii sp. nov. and Deinococcus aquaedulcis sp. nov., two novel resistant bacteria isolated from pearl river estuary.

Two novel species of the genus Deinococcus, designated SYSU M49105T and SYSU M42101T, were isolated from freshwater samples of the Pearl River estuary in Guangdong, China. Phylogenetic analysis using 16S rRNA gene sequence indicated that strains SYSU M49105T and SYSU M42101T showed the highest sequence similarities to Deinococcus aetherius JCM 11751 T (93.6%) and Deinococcus multiflagellatus NBRC 112888 T (97.3%), respectively. Cells of both strains were Gram-staining positive, aerobic, coccus-shaped, oxidase-negative and non-motile. The cell wall contained meso-diaminopimelic acid as their diagnostic diamino acid. MK-8 was the predominant respiratory quinone for both strains. The polar lipid profile of SYSU M49105T contained two unidentified phosphoglycolipids, nine unidentified glycolipids, and five unidentified polar lipids. SYSU M42101T had one unidentified phosphoglycolipid, nine unidentified glycolipids, one unidentified aminophospholipid and four unidentified polar lipids. The major fatty acids of strains SYSU M49105T and SYSU M42101T were summed feature 3 (C16:1 ω7c and/ or C16:1 ω6c) and C16:0. The G + C contents of the novel isolates based on genomic DNAs were 69.6% and 67.4%, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU M49105T and SYSU M42101T should be considered to represent two novel species in the genus Deinococcus, for which the names Deinococcus aestuarii sp. nov. and Deinococcus aquaedulcis sp. nov. were proposed with the type strains SYSU M49105T (= KCTC 43258 T = CGMCC 1.18609 T) and SYSU M42101T (= KCTC 43257 T = CGMCC 1.18614 T), respectively.

Roseomonas ponticola sp. nov., a novel bacterium isolated from Pearl River estuary.

A novel species of the genus Roseomonas, designated SYSU M41301T, was isolated from water sample of the Pearl River estuary in Guangdong, China. Polyphasic, taxonomic and phylogenomic analyses were used to determine the taxonomy position of the strain. Phylogenetic analysis using 16S rRNA gene sequence indicated that strain SYSU M41301T showed the highest sequence similarity to Roseomonas stagni KCTC 22213T (97.9 %) and Roseomonas riguiloci KCTC 23339T (96.4 %). The novel species could be differentiated from other species of the genus Roseomonas by its distinct phenotypic and genotypic characteristics. The isolate was Gram-staining-negative, aerobic, short rod-shape, oxidase-positive and non-motile. The predominant respiratory quinone was ubiquinone 8 (Q-8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and one unidentified polar lipid. The major fatty acids (>10 % of total) were 11-methyl C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/ or C16 : 1 ω6c) and summed feature 8 (C18:  :1 ω7c and/or C18 : 1 ω6c). The G+C content of the novel isolate based on genomic DNA was 72.0 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU M41301T should be considered to represent a novel species in the genus Roseomonas, for which the name Roseomonas ponticola sp. nov. is proposed with the type strain SYSU M41301T (=KCTC 72726T=CGMCC 1.18613T).

Leeia aquatica sp. nov., isolated from freshwater.

A Gram-stain-negative, rod-shaped, obligately aerobic, motile by a single polar flagellum, chemoheterotrophic bacterium, designated strain IMCC25680T, was isolated from surface water in Chungju Lake, Republic of Korea. 16S rRNA gene sequence analysis revealed that strain IMCC25680T was most closely related to Leeia oryzae HW7T with 95.5% sequence similarity and formed a robust clade with L. oryzae HW7T. Whole genome sequencing showed that strain IMCC25680T had a genome 3.6 Mbp long with 60.7 mol% DNA G+C content. Average nucleotide identity and digital DNA-DNA hybridization values between strain IMCC25680T and L. oryzae HW7T were 72.4% and 18.5%, respectively, indicating that the novel strain represents a novel species of the genus Leeia. The major cellular fatty acids of strain IMCC25680T were iso-C16:0 and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The respiratory quinone detected in the strain was ubiquinone-8. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified polar lipids. On the basis of the phylogenetic and phenotypic characterization, strain IMCC25680T was considered to represent a novel species within the genus Leeia, for which the name Leeia aquatica sp. nov. is proposed. The type strain is IMCC25680T (=KACC 19487T =NBRC 113132T).

Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake.

