Unraveling interspecies cross-feeding during anaerobic lignin degradation for bioenergy applications.

Lignin, a major component of plant biomass, remains underutilized for renewable biofuels due to its complex and heterogeneous structure. Although investigations into depolymerizing lignin using fungi are well-established, studies of microbial pathways that enable anaerobic lignin breakdown linked with methanogenesis are limited. Through an enrichment cultivation approach with inoculation of freshwater sediment, we enriched a microbial community capable of producing methane during anaerobic lignin degradation. We reconstructed the near-complete population genomes of key lignin degraders and methanogens using metagenome-assembled genomes finally selected in this study (MAGs; 92 bacterial and 4 archaeal MAGs affiliated into 45 and 2 taxonomic groups, respectively). This study provides genetic evidence of microbial interdependence in conversion of lignin to methane in a syntrophic community. Metagenomic analysis revealed metabolic linkages, with lignin-hydrolyzing and/or fermentative bacteria such as the genera Alkalibaculum and Propionispora transforming lignin breakdown products into compounds such as acetate to feed methanogens (two archaeal MAGs classified into the genus Methanosarcina or UBA6 of the family Methanomassiliicoccaceae). Understanding the synergistic relationships between microbes that convert lignin could inform strategies for producing renewable bioenergy and treating aromatic-contaminated environments through anaerobic biodegradation processes. Overall, this study offers fundamental insights into complex community-level anaerobic lignin metabolism, highlighting hitherto unknown players, interactions, and pathways in this biotechnologically valuable process.

Chryseobacterium gotjawalense sp. nov. Isolated from Soil in the Volcanic Forest Gotjawal, Jeju Island.

Strain wdc7T, a rod-shaped bacterium, was isolated from soil in the Gotjawal Forest on Jeju Island, South Korea. Strain wdc7T was Gram stain-negative, facultatively anaerobic, catalase- and oxidase positive, yellow pigmented, and non-flagellated. It grew at 4-37 °C and pH 5.0-8.0 in 0-3% (w/v) NaCl. 16S rRNA gene sequencing analysis revealed that strain wdc7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium salivictor NBC 122T, with a sequence similarity of 98.51%. Menaquinone 6 was the sole respiratory quinone, and C15:0 anteiso, C15:0 iso, and summed feature 9 were the major fatty acids. The genome length was 3.30 Mbp, with a 37% G + C content. Average amino acid identity, average nucleotide identity, and digital DNA-DNA relatedness between strain wdc7T and C. salivictor NBC 122T were 93.52%, 92.80%, and 49.7%, respectively. Digital genomic and polyphasic analyses showed that strain wdc7T likely represented a new species of the genus Chryseobacterium. We proposed the name Chryseobacterium gotjawalense sp. nov., with wdc7T (= KCTC 92440T = JCM 35602T) as the type strain.

Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium.

Members of the genus Flavobacterium are widely distributed and produce various polysaccharide-degrading enzymes. Many species in the genus have been isolated and characterized. However, few studies have focused on marine isolates or fish pathogens, and in-depth genomic analyses, particularly comparative analyses of isolates from different habitat types, are lacking. Here, we isolated 20 strains of the genus from various environments in South Korea and sequenced their full-length genomes. Combined with published sequence data, we examined genomic traits, evolution, environmental adaptation, and putative metabolic functions in total 187 genomes of isolated species in Flavobacterium categorized as marine, host-associated, and terrestrial including freshwater. A pangenome analysis revealed a correlation between genome size and coding or noncoding density. Flavobacterium spp. had high levels of diversity, allowing for novel gene repertories via recombination events. Defense-related genes only accounted for approximately 3% of predicted genes in all Flavobacterium genomes. While genes involved in metabolic pathways did not differ with respect to isolation source, there was substantial variation in genomic traits; in particular, the abundances of tRNAs and rRNAs were higher in the host-associdated group than in other groups. One genome in the host-associated group contained a Microviridae prophage closely related to an enterobacteria phage. The proteorhodopsin gene was only identified in four terrestrial strains isolated for this study. Furthermore, recombination events clearly influenced genomic diversity and may contribute to the response to environmental stress. These findings shed light on the high genetic variation in Flavobacterium and functional roles in diverse ecosystems as a result of their metabolic versatility. IMPORTANCE The genus Flavobacterium is a diverse group of bacteria that are found in a variety of environments. While most species of this genus are harmless and utilize organic substrates such as proteins and polysaccharides, some members may play a significant role in the cycling for organic substances within their environments. Nevertheless, little is known about the genomic dynamics and/or metabolic capacity of Flavobacterium. Here, we found that Flavobacterium species may have an open pangenome, containing a variety of diverse and novel gene repertoires. Intriguingly, we discovered that one genome (classified into host-associated group) contained a Microviridae prophage closely related to that of enterobacteria. Proteorhodopsin may be expressed under conditions of light or oxygen pressure in some strains isolated for this study. Our findings significantly contribute to the understanding of the members of the genus Flavobacterium diversity exploration and will provide a framework for the way for future ecological characterizations.

