Differential structure and function of phosphorus-mineralizing microbial communities in organic and upper mineral soil horizons across a temperate rainforest chronosequence.

Microbial community structure and function were assessed in the organic and upper mineral soil across a ~4000-year dune-based chronosequence at Big Bay, New Zealand, where total P declined and the proportional contribution of organic soil in the profile increased with time. We hypothesized that the organic and mineral soils would show divergent community evolution over time with a greater dependency on the functionality of phosphatase genes in the organic soil layer as it developed. The structure of bacterial, fungal, and phosphatase-harbouring communities was examined in both horizons across 3 dunes using amplicon sequencing, network analysis, and qPCR. The soils showed a decline in pH and total phosphorus (P) over time with an increase in phosphatase activity. The organic horizon had a wider diversity of Class A (phoN/phoC) and phoD-harbouring communities and a more complex microbiome, with hub taxa that correlated with P. Bacterial diversity declined in both horizons over time, with enrichment of Planctomycetes and Acidobacteria. More complex fungal communities were evident in the youngest dune, transitioning to a dominance of Ascomycota in both soil horizons. Higher phosphatase activity in older dunes was driven by less diverse P-mineralizing communities, especially in the organic horizon.

Cover Crops Modulate the Response of Arbuscular Mycorrhizal Fungi to Water Supply: A Field Study in Corn.

Cover crops (CCs) were found to improve soil health by increasing plant diversity and ground cover. They may also improve water supply for cash crops by reducing evaporation and increasing soil water storage capacity. However, their influence on plant-associated microbial communities, including symbiotic arbuscular mycorrhizal fungi (AMF), is less well understood. In a corn field trial, we studied the response of AMF to a four-species winter CC, relative to a no-CC control, as well as to two contrasting water supply levels (i.e., drought and irrigated). We measured AMF colonization of corn roots and used Illumina MiSeq sequencing to study the composition and diversity of soil AMF communities at two depths (i.e., 0-10 and 10-20 cm). In this trial, AMF colonization was high (61-97%), and soil AMF communities were represented by 249 amplicon sequence variants (ASVs) belonging to 5 genera and 33 virtual taxa. Glomus, followed by Claroideoglomus and Diversispora (class Glomeromycetes), were the dominant genera. Our results showed interacting effects between CC treatments and water supply levels for most of the measured variables. The percentage of AMF colonization, arbuscules, and vesicles tended to be lower in irrigated than drought sites, with significant differences detected only under no-CC. Similarly, soil AMF phylogenetic composition was affected by water supply only in the no-CC treatment. Changes in the abundance of individual virtual taxa also showed strong interacting effects between CCs, irrigation, and sometimes soil depth, although CC effects were clearer than irrigation effects. An exception to these interactions was soil AMF evenness, which was higher in CC than no-CC, and higher under drought than irrigation. Soil AMF richness was not affected by the applied treatments. Our results suggest that CCs can affect the structure of soil AMF communities and modulate their response to water availability levels, although soil heterogeneity could influence the final outcome.

Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin.

Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.

Functionality of methane cycling microbiome during methane flux hot moments from riparian buffer systems.

Riparian buffer systems (RBS) are a common agroforestry practice that involves maintaining a forested boundary adjacent to water bodies to protect the aquatic ecosystems in agricultural landscapes. While RBS have potential for carbon sequestration, they also can be sources of methane emissions. Our study site at Washington Creek in Southern Ontario, includes a rehabilitated tree buffer (RH), a grassed buffer (GRB), an undisturbed deciduous forest (UNF), an undisturbed coniferous forest (CF), and an adjacent agricultural field (AGR). The objective of this study was to assess the diversity and activity of CH4 cycling microbial communities in soils sampled during hot moments of methane fluxes (July 04 and August 15). We used qPCR and high-throughput amplicon sequencing from both DNA and cDNA to target methanogen and methanotroph communities. Methanogens, including the archaeal genera Methanosaeta, Methanosarcina, Methanomassiliicoccus, and Methanoreggula, were abundant in all RBSs, but they were significantly more active in UNF soils, where CH4 emissions were highest. Methylocystis was the most prevalent taxon among methanotrophs in all the riparian sites, except for AGR soils where the methanotrophs community was composed primarily of members of rice paddy clusters (RPCs and RPC-1) and upland soil clusters (TUSC and USCα). The main factors influencing the composition and assembly of methane-cycling microbiomes were soil carbon and moisture content. We concluded that the differences in CH4 fluxes observed between RBSs were primarily caused by differences in the presence and activity of methanogens, which were influenced by total soil carbon and water content. Overall, this study emphasizes the importance of understanding the microbial drivers of CH4 fluxes in RBSs in order to maximize RBS environmental benefits.

