Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA

The impact of chronic nitrogen amendments on bacterial communities was evaluated at Harvard Forest, Petersham, MA, USA. Thirty soil samples (3 treatments × 2 soil horizons × 5 subplots) were collected in 2009 from untreated (control), low nitrogen-amended (LN; 50 kg NH4NO3 ha-1 yr-1) and high nitrogen-amended (HN; 150 kg NH4NO3 ha-1 yr-1) plots. PCR-amplified partial 16S rRNA gene sequences made from soil DNA were subjected to pyrosequencing (Turlapati et al., 2013) and analyses using oligotyping. The parameters M (the minimum count of the most abundant unique sequence in an oligotype) and s (the minimum number of samples in which an oligotype is expected to be present) had to be optimized for forest soils because of high diversity and the presence of rare organisms. Comparative analyses of the pyrosequencing data by oligotyping and operational taxonomic unit clustering tools indicated that the former yields more refined units of taxonomy with sequence similarity of ≥99.5%. Sequences affiliated with four new phyla and 73 genera were identified in the present study as compared to 27 genera reported earlier from the same data (Turlapati et al., 2013). Significant rearrangements in the bacterial community structure were observed with N-amendments revealing the presence of additional genera in N-amended plots with the absence of some that were present in the control plots. Permutational MANOVA analyses indicated significant variation associated with soil horizon and N treatment for a majority of the phyla. In most cases soil horizon partitioned more variation relative to treatment and treatment effects were more evident for the organic (Org) horizon. Mantel test results for Org soil showed significant positive correlations between bacterial communities and most soil parameters including NH4 and NO3. In mineral soil, correlations were seen only with pH, NH4, and NO3. Regardless of the pipeline used, a major hindrance for such a study remains to be the lack of reference databases for forest soils

Glutamate, Ornithine, Arginine, Proline, and Polyamine Metabolic Interactions: The Pathway Is Regulated at the Post-Transcriptional Level

The metabolism of glutamate into ornithine, arginine, proline, and polyamines is a major network of nitrogen-metabolizing pathways in plants, which also produces intermediates like nitric oxide, and γ-aminobutyric acid (GABA) that play critical roles in plant development and stress. While the accumulations of intermediates and the products of this network depend primarily on nitrogen assimilation, the overall regulation of the interacting sub-pathways is not well understood. We tested the hypothesis that diversion of ornithine into polyamine biosynthesis (by transgenic approach) not only plays a role in regulating its own biosynthesis from glutamate but also affects arginine and proline biosynthesis. Using two high putrescine producing lines of Arabidopsis thaliana (containing a transgenic mouse ornithine decarboxylase gene), we studied the: (1) effects of exogenous supply of carbon and nitrogen on polyamines and pools of soluble amino acids; and, (2) expression of genes encoding key enzymes in the interactive pathways of arginine, proline and GABA biosynthesis as well as the catabolism of polyamines. Our findings suggest that: (1) the overall conversion of glutamate to arginine and polyamines is enhanced by increased utilization of ornithine for polyamine biosynthesis by the transgene product; (2) proline and arginine biosynthesis are regulated independently of polyamines and GABA biosynthesis; (3) the expression of most genes (28 that were studied) that encode enzymes of the interacting sub-pathways of arginine and GABA biosynthesis does not change even though overall biosynthesis of Orn from glutamate is increased several fold; and (4) increased polyamine biosynthesis results in increased assimilation of both nitrogen and carbon by the cells

A Fuzzy C-Means Based Feature Selection to Process Medical Data

Classification and Feature selection are crucial steps in medical image data mining to diagnose the problems effectively. Micro Aneurysm, a retinal disease that mostly appears in diabetic patients is identified with a careful examination only. A classifier that recognises the micro aneurysm with the help of fuzzy technique has been proposed here. A Comparison has been made between the proposed approach and with the annealing and boosting approaches

Long-term trends of changes in pine and oak foliar nitrogen metabolism in response to chronic nitrogen amendments at Harvard Forest, MA

We evaluated the long-term (1995–2008) trends in foliar and sapwood metabolism, soil solution chemistry and tree mortality rates in response to chronic nitrogen (N) additions to pine and hardwood stands at the Harvard Forest Long Term Ecological Research (LTER) site. Common stress-related metabolites like polyamines (PAs), free amino acids (AAs) and inorganic elements were analyzed for control, low N (LN, 50 kg NH4NO3 ha−1 year−1) and high N (HN, 150 kg NH4NO3 ha−1 year−1) treatments. In the pine stands, partitioning of excess N into foliar PAs and AAs increased with both N treatments until 2002. By 2005, several of these effects on N metabolites disappeared for HN, and by 2008 they were mostly observed for LN plot. A significant decline in foliar Ca and P was observed mostly with HN for a few years until 2005. However, sapwood data actually showed an increase in Ca, Mg and Mn and no change in PAs in the HN plot for 2008, while AAs data revealed trends that were generally similar to foliage for 2008. Concomitant with these changes, mortality data revealed a large number of dead trees in HN pine plots by 2002; the mortality rate started to decline by 2005. Oak trees in the hardwood plot did not exhibit any major changes in PAs, AAs, nutrients and mortality rate with LN treatment, indicating that oak trees were able to tolerate the yearly doses of 50 kg NH4NO3 ha−1 year−1. However, HN trees suffered from physiological and nutritional stress along with increased mortality in 2008. In this case also, foliar data were supported by the sapwood data. Overall, both low and high N applications resulted in greater physiological stress to the pine trees than the oaks. In general, the time course of changes in metabolic data are in agreement with the published reports on changes in soil chemistry and microbial community structure, rates of soil carbon sequestration and production of woody biomass for this chronic N study. This correspondence of selected metabolites with other measures of forest functions suggests that the metabolite analyses are useful for long-term monitoring of the health of forest trees

Analysis of the Types and Pattern of uses and Control Rights over Multiple uses of Tank Irrigation System in South India

The study examines the property rights related to conservation and sustainable management of tank irrigation systems in South India. Tanks are a symbol of social and cultural entity closely woven in to the livelihood of the common man as it serves a multitude of functions such as irrigation, livestock, fisheries, duck rearing and domestic water supply as well. A study of the types, pattern of uses and control rights over Tank irrigation system is important for the sustainable management and conservation of tank irrigation systems. The research was carried out during 2007-09 by selecting one system tank and 31 non-system tanks drawn from eight tank-chains present in two tank intensive districts (Villupuram and Kancheepuram) of Tamil Nadu state, India. Case study was conducted in the system tank to collect data using Participatory Rural Appraisal PRA method. From each of the 31 non-system tanks, a random sample of key informants ranging 12 to 15 users (totalling 400) who depended on various tank resources was drawn from the 31 non-system tanks for data collection through PRA. The results on the performance of tanks in the light of its multiple uses (or physical resource use efficiency) indicated that agricultural use dominated in terms of its use share performance in absolute terms. Uses such as domestic, Live Stock Drinking (LSD) and fishery performed better next to agriculture. The intensity of property rights in terms of access, withdrawal, management, exclusion and alienation, for the five uses of tank namely irrigation, social forestry, silt, fishing and bund trees were found to be exercised by various groups of users at lower level in most of the tanks. The uses namely domestic, duck rearing, hard grass collection, LSD and brick making were found to be enjoyed by the users at higher level of intensity of PR by the respective user group. The intensity of property rights seems to be high for those uses with less number of users than for the uses like agriculture, fishery, Social Forestry, silt and bund trees wherein there were too many users with competition among them to enjoy the benefits of the resource. Hence existence of a strong users’ institution would facilitate the users to enjoy the property rights over the tank resources at a higher level in an appropriate manner