Intestinal inflammation alters mucosal carbohydrate foraging and monosaccharide incorporation into microbial glycans.

Endogenous carbohydrates released from the intestinal mucus represent a constant source of nutrients to the intestinal microbiota. Mucus-derived carbohydrates can also be used as building blocks in the biosynthesis of bacterial cell wall components, thereby influencing host mucosal immunity. To assess the uptake of endogenous carbohydrates by gut microbes in healthy mice and during intestinal inflammation, we applied azido-monosaccharides that can be tracked on bacterial cell walls after conjugation with fluorophores. In interleukin-10 deficient mice, changes in the gut microbiota were accompanied by decreased carbohydrate hydrolase activities and increased lumenal concentrations of host glycan-derived monosaccharides. Tracking of the monosaccharide N-azidoacetylglucosamine (GlcNAz) in caecum bacteria revealed a preferential incorporation of this carbohydrate by Xanthomonadaceae in healthy mice and by Bacteroidaceae in interleukin-10 deficient mice. These GlcNAz-positive Bacteroidaceae fractions mainly belonged to the species B. acidifaciens and B. vulgatus. Growth of Bacteroides species in the presence of specific monosaccharides changed their stimulatory activity toward CD11c+ dendritic cells. Expression of activation markers and cytokine production was highest after stimulation of dendritic cells with B. vulgatus. The variable incorporation of monosaccharides by related Bacteroides species underline the necessity to investigate intestinal bacteria down to the species level when addressing microbiota-host interactions.

Nevskia lacus sp. nov., a gammaproteobacterium isolated from a eutrophic lake.

A novel Gram-stain negative, rod-shaped and motile bacterial strain, designated strain Seoho-38T, was isolated from a eutrophic lake in South Korea. Polyphasic taxonomic studies were performed to investigate the taxonomic position of the new isolate. The phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain Seoho-38T formed a distinct cluster with Nevskia ramosa Soe1T, Nevskia persephonica G6M-30T, Nevskia soli GR15-1T, Nevskia terrae KIS13-15T and Nevskia aquatilis F2-63T with bootstrap resampling value of 100%. Of those Nevskia strains, the new isolate shows high sequence similarity with N. ramosa Soe1T (98.7%) and N. persephonica G6M-30T (97.2%), and values lower than 96.5% with the other type strains. The new isolate was observed to grow aerobically in 0-1.5% (w/v) NaCl (optimum 0%), at pH 7.0-9.0 (optimum pH 7.0) and temperature 15-36 °C (optimum 20-30 °C) on R2A medium. DNA-DNA relatedness values between strain Seoho-38T and the type strains of reference species in the genus Nevskia were < 24%. The genomic DNA G + C content was determined to be 67.4 mol%. Ubiquinone-8 (Q-8) (95%) and ubiquinone-7 (Q-7) (5%) were identified as the respiratory quinones. The cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phosphoaminolipid, two glycolipids, an aminolipid and four unidentified lipids. The major fatty acid components were found to include summed feature 3 (C16:1ω7c and/or C16:1ω6c), summed feature 8 (C18:0ω7c and/or C18:0ω6c), C16:0 and C14:0. Based on the above polyphasic evidence, strain Seoho-38T (= KCTC 52221T = JCM 31888T) represents a new species of the genus Nevskia, for which the name Nevskia lacus sp. nov. is proposed.

Luteibacter pinisoli sp. nov., a casein degrading bacterium isolated from rhizospheric soil of Pinus koraiensis.

