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Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials

The identification of microorganisms in closely related groups is challenging. The present work focused on the different molecular methodology for the accurate microbial identification in the five commercially available organic agriculture materials enriched with effective microorganisms. From the t...

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Autores principales: Bahuguna, Ashutosh, Joe, Ah-ryeong, Kumar, Vishal, Lee, Jong Suk, Kim, Sung-Youn, Moon, Ji-Young, Cho, Soon-Kil, Cho, Hyunjeong, Kim, Myunghee
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7599497/
https://www.ncbi.nlm.nih.gov/pubmed/33053711
http://dx.doi.org/10.3390/microorganisms8101568
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author Bahuguna, Ashutosh
Joe, Ah-ryeong
Kumar, Vishal
Lee, Jong Suk
Kim, Sung-Youn
Moon, Ji-Young
Cho, Soon-Kil
Cho, Hyunjeong
Kim, Myunghee
author_facet Bahuguna, Ashutosh
Joe, Ah-ryeong
Kumar, Vishal
Lee, Jong Suk
Kim, Sung-Youn
Moon, Ji-Young
Cho, Soon-Kil
Cho, Hyunjeong
Kim, Myunghee
author_sort Bahuguna, Ashutosh
collection PubMed
description The identification of microorganisms in closely related groups is challenging. The present work focused on the different molecular methodology for the accurate microbial identification in the five commercially available organic agriculture materials enriched with effective microorganisms. From the tested five organic agricultural materials, a total of seven distinct bacterial colonies (A-1, B-1, C-1, D-1, E-1, E-2, and E-3) were isolated and processed for sequential identification utilizing HiCrome™ Bacillus agar, biochemical tests with API CHB50, 16S rRNA gene analysis, random amplified polymorphic DNA (RAPD), and species-specific PCR analysis. All the isolated microorganisms were Gram-positive rods and spore former belonging to Bacillus group and appeared as a differential characteristic feature on HiCrome™ Bacillus agar. All isolates showed high-percentage similarities with the different members of Bacillus species in biochemical testing and 16S rRNA gene analysis. The collective identification results revealed isolates, A-1, B-1, and C-1, close to B. velezensis. Further RAPD-PCR and species-specific PCR discriminated and provided confirmatory evidence for D-1 as B. thuringiensis and E-1, E-2, and E-3 as B. licheniformis, respectively. In addition, presence of B. thuringiensis was also confirmed by toxin crystal protein staining. In conclusion, the species-specific primers could be used as a rapid and accurate identification tool to discriminate closely related Bacillus species such as B. subtilis, B. licheniformis, and B. thuringiensis.
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spelling pubmed-75994972020-11-01 Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials Bahuguna, Ashutosh Joe, Ah-ryeong Kumar, Vishal Lee, Jong Suk Kim, Sung-Youn Moon, Ji-Young Cho, Soon-Kil Cho, Hyunjeong Kim, Myunghee Microorganisms Article The identification of microorganisms in closely related groups is challenging. The present work focused on the different molecular methodology for the accurate microbial identification in the five commercially available organic agriculture materials enriched with effective microorganisms. From the tested five organic agricultural materials, a total of seven distinct bacterial colonies (A-1, B-1, C-1, D-1, E-1, E-2, and E-3) were isolated and processed for sequential identification utilizing HiCrome™ Bacillus agar, biochemical tests with API CHB50, 16S rRNA gene analysis, random amplified polymorphic DNA (RAPD), and species-specific PCR analysis. All the isolated microorganisms were Gram-positive rods and spore former belonging to Bacillus group and appeared as a differential characteristic feature on HiCrome™ Bacillus agar. All isolates showed high-percentage similarities with the different members of Bacillus species in biochemical testing and 16S rRNA gene analysis. The collective identification results revealed isolates, A-1, B-1, and C-1, close to B. velezensis. Further RAPD-PCR and species-specific PCR discriminated and provided confirmatory evidence for D-1 as B. thuringiensis and E-1, E-2, and E-3 as B. licheniformis, respectively. In addition, presence of B. thuringiensis was also confirmed by toxin crystal protein staining. In conclusion, the species-specific primers could be used as a rapid and accurate identification tool to discriminate closely related Bacillus species such as B. subtilis, B. licheniformis, and B. thuringiensis. MDPI 2020-10-12 /pmc/articles/PMC7599497/ /pubmed/33053711 http://dx.doi.org/10.3390/microorganisms8101568 Text en © 2020 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Bahuguna, Ashutosh
Joe, Ah-ryeong
Kumar, Vishal
Lee, Jong Suk
Kim, Sung-Youn
Moon, Ji-Young
Cho, Soon-Kil
Cho, Hyunjeong
Kim, Myunghee
Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials
title Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials
title_full Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials
title_fullStr Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials
title_full_unstemmed Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials
title_short Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials
title_sort study on the identification methods for effective microorganisms in commercially available organic agriculture materials
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7599497/
https://www.ncbi.nlm.nih.gov/pubmed/33053711
http://dx.doi.org/10.3390/microorganisms8101568
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