Margaret Fernando’s research while affiliated with United States Department of Agriculture and other places

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Publications (6)


Fig. 2 Temporal changes in soil microbial biomass and key soil metrics under cover crop treatments. (A) Magnitude of change from baseline for selected soil variables in interrow and vine row soils across years 1 to 3 under control, phacelia and rye treatments. (B) Linear regressions of selected variables over time across treatments: control (solid lines), native cover (dashed lines), and introduced cover (dotted lines). SMB -soil microbial biomass; F:B -fungi-tobacteria ratio; AMF -arbuscular mycorrhizal fungi; Actinobacteria -bacterial group; GN: GP -ratio of Gram-negative to Gram-positive bacteria; Copio: Oligo -copiotrophic-to-oligotrophic ratio; Sat: Unsat -ratio of saturated-to-unsaturated fatty acids; GWC -gravimetric water content
Fig. 3 Random Forest-selected soil variables and their correlations with microbial taxa across treatments in interrow and vine row soils. (A) Top 10 soil variables distinguishing treatments in the interrow based on Gini importance and normalized values. (B) Heatmaps showing correlations between selected soil variables and bacterial and fungal taxa (Order level) across treatments (control, phacelia, rye) in the interrow. Microbial taxa were selected using Kruskal-Wallis tests (p < 0.05). Environmental variables were selected via Random Forest and tested for treatment effects using linear mixed-effect models. (C) Top 10 soil variables distinguishing treatments in the vine row. (D) Heatmaps showing correlations between selected soil variables and microbial taxa in the vine row. F: B -fungi-to-bacteria ratio; AMF -arbuscular mycorrhizal fungi; GN: GP -ratio of Gram-negative to Gram-positive bacteria; MUFAmonounsaturated fatty acids; PUFA -polyunsaturated fatty acids; Pred: Prey -predator-to-prey ratio; Copio: Oligo -copiotrophic-to-oligotrophic bacteria ratio; GWC -gravimetric water content. Statistical significance is indicated as *p < 0.05, **p < 0.01, and ***p < 0.001
Fig. 4 Spatial shifts in prokaryotic and fungal community composition across treatments and time. (A) Relative abundance of dominant bacterial and fungal orders over three years of cover crop management in interrow and vine row soils. (B, C) Non-metric multidimensional scaling (NMDS) ordinations showing beta diversity of bacterial (B) and fungal (C) communities under control, rye and phacelia treatments across years 1, 2, and 3. Statistical significance of treatment effects was assessed using Permanova
Interrow cover crops in a semi-arid vineyard increase plant beneficial functional potential of the soil microbiome, both in vine rows and interrows, a benefit that increases with cover crop duration
  • Article
  • Full-text available

June 2025

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15 Reads

Environmental Microbiome

Fernando Igne Rocha

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Jean Carlos Rodriguez-Ramos

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Margaret Fernando

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Lauren Hale

Background Cover crops are recognized for enhancing soil health and providing agroecosystem services, but are not widely adopted, particularly in water-limited regions. In Mediterranean vineyards, where water scarcity and soil degradation challenge productivity, interrow, cool-season cover cropping offers a promising strategy to improve microbial-mediated soil functions. However, the temporal and spatial effects of cover crops on vineyard soil microbiomes and soil health metrics remain poorly understood. This study evaluated the impacts of a California native (phacelia, Phacelia tanacetifolia ) and introduced (rye, Secale cereale L.) plant species as interrow cover crops on soil properties in interrow and vine row soils across three years. Results The study revealed distinct temporal and spatial dynamics in soil microbiomes elicited by the cover crop treatments. By the third year, phacelia exhibited the highest microbial biomass, fungal-to-bacterial ratios, and microbial network complexity. Interrow soils showed stronger responses to cover cropping, including enhanced microbial biomass and differentiation between treatments, while vine row soils demonstrated subtler but significant shifts in microbial metrics. Functional predictions indicated that cover crops reduced fungal pathogen prevalence and supported nutrient cycling processes. Deterministic processes driven by environmental selection became dominant under both treatments, promoting microbial resilience. Random Forest analysis identified NO 3 ⁻ as a key driver of microbial differentiation, with phacelia fostering communities reliant on labile organic inputs. Conclusions This study highlights a crucial benefit of interrow cover crops in improving soil health and enhancing microbial-mediated ecosystem functions in adjacent vine row soils, even after cover crop termination. Long-term application of cover crops offers a sustainable approach to building resilient agroecosystems in water-scarce environments, with implications for sustainable viticulture practices.

