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Dominance of Burkholderia sp. in low pH Environments: from Biogeography to Tolerance Mechanisms

English title Dominance of Burkholderia sp. in low pH Environments: from Biogeography to Tolerance Mechanisms
Applicant Weisskopf Laure
Number 130089
Funding scheme Project funding (Div. I-III)
Research institution Forschungsanstalt Agroscope Reckenholz-Tänikon ART
Institution of higher education Research Institutes Agroscope - AGS
Main discipline Experimental Microbiology
Start/End 01.09.2010 - 28.02.2014
Approved amount 216'000.00
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All Disciplines (3)

Discipline
Experimental Microbiology
Ecology
Molecular Biology

Keywords (2)

Low pH; soil

Lay Summary (English)

Lead
Lay summary
Recent studies have shown that pH plays a major role in the biogeography of micro-organisms. However, the mechanisms that enable specific taxa to establish in low pH environments, while others are excluded have not yet been investigated. In this project, we address this question using Burkholderia as a model genus. The genus Burkholderia (β-Proteobacteria) comprises over 60 species that are characterized by a very versatile metabolism and broad ecological amplitude. Burkholderia sp. are typical soil and rhizosphere inhabitants and engage in a variety of interactions (both mutualistic and parasitic) with other organisms (plants, fungi, animals, humans). We have accumulated evidence that Burkholderia sp. are among those populations that become dominant in acidic soils and we want to investigate the underlying mechanisms responsible for this dominance. The goals of this project are i) to evaluate the role of acid tolerance in the biogeography of the genus Burkholderia, ii) to assess the species-specificity of the acid tolerance and iii) to investigate the mechanisms leading to acid tolerance. This project will lead to a better understanding of the biogeography of the Burkholderia genus and provide valuable information for a broader audience, e.g. for Burkholderia species of agronomical or clinical relevance.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Molecular mechanisms underlying the close association between soil Burkholderia and fungi
Stopnisek Nejc, Zühlke Daniela, Carlier Aurélien, Barberán Albert, Fierer Noah, Becher Dörte, Riedel Katharina, Eberl Leo, Weisskopf Laure (2016), Molecular mechanisms underlying the close association between soil Burkholderia and fungi, in The ISME Journal, 10, 253-264.
Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations
Stopnisek Nejc, Bodenhausen Natacha, Fierer Noah, Frey Beat, Eberl Leo, Weisskopf Laure (2014), Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations, in Environmental Microbiology, 16(6), 1503-1512.
Oxalotrophy, a widespread trait of plant-associated Burkholderia species, is involved in successful root colonization of lupin and maize by Burkholderia phytofirmans.
Kost Thomas, Stopnisek Nejc, Agnoli Kirsty, Eberl Leo, Weisskopf Laure (2014), Oxalotrophy, a widespread trait of plant-associated Burkholderia species, is involved in successful root colonization of lupin and maize by Burkholderia phytofirmans., in Frontiers in microbiology, 4, 421.
Production of bioactive volatiles from different Burkholderia ambifaria strains
Groenhagen Ulrike, Baumgartner Rita, Bailly Aurélien, Gardiner Amber, Eberl Leo, Schulz Stefan, Weisskopf Laure (2013), Production of bioactive volatiles from different Burkholderia ambifaria strains, in Journal of Chemical Ecology, 39(7), 892-906.
The genetic basis of cadmium resistance of Burkholderia cenocepacia
Schwager S Lumjiaktase P Stöckli M Weisskopf L and Eberl L (2012), The genetic basis of cadmium resistance of Burkholderia cenocepacia, in Environmental Microbiology Reports, 4(5), 562-568.
Burkholderia sp are major inhabitants of white lupin cluster roots
Weisskopf Laure Heller Stefanie and Eberl Leo (2011), Burkholderia sp are major inhabitants of white lupin cluster roots, in Applied and Environmental Microbiology, 77(21), 7715-7720.

