Comparison of bacterial and archaeal communities in two fertilizer doses and soil compartments under continuous cultivation system of garlic

Soil microbial communities are affected by interactions between agricultural management (e.g., fertilizer) and soil compartment, but few studies have considered combinations of these factors. We compared the microbial abundance, diversity and community structure in two fertilizer dose (high vs. low NPK) and soil compartment (rhizosphere vs. bulk soils) under 6-year fertilization regimes in a continuous garlic cropping system in China. The soil contents of NO3- and available K were significantly higher in bulk soil in the high-NPK. The 16S rRNA gene-based bacterial and archaeal abundances were positively affected by both the fertilizer dose and soil compartment, and were higher in the high-NPK fertilization and rhizosphere samples. High-NPK fertilization increased the Shannon index and decreased bacterial and archaeal richness, whereas the evenness was marginally positively affected by both the fertilizer dose and soil compartment. Soil compartment exerted a greater effect on the bacterial and archaeal community structure than did the fertilization dose, as demonstrated by both the nonmetric multidimensional scaling and redundancy analysis results. We found that rhizosphere effects significantly distinguished 12 dominant classes of bacterial and archaeal communities, whereas the fertilizer dose significantly identified four dominant classes. In particular, a Linear Effect Size analysis showed that some taxa, including Alphaproteobacteria, Rhizobiales, Xanthomonadaceae and Flavobacterium, were enriched in the garlic rhizosphere of the high-NPK fertilizer samples. Overall, the fertilizer dose interacted with soil compartment to shape the bacterial and archaeal community composition, abundance, and biodiversity in the garlic rhizosphere. These results provide an important basis for further understanding adaptive garlic-microbe feedback, reframing roots as a significant moderating influence in agricultural management and shaping the microbial community.

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.

Response of soil microorganisms and enzymes to the foliar application of Helicur 250 EW fungicide on Horderum vulgare L

The use of fungicides bears the risk of many undesirable outcomes that are manifested in, among other things, changes in the structure and activity of microorganisms. This study aimed at determining the effect of a Helicur 250 EW preparation, used to protect crops against fungal diseases, on the microbiological and biochemical activity of soil and on the development of Horderum vulgare L. The fungicide was sprayed on leaves of spring barley in the following doses (per active substance, i.e. tebuconazole, TEB): 0.046, 0.093, 0.139, 1.395, and 2.790 mg TEB plant^-1. The following indices were analyzed in the study: index of microorganisms resistance (RS) to the effects of fungicide, microorganisms colony development index (CD), microorganisms ecophysiological diversity index (EP), genetic diversity of bacteria, enzymatic activity, and effect of the fungicide on spring barley development (IF_H). The most susceptible to the effects of the fungicide turned out to be fungi. The metagenomic analysis demonstrated that the bacterial community differed in terms of structure and percentage contribution in the soil exposed to the fungicide from the control soil even at the Phylum level. However, Proteobacteria appeared to be the prevailing taxon in both soils. Bacillus arabhattai, B. soli, and B. simplex occurred exclusively in the control soil, whereas Ramlibacter tataounensis, Azospirillum palatum, and Kaistobacter terrae - exclusively in the soil contaminated with the fungicide. Helicur 250 EW suppressed activities of all soil enzymes except for arylsulfatase. In addition, it proved to be a strong inhibitor of spring barley growth and development.

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.

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 (Er_Cd 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.

Potential bacterial bioindicators of urban pollution in mangroves

Despite their ecological and socioeconomic importance, mangroves are among the most threatened tropical environments in the world. In the past two decades, the world's mangrove degradation and loss were estimated to lie between an 35% and >80%. However, appropriate bioindicators for assessing the impact of external factors, and for differentiating polluted from unpolluted areas are still scarce. Here, we determine the physicochemical profiles of the soils of two mangroves, one exposed to and one not exposed to anthropogenic factors. By metagenomic analysis based on 16S rRNA, we generated the bacterial diversity profiles of the soils and estimated their functional profiles. Our results showed that the two examined mangrove forests differed significantly in the physicochemical properties of the soils, especially regarding organic carbon, phosphorus and metal content, as well as in their microbial communities, which was likely caused by anthropogenic pollution. The physicochemical differences between the soils explained 76% of the differential bacterial composition, and 64% depended solely on gradients of phosphorus, metal ions and potassium. We found two genera JL-ETNP-Z39 and TA06 exclusively in polluted and non-polluted mangroves, respectively. Additionally, the polluted mangrove was enriched in Gemmatimonadetes, Cyanobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Nitrospirae. A total of 77 genera were affected by anthropic contamination, of which we propose 33 as bioindicators; 26 enriched, and 7 depleted upon pollution.

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, β-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.

Enhanced diuron remediation by microorganism-immobilized silkworm excrement composites and their impact on soil microbial communities

In response to the potential threats stemming from the constantly increasing consumption of herbicides, bioremediation offers a beneficial technology for reducing the widespread herbicide contamination. In order to facilitate the in-situ degradation of diuron, Arthrobacter globiformis D47 is captured onto a biocompatible carrier to assemble the microorganism-immobilized silkworm excrement (MSE) composites. By characterization, bacterial cells are intensively entrapped in/onto the carriers, showing high survival and stable catalytic degradation of target pollutants. Meanwhile, MES composites display excellent adaptiveness and feasibility under different conditions, and the average half-life of diuron is shortened to 7.69 d in sugarcane field where diuron is regularly sprayed for weed management. Importantly, we assess that the use of MSE may generally boost the overall xenobiotic-degrading ability, likely due to the slight alternation of the diversity and composition of soil microbial communities. Taking together, the presented MSE provides an attractive in situ approach for the efficient diuron removal as well as for the more feasible utilization of various pollutant-degrading microorganisms.

