Development and Validation of Bacterial Consortia for Bioremediation of Detritus in Aquaculture Systems

Cochin University Of Science And Technology

Cereal/legume rotation effects on rhizosphere bacterial community structure in West African soils

The increased use of cereal/legume crop rotation has been advocated as a strategy to increase cereal yields of subsistence farmers in West Africa, and is believed to promote changes in the rhizosphere that enhance early plant growth. In this study we investigated the microbial diversity of the rhizoplane from seedlings grown in two soils previously planted to cereal or legume from experimental plots in Gaya, Niger, and Kaboli, Togo. Soils from these legume rotation and continuous cereal plots were placed into containers and sown in a growth chamber with maize (Zea mays L.), millet (Pennisetum glaucum L.), sorghum (Sorghum bicolor L. Moench.), cowpea (Vigna unguiculata L.) or groundnut (Arachis hypogaea L.). At 7 and 14 days after sowing, 16S rDNA profiles of the eubacterial and ammoniaoxidizing communities from the rhizoplane and bulk soil were generated using denaturing gradient gel electrophoresis (DGGE). Community profiles were subjected to peak fitting analyses to quantify the DNA band position and intensities, after which these data were compared using correspondence and principal components analysis. The data showed that cropping system had a highly significant effect on community structure (p <0.005), irrespective of plant species or sampling time. Continuous cereal-soil grown plants had highly similar rhizoplane communities across crop species and sites, whereas communities from the rotation soil showed greater variability and clustered with respect to plant species. Analyses of the ammonia-oxidizing communities provided no evidence of any effects of plant species or management history on ammonia oxidizers in soil from Kaboli, but there were large shifts with respect to this group of bacteria in soils from Gaya. The results of these analyses show that crop rotation can cause significant shifts in rhizosphere bacterial communities.

Bacterial ecology of ancient Saharan salt-enrichment ponds at Teguidda-n-Tessoumt

Little is known about the bacterial ecology of evaporative salt-mining sites (salterns) of which Teguidda-n-Tessoumt at the fringe of the West-African Saharan desert in Niger is a spectacular example with its many-centuries-old and very colorful evaporation ponds. During the different enrichment steps of the salt produced as a widely traded feed supplement for cattle, animal manure is added to the crude brine, which is then desiccated and repeatedly crystallized. This study describes the dominant Bacteria and Archaea communites in the brine from the evaporation ponds and the soil from the mine, which were determined by PCR-DGGE of 16S rDNA. Correspondence analysis of the DGGE-community fingerprints revealed a change in community structure of the brine samples during the sequential evaporation steps which was, however, unaffected by the brine's pH and electric conductivity (EC). The Archaea community was dominated by a phylogenetically diverse group of methanogens, while the Bacteria community was dominated by gamma proteobacteria. Microorganisms contained in the purified salt product have the potential to be broadly disseminated and are fed to livestock across the region. In this manner, the salt mines represent an intriguing example of long-term human activity that has contributed to the continual selection, cultivation, and dissemination of cosmopolitan microorganisms.

Characterization of Lipid Droplets and Functional Analysis of Lipid Droplet-Associated Proteins in Dictyostelium discoideum

