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The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Despite the importance of propagule pressure to species introductions, few tools exist in microbial ecology to predict the outcomes of agricultural microbial introductions. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the riskrelease relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. Applying ecological modeling approaches like those presented here to microbial inoculants may aid their sustainable use and provide a monitoring tool for microbial inoculants. [ABSTRACT FROM AUTHOR]

Continuous maize (Zea mays L.) (CM) cropping has been proposed to increase soil organic carbon stocks through greater residue return to soils. These residues, however, can contribute to a yield decrease known as the continuous maize yield penalty (CMYP). The objectives of this research were to (1) evaluate the efficacy of residue management practices to mitigate the CMYP when compared to a maize–soybean [Glycine max (L.) Merr.] (MS) rotation and (2) determine effects of long‐term rotation or residue sizing on soil microbial communities and carbon‐cycling enzyme activities. Two long‐term sites (17 and 19 years) with replicated blocks of CM and MS rotation were used. The yield response to management was similar at both sites, with an average CMYP of 2570 kg ha−1 with no residue management, while chopping the residue along with broadcast ammonium sulfate (AMS) reduced the CMYP by 728 kg ha−1 (28.3%). The CMYP was further reduced when a microbial blend was applied with AMS to the sized residues, reducing the CMYP by a total of 1303 kg ha−1 (50.7%). Soil bacterial communities differed by site but were unchanged by crop rotation or residue sizing. Soil fungal assemblage, particularly arbuscular mycorrhizal fungi, was influenced by rotation and site. Sizing of residues resulted in higher soil cellobiohydrolase activity for CM, but not for MS. These findings indicate that the CMYP was not directly associated with the soil bacterial community, and that management to mitigate the CMYP may be aided by elevated levels of fungal diversity under CM. Core Ideas: The yield penalty of continuous maize can be mitigated by agronomic practices without need for residue removal.Residue management practices, when combined, reduced the yield penalty up to 50%.Long‐term crop rotation effects on microbial communities were site‐specific.Soil bacterial communities were relatively similar after 17 or 19 years of continuous maize.Soil fungal assemblage was influenced by crop rotation and site. [ABSTRACT FROM AUTHOR]

Perennial tall grasses show promise as bioenergy crops due to high productivity and efficient nutrient use. Ongoing research on bioenergy grasses seeks to reduce their reliance on synthetic nitrogen (N) fertilizer, the manufacture of which relies on fossil fuel combustion. Excessive use of fertilizers also causes adverse environmental consequences and leads to the evolutionary loss of plant traits beneficial to sustainable N cycle. Notably, perennial tall grasses have exhibited the potential to maintain high biomass yield without the need for N fertilizer or causing soil N depletion. Perennial grasses can be adept at interacting with their microbial partners to facilitate N acquisition and retention via mechanisms such as biological N fixation and nitrification inhibition. These inherent N management traits should be preserved and optimized at the this early stage of bioenergy grass breeding programs. This review examines the impact of external N on bioenergy grass production and explores the potential of leveraging advantageous N‐cycling attributes of perennial tall grasses, laying groundwork for future management and research efforts. With minimized dependency on external N input, the cultivation of perennial energy grasses will pave the way toward more resilient agricultural systems and play a significant role in addressing key global energy and environmental challenges. [ABSTRACT FROM AUTHOR]

Altering plant carbon allocation from leaves to stems is key to improve biomass for forage, fuel, and renewable chemicals. The sorghum dry stalk (D) locus controls a quantitative trait for sugar accumulation, with enhanced carbon allocation in the stems of juicy green (dd) sorghum but reduced carbon allocation in that of dry white (DD) sorghum. However, it remains unclear whether altering sorghum sugar accumulation in stem affects below‐ground microbiome. Here we investigated sorghum rhizosphere soil microbiome in near isogenic lines with different magnitude of carbon allocations and accumulation in the stems. Results showed that enhanced carbon accumulation in stems of juicy green sorghum results in stronger selection in rhizosphere microbiome assembly. The rhizosphere soil microbial communities selected in juicy green sorghum tended to be fast‐growing microbial taxa which possessed potential functions that would promote higher potential capacity to use chemically labile carbon sources and potentially result in higher potential decomposition rates. We found the rhizosphere microbes selected by juicy green sorghum form weaker interactions than dry white sorghum. This is the first comprehensive study revealing how the different magnitude of carbon allocations to stems regulates microbial community assembly, microbial interaction, and microbial functions. This study indicates that future plant modification for bioenergy crops should also consider the impacts on belowground microbial community without compromising the sustainability. [ABSTRACT FROM AUTHOR]

