Gemmobacter denitrificans sp. nov., a denitrifying bacterium, isolated from pond water for Litopenaeus vannamei.

A novel Gram-stain-negative strain, designated JM10B15T, was isolated from pond water for Litopenaeus vannamei collected from Jiangmen City, Guangdong province, south PR China. Cells of the strain were aerobic, rod-shaped, and motile by lateral flagella. JM10B15T could grow at 15-40 °C, pH 6.0-9.5, and in 0-3.0 % NaCl, with optimal growth at 25-35 °C, pH 7.5-8.5, and in 0 % NaCl, respectively. Furthermore, this strain grew well on Reasoner's 2A agar but not on nutrient broth agar or Luria-Bertani agar. JM10B15T was a denitrifying bacterium capable of removing nitrites and nitrates, and three key functional genes, nasA, nirS, and nosZ, were identified in its genome. The results of phylogenetic analyses based on the 16S rRNA gene and genome sequences indicated that JM10B15T belonged to the genus Gemmobacter. JM10B15T showed the highest 16S rRNA sequence similarity to Gemmobacter lutimaris YJ-T1-11T (98.8 %), followed by Gemmobacter aquatilis IFAM 1031T (98.6 %) and Gemmobacter serpentinus HB-1T (98.1 %). The average nucleotide identity and digital DNA-DNA hybridization values between JM10B15T and the other type strains of genus Gemmobacter were 78.1-82.1 % and 18.4-22.1 %, respectively. The major fatty acids of strain JM10B15T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and C18 : 1 ω7c 11-methyl. In addition, the major respiratory quinone of this novel strain was Q-10, and the predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, four unidentified phospholipids, three unidentified lipids, and an unidentified aminophospholipid. Results of analyses of the phylogenetic, genomic, physiological, and biochemical characteristics indicated that JM10B15T represents a novel species of the genus Gemmobacter, for which the name Gemmobacter denitrificans sp. nov. is proposed. The type strain is JM10B15T (=GDMCC 1.4148T=KCTC 8140T).

Sinomonas terricola sp. nov., a plant-beneficial bacterium isolated from litchi rhizosphere soil in Guangdong, China.

A novel plant-beneficial bacterium strain, designated as JGH33T, which inhibited Peronophythora litchii sporangia germination, was isolated on Reasoner's 2A medium from a litchi rhizosphere soil sample collected in Gaozhou City, Guangdong Province, PR China. Cells of strain JGH33T were Gram-stain-positive, aerobic, non-motile, bent rods. The strain grew optimally at 30-37 °C and pH 6.0-8.0. Sequence similarity analysis based on 16S rRNA genes indicated that strain JGH33T exhibited highest sequence similarity to Sinomonas albida LC13T (99.2 %). The genomic DNA G+C content of the isolate was 69.1 mol%. The genome of JGH33T was 4.7 Mbp in size with the average nucleotide identity value of 83.45 % to the most related reference strains, which is lower than the species delineation threshold of 95 %. The digital DNA-DNA hybridization of the isolate resulted in a relatedness value of 24.9 % with its closest neighbour. The predominant respiratory quinone of JGH33T was MK-9(H2). The major fatty acids were C15 : 0 anteiso (43.4 %), C16 : 0 iso (19.1 %) and C17 : 0 anteiso (19.3 %), and the featured component was C18 : 3 ω6c (1.01 %). The polar lipid composition of strain JGH33T included diphosphatidylglycerol, phosphatidylglycerol, dimannosylglyceride, phosphatidylinositol and glycolipids. On the basis of polyphasic taxonomy analyses data, strain JGH33T represents a novel species of the genus Sinomonas, for which the name Sinomonas terricola sp. nov. is proposed, with JGH33T (=JCM 35868T=GDMCC 1.3730T) as the type strain.

Altererythrobacter litoralis sp. nov., a New Carotenoid-Producing Member of the Family Erythrobacteraceae, Isolated from a Tidal Flat Sediment.

