Soil Biochemistry

Volume 8

Jean-Marc Bollag, G. Stotzky

• Éditeur: CRC Press
• Année: 2021
• ISBN:
  9781000447811
• Édition: 1
• Sujet: Scienze biologiche
• Sous-sujet: Biochimica

Stressing the potential application of biochemical processes in soil to environmental biotechnology, this state-of-the-art reference considers the vital role that such biochemical processes have in the environment - emphasizing the activity of micro-organisms in soil.;An up-to-date analysis of biological reactions in soil, Volume 8 of Soil Biochemistry highlights: traditional as well as molecular and immunlogical techniques for detecting specific micro-organisms in soil; the fate of introduced genetically-modified organisms; the problem of competition by the indigenous microbial populations with the introduced organisms; the use of a white rot fungus, Phanerochaete chrysosporium, for bioremediative purposes in soil; the interaction of xenobiotics, such as pesticides, with soil organisms; generic microbial metabolism and degradation pathways; the inhibition of the nitrification process by allelochemicals released by plants; the microbial mineralization of various compounds under anaerobic conditions, explaining its importance in the global carbon cycle; the formation of soil organic matter, particularly in forest soils; and CPMAS 13C-NMR spectroscopy, a major analytical technique to determine the chemicals or chemical groups involved in the humification process.;Presenting a multidisciplinary approach to the field by internationally acclaimed scientists, Soil Biochemistry, Volume 8 is intended for professionals and students in the fields of soil science; microbiology; biochemistry; environmental science, engineering and technology; biogeochemistry; biotechnology; agronomy; plant pathology; and microbial ecology.

1

Detection, Survival, and Activity of Bacteria Added to Soil

CAROLINE S. YOUNG and RICHARD G. BURNS University of Kent, Canterbury, Kent, United Kingdom

I. INTRODUCTION

The microbial world appears to have an almost limitless metabolic potential, and as comprehension of this has increased so has the desire to use the enormous biochemical diversity to advantage. Advances in molecular biology, fermentation technology, and microbial physiology, coupled with the search for and discovery of microorganisms with novel metabolic capabilities, have presented numerous opportunities. Microbial biotechnology is already being exploited in the chemical and pharmaceutical industries, where commercial-scale bioreactors produce antibiotics, insulin, growth hormones, amino acids, proteins, enzymes, vitamins, hemoglobins, and a host of fragrances and flavorings. In addition, the large-scale generation of microbial biomass supplies food for human beings and domestic animals.

Despite many exciting commercial developments and no shortage of imaginative ideas, microorganisms have not yet been applied widely to the environment outside of the laboratory or away from the contained and carefully monitored industrial reactor. This is partly because soil is a heterogeneous environment that cannot be manipulated easily to ensure the success of a potential inoculant.

As a consequence, the activity and persistence of soil microbial amendments are difficult to predict. In addition to these constraints, a major public debate is taking place concerning the safe use of microbes in the environment. This debate is focused on a number of issues, including perceived human health hazards associated with release [1], the potential disruption to the indigenous flora and fauna as a result of the successful establishment of an introduced species [2], and ethical concerns regarding the manipulation of the natural environment. The arguments become more passionate when the deliberate release of genetically modified microorganisms is advocated rather than that of naturally occurring species [3].

Intentional or unintentional introduction of microorganisms to new environments, via natural or anthropogenic dispersal, has been occurring since the beginning of time (e.g., sewage applications to soil, transport of microorganisms over long distances by air and water currents and by animals). This is an important point to bear in mind when risk assessments are made concerning novel inoculants. Unfortunately, there is a dearth of knowledge concerning the effects of allochthonous microorganisms on the microbial ecology of soil, and the best methods for measuring these effects have not been decided. In other words, soil microbiologists are largely ignorant of the multispecies dynamics that occur in natural soil microbial communities, and there are few standardized techniques for counting introduced species or assessing their activities. As a consequence, the capacity to select and manipulate microorganisms in vitro has far outstripped the ability to forecast their behavior when added to soil. This gulf between the potential of microorganisms to enhance soil processes and the information that would allow confident introduction of bacteria, fungi, algae, and viruses to soil is well recognized [4]. In an attempt to bridge this gulf, dozens of major research programs are under way throughout the world involving industry, academia, and government institutes, all aimed at the safe, predictable, and profitable exploitation of soil microbial inoculants.

