Xiao-Lei Wu

Bacterial Community Mapping of the Mouse Gastrointestinal Tract

Keeping mammalian gastrointestinal (GI) tract communities in balance is crucial for host health maintenance. However, our understanding of microbial communities in the GI tract is still very limited. In this study, samples taken from the GI tracts of C57BL/6 mice were subjected to 16S rRNA gene sequence-based analysis to examine the characteristic bacterial communities along the mouse GI tract, including those present in the stomach, duodenum, jejunum, ileum, cecum, colon and feces. Further analyses of the 283,234 valid sequences obtained from pyrosequencing revealed that the gastric, duodenal, large intestinal and fecal samples had higher phylogenetic diversity than the jejunum and ileum samples did. The microbial communities found in the small intestine and stomach were different from those seen in the large intestine and fecal samples. A greater proportion of Lactobacillaceae were found in the stomach and small intestine, while a larger proportion of anaerobes such as Bacteroidaceae, Prevotellaceae, Rikenellaceae, Lachnospiraceae, and Ruminococcaceae were found in the large intestine and feces. In addition, inter-mouse variations of microbiota were observed between the large intestinal and fecal samples, which were much smaller than those between the gastric and small intestinal samples. As far as we can ascertain, ours is the first study to systematically characterize bacterial communities from the GI tracts of C57BL/6 mice.

Degradation of petroleum hydrocarbons (C6–C40) and crude oil by a novel Dietzia strain

A novel bacterial strain, DQ12-45-1b, was isolated from the production water of a deep subterranean oil-reservoir. Morphological, physiological and phylogenetic analyses indicated that the strain belonged to the genus Dietzia with both alkB (coding for alkane monooxygenase) and CYP153 (coding for P450 alkane hydroxylase of the cytochrome CYP153 family) genes and their induction detected. It was capable of utilizing a wide range of n-alkanes (C6-C40), aromatic compounds and crude oil as the sole carbon sources for growth. In addition, it preferentially degraded short-chain hydrocarbons (≤C25) in the early cultivation phase and accumulated hydrocarbons with chain-lengths from C23 to C27 during later cultivation stage with crude oil as the sole carbon source. This is the first study to report the different behaviors of a bacterial species toward crude oil degradation as well as a species of Dietzia degrading a wide range of hydrocarbons.

Removal of silver nanoparticles in simulated wastewater treatment processes and its impact on COD and NH4 reduction

The increasing utilization of silver nanoparticles in industrial and consumer products has raised concern to wastewater treatment utilities due to its antimicrobial activity. In this work, the removal of citrate stabilized silver nanoparticles (Ag-NPs) during the wastewater treatment processes and its impact on treatment performance were examined. During simulated primary clarification, over 90% of the Ag-NPs remained in the wastewater, indicating that the majority of silver nanoparticles in sewage would enter the subsequent treatment units. During sequencing batch reactor processes, silver nanoparticles were effectively removed in each cycle throughout the 15-d experimental duration. Continuous input of silver nanoparticles into the wastewater did not significantly alter chemical oxygen demand (COD) removal. NH(4) removal was reduced at the beginning of the SBR experiment but quickly recovered at the later stage of the experiment. This study demonstrated that in the near future it is unlikely that citrate-stabilized Ag-NPs released into sewage will cause significant adversary effects on the COD and NH(4) removal of activated sludge processes in municipal wastewater treatment plants.

Diverse alkane hydroxylase genes in microorganisms and environments

AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature.

Microbial Communities in Long-Term, Water-Flooded Petroleum Reservoirs with Different in situ Temperatures in the Huabei Oilfield, China

The distribution of microbial communities in the Menggulin (MGL) and Ba19 blocks in the Huabei Oilfield, China, were studied based on 16S rRNA gene analysis. The dominant microbes showed obvious block-specific characteristics, and the two blocks had substantially different bacterial and archaeal communities. In the moderate-temperature MGL block, the bacteria were mainly Epsilonproteobacteria and Alphaproteobacteria, and the archaea were methanogens belonging to Methanolinea, Methanothermobacter, Methanosaeta, and Methanocella. However, in the high-temperature Ba19 block, the predominant bacteria were Gammaproteobacteria, and the predominant archaea were Methanothermobacter and Methanosaeta. In spite of shared taxa in the blocks, differences among wells in the same block were obvious, especially for bacterial communities in the MGL block. Compared to the bacterial communities, the archaeal communities were much more conserved within blocks and were not affected by the variation in the bacterial communities.

