Cover cropping is proposed to enhance soil microbial diversity and activity, with cover crop type affecting microbial groups in different ways. We compared fungal community compositions of bulk soils differing by cover crop treatment, season, and edaphic properties in the third year of an organic, conventionally tilled rotation of corn-soybean-wheat planted with winter cover crops. We used Illumina amplicon sequencing fungal assemblages to evaluate effects of nine treatments, each replicated four times, consisting of six single winter cover crop species, a three-species mixture, a six-species mixture, and fallow. Alpha-diversity of fungal communities was not affected by cover crop species identity, function, or diversity. Sampling season influenced community composition as well as genus-level abundances of arbuscular mycorrhizal (AM) fungi. Cover crop mixtures, specifically the three-species mixture, had distinct AM fungal community compositions, while cereal rye and forage radish monocultures had unique Core OTU compositions. Soil texture, pH, permanganate oxidizable carbon, and chemical properties including Cu, and P were important variables in models of fungal OTU distributions across groupings. These results showed how fungal composition and potential functions were shaped by cover crop treatment as well as soil heterogeneity.Microbial diversity is an important aspect of soil health, as soil microbial communities mediate many biogeochemical processes and are sensitive to disturbances that can lead to long-lasting ecosystem effects 1 . Greater richness and evenness in the representation of bacteria and fungi in soils can help mitigate plant responses to environmental stressors 2 . With the advent of high-throughput DNA sequencing technologies that allow for more detailed genetic information, we can determine if and how microbial compositions shift in response to disturbance and edaphic differences and, to some degree, what those changes may mean for ecosystem processes.Cover cropping is the practice of growing ground-covering crops during the intervals between successive cash crops. Cover cropping imparts numerous benefits to soil, including the addition of organic carbon (C) from roots, root exudates, and aboveground residues and the improvement of soil structure and tilth 3-5 . Ecosystem services provided by cover crops include protection from soil erosion, enhanced soil water-holding capacity, reduced weed colonization and growth, plant resilience to pathogens and increased crop yield 5,6 . Legume cover crops provide biologically fixed nitrogen (N), while grasses take up excess soil inorganic N and improve N retention. A complete suite of ecosystem services is not deliverable by any one cover crop species. Thus, planting mixtures of cover crops has been proposed as a means to provide varied combinations of ecosystem services based on the functional traits of individual cover crop species 5,7-10 .Cover crops may alter microbial community diversity and function by varying the types and composition of exuded C...

Biotic stresses including fungal infections result in increased production of flavonoid compounds, including 3-deoxyanthocyanidins (3-DAs) in the leaf tissues of Sorghum bicolor (L.) Moench. Our objectives were to determine if sorghum genotypic variation influenced root flavonoid and 3-DA concentrations and rhizosphere microbial communities and to identify how these relationships were impacted by abiotic stress. We evaluated root chemicals and rhizosphere microbiomes of five near-isogenic lines of sorghum before and after a late-season frost. Roots were analyzed for total flavonoids, total phenolics, 3-DA concentrations and antioxidant activity. Amplicon sequencing of 16S rRNA genes and ITS regions was performed on rhizosphere soils. Concentrations of luteolinidin (a 3-DA) and total flavonoids differed between several lines before frost, but these relationships changed after frost. Luteolinidin increased in three lines after frost, while total flavonoids decreased in all the lines after frost. Lines that differed in luteolinidin and total flavonoid concentrations before frost were different from those after frost. Rhizosphere community compositions also differed before and after frost, but only fungal community compositions differed among sorghum lines. Bacterial community compositions were highly correlated with total flavonoid and luteolinidin concentrations. Furthermore, a greater number of bacterial taxa were correlated with total flavonoids and luteolinidin compared to fungal taxa. Collectively, this study provides evidence that plant genotypic variation influences root flavonoids and rhizosphere community composition and that these relationships are impacted by frost. Plant-microbe interactions and secondary metabolite production may be important components to include for selective breeding of sorghum for frost stress tolerance.

Cave ecosystems are carbon limited and thus are particularly susceptible to anthropogenic pollution. Yet, how carbon quality and quantity that can modulate the pathways and amount of Mn cycling in caves remains largely unknown. To explore Mn cycling, baseline bacterial, archaeal, and fungal com-munities associated with Mn(III/ IV) oxide deposits were assessed in both relatively 'pristine' and anthropogenically impacted caves in the Appalachian Mountains (USA). Cave sites were then amended with various carbon sources that are commonly associated with anthropogenic input to determine whether they stimulate biotic Mn(II) oxidation in situ. Results revealed patterns between sites that had long-term exogenous carbon loading compared to sites that were relatively 'pristine,' particularly among Bacteria and Archaea. Carbon treatments that stimulated Mn(II) oxidation at several sites resulted in significant changes to the microbial communities, indicating that anthropogenic input can not only enhance biotic Mn(II) oxidation, but also shape community structure and diversity. Additional carbon sources amended with copper were incubated at various cave sites to test the role that Cu(II) plays in in situ biotic Mn(II) oxidation. Media supplemented with 100 lM Cu(II) inhibited bacterial Mn(II) oxidation but stimulated fungal Mn(II) oxidation, implicating fungal use of multicopper oxidase (MCO) enzymes but bacterial use of superoxide to oxidize Mn(II). In sites with low C:N ratios, the activity of the Mn(II) oxidizing enzyme manganese peroxidase (MnP) appears to be limited (particularly by MnP-utilizing Basidiomycetes and/or Zygomycetes).

Worldwide, arable soils have been degraded through erosion and exhaustive cultivation, and substantial proportions of fertilizer nutrients are not taken up by crops. A central challenge in agriculture is to understand how soils and resident microbial communities can be managed to deliver nutrients to crops more efficiently with minimal losses to the environment. Throughout much of the twentieth century, intensive farming has caused substantial loss of organic matter and soil biological function. Today, more farmers recognize the importance of protecting soils and restoring organic matter through reduced tillage, diversified crop rotation, cover cropping, and increased organic amendments. Such management practices are expected to foster soil conditions more similar to those of undisturbed, native plant-soil systems by restoring soil biophysical integrity and re-establishing plant-microbe interactions that retain and recycle nutrients. Soil conditions which could contribute to desirable shifts in microbial metabolic processes include lower redox potentials, more diverse biogeochemical gradients, higher concentrations of labile carbon, and enrichment of carbon dioxide (CO 2 ) and hydrogen gas (H 2 ) in soil pores. This paper reviews recent literature on generalized and specific microbial processes that could become more operational once soils are no longer subjected to intensive tillage and organic matter depletion. These processes include heterotrophic assimilation of CO 2 ; utilization of H 2 as electron donor or reactant; and more diversified nitrogen uptake and dissimilation pathways. Despite knowledge of these processes occurring in laboratory studies, they have received little attention for their potential to affect nutrient and energy flows in soils. This paper explores how soil microbial processes could contribute to in situ nutrient retention, recycling, and crop uptake in agricultural soils managed for improved biological function.