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Ammonium sulfate wastewater can cause eutrophication and black odor of water body. Although ammonia nitrogen can be used as nutrient of microalgae, high ammonia nitrogen levels could inhibit the growth of microalgae. Nitrobacteria can transform ammonia nitrogen into nitrate nitrogen. In this study, mono Chlorella pyrenoidosa culture (mono-C.py), synchronous mixed culture (mixed-a), and asynchronous mixed culture (mixed-b) systems were examined for their ability to treat ammonium sulfate wastewater. Nitrogen removal rate of mixed-b at the end of culture (52.96%) was higher than that of the mono-C.py (46.37%) and the mixed-a (39.11%). Higher total suspended solid concentration (2.40 g/L), crude protein yield (0.76 g/L), and heating value yield (35.73 kJ/L) were obtained in mixed-b, meanwhile with excellent settlement performance (91.43 ± 0.51%). Mechanism analysis of settlement showed that the relative abundance of floc-forming-related bacteria Sphingopyxis and Acidovorax were increased generally, while nitrification/denitrifying members were decreased in mixed-b along with the culture proceeding.

Biobeds are agriculture-based bioremediation tools used to safely contain and microbially degrade on-farm pesticide waste and rinsate, thereby reducing the negative environmental impacts associated with pesticide use. While these engineered ecosystems demonstrate efficient pesticide removal, the microbiomes in these environments remain largely understudied both taxonomically and functionally. This study used metagenomic and metatranscriptomic techniques to characterize the microbial community in a two-cell Canadian biobed system before and after a field season of pesticide application. These culture-independent approaches identified an enrichment of xenobiotic-degrading bacteria, such as Afipia, Sphingopyxis and Pseudomonas, and enrichment and transcription of xenobiotic-degrading genes, such as peroxidases, oxygenases, and hydroxylases, among others; we were able to directly link the transcription of these genes to Pseudomonas, Oligotropha, Mesorhizobium, Rhodopseudomonas, and Stenotrophomonas taxa.

UV irradiation is known to cause harmful effects on microorganisms. As the result, microorganisms have developed protection against exposure to harmful UV irradiation. We suggested that resistance to UV might be specific characteristic of certain genera of microorganisms. So, the aim of the work is to assess whether there is a correlation between UV resistance and the taxonomic position of microorganisms or is it the adaptation of cells to extreme conditions. There were studied 67 strains from extreme ecosystems (phytocenoses and оrnithogenic soil of the Antarctic, hypersaline ecosystems of the Crimea and the Dead Sea, the lake Baikal). Sequence of 16S rRNA genes, phylogenetic analysis and UV resistance were performed according to standard procedures. Phylogenetic analysis revealed live representatives of the following genera: Pseudomonas, Serratia, Rheinheimera, Aeromonas, Buttiauxella, Brevundimonas, Sphingomonas, Sphingopyxis, Dermacoccus, Frondihabitans, Microbacterium, Rhodococcus, Janthinobacterium, Arthrobacter, Micrococcus, Kocuria, Sphingobacterium, Flavobacterium, Chryseobacterium, Bacillus, Staphylococcus, Paenibacillus, Sporosarcina. Gram-positive bacteria were significantly more resistant to UV irradiation (LD99.99 750–1400 J/m2). Gram-negative had lower resistance (LD99.99 35–150 J/m2). Most pigmented strains were more resistant to UV than non-pigmented ones. According to the values of lethal doses of UV irradiation we suggest that investigated microorganisms have effective mechanisms to repair DNA damages. Resistance of microorganisms to UV, as a rule, was not related to the ecological features of their habitat. Thus, there is a correlation between the resistance of microorganisms to UV irradiation and their taxonomic position, which allows to consider UV resistance as a diagnostic feature at the genus level.

Deoxynivalenol (DON) is commonly found in wheat and wheat-derived foods, posing a threat to human health. Biodegradation is an efficient and eco-friendly measure for mycotoxin detoxification. Understanding the mechanism of DON biodegradation is hence of great importance. Herein, we report the application of metabolomics methods for the analysis of DON degradation by a bacterial consortium isolated from wheat leaves collected in Jiangsu Province. Metabolomics analysis combined with a nuclear magnetic resonance analysis revealed the main degradation product, 3-keto-DON, and a minor degradation product, 3-epi-DON. Further study illustrated that DON underwent a two-step epimerization through the intermediate 3-keto-DON. Sequencing analysis of the 16S rRNA metagenome of the microorganismal community suggested that the abundance of three bacterial genera, Achromobacter, Sphingopyxis, and Sphingomonas, substantially increased during the coculture of bacterial consortium and DON. Further investigation revealed that Devosia sp. might be responsible for the epimerization of 3-keto-DON. These findings shed light on the catabolic pathways of DON during biodegradation and illustrate the potential of using metabolomics approaches in biodegradation studies.Key Points• A bacterial consortium was isolated with good deoxynivalenol-degrading potential. • Metabolomics approaches were successfully used to interpret the degradation pathway. • A trace-amount degradation product was determined by metabolomics and NMR analysis. Graphical Abstract .

Two Gram-stain-negative, aerobic, motile and rod-shaped bacteria, one designated as strain AXBT, capable of degrading estrogens, and another, YL23T, capable of degrading estrogen and bisphenol A, were isolated from activated sludge in Xiamen City, PR China. The optimum temperature and pH of both strains were 25–35 °C and pH 7.0–8.0. While strain AXBT could tolerate 3 % (w/v) NaCl, YL23T could only grow between 0–1 % (w/v) NaCl. They contained ubiquinone-10 as the major quinone, spermidine as the major polyamine, summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c) as the major fatty acids and diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as the major polar lipids. The DNA G+C contents of strains AXBT and YL23T were 63.6 and 63.7 mol%, respectively. Based on the results of 16S rRNA gene sequence analysis, strains AXBT and YL23T belonged to the genus Sphingobium . Strain AXBT was most closely related to Sphingobium chlorophenolicum NBRC 16172T (97.5 %) and Sphingobium chungbukense DJ77T (97.2 %), and strain YL23T was most closely related to S. chlorophenolicum NBRC 16172T (97.4 %) and S. quisquiliarum P25T (97.1 %). Average nucleotide identity values between these two strains and S. chlorophenolicum NBRC 16172T, S. chungbukense DJ77T, Sphingobium chinhatense IP26T, Sphingobium quisquiliarum P25T and Sphingobium japonicum UT26ST were from 80.7 to 85.8 %. In conclusion, strains AXBT and YL23T represent novel species of the genus Sphingobium , for which the names Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov. are proposed, respectively. The type strains of S. estronivorans and S. bisphenolivorans are AXBT (=MCCC 1K01232T=DSM 102173T) and YL23T (=MCCC 1K02300T=DSM 102172T), respectively.

rac-Dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in rac-dichlorprop degradation. However, the compositions of the microbial consortia involved in rac-dichlorprop degradation remain largely unknown. In this study, DNA stable isotope probing (SIP) and metagenomic analysis were integrated to reveal the key microbial consortium responsible for rac-dichlorprop degradation in a rac-dichlorprop-degrading enrichment. OTU340 (Sphingobium sp.) and OTU348 (Sphingopyxis sp.) were significantly enriched in the rac-[13C]dichlorprop-labeled heavy DNA fractions. A rac-dichlorprop degrader, Sphingobium sp. strain L3, was isolated from the enrichment by a traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomic analysis of the associations between rac-dichlorprop degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes rdpA and sdpA, involved in the initial degradation of the (R)- and (S)-enantiomers of dichlorprop, respectively, were mostly taxonomically assigned to Sphingobium species, indicating that Sphingopyxis species might harbor novel dichlorprop-degrading genes. In addition, taxonomically diverse bacterial genera such as Dyella, Sphingomonas, Pseudomonas, and Achromobacter were presumed to synergistically cooperate with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. IMPORTANCE Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide rac-dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of the microbial consortium and the interactions between community members during the biodegradation of rac-dichlorprop are unclear. In this study, DNA-SIP and metagenomic analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders Dyella, Sphingomonas, Pseudomonas, and Achromobacter synergistically cooperated with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. Our study provides new insights into the synergistic degradation of rac-dichlorprop at the community level and implies the existence of novel degrading genes for rac-dichlorprop in nature.

