Microbial diversity in rice rhizosphere as influenced by nutrient management: A review

Introduction

The soil microbial diversity concept Soil microbial diversity is composed of species diversity and genetic diversity, as well as ecosystem biodiversity. Species diversity consists of species richness, the total of species present, species evenness, and the distribution of species. However, the traditional species definition was based on higher plants and animals and is not readily applied to prokaryotes or asexual organisms. Microbial diversity has usually been taken as the number of individuals assigned to different taxa and their distribution among taxa. consequently, microorganisms have been referred to collectively as functional groups or guilds. Typically, microbial diversity studies have included the relative diversities of communities across a gradient of stress, disturbance, or other biotic or abiotic differences. In spite of several studies for estimating the fluxes and appraising microbial pools, the composition and functions of soil microbiota are still mostly undiscovered.

Most of the soil microorganisms are still unknown, only a few have been isolated, cultured and identified, and directly related to their function in agroecosystems. Currently, several techniques, viz., analysis of DNA and phospholipid fatty acids (PLFAs)as well as cultivation on Bio log plates are available to facilitate the community-level characterization of soil microorganisms (Widmer et al., 2001; Wang et al., 2011) [8,9] .

Microbial diversity in rice

Irrigated rice fields differ in many ways from other agricultural lands and natural terrestrial ecosystems, including wetlands (Kogel-Knabner et al., 2010). Perhaps the most important difference is that the soil in irrigated rice fields is waterlogged for most of the time, which enhances algal photosynthesis and thus the fertility of the soil is enhanced. The prolonged hydration also influences the ability of microeukaryotes to decompose plant residues in rice field soils. Moreover, water-logged soils are typically anoxic, which limits the growth and activity of aerobic microorganisms, including bacteria, fungi and protitsts Zhang Jian-fu et. al., in a study in 2012 [12] found Grampositive bacteria, Gram-negative bacteria, methaneoxidizing bacteria, sulfate-reducing bacteria, fungi, actinomycete, arthropoda and protozoa were detected in anaerobic environment of paddy soil found that 99% of bacteria seen under microscope are not culturable by common lab techniques. To overcome problems associated with non-culturable bacteria and fungus various methods have been developed to identify and study these microorganisms including various traditional, biochemical and molecular procedures.

Major factors affecting rhizosphere microbial diversity:

Pertinent literature has suggested that different factors like soil P H , salinity, Texture, organic matter content, concentration of nutrient elements, seasonal effects as well as the management practices(irrigation, tillage, cropping, fertilizer and pesticide application, residue incorporation etc.) highly influences the microbial diversity in soil.From the middle of 1990s, much more attention has been paid on the sensitive responds of soil microbial characteristics and molecular ecology footprint to the evolution of ecology system.

Microbial diversity as influenced by Nutruient Management

In recent studies on the effect of long term fertilization on soil physical and chemical properties much more efforts were focused on the impact of long-term fertilization on soil microbial characteristics. Since the soil microbial characteristic is closely related to soil quality, it is very important to understand the soil microbial diversity. Their results show that soil microbial properties respond to the different agricultural managements sensitively, and can reflect the change ofsoil quality. Here we shall emphasise mainly on the different management practices adopted in rice field which in turn influence the rice rhizosphere community.