Cover crop-driven shifts in soil microbial communities could modulate early tomato biomass via plant-soil feedbacks.

Sustainable agricultural practices such as cover crops (CCs) and residue retention are increasingly applied to counteract detrimental consequences on natural resources. Since agriculture affects soil properties partly via microbial communities, it is critical to understand how these respond to different management practices. Our study analyzed five CC treatments (oat, rye, radish, rye-radish mixture and no-CC) and two crop residue managements (retention/R+ or removal/R-) in an 8-year diverse horticultural crop rotation trial from ON, Canada. CC effects were small but stronger than those of residue management. Radish-based CCs tended to be the most beneficial for both microbial abundance and richness, yet detrimental for fungal evenness. CC species, in particular radish, also shaped fungal and, to a lesser extent, prokaryotic community composition. Crop residues modulated CC effects on bacterial abundance and fungal evenness (i.e., more sensitive in R- than R+), as well as microbial taxa. Several microbial structure features (e.g., composition, taxa within Actinobacteria, Firmicutes and Ascomycota), some affected by CCs, were correlated with early biomass production of the following tomato crop. Our study suggests that, whereas mid-term CC effects were small, they need to be better understood as they could be influencing cash crop productivity via plant-soil feedbacks.

Root Functional Trait and Soil Microbial Coordination: Implications for Soil Respiration in Riparian Agroecosystems.

Predicting respiration from roots and soil microbes is important in agricultural landscapes where net flux of carbon from the soil to the atmosphere is of large concern. Yet, in riparian agroecosystems that buffer aquatic environments from agricultural fields, little is known on the differential contribution of CO2 sources nor the systematic patterns in root and microbial communities that relate to these emissions. We deployed a field-based root exclusion experiment to measure heterotrophic and autotrophic-rhizospheric respiration across riparian buffer types in an agricultural landscape in southern Ontario, Canada. We paired bi-weekly measurements of in-field CO2 flux with analysis of soil properties and fine root functional traits. We quantified soil microbial community structure using qPCR to estimate bacterial and fungal abundance and characterized microbial diversity using high-throughput sequencing. Mean daytime total soil respiration rates in the growing season were 186.1 ± 26.7, 188.7 ± 23.0, 278.6 ± 30.0, and 503.4 ± 31.3 mg CO2-C m-2 h-1 in remnant coniferous and mixed forest, and rehabilitated forest and grass buffers, respectively. Contributions of autotrophic-rhizospheric respiration to total soil CO2 fluxes ranged widely between 14 and 63% across the buffers. Covariation in root traits aligned roots of higher specific root length and nitrogen content with higher specific root respiration rates, while microbial abundance in rhizosphere soil coorindated with roots that were thicker in diameter and higher in carbon to nitrogen ratio. Variation in autotrophic-rhizospheric respiration on a soil area basis was explained by soil temperature, fine root length density, and covariation in root traits. Heterotrophic respiration was strongly explained by soil moisture, temperature, and soil carbon, while multiple factor analysis revealed a positive correlation with soil microbial diversity. This is a first in-field study to quantify root and soil respiration in relation to trade-offs in root trait expression and to determine interactions between root traits and soil microbial community structure to predict soil respiration.

Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand.

The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).

Identification of degrader bacteria and fungi enriched in rhizosphere soil from a toluene phytoremediation site using DNA stable isotope probing.

