Carbon/nitrogen ratio as a major factor for predicting the effects of organic wastes on soil bacterial communities assessed by DNA-based molecular techniques

Background, aim, and scope  

Current Australian legislation permits the beneficial application of grease trap waste (GTW) to agricultural soil, viewing it as a beneficial source of organic matter and soil conditioner containing no/low amounts of metals or pathogenic organisms. However, little is known about the influence of GTW on soil bacterial community. A field experiment was established at Menangle in south western Sydney in Australia to quantitatively assess the impacts of different types (GTW CO and GTW CL) and amounts of GTW application on the soil bacterial community and diversity. Furthermore, a municipal solid waste (MSW) compost was simultaneously examined to compare against the other organic wastes. Knowledge about the shifts in microbial community structure and diversity following the applications of organic wastes could help to evaluate the ecological consequences on the soil and thus to develop sound regulatory guidelines for the beneficial reuse of organic wastes in agricultural lands.     

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.     

Effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on methanotroph abundance and methane uptake in a grazed pasture soil

Methane-oxidizing bacteria (methanotrophs) in the soil are a unique group of methylotrophic bacteria that utilize methane (CH₄) as their sole source of carbon and energy which limit the flux of methane to the atmosphere from soils and consume atmospheric methane. A field experiment was conducted to determine the effect of nitrogen application rates and the nitrification inhibitor dicyandiamide (DCD) on the abundance of methanotrophs and on methane flux in a grazed pasture soil. Nitrogen (N) was applied at four different rates, with urea applied at 50 and 100 kg N ha^?1 and animal urine at 300 and 600 kg N ha^?1. DCD was applied at 10 kg ha^?1. The results showed that both the DNA and selected mRNA copy numbers of the methanotroph pmoA gene were not affected by the application of urea, urine or DCD. The methanotroph DNA and mRNA pmoA gene copy numbers were low in this soil, below 7.13?×?10³ g^?1 soil and 3.75?×?10³ μg^?1 RNA, respectively. Daily CH₄ flux varied slightly among different treatments during the experimental period, ranging from ?12.89 g CH₄ ha^?1 day^?1 to ?0.83 g CH₄ ha^?1 day^?1, but no significant treatment effect was found. This study suggests that the application of urea fertilizer, animal urine returns and the use of the nitrification inhibitor DCD do not significantly affect soil methanotroph abundance or daily CH₄ fluxes in grazed grassland soils.     

Response of denitrification genes <Emphasis Type="Italic">nirS</Emphasis>, <Emphasis Type="Italic">nirK</Emphasis>, and <Emphasis Type="Italic">nosZ</Emphasis> to irrigation water quality in a Chinese agricultural soil

Purpose  

Denitrification 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.     

Effects of Cd and Pb on soil microbial community structure and activities

Background, aim, and scope  

Soil contamination with heavy metals occurs as a result of both anthropogenic and natural activities. Heavy metals could have long-term hazardous impacts on the health of soil ecosystems and adverse influences on soil biological processes. Soil enzymatic activities are recognized as sensors towards any natural and anthropogenic disturbance occurring in the soil ecosystem. Similarly, microbial biomass carbon (MBC) is also considered as one of the important soil biological activities frequently influenced by heavy metal contamination. The polymerase chain reaction–denaturing gradient gel electrophoresis (DGGE) has recently been used to investigate changes in soil microbial community composition in response to environmental stresses. Soil microbial community structure and activities are difficult to elucidate using single monitoring approach; therefore, for a better insight and complete depiction of the soil microbial situation, different approaches need to be used. This study was conducted in a greenhouse for a period of 12 weeks to evaluate the changes in indigenous microbial community structure and activities in the soil amended with different application rates of Cd, Pb, and Cd/Pb mix. In a field environment, soil is contaminated with single or mixed heavy metals; so that, in this research, we used the selected metals in both single and mixed forms at different application rates and investigated their toxic effects on microbial community structure and activities, using soil enzyme assays, plate counting, and advanced molecular DGGE technique. Soil microbial activities, including acid phosphatase (ACP), urease (URE), and MBC, and microbial community structure were studied.     

Linkage between community diversity of sulfate-reducing microorganisms and methylmercury concentration in paddy soil

Sulfate-reducing microorganisms (SRM) have been thought to play a key role in mercury (Hg) methylation in anoxic environments. The current study examined the linkage between SRM abundance and diversity and contents of methylmercury (MeHg) in paddy soils collected from a historical Hg mining area in China. Soil profile samples were collected from four sites over a distance gradient downstream the Hg mining operation. Results showed that MeHg content in the soil of each site significantly decreased with the extending distance away from Hg mine. Soil MeHg content was correlated positively with abundance of SRM and the contents of organic matter (OM), NH₄ ⁺, SO₄ ^2?, and Hg. The abundances of SRM based on dissimilatory (bi) sulfite reductase (dsrAB) gene at 0–40 cm depths were higher than those at 40–80 cm depth at all sites. The SRM community composition varied in the soils of different sampling sites following terminal restriction fragment length polymorphism (T-RFLP) and phylogenetic analyses, which appeared to be correlated with contents of MeHg, OM, NH₄ ⁺, and SO₄ ^2? through canonical correspondence analysis. The dominant groups of SRM in the soils examined belonged to Deltaproteobacteria and some unknown SRM clusters that could have potential for Hg methylation. These results advance our understanding of the relationship between SRM and methylmercury concentration in paddy 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.     

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.     

Copper pollution decreases the resistance of soil microbial community to subsequent dry–rewetting disturbance

Dry–rewetting(DW) disturbance frequently occurs in soils due to rainfall and irrigation, and the frequency of DW cycles might exert significant influences on soil microbial communities and their mediated functions. However, how microorganisms respond to DW alternations in soils with a history of heavy metal pollution remains largely unknown.Here, soil laboratory microcosms were constructed to explore the impacts of ten DW cycles on the soil microbial communities in two contrasting soils(fluvo-aquic soil and red soil)under three copper concentrations(zero, medium and high). Results showed that the fluctuations of substrate induced respiration(SIR) decreased with repeated cycles of DW alternation. Furthermore, the resistance values of substrate induced respiration(RS-SIR)were highest in non-copper-stressed(zero) soils. Structural equation model(SEM) analysis ascertained that the shifts of bacterial communities determined the changes of RS-SIR in both soils. The rate of bacterial community variance was significantly lower in noncopper-stressed soil compared to the other two copper-stressed(medium and high) soils,which might lead to the higher RS-SIR in the fluvo-aquic soil. As for the red soil, the substantial increase of the dominant group WPS-2 after DW disturbance might result in the low RS-SIR in the high copper-stressed soil. Moreover, in both soils, the bacterial diversity was highest in non-copper-stressed soils. Our results revealed that initial copper stress could decrease the resistance of soil microbial community structure and function to subsequent DW disturbance.