The Combined Role of Microbes and Forages in Animal Productivity

Agricultural systems, particularly ruminant systems, are underpinned by diverse, functional microbial communities—in the soil, forage, silo, and rumen. We have relied on the jobs they perform on our behalf, but only recently have we been able to look “under the hood” at the membership and mechanisms within these microbiomes and begin to think about optimization. Ensiling is a common method of forage preservation globally and represents a highly intensive intersection between forage and microbiology, which has been shown to have beneficial effects on forage quality and dairy animal performance. However, observations of enhanced productivity, especially in the context of inoculated silages, are inconsistent. A greater understanding of the functions of, and interactions between, forage, silo, and rumen microbiomes are needed to develop best practices that align the interests of producers and their microbial communities

Native soils with their microbiotas elicit a state of alert in tomato plants

Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium). Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam‐disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil. The ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses

Fungal communities are differentially affected by conventional and biodynamic agricultural management approaches in vineyard ecosystems

There is increased need to identify sustainable agricultural methods which avoid environmental degradation. Previous studies have focused on the effect of specific agricultural interventions on large organisms, but we have fewer data evaluating how microbes, which are key components of ecosystems, might be affected. Additionally, previous studies have been constrained as they only examined one habitat in an ecosystem and have not gone on to evaluate the effect of agricultural approach on harvested crops. Here we take an ecosystems approach and evaluate the net effect of conventional versus biodynamic management on agricultural ecosystems by quantifying fungal communities in multiple habitats using metagenomics. We go on to measure biodiversity in the crop and key chemical quality parameters in the product consumed by humans. We find that the method of management significantly affects communities in soil, on plant structures, and on the developing crop in subtle but importantly different ways in terms of number, type, and abundance of species. However, management approach has no effect on communities in the final harvested juice, nor on product traits aligned with quality. This shows that while management approach impacts different habitats in the environment in different ways, this does not automatically flow onto the harvested crop

Rhizobacterial Community Assembly Patterns Vary Between Crop Species

Currently our limited understanding of crop rhizosphere community assembly hinders attempts to manipulate it beneficially. Variation in root communities has been attributed to plant host effects, soil type, and plant condition, but it is hard to disentangle the relative importance of soil and host without experimental manipulation. To examine the effects of soil origin and host plant on root associated bacterial communities we experimentally manipulated four crop species in split-plot mesocosms and surveyed variation in bacterial diversity by Illumina amplicon sequencing. Overall, plant species had a greater impact than soil type on community composition. While plant species associated with different Operational Taxonomic Units (OTUs) in different soils, plants tended to recruit bacteria from similar, higher order, taxonomic groups in different soils. However, the effect of soil on root-associated communities varied between crop species: Onion had a relatively invariant bacterial community while other species (maize and pea) had a more variable community structure. Dynamic communities could result from environment specific recruitment, differential bacterial colonization or reflect broader symbiont host range; while invariant community assembly implies tighter evolutionary or ecological interactions between plants and root-associated bacteria. Irrespective of mechanism, it appears both communities and community assembly rules vary between crop species

Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

Plant health in natural environments depends on interactions with complex and dynamic communities comprising macro- and microorganisms. While many studies have provided insights into the composition of rhizosphere microbiomes (rhizobiomes), little is known about whether plants shape their rhizobiomes. Here, we discuss physiological factors of plants that may govern plant-microbe interactions, focusing on root physiology and the role of root exudates. Given that only a few plant transport proteins are known to be involved in root metabolite export, we suggest novel families putatively involved in this process. Finally, building off of the features discussed in this review, and in analogy to well-known symbioses, we elaborate on a possible sequence of events governing rhizobiome assembly