Lipid droplets (LDs) are the universal storage form of fat as a reservoir of metabolic energy in animals, plants, bacteria and single celled eukaryotes. Dictyostelium LD formation was investigated in response to the addition of different nutrients to the growth medium. LDs were induced by adding exogenous cholesterol, palmitic acid (PA) as well as growth in bacterial suspension, while glucose addition fails to form LDs. Among these nutrients, PA addition is most effective to stimulate LD formation, and depletion of PA from the medium caused LD degradation. The neutral lipids incorporated into the LD-core are composed of triacylglycerol (TAG), steryl esters, and an unknown neutral lipid (UKL) species when the cells were loaded simultaneously with cholesterol and PA. In order to avoid the contamination with other cellular organelles, the LD-purification method was modified. The isolated LD fraction was analysed by mass spectrometry and 100 proteins were identified. Nineteen of these appear to be directly involved in lipid metabolism or function in regulating LD morphology. Together with a previous study, a total of 13 proteins from the LD-proteome were confirmed to localize to LDs after the induction with PA. Among the identified LD-proteins, the localization of Ldp (lipid droplet membrane protein), GPAT3 (glycerol-3-phosphate acyltransferase 3) and AGPAT3 (1-acylglycerol-3-phosphate-acyltransferase 3) were further verified by GFP-tagging at the N-termini or C-termini of the respective proteins. Fluorescence microscopy demonstrated that PA-treatment stimulated the translocation of the three proteins from the ER to LDs. In order to clarify DGAT (diacylglycerol acyltransferase) function in Dictyostelium, the localization of DGAT1, that is not present in LD-proteome, was also investigated. GFP-tagged DGAT1 localized to the ER both, in the presence and absence of PA, which is different from the previously observed localization of GFP-tagged DGAT2, which almost exclusively binds to LDs. The investigation of the cellular neutral lipid level helps to elucidate the mechanism responsible for LD-formation in Dictyostelium cells. Ldp and two short-chain dehydrogenases, ADH (alcohol dehydrogenase) and Ali (ADH-like protein), are not involved in neutral lipid biosynthesis. GPAT, AGPAT and DGAT are three transferases responsible for the three acylation steps of de novo TAG synthesis. Knock-out (KO) of AGPAT3 and DGAT2 did not affect storage-fat formation significantly, whereas cells lacking GPAT3 or DGAT1 decreased TAG and LD accumulation dramatically. Furthermore, DGAT1 is responsible for the accumulation of the unknown lipid UKL. Overexpression of DGAT2 can rescue the reduced TAG content of the DGAT1-KO mutant, but fails to restore UKL content in these cells, indicating that of DGAT1 and DGAT2 have overlapping functions in TAG synthesis, but the role in UKL formation is unique to DGAT1. Both GPAT3 and DGAT1 affect phagocytic activity. Mutation of GPAT3 increases it but a DGAT1-KO decreases phagocytosis. The double knockout of DGAT1 and 2 also impairs the ability to grow on a bacterial lawn, which again can be rescued by overexpression of DGAT2. These and other results are incorporated into a new model, which proposes that up-regulation of phagocytosis serves to replenish precursor molecules of membrane lipid synthesis, whereas phagocytosis is down-regulated when excess fatty acids are used for storage-fat formation.  

Changes of traditional farming systems and their effects on land degradation and socio-economic conditions in the Inle Lake region, Myanmar

At many locations in Myanmar, ongoing changes in land use have negative environmental impacts and threaten natural ecosystems at local, regional and national scales. In particular, the watershed area of Inle Lake in eastern Myanmar is strongly affected by the environmental effects of deforestation and soil erosion caused by agricultural intensification and expansion of agricultural land, which are exacerbated by the increasing population pressure and the growing number of tourists. This thesis, therefore, focuses on land use changes in traditional farming systems and their effects on socio-economic and biophysical factors to improve our understanding of sustainable natural resource management of this wetland ecosystem. The main objectives of this research were to: (1) assess the noticeable land transformations in space and time, (2) identify the typical farming systems as well as the divergent livelihood strategies, and finally, (3) estimate soil erosion risk in the different agro-ecological zones surrounding the Inle Lake watershed area. GIS and remote sensing techniques allowed to identify the dynamic land use and land cover changes (LUCC) during the past 40 years based on historical Corona images (1968) and Landsat images (1989, 2000 and 2009). In this study, 12 land cover classes were identified and a supervised classification was used for the Landsat datasets, whereas a visual interpretation approach was conducted for the Corona images. Within the past 40 years, the main landscape transformation processes were deforestation (- 49%), urbanization (+ 203%), agricultural expansion (+ 34%) with a notably increase of floating gardens (+ 390%), land abandonment (+ 167%), and marshlands losses in wetland area (- 83%) and water bodies (- 16%). The main driving forces of LUCC appeared to be high population growth, urbanization and settlements, a lack of sustainable land use and environmental management policies, wide-spread rural poverty, an open market economy and changes in market prices and access. To identify the diverse livelihood strategies in the Inle Lake watershed area and the diversity of income generating activities, household surveys were conducted (total: 301 households) using a stratified random sampling design in three different agro-ecological zones: floating gardens (FG), lowland cultivation (LL) and upland cultivation (UP). A cluster and discriminant analysis revealed that livelihood strategies and socio-economic situations of local communities differed significantly in the different zones. For all three zones, different livelihood strategies were identified which differed mainly in the amount of on-farm and off-farm income, and the level of income diversification. The gross margin for each household from agricultural production in the floating garden, lowland and upland cultivation was US$ 2108, 892 and 619 ha-1 respectively. Among the typical farming systems in these zones, tomato (Lycopersicon esculentum L.) plantation in the floating gardens yielded the highest net benefits, but caused negative environmental impacts given the overuse of inorganic fertilizers and pesticides. The Revised Universal Soil Loss Equation (RUSLE) and spatial analysis within GIS were applied to estimate soil erosion risk in the different agricultural zones and for the main cropping systems of the study region. The results revealed that the average soil losses in year 1989, 2000 and 2009 amounted to 20, 10 and 26 t ha-1, respectively and barren land along the steep slopes had the highest soil erosion risk with 85% of the total soil losses in the study area. Yearly fluctuations were mainly caused by changes in the amount of annual precipitation and the dynamics of LUCC such as deforestation and agriculture extension with inappropriate land use and unsustainable cropping systems. Among the typical cropping systems, upland rainfed rice (Oryza sativa L.) cultivation had the highest rate of soil erosion (20 t ha-1yr-1) followed by sebesten (Cordia dichotoma) and turmeric (Curcuma longa) plantation in the UP zone. This study indicated that the hotspot region of soil erosion risk were upland mountain areas, especially in the western part of the Inle lake. Soil conservation practices are thus urgently needed to control soil erosion and lake sedimentation and to conserve the wetland ecosystem. Most farmers have not yet implemented soil conservation measures to reduce soil erosion impacts such as land degradation, sedimentation and water pollution in Inle Lake, which is partly due to the low economic development and poverty in the region. Key challenges of agriculture in the hilly landscapes can be summarized as follows: fostering the sustainable land use of farming systems for the maintenance of ecosystem services and functions while improving the social and economic well-being of the population, integrated natural resources management policies and increasing the diversification of income opportunities to reduce pressure on forest and natural resources.

Functional studies of the deubiquitinating enzymes USP19, USP4 and UCH-L1

El marcaje de proteínas con ubiquitina, conocido como ubiquitinación, cumple diferentes funciones que incluyen la regulación de varios procesos celulares, tales como: la degradación de proteínas por medio del proteosoma, la reparación del ADN, la señalización mediada por receptores de membrana, y la endocitosis, entre otras (1). Las moléculas de ubiquitina pueden ser removidas de sus sustratos gracias a la acción de un gran grupo de proteasas, llamadas enzimas deubiquitinizantes (DUBs) (2). Las DUBs son esenciales para la manutención de la homeostasis de la ubiquitina y para la regulación del estado de ubiquitinación de diferentes sustratos. El gran número y la diversidad de DUBs descritas refleja tanto su especificidad como su utilización para regular un amplio espectro de sustratos y vías celulares. Aunque muchas DUBs han sido estudiadas a profundidad, actualmente se desconocen los sustratos y las funciones biológicas de la mayoría de ellas. En este trabajo se investigaron las funciones de las DUBs: USP19, USP4 y UCH-L1. Utilizando varias técnicas de biología molecular y celular se encontró que: i) USP19 es regulada por las ubiquitin ligasas SIAH1 y SIAH2 ii) USP19 es importante para regular HIF-1α, un factor de transcripción clave en la respuesta celular a hipoxia, iii) USP4 interactúa con el proteosoma, iv) La quimera mCherry-UCH-L1 reproduce parcialmente los fenotipos que nuestro grupo ha descrito previamente al usar otros constructos de la misma enzima, y v) UCH-L1 promueve la internalización de la bacteria Yersinia pseudotuberculosis.

