Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.

Most U.S. farms today specialize in either crop or livestock production, failing to harness the potential economic and environmental benefits of integrated crop–livestock systems (ICLS). This specialization is particularly contradictory for organic operations, which aim to promote biodiversity and reduce reliance on outside sources of feed and fertility. This study investigated the challenges and opportunities experienced by farmers interested in integrating crops and livestock on organically managed farms in Iowa, Pennsylvania, and Minnesota. Qualitative methods, including focus groups and interviews, generated four categories of challenges: farming norms, complexity of management, biophysical conditions, and financial costs, and four categories of opportunities: increasing support for ICLS, financial and labor advantages, biophysical improvements, and animal welfare. Discussion of the data analysis demonstrates how most of the challenges of ICLS are mitigated by opportunities. For instance, increasing support for ICLS means there are growing communities of practice in which farmer-to-farmer knowledge exchange and peer support overcome obstacles to success in these systems. Unmitigated challenges that are beyond the control of farmers include regional infrastructure, financing and insurance, and long time horizon for returns. These three unmitigated challenges may require interventions such as policy support, economic incentives and social infrastructure to enable successful farm transitions to ICLS in this region.

Societal Impact Statement: Evidence has emerged that the antioxidant ergothioneine may be important in preventing many inflammatory diseases in humans. However, ergothioneine is not produced by humans or plants and is only made by fungi and some bacteria in soils. As such, humans get ergothioneine from eating fungi (mushrooms) or plants that take it up from the soil. In this study, we found that growing plants with beneficial fungi called arbuscular mycorrhizal fungi increased the amount of ergothioneine in plant tissues. This suggests that promoting agricultural practices that maintain healthy populations of beneficial soil fungi may improve the nutritional quality of crops.Summary: The amino acid ergothioneine (ERGO) has recently gained attention as an antioxidant that benefits human health. ERGO is produced by fungi and mycobacteria in soils and is acquired only from diet. The mechanism by which ERGO is transferred from soil to plant is unknown. Recent work has shown that tillage reduces the amount of ERGO in crops. As tillage also reduces arbuscular mycorrhizal fungi (AMF) populations, we examined the relationship between AMF and plant ERGO uptake. We grew asparagus, black beans, wheat, and oats with a variety of single and mixed species AMF inocula and compared ERGO levels of these plants to plants that were uninoculated. Mycorrhizal inoculation enhanced ERGO content across all plants. There was a positive correlation between AMF colonization level and plant ERGO content. AMF appear to be important mediators of plant ERGO uptake. Future research is needed to identify the mechanism that leads to higher ERGO in plants colonized by AMF in order to promote farming practices that enhance AMF populations and increase crop ERGO concentration in field settings.

Alternative grazing systems that incorporate cover crops may be useful to achieve a longer grazing season and maximize forage production. However, little is known about their impact on soil properties, especially in the presence or absence of cattle grazing in the early spring. The aim of this study was to evaluate the interacting effects of cropping systems with and without cattle grazing in rotation with corn or soybean on the balance and dynamics of soil fertility and enzyme activity. This study was conducted as a system experiment between 2015 and 2019 in Minnesota and Pennsylvania, USA. The experimental design was a randomized complete block design with four replications. Treatments included presence or absence of cattle grazing and two types of cropping systems (pasture-rye-soybean-pasture [P-R-SB-P] and pasture-wheat/vetch-corn-pasture [P-W/V-C-P]. Soil samples were collected six times during the study. Soil properties analyzed were soil pH, organic matter, salinity, K, Ca, Mg, cation exchange capacity (CEC), P, β-glucosidase, alkaline phosphatase, aryl-sulfatase, fluorescein diacetate hydrolysis, ammonium, nitrate, permanganate oxidizable carbon (POXC), N%, C%, S%, and C:N ratio. Grazing increased glucosidase activity, available Ca, Mg, NO₃⁻, NH₄⁺, soil pH, soil C%, S%, and the C:N ratio. In the P-W/V-C-P cropping system, soil pH, available Ca, NO₃⁻, and sulfatase activity were found to increase compared with the P-R-SB-P cropping system. In contrast, soil OM, available K, Mg, CEC, glucosidase, phosphatase, POXC, and total C%, N%, and S% were greater in the P-R-SB-P cropping system compared with the P-W/V-C-P cropping system. The results of this study suggested that rotational grazing can increase soil quality and microbial decomposition under the P-W/V-C-P cropping system, and that this result was greater than under the P-R-SB-P cropping system, leading to a faster nutrient cycling. These results show promise for producers who are seeking methods to diversify their farming operation and reduce the need for external inputs.

