Arsenite Mediates Selenite Resistance and Reduction in Enterobacter sp. Z1, Thereby Enhancing Bacterial Survival in Selenium Environments.

Arsenic (As) is widely present in the environment, and virtually all bacteria possess a conserved ars operon to resist As toxicity. High selenium (Se) concentrations tend to be cytotoxic. Se has an uneven regional distribution and is added to mitigate As contamination in Se-deficient areas. However, the bacterial response to exogenous Se remains poorly understood. Herein, we found that As(III) presence was crucial for Enterobacter sp. Z1 to develop resistance against Se(IV). Se(IV) reduction served as a detoxification mechanism in bacteria, and our results demonstrated an increase in the production of Se nanoparticles (SeNPs) in the presence of As(III). Tandem mass tag proteomics analysis revealed that the induction of As(III) activated the inositol phosphate, butanoyl-CoA/dodecanoyl-CoA, TCA cycle, and tyrosine metabolism pathways, thereby enhancing bacterial metabolism to resist Se(IV). Additionally, arsHRBC, sdr-mdr, purHD, and grxA were activated to participate in the reduction of Se(IV) into SeNPs. Our findings provide innovative perspectives for exploring As-induced Se biotransformation in prokaryotes.

A Coculture of Enterobacter and Comamonas Species Reduces Cadmium Accumulation in Rice.

The accumulation of cadmium (Cd) in plants is strongly impacted by soil microbes, but its mechanism remains poorly understood. Here, we report the mechanism of reduced Cd accumulation in rice by coculture of Enterobacter and Comamonas species. In pot experiments, inoculation with the coculture decreased Cd content in rice grain and increased the amount of nonbioavailable Cd in Cd-spiked soils. Fluorescence in situ hybridization and scanning electron microscopy detection showed that the coculture colonized in the rhizosphere and rice root vascular tissue and intercellular space. Soil metagenomics data showed that the coculture increased the abundance of sulfate reduction and biofilm formation genes and related bacterial species. Moreover, the coculture increased the content of organic matter, available nitrogen, and potassium and increased the activities of arylsulfatase, ß-galactosidase, phenoloxidase, arylamidase, urease, dehydrogenase, and peroxidase in soils. In subsequent rice transcriptomics assays, we found that the inoculation with coculture activated a hypersensitive response, defense-related induction, and mitogen-activated protein kinase signaling pathway in rice. Heterologous protein expression in yeast confirmed the function of four Cd-binding proteins (HIP28-1, HIP28-4, BCP2, and CID8), a Cd efflux protein (BCP1), and three Cd uptake proteins (COPT4, NRAM5, and HKT6) in rice. Succinic acid and phenylalanine were subsequently proved to inhibit rice divalent Cd [Cd(II)] uptake and activate Cd(II) efflux in rice roots. Thus, we propose a model that the coculture protects rice against Cd stress via Cd immobilization in soils and reducing Cd uptake in rice. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Reducing cadmium in rice using metallothionein surface-engineered bacteria WH16-1-MT.

Cadmium (Cd) accumulation in rice grains poses a health risk for humans. In this study, a bacterium, Alishewanella sp. WH16-1-MT, was engineered to express metallothionein on the cell surface. Compared with the parental WH16-1 strain, Cd2+ adsorption efficiency of WH16-1-MT in medium was increased from 1.2 to 2.6 mg/kg dry weight. The WH16-1-MT strain was then incubated with rice in moderately Cd-contaminated paddy soil. Compared with WH16-1, inoculation with WH16-1-MT increased plant height, panicle length and thousand-kernel weight, and decreased the levels of ascorbic acid and glutathione and the activity of peroxidase. Compared with WH16-1, WH16-1-MT inoculation significantly reduced the concentrations of Cd in brown rice, husks, roots and shoots by 44.0 %, 45.5 %, 36.1 % and 47.2 %, respectively. Moreover, inoculation with WH16-1-MT reduced the bioavailability of Cd in soil, with the total Cd proportion in oxidizable and residual states increased from 29 % to 32 %. Microbiome analysis demonstrated that the addition of WH16-1-MT did not significantly alter the original bacterial abundance and community structure in soil. These results indicate that WH16-1-MT can be used as a novel microbial treatment approach to reduce Cd in rice grown in moderately Cd-contaminated paddy soil.

