Amplicon metagenomics for elucidating microbial community changes associated to conventional and organic farming of Beta vulgaris and Solanum lycopersicum


Autoria(s): Ibáñez Solé, Olga
Contribuinte(s)

Zarraonaindia Martínez, Iratxe

F. CIENCIA Y TECNOLOGIA

ZIENTZIA ETA TEKNOLOGIA F.

Grado en Biología

Biologiako Gradua

Data(s)

27/04/2016

27/04/2016

27/04/2016

03/09/2015

Resumo

Soil microbial community changes associated to conventional and organic farming of two relevant crops (Beta vulgaris and Solanum lycopersicum) were analysed through 16s rRNA amplicon sequencing. This study revealed microbial communities in the agricultural soils studied to be similar to other reported nutrient-rich microbiomes, and some significant differences between the microbial communities associated to the two farming practices were found. Some phyla (Chloroflexi and Thermi) were found to be present in different abundances according to soil treatment. As chloroplast interference can be a stumbling block in plant-associated 16s rRNA amplicon metagenomics analysis of aerial plant tissues, two protocols for bacterial cell detachment (orbital shaking and ultrasound treatment) and two protocols for microbial biomass recovery (centrifugation and filtration) were tested regarding their efficiency at excluding plant-DNA. An alternative method to the one proposed by Rastogi et al (2010) for evaluating the chloroplast-amplicon content in post-PCR samples was tested, and the method revealed that filtration was the most efficient protocol in minimising chloroplast interference.

Identificador

http://hdl.handle.net/10810/17961

63574-667698-11

26462-667698

Idioma(s)

eng

es

Direitos

© 2015, la autora

info:eu-repo/semantics/openAccess

Palavras-Chave #microbial communities #agricultural soils #amplicon metagenomics
Tipo

info:eu-repo/semantics/bachelorThesis