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A related group of phosphotriesters known as organophosphate flame retardants (OPFRs) has become emerging contaminants due to its worldwide use. The lack of an easily hydrolysable bond renders OPFRs inert to the well-known phosphotriesterases capable of hydrolyzing the neurotoxic organophosphates. An OPFRs phosphotriesterase gene stpte was cloned from plasmid pStJH of strain Sphingopyxis terrae subsp. terrae YC-JH3 and was heterologously expressed in Escherichia coli. The recombinant protein St-PTE was purified and analyzed. St-PTE showed the highest catalytic activity at pH 8.5 and 35 °C. The optimal substrate for St-PTE is triphenyl phosphate, with kcat/Km of 5.03 × 106 M−1 s−1, two orders of magnitude higher than those of tricresyl phosphate (4.17 × 104 M−1 s−1), 2-ethylhexyl diphenyl phosphate (2.03 × 104 M−1 s−1) and resorcinol bis(diphenyl phosphate) (6.30 × 104 M−1 s−1). St-PTE could break the P–O bond of tri-esters and convert aryl-OPFRs into their corresponding di-ester metabolites, including polymers of resorcinol bis(diphenyl phosphate). Mediated by transposase, the gene of OPFRs phosphotriesterase could be transferred horizontally among closely related strains of Sphingomonas, Sphingobium and Sphingopyxis. Key points: • St-PTE from Sphingopyxis terrae subsp. terrae YC-JH3 could hydrolyze aryl-OPFRs. • Metabolites of RBDPP hydrolyzed by phosphotriesterase were identified. • St-PTE could hydrolyze the P–O cleavage of dimer and trimer of RBDPP. • Phosphotriesterase genes transfer among Sphingomonadaceae mediated by transposase. [ABSTRACT FROM AUTHOR]

Recent molecular studies on endophytic bacterial diversity have revealed a large richness of species. Associations between endobiotic bacterialalgae 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. [ABSTRACT FROM AUTHOR]

A Gram-stain-negative, aerobic, motile and rod-shaped bacterium was isolated from pebbles collected from the coast near Taejongdae Park, Busan, South Korea. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain DHUNG17T belonged to the family Sphingomonadaceae, and it showed the highest sequence similarity found with Sphingopyxis panaciterrulae DCY34T (98.4%) and Sphingopyxis granuli TFAT (98.4%). The strain grew at 10–45 °C, at pH 5.0–9.0 and with 0–12% (w/v) NaCl. Chemotaxonomic data revealed that strain DHUNG17T possessed ubiquinone Q-10 as the predominant respiratory lipoquinone. The predominant fatty acids were C16: 0, C18: 0, summed feature 4 (C16: 1ω7c and/or C15: 0 iso 2-OH) and summed feature 8 (C19: 1ω6c and/or unknown 18.864). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and a sphingoglycolipid and spermidine were detected as the major polyamines. Strain DHUNG17T was able to produce carotenoid-type pigment. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values with its closest neighbors were 79.3–81.7% and 22.0–24.4%, respectively. The genome of strain DHUNG17T is 3,129,415 bp long with a DNA G + C content of 64.7% and encodes 2,951 predicted proteins, 3 rRNAs and 47 tRNAs. Gene related to transportation of polycyclic aromatic hydrocarbons (PAHs) was found in the genome of strain DHUNG17T. According to the genotypic, phylogenetic and chemotaxonomic data, strain DHUNG17T represents a novel species within the genus Sphingopyxis, for which the name Sphingopyxis lutea sp. nov. is proposed. The type strain is DHUNG17T (= KACC 21746T = NBRC 114643T). [ABSTRACT FROM AUTHOR]