Estimation of silage VOC emission impacts of surface-applied additives by GC-MS

Ensiling, the process of microbial acidification and preservation of wet forage for livestock feed that yields silage, produces a significant amount of volatile organic compounds (VOCs). Measurement of the chemical species involved, their emission to the atmosphere, environmental impacts, and economic losses to agricultural producers have been discussed in previous studies. Strategies for mitigation of silage VOC emission are limited and focus primarily on ensiling efficiency and silage additives at time of ensiling. However, one novel strategy employed by some producers to reduce airborne particulates, “wetting down” or applying water to rations at the feed bunk may also impact VOCs emission. We tested this method in parallel with several other chemical solutions with potential nutritional relevance for effects on VOC emission from silage.A headspace gas chromatography (GC) method was adapted for use with a paired mass spectrometer (MS) to profile silage. The effects on corn silage VOC emissions of surface-applied solutions across a range of pH, viscosity, and hydrophobicity were determined by GC-MS VOC headspace measurements. Surface-applied liquid additives included: water, citric acid, malic acid, molasses, sorghum syrup, yucca extract, seaweed extract, vegetable glycerine, olive oil, grape seed oil, and sunflower oil.Sample-to-sample variation among vials containing 5 g fresh weight (fw) silage collected from a bulked, homogenized silo sample was high, highlighting a need for sufficient replication. The most prevalent volatile acid in corn silage, acetic acid, made up the majority of observed VOCs. However, in total, eighteen VOCs were detected across all samples and the effects of treatments were assessed for each individually and for their sum as total VOC emission. Water applied to the surface of silage samples did not significantly alter VOC emissions as compared to silage alone for most VOCs. The largest observed significant effects were from the oil additives. Grape seed oil increased acetaldehyde and acetone values, while sunflower seed oil increased propionic acid and propyl acetate. Several treatments, including vegetable glycerine and seaweed extract, led to numerical decreases in VOC emissions and lower emission variability.More work is needed to understand interactions between silage VOC emissions and surface-applied mitigation strategies, including: constraining silage sample heterogeneity; investigation of the prevalence of oil-based feed additives and potential impacts on whole-farm VOC emissions; and in situ, on-farm measurements of VOC emission from treated piles

Functional Rhizosphere Microbiomes And Effects On Plant-Host Growth, Development, And Abiotic Stress Tolerance

FUNCTIONAL RHIZOSPHERE MICROBIOMES AND EFFECTS ON PLANTHOST GROWTH, DEVELOPMENT, AND ABIOTIC STRESS TOLERANCE Kevin Wayne Panke-Buisse, Ph. D. Cornell University, February, 2016 The rhizosphere microbiome is the community of microorganisms on and surrounding plant roots. This community is important for both above and below ground ecosystem functioning as well as plant growth and development. The depth and complexity of microbe-microbe and plant-microbe interactions within the rhizosphere remain largely uncharacterized. In this dissertation, I explore the rhizosphere system from three directions. First, I propose multiple levels of selection upon extracellular enzyme production and soil organic matter depolymerization as a conceptual framework for explaining the evolution of cooperative rhizospheres. Second, I demonstrate the ability to apply ecosystem-level selection to rhizosphere microcosms to assemble functional microbiomes capable of altering plant flowering phenology and biomass partitioning. I also test the ability of the assembled flowering microbiomes, and sub-communities cultivated from them, to reproduce their function in novel and familiar plant hosts. Flowering microbiomes were able to reproduce their function in several novel Arabidopsis thaliana genotypes and Brassica rapa, a family-level relative. Cultivated sub-communities displayed variability in their effects on host plant growth and development depending on the composition of the cultivation media. Two of the four cultivation media reproduced the flowering effects of the early-flowering whole microbiome from which they were cultivated. These two sub-communities also increased plant biomass in contrast to the decrease in plant biomass associated with the whole microbiome. Third, I investigate the rhizosphere microbiome of 116 closely-related tall fescue varieties under drought stress to assess the role of the rhizosphere microbiome in genotype-specific variations in abiotic stress tolerance. Differences in drought tolerance were primarily associated with shifts in microbial extracellular enzyme production and fungal endophyte infection rates over differences in bacterial community composition. This work adds to the growing understanding of the complex network of interactions within the rhizosphere and presents ecosystem selection and cultivation as a means of enhancing and characterizing microbiomemediated effects on plant growth and development. Furthermore, the parallel investigation of rhizosphere microbiome function between plant genotypes and the response of the microbiome to selective pressure begins to uncover the potential of microbial components in traditional plant breeding programs