Arsenate-Induced Changes in Bacterial Metabolite and Lipid Pools during Phosphate Stress.

Agrobacterium tumefaciens GW4 is a heterotrophic arsenite-oxidizing bacterium with a high resistance to arsenic toxicity. It is now a model organism for studying the processes of arsenic detoxification and utilization. Previously, we demonstrated that under low-phosphate conditions, arsenate [As(V)] could enhance bacterial growth and be incorporated into biomolecules, including lipids. While the basic microbial As(V) resistance mechanisms have been characterized, global metabolic responses under low phosphate remain largely unknown. In the present work, the impacts of As(V) and low phosphate on intracellular metabolite and lipid profiles of GW4 were quantified using liquid chromatography-mass spectroscopy (LC-MS) in combination with transcriptional assays and the analysis of intracellular ATP and NADH levels. Metabolite profiling revealed that oxidative stress response pathways were altered and suggested an increase in DNA repair. Changes in metabolite levels in the tricarboxylic acid (TCA) cycle along with increased ATP are consistent with As(V)-enhanced growth of A. tumefaciens GW4. Lipidomics analysis revealed that most glycerophospholipids decreased in abundance when As(V) was available. However, several glycerolipid classes increased, an outcome that is consistent with maximizing growth via a phosphate-sparing phenotype. Differentially regulated lipids included phosphotidylcholine and lysophospholipids, which have not been previously reported in A. tumefaciens The metabolites and lipids identified in this study deepen our understanding of the interplay between phosphate and arsenate on chemical and metabolic levels.IMPORTANCE Arsenic is widespread in the environment and is one of the most ubiquitous environmental pollutants. Parodoxically, the growth of certain bacteria is enhanced by arsenic when phosphate is limited. Arsenate and phosphate are chemically similar, and this behavior is believed to represent a phosphate-sparing phenotype in which arsenate is used in place of phosphate in certain biomolecules. The research presented here uses a global approach to track metabolic changes in an environmentally relevant bacterium during exposure to arsenate when phosphate is low. Our findings are relevant for understanding the environmental fate of arsenic as well as how human-associated microbiomes respond to this common toxin.

Hyphomicrobium album sp. nov., isolated from mountain soil and emended description of genus Hyphomicrobium.

A soil bacterium, designated XQ2T, was isolated from Lang Mountain in Hunan province, P. R. China. The strain is Gram stain negative, facultative anaerobic, and the cells are motile and rod-shaped. The 16S rRNA gene sequence of strain XQ2T shared the highest similarities with Hyphomicrobium sulfonivorans S1T (97.1%), Pedomicrobium manganicum ACM 3038T (95.9%) and Hyphomicrobium aestuarii DSM 1564T (95.4%) and grouped with H. sulfonivorans S1T. The average nucleotide identity (ANI) values and the DNA-DNA hybridization (dDDH) values between strain XQ2T and H. sulfonivorans S1T were 86.6% and 55.4% respectively. Strain XQ2T had a genome size of 3.91 Mb and the average G+C content was 65.1%. The major fatty acids (> 5%) were C18:1ω6c, C18:1ω7c, C19:0 cyclo ω8c, C16:0 and C18:0. The major respiratory quinone was Q-9 (82.8%) and the minor one was Q-8 (17.2%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid and two unidentified lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain XQ2T represents a novel species of the genus Hyphomicrobium, for which the name Hyphomicrobium album sp. nov. is proposed. The type strain is XQ2T (= KCTC 82378T = CCTCC AB 2020178T). The genus description is also emended.

Sediminibacterium soli sp. nov., isolated from soil.