Sphingopyxis sp. USTB-05, which we previously identified and examined, is a well-known bacterial strain for biodegrading cyanobacterial hepatotoxins of both nodularins (NODs) and microcystins (MCs). Although the pathways for biodegrading the different types of [D-Asp1] NOD, MC-YR, MC-LR and MC-RR by Sphingopyxis sp. USTB-05 were suggested, and several biodegradation genes were successfully cloned and expressed, the comprehensive genomic analysis of Sphingopyxis sp. USTB-05 was not reported. Here, based on second and third generation sequencing technology, we analyzed the whole genome of Sphingopyxis sp. USTB-05, which is 4,679,489 bp and contains 4,312 protein coding genes. There are 88 protein-coding genes related to the NODs and MCs biodegradation, of which 16 genes (bioA, hmgL, hypdh, speE, nspC, phy, spuC, murD, glsA, ansA, ocd, crnA, ald, gdhA, murC and murI) are unique. These genes for the transformation of phenylacetic acid CoA (PA-CoA) to CO2 were also found in Sphingopyxis sp. USTB-05. This study expands the understanding of the pathway for complete biodegradation of cyanobacterial hepatotoxins by Sphingopyxis sp. USTB-05. [ABSTRACT FROM AUTHOR]

This study aimed to isolate waterborne heterotrophic organisms indigenous to water treatment processes with suitable ultraviolet (UV) dose–response profiles for estimation of the UV doses delivered by operational UV disinfection systems. The UV dose–response profiles of two isolated organisms, Flavobacterium succinicans and Sphingopyxis chilensis, were determined. S. chilensis has a UV dose–response with potential for use as an indigenous surrogate for Cryptosporidium inactivation, up to 2.2‐logs in the dose range 2–7 mJ/cm2 of monochromatic UV light at 253.7 nm. F. succinicans was more sensitive and tailing was observed above 4 mJ/cm2 making it unsuitable for UV dose verification above this dose. As a single species in the water samples used in this study, S. chilensis is unlikely to be present in sufficient numbers for routine use as an indigenous surrogate. However, the Sphingomonadaceae family to which it belongs is abundant in various drinking water sources and warrants further investigation. [ABSTRACT FROM AUTHOR]

Sphingopyxis sp. USTB-05, which we previously identified and examined, is a well-known bacterial strain for biodegrading cyanobacterial hepatotoxins of both nodularins (NODs) and microcystins (MCs). Although the pathways for biodegrading the different types of [D-Asp1] NOD, MC-YR, MC-LR and MC-RR by Sphingopyxis sp. USTB-05 were suggested, and several biodegradation genes were successfully cloned and expressed, the comprehensive genomic analysis of Sphingopyxis sp. USTB-05 was not reported. Here, based on second and third generation sequencing technology, we analyzed the whole genome of Sphingopyxis sp. USTB-05, which is 4,679,489 bp and contains 4,312 protein coding genes. There are 88 protein-coding genes related to the NODs and MCs biodegradation, of which 16 genes (bioA, hmgL, hypdh, speE, nspC, phy, spuC, murD, glsA, ansA, ocd, crnA, ald, gdhA, murC and murI) are unique. These genes for the transformation of phenylacetic acid CoA (PA-CoA) to CO2 were also found in Sphingopyxis sp. USTB-05. This study expands the understanding of the pathway for complete biodegradation of cyanobacterial hepatotoxins by Sphingopyxis sp. USTB-05.

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. [ABSTRACT FROM AUTHOR]

The large quantities and the persistent nature of fungicide wastewaters have increased the efforts towards a sustainable technological solution. In this context, fludioxonil-contaminated wastewater was treated in an upflow immobilized cell bioreactor, resulting in chemical oxygen demand (COD) removal efficiency even higher than 80%, whereas the electrical conductivity (EC) of the effluent was gradually increased. Organic-F was mineralized by 94.0 ± 5.2%, which was in accordance with the high fludioxonil removal efficiency (95.4 ± 4.0%). In addition, effluent total Kjeldahl nitrogen (TKN) concentration reduced significantly during bioprocessing. A strong relationship among COD removal, TKN/total nitrogen removal, and effluent EC increase (p < 0.01) was identified. Despite the adequate aeration provided, effluent nitrite and nitrate concentrations were negligible. Illumina sequencing revealed a reduction in the relative abundances of Betaproteobacteria, Chloroflexi, Planctomycetes, and Firmicutes and an increase in the proportion of Alphaproteobacteria and Actinobacteria. A shift in bacterial communities occurred during fludioxonil treatment, resulting in the significant increase of the relative abundances of Empedobacter, Sphingopyxis, and Rhodopseudomonas (from 0.67 ± 0.13% at the start-up to 34.34 ± 1.60% at the end of biotreatment). In conclusion, the immobilized cell bioreactor permitted the proliferation of specialized activated sludge microbiota with an active role in the depuration of postharvest fungicides. [ABSTRACT FROM AUTHOR]

