Chapter 1
Applications of Microorganisms in Agriculture for Nutrients Availability

Fehmida Fasim1* and Bushra Uziar2

1Discipline of Biomedical Science, Sydney Medical School, University of Sydney, Australia

2International Islamic University, Department of Bioinformatics and Biotechnology, Islamabad Capital Territory, Islamabad

*Corresponding author: ffasim@uni.sydney.edu.au

Abstract

Constantly increasing global food demand, over use of Phosphorus (P) containing fertilisers to improve agricultural productivity not only causes pollution of ground and surface water but also depletes soil fertility and leads to accumulation of toxic elements in the soil. Production of healthy agriculture crops is essentially dependant on the available nutrients in soil. In healthy crop production, key nutrients such as phosphorus (P), iron (Fe), nitrogen (N) and potassium (K) play a major role. Chemical fertilizers are in great demand as most soils are deficient in key nutrients. Hence efforts are made for an innovative, alternative and environmentally friendly techniques over conventional chemical fertilizers. Microbes play a pivotal role in increasing the nutrients bioavailability such as mobilization of major nutrients and nitrogen fixation that improve the plant yield and growth. In this review, current findings on the mechanisms utilized by various microbes will be discussed and highlighted. Furthermore, in improving soil fertility the inoculation of microbes in various forms such as sole inoculation, co-inoculation or in combination with organic fertilizer will be debated.

Keywords: Soil depletion, soil microbes, solubilization, co-inoculation, biofertilizer

1.1 Introduction

In developing countries from 1970 to 1995, the global food production had increased by 70% mainly because of new technology called conventional agriculture which was based on chemical fertilizers, synthetic pesticides and irrigation to produce high yields [1, 2]. The use of such technologies are destroying the natural environment in many ways such as surface and ground water contamination, increased pest resistance, soil erosion and reduced biodiversity [3, 4]. Keeping in mind the increasing population and food demand worldwide, sustainable methods are key for food production. To avoid mitigating climate change and land degradation the sustainable methods must sustain this natural resource. This can be done by fine tuning of current technologies or to develop alternate technologies without damaging the environment or natural resources to obtain high yield crops that can meet food demand globally.

About organic and inorganic fertilizers there are numerous myths [5, 6]. Without enough scientific evidence, it appears that mostly these myths are based on conjunctions, perceptions, or for political motives. Regarding chemical fertilizers some legends are listed below:

1.1.1 Land and Soil Deterioration

Soil's physical and chemical properties are destroyed by chemical fertilizers whereas fertility is improved by organic fertilizers [5]. Soil structure by chemical fertilisers is not affected if it is administered in the right quantity. Nitrogen (N) fertilizers tend to acidify soil to a pH of < 5 which can have adverse effects. If administered at an optimal dose it may positively influence soil biota. If applied in high amount then it may alter soil texture, reduce in microbial community and increase soil acidification.

1.1.2 Micro-Nutrients Lacks

Regarding chemical fertilizers there is a popular misconception that macro-nutrients are in low amounts when in fact they are lacking. Organic fertilizers generally contain some micro-nutrients however there are some inorganic fertilizers containing micro-nutrients commercially available too [5].

Adoption of Integrated Soil Fertility management can help restore fertility of soil as explained by Vlek and Vielhauer [7]. This involves a strategy that allows for control of soil nutrients, nitrogen fixation and efficiency in administration.

This strategy encompasses use of biofertilizers which are biocompatible and economically viable plant nutrients to help supplement synthetic fertilisers for a more sustainable agricultural system. The aim is to increase production and sustain balance of the nutrients in soil.

1.2 Biofertilizers

Microbial inoculants or biofertilizers are live or latent cell of strains that are efficient in phosphate solubilization, nitrogen fixation, potassium solubilization, siderophore production used for seed application, soil or composting areas where such microorganism population can increase and enhance several microbial processes to boost the nutrients availability that can be utilised by plants. The history of applying microbial inoculums have passed down generations of farmers. The efficacy of biofertilizers was evident when on small scale culture compost was introduced, it enhanced the decomposition of organic residues and agriculture by-products that resulted in healthy harvest of crops [8].