Bioenergy could help limit global warming to 2°C above pre‐industrial levels while supplying almost a fourth of the world's renewable energy needs by 2050. However, the deployment of bioenergy raises concerns that adoption at meaningful scales may lead to unintended negative environmental consequences. Meanwhile, the full consolidation of a bioenergy industry is currently challenged by a sufficient, resilient, and resource‐efficient biomass supply and an effective conversion process. Here, we provide a comprehensive analysis of how stable isotope approaches have accelerated the development of a robust bioeconomy by advancing knowledge about environmental sustainability, feedstock development, and biological conversion. We show that advances in stable isotope research have generated crucial information to (1) gain mechanistic insight into the potential of bioenergy crops to mitigate climate change as well as their impact on water and nutrient cycling; (2) develop high‐yielding, resilient feedstocks that produce high‐value bioproducts in planta; and (3) engineer microbes to enhance feedstock conversion to bioenergy products. Further, we highlight knowledge gaps that could benefit from future research facilitated by stable isotope approaches. We conclude that advances in mechanistic knowledge and innovations within the field of stable isotopes in cross‐disciplinary research actions will greatly contribute to breaking down the barriers to establishing a robust bioeconomy. [ABSTRACT FROM AUTHOR]

Plants have a surprising capacity to alter their environmental conditions to create adequate niches for survival and stress tolerance. This process of environmental transformation, commonly referred to as "extended phenotypes" or "niche construction", has historically been studied in the domain of ecology, but this is a process that is pervasive across the plant kingdom. Furthermore, research is beginning to show that plants' extended phenotypes shape the assembly and function of closely associated microbial communities. Incorporation and understanding the role that plant-extended phenotypes play in agriculture may offer novel, bioinspired methods to manage our arable soil microbiomes. Here, we review the challenges agriculture faces, the plant extended phenotypes we know to shape the microbiome, and the potential utilization of this knowledge to improve the environmental impact of agriculture. Understanding how plant extended phenotypes shape microbial communities could be a key to creating a sustainable future with both plants and microbiomes in consideration. [ABSTRACT FROM AUTHOR]

Two primer sets for automated ribosomal intergenic spacer analysis (ARISA) are used for assessing the bacterial community composition (BCC) in Lake Mendota, Wisconsin. The analysis has shown that ARISA is a powerful tool for evaluating the changes in BCC through space and time, regardless of the specific primer set used.

Background: Assessments of the soil microbiome provide valuable insight to ecosystem function due to the integral role microorganisms play in biogeochemical cycling of carbon and nutrients. For example, treatment effects on nitrogen cycling functional groups are often presented alongside one another to demonstrate how agricultural management practices affect various nitrogen cycling processes. However, the functional groups commonly evaluated in nitrogen cycling microbiome studies range from phylogenetically narrow (e.g., N-fixation, nitrification) to broad [e.g., denitrification, dissimilatory nitrate reduction to ammonium (DNRA)]. The bioinformatics methods used in such studies were developed for 16S rRNA gene sequence data, and how these tools perform across functional genes of different phylogenetic diversity has not been established. For example, an OTU clustering method that can accurately characterize sequences harboring comparatively little diversity may not accurately resolve the diversity within a gene comprised of a large number of clades. This study uses two nitrogen cycling genes, nifH, a gene which segregates into only three distinct clades, and nrfA, a gene which is comprised of at least eighteen clades, to investigate differences which may arise when using heuristic OTU clustering (abundance-based greedy clustering, AGC) vs. true hierarchical OTU clustering (Matthews Correlation Coefficient optimizing algorithm, Opti-MCC). Detection of treatment differences for each gene were evaluated to demonstrate how conclusions drawn from a given dataset may differ depending on clustering method used. Results: The heuristic and hierarchical methods performed comparably for the more conserved gene, nifH. The hierarchical method outperformed the heuristic method for the more diverse gene, nrfA; this included both the ability to detect treatment differences using PERMANOVA, as well as higher resolution in taxonomic classification. The difference in performance between the two methods may be traced to the AGC method’s preferential assignment of sequences to the most abundant OTUs: when analysis was limited to only the largest 100 OTUs, results from the AGC-assembled OTU table more closely resembled those of the Opti-MCC OTU table. Additionally, both AGC and Opti-MCC OTU tables detected comparable treatment differences using the rank-based ANOSIM test. This demonstrates that treatment differences were preserved using both clustering methods but were structured differently within the OTU tables produced using each method. Conclusion: For questions which can be answered using tests agnostic to clustering method (e.g., ANOSIM), or for genes of relatively low phylogenetic diversity (e.g., nifH), most upstream processing methods should lead to similar conclusions from downstream analyses. For studies involving more diverse genes, however, care should be exercised to choose methods that ensure accurate clustering for all genes. This will mitigate the risk of introducing Type II errors by allowing for detection of comparable treatment differences for all genes assessed, rather than disproportionately detecting treatment differences in only low-diversity genes. [ABSTRACT FROM AUTHOR]