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated strain IMCC25678T, was isolated from an artificial freshwater reservoir, Chungju Lake, in the Republic of Korea. The 16S rRNA gene sequence analysis indicated that strain IMCC25678T belongs to the genus Sphingobacterium with ≤98.7 % sequence similarities to Sphingobacterium species. Whole genome sequencing of strain IMCC25678T revealed a 3.9 Mbp genome size with a DNA G+C content of 42.2 mol%. The IMCC25678T genome shared ≤89.7 % average nucleotide identity and ≤21.4 % digital DNA-DNA hybridization values with closely related species of the genus Sphingobacterium, indicating that the strain represents a novel species. Summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH were found to be the predominant cellular fatty acid constituents in the strain. The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, one unidentified phosphoglycolipid, one unidentified sphingolipid and three unidentified polar lipids. Based on the phylogenetic and phenotypic characteristics, strain IMCC25678T was considered to represent a novel species within the genus Sphingobacterium, for which the name Sphingobacterium chungjuense sp. nov. is proposed. The type strain is IMCC25678T (=KACC 19485T=NBRC 113130T).

Halioglobus maricola sp. nov., isolated from coastal seawater.

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6-97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA-DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-ß-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus, for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

Deinococcus malanensis sp. nov., isolated from radiation-polluted soil.

A Gram-staining positive, non-spore forming, short rod-shaped and coccus-shaped, non-motile, pink-colored, gamma- and UV-resistant strain, designated T93T was isolated from soil of Malan area in Xinjiang Uyghur Autonomous Region, Northwest China. The taxonomic position of the new isolate was determined using a polyphasic approach. Strain T93T shared the highest 16 S rRNA gene sequence similarity with Deinococcus deserti VCD115T (97.54%). The genomic DNA G+C content of the isolate T93T was 61.7 mol%. The predominant menaquinone was MK-8, while the major cellular fatty acids were iso-C16:0, C15:1 ω6c, C16:0, C17:1 ω8c and Summed Feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c). The major polar lipid profiles consisted of diphosphatidylglycerol and phosphatidylinositol mannoside. Based on the phenotypic and genotypic data, strain T93T is considered to represent a novel species of the genus Deinococcus, for which the name Deinococcus malanensis sp. nov. is proposed. The type strain is T93T (= KCTC 33563T = JCM 30331T).

Paenibacillus wulumuqiensis sp. nov. and Paenibacillus dauci sp. nov., two novel species of the genus Paenibacillus.

Two Gram-staining-positive, aerobic, motile, endospore-forming, rod-shaped bacteria, designated strains Y24(T) and H9(T) were isolated from cold spring and carrot (Daucus L.) samples, respectively, in Xinjiang Uyghur Autonomous Region, north-western China. The taxonomic positions of the two new isolates were determined by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA hybridizations showed that strains Y24(T) and H9(T) were two different novel species belonging to the genus Paenibacillus, with Paenibacillus hunanensis FeL05(T) as their closest relative. The genomic DNA G + C contents of the two isolates Y24(T) and H9(T) were 48.1 and 46.6 mol %, respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid. The predominant menaquinone was both as MK-7. The major cellular fatty acids were anteiso-C15:0, C16:0, iso-C16:0, anteiso-C17:0 and iso-C15:0. The polar lipid profiles consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two glycolipids as the major components. On the basis of their phenotypic characteristics, the two isolates represent two different novel species of the genus Paenibacillus, for which the names Paenibacillus wulumuqiensis sp. nov. (type strain Y24(T) = CPCC 100602(T) = JCM 30284(T)) and Paenibacillus dauci sp. nov. (type strain H9(T) = CPCC 100608(T) = JCM 30283(T)) are proposed.

Phytoactinopolyspora endophytica gen. nov., sp. nov., a halotolerant filamentous actinomycete isolated from the roots of Glycyrrhiza uralensis F.

