Bacteria In Agricultural Soils Research Articles

The intrinsic methane mitigation potential and associated microbes add product value to compost

Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h−1 g dw compost−1 and 25.19 ± 6.75 pmol h−1 g dw compost−1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.

Identification of diverse antibiotic resistant bacteria in agricultural soil with H218O stable isotope probing combined with high-throughput sequencing

BackgroundWe aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in 18O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled “heavy” and the unlabelled “light” SIP fractions were sequenced.ResultsAn increase of the 16S rRNA copy numbers in the “heavy” fractions of the treatments with 18O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.ConclusionsThe results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Soil microbiomes are sensitive to current and previous soil conditions, and bacterial ‘bioindicators’ of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

Human Health and Soil Health Risks from Heavy Metals, Micro(nano)plastics, and Antibiotic Resistant Bacteria in Agricultural Soils

Humans are exposed to agricultural soils through inhalation, dermal contact, or the consumption of food. Human health may be at risk when soils are contaminated; while some soil contaminants such as heavy metals (HMs) have been extensively studied, others such as micro(nano)plastics (MNPs) or antibiotic-resistant bacteria (ARB) pose novel threats. This paper investigates the linkages between soil contamination and human health risk by reviewing the state of knowledge on HMs, MNPs, and ARB in agricultural soils. A keyword-based search in Web of Science, Scopus, and Google Scholar was conducted, complemented with a backward snowball search. We analysed main sources of contamination for agricultural soils, risks to human health differentiated by uptake pathway (ingestion, inhalation, dermal), and interactions of contaminants with microorganism, soil fauna, and plants. Results show that the emergence and spread of ARB and antibiotic resistant genes from agricultural soils and their contribution to antibiotic resistances of human pathogens is recognized as a significant threat. Likewise, a growing body of evidence indicates that MNPs are able to enter the food chain and to have potentially harmful effects on human health. For HM, knowledge of the effects on human health is well established. Multiple agricultural practices increase HM concentrations in soils, which may lead to adverse health effects from the ingestion of contaminated products or inhalation of contaminated soil particles. Severe knowledge gaps exist about the pathways of the contaminants, their behaviour in soil, and human uptake. Little is known about long-term exposure and impacts of MNPs, antibiotics and ARB on human health or about the possible combined effects of MNPs, ARB, and HMs. Missing monitoring systems inhibit a comprehensive assessment of human health risks. Our research demonstrates the need for human health risk assessment in the context of agricultural soils, in particular to be able to assess risks related to measures reinforcing the concept of the circular economy.

Tracking antibiotic resistance through the environment near a biosolid spreading ground: Resistome changes, distribution, and metal(loid) co-selection

The application of urban wastewater treatment plants (WWTPs) products to agricultural lands has contributed to the rising level of antibiotic resistance and drawn a critical public health concern. It has not been thoroughly investigated at which spatial scales a biosolid applied area as a potentially predominant source affects surrounding soil resistomes. This study investigated distribution and impact of WWTP biosolids treated with anaerobic digestion on an agricultural area. Heterotrophic plate counts (HPCs) and quantitative polymerase chain reaction (qPCR) were performed for detection of selected antibiotic-resistant bacteria (ARB), selected antibiotic resistance genes (ARGs), intI1 genes, and 16S rRNA genes. Biosolid samples contained significantly higher levels of selected ARGs than the raw agricultural soils (p < 0.05). The average relative abundances of intI1, sul1, blaSHV, and ermB genes were significantly higher in biosolid-amended soils than nearby agricultural soils (p < 0.05). Spatial interpolation analysis of relative gene abundances of intI1, sul1, sul2, and tetW across the studied area further indicated directional trends towards the northwest and southeast directions, highlighting possible airborne spread. Concentrations of Co, Cu, Ni, and Fe were found to be significantly and positively correlated with relative abundances of intI1, sul1, and tetW genes (p < 0.05). The resistance ratios of culturable antibiotic-resistant bacteria in agricultural soils with biosolid amendments were generally identical to those without biosolid amendments. This study will advance the understanding of the antibiotic resistome in agricultural soils impacted by long-term waste reuse and inform the evaluation strategies for future biosolids application and management.