Improved knowledge of the ecology of contaminant-degrading organisms is paramount for effective assessment and remediation of aromatic hydrocarbon-impacted sites. DNA stable isotope probing was used herein to identify autochthonous degraders in rhizosphere soil from a hybrid poplar phytoremediation system incubated under semi-field-simulated conditions. High-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes in metagenomic samples separated according to nucleic acid buoyant density was used to identify putative toluene degraders. Degrader bacteria were found mainly within the Actinobacteria and Proteobacteria phyla and classified predominantly as Cupriavidus, Rhodococcus, Luteimonas, Burkholderiaceae, Azoarcus, Cellulomonadaceae, and Pseudomonas organisms. Purpureocillium lilacinum and Mortierella alpina fungi were also found to assimilate toluene, while several strains of the fungal poplar endophyte Mortierella elongatus were indirectly implicated as potential degraders. Finally, PICRUSt2 predictive taxonomic functional modeling of 16S rRNA genes was performed to validate successful isolation of stable isotope-labeled DNA in density-resolved samples. Four unique sequences, classified within the Bdellovibrionaceae, Intrasporangiaceae, or Chitinophagaceae families, or within the Sphingobacteriales order were absent from PICRUSt2-generated models and represent potentially novel putative toluene-degrading species. This study illustrates the power of combining stable isotope amendment with advanced metagenomic and bioinformatic techniques to link biodegradation activity with unisolated microorganisms. Novelty statement: This study used emerging molecular biological techniques to identify known and new organisms implicated in aromatic hydrocarbon biodegradation from a field-scale phytoremediation system, including organisms with phyto-specific relevance and having potential for downstream applications (amendment or monitoring) in future and existing systems. Additional novelty in this study comes from the use of taxonomic functional modeling approaches for validation of stable isotope probing techniques. This study provides a basis for expanding existing reference databases of known aromatic hydrocarbon degraders from field-applicable sources and offers technological improvements for future site assessment and management purposes.

Riparian land-use systems impact soil microbial communities and nitrous oxide emissions in an agro-ecosystem.

Riparian buffer systems (RBS) are considered a best management practice (BMP) in agricultural landscapes to intercept soil nitrogen (N) and phosphorus (P) leaching and surface runoff into aquatic ecosystems. However, these environmental benefits could be offset by increased greenhouse gas (GHG) emissions, including nitrous oxide (N2O). The main sources of N2O in soil are linked to processes which are mediated by soil microbial communities. These microorganisms play crucial roles in N-cycling and in the reduction of nitrate to N2, and N2O gases. This study was conducted to determine the abundance and diversity of microbial communities and functional genes associated with N-cycling and their influence on N2O emissions in different riparian land-use: undisturbed natural forest (UNF), rehabilitated site (RH), grass buffer (GRB), and an adjacent agricultural land (AGR). Soil was sampled concurrently with N2O emissions on July 13, 2017. DNA was extracted and used to target key N-cycling genes for N-fixation (nifH), nitrification: (amoA), and denitrification (nirS, nirK, and nosZ) via quantitative PCR, and for high throughput sequencing of total bacterial and fungal communities. Non-metric multidimensional scaling (NMDS) was used to examine microbial community composition and indicated significant differences in bacterial (p < 0.001) and fungal (p < 0.0085) communities between sites. Bacterial abundance differed significantly (p = 0.0005) between RBS and AGR sites with the highest populations occurring in the UNF (2.1 × 1010 copies g-1 dry soil), and lowest in AGR (5.3 × 109 copies g-1 dry soil). However, the AGR site had the highest ammonia-oxidizing bacteria (AOB) abundance, indicating that nitrification is highest at this site. The abundance of the nosZ gene was highest in RH and GRB demonstrating the capacity for complete denitrification at these sites, lowering measured N2O. These results suggest N-cycling microbial community dynamics differ among RBS and are influencing N2O emissions in the sites investigated.

Hygienization and microbial metabolic adaptation during anaerobic co-digestion of swine manure and corn stover.

This study assessed the effect of different swine manure (SM)/corn stover (CS) mixtures based on total solids (TS) content with respect to hygienization, microbial community dynamics and methane yields on batch anaerobic co-digestion performance. Different ratios of SM and CS with TS content between 0.69 and 6% digested at 75 d revealed SM had the greatest methane yield at 403.9 mL g-1 volatile solids added (VS) and 86.31% VS reduction. BIOLOG AN microplates and lignocellulolytic enzyme assays proved to be rapid tools for characterizing microbial community metabolism as noted by the different carbon source utilization patterns between TS loadings. Hygienization of fecal indicator bacteria groups was achieved with some (E. coli) but not all groups (Clostridia spp.). The results showed that colorimetric biochemical assays and culture-based techniques can rapidly assess microbial community dynamics during co-digestion, and that TS- in the form of lignocellulosic biomass- influences microbial metabolic activities.

Quantification of toluene phytoextraction rates and microbial biodegradation functional profiles at a fractured bedrock phytoremediation site.

