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Revealing the function of dormant soil microorganisms and the cues for their awakening

Periodic Reporting for period 3 - DormantMicrobes (Revealing the function of dormant soil microorganisms and the cues for their awakening)

Reporting period: 2018-09-01 to 2020-02-29

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 microorganism ensures ecosystem functioning under different environmental conditions. The importance of dormant microorganism 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.
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.
Another goal of the project is to investigate resuscitation and dormancy strategies in soil microorganisms, with a focus on organisms inhabiting biological soil crusts in the Negev Desert. We are using meta-omics techniques in combination with single-cell activity assays to understand the genetic mechanisms that allow dormancy and the dynamics of resuscitation. A process of particular interest in these desert soil crusts is N2 fixation, together with the participating microorganisms (diazotrophs). Re-activated diazotrophs were identified in samples from the Negev Desert via activity assays combined with molecular approaches.
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.
Sampling in the Negev Desert, Israel