A new isolate designated as 1XM1-14T was isolated from a tidal flat sediment of Xiamen Island. The yellow-pigmented colonies and rod-shaped cells were observed. Strain 1XM1-14T could hydrolyze Tweens 20, 40, 60, aesculin, and skim milk, and was chemoheterotrophic and mesophilic, required NaCl for the growth. The 16S rRNA gene-based phylogenetic analysis indicated that strain 1XM1-14T was the most closely related to Altererythrobacter epoxidivorans CGMCC 1.7731T (97.0%), followed by other type strain of the genus Altererythrobacter with identities below 97.0%. The DNA-DNA hybridization and average nucleotide identity values between strain 1XM1-14T and its relatives of the genus Altererythrobacter were below the respective thresholds for prokaryotic species demarcation. The phylogenomic inference further revealed that strain 1XM1-14T formed a separate branch distinct from the type strains of the recognized species within the genus Altererythrobacter. The major cellular fatty acids of strain 1XM1-14T were identified as summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), C17:1 ω6c, and C16:0; the profile of polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified glycolipid, and two unidentified lipids; the respiratory quinone was determined to ubiquinone-10. The genomic size and DNA G+C content of strain 1XM1-14T were 2.5 Mbp and 62.71%. The key carotenoid biosynthetic genes were determined in the genome of strain 1XM1-14T and the generated carotenoids were detected. The combined genotypic and phenotypic characteristics supported the classification of strain 1XM1-14T (= GDMCC 1.2383T = KCTC 82612T) as a novel species in the genus Altererythrobacter, for which the name Altererythrobacter litoralis sp. nov. is proposed.

Semiquantitative Fingerprinting Based on Pseudotargeted Metabolomics and Deep Learning for the Identification of Listeria monocytogenes and Its Major Serotypes.

The rapid identification of pathogenic microorganism serotypes is still a bottleneck problem to be solved urgently. Compared with proteomics technology, metabolomics technology is directly related to phenotypes and has higher specificity in identifying pathogenic microorganism serotypes. Our study combines pseudotargeted metabolomics with deep learning techniques to obtain a new deep semiquantitative fingerprinting method for Listeria monocytogenes identification at the serotype levels. We prescreened 396 features with orthogonal partial least-squares discrimination analysis (OPLS-DA), and 200 features were selected for deep learning model building. A residual learning framework for L. monocytogenes identification was established. There were 256 convolutional filters in the initial convolution layer, and each hidden layer contained 128 filters. The total depth included seven layers, consisting of an initial convolution layer, a residual layer, and two final fully connected classification layers, with each residual layer containing four convolutional layers. In addition, transfer learning was used to predict new isolates that did not participate in model training to verify the method's feasibility. Finally, we achieved prediction accuracies of L. monocytogenes at the serotype level exceeding 99%. The prediction accuracy of the new strain validation set was greater than 97%, further demonstrating the feasibility of this method. Therefore, this technology will be a powerful tool for the rapid and accurate identification of pathogens.

Wavelength-shift-free racetrack resonator hybrided with phase change material for photonic in-memory computing.

The photonic in-memory computing architecture based on phase change materials (PCMs) is increasingly attracting widespread attention due to its high computational efficiency and low power consumption. However, PCM-based microring resonator photonic computing devices face challenges in terms of resonant wavelength shift (RWS) for large-scale photonic network. Here, we propose a PCM-slot-based 1 × 2 racetrack resonator with free wavelength shift for in-memory computing. The low-loss PCMs such as Sb2Se3 and Sb2S3 are utilized to fill the waveguide slot of the resonator for the low insertion (IL) and high extinction ratio (ER). The Sb2Se3-slot-based racetrack resonator has an IL of 1.3 (0.1) dB and an ER of 35.5 (8.6) dB at the drop (through) port. The corresponding IL of 0.84 (0.27) dB and ER of 18.6 (10.11) dB are obtained for the Sb2S3-slot-based device. The change in optical transmittance of the two devices at the resonant wavelength is more than 80%. No shift of the resonance wavelength can be achieved upon phase change among the multi-level states. Moreover, the device exhibits a high degree of fabrication tolerance. The proposed device demonstrates ultra-low RWS, high transmittance-tuning range, and low IL, which provides a new scheme for realizing an energy-efficient and large-scale in-memory computing network.

Characterization of phytopathogen-preying Hyalangium versicolor sp. nov., and proposal for the reclassification of Cystobacter gracilis as Hyalangium gracile comb. Nov.

