Xinxin Wang

Analysis of bacterial community in bulking sludge using culture-dependent and -independent approaches.

The bacterial community of a bulking sludge from a municipal wastewater treatment plant with anoxic-anaerobic-oxic process was investigated by combination of cultivation and 16S rRNA gene clone library analysis for understanding the causes of bulking. A total of 28 species were obtained from 63 isolates collected from six culture media. The most cultivable species belonged to gamma-Proteobacteria including Klebsiella sp., Pseudomonas sp., Aeromonas sp. and Acinetobacter sp. Further analysis of these strains by repetitive sequence based on polymerase chain reaction (rep-PCR) technology showed that rep-PCR yielded discriminatory banding patterns within the same genus using REP and BOX primer sets. While the culture-independent assessment revealed that beta-Proteobacteria was the dominant group in the bulking sample. Sequence analysis revealed that the highest proportion (14.7%) of operational taxonomic units was 98% similar to Candidatus Accumulibacter phosphatis, which is used to remove phosphorous from wastewater. Our results indicated that combining different approaches can produce complementary information, thus generate a more accurate view of microbial community in bulking sludge.

Archaeal community structure along a gradient of petroleum contamination in saline-alkali soil.

The response of archaeal communities to petroleum contamination in saline-alkali soil was characterized by analyses of three soil samples with different total petroleum hydrocarbon concentrations. Through the construction and screening of 16S rRNA gene clone libraries based on DNA extracts from these soils, nine distinct phylogenetic groups were identified. Statistical analyses showed that the distribution of archaeal community structures differ significantly along the gradient of petroleum contamination in these three saline-alkali soils. Five phylogenetic groups were dominant in the control soil, two of which were also abundant in the lightly contaminated soil. Four phylogenetic groups were dominant in heavily contaminated soil, one of which was also abundant in the lightly contaminated soil. The halophilic genus of Haloferax and the haloalkaliphilic genus of Natronomonas were more abundant in heavily contaminated soil. These results suggested that the genera of Haloferax and Natronomonas may have a role in the natural attenuation of petroleum-contaminated saline-alkali soil.

Terrimonas pekingensis sp. nov., isolated from bulking sludge, and emended descriptions of the genus Terrimonas, Terrimonas ferruginea, Terrimonas lutea and Terrimonas aquatica.

A Gram-negative, strictly aerobic, non-motile and non-spore-forming rod that produced white, viscous colonies, designated QH(T), was isolated from bulking sludge collected from a municipal wastewater treatment plant in Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QH(T) belonged to the genus Terrimonas and shared 96.3 % sequence similarity with Terrimonas lutea DY(T), 94.1 % with Terrimonas ferruginea ATCC 13524(T) and 93.8 % with Terrimonas aquatica RIB1-6(T). Strain QH(T) contained iso-C15 : 0, summed feature 3 (comprising one or more of C16 : 1ω7c, C16 : 1ω6c and iso-C15 : 0 2-OH) and iso-C15 : 1 G as the predominant fatty acids. The predominant polar lipid of strain QH(T) and members of the genus Terrimonas was phosphatidylethanolamine. The major isoprenoid quinone of strain QH(T) was MK-7 and the DNA G+C content was 41.0 mol%. DNA-DNA relatedness between strain QH(T) and T. lutea BCRC 17944(T), T. ferruginea BCRC 17943(T) and T. aquatica BCRC 17941(T) was 32, 23 and 22 %, respectively. On the basis of phylogenetic inference, differential phenotypic data and low DNA-DNA relatedness with members of the genus Terrimonas, strain QH(T) represents a novel species, for which the name Terrimonas pekingensis sp. nov. is proposed. The type strain is QH(T) ( = CICC 10452(T)  = NCCB 100397(T)). The descriptions of the genus Terrimonas and T. ferruginea, T. lutea and T. aquatica are also emended.

