A Problem of the Optimal Adaptation of a Bacterial Culture to a Toxic Substrates in Continuous Flow Conditions

A model of bacterial culture, utilizing a toxic substrate in continuous flow conditions' is discussed in the present paper. The relative velocity of microorganisms growth is expressed by means of a formula proposed by us, grounded on the analogy of a model of an irreversibly inhibited enzymatic reaction. It is assumed that the integral parameter characterizing the damage of the bacterial cell by a toxic agent may be considered a slow variable in regard to the variation of the biomass and substrate concentrations. An equation for the evolution of this parameter is proposed. A problem of minimum time adaptation of the bacterial population is proposed as a time optimal control problem that is solved on the basis of the Pontryagin maximum principle. This model provides a possibility of studying some regularities in the adaptation mechanism of the microorganisms destroying toxic substances. The same model can also be used to forecast the optimal regimes in cultivation of bacterial cultures that play an essential role in the biological self-purification of various water pools.     

Displacement Phenomenon of Slow and Fast Growing Species in Microorganisms Association

In the process of the biological treatment of sewage, the multicomponent system of the substrate is converted by an association of microorganisms. The composition of species of microorganisms in the system depends on the substrate available and on the conversion of substrate. For this, a mathematical model is presented, which describes the change of the composition of species according to the rate of growth of the individual species on the basis of load (substrate available/biomass). The diversity of the biological system increases with decreasing load. The model is tested by practical examples.     

Dynamics of planktonic bacteria and heterotrophic microflagellates in the Parker Estuary, northern Massachusetts

The temporal and spatial abundance and activities of members of the planktonic microbial food web in a salt marsh estuary were analysed over the course of a year. Analysis of the data was focused on the factors that control the density and productivity of the heterotrophic bacteria. Temperature exercises a long-term influence on substrate sources, but short-term control is a function of the interaction of grazing and substrate supply. A model has been developed to give a framework for understanding how the microbial food web may work under steady-state assumptions. The model assumptions and predictions appear to be supported by the field data. Equations were generated for estimating substrate flux through the bacteria and estimating bacterial density as a result of grazing and substrate input. The results give some insights into the question of whether the heterotrophic bacteria function as a link to higher organisms or as an energy sink.     

Analytical solutions for bacterial energy taxis (chemotaxis): Traveling bacterial bands

Motile bacteria may form bands that travel with a constant speed of propagation through a medium containing a dissolved substrate, to which they respond energy tactically. We generalize the analytical solution by Keller and Segel for such bands by accounting for (1) the presence of a porous medium, (2) substrate consumption described by a Monod kinetics model, and (3) an energy tactic response model derived by Rivero et al. Specifically, we determine the concentration profiles of the bacteria and the substrate. We also derive various expressions for the band velocity. The band velocity is also shown to equal the energy tactic velocity at the bacterial peak divided by tortuosity.     

Shallow water substrate mapping using hyperspectral remote sensing

During April 2004 the airborne hyperspectral sensor, HyMap, collected data over a shallow coastal region of Western Australia. These data were processed by inversion of a semi-analytical shallow water optical model to classify the substrate. Inputs to the optical model include water column constituent specific inherent optical properties (SIOPs), view and illumination geometry, surface condition (based on wind speed) and normalised reflectance spectra of substrate types. A sub-scene of the HyMap data covering approximately 4 km² was processed such that each 3×3 m² pixel was classed as sand, seagrass, brown algae or various mixtures of these three components. Coincident video data were collected and used to estimate substrate types. We present comparisons of the habitat classifications determined by these two methods and show that the percentage validation of the remotely sensed habitat map may be optimised by selection of appropriate optical model parameters. The optical model was able to retrieve classes for approximately 80% of all pixels in the scene, with validation percentages of approximately 50% for sand and seagrass classification, and 90% for brown algae classification. The semi-analytical model inversion approach to classification can be expected to be applied to any shallow water region where substrate reflectance spectra and SIOPs are known or can be inferred.     