A Gram-staining-negative, aerobic, and rod-shaped with tapered end myxobacterium, designed as strain H56D21T, was isolated from forest soil sampled from the Diaoluo Mountain National Nature Reserve located in Hainan Province, PR China. It showed prey ability on two kinds of phytopathogens including both fungi (Fusarium solani, Fusarium graminearum, and Fusarium oxysporum) and bacteria (Ralstonia solanacearum and Xanthomonas campestris). Phylogenetic analyses based on the 16S rRNA gene and core genes  sequences revealed that strain H56D21T belonged to the genus Hyalangium and was most closely related to Cystobacter gracilis DSM 14753 T and Hyalangium minutum DSM 14724 T. Genome comparison showed 85.6% and 82.3% of average nucleotide identity between strain H56D21T and the above two type strains and 29.8% and 25.1% of digital DNA-DNA hybridization , respectively. The novel strain had a large genome size of 13.56 Mbp and a high  DNA G + C content of 67.1%. Genome annotation identified 46 secondary metabolite biosynthesis gene clusters and 187 CAZymes-encoding genes. The major fatty acids contained iso-C15:0, iso-C15:0 DMA, C16:1 ω5c, and iso-C17:0. The dominant respiratory quinone was menaquinone 8. Based on the phenotypic, chemotaxonomic and phylogenetic analyses, we suggested that strain H56D21T should represent a novel species of the genus Hyalangium with a proposed name of Hyalangium versicolor sp. nov. (type strain H56D21T = GDMCC 1.1944 T = KCTC 82613 T) and Cystobacter gracilis should be reclassified as Hyalangium gracile comb. nov.

Description of Xanthocytophaga agilis sp. nov. and Xanthocytophaga flavus sp. nov. of the new genus Xanthocytophaga gen. nov and the proposal of Rhodocytophagaceae fam. nov. within the order Cytophagales.

Four Gram-staining-negative, aerobic, yellow-pigmented and rod-shaped bacteria, named strains BD1B2-1T, NT2B1T, YF14B1 and DM2B3-1, were isolated from four rhizosphere soil samples of banana in China. Comparison of the 16S rRNA gene sequences showed that all these strains were most closely related to an invalidly published species, 'Rhodocytophaga rosea' 172606-1, with similarities ranging from 87.7 to 88.0%. According to the phylogenomic analysis, the four strains were clustered in an independent lineage and closely related to the genus Rhodocytophaga. The genomic sizes of these strains were approximately 9.49-9.77 Mbp with the DNA G + C contents of 38.8-39.0 mol%. They all contained C16:1 ω5c, iso-C15:0 and iso-C17:0 3-OH as the major fatty acids and menaquinone 7 as the only respiratory quinone. They all had phosphatidylethanolamine as the major polar lipids. Based on phenotypic and phylogenomic characteristics, the four strains should represent two novel species within a novel genus, for which the names Xanthocytophaga agilis gen. nov., sp. nov. (BD1B2-1T = GDMCC 1.2890T = JCM 35374T) and Xanthocytophaga flavus sp. nov. (NT2B1T = GDMCC 1.2889T = JCM 35375T) are proposed; the former is assigned as the type species of the novel genus Xanthocytophaga gen. nov. In addition, based on the phenotypic and phylogenomic data, we proposed to reclassify the existing genus Rhodocytophaga in the family Cytophagaceae into a novel family Rhodocytophagaceae fam. nov. The novel family consists of the type genus Rhodocytophaga and the novel genus Xanthocytophaga.

Status of 18F-PSMA-1007-PET/CT compared with multiparametric MRI in preoperative evaluation of prostate cancer.

