Jun Lou

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

Soil microbiota play a critical role in soil biogeochemical processes and have a profound effect on soil functions. Recent studies have revealed microbial co-occurrence patterns in soil microbial communities, yet the geographic pattern of topological features in soil microbial co-occurrence networks at the continental scale are largely unknown. Here, we investigated the shifts of topological features in co-occurrence networks inferred from soil microbiota along a continental scale in eastern China. Integrating archaeal, bacterial and fungal community datasets, we inferred a meta-community co-occurrence network and analyzed node-level and network-level topological shifts associated with five climatic regions. Both node-level and network-level topological features revealed geographic patterns wherein microorganisms in the northern regions had closer relationships but had a lower interaction influence than those in the southern regions. We further identified topological differences associated with taxonomic groups and demonstrated that co-occurrence patterns were random for archaea and non-random for bacteria and fungi. Given that microbial interactions may contribute to soil functions more than species diversity, this geographic shift of topological features provides new insight into studying microbial biogeographic patterns, their organization and impacts on soil-associated function.

Survival of Escherichia coli O157:H7 in Soils from Jiangsu Province, China

Escherichia coli O157:H7 (E. coli O157:H7) is recognized as a hazardous microorganism in the environment and for public health. The E. coli O157:H7 survival dynamics were investigated in 12 representative soils from Jiangsu Province, where the largest E. coli O157:H7 infection in China occurred. It was observed that E. coli O157:H7 declined rapidly in acidic soils (pH, 4.57 – 5.14) but slowly in neutral soils (pH, 6.51 – 7.39). The survival dynamics were well described by the Weibull model, with the calculated td value (survival time of the culturable E. coli O157:H7 needed to reach the detection limit of 100 CFU g−1) from 4.57 days in an acidic soil (pH, 4.57) to 34.34 days in a neutral soil (pH, 6.77). Stepwise multiple regression analysis indicated that soil pH and soil organic carbon favored E. coli O157:H7 survival, while a high initial ratio of Gram-negative bacteria phospholipid fatty acids (PLFAs) to Gram-positive bacteria PLFAs, and high content of exchangeable potassium inhibited E. coli O157:H7 survival. Principal component analysis clearly showed that the survival profiles in soils with high pH were different from those with low pH.

A glimpse of Escherichia coli O157:H7 survival in soils from eastern China.

Escherichia coli O157:H7 (E. coli O157:H7) is an important food-borne pathogen, which continues to be a major public health concern worldwide. It is known that E. coli O157:H7 survive in soil environment might result in the contamination of fresh produce or water source. To investigate how the soils and their properties affect E. coli O157:H7 survival, we studied E. coli O157:H7 survival dynamics in 14 soils collected in eastern China from the warm-temperate zone to subtropical zone. Results showed that E. coli O157:H7 survival as a function of time can be well described by the Weibull model. The calculated td values (survival time to reach the detection limit, 100 colony forming units per gram oven-dried weight of soil) for the test soils were between 1.4 and 25.8 days. A significantly longer survival time (td) was observed in neutral or alkaline soils from north-eastern China (the warm-temperate zone) than that in acidic soils from south-eastern China (the subtropical zone). Distinct E. coli O157:H7 survival dynamics was related to soil properties. Stepwise multiple regression analysis revealed that the td values were significantly enhanced by soil microbial biomass carbon and total nitrogen, but were significantly reduced by amorphous Al2O3 and relative abundance of Chloroflexi. It should pay more attention to E. coli O157:H7 long survival in soils and its potential environmental contamination risk.

Biodegradation, Biosorption of Phenanthrene and Its Trans-Membrane Transport by Massilia sp. WF1 and Phanerochaete chrysosporium.

Reducing phenanthrene (PHE) in the environment is critical to ecosystem and human health. Biodegradation, biosorption, and the trans-membrane transport mechanism of PHE by a novel strain, Massilia sp. WF1, and an extensively researched model fungus, Phanerochaete chrysosporium were investigated in aqueous solutions. Results showed that the PHE residual concentration decreased with incubation time and the data fitted well to a first-order kinetic equation, and the t1/2 of PHE degradation by WF1, spores, and mycelial pellets of P. chrysosporium were about 2 h, 87 days, and 87 days, respectively. The biosorbed PHE was higher in P. Chrysosporium than that in WF1, and it increased after microorganisms were inactivated and inhibited, especially in mycelial pellets. The detected intracellular auto-fluorescence of PHE by two-photon excitation microscopy also proved that PHE indeed entered into the cells. Based on regression, the intracellular (Kdin) and extracellular (Kdout) dissipation rate constants of PHE by WF1 were higher than those by spores and mycelial pellets. In addition, the transport rate constant of PHE from outside solution into cells (KinS/Vout) for WF1 were higher than the efflux rate constant of PHE from cells to outside solution (KoutS/Vin), while the opposite phenomena were observed for spores and mycelial pellets. The amount of PHE that transported from outside solution into cells was attributed to the rapid degradation and active PHE efflux in the cells of WF1 and P. Chrysosporium, respectively. Besides, the results under the inhibition treatments of 4°C, and the presence of sodium azide, colchicine, and cytochalasin B demonstrated that a passive trans-membrane transport mechanism was involved in PHE entering into the cells of WF1 and P. Chrysosporium.