Thermophilic anaerobic co-digestion of garbage, screened swine and dairy cattle manure.

Methane fermentation characteristics of garbage, swine manure (SM), dairy cattle manure (DCM) and mixtures of these wastes were studied. SM and DCM showed much lower volatile total solid (VTS) digestion efficiencies and methane yield than those of garbage. VTS digestion efficiency of SM was significantly increased when it was co-digested with garbage (Garbage: SM=1:1). Co-digestion of garbage, SM and DCM with respect to the relative quantity of each waste discharged in the Kikuchi (1: 16: 27) and Aso (1: 19: 12) areas indicated that co-digestion with garbage would improve the digestion characteristic of SM and DCM as far as the ratio of DCM in the wastes was maintained below a certain level. When the mixed waste (Garbage: SM: DCM=1:19:12) was treated using a thermophilic UAF reactor, methanogens responsible for the methane production were Methanoculleus and Methanosarcina species. Bacterial species in the phylum Firmicutes were dominant bacteria responsible for the digestion of these wastes. As the percentage of garbage in the mixed wastes used in this study was low (2-3%) and the digestion efficiency of DCM was obviously improved, the co-digestion of SM and DCM with limited garbage was a prospective method to treat the livestock waste effectively and was an attractive alternative technology for the construction of a sustainable environment and society in stock raising area.

Impacts of different nanoparticles on functional bacterial community in activated sludge

Rapidly developing industry raises concerns about the environmental impacts of nanoparticles, but the effects of inorganic nanoparticles on functional bacterial community in wastewater treatment remain unclear. The discriminated effects of silver nanoparticles (Ag-NP) and zinc oxide nanoparticles (ZnO-NP) in a simulated sequencing batch reactor (SBR) system were therefore evaluated by the RNA-based terminal restricted fragment length polymorphism (T-RFLP), 16S rcDNA gene clone library and real-time reverse transcription-PCR (RT-PCR) analyses. Although the COD and NH4-N removal efficiencies were not or slightly reduced by the addition of ZnO-NP and Ag-NP, the functional bacterial community changed remarkably. The denitrification related species were inhibited by high dosage of ZnO-NP and Ag-NP, including Diaphorobacter species, Thauera species and those in the Sphaerotilus-Leptothrix group. However, the bacteria related to sludge bulking, heavy metal resistant and biosorption were increased, especially by ZnO-NPs treatment, including those closely related to Haliscomenobacter hydrossis, Zoogloea ramigera and Methyloversatilis universalis. In addition, Ag-NP and ZnO-NP treatments influenced the functional bacterial community differently. Increasing of bulking related bacteria may help to compensate the COD removal efficiency and to maintain functional redundancy, but could lead to operation failure of activated sludge system when expose to ZnO-NPs.

Removal of ZnO nanoparticles in simulated wastewater treatment processes and its effects on COD and NH4+-N reduction

For many engineered nanoparticles, the primary pathway of release into the environment is via sewage and industrial wastewater discharges. In this work, the removal of uncoated ZnO nanoparticles (ZnO NPs) during simulated wastewater treatment processes and its impact on treatment performance were examined. Simulated primary clarification removed the majority (about 70%) of the dosed ZnO NPs. During simulated sequencing batch reactor (SBR) processes, ZnO NPs were completely removed in each cycle throughout the 11-day experimental duration (two cycles per day). Continuous input of ZnO NPs into the wastewater (at concentrations up to 5 mg L(-1)) did not reduce chemical oxygen demand (COD) removal. NH(4)(+)-N removal was reduced at a dosing concentration of 5 mg L(-1) ZnO NPs per cycle. Inhibition of respiration of nitrifying microorganisms by ZnO NPs corroborated the reduction of NH(4)(+)-N removal. These results indicate that if the wastewater is treated, the release of ZnO NPs into receiving water bodies would be minimal and ZnO NPs would mainly accumulate in biosolids. Uncoated ZnO NPs in wastewater at very high concentrations may have some adverse effects on activated sludge process.

