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Deciphering mechanisms of soil bacterial community assembly under changing hydration regimes

English title Deciphering mechanisms of soil bacterial community assembly under changing hydration regimes
Applicant Or Dani
Number 182734
Funding scheme Project funding (Div. I-III)
Research institution Institut für Biogeochemie und Schadstoffdynamik ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Experimental Microbiology
Start/End 01.01.2019 - 31.12.2019
Approved amount 93'070.00
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All Disciplines (2)

Discipline
Experimental Microbiology
Biophysics

Keywords (3)

Microbial ecology; Bacterial communities; Soil microbiology

Lay Summary (German)

Lead
Bodenmikroorganismen wie Bakterien sind essentiell für die Gesundheit und Produktivität von Böden. Die Vielfalt der im Boden lebenden Bakterien ist immens; die verschiedenen Bakterienarten recyceln gemeinsam abgestorbenes Material und unterstützen das Pflanzenwachstum. Der Einfluss von Umweltfaktoren auf die Organisation und Vielfalt bakterieller Gemeinschaften im Boden ist jedoch noch nicht vollständig aufgeklärt. Von grossem Interesse ist insbesondere die Rolle dynamischer Veränderungen der Bodenfeuchtigkeit (z. B. nach Regen) auf die bakterielle Diversität und Aktivität, da diese in engem Zusammenhang mit Klimaveränderungen steht.
Lay summary

Um diese Fragen besser zu verstehen, haben wir ein experimentelles System entwickelt, mit dem wir untersuchen können, wie Wasserverfügbarkeit die Organisation einer einfachen, repräsentativen Gemeinschaft aus 11 Bakterienarten beeinflusst. In unserem Laborsystem haben wir den Erdboden durch kleine Glasperlen ersetzt. Diese bilden ein experimentelles Ökosystem - den sogenannten Mikrokosmus - welches sich durch ein dreidimensionales Porennetzwerk auszeichnet. Durch Zugabe von Nährstoffen in Form eines definierten Flüssigmediums können wir Bedingungen für das Bakterienwachstum simulieren, welche den Bedingungen in ihrem natürlichen Habitat, dem Erdreich, ähneln. Um die Zusammensetzung unserer repräsentativen Gemeinschaft auszuwerten, haben wir eine molekulare Methode basierend auf DNA-Vervielfachung entwickelt. Unsere ersten Ergebnisse zeigten, dass dynamische Veränderungen des Wassergehalts signifikante Auswirkungen auf die Zusammensetzung und Diversität der Bakteriengemeinschaft haben. In diesem Projekt wollen wir untersuchen, wie die repräsentative Bakteriengemeinschaft auf extreme Veränderungen der Wasserverfügbarkeit wie Trockenheit reagiert. Die Ergebnisse werden uns helfen, die Umweltbedingungen und Mechanismen besser zu verstehen, welche die Vielfalt der Bakterien im Boden, die ein wichtiger Bestandteil der Bodenökosysteme ist, fördern, erhalten oder reduzieren.

Direct link to Lay Summary Last update: 29.09.2018

Responsible applicant and co-applicants

Employees

Publications

Publication
Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media
Kleyer Hannah, Tecon Robin, Or Dani (2019), Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media, in Applied and Environmental Microbiology, 86(1), 1-13.

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
7th Swiss Microbial Ecology Meeting (SME 2019) Poster Hydration dynamics alters species composition of a representative soil bacterial community inhabiting unsaturated porous microcosms 30.01.2019 Auqatis Conference Center, Lausanne, Switzerland Tecon Robin; Or Dani; Kleyer Hannah;


Associated projects

Number Title Start Funding scheme
172493 Evaporation suppression from water reservoirs using floating covers: scientific basis and design considerations 01.08.2017 Project funding (Div. I-III)

Abstract

Soil bacteria are key players for many ecosystem services and for soil ecological functioning. Recent molecular techniques uncovered a tremendous bacterial diversity in soil, however, the underlying mechanisms controlling composition, functioning and maintenance of diverse microbial communities remain largely unknown. In this proposal we aim to link dynamics of soil hydration conditions and nutrient availability in model soil systems with variations in microbial community composition. Understanding factors that shape species abundance is essential to gaining insights into how microbial communities assemble and function under the ever-changing aqueous habitats in soil. The research plan aims to expand ongoing research that has established a unique experimental system for systematic community level observations of a designed a synthetic microbial community combined with a microfluidic quantitative PCR assay designed for absolute quantification of species level changes in community composition. We first assembled a representative soil bacterial community comprised of 11 well-characterized bacterial species spanning a wide range of soil phyla. The community was inoculated onto model porous surfaces mimicking soil habitats with accurate control of hydration status. The activity and composition of the bacterial community established in a sand layer within each microcosm were evaluated using 16S fingerprinting and quantitative PCR. Preliminary results show that the bacterial assembly inoculated at equal proportions of species responds to hydration conditions, with saturated habitats enhancing competition for resources, while unsaturated conditions enhance niche formation that promote coexistence and diversity. The observed shifts in community composition can also be linked to physiological factors such as bacterial cell shapes, motility and their metabolic rate under given conditions. The trends deduced from experiments with the synthetic community under a range of controlled physico-chemical conditions contribute to basic understanding of how diversity is maintained in natural systems. Observations how the community stabilizes during the first hours of the experiment raises the question how the spatial structure of a given environment acts on the bacterial consortium and how extreme hydration conditions (saturated and very dry) would shape community composition and dynamics. To address these questions, two follow-up experiments are planned with the same soil bacterial community subjected to extreme dry conditions in a sand microcosms with defined hydration to answer the question how the consortia responds to extreme dry conditions and as second habitat microcosms with-agar surface as a set-up presenting routine laboratory conditions, the wet scenario. The hypothesis is that a representative soil bacterial community requires a heterogeneous, structured environment to maintain coexistence of dominant and rare species, whereas using standard habitats such as growing cells on an agar surface might select for more competitive species, while less competitive species would decline and eventually disappear. Such insights would enhance our understanding of soil ecological functioning and dominant species under different hydration states, and the mechanisms that maintain high level of biodiversity in soil.
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