An Examination of Fungal and Bacterial Assemblages in Bulk and Rhizosphere Soils under Solanum tuberosum in Southeastern Wyoming, USA

Gordon Custer,Linda Van Diepen,William Stump

doi:10.3390/applmicrobiol1020013

Gordon Custer, Linda Van Diepen + Show 1 more

Open Access

https://doi.org/10.3390/applmicrobiol1020013

Copy DOI

Journal: Applied Microbiology	Publication Date: Jun 22, 2021
Citations: 7	License type: CC BY 4.0

Affiliation: University of Wyoming

Abstract

Solanum tuberosum, commonly known as potato, is the most important non-cereal crop in the world. However, its cultivation is prone to disease and other issues. In recent years, a newfound interest in the soil microbiome and the potential benefits it may convey has led researchers to study plant–microbe interactions in great detail and has led to the identification of putative beneficial microbial taxa. In this survey, we examined fungal and bacterial diversity using high-throughput sequencing in soils under a potato crop in southeastern Wyoming, USA. Our results show decreased microbial diversity in the rhizosphere, with increases in the abundances of arbuscular mycorrhizal fungi as well as pathogenic microbes. We show coarse taxonomic differences in microbial assemblages when comparing the bulk and rhizosphere soils for bacteria but not for fungi, suggesting that the two kingdoms respond differently to the selective pressures of the rhizosphere. Using cooccurrence network analysis, we identify microbes that may serve as keystone taxa and provide benefits to their host plants through competitive exclusion of detrimental pathogenic taxa and increased nutrient availability. Our results provide additional information on the structure and complexity of the potato rhizosphere microbiome and highlight candidate taxa for microbial isolation and inoculation.

Highlights

Increasing human population coupled with predicted climate change scenarios have the potential to manifest in food supply vulnerability [1]
In order to better understand the composition of the potato rhizosphere microbiome, we conducted a survey of both the bulk and rhizosphere microbial assemblages in a potato monoculture in southeastern Wyoming, USA. As both bacteria and fungi are important members of the soil microbiome, we examined both Kingdoms using high-throughput sequencing of the 16s rRNA and fungal internal transcribed spacer (ITS) genes, respectively
Our that differences in α-diversity metrics between bulk and rhizoOur analyses analysesshow show that differences in α-diversity metrics between bulk and sphere soils were specific to bacteria or fungi, andand that in in most rhizosphere soils were specific to bacteria or fungi, that mostcases, cases,the therhizosphere rhizosphere displayed displayed lower lower α-diversity

Summary

Introduction

Increasing human population coupled with predicted climate change scenarios have the potential to manifest in food supply vulnerability [1]. In order to provide a stable food supply in the face of changing climate and other disturbances, researchers and farmers alike are turning to microorganisms, the soil microbiome. Soil microorganisms are known to dramatically affect ecosystem properties such as nutrient cycling [2,3] and ecosystem productivity [4]. The microbial assemblage directly surrounding plant roots, known as the rhizosphere microbiome, plays a large role in plant fitness via mediating abiotic stress [5,6], increasing plant nutrient access [2,7,8,9], and affecting susceptibly to both herbivory [10,11] and pathogens [12]. Rhizosphere assemblages that increase host fitness are positively selected for, and those that act as a detriment to their host are selected against

Methods

Results

Conclusion