Techniques used for measurement of microbial diversity

The most commonly followed methods are as follows: [4] for ricerice (May-July and July-October) cropping system for a period of 5 years where urea was applied as N source with the following treatment levels, L1: 0, L2:207, L3:414, L4:621, L5:828 kg/h/yr. In addition, Ca (H 2 PO 4 ) 2 (397 kg P ha/ yr) and KCl (316 kg K ha/yr) were also applied to each plot as basal fertilizers. It was found that Diversity Shannon index and Evenness index indicated that bacterial functional diversity increased with increasing of urea input, but decreased again with excessive urea application. Table 1(a) With increasing levels of N, PLFA increased but up to a certain point (N157). But no significant difference between N157 and N210 levels was found. Among the growth stages, Grain filling stages exhibited more PLFAvalue due to highest rhizodeposition. Fig. 2(a) [10] with the following soil characteristics: The experiment had a completely randomized block design with eight treatments and four blocks. The plot size was 3.5 m × 3 m. The eight treatments include three mineral fertilizers treatments (N, NP, NPK), farmyard manure alone (M, the main component was swine manure, the content of organic matter was 1.5 g kg -1 ), three mineral plus farmyard manure treatments (NM, NPM, NPKM), and no fertilizer control (CK). All manure, P (as single superphosphate), and K (as KCl) were applied as basal fertilizers, while N (as urea) was split into 70 and 30% as basal application and topdressing for rice at tillering, and 60 and 40% as basal application and 40% as topdressing for wheat at tillering, respectively. The rates of fertilizers used were: manure at 3 × 104 kg ha-1; N at 55.2 kg ha -1 ; P 2 O 5 at 13.2 kg ha -1 ; and KCl, at 31.5 kg ha1 . It was found that in the rice soil, the numbers of bacteria, cellulose decomposing bacteria and nitrifiers were higher. In the rice soil, the numbers of bacteria, cellulose degrading bacteria and nitrifiers were higher. Numbers of microbes were in the order of: bacteria > actinomycetes > fungi.

Among the specific physiology kind group, Azotobacter number was the smallest and ammonifers was the highest in rice soil. Growth of Ammonium Oxidising Bacteria (AOB) by FYM is promoted as it provides a better soil microhabitat condition to AOB by improving the soil nutrition & aggregation structure. [12] conducted a long term paddy in rice -rice ecosystem after 8 yearsandanalyzed for: 1) Bacteria, It has been observed that application of organic manures, especially rice straw, resulted in larger overall bacterial populations than in control or chemical fertilizer Treatments. This was primarily due to higher bacterial counts in the CFS-treated soil. Compared to control, chemical fertilizer application also improved bacterial population. Therefore, both organic amendments and chemical fertilizers could be advantageous in exploiting all types beneficial microflora in soil and increasing the crop production. Use of organic manures that enhance the microbial diversity, biomass and activity along with chemical fertilizer could greatly benefit in the sustainable management of paddy ecosystem. Different letters within a column indicate that difference among the treatments is significant at 5% probability level.

Here, it was seen that, H and U values followed the order: CFS >CFM > CF > NF. This was due to application of organic manures, especially rice straw, resulted in larger overall bacterial populations than in control or chemical fertilizer Treatments. Table 4(b)

Comparative study of the microbial diversity of bulk paddy soil of two rice fields subjected to organic and conventional farming

Lopes et.al., 2010 [3] conducted a study on the of the microbial diversity of bulk paddy soil of two rice fields subjected to organic and conventional farming. Field management of paddy ORG was basal fertilization with mineral gafsa (Fertigafsa, 300 kg P ha -1 ) and organic amendment with a plant residue commercial compost (Fertiormont, 2 t ha -1 ) fertilization (102 kg N, 63 kg P 2 O 5 and 35 kg K 2 O per hectare, as ammonium sulphate, ammonium di-hydrogen phosphate and di-ammonium mono hydrogen phosphate, and potassium chloride, respectively. Soil Sampling was done three times as follows: Initial (Immediately after seeding in April),Second (Tillering in June) and Third (After Harvest in October). No significant differences were observed over the sampling period (P< 0.05). This may be due to of judicious use of fertilizers for six years in conventional treatment which shows similar results for conventional like organic treatment. Increase in Dehydrogenase activity might be due the application of organic matter. Higher urease and arylsulphatase activity might be due to application of ammonium sulphate as source of N.

