Dananjeyan Balachandar

Impact of long-term organic and inorganic nutrient managements on the biological properties and eubacterial community diversity of the Indian semi-arid Alfisol

Intensive cropping with limited nutrient management options in low fertile semi-arid tropical soils will have agricultural sustainability problems in future. A better understanding of soil variables as influenced by long-term nutrient amendments could lead to the identification of more precise indicators to monitor soil fertility that would promote sustainability. Long-term nutrient experiment in semi-arid Alfisol at Coimbatore, India was investigated in two successive years, 2009 and 2010 to assess the enduring effects of organic (OM) and inorganic (IC) nutrient managements on soil variables. The organic amendments induced higher microbial population and enzyme activity compared to IC and control soils. The principal component analysis of observed variables revealed that soil organic carbon, microbial biomass carbon (MBC), dehydrogenase and alkaline phosphatase activity and diazotrophs population could be the possible indicators for predicting soil fertility resulting from long-term nutrient managements. The eubacterial community profile assessed by 16S rRNA gene sequence polymorphism revealed that the abundance and relative ratio of phyla belonging to Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes were considerably affected due to either organic manures or inorganic fertilizers, and organic nutrient management favours bacterial community diversity. These results emphasize the importance of organic nutrient management to maintain soil biological properties in semi-arid Alfisol.

Expression of Zinc Transporter Genes in Rice as Influenced by Zinc-Solubilizing Enterobacter cloacae Strain ZSB14

Zinc (Zn) deficiency in major food crops has been considered as an important factor affecting the crop production and subsequently the human health. Rice (Oryza sativa) is sensitive to Zn deficiency and thereby causes malnutrition to most of the rice-eating Asian populations. Application of zinc solubilizing bacteria (ZSB) could be a sustainable agronomic approach to increase the soil available Zn which can mitigate the yield loss and consequently the nutritional quality of rice. Understanding the molecular interactions between rice and unexplored ZSB is useful for overcoming Zn deficiency problems. In the present study, the role of zinc solubilizing bacterial strain Enterobacter cloacae strain ZSB14 on regulation of Zn-regulated transporters and iron (Fe)-regulated transporter-like protein (ZIP) genes in rice under iron sufficient and deficient conditions was assessed by quantitative real-time reverse transcription PCR. The expression patterns of OsZIP1, OsZIP4, and OsZIP5 in root and shoot of rice were altered due to the Zn availability as dictated by Zn sources and ZSB inoculation. Fe sufficiency significantly reduced the root and shoot OsZIP1 expression, but not the OsZIP4 and OsZIP5 levels. Zinc oxide in the growth medium up-regulated all the assessed ZIP genes in root and shoot of rice seedlings. When ZSB was inoculated to rice seedlings grown with insoluble zinc oxide in the growth medium, the expression of root and shoot OsZIP1, OsZIP4, and OsZIP5 was reduced. In the absence of zinc oxide, ZSB inoculation up-regulated OsZIP1 and OsZIP5 expressions. Zinc nutrition provided to the rice seedling through ZSB-bound zinc oxide solubilization was comparable to the soluble zinc sulfate application which was evident through the ZIP genes’ expression and the Zn accumulation in root and shoot of rice seedlings. These results demonstrate that ZSB could play a crucial role in zinc fertilization and fortification of rice.

Diversity of cultivable Azotobacter in the semi-arid alfisol receiving long-term organic and inorganic nutrient amendments

Monitoring the biological processes and microbial diversity is essential for sustaining the soil health for long-term productivity. In the present study, the impact of long-term nutrient management systems on changes in Azotobacter diversity of Indian semi-arid alfisol was assessed. Three soils, i.e., unfertilized control, soils amended with organic manures (OM), and with inorganic chemical fertilizers (IC) from century-old experimental fields were evaluated for Azotobacter diversity by Amplified Ribosomal DNA Restriction Analysis (ARDRA). Bray–Curtis’s similarity index of the ARDRA data of the isolates was analyzed by non-metric multi-dimensional scaling and hierarchical cluster analysis. The results revealed that the long-term organically managed soil recorded significantly higher soil organic carbon, microbial biomass carbon, and total culturable bacterial counts, whereas the chemical fertilized and control soils remained unaffected. Though the Azotobacter population was significantly higher in OM soil than IC and control soils, the genetic diversity was unaffected due to long-term addition of either organic manures or inorganic chemical fertilizers. This result implies the importance of continuous addition of organic manures and also the optimal use of inorganic chemical fertilizers without disturbing the biological properties of the soil.

