Distribution and abundance of oil-degrading bacteria in seawater of the Yellow Sea and Bohai Sea, China

Petroleum hydrocarbons are widespread in seawater. As an important sea area in northern China, the content and distribution of petroleum hydrocarbons in seawater need our attention because of the high toxicity and lasting polluting effects on the ecological environment of the Yellow Sea and Bohai Sea. In addition, there are few reports comparing the diversity of oil-degrading bacteria before and after enrichment. Therefore, we collected surface seawater from 10 sites in the Yellow Sea and Bohai Sea in the autumn of 2020 to study the distribution characteristics of total petroleum hydrocarbons (TPH) and the diversity of oil-degrading bacteria. The concentration of TPH was 81.65 μg/L-139.55 μg/L at ten sites in the Bohai Sea and the Yellow Sea, which conformed to the China Grade II water quality standard (GB3097-1997). Moreover, the pristine/phytane (PR/PH) value of most sites was close to 1, indicating that the area was obviously polluted by exogenous petroleum hydrocarbons. We found that oil-degrading bacteria in the seawater of the Yellow Sea and the Bohai Sea had a good degradation effect on C11-C14 short chain alkanes (degradation rate of 59.19-73.22 %) and C1-C4 phenanthrene (degradation rate of 48.19-60.74 %). In terms of the diversity of oil-degrading bacteria, Gammaproteobacteria and Alphaproteobacteria dominated the enriched bacterial communities. Notably, the relative abundance of Alcanivorax changed significantly before and after enrichment. We proposed that surface seawater in the Bohai Sea and Yellow Sea could form oil-degrading bacteria mainly composed of Alcanivorax, which had great potential for oil pollution remediation.

A FadR-Type Regulator Activates the Biodegradation of Polycyclic Aromatic Hydrocarbons by Mediating Quorum Sensing in Croceicoccus naphthovorans Strain PQ-2

Bacteria employ multiple transcriptional regulators to orchestrate cellular responses to adapt to constantly varying environments. The bacterial biodegradation of polycyclic aromatic hydrocarbons (PAHs) has been extensively described, and yet, the PAH-related transcriptional regulators remain elusive. In this report, we identified an FadR-type transcriptional regulator that controls phenanthrene biodegradation in Croceicoccus naphthovorans strain PQ-2. The expression of fadR in C. naphthovorans PQ-2 was induced by phenanthrene, and its deletion significantly impaired both the biodegradation of phenanthrene and the synthesis of acyl-homoserine lactones (AHLs). In the fadR deletion strain, the biodegradation of phenanthrene could be recovered by supplying either AHLs or fatty acids. Notably, FadR simultaneously activated the fatty acid biosynthesis pathway and repressed the fatty acid degradation pathway. As intracellular AHLs are synthesized with fatty acids as substrates, boosting the fatty acid supply could enhance AHL synthesis. Collectively, these findings demonstrate that FadR in C. naphthovorans PQ-2 positively regulates PAH biodegradation by controlling the formation of AHLs, which is mediated by the metabolism of fatty acids. IMPORTANCE Master transcriptional regulation of carbon catabolites is extremely important for the survival of bacteria that face changes in carbon sources. Polycyclic aromatic hydrocarbons (PAHs) can be utilized as carbon sources by some bacteria. FadR is a well-known transcriptional regulator involved in fatty acid metabolism; however, the connection between FadR regulation and PAH utilization in bacteria remains unknown. This study revealed that a FadR-type regulator in Croceicoccus naphthovorans PQ-2 stimulated PAH biodegradation by controlling the biosynthesis of the acyl-homoserine lactone quorum-sensing signals that belong to fatty acid-derived compounds. These results provide a unique perspective for understanding bacterial adaptation to PAH-containing environments.