Insects harbor a variety of maternally inherited bacterial symbionts. As such, variation in symbiont presence/absence, in the combinations of harbored symbionts, and in the genotypes of harbored symbiont species provide heritable genetic variation of potential use in the insects’ adaptive repertoires. Understanding the natural importance of symbionts is challenging but studying their dynamics over time can help to elucidate the potential for such symbiont-driven insect adaptation. Toward this end, we studied the seasonal dynamics of six maternally transferred bacterial symbiont species in the multivoltine pea aphid (Acyrthosiphon pisum). Our sampling focused on six alfalfa fields in southeastern Pennsylvania, and spanned 14 timepoints within the 2012 growing season, in addition to two overwintering periods. To test and generate hypotheses on the natural relevance of these non-essential symbionts, we examined whether symbiont dynamics correlated with any of ten measured environmental variables from the 2012 growing season, including some of known importance in the lab. We found that five symbionts changed prevalence across one or both overwintering periods, and that the same five species underwent such frequency shifts across the 2012 growing season. Intriguingly, the frequencies of these dynamic symbionts showed robust correlations with a subset of our measured environmental variables. Several of these trends supported the natural relevance of lab-discovered symbiont roles, including anti-pathogen defense. For a seventh symbiont—Hamiltonella defensa—studied previously across the same study periods, we tested whether a reported correlation between prevalence and temperature stemmed not from thermally varying host-level fitness effects, but from selection on co-infecting symbionts or on aphid-encoded alleles associated with this bacterium. In general, such “hitchhiking” effects were not evident during times with strongly correlated Hamiltonella and temperature shifts. However, we did identify at least one time period in which Hamiltonella spread was likely driven by selection on a co-infecting symbiont—Rickettsiella viridis. Recognizing the broader potential for such hitchhiking, we explored selection on co-infecting symbionts as a possible driver behind the dynamics of the remaining six species. Out of twelve examined instances of symbiont dynamics unfolding across 2-week periods or overwintering spans, we found eight in which the focal symbiont underwent parallel frequency shifts under single infection and one or more co-infection contexts. This supported the idea that phenotypic variation created by the presence/absence of individual symbionts is a direct target for selection, and that symbiont effects can be robust under co-habitation with other symbionts. Contrastingly, in two cases, we found that selection may target phenotypes emerging from symbiont co-infections, with specific species combinations driving overall trends for the focal dynamic symbionts, without correlated change under single infection. Finally, in three cases—including the one described above for Hamiltonella—our data suggested that incidental co-infection with a (dis)favored symbiont could lead to large frequency shifts for “passenger” symbionts, conferring no apparent cost or benefit. Such hitchhiking has rarely been studied in heritable symbiont systems. We propose that it is more common than appreciated, given the widespread nature of maternally inherited bacteria, and the frequency of multi-species symbiotic communities across insects.

Reducing tillage has been widely promoted to reduce soil erosion, maintain soil health, and sustain long-term food production. The effects of reducing tillage on crop nutritional quality in organic and conventional systems, however, has not been widely explored. One possible driver of crop nutritional quality might be the changing soil nitrogen (N) availability associated with reduced tillage in various management systems. To test how reducing tillage affects crop nutritional quality under contrasting conventional and organic farming systems with varied N inputs, we measured nutritional quality (protein, fat, starch, ash, net energy, total digestible nutrients, and concentrations of Ca, K, Mg, P, and S) of maize, wheat, oats, and soybeans harvested from a long-term trial comprised of three farming systems under two tillage regimes: a conventional grain system (CNV); a low-input organic grain system (LEG); and an organic, manure-based grain + forage system (MNR) under conventional full-tillage (FT) and reduced-till (RT) management. Although maize and wheat yields were 10–13% lower under RT management, grain quality metrics including protein, fat, starch, energy, and mineral concentrations were not significantly affected by reducing tillage. Differences in nutrient quality were more marked between farming systems: protein levels in maize were highest in the MNR system (8.1%); protein levels in soybeans were highest in the LEG system (40.4%); levels of protein (12.9%), ash (2.0%), and sulfur (1430 ppm) in wheat were highest in the CNV system, and oat quality was largely consistent between the LEG and MNR systems. As grain quality did not significantly respond to reducing tillage, other management decisions that affect nutrient availability appear to have a greater effect on nutrient quality.