Nitrous oxide (N(2)O) emission from soils is a major contributor to the atmospheric loading of this potent greenhouse gas. It is thought that autotrophic ammonia oxidizing bacteria (AOB) are a significant source of soil-derived N(2)O and a denitrification pathway (i.e. reduction of NO(2) (-) to NO and N(2)O), so-called nitrifier denitrification, has been demonstrated as a N(2)O production mechanism in Nitrosomonas europaea. It is thought that Nitrosospira spp. are the dominant AOB in soil, but little information is available on their ability to produce N(2)O or on the existence of a nitrifier denitrification pathway in this lineage. This study aims to characterize N(2)O production and nitrifier denitrification in seven strains of AOB representative of clusters 0, 2 and 3 in the cultured Nitrosospira lineage. Nitrosomonas europaea ATCC 19718 and ATCC 25978 were analysed for comparison. The aerobically incubated test strains produced significant (P < 0.001) amounts of N(2)O and total N(2)O production rates ranged from 2.0 amol cell(-1) h(-1), in Nitrosospira tenuis strain NV12, to 58.0 amol cell(-1) h(-1), in N. europaea ATCC 19718. Nitrosomonas europaea ATCC 19718 was atypical in that it produced four times more N(2)O than the next highest producing strain. All AOB tested were able to carry out nitrifier denitrification under aerobic conditions, as determined by production of (15)N-N(2)O from applied (15)N-NO(2) (-). Up to 13.5% of the N(2)O produced was derived from the exogenously applied (15)N-NO(2) (-). The results suggest that nitrifier denitrification could be a universal trait in the betaproteobacterial AOB and its potential ecological significance is discussed.

It is well known that atmospheric concentrations of carbon dioxide (CO2) (and other greenhouse gases) have increased markedly as a result of human activity since the industrial revolution. It is perhaps less appreciated that natural and managed soils are an important source and sink for atmospheric CO2 and that, primarily as a result of the activities of soil microorganisms, there is a soil-derived respiratory flux of CO2 to the atmosphere that overshadows by tenfold the annual CO2 flux from fossil fuel emissions. Therefore small changes in the soil carbon cycle could have large impacts on atmospheric CO2 concentrations. Here we discuss the role of soil microbes in the global carbon cycle and review the main methods that have been used to identify the microorganisms responsible for the processing of plant photosynthetic carbon inputs to soil. We discuss whether application of these techniques can provide the information required to underpin the management of agro-ecosystems for carbon sequestration and increased agricultural sustainability. We conclude that, although crucial in enabling the identification of plant-derived carbon-utilising microbes, current technologies lack the high-throughput ability to quantitatively apportion carbon use by phylogentic groups and its use efficiency and destination within the microbial metabolome. It is this information that is required to inform rational manipulation of the plant–soil system to favour organisms or physiologies most important for promoting soil carbon storage in agricultural soil.

SummaryFlavonoids are a diverse class of polyphenolic compounds that are produced as a result of plant secondary metabolism. They are known to play a multifunctional role in rhizospheric plant-microbe and plant-plant communication. Most familiar is their function as a signal in initiation of the legume-rhizobia symbiosis, but, flavonoids may also be signals in the establishment of arbuscular mycorrhizal symbiosis and are known agents in plant defence and in allelopathic interactions. Flavonoid perception by, and impact on, their microbial targets (e.g. rhizobia, plant pathogens) is relatively well characterized. However, potential impacts on 'non-target' rhizosphere inhabitants ('non-target' is used to distinguish those microorganisms not conventionally known as targets) have not been thoroughly investigated. Thus, this review first summarizes the conventional roles of flavonoids as nod gene inducers, phytoalexins and allelochemicals before exploring questions concerning 'nontarget' impacts. We hypothesize that flavonoids act to shape rhizosphere microbial community structure because they represent a potential source of carbon and toxicity and that they impact on rhizosphere function, for example, by accelerating the biodegradation of xenobiotics. We also examine the reverse question, 'how do rhizosphere microbial communities impact on flavonoid signals?' The presence of microorganisms undoubtedly influences the quality and quantity of flavonoids present in the rhizosphere, both through modification of root exudation patterns and microbial catabolism of exudates. Microbial alteration and attenuation of flavonoid signals may have ecological consequences for below-ground plant-microbe and plant-plant interaction. We have a lack of knowledge concerning the composition, concentration and bioavailability of flavonoids actually experienced by microbes in an intact rhizosphere, but this may be addressed through advances in microspectroscopic and biosensor techniques. Through the use of plant mutants defective in flavonoid biosynthesis, we may also start to address the question of the significance of flavonoids in shaping rhizosphere community structure and function.

