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

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

Selection on soil microbiomes reveals reproducible impacts on plant function

Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early- or late-flowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two- to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools

Selection on soil microbiomes reveals reproducible impacts on plant function.

Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early-or lateflowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two-to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools

Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing

International audienceProfiling diverse microbiomes is revolutionizing our understanding of biological mechanisms and ecologically relevant problems, including metaorganism (host + microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci has therefore become an instrumental tool for many researchers. Investigations in many systems are hindered, however, since essential sequencing depth can be lost by amplification of nontarget DNA from hosts or overabundant microorganisms. Here, we introduce “blocking oligos”, a low-cost and flexible method using standard oligonucleotides to block amplification of diverse nontargets and software to aid their design. We apply them primarily in leaves, where exceptional challenges with host amplification prevail. A. thaliana-specific blocking oligos applied in eight different target loci reduce undesirable host amplification by up to 90%. To expand applicability, we designed universal 16S and 18S rRNA gene plant blocking oligos for targets that are conserved in diverse plant species and demonstrate that they efficiently block five plant species from five orders spanning monocots and dicots (Bromus erectus, Plantago lanceolata, Lotus corniculatus, Amaranth sp., Arabidopsis thaliana). These can increase alpha diversity discovery without biasing beta diversity patterns and do not compromise microbial load information inherent to plant-derived 16S rRNA gene amplicon sequencing data. Finally, we designed and tested blocking oligos to avoid amplification of 18S rRNA genes of a sporulating oomycete pathogen, demonstrating their effectiveness in applications well beyond plants. Using these tools, we generated a survey of the A. thaliana leaf microbiome based on eight loci targeting bacterial, fungal, oomycete and other eukaryotic microorganisms and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. This approach has potential to make questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems-based insights into microbial discovery. For fast and easy design for blocking oligos for any nontarget DNA in other study systems, we developed a publicly available R package

Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time

Recent field and laboratory experiments with perennial Boechera stricta and annual Arabidopsis thaliana suggest that the root microbiota influences flowering time. Here we examined in long-term time-course experiments the bacterial root microbiota of the arctic-alpine perennial Arabis alpina in natural and controlled environments by 16S rRNA gene profiling. We identified soil type and residence time of plants in soil as major determinants explaining up to 15% of root microbiota variation, whereas environmental conditions and host genotype explain maximally 11% of variation. When grown in the same soil, the root microbiota composition of perennial A. alpina is largely similar to those of its annual relatives A. thaliana and Cardamine hirsuta. Non-flowering wild-type A. alpina and flowering pep1 mutant plants assemble an essentially indistinguishable root microbiota, thereby uncoupling flowering time from plant residence time-dependent microbiota changes. This reveals the robustness of the root microbiota against the onset and perpetual flowering of A. alpina. Together with previous studies, this implies a model in which parts of the root microbiota modulate flowering time, whereas, after microbiota acquisition during vegetative growth, the established root-associated bacterial assemblage is structurally robust to perturbations caused by flowering and drastic changes in plant stature