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Lake Taihu in China has suffered serious harmful cyanobacterial blooms for decades. The algal blooms threaten the ecological sustainability, drinking water safety, and human health. Although the roles of abiotic factors (such as water temperature and nutrient loading) in promoting Microcystis blooms have been well studied, the importance of biotic factors (e.g. bacterial community) in promoting and meditating Microcystis blooms remains unclear. In this study, we investigated the ecological dynamics of bacterial community, the ratio of toxic Microcystis, as well as microcystin in Lake Taihu. High-throughput 16S rRNA sequencing and principal component analysis (PCA) revealed that the bacteria community compositions (BCCs) clustered into three groups, the partitioning of which corresponded to that of groups according to the toxic profiles (the ratio of toxic Microcystis to total Microcystis, and the microcystin concentrations) of the samples. Further Spearman's correlation network showed that the α-proteobacteria Phenylobacterium strongly positively correlated with the toxic profiles. Subsequent laboratory chemostats experiments demonstrated that three Phenylobacterium strains promoted the dominance of the toxic Microcystis aeruginosa PCC7806 when co-culturing with the non-toxic PCC7806 mcyB- mutant. Taken together, our data suggested that the α-proteobacteria Phenylobacterium may play a vital role in the maintenance of toxic Microcystis dominance in Lake Taihu.

The ecological distribution and activities of soil microbes can reflect the influence of environmental factors on microbes and changes in soil fertility. Understanding the community structure of the soil microbes is of great importance to maintaining soil health in ancient mulberry plantation ecosystems. In this study, the population structure of soil microorganisms in different ages of mulberry plantations was analyzed using high-throughput sequencing technology. A total of 1616, 1568, 1379 and 1477 operational taxonomic units were acquired from samples of 3Y (3-year-old), 35Y (35-year-old), 200Y (200-year-old) and 600Y (600-year-old) soils, respectively. The results exhibited that the highest community diversity was found in 35Y soil, followed by 200Y soil, and showed that the stand age strongly influenced the community structure of soil bacteria. A total of 23 phyla were detected in 12 samples, and the genus of bacteria that predominated the different stand ages mainly included; Phenylobacterium, Cohnella, Lactococcus, Sphingomonas, Bacillus, and Microbispora. The relative abundance of Phenylobacterium accounts for 22.6–53.5% of the total abundance. This study showed that the richness and diversity of the soil bacteria decreased as the stand age increased in ancient mulberry plantations.

Contamination of soil, water and air due to hydrocarbons are a global issue and bioremediation provides probably the best way to remediate the contaminants. The current study shows the biodegradation of crude oil, diesel and used engine oil by a newly isolated Phenylobacterium korensee from contaminated soil of Bahror, Alwar, Rajasthan. Hydrocarbon degrading strain was screened on BHA (Bushnell Haas Agar) media supplemented with 2T engine oil as sole carbon source. The strain was found to be degrading at 1%, 4% and 10% of used 2T engine oil respectively after 14 days. Degradation was confirmed both gravimetrically and by Gas Chromatography Mass Spectroscopy analysis. The degradation was found very well at long term basis. The optimization of growth also studied at temperature and pH basis also. The significance of the study is that the percentage degradation of the complex petroleum supplements used in the study was found to be far higher than some of the previously reported values and this bacterial strain was firstly found from this contaminated site.

A Gram-stain-negative, facultative anaerobic, non-motile and rod-shaped bacterial strain, designated LX32T, was isolated from arsenic and cadmium contaminated farmland soil. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain LX32T was closely related to Phenylobacterium hankyongense HKS-05T (97.7 % sequence similarity), Phenylobacterium kunshanense CCTCC AB 2013085T (97.4 %) and Phenylobacterium deserti CCTCC AB 2016297T (97.1 %). The average nucleotide identity values of the whole genome sequences of LX32T/P. hankyongense HKS-05T, LX32T/P. kunshanense CCTCC AB 2013085T and LX32T/P. deserti CCTCC AB 2016297T were 79.8, 77.9 and 77.5 %, respectively. Its genome size was 4.02 Mb, comprising 3998 predicted genes with a DNA G+C content of 70.1 mol%. The major fatty acids were C15 : 0, C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The polar lipid profiles consisted of phosphatidylglycerol, aminophospholipid, seven glycolipids and two unidentified polar lipids. The predominantly respiratory quinone was ubiquinone-10. Based on polyphasic analyses, the isolate is considered to represent a novel species of the genus Phenylobacterium , for which the name Phenylobacterium soli sp. nov. is proposed. The type strain is LX32T (=KCTC 62522=CCTCC AB 2018055).

