Zhenmei Lu

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in the United State history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared with outside the plume, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep sea. Various other microbial functional genes that are relevant to carbon, nitrogen, phosphorus, sulfur and iron cycling, metal resistance and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could have a significant role in biodegradation of oil spills in deep-sea environments.

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO2. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO2. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO2, and such significant effects of eCO2 on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO2. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO2. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO2 and environmental factors shaping the microbial community structure.

Influence of geogenic factors on microbial communities in metallogenic Australian soils

Links between microbial community assemblages and geogenic factors were assessed in 187 soil samples collected from four metal-rich provinces across Australia. Field-fresh soils and soils incubated with soluble Au(III) complexes were analysed using three-domain multiplex-terminal restriction fragment length polymorphism, and phylogenetic (PhyloChip) and functional (GeoChip) microarrays. Geogenic factors of soils were determined using lithological-, geomorphological- and soil-mapping combined with analyses of 51 geochemical parameters. Microbial communities differed significantly between landforms, soil horizons, lithologies and also with the occurrence of underlying Au deposits. The strongest responses to these factors, and to amendment with soluble Au(III) complexes, was observed in bacterial communities. PhyloChip analyses revealed a greater abundance and diversity of Alphaproteobacteria (especially Sphingomonas spp.), and Firmicutes (Bacillus spp.) in Au-containing and Au(III)-amended soils. Analyses of potential function (GeoChip) revealed higher abundances of metal-resistance genes in metal-rich soils. For example, genes that hybridised with metal-resistance genes copA, chrA and czcA of a prevalent aurophillic bacterium, Cupriavidus metallidurans CH34, occurred only in auriferous soils. These data help establish key links between geogenic factors and the phylogeny and function within soil microbial communities. In particular, the landform, which is a crucial factor in determining soil geochemistry, strongly affected microbial community structures.

Studies on biosorption equilibrium and kinetics of Cd2+ by Streptomyces sp. K33 and HL-12.

The sorption of Cd(2+) by Streptomyces sp. K33 and HL-12 was investigated. The removal efficiency increased with pH, but no obvious differences with different temperatures. Fourier transform infrared (FT-IR) was used to characterize the interaction between Cd(2+) and K33 and HL-12. Results revealed that the presence of amino, carboxyl, hydroxyl and carbonyl groups were responsible for the biosorption of Cd(2+). Strain HL-12 had more changes in the functional groups than K33. Biosorption equilibrium was established earlier by strain K33 than that by HL-12, and K33 had higher adsorption ratio. Langmuir, Freundlich and Dubinin-Radushkevich (D-R) isotherms were used to describe the adsorption experiment, Langmuir model fitted the experiment data best. Strain K33 showed greater sorption capacities with 38.49 mg Cd(2+)/g dry cells. Pseudo-first-order and second-order kinetic models were used to describe the kinetic data, and second-order kinetic model fitted better. About 70% recovery of Cd(2+) could be obtained at pH <or= 3 from metal-loaded biomass of strains HL-12 and K33.

Biodegradation of di-n-butyl phthalate by a stable bacterial consortium, HD-1, enriched from activated sludge.

HD-1, a stable microbial consortium capable of mineralizing di-n-butyl phthalate (DBP), was developed from activated sludge. The dominant microorganisms in the consortium, Gordonia sp., Burkholderia sp. and Achromobacter sp., were identified by denaturing gradient gel electrophoresis (DGGE). The consortium could mineralize approximately 90% of 1200 mg/L DBP after 48 h of cultivation. The optimal DBP degradation conditions were 25-30 °C and pH 8.0-9.0. The addition of yeast (0.5 g/L), sodium acetate (0.5 g/L, 1.0 g/L), Brij 35 (0.2%, 0.5%, 1.0%), or Triton X-100 (0.2%) enhanced DBP degradation. The DBP degradation rate was influenced by the presence of dimethyl phthalate (DMP) and diethyl phthalate (DEP). Only one main intermediate, phthalic acid, could be monitored by gas chromatography-mass spectrometry (GC-MS) during the degradation process. The HD-1 consortium also utilized phenol, o-dihydroxybenzene as the sole carbon and energy source. The results indicate the consortium may represent a promising application for DBP bioremediation.

GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer

The functional gene diversity and structure of microbial communities in a shallow landfill leachate-contaminated aquifer were assessed using a comprehensive functional gene array (GeoChip 3.0). Water samples were obtained from eight wells at the same aquifer depth immediately below a municipal landfill or along the predominant downgradient groundwater flowpath. Functional gene richness and diversity immediately below the landfill and the closest well were considerably lower than those in downgradient wells. Mantel tests and canonical correspondence analysis (CCA) suggested that various geochemical parameters had a significant impact on the subsurface microbial community structure. That is, leachate from the unlined landfill impacted the diversity, composition, structure, and functional potential of groundwater microbial communities as a function of groundwater pH, and concentrations of sulfate, ammonia, and dissolved organic carbon (DOC). Historical geochemical records indicate that all sampled wells chronically received leachate, and the increase in microbial diversity as a function of distance from the landfill is consistent with mitigation of the impact of leachate on the groundwater system by natural attenuation mechanisms.

Assessment of toxicity of tetrahydrofuran on the microbial community in activated sludge.

Activated sludge is widely used to treat industrial wastewater, but its efficiency is affected by a variety of factors, including toxic substances such as tetrahydrofuran (THF). In this study, we examined the toxicity of THF at different concentrations (0-320 mM) on the microbial community in activated sludge. A remarkable dose-dependent decrease in the total organic compound removal rate and culturable bacteria and fungi was observed. At THF concentrations higher than 160 mM, a decrease in pH to 3.0 was observed. The activities of five enzymes (catalase, dehydrogenase, urease, phosphatase and protease) analyzed were all significantly inhibited (p<0.01) at THF concentrations higher than 160 mM, especially dehydrogenase activity, which lost 95.4% of its activity at 320 mM THF. Microbial community analysis by PCR-DGGE revealed a substantial shift in the community structure and a reduction in diversity at a low THF concentration (20mM). These results suggest that THF is much more toxic than reported in the literature, indicating its acute toxicity to microorganisms.

Genetic Linkage of Soil Carbon Pools and Microbial Functions in Subtropical Freshwater Wetlands in Response to Experimental Warming

ABSTRACT Rising climate temperatures in the future are predicted to accelerate the microbial decomposition of soil organic matter. A field microcosm experiment was carried out to examine the impact of soil warming in freshwater wetlands on different organic carbon (C) pools and associated microbial functional responses. GeoChip 4.0, a functional gene microarray, was used to determine microbial gene diversity and functional potential for C degradation. Experimental warming significantly increased soil pore water dissolved organic C and phosphorus (P) concentrations, leading to a higher potential for C emission and P export. Such losses of total organic C stored in soil could be traced back to the decomposition of recalcitrant organic C. Warming preferentially stimulated genes for degrading recalcitrant C over labile C. This was especially true for genes encoding cellobiase and mnp for cellulose and lignin degradation, respectively. We confirmed this with warming-enhanced polyphenol oxidase and peroxidase activities for recalcitrant C acquisition and greater increases in recalcitrant C use efficiency than in labile C use efficiency (average percentage increases of 48% versus 28%, respectively). The relative abundance of lignin-degrading genes increased by 15% under warming; meanwhile, soil fungi, as the primary decomposers of lignin, were greater in abundance by 27%. This work suggests that future warming may enhance the potential for accelerated fungal decomposition of lignin-like compounds, leading to greater microbially mediated C losses than previously estimated in freshwater wetlands.

Phylogenetic and degradation characterization of Burkholderia cepacia WZ1 degrading herbicide quinclorac

Strain WZ1 capable of degrading quinclorac was isolated from a pesticide manufactory soil and considered to be Burkholderia cepacia, belonged to bacteria, Proteobacteria, β‐Proteobacteria, based on morphology, physio‐biochemical properties, whole cell fatty acid analysis and a partial sequencing of 16S rDNA. Strain WZ1 decomposed 90% of quinclorac at original concentration of 1000 mg L− 1 within 11 days. GC/MS analysis showed that the strain degraded quinclorac to 3,7‐dichloro‐8‐quinoline and the cracked residue 2‐chloro, 1,4‐benzenedicarboxylic acid, indicating that the metabolic pathway was initiated by process of decarboxylation followed by cleavage of the aromatic ring. Stain WZ1 was also able to degrade some other herbicides and aromatic compounds, including 2,4,5‐T, phenol, naphthalene and hydrochinone etc. This paper describes for the first time Phylogenetic and degradation characterization of a pure bacterium which, is able to mineralize quinclorac.

Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau

BackgroundGeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau.ResultsA total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (Pu2009<u20090.05) correlated with the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes.ConclusionsHigh overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were significantly impacted by local environmental conditions, and soil C/N is the most important factor to impact the microbial structure in alpine meadow in Qinghai-Tibetan plateau.