Bacteria
Bacteria are ubiquitous in soils worldwide with up to 109 cells per g soil. They not only have a tremendous taxonomic but also metabolic diversity. For example, in term of carbon utilization, bacteria may be saprophytes, photoautrophs or lithoautrophs. Bacteria vary widely also in term of O2 requirement, ranging from obligate aerobes to obligate anaerobes. Bacteria can fix atmospheric nitrogen, produce greenhouse gases, decompose organic residues, etc. and they play a dominant role in the biogeochemical cycles linking to the Nutrient cycling and Carbon and climate regulation functions. Bacteria can also degrade various contaminants, which is of importance for soil and water quality. Moreover, bacteria are engaged in strong interactions with plants. Thus, bacteria can have both detrimental and beneficial effects on plant nutrition and health while their diversity and activity are strongly influenced by plants[1].
The range of approaches to study soil bacteria is broad but their diversity and abundance are now most often assessed by high throughput sequencing and qPCR techniques after DNA/RNA extraction from soil samples while their activities are monitored using enzymatic and respiration assays.
Due to their high taxonomic and metabolic diversity, various microbial groups and activities have been proposed as bioindicators of land use, agricultural practices, soil contamination and plant and soil health [2],[3]. There is a growing interest in applying bacterial trait-based concepts for predicting soil quality and functioning. Trait-based approaches can also be used to identify bacterial life history strategies[4], which are reflecting soil conditions such as high yield, resource acquisition, and stress tolerance strategies.
Text by dr. Laurent PhilippotDepartment of Agroecology, Instituté National de la Recherché Agronomique, Université Bourgogne
[1] Philippot L et al. 2013. Going back to the roots: the microbial ecology of the rhizosphere. Nature Reviews Microbiology 11:789-799.
[2] Griffiths BS et al. 2016. Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function. Ecological Indicators 69: 213-223.
[3] Wessen E and Hallin S. 2011. Abundance of archaeal and bacterial ammonia oxidizers – Possible bioindicator for soil monitoring. . Ecological Indicators 11: 1696-1698.
[4] Malik AA et al. 2020. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. The ISME Journal 14: 1-9.