Development of economical and environment-friendly Microbial Fuel Cells (MFCs) technology should be associated with waste management. However, current knowledge regarding microbiological bases of electricity production from complex waste substrates is insufficient. In the following study, microbial composition and electricity generation were investigated in MFCs powered with waste volatile fatty acids (VFAs) from anaerobic digestion of primary sludge. Two anode sizes were tested, resulting in organic loading rates (OLRs) of 69.12 and 36.21 mg chemical oxygen demand (COD)/(g MLSS∙d) in MFC1 and MFC2, respectively. Time of MFC operation affected the microbial structure and the use of waste VFAs promoted microbial diversity. High abundance of Deftia sp. and Methanobacterium sp. characterized start-up period in MFCs. During stable operation, higher OLR in MFC1 favored growth of exoelectrogens from Rhodopseudomonas sp. (13.2%) resulting in a higher and more stable electricity production in comparison with MFC2. At a lower OLR in MFC2, the percentage of exoelectrogens in biomass decreased, while the abundance of genera Leucobacter, Frigoribacterium and Phenylobacterium increased. In turn, this efficiently decomposed complex organic substances, favoring high and stable COD removal (over 85%). Independent of the anode size, Clostridium sp. and exoelectrogens belonging to genera Desulfobulbus and Acinetobacter were abundant in MFCs powered with waste VFAs.

International audience; Alpine soils are warming strongly, leading to profound alterations in carbon cycling and greenhouse gas budgets, mediated via the soil microbiome. To explore microbial responses to global warming, we incubated eight alpine soils between 4 and 35 °C and linked the temperature dependency of bacterial growth with alterations in community structures and the identification of temperature sensitive taxa. The temperature optimum for bacterial growth was between 27 and 30 °C and was higher in soils from warmer environments. This temperature framing the upper limit of naturally occurring temperatures was a tipping point above which the temperature range for growth shifted towards higher temperatures together with pronounced changes in community structures and diversity based on both 16S rRNA gene and transcript sequencing. For instance, at the highest temperature, we observed a strong increase in OTUs affiliated with Burkholderia-Paraburkholderia, Phenylobacterium, Pseudolabrys, Edaphobacter and Sphingomonas. Dominance at high temperature was explained by a priori adaptation to high temperature, high growth potential as well as stress resistance. At the highest temperature, we moreover observed an overall increase in copiotrophic properties in the community along with high growth rates. Further, temperature effects on community structures depended on the long-term climatic legacy of the soils. These findings contribute to extrapolating from single to multiple sites across a large range of conditions.

Background Bacterial endophytes are widespread inhabitants inside plant tissues that play crucial roles in plant growth and biotransformation. This study aimed to offer information for the exploitation of endophytes by analyzing the bacterial endophytes in different parts of Panax notoginseng. Methods We used high-throughput sequencing methods to analyze the diversity and composition of bacterial endophytes from different parts of P. notoginseng. Results A total of 174,761 classified sequences were obtained from the analysis of 16S ribosomal RNA in different parts of P. notoginseng. Its fibril displayed the highest diversity of bacterial endophytes. Principal coordinate analysis revealed that the compositions of the bacterial endophytes from aboveground parts (flower, leaf, and stem) differed from that of underground parts (root and fibril). The abundances of Conexibacter, Gemmatimonas, Holophaga, Luteolibacter, Methylophilus, Prosthecobacter, and Solirubrobacter were significantly higher in the aboveground parts than in the underground parts, whereas the abundances of Bradyrhizobium, Novosphingobium, Phenylobacterium, Sphingobium, and Steroidobacter were markedly lower in the aboveground parts. Conclusions Our results elucidated the comprehensive diversity and composition profiles of bacterial endophytes in different parts of 3-year-old P. notoginseng. Our data offered pivotal information to clarify the role of endophytes in the production of P. notoginseng and its important metabolites. Electronic supplementary material The online version of this article (10.1186/s13020-018-0198-5) contains supplementary material, which is available to authorized users.

A Gram-stain negative, aerobic, motile, non-spore-forming and rod-shaped bacterial strain, designated YIM 730227T, was isolated from a soil sample, collected from Karak district, Khyber-Pakhtun-Khwa, Pakistan. The bacterium was characterized using a polyphasic taxonomic approach. Pairwise comparison of the 16S rRNA gene sequences showed that strain YIM 730227T is closely related to Phenylobacterium lituiforme FaiI3T (97.5% sequence similarity), Phenylobacterium muchangponense A8T (97.4%), Phenylobacterium panacis DCY109T (97.1%), Phenylobacterium immobile ET (97.1%) and Phenylobacterium composti 4T-6T (97.0%), while also sharing 98.0% sequence similarity with Phenylobacterium hankyongense HKS-05T after NCBI blast, showing it represents a member of the family Caulobacteraceae. The major respiratory quinone was Q-10 and the major fatty acids were C16:0, summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c), C18:1ω7c 11-methyl and C17:0. The polar lipids were phosphatidylglycerol, unidentified glycolipids, phospholipid and unidentified lipid. The G + C content of the genomic DNA was 68.2 mol%. The DNA–DNA relatedness values of strain YIM 730227T with P. hankyongense HKS-05T, P. lituiforme FaiI3T, P. muchangponense A8T, P. panacis DCY109T, P. immobile ET and P. composti 4T-6T were 31.3 ± 0.6, 26.1 ± 0.2, 24.3 ± 0.1, 21.8 ± 0.9, 19.8 ± 0.6 and 18.2 ± 1.1%, respectively, values lower than 70%. Besides the morphological and chemotaxonomic characteristics, phylogenetic analyses of 16S rRNA gene sequences and the biochemical characteristics indicated that the strain YIM 730227T represents a novel member of the genus Phenylobacterium, for which the name Phenylobacterium terrae sp. nov. (type strain YIM 730227T = KCTC62324T = CGMCC 1.16326T) is proposed.

