Performing Department
(N/A)
Non Technical Summary
The proposed project aims to enhance the sustainability of cotton production by investigating the impact of cover crops on the soil microbiome and its subsequent effects on cotton development. The project seeks to achieve two main objectives: 1) investigate the effect of cover crop species on soil microbial community structure and function, and 2) examine the influence of different cover crop species on cotton root development and water- and nutrient-uptake. Soils in the southeastern United States are severely degraded, and methods to improve soil health to are critical to ensure sustainable crop production for the future. Existing knowledge shows that cover crops can increase soil organic carbon storage, improve soil fertility, and enhance soil structure. However, the influence of cover crops on soil microbial communities and their role in cotton development is less understood. Through field experiments and subsequent soil and plant sample analyses, this project will assess the abundance and functionality of microbial communities in different cover crop treatments. This will include measuring microbial biomass, arbuscular mycorrhizal fungi colonization, and amplicon sequencing to analyze soil bacterial and archaeal communities. Additionally, physiological measurements of cotton, including photosynthesis, transpiration, water use efficiency, leaf area index, and nutrient uptake, will be performed, and cotton root characteristics will be measured. The project addresses the AFRI Commodity Board Co-Funding Topic to "develop approaches to enhance the microbiome in cotton production" by providing insights into cover crop influence on the soil microbiome, leading to a better understanding of soil health and impacts on cotton performance.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Goals / Objectives
The long-term goal of this project is to improve sustainability of cotton production by leveraging the benefits of cover crops to enhance plant development, nutrient uptake, and water use efficiency by managing for improved soil microbial structure and function. We propose to address this goal with two specific objectives:Investigate the effect of cover crop species on soil microbial community structure and functionExamine the influence of different cover crop species on cotton root development and water- and nutrient-uptake.
Project Methods
Site DescriptionThe project will utilize existing medium-term (>6 years) field experiments to achieve the proposed objectives. Two cover crop trials were established in 2017 to evaluate different mixtures of winter cover crops included in a cotton (Gossypium hirsutum L.)-legume cash crop rotation. The first in Belle Mina, AL at the Tennessee Valley Research and Extension Center (TVREC) and the second in Headland, AL at the Wiregrass Research and Extension Center (WREC). The cash crop rotation at TVREC consists of cotton-soybean [Glycine max (L.) Merr.], and the rotation at WREC is cotton-peanut (Arachis hypogaea L.) to reflect legume cash crops commonly grown in those regions and elsewhere in the Southeast.This experiment includes eight cover crop treatments that are replicated four times in a one-factor randomized complete block design. The treatments include the following: winter fallow, cereal rye (Secale cereale L.), crimson clover (Trifolium incarnatum L.), andDaikon radish (Raphanus sativus L.) monocultures, and cover crop mixture treatments include all possible combinations of the three cover crop species.Only fallow, monoculture, and the three-species mixture treatments will be sampled for the current proposed study.Cover crops are rolled and chemically terminated, andcover crop biomass samples are collected according to plotprior to termination. Cash crops are planted approximately 2-3 weeks after cover crop termination.Activities for Objective 1--Investigate the effect of cover crop species on soil microbial community structure and functionSoil and Plant Material Sampling Soil samples will be collected from the appropriate plots for fallow, rye, clover, radish, and rye-clover-radish mixture treatments at TVREC and WREC. Soils will be collected approximately 2 weeks after cotton harvest.From each plot, 20 soil cores for 0-10 and 10-30 cm depths will be collected and thoroughly mixed to form one composite sample per depth per plot. After thorough mixing, sub-samples will be taken for mass water content, air-drying for soil chemical analysis, and freezing at -80ºC for molecular analysis. The remaining field-moist soil will be stored at 4ºC for microbial biomass C determination and other appropriate soil health indicators.Root samples for AMF colonization will be collected during the cotton growing season at the fourth true leaf stage. Samples will be collected by uprooting five to ten plants per plot from a 30 cm3 area of soil surrounding the cotton plant. Lateral roots will be removed from the taproot, rinsed, and placed in sealed glass vials containing 0.5 M formalin-acetic acid-alcohol solution for preservation. Samples will be stored at 4ºC until AMF analysis.Soil AnalysesGeneral soil chracterization will