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.

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).

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 β-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.

The drought and high wet soil condition impact on PAH (phenanthrene) toxicity towards nitrifying bacteria

A few previous studies showed that the low soil moisture could interact with the toxic effect of the polycyclic aromatic hydrocarbons (PAHs) towards animals (mostly invertebrates). In the present research the impact of the soil moisture in the wide range (from the drought to high moisture conditions) in three different soil materials on toxic effect of the PAH (phenanthrene) towards soil microorganisms (nitrifying bacteria activity) was evaluated. The three dry soil materials were artificially contaminated with phenanthrene (0, 1, 10, 100 and 1000 mg kg^-1 dry mass of soil) and moistened to the varied levels of the soil moisture (30% WHC (dry), 55% WHC (optimal) and 80% WHC (highly wet conditions)). After 7 days incubation, the nitrification potential was measured. The results of the proposed ANCOVA multiple regression model (adjusted R² = 0.91), showed that the increase of soil moisture enhanced the toxicity of the phenanthrene towards nitrification potential and this combined moisture-phenanthrene effect was soil dependent. Therefore, the effect of the soil moisture in combination with the soil diversity should not be missed in the ecotoxicological risk assessment of the PAHs.

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.

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.

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.

Importance of soil texture to the fate of pathogens introduced by irrigation with treated wastewater

World-wide water scarcity is urging the use of treated wastewater (TWW) for irrigation but this practice may have adverse effects on soil and crop contamination due to the introduction of potential microbial pathogens. The objective of this study was to evaluate the potential health risks caused by TWW irrigation of soils differing in their texture, i.e., soil particle fractions including sand, silt and clay. We predicted that the presence of fecal indicator bacteria (FIB) and pathogens would not be linked to TWW irrigation, yet their abundance would be favored by the smallest soil fraction (~2 nm, e.g., clay) as it provides the largest surface area. To test our hypotheses, culture dependent and independent techniques were used to monitor the presence, abundance and source of FIB and microbial pathogens (bacteria and protists) in water (TWW and potable water) and three irrigated soil types (clay, loam and loamy-sand) in a field study spanning two years. The results showed that FIB and pathogens' abundance were significantly different between water types, yet these differences did not carry to the irrigated soils. The abundance and presence of FIB and potential opportunistic or obligate human pathogens did not significantly differ (p > 0.05) between TWW and potable water irrigated soils. Moreover, the source of the FIB and potential pathogens could not be linked to irrigation with TWW. Yet, soil type significantly altered the potential pathogens' diversity (p < 0.05) and abundance (p < 0.05), and differences were affected by clay content, as predicted. The results gave no indication for potential adverse health effects associated with the application of TWW but demonstrated that clay has a particular stabilizing effect on the potential presence of microbial pathogens.

Responses of soil fungal and archaeal communities to environmental factors in an ongoing antimony mine area

Microorganisms are vital to biogeochemical cycles. However, heavy metal contamination has been implicated in altering the microbial community. Antimony (Sb) and arsenic (As) in soils can alter soil bacterial community composition in previous studies and, therefore, may have effects on soil fungal and archaeal community composition. The aim of this study was to assess the microbial activity and fungal and archaeal community composition in long-term Sb and As contamination areas. We analyzed soil respiration rates from 247.91 μg C/kg SDW h to 1372.93 μg C/kg SDW h, which revealed a positive correlation with concentrations of antimony (r = 0.79). The microbial diversity indices (Shannon and Simpson indices) showed that the abundances of the fungal and archaeal communities were more sensitive to As. Redundancy analysis (RDA) revealed that soil properties and contamination are drivers controlling the fungal and archaeal community. All of these two microbial groups responded strongly to pH. However, the dominant drivers for fungal and archaeal community composition were very different. These differences were related to limiting conditions for different species, with fungal community composition affected strongly by pH, TC, TSb, RI and Sb_DGT, while archaeal community composition was mainly affected by the pH, As_DGT and TAs. Furthermore, soil respiration showed a very strong relationship with fungal community composition with r² = 0,60, p < 0.01. These results showed that microbial responses to contamination gradients of Sb and As were heterogeneous due to the limiting environmental conditions of different microbial taxa.