Coastal profile response to sea level rise: a process‐based approach

Prevailing ideas and calculations of coastal response to sea level rise (SLR) are often based on the Bruun model (Bruun P., Sea‐level rise as a cause of shore erosion, Journal Waterways Harbors Division, ASCE 88 : 117–130, 1962) that predicts upward and landward transfer of an equilibrium profile during SLR through offshore sediment transport on the shoreface. The model is based on a number of assumptions of questionable validity as well as outdated concepts on how sediment is transported across the shoreface. This contribution takes a numerical modelling approach that is based on first‐order processes contributing to the movement of sediment across the shoreface. Using a wave transformation model that predicts hydrodynamic processes driving cross‐shore sediment transport and an energetics‐based model for the coupling between hydrodynamics and sediment transport, we show that cross‐shore sediment transport is mainly onshore directed at the boundary between the lower and the upper shoreface, in agreement with the model proposed by Davidson‐Arnott (Conceptual model of the effects of sea level rise on sandy coasts, Journal of Coastal Research 21 : 1166–1172, 2005). The transition from onshore to offshore directed transport is located well within the surf zone and with a rising sea level this transition point becomes displaced landward and upward. Tests also show that substrate slope is of fundamental importance to the manner in which beaches react to rising sea level. Copyright © 2012 John Wiley & Sons, Ltd.     

The weathering effects of the lichen Lecidea aff. Sarcogynoides (Koerb.) on magaliesberg quartzite

The effect of the weathering processes generated by Lecidea aff. Sarcogynoides (Koerb.) on the substrate was studied by means of a scanning electron microscope. The elements present in the substrate (Magaliesberg quartzite) and in the lichen thallus were determined by X-ray fluorescence spectrometry for the purpose of comparison. The elements present were mostly similar although a few were present in the thallus which were not observed in the quartzite. It is possible that those elements present in the lichen thallus which were not present in the substrate may have been extracted from the atmosphere. The occurrence of small hollows (weathering pits) in which the early stages of plant development occurs, and the disintegration of the rock indicate that Lecidea aff. sarcogynoides (Koerb.) contributes to the chemical weathering processes by chelation and mechanically by the penetration and expansion of hyphae. A model is proposed in which a possible mechanism for these weathering processes is suggested.     

Evidence of distinct contaminant transport patterns in rivers using tracer tests and a multiple domain retention model

Solute transport in rivers is controlled by surface hydrodynamics and by mass exchanges with distinct retention zones. Surface and hyporheic retention processes can be accounted for separately in solute transport models with multiple storage compartments. In the simplest two component model, short term storage can be associated to in-channel transient retention, e.g. produced by riparian vegetation or surface dead zones, and the long-term storage can be associated to hyporheic exchange. The STIR (Solute Transport In Rivers) multiple domain transport model is applied here to tracer test data from three very different Mediterranean streams with distinctive characteristics in terms of flow discharge, vegetation and substrate material. The model is used with an exponential residence time distribution (RTD) to represent surface storage processes and two distinct modeling closures are tested to simulate hyporheic retention: a second exponential RTD and a power-law distribution approximating a known solution for bedform-induced hyporheic exchange. Each stream shows distinct retention patterns characterized by different timescales of the storage time distribution. Both modeling closures lead to very good approximations of the observed breakthrough curves in the two rivers with permeable bed exposed to the flow, where hyporheic flows are expected to occur. In the one case where the occurrence of hyporheic flows is inhibited by bottom vegetation, only the two exponential RTD model is acceptable and the time scales of the two components are of the same magnitude. The significant finding of this work is the recognition of a strong signature of the river properties on tracer data and the evidence of the ability of multiple-component models to describe individual stream responses. This evidence may open a new perspective in river contamination studies, where rivers could possibly be classified based on their ability to trap and release pollutants.     

Über den Einfluss der Strömungsgeschwindigkeit auf die Selbstreinigung in Fliessgewässern

Experiments in model rivers on selfpurification in function of the concentrations of pollutants and of flow velocity have indicated that the ratio of the rates of substrate transports from the flowing wave on to cell surfaces and of active transports in substrate uptake is a determining factor for selfpurification rates. This ratio is decreasing rapidly with decreasing flow velocities of the water. The results were discussed on the basis of the kinetics of active transports.     