PURPOSE: Treatment of primary prostate cancer extremely depends on preoperative stage. The role of 18F-1007-PSMA-PET/CT in preoperative staging has not been well defined. Our aim was to compare the diagnostic performance of 18F-1007-PEMA-PET/CT, mpMRI, and mpMRI + PEMA-PET/CT in local progression and lymph node invasion of prostate cancer using histopathology as the gold standard. MATERIALS AND METHODS: In this retrospective study, all patients with prostate cancer who underwent mpMRI and 18F-PSMA-1007-PET/CT before operation were included. The role of preoperative imaging was evaluated by predicting the sensitivity and specificity of EPE (extraprostatic extension), SVI (seminal vesicle invasion), and lymph node invasion results. RESULTS: Ultimately, 130 patients were included in this study. In the preoperative judgment of EPE and SVI, mpMRI + PSMA-PET/CT had higher sensitivity and specificity. When predicting lymph node metastasis, PSMA-PET/CT was the best choice. The accuracy of mpMRI + PSMA-PET/CT and PSMA-PET/CT in the T and N stages, respectively, was affected by the least factors. CONCLUSIONS: Based on the combined results of mpMRI and 18F-1007-PSMA-PET/CT, the accuracy of the preoperative judgment of prostatic capsule invasion can be improved, which may be conducive to developing intra-fascial technology while ensuring no tumor-touch isolation. PSMA-PET/CT has the advantages over mpMRI alone in terms of lymph node positivity. Compared with PSMA-PET/CT alone, the combined results can improve the sensitivity, but reduce specificity. Therefore, it is recommended to focus on PSMA-PET/CT to decide whether lymph node dissection should be performed.

Gimibacter soli gen. nov. sp. nov., isolated from mangrove soil and insight into its ecological distribution and metabolic potential.

A Gram-stain-negative, facultatively anaerobic, motile and rod-shaped bacterium, designated as 6D33T, was isolated from mangrove soil. Growth was found to occur at 15-32 °C (optimum, 28 °C), at pH 6-9 (optimum, pH 7) and in 0-3 % NaCl (optimum, 1 %, w/v). The results of 16S rRNA gene-based analysis showed that strain 6D33T belonged to the family Temperatibacteraceae, sharing 93.1-94.4 % identity with its close neighbours within the genus Kordiimonas. The phylogenomic results indicated that strain 6D33T formed an independent branch distinct from type strains of the genus Kordiimonas. The overall genome relatedness indices of digital DNA-DNA hybridization, average nucleotide identity and amino acid identity values showed that strain 6D33T represents a novel species of a novel genus. The results of chemotaxonomic characterization indicated that the major cellular fatty acids of strain 6D33T were summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1 ω9c), summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C15 : 0; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and three unidentified lipids; the only respiratory quinone was ubiquinone-10. The genomic size and DNA G+C contents were 3.59 Mbp and 60.84 mol%, respectively. The 16S rRNA gene sequence reads abundance profiles revealed that the rare taxon is prevalent in marine environments, especially in sediments. Genome-scale metabolic reconstruction of strain 6D33T revealed a heterotrophic lifestyle and many pathways responsible for the degradation of aromatic compounds, suggesting application potential in aromatic hydrocarbon removal. Based on its genotypic and phenotypic characteristics, strain 6D33T is concluded to represent a novel species of the novel genus in the family Temperatibacteraceae, for which the name Gimibacter soli gen. nov. sp. nov. is proposed. The type strain of the type species is 6D33T (=GDMCC 1.1959T=KCTC 82335T).

Sphingomonas lycopersici sp. nov., isolated from tomato rhizosphere soil.

Two aerobic, Gram-stain-negative, non-motile and non-spore-forming rods bacterial strains, designated MMSM20T and MMSM24, were isolated from tomato rhizosphere soil and could produce indole-3-acetic acid and siderophore. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that strains MMSM20T and MMSM24 belonged to the genus Sphingomonas and were most closely related to three validly published species Sphingomonas jeddahensis G39T, Sphingomonas mucosissima DSM 17494T and Sphingomonas dokdonensis DSM 21029T. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains MMSM20T and MMSM24 were 97.6 and 81.0 %, respectively, demonstrating that they were conspecific. The ANI and dDDH values between the two strains and the three type strains above were below the threshold values for species delimitation. The genomic DNA G+C contents of strains MMSM20T and MMSM24 were 66.6 and 66.4 mol%, respectively. The major fatty acids of the two strains were identified as C14 : 0 2OH, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c); the predominant quinone was ubiquinone 10; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and unidentified lipids. Results of phenotypic and genotypic analyses supported that strains MMSM20T and MMSM24 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lycopersici sp. nov. is proposed. The type strain is MMSM20T (=GDMCC 1.3401T=JCM 35647T).

Dyella humicola sp. nov., Dyella subtropica sp. nov., Dyella silvatica sp. nov. and Dyella silvae sp. nov., isolated from subtropical forest soil.