The mycotoxin deoxynivalenol (DON), produced in wheat, barley and maize by Fusarium graminearum and Fusarium culmorum, is threatening the health of humans and animals. With its worldwide high incidence in food and feed, mitigation strategies are needed to detoxify DON, maintaining the nutritional value and palatability of decontaminated commodities. A promising technique is biological degradation, where microorganisms are used to biotransform mycotoxins into less toxic metabolites. In this study, bacterial enrichment cultures were screened for their DON detoxification potential, where DON and its potential derivatives were monitored. The residual phytotoxicity was determined through a bioassay using the aquatic plant Lemna minor L. Two bacterial enrichment cultures were found to biotransform DON into a still highly toxic metabolite for plants. Furthermore, a cytotoxic effect was observed on the cellular viability of intestinal porcine epithelial cells. Through liquid chromatography high-resolution mass spectrometry analysis, an unknown compound was detected, and tentatively characterized with a molecular weight of 30.0 Da (i.e., CH2O) higher than DON. Metabarcoding of the subsequently enriched bacterial communities revealed a shift towards the genera Sphingopyxis, Pseudoxanthomonas, Ochrobactrum and Pseudarthrobacter. This work describes the discovery of a novel bacterial DON-derived metabolite, toxic to plant and porcine cells.

According to the characteristics of aniline dyeing wastewater, aerobic biological treatment was adopted herein, and high-throughput sequencing technology was used to analyze the changes to the microbial community structure and diversity in the aerobic sludge acclimation stage. As a result, according to the experimental study on the effects of different biomass, the initial pH value and the salinity with the aerobic biological treatment, the chemical oxygen demand (COD) degradation rate can increase linearly with the increase in biomass under different biomass conditions. The organic matter degradation rate is 6.24 mg/L COD·h−1·(mg/L·MLSS)−1, with a correlation coefficient (R2) of 0.98704. When the initial pH value is less than 7.0 ± 0.2, the COD degradation rate increases with the increase in the initial pH value and then decreases gradually. The optimal sludge concentration is 4 g/L, the optimal initial pH value is in the range of 7.0–8.0, the optimal salinity is 1.7%. When the initial concentration of COD is 3000 mg/L, the COD value gradually stabilizes and decreases to 1500 mg/L after 32 h, the degradation rate reaches 50%, and the pH decreases from 7.5 to 4.5. Sphingopyxis has been detected in sludge samples from the third cycle of acclimation, which can biodegrade aromatic compounds, anthraquinone dyes, and their intermediates, and the relative abundance of Sphingopyxis increased from 0.18% to 5.08%, indicating a potential biodegradation ability of aniline dyeing wastewater.

The aromatic compound phenylacetic acid (PAA) is present in the environment, and released in the catabolism of phenylalanine, 2-phenylethylamine, or environmental contaminants such as ethylbenzene and styrene. PAA was also proposed to be involved in human chronic kidney disease development. Several bacteria and fungi utilize these aromatic acids as sole carbon source either during aerobic or anaerobic conditions. The aromatic structure of PAA makes this compound resistant toward oxidation or reduction, because the stabilizing resonance energy of the aromatic ring system is difficult to overcome. In the case of bacteria that utilize aromatic compounds as growth substrates, the aromatic ring system limits survival due to a lack of carbon source. Sphingopyxis sp. YF1 isolated from Lake Taihu was found to be beneficial in bioremediation of aromatic compounds. This study thus aimed to examine the influence of environmental factors such as temperature, PAA concentration, and pH on the effectiveness of Sphingopyxis sp. YF1 to degrade aromatic compounds using PAA as model compound. Data showed the highest PAA-degrading rate of strain Sphingopyxis sp. YF1 was 7.6 mg/L·h under the condition of 20°C, pH 9 with a 1000 μg/ml concentration of PAA. Evidence indicates that PAA-degrading ability of strain Sphingopyxis sp. YF1 appears to be primarily influenced by the concentration of PAA, followed by temperature and pH. PAA-degrading gene PAAase was identified in this strain using polymerase chain reaction (PCR) method. These results illustrate that the bacteria Sphingopyxis sp. YF1 removes PAA effectively at certain environmental conditions and this proves beneficial in bioremediation of aromatic compounds.

3-Nitro-1,2,4-triazol-5-one (NTO) is one of the main ingredients of many insensitive munitions, which are being used as replacements for conventional explosives. As its use becomes widespread, more research is needed to assess its environmental fate. Previous studies have shown that NTO is biologically reduced to 3-amino-1,2,4-triazol-5-one (ATO). However, the final degradation products of ATO are still unknown. We have studied the aerobic degradation of ATO by enrichment cultures derived from the soil. After multiple transfers, ATO degradation was monitored in closed bottles through measurements of inorganic carbon and nitrogen species. The results indicate that the members of the enrichment culture utilize ATO as the sole source of carbon and nitrogen. As ATO was mineralized to CO2, N2, and NH4+, microbial growth was observed in the culture. Co-substrates addition did not increase the ATO degradation rate. Quantitative polymerase chain reaction analysis revealed that the organisms that enriched using ATO as carbon and nitrogen source were Terrimonas spp., Ramlibacter-related spp., Mesorhizobium spp., Hydrogenophaga spp., Ralstonia spp., Pseudomonas spp., Ectothiorhodospiraceae, and Sphingopyxis. This is the first study to report the complete mineralization of ATO by soil microorganisms, expanding our understanding of natural attenuation and bioremediation of the explosive NTO.

N-Acylhomoserine lactone (AHL)-degrading enzyme is identified from the various environments and applied for quorum-sensing inhibition. In this study, we isolated two AHL-degrading strains, Sphingopyxis sp. EG6 and FD7, from the industrial cooling water samples. When the eight Sphingopyxis type strains were checked for the AHL-degrading activity, two strains, Sphingopyxis alaskensis DSM 13593 and Sphingopyxis bauzanensis DSM 22271, showed high AHL-degrading activity. The complete genome sequences of EG6 and FD7 revealed the presence of gene homolog of qsdS, which encodes AHL-lactonase in Sphingomonas ursincola. The qsdS gene is seated between putative gene homologs involved in 3-isopropylmalate dehydratase large (leuC2) and small (leuD) subunits in the genome of EG6, FD7, DSM 13593, and DSM 22271, but completely disappeared between leuC2 and leuD in the genome sequences of Sphingopyxis type strains without AHL-degrading activity. Purified His-tagged QsdS showed high AHL-degrading activity and catalyzed AHL ring opening by hydrolyzing lactones. In addition, heterologous expression of qsdS in Pseudomonas aeruginosa resulted in reduction of biofilm formation. These results suggested that the AHL-degrading activity in Sphingopyxis is useful as an effective agent for biofilm inhibition.

An aerobic, Gram-stain-negative, rod-shaped, non-motile, mesophilic soil bacterium, strain WS5A3pT, was isolated from a pesticide burial site in north-west Poland. The strain grew at 12–37 °C, at pH 8–9 and with 0–2 % (w/v) NaCl. The main fatty acids detected in WS5A3pT were summed feature 3, summed feature 8 and C16 : 0. The major respiratory quinone was Q-10 and major polar lipids were phosphatidylethanolamine, sphingoglycolipid and phosphatidylglycerol. The G+C content of the genome was 65.1 mol%. Phylogenetic pairwise distance analysis of the 16S rRNA gene placed this strain within the genus Sphingopyxis , with the highest similarity to Sphingopyxis witflariensis W-50T (98.8 %), Sphingopyxis bauzanensis BZ30T and Sphingopyxis ginsengisoli Gsoil 250T (98.3 %) and Sphingopyxis granuli NBRC 100800T (98.09 %). Genomic similarity analyses using ANIb and dDDH algorithms indicated levels of similarity of 81.44, 80.84 and 81.16 % between WS5A3pT and S. witflariensis , S. bauzanensis and S. granuli , respectively for average nucleotide identity and 25.90, 25.00 and 26.10 % for digital DNA–DNA hybridization. Based on the phylogenetic and phenotypic data, strain WS5A3pT should be considered as a representative of a novel Sphingopyxis species. The name Sphingopyxis lindanitolerans sp. nov. is proposed with the type strain WS5A3pT (=DSM 106274T=PCM 2932T).