Long-Term Organic Nutrient Management Fosters the Eubacterial Community Diversity in the Indian Semi-arid Alfisol as Revealed by Length Heterogeneity–PCR

Agricultural practices influence the community structure and functional diversity of soil microorganisms. In the present study, the impact of nutrient-management systems on the changes in the biological properties of Indian semi-arid Alfisol was assessed. The long-term organically managed (OGF) and inorganically fertilized (IGF) soils from century-old experimental plots were compared for eubacterial diversity using amplicon length heterogeneity PCR (LH-PCR) targeting three hypervariable domains (V1, V1_V2, and V3) of 16S rRNA gene. Of these domains, V1_V2 could discriminate the bacterial communities between the soil types. The relative ratios of amplicons differed between OGF and ICF soils, and eubacterial diversity was decreased substantially because of the inorganic chemical fertilizers, as compared to organic amendments. The Bray–Curtis similarity index and diversity indices of amplicons were greater in OGF soil than in ICF soil. This polyphasic approach revealed that the diversity and functionality of the soil eubacterial community were encouraged by long-term organic manures more than inorganic chemical fertilizers.

Arbuscular mycorrhizal fungal diversity in phosphorus-deficient Alfisols of a dry North-western agro-ecosystem of Tamil Nadu, India

Semi-arid tropical soils, characterized by low soil organic carbon (SOC) with limited available macronutrients and micronutrients for crop plants, are predicated to have a yield sustainability problem in the future due to intensive cropping and limited nutrient management adoptions. Arbuscular mycorrhizal fungi (AMF), the functional link between plant and soil, play a pivotal role in nutrient cycling, organic matter stabilization and soil structure and fertility improvement. Hence, so far unexplored or underutilized, native AMF could be a potential resource for fertility management of these semi-arid tropical soils. Hence, in the present investigation, we assessed the abundance and diversity of AMF in phosphorus-deficient agricultural soils of semi-arid tropics of southern India. Our results show that the spore density and infective propagules of AMF were relatively low in these soils. The morpho-typing of extracted AMF spores revealed that these soils were dominated by glomeraceae (six species of Glomus) while species of Gigaspora, Scutellospora and Acaulospora were found in low abundance. The diversity indices assessed for the AMF species were also globally low. The non-metric multi-dimensional scaling and hierarchical cluster analysis of species richness showed variation in the community composition of AMF in the soils. The principal component analysis of the assessed soil variables suggest that the available phosphorus (P), SOC and dehydrogenase and alkaline phosphatase activities had negative impact on spore density and infective propagules of AMF with no effect on species diversity. The regression analyses reveal that the available P is the significant soil variable that drives the AMF abundance and infectivity. This study opens the possibilities of effective utilization of native mycorrhizae for agriculture in semi-arid tropical soils.

Long-term organic nutrient managements foster the biological properties and carbon sequestering capability of a wetland rice soil