Assessment of residual chlorine in soil microbial community using metagenomics

Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic. However, at present, little is known about the impact of residual chlorine on the soil micro-ecological environment. Herein, we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water, and then analyzed the influence on the soil microbial community using metagenomics. After 14-d continuous chlorine treatment, there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil. Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment, it recovered to the original status. The abundance of several resistance genes changed by 7 d and recovered by 14 d. According to our results, the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth (shoot length and fresh weight) and soil micro-ecology. In general, our study assisted with environmental risk assessments relating to the application ofchlorine-containing disinfectants and minimization of risks to the environment during disease control, such as COVID-19.

Croceicoccus hydrothermalis sp. nov., isolated from shallow-sea hydrothermal system off Kueishantao Island

A Gram-stain-negative, strictly aerobic, non-motile, ovoid or short-rod shaped, orange-pigmented bacterial strain, designated as strain JLT1T, was isolated from seawater of the shallow-sea hydrothermal system, near Kueishantao Islet. Growth was observed at 5–45°C (optimum, 30 °C) and pH 5.0–11.0 (optimum, pH 7.0). The salinity range for growth was 0–12 % (optimum, 2–4 %) (w/v) NaCl. JLT1T contained ubiquinone-10 as the main respiratory quinone. Iso-C12 : 0, summed feature 3 (C16 : 1ω7c/ω6c) and summed feature 8 (C18 : 1ω6c/ω7c) were identified as the major cellular fatty acids. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids, eight unidentified glycolipids and an unidentified lipid. The 16S rRNA gene of JLT1T shared the greatest similarity (96.31 %) with those of Croceicoccus pelagius Ery9T and Croceicoccus ponticola GM-16T. The draft genome size of JLT1T is 3.56 Mb, with 3578 potential genes and a genomic DNA G+C content of 63.24 mol %. Average nucleotide identity and digital DNA–DNA hybridization values of JLT1T compared with C. pelagius Ery9T, C. ponticola GM-16T, Croceicoccus sediminis S2-4-2T, Croceicoccus mobilis Ery22T and Croceicoccus marinus E4A9T were 74.5, 73.9, 74.4, 74.3 and 74.8 % and 20.6, 19.2, 20.0, 20.5 and 19.8%, respectively. On the basis of these phylogenetic, chemotaxonomic and phenotypic features, JLT1T is concluded to represent a novel species of the genus Croceicoccus , for which the name Croceicoccus hydrothermalis sp. nov. is proposed. The type strain is JLT1T (=CGMCC 1.15786T =JCM 31508T).

Microbial diversity and community structure in deep-sea sediments of South Indian Ocean

Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.

Effects of Salinity on the Biodegradation of Polycyclic Aromatic Hydrocarbons in Oilfield Soils Emphasizing Degradation Genes and Soil Enzymes

The biodegradation of organic pollutants is the main pathway for the natural dissipation and anthropogenic remediation of polycyclic aromatic hydrocarbons (PAHs) in the environment. However, in the saline soils, the PAH biodegradation could be influenced by soil salts through altering the structures of microbial communities and physiological metabolism of degradation bacteria. In the worldwide, soils from oilfields are commonly threated by both soil salinity and PAH contamination, while the influence mechanism of soil salinity on PAH biodegradation were still unclear, especially the shifts of degradation genes and soil enzyme activities. In order to explain the responses of soils and bacterial communities, analysis was conducted including soil properties, structures of bacterial community, PAH degradation genes and soil enzyme activities during a biodegradation process of PAHs in oilfield soils. The results showed that, though low soil salinity (1% NaCl, w/w) could slightly increase PAH degradation rate, the biodegradation in high salt condition (3% NaCl, w/w) were restrained significantly. The higher the soil salinity, the lower the bacterial community diversity, copy number of degradation gene and soil enzyme activity, which could be the reason for reductions of degradation rates in saline soils. Analysis of bacterial community structure showed that, the additions of NaCl increase the abundance of salt-tolerant and halophilic genera, especially in high salt treatments where the halophilic genera dominant, such as Acinetobacter and Halomonas. Picrust2 and redundancy analysis (RDA) both revealed suppression of PAH degradation genes by soil salts, which meant the decrease of degradation microbes and should be the primary cause of reduction of PAH removal. The soil enzyme activities could be indicators for microorganisms when they are facing adverse environmental conditions.

