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Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines' rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

Pasture degradation hinders livestock production and ecosystem services that support rural smallholder communities throughout Latin America. Silvopastoral systems, with improved pasture cultivars (especially Brachiaria spp.) and multipurpose trees, offer a promising strategy to restore soils and improve livelihoods in the region. However, studies evaluating the impact of such systems on pasture productivity and soil health under realistic smallholder constraints are lacking. We evaluated the impact of improved pasture grass and tree establishment on a suite of soil health indicators in actively grazed, low-input, farmer-managed silvopastoral systems. In August 2013, paired pasture treatments (improved grass with trees vs. traditional pastures) were established on nine farms with similar land-use histories near Matagalpa, Nicaragua. On each farm, one treatment was left as traditional pasture with naturalized grass (Hyparrhenia rufa), while the adjacent treatment was sown with the improved grass (Brachiaria brizantha cv. Marandu) and planted with tree saplings without fertilizer. In August 2015, we measured standing biomass and a suite of chemical, biological, and physical soil health variables. Improved silvopastoral systems with B. brizantha produced more standing grass biomass and supported higher levels of earthworm populations and permanganate oxidizable carbon (POXC) compared to the traditional control. Correlations suggest that earthworms and POXC were associated with incipient improvements to soil aggregate stability and water holding capacity. We report measurable improvements to soil health just two years following the establishment of improved pasture systems under common smallholder management practices and suggest that these systems, even with minimal fertility inputs, have the potential to enhance regional sustainability.

Introduction: Integrated crop-livestock systems (ICLS) use animals to graze crop residues or cover crops before planting fresh produce and provide ecosystem services to support organic vegetable production. However, there is a risk of foodborne pathogen transfer to fresh produce because grazing may introduce enteric foodborne pathogens into the soil via animal feces, which may subsequently be transferred to the produce. Methods: To examine the effect of cover crop use and the risk of cover crop grazing on the contamination of soil and produce by foodborne pathogens in ICLS, a three-year (2019–2021) experimental study was conducted in organically managed plots, which were assigned three different treatments (fallow without cover crop or grazing, cover crop without grazing, or cover crop with grazing by sheep) in a maize/tomato rotation. During the three years of the experiment, a total of 184 pre- and post-graze fecal samples and 96 samples of tomatoes were collected to test for foodborne pathogens (Escherichia coli O157, non-O157 Shiga toxin-producing Escherichia coli (STEC), and Listeria (L.) monocytogenes). Soil samples were collected monthly until 126–171 days after grazing (824 in total) to examine the presence of foodborne pathogens, and generic E. coli (MPN/g) was quantified to compare its persistence among the three treatments. Results and Discussion: We did not detect any foodborne pathogens from harvested tomatoes in 2020 and 2021. One non-O157 STEC positive soil sample (0.1%, 1/824) was detected in the fallow treatment, and one L. monocytogenes-positive (1.1%, 1/92) was detected from the post-graze fecal samples. When assessing proportions of generic E. coli positive and counts of generic E. coli in the soil samples using mixed effect zero-inflated negative binomial models, soil samples collected in the graze cover crop treatment plot showed significant increases in the counts of generic E. coli until 61–82 days post grazing, but no difference was observed after 96–123 days, compared to the baseline of the fallow treatment. Findings from generic E. coli counts support the use of the United States Department of Agriculture (USDA) National Organic Program (NOP) 90- or 120-day interval rule between applying raw manure and harvesting in organic farming into ICLS. Additionally, we confirmed that commercial organic compost application before cover crop seeding in the winter had no significant effect on the proportions and counts of generic E. coli in the soil of the following growing seasons. This longitudinal field trial confirmed that the effect of sheep grazing on foodborne pathogen contamination in ICLS is minimal but further studies comparing the genetic associations between fecal and soil samples would be necessary to distinguish the source of foodborne pathogen contamination.

