Altererythrobacter estronivorus sp. nov., an Estrogen-Degrading Strain Isolated from Yundang Lagoon of Xiamen City in China

Altererythrobacter litoralis sp. nov., a New Carotenoid-Producing Member of the Family Erythrobacteraceae, Isolated from a Tidal Flat Sediment

A new isolate designated as 1XM1-14T was isolated from a tidal flat sediment of Xiamen Island. The yellow-pigmented colonies and rod-shaped cells were observed. Strain 1XM1-14T could hydrolyze Tweens 20, 40, 60, aesculin, and skim milk, and was chemoheterotrophic and mesophilic, required NaCl for the growth. The 16S rRNA gene-based phylogenetic analysis indicated that strain 1XM1-14T was the most closely related to Altererythrobacter epoxidivorans CGMCC 1.7731T (97.0%), followed by other type strain of the genus Altererythrobacter with identities below 97.0%. The DNA-DNA hybridization and average nucleotide identity values between strain 1XM1-14T and its relatives of the genus Altererythrobacter were below the respective thresholds for prokaryotic species demarcation. The phylogenomic inference further revealed that strain 1XM1-14T formed a separate branch distinct from the type strains of the recognized species within the genus Altererythrobacter. The major cellular fatty acids of strain 1XM1-14T were identified as summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), C17:1 ω6c, and C16:0; the profile of polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified glycolipid, and two unidentified lipids; the respiratory quinone was determined to ubiquinone-10. The genomic size and DNA G+C content of strain 1XM1-14T were 2.5 Mbp and 62.71%. The key carotenoid biosynthetic genes were determined in the genome of strain 1XM1-14T and the generated carotenoids were detected. The combined genotypic and phenotypic characteristics supported the classification of strain 1XM1-14T (= GDMCC 1.2383T = KCTC 82612T) as a novel species in the genus Altererythrobacter, for which the name Altererythrobacter litoralis sp. nov. is proposed.

Functional analysis, diversity, and distribution of the ean cluster responsible for 17β-estradiol degradation in sphingomonads

17β-estradiol (E2) is a natural endocrine disruptor that is frequently detected in surface and groundwater sources, thereby threatening ecosystems and human health. The newly isolated E2-degrading strain Sphingomonas colocasiae C3-2 can degrade E2 through both the 4,5-seco pathway and the 9,10-seco pathway; the former is the primary pathway supporting the growth of this strain and the latter is a branching pathway. The novel gene cluster ean was found to be responsible for E2 degradation through the 4,5-seco pathway, where E2 is converted to estrone (E1) by EanA, which belongs to the short-chain dehydrogenases/reductases (SDR) superfamily. A three-component oxygenase system (including the P450 monooxygenase EanB1, the small iron-sulfur protein ferredoxin EanB2, and the ferredoxin reductase EanB3) was responsible for hydroxylating E1 to 4-hydroxyestrone (4-OH-E1). The enzymatic assay showed that the proportion of the three components is critical for its function. The dioxygenase EanC catalyzes ring A cleavage of 4-OH-E1, and the oxidoreductase EanD is responsible for the decarboxylation of the ring A-cleavage product of 4-OH-E1. EanR, a TetR family transcriptional regulator, acts as a transcriptional repressor of the ean cluster. The ean cluster was also found in other reported E2-degrading sphingomonads. In addition, the novel two-component monooxygenase EanE1E2 can open ring B of 4-OH-E1 via the 9,10-seco pathway, but its encoding genes are not located within the ean cluster. These results refine research on genes involved in E2 degradation and enrich the understanding of the cleavages of ring A and ring B of E2.IMPORTANCESteroid estrogens have been detected in diverse environments, ranging from oceans and rivers to soils and groundwater, posing serious risks to both human health and ecological safety. The United States National Toxicology Program and the World Health Organization have both classified estrogens as Group 1 carcinogens. Several model organisms (proteobacteria) have established the 4,5-seco pathway for estrogen degradation. In this study, the newly isolated Sphingomonas colocasiae C3-2 could degrade E2 through both the 4,5-seco pathway and the 9,10-seco pathway. The novel gene cluster ean (including eanA, eanB1, eanC, and eanD) responsible for E2 degradation by the 4,5-seco pathway was identified; the novel two-component monooxygenase EanE1E2 can open ring B of 4-OH-E1 through the 9,10-seco pathway. The TetR family transcriptional regulator EanR acts as a transcriptional repressor of the ean cluster. The cluster ean was also found to be present in other reported E2-degrading sphingomonads, indicating the ubiquity of the E2 metabolism in the environment.

Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes

An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.

Altererythrobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat and reclassification of Altererythrobacter deserti, Altererythrobacter estronivorus and Altererythrobacter muriae as Tsuneonella deserti comb. nov., Croceicoccus estronivorus comb. nov. and Alteripontixanthobacter muriae comb. nov

A yellow-coloured bacterium, designated strain JGD-16^T, was isolated from a tidal flat in Janggu-do, Garorim Bay, Taean-gun, Chungcheongbuk-do, Republic of Korea. Cells were Gram-stain-negative, aerobic, non-flagellated and short ovoid to coccoid-shaped. Growth was observed at 10-37 °C (optimum, 30 °C), pH 6.0-9.0 (pH 8.0) and with 1-5% (w/v) NaCl (2%). Results of 16S rRNA gene sequence analysis indicated that strain JGD-16^T was closely related to Altererythrobacter xiamenensis LY02^T (97.1 %), Altererythrobacter aurantiacus O30^T (96.3 %), Altererythrobacter ishigakiensis JPCCMB0017^T (95.8 %), Altererythrobacter epoxidivorans JCS350^T (95.7 %) and Altererythrobacter insulae BPTF-M16^T (95.3%). Phylogenomic analysis using the maximum-likelihood algorithm showed that strain JGD-16^T formed a clade with the genus Altererythrobacter. The genomic DNA G+C content was 57.8 mol%. The predominant respiratory quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, a sphingoglycolipid, an unidentified glycolipid and an unidentified lipid. The major fatty acids were C_18:1 ω7c (31.5 %) and C_18:3 ω6c (19.6 %). On the basis of its phylogenomic, physiological and chemotaxonomical characteristics, strain JGD-16^T represents a novel species within the genus Altererythrobacter, for which the name Altererythrobacter lutimaris JGD-16^Tsp. nov. is proposed. The type strain is JGD-16^T (=KCTC 72632^T=KACC 21405^T=JCM 33750^T). We also propose the reclassification of Altererythrobacter deserti as Tsuneonella deserti comb. nov., Altererythrobacter estronivorus as Croceicoccus estronivorus comb. nov. and Altererythrobacter muriae as Alteripontixanthobacter muriae comb. nov.

Identification of the EdcR Estrogen-Dependent Repressor in Caenibius tardaugens NBRC 16725: Construction of a Cellular Estradiol Biosensor

In this work, Caenibius tardaugens NBRC 16725 (strain ARI-1) (formerly Novosphingobium tardaugens) was isolated due to its capacity to mineralize estrogenic endocrine disruptors. Its genome encodes the edc genes cluster responsible for the degradation of 17β-estradiol, consisting of two putative operons (OpA and OpB) encoding the enzymes of the upper degradation pathway. Inside the edc cluster, we identified the edcR gene encoding a TetR-like protein. Genetic studies carried out with C. tardaugens mutants demonstrated that EdcR represses the promoters that control the expression of the two operons. These genetic analyses have also shown that 17β-estradiol and estrone, the second intermediate of the degradation pathway, are the true effectors of EdcR. This regulatory system has been heterologously expressed in Escherichia coli, foreseeing its use to detect estrogens in environmental samples. Genome comparisons have identified a similar regulatory system in the edc cluster of Altererythrobacter estronivorus MHB5, suggesting that this regulatory arrangement has been horizontally transferred to other bacteria.

Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557

Rhodococcus equi ATCC13557 was selected as a model organism to study oestrogen degradation based on its previous ability to degrade 17α-ethinylestradiol (EE2). Biodegradation experiments revealed that R. equi ATCC13557 was unable to metabolise EE2. However, it was able to metabolise E2 with the major metabolite being E1 with no further degradation of E1. However, the conversion of E2 into E1 was incomplete, with 11.2 and 50.6% of E2 degraded in mixed (E1-E2-EE2) and E2-only conditions, respectively. Therefore, the metabolic pathway of E2 degradation by R. equi ATCC13557 may have two possible pathways. The genome of R. equi ATCC13557 was sequenced, assembled, and mapped for the first time. The genome analysis allowed the identification of genes possibly responsible for the observed biodegradation characteristics of R. equi ATCC13557. Several genes within R. equi ATCC13557 are similar, but not identical in sequence, to those identified within the genomes of other oestrogen degrading bacteria, including Pseudomonas putida strain SJTE-1 and Sphingomonas strain KC8. Homologous gene sequences coding for enzymes potentially involved in oestrogen degradation, most commonly a cytochrome P450 monooxygenase (oecB), extradiol dioxygenase (oecC), and 17β-hydroxysteroid dehydrogenase (oecA), were identified within the genome of R. equi ATCC13557. These searches also revealed a gene cluster potentially coding for enzymes involved in steroid/oestrogen degradation; 3-carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy-phenyl)propionate hydroxylase, cytochrome P450 monooxygenase, and 3-oxosteroid 1-dehydrogenase. Further, the searches revealed steroid hormone metabolism gene clusters from the 9, 10-seco pathway, therefore R. equi ATCC13557 also has the potential to metabolise other steroid hormones such as cholesterol.

Identification of novel catabolic genes involved in 17β-estradiol degradation by Novosphingobium sp. ES2-1

Novosphingobium sp. ES2-1 is an efficient 17β-estradiol (E2)-degrading bacterium, which can convert E2 to estrone (E1), then to 4-hydroxyestrone (4-OH-E1) for subsequent oxidative cracking. In this study, the molecular bases for this process were elucidated. Two novel monooxygenase systems EstP and EstO were shown to catalyse the oxygenation of E1 and 4-OH-E1, respectively. EstP was a three-component cytochrome P450 monooxygenase system consisting of EstP1 (P450 monooxygenase), EstP2 (ferredoxin) and EstP3 (ferredoxin reductase). Ultraperformance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) analysis revealed that EstP catalysed the 4-hydroxylation of E1 to produce 4-OH-E1. The resultant 4-OH-E1 was further oxidized by a two-component monooxygenase system EstO consisting of EstO1 (flavin-dependent monooxygenases) and EstO2 (flavin reductase). UPLC-HRMS combined with ¹ H-nuclear magnetic resonance analysis demonstrated that EstO catalysed the breakage of C9-C10 to yield a ring B-cleavage product. In addition, the oxygenase component genes estP1 and estO1 exhibited contrary inductive behaviours when exposed to different steroids, suggesting that EstP1-mediated 4-hydroxylation was E2-specific, whereas EstO1-mediated monooxygenation might be involved in the degradation of testosterone, androstenedione, progesterone and pregnenolone. This also implied that the mechanisms of the catabolism of different steroids by the same microorganism might be partially interlinked.

Unraveling the 17β-Estradiol Degradation Pathway in Novosphingobium tardaugens NBRC 16725

We have analyzed the catabolism of estrogens in Novosphingobium tardaugens NBRC 16725, which is able to use endocrine disruptors such as 17β-estradiol, estrone, and estriol as sole carbon and energy sources. A transcriptomic analysis enabled the identification of a cluster of catabolic genes (edc cluster) organized in two divergent operons that are involved in estrogen degradation. We have developed genetic tools for this estrogen-degrading bacterium, allowing us to delete by site-directed mutagenesis some of the genes of the edc cluster and complement them by using expression plasmids to better characterize their precise role in the estrogen catabolism. Based on these results, a catabolic pathway is proposed. The first enzyme of the pathway (17β-hydroxysteroid dehydrogenase) used to transform 17β-estradiol into estrone is encoded out of the cluster. A CYP450 encoded by the edcA gene performs the second metabolic step, i.e., the 4-hydroxylation of estrone in this strain. The edcB gene encodes a 4-hydroxyestrone-4,5-dioxygenase that opens ring A after 4-hydroxylation. The initial steps of the catabolism of estrogens and cholate proceed through different pathways. However, the degradation of estrogens converges with the degradation of testosterone in the final steps of the lower catabolic pathway used to degrade the common intermediate 3aα-H-4α(3'-propanoate)7a-β-methylhexahydro-1,5-indanedione (HIP). The TonB-dependent receptor protein EdcT appears to be involved in estrogen uptake, being the first time that this kind of proteins has been involved in steroid transport.

