Rhizosphere Microbiomes of Potato Cultivated under Bacillus subtilis Treatment Influence the Quality of Potato Tubers.

Plants serve as a niche for the growth and proliferation of a diversity of microorganisms. Soil microorganisms, which closely interact with plants, are increasingly being recognized as factors important to plant health. In this study, we explored the use of high-throughput DNA sequencing of the fungal ITS and bacterial 16S for characterization of the fungal and bacterial microbiomes following biocontrol treatment (DT) with Bacillus subtilis strain Bv17 relative to treatments without biocontrol (DC) during the potato growth cycle at three time points. A total of 5631 operational taxonomic units (OTUs) were identified from the 16S data, and 2236 OTUs were identified from the ITS data. The number of bacterial and fungal OTU in DT was higher than in DC and gradually increased during potato growth. In addition, indices such as Ace, Chao, Shannon, and Simpson were higher in DT than in DC, indicating greater richness and community diversity in soil following the biocontrol treatment. Additionally, the potato tuber yields improved without a measurable change in the bacterial communities following the B. subtilis strain Bv17 treatment. These results suggest that soil microbial communities in the rhizosphere are differentially affected by the biocontrol treatment while improving potato yield, providing a strong basis for biocontrol utilization in crop production.

Molecular characterization and antimicrobial resistance profiles of Mycobacterium tuberculosis complex in environmental substrates from three dairy farms in Eastern Cape, South Africa.

This study analysed 330 environmental substrates from three dairy farms for the occurrence, drug resistance and the genetic mutations of MTBC (Mycobacterium tuberculosis complex) in Eastern Cape, South Africa using PCR, while the Genotype MTBDRplus assay was used for drug susceptibility and genetic mutations analyses. About 17% (55/330) of the samples were positive for MTBC at 16.7% (water), 13.3% (soil) and 20% (hayfeed). Isoniazid resistance was detected in 47.3% (26/55) of the samples while 16.4% (9/55) were multidrug-resistant. Genetic mutations were detected on the rpoB gene (resistance to rifampicin) with frequencies ranging from 53.6% (D516V) to 21.4% (H526D), while mutations on the katG and inhA genes (resistance to isoniazid) ranged between 14.3% and 80%. Incidents of diverse genetic mutations in the environmental matrices suggest possible resistance to other anti-TB drugs not assayed in this study and emphasizes the need for continuous monitoring of drug resistance patterns for timely detection and control of new clonal groups of MTBC.

Comparative transcriptomic analysis reveals novel insights into the response to Cr(VI) exposure in Cr(VI) tolerant ectomycorrhizal fungi Pisolithus sp. 1 LS-2017.

Chromium (Cr) is one of the most toxic heavy metals and a health hazard to millions of people worldwide. Ectomycorrhizal (ECM) fungi can assist plants in phytoremediation of heavy metal contaminated soil. Cr tolerance differs among ECM fungal varieties, but the underlying molecular mechanisms of Cr tolerance in ECM fungi are not clear. This study identified, analysed and compared the Cr(VI)-induced transcriptional changes between Cr(VI)-tolerant strain (Pisolithus sp. 1 LS-2017) and Cr(VI)-sensitive strain (Pisolithus sp. 2 LS-2017) by de novo transcriptomic analysis. The results showed that 93,642 assembled unique transcripts representing the 22,353 (46.76%) unigenes matched the proteins we have known in the Nr database and 47,801 unigenes were got from the Pisolithus spp. For DEGs between the control and 10 mg/L Cr(VI) treatment, cyanoamino acid metabolic, type I diabetes mellitus metabolism, nitrogen metabolism and beta-Alanine metabolism pathways were significantly enriched (p < 0.05) in Pisolithus sp. 1 LS-2017. Two nitrate reductase family genes (nidD, niiA) provide Cr(VI) tolerance for Pisolithus sp. 1 LS-2017 by regulating Cr(VI) reduction. In addition, NO produced by nidD, niiA regulated denitrification can alleviate Cr(VI) induced oxidative stress. In Pisolithus sp. 2 LS-2017, the alcC, aldA and lcf2 gene may alleviate Cr(VI) induced oxidative stress by protecting SH groups and increasing secondary metabolism, reducing detoxify aldehydes to carboxylic acids and producing LCPUFAs respectively; .T gene regulate Cr(VI) induced wound healing by pigmentation and stability of melanin in spore; MKP2 gene accelerate Cr(VI) induced cell death and gpmA gene regulated Cr(VI) induced energy emergency.