Fate of microbial pollutants and evolution of antibiotic resistance in three types of soil amended with swine slurry

Swine waste is a reservoir of microbial pollutants, including pathogens, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB); therefore, soil fertilized with swine waste is an essential pathway for the dissemination of microbial pollutants from concentrated swine farms to the public. To rationalize the intervals of swine wastes application and investigate the effects of soil type on the occurrences of microbial pollutants and antibiotic resistance, pot experiments were conducted with three typical soils, humic acrisol, calcaric cambisols and histosols, being collected from south, northwest and northeast China (soil-R, soil-Y and soil-B, respectively). The soils were amended with swine slurry, digestate and chemical fertilizers and then conducted for 172 days. The influence of microbial pollutants and antibiotic resistance in soil posed by digestate application was similar to that of the chemical fertilizers, while swine slurry posed high risks to the soil. Soil-B which had the highest organic matter and neutral pH was least influenced by the swine slurry amendment. tetG, tetM and ermF were persistent ARGs in the slurry treated soil, and their decay rates fitted to first-order kinetics in the order soil-B> soil-Y > soil-R. Putative pathogens showed strong correlations with ARGs, suggesting a risk of dissemination. The initial 43-82 days was the active phase of microbial pollution in slurry treated soil, during which time heavy metals, moisture content, total organic carbon and the microbial community were key factors contributing to changes in antibiotic resistance. Fertilization intervals of livestock wastes should be lengthened over the ARG active phase.

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.

The Clean India Mission: Public and animal health benefits

The Clean India Mission is a national campaign that aims for complete elimination of open defecation from the country. In India, 564 million people do not have access to toilets and defecate in the open environment. The 'Millennium development goals' have given increased weightage to elimination of open defecation for improving health, nutrition and productivity of developing country populations. The Indian economy bears an estimated annual total loss (in terms of health, education, access time and tourism) of US$ 54 billion due to lack of toilets, poor hygiene and over US$ 38.5 billion in treatment costs for diseases occurring due to poor hygiene. Out of 1415 human pathogens, at least more than 10% of pathogens are transmitted through the faecal-oral route. The practice of open defecation helps pathogens persist in the environment and cause diseases. This review focuses on the current status and harms of open defecation, as well as the public and animal health benefits of implementing 'The Clean India Mission' in India.

Effects of nitrification inhibitors on gross N nitrification rate, ammonia oxidizers, and N2O production under different temperatures in two pasture soils

Australian pasture soil for cattle and sheep industries constitutes the principal land use with considerable N fertilizer consumption, which is one of the causes of local environmental problems. Nitrification plays a key role in regulating soil inorganic N concentration and its environmental diffusion. The effects of different nitrification inhibitors (NIs) on gross N nitrification (n_gross) rate and N₂O production under different temperatures in pasture soils remain unclear. A laboratory incubation experiment was conducted to determine the effect of NIs (dicyandiamide [DCD], 3,4-dimethylpyrazole phosphate [DMPP], and 3-methylpyrazol and 1H-1,2,4-triazol [3MP + TZ]) on N₂O emissions, n_gross and net N nitrification (n_net) rates, and the abundance of ammonia oxidizers, namely, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), in two Australian pasture soils incubated at temperatures of 15, 25, and 35 °C. All NIs reduced both n_gross and n_net rates and N₂O production rate from the two pasture soils but to different extents. The inhibitory rates of NIs on n_gross and n_net reached 6.80-63.8 and 5.91-62.3%, respectively, whereas that on N₂O production rate totaled 4.5-41.4% in the tested soils. NIs reduced nitrification and N₂O production by inhibiting the growth of AOB rather than AOA. The inhibitory effects of NIs were temperature-dependent, that is, decreasing with increasing temperature from 15 to 35 °C. In general, DMPP performed better than DCD and 3MP + TZ at 15 and 35 °C, whereas DCD performed more effectively than the other two NIs at 25 °C. Our results suggest that the utilization of NIs will depend on the conditions present, especially soil temperature. Additionally, AOB is the target of inhibition when mitigating nitrification and N₂O emission by applying NIs in pasture soils.

Standard methods for the assessment of structural and functional diversity of soil organisms: A review

The lack of standardized methods to study soil organisms prevents comparisons across data sets and the development of new global and regional experiments and assessments. Moreover, standardized methods are needed to evaluate the impact of anthropogenic stressors, such as chemicals, on soil organism communities in the regulatory context. The goal of this contribution is to summarize current methodological approaches to measure structural and functional diversity of soil organisms, and to identify gaps and methodological improvements so as to cross data sets generated worldwide. This is urgently needed because several currently ongoing regional and global soil biodiversity studies are not coordinated with one another in terms of methodology, including database development. Therefore, we evaluated the standard methods to sample, identify, determine, and assess soil organisms currently applied or proposed, using well-accepted criteria such as ecological relevance; practicability of usage in terms of resources, time, and costs; and the level of standardization. Methods addressing both the structure and the functions of soil organisms (populations or communities) are included, with a special focus on new molecular methods based on nucleic acid extraction and further analyses by polymerase chain reaction (PCR)-based approaches for microorganisms and invertebrates. We particularly highlight the activities of the Technical Committee (TC) 190 of the International Organization for Standardization (ISO) because ISO guidelines are legally accredited by many national or international authorities when they put conservation laws and regulations into practice. Finally, we propose detailed recommendations regarding gaps in the available set of standards, in order to identify a list of new methods to be standardized. We propose to organize this whole process under the Global Soil Biodiversity Initiative (GSBI) in order to ensure a truly global approach for the assessment of soil biodiversity. Integr Environ Assess Manag 2018;14:463-479. © 2018 SETAC.