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. • S. baekryungensis DSM16222 and Sphingopyxis sp. LPB0140 strains should not be included under genus Sphingopyxis. • Sphingopyxis sp. MG is classified as Sphingopyxs granuli MG. • Core-analysis revealed that 1422 genes were shared for essential pathways and adaptation against stress environment • Polyhydroxybutyrate (bio-degradable plastics) degradation, anaerobic respiration & type IV secretion were most abundant • Exopolysaccharide formation, toxin-antitoxin system and hyaluronic acid production were differentially present families • Genome of S. witflariensis DSM14551, Sphingopyxis sp. MG and Sphingopyxis sp. FD7 suggests probable pathogenic abilities. • PPI depicted that membrane proteins and stress response are integrated with core-proteins • Aromatic compounds degradation and virulence ability are strain specific attributes in genus Sphingopyxis. [ABSTRACT FROM AUTHOR]

Hexachlorocyclohexane (HCH), an organochlorine pesticide imposes several harmful impacts on the ecosystem. β- and δ -isomers of HCH are highly toxic, persistent, and recalcitrant to biodegradation, slow and incomplete degradation of β- and δ - isomers have been reported in a few strains. We have isolated a strain designated as Sphingopyxis strain MC4 that can tolerate and degrade high concentrations of α-, β-, γ- and δ -HCH isomers. To date, no other Sphingopyxis strain has been reported to degrade β- and δ -isomers. To understand the underlying genetic makeup contributing to adaptations, the whole genome of strain MC4 was sequenced. Comparative genome analysis showed that strain MC4 harbors the complete pathway (lin genes) required for HCH degradation. Genetic footprints such as presence of lin genes on genomic islands, IS 6100 elements in close proximity of lin genes, and synteny in lin flanking regions with other strains reflects the horizontal gene transfer in strain MC4. Positive selection and HGT drive the adaptive evolution of strain MC4 under the pressure of HCH contamination that it experienced in its surrounding niche. In silico analyses showed efficient binding of β- and δ -isomers with enzymes leading to rapid degradation that need further validation by cloning and biochemical experiments. [Display omitted] • Rapid degradation of β- and δ -HCH by newly isolated strain MC4. • Comparative genome analysis for adaptive evolution. • Acquisition of lin genes through lateral gene transfer. • Binding energy of LinA and LinB with substrates contributing in degradation efficiency. [ABSTRACT FROM AUTHOR]

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.

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. [ABSTRACT FROM AUTHOR]

The volatile secondary metabolite, isoprene, is released by trees to the atmosphere in enormous quantities, where it has important effects on air quality and climate. Oil palm trees, one of the highest isoprene emitters, are increasingly dominating agroforestry over large areas of Asia, with associated uncertainties over their effects on climate. Microbes capable of using isoprene as a source of carbon for growth have been identified in soils and in the tree phyllosphere, and most are members of the Actinobacteria. Here, we used DNA stable isotope probing to identify the isoprene-degrading bacteria associated with oil palm leaves and inhabiting the surrounding soil. Among the most abundant isoprene degraders of the leaf-associated community were members of the Sphingomonadales, although no representatives of this order were previously known to degrade isoprene. Informed by these data, we obtained representatives of the most abundant isoprene degraders in enrichments, including Sphingopyxis strain OPL5 (Sphingomonadales), able to grow on isoprene as the sole source of carbon and energy. Sequencing of the genome of strain OPL5, as well as a novel Gordonia strain, confirmed their pathways of isoprene degradation and broadened our knowledge of the genetic and taxonomic diversity of this important bacterial trait.