Municipal solid wastes as a resource for environmental recovery: Impact of water treatment residuals and compost on the microbial and biochemical features of As and trace metal-polluted soils.

In this study we evaluated the microbiological and biochemical impact of iron-based water treatment residuals (Fe-WTRs) and municipal solid waste compost (MSWC), alone and combined, on three different soils co-contaminated with arsenic (As) and trace-metals (TM), i.e. Pb, Cu and Zn. Overall, all the amendments considered significantly increased the abundance of culturable heterotrophic bacteria, with MSWC showing the greatest impact across all soils (up to a 24% increase). In most of treated soils this was accompanied by a significant reduction of both the (culturable) fungal/bacterial ratio, and the proportion of culturable As(V)- and As(III)-resistant bacteria with respect to total bacterial population. The catabolic potential and versatility of the resident microbial communities (assessed by community level physiological profile) was highly soil-dependent and substantial increases of both parameters were observed in the amended soils with the higher total As concentration (from approx. 749 to 22,600 mg kg-1). Moreover, both carbon source utilisation profile and 16S rRNA soil metagenome sequencing indicated a significant impact of MSWC and Fe-WTRs on the structure and diversity of soil microbial communities, with Proteobacteria, Actinobacteria and Firmicutes being the most affected taxa. The assessment of selected soil enzyme activities (dehydrogenase, urease and ß-glucosidase) indicated an increase of metabolic functioning especially in soils treated with MSWC (e.g. dehydrogenase activity increased up to 19.5-fold in the most contaminated soil treated with MSWC). Finally, the microbial and biochemical features of treated (and untreated) contaminated soils (i.e. total bacterial counts, catabolic potential and versatility and soil enzyme activities) were highly correlated with the concentrations of labile As and TM in these latter soils and supported a clear role of the tested amendments (especially MSWC) as As- and TM-immobilising agents.

Risk assessment for and microbial community changes in Farmland soil contaminated with heavy metals and metalloids.

Food security and human health can be seriously affected by heavy metal and metalloid (HM) pollution of soil. In this study, the risks posed by HMs and microbial community responses to HM pollution of agricultural soil in southwestern China were investigated. The C, N, P, and S (nutrients) concentrations were 12040.7-15912.7, 1298.06-1832.01, 750.91-2050.35, and 269.17-2115.52 mg/kg, respectively. The As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn concentrations were 3.11-8.20, 1.85-6.56, 22.83-43.96, 11.21-23.30, 0.08-0.81, 11.02-22.97, 24.07-42.96, and 193.63-698.39 mg/kg, respectively. Interpolation analysis indicated that the nutrient and HM concentrations varied spatially rather strongly. The concentrations of all of the elements were higher in soil from the northern sampling sites than in soil from the other sites. HMs in soil were found to pose high levels of risk (RI 898.85, i.e., >600). Cd contributed more than the other HMs to the risk assessment values (ErCd 293.72-1031.94), so was the most serious contaminant. Microbial diversity decreased over time in soil with high HM concentrations (plot S2) and was lower than in soil with low HM concentrations (plot S8). The nutrient and HM concentrations correlated with the microbial community characteristics. Proteobacteria, Acidobacteria, and Chloroflexi were (in decreasing order) the dominant bacterial phyla. We speculate that these phyla may be strongly resistant to HMs. The fourth most common phylum was Actinobacteria. Bacteria in this phylum could be used as biological indicators of the HM pollution status. Soil micro-ecosystems can self-regulate. HM stress will affect the evolution of soil microorganisms and relevant functional genes. The spatiotemporal variability in the microbial community responses to HMs and the spatial analysis and ecological risk assessment results will be useful reference data for the remediation of HM-polluted soil.

