Microbes are the unseen majority in soil and comprise a large portion of lifes genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogenfixing bacteria are responsible for c. 5‐20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.

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The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

Dissolved organic matter (DOM) in soils plays an important role in the biogeochemistry of carbon, nitrogen, and phosphorus, in pedogenesis, and in the transport of pollutants in soils. The aim of this review is to summarize the recent literature about controls on DOM concentrations and fluxes in soi

Controls on the dynamics of dissolved organic matter in soils: a review.

Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.

The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms

Background: Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Results: Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with highthroughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA). Conclusions: The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.

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Molecular ecological network analyses

Borohydride reduction of an aqueous iron salt in the presence of a support material gives supported zero-valent iron nanoparticles that are 10−30 nm in diameter. The material is stable in air once it has dried and contains 22.6% iron by weight. The supported zero-valent iron nanoparticles (“Ferragels”) rapidly separate and immobilize Cr(VI) and Pb(II) from aqueous solution, reducing the chromium to Cr(III) and the Pb to Pb(0) while oxidizing the Fe to goethite (α-FeOOH). The kinetics of the reduction reactions are complex and include an adsorption phase. About 10% of the iron in the material appears to be located at active surface sites. Once these sites have been saturated, the reduction process continues but at a much lower rate, which is likely limited by mass transfer. Rates of remediation of Cr(VI) and Pb(II) are up to 30 times higher for Ferragels than for iron filings or iron powder on a (Fe) molar basis. Over 2 months, reduction of Cr(VI) was 4.8 times greater for Ferragels than for an equal weigh...

Remediation of Cr(VI) and Pb(II) aqueous solutions using supported, nanoscale zero-valent iron

Owing to their vast diversity and as-yet uncultivated status, detection, characterization and quantification of microorganisms in natural settings are very challenging, and linking microbial diversity to ecosystem processes and functions is even more difficult. Microarray-based genomic technology for detecting functional genes and processes has a great promise of overcoming such obstacles. Here, a novel comprehensive microarray, termed GeoChip, has been developed, containing 24 243 oligonucleotide (50 mer) probes and covering 410 000 genes in 4150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation. The developed GeoChip was successfully used for tracking the dynamics of metal-reducing bacteria and associated communities for an in situ bioremediation study. This is the first comprehensive microarray currently available for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. It is particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions.

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GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes

Uranium(VI) adsorption and transport in three natural, heterogeneous subsurface media were investigated in batch and column experiments. The rate of U(VI) adsorption to the natural samples was rapid over the first few hours of the experiments, and then slowed appreciably after 24 to 48 h. The adsorption of U(VI) to the samples was also nonlinear, suggesting a decreasing attraction for the surface with increased surface loading. The extent of adsorption on each of the media was strongly pH-dependent, increasing sharply as the pH increased from 4.5 to 5.5 and then decreasing sharply over the pH range 7.5 to 8.5 as the concentration of dissolved carbonate and U(VI)-carbonate complexes increased. The similarities in the pH-dependent behavior between the three materials despite differences in bulk mineralogy was likely due to the similar Fe contents of the materials. The transport of U(VI) through packed columns of the soils and sediments was significantly retarded but reversible. The local equilibrium assumption and the batch-measured adsorption isotherms dramatically underestimated the degree of retardation observed in the columns. The U(VI) displacement experiments were modeled with the one-dimensional advective-dispersive equation and several different model formulations describing the interactions of U(VI) with the solid phase. These models were able to fit the observed breakthrough curves within 0.1 root mean square error of the initial concentration.

Adsorption and Transport of Uranium(VI) in Subsurface Media

The disposal of toxic metals [e.g., Cr(VI)] generated by the Department of Energy during the cold war era has historically involved shallow land burial in unconfined pits and trenches. The objectiv...

Fate and Transport of Hexavalent Chromium in Undisturbed Heterogeneous Soil

Transport of Naturally Occurring Dissolved Organic Carbon in Laboratory Columns Containing Aquifer Material

There are numerous Cr(III)-contaminated sites on Department of Defense (DoD) and Department of Energy (DOE) lands that are awaiting possible clean up and closure. Ingestion of contaminated soil by children is the risk driver that generally motivates the likelihood of site remediation. The purpose of this study was to develop a simple statistical model based on commen soil properties to estimate the bioaccessibility of Cr(III)-contaminated soil upon ingestion. Thirty-five uncontaminated soils from seven major soil orders, whose properties were similar to numerous U.S. DoD contaminated sites, were treated with Cr(III) and aged. Statistical analysis revealed that Cr(III) sorption (e.g., adsorption and surface precipitation) by the soils was strongly correlated with the clay content, total inorganic C, pH, and the cation exchange capacity of the soils. Soils with higher quantities of clay, inorganic C (i.e., carbonates), higher pH, and higher cation exchange capacity generally sequestered more Cr(III). The amount of Cr(III) bioaccessible from the treated soils was determined with a physiologically based extraction test (PBET) that was designed to simulate the digestive process of the stomach. The bioaccessibility of Cr(III) varied widely as a function of soil type with most soils limiting bioaccessibility to <45 and <30% after 1 and 100 d soil-Cr aging, respectively. Statistical analysis showed the bioaccessibility of Cr(III) on soil was again related to the clay and total inorganic carbon (TIC) content of the soil. Bioaccessibility decreased as the soil TIC content increased and as the clay content decreased. The model yielded an equation based on common soil properties that could be used to predict the Cr(III) bioaccessibility in soils with a reasonable level of confidence.

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Phil Jardine

Papers

GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes

Adsorption and Transport of Uranium(VI) in Subsurface Media

Fate and Transport of Hexavalent Chromium in Undisturbed Heterogeneous Soil

Transport of Naturally Occurring Dissolved Organic Carbon in Laboratory Columns Containing Aquifer Material

Influence of soil geochemical and physical properties on the sorption and bioaccessibility of chromium(III).