A yellow pigmented, Gram-staining negative, motile and rod-shaped novel bacterial strain, designated MAH-14T was isolated from rhizospheric soil and was characterized using a polyphasic approach. The isolated strain was aerobic, oxidase and catalase were positive, optimum growth temperature and pH were 28-30 °C and 6.5, respectively. The novel strain is able to hydrolyze casein, starch, esculin, gelatin, L-tyrosine, DNA, tween 80, tween 20, L-arginine and 4-nitrophenyl-BD-galactopyranoside. On the basis of 16S rRNA gene sequence analysis, strain MAH-14T belongs to the genus Luteibacter and is most closely related to Luteibacter yeojuensis R2A16-10T (98.5%), Luteibacter anthropi CCUG 25036T (98.4%) and Luteibacter rhizovicinus LJ96T (98.3%). In DNA-DNA hybridization experiments, the DNA relatedness between strain MAH-14T and its closest phylogenetic neighbor was below 45.0%. The predominant respiratory quinone and the DNA G + C content of the novel strain were ubiquinone-8 and 63.5 mol%, respectively. The novel strain MAH-14T is able to produce flexirubin-type pigments. The major cellular fatty acids were C15:0 iso, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 9 (C17:1 iso ω9c and/or C16:0 10-methyl). The DNA-DNA hybridization results and results of the genotypic analysis in combination with chemotaxonomic and physiological data revealed that strain MAH-14T represented a novel species within the genus Luteibacter, for which the name Luteibacter pinisoli, is proposed. The type strain is MAH-14T (= KACC 19298T = CGMCC 1.16227T).

Biosynthesis, biotechnological production, and applications of glucosylglycerols.

Glucosylglycerols (GGs) are known as compatible solutes accumulated by some bacteria including cyanobacteria as well as higher plants for their adaptations to salt or desiccation stresses. Since being identified in Japanese sake, their physiological effects and potential applications on human health cares have been explored in the following 15 years. Several different synthesis methods have been successively developed for the production of GGs. However, the efficiency of GG synthesis, especially biological synthesis, is still low. With the recent advances in genome sequencing and synthetic biology tools, systematical screening of enzyme candidates and metabolic engineering approaches is necessary for improving GG synthesis efficiency. In this review, we will summarize GG structure information, protective effects on human skin and digestive system as well as industrial enzymes, together with their synthesis by chemical, enzymatic, and biological in vivo approaches in detail, and provide some prospects on improving GG production.

Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment.

A denitrifying bacterium, designated strain E4-1(T), was isolated from a bioreactor for tannery wastewater treatment, and its taxonomic position was investigated using a polyphasic approach. Strain E4-1(T), a facultative anaerobic bacterium, was observed to grow between 0 and 12 % (w/v) NaCl, between pH 3.0 and 12.0. Cells were found to be oxidase-positive and catalase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E4-1(T) forms a distinct lineage with respect to closely related genera in the family Xanthomonadaceae, and is closely related to Chiayiivirga, Aquimonas and Dokdonella, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93.9 %. The predominant respiratory quinone was determined to be ubiquinone-8 (Q-8) and the major cellular fatty acids were determined to be iso-C15:0, iso-C17:1 ω9c, iso-C11:0 and iso-C11:0 3OH. Based on physiological, biochemical and chemotaxonomic properties together with results of comparative 16S rRNA gene sequence analysis, strain E4-1(T) is considered to represent a novel species in a new genus, for which the name Denitratimonas tolerans gen. nov., sp. nov. is proposed. The type strain is E4-1(T) (=KACC 17565(T) = NCAIM B 025327(T)).

Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China.

A Gram-stain negative, aerobic, rod-shaped bacterial strain, YN2-31A(T), was isolated from rice-field soil, Taoyuan Village, Yunnan province of China. The bacterium was observed to grow at 20-45 °C (optimum 28 °C), at pH 5.0-10.0 (optimum 7.0), and in the presence of 0-2% (w/v) NaCl (optimum 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2-31A(T) is most closely related to Arenimonas daejeonensis DSM 18060(T) (96.1%), Arenimonas malthae DSM 21305(T) (95.9%), Arenimonas donghaensis DSM 18148(T) (95.1%), Arenimonas composti DSM 18010(T) (94.8%) and Arenimonas maotaiensis JCM 19710(T) (94.8%). The major cellular fatty acids (>10%) were found to be iso-C(18:1) ω9c, iso-C(15:0), Sum In Feature 3 (C(16:1) ω7c/C(16:1) ω6c), and C(16:0). The major ubiquinone was identified as Q-8 and the major cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The genomic DNA G+C content was determined to be 72.3 mol%. The results of the phylogenetic, genetic, phenotypic and chemotaxonomic analyses suggest that strain YN2-31A(T) represents a novel species of the genus Arenimonas, for which the name Arenimonas taoyuanensis sp. nov. is proposed. The type strain is YN2-31A(T) (=DSM 26777(T) = CCTCC AB2012964(T)).