A three-step method to prepare dual graphene modified bioelectrode (D-GM-BE) in microbial fuel cell (MFC) in previous studies. This study explored the biodegradation of oxytetracycline (OTC) and electricity generation in O-D-GM-BE MFC. The OTC removal efficiency of graphene modified biocathode and bioanode (O-GM-BC, O-GM-BA) was 95.0% and 91.8% in eight days. The maximum power density generated by O-D-GM-BE MFC was 86.6 ± 5.1 mW m−2, which was 2.1 times of that in OTC control bioelectrode (O-C-BE) MFC. The Rct of O-GM-BA and O-GM-BC were decreased significantly by 78.3% and 76.3%. OTC was biodegraded to monocyclic benzene compounds by bacteria. O-GM-BA was affected strongly by OTC, and Salmonella and Trabulsiella were accounted for 83.0%, while typical exoelectrogens (Geobacter) were still enriched after the maturity of biofilm. In O-GM-BC, bacteria related with OTC biodegradation (Comamonas, Ensifer, Sphingopyxis, Pseudomonas, Dechloromonas, etc.) were enriched, which contributed to the high removal efficiency of OTC.

Biobeds are agriculture-based bioremediation tools used to safely contain and microbially degrade on-farm pesticide waste and rinsate, thereby reducing the negative environmental impacts associated with pesticide use. While these engineered ecosystems demonstrate efficient pesticide removal, their microbiome dynamics remain largely understudied both taxonomically and functionally. As such, further characterization of these parameters may aid in the optimization of biobed management and deployment. This study used metagenomic and metatranscriptomic techniques to characterize the microbial community in a two-cell Canadian biobed system before and after a field season of pesticide application. These culture-independent approaches identified an enrichment of xenobiotic-degrading bacteria, such as Afipia, Sphingopyxis and Pseudomonas, and enrichment and transcription of xenobiotic-degrading genes, such as peroxidases, oxygenases, and hydroxylases, among others; we were able to directly link the transcription of these genes to Pseudomonas, Oligotropha, Mesorhizobium, Rhodopseudomonas, and Stenotrophomonas taxa.

Clone libraries of bacterial 16S rRNA genes (a total of 1,980 clones) were constructed from the leaf blades, petioles, taproots, and lateral roots of sugar beet (Beta vulgaris L.) grown under different fertilization conditions. A principal coordinate analysis revealed that the structures of bacterial communities in above- and underground tissues were largely separated by PC1 (44.5%). The bacterial communities of above-ground tissues (leaf blades and petioles) were more tightly clustered regardless of differences in the tissue types and fertilization conditions than those of below-ground tissues (taproots and lateral roots). The bacterial communities of below-ground tissues were largely separated by PC2 (26.0%). To survey plant growth-promoting bacteria (PGPBs), isolate collections (a total of 665 isolates) were constructed from the lateral roots. As candidate PGPBs, 44 isolates were selected via clustering analyses with the combined 16S rRNA gene sequence data of clone libraries and isolate collections. The results of inoculation tests using sugar beet seedlings showed that eight isolates exhibited growth-promoting effects on the seedlings. Among them, seven isolates belonging to seven genera (Asticcacaulis, Mesorhizobium, Nocardioides, Sphingobium, Sphingomonas, Sphingopyxis, and Polaromonas) were newly identified as PGPBs for sugar beet at the genus level, and two isolates belonging to two genera (Asticcacaulis and Polaromonas) were revealed to exert growth-promoting effects on the plant at the genus level for the first time. These results suggest that a community analysis-based selection strategy will facilitate the isolation of novel PGPBs and extend the potential for the development of novel biofertilizers.

Sphingomonadaceae has a large number of strains that can biodegrade hepatotoxins or environmental pollutants. The latest research reported that certain strains can also produce lutein. Based on the third-generation sequencing technology, we analyzed the whole genome sequence and compared related functional genes of two strains of Sphingomonadaceae isolated from different habitats. The genome of Sphingopyxis USTB-05 was 4,679,489 bp and contained 4312 protein coding genes. The 4,239,716 bp nuclear genome of Sphingomonas morindae NBD5, harboring 3882 protein coding genes, has two sets of chromosomes. Both strains had lutein synthesis metabolism pathway sharing identical synthetic genes of crtB, crtE, crtI, crtQ, crtL, crtR, atoB, dxs, dxr, ispD, ispE, ispDF, gcpE, ispG, ispH, ispA, ispB and ispU. Sphingopyxis USTB-05 had hepatotoxins microcystins and nodularin metabolic pathways related to 16 genes (ald, ansA, gdhA, crnA, phy, ocd, hypdh, spuC, nspC, speE, murI, murD, murC, hmgL, bioA and glsA), while these genes were not found in Sphingomonas morindae NBD5. The unique protein sequences of strain NBD5 and strain USTB-05 were 155 and 199, respectively. The analysis of whole genome of the two Sphingomonadaceae strains provides insights into prokaryote evolution, the new pathway for lutein production and the new genes for environmental pollutant biodegradation.IMPORTANCEUnderstanding the functional genes related to the special functions of strains is essential for humans to utilize microbial resources. The ability of Sphingopyxis USTB-05 to degrade hepatotoxins microcystins and nodularin has been studied in depth, however the complete metabolic process still needs further elucidation. Sphingomonas morindae NBD5 can produce lutein, and it is necessary to determine whether there is a new pathway of lutein. In this study, the whole genome sequencing of Sphingopyxis USTB-05 and Sphingomonas morindae NBD5 were performed for the first time. Lutein synthesis metabolic pathways and synthetic genes were discovered in Sphingomonadaceae. We predicted the existence of new lutein synthesis pathways and revealed most of the genes of the new synthesis pathways. A comparative analysis of the functional genes of the two strains revealed that Sphingopyxis USTB-05 contains a large number of functional genes related to the biodegradation of hepatotoxins or hexachlorocyclohexane. Among them, the functional genes related to the biodegradation and metabolism of hexachlorocyclohexane had not been previously reported. These findings lay the foundation for the biosynthesis of lutein using Sphingomonas morindae NBD5 or Sphingopyxis USTB-05 and the application of Sphingopyxis USTB-05 for the biodegradation of hepatotoxins microcystins and nodularin or environmental pollutants.

A total of 100 environmental samples were investigated for their ability to degrade 1 g/L surfactin as a substrate. Among them, two enrichment cultures, which exhibited microbial growth as well as surfactin degradation, were selected and further investigated. After several successive cultivations, nanopore sequencing of full-length 16S rRNA genes with MinIONTM was used to analyze the bacterial species in the enrichment cultures. Variovorax spp., Caulobacter spp., Sphingopyxis spp., and Pseudomonas spp. were found to be dominant in these surfactin-degrading mixed cultures. Finally, one strain of Pseudomonas putida was isolated as a surfactin-degrading bacterium. This strain degraded 1 g/L surfactin below a detectable level within 14 days, and C13 surfactin was degraded faster than C15 surfactin.

During the study into the microbial biodiversity and bioactivity of the Microcystis phycosphere, a new yellow-pigmented, non-motile, rod-shaped bacterium containing polyhydroxybutyrate granules designated as strain Z10-6T was isolated from highly-toxic Microcystis aeruginosa Kutzing M.TN-2. The new isolate produces active bioflocculating exopolysaccharides. Phylogenetic analysis based on 16S rRNA gene sequences indicated strain Z10-6T belongs to the genus Sphingopyxis with highest similarity to Sphingopyxis solisilvae R366T (98.86%), and the similarity to other Sphingopyxis members was less than 98.65%. However, both low values obtained by phylogenomic calculation of average nucleotide identity (ANI, 85.5%) and digital DNA-DNA hybridization (dDDH, 29.8%) separated the new species from its closest relative. The main polar lipids were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and one unidentified aminophospholipid. The predominant fatty acids were summed feature 8, C17:1ω6c, summed feature 3, C16:0, C18:1ω7c 11-methyl and C14:0 2-OH. The respiratory quinone was ubiqunone-10, with spermidine as the major polyamine. The genomic DNA G + C content was 64.8 mol%. Several biosynthesis pathways encoding for potential new bacterial bioactive metabolites were found in the genome of strain Z10-6T. The polyphasic analyses clearly distinguished strain Z10-6T from its closest phylogenetic neighbors. Thus, it represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis microcysteis sp. nov. is proposed. The type strain is Z10-6T (= CCTCC AB2017276T = KCTC 62492T).