Methanotrophs are a biological resource as they degrade the greenhouse gas methane and various organic contaminants. Several non-methanotrophic bacteria have shown potential to stimulate growth of methanotrophs when co-cultured, and however, the ecology is largely unknown. Effects of Sphingopyxis sp. NM1 on methanotrophic activity and growth of Methylocystis sp. M6 were investigated in this study. M6 and NM1 were mixed at mixing ratios of 9:1, 1:1, and 1:9 (v/v), using cell suspensions of 7.5 × 1011 cells L−1. Methane oxidation of M6 was monitored, and M6 population was estimated using fluorescence in situ hybridization (FISH). Real-time PCR was applied to quantify rRNA and expression of transcripts for three enzymes involved in the methane oxidation pathway. NM1 had a positive effect on M6 growth at a 1:9 ratio (p

The mlr-dependent biodegradation plays an essential role in the natural attenuation of microcystins (MCs) in eutrophic freshwater ecosystems. However, their evolutionary origin is still unclear due to the lack of mlr gene cluster sequences. In this study, a Sphingopyxis sp. strain X20 with high MC-degrading ability was isolated, and the mlrA gene activity was verified by heterologous expression. The whole sequence of the mlr gene cluster in strain X20 was obtained through PCR and thermal asymmetric interlaced (TAIL)-PCR, and then used for evolutionary origin analyses together with the sequences available in GenBank. Phylogenetic analyses of mlr gene clusters suggested that the four mlr genes had the same origin and evolutionary history. Genomic island analyses showed that there is a genomic island on the genome of sphingomonads that is capable of degrading MCs, on which the mlr gene cluster anchors. The concentrated distribution of the mlr gene cluster in sphingomonads implied that these genes have likely been present in the sphingomonads gene pool for a considerable time. Therefore, the mlr gene cluster may have initially entered into the genome of sphingomonads together with the genomic island by a horizontal gene transfer event, and then become inherited by some sphingomonads. The species other than sphingomonads have likely acquired mlr genes from sphingomonads by recently horizontal gene transfer due to the sporadic distribution of MC-degrading species and the mlr genes in them. Our results shed new light on the evolutionary origin of the mlr cluster and thus facilitate the interpretation of characteristic distribution of the mlr gene in bacteria and the understanding of whole mlr pathway.

Biotransformation of arsenic (As) plays an important role in its environmental fate. However, the impact of direct microbial interspecies interactions on valence state and migration of As is rarely reported and cognized. Here, by co-cultivating two aerobic As-reducing bacteria ( Arthrobacter sp. QXT-31 and Sphingopyxis sp. QXT-31) in a culture medium containing initial As (10 μM) and bivalent manganese (Mn, 175 μM), we demonstrated how the interactions between strains affect valence state and partition of As. The results showed that both the strains first reduced As to As via a detoxification mechanism during aerobic growth, with participation of As-reducing gene arsC; the expression of a Mn-oxidizing gene of Arthrobacter sp. QXT-31 was then triggered in the presence of Sphingopyxis sp. QXT-31, and emerging Mn-oxidizing activity oxidized 90% of Mn to Mn oxides; the formed Mn oxides oxidized As to As and adsorbed As; Mn-oxidizing activity decreased significantly in the later stage, resulting to desorption of As from Mn oxides and subsequent bioreduction in aqueous phase. Considering the universality of the two bacterial genera and the interspecies interactions, our study hints at the pervasive impact of direct microbial interspecies interactions on the environmental fate of As in an aquatic ecosystem containing Mn. [ABSTRACT FROM AUTHOR]

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 (EC 50 ) 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. [ABSTRACT FROM AUTHOR]

