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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...

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Autores principales: 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
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
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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.
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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
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