Yu-Rong Liu

Particle size, charge and colloidal stability of humic acids coprecipitated with Ferrihydrite

Humic acids (HA) have a colloidal character whose size and negative charge are strictly dependent on surface functional groups. They are able to complex large amount of poorly ordered iron (hydr)oxides in soil as a function of pH and other environmental conditions. Accordingly, with the present study we intend to assess the colloidal properties of Fe(II) coprecipitated with humic acids (HA) and their effect on Fe hydroxide crystallinity under abiotic oxidation and order of addition of both Fe(II) and HA. TEM, XRD and DRS experiments showed that Fe-HA consisted of Ferrihydrite with important structural variations. DLS data of Fe-HA at acidic pH showed a bimodal size distribution, while at very low pH a slow aggregation process was observed. Electrophoretic zeta-potential measurements revealed a negative surface charge for Fe-HA macromolecules, providing a strong electrostatic barrier against aggregation. Under alkaline conditions HA chains swelled, which resulted in an enhanced stabilization of the colloid particles. The increasing of zeta potential and size of the Fe-HA macromolecules, reflects a linear dependence of both with pH. The increase in the size and negative charge of the Fe-HA precipitate seems to be more affected by the ionization of the phenolic acid groups, than by the carboxylic acid groups. The main cause of negative charge generation of Fe/HA is due to increased dissociation of phenolic groups in more expanded structure. The increased net negative surface potential induced by coprecipitation with Ferrihydrite and the correspondent changes in configuration of the HA could trigger the inter-particle aggregation with the formation of new negative surface. The Fe-HA coprecipitation can reduce electrosteric repulsive forces, which in turn may inhibit the aggregation process at different pH. Therefore, coprecipitation of Ferrihydrite would be expected to play an important role in the carbon stabilization and persistence not only in organic soils, but also in waters containing dissolved organic matter.

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.

Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils.

Copper contamination on Chinas arable land could pose severe economic, ecological and healthy consequences in the coming decades. As the drivers in maintaining ecosystem functioning, the responses of soil microorganisms to long-term copper contamination in different soil ecosystems are still debated. This study investigated the impacts of copper gradients on soil bacterial communities in two agricultural fields with contrasting soil properties. Our results revealed consistent reduction in soil microbial biomass carbon (SMBC) with increasing copper levels in both soils, coupled by significant declines in bacterial abundance in most cases. Despite of contrasting bacterial community structures between the two soils, the bacterial diversity in the copper-contaminated soils showed considerably decreasing patterns when copper levels elevated. High-throughput sequencing revealed copper selection for major bacterial guilds, in particular, Actinobacteria showed tolerance, while Acidobacteria and Chloroflexi were highly sensitive to copper. The thresholds that bacterial communities changed sharply were 800 and 200 added copper mg kg−1 in the fluvo-aquic soil and red soil, respectively, which were similar to the toxicity thresholds (EC50 values) characterized by SMBC. Structural equation model (SEM) analysis ascertained that the shifts of bacterial community composition and diversity were closely related with the changes of SMBC in both soils. Our results provide field-based evidence that copper contamination exhibits consistently negative impacts on soil bacterial communities, and the shifts of bacterial communities could have largely determined the variations of the microbial biomass.

Anaerobic Mercury Methylation and Demethylation by Geobacter bemidjiensis Bem.

Microbial methylation and demethylation are two competing processes controlling the net production and bioaccumulation of neurotoxic methylmercury (MeHg) in natural ecosystems. Although mercury (Hg) methylation by anaerobic microorganisms and demethylation by aerobic Hg-resistant bacteria have both been extensively studied, little attention has been given to MeHg degradation by anaerobic bacteria, particularly the iron-reducing bacterium Geobacter bemidjiensis Bem. Here we report, for the first time, that the strain G. bemidjiensis Bem can mediate a suite of Hg transformations, including Hg(II) reduction, Hg(0) oxidation, MeHg production and degradation under anoxic conditions. Results suggest that G. bemidjiensis utilizes a reductive demethylation pathway to degrade MeHg, with elemental Hg(0) as the major reaction product, possibly due to the presence of genes encoding homologues of an organomercurial lyase (MerB) and a mercuric reductase (MerA). In addition, the cells can strongly sorb Hg(II) and MeHg, reduce or oxidize Hg, resulting in both time and concentration-dependent Hg species transformations. Moderate concentrations (10-500 μM) of Hg-binding ligands such as cysteine enhance Hg(II) methylation but inhibit MeHg degradation. These findings indicate a cycle of Hg methylation and demethylation among anaerobic bacteria, thereby influencing net MeHg production in anoxic water and sediments.