The response of plant endophytes to disease within infected tissues has been well demonstrated, but the corresponding response of endophytes in non-lesion tissues remains unclear. Here, we studied the composition and distribution of bacterial endophytes in potato roots (RE), stems (SE), and tubers (TE), and explored the response of endophytes in non-lesion tissues to potato common scab (PCS), which is a soil-borne disease caused by pathogenic Streptomyces and results in serious losses to the global economy every year. Via high-throughput sequencing, it was seen that the composition of endophytes in roots, stems, and tubers had significant differences (P < 0.05) and the distribution of the bacterial communities illustrated a gradient from soil to root to tuber/stem. PCS significantly reduced bacterial endophytes α-diversity indexes, including ACE and the number of observed operational taxonomic units (OTUs), of RE without significantly reducing the indexes of SE and TE. No significant effect on the composition of endophytes were caused by PCS in roots, tubers, or stems between high PCS severity (H) and low PCS severity (L) infections at the community level, but PCS did have a substantial impact on the relative abundance of several specific endophytes. Rhizobium and Sphingopyxis were significantly enriched in root endophytes with low PCS severity (REL); Delftia and Ochrobactrum were significantly enriched in stem endophytes with low PCS severity (SEL); Pedobacter, Delftia, and Asticcacaulis were significantly enriched in tuber endophytes with high PCS severity (TEH). OTU62, a potential PCS pathogen in this study, was capable of colonizing potato tubers, roots, and stems with few or no symptoms present. Co-occurrence networks showed that the number of correlations to OTU62 was higher than average in these three tissue types, suggesting the importance of OTU62 in endophytic communities. This study clarified the distribution and composition of potato endophytes in tubers, roots, and stems, and demonstrated the response of endophytes in non-lesion tissues to PCS.

Field experiments was conducted to evaluate the effectiveness of sepiolite (S), sepiolite + fungi residues (SFR) and sepiolite + vermicompost (SVC) on in situ immobilization remediation of Cd contaminated soils. The results showed that treatments of S, SFR and SVC decreased soil Cd availability by 15.2–47.8%, 17.5–44.9% and 13.2–44.9%, respectively, when compared with the control groups. Moreover, the content of Cd in edible parts of Lactuca sativa L., Cichorium endivia L. and Brassica campestris L. was experienced a decrease of 15.9–41.9%, 1.6–38.0% and 29.0–37.4% reduction, respectively, under the amended soil. The improvement of soil fertility was obtained under addition of SVC and SFR, while the amounts of available P, K, organic matter, microbial carbon, microbial nitrogen and dehydrogenase activity were increased by 9.6–68.2%, 1.2–28.3%, 37.5–70.5%, 4.1–121.0%, 220–640% and 6.8–56.8%, respectively, in contrast to CK. Moreover, high-throughput sequencing analysis showed that the combined treated soils got higher values of alpha diversity indices, Chao1, ACE and Shannon. The number of dominant phyla (Proteobacteria, Acidobacteria, Gemmatimonadetes, Crenarchaeota) and genera (Aquicella, Lysobacter, Candidatus Nitrososphaera, Sphingopyxis, Mesorhizobium) were enhanced. Therefore, the use of sepiolite and organic amendments could be an adequate strategy to immobilization remediation of Cd–contaminated soils.

Algae and bacteria establish complex relationships reciprocally influencing their growth. Associated bacterial communities alter microalgae metabolism and physiology, affecting biomass yield and quality. In this study, 203 bacterial isolates (33 different genera), recovered from Tetraselmis suecica F&M-M33 cultures, were identified and phenotypically characterized in relation to the microalgal growth-promoting (MGP) features of indol-3-acetic acid (IAA) and siderophore production. IAA production was observed in 30 isolates belonging to 10 genera, whilst siderophore production was observed in 12 isolates belonging to nine genera, indicating that bacteria which are phylogenetically different within the phycosphere community may contribute in similar ways to boosting algal growth. Moreover, strains belonging to a single genus (e.g. Bacillus, Muricauda, Labrenzia and Amorphus) showed different MGP features, but none of these isolates were capable of producing both growth-promoting factors. Twenty-two selected strains were further tested in co-culture assays to evaluate their effect on T. suecica F&M-M33 growth; four induced an increase in microalgal productivity. The exo-metabolome of T. suecica F&M-M33 cultures, either axenically or when co-cultured with either Vitellibacter strain AAD2 or Sphingopyxis flavimaris strain AG5, was determined using a non-targeted metabolomics approach using an Ultra High Performance Liquid Chromatography (UHPLC) system. This allowed for the detection of 133 entities (small chemical molecules, e.g. metabolites), of which 84 were identified. Most of the entities were common in all three cultures, showing that the T. suecica F&M-M33 phycosphere was rich in small peptides and organic acids, and a high number of terpenes were also observed. Seventeen entities were culture-specific, suggesting that they were directly related to microalgae–bacteria interactions.

In this study, the biodegradation towards aryl organophosphate flame retardants (aryl-OPFRs) was investigated by the Rhodococcus-Sphingopyxis consortium, mixture of strain Rhodococcus sp. YC-JH2 and Sphingopyxis sp. YC-JH3. The optimal ratio between the two composition strains was determined as 1:1. Under the optimum condition (pH 8, 35 °C and 0% salinity), the consortium could utilize aryl-OPFRs as sole carbon source and degrade them rapidly with half-life of 4.53, 21.11 and 23.0 h for triphenyl phosphate (TPhP), tricresyl phosphate (TCrP) and 2-ethylhexyl diphenyl phosphate (EHDPP) respectively. The consortium maintained high degrading efficiency under a wide of range of pH (6–10), temperature (20–40 °C) and salinity (0–6%). Besides, the consortium could rapidly degrade high concentration of TPhP and no inhibitory effect towards degradation speed was observed up to 500 mg/L. The effect of metal ions and surfactants was estimated. Most metal ions exhibited significant inhibition, except Zn2+ and Pb2+, which showed no effect or slight promotion. Ionic surfactants could severely reduce the degrading capacity, while nonionic surfactants showed no effect. With abundant inoculation of the consortium, mineralization higher than 75% could be achieved within a week. This study provides efficient microorganisms for bioremediation of aryl-OPFRs contamination.

This study aimed to explore the dynamics of microbial communities and antibiotic resistance genes (ARGs) during biofilm formation on polypropylene random (PPR), polyvinyl chloride and stainless steel pipes in domestic hot water system (DHWS), as well as their interactions. Full-scale classification was used to divide abundant and rare genera with 0.1% and 1% as the thresholds. The biofilm community structure presented a temporal pattern, which was mainly determined by conditionally rare or abundant taxa (CRAT) and conditionally rare taxa (CRT). The dynamics of microbial community during biofilm formation were observed, and the effect of pipe material on conditionally abundant taxa (CAT) and CRAT was greater than CRT and rare taxa (RT). CRAT showed the most complex internal associations and were identified as the core taxa. Notably, CRT and RT with low relative abundance, also played an important role in the network. For potential pathogens, 17 genera were identified in this study, and their total relative abundance was the highest (3.6-28.9%) in PPR samples. Enterococcus of CRAT was the dominant potential pathogen in young biofilms. There were 36 more co-exclusion patterns (140) observed between potential pathogens and nonpathogenic bacteria than co-occurrence (104). A total of 38 ARGs were predicted, and 109 negative and 165 positive correlations were detected between them. Some potential pathogens (Escherichia/Shigella and Burkholderia) and nonpathogenic bacteria (Meiothermus and Sphingopyxis) were identified as the possible hosts of ARGs. This study is helpful for a comprehensive understanding of the biofilm microbial community and ARGs, and provides a reference for the management and biosafety guarantee of newly-built DHWS.

The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.

Background Biofilm formation in dental unit waterlines (DUWL) may lead to health risks for dental staff and patients. Therefore, dental unit waterlines need to be disinfected, for instance by using chemical disinfectants. However, the application of chemical disinfectants may lead to the selection of specific microorganisms. Therefore, the aim of our study was to assess the microbial composition of water-derived biofilms, after a continuous exposure to maintenance doses of commercially available chemical disinfectants, in vitro. Methods The AAA-model was used to grow water derived biofilms. The biofilms were subjected to the maintenance dose of each disinfectant. To determine the microbial composition, the V4 hypervariable region of the 16S rRNA gene was sequenced. The sequences were clustered in operational taxonomic units (OTUs). Results The bacterial composition of biofilms in all treatment groups differed significantly (PERMANOVA F = 4.441, p = 0.001). Pairwise comparisons revealed Anoxyl treated biofilms were significantly different from all groups (p = 0.0001). In the Anoxyl-treated biofilms, the relative abundance of Comamonadaceae and Sphingopyxis was high compared to the Dentosept, Green and Clean and Oxygenal groups. Conclusion We concluded that exposure to low doses of the chlorine-based chemical disinfectant Anoxyl led to a substantially different composition of water derived biofilms compared to biofilms exposed to H2O2-based chemical disinfectants.

