Seasonal fluctuations of bacterial community diversity in agricultural soil and experimental validation by laboratory disturbance experiments.

Natural fluctuations in soil microbial communities are poorly documented because of the inherent difficulty to perform a simultaneous analysis of the relative abundances of multiple populations over a long time period. Yet, it is important to understand the magnitudes of community composition variability as a function of natural influences (e.g., temperature, plant growth, or rainfall) because this forms the reference or baseline against which external disturbances (e.g., anthropogenic emissions) can be judged. Second, definition of baseline fluctuations in complex microbial communities may help to understand at which point the systems become unbalanced and cannot return to their original composition. In this paper, we examined the seasonal fluctuations in the bacterial community of an agricultural soil used for regular plant crop production by using terminal restriction fragment length polymorphism profiling (T-RFLP) of the amplified 16S ribosomal ribonucleic acid (rRNA) gene diversity. Cluster and statistical analysis of T-RFLP data showed that soil bacterial communities fluctuated very little during the seasons (similarity indices between 0.835 and 0.997) with insignificant variations in 16S rRNA gene richness and diversity indices. Despite overall insignificant fluctuations, between 8 and 30% of all terminal restriction fragments changed their relative intensity in a significant manner among consecutive time samples. To determine the magnitude of community variations induced by external factors, soil samples were subjected to either inoculation with a pure bacterial culture, addition of the herbicide mecoprop, or addition of nutrients. All treatments resulted in statistically measurable changes of T-RFLP profiles of the communities. Addition of nutrients or bacteria plus mecoprop resulted in bacteria composition, which did not return to the original profile within 14 days. We propose that at less than 70% similarity in T-RFLP, the bacterial communities risk to drift apart to inherently different states.

δ 15N measurement of organic and inorganic substances by EA-IRMS: a speciation-dependent procedure

Little attention has been paid so far to the influence of the chemical nature of the substance when measuring δ 15N by elemental analysis (EA)-isotope ratio mass spectrometry (IRMS). Although the bulk nitrogen isotope analysis of organic material is not to be questioned, literature from different disciplines using IRMS provides hints that the quantitative conversion of nitrate into nitrogen presents difficulties. We observed abnormal series of δ 15N values of laboratory standards and nitrates. These unexpected results were shown to be related to the tailing of the nitrogen peak of nitrate-containing compounds. A series of experiments were set up to investigate the cause of this phenomenon, using ammonium nitrate (NH4NO3) and potassium nitrate (KNO3) samples, two organic laboratory standards as well as the international secondary reference materials IAEA-N1, IAEA-N2-two ammonium sulphates [(NH4)2SO4]-and IAEA-NO-3, a potassium nitrate. In experiment 1, we used graphite and vanadium pentoxide (V2O5) as additives to observe if they could enhance the decomposition (combustion) of nitrates. In experiment 2, we tested another elemental analyser configuration including an additional section of reduced copper in order to see whether or not the tailing could originate from an incomplete reduction process. Finally, we modified several parameters of the method and observed their influence on the peak shape, δ 15N value and nitrogen content in weight percent of nitrogen of the target substances. We found the best results using mere thermal decomposition in helium, under exclusion of any oxygen. We show that the analytical procedure used for organic samples should not be used for nitrates because of their different chemical nature. We present the best performance given one set of sample introduction parameters for the analysis of nitrates, as well as for the ammonium sulphate IAEA-N1 and IAEA-N2 reference materials. We discuss these results considering the thermochemistry of the substances and the analytical technique itself. The results emphasise the difference in chemical nature of inorganic and organic samples, which necessarily involves distinct thermochemistry when analysed by EA-IRMS. Therefore, they should not be processed using the same analytical procedure. This clearly impacts on the way international secondary reference materials should be used for the calibration of organic laboratory standards.

Effects of Organic and Inorganic Fertilizers on Growth and Yield of Banana (Musa AAA cv. Malindi) in Oman