Co-enhanced activated sludge system by static magnetic field and two halotolerant yeasts for azo dye treatment

The effect of static magnetic field (SMF) on azo dye Acid Red B (ARB) decolorization by the co-culture of activated sludge (AS) and two halotolerant yeasts Candida tropicalis A1 and Pichia occidentalis A2 was investigated. Microbial community structure of the co-cultures before and after treatment with SMFs of different intensity was analyzed through high-throughput sequencing and quantitative real-time polymerase chain reaction. The results showed that ARB decolorization efficiency by the defined co-culture was 1.25-fold to 1.51-fold elevated by 24.6-305.0 mT SMF. The best ARB decolorization and chemical oxygen demand (COD) removal performances by the co-culture were both achieved with 95.0 mT SMF. By contrast, biomass multiplication and sedimentation property of AS systems were not significantly influenced by SMF. Higher activities of intracellular key enzymes were determined (with 95.0 mT SMF) as responsible for better decolorization and COD removal performances. Bacteria belonging to Prolixibacter, Corynebacterium, Pelagibacterium, Demequina, and Sphingobacterium which might be responsible for azo dye decolorization and aromatic compounds biodegradation were significantly enriched only in presence of SMF. Fungal genera Candida and Pichia were also significantly enriched by 41.4-305.0 mT SMF, which might be responsible for higher treatment efficiency. PRACTITIONER POINTS: Dye degradation was enhanced by combination of static magnetic field and yeasts. Improvement of enzyme activity was responsible for better treatment performance. Putative azo-degrading-related bacteria and fungi were selectively enriched. High relative abundance of Candida and Pichia ensured high decolorization effects. Potentially effective improvement of bioprocesses for treating hypersaline wastewater.

Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant

Two Gram-stain-negative, aerobic, motile and rod-shaped bacteria, one designated as strain AXB^T, capable of degrading estrogens, and another, YL23^T, 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 AXB^T could tolerate 3 % (w/v) NaCl, YL23^T 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 C_18:1ω6c and/or C_18:1ω7c) 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 AXB^T and YL23^T were 63.6 and 63.7 mol%, respectively. Based on the results of 16S rRNA gene sequence analysis, strains AXB^T and YL23^T belonged to the genus Sphingobium. Strain AXB^T was most closely related to Sphingobium chlorophenolicum NBRC 16172^T (97.5 %) and Sphingobium chungbukense DJ77^T (97.2 %), and strain YL23^T was most closely related to S. chlorophenolicum NBRC 16172^T (97.4 %) and S. quisquiliarum P25^T (97.1 %). Average nucleotide identity values between these two strains and S. chlorophenolicum NBRC 16172^T, S. chungbukense DJ77^T, Sphingobium chinhatense IP26^T, Sphingobium quisquiliarum P25^T and Sphingobium japonicum UT26S^T were from 80.7 to 85.8 %. In conclusion, strains AXB^T and YL23^T 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 AXB^T (=MCCC 1K01232^T=DSM 102173^T) and YL23^T (=MCCC 1K02300^T=DSM 102172^T), respectively.

Steroids as Environmental Compounds Recalcitrant to Degradation: Genetic Mechanisms of Bacterial Biodegradation Pathways

Steroids are perhydro-1,2-cyclopentanophenanthrene derivatives that are almost exclusively synthesised by eukaryotic organisms. Since the start of the Anthropocene, the presence of these molecules, as well as related synthetic compounds (ethinylestradiol, dexamethasone, and others), has increased in different habitats due to farm and municipal effluents and discharge from the pharmaceutical industry. In addition, the highly hydrophobic nature of these molecules, as well as the absence of functional groups, makes them highly resistant to biodegradation. However, some environmental bacteria are able to modify or mineralise these compounds. Although steroid-metabolising bacteria have been isolated since the beginning of the 20th century, the genetics and catabolic pathways used have only been characterised in model organisms in the last few decades. Here, the metabolic alternatives used by different bacteria to metabolise steroids (e.g., cholesterol, bile acids, testosterone, and other steroid hormones), as well as the organisation and conservation of the genes involved, are reviewed.

