Bacteria-induced mixing in natural waters

Swimming organisms can enhance mixing in their natural environments by creating eddies in their wake and by dragging water along. However, these mixing mechanisms are inefficient for microorganisms, because swimming-induced variations in velocity, temperature, and dissolved substances are evened out before they can be advected. In bioconvection, however, microorganisms induce water movement not by propulsion directly but by locally changing the fluid density, which drives convection. Observations of bioconvection have so far mainly been limited to laboratory settings. We report the first observation and quantification of bioconvection within a stratified natural water body. Using in situ measurements, laboratory experiments, and numerical simulations, we demonstrate that the bacterium Chromatium okenii is capable of mixing 0.3 to 1.2 m thick water layers at around 12 m water depth in the Alpine Lake Cadagno (Switzerland). As many species are capable of driving bioconvection, this phenomenon potentially plays a role in species distributions and influences large-scale phenomena like algal blooms.

Development of a hyphenated analytical methodology for the fractionation and characterization of environmental colloids

Enrica Alasonati

Natural colloids are defined as macromolecules and nanoparticles with sizes ranging between 1 nm and 1 µm. Colloidal pool is complex "ill-defined" mixture of humic substances, exopolymeric substances (EPS), inorganic oxides, clays, etc. Aquatic colloids have been recognized as key mediators in the removal of trace elements, facilitating contaminant transport, organic carbon cycling and micronutrient bioavailability. The residence times of the colloidal pool (and associate contaminants) can be order of magnitude different from those of the particulate fraction, but unlike the "truly" dissolved fraction, can be subjected to different coagulation and sedimentation processes. Colloids may also influence metal bioavailability by affecting free metal ion concentrations, constraining diffusion and affecting the dissociation kinetics of biological processes. The important environmental role of natural colloids is largely influenced by their surface area and closely related colloidal size. Nonetheless, it is currently unclear to what extend colloidal size can influence their behaviour and contaminant (e.g. toxic metals) binding properties. In our view this is partially related to the difficulties in determination of the colloidal size distributions and their impact in metal behaviour, mainly due to the inherent heterogeneity of the environmental colloids and their low concentrations in the environment. Furthermore, in addition to average parameters, there is a lack of appropriate sample collection and processing procedures, as well as analytical techniques to measure simultaneously the size (or related parameter) distributions of the colloid associated metal. The objective of the present work was therefore to develop sensitive analytical procedures for the fractionation of natural colloids and to apply them to improve the current understanding on the fate of the colloids and associated toxic metals in the freshwaters. To achieve these goals, the capabilities of asymmetric flow-field flow fractionation (aFlFFF) coupled to several detectors was explored. aFlFFF is a versatile technique separating colloids according to their diffusion coefficient. The system was hyphenated with multi-angle laser light scattering (MALS), differential refractive index (DRI), UV detector and, when necessary, high resolution inductively coupled plasma mass spectrometry (ICP-MS). Correct interpretation of the experimental results and extrapolation of meaningful molecular parameters by using an analytical tool with such a level of complexity requires improvement of the knowledge of colloids behaviour in the aFlFFF channel and careful optimization of the separation conditions. Given the very complex and dynamic nature of environmental colloids, different experimental procedures was first optimized and validate under lab conditions by using "standardized" colloids (e.g. alginate and EPS isolate from lab bacterial cultures), then applied to characterize colloidal organic matter (COM) isolated from natural water systems. The influence of critical operating parameters, such as crossflow rate, carrier composition and concentration, and sample load, on the alginate retention was carefully evaluated. Combined information obtained simultaneously by DRI and MALS detectors, allowed to set the appropriate combination of optimal parameters for the characterization of alginate, as a model COM. The metal distributions of metal-alginate complexes were probed by aFlFFF - ICP-MS: average values and continuous distributions of molar masses, radius of gyration and hydrodynamic radius, critical for understanding their role as carriers of metal pollutants, were evaluated in presence of lead or cadmium and compared to those in metal-free solutions of alginate. Furthermore, the molecular characteristic of exopolymeric substances (EPS) secreted by bacterium Sinorhizobium meliloti wild type and exoY strains, which is deficient in the production of the succinoglycan, were studied. EPS were collected in the extracellular environment or desorbed from the cell surface using different extraction protocols. EPS fractions with different chemical characteristic and molar mass were found, depending on the strain and extraction protocol. Molecular parameters as the distributions and average values of molar mass and gyration radius, and the polydispersity index have been measured and compared with data obtained by the chemical characterization. Size exclusion chromatography coupled to UV detection was also employed to provide additional information on the small class of size. Moreover, the effect of the cadmium, lead and calcium addition to exopolymeric substances excreted in the extracellular environment was investigated, with the aim to study how does EPS composition, size and mass distributions, can affect the trace metal binding properties of EPS and how the metal addition affects the EPS conformation. Obtained results revealed that cadmium and calcium bound preferentially on the low-size species population and the amount of the bound metal increased with the increasing of the concentration of added metal. In contrast, lead bound on preferentially larger classes of EPS size. The aFlFFF separation parameters were also optimized for the fractionation and characterization of humic substances, as other COM component, and applied to probe the temporal and spatial variability in the size and mass characteristics of COM samples collected in the Amazon River basin. COM characterization demonstrated the existence of a clear decrease of size of the colloidal material when passing from small to large watercourses (spatial variation). No significant changes were found in size distributions of samples collected in different period of the year, during the low and high flow, respectively (temporal variation). The analytical methodology, adapted to determine not only mean characteristics, but the population distributions, developed in the present work, allowed to obtain new information about the colloidal organic matter size distribution, which play utmost role in colloids behaviour and fate in the environment, in particular as toxic metal carriers.

