The microbiology of soils and plant microbe interactions are enormous topics worthy of the many books and research papers on the subjects, some of which are listed in the bibliography. It is not the aim of this section to give a detailed account but simply an introduction to the complexity of plant – microbe interac-tions in the hope of illustrating that ‘no man is an island’: disturbance of these interactions has its consequences. Although the term ‘plant’ includes all plant forms from trees to algae, the current discussion addresses interactions between higher plants and micro-organisms. Such interactions fall into two basic cate-gories: the first category being those involving microbes external to the plant, such as soil bacteria and soil fungi. The second being microbes internal to the plant, which include endophytic bacteria such as those involved in nitrogen fix-ation, internal fungi, and plant pathogens examples of which are Agrobacteriumplasmodium and Agrobacterium tumefaciens (Greene and Zambryski 1993). Thelatter is now used extensively to introduce ‘foreign’ genes into plants. The associations may therefore involve bacteria, fungi or viruses and in some cases, some quite complex interactions involving three or four dif-ferent organisms often bringing great benefit to the plant in environments where nutrients are somewhat deficient.
There are clearly two distinct areas of a higher plant which are inhabited by different communities of micro-organisms: above ground around and on the sur-face of leaves, stems, seeds and flowers and below ground in zones of increasing distance away from the root mass. These rhizospheres, or zones around the roots, which are more accurately envisaged as a continuous gradient of nutrients, are the result of plant metabolic activity constantly drawing from the surrounding soil. Nutrients may also be transferred in the reverse direction that is, to the soil, as is the case with aerating plants exemplified by Phragmites used in reed bed systems. It appears that colonisation of the rhizosphere by bacteria is stimulated by exudate from the plant. The first phase is attraction to the plant roots, the second is a ‘settlement’ phase during which bacteria grow to form colonies and the third is a ‘residence’ phase when a balance is established between root mass and bacterial numbers (Espinosa-Urgel, Kolter and Ramos2002). The microbes in the rhizosphere are, to a large extent, dependent on the plants for a supply of many useable organic substances. As plants die and decay, the components released by the degradative bacteria return to the soil and the cycle begins again. Consequently, plants affect the composition of the microbial community of the ground in which they grow, especially in soils of low fertility. Not all the compounds released from plants are stimulants of microbial growth, some plants may also produce inhibitors. The microbes themselves have an effect on the plant growth characteristics. Some release into the soil, gibberellins and cytokinins, both of which are plant growth factors, and may also affect the flow of organic compounds, termed exudate, from the plant into the rhizosphere. The rate at which exudate is transferred to the soil is affected by many parameters; the presence of surrounding soil bacteria as mentioned above, the reduction of plant mass by harvesting from above ground level, and environmental changes, for example, variations in light or temperature. Both bacteria and fungi contribute to the microbial population in the rhizosphere. Associations of fungi with roots of vascular plants, called mycorrhizae, are quite common and may in some cases be very beneficial to the plant. They may be external, ectomycorrhizal, or internal, endomycorrhizal. Ectomycorrhizal associations more commonly occur in temper-ate regions and often in beech, oak, birch and coniferous trees. Their association involves a limited penetration of the root cortex by the fungi growing as a cov-ering around the tip of the root. They aid the growth of the plants as a result of their mycelia reaching far out into the surrounding soil, thus assisting the plant in nutrient uptake. This quality has received commercial attention. The effect on plant growth and subsequent predation by insect larvae, of some species of fun-gus for example, Pisolithus tinctorius, has received particular attention (Rieske 2001). Bacteria have been found capable of encouraging this association, earn-ing themselves the title of ‘micorrhizal helper bacteria’. Clearly, anything which increases the efficiency of nutrient uptake by crop plants reduces the require-ment for the addition of artificial fertilisers and thus reduces the potential for agrichemical environmental disturbance.
The influence of microbes on the welfare of plants is not confined to the ground and may even affect the weather. An often quoted example is that drawn fromPseudomonas syringae which produces a protein known to act as a point of nucleation of ice crystals. Plants which harbour this bacterium run an increased risk of frost damage especially if their tissue is particularly susceptible as is the case with strawberries. P. syringae has been subjected to genetic engineering which successfully reduced the problem.
Plant – microbe interactions are becoming recognised as having an immediate and direct importance to human health in the role they can play in reducing the effect of ‘sick buildings’. They occur principally because these buildings are closed systems in which people work, breathing in volatile components from plastics, paint, chemicals used in office machinery such as photocopiers andprinters and a range of other sources including furnishing manufactured using synthetic materials. Bacteria resident in the soil of potted plants in the office are able to degrade many of these volatiles, which include phenolics, formaldehyde and trichloroethylene, thus improving the air quality. The plants themselves con-tribute to this improvement, not only by supporting the rhizosphere microbial community. In essence, this is root zone phytotechnology on a small scale.
Although straying away slightly from the remit of this section, it is interesting to point out that soil microbial activity has a major influence in the balance of stable atmospheric gases. These include the greenhouse gases, carbon dioxide, nitrous and nitric oxide and methane, so called because they trap heat re-emitted by earth from energy radiated by the sun. The atmospheric balance of less stable gases which include ammonia, hydrogen sulphide and dimethylsulphide are also subject to microbial activity, as will be apparent from an understanding of the foregoing on metabolism. A final word on soil microbes concerns the degradation of lignin. This is a major constituent of woody plant material and is recalcitrant to degradation. However, filamentous fungi are responsible for its degradation worldwide, augmented in the tropics by bacteria living in the gut of termites. This degradation requires the presence of oxygen, hence wood residing in anaerobic conditions is somewhat protected. Clearly, should the water table drop, exposing to air the wood pilings supporting buildings, for example, there is a danger of invasion by filamentous fungi able to degrade lignin and thus weaken the building structure. This also explains in part the necessity to aerate a compost heap containing any woody plant material to allow invasion by filamentous fungi capable of degrading lignin.
Two categories fulfil this description. The first are the internal fungi or endomy-corrhizae, referred to in the earlier section, together with the endophytic bacteria and the second comprises plant pathogens, which may be bacterial or viral in form. Although the term ‘endophytic’ seems unambiguous, it is sometimes used to describe only bacteria which may be isolated from plants which have been superficially cleansed with disinfectant, or isolated from within plant tissue and which cause no discernible harm to the plant. Thus defined, plant pathogens are excluded from this description. There are endophytic bacteria, called commen-sals, which neither benefit nor harm the plant, but there are also those which are beneficial to plant growth. These are symbiots which achieve this status either by promoting plant growth or by protection against plant pathogens.
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