European Soil-Biology Data Warehouse for Soil Protection
The Section Mesofauna currently chairs the EU COST Action “EUdaphobase”, a European consortium of presently more than 80 participants from 30 countries, including the European Commission as well as European agencies.
At least 18 EU directives presently address the protection of soil, soil ecosystem services and/or soil biodiversity. Furthermore, many soil functions leading to ecosystem services are biotically driven. Soil protection thus requires coordinated efforts for the evaluation of soil biota throughout Europe. Without proper baseline data and reliable tools for soil-state assessment, it is currently difficult to efficiently address such goals. European authorities and stakeholders therefore urgently need reliable tools for monitoring and evaluating the biotic condition of soils within policy assessment. Procedures for assessing soil biodiversity as well as establishing baselines and current states must be based on existing data and knowledge, preferably accumulated from national or local databanks.
The EUdaphobase Action is expanding the Edaphobase soil-biodiversity data platform, creating the structures and procedures necessary for developing an open-access Europe-wide data infrastructure for soil invertebrate, fungi, bacteria and archaea. The goal is to establish a pan-European data and knowledge warehouse for understanding, protecting and sustainably managing soil biodiversity and its functions. A focal approach is to combine available soil biota’s distributional & trait data with environmental metadata to gain insight into functional relationships in soils. The activities follow an information flow from data providers to users of assessment tools. The data warehouse will host and allow open sharing of data. The consortium is developing standardized terminologies, data quality-control protocols and ecological traits used as proxies for soil ecosystem services (ESS). The Action will curate, harmonize, quality check and standardize existing data according to protocols agreed upon during the Action. To operationalize assessments of the state of soil concerning biodiversity and ESS, specific analytical tools will be developed that recognize and visualize (i.e. on maps) functional biological characteristics of soils related to type, use and management practices as well as determine and delineate ecosystem services, baselines, relationships and set the basis for forecasting changes.
The Action is financed by the Horizon 2020 Program of the EU under the Action number CA18237.
Project INPEDIV
Integrative Analysis of the Influence of Pesticides and Land Use on Biodiversity in Germany
In the Leibniz Collaborative Excellence project INPEDIV, we investigate the consequences of organic and conventional farming for biodiversity in protected areas. INPEDIV is an interdisciplinary joint project of seven partner institutes under the lead of the Zoological Research Museum Alexander Koenig and funded by the Leibniz Competition from March 2019 to February 2023. By use of traditional methods and new technologies, we are jointly examining agricultural land use effects with a special focus on pesticides on a broad range of plant and animal taxa. Study sites are located in the Rhineland and in Brandenburg.
Towards these goals, the Senckenberg Görlitz soil zoologists are investigating the relative importance of local and landscape-level factors for diversity and abundance of soil invertebrates and soil-biological activity. Our species-level focus will be on oribatid mites, nematodes and earthworms. We are investigating how their patterns change along gradients of pesticide load, soil nutrient content and management intensity – from farmland to adjacent protected sites.
In close cooperation with colleagues from ZALF and University Bonn, the Görlitz Botany Division studies changes in plant community composition from arable fields to dry grasslands, focusing on the transition zone. Additionally, we measure differences in soil nutrient conditions, and map differences in landscape structure by GIS based analysis of drone imagery.
MetaInvert: Metagenomic monitoring of soil communities
Soils are habitats for a tremendous diversity of animals and microorganisms, whose biological activity is the basis of many soil functions and ecosystem services. Despite their importance, comprehensive monitoring of soil fauna has not yet been possible due to the lack of methods to measure the composition of invertebrate communities, their biomass and their functions on a large scale. In MetaInvert we are therefore developing the necessary genomic resources, laboratory and bioinformatics tools for metagenome-based monitoring of soil invertebrate communities.
For this purpose, we are creating a genome database for initially about 300 species of a broad taxonomic spectrum of soil invertebrates: collembolans, ori-batid mites, nematodes, enchytraeids, tardigrades, diplopods, chilopods, isopods and several other groups.
Accuracy and efficiency of the metagenomic approach will be verified with artificially assembled soil animal communities. These artificial communities allow sensitivity and specificity analyses for taxonomic identification and to obtain biomass information from the number of sequenced DNA fragments.
