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DormantMicrobes Report Summary

Project ID: 636928
Funded under: H2020-EU.1.1.

Periodic Reporting for period 1 - DormantMicrobes (Revealing the function of dormant soil microorganisms and the cues for their awakening)

Reporting period: 2015-09-01 to 2017-02-28

Summary of the context and overall objectives of the project

Soils harbor the most diverse microbial communities on Earth. However, at a certain point of time the vast majority of these microorganisms are dormant and only ca. 20% are active. It is hypothesized that this vast diversity of mostly dormant soil microorganisms ensures ecosystem functioning under different environmental conditions. The importance of dormant microorganisms in global nutrient cycles and the signals that reactivate them are still largely unknown. In this project, we aim to identify the active and dormant community members involved in selected important soil processes, as well as their participation in these processes and the mechanisms that regulate their activity and dormancy. This will generate essential knowledge on the diversity, the genetics and the function of the dormant majority in terrestrial ecosystems, and thus on the stability of microbial key processes under changing conditions.
The overall objectives are (1) to reveal environmental cues that resuscitate dormant microorganisms involved in major soil functions and identify the activated microorganisms; (2) to retrieve genomic information of primarily dormant, but after resuscitation active, microorganisms involved in important soil processes; which will then allow (3) investigating the genetics of microbial dormancy-resuscitation strategies.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Mineral soils contain the largest pool of C on Earth; cellulose is one of the major constituents, as it is a key component of plant structural C. Members of the bacteria and fungi are essential for degrading cellulose and thus are essential for cycling C. We hypothesize that by varying certain edaphic properties, which can limit cellulose degradation (such as N), we will resuscitate different members of the community (both bacteria & fungi). We performed cellulose degradation experiments at different seasons under different edaphic conditions and analyzed them on the process level. The active participants of the process were investigated via stable-isotope probing and next generation sequencing. Our data revealed that N in inorganic or organic form increased cellulolytic activity, presumably due to the activation of different cellulolytic guilds. These data were presented at the 74th Annual Swiss Society for Microbiology Meeting, Bern, Switzerland (invited talk by Dagmar Woebken, “Combining stable isotope labeling experiments and single-cell analysis to elucidate the function of microorganisms in soil”, June 2016), at the DBG-Workshop “Combined analysis of biochemistry and structural complexity of soil via imaging”, Halle, Germany (poster presentation by Florian Strasser, “Influences of carbon and nitrogen availability on microbial-mediated cellulose degradation in an Austrian beech forest soil” July 2016) and at the International Symposium on Microbial Ecology (ISME 16), Montreal, Canada (talk by Stephanie Eichorst, “Exploring the niches of cellulose degradation in a forested soil – from the process to the single-cell scale”, August 2016).
Another goal of the project is to investigate processes and the participating microorganisms in the Negev Desert, Israel, with the process of N2 fixation being of a particular focus. To retrieve samples from the Negev Desert, the team conducted a sampling trip in May 2016. The microorganisms participating in N2 fixation were revealed via activity assays combined with molecular approaches. The results were presented at conferences and in invited talks: At the International Symposium on Microbial Ecology (ISME 16), Montreal, Canada (invited talk by Dagmar Woebken, “Revealing the active participants of N2 fixation in photosynthetic microbial mats”, August 2017), at the 1st Meeting of the Study Group “Diversity and Function of Phototrophic Biofilms in the Seas of Oman”, Hanse-Wissenschaftskolleg, Delmenhorst, Germany (invited talk by Dagmar Woebken, “Combining stable isotope labeling experiments, molecular and single-cell analysis to elucidate the function of microorganisms in microbial mats”, November 2016) and at the Max Planck Institute for Chemistry, Mainz, Germany (invited talk by Dagmar Woebken, “Combining stable istotopes, molecular and single-cell methods to elucidate the function of microorganisms in photosynthetic mats”, February 2017).

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The research on complex C degradation in terrestrial ecosystem has a strong long-term socio-economic advancement potential. As global CO2 levels continue to rise due to anthropogenic activities, it is of utmost importance that we understand the factors determining C sequestration and C release as CO2. Second, our fossil fuel stocks are finite. Alternative, more ‘green’ fuel sources are needed to sustain our societal demands. The breakdown of plant material is an enormous resource for generating renewable biofuels. The proposed research has the potential to identify new target microorganisms with novel cellulose degradation genes for subsequent genetic manipulations for increased biomass-to-biofuel efficiencies and bioenergy applications. Our recent data pointed out another group of microorganisms involved in the breakdown of cellulose, the so-called opportunists. It becomes more and more apparent, that these microorganisms together with the primary degraders play an important role in the degradation of cellulose. Understanding the dynamics of these two groups could advance our knowledge on complex carbon degradation, which is also important for bioenergy applications.
Another progress achieved in this project beyond the expected potential impact is the constant quest to establish single-cell technologies for the investigation of microorganisms in diverse environmental samples. These methods can be transferred to other processes that are investigated by other scientists, thus opening the door to apply these powerful single-cell technologies to a wide array of open questions.

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