Organic phosphorus availability shapes the diversity of phoD-harboring bacteria in agricultural soil

In light of the limited resources of phosphorus (P) fertilizer, investigating the response of organic P (Po)-mineralizing microbial communities on the resource supply can be an avenue to optimize P recycling in agricultural systems. The alkaline phosphomonoesterase (alkaline PAse)-encoding gene PhoD is universally occurring in soil microorganisms. Here we collected 102 soil samples from Chinese agricultural fields to explore the effect of resource supply on the community of phoD-harboring bacteria. The relationships between the community diversity and soil organic carbon (SOC), total nitrogen (TN) and available Po concentration were fitted to the linear and quadric models suggested by the resource competition theory as well as the Michaelis-Menten model suggested by the metabolic theory of ecology. The results revealed that the response of phoD-harboring bacterial diversity to SOC and TN was likely related to the resource competition theory, with highest diversity at moderate SOC and TN concentration. In contrast, the phoD diversity increased with increasing available Po until the stationary value, which was consistent with the metabolic theory of ecology. Random forest models and multiple regression tree analyses identified the Po availability as the most important predictor on the variation of the phoD-harboring bacterial diversity and network topological features prior to the climate, soil texture, pH and all tested soil nutrient variables. This study highlights the critical role that Po plays in structuring phoD-harboring bacterial communities. Furthermore, for the first time, we correlated functional gene diversity to the corresponding enzymatic substrate availability from a metabolic theory perspective, confirming that the relationship follows the Michaelis-Menten model which was well known to predict the substrate regulation on the rate of enzymatic reactions.

Impacts of different sources of animal manures on dissemination of human pathogenic bacteria in agricultural soils

The human pathogenic bacteria (HPB) in animal feces may disseminate to agricultural soils with their land application as organic fertilizer. However, the knowledge about the impacts of different sources and rates of animal manures on the temporal changes of soil HPB remains limited, which hamper our ability to estimate the potential risks of their land application. Here, we constructed an HPB database including 565 bacterial strains. By blasting the 16 S rRNA gene sequences against the database we explored the occurrence and fate of HPB in soil microcosms treated with two rates of swine, poultry or cattle manures. A total of 30 HPB were detected in all of manure and soil samples. Poultry manure at the high level obviously improved the abundance of soil HPB. The application of swine manure could introduce concomitant HPB into the soils. Of which, Pseudomonas syringae pv. syringae B728a and Escherichia coli APEC O78 may deserve more attention because of their survival for a few days in manured soils and being possible hosts of diverse antibiotic resistance genes (ARGs) as revealed by co-occurrence pattern. Bayesian source tracking analysis showed that the HPB derived from swine manure had a higher contribution to soil pathogenic communities than those from poultry or cattle manures in early days of incubation. Mantel test together with variation partitioning analysis suggested that bacterial community and soil physicochemical properties were the dominant factors determining the profile of HPB and contributed 64.7% of the total variations. Overall, our results provided experimental evidence that application of animal manures could facilitate the potential dissemination of HPB in soil environment, which should arouse sufficient attention in agriculture practice and management to avoid the threat to human health.

Identification of Thiobacillus bacteria in agricultural soil in Iran using the 16S rRNA gene

Thiobacillus, as useful soil bacteria, plays an important role in sulfur cycling. The purpose of this study was to identify the species Thiobacillus thioparus, Thiobacillus novellas and Thiobacillus denitrificans in rainfed and irrigated lands soil in Ajabshir, Ilam, Qorveh, Rojintaak, Sonqor, Kermanshah and Research Farm of Razi University in Iran. Sampling was performed as randomized completely with three replications at depth of 0-30cm. The Thiobacillus species were determined via 16S rRNA characteristics. The results of agarose gel electrophoresis indicated that T. thioparus was the highest amount in the irrigated land in Research Farm and its lowest amount was in the Rojintaak rainfed land. These species not found in four locations and conditions including the Ajabshir irrigated, Qorveh rainfed, Research Farm rainfed and Rojintaak irrigated lands. The results of the T. novellas indicated that this was found in Ilam irrigated, Qorveh rainfed, Research Farm irrigated, Rojintaak irrigated and Rojintaak rainfed lands. The highest and lowest amount of T. novellas was indicated in the Rojintaak and Ilam irrigated lands respectively. The T. denitrificans gene showed that this bacterium was observed only in both samples of Ajabshir. Our study showed that Thiobacillus was not detected in all of the soils. If sulfur fertilizer is given to the soil without this bacterium, it is necessary to use sulfur fertilizer with Thiobacillus bacteria inoculation for better sulfur oxidation.