Project VIRMISCO
The Virtual Microscope Slide Collection
Development of standards for the photographic documentation of permanent microscope slide mounts in precarious mounting media
“The scientifically motivated digitisation of cultural heritage materials is considered standard,
not a technical novelty.”
DFG-Practical Guidelines on “Digitalisation” 02/2013 funded by DFG: DFG XY 12/6-1
Digitisation allows science rapid access to research objects while conserving the originals. The linkage of diverse online resources creates a virtual research infrastructure that provides completely novel opportunities for science. To optimise their use in research and to ensure comparability, digitised materials should be produced under the same (documented) conditions. This requires the definition of standards for digitisation. For transparent to semitransparent three-dimensional microscopic objects, such as microinvertebrates or microscopic pieces of fungi, plants or other animals, the definition of standards is still in its initial stages. In this project we are developing standards and recommendations for taking microscopic images of 3D objects.
We therefore recommend as a standard for the digitalisation of three-dimensional objects in permanent preparations of soil organisms: (1) series of photographs with different focal planes (z stack); (2) using a microscope with motor focus; (3) at least one photograph with scale bar and measure of length; (4) bright-field microscopy, especially differential interference contrast microscopy (DIC); (5) the following metadata should be documented: creator of photographs, creation date, producer / type of microscope, producer / type of camera.
The benefits of Virmisco:
- Virtual access to collections
for taxonomic studies, like type material: Loans might become obsolete and prevents material – especially old and fragile one – from damage and loss. - New way for taxonomic publishing: the deposition of z-stacks in VIRMISCO in addition to the description will be a more comprehensible and objective documentation of the studied objects.
- Education and taxonomic training since it constitutes a virtual reference collection.
Virmisco provides more then 4.700 image stacks of ca. 172 taxa and more than 354 types from collection material of the Senckenberg Museum of Natural History Goerlitz; Acari (Gamasina, Uropodina, Oribatida), Collembola, Myriapoda (Diplopoda, Chilopoda, Pauropoda), Nematoda, Plathelminthes, Tardigrada, Insecta (Diptera).
Project Chicken Creek
Primary succession
Together with the Technical University of Cottbus the spatio-temporal colonization dynamics of soil animals are being studied in a 6-ha large, artificially created initial ecosystem since 2005. Until 2009, the investigations were carried out with the framework of the DFG Collaborative Research Centre Transregio 38 of the German Science Foundation. The new soils were inhabited by nematodes and first microarthropods already within the first weeks of site initiation. The Sections Mesofauna, Nematoda, Apterygota, Arachnida and Oribatida are studying the temporal sequence of species additions, the population development of species already present and their spatial distributional dynamics within the site as well as the spatio-temporal community assembly during primary succession. Beyond the dependence of these processes on the simultaneously developing vegetation and soils, the research is focusing on the dependence of assembly processes on the ecological requirements of primary colonizing taxa as well as the temporal development of the various trophic levels of the soil food web.
Project GBOL
German Barcode of Life – Inventory and molecular biological characterisation of animals, plants and fungi in Germany
Within the GBOL-project, a, cooperation of several German research institutes, funded by the BMBF, Senckenberg soil zoologists were going to generate an inventory of soil animals occurring in Germany,
focusing on Collembola, Nematoda, Oribatida and Gamasina (GBOL4), and Myriapoda (as part of GBOL1). The inventory included sampling of genetic fingerprints, as a first step towards an assessment of soil organism biodiversity within Germany at the genetic level.
Based on specimens and molecular data of soil animal species sampled from sites all over Germany we could detect and resolve cryptic species groups, and estimated intraspecific diversity of geographically separated populations.
For further information see www.bolgermany.de
Project BiK-F
Functional adaptation of saprophagous soil animals to climate change
With the research project „Forest of the Future” of the LOEWE research centre “Biodiversity and Climate” (BiK-F), the effects of southern European oak species on central European soil fauna and the decomposition processes they drive were being investigated. The existing oak forests in the Rhine Valley of southern Hesse were confronted with heavy losses due to increasing drought. Therefore, the potential of drought-resistant southern European oak species as future forest trees for Central Europe was being evaluated.
