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Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms

Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from we...

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Autores principales: Klair, Diksha, Dobhal, Shefali, Ahmad, Amjad, Hassan, Zohaib Ul, Uyeda, Jensen, Silva, Joshua, Wang, Koon-Hui, Kim, Seil, Alvarez, Anne M., Arif, Mohammad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9981659/
https://www.ncbi.nlm.nih.gov/pubmed/36876060
http://dx.doi.org/10.3389/fmicb.2023.1039292
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author Klair, Diksha
Dobhal, Shefali
Ahmad, Amjad
Hassan, Zohaib Ul
Uyeda, Jensen
Silva, Joshua
Wang, Koon-Hui
Kim, Seil
Alvarez, Anne M.
Arif, Mohammad
author_facet Klair, Diksha
Dobhal, Shefali
Ahmad, Amjad
Hassan, Zohaib Ul
Uyeda, Jensen
Silva, Joshua
Wang, Koon-Hui
Kim, Seil
Alvarez, Anne M.
Arif, Mohammad
author_sort Klair, Diksha
collection PubMed
description Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and storage tank water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3–V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phylum in the stream source and associated water samples from wetland taro fields. Cyanobacteria was also a dominant phylum in samples from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. In contrast, Oxford Nanopore MinION was a better choice for microbe classification at the genus and species levels as indicated by samples sequenced for full length 16S rRNA. No reliable taxonomic classification results were obtained while using shotgun metagenome data. In functional analyzes, only 12% of the genes were shared by two consortia and 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Full descriptions of microbial communities and their functions are essential for the development of better water management strategies aimed to produce safer fresh produce and to protect plant, animal, human and environmental health. Quantitative comparisons illustrated the importance of selecting the appropriate analytical method depending on the level of taxonomic delineation sought in each microbiome.
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spelling pubmed-99816592023-03-04 Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms Klair, Diksha Dobhal, Shefali Ahmad, Amjad Hassan, Zohaib Ul Uyeda, Jensen Silva, Joshua Wang, Koon-Hui Kim, Seil Alvarez, Anne M. Arif, Mohammad Front Microbiol Microbiology Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and storage tank water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3–V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phylum in the stream source and associated water samples from wetland taro fields. Cyanobacteria was also a dominant phylum in samples from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. In contrast, Oxford Nanopore MinION was a better choice for microbe classification at the genus and species levels as indicated by samples sequenced for full length 16S rRNA. No reliable taxonomic classification results were obtained while using shotgun metagenome data. In functional analyzes, only 12% of the genes were shared by two consortia and 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Full descriptions of microbial communities and their functions are essential for the development of better water management strategies aimed to produce safer fresh produce and to protect plant, animal, human and environmental health. Quantitative comparisons illustrated the importance of selecting the appropriate analytical method depending on the level of taxonomic delineation sought in each microbiome. Frontiers Media S.A. 2023-02-17 /pmc/articles/PMC9981659/ /pubmed/36876060 http://dx.doi.org/10.3389/fmicb.2023.1039292 Text en Copyright © 2023 Klair, Dobhal, Ahmad, Hassan, Uyeda, Silva, Wang, Kim, Alvarez and Arif. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Klair, Diksha
Dobhal, Shefali
Ahmad, Amjad
Hassan, Zohaib Ul
Uyeda, Jensen
Silva, Joshua
Wang, Koon-Hui
Kim, Seil
Alvarez, Anne M.
Arif, Mohammad
Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms
title Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms
title_full Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms
title_fullStr Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms
title_full_unstemmed Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms
title_short Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms
title_sort exploring taxonomic and functional microbiome of hawaiian stream and spring irrigation water systems using illumina and oxford nanopore sequencing platforms
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9981659/
https://www.ncbi.nlm.nih.gov/pubmed/36876060
http://dx.doi.org/10.3389/fmicb.2023.1039292
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