Monitoring the qualitative and quantitative changes of soil organic carbon (SOC) is very much essential to keep the soil viable and productive for long-term sustainability. Impact of long-term (36 years) enforcement of organic and inorganic nutrient management practices on changes in physio-chemical, microbiological properties and enzymatic activities of flooded rice soil was assessed along with soil carbon pools. The results revealed that the fractions of SOC, microbial biomass carbon, culturable microbial counts and dehydrogenase and β-glucosidase activities increased significantly in green manure amended soil. The population of functional microbial groups, namely denitrifiers and methanotrophs was high in farm yard manure applied soil, while methanogens population was high in green manure application. Higher nitrifier population was evident in inorganic or integrated organic and inorganic fertilizer. Continuous application of recommended levels of chemical fertilizers did not greatly affect biological activities in the soil. Fourier Transform Infrared Spectroscopy analysis of humic acid revealed that organic fertilized soil fractions were more aliphatic with greater diversity than did the inorganic fertilized soil fractions. This study emphasizes the importance of organic manure and underscores the recommended dose of inorganic fertilizer to maintain the soil biological properties in flooded rice soil.

Multiplex and quantitative PCR targeting SCAR markers for strain-level detection and quantification of biofertilizers

Biofertilizers are the eco‐friendly bio‐input being used to sustain the agriculture by reducing the chemical inputs and improving the soil health. Quality is the major concern of biofertilizer technology which often leads to poor performance in the field and thereby loses the farmers’ faith. To authenticate the strain as well as its presumed cell load of a commercial product, sequence characterized amplified region (SCAR) markers were developed for three biofertilizer strains viz., Azospirillum brasilense (Sp7), Bacillus megaterium (Pb1) and Azotobacter chroococcum (Ac1). We evaluated the feasibility of multiplex‐PCR and quantitative real‐time PCR for SCAR marker‐based quality assessment of the product as well as the persistence of the strains during crop growth. We showed that multiplex PCR can concurrently discriminate the strains based on the amplicons’ size and detects up to 104 cells per g or per ml of carrier‐based or liquid formulation of biofertilizer, respectively. The detection limit of quantitative PCR targeting SCAR markers is 103 cells per g or ml of biofertilizer. Both the PCR methods detected and quantified them in the maize rhizosphere. Hence SCAR marker‐based quality assessment would be a sensitive tool to monitor the biofertilizer production as well as its persistence in the inoculated crop rhizosphere.

Microbial Populations, Activity and Gene Abundance in Tropical Vertisols Under Intensive Chemical Farming

There are increasing concerns on the environmental impacts of intensive chemical agriculture. The effect of high agrochemical inputs used in intensive chemical farming was assessed on soil microbiological, molecular and biochemical properties in tropical Vertisols in India. Farm field sites under normal cultivation of arable crops using high inputs of fertilizers and pesticides in chili (Capsicum annum L., 5.0× dose for fertilizers and 1.5× dose for pesticides over normal inputs) and black gram (Vigna mungo L. Hepper, 2.2× dose for fertilizers and 2.3× dose for pesticides over normal inputs) were compared with adjacent sites using normal recommended doses. Organic carbon and basal respiration showed no response to high inputs of fertilizers and pesticides in soils of both crops. Labile carbon decreased by 10% in chili soils and increased by 24% in black gram soils under high input farming system. The proportion of soil labile carbon as a fraction of soil organic carbon was unaffected by high inputs. The labile carbon mineralization coefficient (qMLC) increased by 50.0% in chili soils, indicating that the soil microorganisms were under stress due to high agochemical inputs, whereas qMLC decreased by 36.4% in black gram soils. Copiotrophs increased due to high inputs in soils of both chili (63.1%) and black gram (47.1%). Oligotrophs increased by 10.8% in black gram soils but not in chili soils. The abundance of amoA gene reduced by 39.3% in chili soils due to high inputs and increased significantly by 110.8% in black gram soils. β-Glucosidase also increased by 27.2% and 325.0%, respectively. Acid phosphatase activity reduced by 29.2% due to high inputs in chili soils and increased by 105.0% in black gram soils. The use of high agrochemical inputs thus had adverse consequences on biological health in chili but not in black gram soils. In soils cultivated with black gram, the moderating effect of cultivating legumes and their beneficial effect on soil health were evident from the increase in soil labile carbon, lower qMLC, higher amoA gene and enzyme activities. Overall results showed that cultivation of legumes permits intensive chemical farming without deteriorating soil biological health.