Biodegradation of pesticide profenofos by the free and immobilized cells of Pseudoxanthomonas suwonensis strain HNM.

Profenofos is an organophosphate pesticide used extensively in agriculture to control pests. A bacterium capable of degrading profenofos was isolated from pesticide-contaminated soil samples and identified as Pseudoxanthomonas suwonensis strain HNM based on its morphological and biochemical characteristics and phylogenetic analysis of 16S rRNA gene sequences. 4-Bromo-2-chlorophenol was identified as a metabolite of profenofos degradation by HPLC and GC-MS analysis. The organism degraded profenofos by hydrolysis to yield 4-bromo-2-chlorophenol which was further utilized as carbon source for growth. The organism utilized various organophosphate pesticides such as temephos, quinalphos, and chloropyrifos as carbon sources. The optimum conditions for degradation of profenofos by P. suwonensis strain HMN were found to be at pH 7 and 30 °C. We have investigated the rate of degradation of profenofos by the free and immobilized cells of P. suwonensis strain HNM in various matrices such as sodium alginate (SA), sodium alginate-polyvinyl alcohol (SA-PVA), and SA-bentonite clay. The rate of degradation of 3 and 6 mM profenofos by the freely suspended cells were compared with that by immobilized cells in batches and semi-continuous with shaken cultures. The SA-bentonite clay-immobilized cells showed higher rate of degradation of 3 and 6 mM profenofos then freely suspended cells and cells immobilized in SA and SA-PVA. The SA-bentonite clay-immobilized cells of P. suwonensis strain HNM could be reused for more than 32 cycles without losing their degradation capacity. Thus, the immobilized cells are more efficient than freely suspended cells for the degradation of organophosphate pesticide contaminated water.

Wohlfahrtiimonas larvae sp. nov., isolated from the larval gut of Hermetia illucens (Diptera: Stratiomyidae).

A novel, Gram-negative, facultative anaerobic, motile and short rod-shaped bacterium, strain KBL006(T) was isolated from the larval gut of Hermetia illucens, Black soldier fly. The 16S rRNA gene sequence of strain KBL006(T) showed 96.4 % similarity to that of Wohlfahrtiimonas chitiniclastica S5(T). Strain KBL006(T) grew optimally at 30 °C, at pH 8.0 and in the presence of 1-2 % (w/v) NaCl. Oxidase activity and catalase activity were positive. The major fatty acids were C18:1 ω7c, C14:0, and C16:0. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol, and two phospholipids. The G+C content of the genomic DNA was 45.2 mol%. Based on these polyphasic data, strain KBL006(T) is considered to represent a novel species in the genus Wohlfahrtiimonas, for which the name Wohlfahrtiimonas larvae sp. nov. is proposed. The type strain is KBL006(T) (= KACC 16839(T) = JCM 18424(T)).

Co-metabolic transformation of the neonicotinoid insecticide imidacloprid by the new soil isolate Pseudoxanthomonas indica CGMCC 6648.

A new imidacloprid (IMI) degrading bacterium Z-9 (deposited number CGMCC 6648) was isolated and identified as Pseudoxanthomonas indica by 16S rRNA gene analysis. Two metabolites were identified as olefin and 5-hydroxy IMI by liquid chromatography-mass spectrometry and nuclear magnetic resonance analysis. P. indica CGMCC 6648 degraded 70.1% of IMI (1.22 mmol L(-1)) and formed 0.93 mmol L(-1) 5-hydroxy IMI and 0.05 mmol L(-1) olefin IMI in 6 days and in the presence of 100 mmol L(-1) glucose. The half-life of IMI degradation was 3.6 days. P. indica CGMCC 6648 transforms IMI via a co-metabolism mechanism and different carbohydrates have significant effects on 5-hydroxy IMI formation, whereas different organic acids have substantial effects on olefin IMI production. Lactose is the best co-substrate for IMI degradation and 5-hydroxy IMI formation with 0.77 mmol L(-1) degraded and 0.67 mmol L(-1) formed in 48 h, respectively. Pyruvate is the best co-substrate for olefin IMI formation with 0.17 mmol L(-1) produced in 96 h for all carbon sources tested. Pyruvate significantly stimulates the conversion of 5-hydroxy IMI to olefin IMI, whereas glucose slightly inhibits this reaction. P. indica CGMCC 6648 rapidly degrades IMI and forms olefin IMI, which may enhance its potential for biodegradation of IMI and increase its insecticidal activity, which can decrease the IMI dosage required.