A novel endophytic actinomycete, designated strain EGI 60009T, was isolated from the roots of Glycyrrhiza uralensis F. collected from Xinjiang Province, north-west China. The isolate was able to grow in the presence of 0-9% (w/v) NaCl. Strain EGI 60009T had particular morphological properties: the substrate mycelia fragmented into rod-like elements and aerial mycelia differentiated into short spore chains. ll-2, 6-Diaminopimelic acid was the cell-wall diamino acid and rhamnose, galactose and glucose were the cell-wall sugars. MK-9(H4) was the predominant menaquinone. The major fatty acids of strain EGI 60009T were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 0, iso-C17 : 1 and I/anteiso-C17 : 0 B. Mycolic acids were absent. The DNA G+C content of strain EGI 60009T was 70.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain EGI 60009T belongs to the family Jiangellaceae and formed a distinct clade in the phylogenetic tree. 16S rRNA gene sequence similarities between strain EGI 60009T and other members of the genera Jiangella and Haloactinopolyspora were 96.1-96.4 and 95.7-96.0%, respectively. Based on these results and supported by morphological, physiological and chemotaxonomic data and numerous phenotypic differences, a novel species of a new genus, Phytoactinopolyspora endophytica gen. nov., sp. nov., is proposed. The type strain of Phytoactinopolyspora endophytica is EGI 60009T ( = KCTC 29657T = CPCC204078T).

Rufibacter roseus sp. nov., isolated from radiation-polluted soil.

A rose, Gram-stain-negative, aerobic, rod-shaped bacterium that was motile by gliding, and designated strain H359(T), was isolated from radiation-polluted soil (with high Cs(137)) from the Xinjiang Uygur Autonomous Region of PR China and subjected to a polyphasic taxonomic analysis. The isolate grew optimally at 30 °C and pH 7.0. It grew with NaCl up to 4% (w/v). 16S rRNA gene sequence analysis indicated that strain H359(T) belonged to the genus Rufibacter, a member of the family Cytophagaceae, with Rufibacter tibetensis CCTCC AB 208084(T) as its closest phylogenetic relative, having 96.1% 16S rRNA gene sequence similarity to the type strain. Strain H359(T) contained menaquinone-7 (MK-7) as the predominant menaquinone, and the major fatty acids were iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 1ω5c. The polar lipid profile had phosphatidylethanolamine as the major component. The DNA G+C content was 43.9 mol%. Based on phenotypic, genotypic and phylogenetic evidence, strain H359(T) represents a novel species of the genus Rufibacter, for which the name Rufibacter roseus sp. nov. is proposed. The type strain is H359(T) ( =CPCC 100615(T) =KCTC 42217(T)).

Actinotalea suaedae sp. nov., isolated from the halophyte Suaeda physophora in Xinjiang, Northwest China.

A Gram-stain-positive, aerobic, non-motile, coryneform bacterium, designated strain EGI 60002(T), was isolated from the halophyte Suaeda physophora. Cells were coryneform shaped and polymorphic. Phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate was closely related to Actinotalea ferrariae CF5-4(T) (95.8 % gene sequence similarity). The peptidoglycan type of strain EGI 60002(T) was A4ß, containing L-Orn-D-Ser-D-Asp. The cell-wall sugars were mannose, ribose, rhamnose and glucose. The major fatty acids (>5 %) of strain EGI 60002(T) were iso-C14:0, iso-C15:0, anteiso-C15:1 A and anteiso-C15:0. The predominant respiratory quinone was MK-10(H4). The major polar lipids were diphosphatidylglycerol (DPG), one unidentified phosphoglycolipid (PGL) and one unidentified phospholipid (PL1). The genomic DNA G+C content was 72.3 mol%. On the basis of morphological, physiological, chemotaxonomic data, and phylogenetic analysis, strain EGI 60002(T) should be classified as a novel species within the genus Actinotalea, for which the name Actinotalea suaedae sp. nov. is proposed. The type strain is EGI 60002T (=JCM 19624(T) = KACC 17839(T) = KCTC 29256(T)).

Flavobacterium notoginsengisoli sp. nov., isolated from the rhizosphere of Panax notoginseng.

Two novel bacterial strains, designated SYP-B540(T) and SYP-B556, were isolated from rhizospheric soil of Panax notoginseng located at Yunnan Province, China. Both strains were Gram-staining negative, aerobic, non-motile, elongated rod shaped and yellow coloured. They grew optimally at 28 °C and pH 7.0. Analysis of 16S rRNA gene sequences showed that the two strains shared 99.8 % sequence similarity to each other, but lower than 97.6 % to the other known species of the genus Flavobacterium. The predominant respiratory quinone for the two strains was MK-6, and the major fatty acids were iso-C15:0 and summed Feature 3 (comprising 16:1 ω7c and/or 16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine, two unidentified polar lipids and three unidentified amino-phospholipids. The DNA G+C contents of strains SYP-B540(T) and SYP-B556 were 33.3 and 32.7 mol%, respectively. In addition, the DNA-DNA hybridization values of strains SYP-B540(T) and SYP-B556 to their closest phylogenetic neighbors were significantly lower than 70 %. On the basis of the polyphasic taxonomy studies, strains SYP-B540(T) and SYP-B556 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium notoginsengisoli sp. nov. is proposed. The type strain is SYP-B540(T) (=KCTC 32505(T) = NBRC 110012(T) = BCRC 80724(T)).

Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique.

A Gram-positive, aerobic, non-motile, non-spore forming strain, designated DSD51W(T), was isolated using a resuscitative technique from a soil sample collected from Kyoto park, Japan, and characterized by using a polyphasic approach. The morphological and chemotaxonomic properties of the isolate were typical of those of members of the genus Rhodococcus. Strain DSD51W(T) was found to form a coherent cluster with Rhodococcus hoagii ATCC 7005(T), Rhodococcus equi NBRC 101255(T), Rhodococcus defluvii Call(T) and Rhodococcus kunmingensis YIM 45607(T) as its closest phylogenetic neighbours in 16S rRNA gene sequence analysis. However, the DNA-DNA hybridization values with the above strains were 58.2 ± 2.2, 58.4 ± 1.9, 45.1 ± 1.4 and 40.3 ± 4.7 %, respectively. In combination with differences in physiological and biochemical properties, strain DSD51W(T) can be concluded to represent a novel species of the genus Rhodococcus, for which the name Rhodococcus soli sp. nov. is proposed, with the type strain DSD51W(T) (=KCTC 29259(T) = JCM 19627(T) = DSM 46662(T) = KACC 17838(T)).

Sinomonas halotolerans sp. nov., an actinobacterium isolated from a soil sample.

A novel actinobacterial strain, designated CFH S0499(T), was isolated from a soil sample collected from Catba island in Halong Bay, Vietnam. The cells were observed to be Gram-stain positive, aerobic, non-motile, curved rods. The strain was found to grow optimally at 28 °C and pH 7.0. Growth was found to occur at 0-7 % NaCl. Chemotaxonomically, the peptidoglycan type was determined to be of the A3α type, with glutamic acid, glycine, alanine and lysine as the major cell wall amino acids. The whole cell sugars were found to contain mannose, galactose, glucose, ribose and rhamnose. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and two unidentified phospholipids. The major fatty acids were identified as anteiso-C15:0, iso-C15:0, anteiso-C17:0 and iso-C16:0 and the predominant respiratory quinone as MK-9 (H2), with a minor amount of MK-10 (H4) and MK-8 (H2). The G+C content of the genomic DNA was determined to be 71.8 mol%. The 16S rRNA gene sequence analysis showed that strain CFH S0499(T) should be assigned to the genus Sinomonas and is closely related to members of the species Sinomonas atrocyanea DSM 20127(T) (98.3 %), Sinomonas soli CW 59(T) (98.28 %), Sinomonas flava CW 108(T) (98.26 %), Sinomonas mesophila MPLK 26(T) (97.5 %) and Sinomonas notoginsengisoli SYP-B 575(T) (95.8 %). DNA-DNA hybridizations showed low values (49.1-54.5 %) between strain CFH S0499(T) and its four closest neighbours. Based on phenotypic, chemotaxonomic and phylogenetic analysis, strain CFH S0499(T) is concluded to represent a novel species of the genus Sinomonas, for which the name Sinomonas halotolerans sp. nov. is proposed, with CFH S0499(T) as the type strain (=CCTCC AB2014300(T) = KCTC 39116(T)).

Sinomonas notoginsengisoli sp. nov., isolated from the rhizosphere of Panax notoginseng.

A Gram-positive, aerobic, non-motile and pale yellow colour actinobacterial strain, designated SYP-B575(T), was isolated from rhizosphere soil of Panax notoginseng. The optimal growth of the strain was found to occur at 28 °C, pH 7.0 and without NaCl. Phylogenetic analysis indicated that strain SYP-B575(T) clearly belongs to the genus Sinomonas and should be considered as a candidate of novel species within this genus. The 16S rRNA gene sequence similarities between strain SYP-B575(T) and the other Sinomonas type strains ranged from 97.3 to 96.0%. The predominant isoprenoid quinone was identified as MK-9(H2) and the major fatty acids were identified as anteiso-C(15:0) and anteiso-C(17:0). The polar lipids were found to consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and glycolipids. The major cell-wall amino acids were identified as Lys, Ala, Glu, Gly and Ser. The whole-cell sugars were identified as mannose, ribose, rhamnose, glucose and galactose. The G+C content of the genomic DNA was determined to be 66.6 mol%. The DNA-DNA relatedness values between SYP-B575(T) and its closest phylogenetic neighbours were lower than 35.5%. On the basis of this polyphasic taxonomic study, strain SYP-B575(T) represents a novel species of the genus Sinomonas, for which the name Sinomonas notoginsengisoli sp. nov. is proposed. The type strain is SYP-B575(T) (=DSM 27685(T) = KCTC 29237(T)).