Identifying bioaugmentation candidates for bioremediation of polycyclic aromatic hydrocarbons in contaminated estuarine sediment of the Elizabeth River, VA, USA

Estuarine sediments near former creosoting facilities along the Elizabeth River (Virginia, USA) are contaminated by polycyclic aromatic hydrocarbons (PAHs). In this study, we interrogated the bacterial community of the Elizabeth River with both culture-based and culture-independent methods to identify potential candidates for bioremediation of these contaminants. DNA-based stable isotope probing (SIP) experiments with phenanthrene and fluoranthene using sediment from the former Republic Creosoting site identified relevant PAH-degrading bacteria within the Azoarcus, Hydrogenophaga, and Croceicoccus genera. Targeted cultivation of PAH-degrading bacteria from the same site recovered 6 PAH-degrading strains, including one strain highly similar to Hydrogenophaga sequences detected in SIP experiments. Other isolates were most similar to organisms within the Novosphingobium, Sphingobium, Stenotrophomonas, and Alcaligenes genera. Lastly, we performed 16S rRNA gene amplicon microbiome analyses of sediment samples from four sites, including Republic Creosoting, with varying concentrations of PAHs. Analysis of these data showed a striking divergence of the microbial community at the highly contaminated Republic Creosoting site from less contaminated sites with the enrichment of several bacterial clades including those affiliated with the Pseudomonas genus. Sequences within the microbiome libraries similar to SIP-derived sequences were generally found at high relative abundance, while the Croceicoccus sequence was present at low to moderate relative abundance. These results suggest that Azoarcus and Hydrogenophaga strains might be good target candidates for biostimulation, while Croceicoccus spp. might be good targets for bioaugmentation in these sediments. Furthermore, this study demonstrates the value of culture-based and culture-independent methods in identifying promising bacterial candidates for use in a precision bioremediation scheme. KEY POINTS: • This study highlights the importance of using multiple strategies to identify promising bacterial candidates for use in a precision bioremediation scheme. • We used both selective cultivation techniques and DNA-based stable isotope probing to identify bacterial degraders of prominent PAHs at a historically contaminated site in the Elizabeth River, VA, USA. • Azoarcus and Hydrogenophaga strains might be good target candidates for biostimulation in Elizabeth River sediments, while Croceicoccus spp. might be good targets for bioaugmentation.

Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons

Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg^-1), moderate (600 mg kg^-1), and high (1200 mg kg^-1) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHD_α) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11.58, 14.51, and 8.94 mg kg^-1 sediment day^-1) than in the dry-season sediments (3.51, 12.56, and 5.91 mg kg^-1 sediment day^-1) possibly due to higher nutrient accumulation caused by rainfall and higher diversity of potential phenanthrene-degrading bacteria. The results suggested that the mangrove sediment microbiome significantly clustered according to season. Although Gram-negative phenanthrene-degrading bacteria (i.e., Anaerolineaceae, Marinobacter, and Rhodobacteraceae) played a key role in both dry and wet seasons, distinctly different phenanthrene-degrading bacterial taxa were observed in each season. Halomonas and Porticoccus were potentially responsible for the degradation of phenanthrene in the dry and wet seasons, respectively. The knowledge gained from this study contributes to the development of effective and rationally designed microbiome innovations for oil removal.

Growth promotion of a deep-sea bacterium by sensing infrared light through a bacteriophytochrome photoreceptor

Photoreceptors are found in all kingdoms of life and bacteriophytochromes (Bphps) are the most abundant photo-sensing receptors in bacteria. Interestingly, BphPs have been linked to some bacterial physiological responses, yet most of the biological processes they regulate are still elusive, especially in non-photosynthetic bacteria. Here, we show that a bacteriophytochrome (CmoBphp) from a deep-sea bacterium Croceicoccus marinus OT19 perceives infrared light (wavelength at 940 nm) and transduces photo-sensing signals to a downstream intracellular transduction cascade for better growth. We discover that the infrared light-mediated growth promotion of C. marinus OT19 is attributed partly to the enhancement of pyruvate and propanoate metabolism. Further study suggests that CmoBphp plays a crucial role in integrating infrared light with intracellular signalling to control the bacterial growth and metabolism. This is the first report that deep-sea non-photosynthetic bacteria can sense infrared light to control growth through a bacteriophytochrome photoreceptor, thus providing new understandings towards light energy utilization by microorganisms.

PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influences its survival in soil and rhizospheres

Novosphingobium sp. HR1a is a good biodegrader of PAHs and aromatic compounds, and also a good colonizer of rhizospheric environments. It was previously demonstrated that this microbe is able to co-metabolize nutrients existing in root exudates together with the PAHs. We have revealed here that PahT, a regulator of the IclR-family, regulates the central carbon fluxes favouring the degradation of PAHs and mono-aromatic compounds, the ethanol and acetate metabolism and the uptake, phosphorylation and further degradation of mono- and oligo-saccharides through a phosphoenolpyruvate transferase system (PTS). As final products of these fluxes, pyruvate and acetyl-CoA are obtained. The pahT gene is located within a genomic region containing two putative transposons that carry all the genes for PAH catabolism; PahT also regulates these genes. Furthermore, encoded in this genomic region, there are genes that are involved in the recycling of phosphoenolpyruvate, from the obtained pyruvate, which is the motor molecule involved in the saccharide uptake by the PTS system. The co-metabolism of PAHs with different carbon sources, together with the activation of the thiosulfate utilization and an alternative cytochrome oxidase system, also regulated by PahT, represents an advantage for Novosphingobium sp. HR1a to survive in rhizospheric environments.

Bisphenol A biodegradation differs between mudflat and mangrove forest sediments

Bisphenol A (BPA) is one of the widely detected endocrine disrupting chemicals in coastal sediment. Biodegradation is a vital pathway of BPA elimination in sediment. However, the impact of vegetation on BPA degradation in coastal sediment is still unclear. In this study, the differences of BPA biodegradation and the functional microbial community and metabolic pathway were explored between mangrove forest and mudflat sediments. A nearly complete BPA attenuation was detected in 4 days in mudflat sediment but 8 days in forest sediment. Bacterial abundance varied greatly in different sediment types. Bacterial community structure changed with BPA biodegradation, dependent on sediment type. During the degradation, the proportions of Alphaproteobacteria and Gammaproteobacteria were higher in BPA amended microcosms than in un-amended microcosms. With BPA biodegradation, a substantial increase in Novosphingobium and Croceicoccus occurred in forest sediment and mudflat sediment, respectively. Additionally, two divergent BPA biodegradation pathways were proposed based on functional annotation and KEGG pathway database. The abundance of functional genes also varied with BPA biodegradation, dependent on sediment type. Gene pcaGH decreased, while genes ligK and pcaD increased in both sediment types. Gene pcaB showed a remarkable increase in forest sediment but a decrease in mudflat sediment. Therefore, BPA degradation and the associated microbial community and metabolic pathway differed between mudflat and mangrove forest sediments.

Actirhodobacter atriluteus gen. nov., sp. nov., isolated from the surface water of the Yellow Sea

