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Projects / Programmes source: ARRS

Employing the recent advances in metagenomics to explore the karst groundwater microbiome

Research activity

Code Science Field Subfield
1.05.00  Natural sciences and mathematics  Biochemistry and molecular biology   

Code Science Field
B230  Biomedical sciences  Microbiology, bacteriology, virology, mycology 

Code Science Field
1.06  Natural Sciences  Biological sciences 
Keywords
groundwater, metagenomics, novel sequencing techniques, single cell genomics
Evaluation (rules)
source: COBISS
Researchers (13)
no. Code Name and surname Research area Role Period No. of publications
1.  13654  PhD Jerneja Ambrožič Avguštin  Biochemistry and molecular biology  Researcher  2014 - 2017  233 
2.  30435  Gregor Bajc    Technician  2014  31 
3.  25974  PhD Cene Gostinčar  Biotechnology  Researcher  2016 - 2017  292 
4.  09836  PhD Blagajana Herzog-Velikonja  Biochemistry and molecular biology  Researcher  2014 - 2015  121 
5.  37703  PhD Luka Lipoglavšek  Animal production  Researcher  2015 - 2017  49 
6.  20220  PhD Janez Mulec  Biology  Researcher  2014 - 2017  454 
7.  20788  PhD Lejla Pašić  Biochemistry and molecular biology  Researcher  2014 - 2016  87 
8.  12605  PhD Metka Petrič  Geology  Researcher  2014 - 2017  501 
9.  27547  PhD Zala Prevoršek  Animal production  Researcher  2014 - 2017  40 
10.  16064  PhD Marjanca Starčič Erjavec  Biochemistry and molecular biology  Researcher  2014 - 2017  419 
11.  19104  PhD Blaž Stres  Animal production  Principal Researcher  2014 - 2017  348 
12.  32061  PhD Janja Zajc  Plant production  Researcher  2015  124 
13.  07042  PhD Darja Žgur Bertok  Biochemistry and molecular biology  Researcher  2014 - 2017  439 
Organisations (2)
no. Code Research organisation City Registration number No. of publications
1.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  64,121 
2.  0618  Research Centre of the Slovenian Academy of Sciences and Arts  Ljubljana  5105498000  58,441 
Abstract
About ninety-five percent of global liquid freshwater is stored in the terrestrial subsurface, making it the largest terrestrial freshwater biome. Despite the importance of this water source for humanity, these systems are largely understudied from the microbiological point of view. In Slovenia, about half of the population depends on groundwater for its domestic needs. The quality of this water source and the putative presence of pathogens are not properly monitored. Accordingly, very little is known about the composition and the structure of its native prokaryotic communities. Here presented project aims to lay ground for microbiological and ecological studies of groundwater reservoirs of Slovenian karst. It aims to identify and describe the diversity in those pristine reservoirs in which the microbiota is still present in its original splendor. To achieve this, we plan to take advantage of recently emerged approaches in metagenomics. In more detail, we plan to analyze a time-series of short-insert and fosmid libraries constructed in parallel from environmental DNA extracted from pristine groundwater reservoirs. Prior to library construction we plan to separate the suspended cells from the cells that are attached to particulate material. Furthermore, we plan to separate the cells based on their size in order to get information on all members of the community, including commonly overlooked ultramicrobacteria and bacteriophages. We expect the analysis of these community subsets not only to provide an estimate of species richness and the overall genetic potential of the community, but also to identify taxa that are either particularly abundant or ecologically relevant for studied ecosystem. We further plan to learn more about the ecology of these taxa through (i) analysis of its genome segments captured as inserts of fosmid clone libraries or assembled from the short read metagenomes, (ii) through their targeted cultivation based on metagenomic data and (iii) through the analysis of single amplified genomes of these cells as recently made possible by single cell genomics.
Significance for science
This project represented intensive metagenomic research of underground freshwater reservoirs. Despite their utmost importance for humanity as a drinking water resource, these are virtually unexplored from the microbiological point of view. Additional scientific value of this project is the fact that Slovenian karst in some remote parts, for example Alpine karst, still hosts pristine groundwater. The number of pristine habitats in Europe and elsewhere is constantly declining as a result of deteriorating impact of human population. Knowledge on composition, structure and the ecology of pristine populations is necessary to understand their responses to environmental disturbances. Another important output of this project is the archives of prokaryotic diversity. Collecting biomass and DNA samples, metagenomic sequence databases are of utmost importance as these are invaluable resources not only for environmental sciences but also for the future of biotechnology. In the latter field discovery of new utilizable genes, bioproducts and microbes of interest for food, pharmaceutics and fine chemistry industries. Reconstruction of the genomic draft on the basis of shot-gun metagenomic sequences shows us a surprising genetic and genomic diversity in both oligotrophic and cold waters, while demonstrating how new insights can be obtained through the use of newest sequencing technologies to provide a comprehensive insight into the fluctuations of the groups of functional genes of microorganisms, and on this basis, to shed light into their predominant metabolism. The tested experimental and analytical methods and pipelines are now available for extended use by other interested researchers.
Significance for the country
Basic research rarely has a direct impact on the economy. The occurrence of many diseases is conditioned by the environment. Metagenomic collections thus represent a permanent source of data for pathogen studies, their survival mechanisms in the environment and pathogenesis mechanisms that can be studied on the basis of the large amount of sequences obtained in this project. Knowledge about metagenomic techniques and bioinformatics has already been transferred to students and young scientists within master and postdoctoral projects. It is important to point out that most of the metagenomic collections are of a public nature and are freely available to researchers. The popularization of metagenomics can lead to the development of small businesses dedicated to the search for genes that are of interest to industry and thus contribute to the development of the local economy. We expect the project to contribute to the establishment of microbiote protection criteria groundwater, and thus promote the cooperation of scientists and control bodies quality of water. At the same time, the applied approach shows that the composition of all the analytical methods used in this project can be used for routine inspection and control of the quality of drinking water in Slovenia. By the fact that the whole project was carried out within Slovenian public research organizations, where we had to overcome many institutional barriers, we expect the research to have a positive impact on the development of metagenomics in Slovenia. Even if a large number of Slovenian scientists use a metagenomic approach in their studies, they do not fully implement it. They often rely on cooperation with foreign laboratories, which either prepare, or analyze metagenomic libraries. In addition, we have not yet carried out in-depth research involving environmental ones ultramicrobacteria. As part of our project, we managed to connect Slovenian experts in the field of metagenomics, bioinformatics and statistics, which can carry out such research entirely on the domestic territory.
Most important scientific results Annual report 2015, final report
Most important socioeconomically and culturally relevant results Final report
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