There is an urgent need to develop climate smart agroecosystems capable of mitigating climate change and adapting to its effects. In California, high commodity prices and increased frequency of drought have encouraged orchard turnover, providing an opportunity to recycle tree biomass in situ prior to replanting an orchard. Whole orchard recycling (WOR) has potential as a carbon (C) negative cultural practice to build soil C storage, soil health, and orchard productivity. We tested the potential of this practice for long term C sequestration and hypothesized that associated co-benefits to soil health will enhance sustainability and resiliency of almond orchards to water-deficit conditions. We measured soil health metrics and productivity of an almond orchard following grinding and incorporation of woody biomass vs. burning of old orchard biomass 9 years after implementation. We also conducted a deficit irrigation trial with control and deficit irrigation (-20%) treatments to quantify shifts in tree water status and resilience. Biomass recycling led to higher yields and substantial improvement in soil functioning, including nutrient content, aggregation, porosity, and water retention. This practice also sequestered significantly higher levels of C in the topsoil (+5 t ha-1) compared to burning. We measured a 20% increase in irrigation water use efficiency and improved soil and tree water status under stress, suggesting that in situ biomass recycling can be considered as a climate smart practice in California irrigated almond systems.

Production systems that feature temporal and spatial integration of crop and livestock enterprises, also known as integrated crop-livestock systems (ICLS), have the potential to intensify production on cultivated lands and foster resilience to the effects of climate change without proportional increases in environmental impacts. Yet, crop production outcomes following livestock grazing across environments and management scenarios remain uncertain and a potential barrier to adoption, as producers worry about the effects of livestock activity on the agronomic quality of their land. To determine likely production outcomes across ICLS and to identify the most important moderating variables governing those outcomes, we performed a meta-analysis of 66 studies comparing crop yields in ICLS to yields in unintegrated controls across 3 continents, 12 crops, and 4 livestock species. We found that annual cash crops in ICLS averaged similar yields (-7% to +2%) to crops in comparable unintegrated systems. The exception was dual-purpose crops (crops managed simultaneously for grazing and grain production), which yielded 20% less on average than single-purpose crops in the studies examined. When dual-purpose cropping systems were excluded from the analysis, crops in ICLS yielded more than in unintegrated systems in loamy soils and achieved equal yields in most other settings, suggesting that areas of intermediate soil texture may represent a "sweet-spot" for ICLS implementation. This meta-analysis represents the first quantitative synthesis of the crop production outcomes of ICLS and demonstrates the need for further investigation into the conditions and management scenarios under which ICLS can be successfully implemented.

Increasing soil organic carbon (SOC) via organic inputs is a key strategy for increasing long-term soil C storage and improving the climate change mitigation and adaptation potential of agricultural systems. A long-term trial in California's Mediterranean climate revealed impacts of management on SOC in maize-tomato and wheat-fallow cropping systems. SOC was measured at the initiation of the experiment and at year 19, at five depth increments down to 2 m, taking into account changes in bulk density. Across the entire 2 m profile, SOC in the wheat-fallow systems did not change with the addition of N fertilizer, winter cover crops (WCC), or irrigation alone and decreased by 5.6% with no inputs. There was some evidence of soil C gains at depth with both N fertilizer and irrigation, though high variation precluded detection of significant changes. In maize-tomato rotations, SOC increased by 12.6% (21.8 Mg C/ha) with both WCC and composted poultry manure inputs, across the 2 m profile. The addition of WCC to a conventionally managed system increased SOC stocks by 3.5% (1.44 Mg C/ha) in the 0-30 cm layer, but decreased by 10.8% (14.86 Mg C/ha) in the 30-200 cm layer, resulting in overall losses of 13.4 Mg C/ha. If we only measured soil C in the top 30 cm, we would have assumed an increase in total soil C increased with WCC alone, whereas in reality significant losses in SOC occurred when considering the 2 m soil profile. Ignoring the subsoil carbon dynamics in deeper layers of soil fails to recognize potential opportunities for soil C sequestration, and may lead to false conclusions about the impact of management practices on C sequestration.

Agricultural management practices affect bulk soil microbial communities and the functions they carry out, but it remains unclear how these effects extend to the rhizosphere in different agroecosystem contexts. Given close linkages between rhizosphere processes and plant nutrition and productivity, understanding how management practices impact this critical zone is of great importance to optimize plant-soil interactions for agricultural sustainability. A comparison of six paired conventional-organic processing tomato farms was conducted to investigate relationships between management, soil physicochemical parameters, and rhizosphere microbial community composition and functions. Organically managed fields were higher in soil total N and NO3-N, total and labile C, plant Ca, S, and Cu, and other essential nutrients, while soil pH was higher in conventionally managed fields. Differential abundance, indicator species, and random forest analyses of rhizosphere communities revealed compositional differences between organic and conventional systems and identified management-specific microbial taxa. Phylogeny-based trait prediction showed that these differences translated into more abundant pathogenesis-related gene functions in conventional systems. Structural equation modeling revealed a greater effect of soil biological communities than physicochemical parameters on plant outcomes. These results highlight the importance of rhizosphere-specific studies, as plant selection likely interacts with management in regulating microbial communities and functions that impact agricultural productivity.IMPORTANCE Agriculture relies, in part, on close linkages between plants and the microorganisms that live in association with plant roots. These rhizosphere bacteria and fungi are distinct from microbial communities found in the rest of the soil and are even more important to plant nutrient uptake and health. Evidence from field studies shows that agricultural management practices such as fertilization and tillage shape microbial communities in bulk soil, but little is known about how these practices affect the rhizosphere. We investigated how agricultural management affects plant-soil-microbe interactions by comparing soil physical and chemical properties, plant nutrients, and rhizosphere microbial communities from paired fields under organic and conventional management. Our results show that human management effects extend even to microorganisms living in close association with plant roots and highlight the importance of these bacteria and fungi to crop nutrition and productivity.

Introduction: Integrated crop-livestock systems (ICLS) use animals to graze crop residues or cover crops before planting fresh produce and provide ecosystem services to support organic vegetable production. However, there is a risk of foodborne pathogen transfer to fresh produce because grazing may introduce enteric foodborne pathogens into the soil via animal feces, which may subsequently be transferred to the produce. Methods: To examine the effect of cover crop use and the risk of cover crop grazing on the contamination of soil and produce by foodborne pathogens in ICLS, a three-year (2019-2021) experimental study was conducted in organically managed plots, which were assigned three different treatments (fallow without cover crop or grazing, cover crop without grazing, or cover crop with grazing by sheep) in a maize/tomato rotation. During the three years of the experiment, a total of 184 pre- and post-graze fecal samples and 96 samples of tomatoes were collected to test for foodborne pathogens (Escherichia coli O157, non-O157 Shiga toxin-producing Escherichia coli (STEC), and Listeria (L.) monocytogenes). Soil samples were collected monthly until 126-171 days after grazing (824 in total) to examine the presence of foodborne pathogens, and generic E. coli (MPN/g) was quantified to compare its persistence among the three treatments. Results and Discussion: We did not detect any foodborne pathogens from harvested tomatoes in 2020 and 2021. One non-O157 STEC positive soil sample (0.1%, 1/824) was detected in the fallow treatment, and one L. monocytogenespositive (1.1%, 1/92) was detected from the post-graze fecal samples. When assessing proportions of generic E. coli positive and counts of generic E. coli in the soil samples using mixed effect zero-inflated negative binomial models, soil samples collected in the graze cover crop treatment plot showed significant increases in the counts of generic E. coli until 61-82 days post grazing, but no difference was observed after 96-123 days, compared to the baseline of the fallow treatment. Findings from generic E. coli counts support the use of the United States Department of Agriculture (USDA) National Organic Program (NOP) 90- or 120-day interval rule between applying raw manure and harvesting in organic farming into ICLS. Additionally, we confirmed that commercial organic compost application before cover crop seeding in the winter had no significant effect on the proportions and counts of generic E. coli in the soil of the following growing seasons. This longitudinal field trial confirmed that the effect of sheep grazing on foodborne pathogen contamination in ICLS is minimal but further studies comparing the genetic associations between fecal and soil samples would be necessary to distinguish the source of foodborne pathogen contamination. [ABSTRACT FROM AUTHOR]