Influence of rice straw amendment on mercury methylation and nitrification in paddy soils.

UNLABELLED Currently, rice straw return in place of burning is becoming more intensive in China than observed previously. However, little is known on the effect of returned rice straw on mercury (Hg) methylation and microbial activity in contaminated paddy fields. Here, we conduct a microcosm experiment to evaluate the effect of rice straw amendment on the Hg methylation and potential nitrification in two paddy soils with distinct Hg levels. Our results show that amended rice straw enhanced Hg methylation for relatively high Hg content soil, but not for low Hg soil, spiking the same additional fresh Hg. methylmercury (MeHg) concentration was significantly correlated to the dissolved organic carbon (DOC) content and relative abundance of dominant microbes associated with Hg methylation. Similarly, amended rice straw was found to only enhance the potential nitrification rate in soil with relatively high Hg content. These findings provide evidence that amended rice straw differentially modulates Hg methylation and nitrification in Hg contaminated soils possibly resulting from different characteristics in the soil microbial community. This highlights that caution should be taken when returning rice straw to contaminated paddy fields, as this practice may increase the risk of more MeHg production. MAIN FINDING Rice straw amendment enhanced both Hg methylation and nitrification potential in the relatively high, but not low, Hg soil.

Responses of activities, abundances and community structures of soil denitrifiers to short-term mercury stress.

The responses of activities, abundances and community structures of soil denitrifiers to mercury (Hg) stress were investigated through a short-term incubation experiment. Four soil treatments with different concentrations of Hg (CK, Hg25, Hg50, and Hg 100, denoted as 0, 25, 50, and 100 mg Hg/kg dry soil, respectively) were incubated for 28 days. Soil denitrification enzyme activity (DEA) was measured at day 3, 7 and 28. The abundances and community structures of two denitrification concerning genes, nirS (cd(1)-nitrite reductase gene) and nosZ (nitrous oxide reductase gene), were analyzed using real-time PCR and denaturing gradient gel electrophoresis (DGGE). Results showed that soil DEA was significantly stimulated in the treatments of Hg25 and Hg50 compared with others at day 7. Meanwhile, no difference in the abundances of soil nirS and nosZ was found between Hg spiked treatments and CK, except the lower abundance of nirS (P < 0.05) in the Hg added treatments compared with that in the CK at day 28. The community structures of denitrifiers based on nirS gene presented obvious change at day 7 along with the Hg additions, however, no variation was found in all treatments based on the nosZ gene. The results indicated that Hg (Hg25 and Hg50) had a strongly short-term stimulation on soil DEA, and nirS gene is more sensitive than nosZ gene to Hg stress.

Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities

The legacy impacts of past climates on the current distribution of soil microbial communities are largely unknown. Here, we use data from more than 1,000 sites from five separate global and regional datasets to identify the importance of palaeoclimatic conditions (Last Glacial Maximum and mid-Holocene) in shaping the current structure of soil bacterial communities in natural and agricultural soils. We show that palaeoclimate explains more of the variation in the richness and composition of bacterial communities than current climate. Moreover, palaeoclimate accounts for a unique fraction of this variation that cannot be predicted from geographical location, current climate, soil properties or plant diversity. Climatic legacies (temperature and precipitation anomalies from the present to ~20 kyr ago) probably shape soil bacterial communities both directly and indirectly through shifts in soil properties and plant communities. The ability to predict the distribution of soil bacteria from either palaeoclimate or current climate declines greatly in agricultural soils, highlighting the fact that anthropogenic activities have a strong influence on soil bacterial diversity. We illustrate how climatic legacies can help to explain the current distribution of soil bacteria in natural ecosystems and advocate that climatic legacies should be considered when predicting microbial responses to climate change.Analysing data from more than 1,000 sites globally, the authors show that palaeoclimatic legacies explain a greater amount of variation in bacterial community richness and composition than current climate.

