Yuan-Ming Zheng

Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest

To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in alpine and permafrost soils, 12 soils at altitudes of 4000-6550 m above sea level (m a.s.l.) were collected from the northern slope of the Mount Everest (Tibetan Plateau), where the permanent snow line is at 5800-6000 m a.s.l. Communities were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. Archaeal amoA abundance was greater than bacterial amoA abundance in lower altitude soils (<or=5400 m a.s.l.), but this situation was reversed in higher altitude soils (>or=5700 m a.s.l.). Both archaeal and bacterial amoA abundance decreased abruptly in higher altitude soils. Communities shifted from a Nitrosospira amoA cluster 3a-dominated ammonia-oxidizing bacteria community in lower altitude soils to communities dominated by a newly designated Nitrosospira ME and cluster 2-related groups and Nitrosomonas cluster 6 in higher altitude soils. All archaeal amoA sequences fell within soil and sediment clusters, and the proportions of the major archaeal amoA clusters changed between the lower altitude and the higher altitude soils. These findings imply that the shift in the relative abundance and community structure of archaeal and bacterial ammonia oxidizers may result from selection of organisms adapted to altitude-dependent environmental factors in elevated soils.

Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies?

Contemporary environmental disturbances and historical contingencies are considered to be major factors driving current differences in microbial diversity. However, little was known about their relative importance. This study combines culture-independent molecular techniques and advanced statistical analyses to examine quantitatively the relative importance of contemporary disturbances and historical contingencies in influencing large-scale soil bacterial diversity using a large set of manipulated field-based molecular data (212 samples). Contemporary disturbances were represented by applications of different fertilizers N, P, K and organic manure (OM) and historical contingencies by distinct geographic sampling locations and soil profiles. Multivariate regression tree (MRT) analysis showed that diversity estimates were mainly distinguished by sampling locations, which explained 40.8% of the variation in bacterial diversity, followed by soil profiles (19.5%), sampling time (13.1%), OM (3.7%) and P (1.8%). Aggregated boosted tree (ABT) analysis showed that the relative importance of different categorical factors on soil bacterial diversity variation was ranked as sampling locations, soil profiles, sampling time, OM and P. Both MRT and ABT analyses showed that historical contingencies were the dominant factor driving variation in bacterial diversity across a regional scale (about 1000 km), whereas some contemporary disturbances also caused variation in bacterial diversity at a local scale. This study demonstrated that past events and contemporary disturbances had similar influence on soil bacterial diversity to that documented for macroorganisms, indicating that there might be some common aspects of biogeography to all organisms.

Biogenic Mn oxides for effective adsorption of Cd from aquatic environment

Biogenic Mn oxides exert important controls on trace metal cycling in aquatic and soil environments. A Mn-oxidizing bacterium Bacillus sp. WH4 was isolated from Fe-Mn nodules of an agrudalf in central China. The biogenic Mn oxides formed by mediation of this Mn oxidizing microorganism were identified as short-ranged and nano-sized Mn oxides. Cd adsorption isotherms, pH effect on adsorption and kinetics were investigated in comparison with an abiotic Mn oxide todorokite. Maximum adsorption of Cd to the biogenic Mn oxides and todorokite was 2.04 and 0.69 mmol g(-1) sorbent, respectively. Thus, the biogenic Mn oxides were more effective Cd adsorbents than the abiotic Mn oxide in the aquatic environment. The findings could improve our knowledge of biogenic Mn oxides formation in the environment and their important roles in the biogeochemical cycles of heavy metals.

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

PurposeDenitrification is an important biochemical process in global nitrogen cycle, with a potent greenhouse gas product N2O. Wastewater irrigation can result in the changes of soil properties and microbial communities of agricultural soils. The purpose of this study was to examine how the soil denitrification genes responded to different irrigation regimes.Materials and methodsSoil samples were collected from three rural districts of Beijing (China) with three different irrigation regimes: clean groundwater (CW), reclaimed water (RW), and wastewater (WW). The abundance and diversity of three denitrification microbial genes (nirS, nirK, and nosZ) were examined by real-time polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) molecular approaches.Results and discussionThe abundance of nirS in the WW treatment was higher than that in the CW treatment, and no significant difference was found between the RW and CW or WW treatments. The abundance of nirK gene of the RW and WW treatments was higher than that of the CW treatment. There was no difference for nosZ gene among the three treatments. Correspondence analysis based on the DGGE profiles showed that there was no obvious difference in the nosZ gene composition, but nirS and nirK genes changed with different irrigation regimes.ConclusionsIrrigation with unclean water sources enhanced the soil NO3− content and changed the abundance and composition of soil denitrifiers, and different functional genes had different responses. Irrigation with unclean water sources increased the abundance of nirK gene and changed the community structures of nirS and nirK genes, while nosZ gene was relatively stable in the soil. These results could be helpful to explore the mechanisms of the variation of denitrification processes under long-term wastewater irrigation and partially explain the reason of more N2O output in the field with wastewater irrigation.