The agricultural imprints on soil microbial processes manifest at various timescales, leaving many temporal patterns to present slowly. Unfortunately, the lack of long-term continuous agricultural field sites in North America has left gaps in our understanding of agricultural management on biogeochemical processes and their controlling microbiota. Nitrification, ammonium oxidation by bacteria and archaea, is a critical control point in terrestrial nitrogen fluxes by oxidizing cationic ammonium to anionic nitrate, promoting nitrate leaching. Moreover, nitrous oxide is produced during nitrification, contributing to massive nitrous oxide emissions from fertilized agroecosystems. Nitrification is sensitive to many macro and micro-ecological filters, as nitrifiers are obligate aerobes and are sensitive to numerous non-growth substrates and metal ions. This study sought to understand the long-term implications of various rotation and fertilizer regimes on nitrification potential and nitrifying bacterial communities in the Morrow Plots (Urbana, IL). The Morrow Plots was established in 1876 and are the longest continuous field experiments in North America, making it the only site in America capable of assessing the impact of over 140 years of agricultural management on nitrification. The Morrow Plots contrasts fertilizer (manure, inorganic, unfertilized) and rotation (continuous corn, corn-soy, corn-oat alfalfa), allowing us to explore how conventional vs. regenerative agriculture practices impact nitrifier communities. The results of this study suggest that fertilizer and rotation interact to promote distinct bacterial nitrifier communities. Nitrification potential is highest in manure corn-oat-alfalfa plots, suggesting ammonium availability is not solely responsible for active nitrifier communities. Various soil chemical variables, like CEC, Mg, and Ca, significantly influenced nitrifier community beta-diversity, using 16S rRNA amplicon sequencing, suggesting long-term accumulation of specific cations diverge microbial community assembly. While this study only uses nitrification potential enzyme activity instead of isotope analyses, it sheds light on the importance of various physiochemical drivers on nitrification potential and communities. The results support the need for a more precise exploration of the mechanisms controlling field-scale nitrification rates over large temporal scales. Put together, this study supports the importance of long-term field sites for understanding agricultural manipulations of microbial biogeochemical cycling and sheds light on the micronutrients influencing nitrifier communities and potential activity. [ABSTRACT FROM AUTHOR]

Biological nitrification inhibition (BNI) and plant–microbe competition for ammonium (NH4+) by sorghum (Sorghum bicolor (L.) Moench) have the potential to suppress nitrification, reducing nitrate (NO3−) and nitrous oxide (N2O) production for more sustainable bioenergy feedstock production. However, it is unknown how variability in environmental factors, field management, and plant growth affect the suppression of nitrification. We conducted a field trial with four genotypes of energy sorghum and four fertilization rates in central Illinois, USA, and measured soil N pools, potential nitrification and denitrification rates, and microbial community composition in bulk and rhizosphere soils to assess nitrification suppression throughout the 2018 and 2019 growing seasons. Concentrations of NO3− and NH4+ were very low in rhizosphere soil regardless of fertilization level, suggesting strong N demand by plants and microbes. Potential nitrification was lower in the rhizosphere soil than bulk soil, and this suppression was strongest mid‐season ~2 months after planting in both years (20% suppression in 2018 and 58% in 2019). Since precipitation was lower during the mid‐growing season of 2019 compared to 2018, we speculate that hydrophilic BNI root exudates accumulated in the rhizosphere and suppressed nitrification more than in 2018 when soil moisture was higher. Unfertilized plots had greater nitrification suppression than fertilized plots during the mid‐season in 2018, but otherwise nitrification suppression was insensitive to fertilizer treatment. Potential denitrification was stimulated in the rhizosphere compared to bulk soil in both study years, suggesting that heterotrophic activity was stimulated by plant carbon inputs, possibly further suppressing slower‐growing chemoautotrophic nitrifying microbes. Overall, we found inter‐ and intra‐annual variation in nitrification suppression in the rhizosphere of field‐grown biomass sorghum, suggesting that plant phenology and environmental conditions should be considered when devising strategies to improve the nitrogen sustainability of this annual bioenergy crop. [ABSTRACT FROM AUTHOR]

