Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach
Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea....
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Hanrimwon Publishing Company
2021-12-01
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| Series: | The Plant Pathology Journal |
| Subjects: | |
| Online Access: | http://www.ppjonline.org/upload/pdf/PPJ-OA-07-2021-0106.pdf |
| _version_ | 1818068466355142656 |
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| author | Mahesh Adhikari Sang Woo Kim Hyun Seung Kim Ki Young Kim Hyo Bin Park Ki Jung Kim Youn Su Lee |
| author_facet | Mahesh Adhikari Sang Woo Kim Hyun Seung Kim Ki Young Kim Hyo Bin Park Ki Jung Kim Youn Su Lee |
| author_sort | Mahesh Adhikari |
| collection | DOAJ |
| description | Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions. |
| first_indexed | 2024-12-10T15:40:01Z |
| format | Article |
| id | doaj.art-8ab6c8996dc9443c9fe9afca66d4c46d |
| institution | Directory Open Access Journal |
| issn | 1598-2254 2093-9280 |
| language | English |
| last_indexed | 2024-12-10T15:40:01Z |
| publishDate | 2021-12-01 |
| publisher | Hanrimwon Publishing Company |
| record_format | Article |
| series | The Plant Pathology Journal |
| spelling | doaj.art-8ab6c8996dc9443c9fe9afca66d4c46d2022-12-22T01:43:07ZengHanrimwon Publishing CompanyThe Plant Pathology Journal1598-22542093-92802021-12-0137652153210.5423/PPJ.OA.07.2021.01062281Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing ApproachMahesh AdhikariSang Woo KimHyun Seung KimKi Young KimHyo Bin ParkKi Jung KimYoun Su LeeKnowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.http://www.ppjonline.org/upload/pdf/PPJ-OA-07-2021-0106.pdfbacterial diversitymicrobiomenext generation sequencingwatermelon |
| spellingShingle | Mahesh Adhikari Sang Woo Kim Hyun Seung Kim Ki Young Kim Hyo Bin Park Ki Jung Kim Youn Su Lee Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach The Plant Pathology Journal bacterial diversity microbiome next generation sequencing watermelon |
| title | Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach |
| title_full | Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach |
| title_fullStr | Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach |
| title_full_unstemmed | Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach |
| title_short | Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach |
| title_sort | bacterial community and diversity from the watermelon cultivated soils through next generation sequencing approach |
| topic | bacterial diversity microbiome next generation sequencing watermelon |
| url | http://www.ppjonline.org/upload/pdf/PPJ-OA-07-2021-0106.pdf |
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