Accompanying research was investigating the effects the litter of these oak species (Quercus ilex, Q. frainetto and Q. pubescens) could had on central European soil-animal communities and their functions. A long-term monitoring programme was documenting possible changes on existing litter decomposer communities. Laboratory preference and metabolic studies were examining the ability of the most important primary litter “fragmenters” to ingest and assimilate the litter of these oak species in comparison to domestic tree species (Q. robur, Fagus sylvatica). Litter-bag experiments were measuring the decomposition rates and vectors of the litter from the same domestic and foreign tree species in the field.
Project Antarctis
The role of human activities in the introduction of non-native species into Antarctica and in the distribution of organisms within the Antarctic
UBA Research & Development Project 01.10.2009 – 30.09.2011
FKZ 3709 85 157a
The main goal of the present project was to assess the potential influence on Antarctic terrestrial ecosystems by increasing tourism. The project aimed at estimating the anthropogenic influence on the distribution of organisms within as well as on the introduction of non-native species into Antarctica, both in areas frequently visited by tourists and near research stations. Furthermore, the efficiency of possible preventive and precautionary measures was be investigated and evaluated.
Changes in species’ distributions are best considered within the framework of landscape ecology, which is, however, difficult to study in continents such as Antarctica. Due to their very small radius of action and their extreme habitat fidelity, soil organisms allowed the study of landscape-level processes at very small spatial scales. Taxonomically, soil organisms have been relatively well studied in Antarctica and are important, species- and individual-rich components of terrestrial ecosystems, especially in biotically relatively simple ecosystems as in Antarctica. Therefore, the present study will concentrated on soil organisms (flora and fauna), which allowed the research questions to be answered in a necessarily limited area of the Antarctic Peninsula.
Although literature concerning Antarctic soil flora and fauna as well as biological databanks for the Antarctica exist, with which taxonomic results could be compared, data from the possible origins of neobiota, e.g., the southern regions of South America, was practically non-existent. It was thus nearly impossible to evaluate whether detected but unknown species were undescribed endemics of Antarctica or originated from southern hemispheric continents. The evaluation of possible anthropogenic affects on species’ distributions was therefore be approached indirectly at different levels:
- Changes in the ß-diversity, i.e. the biodiversity of different microhabitats, within single locations. Especially in fragile and ecologically limited ecosystems as in Antarctica, undisturbed sites contain diverse microhabitats. These microhabitats harbour different species compositions and community structures, i.e. ß-diversity is high. In locations with high tourism pressure, species introduction can be higher between microhabitats of a single location than between continents, resulting in a biotic homogenisation of microhabitats and an overall reduction in the ß-diversity of a location.
- Zoogeographical distribution patterns. Different locations along the coast of Antarctica will be sampled, allowing the evaluation of the biogeographical distribution patterns of the registered species at larger spatial scales. In sites with high tourism pressure, a species composition containing more species with a wide distribution range and fewer locally endemic species than undisturbed sites, can indicate an anthropogenic influence on the distribution patterns of Antarctic organisms. Depending on the presence of locally endemic or more widely distributed species, possibly endangered locations (i.e., those with high levels of endemism) will be identified that should be exempted from tourism.
- Possible direct proof of introduced species. Despite the lack of taxonomic knowledge of southern-hemispheric soil organisms, introduction of some non-native species in Sub Antarctic islands, where the climatic conditions are not as harsh, is known. Registration of these species on the Antarctic continent – while not very probable due to climatic differences – will directly and explicitly indicate the introduction of none-native species.
- Evaluation of possible direct mechanisms of species introduction (“bootwashing”). A likely mechanism of species’ introduction is direct dispersal by, i.e., the footwear of visiting tourists. Therefore, the shoes and boots of tourists will be sampled and studied before and after visiting locations on the Antarctic continent for the presence of soil organisms.
The research project was commissioned by the German Federal Environment Agency and is carried out by the Senckenberg Museum of Natural History Görlitz, Germany, in close co-operation with international experts on soil invertebrates (Mikhail Potapov, Moscow; Alexander Brückner, Vienna; Sandra McInnes, Oxford). It is graciously supported by two cruise tour operators (Hapag-Lloyd and Delphin Tours) and their expedition leaders.