Characterization of soil heavy metal contamination and potential health risk in metropolitan region of northern China

Soil in metropolitan region suffers great contamination risk due to the rapid urbanization especially in developing countries. Beijing and Tianjin, together with their surrounding regions, form a mega-metropolitan region in northern China. To assess the soil environmental quality, a total of 458 surface soil samples were collected from this area. Concentrations of Cr, Cu, Pb, Zn, As, Cd, and Hg were analyzed and compared to the Chinese environmental quality standards for soil. Multivariate analysis was carried out to identify the possible sources and Geographic Information Systems techniques were applied to visualize the spatial data. It was found that the primary inputs of As were due to pedogenic sources, whereas Hg was mainly of anthropogenic source. Other elements including Cr, Cu, Pb, Zn, and Cd were from both lithogenic and anthropogenic origins. Health risk assessment based on the maximum heavy metal concentration indicated that As derived from sewage irrigation area can result in carcinogenic lifetime risk due to ingestion and/or dermal contact of soil. The potential non-carcinogenic risk for children is significant for Pb and the cumulative effect of multiple metals is of concern for children in the vicinity of mining site. The results increased our knowledge for understanding natural and anthropogenic sources as well as health risk for metals in metropolitan soil.

Material flow analysis of phosphorus through food consumption in two megacities in northern China.

The key stocks and flows of phosphorus (P) through food consumption in Beijing and Tianjin, two megacities in northern China, were explored using a material flow analysis (MFA) approach to construct a static model of P metabolism. A total of 4498 t P has accumulated with 72% of P flow imported through food consumption eventually remaining in Beijing in 2008. Around 64% of the total inflow of P (2670 t) remained in Tianjin in 2008. P in the uncollected sewage from both urban and rural residents and the effluents from sewage treatment plants has significant negative effects on water quality. An average of 55% the P flow remained in the sewage sludge through urban food consumption. The key problems in P metabolism and management in megacities are identified based on the quantitative analysis of P cycling through food consumption. Relevant solutions for improving P recycling efficiency are also discussed. It is important to link P flows with environmental regulations and to establish a strong coordination between urban and rural areas for nutrient recycling to attain sustainable development of megacities.

Soil pH determines the alpha diversity but not beta diversity of soil fungal community along altitude in a typical Tibetan forest ecosystem

PurposeDespite their symbiotic relationship with trees and the vital role as decomposer in forest, soil fungi received limited attention regarding their changes with altitude in forest ecosystems. This study aimed to determine the diversity patterns of soil fungi along an altitudinal gradient on Mt. Shegyla, a typical forest ecosystem on the Tibetan Plateau.Materials and methodsHigh-throughput barcoded pyrosequencing and quantitative PCR approaches were employed to measure the community composition, diversity, and abundance patterns of soil fungal 18S ribosomal RNA (rRNA) gene in 20 samples collected along the altitudinal gradient of Mt. Shegyla.Results and discussionAbundant taxa in the fungal community were Agaricomycetes and Leotiomyceta on Mt. Shegyla. Fungal abundance decreased significantly with increasing altitude. Beta diversity of the fungal community, as measured using weighted UniFrac distance, was significantly related to altitude. Significant correlation was observed between altitude and alpha diversity including richness and phylodiversity, but not with evenness. Network analysis revealed that Ceramothyrium and Clavulina were two important hubs in the community, and an uncultured fungal taxon that previously detected in glacier forefront dominated this network. Distance-based linear model identified soil pH as the dominant driver which significantly related with fungal alpha diversity including richness, phylodiversity, and evenness. However, fungal abundance and the first component of PCoA on weighted UniFrac matrix (beta diversity) did not change significantly with pH.ConclusionsThese results provided strong evidence that soil pH was the dominant driver for structuring altitudinal alpha diversity pattern but not beta diversity pattern or community abundance of soil fungi in this typical forest on the Tibetan Plateau.

Mercury in soils of three agricultural experimental stations with long-term fertilization in China.

Mercury (Hg) in the agricultural ecosystem is a global concern because of its high potential toxicity. The objectives of this study were to determine the concentration and distribution of Hg in soils from three long-term experimental stations, i.e., Taoyuan (TY) and Qiyang (QY) in Hunan Province and Fengqiu (FQ) in Henan Province of China, and thus to assess the possible food and health risk of long-term applications of fertilizers. Soil samples at each site were collected from different fertilization plots and also from soil profiles with depths 0-100 cm. There were significant differences in soil Hg concentrations in 0-20 cm (A) or 20-40 cm (B) horizon among the three experimental stations. QY station showed significantly higher Hg concentrations than TY and FQ stations. However, there were no significant differences in soil Hg concentrations between A and B horizons at each station. It was concluded that the soil Hg concentrations at the three sites were mainly controlled by the parent materials. Moreover, chemical fertilizer, especially phosphorous fertilizers, could influence the soil Hg concentrations to some extent at the station with lower soil Hg concentrations, for example, at TY station. There were minimal amounts of Hg resulting from applications of the other chemical fertilizers and organic manure, and thus the fertilization had very low risk to the food security of the agro-ecosystems in the terms of Hg inputs and contamination.

Ecological Drivers of Biogeographic Patterns of Soil Archaeal Community

Knowledge about the biogeography of organisms has long been a focus in ecological research, including the mechanisms that generate and maintain diversity. In this study, we targeted a microbial group relatively underrepresented in the microbial biogeographic literature, the soil Archaea. We surveyed the archaeal abundance and community composition using real-time quantitative PCR and T-RFLP approaches for 105 soil samples from 2 habitat types to identify the archaeal distribution patterns and factors driving these patterns. Results showed that the soil archaeal community was affected by spatial and environmental variables, and 79% and 51% of the community variation was explained in the non-flooded soil (NS) and flooded soil (FS) habitat, respectively, showing its possible biogeographic distribution. The diversity patterns of soil Archaea across the landscape were influenced by a combination of stochastic and deterministic processes. The contribution from neutral processes was higher than that from deterministic processes associated with environmental variables. The variables pH, sample depth and longitude played key roles in determining the archaeal distribution in the NS habitat, while sampling depth, longitude and NH4 +-N were most important in the FS habitat. Overall, there might be similar ecological drivers in the soil archaeal community as in macroorganism communities.

Microbes influence the fractionation of arsenic in paddy soils with different fertilization regimes.

Sequential extraction procedures were used to investigate the influence of the microbes on the distribution of arsenic in a Chinese paddy soil under different long-term fertilization treatments. The paddy soil with four long-term fertilization treatments (CK, M, NPK and NPK+M) and three levels of arsenate addition (0, 50, 100 mg As kg(-1) dry soil), were selected to construct microcosms for laboratory incubation. After the incubation, soil samples were sequentially extracted to determine As in various fractions, i.e. water soluble (F0), exchangeable (F1), bound to carbonates (F2), bound to Fe and Mn oxides (F3), bound to organic matter and sulfides (F4), and residual (F5, mineral matrix). Results showed that most of the As was fixed by mineral matrix (F5, ratios ranging from 46.22% to 96.37%), followed by As bound to Fe and Mn oxides (F3, ratios ranging from 3.14% to 28.18%), and the ratios of the other four fractions (F0, F1, F2 and F4) were mostly less than 10%. The microbes in the paddy soil could make As transform from inactive fraction (F5) to relatively active fractions (F0, F1, F2 and F3) and thus increase its environmental risk. With the increase of the As addition levels and with the application of manure or chemical NPK fertilizers, As was distributed more in the relatively active fractions (F0, F1, F2, F3 and F4) in the paddy soil mediated by the microbes. In addition, Fe and Mn oxides could play an important role in decreasing the As leaching potential from the mineral matrix to soil solution and thus abate the As risk to human health.