A Gram-stain-negative, facultative anaerobic strain, designated WSJ-3T, was isolated from soil. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WSJ-3T belongs to genus Sediminibacterium and exhibits the highest sequence similarities to Sediminibacterium roseum SYL130T (97.0%), Sediminibacterium goheungense DSM 28323T (96.9%), Sediminibacterium aquarii AA5T (96.7%), and Sediminibacterium salmoneum NBRC 103935T (95.2%). The average nucleotide identity values of strain WSJ-3T/S. roseum SYL130T and strain WSJ-3T/S. goheungense DSM 28323T are 72.2% and 70.4%, respectively, and digital DNA-DNA hybridization values for these are 19.2% and 19.1%, respectively. Strain WSJ-3T has a genome size of 3.88 Mb, with a DNA G + C content of 50.1 mol% and comprises of 3263 predicted genes. A phylogenetic tree constructed using the genomic core protein coding sequences revealed that strain WSJ-3T clusters with S. roseum SYL130T. Strain WSJ-3T has menaquinone-7 as the only respiratory quinone and phosphatidylethanolamine, three unidentified phospholipids, four unidentified aminophospholipids, two unidentified aminolipids, and three unidentified lipids as the polar lipids. The major fatty acids of strain WSJ-3T are iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. On the basis of the polyphasic results, the isolate represents a novel species of the genus Sediminibacterium, for which the name Sediminibacterium soli sp. nov. is proposed. The type strain is WSJ-3T (= KCTC 72839T = CCTCC AB 2019408T).

NemA Catalyzes Trivalent Organoarsenical Oxidation and Is Regulated by the Trivalent Organoarsenical-Selective Transcriptional Repressor NemR.

Synthetic aromatic arsenicals such as roxarsone (Rox(V)) and nitarsone (Nit(V)) have been used as animal growth enhancers and herbicides. Microbes contribute to redox cycling between the relatively less toxic pentavalent and highly toxic trivalent arsenicals. In this study, we report the identification of nemRA operon from Enterobacter sp. Z1 and show that it is involved in trivalent organoarsenical oxidation. Expression of nemA is induced by chromate (Cr(VI)), Rox(III), and Nit(III). Heterologous expression of NemA in Escherichia coli confers resistance to Cr(VI), methylarsenite (MAs(III)), Rox(III), and Nit(III). Purified NemA catalyzes simultaneous Cr(VI) reduction and MAs(III)/Rox(III)/Nit(III) oxidation, and oxidation was enhanced in the presence of Cr(VI). The results of electrophoretic mobility shift assays and fluorescence assays demonstrate that the transcriptional repressor, NemR, binds to either Rox(III) or Nit(III). NemR has three conserved cysteine residues, Cys21, Cys106, and Cys116. Mutation of any of the three resulted in loss of response to Rox(III)/Nit(III), indicating that they form an Rox(III)/Nit(III) binding site. These results show that NemA is a novel trivalent organoarsenical oxidase that is regulated by the trivalent organoarsenical-selective repressor NemR. This discovery expands our knowledge of the molecular mechanisms of organoarsenical oxidation and provides a basis for studying the redox coupling of environmental toxic compounds.

Fibrisoma montanum sp. nov., isolated from soil of Mountain Danxia, China.

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium, designated HYT19T, was isolated from soil of Mountain Danxia in southern China. It showed the highest similarity of 16S rRNA gene sequence (97.0%) and formed a monophyletic clade with Fibrisoma limi BUZ 3T. Strain HYT19T grew at 16-37 °C (optimum 28-30 °C) and at pH 6-7. The draft genome size of strain HYT19T was 7.8 Mb with a DNA G+C content of 54.0 mol%. The digital DDH and average nucleotide identity values between strain HYT19T and F. limi BUZ 3T were 28.8% and 85.1%, respectively. MK-7 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, unidentified aminophospholipid, two unidentified aminolipids, unidentified phospholipid and unidentified lipid. The strain contained C16:1ω5c, iso-C15:0, summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0, iso-C17:0 3-OH and anteiso-C15:0 as the major fatty acids. On the basis of phylogenetic, genomic, phenotypic and chemotaxonomic analysis, we propose a new species Fibrisoma montanum sp. nov. of genus Fibrisoma. The type strain is HYT19T (= CCTCC AB 2018342T = JCM 33105T).

Mucilaginibacter hurinus sp. nov., isolated from briquette warehouse soil.