Impact of sugarcane bagasse-derived biochar on heavy metal availability and microbial activity: A field study

In the current study, we conducted a field experiment using the test plant, Brassica chinesis L. (pak choi), to investigate the effect of sugarcane bagasse-derived biochar on the bioavailability of cadmium (Cd), copper (Cu) and lead (Pb), and the health of soil microbiota in a contaminated soil. Biochar application significantly (P < 0.05) increased pak choi yield. Bioavailability of heavy metals to plant shoots and roots decreased with increasing biochar application rates (at 0, 1.5, 2.25 and 3.0 t ha^-1). Sequential extraction of the biochar-treated and -untreated soil revealed that exchangeable Cd reduced whereas organically-bound fraction increased with increasing biochar rate. The labile fractions of Cu and Pb decreased, but the residual fraction increased in biochar-treated soils compared to the control. Urease, catalase and invertase activities, and the populations of bacteria and actinomycetes were significantly enhanced, whereas fungi population declined in biochar-treated soils. This study highlights that sugarcane bagasse biochar has the potential to support the remediation of soils contaminated with heavy metals, and as such can improve the yield and quality of agricultural crops.

Isolation and characterization of a quinclorac-degrading Actinobacteria Streptomyces sp. strain AH-B and its implication on microecology in contaminated soil

Quinclorac, a highly selective auxin herbicide, is widely used for controlling weeds in rice field. However, the residual quinclorac is toxic to many crops, vegetables, and aquatic animals, resulting in one of the major problems in crop rotation. Here, we investigated the degradation of quinclorac by strain AH-B, which was isolated from long-term quinclorac-contaminated soil using continuous circulating fluidized bed reactor and subjected to atmospheric and room temperature plasma mutation. Morphological examination, 16S rRNA gene sequencing, and phylogenetic analysis revealed that strain AH-B was Streptomyces sp. The quinclorac degradation efficiency of AH-B in liquid medium was 97.2% after 18 days when the initial quinclorac concentration was 20 mg L^-1. The degradation products were 3-chloro-7-methoxy-8-quinoline-carboxylic, 3-chloro-7-methyl-8-quinoline-carboxylic, 3-chloro-7-oxyethyl-8-quinoline-carboxylic, and 3,7-dichloro-6-methyl-8-quinoline-carboxylic. The inoculum size, initial quinclorac concentration, pH, and temperature were found to affect quinclorac degradation efficiency of AH-B. High-performance liquid chromatography-electrospray ionization tandem mass spectrometry analysis revealed that quinclorac degradation by AH-B produced many products. In soil with initial quinclorac content of 1 mg kg^-1 dry soil, addition of AH-B resulted in 87.5% quinclorac degradation after 42 days, while that in the control (without AH-B) was 22.4%. Furthermore, microecological analysis using next-generation sequencing of 16S rRNA geneshowed that some bacterial species, such as Bacterioides and Proteobacteria, could survive in quinclorac-contaminated soil, while some bacteria, such as Firmicutes, were very sensitive to quinclorac. Besides, some fungal species, such as Basidiomycota, could also survive quinclorac-contamination. After 42 days, the diversity of bacteria and fungi in soil treated with AH-B was higher than that in the control, implying that bioaugmentation with strain AH-B could reduce quinclorac toxicity to microorganisms in soil.

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.

Continuous cropping of endangered therapeutic plants via electron beam soil-treatment and neutron tomography

Various medicinal plants are threatened with extinction owing to their over-exploitation and the prevalence of soil borne pathogens. In this study, soils infected with root-rot pathogens, which prevent continuous-cropping, were treated with an electron beam. The level of soil-borne fungus was reduced to ≤0.01% by soil electron beam treatment without appreciable effects on the levels of antagonistic microorganism or on the physicochemical properties of the soil. The survival rate of 4-year-old plant was higher in electron beam-treated soil (81.0%) than in fumigated (62.5%), virgin (78%), or untreated-replanting soil (0%). Additionally, under various soils conditions, neutron tomography permitted the monitoring of plant health and the detection of root pathological changes over a period of 4-6 years by quantitatively measuring root water content in situ. These methods allow continual cropping on the same soil without pesticide treatment. This is a major step toward the environmentally friendly production of endangered therapeutic herbs.

Phthalate esters and organochlorine pesticides in agricultural soils and vegetables from fast-growing regions: a case study from eastern China

The present study investigated phthalate esters (PAEs) and organochlorine pesticides (OCPs) in agricultural soils and vegetables from eastern China. The concentrations of PAEs ranged from 109 to 5560 ng/g in soils and 60.1 to 2390 ng/g in cabbages, with average concentrations of 946 and 601 ng/g, respectively. The concentrations of OCPs ranged from <0.1 to 662 ng/g in soils and <0.1 to 42.8 ng/g in cabbages, with average concentrations of 134 and 11.6 ng/g, respectively. OCPs were mainly in the 0-30 cm surface soil layers, while PAEs could infiltrate in deep soil profiles to 70-80 cm layer. Potential source analysis traced the occurrence of OCPs to both historical application and current usage, whereas building materials and agricultural plastic film were possible input sources of PAEs in the ambient environment. OCPs showed no apparent effect on soil microbial communities, whereas significant negative relationship was observed between PAEs and fungi in soils (R = -0.54, p < 0.01). Human health risk assessment data revealed marginal noncarcinogenic risks and low carcinogenic risks in these soils. Notably, PAEs posed a comparable or higher risk level compared with that of OCPs. This study suggests the need for better regulation on pollution control and management of PAE-elevated sites to protect soil quality and food safety.

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.

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.

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 C_t/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.

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.

Impact of the Fenton-like treatment on the microbial community of a diesel-contaminated soil

Fenton-like treatment (FLT) is an ISCO technique relying on the iron-induced H₂O₂ activation in the presence of additives aimed at increasing the oxidant lifetime and maximizing iron solubility under natural soil pH conditions. The efficacy of FLT in the clean-up of hydrocarbon-contaminated soils is well established at the field-scale. However, a better assessment of the impact of the FLT on density, diversity and activity of the indigenous soil microbiota, might provide further insights into an optimal combination between FLT and in-situ bioremediation (ISB). The aim of this work was to assess the impacts of FLT on the microbial community of a diesel-contaminated soil collected nearby a gasoline station. Different FLT conditions were tested by varying either the H₂O₂ concentrations (2 and 6%) or the oxidant application mode (single or double dosage). The impact of these treatments on the indigenous microbial community was assessed immediately after the Fenton-like treatment and after 30, 60 and 90 d and compared with enhanced natural attenuation (ENA). After FLT, a dramatic decrease in bacterial density, diversity and functionality was evident. Although in microcosms with double dosing at 2% H₂O₂ a delayed recovery of the indigenous microbiota was observed as compared to those subjected to single oxidant dose, after 60 d incubation the respiration rate increased from 0.036 to 0.256 μg CCO₂ g^-1soil h^-1. Irrespective of the oxidant dose, best degradation results after 90 d incubation (around 80%) were observed with combined FLT, relying on double oxidant addition, and bioremediation.

Salinity induced effects on the growth rates and mycelia composition of basidiomycete and zygomycete fungi

Soil salinization, as the combination of primary and secondary events, can adversely affect organisms inhabiting this compartment. In the present study, the effects of increased salinity were assessed in four species of terrestrial fungi: Lentinus sajor caju, Phanerochaete chrysosporium, Rhizopus oryzae and Trametes versicolor. The mycelial growth and biochemical composition of the four fungi were determined under three exposure scenarios: 1) exposure to serial dilutions of natural seawater (SW), 2) exposure to serial concentrations of NaCl (potential surrogate of SW); and 3) exposure to serial concentrations of NaCl after a period of pre-exposure to low levels of NaCl. The toxicity of NaCl was slightly higher than that of SW, for all fungi species: the conductivities causing 50% of growth inhibition (EC₅₀) were within 14.9 and 22.0 mScm^-1 for NaCl and within 20.2 and 34.1 mScm^-1 for SW. Phanerochaete chrysosporium showed to be the less sensitive species, both for NaCl and SW. Exposure to NaCl caused changes in the biochemical composition of fungi, mainly increasing the production of polysaccharides. When fungi were exposed to SW this pattern of biochemical response was not observed. Fungi pre-exposed to low levels of salinity presented higher EC₅₀ than fungi non-pre-exposed, though 95% confidence limits overlapped, with the exception of P. chrysosporium. Pre-exposure to low levels of NaCl also induced changes in the biochemical composition of the mycelia of L. sajor caju and R. oryzae, relatively to the respective control. These results suggest that some terrestrial fungi may acquire an increased tolerance to NaCl after being pre-exposed to low levels of this salt, thus, suggesting their capacity to persist in environments that will undergo salinization. Furthermore, NaCl could be used as a protective surrogate of SW to derive safe salinity levels for soils, since it induced toxicity similar or higher than that of SW.

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils

Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer.

Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites

Derelict mines pose potential risks to environmental health. Several factors such as soil structure, organic matter, and nutrient content are the greatly affected qualities in mined soils. Soil microbial communities are an important element for successful reclamation because of their major role in nutrient cycling, plant establishment, geochemical transformations, and soil formation. Yet, microorganisms generally remain an undervalued asset in mined sites. The microbial diversity in derelict mine sites consists of diverse species belonging to four key phyla: Proteobacteria, Acidobacteria, Firmicutes, and Bacteroidetes. The activity of plant symbiotic microorganisms including root-colonizing rhizobacteria and ectomycorrhizal fungi of existing vegetation in the mined sites is very high since most of these microbes are extremophiles. This review outlines the importance of microorganisms to soil health and the rehabilitation of derelict mines and how microbial activity and diversity can be exploited to better plan the soil rehabilitation. Besides highlighting the major breakthroughs in the application of microorganisms for mined site reclamation, we provide a critical view on plant-microbiome interactions to improve revegetation at the mined sites. Also, the need has been emphasized for deciphering the molecular mechanisms of adaptation and resistance of rhizosphere and non-rhizosphere microbes in abandoned mine sites, understanding their role in remediation, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.

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.

Dimethyl pyrazol-based nitrification inhibitors effect on nitrifying and denitrifying bacteria to mitigate N2O emission

Nitrous oxide (N2O) emissions have been increasing as a result of intensive nitrogen (N) fertilisation. Soil nitrification and denitrification are the main sources of N2O, and the use of ammonium-based fertilisers combined with nitrification inhibitors (NIs) could be useful in mitigating N2O emissions from agricultural systems. In this work we looked at the N2O mitigation capacity of two dimethylpyrazol-based NIs, 3,4-dimethylpyrazole phosphate (DMPP) and 2-(N-3,4-dimethyl-1H-pyrazol-1-yl) succinic acid isomeric mixture (DMPSA), on soil nitrifying and denitrifying microbial populations under two contrasting soil water contents (40% and 80% soil water filled pore space; WFPS). Our results show that DMPP and DMPSA are equally efficient at reducing N2O emissions under 40% WFPS conditions by inhibiting bacterial ammonia oxidation. In contrast, at 80% WFPS DMPSA was less efficient than DMPP at reducing N2O emissions. Interestingly, at 80% WFPS, where lowered oxygen availability limits nitrification, both DMPP and DMPSA not only inhibited nitrification but also stimulated N2O reduction to molecular nitrogen (N2) via nitrous oxide reductase activity (Nos activity). Therefore, in this work we observed that DMP-based NIs stimulated the reduction of N2O to N2 by nitrous oxide reductase during the denitrification process.

Distribution of ion contents and microorganisms during the electro-bioremediation of petroleum-contaminated saline soil

This study investigated the distribution of ion contents and microorganisms during the electro-bioremediation (EK-Bio) of petroleum-contaminated saline soil. The results showed that soil ions tend to accumulate around the electrodes, and the concentration was correlated with the distance from the electrodes. The average soil ion content was 7.92 g/kg around the electrodes (site A) and 0.55 g/kg at the furthest distance from the electrodes (site B) after 112 days of treatment, while the initial average content was 3.92 g/kg. Smooth linear (R² = 0.98) loss of soil ions was observed at site C, which was closer to the electrodes than site B, and had a final average soil ion content of 1.96 g/kg. The dehydrogenase activity was much higher in EK-Bio test soil than in the Bio test soil after 28 days of treatment, and followed the order: site C > site B > site A. However, the soil dehydrogenase activity dropped continuously when the soil ion reached very high and low concentrations at sites A and B. The soil microbial community varied in sample sites that had different ion contents, and the soil microbial diversity followed the order: site C > site B > site A. The applied electric field clearly enhanced the biodegradation efficiency for soil petroleum contaminants. However, the biodegradation promotion effects were weakening in soils where the ion contents were extremely high and low (sites A and B). These results can provide useful information for EK-Bioremediation of organic-contaminated saline soil.

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, β-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.

Microbial diversity in solar greenhouse soils in Round-Bohai Bay-Region, China: The influence of cultivation year and environmental condition

Round-Bohai Bay (RBB)-Region is an important crop production area in China, where vegetables are mainly produced in solar greenhouses. However, excessive fertilization and monoculture have caused serious deterioration of soil quality in this region. Soil microbial communities play pivotal roles in many ecosystem processes and are recognized as integrative components of soil quality. Therefore, in this study, we investigated bacterial and fungal diversity in solar greenhouse soils covering a wide range of cultivation year (CY) and sampling site (SS), by using pyrosequencing technology. Surprisingly, CY and SS had little influence on bacterial and fungal relative abundance and diversity. However, environmental factors (EF) and soil available potassium (K) in particular made a significant contribution to the variation of soil bacterial and fungal communities. Specifically, K showed significant (P < 0.05) correlations with dominant bacterial phyla Bacteroidetes, Acidobacteria, Chloroflexi, and Planctomycetes and fungal phyla Ascomycota and Basidiomycota. These results suggested that soil EF appeared more important than CY and SS in shaping the compositions of bacterial and fungal communities. In addition, since fertilizer K has been in the long-term abused in RBB-Region, future vegetable production should pay more attention to K input to reduce the negative effect on soil microbial communities.

Review of the ecotoxicological effects of emerging contaminants to soil biota

In recent years, emerging contaminants (e.g. pesticides and their metabolites, pharmaceuticals, personal and house care products, life-style compounds, food additives, industrial products and wastes, as well as nanomaterials) have become a problem to the environment. In fact, the cumulative use of a panoply of chemical substances in agriculture, industrial activities, in our homes and in health care services has led to their recent appearance in detectable levels in soils, surface, and groundwater resources, with unpredictable consequences for these ecosystems. Few data exist regarding the toxicity and potential for bioaccumulation in biota. When available, data were obtained only for some representatives of the main groups of chemical substances, and for a limited number of species, following non-standard protocols. This makes difficult the calculation of predicted no effect concentrations (PNEC) and the existence of sufficient data to set limits for their release into the environment. This is particularly concerning for the soil compartment, since only recently the scientific community, regulators, and the public have realised the importance of protecting this natural resource and its services to guarantee the sustainability of terrestrial ecosystems and human well-being. In this context, this review paper aims to identify the major groups of soil emerging contaminants, their sources, pathways and receptors, and in parallel to analyse existing ecotoxicological data for soil biota.

Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers

Due to the intimate association between plants and their microbial symbionts, an examination of the influence of agricultural practices on phytobiome structure and diversity could foster a more comprehensive understanding of plant health and produce safety. Indeed, the impact of upstream crop producti006Fn practices cannot be overstated in their role in assuring an abundant and safe food supply. To assess whether fertilizer type impacted rhizosphere and phyllosphere bacterial communities associating with tomato plants, the bacterial microbiome of tomato cv. 'BHN602' grown in soils amended with fresh poultry litter, commercially available sterilized poultry litter pellets, vermicompost or synthetic fertilizer was described. Culture independent DNA was extracted from bulk and rhizosphere soils, and washes of tomato blossoms and ripe fruit. PCR amplicons of hypervariable regions of the 16S rRNA gene were sequenced and profiled using the QIIME pipeline. Bulk and rhizosphere soil, and blossom and fruit surfaces all supported distinct bacterial communities according to principal coordinate analysis and ANOSIM (R=0.87, p=0.001 in year 1; R=0.93, p=0.001 in year 2). Use of microbiologically diverse organic fertilizers generally did not influence bacterial diversity, community structure or relative abundance of specific taxa on any plant organ surface. However, statistically significant differences in sand and silt contents of soil (p<0.05) across the field and corresponding shifts in water activity were positively (R²=0.52, p=0.005) and negatively (R²=0.48, p=0.009) correlated with changes in bacterial community structure in the rhizosphere, respectively. Over two harvest seasons, this study demonstrated that the application of raw poultry manure, poultry litter pellets and vermicompost had little effect on the tomato microbiome in the rhizosphere and phyllosphere, when compared to synthetically fertilized plants. Plant anatomy, and other factors related to field location, possibly associated with edaphic and air characteristics, were more influential drivers of different tomato organ microbiomes than were diverse soil amendment applications.

Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation

Diversity, distribution and composition of bacterial community of soils contaminated long-term with both polycyclic aromatic hydrocarbons (PAHs) and heavy metals were explored for the first time following 454 pyrosequencing. Strikingly, the complete picture of the Gram positive (+ve) and Gram negative (-ve) bacterial profile obtained in our study illustrates novel postulates that include: (1) Metal-tolerant and PAH-degrading Gram -ves belonging to the class Alphaproteobacteria persist relatively more in the real contaminated sites compared to Gram +ves, (2) Gram +ves are not always resistant to heavy metal toxicity, (3) Stenotrophomonas followed by Burkholderia and Pseudomonas are the dominant genera of PAH degraders with high metabolic activity in long-term contaminated soils, (4) Actinobacteria is the predominant group among the Gram +ves in soils contaminated with high molecular weight PAHs that co-exist with toxic heavy metals like Pb, Cu and Zn, (5) Microbial communities are nutrient-driven in natural environments and (6) Catabolically potential Gram +/-ves with diverse applicability to remediate the real contaminated sites evolve eventually in the historically-polluted soils. Thus, the most promising indigenous Gram +/-ve strains from the long-term contaminated sites with increased catabolic potential, enzymatic activity and metal tolerance need to be harnessed for mixed contaminant cleanups.

Testing an Alternative Method for Estimating the Length of Fungal Hyphae Using Photomicrography and Image Processing

This study aimed to develop and test an unbiased and rapid methodology to estimate the length of external arbuscular mycorrhizal fungal (AMF) hyphae in soil. The traditional visual gridline intersection (VGI) method, which consists in a direct visual examination of the intersections of hyphae with gridlines on a microscope eyepiece after aqueous extraction, membrane-filtration, and staining (e.g., with trypan blue), was refined. For this, (i) images of the stained hyphae were taken by using a digital photomicrography technique to avoid the use of the microscope and the method was referred to as “digital gridline intersection” (DGI) method; and (ii), the images taken in (i) were processed and the hyphal length was measured by using ImageJ software, referred to as the “photomicrography–ImageJ processing” (PIP) method. The DGI and PIP methods were tested using known grade lengths of possum fur. Then they were applied to measure the hyphal lengths in soils with contrasting phosphorus (P) fertility status. Linear regressions were obtained between the known lengths (L_known) of possum fur and the values determined by using either the DGI (L_DGI) (L_DGI = 0.37 + 0.97 × L_known, r² = 0.86) or PIP (L_PIP) methods (L_PIP = 0.33 + 1.01 × L_known, r² = 0.98). There were no significant (P > 0.05) differences between the L_DGI and L_PIP values. While both methods provided accurate estimation (slope of regression being 1.0), the PIP method was more precise, as reflected by a higher value of r² and lower coefficients of variation. The average hyphal lengths (6.5–19.4 m g^–1) obtained by the use of these methods were in the range of those typically reported in the literature (3–30 m g^–1). Roots growing in P-deficient soil developed 2.5 times as many hyphae as roots growing in P-rich soil (17.4 vs 7.2 m g^–1). These tests confirmed that the use of digital photomicrography in conjunction with either the grid–line intersection principle or image processing is a suitable method for the measurement of AMF hyphal lengths in soils for comparative investigations.

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity

Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable.