An investigation on the soil microbe populations from an agricultural inning area at the Pearl River estuary in Guangdong province, China was conducted via high through-put sequencing. The results revealed abundant diversity in the soil bacterial and fungal populations. In total, 197103 sequence tags were obtained from soil samples, most of which represented bacterial genera Actinomycetes, Bacillus and Marinobacter, while a majority of 118378 tags obtained were derived from fungal genera Clostridium, Devosia, Bradyrhizobium, Bdellovibrio, Phenylobacterium, Penicillium, and Emericella. Furthermore, nine physiological indexes (pH, available phosphorous, basic-group nitrogen, available potassium, catalase, sucrose, urease, phosphatase, and organic matters) were measured in three soil samples, and the association between these physiological indexes and microbe population composition was examined. The results revealed obvious inter-sample differences associated with ten dominating microbial groups: genera Clostridium, Devosia, Bradyrhizobium, Bdellovibrio, Phenylobacterium, and Penicillium were mainly impacted by pH (with a positive correlation), genera Sphingomonas and Acinetobacter mainly by available phosphorous (positive correlation), and genera Gemmatimonas and Pseudomonas by both pH and available phosphorous (negative correlation). Our study suggested that regulation of microbial species/populations might help improve soil environment to facilitate the growth of crops’ above-ground parts, and this provides practical information for inning agriculture.

A Gram-stain-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated HKS-05T, was isolated from ginseng field soil. This bacterium was characterized to determine its taxonomic position by using the polyphasic approach. HKS-05T grew at 10–37 °C and at pH 6.0–8.0 on R2A agar. On the basis of 16S rRNA gene sequence similarity, HKS-05T was shown to represent a member of the family Caulobacteraceae and to be related to Phenylobacterium lituiforme FaiI3T (98.1 % sequence similarity), ‘ Phenylobacterium zucineum ’ HLK1 (97.9 %), Phenylobacterium muchangponense A8T (97.7 %), Phenylobacterium composti 4T-6T (97.2 %) and Phenylobacterium immobile ET (97.1 %). The major respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids were phosphatidylglycerol, unidentified glycolipids and unidentified polar lipids. The G+C content of the genomic DNA was 70.4 mol%. DNA–DNA relatedness values between HKS-05T and its closest phylogenetically neighbours were low. HKS-05T could be differentiated genotypically and phenotypically from the species of the genus Phenylobacterium with validly published names. The isolate therefore represents a novel species, for which the name Phenylobacterium hankyongense sp. nov. is proposed, with the type strain HKS-05T (=KACC 18628T=LMG 30081T)

The microbiota has been reported to be closely associated with carcinogenesis and cancer progression. However, its involvement in the pathology of thymoma remains unknown. In this study, we aimed to identify thymoma-specific microbiota using resected thymoma samples. Nineteen thymoma tissue samples were analyzed through polymerase chain reaction amplification and 16S rRNA gene sequencing. The subjects were grouped according to histology, driver mutation status in the GTF2I gene, PD-L1 status, and smoking habits. To identify the taxa composition of each sample, the operational taxonomic units (OTUs) were classified on the effective tags with 97% identity. The Shannon Index of the 97% identity OTUs was calculated to evaluate the alpha diversity. The linear discriminant analysis effect size (LEfSe) method was used to compare the relative abundances of all the bacterial taxa. We identified 107 OTUs in the tumor tissues, which were classified into 26 genera. Sphingomonas and Phenylobacterium were identified as abundant genera in almost all the samples. No significant difference was determined in the alpha diversity within these groups, however, type A thymoma tended to exhibit a higher bacterial diversity than type B thymoma. Through the LEfSe analysis, we identified the following differentially abundant taxa: Bacilli, Firmicutes, and Lactobacillales in type A thymoma, Proteobacteria in type B thymoma, Gammaproteobacteria in tumors harboring the GTF2I mutation, and Alphaproteobacteria in tumors without the GTF2I mutation. In conclusion, Sphingomonas and Phenylobacterium were identified as dominant genera in thymic epithelial tumors. These genera appear to comprise the thymoma-specific microbiota.

