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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.

Recent molecular studies on endophytic bacterial diversity have revealed a large richness of species. Associations between endobiotic bacterial-algae interactions have been studied for more than 40 years but were, up to now, never molecularly analyzed within the filamentous Cyanobacteria Phormidium. Therefore, the endophytic bacteria associated with fresh microalgae Phormidium, a group of ubiquitous photosynthetic organisms that play an important role in aquatic ecosystems, has been investigated. To study this partnership, Phormidium sp. was cultured in BG-11 medium using optimal conditions, and after the incubation period, cell biomass was obtained. Total genomic DNA from biomass was extracted and used for endophytic bacteria determination by using the 16S rRNA gene. Sequencing results revealed that a total of seven endophytic bacteria living within the cytoplasm of the host Phormidium sp. have been identified, including six bacteria belonging to three genera, namely Sphingomonas, Sphingopyxis, and Stenotrophobacter and while one bacteria remained unidentified due to low sequence homology in the GenBank database. The results highlighted the importance of endophytic bacteria associated with Phormidium sp. for the first time by using sequence-based identification.

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.