• Biodegradation mechanisms of MC-LR and its key bioactive moiety Adda were elucidated. • Multi-omic profiles of Sphingopyxis sp. YF1 in Adda degradation were firstly revealed. • The aminotransferase and beta oxidation enzymes played important roles in Adda biodegradation. • Some novel MC-LR and Adda biodegradation products were identified successfully. Microcystins (MCs) are harmful to the ecology and public health. Some bacteria can degrade MCs into Adda, but few can destroy Adda. Adda is the key bioactive moiety of MCs and mainly contributes to hepatotoxicity. We had previously isolated an indigenous novel bacterial strain named Sphingopyxis sp. YF1 that can efficiently degrade MCs and its key bioactive moiety Adda, but the mechanisms remained unknown. Here, the biodegradation mechanisms and pathways of Adda were systematically investigated using multi-omics analysis, mass spectrometry and heterologous expression. The transcriptomic and metabolomic profiles of strain YF1 during Adda degradation were revealed for the first time. Multi-omics analyses suggested that the fatty acid degradation pathway was enriched. Specifically, the expression of genes encoding aminotransferase , beta oxidation (β-oxidation) enzymes and phenylacetic acid (PAA) degradation enzymes were significantly up-regulated during Adda degradation. These enzymes were further proven to play important roles in the biodegradation of Adda. Simultaneously, some novel potential degradation products of Adda were identified successfully, including 7‑methoxy-4,6-dimethyl-8-phenyloca-2,4-dienoic acid (C 17 H 22 O 3), 2-methyl-3‑methoxy-4-phenylbutyric acid (C 12 H 16 O 3) and phenylacetic acid (PAA, C 8 H 8 O 2). In summary, the Adda was converted into PAA through aminotransferase and β-oxidation enzymes, then the PAA was further degraded by PAA degradation enzymes, and finally to CO 2 via the tricarboxylic acid cycle. This study comprehensively elucidated the novel MC-LR biodegradation mechanisms, especially the new enzymatic pathway of Adda degradation. These findings provide a new perspective on the applications of microbes in the MCs polluted environment. [Display omitted] [ABSTRACT FROM AUTHOR]

Water blooms dominated by cyanobacteria are capable of producing hepatotoxins known as microcystins. These toxins are dangerous to people and to the environment. Therefore, for a better understanding of the biological termination of this increasingly common phenomenon, bacteria with the potential to degrade cyanobacteria-derived hepatotoxins and the degradative activity of culturable bacteria were studied. Based on the presence of the mlrA gene, bacteria with a homology to the Sphingopyxis and Stenotrophomonas genera were identified as those presenting potential for microcystins degradation directly in the water samples from the Sulejów Reservoir (SU, Central Poland). However, this biodegrading potential has not been confirmed in in vitro experiments. The degrading activity of the culturable isolates from the water studied was determined in more than 30 bacterial mixes. An analysis of the biodegradation of the microcystin-LR (MC-LR) together with an analysis of the phylogenetic affiliation of bacteria demonstrated for the first time that bacteria homologous to the Aeromonas genus were able to degrade the mentioned hepatotoxin, although the mlrA gene was not amplified. The maximal removal efficiency of MC-LR was 48%. This study demonstrates a new aspect of interactions between the microcystin-containing cyanobacteria and bacteria from the Aeromonas genus.