Characterization and Genomic Analysis of a Highly Efficient Dibutyl Phthalate-Degrading Bacterium Gordonia sp. Strain QH-12

A bacterial strain QH-12 isolated from activated sludge was identified as Gordonia sp. based on analysis of 16S rRNA gene sequence and was found to be capable of utilizing dibutyl phthalate (DBP) and other common phthalate esters (PAEs) as the sole carbon and energy source. The degradation kinetics of DBP under different concentrations by the strain QH-12 fit well with the modified Gompertz model (R2 > 0.98). However, strain QH-12 could not utilize the major intermediate product phthalate (phthalic acid; PA) as the sole carbon and energy source, and only a little amount of PA was detected. The QH-12 genome analysis revealed the presence of putative hydrolase/esterase genes involved in PAEs-degradation but no phthalic acid catabolic gene cluster was found, suggesting that a novel degradation pathway of PAEs was present in Gordonia sp. QH-12. This information will be valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs-degrading Gordonia sp. strains.

Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge

A phthalate esters-degrading bacterial strain, designated QH-11T, was isolated from an activated sludge wastewater treatment plant in Beijing, PR China. The cells were aerobic, Gram-stain-positive, non-motile, catalase-positive, oxidase-negative, short rods and formed white colonies on trypticase soy agar. This isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and whole-cell hydrolysates contained arabinose and ribose. Diphosphatidylglycerol and phosphatidylethanolamine were the predominant polar lipids. According to the results of full-length of 16S rRNA gene sequence analysis, QH-11T represented a member of the genus Gordonia and showed the highest sequence similarity to Gordonia hydrophobica DSM 44015T (99.2 %), but was distinguishable by a low level of DNA-DNA relatedness (37.8 %). Genome-based comparisons indicated a clear distinction from the top ten most similar type strains (16S rRNA gene sequence) with pairwise average nucleotide identities (ANI) between 74.6 and 83.4 %. The predominant respiratory quinone was MK-9(H2), the mycolic acids present had 56 to 62 carbon atoms, and the major fatty acids were C16 : 0 (33.3 %), C17 : 1ω8c (23.4 %) and C18 : 1ω9c (17.9 %). The DNA G+C content was 68.0 mol%. On the basis of the results of DNA-DNA hybridization, ANI and physiological and biochemical tests, it is proposed that QH-11T represents a novel species of the genus Gordonia, for which the name Gordonia phthalatica sp. nov. is proposed. The type strain is QH-11T (CICC 24107T =KCTC 39933T).

Draft Genome Sequence of Paenibacillus polymyxa EBL06, a Plant Growth-Promoting Bacterium Isolated from Wheat Phyllosphere

ABSTRACT Paenibacillus polymyxa strain EBL06 is a plant growth-promoting bacterium with high antifungal activity. The estimated genome of this strain is 5.68 Mb in size and harbors 4,792 coding sequences (CDSs).

Dibutyl phthalate contamination remolded the fungal community in agro-environmental system

Dibutyl phthalate (DBP) is a typical soil contaminant that is widely used as plasticizer in modern agricultural production. In this study, an experiment was conducted to evaluate fungal community succession in a soil-vegetable ecosystem under different DBP concentrations. By using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region, it was shown that DBP contamination caused significant changes to the soil fungal community, in terms of both α and β diversities. The largest changes in fungal α and β diversities were detected under 50 mg/kg DBP concentration at the first day of addition. The bulk soils, rhizosphere soils and the phyllosphere harbored different fungal communities, while the abundance of saprotrophs and plant pathogens in the phyllosphere have been increased under DBP contamination. From correlation analysis and partial Mantel test, the change in fungal community α diversity was the result of multiple factors (DBP concentration, bacterial community and soil properties) while the β diversity of fungal community was mainly co-varied with the bacterial community after DBP contamination. Moreover, molecular ecological network analysis demonstrated that DBP contamination was detrimental to mutualistic relationships among fungal species and destabilized the network structure. Overall, the fungal communities in soils and around vegetables were largely remolded by DBP contamination that provides new insight into DBP contamination impacts on agricultural ecosystems.

Draft Genome Sequence of Sphingobium yanoikuyae TJ, a Halotolerant Di-n-Butyl-Phthalate-Degrading Bacterium

ABSTRACT Sphingobium yanoikuyae TJ is a halotolerant di-n-butyl-phthalate-degrading bacterium, isolated from the Haihe estuary in Bohai Bay, Tianjin, China. Here, we report the 5.1-Mb draft genome sequence of this strain, which will provide insights into the diversity of Sphingobium spp. and the mechanism of phthalate ester degradation in the estuary.