Collaboration

Group / person Country
Types of collaboration
University of Colorado at Boulder United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
University of Aberdeen Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
University of Greifswald Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
WSL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
ETH Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Mikrobiologisch-infektiologisches Kolloquium an der Universität Greifswald Individual talk Bacteria-fungi interactions in the soil, the rhizosphere and the phyllosphere 28.01.2016 Greifswald, Germany Weisskopf Laure;
Netherland Institute of Ecology (NIOO) Colloquium (invited seminar) Individual talk Bacteria-fungi interactions in the soil, the rhizosphere and the phyllosphere 15.06.2015 Wageningen, Netherlands Weisskopf Laure;
BAGECO12 Poster Biogeography of soil Burkholderia populations 09.06.2013 Ljubljana, Slovenia Stopnisek Nejc;
BAGECO12 Poster Warning - bacterial stink bomb! The potential of non cyanogenic Pseudomonas for biological control of Phytophthora infestans 09.06.2013 Ljubljana, Slovenia Weisskopf Laure;
Swiss Microbial Ecology Meeting Individual talk The smell of bacteria and its impact on plants and phytopathogenic fungi 04.02.2013 Murten, Switzerland Weisskopf Laure;
Swiss Microbial Ecology Meeting Individual talk Biogeography of soil Burkholderia populations 04.02.2013 Murten, Switzerland Stopnisek Nejc;
ISME 14 The Power of the Small Individual talk A smelly world: how bacterial volatiles influence the growth of plants and of phytopathogenic fungi 19.08.2012 Copenhagen, Denmark Weisskopf Laure;
ISME 14 The Power of the Small Poster Influence of acidity on the abundance and diversity of soil Burkholderia populations 19.08.2012 Copenhagen, Denmark Stopnisek Nejc;
VAAM-Jahrestagung 2012 Poster Biogeography of soil Burkholderia populations 18.03.2012 Tübingen, DE, Germany Stopnisek Nejc;
FEMS Microbiology Congress 2011 Poster Reactions of Plants to Bacterial Volatiles: From Love to Hatred 26.06.2011 Geneva, Switzerland Weisskopf Laure;
FEMS Microbiology Congress 2011 Poster Influence of acidity on the abundance and diversity of soil Burkholderia populations 26.06.2011 Geneva, Switzerland Stopnisek Nejc;
Ecology of Soil Microorganisms Poster Influence of acidity on the abundance and diversity of soil Burkholderia populations: from biogeography to low pH tolerance mechanisms 27.04.2011 Prague, Czech Republic Stopnisek Nejc;
Ecology of Soil Microorganisms Poster BURKHOLDERIA SPECIES ARE MAJOR INHABITANTS OF WHITE LUPIN’S CLUSTER ROOTS 27.04.2011 Prague, Czech Republic Weisskopf Laure;
International Symposium on Soil Metagenomics Poster Influence of acidity on the abundance and diversity of soil Burkholderia populations: from biogeography to low pH tolerance mechanisms 08.12.2010 Braunschweig, Germany Stopnisek Nejc; Weisskopf Laure;


Communication with the public

Communication Title Media Place Year
Talks/events/exhibitions Frühlingsfest Botanischer Garten German-speaking Switzerland 2012
Talks/events/exhibitions Vortrag für die Freunde des Botanischen Gartens German-speaking Switzerland 2012

Associated projects

Number Title Start Funding scheme
149271 Elucidating the mechanisms underlying volatile-mediated growth inhibition of Phytophthora infestans by rhizosphere bacteria 01.03.2014 Project funding (Div. I-III)

Abstract

Recent studies have shown that pH plays a major role in the biogeography of micro-organisms. However, the mechanisms that enable specific taxa to establish in low pH environments, while others are excluded have not yet been investigated. In this project, we address this question using Burkholderia as a model genus. The genus Burkholderia (ß-Proteobacteria) comprises over 50 species that are characterized by a very versatile metabolism and broad ecological amplitude. Burkholderia sp. are typical soil and rhizosphere inhabitants and engage in a variety of interactions (both mutualistic and parasitic) with other organisms (plants, fungi, animals, humans). We have accumulated evidence that Burkholderia sp. are among those populations that become dominant in acidic soils and we want to investigate the underlying mechanisms responsible for this dominance.The goals of this project are:i)to evaluate the role of acid tolerance in the biogeography of the genus Burkholderiaii)to assess the species-specificity of the acid toleranceiii)to investigate the mechanisms leading to acid toleranceIn order to reach these goals, we plan the following experiments/analyses:i)Taking advantage of an available soil DNA sample collection of continental scale (98 soil DNA samples from across North and South America), we will analyze the dominance of Burkholderia sp. using a quantitative PCR approach. The intra-generic specificity of the acid tolerance will be evaluated by cloning-sequencing of 16S rRNA and recA genes in a subset of samples.ii)The existence of a causal link between low pH and Burkholderia dominance will be tested using a microcosm design allowing for pH manipulation. Changes in Burkholderia abundance and species diversity will be monitored using the same methods as mentioned for i). In addition, Burkholderia strains will be isolated, identified and submitted to low pH tolerance in vitro assays.iii)Tolerance mechanisms will be elucidated by using a combination of molecular analyses (taking advantage of available tools, e.g. a transposon mutant bank and other Burkholderia mutants in putative acid tolerance factors) and of physiological tests on our vast Burkholderia strain collection (growth in low pH media, competition experiments with other soil/rhizosphere strains).This project will lead to a better understanding of the biogeography of the Burkholderia genus and provide valuable information for a broader audience (e.g. for Burkholderia species of agronomical or clinical relevance). Moreover, it will bring the first step towards an understanding of the mechanisms underlying low pH tolerance in Burkholderia sp., a question that has not yet been addressed at all.
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