Four novel bacterial strains, designated RBB1W86T, RXD159T, RBB189T and RLT163T, were isolated from subtropical forest soil of the Nanling National Nature Reserve located in Guangdong Province, PR China. 16S rRNA gene phylogeny indicated their affiliation to the genus Dyella, among which strains RBB1W86T and RXD159T were closely related to Dyella halodurans CGMCC 1.15435T with 16S rRNA gene sequence similarities of 98.8 and 99.5 %, respectively, and strains RBB189T and RLT163T were closely related to Dyella tabacisoli CGMCC 1.16273T (98.8 %) and Dyella japonica JCM 21530T (99.4 %), respectively. Phylogenomic analysis based on 92 core genes showed consistent phylogeny with the 16S rRNA gene phylogeny for strains RBB1W86T, RBB189T and RLT163T, while strain RXD159T showed a closer relationship with D. tabacisoli CGMCC 1.16273T and strain RBB189T. The genome-derived average nucleotide identity (ANI) values between the newly isolated strains and their closely related species were 70.18‒90.20 %, and the corresponding digital DNA-DNA hybridization (dDDH) values were 20.80‒40.30 %. Meanwhile, the ANI and dDDH values between each pair of the newly isolated strains were 75.80‒79.77 % and 21.30‒23.30 %, respectively. They all took iso-C15 : 0 and summed feature 9 (10-methyl C16  : 0 and/or iso-C17  : 1 ω9c) as the major fatty acids. Moreover, C16 : 0, iso-C16 : 0, iso-C17 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) were also variously distributed as major components. They all took ubiquinone 8 as the only predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Phosphatidylmethylethanolamine was only present in strain RBB189T as another major component. Based on the results of phenotypic, genotypic and chemotaxonomic analyses, the newly isolated strains could be clearly distinguished from their closely related species and should represent four distinct novel species of the genus Dyella, for which the names Dyella humicola sp. nov. (type strain RBB1W86T=GDMCC 1.1901T=KACC 21988T), Dyella subtropica sp. nov. (type strain RXD159T=GDMCC 1.1902T=KACC 21989T), Dyella silvatica sp. nov. (type strain RBB189T=GDMCC 1.1900T=KACC 21990 T) and Dyella silvae sp. nov. (type strain RLT163T=GDMCC 1.1916T=KACC 21991T) are proposed.

Marivirga aurantiaca sp. nov., a halophilic nitrite-reducing bacterium, isolated from intertidal surface sediments.

A novel Gram-stain-negative strain, designated S37H4T, was isolated from an intertidal surface sediment sample collected from Zhanjiang City, Guangdong province, south PR China. Cells of the strain were aerobic, non-flagellated, long rod-shaped and motile by gliding. S37H4T could grow at 4-40 °C, pH 7.0-8.5 and in 2.0-15.0 % NaCl, with optimal growth at 25-30 °C, pH 7.5 and 9.0 % NaCl, respectively. S37H4T was capable of nitrite removal under high-salt conditions, and there were three denitrification genes, nirK, norB and nosZ, in its genome. The results of phylogenetic analyses based on the 16S rRNA gene and genome sequences indicated that S37H4T represented a member of the genus Marivirga and formed a subclade with Marivirga lumbricoides JLT2000T. S37H4T showed the highest 16S rRNA sequence similarity to M. lumbricoides JLT2000T (98.3 %) and less than 97.0 % similarity with other type strains of species of the genus Marivirga. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between S37H4T and the reference type strains of species of the genus Marivirga were 70.7-74.3 % and 18.2-19.2 %, respectively. The major fatty acids of S37H4T were iso-C15 : 0, iso-C15 : 1G, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The major respiratory quinone of this novel strain was MK-7, and the predominant polar lipids were identified as phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and three unidentified lipids. The results of analyses of phylogenetic, genomic, physiological and biochemical characteristics indicated that S37H4T represented a novel species of the genus Marivirga, for which the name Marivirga aurantiaca sp. nov. is proposed. The type strain is S37H4T (= GDMCC 1.1866T = KACC 21922T).

Tahibacter harae sp. nov., isolated from pig farm soil in Guangdong, PR China.

