rganic farming is characterized by management practices that promote soil biodiversity and beneficial ecological interactions to offset the need for synthetic inputs such as inorganic fertilizers and biocides. Pest and nutrient management in organic agriculture is largely accomplished through various diversification methods, including cover crops, crop rotations, trap crops and promotion of active soil microbial communities [1][2][3][4][5] . Although organic agriculture is often thought to be less productive in terms of yield as compared to conventional farming, it offers great potential to enhance ecosystem services and agricultural sustainability [5][6][7] .Accumulating evidence suggests that organic management practices also reduce pest populations and increase resilience to pest damage 8,9 . Decreased insect pests on long-term organic farms have largely been attributed to practices that limit pest build-up, increase predator biodiversity, and increase the numbers of beneficial insects [9][10][11][12][13] . The nitrogen contents of plants grown on organic farms are often lower than those of conventional systems 11,12 . Plants that are nitrogen-limited are often less attractive to herbivores, which could also explain the lower pest pressure observed in organic systems 12,14,15 . However, very little is known about the impact of organic management for plant defence capacity.Organic management strategies can increase microbial activity and biomass in soils 1,2,16 , alter microbial communities 17 and in some cases enhance plant associations with beneficial microbes in the rhizosphere 3,4 . Microorganisms that associate with plant roots play a critical role in resistance to abiotic and biotic stress [18][19][20] . Mycorrhizal fungi have been shown to induce plant systemic resistance 21,22 and can reduce susceptibility to pathogens 23 and herbivores 24 . Plant growth-promoting rhizobacteria commonly found in soil microbial pools, as well as commercial inoculants, induce defences and other physiological changes in the host plant that influence above-ground herbivores 19,[25][26][27][28] . Despite the known interactions between organic management, plant-microbe associations and changes in crop resistance, the potential of these interactions to reduce pest damage in agricultural systems remains largely untapped.In this study, we report that organic management influences pest populations through changes in plant resistance. We explore linkages between insect settling and performance, rhizosphere communities and phytohormones related to plant defence with tomato (Solanum lycopersicum) and the beet leafhopper (Circulifer tenellus), an important pest of California's processing tomato industry 29 . We demonstrate that tomatoes grown using conventional management are preferentially settled by leafhopper pests and have lower salicylic acid (SA) levels compared to tomatoes grown using organic management. Our results indicate that differences in insect preference were due at least partially to changes in SA accumulation and rhi...

Root-associated microbial communities influence plant phenotype, growth and local abundance, yet the factors that structure these microbial communities are still poorly understood. California landscapes contain serpentine soils, which are nutrient-poor and high in heavy metals, and distinct from neighboring soils. Here, we surveyed the rhizoplane of serpentine-indifferent plants species growing on serpentine and non-serpentine soils to determine the relative influence of plant identity and soil chemistry on rhizoplane microbial community structure using 16S rRNA metabarcoding. Additionally, we experimentally examined if locally adapted microorganisms enhance plant growth in serpentine soil. Plant species, soil chemistry, and the interaction between them were important in structuring rhizoplane bacterial communities in both the field and experimental soils. In the experiment, rhizoplane microbial community source influenced seedling survival, but plant growth phenotypes measured were largely invariant to microbial community with a few exceptions. Results from the field sampling suggest that plant species associate with specific microbial communities even across chemically distinct soils, and that microbial communities can differentially influence seedling survival on harsh serpentine soils.

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 NO 3 -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.

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Serpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA gene barcoding to compare bacterial species composition at seedling, vegetative, early-, and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on non-serpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.

42Lower insect pest populations found on long-term organic farms have largely been 43 attributed to increased biodiversity and abundance of beneficial predators. However, 44 potential induction of plant defenses has largely been ignored. This study aims to 45 determine whether host plant resistance mediates decreased pest populations in 46 organic systems, and to identify the underpinning mechanisms. We demonstrate that 47Organic farming is characterized by management practices that promote biodiversity 82 and beneficial ecological interactions to offset synthetic inputs such as inorganic 83 fertilizers and biocides. Pest and nutrient management in organic agriculture is largely 84 accomplished through diversification methods such as cover crops, crop rotations, 85 and trap crops. Organic agriculture is often thought to be less productive in terms of 86 yield as compared to conventional farming, even though it offers great potential as a 87 more sustainable agricultural system (4, 5, 6) and can enhance the provision of 88 multiple ecosystem services, such as carbon sequestration, nutrient and water 89 retention, and biodiversity conservation (1-3). 90 91Accumulating evidence suggests that organic management practices also reduce pest 92 populations and increase resilience to pest damage (7-9). Enhancing natural pest 93 control in organic systems could help reduce costs, stabilize production, and increase 94 the ability of organic practices to meet global demand. Decreased insect pests on long-95

Serpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA barcoding to compare bacterial species composition at seedling, vegetative, early-, and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on non-serpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.

Prolonged water stress can reduce plant growth and fitness and may shift rhizoplane microbial communities. Although drought affects microbial structure of many plant species, it is still poorly understood whether closely related plant species host distinct microbial communities or respond similarly to drought. To explore this question, eight members of the Streptanthus clade with varying affinity to serpentine were subjected to three watering regimes. Rhizoplane bacterial communities were described using 16S rRNA gene amplicon sequencing and we explored the impact of watering treatment and plant species on alpha diversity, differential abundance, and beta diversity of soil bacterial communities. Among most plant species, reduced watering also reduced alpha diversity, but plant species did not strongly impact alpha diversity. Drought treatment reduced microbial community dissimilarity among samples: bacterial communities were more similar when plants received less water. Watering altered the relative abundance of bacterial genera within Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, and Acidobacteria, which responded similarly in the rhizoplane of most plant species. These results suggest that prolonged water stress in Streptanthus spp. can result in convergent microbial communities among plant species. We suggest the functional consequences of these shifts be examined to assess effects on plant and microbial fitness under drought conditions.