Relative abundance of denitrifying and DNRA bacteria and their activity determine nitrogen retention or loss in agricultural soil

Dissimilatory nitrate reduction to ammonium (DNRA) competes with denitrification for nitrate (NO3−) and can result in conservation of nitrogen (N), whereas denitrification leads to gaseous losses in the form of nitrogen gas or the greenhouse gas nitrous oxide (N2O). Thus, promoting DNRA bacteria in agricultural soils would be tractable, but little is known about what controls them in these systems and if management or cropping regimes can affect the competition between denitrifiers and DNRA bacteria. We hypothesized that cropping systems conserving soil organic matter (SOM) and resulting in higher C/NO3− ratios would favour DNRA over denitrification, and thereby lower the N2O emissions due to shifts in the abundances of the microbial communities involved. To test this hypothesis, we compared soil of an annual cereal rotation with a ley rotation (including barley) from a long-term field experiment, each with two different N fertilizer application rates. We quantified the gross rates of denitrification and DNRA in a15N tracing experiment and quantified the abundances of the functional genes for denitrification (nirK, nirS), DNRA (nrfA) and N2O reduction (nosZI, nosZII). The annual crop rotation had changed the soil properties, whereas the ley rotation prevented depletion of SOM resulting in higher C/NO3− ratios. The abundances of both nrfA and nosZ relative to the nir genes were higher in the ley soils, which correlated with significantly higher DNRA rates and lower N2O production, compared to the annual cereal rotation. We conclude that conservation of soil N and mitigation of N2O emissions can be mediated by the soil microbiome by management of SOM.

English

English

Oxygen uptake and denitrification in soil aggregates

A mathematical model of oxygen uptake by bacteria in agricultural soils is presented with the goal of predicting anaerobic regions in which denitrification occurs. In an environment with a plentiful supply of oxygen, micro-organisms consume oxygen through normal respiration. When the local oxygen concentration falls below a threshold level, denitrification may take place leading to the release of nitrous oxide, a potent agent for global warming. A two-dimensional model is presented in which one or more circular soil aggregates are located at a distance below the ground level at which the prevailing oxygen concentration is prescribed. The level of denitrification is estimated by computing the area of any anaerobic cores, which may develop in the interior of the aggregates. The oxygen distribution throughout the model soil is calculated first for an aggregated soil for which the ratio of the oxygen diffusivities between an aggregate and its surround is small via an asymptotic analysis. Second, the case of a non-aggregated soil featuring one or more microbial hotspots, for which the diffusion ratio is arbitrary, is examined numerically using the boundary-element method. Calculations with multiple aggregates demonstrate a sheltering effect whereby some aggregates receive less oxygen than their neighbours. In the case of an infinite regular triangular network representing an aggregated soil, it is shown that there is an optimal inter-aggregate spacing which minimises the total anaerobic core area.

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils. By integrating WGA-X with calibrated index-cell sorting and high-throughput genomic sequencing, we are able to analyze genomic sequences and cell sizes of hundreds of individual, uncultured bacteria, archaea, protists, and viral particles, obtained directly from marine and soil samples, in a single experiment. This approach may find diverse applications in microbiology and in biomedical and forensic studies of humans and other multicellular organisms.

