Soils are considered a hotspot for microbial diversity, from which bacteria are the most diverse members. Soil microorganisms contribute strongly to the services provided by soils, including promotion of plant growth, driving food, feed and fuel production, the sequestration of carbon and the degradation of pollutants.
The Biodiversity Exploratories, a German Science Foundation funded research project (DFG Priority Programme 1374), were created as a scientific infrastructure to address critical questions about changes in biodiversity and to evaluate the impacts of those changes for ecosystem processes. They are comprised of three large-scale and long-term research sites in Germany: the Biosphere Reserve Schorfheide-Chorin, the National Park Hainich and the Biosphere Reserve Schwäbische Alb.
Within the scope of the Biodiversity Exploratories, the Core project Microorganisms investigates soil microbial diversity and community composition of grassland and forest ecosystems along land use gradients in three research sites. This project is involved in centralized soil sampling campaigns and is responsible for the provisioning of soil nucleic acid extracts as a service to contributing projects studying microorganisms. Furthermore, the Core project Microorganisms analyses the diversity of soil bacteria and fungi, including arbuscular mycorrhizal fungi by barcoding sequencing as contribution to long term biodiversity monitoring. Using metagenome analyses it also provides functional analyses as well as diversity analysis of additional microbe groups such as Archaea and micro-eukaryotes.
Recently a new experiment (Forest gap Experiment – FOX), for which the Core project Microrganisms contributes, was set up in 29 different forest locations of the Biodiversity Exploratories which differ in management, biodiversity and ecosystem functions. This aims at understanding the changes driven by forest manipulation on biodiversity, namely by opening the canopy and logging. Four treatments were set up: 1) Gap - creating an opening in the canopy with a diameter of around 30m with removal of felled trees; 2) Gap and deadwood - creating a gap as before, but leaving felled trees as deadwood; 3) Deadwood enrichment - no gap but placing a certain amount of deadwood; 4) Control - no gap or additional deadwood.
The team from DSMZ (from the Department of Microbial Ecology and Diversity Research) was responsible for the campaign carried out in the National Park Hainich in Thuringia (9 locations). Despite the current pandemic and low temperatures, 342 soil cores comprising 117 samples were successfully retrieved last November.
After having carefully planned the equipment we needed in an environment which is completely different than a laboratory and having packed all our boxes into the cars we headed south towards the National Park Hainich.
As light is limited in winter months we worked in the forest from sunrise to sunset. Wearing several layers of outdoor and protective clothing, while transporting equipment such as a hammer, split tubes, cooling boxes, ethanol and measuring tapes we hiked through the woods resembling a bit like the Seven Dwarfs. Trying to find the correct sampling location under these conditions was the first workout of the day. Another challenge was to move from plot to plot through the forest. We had to struggle with sometimes quite steep, muddy and slippery grounds, circumvent tree trunks and branches hidden by big layers of leaves, and dodge dense 2 m high thickets of young trees.
At the sampling location, the cardinal points were determined using a compass and sampling points were measured in (at certain coordinates or in cross formation). At these points the various layers of litter (mostly leaves and seeds) were noted and collected. To take the soil samples, a large hammer was used to insert a sampler (5 cm diameter split tube) into the soil. The tube was pulled out of the ground, the soil A horizon was measured and a sample taken. Everything needed to be explicitly documented and you will only understand why a pencil is your best friend while being in the rain when every other pen would quit its job.
Returning to the field lab, where samples are processed, it’s already dark, but our evening routine is just starting: sieving, sieving, sieving! The samples need to be prepared: roots and stones are removed, soil is weighed and subsamples are stored at +4°C or -20°C. After all samples for the day are complete it is usually very late in the evening and only now we could call it “a day”.