The rhizosphere encompasses the millimeters of soil surrounding a plant root where complex biological and ecological processes occur. This review describes recent advances in elucidating the role of root exudates in interactions between plant roots and other plants, microbes, and nematodes present in the rhizosphere. Evidence indicating that root exudates may take part in the signaling events that initiate the execution of these interactions is also presented. Various positive and negative plant-plant and plant-microbe interactions are highlighted and described from the molecular to the ecosystem scale. Furthermore, methodologies to address these interactions under laboratory conditions are presented.

The Role of Root Exudates in Rhizosphere Interactions with Plants and Other Organisms

SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and oftenconfusingterminologyaswellasunnecessarilypolarizingdebates. Thus,wereviewrecentliteratureonmicrobialcommunityassembly, using the framework of Vellend (Q. Rev. Biol. 85:183‐206, 2010) in an effort to synthesize and unify these contributions. We begin by discussingpatternsinmicrobialbiogeographyandthendescribefour basic processes (diversification, dispersal, selection, and drift) that contributetocommunityassembly.Wealsodiscussdifferentcombinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generatehypothesesdescribinghowthesedifferencesmaybeimportantforcommunityassembly.Weendbydiscussingtheimplications ofmicrobialassemblyprocessesforecosystemfunctionandbiodiversity.

/pdf/patterns-and-processes-of-microbial-community-assembly-1nnu7tbo44.pdf

Patterns and Processes of Microbial Community Assembly

Premise of the study Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million fungi on the Earth. Because only 70000 fungi had been described at that time, the estimate has been the impetus to search for previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods suggest that as many as 5.1 million fungal species exist. Methods Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and identify fungal taxa. Key results Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a monophyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making significant advances in species discovery, but many fungi remain to be discovered. Conclusions Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world's unknown fungi in less than 1000 years predicted at current new species acquisition rates.

The Fungi: 1, 2, 3 … 5.1 million species?

Although belowground ecosystems have been studied extensively and soil biota play integral roles in biogeochemical processes, surprisingly we have a limited understanding of global patterns in belowground biomass and community structure. To address this critical gap, we conducted a meta-analysis of published data (> 1300 datapoints) to compare belowground plant, microbial and faunal biomass across seven of the major biomes on Earth. We also assembled data to assess biome-level patterns in belowground microbial community composition. Our analysis suggests that variation in microbial biomass is predictable across biomes, with microbial biomass carbon representing 0.6-1.1% of soil organic carbon (r(2) = 0.91) and 1-20% of total plant biomass carbon (r(2) = 0.42). Approximately 50% of total animal biomass can be found belowground and soil faunal biomass represents < 4% of microbial biomass across all biomes. The structure of belowground microbial communities is also predictable: bacterial community composition and fungal : bacterial gene ratios can be predicted reasonably well from soil pH and soil C : N ratios respectively. Together these results identify robust patterns in the structure of belowground microbial and faunal communities at broad scales which may be explained by universal mechanisms that regulate belowground biota across biomes.

/pdf/global-patterns-in-belowground-communities-5fwnuh5vd9.pdf

Global patterns in belowground communities.

Soil health is presented as an integrative property that reflects the capacity of soil to respond to agricultural intervention, so that it continues to support both the agricultural production and the provision of other ecosystem services. The major challenge within sustainable soil management is to conserve ecosystem service delivery while optimizing agricultural yields. It is proposed that soil health is dependent on the maintenance of four major functions: carbon transformations; nutrient cycles; soil structure maintenance; and the regulation of pests and diseases. Each of these functions is manifested as an aggregate of a variety of biological processes provided by a diversity of interacting soil organisms under the influence of the abiotic soil environment. Analysis of current models of the soil community under the impact of agricultural interventions (particularly those entailing substitution of biological processes with fossil fuel-derived energy or inputs) confirms the highly integrative pattern of interactions within each of these functions and leads to the conclusion that measurement of individual groups of organisms, processes or soil properties does not suffice to indicate the state of the soil health. A further conclusion is that quantifying the flow of energy and carbon between functions is an essential but non-trivial task for the assessment and management of soil health.