A novel bacterial strain, designated ZR32T, was isolated from briquette warehouse soil in Ulsan (Korea). The strain was aerobic, showing pink-colored colonies on R2A agar. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZR32T was closely related to Mucilaginibacter soli R9-65T (97.0%), Mucilaginibacter gynuensis YC7003T (96.9%), and Mucilaginibacter lutimaris BR-3T (96.8%). The values of DNA-DNA relatedness related two highest strains M. soli R9-65T and M. gynuensis YC7003T were 31.2 ± 6.9% and 19.7 ± 0.3%, respectively. Its genome size was 3.9 Mb, comprising 3402 predicted genes. The DNA G+C content of strain ZR32T was 43.0 mol%. The major cellular fatty acids (> 5% of total) were summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0, C16:1ω5c, iso-C15:0, iso-C17:0 3-OH, and C17:1ω9c. The major respiratory quinine was menaquinone-7 (MK-7). The major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, one unidentified sphingolipid, and one unidentified polar lipid. Strain ZR32T showed distinctive characteristics such as the temperature and pH for growth ranges, being positive for ß-glucosidase, salicin production, negative for N-acetyl-glucosamine assimilation, being resistant to carbenicillin and piperacillin to related species. On the basis of phenotypic, chemotaxonomic, and phylogenetic data, strain ZR32T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter hurinus sp. nov. is proposed. The type strain is ZR32T (= KCTC 62193 = CCTCC AB 2017285).

Larkinella punicea sp. nov., isolated from manganese mine soil.

Strain ZZJ9T is a Gram-stain-negative, rod-shaped, aerobic bacterium isolated from manganese mine soil. Strain ZZJ9T showed the highest 16S rRNA gene sequence similarities with Larkinella rosea 15J16-1T3AT (97.1%), Larkinella terrae 15J8-8T (97.0%), Larkinella knui 15J6-3T6T (96.8%), and Larkinella ripae 15J11-1T (95.3%). The genome size of strain ZZJ9T was 8.01 Mb and the DNA G+C content was 51.8 mol%. ANI values among strain ZZJ9T and Larkinella rosea 52004 T, Larkinella knui KCTC 42998T, and Larkinella terrae 52001T were 80.5%, 82.7%, and 80.5%, respectively. dDDH values among strain ZZJ9T and Larkinella rosea 52004T, Larkinella knui KCTC 42998T, and Larkinella terrae 52001T were 23.5%, 26.0%, and 23.6%, respectively. Furthermore, the genome of strain ZZJ9T contained 6302 predicted protein-coding genes and 3114 (49%) of them had classificatory functions. The major quinone of strain ZZJ9T was menaquinone-7 and the main cellular fatty acids were C16:1ω5c (39.5%), iso-C15:0 (25.6%), and iso-C17:0 3OH (11.5%). The polar lipids of strain ZZJ9T were phosphatidylethanolamine, unidentified lipid, and two unidentified aminolipids. Based on the results of phylogenetic, genome, phenotypic, and chemotaxonomic analytical, strain ZZJ9T represents a novel species of the genus Larkinella, for which the name Larkinella punicea sp. Nov. is proposed. The type strain is ZZJ9T (= KCTC 62876T = CCTCC AB 2018215T).

Luteimonas gilva sp. nov., isolated from farmland soil.

A Gram-stain-negative, rod-shaped bacterium, strain H23T, was isolated from farmland soil sampled in Enshi City, Hubei Province, PR China. The isolate grew optimally at 28-32 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain H23T belonged to the genus Luteimonas with the highest degree of 16S rRNA gene sequence similarity to Luteimonas cucumeris Y4T (97.41 %). The DNA G+C content was 65.88 mol%. The average nucleotide identity and the Genome-to-Genome Distance Calculator results also showed low relatedness (below 95 and 70 %, respectively) between strain H23T and type strains in the genus Luteimonas. Ubiquinone-8 was the predominant quinone. The major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1 ω9c. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified phospholipids. Low digital DNA-DNA hybridization values, as well as physiological and biochemical differences, such as no casein hydrolysis, being catalase-negative, and tesing positive for cystine arylamidase, α-chymotrypsin and N-acetyl-ß-glucosaminidase, could distinguish strain H23T from its closely related species. Strain H23T is considered to represent a novel species in the genus Luteimonas, for which the name Luteimonas gilva sp. nov. is proposed, with strain H23T (=CCTCC AB 2019255T=KCTC 72593T) as the type strain.

Sphingomonas montanisoli sp. nov., isolated from mountain soil.

