Davey L. Jones

Organic acids in the rhizosphere: a critical review

Organic acids, such as malate, citrate and oxalate, have been proposed to be involved in many processes operating in the rhizosphere, including nutrient acquisition and metal detoxification, alleviation of anaerobic stress in roots, mineral weathering and pathogen attraction. A full assessment of their role in these processes, however, cannot be determined unless the exact mechanisms of plant organic acid release and the fate of these compounds in the soil are more fully understood. This review therefore includes information on organic acid levels in plants (concentrations, compartmentalisation, spatial aspects, synthesis), plant efflux (passive versus active transport, theoretical versus experimental considerations), soil reactions (soil solution concentrations, sorption) and microbial considerations (mineralization). In summary, the release of organic acids from roots can operate by multiple mechanisms in response to a number of well-defined environmental stresses (e.g., Al, P and Fe stress, anoxia): These responses, however, are highly stress- and plant-species specific. In addition, this review indicates that the sorption of organic acids to the mineral phase and mineralisation by the soils microbial biomass are critical to determining the effectiveness of organic acids in most rhizosphere processes.

Optimisation of the anaerobic digestion of agricultural resources

It is in the interest of operators of anaerobic digestion plants to maximise methane production whilst concomitantly reducing the chemical oxygen demand of the digested material. Although the production of biogas through anaerobic digestion is not a new idea, commercial anaerobic digestion processes are often operated at well below their optimal performance due to a variety of factors. This paper reviews current optimisation techniques associated with anaerobic digestion and suggests possible areas where improvements could be made, including the basic design considerations of a single or multi-stage reactor configuration, the type, power and duration of the mixing regime and the retention of active microbial biomass within the reactor. Optimisation of environmental conditions within the digester such as temperature, pH, buffering capacity and fatty acid concentrations is also discussed. The methane-producing potential of various agriculturally sourced feedstocks has been examined, as has the advantages of co-digestion to improve carbon-to-nitrogen ratios and the use of pre-treatments and additives to improve hydrolysis rates or supplement essential nutrients which may be limiting. However, perhaps the greatest shortfall in biogas production is the lack of reliable sensory equipment to monitor key parameters and suitable, parallelised control systems to ensure that the process continually operates at optimal performance. Modern techniques such as software sensors and powerful, flexible controllers are capable of solving these problems. A direct comparison can be made here with, for instance, oil refineries where a more mature technology uses continuous in situ monitoring and associated feedback procedures to routinely deliver continuous, optimal performance.

Carbon flow in the rhizosphere: carbon trading at the soil-root interface

The loss of organic and inorganic carbon from roots into soil underpins nearly all the major changes that occur in the rhizosphere. In this review we explore the mechanistic basis of organic carbon and nitrogen flow in the rhizosphere. It is clear that C and N flow in the rhizosphere is extremely complex, being highly plant and environment dependent and varying both spatially and temporally along the root. Consequently, the amount and type of rhizodeposits (e.g. exudates, border cells, mucilage) remains highly context specific. This has severely limited our capacity to quantify and model the amount of rhizodeposition in ecosystem processes such as C sequestration and nutrient acquisition. It is now evident that C and N flow at the soil–root interface is bidirectional with C and N being lost from roots and taken up from the soil simultaneously. Here we present four alternative hypotheses to explain why high and low molecular weight organic compounds are actively cycled in the rhizosphere. These include: (1) indirect, fortuitous root exudate recapture as part of the root’s C and N distribution network, (2) direct re-uptake to enhance the plant’s C efficiency and to reduce rhizosphere microbial growth and pathogen attack, (3) direct uptake to recapture organic nutrients released from soil organic matter, and (4) for inter-root and root–microbial signal exchange. Due to severe flaws in the interpretation of commonly used isotopic labelling techniques, there is still great uncertainty surrounding the importance of these individual fluxes in the rhizosphere. Due to the importance of rhizodeposition in regulating ecosystem functioning, it is critical that future research focuses on resolving the quantitative importance of the different C and N fluxes operating in the rhizosphere and the ways in which these vary spatially and temporally.