Lithospheric necking: a dynamic model for rift morphology

Rifting is examined in terms of the growth of a necking instability in a lithosphere consisting of a strong plastic or viscous surface layer of uniform strength overlying a weaker viscous substrate in which strength is either uniform or decreases exponentially with depth. As the lithosphere extends, deformation localizes about a small imposed initial perturbation in the strong layer thickness. For a narrow perturbation, the resulting surface topography consists of a central depression and uplifted flanks; the layer thins beneath the central depression. The width of the rift zone is related to the dominant wavelength of the necking instability, which in turn is controlled by the layer thickness and the mechanical properties of the lithosphere. For an initial thickness perturbation with a width less than the dominant wavelength, deformation concentrates into a zone comparable to the dominant wavelength. If the initial perturbation is wider than the dominant wavelength, then the width of the zone of deformation is controlled by the width of the initial perturbation; deformation concentrates in the region of enhanced thinning and develops periodically at the dominant wavelength. A surface layer with limiting plastic (stress exponent n = ∞) behavior produces a rift-like structure with a width typical of continental rifts for a strong layer thickness consistent with various estimates of the maximum depth of brittle deformation in the continental lithosphere. The width of the rift is essentially independent of the layer/substrate strength ratio. For a power law viscous surface layer (n = 3), the dominant wavelength varies with layer/substrate strength ratio to the one-third power and is always larger than for a plastic surface layer of the same thickness. The great widths of rift zones on Venus may be explained by unstable extension of a strong viscous surface layer.     

The influence of biogeochemical conditions and level of model complexity when simulating cometabolic biodegradation in sorbent-water systems

Eighteen models with different levels of complexity for representing sorption, mass transfer, and biodegradation are used to simulate the biodegradation of toluene (primary substrate) and TCE (cometabolic substrate). The simulations are conducted for hypothetical completely mixed systems of various scenarios with regard to sorbent, microbial composition, and solute concentrations. The purpose of the suite of simulations is to investigate the sensitivity of different modeling approaches in simulating the bio-attenuation of co-existing solutes in sorbent-water systems. The sensitivity of results to the modeling approach depends on the biogeochemical conditions of the system. For example, the results are insensitive to the type of sorption model in systems with low sorption strength and slow biodegradation rates, and insensitive to the biodegradation rate model if mass transfer controlled. Differences among model results are generally greater when evaluated in terms of total mass removal rather than aqueous phase concentration reduction. The fate of the cometabolite is more sensitive to the proper consideration of co-solute effects than is the fate of the primary substrate. For a given system, graphical comparison of a characteristic mass transfer rate coefficient (α_mt) versus a characteristic biodegradation rate coefficient (α_bio) provides an indication of how sensitivity to the different processes may be expected to change with time and can guide the selection of an appropriate level of model complexity.     

Modeling of Trace Organics Biotransformation in the Subsurface

Biofilm processes are potentially important for transformations of organic micropollutants in ground water. Some theoretical hypotheses and empirical observations suggest that a concentration threshold exists for some compounds below which the concentration cannot be reduced by bacterial action. However, in the presence of one compound at a relatively high concentration, termed the primary substrate, another compound present at trace concentrations, termed the secondary substrate, can be biotransformed as well. These concepts were evaluated through laboratory column studies with several halogenated organic compounds of importance in ground water. A biofilm model can successfully describe utilization of trace substrates, and application to modeling the subsurface is discussed. A simplified batch model with first-order kinetics may be adequate for describing subsurface microbial processes when low active organism and pollutant concentrations exist over a large scale.     

Basic Equations to Describe the Kinetic Isotope Effect during Microbial Substrate Transformation

The redistribution of stable isotopes allows specifying the pathway of substrate utilization and identifying the relevant kinetic parameters. To describe degradation kinetics and identify predominant metabolic pathway for microbial substrate transformation, new basic equations, which take into account the dynamics of heavier isotope in the substrate, intermediates, and products were added to the common model of microbial substrate transformation, which did consider isotope differences at any step of substrate transformation. Using the unified approach, we showed that the dynamic changes of isotope fractionation depend on the kinetic coefficients, the initial conditions, and the microorganisms participating in the reactions during microbial denitrification, anaerobic oxidation of methane by sulphate and nitrite, aerobic oxidation of methane gas, and anaerobic digestion of cellulose.     

