Mining of unexplored habitats for novel chitinases - chiA as a helper gene proxy in metagenomics
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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; Sørensen, Søren Johannes; van Elsas, Jan Dirk.
In: Applied Microbiology and Biotechnology, Vol. 94, No. 5, 2012, p. 1347-1358.Research output: Contribution to journal › Journal article › Research › peer-review
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T1 - Mining of unexplored habitats for novel chitinases - chiA as a helper gene proxy in metagenomics
AU - Cretoiu, Mariana Silvia
AU - Kielak, Anna Maria
AU - Abu Al-Soud, Waleed
AU - Sørensen, Søren Johannes
AU - van Elsas, Jan Dirk
PY - 2012
Y1 - 2012
N2 - 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.
AB - 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.
KW - Animals
KW - Chitinase
KW - Cluster Analysis
KW - DNA, Bacterial
KW - Denaturing Gradient Gel Electrophoresis
KW - Ecosystem
KW - Environmental Microbiology
KW - Genes, Bacterial
KW - Genetic Variation
KW - Metagenome
KW - Metagenomics
KW - Polygonaceae
KW - Polymerase Chain Reaction
KW - Porifera
KW - Sequence Analysis, DNA
U2 - 10.1007/s00253-012-4057-5
DO - 10.1007/s00253-012-4057-5
M3 - Journal article
C2 - 22526805
VL - 94
SP - 1347
EP - 1358
JO - Applied Microbiology and Biotechnology
JF - Applied Microbiology and Biotechnology
SN - 0175-7598
IS - 5
ER -
ID: 40801841