Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1

The multiple symbiotic partnerships between closely related species of the haptophyte algae Braarudosphaera bigelowii and the nitrogen-fixing cyanobacteria Candidatus Atelocyanobacterium thalassa (UCYN-A) contribute importantly to the nitrogen and carbon cycles in vast areas of the ocean. The divers...

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Published in:Frontiers in Microbiology
Main Authors: Salas, Krystal, Cabello, Ana M., Turk-Kubo, Kendra A., Zehr, Jonathan P., Cornejo-Castillo, Francisco M.
Format: Text
Language:English
Published: Frontiers Media S.A. 2023
Subjects:
Online Access:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150950/
http://www.ncbi.nlm.nih.gov/pubmed/37138636
https://doi.org/10.3389/fmicb.2023.1130695
id ftpubmed:oai:pubmedcentral.nih.gov:10150950
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spelling ftpubmed:oai:pubmedcentral.nih.gov:10150950 2023-06-11T04:10:39+02:00 Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1 Salas, Krystal Cabello, Ana M. Turk-Kubo, Kendra A. Zehr, Jonathan P. Cornejo-Castillo, Francisco M. 2023-04-17 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150950/ http://www.ncbi.nlm.nih.gov/pubmed/37138636 https://doi.org/10.3389/fmicb.2023.1130695 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150950/ http://www.ncbi.nlm.nih.gov/pubmed/37138636 http://dx.doi.org/10.3389/fmicb.2023.1130695 Copyright © 2023 Salas, Cabello, Turk-Kubo, Zehr and Cornejo-Castillo. 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. Front Microbiol Microbiology Text 2023 ftpubmed https://doi.org/10.3389/fmicb.2023.1130695 2023-05-07T01:11:44Z The multiple symbiotic partnerships between closely related species of the haptophyte algae Braarudosphaera bigelowii and the nitrogen-fixing cyanobacteria Candidatus Atelocyanobacterium thalassa (UCYN-A) contribute importantly to the nitrogen and carbon cycles in vast areas of the ocean. The diversity of the eukaryotic 18S rDNA phylogenetic gene marker has helped to identify some of these symbiotic haptophyte species, yet we still lack a genetic marker to assess its diversity at a finer scale. One of such genes is the ammonium transporter (amt) gene, which encodes the protein that might be involved in the uptake of ammonium from UCYN-A in these symbiotic haptophytes. Here, we designed three specific PCR primer sets targeting the amt gene of the haptophyte species (A1-Host) symbiotic with the open ocean UCYN-A1 sublineage, and tested them in samples collected from open ocean and near-shore environments. Regardless of the primer pair used at Station ALOHA, which is where UCYN-A1 is the pre-dominant UCYN-A sublineage, the most abundant amt amplicon sequence variant (ASV) was taxonomically classified as A1-Host. In addition, two out of the three PCR primer sets revealed the existence of closely-related divergent haptophyte amt ASVs (>95% nucleotide identity). These divergent amt ASVs had higher relative abundances than the haptophyte typically associated with UCYN-A1 in the Bering Sea, or co-occurred with the previously identified A1-Host in the Coral Sea, suggesting the presence of new diversity of closely-related A1-Hosts in polar and temperate waters. Therefore, our study reveals an overlooked diversity of haptophytes species with distinct biogeographic distributions partnering with UCYN-A, and provides new primers that will help to gain new knowledge of the UCYN-A/haptophyte symbiosis. Text Bering Sea PubMed Central (PMC) Bering Sea Frontiers in Microbiology 14
institution Open Polar
collection PubMed Central (PMC)
op_collection_id ftpubmed
language English
topic Microbiology
spellingShingle Microbiology
Salas, Krystal
Cabello, Ana M.
Turk-Kubo, Kendra A.
Zehr, Jonathan P.
Cornejo-Castillo, Francisco M.
Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1
topic_facet Microbiology
description The multiple symbiotic partnerships between closely related species of the haptophyte algae Braarudosphaera bigelowii and the nitrogen-fixing cyanobacteria Candidatus Atelocyanobacterium thalassa (UCYN-A) contribute importantly to the nitrogen and carbon cycles in vast areas of the ocean. The diversity of the eukaryotic 18S rDNA phylogenetic gene marker has helped to identify some of these symbiotic haptophyte species, yet we still lack a genetic marker to assess its diversity at a finer scale. One of such genes is the ammonium transporter (amt) gene, which encodes the protein that might be involved in the uptake of ammonium from UCYN-A in these symbiotic haptophytes. Here, we designed three specific PCR primer sets targeting the amt gene of the haptophyte species (A1-Host) symbiotic with the open ocean UCYN-A1 sublineage, and tested them in samples collected from open ocean and near-shore environments. Regardless of the primer pair used at Station ALOHA, which is where UCYN-A1 is the pre-dominant UCYN-A sublineage, the most abundant amt amplicon sequence variant (ASV) was taxonomically classified as A1-Host. In addition, two out of the three PCR primer sets revealed the existence of closely-related divergent haptophyte amt ASVs (>95% nucleotide identity). These divergent amt ASVs had higher relative abundances than the haptophyte typically associated with UCYN-A1 in the Bering Sea, or co-occurred with the previously identified A1-Host in the Coral Sea, suggesting the presence of new diversity of closely-related A1-Hosts in polar and temperate waters. Therefore, our study reveals an overlooked diversity of haptophytes species with distinct biogeographic distributions partnering with UCYN-A, and provides new primers that will help to gain new knowledge of the UCYN-A/haptophyte symbiosis.
format Text
author Salas, Krystal
Cabello, Ana M.
Turk-Kubo, Kendra A.
Zehr, Jonathan P.
Cornejo-Castillo, Francisco M.
author_facet Salas, Krystal
Cabello, Ana M.
Turk-Kubo, Kendra A.
Zehr, Jonathan P.
Cornejo-Castillo, Francisco M.
author_sort Salas, Krystal
title Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1
title_short Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1
title_full Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1
title_fullStr Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1
title_full_unstemmed Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1
title_sort primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium ucyn-a1
publisher Frontiers Media S.A.
publishDate 2023
url http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150950/
http://www.ncbi.nlm.nih.gov/pubmed/37138636
https://doi.org/10.3389/fmicb.2023.1130695
geographic Bering Sea
geographic_facet Bering Sea
genre Bering Sea
genre_facet Bering Sea
op_source Front Microbiol
op_relation http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150950/
http://www.ncbi.nlm.nih.gov/pubmed/37138636
http://dx.doi.org/10.3389/fmicb.2023.1130695
op_rights Copyright © 2023 Salas, Cabello, Turk-Kubo, Zehr and Cornejo-Castillo.
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.
op_doi https://doi.org/10.3389/fmicb.2023.1130695
container_title Frontiers in Microbiology
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