Biological diversity

Soil biota along redox gradient and role of this gradient in invertebrate microbial interactions

This research programme is dedicated to the study of diversity of functional groups of organisms and their interactions in soil and sediment niches differing in availability of oxygen. We focus on several important soil microsites, namely soil aggregates, invertebrate intestine and animal faeces and on aeration gradient in sediment. We determine the genetic and other bioindicators specific for selected biocenosis in hot-spot soil niches in dependence on oxygen availability. We characterise the biodiversity in hot-spot niches with respect to availabilty of oxygen and to organic matter transformation. We study the impact of bulk soil biodiversity on transformation of organic matter and soil biota interactions in soil hot-spot niches affected by oxygen availability. The role of soil microbial diversity in processes associated with organic matter transformation is assessed, in particular its role in the degradation and elimination of anthropogenic pollutants under different aeration conditions. In the sediment, we study the effect of environmental conditions on microbial functioning with focus on methanotrophy, denitrification and iron cycle along the oxygen gradient.

Key question

Functional diversity of groups of organisms with different requirements to aeration status substantially differs in soil and sediment niches differing in availability of oxygen. This functional diversity affects soil structure, stable soil organic matter formation and sediment organic matter decomposition and iron cycling. We focus on several important soil microsites, namely soil aggregates and invertebrate and vertebrate intestine and faeces, as well as on oxygen gradient in the sediment.

Project team

Roey Angel

Environmental microbiologist

Hana Šantrůčková

Senior Scientist

Alica Chroňáková

Soil Scientist

Ana Catalina Lara R.

Molecular biologist and bioinformatics


Diversity of the microbial community and selected functional microbial groups are studied in hot-spot niches of the active and stable part of microbiome, e.g. invertebrate and vertebrate faeces, invertebrate intestine, soil aggregates, sediment, litter, under oxic and anoxic conditions combining selective cultivation, PCR, quantitative PCR, fingerprinting techniques (PLFA or DGGE or TRFLP), microscopic techniques (CARD-FISH) and metagenomic amplicon sequencing (active and stable part of microbiome, RNA- and DNA- based approaches). The soil, leaf litter and/or sediment differing in quality of OM and microbial biodiversity and representatives of important functional groups of soil macrofauna – endogeic earthworms and/or leaf litter consuming millipedes are used in micro- and mesocosms experiments run under different aeration and redox conditions. The cultivable isolates are consequently characterized to acquire signature biomarkers/bioindicators suitable for monitoring and next experiments. In the sediment diversity of methanotrophic, methanogenic, denitrifiers and iron reducing bacteria is of the main interest. The digestive tract of soil macrofauna is studied in detail of aerobic/anaearobic microenvironments.

Animals are fed on soil and/or litter differing in OM quality and microbial diversity. Parts of animals are dissected for microsensoric measurements, enzymatic activity measurement and microbial characterizations based on markers defined above. Standardized microcosms incubation experiments in different aeration and redox conditions are coupled to previous activities to observe in detailed enzymatic activity, microbial characteristics and OM quality under controlled conditions. The studied niches are characterized by microsensors. The acquired information on the link between soil and sediment biodiversity, micro-zoo edafon-interactions, OM quality, transformation and stabilisation under laboratory conditions are related to standardized ecosystems in the manipulation experiment as well as to ecosystems with different gradient of soil and sediment biodiversity and OM quality and quantity and affected by human activities. Standardized microcosms are used to gain an insight into hot-spots niches of agricultural soils affected by additions of OM of different quality including animal wastes with respect (i) on changes of soil biodiversity, OM quality, and (ii) soil ability to eliminate pollutants and contaminations.