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

Frontiers in Microbiology

Microbiology

Shefali Dobhal¹  Koon-Hui Wang¹  Anne M. Alvarez¹  Mohammad Arif¹  Diksha Klair¹  Amjad Ahmad²  Joshua Silva²  Jensen Uyeda²  Zohaib Ul Hassan³  Seil Kim³ 

[1] Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States;Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States;Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea;Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea;Department of Bio-Medical Measurement, University of Science and Technology (UST), Daejeon, Republic of Korea;

关键词: irrigation water;    microbiome;    taxonomic diversity;    Illumina;    metagenomics;    shotgun analyses;   

DOI  :  10.3389/fmicb.2023.1039292

 received in 2022-09-13, accepted in 2023-01-16,  发布年份 2023

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

Unknown   
Copyright © 2023 Klair, Dobhal, Ahmad, Hassan, Uyeda, Silva, Wang, Kim, Alvarez and Arif.