Sphingopyxis granuli strain TFA is an alpha-proteobacterium that belongs to the sphingomonads, a group of bacteria well-known for its degradative capabilities and oligotrophic metabolism. Strain TFA is the only bacterium in which the mineralisation of the aromatic pollutant tetralin has been completely characterized at biochemical, genetic, and regulatory levels and the first Sphingopyxis characterised as facultative anaerobe. Here we report additional metabolic features of this alpha-proteobacterium using metabolic modelling and the functional integration of genomic and transcriptomic data. The genome-scale metabolic model (GEM) of strain TFA, which has been manually curated, includes information on 743 genes, 1114 metabolites and 1397 reactions. This represents the largest metabolic model for a member of the Sphingomonadales order thus far. The predictive potential of this model was validated against experimentally calculated growth rates on different carbon sources and under different growth conditions, including both aerobic and anaerobic metabolisms. Moreover, new carbon and nitrogen sources were predicted and experimentally validated. The constructed metabolic model was used as a platform for the incorporation of transcriptomic data, generating a more robust and accurate model. In silico flux analysis under different metabolic scenarios highlighted the key role of the glyoxylate cycle in the central metabolism of strain TFA., This research was funded by Ministerio de Ciencia, Innovación y Universidades,grant numbers BIO2014-57545-R, BIO2014-59528-JIN, and BIO2016-79736-R.

The choice of the study objective was affected by numerous controversies and concerns around bisphenol F (BPF) and bisphenol S (BPS)&mdash, analogues of bisphenol A (BPA). The study focused on the determination and comparison of the scale of the BPA, BPF, and BPS impact on the soil microbiome and its enzymatic activity. The following parameters were determined in soil uncontaminated and contaminated with BPA, BPF, and BPS: the count of eleven groups of microorganisms, colony development (CD) index, microorganism ecophysiological diversity (EP) index, genetic diversity of bacteria and activity of dehydrogenases (Deh), urease (Ure), catalase (Cat), acid phosphatase (Pac), alkaline phosphatase (Pal), arylsulphatase (Aryl) and &beta, glucosidase (Glu). Bisphenols A, S and F significantly disrupted the soil homeostasis. BPF is regarded as the most toxic, followed by BPS and BPA. BPF and BPS reduced the abundance of Proteobacteria and Acidobacteria and increased that of Actinobacteria. Unique types of bacteria were identified as well as the characteristics of each bisphenol: Lysobacter, Steroidobacter, Variovorax, Mycoplana, for BPA, Caldilinea, Arthrobacter, Cellulosimicrobium and Promicromonospora for BPF and Dactylosporangium Geodermatophilus, Sphingopyxis for BPS. Considering the strength of a negative impact of bisphenols on the soil biochemical activity, they can be arranged as follows: BPS &gt, BPF &gt, BPA. Urease and arylsulphatase proved to be the most susceptible and dehydrogenases the least susceptible to bisphenols pressure, regardless of the study duration.

Rough-skinned newts (Taricha granulosa) use tetrodotoxin (TTX) to block voltage-gated sodium (Nav) channels as a chemical defense against predation. Interestingly, newts exhibit extreme population-level variation in toxicity attributed to a coevolutionary arms race with TTX-resistant predatory snakes, but the source of TTX in newts is unknown. Here, we investigated whether symbiotic bacteria isolated from toxic newts could produce TTX. We characterized the skin-associated microbiota from a toxic and non-toxic population of newts and established pure cultures of isolated bacterial symbionts from toxic newts. We then screened bacterial culture media for TTX using LC-MS/MS and identified TTX-producing bacterial strains from four genera, including Aeromonas, Pseudomonas, Shewanella, and Sphingopyxis. Additionally, we sequenced the Nav channel gene family in toxic newts and found that newts expressed Nav channels with modified TTX binding sites, conferring extreme physiological resistance to TTX. This study highlights the complex interactions among adaptive physiology, animal-bacterial symbiosis, and ecological context., eLife digest Rough-skinned newts produce tetrodotoxin or TTX, a deadly neurotoxin that is also present in some pufferfish, octopuses, crabs, starfish, flatworms, frogs, and toads. It remains a mystery why so many different creatures produce this toxin. One possibility is that TTX did not evolve in animals at all, but rather it is made by bacteria living on or in these creatures. In fact, scientists have already shown that TTX-producing bacteria supply pufferfish, octopus, and other animals with the toxin. However, it was not known where TTX in newts and other amphibians comes from. TTX kills animals by blocking specialized ion channels and shutting down the signaling between neurons, but rough-skinned newts appear insensitive to this blockage, making it likely that they have evolved defenses against the toxin. Some garter snakes that feed on these newts have also evolved to become immune to the effects of TTX. If bacteria are the source of TTX in the newts, the emergence of newt-eating snakes resistant to TTX must be putting evolutionary pressure on both the newts and the bacteria to boost their anti-snake defenses. Learning more about these complex relationships will help scientists better understand both evolution and the role of beneficial bacteria. Vaelli et al. have now shown that bacteria living on rough-skinned newts produce TTX. In the experiments, bacteria samples were collected from the skin of the newts and grown in the laboratory. Four different types of bacteria from the samples collected produced TTX. Next, Vaelli et al. looked at five genes that encode the channels normally affected by TTX in newts and found that all them have mutations that prevent them from being blocked by this deadly neurotoxin. This suggests that bacteria living on newts shape the evolution of genes critical to the animals’ own survival. Helpful bacteria living on and in animals have important effects on animals’ physiology, health, and disease. But understanding these complex interactions is challenging. Rough-skinned newts provide an excellent model system for studying the effects of helpful bacteria living on animals. Vaelli et al. show that a single chemical produced by bacteria can impact diverse aspects of animal biology including physiology, the evolution of their genes, and their interactions with other creatures in their environment.

Members of genus Sphingopyxis are frequently found in diverse eco-environments worldwide and have been traditionally considered to play vital roles in the degradation of aromatic compounds. Over recent decades, many aromatic-degrading Sphingopyxis strains have been isolated and recorded, but little is known about their genetic nature related to aromatic compounds biodegradation. In this study, bacterial genomes of 19 Sphingopyxis strains were used for comparative analyses. Phylogeny showed an ambiguous relatedness between bacterial strains and their habitat specificity, while clustering based on Cluster of Orthologous Groups suggested the potential link of functional profile with substrate-specific traits. Pan-genome analysis revealed that 19 individuals were predicted to share 1,066 orthologous genes, indicating a high genetic homogeneity among Sphingopyxis strains. Notably, KEGG Automatic Annotation Server results suggested that most genes pertaining aromatic compounds biodegradation were predicted to be involved in benzoate, phenylalanine, and aminobenzoate metabolism. Among them, β-ketoadipate biodegradation might be the main pathway in Sphingopyxis strains. Further inspection showed that a number of mobile genetic elements varied in Sphingopyxis genomes, and plasmid-mediated gene transfer coupled with prophage- and transposon-mediated rearrangements might play prominent roles in the evolution of bacterial genomes. Collectively, our findings presented that Sphingopyxis isolates might be the promising candidates for biodegradation of aromatic compounds in pollution sites.

Kuwait is a country with a very high dust loading; in fact it bears the world’s highest particulate matter concentration in the outdoor air. The airborne dust often has associated biological materials, including pathogenic microbes that pose a serious risk to the urban ecosystem and public health. This study has established the baseline taxonomic characterization of microbes associated with dust transported into Kuwait from different trajectories. A high volume air sampler with six-stage cascade impactor was deployed for sample collection at a remote as well as an urban site. Samples from three different seasons (autumn, spring and summer) were subjected to targeted amplicon sequencing. A set of ~ 50 and 60 bacterial and fungal genera, respectively, established the core air microbiome. The predominant bacterial genera (relative abundance ≥ 1%) wereBrevundimonas(12.5%),Sphingobium(3.3%),Sphingopyxis(2.7%),Pseudomonas(2.5%),Sphingomonas(2.4%),Massilia(2.3%),Acidovorax(2.0%),Allorhizobium(1.8%),Halomonas(1.3%), andMesorhizobium(1.1%), and the fungal taxa wereCryptococcus(12%) followed byAlternaria(9%),Aspergillus(7%),Candida(3%),Cladosporium(2.9%),Schizophyllum(1.6%),Fusarium(1.4%),Gleotinia(1.3%) andPenicillium(1.15%). Significant spatio-temporal variations were recorded in terms of relative abundances, α-diversities, and β-diversities of bacterial communities. The dissimilarities were less pronounced and instead the communities were fairly homogenous. Linear discrimant analysis revealed three fungal genera known to be significantly differentially abundant with respect to different size fractions of dust. Our results shed light on the spatio-temporal distribution of airborne microbes and their implications in general health.