Co-metabolic degradation of benzo(e)pyrene by halophilic bacterial consortium at different saline conditions.

Polyaromatic hydrocarbons (PAHs) with high molecular weight (more than three benzene rings) were difficult to degrade in saline environment. The present study details about the bacterial consortium enriched from industrial sludge from salt manufacturing company, Tuticorin, Tamilnadu (India), which was capable of degrading 1, 4 dioxane (Emerging micropollutant) and also phenanthrene as sole carbon source under saline condition. The halophilic bacterial consortium was able to degrade low molecular weight (LMW) phenanthrene, but unable to degrade high molecular weight (HMW) benzo(e)pyrene. To overcome this problem, phenanthrene was added as co-substrate along with benzo(e)pyrene which enhanced the biodegradation process by co-metabolism under saline conditions. The consortium potentially degraded 80% and 99% of benzo(e)pyrene in 7 days and phenanthrene in 5 days at 30 g l⁻¹ of NaCl concentration. When the saline concentration increased to 60 g l⁻¹, degradation of phenanthrene (97% in 8 days) and benzo(e)pyrene (65% in 10 days) was observed. Further increase in saline concentration to 90 g I⁻¹ of NaCI showed reduction in the percent degradation of phenanthrene and benzo(e)pyrene leads to 30.3% and 9% respectively in 6 days. Potential bacterial strains, present in PAHs degrading bacterial consortium were identified as Achromobacter sp. AYS3 (JQ419751), Marinobacter sp. AYS4 (JQ419752) and Rhodanobacter sp. AYS5 (JQ419753). The present study details about the effect of salinity on PAHs degradation and vital role of co-metabolism on biodegradation of benzo(e)pyrene with phenanthrene under saline conditions.

Production, characterization, and application of Pseudoxanthomonas taiwanensis biosurfactant: a green chemical for microbial enhanced oil recovery (MEOR).

Biosurfactants, as microbial bioproducts, have significant potential in the field of microbial enhanced oil recovery (MEOR). Biosurfactants are microbial bioproducts with the potential to reduce the interfacial tension (IFT) between crude oil and water, thus enhancing oil recovery. This study aims to investigate the production and characterization of biosurfactants and evaluate their effectiveness in increasing oil recovery. Pseudoxanthomonas taiwanensis was cultured on SMSS medium to produce biosurfactants. Crude oil was found to be the most effective carbon source for biosurfactant production. The biosurfactants exhibited comparable activity to sodium dodecyl sulfate (SDS) at a concentration of 400 ppm in reducing IFT. It was characterized as glycolipids, showing stability in emulsions at high temperatures (up to 120 °C), pH levels ranging from 3 to 9, and NaCl concentrations up to 10% (w/v). Response surface methodology revealed the optimized conditions for the most stable biosurfactants (pH 7, temperature of 40 °C, and salinity of 2%), resulting in an EI24 value of 64.45%. Experimental evaluations included sand pack column and core flooding studies, which demonstrated additional oil recovery of 36.04% and 12.92%, respectively. These results indicate the potential application of P. taiwanensis biosurfactants as sustainable and environmentally friendly approaches to enhance oil recovery in MEOR processes.

Comparative genomic analysis and benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) degradation pathways of Pseudoxanthomonas spadix BD-a59.