Organic acid behavior in soils - misconceptions and knowledge gaps

Organic acids have been hypothesized to perform many functions in soil including root nutrient acquisition, mineral weathering, microbial chemotaxis and metal detoxification. However, their role in most of these processes remains unproven due to a lack of fundamental understanding about the reactions of organic acids in soil. This review highlights some of the knowledge gaps and misconceptions associated with the behavior of organic acids in soil with particular reference to low-molecular-weight organic acids (e.g., citrate, oxalate, malate) and plant nutrient acquisition. One major concern is that current methods for quantifying organic acids in soil may vastly underestimate soil solution concentrations and do not reveal the large spatial heterogeneity that may exist in their concentration (e.g., around roots or microbes). Another concern relates to the interaction of organic acids with the soils solid phase and the lack of understanding about the relative importance of processes such as adsorption versus precipitation, and sorption versus desorption. Another major knowledge gap concerns the utilization of organic acids by the soil microbial community and the forms of organic acids that they are capable of degrading (e.g., metal-complexed organic acids, adsorbed organic acids etc). Without this knowledge it will be impossible to obtain accurate mathematical models of organic acid dynamics in soil and to understand their role and importance in ecosystem processes. Fundamental research on organic acids and their interaction with soil still needs to be done to fully elucidate their role in soil processes.

The role of the natural environment in the emergence of antibiotic resistance in Gram-negative bacteria

During the past 10 years, multidrug-resistant Gram-negative Enterobacteriaceae have become a substantial challenge to infection control. It has been suggested by clinicians that the effectiveness of antibiotics is in such rapid decline that, depending on the pathogen concerned, their future utility can be measured in decades or even years. Unless the rise in antibiotic resistance can be reversed, we can expect to see a substantial rise in incurable infection and fatality in both developed and developing regions. Antibiotic resistance develops through complex interactions, with resistance arising by de-novo mutation under clinical antibiotic selection or frequently by acquisition of mobile genes that have evolved over time in bacteria in the environment. The reservoir of resistance genes in the environment is due to a mix of naturally occurring resistance and those present in animal and human waste and the selective effects of pollutants, which can co-select for mobile genetic elements carrying multiple resistant genes. Less attention has been given to how anthropogenic activity might be causing evolution of antibiotic resistance in the environment. Although the economics of the pharmaceutical industry continue to restrict investment in novel biomedical responses, action must be taken to avoid the conjunction of factors that promote evolution and spread of antibiotic resistance.

Through form to function: root hair development and nutrient uptake.

Root hairs project from the surface of the root to aid nutrient and water uptake and to anchor the plant in the soil. Their formation involves the precise control of cell fate and localized cell growth. We are now beginning to unravel the complexities of the molecular interactions that underlie this developmental regulation. In addition, after years of speculation, nutrient transport by root hairs has been demonstrated clearly at the physiological and molecular level, with evidence for root hairs being intense sites of H(+)-ATPase activity and involved in the uptake of Ca(2+), K(+), NH(4)(+), NO(3)(-), Mn(2+), Zn(2+), Cl(-) and H(2)PO(4)(-).

HOW ROOTS CONTROL THE FLUX OF CARBON TO THE RHIZOSPHERE

What determines the way in which roots provide carbon to and interact with other components of the soil? Roots lose metabolites and signal molecules to the soil at rates of significance to soil organisms, and we need to know if the mechanisms of passive diffusion identified in hydroponics apply in soil, and whether other, active mechanisms complement them. New insights from biosensors into the heterogeneity and localization of exudation are transforming our understanding of root-microorganism relations. We need to know more about compounds that are exuded at subnutritional rates in soil and may act as signal molecules modifying the biology of soil organisms. Insights into one suite of such compounds is coming from studies of border cells. These cells are lost from the root cap at a rate regulated by the root and secrete compounds that alter the environment of and gene expression in soil microorganisms and fauna. The amount of root places an upper limit on the effect roots can have; carbon flow to the rhizosphere is a function of root growth. Top-down metabolic control analysis shows that the control over the rate at which roots grow is shared between root and shoot, with most control being in the shoot.