Growth of non-phototrophic microorganisms using solar energy through mineral photocatalysis

Phototrophy and chemotrophy are two dominant modes of microbial metabolism. To date, non-phototrophic microorganisms have been excluded from the solar light-centered phototrophic metabolism. Here we report a pathway that demonstrates a role of light in non-phototrophic microbial activity. In lab simulations, visible light-excited photoelectrons from metal oxide, metal sulfide, and iron oxide stimulated the growth of chemoautotrophic and heterotrophic bacteria. The measured bacterial growth was dependent on light wavelength and intensity, and the growth pattern matched the light absorption spectra of the minerals. The photon-to-biomass conversion efficiency was in the range of 0.13-1.90‰. Similar observations were obtained in a natural soil sample containing both bacteria and semiconducting minerals. Results from this study provide evidence for a newly identified, but possibly long-existing pathway, in which the metabolisms and growth of non-phototrophic bacteria can be stimulated by solar light through photocatalysis of semiconducting minerals.

Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil

Four bacterial strains, SL014B-41A4(T), SL014B-20A1(T), SL014B-76A1 and SL014B-79A, isolated from a crude oil-contaminated saline soil of Shengli Oilfield, China, were investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SL014B-41A4(T) belonged to the genus Salinarimonas in the order Rhizobiales, with the highest sequence similarity with Salinarimonas rosea YIM YD3(T) (98.3 %). The DNA-DNA relatedness of strain SL014B-41A4(T) to S. rosea YIM YD3(T) was 27.03 ± 3.0 %. Strain SL014B-41A4(T) was Gram-negative staining, facultatively anaerobic and produced deep red pigment in artificial seawater medium. Cells of strain SL014B-41A4(T) were rod-shaped (0.6-4.0 × 1.25-25 µm), motile with a single polar flagellum and often formed branches. The strain contained Q-10 as the predominant respiratory ubiquinone and C(18 : 1)ω7c (57.5 %), C(16 : 0) (16.4 %) and 10-methyl C(19 : 0) (9.1 %) as the major fatty acids. Strains SL014B-20A1(T), SL014B-76A1 and SL014B-79A were actinobacteria and belonged to the genus Tessaracoccus in the family Propionibacteriaceae of the order Actinomycetales with the highest 16S rRNA gene sequence similarities with Tessaracoccus flavescens SST-39(T) (96.4 %), Tessaracoccus lubricantis KISS-17Se(T) (96.2 %) and Tessaracoccus bendigoensis Ben 106(T) (94.7 %). Strains SL014B-20A1(T), SL014B-76A1 and SL014B-79A were Gram-positive staining, facultatively anaerobic, non-endospore-forming, non-motile, acid-fast and oval to rod-shaped (0.48 × 0.5-1.0 µm). These three novel strains had ll-diaminopimelic acid (DAP) as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-9(H(4)) as the only menaquinone and anteiso-C(15 : 0) (67.11-76.14 %) as the major cellular fatty acid. The G+C contents of the genomic DNA of strain SL014B-41A4(T) and strains SL014B-20A1(T), SL014B-76A1 and SL014B-79A were 67.68 mol% and 65.65-67.17 mol%, respectively. Based on phenotypic and genotypic characteristics, strain SL014B-41A4(T) represents a novel species of the genus Salinarimonas, for which the name Salinarimonas ramus is proposed, with strain SL014B-41A4(T) ( = DSM 22962(T) = CGMCC 1.9161(T)) as the type strain. Strains SL014B-20A1(T), SL014B-76A1 and SL014B-79A represent a novel species of the genus Tessaracoccus, for which the name Tessaracoccus oleiagri is proposed, with strain SL014B-20A1(T) ( = DSM 22955(T) = CGMCC 1.9159(T)) as the type strain.