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Do native and introduced cover crops differ in their ability to suppress weeds and reduce seedbanks? A Case study in a Table Grape Vineyard

June 2023

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32 Reads

Cover cropping is considered a valuable tool for integrated weed management. However, weed suppression by cover crops can be inconsistent. We hypothesized that a native cover crop species may have greater capacity to suppress weeds than an introduced species owing to adaptive advantages. A study was conducted from 2020 to 2022 in a newly-established Autumn King tablegrape vineyard in Parlier, CA. Two cover crop treatments, a native plant species, phacelia (Phacelia tanacetifolia), or an introduced species, rye (Secale cereale L. Merced), were compared to a no cover crop, herbicide-managed control for impacts on weed control. Cover crops were sown in 2019 in the center 1.8 m of the 3.6 m space between the grapevine rows. The experimental design was a randomized complete block with four replications. Percent cover, weed density, and weed biomass in different seasons were assessed in the inter-row spaces and the vine rows. Soil samples were collected in 2021 from the grape row and interrow spaces to assess the weed seedbank. After the cover crops were terminated, percent weed cover was lower in the interrow of the phacelia compared to the no cover crop plots at two sampling times. When cover crops were actively growing (winter/spring), phacelia plots had a 7-fold higher cover crop to weed biomass ratio compared to that of the rye plots, thus indicating greater weed suppression. However, weed seedling emergence from the seedbank samples of the cover crop plots were 2- to 4-fold greater (in the phacelia and rye, respectively) than from the no cover crop plots. In summary, phacelia suppressed weeds more than rye; however, they both resulted in a bigger weed seedbank size compared to the herbicide-managed no cover crop plots, so additional management practices will be needed for long term weed management with cover crops in vineyards.


Conceptual diagram of a summary of possible interactions during the actively growing phase of the cover crop (left) and after the cover crop is terminated and left as a surface residue on the soil (right).
The Potential of Cover Crops for Weed Management: A Sole Tool or Component of an Integrated Weed Management System?

February 2023

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500 Reads

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35 Citations

Cover crops are an important component of integrated weed management programs in annual and perennial cropping systems because of their weed suppressive abilities. They influence weed populations using different mechanisms of plant interaction which can be facilitative or suppressive. However, the question often arises if cover crops can be solely relied upon for weed management or not. In this review we have tried to provide examples to answer this question. The most common methods of weed suppression by an actively growing cover crop include competition for limited plant growth resources that result in reduced weed biomass, seed production, and hence reductions in the addition of seeds to the soil seedbank. Cover crop mulches suppress weeds by reducing weed seedling emergence through allelopathic effects or physical effects of shading. However, there is a great degree of variability in the success or failure of cover crops in suppressing weeds that are influenced by the cover crop species, time of planting, cover crop densities and biomass, time of cover crop termination, the cash crop following in the rotation, and the season associated with several climatic variables. Several studies demonstrated that planting date was important to achieve maximum cover crop biomass, and a mixture of cover crop species was better than single cover crop species to achieve good weed suppression. Most of the studies that have demonstrated success in weed suppression have only shown partial success and not total success in weed suppression. Therefore, cover crops as a sole tool may not be sufficient to reduce weeds and need to be supplemented with other weed management tools. Nevertheless, cover crops are an important component of the toolbox for integrated weed management.


Citations (2)


... Modern agricultural systems face the challenge of maintaining productivity while mitigating the impacts of soil degradation, water scarcity, and declining ecosystem services associated with monocultures [1]. Cover crops provide multifaceted benefits, including improving soil structure, reducing topsoil loss, and enhancing soil microbial activity, but concerns over their water use has limited adoption in semi-arid regions [2][3][4][5]. Agricultural production in Mediterranean climates, classified by cool, wet winters, and hot, dry summers, is often reliant on irrigation inputs. Notably, Southern California and the San Joaquin Valley of California receive ~ 0-1 mm average monthly rainfall June through September [6], but produced a table grape crop valued at $2.3 billion USD in 2023 [7]. ...

Reference:

Interrow cover crops in a semi-arid vineyard increase plant beneficial functional potential of the soil microbiome, both in vine rows and interrows, a benefit that increases with cover crop duration
A native plant species cover crop positively impacted vineyard water dynamics, soil health, and vine vigor
  • Citing Article
  • March 2024

Agriculture Ecosystems & Environment

... Moreover, they can be adapted to diverse climatic conditions and agroecosystems, including semi-arid regions before an irrigated summer cash crop, cold-temperate areas before a spring cereal crop, tropical and subtropical zones before a rain-fed summer crop, and even rice paddies during the fallow season [7]. Cover crops are generally composed of legumes (Fabaceae), grasses (Poaceae), and brassicas (Brassicaceae) plant families [11]. The practice of cover cropping has been used since ancient times in the Mediterranean, where leguminous plants were ploughed into fallow fields after an early harvest in order to reinvigorate the soil [8,12]. ...

The Potential of Cover Crops for Weed Management: A Sole Tool or Component of an Integrated Weed Management System?