Global dRNA-seq analysis of transcription start sites combined with in silico annotation using Infernal software revealed the expression of 91 putative non-coding sRNA in Sphingopyxis granuli TFA cells grown on different carbon sources. Excluding housekeeping sRNAs, only one additional sRNA, which belongs to the Rfam SuhB family (RF00519), was detected by Infernal but with an incorrect size according to the experimental results. SuhB is highly conserved across the Sphingopyxis genus. Expression data revealed that SuhB is present in rapidly growing TFA cells. A suhB deletion mutant exhibited de-repression of tetralin degradation (thn) gene expression and higher amounts of their LysR-type activator, ThnR, under conditions of carbon catabolite repression (CCR). Interaction between SuhB and the 5'UTR of thnR mRNA was demonstrated in vitro. Moreover, co-immunoprecipitation experiments, combined with fluorescence measurements of gfp fusions to the 5'UTR of thnR mRNA and the phenotype of an hfq deletion mutant, suggest the involvement of Hfq in this interaction. Taken together, these data support an Hfq-mediated repressive role for SuhB, on ThnR mRNA translation that prevents thn gene induction. SuhB, which is a highly conserved sRNA in the Sphingopyxis genus, is the first identified element directly involved in CCR of thn gene expression in S. granuli strain TFA.

The biodegradation characteristics and primary metabolic pathway of hydrocortisone were investigated in different aquifer media-water systems. The aquifer media from Beijing Chaobai river (BJ), Hebei Hutuo river (HB), and Tianjin Duliujian river (TJ), having different properties were used. The results showed that the attenuation rates of hydrocortisone were 0.175, 0.119 and 0.096 d−1 in BJ, HB, TJ respectively and all of them followed the first-order rate kinetics. The main metabolic pathway of hydrocortisone in the BJ system began with the hydration of C-4 and C-5 double bond on ring A, and the A-ring was subsequently cleaved. In the case of the HB system, the primary biotransformation pathway started from the side chain degradation and oxidation of C-12 on ring D to form a ketone group, and the D-ring was subsequently carboxylated and cleaved. The differences in attenuation rates and metabolic pathways were associated with community structures of bacteria and archaea in different systems. The biodegradation of A-ring had a greater influence on the decay rate than D-ring. The results from microbial community structure analysis using 454 pyrosequencing of 16s rRNA genes showed that the microbial community structure transformed to microflora with good degrading capacity towards hydrocortisone by hydrocortisone amendment. The potential bio-transformers were seven major bacterial genera (Methylophilus, Sphingopyxis, Arenimonas, hgcI_clade, Methylobacillus, Methylotenera and Fluviicola) and two major archaeal genera (Candidatus_Nitrososphaera and Woesearchaeota_DHVEG-6), respectively.

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for ~ 16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.

Objectives: To investigate the presence of Legionella spp in cooling tower water. Legionella proliferation in cooling tower water has serious public health implications as it can be transmitted to humans via aerosols and cause Legionnaires’ disease. Methods: Samples of cooling tower water were collected from King Fahd Hospital of the University (KFHU) (Imam Abdulrahman Bin Faisal University, 2015/2016). The water samples were analyzed by a standard Legionella culture method, real-time polymerase chain reaction (RT-PCR), and 16S rRNA next-generation sequencing. In addition, the bacterial community composition was evaluated. Results: All samples were negative by conventional Legionella culture. In contrast, all water samples yielded positive results by real-time PCR (10 5 to 10 6 GU/L). The results of 16S rRNA next generation sequencing showed high similarity and reproducibility among the water samples. The majority of sequences were Alpha-, Beta-, and Gamma-proteobacteria, and Legionella was the predominant genus. The hydrogen-oxidizing gram-negative bacterium Hydrogenophaga was present at high abundance, indicating high metabolic activity. Sphingopyxis , which is known for its resistance to antimicrobials and as a pioneer in biofilm formation, was also detected. Conclusion: Our findings indicate that monitoring of Legionella in cooling tower water would be enhanced by use of both conventional culturing and molecular methods. Saudi Med J 2018; Vol. 39 (2): 137-141 doi: 10.15537/smj.2018.2.21587 How to cite this article: Farhat M, Shaheed RA, Al-Ali HH, Al-Ghamdi AS, Al-Hamaqi GM, Maan HS, et al. Legionella confirmation in cooling tower water. Comparison of culture, real-time PCR and next generation sequencing. Saudi Med J . 2018 Feb;39(2):137-141. doi: 10.15537/smj.2018.2.21587.

During a study of oil-degrading bacteria, three yellow-coloured, Gram-stain-negative, non-motile and rod-shaped bacteria, designated strains Ktm-14T, Ktm-17 and Ktm-18, were isolated from oil-contaminated soil of Biratnagar, Morang, Nepal. The strains were able to grow at 15–37 °C, pH 4.5–10.0 and 0–2 % (w/v) NaCl concentration. Strains Ktm-14T, Ktm-17 and Ktm-18 were characterized by multiple taxonomic approaches. Based on 16S rRNA gene sequence analysis, strains Ktm-14T, Ktm-17 and Ktm-18 belonged to the genus Sphingopyxis and shared highest sequence similarity with Sphingopyxis ginsengisoli Gsoil 250T (98.94 %). The only respiratory quinone was ubiquinone-10 and the predominant polyamine was spermidine. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and sphingoglycolipids. The predominant fatty acids were C17 : 1ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The DNA G+C content values of strains Ktm-14T, Ktm-17 and Ktm-18 were 65.8, 65.9 and 65.6 mol%, respectively. The DNA–DNA relatedness between Ktm-14T and Ktm-17 and Ktm-18 were higher than 70 % but with closely related reference strains were less than 40 %. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished strain Ktm-14T from its closest phylogenetic neighbours. Thus, strain Ktm-14T represents a novel species of the genus Sphingopyxis , for which the name Sphingopyxis nepalensis sp. nov. is proposed. The type strain is Ktm-14T (=KEMB 9005-694T=KACC 19389T=JCM 32250T), and strains Ktm-17 and Ktm-18 represent two additional strains.

Currently, studies worldwide have comprehensively recognized the importance of Sphingomonadaceae bacteria and the mlrCABD gene cluster in microcystin (MC) degradation. However, knowledge about their degradation of nodularin (NOD) is still unclear. In this study, the degradation mechanism of NOD by Sphingopyxis sp. m6, an efficient MC degrader isolated from Lake Taihu, was investigated in several aspects, including degradation ability, degradation products, and potential application. The strain degraded NOD of 0.50 mg/L with a zero-order rate constant of 0.1656 mg/L/d and a half-life of 36 h. The average degradation rate of NOD was significantly influenced by the temperature, pH, and initial toxin concentrations. Moreover, four different biodegradation products, linear NOD, tetrapeptide H-Glu-Mdhb-MeAsp-Arg-OH, tripeptide H-Mdhb-MeAsp-Arg-OH, and dipeptide H-MeAsp-Arg-OH, were identified, of which the latter two are the first reported. Furthermore, the four mlr genes were upregulated during NOD degradation. The microcystinase MlrA encoded by the mlrA gene hydrolyzes the Arg-Adda bond to generate linear NOD as the first step of NOD biodegradation. Notably, recombinant MlrA showed higher degradation activity and stronger environmental adaptability than the wild strain, suggesting future applications in NOD pollution remediation. This research proposes a relatively complete NOD microbial degradation pathway, which lays a foundation for exploring the mechanisms of NOD degradation by MC-degrading bacteria.