Microbial attenuation of atrazine in agricultural soils: Biometer assays, bacterial taxonomic diversity, and catabolic genes

The purpose of this study was to examine the potential biomineralization of atrazine and identification of atrazine-degrading bacteria in agricultural soils. Different atrazine application histories of soils impacted the kinetics of biomineralization but not the presence of catabolic genes of two atrazine degradative pathways (Trz and Atz). Biomineralization was based on the measurement of 14CO2 from [U-ring-14C]-atrazine in surface soil (0–7 cm) samples incubated in biometers. Aerobic atrazine biomineralization rate constants (k) varied in the range of 0.004–0.508 d−1 depending on the specific soil sample and glucose amendment. The corresponding k-values for anaerobic biometers ± nitrate, ferrihydrite or sulfate were 0.002–0.360 d−1. Glucose enhancement of atrazine biomineralization was not consistent. Aerobic enrichments from soil samples and in-situ incubated BioSep beads yielded mixed cultures, four of which were characterized by 16S rRNA gene amplification, cloning and sequencing. Twelve pure cultures were isolated from enrichments and they were primarily Arthrobacter spp. (10/12). The presence of eight atrazine catabolic genes representing two degradative pathways was investigated in seven bacterial isolates by PCR amplification and sequencing. Several combinations of atrazine catabolic genes were detected; each contained at least atzBC. A complete set of genes for the Atz pathway was not found among the isolates. Our data indicate that atrazine metabolism involves multiple microorganisms and cooperative pathways diverging from atrazine metabolites.

Monitoring of indicator and multidrug resistant bacteria in agricultural soils under different irrigation patterns

The presence of multidrug-resistant bacteria has been proposed as an environmental impact indicator of wastewater use in agricultural soils. Nevertheless, the effect of untreated wastewater discharge on occurrence and persistence of these type of bacteria in soils is unclear. In this study, multidrug-resistant bacteria and microbial indicators of fecal contamination (coliforms and Salmonella) were determined at different depths (0–15, 15–30 and 30–50cm), in active agricultural soils under different untreated wastewater irrigation pattern (a zone with past and present wastewater irrigation; a zone with wastewater irrigation until 2003; and a zone that had never been irrigated with wastewater) in Chihuahua, Mexico. A total of 94 multidrug-resistant strains were recovered from all tested soil samples, even from those that have never been irrigated with wastewater. Higher presence (P<0.05) of multidrug-resistant bacteria was found in soils currently irrigated with untreated wastewater than in soils that has not been irrigated with wastewater for more than 10 years; the later had presence of multidrug-resistant bacteria that was statistically higher than soils that had never been irrigated with wastewater. Wastewater irrigation showed an impact on proliferation of antibiotic-resistant Gram negative bacteria in soils actually irrigated but not in Gram positive bacteria. No statistical difference was found for coliforms and Salmonella between the three soil groups. The effect of depth in multidrug-resistance bacteria presence was negligible. Although multidrug-resistant bacteria was also isolate from soils without wastewater irrigation, their persistence in a highest number in soils irrigated with wastewater suggest that use of untreated wastewater for irrigation enhance the proliferation of multidrug-resistant microorganisms which can be monitoring in soils even after a long period of time after the last irrigation.

Fate of classical faecal bacterial markers and ampicillin-resistant bacteria in agricultural soils under Mediterranean climate after urban sludge amendment