A novel bacterial strain, designated YIM 73061T, was isolated from the Cholistan desert in Punjab, Pakistan, and characterized by using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed the highest levels of sequence similarity with respect to Phenylobacterium conjunctum FWC21T (97.6 %), Phenylobacterium lituiforme FaiI3T (97.4 %), Phenylobacterium composti 4T-6T (97.0 %) and Phenylobacterium aquaticum W2-3-4T (96.8 %). Cells were Gram-stain-negative, aerobic and motile rods that formed orange colonies. The strain was oxidase- and catalase-positive. Growth occurred at 20–40 °C (optimum, 30–37 °C) at pH 5.0–8.0 (optimum, pH 7.0) and with 0–1 % (w/v) NaCl (optimum, 0–0.5 %). The major cellular fatty acids (>10 %) were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol and four unidentified glycolipids. The major isoprenoid quinone was ubiquinone-10 (Q-10). The G+C content of the genomic DNA was 66.8 mol%. Strain YIM 73061T showed low levels of DNA–DNA relatedness to P. conjunctum FWC21T (27.2±2.6 %), P. lituiforme FaiI3T (24.6±1.1 %) and P. composti 4T-6T (18.4±3.1 %). On the basis of phylogenetic inference, chemotaxonomic characteristics and phenotypic data, strain YIM 73061T should be classified as representing a novel species, for which the name Phenylobacterium deserti sp. nov. is proposed. The type strain is YIM 73061T (=DSM 103871T=CCTCC AB 2016297T).

Soda lime is a by-product of the Solvay soda process for the production of sodium carbonate from limestone and sodium chloride. Due to a high salt concentration and alkaline pH, the lime is considered as a potential habitat of haloalkaliphilic and haloalkalitolerant microbial communities. This artificial and unique environment is nutrient-poor and devoid of vegetation, due in part to semi-arid, saline and alkaline conditions. Samples taken from the surface layer of the lime and from the depth of 2 m (both having pH ~11 and ECe up to 423 dS m−1) were investigated using culture-based (culturing on alkaline medium) and culture-independent microbiological approaches (microscopic analyses and pyrosequencing). A surprisingly diverse bacterial community was discovered in this highly saline, alkaline and nutrient-poor environment, with the bacterial phyla Proteobacteria (representing 52.8% of the total bacterial community) and Firmicutes (16.6%) showing dominance. Compared to the surface layer, higher bacterial abundance and diversity values were detected in the deep zone, where more stable environmental conditions may occur. The surface layer was dominated by members of the genera Phenylobacterium, Chelativorans and Skermanella, while in the interior layer the genus Fictibacillus was dominant. The culturable aerobic, haloalkaliphilic bacteria strains isolated in this study belonged mostly to the genus Bacillus and were closely related to the species Bacillus pseudofirmus, B. cereus, B. plakortidis, B. thuringensis and B. pumilus. Electronic supplementary material The online version of this article (doi:10.1007/s10482-017-0866-y) contains supplementary material, which is available to authorized users.

The aim of this study was to investigate the impacts of red mud on lignin degradation, humic substance formation and laccase-producing bacterial community in composting to better improve composting performances. The results indicated that the organic matter contents of final compost products in the treatment group with red mud (T) decreased by 25.74%, which was more than the control group without red mud (CK) (12.09%). The final lignin degradation ratio and humic substance concentration of the T were 18.67% and 22.80% higher than that of the CK, respectively. The final C/N values of compost in the CK and T were 11.32 and 10.66, respectively, which were both less than 15, suggesting that compost reached maturity. Redundancy analysis showed that temperature was the main factors driving the variation of laccase-producing bacterial community. Pearson analysis suggested that Pseudomonas, Phenylobacterium, and Caulobacter were the most significantly correlated with lignin degradation and humification in the T.

A Gram-stain-negative, rod-shaped and aerobic bacterium, designated HYN0004T, was isolated from lake water. The strain grew at 15–35 °C and pH 7.0–9.0 on R2A. The isoprenoid quinone was Q10 and major polar lipids were phosphatidylglycerol and one unidentified glycolipid. The genome was 2.83 Mb with a DNA G+C content of 69.9 mol%. 16S rRNA gene sequence analyses revealed that HYN0004T represented a member of the genus Phenylobacterium and shared sequence similarities with Phenylobacterium conjunctum (97.8 %), Phenylobacterium koreense (97.5 %), Phenylobacterium aquaticum (97.2 %), and Phenylobacterium heamatophilum (97.0 %). In addition to the low sequence similarities, the phylogenetic tree shapes indicated that HYN0004Trepresents an independent species of this genus. The genomic and phenotypic properties, including small genome size, inability to carry out numerous enzymatic reactions and high ratio of C18 : 1ω6c and/or C18 : 1ω7c in fatty acids, verified the differentiation between HYN0004T and related species. Thus, we propose a novel species of the genus Phenylobacterium , named as Phenylobacterium parvum sp. nov. The type strain is HYN0004T (=KACC 19185T=NBRC 112736T).