Methane mitigation in landfill top cover soils is mediated by methanotrophs whose optimal methane (CH4) oxidation capacity is governed by environmental and complex microbial community interactions. Optimization of CH4 remediating bio-filters need to take microbial responses into account. Divalent copper (Cu2+) and iron (Fe2+) are present in landfills at variable ratios and play a vital role in methane oxidation capacity and growth of methanotrophs. This study, as a first of its kind, therefore quantified effects of variable Cu2+ and Fe2+ (5:5, 5:25 and 5:50 μM) ratios on mixed methanotrophic communities enriched from landfill top cover (LB) and compost soils (CB). CH4 oxidation capacity, CH4 removal efficiencies, fatty acids content/profiles and polyhydroxybutyrate (PHB; a biopolymer) contents were also analysed to quantify performance and potential co-product development. Mixed methanotroph cultures were raised in 10 L continuous stirred tank reactors (CSTRs, Bioflo® & Celligen® 310 Fermentor/Bioreactor; John Morris Scientific, Chatswood, NSW, Australia). Community structure was determined by amplifying the V3-V4 region of 16s rRNA gene. Community structure and, consequently, fatty acid-profiles changed significantly with increasing Cu2+/Fe2+ ratios, and responses were different for LB and CB. Effects on methane oxidation capacities and PHB content were similar in the LB- and CB-CSTR, decreasing with increasing Cu2+/Fe2+ ratios, while biomass growth was unaffected. In general, high Fe2+ concentration favored growth of the type -II methanotroph Methylosinus in the CB-CSTR, but methanotroph abundances decreased in the LB-CSTR. Increase in Cu2+/Fe2+ ratio increased the growth of Sphingopyxis in both systems, while Azospirllum was co-dominant in the LB- but absent in the CB-CSTR. After 13 days, methane oxidation capacities and PHB content decreased by ∼50% and more in response to increasing Fe2+ concentrations. Although methanotroph abundance was ∼2% in the LB- (compared to >50% in CB-CSTR), methane oxidation capacities were comparable in the two systems, suggesting that methane oxidation capacity was maintained by the dominant Azospirllum and Sphingopyxis in the LB-CSTR. Despite similar methanotroph inoculum community composition and controlled environmental variables, increasing Cu2+/Fe2+ ratios resulted in significantly different microbial community structures in the LB- and CB-CSTR, indicative of complex microbial interactions. In summary, our results suggest that a detailed understanding of allelopathic interactions in mixed methanotrophic consortia is vital for constructing robust bio-filters for CH4 emission abatement.

Environmental endocrine-disrupting compounds (EDCs) are a growing concern as studies reveal their persistence and detrimental effects on wildlife. Microorganisms are known to affect the transformation of steroid EDCs; however, the diversity of estrogen-degrading microorganisms and the range of transformations they mediate remain relatively little studied. In mesocosms, low concentrations of added estrone (E1) and 17β-estradiol (E2) were removed by indigenous microorganisms from Las Vegas Wash water within 2 wk. Three bacterial isolates, sp. strain LVW-9, sp. strain LVW-12, and sp. strain LVW-PC, were enriched from Las Vegas Wash water on E1 and E2 and used for EDC transformation studies. In the presence of alternative carbon sources, LVW-9 and LVW-12 catalyzed near-stoichiometric reduction of E1 to E2 but subsequently reoxidized E2 back to E1; whereas LVW-PC minimally reduced E1 to E2 but effectively oxidized E2 to E1 after a 20-d lag. In the absence of alternative carbon sources, LVW-12 and LVW-PC oxidized E2 to E1. This report documents the rapid and sometimes reversible microbial transformation of E1 and E2 and the slow degradation of 17α-ethinylestradiol in urban stream water and extends the list of known estrogen-transforming bacteria to the genera and . These results suggest that discharge of steroid estrogens via wastewater could be reduced through tighter control of redox conditions and may assist in future risk assessments detailing the environmental fate of estrogens through evidence that microbial estrogen transformations may be affected by environmental conditions or growth status.

© 2016 A mercury resistant bacterial strain SE2 was isolated from contaminated soil. The 16s rRNA gene sequencing confirms the strain as Sphingopyxis belongs to the Sphingomonadaceae family of the α-Proteobacteria group. The isolate showed high resistance to mercury with estimated concentrations of Hg that caused 50% reduction in growth (EC50) of 5.97 and 6.22 mg/L and minimum inhibitory concentrations (MICs) of 32.19 and 34.95 mg/L in minimal and rich media, respectively. The qualitative detection of volatilized mercury and the presence of mercuric reductase enzyme proved that the strain SE2 can potentially remediate mercury. ICP-QQQ-MS analysis of the remaining mercury in experimental broths indicated that a maximum of 44% mercury was volatilized within 6 hr by live SE2 culture. Furthermore a small quantity (23%) of mercury was accumulated in live cell pellets. While no volatilization was caused by dead cells, sorption of mercury was confirmed. The mercuric reductase gene merA was amplified and sequenced. Homology was observed among the amino acid sequences of mercuric reductase enzyme of different organisms from α-Proteobacteria and ascomycota groups.

Microalgal aggregation is a key to many ecosystem functions in aquatic environments. Yet mechanistic understanding of microalgae aggregation, especially the interactions with ubiquitous bacteria populations, remains elusive. We reported an experimental study illustrating how the emerging bacterial populations interacted with a model microalga (Chlamydomonas microsphaera) cells and the consequent aggregation patterns. Results showed that the emergence of bacterial populations significantly stimulated C. microsphaera aggregation. Both bacterial and C. microsphaera motilities were remarkably excited upon coculturing, with the mean cell velocity being up to 2.67 and 1.80 times of those of separate bacterial and C. microsphaera cultures, respectively. The stimulated bacterial and C. microsphaera cell velocity upon coculturing would likely provide a mechanism for enhanced probability of cell-cell collisions that led to amplified aggregation of C. microsphaera population. Correlation analysis revealed that bacterial resource foraging (for polysaccharides) was likely a candidate mechanism for stimulated cell motility in an organic carbon source-limited environment, whereby C. microsphaera-derived polysaccharides serve as the sole organic carbon source for heterotrophic bacteria which in turns facilitates bacteria-C. microsphaera aggregation. Additional analysis showed that bacterial populations capable of successive decomposing algal-derived organic matters dominated the cocultures, with the top five abundant genera of Brevundimonas (24.78%), Shinella (17.94%), Sphingopyxis (11.62%), Dongia (5.82%) and Hyphomicrobium (5.45%). These findings provide new insights into full understanding of microalgae-bacteria interactions and consequent microbial aggregation characteristics in aquatic ecosystems.

Isoprene is a climate-active gas and one of the most abundant biogenic volatile organic compounds (BVOC) released into the atmosphere. In the terrestrial environment, plants are the primary producers of isoprene, releasing between 500 and 750 million tons per year to protect themselves from environmental stresses such as direct radiation, heat, and reactive oxygen species. While many studies have explored isoprene production, relatively little is known about consumption of isoprene by microbes and the most well-characterized isoprene degrader is a Rhodococcus strain isolated from freshwater sediment. In order to identify a wider range of bacterial isoprene-degraders in the environment, DNA stable isotope probing (DNA-SIP) with 13C-labeled isoprene was used to identify active isoprene degraders associated with soil in the vicinity of a willow tree. Retrieval by PCR of 16S rRNA genes from the 13C-labeled DNA revealed an active isoprene-degrading bacterial community dominated by Proteobacteria, together with a minor portion of Actinobacteria, mainly of the genus Rhodococcus. Metagenome sequencing of 13C-labeled DNA from SIP experiments enabled analysis of genes encoding key enzymes of isoprene metabolism from novel isoprene degraders. Informed by these DNA-SIP experiments and working with leaves and soil from the vicinity of tree species known to produce high amounts of isoprene, four novel isoprene-degrading strains of the genera Nocardioides, Ramlibacter, Variovorax and Sphingopyxis, along with strains of Rhodococcus and Gordonia, genera that are known to contain isoprene-degrading strains, were isolated. The use of lower concentrations of isoprene during enrichment experiments has revealed active Gram-negative isoprene-degrading bacteria associated with isoprene-emitting trees. Analysis of isoprene-degradation genes from these new isolates provided a more robust phylogenetic framework for analysis of isoA, encoding the α-subunit of the isoprene monooxygenase, a key molecular marker gene for cultivation-independent studies on isoprene degradation in the terrestrial environment.

