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...

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Bibliographic Details
Published in:Applied Microbiology and Biotechnology
Main Authors: Cretoiu, Mariana Silvia, Kielak, Anna Maria, Abu Al-Soud, Waleed, Sorensen, Soren J., van Elsas, Jan Dirk, Sørensen, S.J.
Format: Article in Journal/Newspaper
Language:English
Published: 2012
Subjects:
chiA
Bacterial community
Environment
Functional screening
chiA pyrosequencing
16S RIBOSOMAL-RNA
BACTERIAL CHITINASES
MICROBIAL ECOLOGY
DIVERSITY
SOIL
COMMUNITY
CHITOSAN
DEGRADATION
HYDROLASES
Arctic
Oxyria digyna
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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Summary: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.

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