A soil bacterium, designated ZX9611T, was isolated from Taihang Mountain in Henan province, PR China. The strain was Gram-stain-negative and strictly aerobic. The cells were motile, rod-shaped and formed light pink-colored colonies. The 16S rRNA gene sequence of ZX9611T shared the highest similarities with those of Sphingomonas crocodyli CCP-7T (97.0%), Sphingomonas jatrophae S5-249T (96.6%) and Sphingomonas starnbergensis 382T (95.9%). Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that ZX9611T clustered with S. crocodyli CCP-7T, S. jatrophae S5-249T and S. starnbergensis 382T. The average nucleotide identity (ANI) values between ZX9611T and two type strains (S. crocodyli BCRC 81096T and S. jatrophae DSM 27345T) were 88.3 and 68.6% respectively. ZX9611T exhibited genome-sequence-based digital DNA-DNA hybridization (dDDH) values of 53.3 % and 15.3 %, compared with S. crocodyli BCRC 81096T and S. jatrophae DSM 27345T, respectively. ZX9611T had a genome size of 4.12 Mb and an average DNA G+C content of 64.8 %. ZX9611T had major fatty acids (>5 %) including summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and the major polyamine was sym-homospermidine. The only respiratory quinone was ubiquinone-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZX9611T represents a novel species of genus Sphingomonas, for which the name Sphingomonas montanisoli sp. nov. is proposed. The type strain is ZX9611T (=KCTC 72622T=CCTCC AB 2019350T).

Runella aurantiaca sp. nov., isolated from sludge of a manganese mine.

A Gram-stain-negative, filamentous rod-shaped, aerobic and non-motile strain, YX9T, was isolated from sludge of a manganese mine. Analysis of the 16S rRNA gene sequence revealed that strain YX9T formed the same branch within the members of the genus Runella and showed high relatedness to Runella slithyformis DSM 19594T (98.1 %), Runella palustris HMF3829T (96.0 %) and Runella zeae NS12T (95.4 %). The genome length of strain YX9T was 7.21 Mb, had 5985 coding sequences and a DNA G+C content of 44.8 mol%. The average nucleotide identity value of the draft genomes between strain YX9T and R. slithyformis DSM 19594T was 80.7 %. The major fatty acids of strain YX9T were iso-C15 : 0, C16:1 ω5c and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant respiratory quinone was menaquinone 7. The polar lipids of strain YX9T were phosphatidylethanolamine, four unidentified lipids, two aminolipids, a phospholipid and a glycolipid. Based on the results of genotypic and phenotypic studies, strain YX9T represents a novel species within the genus Runella, for which the name Runellaaurantiaca sp. nov. is proposed (=KCTC 62875T=CCTCC AB 2018214T).

Immobilization of Cd Using Mixed Enterobacter and Comamonas Bacterial Reagents in Pot Experiments with Brassica rapa L.

Enterobacter sp. A11 and Comamonas sp. A23 were isolated and identified. Coculturing these two strains with Cd(II) led to the production of biofilm, H2S, and succinic acid (SA), and Cd(II) was adsorbed by cells and formed CdS precipitates. After centrifugation, 97% Cd(II) was removed from the coculture. Proteomic and metabolomic analyses of the cocultured bacteria revealed that H2S and SA production pathways, metal transportation, and TCA cycle were active under Cd(II) stress. In vitro addition of SA enhanced the production of H2S and biofilm formation and Cd(II) adsorption. Two-season greenhouse pot experiments with Brassica rapa L. were performed with and without the coculture bacteria. Compared with the control, the average Cd amounts of the two-season pot experiments of the aboveground plants were decreased by 71.3%, 62.8%, and 38.6%, and the nonbioavailable and immobilized Cd in the soils were increased by 211.8%, 213.4%, and 116.7%, for low-, medium-, and high- Cd-spiked soils, respectively. The two strains survived well in soil during plant growth using plate counting, quantitative real-time PCR, and metagenomics analysis. Our results indicate that the combination of Enterobacter and Comamonas strains with the production of H2S and biofilm are important effectors for the highly efficient immobilization of Cd.

Surfactants Enhanced Soil Arsenic Phytoextraction Efficiency by Pteris vittata L.

Soil arsenic (As) pollution has become a global problem. It is urgent to improve the phytoextraction efficiency of soil As. This study found chemical activators (Span 80/SDS and GSH/Span 80/SDS) that can significantly improve the availability of As and the phytoextraction efficiency of As by Pteris vittata L. in As-contaminated soil. Compared with the control, in the soil screening experiment, Span 80/SDS and GSH/Span 80/SDS significantly increased available As in soil by 73.4% and 81.4%, respectively. And in the soil pot experiment, the Span 80/SDS and GSH/Span 80/SDS significantly increased the As concentration in the pinnae of Pteris vittata L. by 53.4% and 41.2%, respectively, and the total As amount extraction by Pteris vittata L. increased significantly by 31.7% and 94.2%, respectively. The results suggest that adding Span 80/SDS and GSH/Span 80/SDS to As-contaminated soil can be considered as an effectively method to improve the efficiency of phytoextraction.

