Recruitment of microorganisms to the rhizosphere varies among plant genotypes, yet an understanding of whether the microbiome can be altered by selection on the host is relatively unknown. Here, we ...performed a common garden study to characterize recruitment of rhizosphere microbiome, functional groups, for 20 expired Plant Variety Protection Act maize lines spanning a chronosequence of development from 1949 to 1986. This time frame brackets a series of agronomic innovations, namely improvements in breeding and the application of synthetic nitrogenous fertilizers, technologies that define modern industrial agriculture. We assessed the impact of chronological agronomic improvements on recruitment of the rhizosphere microbiome in maize, with emphasis on nitrogen cycling functional groups. In addition, we quantified the microbial genes involved in nitrogen cycling and predicted functional pathways present in the microbiome of each genotype. Both genetic relatednesses of host plant and decade of germplasm development were significant factors in the recruitment of the rhizosphere microbiome. More recently developed germplasm recruited fewer microbial taxa with the genetic capability for sustainable nitrogen provisioning and larger populations of microorganisms that contribute to N losses. This study indicates that the development of high-yielding varieties and agronomic management approaches of industrial agriculture inadvertently modified interactions between maize and its microbiome.
Background and aims Soil microbial communities influence nutrient cycling, chemistry and structure of soil, and plant productivity. In turn, agronomic practices such as fertilization and crop ...rotation alter soil physical and chemical properties and consequently soil microbiomes. Understanding the long-term effects of agronomic practices on soil microbiomes is essential for improving agronomic practices to optimize these microbial communities for agricultural sustainability. We examine the composition and substrate-utilization profiles of microbial communities at the Morrow Plots in Illinois. Methods Microbial community composition is assessed with 16S rRNA gene sequencing and subsequent bioinformatic analyses. Community-level substrate utilization is characterized with the BIOLOG EcoPlate. Results Fertilizer and rotation treatments significantly affected microbial community structure, while substrate utilization was affected by fertilizer, but not croprotation treatments. Differences in relative abundance and occurrence of bacterial taxa found in fertilizer treatments can explain the observed differences in community level substrate utilization. Conclusion Long-term fertilization and crop-rotation treatments affect soil microbial community composition and physiology, specifically through chronic nutrient limitation, long-term influx of microbes and organic matter via manure application, as well as through changes in soil chemistry. Relatively greater abundance of Koribacteraceae and Solibacterales taxa in soils might prove useful as indicators of soil degradation.
While large inputs of synthetic nitrogen fertilizers enable our current rate of crop production and feed a growing global population, these fertilizers come at a heavy environmental cost. Driven by ...microbial processes, excess applied nitrogen is lost from agroecosystems as nitrate and nitrous oxide (N2O) contaminating aquatic ecosystems and contributing to climate change. Interest in nitrogen-fixing microorganisms as an alternative to synthetic fertilizers is rapidly accelerating. Microbial inoculants offer the promise of a sustainable and affordable source of nitrogen, but the impact of inoculants on nitrogen dynamics at an ecosystem level is not fully understood. This review synthesizes recent studies on microbial inoculants as tools for nutrient management and considers the ramifications of inoculants for nitrogen transformations beyond fixation.
Nitrogen-fixing microbial inoculants are widely studied as alternatives to synthetic nitrogen fertilizers.Some microbial inoculants may aid in mitigating nitrous oxide (N2O) emissions from agriculture. However, other inoculant formulations can exacerbate N2O emissions, further contributing to greenhouse gas emissions.Although nitrate leaching from agroecosystems poses a serious environmental threat, whether inoculants mitigate or exacerbate nitrification is poorly understood.Microbial inoculants can have off-target effects, including disruption of resident microbial community structure and increased nitrogen losses.
Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. ...Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes.
Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA bacterial and archaeal, nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system.
Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.
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.
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.
Perennial tall grasses sustain high biomass yield with minimal synthetic nitrogen (N) fertilizer, potentially by leveraging biological N fixation and nitrification inhibition. Enhancing these traits through research and breeding can further reduce their reliance on N fertilizer and thereby support more resilient and environmentally sustainable agricultural systems, while also tackling global energy challenges.