This field study evaluated the efficacy of a mature hybrid poplar phytoremediation system for the remediation of toluene in a fractured bedrock aquifer site. Phytoextraction activity of the trees and the ecology and biodegradation potential of root-colonizing bacteria that ultimately influence how much toluene is transported from the roots and phytoextracted to the aboveground point of measurement were explored. Peak-season toluene mass removal rates ranging from 313 to 743 µg/day were quantified using passive in planta contaminant sampling techniques and continuous heat dissipation transpiration measurements in tree stems. Root bacterial microbiome structure and biodegradation potential were evaluated via high-throughput sequencing and predictive metagenomic functional modelling of bacterial 16S rRNA genes in roots. Poplar roots were colonized mostly by Proteobacteria, Actinobacteria, and Bacteroidetes. Distinct, more uniform communities were observed in roots associated with trees planted in the toluene source area compared to other areas, with differences apparent at lower taxonomic levels. Significant enrichment of Streptomyces in roots was observed in the source area, implicating that genus as a potentially important poplar endophyte at toluene-impacted sites. Moreover, significantly greater aerobic toluene biodegradation capacity was predicted in these roots compared to other areas using taxonomic functional modelling. Together with passive sampling, the molecular results provided supporting evidence of biodegradation activity in the source area and contextualized the detected phytoextraction patterns. These results support the application of phytoremediation systems for aromatic hydrocarbons in environments with complex geology and demonstrate field-validated monitoring techniques to assess phytoextraction and biodegradation in these systems.

Assessing toluene biodegradation under temporally varying redox conditions in a fractured bedrock aquifer using stable isotope methods.

In complex hydrogeological settings little is known about the extent of temporally varying redox conditions and their effect on aromatic hydrocarbon biodegradation. This study aims to assess the impact of changing redox conditions over time on aromatic hydrocarbon biodegradation in a fractured bedrock aquifer using stable isotope methods. To that end, four snapshots of highly spatio-temporally resolved contaminant and redox sensitive species concentrations, as well as stable isotope ratio profiles, were determined over a two-years time period in summer 2016, spring 2017, fall 2017 and summer 2018 in a toluene contaminated fractured bedrock aquifer. The concentration profiles of redox sensitive species and stable isotope ratio profiles for dissolved inorganic carbon (DIC) and sulfate (δ13CDIC, δ34SSO4, δ18OSO4) revealed that the aquifer alternates between oxidising (spring 2017/summer 2018) and reducing conditions (summer 2016/fall 2017). This alternation was attributed to a stronger aquifer recharge with oxygen-rich meltwater in spring 2017/summer 2018 compared to summer 2016/fall 2017. The temporally varying redox conditions coincided with various extents of toluene biodegradation revealed by the different magnitude of heavy carbon (13C) and hydrogen (2H) isotope enrichment in toluene. This indicated that the extent of toluene biodegradation and its contribution to plume attenuation was controlled by the temporally changing redox conditions. The highest toluene biodegradation was observed in summer 2016, followed by spring 2017 and fall 2017, whereby these temporal changes in biodegradation occurred throughout the whole plume. Thus, under temporally varying recharge conditions both the core and the fringe of a contaminant plume can be replenished with terminal electron acceptors causing biodegradation in the whole plume and not only at its distal end as previously suggested by the plume fringe concept. Overall, this study highlights the importance of highly temporally resolved groundwater monitoring to capture temporally varying biodegradation rates and to accurately predict biodegradation-induced contaminant attenuation in fractured bedrock aquifers.

Wildfire severity reduces richness and alters composition of soil fungal communities in boreal forests of western Canada.

Wildfire is the dominant disturbance in boreal forests and fire activity is increasing in these regions. Soil fungal communities are important for plant growth and nutrient cycling postfire but there is little understanding of how fires impact fungal communities across landscapes, fire severity gradients, and stand types in boreal forests. Understanding relationships between fungal community composition, particularly mycorrhizas, and understory plant composition is therefore important in predicting how future fire regimes may affect vegetation. We used an extreme wildfire event in boreal forests of Canada's Northwest Territories to test drivers of fungal communities and assess relationships with plant communities. We sampled soils from 39 plots 1 year after fire and 8 unburned plots. High-throughput sequencing (MiSeq, ITS) revealed 2,034 fungal operational taxonomic units. We found soil pH and fire severity (proportion soil organic layer combusted), and interactions between these drivers were important for fungal community structure (composition, richness, diversity, functional groups). Where fire severity was low, samples with low pH had higher total fungal, mycorrhizal, and saprotroph richness compared to where severity was high. Increased fire severity caused declines in richness of total fungi, mycorrhizas, and saprotrophs, and declines in diversity of total fungi and mycorrhizas. The importance of stand age (a surrogate for fire return interval) for fungal composition suggests we could detect long-term successional patterns even after fire. Mycorrhizal and plant community composition, richness, and diversity were weakly but significantly correlated. These weak relationships and the distribution of fungi across plots suggest that the underlying driver of fungal community structure is pH, which is modified by fire severity. This study shows the importance of edaphic factors in determining fungal community structure at large scales, but suggests these patterns are mediated by interactions between fire and forest stand composition.