The role of biogenic manganese oxide (BMO) materials on the stabilization of arsenic (As) in contaminated soil was investigated. Experimental results indicated that the addition of BMO was proved to be highly effective to stabilize As in soils. Bioavailable As content was decreased from 4.56 mg kg−1 in the control samples to 1.72–1.86 mg kg−1 in BMO-treated soils. X-ray absorption near edge structure (XANES) results confirmed that BMO was mainly responsible for oxidizing As(III) to As(V). Sequential extraction results indicated that the transformation of As fractions was from non-specifically adsorbed fraction to poorly-crystalline hydrous oxides fraction and residual fraction, which can decrease the risk of As in contaminated soils. Moreover, BMO had a higher efficiency in stabilizing As than two types of abiotic Mn oxides. High throughput sequencing analysis indicated that the bacterial community and diversity were significantly changed after BMO treatment. The abundance of Proteobacteria phylum, including Massilia, Phenylobacterium and Sphingomonas genera significantly increased with the increasing amount of BMO. These findings suggested that BMO can be considered as a low cost, high effectiveness and environmental friendliness material for the remediation of As contaminated soils.

Two common organic wastes from agriculture (rice straw) and forestry (sawdust) were applied to a petroleum-contaminated soil to estimate their effectiveness in the removal of total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs). Rice straw was the more effective amendment than the other treatments in reducing TPH contents and addition of sawdust resulted in a significant decrease in PAH removal, particularly high-molecular-weight (5-6 ring) PAHs. Principal coordinates analysis (PCoA) indicates that rice straw treatment separated only the bacterial community but sawdust greatly affected both the soil bacterial and fungal communities. Moreover, the abundance of some petroleum degraders such as the bacteria Sphingomonas, Idiomarina and Phenylobacterium and the fungi Humicola, Wallemia and Graphium was promoted by inputs of the two agricultural and forestry wastes. These results highlight the potential of waste applications in accelerating hydrocarbon biodegradation which may be attributed to the enrichment of keystone taxa that show strong positive associations with hydrocarbon degradation.

In situ remediation of contaminated sediment using microbes is a promising environmental treatment method. This study used bioaugmentation to investigate the biodegradation of tetrabromobisphenol A (TBBPA) in sediment microcosms collected from an electronic-waste recycling site. Treatments included adding possible biodegradation intermediates of TBBPA, including 2,4-dibromophenol (2,4-DBP), 2,4,6-tribromophenol (TBP), and bisphenol A (BPA) as co-substrates. Bioaugmentation was done with Ochrobactrum sp. T (TBBPA-degrader) and a mixed culture of Ochrobactrum sp. T, Bacillus sp. GZT (TBP-degrader) and Bacillus sp. GZB (BPA-degrader). Results showed that bioaugmentation with Ochrobactrum sp. T significantly improved TBBPA degradation efficiencies in sediment microcosms (P < 0.01); aerobic conditions increased the microbes' degradation activities. Co-substrates 2,4-DBP, TBP and BPA inhibited biodegradation of TBBPA. A metagenomic analysis of total 16S rRNA genes from the treated sediment microcosms showed that the following dominant genera: Ochrobactrum, Parasegetibacter, Thermithiobacillus, Phenylobacterium and Sphingomonas. The genus level of Ochrobactrum increased with increased degradation time, within 10-week of incubation. Microbes from genus Ochrobactrum are mainly linked to enhance the TBBPA biodegradation.

Bisphenol A (BPA) is a synthetic chemical primarily used to produce polycarbonate plastics and epoxy resins. Significant industrial and consumer's consumption of BPA-containing products has contributed to extensive contamination in different environmental matrices. In this study, microcosms bioaugmented with Bacillus sp. GZB were constructed to investigate BPA biodegradation, identify the main bacterial community, and evaluate bacterial community responses in the microcosms. Under aerobic conditions, BPA was quickly depleted as a result of bioaugmentation with Bacillus sp. GZB in water-sediment contaminated with pollutants. The pollutants used were generally associated with the electronic wastes (mobile phones, computers, televisions) dismantling process. Adding BPA affected the bacterial community composition in the water-sediment. Furthermore, BPA biodegradation was enhanced by adding electron donors/co-substrates: humic acid, NaCl, glucose, and yeast extract. Metagenomic analysis of the total 16S rRNA genes from the BPA-degrading microcosms with bioaugmentation illustrated that the genera Bacillus, Thiobacillus, Phenylobacterium, and Cloacibacterium were dominant after a 7-week incubation period. A consortium of microorganisms from different bacterial genera may be involved in BPA biodegradation in electronic waste contaminated water-sediment. This study provides new insights about BPA bioaugmentation and bacterial ecology in the BPA-degrading environment.

