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

https://web.science.uu.nl/pmi/publications/PDF/2012/TiPS-Berendsen-2012.pdf

The rhizosphere microbiome and plant health

Dissimilatory Fe(III) and Mn(IV) reduction.

Removal of nutrients in various types of constructed wetlands.

Particular bacterial strains in certain natural environments prevent infectious diseases of plant roots. How these bacteria achieve this protection from pathogenic fungi has been analysed in detail in biocontrol strains of fluorescent pseudomonads. During root colonization, these bacteria produce antifungal antibiotics, elicit induced systemic resistance in the host plant or interfere specifically with fungal pathogenicity factors. Before engaging in these activities, biocontrol bacteria go through several regulatory processes at the transcriptional and post-transcriptional levels.

/pdf/biological-control-of-soil-borne-pathogens-by-fluorescent-4524lno10w.pdf

Biological control of soil-borne pathogens by fluorescent pseudomonads

. Abstract Membrane-covered platinum electrodes with a tip diameter of 2-8 pm were used for an amperometric assay of dissolved oxygen in marine sediments. The oxygen profile extended to 3-5mm depth in nonilluminated sediment; even at high light intensities and at low tem- peratures it did not extend below lo-mm depth in a homogeneous sandy sediment. Oxygen profiles recorded during light-dark cycles were used to estimate the rates of oxygen produc- tion and consumption and also to calculate the apparent diffusion coefficient for oxygen in the sediment. Apparently macrofaunal activity, rather than molecular diffusion and water turbulence, was important for the occasional transport of oxygen into deeper layers and thus for the provision of oxidized conditions (positive redox potential) down to 5-10 cm below the sediment surface.

https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.4319/lo.1980.25.3.0403

Distribution of oxygen in marine sediments measured with microelectrodes1

The addition of 20 mM MoO42− (molybdate) to a reduced marine sediment completely inhibited the SO42− reduction activity by about 50 nmol g−1 h−1 (wet sediment). Acetate accumulated at a constant rate of about 25 nmol g−1 h−1 immediately after MoO42− addition and gave a measure of the preceding utilization rate of acetate by the SO42−-reducing bacteria. Similarly, propionate and butyrate (including isobutyrate) accumulated at constant rates of 3 to 7 and 2 to 4 nmol g−1 h−1, respectively. The rate of H2 accumulation was variable, and a range of 0 to 16 nmol g−1 h−1 was recorded. An immediate increase of the methanogenic activity by 2 to 3 nmol g−1 h−1 was apparently due to a release of the competition for H2 by the absence of SO42− reduction. If propionate and butyrate were completely oxidized by the SO42−-reducing bacteria, the stoichiometry of the reactions would indicate that H2, acetate, propionate, and butyrate account for 5 to 10, 40 to 50, 10 to 20, and 10 to 20%, respectively, of the electron donors for the SO42−-reducing bacteria. If the oxidations were incomplete, however, the contributions by propionate and butyrate would only be 5 to 10% each, and the acetate could account for as much as two-thirds of the SO42− reduction. The presence of MoO42− seemed not to affect the fermentative and methanogenic activities; an MoO42− inhibition technique seems promising in the search for the natural substrates of SO42− reduction in sediments.

Volatile Fatty Acids and Hydrogen as Substrates for Sulfate-Reducing Bacteria in Anaerobic Marine Sediment

According to guidelines for the approval of pesticides, side-effects on soil microorganisms should be determined by studying functional parameters such as carbon or nitrogen mineralisation. However, the microbial diversity may have been markedly changed following pesticide use despite unaltered metabolism, and such changes may affect soil fertility. This review evaluates new methods for measuring pesticide effects on bacterial diversity, and discusses how sampling should take temporal and spatial heterogeneity into account. Future research on pesticide approval protocols should establish the relationships between mineralisation assays and new and rapid bacterial diversity profiling methods, and should include the possible ecological implications of altered bacterial diversity for soil fertility.

Pesticide effects on bacterial diversity in agricultural soils – a review

Studies were carried out to elucidate the nature and importance of Fe3+ reduction in anaerobic slurries of marine surface sediment. A constant accumulation of Fe2+ took place immediately after the endogenous NO3− was depleted. Pasteurized controls showed no activity of Fe3+ reduction. Additions of 0.2 mM NO3− and NO2− to the active slurries arrested the Fe3+ reduction, and the process was resumed only after a depletion of the added compounds. Extended, initial aeration of the sediment did not affect the capacity for reduction of NO3− and Fe3+, but the treatments with NO3− increased the capacity for Fe3+ reduction. Addition of 20 mM MoO42− completely inhibited the SO42− reduction, but did not affect the reduction of Fe3+. The process of Fe3+ reduction was most likely associated with the activity of facultative anaerobic, NO3−-reducing bacteria. In surface sediment, the bulk of the Fe3+ reduction may be microbial, and the process may be important for mineralization in situ if the availability of NO3− is low.

Reduction of ferric iron in anaerobic, marine sediment and interaction with reduction of nitrate and sulfate.

A method has been developed for measurement of denitrification activity in sediments by application of the acetylene inhibition technique. Acetylene-saturated water was injected, at close intervals, into sediment cores which were then incubated for a few hours at the in situ temperature. Frozen segments of the cores were assayed for accumulation of N2O by a combined gas extraction and detection system. The segments were thawed under a stream of helium from which N2O (and other gases) was collected in a liquid N2 trap, and the quantity of N2O was measured by gas chromatography. The maximum rate of denitrification in a coastal marine sediment was 35 nmol of N per cm3 of sediment per day at 2.5°C, and the rate of denitrification for the total sediment was 0.99 nmol of N per m2 per day.

Jan Tind Sørensen

Papers

Distribution of oxygen in marine sediments measured with microelectrodes1

Volatile Fatty Acids and Hydrogen as Substrates for Sulfate-Reducing Bacteria in Anaerobic Marine Sediment

Pesticide effects on bacterial diversity in agricultural soils – a review

Reduction of ferric iron in anaerobic, marine sediment and interaction with reduction of nitrate and sulfate.

Denitrification rates in a marine sediment as measured by the acetylene inhibition technique.