Leveraging microbiome rediversification for the ecological rescue of soil function.

BACKGROUND: Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples. RESULTS: Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions. CONCLUSIONS: In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.

Nutrition vs association: plant defenses are altered by arbuscular mycorrhizal fungi association not by nutritional provisioning alone.

BACKGROUND: While it is known that arbuscular mycorrhizal fungi (AMF) can improve nutrient acquisition and herbivore resistance in crops, the mechanisms by which AMF influence plant defense remain unknown. Plants respond to herbivory with a cascade of gene expression and phytochemical biosynthesis. Given that the production of defensive phytochemicals requires nutrients, a commonly invoked hypothesis is that the improvement to plant defense when grown with AMF is simply due to an increased availability of nutrients. An alternative hypothesis is that the AMF effect on herbivory is due to changes in plant defense gene expression that are not simply due to nutrient availability. In this study, we tested whether changes in plant defenses are regulated by nutritional provisioning alone or the response of plant to AMF associations. Maize plants grown with or without AMF and with one of three fertilizer treatments (standard, 2 × nitrogen, or 2 × phosphorous) were infested with fall armyworm (Spodoptera frugiperda; FAW) for 72 h. We measured general plant characteristics (e.g. height, number of leaves), relative gene expression (rtPCR) of three defensive genes (lox3, mpi, and pr5), total plant N and P nutrient content, and change in FAW mass per plant. RESULTS: We found that AMF drove the defense response of maize by increasing the expression of mpi and pr5. Furthermore, while AMF increased the total phosphorous content of maize it had no impact on maize nitrogen. Fertilization alone did not alter upregulation of any of the 3 induced defense genes tested, suggesting the mechanism through which AMF upregulate defenses is not solely via increased N or P plant nutrition. CONCLUSION: This work supports that maize defense may be optimized by AMF associations alone, reducing the need for artificial inputs when managing FAW.

Cover crop functional types differentially alter the content and composition of soil organic carbon in particulate and mineral-associated fractions.

Cover crops (CCs) can increase soil organic carbon (SOC) sequestration by providing additional OC residues, recruiting beneficial soil microbiota, and improving soil aggregation and structure. The various CC species that belong to distinct plant functional types (PFTs) may differentially impact SOC formation and stabilization. Biogeochemical theory suggests that selection of PFTs with distinct litter quality (C:N ratio) should influence the pathways and magnitude of SOC sequestration. Yet, we lack knowledge on the effect of CCs from different PFTs on the quantity and composition of physiochemical pools of SOC. We sampled soils under monocultures of three CC PFTs (legume [crimson clover]; grass [triticale]; and brassica [canola]) and a mixture of these three species, from a long-term CC experiment in Pennsylvania, USA. We measured C content in bulk soil and C content and composition in contrasting physical fractions: particulate organic matter, POM; and mineral-associated organic matter, MAOM. The bulk SOC content was higher in all CC treatments compared to the fallow. Compared to the legume, monocultures of grass and brassica with lower litter quality (wider C:N) had higher proportion of plant-derived C in POM, indicating selective preservation of complex structural plant compounds. In contrast, soils under legumes had greater accumulation of microbial-derived C in MAOM. Our results for the first time, revealed that the mixture contributed to a higher concentration of plant-derived compounds in POM relative to the legume, and a greater accumulation of microbial-derived C in MAOM compared to monocultures of grass and brassica. Mixtures with all three PFTs can thus increase the short- and long-term SOC persistence balancing the contrasting effects on the chemistries in POM and MAOM imposed by monoculture CC PFTs. Thus, despite different cumulative C inputs in CC treatments from different PFTs, the total SOC stocks did not vary between CC PFTs, rather PFTs impacted whether C accumulated in POM or MAOM fractions. This highlights that CCs of different PFTs may shift the dominant SOC formation pathways (POM vs. MAOM), subsequently impacting short- and long-term SOC stabilization and stocks. Our work provides a strong applied field test of biogeochemical theory linking litter quality to pathways of C accrual in soil.

Farm-scale differentiation of active microbial colonizers.

Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.

Cover crop mixture expression is influenced by nitrogen availability and growing degree days.

Cover crop mixtures can provide multiple ecosystem services but provisioning of these services is contingent upon the expression of component species in the mixture. From the same seed mixture, cover crop mixture expression varied greatly across farms and we hypothesized that this variation was correlated with soil inorganic nitrogen (N) concentrations and growing degree days. We measured fall and spring biomass of a standard five-species mixture of canola (Brassica napus L.), Austrian winter pea (Pisum sativum L), triticale (x Triticosecale Wittm.), red clover (Trifolium pratense L.) and crimson clover (Trifolium incarnatum L.) seeded at a research station and on 8 farms across Pennsylvania and New York in two consecutive years. At the research station, soil inorganic N (soil iN) availablity and cumulative fall growing degree days (GDD) were experimentally manipulated through fertilizer additions and planting date. Farmers seeded the standard mixture and a "farm-tuned" mixture of the same five species with component seeding rates adjusted to achieve farmer-desired services. We used Structural Equation Modeling to parse out the effects of soil iN and GDD on cover crop mixture expression. When soil iN and fall GDD were high, canola dominated the mixture, especially in the fall. Low soil iN favored legume species while a shorter growing season favored triticale. Changes in seeding rates influenced mixture composition in fall and spring but interacted with GDD to determine the final expression of the mixture. Our results show that when soil iN availability is high at the time of cover crop planting, highly competitive species can dominate mixtures which could potentially decrease services provided by other species, especially legumes. Early planting dates can exacerbate the dominance of aggressive species. Managers should choose cover crop species and seeding rates according to their soil iN and GDD to ensure the provision of desired services.

Effects of the insecticide phosmet on solitary bee foraging and nesting in orchards of Capitol Reef National Park, Utah.

Capitol Reef National Park, in southcentral Utah, contains 22 small orchards planted with antique fruit varieties by Mormon pioneers beginning over a century ago. The orchards continue to be managed in a pick-and-pay program, which includes spraying with phosmet to suppress codling moth (Cydia pomonella L.). The park is also home to a rich diversity of flowering plants, many of which are rare, bee-pollinated, and have populations within 1 km of the orchards. Over 3 yr, we studied the short-term effects of phosmet spraying on bee populations: (1) foraging on plants within the orchard understory and adjacent to it; and (2) nesting in, and at several distances from, the orchards. We recorded a rich bee fauna (47 taxa) in the orchards and on plants nearby. In 2 yr (2002 and 2004), we found no difference in the number of native bee visits to several species of plants flowering in and near to orchards immediately before and 1 d after spraying. Conversely, our nesting studies using the semidomesticated alfalfa leafcutting bee, Megachile rotundata (F.), showed strong significant declines in the number of adult males, nesting females, and progeny production subsequent to spraying at distances up to 160 m from sprayed orchards where the bees were presumably foraging. We showed that M. rotundata is negatively affected by phosmet spraying and suggest that caution should be exercised in its use in areas where bees are apt to forage.