Convergencia de vías de señalización en un modelo de apoptosis

La sepsis es un evento inflamatorio generalizado del organismo inducido por un daño causado generalmente por un agente infeccioso. El patógeno más frecuentemente asociado con esta entidad es el Staphylococcus aureus, responsable de la inducción de apoptosis en células endoteliales debida a la producción de ceramida. Se ha descrito el efecto protector de la proteína C activada (PCA) en sepsis y su relación con la disminución de la apoptosis de las células endoteliales. En este trabajo se analizó la activación de las quinasas AKT, ASK1, SAPK/JNK y p38 en un modelo de apoptosis endotelial usando las técnicas de Western Blotting y ELISA. Las células endoteliales (EA.hy926), se trataron con C2-ceramida (130μM) en presencia de inhibidores químicos de cada una de estas quinasas y PCA. La supervivencia de las células en presencia de inhibidores químicos y PCA fue evaluada por medio de ensayos de activación de las caspasas 3, 7 y 9, que verificaban la muerte celular por apoptosis. Los resultados evidencian que la ceramida reduce la activación de AKT y aumenta la activación de las quinasas ASK, SAPK/JNK y p38, en tanto que PCA ejerce el efecto contrario. Adicionalmente se encontró que la tiorredoxina incrementa la activación/fosforilación de AKT, mientras que la quinasa p38 induce la defosforilación de AKT.

Nitrifying and denitrifying bacterial communities in the sediment and rhizosphere of a free water surface constructed wetland

La contínua descàrrega de nutrients, sobretot fosfats i nitrogen, és la major causa d'eutrofització dels ecosistemes aquàtics. Els sistemes de tractament basats en aiguamolls construïts s'han emprat per reduir ells nivells de nitrogen a l'aigua com a alternativa de baix cost als mètodes de depuració convencionals. L'eliminació del nitrogen a aquests sistemes depèn en bona part de la vegetació, i l'alternança de condicions aeròbiques i anaeròbiques per promoure els processos de nitrificació i desnitrificació. En aquest treball hem volgut investigar les activitats microbianes de nitrificació i desnitrificació en relació a dues espècies de plantes macròfites en un sistema d'aiguamolls de tractament de flux superficial (FS-SAC), dissenyat per minimitzar l'impacte de l'alliberament d'aigua carregada de nutrients a la reserva natural dels Aiguamolls de l'Empordà (Girona, Espanya).

Characterization and efficacy of bacterial strains for biological control of soil-borne diseases caused by Phytophthora cactorum and Meloidogyne javanica on Rosaceous plants

S'avaluaren 58 soques de Pseudomonas fluorescens i Pantoea agglomerans per la seva eficàcia en el biocontrol de la malaltia causada per l'oomicet Phytophthora cactorum en maduixera i pel nematode formador de gal·les Meloidogyne javanica en el portaempelt GF-677. Es desenvolupà un mètode ex vivo d'inoculació de fulla amb l'objectiu de seleccionar soques bacterianes com a agents de control biològic de P. cactorum en maduixera. Tres soques de P. fluorescens es seleccionaren com a soques eficaces en el biocontrol del patogen en fulles i en la reducció de la malaltia en plantes de maduixera. La combinació de soques semblà millorar la consistència del biocontrol en comparació amb les soques aplicades individualment. Tres soques de P. fluorescens es seleccionaren per la seva eficàcia en la reducció de la infecció de M. javanica en portaempelts GF-677. La combinació d'aquestes soques no incrementà l'eficàcia del biocontrol, però semblà reduir la seva variabilitat.

Bacterial biofilms in cholesteatomas of Mongolian gerbils

This paper studies cholesteatomas of Mongolian gerbils and the presence of bacterial biofilms.