Analyzing Gut Microbial Community in Varroa destructor-Infested Western Honeybee (Apis mellifera).

The western honeybee Apis mellifera L., a vital crop pollinator and producer of honey and royal jelly, faces numerous threats including diseases, chemicals, and mite infestations, causing widespread concern. While extensive research has explored the link between gut microbiota and their hosts. However, the impact of Varroa destructor infestation remains understudied. In this study, we employed massive parallel amplicon sequencing assays to examine the diversity and structure of gut microbial communities in adult bee groups, comparing healthy (NG) and Varroa-infested (VG) samples. Additionally, we analyzed Varroa-infested hives to assess the whole body of larvae. Our results indicated a notable prevalence of the genus Bombella in larvae and the genera Gillamella, unidentified Lactobacillaceae, and Snodgrassella in adult bees. However, no statistically significant difference was observed between NG and VG. Furthermore, our PICRUSt analysis demonstrated distinct KEGG classification patterns between larval and adult bee groups, with larvae displaying a higher abundance of genes involved in cofactor and vitamin production. Notably, despite the complex nature of the honeybee bacterial community, methanogens were found to be present in low abundance in the honeybee microbiota.

Complete genome sequence of Halomonas alkaliantarctica MSP3 isolated from marine sediment, Jeju Island.

As a moderate halophilic-heterotrophic bacterium, Halomonas alkaliantarctica MSP3 was isolated from marine sediment located in Jeju island, South Korea. The complete genome of strain MSP3 was sequenced and analyzed to reveal its genetic features and metabolic potential. The genome size of MSP3 was about 4.23 Mbp with 54.7% G + C content, and it contained 3811 protein-coding sequences and 79 RNA genes (61 tRNA and 18 rRNA). According to the genome annotation, it was revealed that the strain MSP3 harbors genes encoding for urease and urea transporters, which play a crucial role in the process of urea degradation and utilization. In addition, it is noteworthy that the MSP3 strain possesses genes encoding for both cytochrome c oxidase and cytochrome bd oxidase, thereby conferring upon it the ability to adapt to various levels of oxygen (oxic to microoxic) and to execute denitrification processes in the absence of oxygen. Moreover, it was observed that strain MSP3 had genes for the glyoxylate cycle, which is an alternative pathway to the TCA cycle. Furthermore, it was observed that the MSP3 strain exhibited the ability to thrive across a diverse spectrum of NaCl concentrations, ranging from 2% to 10% (w/v). Collectively, strain MSP3 may possess an advantage over competitors within the marine ecosystem, particularly in conditions where carbon substrates are restricted. The genomic-based assumption could potentially be substantiated by the presence of a multitude of transporter genes within the genome.

Sulfitobacter albidus sp. nov., isolated from marine sediment of Jeju Island.