Background: Sphingomonads are Alphaproteobacteria that belong to the Sphingomonas, Novosphingobium, Sphingopyxis or Sphingobium genera, They are physiologically diverse and broadly distributed in nature, playing important roles in oligotrophic environments and in the degradation of recalcitrant polyaromatic compounds, Sphingopyxis is a poorly studied genus of which only one representative (S. alaskensis RB2256) has been deeply characterized. In this paper we analyze the genomic features of S. granuli strain TFA (formerly Sphingomonas macrogoltabida) in comparison with the available Sphingopyxis sequenced genomes, to describe common characteristics of this genus and to highlight unique characteristics of strain TFA. Results: The TFA genome has been assembled in a single circular chromosome of 4.7 Mb. Genomic sequence analysis and proteome comparison re-assigned the TFA strain to the Sphingopyxis genus and the S. granuli species. Some regions of the TFA genome show high similarity (ca. 100 %) to other bacteria and several genomic islands have been detected. Pathways for aromatic compound degradation have been predicted but no growth of TFA has been detected using these as carbon or nitrogen sources. Genes for nitrate respiration have been identified as TFA exclusive. Experimental data on anaerobic growth of TFA using nitrate as a terminal electron acceptor are also provided. Conclusions: Sphingopyxis representatives form a compact phylogenetic group (with the exception of S. baekryungensis DSM 16222) that share several characteristics, such as being naturally resistant to streptomycin, having only one ribosomal operon, a low number of prophages and CRISPR sequences, absence of selenoproteins and presence of ectoin and other biosynthesis pathways for secondary metabolites. Moreover, the TFA genome organization shows evidence of the presence of putative integrative and conjugative elements (ICE) responsible for the acquisition of several characteristics by horizontal transfer mechanisms. Sphingopyxis representatives have been described as strict aerobes but anaerobic growth using nitrate as a terminal electron acceptor might confer an environmental advantage to the first S. granuli strain characterized at genomic level. [ABSTRACT FROM AUTHOR]

In natural or engineered environments, diverse interspecific interactions among two or more microbial taxa may profoundly affect the transformation of organic compounds in the media. Little is known, however, about how these organisms and interactions affect the transformation of heavy metals. Recently, we found an interaction between two non-Mn(II)-oxidizing (when in monoculture) strains, Arthrobacter sp. QXT-31 and Sphingopyxis sp. QXT-31, which, when cultured in combination, resulted in Mn(II)-oxidizing activity in synthetic media. In order to study the occurrence likelihood of cooperative Mn(II) oxidation in natural water and discharged effluent, we initially identified an optimal ratio of the two strains in a combined culture, as well as the impacts of external factors on the cooperative oxidation. Once preferred initial conditions were established, we assessed the degree and rate of Mn(II) oxidation mediated by the combined QXT-31 strains (henceforth referred to as simply ‘QXT-31’) in three different water types: groundwater, domestic sewage and coking wastewater. Results showed that Mn(II) oxidation only occurred when the two strains were within a specific ratios range. When introduced to the test waters at the preferred ratio, QXT-31 demonstrated high Mn(II)-oxidizing activities, even when relative abundance of QXT-31 was very low (roughly 1.6%, calculated by 454 pyrosequencing events on 16S rcDNA). Interestingly, even under low relative abundance of QXT-31, removal of total organic carbon and total nitrogen in the test waters was significantly higher than the control treatments that were not inoculated with QXT-31. Data from our study indicate that cooperative Mn(II) oxidation is most likely to occur in natural aquatic ecosystems, and also suggests an alternative method to treat wastewater containing high concentrations of Mn(II). [ABSTRACT FROM AUTHOR]

Abstract: Simultaneous removal of methane and malodor-causing volatile sulfur compounds (MVSCs), both emitted from landfills, is a desirable characteristic for methane-mitigation approaches. A methanotrophic bacterium was isolated from a microbial consortium, enriched with methane and dimethyl sulfide (DMS). It grew in the complex nutrient medium R2A without methane, and stably exhibited methanotrophic activity after facultative growth. It was identified as Sphingopyxis sp. MD2 by comparison of the 16S rRNA gene. It belongs to Sphingomonadales, whose members have not shown methanotrophic activity, phylogenetically distinct from orders of known methanotrophs. The MD2 biomass increased at a growth rate of 1.18d−1 when methane was used as the sole growth substrate. An inhibition test with allylthiourea and PCR/sequencing confirmed the presence of particulate methane monooxygenase in MD2. DMS decreased the methane oxidation rate (2634±146μmolegDCW−1 h−1) by 12%, while H2S had no effect on the methane oxidation rate. Interestingly, methanethiol (MT) enhanced the methane oxidation rate by more than 50%. MD2 degraded H2S and MT, regardless of the presence of methane. MD2 also degraded DMS in the presence of methane, indicating co-metabolism. These combined results indicate that MD2 may be a promising biological resource for simultaneous removal of methane and MVSCs. [Copyright &y& Elsevier]