Impact of long-term phosphorus fertilizer inputs on bacterial phoD gene community in a maize field, Northeast China.

The bacterial phoD gene encodes alkaline phosphomonoesterase, an enzyme which plays an important role in the release of plant-available inorganic phosphorus (P) from organic P in soil. However, the relationships between phoD gene community, alkaline phosphomonoesterase activity, and P availability in soil are poorly understood. In this study, we investigated how alkaline phosphomonoesterase activity, phoD gene abundance, and community structure are influenced by plant-available P using soils (0-10, 10-20 and 20-40 cm) from a long-term field trial in which a continuous maize (Zea mays L.) crop had received different levels of P fertilizer inputs (30, 60 kg P ha-1 year-1) for 28 years. Quantitative PCR and high-throughput sequencing were used to analyze phoD gene abundance and community composition. Alkaline phosphomonoesterase enzyme activity was negatively correlated with soil available P, which was reflected in corresponding data for phoD gene abundance. On the other hand, positive correlations were determined between phoD gene α-diversity and available P, while shifts in phoD gene community structure were related to changes in soil pH and P availability. The relative abundance of Pseudomonas was negatively correlated with P availability and positively correlated with alkaline phosphomonoesterase activity, suggesting that Pseudomonas may play an important role in soil organic P mineralization. The findings of this study demonstrated that changes of soil P availability as a result of long-term P fertilizer inputs significantly affected alkaline phosphomonoesterase activity by regulating phoD gene abundance, diversity, as well as altering the phoD gene community composition.

Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis.

Biodegradation is an important mechanism of action of phytoremediation systems, but performance evaluation is challenging. We applied metagenomic molecular approaches and compound-specific stable carbon isotope analysis to assess biodegradation of toluene in the vadose zone at an urban pilot field system where hybrid poplars were planted to remediate legacy impacts to an underlying shallow fractured bedrock aquifer. Carbon isotope ratios were compared spatio-temporally between toluene dissolved in groundwater and in the vapor phase. Enrichment of 13C from toluene in the vapor phase compared to groundwater provided evidence for biodegradation in the vadose zone. Total bacterial abundance (16S rRNA) and abundance and expression of degradation genes were determined in rhizosphere soil (DNA and RNA) and roots (DNA) using quantitative PCR. Relative abundances of degraders in the rhizosphere were on average higher at greater depths, except for enrichment of PHE-encoding communities that more strongly followed patterns of toluene concentrations detected. Quantification of RMO and PHE gene transcripts supported observations of active aerobic toluene degradation. Finally, spatially-variable numbers of toluene degraders were detected in poplar roots. We present multiple lines of evidence for biodegradation in the vadose zone at this site, contributing to our understanding of mechanisms of action of the phytoremediation system.

Spatial variability of microbial communities in a fractured sedimentary rock matrix impacted by a mixed organics plume.

Dissolved phase contaminants, transported by diffusion into the low permeability matrix of fractured sedimentary rock, pose a challenge to groundwater cleanup efforts because this stored mass may persist even when the upgradient source zone is removed. In this context, if contaminant biodegradation takes place within the low permeability matrix, plume persistence may be substantially reduced. Therefore, it is important to characterize microbial communities within the low permeability, rock matrix pores, instead of only from groundwater samples, which represent biomass from fast flowing fractures. This research relies on depth-discrete data from both core and groundwater samples collected from two locations representing a mid-plume and plume front condition within an aged, mixed organic contaminant plume in a sedimentary rock aquifer. Results from multiple analyte measurements on rock and groundwater indicate that biodegradation in the lower permeability matrix of fractured sedimentary rocks and the microbial consortia is spatially variable due to differences in hydrochemistry, redox conditions, and contaminant concentrations. Dechlorinating microorganisms were detected in the sandstone matrix at both locations, but the detected microbial diversity calculated with PCR-DGGE was significantly higher in samples collected from the core located closer to the source zone, where contaminant concentrations are higher and contaminant compositions more diverse, compared to samples from the plume front location.

Effects of 30 Years of Crop Rotation and Tillage on Bacterial and Archaeal Ammonia Oxidizers.