Strain JK7-1T isolated from marine sediment collected from Jeju Island of South Korea was strictly aerobic, Gram-stain-negative, catalase-positive, oxidase-positive, motile, and rod-shaped bacterium that is circular and convex with white pigment. Strain JK7-1T could grow at 10-30 °C and pH 6-9 with 1-6% (w/v) NaCl. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain JK7-1T belonged to genus Sulfitobacter, sharing high sequence similarities with Sulfitobacter undariae W-BA2T (97.90%), Sulfitobacter donghicola KCTC 12864T (97.61%), and Sulfitobacter mediterraneus KCTC 32188T (97.47%). Strain JK7-1T possessed only ubiquinone-10 (Q-10) as a sole respiratory quinone and summed feature 8 as the major fatty acid (81.02%). A dominant polar lipid phosphatidylglycerol was identified in strain JK7-1T. Strain JK7-1T had a complete genome of 3,441,674 bp in length with a mean G + C content of 63.96%. Polyphasic and genomic analyses revealed that strain JK7-1T represented a novel species in the genus Sulfitobacter, for which a name of Sulfitobacter albidus sp. nov. was proposed. Its type strain is JK7-1T (= KCTC 72819T = NBRC 114632T = KMM 6821T).

Genomic sequence of the non-pathogen Neisseria sp. strain MA1-1 with antibiotic resistance and virulence factors isolated from a head and neck cancer patient.

Recent research has claimed virulence factors or antimicrobial resistance in commensal or non-pathogenic Neisseria spp. This study aimed to isolate and analyze commensal microorganisms related to the genus Neisseria from the oral cavity of a patient with head and neck cancer. We successfully isolated strain MA1-1 and identified its functional gene contents. Although strain MA1-1 was related to Neisseria flava based on 16S rRNA gene sequence similarity, genomic relatedness analysis revealed that strain MA1-1 was closely related to Neisseria mucosa, reported as a commensal Neisseria species. The strain MA1-1 genome harbored genes for microaerobic respiration and the complete core metabolic pathway with few transporters for nutrients. A number of genes have been associated with virulence factors and resistance to various antibiotics. In addition, the comparative genomic analysis showed that most genes identified in the strain MA1-1 were shared with other Neisseria spp. including two well-known pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. This indicates that the gene content of intra-members of the genus Neisseria has been evolutionarily conserved and is stable, with no gene recombination with other microbes in the host. Finally, this study provides more fundamental interpretations for the complete gene sequence of commensal Neisseria spp. and will contribute to advancing public health knowledge.

Complete genome sequence of marine photoheterotophic bacterium Erythrobacter sp. JK5.

Erythrobacter sp. JK5, a marine heterotrophic bacterium, was isolated from marine sediment in Jeju island, the Republic of Korea. Here, we report information on the complete genome of strain JK5, including a putative capability for photosynthesis. The genome of JK5 consisted of 3.34 Mbp with 64.2% G + C content, and contained 3210 protein-coding sequences and three rRNA genes. Genomic analysis revealed that strain JK5 might be grown under oxic, microoxic, or anoxic conditions using two types of terminal oxidase (high and low oxygen affinity) or nitrate reductase. The types IV and VI secretion systems presented in strain JK5 genome might reveal a survival advantage against their ecological competitors in the marine environment.

Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment.

A Gram-stain-negative, rod-shaped, and strictly aerobic bacterium designated strain G2-bT was isolated from the marine sediment around Jeju Island, South Korea. Strain G2-bT was found to be catalase- and oxidase-positive, white-pigmented, motile with polar flagellum, and to grow optimally at 25 °C, pH 7.0 in the presence of 4% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain G2-bT belongs to the genus Salinimonas and was closely related Salinimonas sediminis N102T (96.7% sequence similarity), Salinimonas iocasae KX18D6T (95.4%), Salinimonas lutimaris DPSR-4T (94.7%), and Salinimonas chungwhensis BH030046T (94.6%). Strain G2-bT possessed ubiquinone 8 as the sole respiratory quinone, summed feature 3 and summed feature 8 as the major fatty acids, and phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genome size and G + C content of the strain G2-bT were determined to be 3,765,169 bp, and 49.7%, respectively, as a complete circular genome. Based on the genomic analyses (e.g., average nucleotide identity and digital DNA-DNA hybridization), the strain G2-BT likely represents a new species in the genus Salinimonas, for which we propose to name this novel bacterium Salinimonas marina sp. nov., and the type strain is designated G2-BT (= KCTC 72817T = VTCC 910110T).