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped bacterial strain designated W2-3-4T was isolated from the reservoir of a water purifier. This bacterium was characterized to determine its taxonomic position by using a polyphasic approach. Strain W2-3-4T grew well at 25-30 °C on nutrient and R2A agars. On the basis of 16S rRNA gene sequence similarity, strain W2-3-4T was shown to belong to the family Caulobacteraceaeand to be related to Phenylobacterium conjunctumFWC21T (98.0 % sequence similarity) and Phenylobacterium haematophilum CCUG 26751T (97.2 %). Lower sequence similarities were found with the type strains of all other recognized members of the genus Phenylobacterium (95.7-97.1 %). The G+C content of the genomic DNA was 68.7 mol%. The major respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, C18 : 1ω7c 11-methyl and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids were phosphatidylglycerol, an unknown phospholipid, four unknown glycolipids and three unidentified polar lipids. DNA-DNA relatedness values between strain W2-3-4Tand its closest phylogenetically neighbours were below 7 %. Strain W2-3-4T could be differentiated genotypically and phenotypically from recognized species of the genus Phenylobacterium. The isolate therefore represents a novel species, for which the name Phenylobacterium aquaticum sp. nov. is proposed, with the type strain W2-3-4T (=KACC 18306T=LMG 28593T).

Painful granulomatous lesions appeared on the face of a 36-year-old man with myelodysplastic syndrome. Skin biopsy revealed chronic inflammatory granuloma. Bacterial cultures of the lesions and blood indicated the same unknown Gram-negative rod bacterium. The 16S ribosomal RNA sequence of the unknown bacterium yielded Phenylobacterium. Thus, we diagnosed cutaneous infectious granuloma caused by Phenylobacterium and myelodysplastic syndrome/refractory cytopenia with multi-lineage dysplasia. After treatment with combined antibacterials that were selected based on the tests for drug sensitivity, the lesions disappeared with only scars remaining and without any signs of relapse after 1 year. This is the first case report of cutaneous infectious granuloma caused by Phenylobacterium.

Rotifer growth performance and microbial community changes associated with rotifer cultures were monitored while different feed types (Nannochloropsis oculata paste and the commercial yeast based feed CS-3000), different regimes (daily changes, changes per batch and no changes) and mixtures of three probionts (Phenylobacterium sp.; Gluconobacter sp. and Paracoccus denitrificans) were provided. It was shown that the dominant bacterial species in the cultures receiving either N. oculata or CS-3000 were different. However, in cultures receiving both feeds (either switching between feeds on a daily basis or on a batch basis), a high similarity in microbial community fingerprint was found. The presence of probionts was detected by the end of four batch culture cycles in spite of strong shifts of the bacterial community. By group discriminant analysis, it was found that Phenylobacterium sp. and Paracoccus sp. contributed positively to the CS-3000-fed group, while Gluconobacter sp. contributed positively to the N. oculata-fed group, although they did not appear as very dominant species.

Antibiotic ciprofloxacin is ubiquitous in the environment. However, little is known about ciprofloxacin dissipation by microbial community. The present study investigated the biodegradation potential of ciprofloxacin by mixed culture and the influential factors and depicted the structure of ciprofloxacin-degrading microbial community. Both the original microbiota from drinking water biofilter and the microbiota previously acclimated to high levels of ciprofloxacin could utilize ciprofloxacin as sole carbon and nitrogen sources, while the acclimated microbiota had a much stronger removal capacity. Temperature rise and the presence of carbon or nitrogen sources favored ciprofloxacin biodegradation. Many novel biotransformation products were identified, and four different metabolic pathways for ciprofloxacin were proposed. Bacterial community structure illustrated a profound shift with ciprofloxacin biodegradation. The ciprofloxacin-degrading bacterial community was mainly composed of classes Gammaproteobacteria, Bacteroidia, and Betaproteobacteria. Microorganisms from genera Pseudoxanthomonas, Stenotrophomonas, Phenylobacterium, and Leucobacter might have links with the dissipation of ciprofloxacin. This work can provide some new insights towards ciprofloxacin biodegradation.