Abstract Since the first estimate of prokaryotic abundance in soil was published, researchers have attempted to assess the abundance and distribution of species and relate this information on community structure [...]

Foam accumulation in swine manure deep-pits has been linked to explosions and flash fires that pose devastating threats to humans and livestock. It is clear that methane accumulation within these pits is the fuel for the fire; it is not understood what microbial drivers cause the accumulation and stabilization of methane. Here, we conducted a 13-month field study to survey the physical, chemical, and biological changes of pit-manure across 46 farms in Iowa. Our results showed that an increased methane production rate was associated with less digestible feed ingredients, suggesting that diet influences the storage pit's microbiome. Targeted sequencing of the bacterial 16S rRNA and archaeal mcrA genes was used to identify microbial communities' role and influence. We found that microbial communities in foaming and non-foaming manure were significantly different, and that the bacterial communities of foaming manure were more stable than those of non-foaming manure. Foaming manure methanogen communities were enriched with uncharacterized methanogens whose presence strongly correlated with high methane production rates. We also observed strong correlations between feed ration, manure characteristics, and the relative abundance of specific taxa, suggesting that manure foaming is linked to microbial community assemblage driven by efficient free long-chain fatty acid degradation by hydrogenotrophic methanogenesis. [ABSTRACT FROM AUTHOR]

A comparative study was conducted to understand the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial functions was found to be influenced by composition of bacterial communities and soil fertility and the denitrifying populations could potential use for the development of predictive models for restoration of biogeochemical transformations and improve the success of wetland restoration efforts.

The functionality of the terminal restriction fragment length polymorphism (T-RFLP) method is expanded by automating the task of phylogenetic assignment from the T-RF profiles produced by multiple digests. The use of multiple digests increases the specificity of polygenetic inferences derived from the T-RFLP profiles, and automation of this task makes this type of analysis accessible for analysis of complex communities.

Summary: Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio‐environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers. [ABSTRACT FROM AUTHOR]

Biochar application is a promising approach to decrease nitrous oxide (N 2 O) emissions from agricultural soils, yet little is known about how biochar affects N 2 O-producing and consuming microbial processes under changing field conditions. We conducted a field study to assess if growing season patterns in soil N 2 O emissions were correlated with the underlying microbial processes of nitrification and denitrification. We measured soil N 2 O emissions, potential nitrification and denitrification rates, and the abundance of key soil nitrogen (N)-cycling functional genes in an intensive maize production field trial in Illinois, USA that included the following four treatments: Control (unamended), Biochar (100 Mg ha −1 ), Nitrogen (269 kg N ha −1 as Urea Ammonium Nitrate fertilizer), and Biochar + Nitrogen (100 Mg ha −1 and 269 kg N ha −1 , respectively). Biochar increased potential nitrification rates when soil ammonium concentrations were high following fertilizer application, thus enhancing N 2 O emissions in the Biochar + Nitrogen treatment early in the season which were likely nitrification-associated. However, over the full growing season, biochar application reduced cumulative N 2 O emissions in Biochar + Nitrogen plots to levels similar to the unamended Control. This could be attributed to biochar suppression of potential denitrification throughout the growing season. The treatments amended with biochar avoided large pulses of N 2 O emissions following intense rain events in the mid-season, while also sustaining lower N 2 O emissions in the late-season. Our study demonstrates that biochar can have dynamic effects on soil N 2 O emissions and the underlying microbial processes that depend on changing edaphic conditions, such as soil inorganic nitrogen availability and moisture, over the growing season. [ABSTRACT FROM AUTHOR]