Transport and distribution of lindane and simazine in a riverine environment: measurements in bed sediments and modelling

Aquatic sediments often remove hydrophobic contaminants from fresh waters. The subsequent distribution and concentration of contaminants in bed sediments determines their effect on benthic organisms and the risk of re-entry into the water and/or leaching to groundwater. This study examines the transport of simazine and lindane in aquatic bed sediments with the aim of understanding the processes that determine their depth distribution. Experiments in flume channels (water flow of 10 cm s(-1)) determined the persistence of the compounds in the absence of sediment with (a) de-ionised water and (b) a solution that had been in contact with river sediment. In further experiments with river bed sediments in light and dark conditions, measurements were made of the concentration of the compounds in the overlying water and the development of bacterial/algal biofilms and bioturbation activity. At the end of the experiments, concentrations in sediments and associated pore waters were determined in sections of the sediment at 1 mm resolution down to 5 mm and then at 10 mm resolution to 50 mm depth and these distributions analysed using a sorption-diffusion-degradation model. The fine resolution in the depth profile permitted the detection of a maximum in the concentration of the compounds in the pore water near the surface, whereas concentrations in the sediment increased to a maximum at the surface itself. Experimental distribution coefficients determined from the pore water and sediment concentrations indicated a gradient with depth that was partly explained by an increase in organic matter content and specific surface area of the solids near the interface. The modelling showed that degradation of lindane within the sediment was necessary to explain the concentration profiles, with the optimum agreement between the measured and theoretical profiles obtained with differential degradation in the oxic and anoxic zones. The compounds penetrated to a depth of 40-50 rum over a period of 42 days. (C) 2004 Society of Chemical Industry.

Determination of the impact of continuous defoliation of Lolium perenne and Trifolium repens on bacterial and fungal community structure in rhizosphere soil

To determine the effects of defoliation on microbial community structure, rhizosphere soil samples were taken pre-, and post-defoliation from the root tip and mature root regions of Trifolium repens L. and Lolium perenne L. Microbial DNA isolated from samples was used to generate polymerase chain reaction-denaturing gradient gel electrophoresis molecular profiles of bacterial and fungal communities. Bacterial plate counts were also obtained. Neither plant species nor defoliation affected the bacterial and fungal community structures in both the root tip and mature root regions, but there were significant differences in the bacterial and fungal community profiles between the two root regions for each plant. Prior to defoliation, there was no difference between plants for bacterial plate counts of soils from the root tip regions; however, counts were greater in the mature root region of L. perenne than T. repens. Bacterial plate counts for T. repens were higher in the root tip than the mature root region. After defoliation, there was no effect of plant type, position along the root or defoliation status on bacterial plate counts, although there were significant increases in bacterial plate counts with time. The results indicate that a general effect existed during maturation in the root regions of each plant, which had a greater impact on microbial community structure than either plant type or the effect of defoliation. In addition there were no generic consequences with regard to microbial populations in the rhizosphere as a response to plant defoliation.

Degradation of atrazine and isoproturon in surface and sub-surface soil materials undergoing different moisture and aeration conditions

The influence of different moisture and aeration conditions on the degradation of atrazine and isoproturon was investigated in environmental samples aseptically collected from surface and sub-surface zones of agricultural land. The materials were maintained at two moisture contents corresponding to just above field capacity or 90% of field capacity. Another two groups of samples were adjusted with water to above field capacity, and, at zero time, exposed to drying-rewetting cycles. Atrazine was more persistent (t(1/2) = 22-3S days) than isoproturon (t(1/2) = 5-17 days) in samples maintained at constant moisture conditions. The rate of degradation for both herbicides was higher in samples maintained at a moisture content of 90% of field capacity than in samples with higher moisture contents. The reduction in moisture content in samples undergoing desiccation from above field capacity to much lower than field capacity enhanced the degradation of isoproturon (t(1/2) = 9-12 days) but reduced the rate of atrazine degradation (t(1/2) = 23-35-days). This demonstrates the variability between different micro-organisms in their susceptibility to desiccation. Under anaerobic conditions generated in anaerobic jars, atrazine degraded much more rapidly than isoproturon in materials taken from three soil profiles (0-250 cm depth). It is suggested that some specific micro-organisms are able to survive and degrade herbicide under severe conditions of desiccation. (C) 2004 Society of Chemical Industry.