Amino acid biodegradation and its potential effects on organic nitrogen capture by plants

It has been reported that plant roots can directly utilise soil organic-N in the form of amino acids without prior mineralisation by the soils microbial biomass. To critically assess this, however, requires a knowledge of microbial amino acid-N turnover times in soil. The effects of soil type, depth and temperature on the uptake and partitioning of a mixture of 15 14C-labelled amino acids by the soils microbial biomass was therefore studied in 10 contrasting soil types. The results indicated that the degradation of amino acids was soil dependent but that the mean half-life in topsoils at 18°C was 1.7±0.6 h, whilst in subsoils the mean half-life was 12.2±3.3 h. On average 34% of the amino acid-C was respired as CO2 whilst 66% was utilised for new cell biomass. Amino acid decomposition increased with soil temperature, however, rapid rates of amino acid uptake and assimilation were also observed at 5°C (mean half-life in topsoil=2.9±1.5 h). Little correlation was observed between amino acid half-life and either microbial yield, soil arginase activity or organic matter content (r2<0.40), however, decomposition did appear to be weakly related with soil respiration. The high concentration of amino acids used here (5 mM) was intended to simulate amino acid release after root cell lysis. For previously reported lower concentrations in the bulk soil solution, half lives can be predicted to be even less based on microbial amino acid transport kinetics. The significance of this previously overlooked microbial decomposition of amino acids in the utilisation of organic N by plants is discussed.

Soil microbial community patterns related to the history and intensity of grazing in sub-montane ecosystems

Long-term variations in the frequency and intensity of sheep (Ovis aries) grazing have led to the development of ubiquitous plant successional transitions in sub-montane regions of the UK. In this study, we measured a range of soil microbial properties across these successional transitions in three biogeographic regions of the UK, to establish how gradients of grazing-influence (in terms of the history and intensity of sheep grazing) alter the biomass, activity, and structure of soil microbial communities. We also measured soil physicochemical variables to relate changes in soil microbial community arrangement along these grazing-related successional transitions to key soil properties. Our results from three locations show that microbial communities of soils display some consistent and ‘broad-scale’ trends along successional transitions that are related to the history and intensity of grazing. We show that microbial biomass of soil is maximal at low-to-intermediate levels of grazing influence and that the phenotypic evenness (a component of diversity) of the microbial community declines as the intensity of grazing increases. We also provide evidence that soil microbial communities of heavily grazed sites are dominated by bacterial-based energy channels of decomposition, whereas in systems that are less intensively grazed, or completely unmanaged, fungi have a proportionally greater role. Further studies are needed to establish the significance of these changes in relation to soil-level ecosystem processes of decomposition and nutrient cycling. The data show that human disturbances can have profound effects on the biomass and structure of the soil communities that regulate soil processes in these ecosystems and that these effects are consistent across sites.

Critical evaluation of municipal solid waste composting and potential compost markets

Mechanical biological treatment (MBT) of mixed waste streams is becoming increasingly popular as a method for treating municipal solid waste (MSW). Whilst this process can separate many recyclates from mixed waste, the resultant organic residue can contain high levels of heavy metals and physical and biological contaminants. This review assesses the potential end uses and sustainable markets for this organic residue. Critical evaluation reveals that the best option for using this organic resource is in land remediation and restoration schemes. For example, application of MSW-derived composts at acidic heavy metal contaminated sites has ameliorated soil pollution with minimal risk. We conclude that although MSW-derived composts are of low value, they still represent a valuable resource particularly for use in post-industrial environments. A holistic view should be taken when regulating the use of such composts, taking into account the specific situation of application and the environmental pitfalls of alternative disposal routes.