Metagenomic characterization of antibiotic resistance genes in Antarctic soils.

Antibiotic resistance genes (ARGs) are considered environmental pollutants. Comprehensive characterization of the ARGs in pristine environments is essential towards understanding the evolution of antibiotic resistance. Here, we analyzed ARGs in soil samples collected from relatively pristine Antarctica using metagenomic approaches. We identified 79 subtypes related to 12 antibiotic classes in Antarctic soils, in which ARGs related to multidrug and polypeptide were dominant. The characteristics of ARGs in Antarctic soils were significantly different from those in active sludge, chicken feces and swine feces, in terms of composition, abundance and potential transferability. ARG subtypes (e.g., bacA, ceoB, dfrE, mdtB, amrB, and acrB) were more abundant than others in Antarctic soils. Approximately 60% of the ARGs conferred antibiotic resistance via an efflux mechanism, and a low fraction of ARGs (∼16%) might be present on plasmids. Culturable bacterial consortiums isolated from Antarctic soils were consistently susceptible to most of the tested antibiotics frequently used in clinical therapies. The amrB and ceoB carried by culturable species did not express the resistance to aminoglycoside and fluoroquinolone at the levels of clinical concern. Our results suggest that the wide use of antibiotics may have contributed to developing higher antibiotic resistance and mobility.

Negative effect of copper nanoparticles on the conjugation frequency of conjugative catabolic plasmids.

Due to their antimicrobial properties, copper nanoparticles (CuNPs) have been proposed to be used in agriculture for pest control. Pesticides removal is mainly done by microorganisms, whose genes usually are found in conjugative catabolic plasmids (CCP). The aim of this work was to evaluate if CuNPs at subinhibitory concentrations modify the conjugation frequency (CF) of two CCP (pJP4 and pADP1). CuNPs were characterized by scanning electron microscopy with an X-ray detector, dynamic light scattering and X-ray diffraction. Mating assays were done in LB broth supplemented with CuNPs (10, 20, 50 and 100 µg mL-1) or equivalent concentrations of CuSO4. Interestingly, we observed that in LB, Cu+2 release from CuNPs is fast as evaluated by atomic absorption spectrophotometry. Donor and recipient strains were able to grow in all copper concentrations assayed, but CF of mating pairs was reduced to 10% in the presence of copper at 20 or 50 µg Cu mL-1 compared to control. Thus, our results indicated that both copper forms, CuNPs or CuSO4, negatively affected the transfer of catabolic plasmids by conjugation. Since dissemination of degradative genes by conjugation contribute to degradation of pesticides by microorganisms, this work improves our understanding of the risks of using copper in agriculture soils, which could affect the biodegradative potential of microbial communities.

Alleviation of cadmium toxicity to tobacco (Nicotiana tabacum) by biofertilizers involves the changes of soil aggregates and bacterial communities.

Tobacco leaves usually accumulate and concentrate high levels of cadmium (Cd) when growing in contaminated soil, and the transfer of Cd through tobacco smoke to human body could cause serious health risks. In this study, we explored the impact of biofertilizers on alleviating Cd-induced growth inhibition of tobacco leaves. Tobacco (Nicotiana tabacum L.) was planted in three naturally Cd-polluted soils from Chinese main tobacco-planting areas. Adding biofertilizer alleviated Cd-induced degradation of tobacco leaves quality, represented by the balanced K, Cl, N, nicotine or sugar contents and their ratios; Cd reduction rate of tobacco leaves was increased and soil extractable Cd was decreased, when compared with CK (no extra biofertilizer addition). The following changing tendencies were believed to be responsible for immobilizing soil Cd and alleviating its toxicity to tobacco leaves: the re-distribution of Cd from the fraction of smaller soil aggregates to the fraction of larger soil aggregates; and the shift of major soil microbes by increasing the abundance of beneficial taxa such as those from the phyla Actinobacteria, Proteobacteria or Chloroflexi. In all biofertilizer treatments, the effectiveness in mitigating Cd toxicity to tobacco leaves was dependent on the type of biofertilizer and soil applied. This study provides a feasible way to control or reduce Cd toxicity for sustainable tobacco production.