include Mehlich1-extractable nutrients, soil pH, and soil organic C and N. Soil penetration resistance will be measured in years one and three during the cotton growing season at the four true leaf stage. Measurements will be collected using a tractor-mounted hydraulic, five-probe penetrometer.Microbial abundance will be determined by quantifying microbial biomass C and the absolute abundance of bacterial and archaeal 16S rRNA genes.Quantitative PCR (qPCR) assays will be performed to determine the abundance of archaea and bacteria, as well asfour functional genes, including beta-glucosidase, bacterial ammonia monooxygenase archaeal ammonia monooxygenase, and nitrogenase reductase. Standard curves for quantification will be prepared by 10-fold serial dilution of plasmid DNA containing the appropriate target genes.Percent AMF colonization of cotton roots will be determined by stainingwith acid fuschin andexaminingfor AMF colonization.Amplicon sequencing will be used to assess changes in bacterial and archaeal communities in the soil. Purified DNA will be sequenced by HudsonAlpha Discovery (Huntsville, AL). The V4 region of the 16S rRNA genes will be targeted for community profiling of bacteria and archaea using the primer set 515F and 806R. The 16S metagenomic library will be constructed using standard protocols and sequenced on an Illumina MiSeq platform. Blanks from DNA extraction and a mock microbial community standard from Zymo Research will be included in sequencing runs to assess the accuracy of taxonomic identification and bias in composition profiling.Expected Results Under Objective 1, we expect to determine if microbial community structure varies under different cover crop treatments and the influence of cover crop treatment on soil microbiome under cotton. Key taxa of microbial communities in each treatment will be identified and the dominant factors affecting soil microbial communities will be identified as well. Analyses of AMF and function genes will allow us to glean information on soil nutrient supplies for cotton production.Activities for Objective 2--Examine the influence of cover crop species on cotton root development and water- and nutrient-uptakeCotton Physiological Measurements To examine the effect of the cover crop on cotton growth and development, plant physiological measurements, including leaf photosynthesis, transpiration, water use efficiency, and leaf area index (LAI) will be performed. To determine if cover crops impact the water and nutrient uptake, above-ground biomass will be hand-harvested from a two-meter section in each plot approximately two weeks after the bolls reach 60% open stage. The collected biomass will be subsequently divided into different components, including stems, leaves, bolls, burs, seeds, and lint. Each biomass component will be dried at 60°C, weighed, andfinely ground using a Wiley mill. Leaf samples will be ground again with a Genogrinder to obtain leaf powder for C isotope analysis. This analysis provides information on the water uptake and water use efficiency of plants during the growing season.The seed cotton samples will be ginnedto separate lint and seed. Subsequently,concentrations of N, P, K, Ca, Mg, S, Zn, Fe, and B nutrients in each component will be determined using an inductively coupled plasma mass spectroscometer. Nutrient uptake will be calculated by multiplying the nutrient concentration in each biomass component by its corresponding dry weight. Later, the nutrient uptake from all biomass components will be added to obtain the total uptake. The nutrient use efficiency for each nutrient, precisely, internal nutrient use efficiency, which considers both soil and fertilizer sources of nutrients, will be determined by calculating the lint yield production per unit of nutrient uptake.Roots are the main driver of water and nutrient uptake, and it has been documented that in less compacted soils, root growth is improved. As we have observed that some cover crops can reduce soil compaction and alter some root characteristics inpreliminary results, we will measure how different cover crops influence root characteristics in two ways. First, nondestructive root characteristics will be measured during the entire growing season by installing two mini-rhizotron accession tubes per plot. Root images will be taken with a mini-rhizotron every month, and root length, diameter, and density will be estimated. These measurements will inform us if some of the cover crop treatments are able to increase the length and density of the roots at different soil depths throughout the cotton growingseason.Expected Results With this study we expect to understand the effects of different cover crops on the physiological response of cotton in different environments. We expect to see that cover crops that have more "hairy" roots can loosen the soil and that can increase cotton root growth and, therefore, water and nutrient uptake, which could result in higher biomass and in some cases, yield. This project will help inform us to which cover crops can be more beneficial for cotton production and which physiological characteristics are improved using cover crops.