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

Soil moisture and nitrogen (N) are two important factors influencing N2O emissions and the growth of microorganisms. Here, we carried out a microcosm experiment to evaluate effects of soil moisture level and N fertilizer type on N2O emissions and abundances and composition of associated microbial communities in the two typical arable soils. The abundances and community composition of functional microbes involved in nitrification and denitrification were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP), respectively. Results showed that N2O production was higher at 90% water-filled pore (WFPS) than at 50% WFPS. The N2O emissions in the two soils amended with ammonium were higher than those amended with nitrate, especially at relatively high moisture level. In both soils, increased soil moisture stimulated the growth of ammonia-oxidizing bacteria (AOB) and nitrite reducer (nirK). Ammonium fertilizer treatment increased the population size of AOB and nirK genes in the alluvial soil, while reduced the abundances of ammonia-oxidizing archaea (AOA) and denitrifiers (nirK and nosZ) in the red soil. Nitrate addition had a negative effect on AOA abundance in the red soil. Total N2O emissions were positively correlated to AOB abundance, but not to other functional genes in the two soils. Changed soil moisture significantly affected AOA rather than AOB community composition in both soils. The way and extent of N fertilizers impacted on nitrifier and denitrifier community composition varied with N form and soil type. These results indicate that N2O emissions and the succession of nitrifying and denitrifying communities are selectively affected by soil moisture and N fertilizer form in the two contrasting types of soil.

Response of ammonia-oxidizing archaea and bacteria to long-term industrial effluent-polluted soils, Gujarat, Western India

Soil nitrifiers have been showing an important role in assessing environmental pollution as sensitive biomarkers. In this study, the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in long-term industrial waste effluent (IWE) polluted soils. Three different IWE polluted soils characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) were collected in triplicate along Mahi River basin, Gujarat, Western India. Quantitative numbers of ammonia monooxygenase α-subunit (amoA) genes as well as 16S rRNA genes indicated apparent deleterious effect of IWE on abundance of soil AOA, AOB, bacteria, and archaeal populations. Relatively, AOB was more abundant than AOA in the highly contaminated soil R3, while predominance of AOA was noticed in uncontaminated (R1) and moderately contaminated (R2) soils. Soil potential nitrification rate (PNR) significantly (P < 0.05) decreased in polluted soils R2 and R3. Reduced diversity accompanied by apparent community shifts of both AOB and AOA populations was detected in R2 and R3 soils. AOB were dominated with Nitrosospira-like sequences, whereas AOA were dominated by Thaumarchaeal “group 1.1b (Nitrososphaera clusters).” We suggest that the significant reduction in abundance and diversity AOA and AOB could serve as relevant bioindicators for soil quality monitoring of polluted sites. These results could be further useful for better understanding of AOB and AOA communities in polluted soils.

Response of bacterial pdo1, nah, and C12O genes to aged soil PAH pollution in a coke factory area

Soil pollution caused by polycyclic aromatic hydrocarbons (PAHs) is threatening human health and environmental safety. Investigating the relative prevalence of different PAH-degrading genes in PAH-polluted soils and searching for potential bioindicators reflecting the impact of PAH pollution on microbial communities are useful for microbial monitoring, risk evaluation, and potential bioremediation of soils polluted by PAHs. In this study, three functional genes, pdo1, nah, and C12O, which might be involved in the degradation of PAHs from a coke factory, were investigated by real-time quantitative PCR (qPCR) and clone library approaches. The results showed that the pdo1 and C12O genes were more abundant than the nah gene in the soils. There was a significantly positive relationship between the nah or pdo1 gene abundances and PAH content, while there was no correlation between C12O gene abundance and PAH content. Analyses of clone libraries showed that all the pdo1 sequences were grouped into Mycobacterium, while all the nah sequences were classified into three groups: Pseudomonas, Comamonas, and Polaromonas. These results indicated that the abundances of nah and pdo1 genes were positively influenced by levels of PAHs in soil and could be potential microbial indicators reflecting the impact of soil PAH pollution and that Mycobacteria were one of the most prevalent PAHs degraders in these PAH-polluted soils. Principal component analysis (PCA) and correlation analyses between microbial parameters and environmental factors revealed that total carbon (TC), total nitrogen (TN), and dissolved organic carbon (DOC) had positive effects on the abundances of all PAH-degrading genes. It suggests that increasing TC, TN, and DOC inputs could be a useful way to remediate PAH-polluted soils.