Soil Zoology

Cross-sectional projects

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 for 3 years – March 2019 to February 2022. 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.

Leibniz Logo_funded by_klein

Project BonaRes ‑ Soil as a sustainable resource for the bioeconomy

Within the BMBF-sponsored research initiative BonaRes , a new knowledge centre for soil functions and services in Germany has been developed: the BonaRes – Centre for Soil Research. The Centre is a cooperative project of the Helmholtz-Centre for Environmental Research – UFZ, the Leibniz Centre for Agricultural Landscape Research (ZALF), the Senckenberg Museum of Natural History Görlitz (SMNG), the Technical University of Munich, the Federal Institute for Geosciences and Natural Resources (BGR) and the Justus-Liebig-Universität Gießen.

The main goals are to examine the effects of land use on soil functions and to develop strategies for a sustainable use and management of soils. Towards these goals, a soil information system is being established that collects the expertise of scientists from different areas of soil research (i.e., soil science, microbiology and zoology). Within this collaboration, the SMNG is primarily responsible for soil zoology as well as linking Edaphobase with the BonaRes Centre.

Soils are a complex system, in which many factors and processes work together to produce complicated interactive structures. The manifold physical, chemical and biological interactions result in soil functions and ecosystem services such as nutrient cycling, water filtration, or the development and stabilization of soil structure. Agricultural primary production ultimately depends on these processes. The comprehensive understanding of soil systems is essential to securing or increasing harvests in the long term.

To this end, within the BonaRes Centre, the SMNG works on the identification and quantification of biological drivers of soil functions, the development of indicators for assessing these functions, the analysis of effects of agricultural management practices on soil fauna, as well as the provision of biological parameters for models of soil functions.

The project is funded by the Federal Ministry of Education and Research (BMBF), Project Management Jülich (PtJ), under the project number (FKZ) 031B0511D.

 

 

Edaphobase – open access Data Warehouse for Soil Biodiversity

Edaphobase is a non-commercial data infrastructure developed and hosted by the Senckenberg Museum of Natural History Görlitz in Germany, combining data from heterogeneous sources on soil animals, their distribution and habitat parameters of their sites of occurrence and making this data available to the public in open access. Edaphobase lives from the cooperation with numerous soil zoologists who upload their data to the database and thus make them available for overarching analyses and insight. The database currently focusses on Europe-wide soil-biodiversity data, but includes data from around the globe.

Edaphobase currently includes data on Nematoda, Collembola, Oribatida, Gamasina, Chilopoda, Diplopoda, Isopoda, Enchytraeidae, and Lumbricidae. The data model allows adding additional taxonomic groups easily, as long as the current (nomenclaturally complete) taxonomy and systematics of the group are provided. Edaphobase combines data on the taxonomy, zoogeography and ecology of these organisms in a comprehensive manner.

The data in Edaphobase originate from the scientific literature, unpublished results of field studies (theses, reports), collections of museums and research institutions as well as raw data from research studies and well-founded observations. Data types comprise modern taxonomic nomenclatures and synonyms, geographical references, quantities of collected organisms, soil parameters, vegetation, meteorological data, sampling and extraction methods, identification methods, preparation techniques and behavioural data. Altogether, data can be entered into (currently) ca. 620 available data fields in the above-mentioned categories.

Edaphobase is strongly geared towards common data re-use and provision of data and online analysis tools. It follows the FAIR principles and can offer DOIs for submitted data sets. Metadata are defined (including mandatory and recommended fields; in line with i.e. DataCite and INSPIRE standards), as are all data fields in the data base (including formats, units, etc.).

The database is publically available (open access) via a web-based data-query browser portal. All data (provided it is not anonymized or in an embargo period) can be queried and collated via multiple filters and be downloaded by registered users. Simple queries are possible as well as more sophisticated analyses of different data groups. Specific applications include, e.g., mapping taxa’s distributions, the elucidation of species-specific habitat preferences (niche space), or environmental correlations with population densities.

Edaphobase is a data provider to the Global Biodiversity Information Facility (GBIF).

 

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 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.

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).

 

Contact:

Dr. Axel Christian,
Tel. +49 3581 476052-01
axel.christian@senckenberg.de

Dr. Peter Decker,
Tel. +49 3581 476055-83
peter.decker@senckenberg.de
 
 
Virmisco: www.virmisco.org