A novel bacterium within the genus Sphingopyxis is described and its suitability as a bioremediation inoculum is evaluated. Sphingopyxis sp. strain M2R2 was isolated from a polycyclic aromatic hydrocarbon–polluted site and can use both phenanthrene and naphthalene as a sole carbon source in liquid and solid media. It can also co-metabolize fluorene in the presence of phenanthrene. Strain M2R2 can mineralize phenanthrene to CO2 and can utilize the substrate in the presence of glucose. Strain M2R2 is capable of nonchemotactic, passive spreading motility on and through agar media, which is induced by the presence of phenanthrene. It is also capable of motility through phenanthrene-spiked packed sand. The range of materials through which this bacterium can travel along with its high spreading velocity make Sphingopyxis sp. strain M2R2 a good candidate for further field study and inclusion in bioremediation strategies of polycyclic aromatic hydrocarbon polluted soils. [ABSTRACT FROM AUTHOR]

Abstract: A novel bacterium capable of degrading two microcystin analogues, microcystin-LR and -LA (MCLR and MCLA), was isolated from a biological sand filter which was previously shown to effectively remove these toxins from source waters. Based on phylogenetic analysis of the 16S rRNA gene sequence, the isolated organism, LH21, most likely belonged to the genus Sphingopyxis and of the previously cultured species clustered with Sphingopyxis witflariensis. Using polymerase chain reaction (PCR), isolate LH21 was shown to contain homologues to each of the four genes, mlrA, mlrB, mlrC and mlrD previously associated with the degradation of MCLR by Sphingomonas sp. ACM-3962. Isolate LH21 was able to effectively degrade MCLR and MCLA in batch experiments under environmentally relevant conditions, with complete removal observed within 5h after re-exposure of the toxins. [Copyright &y& Elsevier]

Abstract: Microcystin-LR and -LA were readily biodegraded by a bacterium, Sphingpoyxis sp. LH21, in a treated reservoir water. Detection of the microcystins was conducted using high-performance liquid chromatography (HPLC), protein phosphatase 2A (PP2A) inhibition assay and a cell-based cytotoxicity assay. The HPLC results correlated well with the two assays. The decrease in cytotoxicity, coupled with the associated decrease in microcystin concentrations, indicated that no cytotoxic by-products were being generated, highlighting the applicability of biodegradation as a feasible treatment option for effective microcystin removal. [Copyright &y& Elsevier]

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. [ABSTRACT FROM AUTHOR]

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. Image 1 • Sphingopyxis is well delineated genera in sphingomonads group with 20 validly published species. • Sphingopyxis strains are recovered from diverse environmental niches. • Sphingopyxis strains harbour bio-degradative capabilities for various environmental contaminants. • Sphingopyxis strains able to synthesize ectoine, polyhydroxyalkanoates and carotenoids secondary metabolites. [ABSTRACT FROM AUTHOR]

Bacterial degradation of butralin to 5- tert -butyl-3-nitrobenzene-1,2-diamine by flavin-nitroreductase NfnB. • Herbicide butralin degrading bacteria was isolated from the agricultural field. • A gene encoding a novel multi-functional flavin-nitroreductase NfnB was identified. • NfnB was expressed in E. coli and purified to homogeneity. • NfnB biotransformed butralin to 5- tert -butyl-3-nitrobenzene-1,2- diamine. • A novel pathway for butralin biotransformation by the isolated strain was proposed. 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. [ABSTRACT FROM AUTHOR]