Parasphingorhabdus halotolerans sp. nov. isolated from marine sediment in Jeju Island.

A Gram-stain-negative, catalase- and oxidase-positive, rod-shaped bacterium, designated as JK6T was isolated from a coastal marine sediment in Jeju Island. Strain JK6T was characterized by polyphasic investigation including genome features. It grew at pH 5.0-9.0 (optimum 7.5), 18-30 °C (optimum 25 °C) and 1.0-7.0% (w/v) NaCl (optimum 2.0%). Strain JK6T utilized D-mannose, D-glucose, L-fucose, propionate and acetate as carbon and energy sources. The sole quinone was ubiquinone-10, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and sphingolipid. Strain JK6T was closely related to Parasphingorhabdus flavimaris SW-151T (98.2%), Parasphingorhabdus marina DSM 22363T (97.6%) and Parasphingorhabdus litoris FR1093T (97.6%) based on 16S rRNA gene sequence similarity. Genome length and GC content were 3.29 Mbp and 53.0%, respectively. Digital DNA-DNA relatedness, average nucleotide identity, and average amino acid identity between strain JK6T and P. flavimaris SW-151T were 16.6%, 73.9%, and 77.6%, respectively. These results showed that the strain can be recognized as a novel bacterium named Parasphingorhabdus halotolerans. The type strain of Parasphingorhabdus halotolerans sp. nov. is JK6T (= KCTC 72818T = VTCC 910111T).

Draconibacterium halophilum sp. nov., A Halophilic Bacterium Isolated from Marine Sediment.

A Gram-stain-negative, long-rod shaped, and facultatively anaerobic bacterium, designated as strain M1T, was isolated from the marine sediment of Jeju Island, South Korea. Strain M1T was found to be catalase- and oxidase-positive, light yellow-pigmented, non-motile, and non-flagellated, growing optimally at 30 °C, pH 7.0, and in the presence of 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain M1T belongs to the genus Draconibacterium and is closely related to Draconibacterium orientale FH5T (97.2%), Draconibacterium sediminis JN14CK-3 T (96.5%), "Draconibacterium filum" F2T (96.5%) and Draconibacterium mangrovi GM2-18 T (96.3% sequence similarity). The values for digital DNA-DNA hybridization ranged from 37.6 to 38.3% against D. orientale FH5T, D. sediminis KN14CK-3 T, and D. mangrovi GM2-18 T, clearly indicating that strain M1T represents a distinct species of the genus Draconibacterium. Strain M1T has a 40.0% G + C content estimated by genome sequence, menaquinone 7 as the sole respiratory quinone, C15:0 anteiso and C15:0 iso as the major fatty acids, and phosphatidylethanolamine, an unidentified phospholipid, and unidentified lipids as the polar lipids. Based on the polyphasic characteristics, it is suggested that strain M1T be assigned to the genus Draconibacterium as the type strain of a novel species, for which the name Draconibacterium halophilum sp. nov. is proposed. The type strain is M1T (= KCTC 72809 T = VTCC 910107 T).

Kineobactrum salinum sp. nov., isolated from marine sediment.

Strain M2T, isolated from marine sediment collected at Jeju Island, was an aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, rod-shaped bacterium that formed circular, raised, yellow colonies. Strain M2T grew at 15-42 °C, pH 5.5-9.0 and with 1-9 % (w/v) NaCl. Phylogenetic analysis based on its 16S rRNA gene sequences indicated that strain M2T was closely related to Kineobactrum sediminis F02T (98.0 % sequence similarity). Ubiquinone-8 was determined to be the sole respiratory quinone. Summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) were identified as the predominant fatty acids. The DNA G+C content and digital DNA-DNA relatedness between strain M2T and K. sediminis F02T were 60.7 mol% and 19.5 %, respectively. Phosphatidylglycerol and phosphatidylethanolamine were identified as the major polar lipids. Thus, polyphasic characterization revealed that strain M2T represents a novel species in the genus Kineobactrum, for which the name Kineobactrum salinum sp. nov. is proposed. The type strain is M2T (=KCTC 72815T=VTCC 910108T).

Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches.

Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 µM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.

Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea.

Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.

Formosa sediminum sp. nov., a starch-degrading bacterium isolated from marine sediment.

A novel bacterium, designated strain PS13T, was isolated from marine sediment collected from the coast of Jeju Island. Strain PS13T was a Gram stain-negative, catalase- and oxidase-positive, aerobic, yellow-pigmented, motile by gliding, and rod-shaped bacterium. Strain PS13T grew optimally at 25 °C and pH 8.0 and in the presence of 3 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain PS13T belonged to the genus Formosa and was closely related to Formosa algae KMM3553T (98.3 % sequence similarity). The DNA-DNA relatedness (17.3-21.8 %) and average nucleotide identity (83.6-84.6 %) values clearly indicated that strain PS13T represents a distinct species of the genus Formosa. The major fatty acids were C15 : 0 iso, C16 : 1 ω6c/C16 : 1 ω7c and C15 : 1 iso G. The genomic DNA G+C content of the strain PS13T was 32.2 mol%. On the basis of polyphasic characteristics, it is suggested that strain PS13T be assigned to the genus Formosa as the type strain of a novel species, for which the name Formosa sediminum PS13T (=KCCM 43301T=CECT 9918T) sp. nov. is proposed.

Ferrovibrio terrae sp. nov., isolated from soil.

Designated strain K5T was isolated from soil on Jeju Island. The bacterium was aerobic, Gram-stain-negative, oxidase-positive, catalase-low activity, motile, short-rod shaped, opaque and formed white colonies that were circular, raised and had entire margins. Strain K5T was able to grow at 15-40 °C, pH 4-9 and at 0-2 % (w/v) NaCl concentration. Phylogenetic analysis based on its 16S rRNA gene sequences indicated that strain K5T is closely related to Ferrovibrio soli A15T (98.9 % sequence similarity), Ferrovibrio denitrificans Sp-1T (98.7 %) and Ferrovibrio xuzhouensis LM-6T (97.4 %). The sole respiratory quinone was determined to be ubiquinone-10. The dominant fatty acids of strain K5T were summed feature 8 (C18 : 1 ω7c / C18 : 1ω6c, 29.8 %), C19 : 0 cyclo ω8c (20.2 %) and C16 : 0 (24.4 %). DNA G+C content was 63.6 % and DNA-DNA relatedness between strain K5T and other three members of the genus Ferrovibrio ranged from 24 to 28 %. The major polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine and aminolipids. Moreover, polyphasic characterization revealed that strain K5T represents a novel species in the genus Ferrovibrio, for which the name Ferrovibrio terrae sp. nov. is proposed. The type strain is K5T (=KCCM 43295T=LMG 30611T).

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System.

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis.

Rhizocompartments and environmental factors affect microbial composition and variation in native plants.

Molecular analysis based on large-scale sequencing of the plant microbiota has revealed complex relationships between plants and microbial communities, and environmental factors such as soil type can influence these relationships. However, most studies on root-associated microbial communities have focused on model plants such as Arabidopsis, rice or crops. Herein, we examined the microbiota of rhizocompartments of two native plants, Sedum takesimense Nakai and Campanula takesimana Nakai, using archaeal and bacterial 16S rRNA gene amplicon profiling, and assessed relationships between environmental factors and microbial community composition. We identified 390 bacterial genera, including known plant-associated genera such as Pseudomonas, Flavobacterium, Bradyrhizobium and Rhizobium, and uncharacterized clades such as DA101 that might be important in root-associated microbial communities in bulk soil. Unexpectedly, Nitrososphaera clade members were abundant, indicating functional association with roots. Soil texture/type has a greater impact on microbial community composition in rhizocompartments than chemical factors. Our results provide fundamental knowledge on microbial diversity, community and correlations with environmental factors, and expand our understanding of the microbiota in rhizocompartments of native plants.