In the process of exploring the microbial diversity of pig farms, a Gram-stain-negative, aerobic, rod-shaped, non-spore-forming, non-motile bacterial strain, designated P2KT, was isolated from soil sample collected at a pig farm, Guangdong Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain P2KT belonged to the genus Tahibacter, with the highest sequence similarity to Tahibacter aquaticus PYM5-11T (98.6%) and Tahibacter caeni BUT-6T (98.3 %). The genome size of strain P2KT was 6.0 Mb with a DNA G+C content of 68.3 mol%. Average nucleotide identity values between strain P2KT and the type strains of the genus Tahibacter were 81.1-81.6 %. The digital DNA-DNA hybridization values between P2KT and these relative species were 24.5-25.6%. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, an unknown aminolipids, two unknown lipids and three unknown phospholipids. The major respiratory quinone of strain P2KT was ubiquinone Q-8, and the main fatty acids (>10.0 % of total fatty acids) of strain P2KT were iso-C15:0, iso-C16:0 and summed feature 9 (C16:0 10-methyl and/or iso-C17:1 ω9c). Based on phenotypic and genotypic data, strain P2KT represents a novel species within the genus Tahibacter, for which the name Tahibacter harae sp. nov. is proposed, with the type strain P2KT (=GDMCC 1.3107T=JCM 35231T).

Curtobacterium caseinilyticum sp. nov., Curtobacterium subtropicum sp. nov. and Curtobacterium citri sp. nov., isolated from citrus phyllosphere.

Three novel Gram-stain-positive, aerobic and rod-shaped bacterial strains, designated RHCKG28T, RHCJP20T and RHCKG23T, were isolated from phyllosphere of healthy citrus leaves collected from Renhua County in Guangdong Province, PR China. 16S rRNA gene sequences comparison and phylogenetic analyses showed that they all belonged to the genus Curtobacterium, among which strain RHCKG28T showed the highest similarity to Curtobacterium herbarum NBRC 103064T (99.3 %), while strains RHCJP20T and RHCKG23T showed 99.2 and 99.0 % similarity to Curtobacterium citreum JCM 1345T, respectively. Phylogenomic analysis showed that the three novel strains were most closely related to C. citreum JCM 1345T and Curtobacterium albidum JCM 1344T. The novel strains could be distinguished from their closely related type strains in terms of enzyme activities, substrate assimilation and fatty acid profiles. In addition, the average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and closely related type strains were 84.4‒89.5 % and 24.5‒34.1 %, respectively, which were below the threshold values for species delimitation. They all took anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major fatty acids, menaquinone 9 (MK-9) as the sole predominant respiratory quinone, and ornithine as the principal cell-wall diamino acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and several unidentified glycolipids. The phenotypic, genotypic and chemotaxonomic data supported that they represent three distinct novel species of the genus Curtobacterium, for which the names Curtobacterium caseinilyticum sp. nov., Curtobacterium subtropicum sp. nov. and Curtobacterium citri sp. nov. are proposed, with RHCKG28T (=GDMCC 1.2667T=JCM 34828T), RHCJP20T (=GDMCC 1.2668T=JCM 34829T) and RHCKG23T (=GDMCC 1.2669T=JCM 34830T) as the type strains, respectively.

Tsuneonella litorea sp. nov., a novel carotenoid-producing bacterium isolated from coastal sediment.

A Gram-stain-negative, aerobic, non-motile and pleomorphic bacterium designated as YG55T was isolated from a coastal sediment sample. Growth was found to occur at 10-37 °C (optimum, 28 °C), at pH 6-9 (optimum, pH 8) and in 0-6 % NaCl (optimum, 1 %). The results of 16S rRNA gene-based analysis showed that strain YG55T was related to the members of the genus Tsuneonella and shared the highest identity of 99.4 % with Tsuneonella dongtanensis GDMCC 1.2307T, followed by Tsuneonella troitsensis JCM 17037T (98.4 %). The phylogenomic results indicated that strain YG55T formed an independent branch distinct from the reference type strains. The 22.7 and 21.8 % digital DNA-DNA hybridization (dDDH) values and 83.0 and 81.8 % average nucleotide identity (ANI) values between strain YG55T and the two relatives were below the species definition thresholds of 70 % (dDDH) and 95-96 % (ANI), indicating that the strain represents a novel genospecies. The results of chemotaxonomic characterization indicated that the major cellular fatty acids of strain YG55T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), C14 : 0 2OH and C16 : 0; the main polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid; the respiratory quinone was ubiquinone-10. The genomic size and DNA G+C contents were 3.03 Mbp and 66.98 %. The strain contained carotenoid biosynthesis genes and could produce carotenoids. Based on its genotypic and phenotypic characteristics, strain YG55T is concluded to represent a novel species of the genus Tsuneonella, for which the name Tsuneonella litorea sp. nov. is proposed. The type strain is YG55T (=GDMCC 1.2590 T=KCTC 82812T).

Fungal Communities Are More Sensitive to the Simulated Environmental Changes than Bacterial Communities in a Subtropical Forest: the Single and Interactive Effects of Nitrogen Addition and Precipitation Seasonality Change.

Increased nitrogen deposition (N factor) and changes in precipitation patterns (W factor) can greatly impact soil microbial communities in tropical/subtropical forests. Although knowledge about the effects of a single factor on soil microbial communities is growing rapidly, little is understood about the interactive effects of these two environmental change factors. In this study, we investigated the responses of soil bacterial and fungal communities to the short-term simulated environmental changes (nitrogen addition, precipitation seasonality change, and their combination) in a subtropical forest in South China. The interaction between N and W factors was detected significant for affecting some soil physicochemical properties (such as pH, soil water, and NO3- contents). Fungi were more susceptible to treatment than bacteria in a variety of community traits (alpha, beta diversity, and network topological features). The N and W factors act antagonistically to affect fungal alpha diversity, and the interaction effect was detected significant for the dry season. The topological features of the meta-community (containing both bacteria and fungi) network overrode the alpha and beta diversity of bacterial or fungal communities in explaining the variation of soil enzyme activities. The associations between Ascomycota fungi and Gammaproteobacteria or Alphaproteobacteria might be important in mediating the inter-kingdom interactions. In summary, our results suggested that fungal communities were more sensitive to N and W factors (and their interaction) than bacterial communities, and the treatments' effects were more prominent in the dry season, which may have great consequences in soil processes and ecosystem functions in subtropical forests.

Pseudomonas citri sp. nov., a potential novel plant growth promoting bacterium isolated from rhizosphere soil of citrus.

A novel potential plant growth promoting bacterium, designated OPS13-3T, was isolated from rhizosphere soil of citrus in Aotou Town of Guangzhou, Guangdong Province, PR China. It showed high ability to dissolve insoluble inorganic phosphate and organic phosphorus and to produce 3-indoleacetic acid (IAA) and siderophore. Cells of the novel strain were Gram-stain-negative, rod-shaped, aerobic and motile with polar flagellum. It shared the highest 16S rRNA gene similarity with Pseudomonas mucoides CCUG 74874T (98.7%) and P. bijieensis LMG 31948T (98.7%). Phylogenetic analyses based the 16S rRNA gene and genome sequences revealed that strain OPS13-3T belonged to the genus Pseudomonas, and was most closely related to P. mediterranea ICMP 14184T and P. corrugate ICMP 5819T. The average nucleotide identity (ANI) and DNA-DNA hybridization (dDDH) values between the novel strain and closely relatives with high 16S rRNA gene similarities were 80.8‒87.5% and 24.7‒34.6%, respectively, which were much below the threshold values for species delimitation. The major fatty acids included C16:0, C10:0 3-OH and summed feature 3 (C16:1ω7c and/or C16:1ω6c). It took ubiquinone 9 as the predominant respiratory quinone and the polar lipids contained phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), three unidentified phospholipids, an unidentified aminophospholipid and an unidentified lipid. Based on the phylogenetic, phenotypic and chemotaxonomic analyses and genome comparison, strain OPS13-3T should be considered as a novel species of the genus Pseudomonas, for which the name Pseudomonas citri sp. nov. is proposed (type strain OPS13-3T = GDMCC 1.3118T = JCM 35385T).

Bacillus velezensis RC116 Inhibits the Pathogens of Bacterial Wilt and Fusarium Wilt in Tomato with Multiple Biocontrol Traits.

Soil-borne plant diseases seriously threaten the tomato industry worldwide. Currently, eco-friendly biocontrol strategies have been increasingly considered as effective approaches to control the incidence of disease. In this study, we identified bacteria that could be used as biocontrol agents to mitigate the growth and spread of the pathogens causing economically significant diseases of tomato plants, such as tomato bacterial wilt and tomato Fusarium wilt. Specifically, we isolated a strain of Bacillus velezensis (RC116) from tomato rhizosphere soil in Guangdong Province, China, with high biocontrol potential and confirmed its identity using both morphological and molecular approaches. RC116 not only produced protease, amylase, lipase, and siderophores but also secreted indoleacetic acid, and dissolved organophosphorus in vivo. Moreover, 12 Bacillus biocontrol maker genes associated with antibiotics biosynthesis could be amplified in the RC116 genome. Extracellular secreted proteins of RC116 also exhibited strong lytic activity against Ralstonia solanacearum and Fusarium oxysporum f. sp. Lycopersici. Pot experiments showed that the biocontrol efficacy of RC116 against tomato bacteria wilt was 81%, and consequently, RC116 significantly promoted the growth of tomato plantlets. Based on these multiple biocontrol traits, RC116 is expected to be developed into a broad-spectrum biocontrol agent. Although several previous studies have examined the utility of B. velezensis for the control of fungal diseases, few studies to date have evaluated the utility of B. velezensis for the control of bacterial diseases. Our study fills this research gap. Collectively, our findings provide new insights that will aid the control of soil-borne diseases, as well as future studies of B. velezensis strains.

Genome-based analyses of the genus Acidovorax: proposal of the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the reclassification of Acidovorax antarcticus as Comamonas antarctica comb. nov. and emended description of the genus Acidovorax.

The genus Acidovorax is a genetically heterogeneous species clustering that comprises many environmental and plant-pathogenic taxa. To better understand the evolutionary relationships among the Acidovorax species, 22 available genome sequences of type strains including the genera Acidovorax and Comamonas were used to conduct the genome-based analyses. Three well-supported monophyletic clusters of the Acidovorax species were determined based on the phylogenomic tree reconstructed using core genes, while they were not grouped in the 16S rRNA gene-based phylogenetic tree. The species arrangements of the genus Acidovorax were further confirmed by the comparisons of the digital DNA-DNA hybridization and average nucleotide identity (ANI) values. The ANI, average amino acid identity, and the percentage of conserved proteins values among the inter-clusters were approximately 83, 81, and 61%, respectively, and thus were proposed as practical thresholds for genus delineation. Besides, Acidovorax antarcticus was much closer to members of the genus Comamonas rather than those of the genus Acidovorax based on the genome-based analysis. Taken together, we propose the division of the current genus Acidovorax into the emended genus Acidovorax and the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the transfer of Acidovorax antarcticus into the genus Comamonas as Comamonas antarctica comb. nov.

Flavobacterium proteolyticum sp. nov., isolated from aquaculture water.

A novel aerobic, yellow, and rod-shaped bacterial isolate, designated as 1Y8AT, was isolated from aquaculture water sampled in Jiangmen, Guangdong province, P. R. China. Here, the taxonomic position of strain 1Y8AT was conducted based on phenotypic, genomic, and chemotaxonomic characteristics. Strain 1Y8AT was observed to grow at 10-37 °C (optimum 28 °C), at pH 6.0-9.0 (optimum 7.0) and in 0-2% NaCl (optimum 1%, w/v). The 16S rRNA gene-based analysis showed that strain 1Y8AT was closely related to "Flavobacterium sasangense" YC6274T (99.3%), Flavobacterium aquaticum JC164T (98.4%), Flavobacterium cucumis R2A45-3T (98.0%), Flavobacterium celericrescens TWA-26T (98.0%), and Flavobacterium cheniae NJ-26T (97.2%). The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain 1Y8AT and reference strains above were far below the recognized thresholds of 70% dDDH and 95-96% ANI for species definition, implying that the strain represents a novel genospecies. The phylogenomic analysis indicated that strain 1Y8AT formed an independent branch distinct from known species. The major cellular fatty acids of strain 1Y8AT were iso-C15:0, iso-C15:1 G and C15:0; the polar lipids comprised phosphatidylethanolamine, glycolipid, and two lipids; the respiratory quinone was MK-6. The G + C content of genomic DNA was 32.5%. Based on the genotypic and phenotypic characteristics such as the utilization of D-glucose and casein hydrolysis, strain 1Y8AT is concluded to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium proteolyticum sp. nov. is proposed. The type strain of the species is 1Y8AT (= GDMCC 1.1933T = KACC 22081T).