The use of sewage sludge or biosolids as agricultural amendments may pose environmental and human health risks related to pathogen or antibiotic-resistant microorganism transmission from soils to vegetables or to water through runoff. Since the survival of those microorganisms in amended soils has been poorly studied under Mediterranean climatic conditions, we followed the variation of soil fecal bacterial markers and ampicillin-resistant bacteria for two years with samplings every four months in a split block design with three replica in a crop soil where two different types of biosolids (aerobically or anaerobically digested) at three doses (low, 40; intermediate, 80; and high, 160Mg·ha−1) were applied. Low amounts of biosolids produced similar decay rates of coliform populations than in control soil (−0.19 and −0.27log10CFUs·g−1drysoilmonth−1 versus −0.22) while in the case of intermediate and high doses were close to zero and their populations remained 24months later in the range of 4–5log10CFUs·g−1ds. Enterococci populations decayed at different rates when using aerobic than anaerobic biosolids although high doses had higher rates than control (−0.09 and −0.13log10CFUs·g−1dsmonth−1 for aerobic and anaerobic, respectively, vs −0.07). At the end of the experiment, counts in high aerobic and low and intermediate anaerobic plots were 1 log10 higher than in control (4.21, 4.03, 4.2 and 3.11log10CFUs·g−1 ds, respectively). Biosolid application increased the number of Clostridium spores in all plots at least 1 log10 with respect to control with a different dynamic of decay for low and intermediate doses of aerobic and anaerobic sludge. Ampicillin-resistant bacteria increased in amended soils 4months after amendment and remained at least 1 log10 higher 24months later, especially in aerobic and low and intermediate anaerobic plots due to small rates of decay (in the range of −0.001 to −0.008log10CFUs·g−1dsmonth−1 vs −0.016 for control). Aerobic plots had relative populations of ampicillin-resistant bacteria higher than anaerobic plots with different positive trends. Dose (22%) and time (13%) explained most of the variation of the bacterial populations. Dynamics of fecal markers did not correlate with ampicillin-resistant bacteria thus making necessary to evaluate specifically this trait to avoid possible risks for human and environmental health.

Presence of diverse Candidatus Methylomirabilis oxyfera-like bacteria of NC10 phylum in agricultural soils.

To better explore the distribution and diversity of Candidatus Methylomirabilis oxyfera (M.oxyfera)-like bacteria of NC10 phylum in soil environments. The vertical distribution and diversity of NC10 phylum bacteria were investigated in an agricultural field (surface layer, 0-10cm; subsurface layer, 20-30cm; deep layers, 50-60 and 90-100cm) by using Illumina-based 16S rRNA (V3-V4 region) gene sequencing of soil DNA samples and quantitative PCR assays. It was found that the NC10-related reads accounted for 0·8-4·5% of the 16S rRNA pool in each examined core sample, with greater percentage being observed in deep soils than in surface soils and subsurface soils. The recovered NC10-related reads showed 85·1-96·9% identity to the 16S rRNA gene of M.oxyfera. A high diversity of NC10 phylum bacteria was observed in the examined soil cores. A total of 115 operational taxonomic units (OTU) were detected based on 3% sequence divergence in the recovered 16S rRNA genes. Phylogenetic analysis showed that four distinct groups of NC10 phylum bacteria (groups A, B, C and D) were present in the examined soil cores, with group B members being the dominant bacteria. The group A members, which are identified as the dominant bacteria responsible for anaerobic methane oxidation (AMO) coupled to nitrite reduction, can mainly be detected at 50-60cm. Quantitative PCR further confirmed the presence of NC10 phylum bacteria, ranging from 3·8×10(6) to 9·3×10(6) copiesg(-1) soil. The results showed the presence of diverse NC10 phylum bacteria in agricultural soils by using Illumina-based 16S rRNA gene sequencing and qPCR assays. The greatest level of diversity of NC10 phylum bacteria was reported to date in this study, which improved our understanding of the distribution of NC10 phylum bacterial communities in soil environments.

Identification and Characterization of a NaCl-Responsive Genetic Locus Involved in Survival during Desiccation in Sinorhizobium meliloti

The Rhizobiaceae are a bacterial family of enormous agricultural importance due to the ability of its members to fix atmospheric nitrogen in an intimate relationship with plants. Their survival as naturally occurring soil bacteria in agricultural soils as well as popular seed inocula is affected directly by drought and salinity. Survival after desiccation in the presence of NaCl is enabled by underlying genetic mechanisms in the model organism Sinorhizobium meliloti 1021. Since salt stress parallels a loss in water activity, the identification of NaCl-responsive loci may identify loci involved in survival during desiccation. This approach enabled identification of the loci asnO and ngg by their reduced ability to grow on increased NaCl concentrations, likely due to their inability to produce the osmoprotectant N-acetylglutaminylglutamine (NAGGN). In addition, the mutant harboring ngg::Tn5luxAB was affected in its ability to survive desiccation and responded to osmotic stress. The desiccation sensitivity may have been due to secondary functions of Ngg (N-acetylglutaminylglutamine synthetase)-like cell wall metabolism as suggested by the presence of a d-alanine-d-alanine ligase (dAla-dAla) domain and by sensitivity of the mutant to β-lactam antibiotics. asnO::Tn5luxAB is expressed during the stationary phase under normal growth conditions. Amino acid sequence similarity to enzymes producing β-lactam inhibitors and increased resistance to β-lactam antibiotics may indicate that asnO is involved in the production of a β-lactam inhibitor.