Arthrobacter dokdonellae sp. nov., isolated from a plant of the genus Campanula.

A Gram-stain-positive, oxidase- and catalase-positive motile, aerobic, and rod-shaped bacterial strain, designated as DCT-5T, was isolated from a native plant belonging to the genus Campanula at Dokdo island, Republic of Korea. Growth of the strain DCT-5T was observed at 15-37°C (optimum 30°C) on R2A broth, pH 6.0-8.0 (optimum 7.0), and 0-5% (w/v) NaCl concentration (optimum 0%). The 16S rRNA gene sequence analysis revealed that strain DCT-5T was most closely related to Arthrobacter silviterrae KIS14-16T, Arthrobacter livingstonensis LI2T, Arthrobacter stackebrandtii CCM 2783T, Arthrobacter cryoconiti Cr6-08T, Arthrobacter ramosus CCM 1646T, and Arthrobacter psychrochitiniphilus GP3T with pairwise sequence similarities of 98.76%, 97.47%, 97.25%, 97.11%, 97.11%, and 97.00%, respectively. The DNA G+C content of strain DCT-5T was 64.7 mol%, and its DNA-DNA relatedness values with A. silviterrae KIS14-16T, A. livingstonensis LI2T, A. stackebrandtii CCM 2783T, A. psychrochitiniphilus GP3T, A. ramosus CCM 1646T, and A. cryoconiti Cr6-08T were 32.57 ± 2.02%, 28.75 ± 0.88%, 31.93 ± 1.15%, 34.73 ± 1.86%, 29.12 ± 1.56%, and 27.23 ± 0.88%, respectively. The major quinone was MK-9(H2) and major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C15:0, and iso-C16:0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), unidentified glycolipid (GL), two unidentified aminophospholipids (APLs), and three unidentified lipids (Ls). The peptidoglycan type was A3α. On the basis of phenotypic, phylogenetic, genotypic, and chemotaxonomic characteristics, strain DCT-5T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter dokdonellae sp. nov. is proposed. The type strain is DCT-5T (= KCTC 49189T = LMG 31284T).

Pusillimonas thiosulfatoxidans sp. nov., a thiosulfate oxidizer isolated from activated sludge.

A Gram-stain-negative, motile bacterium, designated strain YE3T, was isolated from activated sludge obtained from a municipal wastewater treatment plant in Daejeon Metropolitan City, Republic of Korea. The cells were oxidase- and catalase-positive, and grew under aerobic conditions at 10-40 °C (optimum, 30 °C), with 1.0-8.0 % (w/v) NaCl (1.0 %) and at pH 5.5-9.0 (pH 7.0). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YE3T was most closely related to Pusillimonasharenae KACC 14927T (98.2 % sequence similarity) and Pusillimonasginsengisoli KCTC 22046T (98.0 %). DNA-DNA relatedness values for strain YE3T and P. harenae KACC 14927T, P. ginsengisoli KCTC 22046T and P. soli KCTC 22455T were 28.7±2.27 %, 21.3±1.16 %, and 14.0±0.67 %, respectively. The genomic G+C content of the type strain YE3T was 59.3 mol%, as determined by whole-genome sequencing. The dominant fatty acids were C16 : 0 (39.2 %) and C17 : 0cyclo (37.5 %). The major polar lipids of strain YE3T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Two aminophospholipids and four unidentified lipids were also detected. Furthermore, strain YE3T was able to oxidize thiosulfate under heterotrophic conditions. Based on the phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, strain YE3T represents a novel species of the genus Pusillimonas, for which the name Pusillimonas thiosulfatoxidans sp. nov. is proposed. The type strain is YE3T (=KCTC 62737T=NBRC 113113T).