Mining of unexplored habitats for novel chitinases - chiA as a helper gene proxy in metagenomics

TY - JOUR

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 - 2012/6

Y1 - 2012/6

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

SN - 0175-7598

VL - 94

SP - 1347

EP - 1358

JO - Applied Microbiology and Biotechnology

JF - Applied Microbiology and Biotechnology

IS - 5

ER -