Application of PCR primer sets for detection of &amp;lt;i&amp;gt;Pseudomonas&amp;lt;/i&amp;gt; sp. functional genes in the plant rhizosphere

Plant growth promoting pseudomonads play an important role in disease suppression and there is considerable interest in development of bio-marker genes that can be used to monitor these bacteria in agricultural soils. Here, we report the application ofa PCR primer sets targeting genes encoding the main antibiotic groups. Distribution of the genes was variably distributed across type strains of 28 species with no phylogenetic groupingfor the detected antibioticsgenes, phlD for 2,4-diacetylphloroglucinol (2,4-DAPG) and phzCD for phenazine-1-carboxylic acid or hcnBC for hydrogen cyanide production. Analysis of field soils showed that primer sets for phlD and phzCD detected these genes in a fallowed neutral pH soil following wheat production, but that the copy numbers were below the detection limits in bulk soils having an acidic pH. In contrast, PCR products for the phzCD, pltc and hcnBc genes were detectable in mature root zones following plantingwith wheat. The ability to rapidly characterize populations of antibiotics producers using specific primer sets will improve our ability to assess the impacts of management practices on the functional traits of Pseudomonas spp. populations in agricultural soils.

Humic Acid-Oxidizing, Nitrate-Reducing Bacteria in Agricultural Soils

ABSTRACTThis study demonstrates the prevalence, phylogenetic diversity, and physiology of nitrate-reducing microorganisms capable of utilizing reduced humic acids (HA) as electron donors in agricultural soils. Most probable number (MPN) enumeration of agricultural soils revealed large populations (104 to 106 cells g−1 soil) of microorganisms capable of reducing nitrate while oxidizing the reduced HA analog 2,6-anthrahydroquinone disulfonate (AH2DS) to its corresponding quinone. Nitrate-dependent HA-oxidizing organisms isolated from agricultural soils were phylogenetically diverse and included members of the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Advective up-flow columns inoculated with corn plot soil and amended with reduced HA and nitrate supported both HA oxidation and enhanced nitrate reduction relative to no-donor or oxidized HA controls. The additional electron donating capacity of reduced HA could reasonably be attributed to the oxidation of reduced functional groups. Subsequent 16S rRNA gene-based high-density oligonucleotide microarray (PhyloChip) indicated that reduced HA columns supported the development of a bacterial community enriched with members of the Acidobacteria, Firmicutes, and Betaproteobacteria relative to the no-donor control and initial inoculum. This study identifies a previously unrecognized role for HA in stimulating denitrification processes in saturated soil systems. Furthermore, this study indicates that reduced humic acids impact soil geochemistry and the indigenous bacterial community composition.

Effects of land application of municipal biosolids on nitrogen-fixing bacteria in agricultural soil

Effects of municipal biosolids on microbial N2-fixation in agricultural soil were assessed in a 3-month laboratory study which included analysis of metals, pharmaceuticals, and personal care products. Reference agricultural soil was amended with organic manure or municipal biosolids from a southern Ontario wastewater plant, with a biosolids-only treatment included to evaluate metabolic activity in this inoculum. Microbial N2-fixation in reference and manure-amended soils were similar (p = 0.144) over 3 months and lower than in biosolids-amended soil (p = 0.001); however, differences among soil treatments decreased over time, with no significant difference at test termination. In general, one-time application of biosolids caused short-term stimulation of N2-fixing activity with a return to reference conditions within 3 months. Although no residual effects were detected, biosolids introduced elevated levels of metals, pharmaceuticals, personal care products (particularly analgesics), and viable bacteria; long-term effects caused by repeat applications (as commonly practiced) requires further investigation.