The Sultanate of Oman is located on the south-eastern coast of the Arabian Peninsula, which lies on the south-western tip of the Asian continent. The strategic geographical locations of the Sultanate with its many maritime ports distributed on the Indian Ocean have historically made it one of the Arabian Peninsula leaders in the international maritime trade sector. Intensive trading relationships over long time periods have contributed to the high plant diversity seen in Oman where agricultural production depends entirely on irrigation from groundwater sources. As a consequence of the expansion of the irrigated area, groundwater depletion has increased, leading to the intrusion of seawater into freshwater aquifers. This phenomenon has caused water and soil salinity problems in large parts of the Al-Batinah governorate of Oman and threatens cultivated crops, including banana (Musa spp.). According to the Ministry of Agriculture and Fisheries, the majority of South Al-Batinah farms are affected by salinity (ECe > 4 dS m-1). As no alternative farmland is available, the reclamation of salt-affected soils using simple cultural practices is of paramount importance, but in Oman little scientific research has been conducted to develop such methods of reclamation. This doctoral study was initiated to help filling this research gap, particularly for bananas. A literature review of the banana cultivation history revealed that the banana germplasm on the Arabian Peninsula is probably introduced from Indonesia and India via maritime routes across the Indian Ocean and the Red Sea. In a second part of this dissertation, two experiments are described. A laboratory trial conducted at the University of Kassel, in Witzenhausen, Germany from June to July 2010. This incubation experiment was done to explore how C and N mineralization of composted dairy manure and date palm straw differed in alkaline non-saline and saline soils. Each soil was amended with four organic fertilizers: 1) composted dairy manure, 2) manure + 10% date palm straw, 3) manure + 30% date palm straw or 4) date palm straw alone, in addition to un-amended soils as control. The results showed that the saline soil had a lower soil organic C content and microbial biomass C than the non-saline soil. This led to lower mineralization rates of manure and date palm straw in the saline soil. In the non-saline soil, the application of manure and straw resulted in significant increases of CO2 emissions, equivalent to 2.5 and 30% of the added C, respectively. In the non-amended control treatment of the saline soil, the sum of CO2-C reached only 55% of the soil organic C in comparison with the non-saline soil. In which 66% of the added manure and 75% of the added straw were emitted, assuming that no interactions occurred between soil organic C, manure C and straw C during microbial decomposition. The application of straw always led to a net N immobilization compared to the control. Salinity had no specific effect on N mineralization as indicated by the CO2-C to Nmin ratio of soil organic matter and manure. However, N immobilization was markedly stronger in the saline soil. Date palm straw strongly promoted saprotrophic fungi in contrast to manure and the combined application of manure and date palm straw had synergistic positive effects on soil microorganisms. In the last week of incubation, net-N mineralization was observed in nearly all treatments. The strongest increase in microbial biomass C was observed in the manure + straw treatment. In both soils, manure had no effect on the fungi-specific membrane component ergosterol. In contrast, the application of straw resulted in strong increases of the ergosterol content. A field experiment was conducted on two adjacent fields at the Agricultural Research Station, Rumais (23°41’15” N, 57°59’1” E) in the South of Al-Batinah Plain in Oman from October 2007 to July 2009. In this experiment, the effects of 24 soil and fertilizer treatments on the growth and productivity of Musa AAA cv. 'Malindi' were evaluated. The treatments consisted of two soil types (saline and amended non-saline), two fertilizer application methods (mixed and ring applied), six fertilizer amendments (1: fresh dairy manure, 2: composted dairy manure, 3: composted dairy manure and 10% date palm straw, 4: composted dairy manure and 30% date palm straw, 5: only NPK, and 6: NPK and micronutrients). Sandy loam soil was imported from another part of Oman to amended the soil in the planting holes and create non-saline conditions in the root-zone. The results indicate that replacing the saline soil in the root zone by non-saline soil improved plant growth and yield more than fertilizer amendments or application methods. Particularly those plants on amended soil where NPK was applied using the ring method and which received micronutrients grew significantly faster to harvest (339 days), had a higher average bunch weight (9.5 kg/bunch) and were consequently more productive (10.6 tonnes/hectare/cycle) compared to the other treatments.

Determination of labile inorganic and organic species of Al and Cu in river waters using the diffusive gradients in thin films technique

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Laboratory shearing experiments at low sliding velocities of IODP Hole 343-C0019E

The 2011 Tohoku-Oki earthquake demonstrated that the shallowest reaches of plate boundary subduction megathrusts can host substantial coseismic slip that generates large and destructive tsunamis, contrary to the common assumption that the frictional properties of unconsolidated clay-rich sediments at depths less than View the MathML source should inhibit rupture. We report on laboratory shearing experiments at low sliding velocities (View the MathML source) using borehole samples recovered during IODP Expedition 343 (JFAST), spanning the plate-boundary décollement within the region of large coseismic slip during the Tohoku earthquake. We show that at sub-seismic slip rates the fault is weak (sliding friction µs=0.2-0.26), in contrast to the much stronger wall rocks (µs>~0.5). The fault is weak due to elevated smectite clay content and is frictionally similar to a pelagic clay layer of similar composition. The higher cohesion of intact wall rock samples coupled with their higher amorphous silica content suggests that the wall rock is stronger due to diagenetic cementation and low clay content. Our measurements also show that the strongly developed in-situ fabric in the fault zone does not contribute to its frictional weakness, but does lead to a near-cohesionless fault zone, which may facilitate rupture propagation by reducing shear strength and surface energy at the tip of the rupture front. We suggest that the shallow rupture and large coseismic slip during the 2011 Tohoku earthquake was facilitated by a weak and cohesionless fault combined with strong wall rocks that drive localized deformation within a narrow zone.