A Gram-stain-negative, aerobic, orange-pigmented bacterial strain, designated HHU K3-1 ^T, was isolated from the surface water of the Yellow Sea. The strain was observed to grow on 2216E agar medium, and growth occurred at pH 6.0-8.0 (optimum 7.0), 28-37 °C (optimum 28 °C), and in the presence of 0.5-5% (w/v) NaCl (optimum 1-3%). The major fatty acids (> 10%) were summed feature 3 (C_16:1ω6c/C_16:1ω7c), C_17:1ω6c and summed feature 8 (C_18:1ω6c/C_18:1ω7c). Strain HHU K3-1 ^T was found to contain ubiquinone-10 as the predominant quinone and the major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and sphingoglycolipid (SGL). The 16S rRNA gene sequence analysis indicated that strain HHU K3-1 ^T shared highest similarities with Pelagerythrobacter marensis KCTC 22370 ^T (97.7%) and Qipengyuania oceanensis MCCC 1A09965^T (96.9%). However, a phylogenetic tree based on 288 orthologous clusters (OCs) indicated that HHU K3-1 ^T was close related to Parapontixanthobacter aurantiacus MCCC 1A09962^T. The pairwise AAI and evolutionary distance between HHU K3-1 ^T and Parapontixanthobacter aurantiacus MCCC 1A09962^T are 67.1% and 0.43, respectively, which meet the recently proposed standard to differentiate genera in the family Erythrobacteraceae. On the basis of the result obtained by the polyphasic taxonomic study, strain HHU K3-1 ^T can be considered to represent a novel genus in the family Erythrobacteraceae, for which the name Actirhodobacter atriluteus gen. nov., sp. nov. is proposed. The type strain is HHU K3-1 ^T (= MCCC 1K04225^T = KCTC 72834 ^T = CGMCC 1.17395 ^T).

Croceicoccus bisphenolivorans sp. nov., a bisphenol A-degrading bacterium isolated from seawater

A bisphenol A-degrading bacterium, designated as strain H4^T, was isolated from surface seawater, which was sampled from the Jiulong River estuary in southeast PR China. Strain H4^T is Gram-stain-negative, aerobic, short rod-shaped, lacking bacteriochlorophyll a, motile with multifibrillar stalklike fascicle structures and capable of degrading bisphenol A. Growth of strain H4^T was observed at 24-45 °C (optimum, 32 °C), at pH 5.5-9 (optimum, pH 7.0) and in 0-7 % NaCl (optimum, 2 %; w/v) . The 16S rRNA gene sequence of strain H4^T showed highest similarity to Croceicoccus pelagius Ery9^T (98.7 %), Croceicoccus sediminis (98.3 %), Croceicoccus naphthovorans PQ-2^T (98.1 %) and Croceicoccus ponticola GM-16^T (97.6 %), followed by Croceicoccus marinus E4A9^T (96.7 %) and Croceicoccus mobilis Ery22^T (96.0 %). Phylogenetic analysis revealed that strain H4^T fell within a clade comprising the type strains of Croceicoccus species and formed a phyletic line with them that was distinct from other members of the family Erythrobacteraceae. The sole respiratory quinone was quinone 10 (Q-10). The predominant fatty acids (>5 % of the total fatty acids) of strain H4^T were summed feature 8 (C_18 : 1  ω6c and/or C_18 : 1  ω7c), summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c), C_17 : 1  ω6c and C_14 : 02-OH. The genomic DNA G+C content was 62.8 mol%. In the polar lipid profile, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, two sphingoglycolipids and three unknown lipids were the major compounds. Based on the genotypic and phenotypic data, strain H4^T represents a novel species of the genus Croceicoccus, for which the name Croceicoccus bisphenolivorans sp. nov. is proposed. The type strain is H4^T (=DSM 102182^T=MCCC1 K02301^T).

The LuxI/LuxR-Type Quorum Sensing System Regulates Degradation of Polycyclic Aromatic Hydrocarbons via Two Mechanisms

Members of the Sphingomonadales are renowned for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). However, little is known about the regulatory mechanisms of the degradative pathway. Using cross-feeding bioassay, a functional LuxI/LuxR-type acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) system was identified from Croceicoccus naphthovorans PQ-2, a member of the order Sphingomonadales. Inactivation of the QS system resulted in a significant decrease in PAHs degradation. The QS system positively controlled the expression of three PAH-degrading genes (ahdA1e, xylE and xylG) and a regulatory gene ardR, which are located on the large plasmid. Interestingly, the transcription levels of these three PAH-degrading genes were significantly down-regulated in the ardR mutant. In addition, bacterial cell surface hydrophobicity and cell morphology were altered in the QS-deficient mutant. Therefore, the QS system in strain PQ-2 positively regulates PAH degradation via two mechanisms: (i) by induction of PAH-degrading genes directly and/or indirectly; and (ii) by an increase of bacterial cell surface hydrophobicity. The findings of this study improve our understanding of how the QS system influences the degradation of PAHs, therefore facilitating the development of new strategies for the bioremediation of PAHs.