Restoration of carbon and microbial activity in salt-induced soil by application of peanut shell biochar during short-term incubation study

For the present study, soil samples of four artificially-induced salinity gradients (S0: control, S1: 2.0, S2: 4.0, S3: 6.0 ECiw) was incubated with fine-textured peanut shell biochar at various ratios (B0: control, B1: 2.5%, B2: 5.0%, B3: 10% w/w) for 30 days. At 1, 3, 7, 15, 30 days of incubation, samples were analyzed for soil carbon and selected enzyme activities. Results showed that biochar could increase soil organic carbon on application of highest rate of biochar addition (B3), hence potentially restored the saline soils by less C mineralization, and more sequestration of soil C. However, soil enzyme activities were biochar rate(s), day(s) of incubation and enzyme dependent. The lowest rate of biochar addition (B1) showed highest dehydrogenase (20.5 μg TPF g(-1) soil h(-1)), acid phosphatase (29.1 μg PNP g(-1) soil h(-1)) and alkaline phosphatase (16.1 μg PNP g(-1) soil h(-1)) whereas the higher rate (B2) increased the urease (5.51 μg urea-N g(-1) soil h(-1)) and fluorescein diacetate hydrolyzing activities (3.95 μg fluorescein g(-1) OD soil h(-1)) in soil. All the positive changes persisted at higher levels of salinity (S2, S3) suggesting biochar-amended soil may be potential for better nutrient cycling. Soil enzymes were found to be correlated with soil carbon and with each other while principal component analysis (PCA) extracted the most sensitive parameters as the acid and alkaline phosphatases and urease activities in the present experimental condition. This is the first time report of examining soil microbial environment using peanut shell biochar under a degraded (saline) soil.

Chestnut green waste composting for sustainable forest management: Microbiota dynamics and impact on plant disease control

Making compost from chestnut lignocellulosic waste is a possible sustainable management strategy for forests that employs a high-quality renewable organic resource. Characterization of the microbiota involved in composting is essential to better understand the entire process as well as the properties of the final product. Therefore, this study investigated the microbial communities involved in the composting of chestnut residues obtained from tree cleaning and pruning. The culture-independent approach taken highlighted the fact that the microbiota varied only slightly during the process, with the exception of those of the starting substrate and mature compost. The statistical analysis indicated that most of the bacterial and fungal species in the chestnut compost persisted during composting. The dominant microbial population detected during the process belonged to genera known to degrade recalcitrant lignocellulosic materials. Specifically, we identified fungal genera, such as Penicillium, Fusarium, Cladosporium, Aspergillus and Mucor, and prokaryotic species affiliated with Bacilli, Actinobacteria, Flavobacteria and γ-Proteobacteria. The suppressive properties of compost supplements for the biocontrol of Sclerotinia minor and Rhizoctonia solani were also investigated. Compared to pure substrate, the addition of compost to the peat-based growth substrates resulted in a significant reduction of disease in tomato plants of up to 70 % or 51 % in the presence of Sclerotinia minor or Rhizoctonia solani, respectively. The obtained results were related to the presence of putative bio-control agents and plant growth-promoting rhizobacteria belonging to the genera Azotobacter, Pseudomonas, Stenotrophomonas, Bacillus, Flavobacterium, Streptomyces and Actinomyces in the chestnut compost. The composting of chestnut waste may represent a sustainable agricultural practice for disposing of lignocellulosic waste by transforming it into green waste compost that can be used to improve the fitness of agricultural plants.

[Microscopic soil fungi - bioindicators organisms contaminated soil]

In the paper there are considered methodological issues for the evaluation of soil biota in terms of oil pollution. Experimental studies have shown that under the exposure of a various levels of oil pollution meeting certain gradations of the state and optimal alteration in microbocenosis in sod-podzolic soils, there is occurred a transformation of structure of the complex of micromycetes and the accumulation of toxic species, hardly typical for podzolic soils - primarily represantatives of the genus Aspergillus (A.niger and A. versicolor), Paecilomyces (P.variotii Bainer), Trichoderma (T.hamatum), the genus of phytopathogens Fusarium (F.oxysporum), dermatophytes of genus Sporothrix (S. schenckii) and dark-colored melanin containing fungi of Dematiaceae family. Besides that there are presented data on the study of microbiocenosis of the urban soil, the urban soil differed from the zone soil, but shaped in similar landscape and climatic conditions, and therefore having a tendency to a similar response from the side of microorganisms inhabiting the soil. Isolated complex of soil microscopic fungi is described by many authors as a complex, characteristic for soils of megalopolises. This allowed authors of this work to suggest that in urban soils the gain in the occurrence of pathogenic species micromycetes also increases against a background of chronic, continuously renewed inflow of petroleum hydrocarbons from various sources of pollution. Because changes in the species composition of micromycetes occurred in accordance with the increasing load of oil, so far as microscopic soil fungi can be recommended as a bioindicator organisms for oil. In the article there is also provided information about the distinctive features of modern DNA identification method of soil microscopic fungi and accepted in our country methodology of isolation of micromycetes with the use of a nutrient Czapek medium.

[SANITARY DANGEROUS FILAMENTOUS MICROORGANISMS IN SOILS OF THE CITY OF VORONEZH]

On the example of urban soils of the city of Voronezh there was revealed dependence of the degree of the disturbance of complexes of filamentous microorganisms on soil contamination levels. For the complex of micromycetes in the recreational area of the city disturbances are reversible and correspond to the adaptive range of "stress". In the transport an irreversible transition originates to the adaptive range of "resistance". There are accumulated toxigenic, opportunistic and allergenic fungi species that is harmful to the health of the urban population. The complex of soil actinomycetes is more sustainable. Microbiological indices (lists of indicative species of fungi) should be used for the monitoring of urban soils.