Soil Microbial Ecology 
Ecology is important for understanding your soil
Ecology aims to understand the distribution and abundance of organisms, and their functions in a community. An organism's ecology is moderated by interactions with both the non-living environment and with other organisms. An ecosystem, for example a soil ecosystem, is a community of interacting organisms. Species-rich ecosystems with many interactions are more stable.
Healthy soils are diverse ecosystems
Healthy soils are complex ecosystems containing many species. Specific soil fungi and bacteria are associated with plant roots. Rhizosphere fungi and bacteria are functionally important to their plants.
Healthy soils have a highly diverse microbiota. Recent research estimates that 1 gram of a typical soil sample contains 10 000 species of bacteria or 1010 bacterial cells per square centimeter (Fierer et al, 2011). The latest genetics techniques are allowing us to discover soil microbiota that could not previously be studied.
A unique microbiota are specifically associated with plant roots. Plant rhizosphere soil contains a very different community of bacteria and fungi compared to the soil matrix. Many rhizosphere bacteria require metabolically active plant root cells to persist, and many fungi live symbiotically within plant roots.
Root-associated microbiota have functional significance for plants:
- Mycorrhizal fungi increase plant mobilisation and uptake of nutrients, especially phosphate
- Mycorrhizal fungi have a large surface area and can uptake water efficiently, this is transferred to plants
- Bacteria release many soil nutrients in a bioavailable form for plant uptake
- Specialised bacteria fix atmospheric nitrogen for plant use
- Bacteria and fungi can suppress competing pathogens that cause plant diseases.
A diverse soil microbiota results in improved soil ecosystem service
Soils with high microbial diversity suppress plant diseases spread in soil. Higher soil bacterial and fungal diversity increases soil functioning including higher soil nutrient cycling, increases soil decomposition rates, and higher plant productivity.
Diverse soils can be disease-suppressive. Increase soil; microbial diversity reduced both the size of a soil bacterial plant pathogen population, and its competititve ability, and therefore also its likelihood of survival (Van Elsas, 2012).
Increase mycorrhizal fungal species diversity causes higher plant shoot biomass, root biomass, increased overall plant phosphate uptake and plant productivity (Van der Heijden et al, 1998, Bevan et al, 2013).
Increased microbial diversity increases bacterial nutrient (nitrogen) cycling rates and wheat straw decomposition rates (Bell et al, 2005, Philippt et al, 2013, Baumann et al, 2013).
The rhizosphere - A complex and diverse interacting ecoystem.
Plant roots and soil microbiota interact via chemicals secreted by plant roots. Plant root secretions provide rhizosphere fungi and bacteria with abundant carbon-based food. Plant root secretitions can stimulate or suppress soil fungi and bacteria.
Diversity and stability in microbial populations
Microbes usually occupy subtly different microhabitates (niches) in soil. Some bacteria have resistant spores that can remain in soil to wait for a burst of food availability. If conditions become suitable, the population size of microbes that can consume available food will grow rapidly and exponentially. Soild with high microbial species diversity are more resilient to environmental change because they are more likely to contain species able to grow in any novel conditions.
A diversity of bacterial chemical signalling
Microbes secrete small molecules into their environment, and respond to molecules secreted by others. Some responses to signalling molecules ("quorum sensing") result in adaptations to new conditions, which benefit select groups over others. Signalling molecules from other organisms can block the signal cascade (called "quorum quenching"). Plant roots encourage beneficial associations with certain bacteria and fungi by secreting "elicitor" molecules, these lead to symbiotic associations.
Soil priming
Priming occurs when the addition of modest amounts of soil organic materials have a strong short-term effect on soil microbial activity and organic carbon breakdown. Soil priming occurs naturally when organic matter derived from photosynthesis is pumped into the rhizosphere soil via plant root secretions. Some compounds have significant soil priming effects, even at low concentration.
Addition of organic matter to the soil can cause an exponential increase in specific groups of soil microbes. These can rapidly consume both the organic matter added to the soil plus existing soil organic matter when added material runs out. Most natural organic matter additions into soil are via plant secretions into the soil rhizosphere, rather than plant litter.
Different organic materials have different soil priming effects, because different groups of microbes are stimulated. Simple organic matter additions include sugars and organic acids and cause priming via many microbes. Complex organic matter addititons include straw, wood cellulose, and lignin, and cause priming via specialist microbes.