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Arbuscular mycorrhiza fungi (AMF) which form a symbiosis association with more than 80% terrestrial plants are not only important for natural ecosystems, but also for sustainable agricultural production. The aim of first part of study was to characterize AM fungal populations collected from different agroclimatic zone of tropical agricultural soil in order to better understand the processes influencing AMF diversity and to determine the environmental factors affecting AMF populations, especially in the context of agricultural management practices. Spores of arbuscular mycorrhizal fungi (AMF) were collected from trap cultures (Northern India) and based on their morphology were grouped into morphotypes. The small subunit, internal transcribed spacer and large subunit gene of ribosomal DNA used as molecular marker and fatty acid methyl ester profiles (FAME) used as biomarker to resolve population structure of AM fungi. Organic sites contributed the 18 AM species belonging to Genera Rhizophagus and Funneliformis and 7 AM fungi of Acaulospora, Gigaspora, Enterospora and Scutellospora. In contrast, conventional sites selectively favour only smaller size AM species belonging to genera Rhizophagus and Funneliformis species. Organically managed farmland contributed the largest number of AMF species richness and diversity index as compared sites with conventional agricultural practices, which suggests that factors contributing to the diversity of AMF are indeed complex: for example, chemically managed farmland not only causes loss of fungal biodiversity but also selectively favors smaller spores (Rhizophagus sp.), thereby affecting ecosystem functioning adversely. The present study showed that both abundance and diversity of AMF is favored by low-input agriculture incorporating planting on raised beds (RB) and organic practices such as zero tillage that do not disturb the physical properties of soil.
Other part of the work based on difficulties in obtaining sterile axenic cultures and heterogeneity in nuclear-encoded ribosomal DNA (n-rDNA) sequences within a single arbuscular mycorrhizal spore make genetic analysis of arbuscular mycorrhizal fungi (AMF) a complicated task, and currently available methods of genotyping are inadequate for identification to the species level. Therefore, we applied a multipronged approach on different isolates grown in root organ culture (ROC) belonging to the genus Rhizophagus which were not characterized at species level. Each strain was characterized using the fatty acid methyl ester profile (FAME), partial sequencing of a small subunit-internal transcribed spacer (SSU-ITS) and a large subunit (LSU) region of n-rDNA, and morphological examination of spores. Neighbor-joining trees obtained from the SSU-ITS rDNA sequences were broadly similar to those obtained from the LSU rDNA sequences. FAME profiles of the same isolates used for molecular characterization were obtained using fatty acid datasets, and results were compared to a neighbor-joining tree of n-rDNA sequence. Based on the results of these studues, a combination of morphology, biomarkers (FAME), and molecular sequencing (of highly variable D1-D2 of LSU and ITS) is recommended for phylogenetic analysis and characterization of species/strain of Glomeromycota. Study revealed that comparative characterization of ten Rhizophagus isolates propagated in root organ culture revealed that single methods is not sufficient to resolve arbuscular mycorrhizal fungi upto species/isolates level. Present investigation critically discussed about constraints and advantages of current methodology used for AM identification and comparative studies with conventional methods. This study was conducted to reconcile the different selected isolates into their true taxonomic position but it was made clear that any single method employed for classification was inadequate. Due to this a combined profile obtained for each isolate which highlighted the similarities and differences between each, thus emphasizing their uniqueness.
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