Understanding how historical and contemporary environmental conditions interact to affect the relationship between community structure and function is necessary to predict the response of microbial ...community function to a changing environment. We focused on nitrogen transformations – denitrification and nitrification – which directly impact nitrate concentration in wetland ecosystems. Nitrate removal can occur via denitrification, while nitrate can be generated through nitrification; these two microbial transformations are strongly influenced by hydrology and redox conditions. We carried out a manipulative mesocosm experiment to determine how microbial communities adapted to different hydrologic conditions (upland vs. wetland) respond to experimental soil moisture treatments (dry, wet-dry, saturated). We assessed local soil characteristics (e.g., soil moisture, inorganic nitrogen), and microbial community composition and activity of denitrifiers and ammonia oxidizers (targeted by the nosZ and amoA genes, respectively) before and after moisture treatments. Wetland soils were characterized by higher soil fertility compared to upland soils. In response to the drying/flooding treatments, we observed a small but significant change in community composition of denitrifier assemblages, but no change in the ammonia oxidizer communities. In addition, potential denitrification rates significantly increased under wetter conditions (upland: 62–118% increase; wetland: 78–96% increase), whereas potential nitrification rates generally showed no significant change following experimental drying/flooding treatments, regardless of the hydrologic history. Based on these results, fluctuations in soil moisture are expected to influence denitrification rates to a greater extent than nitrification rates, ultimately influencing nitrate pools in this wetland. This imbalance in microbial functional response may result in a shift in dominant nitrogen cycling transformations within a wetland as a consequence of the different responses of these nitrogen-cycling functional guilds to changes in soil moisture. A shift in nitrogen transformations can be most noticeable under fluctuating hydrologic conditions, and there is potential for the wetland to be resilient to hydrologic change if soil microbes are exposed to dynamic hydrology over the long-term.
•Microorganisms are influenced by historical and contemporary abiotic conditions.•We manipulated moisture conditions for microbes adapted to contrasting hydrology.•Denitrification responded to moisture treatments more than nitrification.•Microbial communities remained relatively unchanged in response to drying/wetting.•Sensitivity to drying/wetting depends on historical hydrologic conditions.
Snake Fungal Disease (SFD), caused by Ophidiomyces ophiodiicola, is the most recently described fungal disease afflicting wildlife populations across North America and Europe. It has been proposed as ...a significant conservation threat yielding high mortality and yet much its ecology is unknown. We collected 144 skin swabs from Eastern Massasaugas (Sistrurus catenatus) in 2015 and 2016 to determine document ongoing prevalence and assess differences in microbial assemblages between positive and negative individuals. Alpha diversity of fungi was reduced in SFD positive animals, while beta diversity identified distinct assemblages of microbes between SFD-positive and -negative samples. Ophidiomyces was present on the skin of affected animals, even on body sites distant to lesions indicating that the microbiome on entire surface of the skin is altered. Ophidiomyces was not detected in any non-SFD snake. There were smaller, but significant, influences of year sampled. Bacterial genera Janthinobacterium and Serratia were significantly increased in SFD snakes, while Xylanimicrobium, Cellulosimicrobium, and Rhodococcus were the only bacterial taxa significantly reduced. The relative abundance of fungi within the orders Pleosporales and Canopdiales was reduced in SFD-positive samples, though Pyrenochaetopsis pratorum was the only species found to differ significantly. This is the first study to determine the impact that this fungal pathogen has on the skin microbiome.
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.
The gastrointestinal (GI) microbiome contributes significantly to host nutrition and health. However, relationships involving GI microbes, their hosts and host macrohabitats remain to be established. ...Here, we define clear patterns of variation in the GI microbiomes of six groups of Mexican black howler monkeys (Alouatta pigra) occupying a gradation of habitats including a continuous evergreen rainforest, an evergreen rainforest fragment, a continuous semi-deciduous forest and captivity. High throughput microbial 16S ribosomal RNA gene sequencing indicated that diversity, richness and composition of howler GI microbiomes varied with host habitat in relation to diet. Howlers occupying suboptimal habitats consumed less diverse diets and correspondingly had less diverse gut microbiomes. Quantitative real-time PCR also revealed a reduction in the number of genes related to butyrate production and hydrogen metabolism in the microbiomes of howlers occupying suboptimal habitats, which may impact host health.
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