Cargando…
Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health
The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-ge...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8953465/ https://www.ncbi.nlm.nih.gov/pubmed/35324742 http://dx.doi.org/10.3390/toxics10030117 |
_version_ | 1784675857350000640 |
---|---|
author | Kim, Heejung Park, Yong-Ha Yang, Jae E. Kim, Hyuck-Soo Kim, Sung-Chul Oh, Eun-Ji Moon, Jinah Cho, Wonsil Shin, Wonsik Yu, Chaerim |
author_facet | Kim, Heejung Park, Yong-Ha Yang, Jae E. Kim, Hyuck-Soo Kim, Sung-Chul Oh, Eun-Ji Moon, Jinah Cho, Wonsil Shin, Wonsik Yu, Chaerim |
author_sort | Kim, Heejung |
collection | PubMed |
description | The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-generation sequencing (NGS)-based molecular-biological methods have revealed information on soil biodiversity; however, whether this biodiversity is related to soil health remains unclear. In this study, we performed NGS on grassland surface soil to compare the prokaryotic and eukaryotic genetic diversity to determine the chemical soil quality and examined markers associated with soil health. Microorganisms associated with the nitrogen cycle, bioremediation, plant pathogenicity, antibiotic production, and material degradation showed potential for use as markers. To propose a framework for soil health assessment, we not only used traditional indicators, such as chemical and physical measures, but also assessed metagenomics data of soil by land use to identify the major factors influencing the microbial structure in soil. Moreover, major keystone species were identified. Furthermore, the microbial genetic diversity of generally healthy surface soil, such as forests, farmland, and parks, was determined. These findings provide basic data for exploring soil health-related biomarkers. |
format | Online Article Text |
id | pubmed-8953465 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-89534652022-03-26 Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health Kim, Heejung Park, Yong-Ha Yang, Jae E. Kim, Hyuck-Soo Kim, Sung-Chul Oh, Eun-Ji Moon, Jinah Cho, Wonsil Shin, Wonsik Yu, Chaerim Toxics Article The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-generation sequencing (NGS)-based molecular-biological methods have revealed information on soil biodiversity; however, whether this biodiversity is related to soil health remains unclear. In this study, we performed NGS on grassland surface soil to compare the prokaryotic and eukaryotic genetic diversity to determine the chemical soil quality and examined markers associated with soil health. Microorganisms associated with the nitrogen cycle, bioremediation, plant pathogenicity, antibiotic production, and material degradation showed potential for use as markers. To propose a framework for soil health assessment, we not only used traditional indicators, such as chemical and physical measures, but also assessed metagenomics data of soil by land use to identify the major factors influencing the microbial structure in soil. Moreover, major keystone species were identified. Furthermore, the microbial genetic diversity of generally healthy surface soil, such as forests, farmland, and parks, was determined. These findings provide basic data for exploring soil health-related biomarkers. MDPI 2022-03-01 /pmc/articles/PMC8953465/ /pubmed/35324742 http://dx.doi.org/10.3390/toxics10030117 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Kim, Heejung Park, Yong-Ha Yang, Jae E. Kim, Hyuck-Soo Kim, Sung-Chul Oh, Eun-Ji Moon, Jinah Cho, Wonsil Shin, Wonsik Yu, Chaerim Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health |
title | Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health |
title_full | Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health |
title_fullStr | Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health |
title_full_unstemmed | Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health |
title_short | Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health |
title_sort | analysis of major bacteria and diversity of surface soil to discover biomarkers related to soil health |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8953465/ https://www.ncbi.nlm.nih.gov/pubmed/35324742 http://dx.doi.org/10.3390/toxics10030117 |
work_keys_str_mv | AT kimheejung analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth AT parkyongha analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth AT yangjaee analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth AT kimhyucksoo analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth AT kimsungchul analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth AT oheunji analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth AT moonjinah analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth AT chowonsil analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth AT shinwonsik analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth AT yuchaerim analysisofmajorbacteriaanddiversityofsurfacesoiltodiscoverbiomarkersrelatedtosoilhealth |