A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants.

The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint-based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome scale metabolic models of bacteria associated with a specific disease-suppressive vs disease-conducive apple rhizospheres were drafted based on genome-resolved metagenomes, comprising an in silico native microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.

Effect of Rootstock Genotype and Arbuscular Mycorrhizal Fungal (AMF) Species on Early Colonization of Apple.

The effect of plant cultivar on the degree of mycorrhization and the benefits mediated by arbuscular mycorrhizal fungi (AMF) have been documented in many crops. In apple, a wide variety of rootstocks are commercially available; however, it is not clear whether some rootstock genotypes are more susceptible to mycorrhization than others and/or whether AMF species identity influences rootstock compatibility. This study addresses these questions by directly testing the ability/efficacy of four different AMF species (Rhizophagus irregularis, Septoglomus deserticola, Claroideoglomus claroideum or Claroideoglomus etunicatum) to colonize a variety of commercially available Geneva apple rootstock genotypes (G.11, G.41, G.210, G.969, and G.890). Briefly, micropropagated plantlets were inoculated with individual species of AMF or were not inoculated. The effects of the rootstock genotype/AMF interaction on mycorrhization, plant growth, and/or leaf nutrient concentrations were assessed. We found that both rootstock genotype and the identity of the AMF are significant sources of variation affecting the percentage of colonization. However, these factors largely operate independently in terms of the extent of root colonization. Among the AMF tested, C. etunicatum and R. irregularis represented the most compatible fungal partners, regardless of apple rootstock genotype. Among the rootstocks tested, semi-dwarfing rootstocks appeared to have an advantage over dwarfing rootstocks in regard to establishing and maintaining associations with AMF. Nutrient uptake and plant growth outcomes were also influenced in a rootstock genotype/AMF species-specific manner. Our findings suggest that matching host genetics with compatible AMF species has the potential to enhance agricultural practices in nursery and orchard systems.

A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data.

BACKGROUND: The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment. RESULTS: This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from 'sick' vs 'healthy/recovered' rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The potential of two of these metabolites (dopamine and vitamin B12) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant's potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at https://github.com/ot483/NetCom2 . CONCLUSIONS: This research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems. Video Abstract.

Toward a holistic view of orchard ecosystem dynamics: A comprehensive review of the multiple factors governing development or suppression of apple replant disease.

Replant diseases are a common occurrence in perennial cropping systems. In apple, progress toward the development of a universally effective disease management strategy, beyond the use of broad-spectrum soil fumigants, is impeded by inconsistencies in defining replant disease etiology. A preponderance of evidence attributes apple replant disease to plant-induced changes in the soil microbiome including the proliferation of soilborne plant pathogens. Findings from alternative studies suggest that the contribution of abiotic factors, such as the accumulation of phenolic detritus from previous orchard plantings, may play a part as well. Engineering of the resident soil microbiome using resource-based strategies is demonstrating potential to limit activity of replant pathogens and improve productivity in newly established orchards. An understanding of factors promoting the assembly of a disease-suppressive soil microbiome along with consideration of host factors that confer disease tolerance or resistance is imperative to the developing a more holistic view of orchard ecosystem dynamics. Here, we review the literature concerning the transition of orchard soil from a healthy state to a replant disease-conducive state. Included in the scope of this review are studies on the influence of soil type and geography on the apple replant pathogen complex. Furthermore, several tolerance and innate resistance mechanisms that have been described in apple to date, including the role of root chemistry/exudates are discussed. Finally, the interplay between apple rootstock genotype and key resource-based strategies which have been shown to "reshape" the plant holobiont in favor of a more prophylactic or disease-suppressive state is highlighted.

Comparative Analysis of the Apple Root Transcriptome as Affected by Rootstock Genotype and Brassicaceae Seed Meal Soil Amendment: Implications for Plant Health.

Brassicaceae seed meal (SM) soil amendment has been utilized as an effective strategy to control the biological complex of organisms, which includes oomycetes, fungi, and parasitic nematodes, that incites the phenomenon termed apple replant disease. Soil-borne disease control attained in response to Brassicaceae SM amendment is reliant on multiple chemical and biological attributes, including specific SM-generated modifications to the soil/rhizosphere microbiome. In this study, we conducted a comparative analyses of apple root gene expression as influenced by rootstock genotype combined with a seed meal (SM) soil amendment. Apple replant disease (ARD) susceptible (M.26) and tolerant (G.210) rootstocks cultivated in SM-amended soil exhibited differential gene expression relative to corresponding non-treated control (NTC) orchard soil. The temporal dynamics of gene expression indicated that the SM-amended soil system altered the trajectory of the root transcriptome in a genotype-specific manner. In both genotypes, the expression of genes related to plant defense and hormone signaling were altered in SM-amended soil, suggesting SM-responsive phytohormone regulation. Altered gene expression was temporally associated with changes in rhizosphere microbiome density and composition in the SM-treated soil. Gene expression analysis across the two rootstocks cultivated in the pathogen-infested NTC soil showed genotype-specific responses indicative of different defensive strategies. These results are consistent with previously described resistance mechanisms of ARD "tolerant" rootstock cultivars and also add to our understanding of the multiple mechanisms by which SM soil amendment and the resulting rhizosphere microbiome affect apple rootstock physiology. Future studies which assess transcriptomic and metagenomic data in parallel will be important for illuminating important connections between specific rhizosphere microbiota, gene-regulation, and plant health.

Energetic differences between bacterioplankton trophic groups and coral reef resistance.

Coral reefs are among the most productive and diverse marine ecosystems on the Earth. They are also particularly sensitive to changing energetic requirements by different trophic levels. Microbialization specifically refers to the increase in the energetic metabolic demands of microbes relative to macrobes and is significantly correlated with increasing human influence on coral reefs. In this study, metabolic theory of ecology is used to quantify the relative contributions of two broad bacterioplankton groups, autotrophs and heterotrophs, to energy flux on 27 Pacific coral reef ecosystems experiencing human impact to varying degrees. The effective activation energy required for photosynthesis is lower than the average energy of activation for the biochemical reactions of the Krebs cycle, and changes in the proportional abundance of these two groups can greatly affect rates of energy and materials cycling. We show that reef-water communities with a higher proportional abundance of microbial autotrophs expend more metabolic energy per gram of microbial biomass. Increased energy and materials flux through fast energy channels (i.e. water-column associated microbial autotrophs) may dampen the detrimental effects of increased heterotrophic loads (e.g. coral disease) on coral reef systems experiencing anthropogenic disturbance.

Unraveling the unseen players in the ocean - a field guide to water chemistry and marine microbiology.

Here we introduce a series of thoroughly tested and well standardized research protocols adapted for use in remote marine environments. The sampling protocols include the assessment of resources available to the microbial community (dissolved organic carbon, particulate organic matter, inorganic nutrients), and a comprehensive description of the viral and bacterial communities (via direct viral and microbial counts, enumeration of autofluorescent microbes, and construction of viral and microbial metagenomes). We use a combination of methods, which represent a dispersed field of scientific disciplines comprising already established protocols and some of the most recent techniques developed. Especially metagenomic sequencing techniques used for viral and bacterial community characterization, have been established only in recent years, and are thus still subjected to constant improvement. This has led to a variety of sampling and sample processing procedures currently in use. The set of methods presented here provides an up to date approach to collect and process environmental samples. Parameters addressed with these protocols yield the minimum on information essential to characterize and understand the underlying mechanisms of viral and microbial community dynamics. It gives easy to follow guidelines to conduct comprehensive surveys and discusses critical steps and potential caveats pertinent to each technique.