Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales.
Wilpiszeski RL, Aufrecht JA, Retterer ST, Sullivan MB, Graham DE, Pierce EM, Zablocki OD, Palumbo AV, Elias DA
Appl Environ Microbiol. May 2019
COMMENT: This article reviews the state of knowledge about soils’ geochemical properties and their relation to microbial communities. The works addresses main technologies and experimental approaches to study soils and their biological counterparts.
Since soil is considered to be the basis of trophic chain for terrestrial life, a deeper knowledge about soil composition and dynamics turns out to be essential. In this sense, studies that relate the soil microbiome with its geochemical properties are key to understand the role of soil dynamics in the environment and in agricultural production.
Soils are complex three-dimensional structures made up from packed aggregates and pores within them. Aggregates are the functional units of a soil ecosystem, and can be seen as small-scale habitats in which microorganisms live and perform their metabolic activities. The structure of these aggregates, both at the geochemical and the microbial level have a decisive impact in soil properties.
Both the soil functional diversity and hydrological connectivity depend on the structure of soil aggregates. In this sense, aggregates could be understood as microbial niches which are interconnected.
Intra -aggregate communities can thus act as self-contained ‘microbial villages’ that are intermittently connected for nutrient exchange and gene ransfer
Viruses are very abundant in soils but their relation to microbial communities’ dynamics is still poorly understood. They are assumed to play a pivotal role in bacterial mortality and growth, as well as in horizontal gene transfer.
Characterization of microbiomas at different scales includes several approaches for the isolation of microbial communities from natural soils (from sieving to more complex techologies, such as advanced flow cytometry or microdissection) and characterization of aggregate-scale communities. This has been addressed by using a wide variety of nano-scale technologies. Even artificially created aggregates have been constructed using 3D printing technologies. This creates complex surfaces of controlled composition which can be completed with bacterial communities that mimic natural soils.
Although many approaches have rendered valuable results that help to understand the complexity of microbiomes in soil aggregates, there are still major challenges that have to be overcome, like isolation of aggregates with intact microbial communities, assessment of community interactions between aggregates and technical challenges to study structure-function relationships.