In the Antarctic summer of 2009/2010 soil samples were taken from nine different sites of the Antarctic Peninsula; six of which were frequently visited by tourists, three by research personal .
Sampling occurred in a statistical block design, comparing areas of high human impact with closely neighbouring areas without impact. Samples were transported back to Germany, where soil animals were extracted by various methods – on average 1-2 weeks after sampling – and then sorted into the animal groups Collembola, Oribatida, Gamasina, Prostigmata, Nematoda and Tardigrada. All animals were individually embedded on microscopic slides and determined to species level by the participating European taxonomic specialists. Ground vegetation occurring on the samples (mostly mosses, lichens and algae) were determined directly after animal extraction. Soil chemical and physical analyses of the samples were subsequently performed to ensure comparability of the contrasted sampling areas.
Determination of some animal groups is still ongoing. To date over 70 species of soil organisms have been identified, with many more still expected. Antarctic sites frequented by tourists are generally areas with high wildlife density (penguins, seals). The influence of this wildlife on soils and soil organisms can mask human trampling effects. Despite such difficulties, reduced
Example of the microarthropod densities in the sampling sites of one location (Arctowski Station, King George Island) densities in human-impacted areas could be detected for soil animals in general and especially for Collembola and Oribatida. These preliminary results were, however, site specific. Due to the still ongoing determination, effects on total species richness have not yet been determined. Nonetheless, based on data from Collembola and Oribatida, a reduced variability between species assemblages of human-impacted sites could be statistically identified, albeit somewhat marginally. This indicates a reduced ß-diversity of soil animal communities (“community homogenization”) within these localities due to human influence. This must still be confirmed with the data from all organism groups. As of yet, possibly introduced non-indigenous species (Collembola, Prostigmata) have only been identified from one location (Deception Island). Especially this site has a long history of human activity and, in particular, has warmer soils due to volcanic activity, which allows occurrence of species not adapted to Antarctic environmental conditions.
In the Antarctic summer of 2010/2011 seven sites – five of which were different from the previous year – were sampled as described above.
Sample processing, again as stated above, is presently ongoing. Additionally, on one cruise ship tour, the efficacy of on-board boot-washing techniques was tested by spot tests of a representative subset of the passenger’s boots after they were returned to the passenger’s lockers. Preliminary results show that boot-washing was not 100% effective, as sporadic individuals of soil animals (mainly Nematoda) could be identified from the boots after disinfection and boot-washing. This is most probably not due to an inherent inefficiency of the boot-washing methods, but rather to tourist behaviour regarding the methods. Furthermore, it could not be determined whether the soil animals remained
viable after disinfection, which should be tested by direct ecotoxicological experiments with the disinfectant. Final results of the study are expected by mid-2012.
Besides direct comparison of the identities of registered species with known non-native species, the biological data will be analysed using various biodiversity parameters (α-, β- and γ-diversity) of microhabitats, locations and all locations together. Comparison of the ß-diversity within anthropogenically influenced and relatively uninfluenced sites will allow identification of the level of disturbance on species’ distributions and thus potential introduction of species at small spatial scales. Based on the observed distribution of registered species throughout all sampling sites, species will be indentified that have wide and limited (= “locally endemic”) distributions. The proportions of these species groups will then be evaluated for each sampled location. A comparison of these proportions in touristically frequently and infrequently visited locations will provide an indication of anthropogenic species dispersal at larger spatial scales.
Project Partners
German Federal Environmental Agency (Section I 3.5 – Protection of the Antarctic)
Fritz Hertel
Senckenberg Museum für Naturkunde Goerlitz, Germany
Dr. Axel Christian (Gamasida)
Dr. Karin Hohberg (Nematoda)
Dr. Volker Otte (Mosses, Lichens)
Dr. David Russell (Actinedida)
Pedagogical University Moscow, Russia
Dr. Mikhail Potapov (Collembola)
University of Natural Resources and Life Sciences Vienna, Austria
Prof. Dr. Alexander Brückner (Oribatida)
British Antarctic Survey, Cambridge, UK
Dr. Sandra McInnes (Tardigrada)