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

Project Information

DormantMicrobes

Grant agreement ID: 636928

DOI

10.3030/636928

Project closed

EC signature date 22 April 2015

Start date 1 September 2015

End date 30 April 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 356,25

EU contribution

€ 1 499 356,25

Coordinated by

UNIVERSITAT WIEN
Austria

Periodic Reporting for period 4 - DormantMicrobes (Revealing the function of dormant soil microorganisms and the cues for their awakening)

Reporting period: 2020-03-01 to 2022-04-30

Summary of the context and overall objectives of the project

Soils harbor the most diverse microbial communities on Earth; however, the vast majority of these microorganisms are dormant at a given time. It is hypothesized that this vast diversity of mostly dormant soil microorganism ensures ecosystem functioning under different environmental conditions. The mechanisms for dormancy, the signals that reactivate them and the importance of dormant microorganism in global nutrient cycles are still largely unknown. In this project, we aimed to identify the active and dormant community members involved in selected important soil processes, as well as the mechanisms that regulate their activity and dormancy. This will generate essential knowledge on the diversity, the genetic potential and the function of the dormant majority in terrestrial ecosystems, and thus on the stability of microbial key processes under changing conditions.
In this project, we were able to identify environmental cues that resuscitate dormant microorganisms involved in major soil functions and the activated microorganisms. By combining state-of-the-art -omics and single-cell activity analysis, we further revealed major dormancy mechanisms that soil microorganisms employ for survival and resuscitation dynamics in situations when the environmental stress ceases. In addition to these important insights into the survival strategies and thus resilience of soil microorganisms, this project considerably advanced the application of single-cell methods to microorganisms in diverse soil environments.

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

Soil microorganisms are the drivers of major nutrient cycles on Earth. However, as most soil microorganisms are dormant, it is important to elucidate the active participants in soil processes. In this project, we explored the active microorganisms involved in two major processes in soil - degradation of plant polymeric material (cellulose) and fixation of atmospheric N2 gas. Cellulose is a key component of plant material, and one of the major constituents of the soil carbon pool. Bacteria and fungi work in tandem to mediate the decomposition of this polymer, yet their activities, interactions and ecological niches have yet to be explored. To that end, we investigated microbial-mediated cellulose degradation to explore the influence of background nutrient on process dynamics and niche availability for the bacterial-fungal cellulose-degrading consortium. We found that the cellulose-degrading consortium had a clear niche differentiation depending on carbon- and nitrogen-availability and time. Although historically fungi are presumed to be the most important participants of this process, our data suggest that bacteria exploit a clear, yet context-dependent functional niche. Network analysis further revealed, that there are in fact stable co-occurrence patterns between fungi and bacteria independent of nutrient amendments and time underlining the consortia nature of cellulose degradation in soil. In the process of N2 fixation, we investigated the dependence of active diazotrophs on different C and thus energy sources, which in soil are provided via plant root exudation. Active diazotrophs were identified in the vicinity of plant roots, which represent a reactivation hotspot for diazotrophs. Sequence analysis revealed that the active diazotroph community was plant-specific and differed significantly from the diazotroph seedbank, suggesting plant-specific resuscitation effects. Another goal of the project was to investigate dormancy strategies of soil microorganisms inhabiting arid soils, namely biological soil crusts in the Negev Desert. We used meta-omics techniques in combination with single-cell activity assays to understand the genetic mechanisms for dormancy and the resuscitation dynamics of microorganisms inhabiting these crusts, which explain their capability to persist in this inhospitable environment. The results of this project were disseminated via scientific publications and presentations at scientific conferences by the team to the scientific audience and to the non-scientific public in articles, interviews and other outreach activities.

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)

Soils often represent inhospitable habitats for microorganisms, and thus, the vast majority of soil microorganisms is in a dormant state. The capacity of soil microorganisms to survive unfavorable conditions is important to ensure ecosystem functioning under different environmental conditions, which is particularly relevant in the era of climate change. In this project, we have particularly revealed survival mechanisms of microorganisms living in arid ecosystems, where water limitation represents a major stress. As drylands are expanding, maintenance of soil biodiversity will heavily depend on the capacity of soil microorganisms to survive these harsh conditions.
This project has provided important insights how microorganisms persist in arid environments, revealing their dormancy mechanisms and resuscitation dynamics. With this, we have generated a framework, which now allows investigating other soil systems for the capacity of microbial resilience against aridity. Another progress achieved in this project is the application of state-of-the-art single-cell technologies to challenging environmental samples. These methods allowing single-cell activity measurements can be transferred to other systems and processes, thus opening the door to apply these powerful single-cell technologies to a wide array of open questions.

Sampling in the Negev Desert, Israel