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 |
---|---|
Main Authors: | , , , , |
Format: | Text |
Language: | English |
Published: |
Springer-Verlag
2012
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353111 http://www.ncbi.nlm.nih.gov/pubmed/22526805 https://doi.org/10.1007/s00253-012-4057-5 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:3353111 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:3353111 2023-05-15T15:07:57+02:00 Mining of unexplored habitats for novel chitinases—chiA as a helper gene proxy in metagenomics Cretoiu, Mariana Silvia Kielak, Anna Maria Al-Soud, Waleed Abu Sørensen, Søren J. van Elsas, Jan Dirk 2012-04-25 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353111 http://www.ncbi.nlm.nih.gov/pubmed/22526805 https://doi.org/10.1007/s00253-012-4057-5 en eng Springer-Verlag http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353111 http://www.ncbi.nlm.nih.gov/pubmed/22526805 http://dx.doi.org/10.1007/s00253-012-4057-5 © The Author(s) 2012 Methods and Protocols Text 2012 ftpubmed https://doi.org/10.1007/s00253-012-4057-5 2013-09-04T07:18:04Z 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. Text Arctic Oxyria digyna PubMed Central (PMC) Arctic Applied Microbiology and Biotechnology 94 5 1347 1358 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Methods and Protocols |
spellingShingle |
Methods and Protocols Cretoiu, Mariana Silvia Kielak, Anna Maria Al-Soud, Waleed Abu Sørensen, Søren J. van Elsas, Jan Dirk Mining of unexplored habitats for novel chitinases—chiA as a helper gene proxy in metagenomics |
topic_facet |
Methods and Protocols |
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 |
Text |
author |
Cretoiu, Mariana Silvia Kielak, Anna Maria Al-Soud, Waleed Abu Sørensen, Søren J. van Elsas, Jan Dirk |
author_facet |
Cretoiu, Mariana Silvia Kielak, Anna Maria Al-Soud, Waleed Abu Sørensen, Søren J. van Elsas, Jan Dirk |
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 |
publisher |
Springer-Verlag |
publishDate |
2012 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353111 http://www.ncbi.nlm.nih.gov/pubmed/22526805 https://doi.org/10.1007/s00253-012-4057-5 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Oxyria digyna |
genre_facet |
Arctic Oxyria digyna |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353111 http://www.ncbi.nlm.nih.gov/pubmed/22526805 http://dx.doi.org/10.1007/s00253-012-4057-5 |
op_rights |
© The Author(s) 2012 |
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 |
_version_ |
1766339373873233920 |