EPFL2009

Retention of atmospherically deposited nitrogen in soil

Isabelle Morier Jaquet

Since a few decades, the balance of the nitrogen (N) cycle has been deeply disturbed by human activies. The global impact of these activities on the N cycle can be described as a doubling of the transfer from the vast and unreactive atmospheric pool to biologically available forms (N fixation). The main sources responsible for the increase of reactive N emissions are the use of artificial fertilisers (NH3) as well as the combustion processes (NOx). Reactive N is then transformed, transported by both the atmosphere and the hydrosphere and, finally, deposited on both the terrestrial and the aquatic ecosystems with potentially strong impacts. Amongst the terrestrial ecosystems, the temperate forests are particularly sensitive to reactive N increases for various reasons: they are located near to strongly anthropised areas and are thus subjected to strong depositions; they are naturally N-limited and their biochemical cycle can indeed be strongly influenced by additional N, which leads to eutrophication and potential impacts such as soil acidification, nitrate leaching and losses of biodiversity within microorganisms, plants and fauna communities. Previous studies carried out in temperate forest ecosystems have shown that the soil, namely the soil organic matter, acts as a main deposited N sink for the ecosystem. However, biogeochemical reactions responsible for N retention in the soil are still not fully understood. Moreover, the majority of the concerned studies were conducted in acidic or hydromorphous soils and very little is known today about the fate of N deposition under other soil physico-chemical conditions. Consequently, the present research aims at filling some of the gaps described above and deals with two main topics concerning the retention of atmospherically deposited N in soils that are (1) the characterisation of the retention of atmospherically deposited N in the soil, in terms of both duration and quantity, more specifically, in a well drained calcareous soil and (2) the mechanisms and processes responsible for such a retention. From a practical point of view, the retention of N deposition in the soil was characterised by means of a 15N field labelling experiment simulating N atmospheric deposition and conducted at the Grandvillard research site, in the riparian zone of La Sarine River (Swiss Prealps). The stand is a beech forest mixed with planted spruces. The soil consists of a well drained calcareous fluvisol with a fast organic matter turnover. We tracked the N tracers (15NH4+ or 15NO3-, corresponding to the main forms of deposition) from short-term (hours, days or weeks) to longer-term intervals (one year), by measuring the partitioning of 15N into different biochemical soil fractions (extractable N, microbial N, roots N and N immobilised in soil). Aiming at studying the mechanisms and processes responsible for N retention, we performed two laboratory experiments. The first one was an acid hydrolysis, in order to determine the proportion of N deposition retained in the hydrolysable fraction (i.e. the more labile N forms, including the most bioavailable ones) as well as in the non-hydrolysable fraction covering the more recalcitrant N compounds. Within the framework of this experiment, we compared the results obtained in Grandvillard and in an aditional constrasting site (Alptal). The second experiment was a short-term (one hour to one week) laboratory incubation of sterilised and not sterilised soils, which purpose was to highlight the relative importance of biotic and abiotic processes in N immobilisation. Soils were labelled with either 15NH4+ or 15NO3- and subjected to 15N CPMAS NMR spectroscopy analysis, which is a powerful technique to identify