Quinones and other oxygenated polycyclic aromatic hydrocarbons (oxy-PAHs) are toxic and/or genotoxic compounds observed to be cocontaminants at PAH-contaminated sites, but their formation and fate in contaminated environmental systems have not been well studied. Anthracene-9,10-dione (anthraquinone) has been found in most PAH-contaminated soils and sediments that have been analyzed for oxy-PAHs. However, little is known about the biodegradation of oxy-PAHs, and no bacterial isolates have been described that are capable of growing on or degrading anthraquinone. PAH-degrading Mycobacterium spp. are the only organisms that have been investigated to date for metabolism of a PAH quinone, 4,5-pyrenequinone. We utilized DNA-based stable-isotope probing (SIP) with [U- 13 C]anthraquinone to identify bacteria associated with anthraquinone degradation in PAH-contaminated soil from a former manufactured-gas plant site both before and after treatment in a laboratory-scale bioreactor. SIP with [U- 13 C]anthracene was also performed to assess whether bacteria capable of growing on anthracene are the same as those identified to grow on anthraquinone. Organisms closely related to Sphingomonas were the most predominant among the organisms associated with anthraquinone degradation in bioreactor-treated soil, while organisms in the genus Phenylobacterium comprised the majority of anthraquinone degraders in the untreated soil. Bacteria associated with anthracene degradation differed from those responsible for anthraquinone degradation. These results suggest that Sphingomonas and Phenylobacterium species are associated with anthraquinone degradation and that anthracene-degrading organisms may not possess mechanisms to grow on anthraquinone.

Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or stable-isotope-labeled (13C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the 13C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes., IMPORTANCE The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential.

We established artificial consortia of bacteria inoculated from soil and a green alga, Chlorella vulgaris NIES-227. The bacteria and the alga were mixed in a tube or partitioned in a dialysing culture vessel, and the bacterial composition was examined after cultivation. The community of bacteria formed in the consortia included those phylogenetically closely related to the genera Phenylobacterium, Brevundimonas, Phyllobacterium, Afipia, Sphingomonas, Sandaracinobacter, Ramlibacter, Ralstonia, Cellvibrio, and so on. The community also included bacteria belonging to unknown genera within the phyla Bacteroidetes, Verrucomicrobia, and Acidobacteria. It was indicated that Ralstonia sp. and Cellvibrio sp. were attached to the algal cells and Phenylobacterium sp. Ramlibacter sp., Methylophilus sp., and Rhizobiaceae bacterium were not. It was suggested that bacteria belonging to the phylum Bacteroidetes and the class Alphaproteobacteria could be hemi-selectively enriched by the alga.

Three strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from fresh water and human blood. As determined by analyses of 16S rRNA gene sequences, the prosthecate strain FWC 38T was affiliated to the alphaproteobacterial genus Caulobacter, with Caulobacter henricii (96.8 %) and Caulobacter fusiformis (96.8 %) as its closest relatives. The non-prosthecate strain LMG 11050T and the prosthecate strain FWC 21T both belonged to the genus Phenylobacterium with Phenylobacterium koreense (96.9 %) and Phenylobacterium immobile (96.3 %) as the closest relatives. This affiliation was supported by chemotaxonomic data (polar lipids and cellular fatty acids). Physiological and biochemical tests allowed genotypic and phenotypic differentiation of the novel strains from all hitherto recognized species of the genera Caulobacter and Phenylobacterium. The strains therefore represent novel species, for which the names Caulobacter mirabilis sp. nov. (type strain FWC 38T=LMG 24261T=CCUG 55073T), Phenylobacterium conjunctum (type strain FWC 21T=LMG 24262T=CCUG 55074T), the first described prosthecate Phenylobacterium species, and Phenylobacterium haematophilum sp. nov. (type strain LMG 11050T=CCUG 26751T) are proposed. Marker nucleotides within the 16S rRNA genes were determined for the genera Asticcacaulis, Brevundimonas, Caulobacter and Phenylobacterium and the description of the genus Phenylobacterium is emended.

A Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, Slu-01T, was isolated from activated sludge from a wastewater treatment plant in Daejeon, South Korea. After 3 days on R2A medium, strain Slu-01T developed colourless colonies (0·7–1·2 mm). The non-motile rods (0·7–1·0×1·0–2·0 μm) were slightly curved and occurred singly and in pairs. No filamentous cells were found. On the basis of 16S rRNA gene sequence similarity, strain Slu-01T was shown to belong to the family Caulobacteraceae and was most closely related to Phenylobacterium immobile (96·6 %) and Phenylobacterium lituiforme (96·5 %). The genomic DNA G+C content of strain Slu-01T was 68·1 mol%, within the range of 67·3–68·4 mol% for the genus Phenylobacterium. Chemotaxonomic data (major ubiquinone, Q-10; major fatty acids C18 : 1 ω7c, C16 : 0, C15 : 0 and C17 : 0) and 16S rRNA gene sequence analysis supported the affiliation of strain Slu-01T to the genus Phenylobacterium. However, DNA–DNA hybridization data and phenotypic properties showed that strain Slu-01T could be distinguished from the two other Phenylobacterium species with validly published names. Thus, it is suggested that strain Slu-01T represents a novel species of the genus Phenylobacterium, for which the name Phenylobacterium koreense is proposed. The type strain is Slu-01T (=KCTC 12206T=IAM 15119T).