A. Examples of Soil Inoculants

As the 21st century approaches and the world’s population continues to expand at an alarming rate, it will be necessary to consider novel ways to increase food production while, at the same time, preserving the environment. To achieve these objectives, the widespread and routine introduction of beneficial microorganisms into soil will probably have an important role. This is not a new idea, but the potential applications of microbial inoculants have increased in recent years and many of these uses are concerned with the maintenance and improvement of soil fertility and the promotion of plant growth [5]. The benefits may result from the involvement of inoculants in fundamental chemical and biological processes that are essential to plant nutrition (e.g., release of nitrate, solubilization of phosphate), the enhancement of nodulation and nitrogen fixation (e.g., effective rhizobial strains, the production of plant growth-promoting agents (e.g., auxins, cytokinins), the initiation and retention of soil aggregate stability (e.g., polysaccharide production, filamentous growth), or the suppression of plant pathogens by antagonistic metabolites (e.g., enzymes, antibiotics).

Nitrogen Fixation

For the past 70 years, the most widely adopted use of microbial inoculants has involved rhizobia and legumes. The first patents for rhizobial inoculants were issued at the beginning of the century, and commercial exploitation followed soon after. Given the importance of legumes as edible seeds and sources of protein, oils, animal fodder, and green manure, many of these early bacterial formulations sold well. The demand existed then, as it does today, because nodulation does not occur in soils in the absence of appropriate Rhizobium species. Cultures were mixed with seed before sowing or, less efficiently, were poured onto the soil at planting. Very often these preparations contained very low numbers of viable rhizobia (because of losses during storage and preparation by the farmer) or did not survive long enough, either in soil or on the seed, to infect the plant. As a result, low success rates were common (as measured by nodulation of the host legume) and applications of nitrogen fertilizer were still required. Many of these problems still exist today, and much recent research is aimed at selecting or genetically manipulating Rhizobium to produce “improved” strains which will outcomplete indigenous rhizobia and form effective nodules in a high proportion of the crop [6]. In addition, application techniques are being modified to deliver a high viable inoculum at seed germination [7]. Many of the ecological constraints limiting the success of rhizobia added to soil are described in detail elsewhere [8] and are relevant to the understanding of other bacterial inoculants.

It is often assumed that enhancement of plant growth after inoculation is a direct response to the introduced bacteria. In the case of rhizobia, the appearance of nodules, coupled with sensitive measurements of nitrogen fixation using ¹⁵N and acetylene reduction techniques, permits unequivocal correlation of plant response with the inoculant. However, there is a danger of confusing cause and effect when assessing the function of other microbial inoculants. An example is provided by the many experiments in which soil has been amended with a free-living nitrogen-fixing genus Azotobacter. Improvements in germination, plant growth, or yield after soil and seed treatments (bacterization) with Azotobacter chromococcum have been attributed solely to N fixation [9], although there are many alternative explanations [10]. These include the direct physical protection from soil pathogens or plant growth inhibitors resulting from a dense initial seed coating of the inoculant, an indirect disruption of the developing rhizosphere population away from “harmful” and toward “beneficial” bacteria, a “green manuring” effect caused by the addition of large amounts of microbial biomass and the subsequent release of plant nutrients as the cells are lysed and degraded, and the production of plant growth regulators by the inoculant species. The significance of microbial metabolites as growth promoters and the caution that should be exercised when interpreting a plant response are illustrated by the work of Frankenberger and colleagues [11, 12, 13]. They showed an increase in growth of Zea mays and Lycopersicon esculentum after the addition of L-methionine and L-ethionine to soil, possibly as a result of the microbial formation of ethylene from the amino acid precursors. Furthermore, radish yields were enhanced in glasshouse and field experiments after application of the auxin precursor, L-tryptophan. However, even these data are not conclusive, as the increase in plant growth could have been a response to auxins produced by the soil microbiota, a change in the rhizosphere population, or even something nonmicrobiological, such as direct uptake of L-tryptophan by the plant and its subsequent metabolism within plant tissues.

A number of nonleguminous plant roots are colonized by diazotrophs and there have been numerous attempts to enhance this association. Azospirillum species, in particular, have received attention [14], because their intimate association with the rhizosphere of many agriculturally important cereals suggests that fixed nitrogen may be readily accessible to the plant. However, once again the direct contribution of nitrogen fixation to increased crop yields has been questioned and growth regulators have been implicated [15].

Inoculating rice soils with cyanobacteria has long been a standard practice in India, even though results have generally been inconsistent [16]. In contrast, there are comparatively few studies of the colonization of cyanobacteria in temperate soils and, in those that exist, the increased nitrogen fixation...