Pseudoxanthomonas spadix BD-a59, isolated from gasoline-contaminated soil, has the ability to degrade all six BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds. The genomic features of strain BD-a59 were analyzed bioinformatically and compared with those of another fully sequenced Pseudoxanthomonas strain, P. suwonensis 11-1, which was isolated from cotton waste compost. The genome of strain BD-a59 differed from that of strain 11-1 in many characteristics, including the number of rRNA operons, dioxygenases, monooxygenases, genomic islands (GIs), and heavy metal resistance genes. A high abundance of phage integrases and GIs and the patterns in several other genetic measures (e.g., GC content, GC skew, Karlin signature, and clustered regularly interspaced short palindromic repeat [CRISPR] gene homology) indicated that strain BD-a59's genomic architecture may have been altered through horizontal gene transfers (HGT), phage attack, and genetic reshuffling during its evolutionary history. The genes for benzene/toluene, ethylbenzene, and xylene degradations were encoded on GI-9, -13, and -21, respectively, which suggests that they may have been acquired by HGT. We used bioinformatics to predict the biodegradation pathways of the six BTEX compounds, and these pathways were proved experimentally through the analysis of the intermediates of each BTEX compound using a gas chromatograph and mass spectrometry (GC-MS). The elevated abundances of dioxygenases, monooxygenases, and rRNA operons in strain BD-a59 (relative to strain 11-1), as well as other genomic characteristics, likely confer traits that enhance ecological fitness by enabling strain BD-a59 to degrade hydrocarbons in the soil environment.

Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent.

A Gram-staining-negative, non-endospore-forming, non-flagellated, non-motile and rod-shaped bacterium, designated strain LM2-5(T), was isolated from activated sludge in a sequencing batch reactor used for the treatment of triphenylmethane dye effluent. The taxonomy of strain LM2-5(T) was studied by phenotypic, chemotaxonomic and phylogenetic methods. Strain LM2-5(T) was aerobic, heterotrophic and positive for oxidase but negative for catalase activity. It grew at 16-37 °C (optimum 25 °C) and at pH 5.0-8.5 (optimum between pH 6.5 and pH 7.0). NaCl was not obligatory for growth but was tolerated at concentrations up to 2.0 % (w/v) NaCl. The novel strain formed yellow colonies on trypticase soy agar. Cells of strain LM2-5(T) were rods that measured 0.3-0.5 µm in width and 3.0-5.0 µm in length. The predominant respiratory quinone was Q-8. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The genomic DNA G+C content was 66.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain LM2-5(T) clustered with members of the genus Dokdonella and appeared most closely related to Dokdonella koreensis DS-123(T) (96.4 % sequence similarity), Dokdonella fugitiva A3(T) (96.1 %), Dokdonella soli KIS28-6(T) (95.7 %) and Dokdonella ginsengisoli Gsoil 191(T) (95.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain LM2-5(T) was considered to represent a novel species of the genus Dokdonella, for which the name Dokdonella immobilis is proposed. The type strain is LM2-5(T) ( = CGMCC 1.7659(T)  = JCM 15763(T)).

Diesel oil removal by immobilized Pseudoxanthomonas sp. RN402.

Pseudoxanthomonas sp. RN402 was capable of degrading diesel, crude oil, n-tetradecane and n-hexadecane. The RN402 cells were immobilized on the surface of high-density polyethylene plastic pellets at a maximum cell density of 10(8) most probable number (MPN) g(-1) of plastic pellets. The immobilized cells not only showed a higher efficacy of diesel oil removal than free cells but could also degrade higher concentrations of diesel oil. The rate of diesel oil removal by immobilized RN402 cells in liquid culture was 1,050 mg l(-1) day(-1). Moreover, the immobilized cells could maintain high efficacy and viability throughout 70 cycles of bioremedial treatment of diesel-contaminated water. The stability of diesel oil degradation in the immobilized cells resulted from the ability of living RN402 cells to attach to material surfaces by biofilm formation, as was shown by CLSM imaging. These characteristics of the immobilized RN402 cells, including high degradative efficacy, stability and flotation, make them suitable for the purpose of continuous wastewater bioremediation.

The copper resistance mechanism in a newly isolated Pseudoxanthomonas spadix ZSY-33.