Determination of Water- and Methanol-Extractable Pentachlorophenol in Soils Using Vortex-assisted Liquid-Liquid Extraction and Gas Chromatography

Abstract An analytical procedure for determination of water- and methanol-extractable pentachlorophenol (PCP) in soils was developed using vortex-assisted liquid-liquid extraction (VALLE) and gas chromatography (GC). Significant extraction parameters such as vortex speed and liquid-liquid volume ratio were optimized for extracting PCP from solution. The recovery of PCP was the highest (97.4%) with good reproducibility and a small relative standard deviation (RSD, 0.5%) when the vortex speed was at 2000 rpm. Meanwhile, when the volume ratio of derivatization solution to n-hexane was at 10:4, the recovery of PCP was 103% with a RSD of 0.7%. The linearity of the calibration curve for PCP determination ranged from 1.25 μg L−1 to 4000 μg L−1, with a correlation coefficient (R2) of 0.9999. The detection limit of PCP in water samples was below 0.2 μg L−1 and the measuring range was relatively wide, and suitable for trace- and micro-analysis of PCP. Compared with traditional extraction methods (liquid-liquid and solid-phase), VALLE consumes less extractant, requires fewer steps, and achieves higher recovery (96.8%) and smaller RSD (3.7%). The reliability of VALLE was verified in four distinct types (paddy, red, black and alluvial) of soil samples spiked with 1 and 10 mg kg−1 PCP. The total recoveries of PCP in the soil samples were in the range of 89.5%–98.9% by water extraction and 88.7%–98.4% by 3 consecutive extractions with methanol in a sequential procedure. The results indicated that VALLE-GC satisfied the requirements for extracting and determining water- and methanol-extractable PCP in soils polluted by PCP at varying levels.

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

Microbial ecological studies have been remarkably promoted by the high-throughput sequencing approach with explosive information of taxonomy and relative abundance. However, relative abundance does not reflect the quantity of the microbial community and the inter-sample differences among taxa. In this study, we refined and applied an integrated high-throughput absolute abundance quantification (iHAAQ) method to better characterize soil quantitative bacterial community through combining the relative abundance (by high-throughput sequencing) and total bacterial quantities (by quantitative PCR). The proposed iHAAQ method was validated by an internal reference strain EDL933 and a laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene biodegradation study showed that for some bacterial taxa, the changes of relative and absolute abundances were coincident, while for others the changes were opposite. With the addition of a microbial activity inhibitor (NaN3), the absolute abundances of soil bacterial taxa, including several dominant genera of Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their relative abundances increased after 28 days of incubation. We conclude that the iHAAQ method can offer more comprehensive information to reflect the dynamics of soil bacterial community with both relative and absolute abundances than the relative abundance from high-throughput sequencing alone.

Use of an improved high-throughput absolute abundance quantification method to characterize soil bacterial community and dynamics

High-throughput sequencing has dramatically expanded our understanding of bacterial communities based on the information of the species types and their relative abundances. Recently, researchers have also become aware of a deficiency in not considering the absolute abundance in this technique. Combining two or more different methods has typically been used to achieve absolute quantification of microbial communities. However, making a combination of different methods not only is time-consuming but also involves potential uncertainty due to variations in the experimental conditions. To simplify the experimental procedure and improve the high-throughput absolute abundance quantification (HAAQ) of a soil bacterial community, we propose an HAAQ method that uses an internal standard strain (ISS) HAAQ-GFP to simultaneously obtain both the relative and absolute abundances in the soil bacterial community. The results showed that a soil bacterial community and its dynamics can be better characterized by the HAAQ method when the optimal concentrations of ISS HAAQ-GFP (105 to 107cellsg-1) were used, and a 16S rRNA gene copy number adjustment was applied. Based on the HAAQ method, we first found that soil bacterial absolute abundances at the genus level fitted well to the partial log-normal distribution function, and most genera concentrations were in the range of 103.5 to 106.5cellsg-1 in the test soils. Our case studies also indicated that more comprehensive descriptions of soil bacterial communities and their dynamics can be achieved by both the relative and absolute abundances than by the relative abundance alone. The improved HAAQ method can be potentially applied to other microbial ecological studies and to stimulating the development of quantitative bacterial ecology studies.

Pentachlorophenol dissipation and ferrous iron accumulation in flooded paddy soils with contrasting organic matter contents and incorporation of legume green manures

PurposeThe effects of different amendment rates (1 and 3%) of Chinese milk vetch (Astragalus sinicus L.) and bird vetch (Vicia cracca L.) on the dissipation of extractable pentachlorophenol (PCP) residues were investigated in two flooded paddy soils with contrasting soil organic matter (SOM) contents. Following incorporation of the legume green manures, whether acetate-extractable ferrous iron [Fe(II)NaOAc] is useful for revealing the reductive dechlorination mechanism of PCP in flooded paddy soils was verified.Materials and methodsThe kinetic parameters of PCP dissipation and Fe(II)NaOAc accumulation were estimated using logistic curve fitting. Correlation and regression analyses were performed on PCP, Fe(II)NaOAc, water-soluble organic carbon (WSOC), pH, and oxidation-reduction potential data.Results and discussionThe kinetic parameters of PCP dissipation and Fe(II)NaOAc accumulation varied significantly with the amendment rate of legume green manure. The changes in pH value and WSOC content varied significantly with the level of SOM and with the amendment rate of legume green manure. At a low amendment rate of green manure, the pH increase and WSOC consumption greatly enhanced Fe(II)NaOAc accumulation and contributed to PCP dissipation. The rate of PCP dissipation decreased with decreasing pH and WSOC accumulation, especially in the high-SOM soil amended with the higher rate of green manure. Legume green manure species had no effect on PCP dissipation.ConclusionsIn terms of soil chemistry, Fe(II)NaOAc was found to be the key variable that could explain the mechanisms involved in the reductive dissipation of PCP in flooded paddy soils with contrasting SOM contents and incorporation of legume green manures.