Application of Nematode Community Analyses-Based Models towards Identifying Sustainable Soil Health Management Outcomes: A Review of the Concepts

The Bacterial Gq Signal Transduction Inhibitor FR900359 Impairs Soil-Associated Nematodes

The cyclic depsipeptide FR900359 (FR) is derived from the soil bacterium Chromobacterium vaccinii and known to bind Gq proteins of mammals and insects, thereby abolishing the signal transduction of their Gq protein-coupled receptors, a process that leads to severe physiological consequences. Due to their highly conserved structure, Gq family of proteins are a superior ecological target for FR producing organisms, resulting in a defense towards a broad range of harmful organisms. Here, we focus on the question whether bacteria like C. vaccinii are important factors in soil in that their secondary metabolites impair, e.g., plant harming organisms like nematodes. We prove that the Gq inhibitor FR is produced under soil-like conditions. Furthermore, FR inhibits heterologously expressed Gαq proteins of the nematodes Caenorhabditis elegans and Heterodera schachtii in the micromolar range. Additionally, in vivo experiments with C. elegans and the plant parasitic cyst nematode H. schachtii demonstrated that FR reduces locomotion of C. elegans and H. schachtii. Finally, egg-laying of C. elegans and hatching of juvenile stage 2 of H. schachtii from its cysts is inhibited by FR, suggesting that FR might reduce nematode dispersion and proliferation. This study supports the idea that C. vaccinii and its excreted metabolome in the soil might contribute to an ecological equilibrium, maintaining and establishing the successful growth of plants.

A Nematode Community-Based Integrated Productivity Efficiency (IPE) Model That Identifies Sustainable Soil Health Outcomes: A Case of Compost Application in Carrot Production

Percent soil organic matter (SOM), pH and crop yield are among the biophysicochemical process-driven soil health indicators (SHIs). However, identifying sustainable soil health conditions using these SHIs is limited due to the lack of Integrated Productivity Efficiency (IPE) models. We define IPE as a concept that identifies best-to-worst-case soil health outcomes by assessing the effect of agronomic practices on weighted abundance of functional guilds (WAFG) of beneficial soil organisms and SHIs simultaneously. Expressing WAFG of all beneficial nematodes (x-axis) and SHIs (y-axis) as a percent of untreated control and regression of x and y reveals four quadrants describing worst-to-best-case outcomes for soil health and sustainability. We tested the effects of composted cow manure (AC) and plant litter (PC) applied at 135 (1×), 203 (1.5×), and 270 (2×) kg N/ha on WAFG, SOM, pH, and yield in a sandy clay loam field of a processing carrot cultivar over three growing seasons. Untreated control and urea at 1× served as experimental controls. Data that varied by time and were difficult to make sense of were separated into sustainable, unsustainable, or requiring specific modification to be sustainable categories by the IPE model. Within the sustainable category, all AC treatments and 2× rate of PC treatments had the best integrated efficiency outcomes across the SHIs. The IPE model provides a platform where other biophysicochemical process-driven SHIs could be integrated.

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.