Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics
The main objective of this study was to assess the abundance and diversity of chitin-degrading microbial communities in ten terrestrial and aquatic habitats in order to provide guidance to the subsequent exploration of such environments for novel chitinolytic enzymes. A combined protocol which encom...
Published in: | Applied Microbiology and Biotechnology |
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Main Authors: | , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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2012
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Online Access: | https://hdl.handle.net/11370/3dfe7064-dc7f-4a13-be9e-5d380e931774 https://research.rug.nl/en/publications/3dfe7064-dc7f-4a13-be9e-5d380e931774 https://doi.org/10.1007/s00253-012-4057-5 https://pure.rug.nl/ws/files/136041520/Mining_of_unexplored_habitats_for_novel_chitinases_chiA_as_a_helper_gene_proxy.pdf |
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ftunigroningenpu:oai:pure.rug.nl:publications/3dfe7064-dc7f-4a13-be9e-5d380e931774 2024-06-02T08:02:25+00:00 Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics Cretoiu, Mariana Silvia Kielak, Anna Maria Abu Al-Soud, Waleed Sorensen, Soren J. van Elsas, Jan Dirk Sørensen, S.J. 2012-06 application/pdf https://hdl.handle.net/11370/3dfe7064-dc7f-4a13-be9e-5d380e931774 https://research.rug.nl/en/publications/3dfe7064-dc7f-4a13-be9e-5d380e931774 https://doi.org/10.1007/s00253-012-4057-5 https://pure.rug.nl/ws/files/136041520/Mining_of_unexplored_habitats_for_novel_chitinases_chiA_as_a_helper_gene_proxy.pdf eng eng https://research.rug.nl/en/publications/3dfe7064-dc7f-4a13-be9e-5d380e931774 info:eu-repo/semantics/openAccess Cretoiu , M S , Kielak , A M , Abu Al-Soud , W , Sorensen , S J , van Elsas , J D & Sørensen , S J 2012 , ' Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics ' , Applied Microbiology and Biotechnology , vol. 94 , no. 5 , pp. 1347-1358 . https://doi.org/10.1007/s00253-012-4057-5 chiA Bacterial community Environment Functional screening chiA pyrosequencing 16S RIBOSOMAL-RNA BACTERIAL CHITINASES MICROBIAL ECOLOGY DIVERSITY SOIL COMMUNITY CHITOSAN DEGRADATION HYDROLASES article 2012 ftunigroningenpu https://doi.org/10.1007/s00253-012-4057-5 2024-05-07T17:58:48Z The main objective of this study was to assess the abundance and diversity of chitin-degrading microbial communities in ten terrestrial and aquatic habitats in order to provide guidance to the subsequent exploration of such environments for novel chitinolytic enzymes. A combined protocol which encompassed (1) classical overall enzymatic assays, (2) chiA gene abundance measurement by qPCR, (3) chiA gene pyrosequencing, and (4) chiA gene-based PCR-DGGE was used. The chiA gene pyrosequencing is unprecedented, as it is the first massive parallel sequencing of this gene. The data obtained showed the existence across habitats of core bacterial communities responsible for chitin assimilation irrespective of ecosystem origin. Conversely, there were habitat-specific differences. In addition, a suite of sequences were obtained that are as yet unregistered in the chitinase database. In terms of chiA gene abundance and diversity, typical low-abundance/diversity versus high-abundance/diversity habitats was distinguished. From the combined data, we selected chitin-amended agricultural soil, the rhizosphere of the Arctic plant Oxyria digyna and the freshwater sponge Ephydatia fluviatilis as the most promising habitats for subsequent bioexploration. Thus, the screening strategy used is proposed as a guide for further metagenomics-based exploration of the selected habitats. Article in Journal/Newspaper Arctic Oxyria digyna University of Groningen research database Arctic Applied Microbiology and Biotechnology 94 5 1347 1358 |
institution |
Open Polar |
collection |
University of Groningen research database |
op_collection_id |
ftunigroningenpu |
language |
English |
topic |
chiA Bacterial community Environment Functional screening chiA pyrosequencing 16S RIBOSOMAL-RNA BACTERIAL CHITINASES MICROBIAL ECOLOGY DIVERSITY SOIL COMMUNITY CHITOSAN DEGRADATION HYDROLASES |
spellingShingle |
chiA Bacterial community Environment Functional screening chiA pyrosequencing 16S RIBOSOMAL-RNA BACTERIAL CHITINASES MICROBIAL ECOLOGY DIVERSITY SOIL COMMUNITY CHITOSAN DEGRADATION HYDROLASES Cretoiu, Mariana Silvia Kielak, Anna Maria Abu Al-Soud, Waleed Sorensen, Soren J. van Elsas, Jan Dirk Sørensen, S.J. Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics |
topic_facet |
chiA Bacterial community Environment Functional screening chiA pyrosequencing 16S RIBOSOMAL-RNA BACTERIAL CHITINASES MICROBIAL ECOLOGY DIVERSITY SOIL COMMUNITY CHITOSAN DEGRADATION HYDROLASES |
description |
The main objective of this study was to assess the abundance and diversity of chitin-degrading microbial communities in ten terrestrial and aquatic habitats in order to provide guidance to the subsequent exploration of such environments for novel chitinolytic enzymes. A combined protocol which encompassed (1) classical overall enzymatic assays, (2) chiA gene abundance measurement by qPCR, (3) chiA gene pyrosequencing, and (4) chiA gene-based PCR-DGGE was used. The chiA gene pyrosequencing is unprecedented, as it is the first massive parallel sequencing of this gene. The data obtained showed the existence across habitats of core bacterial communities responsible for chitin assimilation irrespective of ecosystem origin. Conversely, there were habitat-specific differences. In addition, a suite of sequences were obtained that are as yet unregistered in the chitinase database. In terms of chiA gene abundance and diversity, typical low-abundance/diversity versus high-abundance/diversity habitats was distinguished. From the combined data, we selected chitin-amended agricultural soil, the rhizosphere of the Arctic plant Oxyria digyna and the freshwater sponge Ephydatia fluviatilis as the most promising habitats for subsequent bioexploration. Thus, the screening strategy used is proposed as a guide for further metagenomics-based exploration of the selected habitats. |
format |
Article in Journal/Newspaper |
author |
Cretoiu, Mariana Silvia Kielak, Anna Maria Abu Al-Soud, Waleed Sorensen, Soren J. van Elsas, Jan Dirk Sørensen, S.J. |
author_facet |
Cretoiu, Mariana Silvia Kielak, Anna Maria Abu Al-Soud, Waleed Sorensen, Soren J. van Elsas, Jan Dirk Sørensen, S.J. |
author_sort |
Cretoiu, Mariana Silvia |
title |
Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics |
title_short |
Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics |
title_full |
Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics |
title_fullStr |
Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics |
title_full_unstemmed |
Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics |
title_sort |
mining of unexplored habitats for novel chitinases-chia as a helper gene proxy in metagenomics |
publishDate |
2012 |
url |
https://hdl.handle.net/11370/3dfe7064-dc7f-4a13-be9e-5d380e931774 https://research.rug.nl/en/publications/3dfe7064-dc7f-4a13-be9e-5d380e931774 https://doi.org/10.1007/s00253-012-4057-5 https://pure.rug.nl/ws/files/136041520/Mining_of_unexplored_habitats_for_novel_chitinases_chiA_as_a_helper_gene_proxy.pdf |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Oxyria digyna |
genre_facet |
Arctic Oxyria digyna |
op_source |
Cretoiu , M S , Kielak , A M , Abu Al-Soud , W , Sorensen , S J , van Elsas , J D & Sørensen , S J 2012 , ' Mining of unexplored habitats for novel chitinases-chiA as a helper gene proxy in metagenomics ' , Applied Microbiology and Biotechnology , vol. 94 , no. 5 , pp. 1347-1358 . https://doi.org/10.1007/s00253-012-4057-5 |
op_relation |
https://research.rug.nl/en/publications/3dfe7064-dc7f-4a13-be9e-5d380e931774 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1007/s00253-012-4057-5 |
container_title |
Applied Microbiology and Biotechnology |
container_volume |
94 |
container_issue |
5 |
container_start_page |
1347 |
op_container_end_page |
1358 |
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1800746913043054592 |