Foliar Roundup application has minor effects on the compositional and functional diversity of soil microorganisms in a short-term greenhouse experiment.

The herbicide Roundup (and glyphosate, its active ingredient) is extensively used for weed control on a worldwide scale. It is absorbed after foliar application and quickly translocated inside the plant. In this study, we investigated the effects of Roundup speed, a commercial glyphosate formulation, on the structural composition (dominance of microbial groups, phospholipid fatty acid analysis - PLFA) and functional diversity (use of carbon sources, Multiple Substrate Induced Respiration - MSIR) of soil microorganisms. We specifically aimed at understanding the potential impact of biotic interactions on herbicide effects and included plants, earthworms, and endomycorrhizal fungi in the experimental setup. For this, we grew clover (Trifolium repens) in the greenhouse and added mycorrhizal inoculum (Glomus mosseae) and earthworms (Lumbricus terrestris) to the pots. Two weeks after foliar Roundup application and subsequent plant death, the pots were destructively sampled. The application resulted in a significant increase of microbial respiration (SIR) by approximately 30%. A multivariate analysis of the MSIR data exhibited small but significant differences between the microbial communities of treated and untreated pots, while no significant difference was apparent for the PLFA data. Bacterial PLFAs generally decreased following herbicide application, while mycorrhizal and fungal PLFAs were not affected. We did not find a consistent difference between the fatty acid markers of gram negative and gram positive bacteria. For all investigated parameters, there were highly significant differences between the upper (0-5 cm depth) and lower (5-10 cm) soil layers. The fact that rooting density differed by a factor of 3.5 between the two layers indicated that herbicide effects were especially pronounced in the clover rhizosphere and were likely due to changes in root exudate composition. We found significant, though very small, interactions between Roundup and other experimental factors (especially mycorrhizal inoculum).

New insights into the impact of nZVI on soil microbial biodiversity and functionality.

Nanoscale zero-valent iron (nZVI) is a strong reducing agent used for in situ remediation of soil. The impacts of nZVI (5-10% w/w) on the soil microbial biodiversity and functionality of two soils (Lufa 2.2 and 2.4) were assessed. Illumina MiSeq technology was used to evaluate the structure of soil microbiomes after 21 days of exposure. Proteobacteria, Verrucomicrobia, Firmicutes and Actinobacteria were the most abundant phyla in both soils. However, the dynamics of bacterial community composition following nZVI addition differed. nZVI exposure induced pronounced shifts in the microbial composition of soil 2.4, but not in soil 2.2; an increase in Verrucomicrobia abundance was the unique common taxonomic pattern observed in both soils. The PICRUSt approach was applied to predict the functional composition of each metagenome. Environmental information processing function (membrane transport) was decreased in both nZVI-spiked soils, although soil 2.4 samples were enriched in functions involved in cellular processes and metabolism. The effects of nZVI on autochthonous bacterial communities clearly varied with the soil type assessed; changes at the phylogenetic level appeared to be more abundant than those observed at the functional level, and thus, the overall effort of the soil ecosystem might involve the maintenance of functionality following nZVI exposure.

Soil nutrients status affected by simple and enriched biochar application under salinity conditions.

In order to study the effect of biochar application as simple and enriched, on the soil nutrients status in the salinity conditions, a research was conducted as a factorial arrangement based on completely randomized design (CRD) with three replicates. The biochar (grape pruning residues) was applied in three levels (0, 2% biochar, and 2% enriched biochar by rock phosphate and cow manure). Also, the salinity treatment was considered in three levels (2, 4.5, and 9 dSm-1). After treating the soil, it was incubated in polyethylene containers for a 70-day period at 25 °C and 70% field capacity moisture regime. The results showed that salinity significantly affected the soil pH, electrical conductivity (EC), calcium, magnesium, sodium, basal respiration, and nitrifying bacteria frequency (P < 0.001) and chloride concentration (P < 0.01). Also, the biochar significantly affected the pH, organic carbon, concentration of total nitrogen, phosphorous, solution potassium, sodium, iron, zinc, copper, basal respiration, and nitrifying bacteria frequency (P < 0.001) of the soil. The interaction effect of biochar and salinity levels was significant on soil sodium concentration (P < 0.01) and pH (P < 0.05). In comparison with the control treatment, the enriched biochar, decreased soil pH (about 1.4%) and increased the phosphorous, iron, and zinc up to 36%, 29%, and 36%, respectively and simple biochar increased the Nitrogen and Potassium up to 46% and 48%, respectively. In general, it was concluded that both types of the biochars lowered the sodium concentration of the soil in different salinity levels due to high potential of biochar for sodium absorption which this ability may be considered in saline soils remediation.