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) both mediate soil nitrification and may have specialized niches in the soil. Little is understood of how these microorganisms are affected by long-term crop rotation and tillage practices. In this study, we assessed abundance and gene expression of AOB and AOA under two contrasting crop rotations and tillage regimes at a 30-yr-old long-term experiment on a Canadian silt loam soil. Continuous corn ( L.) (CC) was compared with a corn-corn-soybean [ (L.) Merr.]-winter wheat ( L.) rotation under-seeded with red clover ( L.) (RC), with conventional tillage (CT) and no-till (NT) as subplot treatments. Soil sampling was performed during the first corn year at four time points throughout the 2010 season and at three discrete depths (0-5, 5-15, and 15-30 cm). Overall, AOA abundance was found to be more than 10 times that of AOB, although AOA transcriptional activity was below detectable levels across all treatments. Crop rotation had a marginally significant effect on AOB abundance, with 1.3 times as many gene copies under the simpler CC rotation than under the more diverse RC rotation. More pronounced effects of depth on AOB abundance and gene expression were observed under NT versus CT management, and NT supported higher abundances of total archaea and AOA than CT across the growing season. We suggest that AOB may be more functionally important than AOA in this high-input agricultural soil but that NT management can promote enhanced soil archaeal populations.

Metagenomic Comparison of Antibiotic Resistance Genes Associated with Liquid and Dewatered Biosolids.

Municipal biosolids (MBs) that are land-applied in North America are known to possess an active microbial population that can include human pathogens. Activated sludge is a hotspot for the accumulation of antibiotics and has been shown to be a selective environment for microorganisms that contain antibiotic resistance genes (ARGs); however, the prevalence of ARGs in MBs is not well characterized. In this study, we enriched the plasmid metagenome from raw sewage sludge and two CP2 MBs, a mesophilic anaerobic digestate and a dewatered digestate, to evaluate the presence of ARGs in mobile genetic elements. The CP2-class biosolids are similar to Class B biosolids in the United States. The CP2 biosolids must meet a microbiological cut off of 2 × 10 colony-forming units (CFU) per dry gram or 100 mL of biosolids. The enriched plasmid DNA was sequenced (Illumina MiSeq). Sequence matching against databases, including the Comprehensive Antibiotic Resistance Database (CARD), MG-RAST, and INTEGRALL, identified potential genes of interest related to ARGs and their ability to transfer. The presence and abundance of different ARGs varied between treatments with heterogeneity observed among the same sample types. The MBs plasmid-enriched metagenomes contained ARGs associated with resistance to a variety of antibiotics, including ß-lactams, rifampicin, quinolone, and tetracycline as well as the detection of extended spectrum ß-lactamase genes. Cultured bacteria from CP2 MBs possessed antibiotic resistances consistent with the MBs metagenome data including multiantibiotic-resistant isolates. The results from this study provide a better understanding of the ARG and MGE profile of the plasmid-enriched metagenome of CP2 MBs.

Micrometeorological measurements over 3 years reveal differences in N2 O emissions between annual and perennial crops.

Perennial crops can deliver a wide range of ecosystem services compared to annual crops. Some of these benefits are achieved by lengthening the growing season, which increases the period of crop water and nutrient uptake, pointing to a potential role for perennial systems to mitigate soil nitrous oxide (N2 O) emissions. Employing a micrometeorological method, we tested this hypothesis in a 3-year field experiment with a perennial grass-legume mixture and an annual corn monoculture. Given that N2 O emissions are strongly dependent on the method of fertilizer application, two manure application options commonly used by farmers for each crop were studied: injection vs. broadcast application for the perennial; fall vs. spring application for the annual. Across the 3 years, lower N2 O emissions (P < 0.001) were measured for the perennial compared to the annual crop, even though annual N2 O emissions increased tenfold for the perennial after ploughing. The percentage of N2 O lost per unit of fertilizer applied was 3.7, 3.1 and 1.3 times higher for the annual for each consecutive year. Differences in soil organic matter due to the contrasting root systems of these crops are probably a major factor behind the N2 O reduction. We found that a specific manure management practice can lead to increases or reductions in annual N2 O emissions depending on environmental variables. The number of freeze-thaw cycles during winter and the amount of rainfall after fertilization in spring were key factors. Therefore, general manure management recommendations should be avoided because interannual weather variability has the potential to determine if a specific practice is beneficial or detrimental. The lower N2 O emissions of perennial crops deserve further research attention and must be considered in future land-use decisions. Increasing the proportion of perennial crops in agricultural landscapes may provide an overlooked opportunity to regulate N2 O emissions.