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Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes

Kinetoplastid flagellates are generally abundant in the deep sea and recently they were even found to be dominant in the hypolimnion of a deep freshwater lake. Therefore, to understand the distribution of kinetoplastids in deep freshwater lakes, we have collected vertical samples from five lakes in...

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Autores principales: Mukherjee, Indranil, Hodoki, Yoshikuni, Okazaki, Yusuke, Fujinaga, Shohei, Ohbayashi, Kako, Nakano, Shin-ichi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6805782/
https://www.ncbi.nlm.nih.gov/pubmed/31681232
http://dx.doi.org/10.3389/fmicb.2019.02375
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author Mukherjee, Indranil
Hodoki, Yoshikuni
Okazaki, Yusuke
Fujinaga, Shohei
Ohbayashi, Kako
Nakano, Shin-ichi
author_facet Mukherjee, Indranil
Hodoki, Yoshikuni
Okazaki, Yusuke
Fujinaga, Shohei
Ohbayashi, Kako
Nakano, Shin-ichi
author_sort Mukherjee, Indranil
collection PubMed
description Kinetoplastid flagellates are generally abundant in the deep sea and recently they were even found to be dominant in the hypolimnion of a deep freshwater lake. Therefore, to understand the distribution of kinetoplastids in deep freshwater lakes, we have collected vertical samples from five lakes in Japan. The abundance of kinetoplastids was enumerated by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization, and the diversity was determined by 18S amplicon sequencing using universal eukaryote and kinetoplastid-specific primers. Kinetoplastids were abundant in the deep waters of all the lakes, contributing up to 53.6% of total nanoeukaryotes. Despite this significant contribution, kinetoplastids remain undetected by amplicon sequencing using universal primers that are widely used in eukaryotic diversity studies. However, they were detected with specific primers, and the communities were characterized by both ubiquitous and lake-specific unique OTUs. Oligotyping of a ubiquitous and dominant OTU revealed the presence of lake-specific sequence types (oligotypes). Remarkably, we also detected diplonemids (a sister group of kinetoplastids and considered to be specific in the marine habitat) using kinetoplastid-specific primers, showing their presence in freshwaters. Underestimation of kinetoplastids and diplonemids using universal primers indicates that euglenozoan flagellates are overlooked in diversity studies worldwide. The present study highlighted the importance of kinetoplastids in the hypolimnion of deep lakes, thereby indicating their role in material cycling in deep waters.
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spelling pubmed-68057822019-11-01 Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes Mukherjee, Indranil Hodoki, Yoshikuni Okazaki, Yusuke Fujinaga, Shohei Ohbayashi, Kako Nakano, Shin-ichi Front Microbiol Microbiology Kinetoplastid flagellates are generally abundant in the deep sea and recently they were even found to be dominant in the hypolimnion of a deep freshwater lake. Therefore, to understand the distribution of kinetoplastids in deep freshwater lakes, we have collected vertical samples from five lakes in Japan. The abundance of kinetoplastids was enumerated by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization, and the diversity was determined by 18S amplicon sequencing using universal eukaryote and kinetoplastid-specific primers. Kinetoplastids were abundant in the deep waters of all the lakes, contributing up to 53.6% of total nanoeukaryotes. Despite this significant contribution, kinetoplastids remain undetected by amplicon sequencing using universal primers that are widely used in eukaryotic diversity studies. However, they were detected with specific primers, and the communities were characterized by both ubiquitous and lake-specific unique OTUs. Oligotyping of a ubiquitous and dominant OTU revealed the presence of lake-specific sequence types (oligotypes). Remarkably, we also detected diplonemids (a sister group of kinetoplastids and considered to be specific in the marine habitat) using kinetoplastid-specific primers, showing their presence in freshwaters. Underestimation of kinetoplastids and diplonemids using universal primers indicates that euglenozoan flagellates are overlooked in diversity studies worldwide. The present study highlighted the importance of kinetoplastids in the hypolimnion of deep lakes, thereby indicating their role in material cycling in deep waters. Frontiers Media S.A. 2019-10-16 /pmc/articles/PMC6805782/ /pubmed/31681232 http://dx.doi.org/10.3389/fmicb.2019.02375 Text en Copyright © 2019 Mukherjee, Hodoki, Okazaki, Fujinaga, Ohbayashi and Nakano. http://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
Mukherjee, Indranil
Hodoki, Yoshikuni
Okazaki, Yusuke
Fujinaga, Shohei
Ohbayashi, Kako
Nakano, Shin-ichi
Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes
title Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes
title_full Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes
title_fullStr Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes
title_full_unstemmed Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes
title_short Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes
title_sort widespread dominance of kinetoplastids and unexpected presence of diplonemids in deep freshwater lakes
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6805782/
https://www.ncbi.nlm.nih.gov/pubmed/31681232
http://dx.doi.org/10.3389/fmicb.2019.02375
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