Deciphering the associated risk on soil microbes upon use of biopesticides in rice ecosystem.

Plant species, viz Cleistanthus collinus, Lantana camara, and Strychnos nux-vomica are being traditionally used for pest management in rice. However, limited investigation has been carried out to understand the toxic effect of these materials on soil microbes. Hot water extracts of these plants were evaluated for their effects on soil microbial population and enzyme activities along with neem oil and chlorpyrifos as check. Soil microbial population, viz bacteria, fungi, phosphate-solubilizing bacteria (PSB), and asymbiotic nitrogen fixers were unchanged after application of plant extracts. Maximum population of bacteria including PSB and asymbiotic nitrogen fixers were observed in control, whereas, S. nux-vomica, and C. collinus-treated soil had higher number of actinomycetes and fungal population, respectively. Soil microbial biomass did not vary differently among the plant extracts. Application of plant extracts did not alter dehydrogenase, ß-glycosidase, acid phosphatase, alkaline phosphatase, and urease content in soil. Secondary metabolites present in these plant extracts may be responsible for variable effects on soil microbes. Chlorpyrifos had a fleeting negative effect on soil microbes and enzymes in comparison to plant extracts. All the three plants did not have any negative effect on soil microbes and enzymes and can be safely recommended in rice pest management.

Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated manure-soil microcosms.

The aim of this study was to investigate the fate of nine potential indicator antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, intI1) and the diversity of bacterial communities in response to poultry manure applications to arable soil over a 90 day period. Quantitative real time PCR and Illumina high-throughput sequencing of 16S rDNA gene were used to quantify and trace ARG fate. The levels of all genes dramatically decreased over time and intI1, sul1, sul2 and tetM always had the greatest abundance and lowest dissipation rates. This indicated that more effort should be focused on the ARG elimination from manure rather than waiting for subsequent attenuation in the environment. Our sequencing results documented dramatic changes in the microbial community structure and diversity during these experiments. In poultry manure groups, Bacteroidetes and Actinobacteria were the two dominant phyla while Acidobacteria dominated the control groups. Moreover, the relative abundance of genera Corynebacterium, Pseudomonas, Ochrobactrum, Actinomadura and Bacillus, which contained potential opportunistic pathogens, changed over time suggesting that poultry manure not only strongly influenced bacterial community composition, but also selected specific bacterial communities. This study provides a glimpse of ARG fates and bacterial community diversity in soil after the application of poultry manure.

Biodiversity of soil bacteria exposed to sub-lethal concentrations of phosphonium-based ionic liquids: Effects of toxicity and biodegradation.

Little is known about the effect of ionic liquids (ILs) on the structure of soil microbial communities and resulting biodiversity. Therefore, we studied the influence of six trihexyl(tetradecyl)phosphonium ILs (with either bromide or various organic anions) at sublethal concentrations on the structure of microbial community present in an urban park soil in 100-day microcosm experiments. The biodiversity decreased in all samples (Shannon's index decreased from 1.75 down to 0.74 and OTU's number decreased from 1399 down to 965) with the largest decrease observed in the microcosms spiked with ILs where biodegradation extent was higher than 80%. (i.e. [P66614][Br] and [P66614][2,4,4]). Despite this general decrease in biodiversity, which can be explained by ecotoxic effect of the ILs, the microbial community in the microcosms was enriched with Gram-negative hydrocarbon-degrading genera e.g. Sphingomonas. It is hypothesized that, in addition to toxicity, the observed decrease in biodiversity and change in the microbial community structure may be explained by the primary biodegradation of the ILs or their metabolites by the mentioned genera, which outcompeted other microorganisms unable to degrade ILs or their metabolites. Thus, the introduction of phosphonium-based ILs into soils at sub-lethal concentrations may result not only in a decrease in biodiversity due to toxic effects, but also in enrichment with ILs-degrading bacteria.

