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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Research Project #436587

Research Project: Development of a Fast, Cost-effective Approach for Quantification of Microbial Community Shift in Chitin Amended Soil

Location: Sugarbeet and Bean Research

Project Number: 5050-43640-003-05-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2019
End Date: Aug 30, 2021

This research aims to address the following two critical issues: 1. Determining or quantifying the efficacy of chitin fungal biomass on the chemical and biochemical properties of treated soil and on the diversity of soil microbial community; 2. Exploring the feasibility of using visible and near-infrared (VNIR) spectroscopy as a fast and low-cost alternative method for analyzing the properties and microbial community changes of chitin treated soil.

Laboratory soil microcosm tests will be conducted to investigate the effects of the fungal chitin biomass on soil properties and microbial community shift (Objective 1), and while for developing a VNIR technique will be developed, by utilizing this data, for rapid assessment of chitin fungal biomass treated soil (Objective 2). Rhizopus oryzae will be grown on cull potatoes to accumulate chitin in the fungal biomass. A simple heat dehydration treatment will be used to dry and stop biological activity of R. oryzae. The dried fungal biomass will then be grinded to pass through 2 mm mesh sieve as the fungal chitin fertilizer. Soil samples will be collected at the Montcalm Research Farm at Lakeview, Michigan. The soil samples will be homogenized. Four replicates of microcosms containing 500 g of soil will be prepared with different commercial chitin and fungal biomass contents. Three levels of fungal biomass fertilizer (0, 0.8, 8 g/100 g soil) will be applied. Based on the 25% of chitin content in fungal biomass, equivalent amounts of commercial chitin (derived from shrimp shell) at three levels (0, 0.2, 2 g/100g soil) will be added into soil as a chitin control. The microcosms will be incubated at room temperature. The soil samples will be removed from each microcosm after different days of inoculation for the following analyses:. 1. The contents of nitrogen (N), carbon (C), hydrogen (H), sulfur (S), phosphate fraction, chitinase activity, and pH in soil samples will be measured. Data will be analyzed to compare the differences of chemical and biochemical properties among each treatment. 2. Changes of microbial communities at various chitin conditions (control without chitin, shrimp chitin, fungal biomass chitin) and different incubation times will be studied. 1) Total soil DNA will be isolated from each soil sample (250 mg) as a template DNA. 2) 16S rRNA and 18S rRNA-based gene sequencing analyses will be employed to understand the prokaryote and eukaryote populations, respectively. Fastq files from the high-throughput sequencing will be analyzed to generate taxonomic/phylogenetic data for statistical analysis. 3) Typical potato pathogens will be monitored and quantified. The diversity and distribution of the predominant fungal species and bacterial populations will be profiled in response to the addition of chitin content in the soil samples. The detailed microbial population shifting regarding different soil chitin conditions will be delineated from this subtask. 3. VNIR reflectance spectra of 400-1,700 nm will be acquired from soil samples at different incubation times. Calibration models will be developed and validated, using such methods as partial least squares and support vector machine, to predict the soil chemical and biochemical properties (e.g., N, C, H, pH, chitinase activity, etc.) and possibly levels of the pathogens in the soil samples.