The volatile secondary metabolite, isoprene, is released by trees to the atmosphere in enormous quantities, where it has important effects on air quality and climate. Oil palm trees, one of the highest isoprene emitters, are increasingly dominating agroforestry over large areas of Asia, with associated uncertainties over their effects on climate. Microbes capable of using isoprene as a source of carbon for growth have been identified in soils and in the tree phyllosphere, and most are members of the Actinobacteria. Here, we used DNA stable isotope probing to identify the isoprene-degrading bacteria associated with oil palm leaves and inhabiting the surrounding soil. Among the most abundant isoprene degraders of the leaf-associated community were members of the Sphingomonadales, although no representatives of this order were previously known to degrade isoprene. Informed by these data, we obtained representatives of the most abundant isoprene degraders in enrichments, including Sphingopyxis strain OPL5 (Sphingomonadales), able to grow on isoprene as the sole source of carbon and energy. Sequencing of the genome of strain OPL5, as well as a novel Gordonia strain, confirmed their pathways of isoprene degradation and broadened our knowledge of the genetic and taxonomic diversity of this important bacterial trait. [ABSTRACT FROM AUTHOR]

Microcystin-leucine-arginine (MC-LR), a cyclic potentially carcinogenic hepatotoxin, occurs frequently in aquatic habitats worldwide and seriously threatens ecosystem and public health. Limited effectiveness of physicochemical treatments to remove MC-LR from drinking water has led to a search for alternative cost-effective and environment friendly biodegradation strategies. Obtaining MC-degrading bacteria and understanding their MC-degrading mechanisms are outstanding challenges. Here, a novel indigenous bacterium named Sphingopyxis sp. YF1 with a high efficient capacity for MC-degradation was successfully isolated from eutrophic Lake Taihu. Through integrating mass spectrometer and multi-omics analyses accompanied by functional verification of certain genes and proteins, a complete MC-degradation pathway was firstly identified, in which MC-LR was sequentially degraded into linearized MC-LR, tetrapeptide, Adda, phenylacetic acid, and finally potential product CO 2. Some specific proteins such as microcystinase, linearized-microcystinase, tetrapeptidease and PAAase responsible for this pathway were identified. This study pioneeringly demonstrated that MC-LR can be completely degraded through natural remediation processes and revealed a significant potential for MC-LR biodegradation in both natural environment and engineered systems. Image 1 • New MC-degrading genes and products were explored through a multi-omic approach. • A complete MC degradation pathway was identified. • A novel bacterium with high MC-degrading rate was isolated from Lake Taihu. • Proteomics data of MC-degrading bacteria were obtained for the first time. • A series of key enzymes responsible for detoxifying MC-LR were identified. [ABSTRACT FROM AUTHOR]

The mlr-dependent biodegradation plays an essential role in the natural attenuation of microcystins (MCs) in eutrophic freshwater ecosystems. However, their evolutionary origin is still unclear due to the lack of mlr gene cluster sequences. In this study, a Sphingopyxis sp. strain X20 with high MC-degrading ability was isolated, and the mlrA gene activity was verified by heterologous expression. The whole sequence of the mlr gene cluster in strain X20 was obtained through PCR and thermal asymmetric interlaced (TAIL)-PCR, and then used for evolutionary origin analyses together with the sequences available in GenBank. Phylogenetic analyses of mlr gene clusters suggested that the four mlr genes had the same origin and evolutionary history. Genomic island analyses showed that there is a genomic island on the genome of sphingomonads that is capable of degrading MCs, on which the mlr gene cluster anchors. The concentrated distribution of the mlr gene cluster in sphingomonads implied that these genes have likely been present in the sphingomonads gene pool for a considerable time. Therefore, the mlr gene cluster may have initially entered into the genome of sphingomonads together with the genomic island by a horizontal gene transfer event, and then become inherited by some sphingomonads. The species other than sphingomonads have likely acquired mlr genes from sphingomonads by recently horizontal gene transfer due to the sporadic distribution of MC-degrading species and the mlr genes in them. Our results shed new light on the evolutionary origin of the mlr cluster and thus facilitate the interpretation of characteristic distribution of the mlr gene in bacteria and the understanding of whole mlr pathway. [ABSTRACT FROM AUTHOR]