Table 1. Pressure, temperature and isotope ratios between H2O and CO2 for all experiments

Traditionally, the application of stable isotopes in Carbon Capture and Storage (CCS) projects has focused on d13C values of CO2 to trace the migration of injected CO2 in the subsurface. More recently the use of d18O values of both CO2 and reservoir fluids has been proposed as a method for quantifying in situ CO2 reservoir saturations due to O isotope exchange between CO2 and H2O and subsequent changes in d18OH2O values in the presence of high concentrations of CO2. To verify that O isotope exchange between CO2 and H2O reaches equilibrium within days, and that d18OH2O values indeed change predictably due to the presence of CO2, a laboratory study was conducted during which the isotope composition of H2O, CO2, and dissolved inorganic C (DIC) was determined at representative reservoir conditions (50°C and up to 19 MPa) and varying CO2 pressures. Conditions typical for the Pembina Cardium CO2 Monitoring Pilot in Alberta (Canada) were chosen for the experiments. Results obtained showed that d18O values of CO2 were on average 36.4±2.2 per mil (1 sigma, n=15) higher than those of water at all pressures up to and including reservoir pressure (19 MPa), in excellent agreement with the theoretically predicted isotope enrichment factor of 35.5 per mil for the experimental temperatures of 50°C. By using 18O enriched water for the experiments it was demonstrated that changes in the d18O values of water were predictably related to the fraction of O in the system sourced from CO2 in excellent agreement with theoretical predictions. Since the fraction of O sourced from CO2 is related to the total volumetric saturation of CO2 and water as a fraction of the total volume of the system, it is concluded that changes in d18O values of reservoir fluids can be used to calculate reservoir saturations of CO2 in CCS settings given that the d18O values of CO2 and water are sufficiently distinct.

Seawater carbonate chemistry and biological processes of Mytilus edulis during experiments, 2010

Marine organisms are exposed to increasingly acidic oceans, as a result of equilibration of surface ocean water with rising atmospheric CO2 concentrations. In this study, we examined the physiological response of Mytilus edulis from the Baltic Sea, grown for 2 months at 4 seawater pCO2 levels (39, 113, 243 and 405 Pa/385, 1,120, 2,400 and 4,000 µatm). Shell and somatic growth, calcification, oxygen consumption and excretion rates were measured in order to test the hypothesis whether exposure to elevated seawater pCO2 is causally related to metabolic depression. During the experimental period, mussel shell mass and shell-free dry mass (SFDM) increased at least by a factor of two and three, respectively. However, shell length and shell mass growth decreased linearly with increasing pCO2 by 6-20 and 10-34%, while SFDM growth was not significantly affected by hypercapnia. We observed a parabolic change in routine metabolic rates with increasing pCO2 and the highest rates (+60%) at 243 Pa. excretion rose linearly with increasing pCO2. Decreased O:N ratios at the highest seawater pCO2 indicate enhanced protein metabolism which may contribute to intracellular pH regulation. We suggest that reduced shell growth under severe acidification is not caused by (global) metabolic depression but is potentially due to synergistic effects of increased cellular energy demand and nitrogen loss.

Seawater carbonate chemistry, mass, size and regenerative capacity of Luidia clathrata during experiments, 2011

The present study examines sublethal effects of near-future (year 2100) ocean acidification (OA) on regenerative capacity, biochemical composition, and behavior of the sea star Luidia clathrata, a predominant predator in sub-tropical soft-bottom habitats. Two groups of sea stars, each with two arms excised, were maintained on a formulated diet in seawater bubbled with air alone (pH 8.2, approximating a pCO2 of 380 µatm) or with a controlled mixture of air/C02 (pH 7.8, approximating a pCO2 of 780 µatm). Arm length, total body wet weight, and righting responses were measured weekly. After 97 days, a period of time sufficient for 80% arm regeneration, pyloric caecal indices, and protein, carbohydrate, lipid, and ash levels were determined for body wall and pyloric caecal tissues of intact and regenerating arms of individuals held in both seawater pH treatments. The present study indicates that predicted near-term levels of ocean acidification (seawater pH 7.8) do not significantly impact whole animal growth, arm regeneration rates, biochemical composition, or righting behavior in this common soft bottom sea star.

Seawater carbonate chemistry, Acropora digitifera growth and skeletal U/Ca ratios during experiments, 2011

The impact of ocean acidification caused by the increasing atmospheric CO2 has been studied in marine calcifiers, including hermatypic corals. However, the effect of elevated pCO2 on the early developmental life-cycle stage of corals has been little studied. In this study, we reared polyps of Acropora digitifera in seawater at pHT 6.55, 7.31, 7.64, 7.77, and 8.03, controlled by CO2 bubbling. We measured the dry weights of polyp skeletons after the 40-d experiment to investigate the relationship between the seawater aragonite saturation state and polyp growth. In addition, we measured skeletal U/Ca ratio to estimate their pH dependence. Skeletal weights of coral polyps increased with the aragonite saturation state and reached an apparent saturation plateau above pH 7.77. U/Ca ratios had a strong inverse relationship with pH and a negligible relationship with skeletal growth rate (polyp weight), suggesting that skeletal U/Ca could be useful for reconstructing paleo-pH.