the N organic molecules in soils. Within the framework of the field labelling experiment, more than half of the tracers (either 15NO3- or 15NH4+) was recovered in the soil between one hour and one year after labelling. Therefore, the general assumption that non-fertilised temperate forest soils are the main sink for deposited N can be confirmed. Since previous studies showing the importance of the soil for the retention of deposited N were all conducted on either acidic or hydromorphous soils, our results allow us to extend the validity of their general conclusions to a wider range of unfertilised temperate forest soils. We further showed that the main forms of N deposition (i.e. NO3-and NH4+) were retained in the soil within the same range of magnitude, in spite of their different biochemical pathways. N retention occurred mainly in the soil organic layers and, consequently, our results confirme the importance of the organic fraction in the deposited N retention. Since deposited N was retained in the soil in the very short term, we confirmed the presence of very fast processes and demonstrated that the very short term dynamics determined the fate of deposited N in the longer term: the main processes were i) a loss of deposited N as extractable through lixiviation (and lateral fluxes) and ii) a retention as N immobilised in soil. Furthermore, we demonstrated that N immobilisation brought deposited N both into the hydrolysable and into the recalcitrant fractions of soil N within short-time range (i.e. one week) . We also demonstrated that the hydrolysability (hydrolysable N/ total N) was constant over the year. Within the framework of the laboratory incubation of soils subjected to the 15N CPMAS NMR spectroscopy analysis, we showed that all NMR spectra were dominated by a single signal corresponding to the amide-peptide structure, whatever the soil layer concerned (organic or organo-mineral), the form added (NO3- or NH4+) and whether the soil was sterilised or not. Such dominance of proteinaceous compounds was in agreement with the results obtained in humic substances and in various soils all over the world. Further to the extractable 15N dynamics during the incubation, we proposed that biotic processes were dominant in the short-term N immobilisation. However, an abiotic fixation of less importance was not excluded for 15NO3-. Considering our results, we propose two mechanisms responsible for the retention of deposited N in soil in the long term. The first mechanism is a rapid and stable immobilisation in the recalcitrant pool of soil organic matter. Our results showed that biotic and abiotic processes could be involved: the afore-mentioned process of abiotic nitrate fixation could lead to the N immobilisation in heterocycles whereas N incorporated in amides and then stabilised in soil organic matter seemed to be the major pathway. The second mechanism of retention we are proposing is the biological recycling within the soil or the soil-plant system: on a short scale, microbial recycling seemed to be very rapid because deposited N was mainly present under a biosynthesised form (amides), in spite of the low amounts of tracer found in the microbes. Within the soil profile, roots recycling was probably efficient: fine roots, which are often the major contributors of soil organic matter were an important sink for N deposition all over the year. The combination of various scales and techniques allowed the connection between the dynamics of N retention in soil organic layers observed and the mechanisms responsible for it (i.e. rapid immobilisation in a recalcitrant pool and biological recycling through micro-organisms and plants). The results of this multi-scale approach suggest further developments and impacts for the modelling of the long-term fate of deposited N.