Biochemical Mechanisms and Catabolic Enzymes Involved in Bacterial Estrogen Degradation Pathways

Estrogens have been classified as group 1 carcinogens by the World Health Organization and represent a significant concern given that they are found in surface waters worldwide, and long-term exposure to estrogen-contaminated water can disrupt sexual development in animals. To date, the estrogen catabolic enzymes and genes remain unknown. Using a tiered functional genomics approach, we identified three estrogen catabolic gene clusters in Sphingomonas sp. strain KC8. We identified several estrone-derived compounds, including 4-hydroxyestrone, a meta-cleavage product, and pyridinestrone acid. The yeast-based estrogen assay suggested that pyridinestrone acid exhibits negligible estrogenic activity. We characterized 17β-estradiol dehydrogenase and 4-hydroxyestrone 4,5-dioxygenase, responsible for the 17-dehydrogenation and meta-cleavage of the estrogen A ring, respectively. The characteristic pyridinestrone acid was detected in estrone-spiked samples collected from two wastewater treatment plants and two suburban rivers in Taiwan. The results significantly expand our understanding of microbial degradation of aromatic steroids at molecular level.

Altererythrobacter salegens sp. nov., a slightly halophilic bacterium isolated from surface sediment

A Gram-negative, rod-shaped and slightly halophilic bacterium, strain XY-R17T, was isolated from the surface sediment of Mai Po Inner Deep Bay Ramsar Site birdwatch in Hong Kong. The 16S rRNA gene sequence of strain XY-R17T exhibited 96.5 % similarity to that of the type strain of Altererythrobacter atlanticus. Optimal growth occurred at pH 7.0-7.5, 3-8 % (w/v) NaCl and at 30 °C. The major respiratory quinone was ubiquinone-10. The principal fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), 11-methyl C18 : 1ω7c and C17 : 1ω6c .The polar lipid profile consisted of the major compounds sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and two unknown lipids. The DNA G+C content was 64.7 mol%. Based on its phenotypic properties, chemotaxonomic characteristics and phylogenetic distinctiveness, strain XY-R17T should be designated as a novel species of the genus Altererythrobacter. Therefore, the name Altererythrobacter salegens sp. nov. (type strain XY-R17T=KCTC 52267T=MCCC 1K01500T) is proposed.

Altererythrobacter soli sp. nov., isolated from desert sand

An alkaliphilic strain designed MN-1T was isolated from a desert sand sample collected from Tengger desert, north-western China. To delineate its taxonomic position, this Gram-stain-negative, rod-shaped, strictly aerobic bacterium was subjected to a polyphasic taxonomic study. Growth was observed at temperatures from 4 to 37 °C (optimum 30-32 °C), at salinities from 0 to 2 % (optimum 1 %) and at pH from 6.5 to 12.0 (optimum 7.0-9.0). Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain MN-1T was a member of the genus Altererythrobacterbut could be distinguished from recognized species of this genus. Compared to the reference strains, the novel strain was flagellated and motile by means of polar flagella. The predominant respiratory quinone was ubiquinone-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid, one unidentified phospholipid and four unidentified lipids. The predominant fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. These chemotaxonomic traits were in agreement with the characteristics of the genus Altererythrobacter. Strain MN-1T was most closely related to Altererythrobacter xinjiangensis S3-63T (96.9 % 16S rRNA gene sequence similarity), followed by Altererythrobacter dongtanensis JM27T (96.4 %) and Altererythrobacter marinus H32T (96.1 %). The G+C content of the genomic DNA of strain MN-1T was 67.0 mol%. On the basis of data from this polyphasic taxonomic study, strain MN-1T is proposed as the type strain of a novel species of the genus Altererythrobacter, named as Altererythrobacter soli sp. nov. (=KCTC 52135T=MCCC 1K02066T).