Integrated Nutrient Management on Microbial Population in

INM on soil microbial biomass carbon and bacterial populations under rice system

Nath et. al., (2011) [6] studied the effect of INM on soil microbial biomass carbon and bacterial populations under rice system with the objective of investigating how INM have affected microbial biomass and the specific bacterial population under rice ecosystem. The RD of fertilizers were 40:20:20 (N:P 2 O 5 :K 2 O kg/ha) for rice. The N, P and K were supplied through urea, single superphosphate and muriate of potash, respectively. Full doses of P and K were applied as basal, while N applied in three splits (50% as basal, 25% at tillering and 25% at panicle initiation) in rice. of the organic inputs, either integration of compost (2 tonnes/ha) with bio fertilizersor application of enriched compost (2 tonnes/ha) amid 25%NP fertilizer in treatment T 5 and T 7 resulted higher MBC at167.66 and 183.66 μg/g respectively, whereas the lowest (43.23 μg/g) was obtained from the control plots. Build-up of microbial biomass is mainly due to the microbial biomass contained in the organic residues & addition of substrate C, stimulating the indigenous soil micro-biota. Favourable effects stabilized specific populations of Azo spirillum and PSB were related to the application of compost and enriched compost& added micro organisms. Application of biofertilizers, besides showing their primary effect are also known to produce diverse growth promoting substances that might contribute to intense proliferation of microbial growth and augmented MBC. Table 7(a)

Biochar amendment on soil bacterial abundance

Biochar is the product of the thermal degradation of organic materials in the absence of air (Pyrolysis) and is used as a soil amendment. (Lehmann et al., 2011) selected three Sites for for studying the effect of Biochar amendment on soil bacterial abundance as:Site A: Added N @ 300 kg/ha; Site B and Site C: added N @ 240kg/ha. On average, the biochar material contained on dry base organic carbon of 467 g kg -1 , total N of 5.9 g kg -1 , ash of 20.8% with a bulk density of 0.59 g cm 3 and p H (H 2 O) of 10.42 as well as a CEC of 21.7 cmol kg -1 . The treatments were selected as: C0: 0 (Control), C1: 20 t/ha and C2:40 t/ha of biochar.

Conclusion:

Soil biological properties viz. microbial biomass, soil respiration, population etc. increases with increasing of urea input on the whole. However, soil microbial functional diversity was correlated to soil moisture content. Excessive urea application caused significant water stress and microbial diversity depression after rice yellow ripening stages.

Application of chemical fertilizers alone could not be enough to support the microbial diversity and beneficial activities in paddy soil. Therefore, use of organic manures that enhance the microbial diversity, biomass and activity along with chemical fertilizer could greatly benefit in the sustainable management of agro-ecosystems. Organic amendments along with low amount of chemical fertilizer have a great potential to enhance paddy soil microbial biomass and microbial activity. Different long term fertilization would change the microbes 'numbers and AOB communities in paddy soil. Farmyard manure plus mineral fertilizer was most effective for protecting the soil microorganism and maintaining the soil bio fertility.

In paddy ecosystems, when organic C and N were limiting, strong competition for them in the rhizosphere soil would decrease microbial activity, thus having a negative role in denitrification and other processes. Nitrification could also be an important N 2 O source, especially under organic C and N limitation, for rhizosphere microbial activity. Regular use of organic inputs (enriched compost) coupled with reduced chemical fertilizer can improve biological properties of soil under rice ecosystem such as microbial biomass carbon, microbial populations well as organic carbon concentration in soil under the sequence. Study suggests functional redundancy of the microbial communities of organically and conventionally farmed rice field soil. Biochar plays a potential role in enhancing bacterial abundance, community diversity as well as modifying more or less the community compositions, particularly the bacteria involved in N cycling. Moreover, application of biochar has positive impact on the soil by increasing its microbial biomass carbon content. It did not affect microbial biomass nitrogen content of the soil. Further, the methanogenic archaeal diversity remains unchanged in one cropping season but its activity at varying biochar concentration may be one of the possible reasons to facilitate methane flux differentially.

Future perspectives

Understanding of microbial diversity and function in soils is limited because of the taxonomic and methodological limitations associated with studying these organisms. The level of microbial diversity and function in the soil, the link between structural diversity and function may be studied in order to understand the complexity of interacting biological, chemical, and physical factors.

References

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