RICERCA ITALIANA     

New method for the analysis of biodiversity: application of pyrosequencing to the study of soil organisms

Università degli Studi di Milano-Bicocca

Abstract

The study of biodiversity is becoming more and more central in the international scientific community. Our project meets this interest and proposes an innovative approach to the biodiversity investigation: the pyrosequencing on a massive environmental scale. Pyrosequencing allows to analyse a high number of samples in a short period of time, factors really useful in an environmental study on a large scale. This approach could be considered a pivotal project for biodiversity researches. Recently, most of the molecular environmental studies follow a metagenomic approach (i.e. a study in which a collection of genes sequenced from the environment could be analyzed in way analogous to the study of a single genome): based on data from Genomes OnLine Database, Release 2.0 (http://www.genomesonline.org/gold.cgi) there are 115 metagenomic projects ongoing by now. However, in these kind of projects the huge amount of data, makes really complex and expensive the data management, with often the loss of taxonomic details. Our method, due to its concentration on only a fraction of the gene sequences obtainable, permits to achieve a high level of efficiency (comparable to that of a metagenomic approach) coupled with a higher taxonomic accuracy.
Research units involved in this project possess all the necessary skills (i.e. traditional and molecular taxonomists, molecular evolutionists) and are the ideal candidates to develop an integrated approach to the study of biodiversity. The >>>

Principal Investigator

Maurizio Casiraghi Università degli Studi di MILANO-BICOCCA

Research Objectives

The main aim of the project is the application of an innovative method for the study of biodiversity on a vast scale. In particular, the technique used, in addition to the actually available, is
the pyrosequencing on a massive scale. Through this method it is possible to reach a high analytic power in a little amount of time, allowing a screening of a high number of samples with optimal species-specific and geographical assignations through a system of specific markers for each sample. These markers will be automatically recognized by the identification system developed in our project. These factors make pyrosequencing particularly suited for biodiversity investigations.
Model of our studies will be the soil ecological community from chestnut (Castanea sativa) forests, for which a moderate degree of biodiversity is expected. This kind of habitat is spread all over Italy, and it is characterized by a limited anthropogenic impact from the agronomic point of view (there are no fertilizations, plowing, harrowing, etc.), a possible source of bias to the composition of soil biotic communities.
In our investigation we do not follow a metagenomic approach (i.e. a study in which a collection of genes sequenced from the environment could be analyzed in way analogous to the study of a single genome), but we will study some key organisms: carabid coleopterans, terrestrial isopods, soil nematodes and ascomycetous fungi. These taxonomic groups have been chosen because >>>

First Results

In this project we foresee the achieving of the following results:

1) development and validation of an innovative system for biodiversity study.
The result will be pursued by mean of a pyrosequencing on a massive environmental scale. Model of the approach will be the biotic community of soils from chestnut (Castanea sativa) forests, using some taxonomic groups as reference (e.g. carabids coleopterans, terrestrial isopods, nematodes and ascomycetous fungi).
It has to be underlined that these results are really innovative, and represent a pivotal project for these kind of researches. Nowadays, many environmental sampling on molecular basis are directed to metagenomic approaches (i.e. a study in which a collection of genes sequenced from the environment could be analyzed in way analogous to the study of a single genome), an approach in which a elevated quantity of information are managed, with high costs, complex analyses and sometimes with a reduced care to the taxonomic data. We believe that the approach we propose could represent a bridge between the traditional approach to biodiversity studies (correct but in many case time consuming for many high qualified researchers) and the metagenomic approach (necessary a huge project with a considerable money investment). This is possible thank to the high number of samples analysable and to the high accuracy of the species identification (see point 16 for details).
The choice to direct this >>>

Timescale

24 months

National and international background

Biological diversity means the full range of variety and variability within and among living organisms and the ecological complexes in which they occur, and encompasses ecosystem or community diversity, species diversity, and genetic diversity. The study of biodiversity has become quite ‘fashionable’ in the last years, because of the possibilities to use unknown organisms/molecules for medical and technological purposes and because of the impact of human activities on it. In spite of many studies, most of the Earth biodiversity (past and present) is still unknown, as well as the complex dynamics of its evolution and the interactions among its various components.
Characterization of biodiversity is ultimately based on: (a) genetics, which depicts the levels of intra-specific and inter-specific variation; (b) systematics, which provides an organized assessment of organisms and returns their evolutionary history (phylogeny); (c) ecology, which investigates structure and function of ecosystems where genetic diversity and taxonomy are naturally integrated. Modern science implements and combines traditional methodologies and technological
innovation, aiming at producing shared international standards. Molecular biology supply the adequate tools for a reliable study of biodiversity (Blaxter, 2004; Lee, 2004; Powers, 2004) and as a natural consequence of the development of techniques for the study of DNA, genetic characterization is the pivotal tool for the study of >>>