Increased biomass and quality and reduced heavy metal accumulation of edible tissues of vegetables in the presence of Cd-tolerant and immobilizing Bacillus megaterium H3.

A Cd-resistant and immobilizing Bacillus megaterium H3 was characterized for its impact on the biomass and quality and heavy metal uptake of edible tissues of two vegetables (Brassica campestris L. var. Aijiaohuang and Brassica rapa L. var. Shanghaiqing) grown in heavy metal-polluted soil. The impact of strain H3 on the soil quality was also evaluated. The increase in the edible tissue biomass and the contents of soluble proteins and vitamin C of the vegetables inoculated with strain H3 ranged from 18% to 33%, 17% to 31%, and 15% to 19%, respectively, compared with the controls. Strain H3 significantly decreased the edible tissue Cd and Pb contents of the two greens (41-80%), DTPA-extractable Cd content (35-47%) of the rhizosphere soils, and Cd and Pb translocation factors (25-56%) of the greens compared with the controls. Moreover, strain H3 significantly increased the organic matter content (17-21%) and invertase activity (13-14%) of the rhizosphere soils compared with the controls. Our results demonstrated the increased edible tissue biomass and quality, decreased Cd and Pb uptake of the edible tissues, and improved soil quality in the presence of strain H3. The results also suggested an effective bacterial-enhanced technique for decreased metal uptake of greens and improved vegetable and soil qualities in the metal-contaminated soils.

Root-induced changes of Zn and Pb dynamics in the rhizosphere of sunflower with different plant growth promoting treatments in a heavily contaminated soil.

Root induced changes are deemed to have an important role in the success of remediation techniques in contaminated soils. Here, the effects of two nano-particles [SiO2 and zeolite] with an application rate of 200mgkg-1, and two bacteria [Bacillus safensis FO-036b(T) and Pseudomonas fluorescens p.f.169] in the rhizosphere of sunflower on Zn and Pb dynamics were studied in greenhouse conditions. The treatments reduced the exchangeable Zn (from 13.68% to 30.82%) and Pb (from 10.34% to 25.92%) in the rhizosphere compared to the control. The EC and microbial respiration/population of the rhizosphere and bulk soil had an opposite trend with the exchangeable fraction of Zn and Pb, but dissolved organic carbon followed a similar trend with the more bioavailable fractions. As a result, the accumulation of Pb and Zn in the plant tissues was significantly (p < 0.05) reduced by the application of amendments, which might be due to the shift of the metals to immobile forms induced by the nature of the treatments and changes in the rhizosphere process. The empirical conditions of this research produced the intensification of the rhizosphere process because the findings highlight those changes in the rhizosphere EC, pH and dissolved organic carbon can affect the efficiency of zeolite/SiO2 NPs and bacteria to immobilize Pb and Zn in the soil, depending on the chemical character of the metals and the treatments. Generally, the affinity of the biotic treatment for Pb was more than the abiotic and conversely, the abiotic treatment showed a higher ability to immobilize Zn than the biotic treatment.

No evidential correlation between veterinary antibiotic degradation ability and resistance genes in microorganisms during the biodegradation of doxycycline.