In biofertilizer making several things are considered such as growth profile of the selected microbe, organism's optimum conditions and inoculum formulation. For the success of biological product critical steps are inocula formulation, application method and product storage.

Generally, six key steps are required in making a biofertilizer, 1) organism selection, 2) solation, 3) method selection and carrier material, 4) propagation method selection, 5) prototype testing and 6) large scale testing. In late 1940's, Malaysia started using industrial scale microbial inoculants and took guide by Brady rhizobium on legumes topped up in 1970's. Malaysian Rubber Board (MRB), a government research institute has conducted research on Rhizobium inoculums for use on leguminous cover crops of young rubber trees in the large-scale plantations. Since 1980 many research projects on Mycorrhiza were conducted at University Putra Malaysia (UPM) and led to Azospirillum nitrogen to oil palm seedlings [8].

1.3 Rhizosphere

Root network is surrounded by a narrow zone of soil termed as rhizosphere [9], and the bacteria that colonises in the root environment are termed 'rhizobacteria' [10]. These roots not only provide mechanical support, nutrient uptake and facilitate water but also synthesize various compounds [9]. Heterogeneous, multifaceted and active microbial communities are attracted to the compounds produced by roots. In a nutshell they act as chemical attractants commonly called as root exudates. The chemical and physical properties of soil are modified by wide variety of chemical compounds (root exudate) and thus control the structure of the microbial community found in the proximate area of root surface [11]. Some microorganisms are attracted whereas some are repelled by the exudates. Exudate composition depends upon plant species, physiological state and surrounding microbes [12]. In addition, these exudates enhance symbiotic plant interaction and growth inhibition to the hostile plant species [13, 14]. In the rhizosphere microbial activity also affects nutrient availability and root patterns thereby by modifying the quantity as well as quality of root exudates. Small organic molecule fractions derived by plants are metabolized further as nitrogen and carbon sources by microbes present in the vicinity. On the other hand, molecules obtained from microbes are regained by plants for growth and development [12]. Critical determinants of rhizosphere function are carbon fluxes. 5 to 15 percent of fixed carbon is obtained through root exudation and transported to rhizosphere [15]. Any amount of soil associated or influenced by plants roots or their hairs as well as any plant produced materials encompass the rhizosphere [16]. Basically, rhizosphere can be grouped into three but interacting constituents a) rhizosphere (soil), b) rhizoplane (root surface), and c) root (itself). Rhizosphere is an area of soil which affects the microbial activity through the release of substrates by roots whereas rhizoplane is the root surface covered by soil particles and roots by microbes known as root colonization [17].

1.4 Plant Growth Promoting Bacteria

Plant growth promoting rhizobacteria (PGPR) are bacteria that colonise the rhizosphere. When PGPR are introduced to roots, seeds, or into soil either directly or indirectly they stimulate plant growth. They play an essential role in plant growth by increasing nutrient uptake, suppress plant pathogens and induce plant resistance to pathogens. The term PGPR was first coined by Kloepper and co-worker's in the late 1970s [18]. PGPR are found widely in various genera such as Azospirillum, Agrobacterium, Acinetobacter, Arthrobacter, Bradyrhizobium, Bacillus, Burkholderia, Pantoea, Cellulomonas, Frankia, Rhizobium, Thiobacillus, Pseudomonas, Serratia, Streptomyces. Rhizobacteria are most widely studied PGPR that colonizes the root surfaces and the rhizosphere [18, 19]. Some of these PGPR also enter root interior and establish endophytic populations as reviewed recently by Gray and Smith [19, 20].

Many of them can surpass the endodermis barrier and enter the vascular system by crossing the root cortex and bloom as endophytes in stem, tubers, leave and other parts [19, 21-23] Endophytic colonization is characteristic of PGPR (the attribute of selective adaptation to specific ecological niches) [19, 21], as a result friendly association between the host plant and bacteria is formed [21, 23] excluding any damage to the host plants...