Free-living diazotrophs in soil

Microbial physiology
Nutrient cycles
Technology / method development

The terrestrial nitrogen (N) cycle is essential for the Earth’s biosphere and intimately linked by microbial activity. Understanding the microorganism providing biologically available N through N2 fixation in a process called diazotrophy is imperative as N is a limiting factor for primary production and thereby CO2 sequestration. Non-symbiotic (free-living) microorganisms can contribute greatly to N2 fixation in terrestrial environments. However, we still have a very limited understanding of these microorganisms, because cultivation of diazotrophs is very challenging and only a small fraction can be cultivated in the laboratory. The advent of molecular biological techniques has provided first insights into the vast genetic diversity and distribution of diazotrophs in many different environments, but we still have very limited understanding of the microorganisms with the potential to fix N2, the active drivers in this important process and the factors influencing their activity. This project aims to fill this gap by using a unique and cultivation-independent approach that combines biogeochemical assays, stable isotope probing, next generation sequencing, and single cell techniques.

We are testing the recent hypothesis suggesting that diazotroph diversity positively influences N2 fixation activity. Using massive parallel sequencing of the functional gene for N2 fixation, dinitrogenase gene (nifH), we are documenting changes in nifH diversity across different ecosystems, seasons, and correlating these diversity data with soil properties and N2 fixation activity.  We are also documenting the influence of different C sources on N2 fixation activity using  15N2-DNA SIP, functional transcript sequencing, and a FISH-NanoSIMS approach. In summary, this integrated combination of cutting-edge methods has great potential to (i) advance our understanding of terrestrial diazotrophy and the factors controlling this important process, (ii) allow comparing the in situ activities of different microbial groups and the analysis of within population heterogeneities in an unprecedented way, but also (iii) encourage other scientists to apply this function-driven approach to terrestrial environments and tackle the many other un-answered questions of microbial function in these ecosystems.

This project is funded by the FWF - Austrian Science Fund (project No. P 25700-B20).



Selected Publications:

Angel R, Nepel M, Panhölzl C, Schmidt H, Herbold CW, Eichorst SA and Woebken D. (2018) Evaluation of primers targeting the diazotroph functional gene and development of NifMAP. Front Microbiol. 9(703):1-15. {doi:10.3389/fmicb.2018.00703}

Angel R, Panhölzl C, Gabriel R, Herbold C, Wanek W, Richter A, Eichorst SA and Woebken D. (2018) Application of stable-isotope labelling techniques for the detection of active diazotrophs. Environ Microbiol 20:44-61. {doi:10.1111/1462-2920.13954}

Herbold C, Pelikan C, Kuzyk O, Hausmann B, Angel R, Berry D, and Loy A. (2015) A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes. Front Microbiol 6(731):1-8. {doi:10.3389/fmicb.2015.00731}.

Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, and Woebken D. (2015) Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol Ecol 91: fiv106.{doi:10.1093/femsec/fiv106}

Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer SW, Lopez Cortes A, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM. (2015) Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J 9:485-496. {doi:10.1038/ismej.2014.144}

Eichorst SA and Woebken D. (2014) Investigation of microorganisms at the single-cell level using Raman Microspectroscopy and Nanometer-scale Secondary Ion Mass Spectrometry. In: Skovhus TL, Caffrey S, editors. Molecular Methods and Applications in Microbiology. Norfolk, UK: Caister Academic Press; p 203-211.