/pdf/soil-health-in-agricultural-systems-1k67gevu9p.pdf

Soil health in agricultural systems

Methods of studying soil microbial diversity

http://envismadrasuniv.org/Bioremediation/pdf/The%20effects%20of%20perennial.pdf

The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil

A phytotoxicity bioassay was used to select plant species for phytoremediation that were able to germinate and grow in petroleum-contaminated soil from an industrial site in Canada. Perennial ryegrass (Lolium perenne var. “Affinity”) and alfalfa (Medicago sativa L.) were more successful at germination and root growth than were little bluestem (Schizachyrum scoparium) and crown vetch (Coronilla varia). The phytotoxicity assay provides a rapid, efficient mechanism of prescreening potential plant species and eliminating those not able to germinate and establish in soil conditions present at the contaminated site. This bioassay can potentially reduce the number of pot or greenhouse degradation studies that need to be conducted before plant species can be chosen for petroleum phytoremediation.

Phytotoxicity Assay to Assess Plant Species for Phytoremediation of Petroleum-Contaminated Soil

Phytoremediation is the use of selected plants to decontaminate polluted environments. Arbuscular mycorrhizal fungi (AMF) may potentially be useful for phytoremediation, but it is not known how petroleum hydrocarbons influence AMF spore germination and hyphal growth. To address this question, germination of spores and germ tube growth of Glomus intraradices Schenck and Smith and Glomus aggregatum Schenck and Smith were assessed in soil contaminated with up to 3% (w/v) of F2 diesel oil or HAGO reference oil. Hyphal growth, colonization and progeny spore production were assessed in vitro using transformed root cultures of Daucus carota and G. intraradices spores in a F2 diesel contaminated medium. In addition, extraradical hyphal growth of G. intraradices colonizing Daucus carota in the presence of F2 diesel was studied. Neither F2 diesel nor HAGO reference oil affected spore germination or germ tube growth in soil. However, in the presence of plant roots, germ tube growth of G. intraradices was reduced and delayed in the presence of F2 diesel and root colonization was not detected. Hyphal growth of pre-colonized carrot roots by G. intraradices was reduced and delayed in F2 contaminated medium compared to controls. F2 diesel did not inhibit spore germination of these AMF species but did reduce colonization, germ tube and hyphal growth. These results suggest that AMF inoculum can be established in petroleum-contaminated sites. However, it may prove beneficial to plant pre-colonized plants to increase the probability of sufficient AMF colonization and growth. The likely mechanism(s) of petroleum toxicity in this plant-microbe system was discussed.

Toxicity of diesel fuel to germination, growth and colonization of Glomus intraradices in soil and in vitro transformed carrot root cultures

Why Bioremediation?




Natural Attenuation




Environmental Constraints to Soil Bioremediation




Contaminant Variables That Affect Their Degradability in Soil




Microbiological Factors




Monitoring Bacteria Introduced into Soil




Enhancing Bacterial Degrading Genes Through Molecular Biology




Encapsulation of Microbial Cells for Use in Soil Bioremediation




Monitoring of Biodegradation Rates




Metals and Radionuclides




Phytoremediation





Keywords:

bioremediation;
bioremediation, soils;
biotechnology;
soils

Jennifer L. Kirk

Papers

Methods of studying soil microbial diversity

The effects of perennial ryegrass and alfalfa on microbial abundance and diversity in petroleum contaminated soil

Phytotoxicity Assay to Assess Plant Species for Phytoremediation of Petroleum-Contaminated Soil

Toxicity of diesel fuel to germination, growth and colonization of Glomus intraradices in soil and in vitro transformed carrot root cultures

Bioremediation of Soils