A Gram-negative bacterium designated AC-49T was isolated from an alkaline groundwater with a pH 11.4. This organism formed rod-shaped cells, was strictly aerobic, catalase and oxidase positive, with an optimum growth temperature of 35 degrees C and an optimum pH value of 8.0. Strain AC-49T assimilated primarily amino acids and some Krebs cycle metabolites, did not use sugars for growth. The organism did not grow on L-phenylalanine or antipyrin. The G+ C content of DNA was 66.9 mol%. The phylogenetic analyses based on the 16S rRNA sequencing showed that the closest relatives of strain AC-49T were Phenylobacterium lituiforme and Phenylobacterium immobile, indicating that the organism is a member of the order Caulobacterales of the Alphaproteobacteria. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strain AC-49T, represents a novel species of the genus Phenylobacterium for which we propose the name Phenylobacterium falsum sp. nov.

Summary The phylogenetic position of a chloridazon-degrading bacterium was evaluated by oligonucleotide cataloguing of its 16S rRNA. The herbicide-degrading organism lacks close relationship to any bacterium investigated so far with this method. Phylogenetically the organism tested is a member of Group I of phototrophic purple non-sulfur bacteria, showing a remote relationship to Pseudomonas diminuta, Rhizobium leguminosarum, Rhodopseudomonas sphaeroides, Rhodopseudomonas capsulata, Rhodopseudomonas viridis, Rhodomicrobium vannielii and Aquaspirillum itersonii (similarity coefficients ranging between 0.46 and 0.51). The isolated position of the chloridazon-degrading organism together with the use of unusual carbon sources favour the description of a new genus, for which the name Phenylobacterium will be proposed.

1. Four strains of bacteria growing with aminopyrine as sole source of carbon were isolated from soil and were identified as strains of Phenylobacterium immobilis. 2. Strain M13 and strain E, the type species of Phenylobacterium immobilis (DSM 1986), which had been isolated by enrichment with chloridazon (5-amino-4-chloro-2-phenyl-2H-pyridazin-3-one) were used to investigate the bacterial degradation of aminopyrine. 3. Three metabolites were isolated and identified as: 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydro-2,3-dihydroxy-4,6-cyc lohexadien-1-yl)-3H-pyrazol-3-one, 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydroxyphenyl)-3H-pyrazol-3 -one and 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-3H-pyrazol-3-one. 4. An enzyme extract from cells of strain m13 was shown to further metabolize the catechol derivative of aminopyrine, with the formation of 2-pyrone-6-carboxylic acid. 5. Results indicate that the benzene ring of aminopyrine is the principal site of microbial metabolism.

Bacteria which utilize the xenobiotic compounds chloridazon, antipyrin, and pyramidon as sole carbon sources were isolated from various soil samples. The 22 strains isolated are similar with respect to morphological, physiological, biochemical, serological, and genetic properties. These bacteria are aerobic gram-negative rods or coccal rods (0.7 to 1.0 by 1.0 to 2.0 μm) that occur singly, in pairs, or in short chains and are nonmotile and nonsporeforming. Physiological and biochemical characteristics and susceptibility to antibiotics were determined. The strains need vitamin B12 as a growth factor; they are catalase positive and weakly oxidase positive and show slight H2S production. All of the other tests which we performed were negative. The nutritional spectrum is extraordinarily limited, with optimal growth on chloridazon, antipyrin, pyramidon, and l-phenylalanine. Most sugars, alcohols, amino and carboxylic acids, and ordinary complex media are not utilized. The bacteria are osmotically sensitive. They are a serologically uniform group of organisms, which are harmless to rats and rabbits. Their guanine-plus-cytosine contents range between 65 and 68.5 mol%. The chloridazon-degrading bacteria are characterized as a new genus, Phenylobacterium, with a single species, Phenylobacterium immobile. The type strain Phenylobacterium immobile strain E (= DSM 1986), is not closely related to any other gram-negative bacterium, as shown by a 16S ribosomal ribonucleic acid partial sequence analysis. This organism is a member of group I of the purple nonsulfur bacteria, but is phylogenetically isolated in this group. Phenylobacterium immobile is remotely related to Pseudomonas diminuta, Rhizobium leguminosarum, rhodopseudomonads, and Aquaspirillum itersonii. Like other members of this group, Phenylobacterium immobile contains 2,3-diamino-2,3-dideoxy-d-glucose in its lipopolysaccharide. The murein equals a normal murein from a gram-negative bacterium. All citric acid cycle enzymes are detectable in Phenylobacterium immobile.