Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea
Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the...
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Veröffentlicht in: | Gene 2016-02, Vol.576 (2), p.626-636 |
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creator | Alzubaidy, Hanin Essack, Magbubah Malas, Tareq B. Bokhari, Ameerah Motwalli, Olaa Kamanu, Frederick Kinyua Jamhor, Suhaiza Ahmad Mokhtar, Noor Azlin Antunes, André Simões, Marta Filipa Alam, Intikhab Bougouffa, Salim Lafi, Feras F. Bajic, Vladimir B. Archer, John A.C. |
description | Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide.
In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in ‘metabolism of aromatic compounds’, ‘mobile genetic elements’, ‘potassium metabolism’ and ‘pathways that utilize osmolytes’ in the rhizosphere microbiomes.
To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea. |
doi_str_mv | 10.1016/j.gene.2015.10.032 |
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To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.</description><identifier>ISSN: 0378-1119</identifier><identifier>EISSN: 1879-0038</identifier><identifier>DOI: 10.1016/j.gene.2015.10.032</identifier><identifier>PMID: 26475934</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Aromatic hydrocarbon degradation ; Avicennia - genetics ; Avicennia - metabolism ; Avicennia - microbiology ; Avicennia marina ; Firmicutes ; Indian Ocean ; Metagenomics ; Microbial diversity ; Microbiota ; Mobile genetic elements ; Osmolytes ; Potassium metabolism ; Proteobacteria ; Rhizosphere ; Saudi Arabia ; Sediments</subject><ispartof>Gene, 2016-02, Vol.576 (2), p.626-636</ispartof><rights>2015 The Authors</rights><rights>Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c569t-5354b644cc36a370186a4ac6e18b32955c1b7fded1ef3cf2ac1412bfc416c34a3</citedby><cites>FETCH-LOGICAL-c569t-5354b644cc36a370186a4ac6e18b32955c1b7fded1ef3cf2ac1412bfc416c34a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.gene.2015.10.032$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>315,781,785,3551,27926,27927,45997</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26475934$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Alzubaidy, Hanin</creatorcontrib><creatorcontrib>Essack, Magbubah</creatorcontrib><creatorcontrib>Malas, Tareq B.</creatorcontrib><creatorcontrib>Bokhari, Ameerah</creatorcontrib><creatorcontrib>Motwalli, Olaa</creatorcontrib><creatorcontrib>Kamanu, Frederick Kinyua</creatorcontrib><creatorcontrib>Jamhor, Suhaiza Ahmad</creatorcontrib><creatorcontrib>Mokhtar, Noor Azlin</creatorcontrib><creatorcontrib>Antunes, André</creatorcontrib><creatorcontrib>Simões, Marta Filipa</creatorcontrib><creatorcontrib>Alam, Intikhab</creatorcontrib><creatorcontrib>Bougouffa, Salim</creatorcontrib><creatorcontrib>Lafi, Feras F.</creatorcontrib><creatorcontrib>Bajic, Vladimir B.</creatorcontrib><creatorcontrib>Archer, John A.C.</creatorcontrib><title>Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea</title><title>Gene</title><addtitle>Gene</addtitle><description>Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide.
In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in ‘metabolism of aromatic compounds’, ‘mobile genetic elements’, ‘potassium metabolism’ and ‘pathways that utilize osmolytes’ in the rhizosphere microbiomes.
To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.</description><subject>Aromatic hydrocarbon degradation</subject><subject>Avicennia - genetics</subject><subject>Avicennia - metabolism</subject><subject>Avicennia - microbiology</subject><subject>Avicennia marina</subject><subject>Firmicutes</subject><subject>Indian Ocean</subject><subject>Metagenomics</subject><subject>Microbial diversity</subject><subject>Microbiota</subject><subject>Mobile genetic elements</subject><subject>Osmolytes</subject><subject>Potassium metabolism</subject><subject>Proteobacteria</subject><subject>Rhizosphere</subject><subject>Saudi Arabia</subject><subject>Sediments</subject><issn>0378-1119</issn><issn>1879-0038</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkE1rGzEQhkVpaFynf6CHoqNzWEejr92FXoxJ2kAgkLTkKLTaWVvGu3KltSH59ZFx2mPJXDS8PPOCHkK-ApsDA321ma9wwDlnoHIwZ4J_IBOoyrpgTFQfyYSJsioAoD4nn1PasDxK8U_knGtZqlrICXl6WPuXkHZrjEh772JofOjziqPN7SFHiYaOrqJ9pr0dVjEcMNHZ4uAdDoO3OYx-sJfUD3RcI33Alj6ivSBnnd0m_PL2Tsnvm-tfy5_F3f2P2-XirnBK12OhhJKNltI5oa0oGVTaSus0QtUIXivloCm7FlvATriOWwcSeNM5CdoJacWUzE69uxj-7DGNpvfJ4XZrBwz7ZKDUXGimqvodqAJZVZKrjPITmn2kFLEzu-jzR58NMHN0bzbm6N4c3R-z7D4ffXvr3zc9tv9O_srOwPcTgFnIwWM0yXkcHLY-ohtNG_z_-l8BglWUsg</recordid><startdate>20160201</startdate><enddate>20160201</enddate><creator>Alzubaidy, Hanin</creator><creator>Essack, Magbubah</creator><creator>Malas, Tareq B.</creator><creator>Bokhari, Ameerah</creator><creator>Motwalli, Olaa</creator><creator>Kamanu, Frederick Kinyua</creator><creator>Jamhor, Suhaiza Ahmad</creator><creator>Mokhtar, Noor Azlin</creator><creator>Antunes, André</creator><creator>Simões, Marta Filipa</creator><creator>Alam, Intikhab</creator><creator>Bougouffa, Salim</creator><creator>Lafi, Feras F.</creator><creator>Bajic, Vladimir B.</creator><creator>Archer, John A.C.</creator><general>Elsevier B.V</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>20160201</creationdate><title>Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea</title><author>Alzubaidy, Hanin ; 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A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide.
In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in ‘metabolism of aromatic compounds’, ‘mobile genetic elements’, ‘potassium metabolism’ and ‘pathways that utilize osmolytes’ in the rhizosphere microbiomes.
To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>26475934</pmid><doi>10.1016/j.gene.2015.10.032</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Aromatic hydrocarbon degradation Avicennia - genetics Avicennia - metabolism Avicennia - microbiology Avicennia marina Firmicutes Indian Ocean Metagenomics Microbial diversity Microbiota Mobile genetic elements Osmolytes Potassium metabolism Proteobacteria Rhizosphere Saudi Arabia Sediments |
title | Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea |
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