Biodegradation of antibiotic residues in the environment by microorganisms may lead to the generation of antibiotic resistance genes (ARGs), which are of great concern to human health. The aim of this study was to determine whether there is a relationship between the ability to degrade antibiotic doxycycline (DOX) and the development of resistance genes in microorganisms. We isolated and identified ten bacterial strains from a vegetable field that had received long-term manure application as fertilizer and were capable of surviving in a series of DOX concentrations (25, 50, 80, and 100mg/L). Our results showed no evidential correlation between DOX degradation ability and the development of resistance genes among the isolated microorganisms that had high DOX degradation capability (P > 0.05). This was based on the fact that Escherichia sp. and Candida sp. were the most efficient bacterial strains to degrade DOX (92.52% and 91.63%, respectively), but their tetracycline resistance genes showed a relatively low risk of antibiotic resistance in a 7-day experiment. Moreover, the tetM of the ribosomal protection protein genes carried by these two preponderant bacteria was five-fold higher than that carried by other isolates (P < 0.05). Pearson correlations between the Ct/C0 of DOX and tet resistance genes of three isolates, except for Escherichia sp. and Candida sp., showed remarkable negative correlations (P < 0.05), mainly because tetG markedly increased during the DOX degradation process. Our results concluded that the biodegradation of antibiotic residues may not necessarily lead to the development of ARGs in the environment. In addition, the two bacteria that we isolated, namely, Escherichia sp. and Candida sp., are potential candidates for the engineering of environmentally friendly bacteria.

Microbial functional diversity responses to 2 years since biochar application in silt-loam soils on the Loess Plateau.

The structure and function of soil microbial communities have been widely used as indicators of soil quality and fertility. The effect of biochar application on carbon sequestration has been studied, but the effect on soil microbial functional diversity has received little attention. We evaluated effects of biochar application on the functional diversities of microbes in a loam soil. The effects of biochar on microbial activities and related processes in the 0-10 and 10-20cm soil layers were determined in a two-year experiment in maize field on the Loess Plateau in China. Low-pyrolysis biochar produced from maize straw was applied into soils at rates of 0 (BC0), 10 (BC10) and 30 (BC30)tha-1. Chemical analysis indicated that the biochar did not change the pH, significantly increased the amounts of organic carbon and nitrogen, and decreased the amount of mineral nitrogen and the microbial quotient. The biochar significantly decreased average well colour development (AWCD) values in Biolog EcoPlates™ for both layers, particularly for the rate of 10tha-1. Biochar addition significantly decreased substrate richness (S) except for BC30 in the 0-10cm layer. Effects of biochar on the Shannon-Wiener index (H) and Simpson's dominance (D) were not significant, except for a significant increase in evenness index (E) in BC10 in the 10-20cm layer. A principal component analysis clearly differentiated the treatments, and microbial use of six categories of substrates significantly decreased in both layers after biochar addition, although the use of amines and amides did not differ amongst the three treatments in the deeper layer. Maize above ground dry biomass and height did not differ significantly amongst the treatments, and biochar had no significant effect on nitrogen uptake by maize seedlings. H was positively correlated with AWCD, and negatively with pH. AWCD was positively correlated with mineral N and negatively with pH. Our results indicated that shifts in soil microbial functional diversity affected by biochar were not effective indicators of soil quality in earlier maize growth periods in this region.

Imidacloprid application changes microbial dynamics and enzymes in rice soil.

Extensive use of imidacloprid in rice ecosystem may alter dynamics of microorganisms and can change soil biochemical properties. The objective of this study was to assess the effect of imidacloprid on growth and activities of microbes in tropical rice soil ecosystem. Four treatments, namely, recommended dose (at 25g a.i. ha-1, RD), double the recommended dose (at 50g a.i. ha-1, 2RD), five times the recommended dose (at 125g a.i. ha-1, 5RD) & ten times the recommended dose (at 250g a.i. ha-1, 10RD) along with control were imposed under controlled condition. Dissipation half lives of imidacloprid in soil were 19.25, 20.38, 21.65 and 33.00 days for RD, 2RD, 5RD and 10RD, respectively. In general bacteria, actinomycetes, fungi and phosphate solubilising bacteria population were disturbed due to imidacloprid application. Changes in diversity indices within bacterial community confirmed that imidacloprid application significantly affected distribution of bacteria. Total soil microbial biomass carbon content was reduced on imidacloprid application. Except dehydrogenase and alkaline phosphatase activities, all other soil enzymes namely, ß-glycosidase, fluorescien diacetate hydrolase, acid phosphatase and urease responded negatively to imidacloprid application. The extent of negative effect of imidacloprid depends on dose and exposure time. This study concludes imidacloprid application had transient negative effects on soil microbes.

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.

Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24µg pot-1, respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg-1 cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems.