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.

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.

Hyalangiumruber sp. nov, characterization of a novel myxobacterium strain s54d21 and their secondary metabolites.

Myxobacteria are special bacteria with wide adaptability, which are rich sources of structurally diverse natural products with intriguing biological properties. Here, a gram-negative myxobacterium strain s54d21T was isolated from the sediment of a wetland park in China using the Escherichia coli baiting method. Based on 16S rRNA gene sequence and genomic data, the strain was demonstrated to be a novel species of a rare genus Hyalangium, designated Hyalangium ruber sp. nov (type strain s54d21T = GDMCC 1.1945T = JCM 39263T). The subsequent chemical investigation of the strain s54d21T led to the isolation of three rare 3,5,6-trisubstituted 2(1H)-pyrazinones, namely, hyalanones A-C (1-3), together with a known macrolactin A (4). Those new structures and their absolute configurations were unambiguously assigned by extensive analyses of spectroscopic data and density functional theory (DFT) calculations. In biological assays, compound 4 exhibited moderate cytotoxic activities against human cell lines RKO, A549, and NCM460 with IC50 values ranging from 27.21 to 32.14 µM.

Unveiling the Broad Substrate Specificity of Deoxynivalenol Oxidation Enzyme DepA and Its Role in Detoxifying Trichothecene Mycotoxins.

DepA, a pyrroloquinoline quinone (PQQ)-dependent enzyme isolated from Devosia mutans 17-2-E-8, exhibits versatility in oxidizing deoxynivalenol (DON) and its derivatives. This study explored DepA's substrate specificity and enzyme kinetics, focusing on DON and 15-acetyl-DON. Besides efficiently oxidizing DON, DepA also transforms 15-acetyl-DON into 15-acetyl-3-keto-DON, as identified via LC-MS/MS and NMR analysis. The kinetic parameters, including the maximum reaction rate, turnover number, and catalytic efficiency, were thoroughly evaluated. DepA-PQQ complex docking was deployed to rationalize the substrate specificity of DepA. This study further delves into the reduced toxicity of the transformation products, as demonstrated via enzyme homology modeling and in silico docking analysis with yeast 80S ribosomes, indicating a potential decrease in toxicity due to lower binding affinity. Utilizing the response surface methodology and central composite rotational design, mathematical models were developed to elucidate the relationship between the enzyme and cofactor concentrations, guiding the future development of detoxification systems for liquid feeds and grain processing. This comprehensive analysis underscores DepA's potential for use in mycotoxin detoxification, offering insights for future applications.

Tomato plant growth promotion and drought tolerance conferred by three arbuscular mycorrhizal fungi is mediated by lipid metabolism.

Arbuscular mycorrhizal fungi (AMF) can promote plant growth and enhance plant drought tolerance with varying effect size among different fungal species. However, the linkage between the variation and the lipid metabolism, which is exclusively derived from plants, has been little explored thus far. Here, we established AM symbiosis between tomato (Solanum lycopersicum) plants and three AMF species (Rhizophagus intraradices, Funneliformis mosseae, Rhizophagus irregularis) under well watered (WW) or drought stressed (DS) conditions in pot experiment. The plant biomass, chlorophyll fluorescence Fv/Fm, shoot P content and mycorrhizal colonization were determined. Meanwhile, fatty acid (FA) profiles and relative expression of genes encoding for nutrition exchange (SlPT4, SlPT5, RAM2, STR/STR2) in roots were also monitored. DS significantly decreased plant biomass while AMF significantly increased it, with three fungal species varying in their growth promoting capacity and drought tolerance capacity. The growth promoting effect of R. irregularis was lower than those of R. intraradices and F. mosseae, and was associated with higher mycorrhizal colonization and more consumption of lipids. However, the drought tolerance capacity of R. irregularis was greater than those of R. intraradices and F. mosseae, and was associated with less decrease in mycorrhizal colonization and lipid content. We also found that AMF mediated plant drought tolerance via regulating both AM specific FAs and non-AM specific FAs in a complementary manner. These data suggest that lipid metabolism in AM plays a crucial role in plant drought tolerance mediated by AMF.

Characterization and engineering of plastic-degrading polyesterases jmPE13 and jmPE14 from Pseudomonas bacterium.

Polyester plastics are widely used in daily life, but also cause a large amount of waste. Degradation by microbial enzymes is the most promising way for the biobased upcycling of the wastes. However, there is still a shortage of high-performance enzymes, and more efficient polyester hydrolases need to be developed. Here we identified two polyester hydrolases, jmPE13 and jmPE14, from a previously isolated strain Pseudomonas sp. JM16B3. The proteins were recombinantly expressed and purified in E. coli, and their enzymatic properties were characterized. JmPE13 and jmPE14 showed hydrolytic activity towards polyethylene terephthalate (PET) and Poly (butylene adipate-co-terephthalate) (PBAT) at medium temperatures. The enzyme activity and stability of jmPE13 were further improved to 3- and 1.5-fold, respectively, by rational design. The results of our research can be helpful for further engineering of more efficient polyester plastic hydrolases and their industrial applications.

Global rewiring of lipid metabolism to produce carotenoid by deleting the transcription factor genes ino2/ino4 in Saccharomyces cerevisiae.

The transcription factor complex INO2 and INO4 in Saccharomyces cerevisiae plays a vital role in lipid biosynthesis by activating multiple genes in the biosynthetic pathways of phospholipid, fatty acid, and sterol. Previous studies have reported conflicting results regarding the effects of ino2 and ino4 gene expression levels on target chemicals. Therefore, this study aimed to examine the influence of different ino2 and ino4 expression levels on carotenoid production (e.g., lycopene), which shares a common precursor, acetyl-CoA, with lipid metabolism. Surprisingly, 2.6- and 1.8-fold increase in lycopene yield in the ino2 and ino4 deletion strains were found, respectively. In contrast, ino2 overexpression did not promote lycopene accumulation. Additionally, there was a decrease in intracellular free fatty acids in the ino2 deletion strain. Comparative transcriptome analysis revealed a significant downregulation of genes related to lipid biosynthesis in the ino2 deletion strain. To our knowledge, this is the first report showing that deletion of transcription factor genes ino2 and ino4 can facilitate lycopene accumulation. These findings hold significant implications for the development of metabolically engineered S. cerevisiae with enhanced carotenoid production.

Secretory CAZymes profile and GH19 enzymes analysis of Corallococcus silvisoli c25j21.

Extracellular enzymes play important roles in myxobacteria degrading macromolecules and preying on other microorganisms. Glycoside hydrolases 19 (GH19) are widely present in myxobacteria, but their evolution and biological functions have not been fully elucidated. Here we investigated the comparative secretory proteome of Corallococcus silvisoli c25j21 in the presence of cellulose and chitin. A total of 313 proteins were detected, including 16 carbohydrate-active enzymes (CAZymes), 7 of which were induced by cellulose or chitin, such as GH6, GH13, GH19, AA4, and CBM56. We further analyzed the sequence and structural characteristics of its three GH19 enzymes to understand their potential functions. The results revealed that myxobacterial GH19 enzymes are evolutionarily divided into two clades with different appended modules, and their different amino acid compositions in the substrate binding pockets lead to the differences in molecular surface electrostatic potentials, which may, in turn, affect their substrate selectivity and biological functions. Our study is helpful for further understanding the biological functions and catalytic mechanisms of myxobacterial CAZymes.

Undescribed α-pyrone-containing mycotoxins and an eremophilane-type sesquiterpenoid isolated from Aspergillus aureoterreus and their cytotoxicity.

Four previously undescribed and highly oxygenated α-pyrone-containing mycotoxins designated citreoviridins (E‒H), and an unreported eremophilane-type sesquiterpenoid namely aureoterrolide N, were isolated from the culture broth of Aspergillus aureoterreus. Those isolates were inferred from extensive spectroscopic methods and theoretical computation, where their absolute configurations were unambiguously determined by coupling constants following an empirical rule for the acyclic vicinal diol, theoretical ECD calculation, and NMR computation using the GIAO method and DP4+ analysis. Among them, citreoviridins E‒H are four stereoisomers of a citreoviridin derivative, featuring a methylated α-pyrone, an oxidized polyene linker, and a tetrahydrofuran ring. Cytotoxicity assay of all isolates demonstrated that aureoterrolide N exhibited weak inhibitory effect against human cancer cell line HL-60 with an inhibition rate of 55.2% at 40.0 µM.

Design of a dual-responding genetic circuit for high-throughput identification of L-threonine-overproducing Escherichia coli.

L-threonine is a crucial amino acid that is extensively employed in the realms of food, animal feed and pharmaceuticals. Unfortunately, the lack of an appropriate biosensor has hindered the establishment of a robust high-throughput screening (HTS) system for the identification of the desired strains from random mutants. In this study, a dual-responding genetic circuit that capitalizes on the L-threonine inducer-like effect, the L-threonine riboswitch, and a signal amplification system was designed for the purpose of screening L-threonine overproducers. This platform effectively enhanced the performance of the enzyme and facilitated the identification of high L-threonine-producing strains from a random mutant library. Consequently, pathway optimization and directed evolution of the key enzyme enhanced L-threonine production by 4 and 7-fold, respectively. These results demonstrate the potential of biosensor design for dynamic metabolite detection and offer a promising tool for HTS and metabolic regulation for the development of L-threonine-hyperproducing strains.

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).

Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, Shewanella zhuhaiensis sp. nov., Isolated from a Tidal Flat Sediment.

A new, facultatively anaerobic, light-yellow, and rod-shaped bacterium designated as 3B26T isolated from Qi'ao Island's tidal flat sediment was identified. Strain 3B26T can hydrolyze gelatin, aesculin, and skim milk. The major cellular fatty acids were identified as iso-C15:0, referred to as summed feature 3, and C16:0; the polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and phospholipid; and the quinones contained Q-7, Q-8, MK-7, and MMK7. The genomic size of strain 3B26T was 4,682,650 bp, and its genomic DNA G + C content was 54.8%. While a 16S rRNA gene-based phylogenetic analysis confirmed that strain 3B26T belongs to the genus Shewanella, both phylogenomic inference and genomic comparison revealed that strain 3B26T is distinguishable from its relatives, and digital DNA-DNA hybridization (dDDH) values of 24.4-62.6% and average nucleotide identities (ANIs) of 83.5-95.6% between them were below the 70% dDDH and 96% ANI thresholds for bacterial species delineation. Genomic functional analysis demonstrated that strain 3B26T possesses complete gene clusters of eicosapentaenoic acid biosynthesis and denitrification. Based on the evidence above, strain 3B26T is considered to represent a novel species of the genus Shewanella, and the name Shewanella zhuhaiensis sp. nov. (type strain 3B26T = GDMCC 1.2057T = KCTC 82339T) is proposed.

Advances in the Discovery and Engineering of Gene Targets for Carotenoid Biosynthesis in Recombinant Strains.

Carotenoids are naturally occurring pigments that are abundant in the natural world. Due to their excellent antioxidant attributes, carotenoids are widely utilized in various industries, including the food, pharmaceutical, cosmetic industries, and others. Plants, algae, and microorganisms are presently the main sources for acquiring natural carotenoids. However, due to the swift progress in metabolic engineering and synthetic biology, along with the continuous and thorough investigation of carotenoid biosynthetic pathways, recombinant strains have emerged as promising candidates to produce carotenoids. The identification and manipulation of gene targets that influence the accumulation of the desired products is a crucial challenge in the construction and metabolic regulation of recombinant strains. In this review, we provide an overview of the carotenoid biosynthetic pathway, followed by a summary of the methodologies employed in the discovery of gene targets associated with carotenoid production. Furthermore, we focus on discussing the gene targets that have shown potential to enhance carotenoid production. To facilitate future research, we categorize these gene targets based on their capacity to attain elevated levels of carotenoid production.

Pan-Genome Analyses of the Genus Cohnella and Proposal of the Novel Species Cohnella silvisoli sp. nov., Isolated from Forest Soil.

Two strains, designated NL03-T5T and NL03-T5-1, were isolated from a soil sample collected from the Nanling National Forests, Guangdong Province, PR China. The two strains were Gram-stain-positive, aerobic, rod-shaped and had lophotrichous flagellation. Strain NL03-T5T could secrete extracellular mucus whereas NL03-T5-1 could not. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains belong to the genus Cohnella, were most closely related to Cohnella lupini LMG 27416T (95.9% and 96.1% similarities), and both showed 94.0% similarity with Cohnella arctica NRRL B-59459T, respectively. The two strains showed 99.8% 16S rRNA gene sequence similarity between them. The draft genome size of strain NL03-T5T was 7.44 Mbp with a DNA G+C content of 49.2 mol%. The average nucleotide identities (ANI) and the digital DNA-DNA hybridization (dDDH) values between NL03-T5T and NL03-T5-1 were 99.98% and 100%, indicating the two strains were of the same species. Additionally, the ANI and dDDH values between NL03-T5T and C. lupini LMG 27416T were 76.1% and 20.4%, respectively. The major cellular fatty acids of strain NL03-T5T included anteiso-C15:0 and iso-C16:0. The major polar lipids and predominant respiratory quinone were diphosphatidylglycerol (DPG) and menaquinone-7 (MK-7). Based on phylogenetic analysis, phenotypic and chemotaxonomic characterization, genomic DNA G+C content, and ANI and dDDH values, strains NL03-T5T and NL03-T5-1 represent novel species in the genus Cohnella, for which the name Cohnella silvisoli is proposed. The type strain is NL03-T5T (=GDMCC 1.2294T = JCM 34999T). Furthermore, comparative genomics revealed that the genus Cohnella had an open pan-genome. The pan-genome of 29 Cohnella strains contained 41,356 gene families, and the number of strain-specific genes ranged from 6 to 1649. The results may explain the good adaptability of the Cohnella strains to different habitats at the genetic level.

Potential functions of the shared bacterial taxa in the citrus leaf midribs determine the symptoms of Huanglongbing.

Instruction: Citrus is a globally important fruit tree whose microbiome plays a vital role in its growth, adaptability, and resistance to stress. Methods: With the high throughput sequencing of 16S rRNA genes, this study focused on analyzing the bacterial community, especially in the leaf midribs, of healthy and Huanglongbing (HLB)-infected plants. Results: We firstly identified the shared bacterial taxa in the midribs of both healthy and HLB-infected plants, and then analyzed their functions. Results showed that the shared bacterial taxa in midribs belonged to 62 genera, with approximately 1/3 of which modified in the infected samples. Furthermore, 366 metabolic pathways, 5851 proteins, and 1833 enzymes in the shared taxa were predicted. Among these, three metabolic pathways and one protein showed significant importance in HLB infection. With the random forest method, six genera were identified to be significantly important for HLB infection. Notably, four of these genera were also among the significantly different shared taxa. Further functional characterization of these four genera revealed that Pseudomonas and Erwinia likely contributed to plant defense against HLB, while Streptomyces might have implications for plant defense against HLB or the pathogenicity of Candidatus Liberibacter asiaticus (CLas). Disccusion: Overall, our study highlights that the functions of the shared taxa in leaf midribs are distinguished between healthy and HLB-infected plants, and these microbiome-based findings can contribute to the management and protection of citrus crops against CLas.

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.

Exogenous myristate promotes the colonization of arbuscular mycorrhizal fungi in tomato.

Arbuscular mycorrhizal fungi (AMF) can establish symbiotic associations with the roots of most terrestrial plants, thereby improving the tolerance of the host plants to biotic and abiotic stresses. Although AMF cannot synthesize lipids de novo, they can obtain lipids from the root cells for their growth and development. A recent study reveals that AMF can directly take up myristate (C14:0 lipid) from the environment and produce a large amount of hyphae in asymbiotic status; however, the effect of environmental lipids on AM symbiosis is still unclear. In this study, we inoculated tomato (Solanum lycopersicum) with AMF in an in vitro dual culture system and a sand culture system, and then applied exogenous myristate to the substrate, in order to explore the effect of exogenous lipids on the mycorrhizal colonization of AMF. We investigated the hyphae growth, development, and colonization of AMF, and examined the gene expression involved in phosphate transport, lipid biosynthesis, and transport. Results indicate that exogenous lipids significantly stimulated the growth and branching of hyphae, and significantly increased the number of hyphopodia and mycorrhizal colonization of AMF, with arbuscular abundance and intraradical spores or vesicles being the most promoted. In contrast, exogenous myristate decreased the growth range and host tropism of the germ tubes, and largely inhibited the exchange of nutrition between symbionts. As a result, exogenous myristate did not affect the plant growth. This study suggests that lipids promote mycorrhizal colonization by enhancing the growth and development of AMF hyphae and increasing their contact opportunities with plant roots. To the best of our knowledge, this is the first report that shows that lipids promote the colonization of AMF. Our study highlights the importance of better understanding the roles of environmental lipids in the establishment and maintenance of AM symbiosis and, thus, in agricultural production.

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.

Phenylalanine-mediated changes in the soil bacterial community promote nitrogen cycling and plant growth.

Soil amino acids (AAs) are the most active components of soil N, which can be mineralized or absorbed by bacteria as N and C sources. We hypothesized that exogenous AAs could regulate the bacterial community and affect soil N cycling, and the effect sizes could vary depending on individual AAs. Here, we applied feather (keratin)-based compost rich in AAs to Poncirus trifoliata (L.) to evaluate the regulation of bacterial community by AAs; furthermore, we applied six individual AAs to test their effects. The compost significantly increased soil hydrolysable AA content, ammonia monooxygenase gene abundance, and plant growth and changed bacterial community structure. Redundancy analysis revealed that the effects of AAs on the bacterial community composition were greater than those of soil chemical properties, and phenylalanine (Phe) was the most effective among thirteen individual AAs. When applied individually, Phe caused the greatest increase in N cycling-related enzyme activity and plant growth and most significantly altered the bacterial community structure among the six exogenous AAs. Notably, Phe significantly increased the relative abundances of Burkholderia-Caballeronia-Paraburkholderia, Azospirillum, Cupriavidus, and Achromobacter, whose abundances were significantly positively correlated with plant biomass, and significantly reduced the relative abundances of Arachidicoccus, Pseudopedobacter, Sphingobacterium, and Paenibacillus, whose abundances were significantly negatively correlated with plant biomass. We demonstrate that soil AAs strongly shape the bacterial community. Particularly, Phe enhances N cycling and plant growth by increasing the potentially beneficial bacterial taxa and inhibiting the potentially harmful bacterial taxa, which needs further validation.

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).