Genomic-based taxonomic classification of the family Erythrobacteraceae

The family Erythrobacteraceae, belonging to the order Sphingomonadales, class Alphaproteobacteria, is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter, Croceibacterium, Croceicoccus, Erythrobacter, Erythromicrobium, Porphyrobacter and Qipengyuania. As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter. This study is the first genomic-based study of the family Erythrobacteraceae, and will contribute to further insights into the evolution of this family.

Croceibacterium gen. nov., with description of Croceibacterium ferulae sp. nov., an endophytic bacterium isolated from Ferula sinkiangensis K. M. Shen and reclassification of Porphyrobacter mercurialis as Croceibacterium mercuriale comb. nov

A novel endophytic bacterium, designated strain SX2RGS8^T, was isolated from the surface-sterilized roots of an endangered medicinal plant (Ferula sinkiangensis K. M. Shen) collected from Xinjiang, north-western PR China. The taxonomic position of the candidate was investigated using a polyphasic approach. Strain SX2RGS8^T was found to be aerobic, Gram-stain-negative, oxidase-negative, catalase-positive and axiolitic-shaped. Strain SX2RGS8^T grew at 4-45 °C (optimum, 28 °C), pH 4.0-10.0 (pH 7.0) and in the presence of 0-5 % (w/v) NaCl. The polar lipids detected for strain SX2RGS8^T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified phosphoglycolipids, an unidentified phospholipid and unidentified lipids. The major respiratory quinone of strain SX2RGS8^T was ubiquinone 10 and the major fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was determined to be 66.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate belonged to the family Erythrobacteraceae and showed 99.2 % (Porphyrobacter mercurialis), 95.5 % (Porphyrobacter donghaensisi) and 95.4 % (Porphyrobacter colymbi) similarities to its closest relatives. The isolate contained carotenoids, but no bacteriochlorophyll a. On the basis of phenotypic, genotypic and phylogenetic data, strain SX2RGS8^T represents a novel species of a novel genus in the family Erythrobacteraceae, for which the name Croceibacterium ferulae gen. nov., sp. nov. is proposed. The type strain is SX2RGS8^T (=CGMCC 1.16402^T=KCTC 62090^T). In addition, Porphyrobacter mercurialis Coil et al. 2016 is proposed to be transferred to this new genus as Croceibacterium mercuriale comb. nov.

Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales

The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C₄₀ carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales. Comparative analyses of the genomes of 41 strains of this order revealed that there were different patterns of clustering of carotenoid biosynthesis (crt) ORFs, with four ORF clusters being the most common. The analyses also revealed that co-occurrence of crtY and crtI is an evolutionarily conserved feature in Sphingomonadales and other carotenogenic bacteria. The comparisons facilitated the categorisation of bacteria of this order into four groups based on the presence of different crt ORFs. Yellow coloured strains most likely accumulate nostoxanthin, and contain six ORFs (group I: crtE, crtB, crtI, crtY, crtZ, crtG). Orange coloured strains may produce adonixanthin, astaxanthin, canthaxanthin and erythroxanthin, and contain seven ORFs (group II: crtE, crtB, crtI, crtY, crtZ, crtG, crtW). Red coloured strains may accumulate astaxanthin, and contain six ORFs (group III: crtE, crtB, crtI, crtY, crtZ, crtW). Non-pigmented strains may contain a smaller subset of crt ORFs, and thus fail to produce any carotenoids (group IV). The functions of many of these ORFs remain to be characterised.

Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9T

Croceicoccus marinus E4A9^Twas isolated from deep-sea sediment collected from the East Pacific polymetallic nodule area. The strain is able to produce esterase, which is widely used in the food, perfume, cosmetic, chemical, agricultural and pharmaceutical industries. Here we describe the characteristics of strain E4A9, including the genome sequence and annotation, presence of esterases, and metabolic pathways of the organism. The genome of strain E4A9^T comprises 4,109,188 bp, with one chromosome (3,001,363 bp) and two large circular plasmids (761,621 bp and 346,204 bp, respectively). Complete genome contains 3653 coding sequences, 48 tRNAs, two operons of 16S–23S-5S rRNA gene and three ncRNAs. Strain E4A9^T encodes 10 genes related to esterase, and three of the esterases (E3, E6 and E10) was successfully cloned and expressed in Escherichia coli Rosetta in a soluble form, revealing its potential application in biotechnological industry. Moreover, the genome provides clues of metabolic pathways of strain E4A9^T, reflecting its adaptations to the ambient environment. The genome sequence of C. marinus E4A9^T now provides the fundamental information for future studies.

Bacterial communities associated with sulfonamide antibiotics degradation in sludge-amended soil

This study investigated the degradation of sulfonamide antibiotics (SAs) and microbial community changes in sludge-amended soil. In batch experiments, SA degradation was enhanced by addition of spent mushroom compost (SMC), SMC extract, and extract-containing microcapsule, with SMC showing higher SA degradation rate than the other additives in soil-sludge mixtures. In bioreactor experiments, the degradation of SAs in soil-sludge mixtures was in the order of sulfamethoxazole > sulfadimethoxine > sulfamethazine during four times of SA addition. SA removal was higher in soil-sludge mixtures than in soil alone. The bacterial composition differed in soil-sludge mixtures with and without SMC. In total, 44 differentially distributed bacterial genera were identified from different experimental settings and stages. Four bacterial genera, Acinetobacter, Alcaligenes, Brevundimonas, and Pseudomonas, were previously found involved in SA degradation, and 20 of the 44 bacterial genera were previously found in aromatic hydrocarbon degradation. Therefore, these bacteria have high potential to be SA degradation bacteria in this study.

Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment

A Gram-reaction-negative, non-motile, facultatively aerobic bacterium, designated strain M1T, was isolated from a subterrestrial sediment sample of Qiangtang Basin in Qinghai-Tibetan plateau, China. The strain formed rough yellow colonies on R2A plates. Cells were oval or short rod-shaped, catalase-positive and oxidase-negative. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate belonged to the family Erythrobacteraceae and showed 96.2–96.4 % 16S rRNA gene sequence similarities to its closest relatives. Chemotaxonomic analysis revealed ubiquinone-10 (Q10) as the dominant respiratory quinone of strain M1T and C17 : 1ω6c (44.2 %) and C18 : 1ω7c (13.7 %) as the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid, three unidentified glycolipids, one unidentified phosphoglycolipid and one unidentified lipid. The DNA G+C content of strain M1T was 73.7 mol%. On the basis of phenotypic, phylogenetic and genotypic data presented in this study, strain M1T represents a novel species of a new genus in the family Erythrobacteraceae, for which the name Qipengyuania sediminis gen. nov., sp. nov. is proposed. The type strain of the type species is M1T ( = CGMCC 1.12928T = JCM 30182T).

Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter

A novel, Gram-negative, non-spore-forming, pleomorphic yellow-orange bacterial strain was isolated from a stadium seat. Strain Coronado^T falls within the Erythrobacteraceae family and the genus Porphyrobacter based on 16S rRNA phylogenetic analysis. This strain has Q-10 as the predominant respiratory lipoquinone, as do other members of the family. The fatty acid profile of this strain is similar to other Porphyrobacter, however Coronado^T contains predominately C18:1ω7cis and C16:0, a high percentage of the latter not being observed in any other Erythrobacteraceae. This strain is catalase-positive and oxidase-negative, can grow from 4 to 28 °C, at NaCl concentrations 0.1–1.5%, and at pH 6.0–8.0. On the basis of phenotypic and phylogenetic data presented in this study, strain Coronado^T represents a novel species in the Porphyrobacter genus for which the name Porphyrobacter mercurialis sp. nov. is proposed; the type strain is Coronado^T (=DSMZ 29971, =LMG 28700).