Resolving the heavy metal resistance mechanisms of microbes is crucial for understanding the bioremediation of the ecological environment. In this study, a multiple heavy metal resistance bacterium, Pseudoxanthomonas spadix ZSY-33 was isolated and characterized. The copper resistance mechanism was revealed by analysis of the physiological traits, copper distribution, and genomic and transcriptomic data of strain ZSY-33 cultured with different concentrations of copper. The growth inhibition assay in basic medium showed that the growth of strain ZSY-33 was inhibited in the presence of 0.5 mM copper. The production of extracellular polymeric substances increased at a lower concentration of copper and decreased at a higher concentration of copper. Integrative analysis of genomic and transcriptomic, the copper resistance mechanism in strain ZSY-33 was elucidated. At a lower concentration of copper, the Cus and Cop systems were responsible for the homeostasis of intracellular copper. As the concentration of copper increased, multiple metabolism pathways, including the metabolism of sulfur, amino acids, and pro-energy were cooperated with the Cus and Cop systems to deal with copper stress. These results indicated a flexible copper resistance mechanism in strain ZSY-33, which may acquire from the long-term interaction with the living environment.

Complete genome sequence of the BTEX-degrading bacterium Pseudoxanthomonas spadix BD-a59.

Pseudoxanthomonas spadix BD-a59, able to metabolize all six BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds, was isolated from gasoline-contaminated sediment. Here, we report the complete 3.45-Mb genome sequence and annotation of strain BD-a59. These advance the understanding of strain BD-a59's genomic properties and pollutant metabolic versatility.

Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities.

We report the first genome sequences for six strains of Rhodanobacter species isolated from a variety of soil and subsurface environments. Three of these strains are capable of complete denitrification and three others are not. However, all six strains contain most of the genes required for the respiration of nitrate to gaseous nitrogen. The nondenitrifying members of the genus lack only the gene for nitrate reduction, the first step in the full denitrification pathway. The data suggest that the environmental role of bacteria from the genus Rhodanobacter should be reevaluated.

Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.

The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

Metabolic characterization and genes for the conversion of biphenyl in Dyella ginsengisoli LA-4.

A complete bph gene cluster (bphLA-4) containing 12,186 bp was amplified from Dyella ginsengisoli LA-4. The bphLA-4 was composed of bphABCXD, and an additional gene encoding a meta-fission product hydrolase was located in the bphX region. BphLA-4 was independently transcribed by the two operons, bphA1A2orf1A3A4BCX0 and bphX1orf2X2X3D, and significantly differed from bphKF707. Both benzoate and catechol induced the expression of both operons. 2-Hydroxypenta-2,4-dienoate was identified as the intermediate of the biphenyl degradation by strain LA-4. This finding suggested that there existed a novel lower pathway of biphenyl degradation in strain LA-4.

Novel indole-mediated potassium ion import system confers a survival advantage to the Xanthomonadaceae family.

Interspecific and intraspecific communication systems of microorganisms are involved in the regulation of various stress responses in microbial communities. Although the significance of signaling molecules in the ubiquitous family Xanthomonadaceae has been reported, the role bacterial communications play and their internal mechanisms are largely unknown. Here, we use Lysobacter enzymogenes, a member of Xanthomonadaceae, to identify a novel potassium ion import system, LeKdpXFABC. This import system participates in the indole-mediated interspecies signaling pathway and matters in environmental adaptation. Compared with the previously reported kdpFABC of Escherichia coli, LekdpXFABC contains a novel indispensable gene LekdpX and is directly regulated by the indole-related two-component system QseC/B. QseC autophosphorylation is involved in this process. The operon LekdpXFABC widely exists in Xanthomonadaceae. Moreover, indole promotes antimicrobial product production at the early exponential phase. Further analyses show that indole enhances potassium ion adsorption on the cell surface by upregulating the production of O-antigenic polysaccharides. Finally, we confirm that LeKdpXFABC mediation by indole is subject to the intraspecific signaling molecules DSFs, of which the biosynthesis genes always exist together with LekdpXFABC. Therefore, as a new idea, the signal collaborative strategy of indole and DSFs might ensure the persistent fitness advantage of Xanthomonadaceae in variable environments.