Members of genus Sphingopyxis are known to thrive in diverse environments. Genomes of 21 Sphingopyxis strains were selected. Phylogenetic analysis was performed using GGDC, AAI and core-SNP showed agreement at sub-species level. Based on our results, we propose that both S. baekryungensis DSM16222 and Sphingopyxis sp. LPB0140 strains should not be included under genus Sphingopyxis. Core-analysis revealed, 1422 genes were shared which included essential pathways and genes for conferring adaptation against stress environment. Polyhydroxybutyrate degradation, anaerobic respiration, type IV secretion were notable abundant pathways and exopolysaccharide, hyaluronic acid production and toxin-antitoxin system were differentially present families. Interestingly, genome of S. witflariensis DSM14551, Sphingopyxis sp. MG and Sphingopyxis sp. FD7 provided a hint of probable pathogenic abilities. Protein-Protein Interactome depicted that membrane proteins and stress response has close integration with core-proteins while aromatic compounds degradation and virulence ability formed a separate network. Thus, these should be considered as strain specific attributes.

This study investigated the treatment performance of activated sludge on Pb(II)-containing wastewater, including contaminant removal efficiency, extracellular polymeric substances, pbrT gene content and the microbial community. The average removal efficiencies of ammonia nitrogen, chemical oxygen demand, total phosphorus, total nitrogen and Pb(II) were 40% ± 4%, 91% ± 3%, 95% ± 3%, 51% ± 5% and 92% ± 9% during the stable operation stage, respectively. Moreover, the extracellular polymeric substance -protein contents increased significantly from day 0 to day 60 (p

A microbial depolymerization process of polyethylene glycol 4000 was investigated mathematically. Weight distributions before and after cultivation of Sphingopyxis macrogoltabidus strain 103 were introduced into inverse probelms for a molecular factor and a time factor of a degradation rate. Once those inverse problems were solved numerically, the microbial depolymerization process of polyethylene glycol 4000 was simulated.

Three bacterial consortia, named YC-SY1, YC-BJ1 and YC-GZ1, were enriched from different areas of China. Bacterial consortia YC-SY1, YC-BJ1 and YC-GZ1 could efficiently degrade triphenyl phosphate (TPhP) (100 mg/L) by approximately 79.4%, 99.8% and 99.6%, tricresyl phosphate (TCrP) by 90.6%, 91.9% and 96.3%, respectively, within 4 days. And they could retain high degrading efficiency under a broad range of temperature (15–40 ℃), pH (6.0–10.0) and salinity (0–4%). A total of 10 bacterial isolates were selected and investigated their degradation capacity. Among these isolates, two were significantly superior to the others. Strain Rhodococcus sp. YC-JH2 could utilize TPhP (50 mg/L) as sole carbon source for growth with 37.36% degradation within 7 days. Strain Sphingopyxis sp. YC-JH3 could efficiently degrade 96.2% of TPhP (50 mg/L) within 7 days, except that no cell growth was observed. Combined with 16S diversity analysis, our results suggest that the effective components of three bacterial consortia responsible for TPhP and TCrP degradation were almost the same, that is, bacteria capable of degrading TPhP and TCrP are limited, in this study, the most efficient component is Sphingopyxis . This study provides abundant microorganism sources for research on organophosphorus flame retardants (OPFRs) metabolism and bioremediation towards OPFRs-contaminated environments.

GY1, a novel microbial consortium with efficient ability to degrade decabromodiphenyl ether (BDE-209) has been isolated and the sequencing analysis has been conducted. The results revealed that Hyphomicrobium, Pseudomonas, Aminobacter, Sphingopyxis, Chryseobacterium, Bacillus, Pseudaminobacter, Stenotrophomonas, Sphingobacterium and Microbacterium were the dominant genera, and the function genes involved in BDE-209 conversion were predicted by PICRUSt. When BDE-209 concentration increased from 0.5 to 10mg/L, its degradation efficiency declined from 57.2% to 22.3%. Various kinds of debrominated metabolites were detected during the biodegradation process, including BDE-208, BDE-207, BDE-206, BDE-205, BDE-190, BDE-181, BDE-155, BDE-154, BDE-99, BDE-47, BDE-17 and BDE-7. Also, the proportion of necrotic cells was observed during GY1 mediated degradation of BDE-209 to reveal the changes of cells viability under BDE-209 stress. Subsequent analysis showed that the reaction of BDE-209 with GY1 was a detoxification process and bioaugmentation with GY1 effectively enhanced BDE-209 degradation in actual water and water-sediment system.

Two types of solid bacterial agents for the simultaneous removal of methane and odor were designed using humic soil (De-MO-1) and the mixture of humic soil and tobermolite (De-MO-2) as biocarriers. The bacterial consortium, having the removability of methane and dimethyl sulfide (DMS), was immobilized in the biocarriers, and then stored at room temperature for 375 days without additional treatment. Although the lag period, of which the incubation time required for removing methane and DMS, tended to increase over the storage period, the removability of methane and DMS was maintained during 375 days in both bacterial agents. Key bacteria associated with the removal of methane and odors (Streptomyces, Promicromonospora, Paracoccus, Lysobacter, Sphingopyxis and Methylosystis) could keep their abundance during the storage period. The richness and evenness values of the bacterial communities in De-MO-1 and De-MO-2 ranged 4.89 ∼ 6.50 and 0.89 ∼ 0.98, respectively, indicating that high bacterial diversity was maintained during the storage period. The results suggest that De-MO-1 and De-MO-2, designed for the simultaneous removal of methane and odors, had shelf stabilities over one year.

An enrichment culture strategy was used to obtain natural consortia from soil in order to study the biodegradability of poly(ether-urethanes) (PUE). PUE were synthesized with different aliphatic diisocyanate group, termed PUIPDI and PUHMDI. In addition, PUE/acrylic hybrids, termed PUH90:DEA10 and PUH70:DEA30 consisted of PUHMDI and increasing ratio of 2-(diethylamino)ethyl methacrylate (DEA) were tested. PUIPDI was biodeteriorated through urea-bond hydrolysis by a consortium dominated by Acinetobacter. A higher biodeterioration rate was demonstrated for PUHMDI, which exhibited large surface holes and a greater weight loss. The hydrolysis of ester-urethane bonds and the oxidation of soft-segment ether bonds were the key reactions identified, possibly by Acinetobacter, Mycobacterium, Sphingopyxis and Pseudomonas, which were present in this consortium. Diverse metabolic functions were also predicted. The addition of DEA favored the biodegradability of PUH:DEA hybrids demonstrated by the increased weight loss, swelling degree and the hydrolysis of DEA-ester bond. Urethane and ether bonds degradation were also detected. PUH:DEA hybrids selected even bacterial consortia, most likely by allowing better access to the nutrients. Pseudomonadaceae and Bradyrhizobiaceae families got relevance in these consortia and their outstanding features were cell mobility and quorum sensing. This work has provided a deeper insight into PUE biodegradation by proposing the chemical mechanisms, bacterial taxa and functions that could be implicated.

Butralin (N-sec- Butyl-4-tert-butyl-2,6-dinitroaniline) is a highly persistent dinitroaniline herbicide frequently detected in the environment. In this study, butralin-degrading soil bacterium, Sphingopyxis sp. strain HMH was isolated from agricultural soil samples. Based on whole genome sequence analysis of the strain HMH, the gene encoding a nitroreductase NfnB was identified and expressed in Escherichia coli (E. coli), and protein was purified to homogeneity. NfnB is a flavin-nitroreductase, found to be a functional tetramer, composed of subunit molecular mass of 25 kDa. The metabolites from butralin degradation by strain HMH and purified NfnB were identified using ultra performance liquid chromatography high resolution mass spectrometry (UPLC-HRMS), and a novel mechanism of butralin degradation was proposed. NfnB selectively nitro-reduced butralin into N- (sec-Butyl)-4-(tert-butyl)-6-nitrobenzene- 1,2-diamine, followed by formation of 5-(tert-Butyl)-3 -nitrobenzene-1,2-diamine and butanone by N- dealkylation through possible hydroxylation reaction onto the carbon linked amine of the N-(sec-Butyl) moiety. In our study, we could not detect the hydroxylated product 2-(2-Amino-4-tert-butyl-6-nitro- phenylamino)-butan-2-ol) (carbinolamine), instead its Schiff base product (E)-2-(Butan-2-yildeneamino)-5- (tert-butyl)-3-nitroaniline was detected. The release of butanone was further confirmed by derivatization with 2,4- dinitrophenylhydrazine (DNPH) followed by MS analysis. In conclusion, this study explores a novel multi-functional flavin- nitroreductase family enzyme NfnB, catalyzing unique and sequential nitroreduction and N-dealkylation through oxidative hydroxylation of dinitroaniline herbicide butralin.