Transcriptomics analysis defines global cellular response of Agrobacterium tumefaciens 5A to arsenite exposure regulated through the histidine kinases PhoR and AioS.

In environments where arsenic and microbes coexist, microbes are the principal drivers of arsenic speciation, which directly affects bioavailability, toxicity and bioaccumulation. Speciation reactions influence arsenic behaviour in environmental systems, directly affecting human and agricultural exposures. Arsenite oxidation decreases arsenic toxicity and mobility in the environment, and therefore understanding its regulation and overall influence on cellular metabolism is of significant interest. The arsenite oxidase (AioBA) is regulated by a three-component signal transduction system AioXSR, which is in turn regulated by the phosphate stress response, with PhoR acting as the master regulator. Using RNA-sequencing, we characterized the global effects of arsenite on gene expression in Agrobacterium tumefaciens 5A. To further elucidate regulatory controls, mutant strains for histidine kinases PhoR and AioS were employed, and illustrate that in addition to arsenic metabolism, a host of other functional responses are regulated in parallel. Impacted functions include arsenic and phosphate metabolism, carbohydrate metabolism, solute transport systems and iron metabolism, in addition to others. These findings contribute significantly to the current understanding of the metabolic impact and genetic circuitry involved during arsenite exposure in bacteria. This informs how arsenic contamination will impact microbial activities involving several biogeochemical cycles in nature.

Pedobacter paludis sp. nov., isolated from wetland soil.

A Gram-stain-negative, aerobic, non-motile, rod-shaped and non-spore-forming bacterium, designated YXT, was isolated from wetland soil. Compared to strain YXT, Pedobacter yonginense HMD1002T had the highest 16S rRNA gene sequence identity (97.8%), and the remaining strains had the identities below 97%. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain YXT grouped with P. yonginense HMD1002T. The values of DNA-DNA hybridization and genomic orthologous average nucleotide identity (orthoANI) between strain YXT and Pedobacter yonginense KCTC 22721T were 58.5% and 82.0%, respectively. The genome size of strain YXT was 5.0 Mb, comprising 4369 predicted genes with a DNA G+C content of 37.3 mol %. Strain YXT had menaquinone-7 as the only respiratory quinone and polar lipids of phosphatidylethanolamine, sphingolipid, aminolipid and three unidentified lipids. The predominant cellular fatty acids (> 10%) of strain YXT were summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c), iso-C15:0 and iso-C17:0 3-OH. Strain YXT could be distinguished from the other Pedobacter members based on the data of phylogenetic distance, DNA-DNA hybridization, genomic orthoANI, RecA MLSA, core-protein comparison, and hydrolyses of L-arginine, utilization of D/L-lactate, L-alanine, 5-ketonic gluconate and glycogen. Therefore, strain YXT represents a novel species of the genus Pedobacter, for which the name Pedobacter paludis sp. nov. is proposed. The type strain is YXT (= KCTC 62520T = CCTCC AB 2018029T).

Sphingosinicella humi sp. nov., isolated from arsenic-contaminated farmland soil and emended description of the genus Sphingosinicella.