We developed a joint bioaugmentation and biostimulation approach for the clean up of soil contaminated with high (168.7 and 337.4 microg g(-1)) concentrations of the herbicide atrazine (2-chloro-4-(ethylamino)-6-isopropylamino-s-triazine). Pseudomonas sp. strain ADP (P. ADP) was used for bioaugmentation (approximately 10(7) cells g(-1) soil), and citrate (concentration range 5.8-40 mg g(-1) soil) and succinate (6.2-30.8 mg g(-1)) were used for biostimulation. The study soil had indigenous potential for atrazine mineralization (54.4 +/- 2% of 168.7 microg g(-1) mineralized after 67 day), but rapid mineralization only took place after a prolonged acclimation phase (approximately 28 days). Inoculation with P. ADP alone resulted in a limited improvement in mineralization (e.g., 30.6 +/- 1% mineralization of 168.7 microg g(-1) of atrazine in inoculated soil cf. < 0.5% in noninoculated in 7 days). Quantification of surviving numbers of P. ADP revealed a 10-fold decline from initial levels. However, bioaugmentation together with citrate or succinate biostimulation markedly increased P. ADP cell survival and atrazine mineralization (e.g., addition of 11.6 mg g(-1) of citrate increased mineralization of 337.4 microg g(-1) of atrazine from < 2 to 79.9 +/- 1% in 13 days). A critical parameter in determining the extent of atrazine mineralization by P. ADP was C(s):N(atz) (soluble carbon to atrazine nitrogen ratio): C(s):N(atz) > 40 was required for maximal atrazine mineralization. We suggest our observations may be used as a framework for rational bioremediation of field soils contaminated with atrazine.

Pseudomonas sp. strain ADP uses the herbicide atrazine as the sole nitrogen source. We have devised a simple atrazine degradation assay to determine the effect of other nitrogen sources on the atrazine degradation pathway. The atrazine degradation rate was greatly decreased in cells grown on nitrogen sources that support rapid growth of Pseudomonas sp. strain ADP compared to cells cultivated on growth-limiting nitrogen sources. The presence of atrazine in addition to the nitrogen sources did not stimulate degradation. High degradation rates obtained in the presence of ammonium plus the glutamine synthetase inhibitor MSX and also with an Nas ؊ mutant derivative grown on nitrate suggest that nitrogen regulation operates by sensing intracellular levels of some key nitrogen-containing metabolite. Nitrate amendment in soil microcosms resulted in decreased atrazine mineralization by the wild-type strain but not by the Nas ؊ mutant. This suggests that, although nitrogen repression of the atrazine catabolic pathway may have a strong impact on atrazine biodegradation in nitrogen-fertilized soils, the use of selected mutant variants may contribute to overcoming this limitation.Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is a herbicide of the s-triazine family used for broad-leaf weed control in both crop and noncrop lands. Its widespread use and high mobility in soil have led to its frequent detection in surface water and groundwater at concentrations exceeding the maximum levels allowed (21,22,30,37). The high incidence of atrazine-contaminated water and the increasing concern about the toxicological and ecotoxicological properties of atrazine (3,6,16,17) have boosted research directed toward bioremediation of atrazine-polluted sites.A few laboratories have reported the isolation of bacteria with the ability to utilize atrazine, achieving in some cases the complete mineralization of the herbicide (see reference 29 and references therein). The best-characterized atrazine-mineralizing bacterial strain is Pseudomonas sp. strain ADP (23), which uses atrazine as the sole nitrogen source by means of a catabolic pathway comprising six enzymatic steps (25,40). The complete degradative pathway is encoded in the 108-kbp conjugative catabolic plasmid pADP-1, which was recently sequenced (25). The atzA, atzB, and atzC genes, responsible for the conversion of atrazine to cyanuric acid, are harbored at three distant positions within a large (Ͼ40 kbp) unstable region in pADP-1. Loss of one or more of these genes is the cause of the frequent appearance of Atr Ϫ (unable to utilize atrazine) mutants in nonselective medium (10). The genes involved in the s-triazine ring cleavage and ammonium release are clustered at a different location in pADP-1, to form the atzDEF operon (25). The atzA, atzB, and atzC genes have been shown to be widespread and plasmid borne in a number of independent isolates from different parts of the world (9, 10, 31, 39, 40).The influence of nitrogen compounds on the efficiency of atrazine catabo...

Cocoa pod husk (CPH) is the main by-product (ca. 70-75% weight of whole fruit) of the cocoa harvest, an important and economic crop in developing countries. It is a rich source of minerals (particularly potassium), fibre (including lignin, cellulose, hemicellulose and pectin) and antioxidants (e.g. phenolic acids). An existing practise is the return of CPH to soil with potential benefits (or disadvantages) for cocoa productivity and soil sustainability that have not been fully characterised. Currently, alternative low-value applications of CPH include its use as animal feed, as a starting material for soap making and activated carbon. Other biotechnological valorisation potentials for CPH and its fractions include the production of bio-fuels and their incorporation in food systems. Physical, chemical or biological pretreatment approaches are needed in order to achieve desirable fractions in a cost-effective and sustainable manner for novel applications in food and non-food sectors.

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