EPFL2006

An experimental study on main flow, secondary flow and turbulence in open-channel bends with emphasis on their interaction with the outer-bank geometry

Alexandre José Pessanha De Oliveira Caimoto Duarte

This research focus on the influence of bank inclination and roughness on the near-bank flow patterns which is relevant for bank protection, bank erosion and design of stable river configuration. Foregoing studies have been carried out mostly in rectangular channels which are far from being representative of natural conditions. In straight-channel flows large scale vortical structures, such as secondary currents or circulation cells of Prandtl's second kind, play a fundamental role. In curved flows mainly two circulation cells are generated, the center-region cell and the outer-bank cell. The outer-bank cell has a fundamental role in protecting the outer-bank by constraining the center-region cell and thereby decreasing the downstream velocity and turbulence. It is still not clear how the secondary circulation cells interact with varying channel shape and wetted perimeter roughness distribution in straight as in curved flows. This work is a part of a joint research program. The project other three partners are: Delft University of Technology (TUD), WL | Delft Hydraulics (WL) and the Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB). The main goal is to improve the understanding of flow underlying mechanisms and to improve existing hydrodynamic and morphodynamic tools. Despite the broader program where this research project is inserted, it is also self-contained. This research project is situated in the discipline of fluid dynamics applied to open-channel flows in the topic of dynamics of the mean-flow field and the turbulence in straight and curved channels. The two main goals are: i) To investigate, systematically in laboratory controlled conditions the influence of the outer bank inclination and roughness on the patterns of main flow, secondary flow, turbulence and outer-bank shear stress in straight and curved flows; ii) To give insight in the flow mechanisms responsible for the observed patterns. The channel width of B = 1.3 m, water depth of H = 0.16 m and a bulk velocity of U = 0.43 m/s were kept constant. The bank inclination was varied between 90°, 45° and 30° whereas the bank roughness was varied between smooth PVC, sand (d = 0.002 m) and d = 0.03 m materials (simulating riprap). The measurements were performed using the Acoustic Doppler Velocimetry Profiler (ADVP). The ADVP is fundamental for the accomplishment of these goals due to its accuracy and profiler capabilities. Straight channel results reveal that rectangular and trapezoidal channels have different flow patterns. The trapezoidal channels have less circulation cells than rectangular channels and a bed shear stress distribution with fewer oscillations. In trapezoidal channels the bed shear stress is higher than the cross-section averaged shear stress regardless the bank/bed roughness ratio. The bank shear stress value increases with outer-bank roughness. The experimental measurements were compared with methods of estimating mean and maximum bed and bank shear stresses, Chow (1959) and Knight et al. (1994). Chow (1959) wetted perimeter shear stress distribution is in agreement with the experiments for the trapezoidal channel experiments with homogeneous roughness distribution whereas for heterogeneous roughness distribution no agreement is verified. Knight (1994) estimations are in good agreement with measurements suggesting its applicability as engineering expedite process. In the curved flow experiments focus is given to the outer-bank roughness and inclination effect on the outer-bank flow region mainly on the outer-bank cell. Curved channel flow results reveal that the outer-bank roughness and inclination has a strong effect on the outer-bank cell, and as consequence, on the center-region cell and downstream velocity evolution along the bend. In all experiments the outer-bank cell constrains the outward limit of the center-region cell regardless its size or strength. In curved flows with rectangular channel, the outer-bank cell size increases with increasing outer-bank roughness and so further protect the bed close to the outer-bank. In curved flows with trapezoidal channel, the outer-bank cell is located over the outer-bank toe close to the free-surface even for low-bank inclination, however, the outer-bank basal zone is more exposed to higher shear stresses. In curved flows with trapezoidal channel, low outer-bank angle and varying bank roughness, the outer-bank cell does not increase with increasing outer-bank roughness. The mechanisms underlying the outer-bank cell are disclosed by analyzing the downstream vorticity equation main terms. The centrifugal term and the cross-stream shear term favor the outer-bank cell rotation sense but cross-stream turbulent anisotropy

EPFL2008