A Gram-stain-negative, strictly aerobic bacterium, designated strain QZX222T, was isolated from arsenic-contaminated farmland soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QZX222T was clustered with Sphingosinicella vermicomposti YC7378T (97.0 %), Sphingosinicellaxenopeptidilytica 3-2W4T (96.1 %), Sphingosinicella microcystinivorans Y2T (96.0 %) and Sphingosinicella soli KSL-125T (95.9 %). Compared to strain QZX222T, Spingomonas olgophenolica JCM 12082T and Sphingobium boeckii 469T had 16S rRNA gene similarities of 96.2 and 95.9 %, respectively, but they located in other phylogenetic clusters. DNA-DNA hybridization and genomic ANI values between strain QZX222T and Sphingosinicella vermicomposti DSM 21593T (KCTC 22446T) were 34.8 and 75.0 %, respectively. The genome size of strain QZX222T was 3.0 Mb including 2982 predicted genes. The strain had a DNA G+C content of 65.9 mol%. Strain QZX222T had ubiquinone Q-10 as the major respiratory quinone and homospermidine as the major polyamine. The major fatty acids (>10 %) of strain QZX222T were C17 : 1ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 1ω8c. The polar lipids were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. Strain QZX222T could be distinguished from other Sphingosinicella strains based on the results of phylogenetic and genomic analyses, DNA-DNA hybridization, white colour colony, hydrolysis of urea, alkaline phosphatase activity, lack of phosphatidylmonomethylethanolamine, and presence of phosphatidylcholine. Therefore, strain QZX222T represents a novel species of Sphingosinicella, for which the name Sphingosinicellahumi sp. nov. is proposed. The type strain is QZX222T (=KCTC 62519T=CCTCC AB 2018030T).

Nocardioides gansuensis sp. nov., isolated from geopark soil.

A novel bacterial strain, designated WSJ-1T, was isolated from geopark soil in Gansu province, PR China. The highest 16S rRNA gene sequence similarities were to those of Nocardioides sediminis MSL-01T (97.10 %), Nocardioides aquiterrae GW-9T (97.08 %) and Nocardioides terrigena DS-17T (96.94 %). Strain WSJ-1T grouped with N. terrigena DS-17T and N. sediminis MSL-01T in 16S rRNA gene-based phylogenetic trees. The DNA-DNA relatedness of WSJ-1T/N. sediminis JCM19559T and WSJ-1T/N. aquiterrae JCM11813T were 44.8 and 29.2 %, respectively. Average nucleotide identity values of whole genome sequences of WSJ-1T/N. terrigena KCTC19217T and WSJ-1T/N. sediminis KCTC19271T were 78.83 and 78.83 %, respectively. Its genome size was 4.76 Mb, comprising 4517 predicted genes with a DNA G+C content of 70.9 %. Strain WSJ-1T contained menaquinone-8(H4) as the major respiratory quinone and ll-2,6-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. The major cellular fatty acids were iso-C16 : 0, C18 : 1ω9c and C17 : 1ω8c. Based on the polyphasic analyses, the isolate is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioidesgansuensis sp. nov. is proposed. The type strain is WSJ-1T (=KCTC 49117T=CCTCC AB 2018027T).

Nocardioides silvaticus sp. nov., isolated from forest soil.

A Gram-stain-positive, non-motile, rod-shaped bacterial strain S-34T was isolated from forest soil. According to 16S rRNA gene sequence analysis, strain S-34T was related to Nocardioides members and showed the highest similarities to Nocardioides thalensis NCCP-696T (97.3 %) and Nocardioides panacisoliGsoil 346T (97.0 %), Nocardioides litorisoli X-2T (96.5 %) and Nocardioides immobilis FLL521T (96.4 %). Phylogenetic trees showed that strain S-34T fell within the cluster containing strain S-34T and N. immobilis FLL521T. The levels of DNA-DNA relatedness between strain S-34T and N. thalensis CCTCC AB 2016296T and between strain S-34T and N. panacisoli KCTC 19470T were 50.6 and 58.8 %, respectively. The genome orthoANI value between strain S-34T and N. immobilis CCTCC AB 2017083T was 82.4 %. Strain S-34T had ll-diaminopimelic acid in the cell-wall peptidoglycan, diphosphatidylglycerol, phosphatidylglycerol, four unknown phospholipids and one unknown lipid as the polar lipids, meanquinone-8(H4) as the only respiratory quinone and iso-C16 : 0, C17:1ω8c, C17:1ω6c, C17 : 0 and C17 : 0 10-methyl (tbsa) as the major fatty acids. The genome length of strain S-34T was 4.53 Mb containing 52 contigs and with a DNA G+C content of 71.2 mol%. Strain S-34T could be distinguished from the other Nocardioides members mainly based on the data of phylogenetic analyses, DNA-DNA hybridization, polar lipids and some biochemical differences. Therefore, strain S-34T represents a novel species of the genus Nocardioides, for which the name Nocardioidessilvaticus sp. nov. is proposed. The type strain is S-34T (=KCTC 49137T=CCTCC AB 2018079T).