Gordonia jinhuaensis sp. nov., a novel actinobacterium, isolated from a VBNC (viable but non-culturable) state in pharmaceutical wastewater.

A Gram-stain positive, aerobic, non-motile and rod-shaped actinobacterial strain, designated as ZYR 51(T), was isolated from pharmaceutical wastewater in Jinhua city, Zhejiang province, Eastern China. Isolation was aided by using a resuscitation-promoting factor, suggesting the strain was recovered from a viable but non-culturable state. Strain ZYR 51(T) was characterized by a polyphasic taxonomic approach. Growth was found to occur at 10-45 °C, pH 6.0-10.0 and 0-9 % NaCl (w/v). Based on the 16S rRNA gene sequence, phylogenetic analysis clearly demonstrated that strain ZYR 51(T) belongs to the genus Gordonia and showed low level similarities (below 97 %) with all other members of this genus. The strain was found to possess meso-diaminopimelic acid (meso-DAP), along with MK-9(H2) as the predominant menaquonine. Mycolic acids were found to be present. C16:0 (34.9 %), 10-methyl C18:0 (30.3 %), iso-C18:0(8.2 %), and summed feature 3 (C16:1 ω6c and/or C16:1ω7c as define by MIDI; 18.8 %) were identified as the major cellular fatty acids. The polar lipid profile of strain ZYR 51(T) was found to consist of diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and some unknown lipids. The genomic DNA G+C content of strain ZYR 51(T) was determined to be 67.7 mol%. The combined genotypic and phenotypic data showed that the strain represents a novel species of the genus Gordonia, for which the name Gordonia jinhuaensis sp. nov. is proposed, with the type strain is ZYR 51(T) (=CGMCC 1.12827(T) = NBRL B-59111(T) = NBRC 110001(T)).

Metabolic Versatility of the Family Halieaceae Revealed by the Genomics of Novel Cultured Isolates.

The family Halieaceae (OM60/NOR5 clade) is a gammaproteobacterial group abundant and cosmopolitan in coastal seawaters and plays an important role in response to phytoplankton blooms. However, the ecophysiology of this family remains understudied because of the vast gap between phylogenetic diversity and cultured representatives. Here, using six pure cultured strains isolated from coastal seawaters, we performed in-depth genomic analyses to provide an overview of the phylogeny and metabolic capabilities of this family. The combined analyses of 16S rRNA genes, genome sequences, and functional genes relevant to taxonomy demonstrated that each strain represents a novel species. Notably, two strains belonged to the hitherto-uncultured NOR5-4 and NOR5-12 subclades. Metabolic reconstructions revealed that the six strains likely have aerobic chemo- or photoheterotrophic lifestyles; five of them possess genes for proteorhodopsin or aerobic anoxygenic phototrophy. The presence of blue- or green-tuned proteorhodopsin in Halieaceae suggested their ability to adapt to light conditions varying with depth or coastal-to-open ocean transition. In addition to the genes of anaplerotic CO2 fixation, genes encoding a complete reductive glycine pathway for CO2 fixation were found in three strains. Putative polysaccharide utilization loci were detected in three strains, suggesting the association with phytoplankton blooms. Read mapping of various metagenomes and metatranscriptomes showed that the six strains are widely distributed and transcriptionally active in marine environments. Overall, the six strains genomically characterized in this study expand the phylogenetic and metabolic diversity of Halieaceae and likely serve as a culture resource for investigating the ecophysiological features of this environmentally relevant bacterial group. IMPORTANCE Although the family Halieaceae (OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure cultured Halieaceae strains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family. The cultured strains exhibited diverse metabolic potential by harboring genes for anaplerotic CO2 fixation, proteorhodopsin, and aerobic anoxygenic phototrophy. Polysaccharide utilization loci detected in some of these strains also indicated an association with phytoplankton blooms. The cultivation of novel strains of Halieaceae and their genomic characteristics largely expanded the phylogenetic and metabolic diversity, which is important for future ecophysiological studies.

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts.

BACKGROUND: Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts' metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments. RESULTS: Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders. CONCLUSIONS: Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract.