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Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.

Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189T and 14171R-81T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189T and 14171R-81T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01T (96.3% and 98.0%, respectively). The genome of strain 12200R-189T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189T, 14171R-81T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189T grew at a temperature range of 15-40°C, pH 6.0-9.0, and 0-3% NaCl (w/v), whereas strain 14171R-81T grew at a temperature range of 10-37°C, pH 6.0-8.0, and 0-1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C15:0, anteiso-C15:0, and iso-C16:0. The polar lipids of strain 12200R-189T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R-189T and 14171R-81T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189T (= KACC 19916T = CCTCC AB 2020027T) and 14171R-81T (= KACC 19915T = CCTCC AB 2020026T).

A Gram-negative, aerobic, and long rod-shaped bacterium, designated as H33E-04T, was isolated from the soil of reclaimed land, Republic of Korea. The strain grew at a temperature range of 15–40 °C, pH 5.0–10.0, and 0–2% NaCl (w/v). The phylogenetic analysis based on 16S rRNA gene sequences showed that strain H33E-04T was in the same clade with Chitinophaga pinensis DSM 2588T, Chitinophaga filiformis IFO 15056T, and Chitinophaga ginsengisoli Gsoil 052T with 98.4%, 97.9%, and 97.8% sequence similarities, respectively. The de novo genome assembly revealed that the DNA G + C content of the strain was 46.2 mol%. Comparative genome analysis between strain H33E-04T and C. pinensis DSM 2588 T showed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values were 79.9% and 23.4%, respectively. The major respiratory quinone was menaquinone-7 (MK-7) and the predominant cellular fatty acids were iso-C15:0 (31.7%), C16:1 ω5c (31.2%), and iso-C17:0 3-OH (11.8%), supporting the affiliation of strain H33E-04T with the genus Chitinophaga. Based on phylogenetic, physiological, and chemotaxonomic characteristics, strain H33E-04T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga agri sp. nov. is proposed. The type strain of Chitinophaga agri is H33E-04T (= KACC 21303T = NBRC114512T).

A bacterial strain, designated CJ1-R5T, was isolated from the flower of the royal azalea plant (Rhododendron schlippenbachii) collected in Jeju Island, Republic of Korea. The strain was a Gram-negative, strictly aerobic, motile, rod-shaped bacterium, growing at a temperature range of 4–33 °C (optimum 28–30 °C), pH 5.0–9.0 (optimum pH 7.0–8.0), and 0–1% NaCl (optimum 0%). The 16S rRNA sequence analysis of strain CJ1-R5T revealed the highest sequence similarity (97.9%) with Xylophilus ampelinus ATCC 33914T, and sequence similarities of less than 97.2% with other validly named species. Phylogenetic tree analysis based on the 16S rRNA gene sequences showed that strain CJ1-R5T clustered with Xylophilus ampelinus ATCC 33914T and two uncultured bacterial clones. The only quinone observed in strain CJ1-R5T was ubiquinone-8. The polar lipids observed were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and two unidentified lipids. The major fatty acids were C16:0, C17:0 cyclo, and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The genome size of strain CJ1-R5T was 5.85 Mbp. The genomic G + C content was 68.4 mol%. ANI and dDDH values between strain CJ1-R5T and Xylophilus ampelinus ATCC 33914T were 79.0% and 22.5%, respectively. Based on the polyphasic taxonomic data, strain CJ1-R5T is considered to represent a novel species, for which the name Xylophilus rhododendri sp. nov. is proposed. The type strain is CJ1-R5T (= KACC 21265T = CCTCC AB2020030T)

In this study, two endophytic bacterial strains designated JS21-1T and S6-262T isolated from leaves of Elaeis guineensis and stem tissues of Jatropha curcas respectively, were subjected for polyphasic taxonomic approach. On R2A medium, colonies of strains JS21-1T and S6-262T are orange and yellow, respectively. Phylogenetic analyses using 16S rRNA gene sequencing and whole-genome sequences placed the strains in distinct clades but within the genus Sphingomonas. The DNA G + C content of JS21-1T and S6-262T were 67.31 and 66.95%, respectively. Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values of strains JS21-1T and S6-262T with phylogenetically related Sphingomonas species were lower than 95% and 70% respectively. The chemotaxonomic studies indicated that the major cellular fatty acids of the strain JS21-1T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C14:0 2OH; strain S6-262T possessed summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major quinone was Q10, and the unique polyamine observed was homospermidine. The polar lipid profile comprised of mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and certain uncharacterised phospholipids and lipids. Based on this polyphasic evidence, strains JS21-1T and S6-262T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov. are proposed, respectively. The type strain of Sphingomonas palmae sp. nov. is JS21-1T (= DSM 27348T = KACC 17591T) and the type strain of Sphingomonas gellani sp. nov. is S6-262T (= DSM 27346T = KACC 17594T).

A novel bacterial strain, S-12T, of a member of the genus Phreatobacter was isolated from a cathode of a microbial fuel cell from Suwon City, South Korea. Cells were Gram-staining-negative, aerobic, non-sporulating rods, motile by means of a polar flagellum, and formed white round colonies. The strain grew at the range of 10–40 °C (optimum, 28–30 °C), pH 6.0–10.0 (optimum 7.0–8.0) and 0–1 % NaCl. The 16S rRNA gene sequence analysis showed the relatedness of S-12T to Phreatobacter stygius YC6-17T (98.2 %) and Phreatobacter oligotrophus PI_21T (98.1 %). The major respiratory quinone was ubiquinone Q-10. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified lipid. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was 69.3 mol%. On the basis of its differences from species of the genus Phreatobacter with validly published names, strain S-12T is identified as representing a novel species, for which the proposed name is Phreatobacter cathodiphilus sp. nov., with S-12T as the type strain (=KACC 18497T=JCM 31612T).

Two yellow-pigmented isolates, S5-249T and L9-754T, originating from surface-sterilized plant tissues of Jatropha curcas L. (Jatropha) cultivars were characterized using a polyphasic taxonomic approach. Strains S5-249T and L9-754T had 16S rRNA genes sharing 94.2 % sequence similarity with each other and 91.6–97.2 % sequence similarity with those of other species in the genus Sphingomonas , suggesting that they represent two potentially novel species. The 16S rRNA gene sequences of strains S5-249T and L9-754T shared the highest similarity to that of Sphingomonas sanguinis NBRC 13937T (96.1 and 97.2 %, respectively). The genomic DNA G+C contents of strains S5-249T and L9-754T were 66.9 and 68.5 mol%, respectively. The respiratory quinone was determined to be Q-10, and the major polyamine was homospermidine. Strains S5-249T and L9-754T contained summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), C16 : 1, C14 : 0 2-OH and summed feature 4 (C16 : 1ω7t, iso-C15 : 0 2-OH and C16 : 1ω7c) as the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The average nucleotide identity (ANI) values between S. sanguinis NBRC 13937T and the two type strains (S5-249T and L9-754T) were 72.31 and 77.73 %, respectively. Digital DNA–DNA hybridization (dDDH) studies between the novel strains (S5-249T and L9-754T) and other species of the genus Sphingomonas were well below the thresholds used to discriminate between bacterial species. The results of dDDH and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the species of the genus Sphingomonas with validly published names. These data strongly support the classification of the strains as representatives of novel species, for which we propose the names Sphingomonas jatrophae sp. nov. (type strain S5-249T=DSM 27345T=KACC 17593T) and Sphingomonas carotinifaciens sp. nov. (type strain L9-754T=DSM 27347T=KACC 17595T).

The taxonomic position of a bacterial strain designated T16R-228T, isolated from a rhizosphere soil sample of a tomato plant collected from a farm in Buyeo, Chungcheongnam-do, Republic of Korea, was determined using a polyphasic approach. On the basis of morphological, genetic and chemotaxonomic characteristics, it was determined to belong to the genus Paenibacillus . It was an aerobic, Gram-stain-positive, non-motile, catalase-negative, oxidase-negative rod with peritrichous flagella. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, hydroxyl- phosphatidylethanolamine and one unidentified polar lipid. Menaquiones were MK-7. Predominant cellular fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. DNA G+C content was 56.8 mol%. The phylogenetic tree constructed based on the 16S rRNA gene sequences showed the strain formed a clade with P. mucilaginosus VKPM B-7519T, P. edaphicus T7T, P. ehimensis KCTC 3748T, P. koreensis YC300T, P. tianmuensis B27T and P. elgii SD17T, showing the highest sequence similarity with P. mucilaginosus VKPM B-7519T (96.5 %). The polyphasic data supported that strain T16R-228T was clearly distinguished from its closely related species and represents a novel species of the genus Paenibacillus for which the name Paenibacillus solanacearum is proposed. The type strain is T16R-228T (=KACC 18654T=NBRC 111896T).

An aerobic, Gram-stain-negative, non-spore-forming, non-flagellated, rod-shaped or filamentous bacterial strain, T16R-86T, was isolated from rhizosphere of a tomato plant collected from a farm on Buyeo-gun, Chungcheongnam-do, South Korea. It grew at the temperature range 10–37 °C (optimum, 28 °C) and pH range 6.0–9.0 (optimum, pH 7.0), and tolerated up to 2 % (w/v) NaCl. According to 16S rRNA gene sequence analysis, strain T16R-86T shared the highest similarity with Chitinophaga barathri YLT18T (96.8 %) and C. pinensis DSM 2588T (96.7 %), forming a subcluster with C. barathri YLT18T, C. cymbidii R156-2T and C. niabensis JS13-10T in the phylogenetic tree. The major fatty acids were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone MK-7. Polar lipids were phosphatidylethanolamine, five unknown aminolipids, an unknown aminophospholipid, one unknown phospholipid and two unknown lipids. The DNA G+C content was 53.6 mol%. The phenotypic, chemotaxonomic and phylogenetic data showed that strain T16R-86T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga rhizosphaerae sp. nov. is proposed. The type strain is T16R-86T (=KACC 18790T=JCM 31600T).

A bacterial strain, designated T20R-70T, was isolated from tomato rhizosphere soil collected in Yecheon-gun, Gyeongsangbuk-do in South Korea. Growth was observed within the ranges 10–40 °C (optimally at 28–30 °C), pH 7.0–8.0 (optimally at pH 7.0) and 0–1 % NaCl (optimally at 0 %). The 16S rRNA gene sequence showed the highest similarities with those of Lysobacter hankyongensis KTCe-2T (98.7 %), Lysobacter brunescens KCTC 12130T (98.0 %), ‘ Lysobacter daecheongensis ' Dae08 (97.2 %) and Lysobacter oligotrophicus 107-E2T (97.1 %). The phylogenetic tree showed that strain T20R-70T formed a clade with Lysobacter hankyongensis KTCe-2T and Lysobacter brunescens KCTC 12130T. The dominant fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0, iso-C17 : 1ω9c and summed feature 3 (including iso-C15 : 0 2-OH and/or iso-C16 : 1ω7c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was Q-8. DNA–DNA hybridization data revealed that strain T20R-70T had a hybridization value of 42±4 % (mean±sd) to the most closely related species of the genus Lysobacter . The DNA G+C content was 63.0 mol%. The physiological, biochemical and chemotaxonomic data allowed the discrimination of the new isolate from its phylogenetic relatives. Strain T20R-70T is thus considered to be a representative of a novel species of the genus Lysobacter , for which the name Lysobacter solanacearum sp. nov. is proposed. The type strain is T20R-70T (=KACC 18656T=NBRC 111881T).

A bacterial strain, designated 5GHs33-3T, was isolated from greenhouse soil collected from Yongin region, Gyeonggi province, South Korea. The strain was an aerobic, Gram-stain-positive, flagellated, rod-shaped bacterium. Strain 5GHs33-3T grew at 4–37 °C (optimally at 28–30 °C), pH 6.0–10.0 (optimally at pH 7.0) and with 0–7 % (w/v) NaCl (optimally with 0 %). The 16S rRNA gene sequence analysis revealed that strain 5GHs33-3T had high sequence similarity with Actinotalea suaedae EGI 60002T (98.4 %), Actinotalea ferrariae CF5-4T (96.4 %) and Actinotalea fermentans DSM 3133T (96.2 %), and less than 95.5 % sequence similarity against all the other species with validly published names. The phylogenetic tree revealed that strain 5GHs33-3T formed a robust independent monophyletic line with Actinotalea suaedae EGI 60002T. The predominant fatty acids of strain 5GHs33-3T were anteiso-C15 : 0 and iso-C14 : 0. The only quinone was MK-8(H4). Polar lipids were diphosphatidylglycerol, phosphatidylinositol, an unknown phosphoglycolipid and unknown lipids. The peptidoglycan type was A4β, with ornithine as the diagnostic diamino acid and an interpeptide bridge comprising l-Glu. The DNA G+C content is 69.0 mol%. Based on phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analyses, strain 5GHs33-3T represents a novel species of a new genus of the family Cellulomonadaceae , for which the name Pseudactinotalea terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs33-3T (=KACC 16542T=NBRC 111006T). We also propose the reclassification of Actinotalea suaedae as Pseudactinotalea suaedae comb. nov. (type strain EGI 60002T=JCM 19624T=KACC 17839T=KCTC 29256T).

Plant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots under natural systems, we characterized the bacterial, archaeal, and fungal communities of three belowground compartments (rhizosphere, endosphere, and bulk soil) of tomato plants collected from 23 greenhouses in 7 geographic locations of South Korea. The microbial diversity and structure varied by rhizocompartment, with the most distinctive community features found in the endosphere. The bacterial and fungal communities in the bulk soil and rhizosphere were correlated with soil physicochemical properties, such as pH, electrical conductivity, and exchangeable cation levels, while this trend was not evident in the endosphere samples. A small number of core bacterial operational taxonomic units (OTUs) present in all samples from the rhizosphere and endosphere represented more than 60% of the total relative abundance. Among these core microbes, OTUs belonging to the genera Acidovorax, Enterobacter, Pseudomonas, Rhizobium, Streptomyces, and Variovorax, members of which are known to have beneficial effects on plant growth, were more relatively abundant in the endosphere samples. A co-occurrence network analysis indicated that the microbial community in the rhizosphere had a larger and more complex network than those in the bulk soil and endosphere. The analysis also identified keystone taxa that might play important roles in microbe-microbe interactions in the community. Additionally, profiling of predicted gene functions identified many genes associated with membrane transport in the endospheric and rhizospheric communities. Overall, the data presented here provide preliminary insight into bacterial, archaeal, and fungal phylogeny, functionality, and interactions in the rhizocompartments of tomato roots under real-world environments.

A bacterial strain designated 5GH32-13T was isolated from greenhouse soil in Yongin-city, Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, motile rods of two different shapes. The strain was catalase-positive and oxidasenegative. Flexirubin-like pigments were not detected. β-Carotene was produced. The strain grew in the range of 10-37°C (optimum of 28-30°C) and pH 6-8 (optimum of pH 7) and tolerated up to 1% (w/v) NaCl (optimum of 0%). According to the 16S rRNA gene sequence comparison, strain 5GH32-13T shared a sequence similarity of less than 96.0% with all validly named taxa, having the highest sequence similarity with Pseudoflavitalea soli KIS20-3T (95.8%), Pseudoflavitalea rhizosphaerae T16R-265T (95.4%), Flavitalea gansuensis JCN-23T (95.3%), Pseudobacter ginsenosidimutans Gsoil 221T (95.3%), and Flavitalea populi HY-50RT (95.2%). A phylogenetic tree showed that strain 5GH32-13T was not grouped consistently into any specific genus. Its only polyamine was homospermidine, and its major fatty acids (> 10% of total fatty acids) were iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. The strain’s only respiratory quinone was MK-7, and its polar lipids were phosphatidylethanolamine, one unidentified phospholipid, six unidentified aminolipids and four unidentified lipids. Its DNA G + C content was 47.5 mol%. The results from chemotaxonomic, phenotypic and phylogenetic analyses indicated that strain 5GH32-13T represents a novel species of a novel genus of the family Chitinophagaceae, and the name Paraflavitalea soli gen. nov., sp. nov. is proposed. The type strain is 5GH32-13T (= KACC 17331T = JCM 33061T).

A Gram-stain-positive, rod-shaped, non-endospore-forming motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13arT was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4-35°C (optimum, 28-30°C), pH 5.0-9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13arT belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88T (98.5%), Paenibacillus hordei RH-N24T (98.4%) and Paenibacillus nicotianae YIM h-19T (98.1%). The major fatty acid was anteiso-C15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13arT represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13arT (= KACC 18728T = NBRC 112013T).

Soil microorganisms play an essential role in soil ecosystem processes such as organic matter decomposition, nutrient cycling, and plant nutrient availability. The land use for greenhouse cultivation has been increasing continuously, which involves an intensive input of agricultural materials to enhance productivity; however, relatively little is known about bacterial communities in greenhouse soils. To assess the effects of environmental factors on the soil bacterial diversity and community composition, a total of 187 greenhouse soil samples collected across Korea were subjected to bacterial 16S rRNA gene pyrosequencing analysis. A total of 11,865 operational taxonomic units at a 97% similarity cutoff level were detected from 847,560 sequences. Among nine soil factors evaluated; pH, electrical conductivity (EC), exchangeable cations (Ca2+, Mg2+, Na+, and K+), available P2O5, organic matter, and NO3-N, soil pH was most strongly correlated with bacterial richness (polynomial regression, pH: R2 = 0.1683, P 1%), the relative abundances of Proteobacteria, Gemmatimonadetes, Acidobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were also more strongly correlated with pH and EC values, compared with other soil cation contents, such as Ca2+, Mg2+, Na+, and K+. Our results suggest that, despite the heterogeneity of various environmental variables, the bacterial communities of the intensively cultivated greenhouse soils were particularly influenced by soil pH and EC. These findings therefore shed light on the soil microbial ecology of greenhouse cultivation, which should be helpful for devising effective management strategies to enhance soil microbial diversity and improving crop productivity.

Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.

A rod-shaped, yellow, Gram-stain-negative, non-flagellated, aerobic bacterium, designated 5516J-17T, was isolated from an air sample collected from Jeju Island, Republic of Korea. It grew in the temperature range of 10-37 °C (optimum 28-30 °C), pH 6.0-11.0 (optimum, pH 7.0) and 0-1 % NaCl (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain 5516J-17T belongs to the genus Spirosoma, showing 96.9 % sequence similarity to the most closely related species, Spirosoma linguale DSM 74T. The cellular fatty acids comprised large amounts (>10 % of total fatty acids) of summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:1ω5c, and moderate amounts (5-10 % of total fatty acids) of iso-C17:0 3-OH, iso-C15:0 and C16:0. The DNA G+C content was 55.7 mol % and MK-7 was the predominant isoprenoid quinone. Polar lipids were phosphatidylethanolamine, two unknown aminophospholipids, one unknown aminolipid and one unknown lipid. On the basis of this phenotypic and polyphasic taxonomy study, it is suggested that strain 5516J-17T represents a novel species within the genus Spirosoma, with the proposed name Spirosoma aerophilum. The type strain is 5516J-17T (= KACC 17323T = DSM 28388T = JCM 19950T).

A novel bacterium, strain 7515T-26T, was isolated from an air sample collected in Taean region, Republic of Korea. Cells were aerobic, Gram-stain-positive, non-flagellated cocci, growing in the temperature, pH and NaCl ranges of 10-33 °C, pH 5.0-9.0 and 0-2 % (w/v). It shared high 16S rRNA gene sequence similarity with Friedmanniella lacustris EL-17AT (97.6 %), Friedmanniella lucida FA2T (96.9 %) and Friedmanniella luteola FA1T (96.9 %), showing high sequence similarities of 96.5-97.6 % with members of the genus Friedmanniella. Phylogenetic trees based on 16S rRNA gene sequences showed that strain 7515T-26T and members of the genus Friedmanniella formed a compact cluster separable from other genera. The isolate contained anteiso-C15 : 0, iso-C14 : 0 3-OH and iso-C15 : 0 as the major cellular fatty acids, and MK-9(H4) as the predominant isoprenoid quinone. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown phospholipids and one unknown lipid, and the DNA G+C content was 73.1 mol%. The peptidoglycan type was A3γ. It showed DNA-DNA hybridization values of less than 70 % with F. lacustris EL-17AT. On the basis of the evidence from this polyphasic study, a novel species, Friedmanniella aerolata sp. nov., is proposed. The type strain is 7515T-26T ( = KACC 17306T = DSM 27139T).

A yellow-colored bacterium with gliding motility, strain KIS68-18T, was isolated from a soil sample at Bijin Island in Tongyeong city, Republic of Korea. The cells were strictly aerobic, Gram-staining-negative, non-spore-forming, and rod-shaped. The strain grew at the range of 10-35°C (optimum, 25-30°C), pH 5.5-8.0 (optimum, 6.0-7.5), and 0-0.5% (w/v) NaCl. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KIS68-18T was closely related to Chryseolinea serpens DSM 24574T (98.9%) and had low sequence similarities (below 92.6%) with other members of the family 'Cytophagaceae' in the phylum Bacteroidetes. The major respiratory quinone system was MK-7 and the predominant cellular fatty acids were C16:1ω5c (38.8%), iso-C15:0 (18.5%), and summed feature 3 (C16:1ω7c and/or C16:1ω6c, 10.6%). The polar lipids consisted of phosphatidylethanolamine, one unidentified phospholipid, three unidentified aminophospholipids, two unidentified aminolipids, and five unidentified lipids. The DNA G + C content was 50.9%. Based on the phylogenetic, physiological, and chemotaxonomic data, stain KIS68-18T represents a novel species of the genus Chryseolinea, for which the name Chryseolinea soli sp. nov. is proposed. The type strain of Chryseolinea soli is KIS68-18T (= KACC 17327T = NBRC 113100T).

A dark-pink-coloured bacterial strain, B4Y-8T, was isolated from a soil cultivated with ginseng. The 16S rRNA gene sequence of this strain showed highest similarity with Mucilaginibacter litoreus BR-18T (96.8 %), Mucilaginibacter lutimaris BR-3T (96.6 %) and Mucilaginibacter defluvii A5T (96.2 %) among the type strains of species of the genus Mucilaginibacter. Strain B4Y-8T was a strictly aerobic, Gram-stain-negative, non-motile, short-rod-shaped bacterium producing a large amount of extracellular polymeric substance. The strain grew at 10–35 °C (optimum, 25 °C), at pH 3.0–11.0 (optimum, pH 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). The DNA G+C content of strain B4Y-8T was 49.0 mol%. It contained menaquinone 7 (MK-7) as the major isoprenoid quinone, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C15 : 0 as the major fatty acids. On the basis of evidence from the present polyphasic taxonomic study, strain B4Y-8T should be classified as representing a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter ginsengisoli sp. nov. is proposed. The type strain is B4Y-8T ( = KACC 18152T = JCM 30759T).

Strain GP20-2(T) was isolated from a soil cultivated with ginseng in Korea. The 16S rRNA gene sequence of this strain showed the highest sequence similarity with Sphingomonas daechungensis CH15-11(T) (96.7%) and Sphingomonas sediminicola Dae 20(T) (96.2%) among the type strains. The strain GP20-2(T) was a strictly aerobic, Gram-negative, non-motile, rod-shaped bacterium that formed very tiny colonies, less than 0.3 mm in diameter after 10 days on R2A agar. The strain grew at 10-35-C (optimum, 35-C), at a pH of 5.0-8.0 (optimum, pH 6.0), and in the absence of NaCl. The DNA G+C content of strain GP20-2(T) was 67.2 mol%. It contained ubiquinone Q-10 as the major isoprenoid quinone, and summed feature 8 (C18:1ω6c and/or C18:1ω7c, 49.8%) and C16:0 (17.0%) as the major fatty acids. On the basis of evidence from our polyphasic taxonomic study, we concluded that strain GP20-2(T) should be classified as a novel species of the genus Sphingomonas, for which the name Sphingomonas parvus sp. nov. is proposed. The type strain is GP20-2(T) (=KACC 12865(T) =DSM 100456(T)).

A bacterial strain, PSGM2-16T, was isolated from a pot of paddy soil grown with rice in Suwon region, Republic of Korea, and was characterized as having aerobic, Gram-stain-positive, short-rod-shaped cells with one polar flagellum. The 16S rRNA gene sequence of strain PSGM2-16T revealed the highest sequence similarities with Knoellia locipacati DMZ1T (97.4 %), Fodinibacter luteus YIM C003T (97.2 %) and Lapillicoccus jejuensis R-Ac013T (97.0 %), and the phylogenetic tree showed that strain PSGM2-16T formed a subgroup with Ornithinibacter aureus HB09001T and F. luteus YIM C003T within the family Intrasporangiaceae. The major fatty acids (>10 % of the total fatty acids) of strain PSGM2-16T were iso-C16 : 0, C17 : 1ω8c and iso-C14 : 0. The predominant menaquinone was MK-8(H4). The polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three aminophospholipids and two phospholipids. The peptidoglycan was type A4γ with meso-diaminopimelic acid as the diagnostic diamino acid. DNA–DNA hybridization values between strain PSGM2-16T and closely related taxa were much less than 70 %. The genomic DNA G+C content of strain PSGM2-16T was 70.0 mol%. On the basis of the evidence presented, it is concluded that strain PSGM2-16T represents a novel species of a new genus in the family Intrasporangiaceae, for which the name Oryzobacter terrae gen. nov., sp. nov. is proposed. The type strain of the type species is PSGM2-16T ( = KACC 17299T = DSM 27137T = NBRC 109598T).

A Gram-staining-negative, aerobic, non-flagellated, rod-shaped bacterial strain, KIS55-21(T), was isolated from a soil sample from Chuja Island, Jeju Province, Republic of Korea. Strain KIS55-21(T) grew optimally at pH 7.0, at 28-30°C and in the presence of 0% (w/v) NaCl. Neighbor-joining and maximum-likelihood trees based on the 16S rRNA gene sequences revealed that strain KIS55-21(T) fell within the family Xanthomonadaceae and was closely related to Metallibacterium scheffleri DKE(T). Strain KIS55-21(T) exhibited the highest 16S rRNA gene sequence similarity (92.6%) to that of M. scheffleri DKE(T), with similarities of less than 92.0% to those of the genera Dokdonella, Rhodanobacter, Aquimonas, and Frateuria. Strain KIS55-21(T) contained ubiquinone-8 (Q-8) as the predominant ubiquinone, iso-C17:0, summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl), anteiso-C17:0 and C16:0 as the major fatty acids, and phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylmonomethylethanolamine as the main polar lipids. The DNA G+C content of strain KIS55-21(T) was 65.9 mol%. Differential phenotypic and chemotaxonomic properties and phylogenetic data of strain KIS55-21(T) demonstrated that this strain is distinguishable from closely related genera within the family Xanthomonadaceae. On the basis of the data presented, strain KIS55-21(T) is considered to represent a novel genus and species, for which the name Chujaibacter soli gen. nov., sp. nov. is proposed. The type strain is KIS55-21(T) (=KACC 16971(T) =DSM 28578(T)).

Two strains of species of the genus Marmoricola , designated KIS18-7T and JOS5-1T, were isolated from soil samples in Korea. The 16S rRNA gene sequence of strain KIS18-7T showed highest similarities with Marmoricola scoriae Sco-D01T (97.8 %), Marmoricola aequoreus SST-45T (97.6 %) and Marmoricola aurantiacus BC 361T (97.3 %), and strain JOS5-1T had highest sequence similarities with M. aequoreus SST-45T (97.5 %) and Marmoricola bigeumensis MSL-05T (97.3 %). The sequence similarity between KIS18-7T and JOS5-1T was 98.1 %. Phylogenetic analysis showed that these strains grouped with species of the genus Marmoricola . The major fatty acids of strain KIS18-7T were iso-C16 : 0 and C17 : 1ω8c, and C17 : 1ω8c, C18 : 0 10-methyl (TBSA), C18 : 1ω9c, C17 : 0 10-methyl and C16 : 0 2-OH for strain JOS5-1T. Strain KIS18-7T contained the polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylcholine, while strain JOS5-1T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown aminolipid and two unknown phospholipids. The peptidoglycan of both strains contained ll-diaminopimelic acid as the diagnostic diamino acid and a single glycine residue as the interpeptide bridge (type A3γ). The major menaquinone of both strains was MK-8(H4). The G+C contents of the DNA of strains KIS18-7T and JOS5-1T were 68.0 mol% and 62.9 mol%, respectively. These data demonstrate that strains KIS18-7T and JOS5-1T are representatives of two novel species of the genus Marmoricola , for which the names Marmoricola solisilvae sp. nov. (type strain KIS18-7T = KACC 17307T = DSM 27140T = NBRC 109601T) and Marmoricola terrae sp. nov. (type strain JOS5-1T = KACC 17308T = DSM 27141T = NBRC 109602T) are proposed.

A Gram-stain-negative, variably shaped, non-flagellated, yellow-pigmented, aerobic bacterium, designated strain SGM2-10T, was isolated from a paddy soil sample from the Suwon region, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was related most closely to Parasegetibacter luojiensis RHYL-37T. Strain SGM2-10T showed highest 16S rRNA gene sequence similarity to P. luojiensis RHYL-37T (95.1 %), Flavitalea populi HY-50RT (95.0 %) and Flavitalea gansuensis JCN-23T (94.4 %). No other species in the family Chitinophagaceae shared more than 94.1 % 16S rRNA gene sequence similarity with strain SGM2-10T. The major fatty acids of strain SGM2-10T were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The only menaquinone was MK-7. The polar lipids comprised phosphatidylethanolamine, seven unknown lipids and ten unknown aminolipids. The G+C content of the DNA of strain SGM2-10T was 46.7 mol%. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain SGM2-10T represents a novel species of the genus Parasegetibacter , for which the name Parasegetibacter terrae sp. nov. is proposed. The type strain is SGM2-10T ( = KACC 17341T = JCM 19942T). The description of the genus Parasegetibacter has also been emended.

A novel actinomycete strain, designated KIS14-16T, was isolated from forest soil in Ongjin county, South Korea and characterized using polyphasic taxonomy. The cells are aerobic, Gram-stain-positive, non-flagellated and short rods. The strain grew in a temperature range of 4–33 °C (optimum, 28–30 °C) and pH range of 5.0–10.0 (optimum, 7.0) and in the presence of 0–5 % (w/v) NaCl (optimum, 0 %). Comparison of 16S rRNA gene sequences showed that strain KIS14-16T is a member of the genus Arthrobacter exhibiting high sequence similarity with A. livingstonensis LI2T (97.7 %), A. cryoconiti Cr6-08T (97.6 %), A. psychrochitiniphilus GP3T (97.4 %), A. stackebrandtii CCM 2783T (97.1 %) and A. globiformis DSM 20124T (96.3 %). DNA–DNA relatedness and phenotypic data distinguished strain KIS14-16T from phylogenetically related type strains. The peptidoglycan type of strain KIS14-16T was A3α, with an interpeptide bridge comprising l-Lys, l-Thr, Gly and l-Ala4. Strain KIS14-16T contained a large amount of MK-9(H2) and relatively small amounts of MK-10(H2) and MK-8(H2). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and dimannosylglyceride. The major fatty acids (>10 %) were anteiso-C15 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 63.9 mol%. On the basis of these phenotypic, chemotaxonomic and phylogenetic data, strain KIS14-16T should be designated as a representative novel species of the genus Arthrobacter , for which the name Arthrobacter silviterrae sp. nov. is proposed. The type strain is KIS14-16T (=KACC 17303T=DSM 27180T=NBRC 109660T).

A novel Gram-stain-negative bacterial strain, designated T16R-256T, was isolated from the rhizosphere soil of tomato plants grown in a greenhouse in Yecheon-gun, Gyeongsangbuk-do, Republic of Korea and characterized using polyphasic taxonomy. Cells were aerobic, non-flagellated and rod-shaped. Colonies were light yellow, convex and round. The strain grew in the temperature range of 15–37 °C (optimally at 28–30 °C) and pH range of 7.0–9.0 (optimally at 7.0–8.0) and in 4 % NaCl (w/v). A comparison of 16S rRNA gene sequences showed that strain T16R-256T is a member of the genus Parapedobacter , exhibiting high sequence similarity with Parapedobacter pyrenivorans P-4T (94.2 %), Parapedobacter indicus RK1T (93.7 %), Parapedobacter koreensis Jip14T (93.7 %), Parapedobacter luteus 4M29T (93.6 %) and Parapedobacter soli DCY14T (93.4 %). The major polar lipids were phosphatidylethanolamine, sphingolipid, one aminophospholipid, two aminolipids and three unknown lipids. The major fatty acids (>10 % of the total fatty acids) were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 2-OH/C16 : 1ω7c. Strain T16R-256T contained MK-7 as the predominant respiratory quinone and homospermidine as the major polyamine. The genomic DNA G+C content of the type strain was 55.5 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain T16R-256T should be designated as representative of a novel species of the genus Parapedobacter , for which the name Parapedobacter lycopersici sp. nov. is proposed. The type strain is T16R-256T (=KACC 18788T=JCM 31602T).

A yellow, aerobic, Gram-stain-negative, non-motile, rod-shaped and non-flagellated bacterial strain, designated T16R-129T, was isolated from the rhizosphere of a tomato plant collected at a farm located on Buyeo-gun of Chungcheongnam-do, South Korea. Strain T16R-129T grew at 15–40 °C and pH 7.0–9.0, and did not require NaCl for growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain T16R-129T clustered with members of the genus Terrimonas , and it shared highest similarity with Terrimonas arctica R9-86T (96.1 %), Terrimonas pekingensis QHT (95.9 %), Terrimonas lutea DYT (94.9 %), Terrimonas crocea M1-33108T (95.4 %) and Terrimonas rhizosphaerae CR94T (95.3 %). The major isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipids of strain T16R-129T were phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and five unidentified polar lipids. The G+C content of the genomic DNA was 46.0 mol%. On the basis of data from this polyphasic taxonomic study, strain T16R-129T represents a novel species in the genus Terrimonas , for which the name Terrimonas terrae sp. nov. is proposed; the type strain is T16R-129T (=KACC 18787T=JCM 31603T).

One strain, designated 63MJ-1T, was isolated from fresh faeces of broad-winged katydids collected in Jinan-gun, Jeollabuk-do, the Republic of Korea. The organism stained Gram-positive and was an aerobic, non-flagellated and short-rod-shaped bacterium. The organism grew in the range of 4–35 °C (optimum, 28–30 °C) and pH 6.0–9.0 (optimum, pH 7.0), and in the presence of 5 % NaCl (w/v), but not in media containing 7 % NaCl. According to the 16S rRNA gene sequence analysis, strain 63MJ-1T showed the highest sequence similarities with Nakamurella panacisegetis P4-7T (95.9 %), Nakamurella endophytica 2Q3S-4-2T (95.8 %) and Nakamurella multipartita DSM 44233T (95.7 %). Phylogenetic trees also indicated that strain 63MJ-1T formed one robust cluster with members of the genus Nakamurella . The predominant quinone of strain 63MJ-1T was MK-8(H4). Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, an unidentified aminophospholipid and two unidentified lipids. The major fatty acids were C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. The peptidoglycan type was A1γ with meso-diaminopimelic acid as the diagnostic amino acid. The DNA G+C content was 64.6 mol%. Based on the phylogenetic, physiological and chemotaxonomic data, it was demonstrated that strain 63MJ-1T represents a novel species of the genus Nakamurella , for which the name Nakamurella intestinalis sp. nov. is proposed. The type strain is 63MJ-1T (=KACC 18662T=NBRC 111844T).

A bacterial strain, designated T16E-198T, was isolated from the rhizosphere of tomato plant collected from a farm on Buyeo-gun, Chungcheongnam-do, South Korea. The strain was aerobic, Gram-stain-negative, rod-shaped, non-flagellated and yellow-pigmented. Strain T16E-198T was mesophilic, catalase- and oxidase-positive and with flexirubin-type pigments. A phylogenetic tree based on 16S rRNA gene sequences showed that strain T16E-198T formed a lineage with Parafilimonas terrae 5GHs7-2T, sharing highest sequence similarity of 98.4 % with it and less than 93 % with all the other validly published species. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The predominant menaquinone was MK-7. The polar lipids were phosphatidylethanolamine, one unknown aminophospholipid, five unknown aminolipids and five unknown lipids. The DNA G+C content was 41.2 mol%. On the basis of the phenotypic, phylogenetic and chemotaxonomic data presented, strain T16E-198T is considered to represent a novel species of the genus Parafilimonas , for which the name Parafilimonas rhizosphaerae sp. nov. is proposed; the type strain is T16E-198T (=KACC 18786T=JCM 31601T).

One strain, designated KIS31-44T, was isolated from a soil sample collected from Dokdo Island, South Korea. The strain is Gram-stain-positive, aerobic, non-spore-forming and non-motile. It grows optimally at 28–30°C, at pH 7.0 and 0% NaCl. 16S rRNA gene sequence analysis showed that strain KIS31-44T belonged to the genus Nocardioides and shared the highest sequence similarities with Nocardioides aestuarii JC2056T (95.5%) and Nocardioides terrae VA15T (95.0%). The major fatty acids of strain KIS31-44T were C17:1 ω6c, C18:1 ω9c, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), iso-C16:0, C18:0 10-methyl (TBSA), C16:0 2-OH, C17:0 10-methyl, and iso-C16:1 H. The major isoprenoid quinone was MK-8 (H4). The strain contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the major polar lipids. The peptidoglycan structure was A3γ-type with ll-diaminopimelic acid. Based on these data, the isolate represents one novel species in the genus Nocardioides, for which the name Nocardioides paucivorans sp. nov. (type strain KIS31-44T =DSM 27142T =KACC 17309T) is proposed.

A Gram-stain-negative, short rod-shaped, non-flagellated, yellow bacterium, designated strain 5GHs7-2T, was isolated from a greenhouse soil sample in South Korea. 16S rRNA gene sequence analysis of strain 5GHs7-2T indicated that the isolate belonged to the family Chitinophagaceae , and exhibited the highest sequence similarities with members of the genera Terrimonas (89.2–92.6 %), Sediminibacterium (90.8–91.4 %) and Chitinophaga (89.2–91.7 %), Filimonas lacunae YT21T (91.7 %), members of the genus Segetibacter (90.2–91.6 %), Parasegetibacter luojiensis RHYL-37T (90.9 %) and Flavihumibacter petaseus T41T (91.2 %). Flexirubin-type pigments were present. The major cellular fatty acids of the novel strain were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipid profile consisted of a large amount of phosphatidylethanolamine, and moderate and small amounts of several unknown aminolipids and lipids. The only respiratory quinone of strain 5GHs7-2T was MK-7, and the DNA G+C content was 47.6 mol%. On the basis of the evidence presented, it is concluded that strain 5GHs7-2T represents a novel species of a new genus in the family Chitinophagaceae , for which the name Parafilimonas terrae gen. nov., sp. nov. is proposed. The type strain of the type species is 5GHs7-2T ( = KACC 17343T = DSM 28286T).

A bacterial strain, designated RHs22T, was isolated from a soil sample cultivated with rice in the Suwon region of South Korea. The cells were aerobic, Gram-stain-negative, non-spore-forming, non-flagellated rods or occasionally filaments. The strain grew at 10–37 °C (optimum, 28–30 °C), at pH 5.0–10.0 (optimum, 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). Phylogenetically, the strain was closely related to members of the genus Spirosoma , as its 16S rRNA gene sequence had similarity of 90.3–92.1 % with respect to those of members of the genus Spirosoma , showing the highest sequence similarity with Spirosoma panaciterrae DSM 21099T. Strain RHs22T revealed relatively low sequence similarities of less than 90 % with all the other species with validly published names. It contained MK-7 as the predominant menaquinone and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 1ω5c, iso-C15 : 0 and iso-C17 : 0 3-OH as the main fatty acids. The polar lipids of strain RHs22T were phosphatidylethanolamine, one unknown aminolipid, two unknown aminophospholipids, one unknown phospholipid and five unknown lipids. The DNA G+C content was 57.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data obtained in this study indicate that strain RHs22T represents a novel species of the genus Spirosoma , for which the name Spirosoma oryzae sp. nov. is proposed. The type strain is RHs22T ( = KACC 17324T = DSM 28354T). An emended description of the genus Spirosoma is also proposed.

A novel strain, designated 5GHs31-2T, was isolated from a greenhouse soil sample collected from Yongin city, South Korea. Cells of strain 5GHs31-2T were Gram-stain-negative, rod-shaped, polar flagellated and yellow-pigmented. The isolate was aerobic, catalase-negative and oxidase-positive and grew optimally at 28–30 °C and pH 7.0. Strain 5GHs31-2T revealed the highest 16S rRNA gene sequence similarities with Fulvimonas soli LMG 19981T (97.6 %), Dyella thiooxydans ATSB10T (97.5 %) and Frateuria terrea VA24T (97.4 %). Furthermore, the neighbour-joining tree showed that strain 5GHs31-2T was a representative of a member of the genus Fulvimonas . Strain 5GHs31-2T contained iso-C16 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 0 and iso-C17 : 0 as the major fatty acids, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an aminolipid as the main polar lipids and Q-8 as the predominant quinone. The genomic DNA G+C content of 5GHs31-2T was 73.0 mol%. According to DNA–DNA hybridization experiments, DNA–DNA relatedness values between strain 5GHs31-2T and its closest phylogenetic neighbours were below 70 %. Based on the taxonomic data, strain 5GHs31-2T represents a novel species of the genus Fulvimonas , for which the name Fulvimonas yonginensis sp. nov. is proposed. The type strain is 5GHs31-2T ( = KACC 16952T = DSM 28344T).

A bacterial strain, ABC02-12T, was isolated from spent mushroom compost, a waste product of button mushroom cultivation. Cells of the strain were Gram-stain-negative, catalase- and oxidase-positive, non-spore-forming, aerobic flagellated rods. Optimum growth occurred at 28 °C and pH 7.0. 16S rRNA gene sequence analysis showed that strain ABC02-12T shared the highest sequence similarities with Paenalcaligenes hominis CCUG 53761AT (96.0 %), Alcaligenes faecalis subsp. parafaecalis GT (95.7 %), Alcaligenes faecalis subsp. faecalis IAM 12369T (95.4 %) and Pusillimonas noertemannii BN9T (95.3 %). According to the phylogenetic tree, strain ABC02-12T formed a robust cluster with Paenalcaligenes hominis CCUG 53761AT and Paenalcaligenes hermetiae KBL009T. The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The major fatty acids (>5 % of total fatty acids) were C16 : 0, C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3), C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8), C17 : 0 cyclo, and iso-C16 : 1 I, C14 : 0 3-OH and/or an unknown fatty acid (summed feature 2). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminolipid. Putrescine was the principal polyamine, with small amounts of 2-hydroxyputrescine and cadaverine. On the basis of the evidence presented in this study, strain ABC02-12T is a representative of a novel species within the genus Paenalcaligenes , for which the name Paenalcaligenes suwonensis sp. nov. is proposed. The type strain is ABC02-12T ( = KACC 16537T = NBRC 108927T).

A Gram-stain-negative, non-motile, aerobic rod, designated 8604S-37T, was isolated from an outdoor air sample collected in Suwon region, Republic of Korea. The isolate was catalase-positive and oxidase-negative. 16S rRNA gene sequence analysis indicated that strain 8604S-37T was most closely related to Diaphorobacter nitroreducens NA10BT and Diaphorobacter oryzae RF3T, with which it shared 97.0 % 16S rRNA gene sequence similarity. Strain 8604S-37T grew at 10–37 °C (optimum 28 °C; no growth occurred at 4 or 40 °C) and pH 5–9 (optimum pH 7). The strain tolerated up to 3 % NaCl (w/v) (optimum 0 %). The only respiratory quinone was ubiquinone-8 (Q-8). The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown aminolipid. The major fatty acids were C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C17 : 0 cyclo, and the predominant hydroxy fatty acid was C10 : 0 3-OH. Strain 8604S-37T exhibited less than 50 % DNA–DNA relatedness with Diaphorobacter nitroreducens KACC 13856T and Diaphorobacter oryzae KACC 16857T. The DNA G+C content was 65 mol%. Strain 8604S-37T represents a novel species of the genus Diaphorobacter , for which the name Diaphorobacter aerolatus sp. nov. is proposed. The type strain is 8604S-37T ( = KACC 16536T = NBRC 108926T). An emended description of the genus Diaphorobacter is also proposed.

An orange-colored bacterial strain, ICM 1-15(T), was isolated from greenhouse soil. The 16S rRNA gene sequence of this strain showed the highest sequence similarity with Niabella ginsengisoli GR10-1(T) (95.2%) and Niabella yanshanensis CCBAU 05354(T) (95.0%) among the type strains. The strain ICM 1-15(T) was a strictly aerobic, Gram-negative, non-spore-forming, non-motile, flexirubin pigment-producing, short rod-shaped bacterium. The strain grew at 15-35°C (optimum, 25°C), at a pH of 5.0-8.5 (optimum, pH 6.5), and in the presence of 0-3% NaCl (optimum, 1%). The DNA G+C content of strain ICM 1-15(T) was 43.6 mol%. It contained MK-7 as the major isoprenoid quinone and iso-C15:0 (38.9%), iso-C15:1 G (20.3%), and iso-C17:0 3-OH (12.9%) as the major fatty acids. On the basis of evidence from our polyphasic taxonomic study, we concluded that strain ICM 1-15(T) should be classified within a novel species of the genus Niabella, for which the name Niabella terrae sp. nov. is proposed. The type strain is ICM 1-15(T) (=KACC 17443(T) =JCM 19502(T)).

An aerobic, Gram-stain-negative, motile, mesophilic bacterium, designated strain 7515T-07T, was isolated from an air sample in the Taean region, Republic of Korea. The strain grew at 4–40 °C (optimum, 30 °C) and pH 5.0–9.0 (optimum, pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 7515T-07T was related to members of the genus Roseomonas and had highest 16S rRNA gene sequence similarity with Roseomonas ludipueritiae 170/96T (96.7 %). 16S RNA gene sequence similarity between strain 7515T-07T and Roseomonas gilardii ATCC 49956T (the type species of the genus Roseomonas ) was 93.4 %. Strain 7515T-07T contained Q-10 as the ubiquinone and C18 : 1ω7c and C19 : 0 cyclo ω8c as the dominant fatty acids (>10 %). The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified aminolipids. The DNA G+C content was 73.0 mol%. Combined data from phenotypic, phylogenetic and chemotaxonomic studies demonstrated that strain 7515T-07T is a representative of a novel species of the genus Roseomonas , for which the name Roseomonas aerophila sp. nov. is proposed. The type strain is 7515T-07T ( = KACC 16529T = NBRC 108923T).

A bacterial isolate designated GR24-2T was isolated from Korean soil used for cultivating ginseng (Panax ginseng C. A. Meyer). The strain was aerobic, Gram-negative, motile, and rod-shaped. It grew optimally at 28–30°C, pH 7.0, and in a range of 0–1% NaCl. Phylogenetically, the strain clustered with members of the genus Rhodanobacter. The strain exhibited the highest sequence similarities (>98%) with R. panaciterrae LnR5-47T (98.4%), R. soli DCY45T (98.2%), and R. ginsengisoli GR17-7T (98.0%). However, it also showed high sequence similarities (>97%) with some other Rhodanobacter and Dyella species. The strain contained Q-8 as the predominant respiratory quinone. The major fatty acids (greater than 10% of the total fatty acids) were iso-C17:1 ω9c (24.5%), iso-C16:0 (22.8%), anteiso-C15:0 (10.5%), and iso-C15:0 (10.1%). Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown aminophospholipid. The DNA G+C content of strain GR24-2T was 65.6 mol%. The strain showed less than 70% DNA relatedness values between the closely related Rhodanobacter and Dyella species. The phylogeny, phenotype, DNA-DNA hybridization, and chemotaxonomic data generated in this study reveal that the isolate is a novel species of the genus Rhodanobacter. The name proposed for this strain is Rhodanobacter umsongensis sp. nov. (type strain GR24-2T =KACC 12917T =DSM 21300T).

A bacterial strain, designated HOR6-4T, was isolated from the epidermal tissue of a root of a Phalaenopsis orchid. Strain HOR6-4T was characterized using a polyphasic approach. The cells were aerobic, Gram-stain-positive, non-motile coccoids. Phylogenetic analysis of its 16S rRNA gene sequence revealed a clear affiliation with the family Dermacoccaceae . Strain HOR6-4T showed relatively low 16S rRNA gene sequence similarity (below 95.9 %) to type strains of species with validly published names, showing the highest sequence similarities to the type strains of Flexivirga alba (95.8 %) and Yimella lutea (95.5 %). The DNA G+C content of strain HOR6-4T was 64.7 mol%. Strain HOR6-4T had anteiso-C17 : 0 (19.3 %), 10-methyl C18 : 0 (tuberculostearic acid; 13.5 %) and 10-methyl C17 : 0 (11.7 %) as the major fatty acids and contained MK-8(H4) and MK-8(H6) as the predominant quinones. Polar lipids were diphosphatidylglycerol, phosphatidylinositol, three aminophospholipids, two phospholipids and an aminolipid. The peptidoglycan type was A4α, with an l-Lys–l-Thr–d-Glu interpeptide bridge with a glycine residue bound to the alpha-carboxyl group of d-Glu in position 2 of the peptide subunit. Mycolic acids were not present. On the basis of comparative analysis of phenotypic and phylogenetic traits, strain HOR6-4T is considered to represent a novel species in a new genus in the family Dermacoccaceae , for which the name Rudaeicoccus suwonensis gen. nov., sp. nov. is proposed. The type strain of Rudaeicoccus suwonensis is HOR6-4T ( = KACC 12637T = DSM 19560T).

A novel actinomycete strain, 7402J-48T, was isolated from an air sample collected from Jeju island, Republic of Korea. Cells were Gram-positive, aerobic, flagellated, short rods. Strain 7402J-48T showed highest 16S rRNA gene sequence similarity (98.6 %) with Angustibacter luteus TT07R-79T, and had relatively low sequence similarities (below 95.1 %) with other members of the family Kineosporiaceae . The cell wall of strain 7402J-48T contained alanine, glutamic acid and 2,6-diaminopimelic acid, suggesting A1γ-type peptidoglycan. The menaquinones were MK-9(H4) and MK-8(H4). The acyl type of the cell-wall muramic acid was acetyl. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown lipid were present. The cellular fatty acid profile comprised a large amount of anteiso-C15 : 0, moderate amounts of C16 : 0, summed feature 3 (including C16 : 1ω7c and/or C16 : 1ω6c), C17 : 0, iso-C15 : 0, C16 : 0 N alcohol and C17 : 1ω8c, and small amounts of other fatty acids. The DNA G+C content of strain 7402J-48T was 73 mol%. Based on its phenotypic and genotypic characteristics, strain 7402J-48T ( = KACC 15527T = NBRC 108730T) is proposed as the type strain of a novel species, Angustibacter aerolatus sp. nov. An emended description of the genus Angustibacter is provided.

A Gram-stain-negative, non-motile, strictly aerobic, yellow-pigmented bacterium, designated strain 5G38T, was isolated from a field cultivated with Chinese cabbage in Korea. The strain grew at 5–40°C and at pH 6.0–8.0. 16S rRNA gene sequence analysis revealed that strain 5G38T represented a distinct lineage within the family Sphingobacteriaceae and showed the highest 16S rRNA gene sequence similarity of 95.2% with Pedobacter koreensis WPCB189T, followed by Pedobacter agri PB92T (94.6%), Pedobacter suwonensis 15–52T (94.4%), Pedobacter rhizosphaerae 01–96T (94.4%), Pedobacter sandarakinus DS-27T (94.4%), and Nubsella zeaxanthinifaciens TDMA-5T (94.3%). Strain 5G38T formed monophyletic clade with Nubsella zeaxanthinifaciens in the cluster comprised of species of the genus Pedobacter. Chemotaxonomic characteristics of the novel strains, including DNA G+C content of genomic DNA (37.0 mol%), the predominant respiratory quinine (MK-7), and the major fatty acids which were iso-C15:0, summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH) and iso-C17:0 3-OH, are similar to those of the genus Pedobacter. However, the novel strains can be distinguished from the other species of Pedobacter by physiological properties. The name Pedobacter namyangjuensis sp. nov. is therefore proposed for strain 5G38T (KACC 13938T =NBRC 107692T) as the type strain. Furthermore, the reclassification of Nubsella zeaxanthinifaciens as Pedobacter zeaxanthinifaciens comb. nov. is proposed.

A Gram-stain-negative, rod-shaped, white bacterium, designated strain T16R-88T, was isolated from a rhizosphere soil sample collected in Buyeo-gun of Chungcheongnam-do, South Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain T16R-88T formed a lineage within the genus Pedobacter . It showed highest sequence similarities to Pedobacter ginsengisoli Gsoil 104T (97.4 %), Pedobacter nutrimenti J22T (97.2 %), Pedobacter nyackensis NWG-II14T (97.1 %), Pedobacter seoulensis THG-G12T (97.1 %) and Pedobacter panaciterrae Gsoil 042T (97.0 %). The predominant respiratory quinone was menaquinone MK-7. The major cellular fatty acids (>10 % of the total fatty acids) were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), iso-C17 : 0 3-OH and iso-C15 : 0. The polar lipids consisted of phosphatidylethanolamine, sphingolipid, one unidentified aminophospholipid, three unidentified aminolipids, three unidentified lipids and one unidentified phospholipid. DNA–DNA hybridization values between strain T16R-88T and its most closely related species were below 70 %. The DNA G+C content was 35.6 mol%. On the basis of the evidence presented in this study, strain T16R-88T represents a novel species of the genus Pedobacter , for which the name Pedobacter lycopersici sp. nov. is proposed. The type strain is T16R-88T (=KACC 18652T=NBRC 111984T).

Strain 63MJ-2T was isolated from the feces of broad-winged katydid (Pseudorhynchus japonicus) collected in Korea. The 16S rRNA gene sequence of this strain showed the highest sequence similarity with that of Siphonobacter aquaeclarae P2T (96.1%) and had low similarities (below 86.3%) with those of other members of family ‘Flexibacteraceae’. The strain 63MJ-2T is a strictly aerobic, Gram-stain-negative, non-motile, rod-shaped bacterium. The strain grew at 4–35°C (optimum, 25–30°C), pH of 5.0–9.0 (optimum, 6.0–7.0), and 0–2.0% (optimum, 1.0–2.0) (w/v) NaCl. The DNA G+C content of strain 63MJ-2T was 43.5 mol%. The major fatty acids were C16:1ω5c (42.5%), iso-C17:0 3-OH (18.7%), and summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c, 18.0%). The major menaquinone was MK-7 and polar lipids were phosphatidylethanolamine, six unknown aminolipids, and five unknown lipids. Based on the evidence from our polyphasic taxonomic study, we conclude that strain 63MJ-2T should be classified as a novel species of the genus Siphonobacter, and propose the name Siphonobacter intestinalis sp. nov. The type strain is 63MJ-2T (=KACC 18663T =NBRC 111883T).

The microbiome in the rhizosphere–the region surrounding plant roots–plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culture-dependent approach, two culture media (Reasoner’s 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria. A total of 689 bacterial isolates were clustered into 164 operational taxonomic units (OTUs) at 97% sequence similarity, and these were found to belong to five bacterial phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122 OTUs were retrieved from the antibiotic-containing media, and 80 OTUs were recovered by one specific antibiotic-containing medium. In the culture-independent approach, we conducted Illumina MiSeq amplicon sequencing of the 16S rRNA gene and obtained 19,215 high-quality sequences, which clustered into 478 OTUs belonging to 16 phyla. Among the total OTUs from the MiSeq dataset, 22% were recovered in the culture collection, whereas 41% of OTUs in the culture collection were not captured by MiSeq sequencing. These results showed that antibiotics were effective in isolating various taxa that were not readily isolated on antibiotic-free media, and that both contrasting approaches provided complementary information to characterize bacterial diversity in the tomato rhizosphere.

A novel siderophore-producing actinomycete, designated PL19T, was isolated from the Scots-pine needle-like leaves collected from TNAU campus, Coimbatore, India. The isolate was chemoorganotrophic in nutrition and able to grow at 30 °C, and the optimum pH and NaCl facilitated the growth pH 6-11 and 0-8 % (w/v), respectively. The cells are filamentous and the mycelia formed are basically of wide and intricately branched substrate mycelium from which aerial mycelia arises, later gets differentiated into spores that are warty and arranged spirally. The 16S rRNA gene of strain PL19T was sequenced and was highly similar to the type strains of species of the genus Streptomyces, including Streptomyces barkulensis RC1831T (98.8 % pairwise similarity), Streptomyces fenghuangensis GIMN4.003T (98.2 %), Streptomyces nanhaiensis SCSIO 01248T (98.0 %), Streptomyces radiopugnans R97T (97.9 %), Streptomyces atacamensis C60T (97.8 %) and Streptomyces macrosporus NBRC 14749T (97.2 %), all of which were subjected to taxonomical characterization using a polyphasic approach. The strains showed unique carbon utilization patterns, and it possesses iso-C16 : 0 anteiso-C15 : 0 and anteiso-C17 : 0 as a major cellular fatty acids. The cell-wall was dominated with ll-type diaminopimelic acid, and the menaquinone type was MK-9(H6, H8). These chemotaxonomic evidences placed strain PL19T within the genus Streptomyces. The determination of G+C ratio (69.5 mol%) and DNA-DNA hybridization values (13.4-31.8 % with the phylogenetically related species) helped in further hierarchical classification of strain PL19T. Based on morphological, physiological and chemotaxonomic data as well as DNA-DNA hybridization values, strain PL19T could be distinguished from the evolutionarily closest species currently available. All these collective data show that strain PL19T represents a novel species of the genus Streptomyces, for which the name Streptomyces pini sp. nov. is proposed. The type strain is PL19T (=NRRL B-24728T=ICMP 17783T).

A bacterial strain, designated T16R-265T, was isolated from rhizosphere of tomato in Buyeo-gun, Chungcheongnam-do, South Korea. The strain was Gram-stain-negative, aerobic, non-flagellated and rod- or long-rod-shaped. It grew at the range of 10-40 °C (optimum 28-30 °C), pH 6.0-9.0 (optimum pH 7.0) and with 0-3 % (w/v) NaCl (optimum 0 %). 16S rRNA gene sequence analysis showed that strain T16R-265T had the highest sequence similarity (98.0 %) with Flavitalea soli KIS20-3T and low sequence similarities of below 95 % with all other taxa. The phylogenetic tree revealed that the strain formed a robust monophyletic line with Flavitalea soli KIS20-3T separable from other clades. The predominant quinone of strain T16R-265T was MK-7, the polar lipids consisted of large amounts of phosphatidylethanolamine and an unknown lipid, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. DNA-DNA hybridization values with Flavitalea soli KACC 17319T were below 70 %. The DNA G+C content of strain T16R-265T is 46.2 mol%. Based on phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analyses, strain T16R-265T represents a novel species of a new genus, for which the name Pseudoflavitalea rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of the type species is T16R-265T (=KACC 18655T=NBRC 111880T). We also propose the reclassification of Flavitalea soli as Pseudoflavitalea soli comb. nov. (type strain KIS20-3T=KACC 17319T=JCM 19937T).

The effects of PCR cycle number and DNA polymerase type on 16S rRNA gene pyrosequencing analysis were investigated using an artificially prepared bacterial community (mock community). The bacterial richness was overestimated at increased PCR cycle number mostly due to the occurence of chimeric sequences, and this was more serious with a DNA polymerase having proofreading activity than with Taq DNA polymerase. These results suggest that PCR cycle number must be kept as low as possible for accurate estimation of bacterial richness and that particular care must be taken when a DNA polymerase having proofreading activity is used.

A novel isolate, designated 6408J-67(T), was isolated from an air sample collected from Jeju Island, Republic of Korea. Its phenotypic, genotypic, and chemotaxonomic properties were compared with those of members of the family Microbacteriaceae. The Gram-positive, aerobic, motile rod formed light yellow, smooth, circular and convex colonies. Optimal growth occurred at 30°C and pH 7.0. 16S rRNA gene sequence data showed that the isolate was a novel member of the family Microbacteriaceae, with the highest sequence similarity (97.4%) to Labedella gwakjiensis KSW2-17(T) and less (97%) sequence similarity with other taxa. The major cellular fatty acids (10% of the total) were anteiso-C(15:0), iso-C(14:0), and iso-C(16:0). The strain also contained MK-13, MK-12, and MK-14 as the major menaquinones, as well as diphosphatidylglycerol, phosphatidylglycerol, and two unknown glycolipids. Its peptidoglycan structure was B1β with 2,4-diaminobutyric acid as a diamino acid. Mycolic acids were absent. The DNA G+C content was 68.3 mol%. Based on these phenotypic and genotypic findings, strain 6408J-67(T) represents a novel species of a new genus within the family Microbacteriaceae, for which the name Diaminobutyricimonas aerilata gen. nov., sp. nov. is proposed. The type strain is 6408J-67(T) (=KACC 15518(T) =NBRC 108726(T)).

The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.