The interactions between microbes and plants make the major contribution to the biotic components of soils, the most diverse habitats on Earth. Plants play central roles in providing nutrient input into the soil, both through microbially-mediated decomposition of plant matter, and through the direct provision of photosynthate derived root exudates. These nutrients support large and diverse microbial communities, many of which provide direct benefit to the plant. The interplay between plants and their microbial co-habitants is regulated by extensive chemical signalling. Most of what we know about these complex community interactions has been derived through study of organisms in pure culture, but it is well known that the vast majority of microbes have not been cultivated. We now have the opportunity to explore the interactions between plants and microbes through cultivation-independent study of the microbial communities. While high-throughput DNA sequence analysis is an important tool for these studies, the immense richness and diversity of such communities present a strong mandate for the use of functional metagenomics strategies that involve a broad variety of screening methodologies to discover and study the currently unknown key biological processes.

Further reading

• Environmental Molecular Microbiology
• Metagenomics: Theory, Methods and Applications
• Environmental Microbiology

Labels: Biotic components of soils, metagenomics, microbial communities, plant-microbe interactions

A new update on research in Microbial Ecology

Microbial Diversity and Phylogeny
Genomics and Metagenomics
Metaproteomics
Nucleic-Acid-based Characterization
Microarrays in Microbial Ecology
The Soil Environment
Plant Microbial Communities
Marine Microbial Environments
Ocean microbial communities
Human Microbial Environment
Wastewater Treatment
Bacterial Biofilms

Read more at: Microbial Ecology

Labels: Bacterial Biofilms, ecology, genomics, metagenomics, Metaproteomics, microarrays, microbial communities, Microbial Diversity, Microbial Environments, Phylogeny, Soil Environment, Wastewater

Microbial ecology is currently experiencing a renaissance spurred by the rapid development of molecular techniques and "omics" technologies in particular. As never before, these tools have allowed researchers in the field to produce a massive amount of information through in situ measurements and analysis of natural microbial communities, both vital approaches to the goal of unraveling the interactions of microbes with their environment and with one another. While genomics can provide information regarding the genetic potential of microbes, proteomics characterizes the primary end-stage product, proteins, thus conveying functional information concerning microbial activity.

Advances in mass spectrometry instrumentation and methodologies, along with bioinformatics approaches, have brought this analytic chemistry technique to relevance in the biological realm due to its powerful applications in proteomics. Mass spectrometry-enabled proteomics, including "bottom-up" and "top-down" approaches, is capable of supplying a wealth of biologically-relevant information, from simple protein cataloging of the proteome of a microbial community to identifying post-translational modifications of individual proteins.

from Brian D. Dill, Jacque C. Young, Patricia A. Carey and Nathan C. VerBerkmoes in Environmental Molecular Microbiology

Further reading:

• Environmental Molecular Microbiology
• Metagenomics: Theory, Methods and Applications
• Environmental Microbiology

Labels: Bioinformatics, genomics, Mass spectrometry, Metaproteomics, microbial communities, Microbial community, microbial ecology, Omics technologies, Proteome, Proteomics

Until fairly recently, the living soil has been considered as a functional black box that is intrinsically too difficult to be unravelled into its core components. However, this concept has changed with the advent of the modern methodologies. The intricacies of microbial life in soil has been impacted by the advanced, mainly molecular-based, approaches that have been unleashed on the soil habitat in recent years. The application of molecular and other advanced methods (cultivation-independent analyses) has provided exciting new insights into microbial life in soil.

Soil is an extremely diverse and complex habitat containing many microsites and gradients that form a range of different biogeochemical interfaces. Depending on the proportion of sand, silt and clay, the surface area in soil can vary from 11 cm² up to 8 million cm² per gram of soil read more.... The aggregates formed by minerals, soil organic matter, fungal hyphae, roots and plant debris offer a range of potential niches for microorganisms with different lifestyles. The architecture of the soil pore network essentially defines the habitat colonized by the microorganisms and the pore space strongly influences the nature and extent of the interactions between the organisms inhabiting the soil. The heterogeneous physical structure of soil affects the spatial distribution of water, oxygen and nutrients, which in turn influences the composition and activity of the microbial communities themselves. As an example, the spatial distribution of bacteria in topsoil and subsoil was found to be different, but lateral variations in spatial distributions are also likely to occur.

In terms of their occurrence in microsites, bacteria can be found in soil as single cells but most often they occur as microcolonies, i.e. small agglomerates of cells that can be regarded as primative soil biofilms read more.... Microorganisms are the major drivers of geochemical and biotransformation processes in soil. In concert with the soil's inorganic and organic constituents, microbes are influential in actively shaping the architecture of the soil matrix by the formation and restructuring of soil aggregates. In addition, the diversity of microbial communities is extremely high in most soils. There are only a few quantitative estimates of the numbers of microbial taxa that can co-exist in just a single gram of soil, but an advanced analysis of nucleic acid-based analyses, based on re-association kinetics, has suggested that prokaryotic diversity can reach 1 million species genomes per g, which by far exceeds the common estimates of bacterial richness in soil obtained from cultivation-based studies read more....

A major driving force that spurs the microbial diversity of soil is the enormous heterogeneity of the soil habitat, allowing the formation of numerous niches. Different factors, such as the presence or absence of water, soil pH, temperature, redox potential and the soil organic matter content do not only influence the types of microbes colonizing the respective microniche but also their activity. All these factors can vary greatly between the different microhabitats and, thus, not only the composition but also the activity and interactions of the microbiota will largely vary due to the spatial and temporal heterogeneity between as well as within the microsites.

A key determinant of microbial fitness in soil is the ability of microbial cells to fine-tune their cellular metabolism to the abiotic and biotic conditions that prevail locally. In addition, the rate of adaptation of microorganisms to changing environmental conditions might be enhanced by horizontal gene transfer processes read more.... Undoubtedly, the most important prerequisite for microbial life in soil is the availability of water. Next to being indispensable for microbial life, the water in soil carries dissolved gases, ions and nutrients to microorganisms, and, in cases of saturation, may quickly establish anaerobic conditions. For instance, an increase of the moisture content of soil can greatly influence the microbial communities that are locally present, in particular by connecting pore spaces in and among aggregates that were unconnected without water, thus increasing the aggregate connectivity. Predation by protozoa or Bdellovibrio species will therefore be particularly enhanced in relatively wet soils.

from Kornelia Smalla and Jan Dirk van Elsas in Environmental Molecular Microbiology

Further reading:

• Environmental Molecular Microbiology
• Metagenomics: Theory, Methods and Applications
• Environmental Microbiology

Labels: Cultivation-independent analysis, microbial communities, microbial ecology, soil microbiology

Metagenomics is a rapidly growing field of research that has had a dramatic effect on the way we view and study the microbial world. By permitting the direct investigation of bacteria, viruses and fungi irrespective of their culturability and taxonomic identities, metagenomics has changed microbiological theory and methods and has also challenged the classical concept of species. This new field of biology has proven to be rich and comprehensive and is making important contributions in many areas including ecology, biodiversity, bioremediation, bioprospection of natural products, and in medicine.

from Diana Marco in Metagenomics: Theory, Methods and Applications

Labels: archaea, archaeal metagenomics, bioremediation, horizontal gene transfer, metagenomics, microbial communities, microbiome, plant-microbe interactions