Resistance of salt marsh substrates to near-instantaneous hydrodynamic forcing

Salt marshes deliver vital ecosystem services by providing habitats, storing pollutants and atmospheric carbon, and reducing flood and erosion risk in the coastal hinterland. Net losses in salt marsh areas, both modelled globally and measured regionally, are therefore of concern. Amongst other controls, the persistence of salt marshes in any one location depends on the ability of their substrates to resist hydrodynamic forcing at the marsh front, along creek margins and on the vegetated surface. Where relative sea level is rising, marsh elevation must keep pace with sea-level rise and landward expansion may be required to compensate for areal loss at exposed margins. This paper reviews current understanding of marsh substrate resistance to the near-instantaneous (seconds to hours) forcing induced by hydrodynamic processes. It outlines how variability in substrate properties may affect marsh substrate stability, explores current understanding of the interactions between substrate properties and erosion processes, and how the cumulative impact of these interactions may affect marsh stability over annual to decadal timescales. Whilst important advances have been made in understanding how specific soil properties affect near-instantaneous marsh substrate stability, less is known about how these properties interact and alter bulk substrate resistance to hydrodynamic forcing. Future research requires a more systematic approach to quantifying biological and sedimentological marsh substrate properties. These properties must then be linked to specific observable erosion processes, particularly at the marsh front and along creek banks. A better understanding of the intrinsic dynamics and processes acting on, and within, salt marsh substrates will facilitate improved prediction of marsh evolution under future hydrodynamic forcing scenarios. Notwithstanding the additional complications that arise from morphodynamic feedbacks, this would allow us to more accurately model the future potential protection from flooding and erosion afforded by marshes, while also increasing the effectiveness of salt marsh restoration and recreation schemes. © 2020 The Authors. Earth Surface Processes and Landforms published by John Wiley & Sons Ltd     

Incipient motion of gravel in a bottomless arch culvert

Incipient motion was investigated for four gravel substrate materials in a bottomless arch culvert and a rectangular flume.Different methods for calculating Shields parameter at incipient motion(θ_c) based upon local flow parameters were explored.An incipient motion region for bottomless arch culverts in fully turbulent flow was defined with two bounding curves on Shields diagram.The variation ofθ_c as a function of relative roughness was examined.Also,a method that utilizes measured flow velocities to determine stable substrate particle diameters for bottomless arched culverts is presented as an alternative to the Shields diagram.     

Population dynamics and tolerance to desiccation in a crustacean ostracod adapted to life in small ephemeral water bodies

Given their small size, isolation and unpredictability, temporary rockpools present high environmental stress and impoverished communities of species that have adapted to such stressful conditions. Special adaptations of the invertebrates living in these habitats include tolerance to desiccation and fast ontogenetic development in order to maintain stable populations and face high risk of extinction. Dozens of small rockpools (mostly with Ø < 1 m) can be found in east Spain on limestone substrate, where the only known Iberian populations of Heterocypris bosniacaPetkovski et al. (2000), an ostracod species with geographic parthenogenesis, have been recently found. In this survey, two of these rockpools have been monitored during the main hydroperiod between the fall of 2005 and summer 2006 to test the ability of H. bosniaca parthenogenetic populations to face unpredictable hydroperiod dynamics. Pools were visited weekly, and limnological data and ostracod samples were obtained from either water or substrate in dry periods. Ostracod individuals were counted and assigned to growth instars to monitor population changes. In the laboratory, experimental cultures allowed the estimation of survival dependence on the substrate desiccation rate. Throughout the hydrological cycle studied, several hatching periods were observed, usually preceded by desiccation, followed by substrate hydration and water dilution by rain. The demographic changes observed indicate that H. bosniaca populations are able to persist in intermittently inundated environments and produce several generations per annual hydrological cycle. In addition, adult individuals were able to survive in the wet mud of dry pools for longer than five weeks. The experimental data suggest a lower average survival time when exposed to desiccation processes, and that the velocity of substrate water loss is a determining factor for the survival rate of ostracods resisting dry events in temporary ponds. As shown by ostracods’ life histories in temporary aquatic environments undergoing unpredictable desiccation events, a combined strategy of adult tolerance to short periods of water scarcity and rapid hatching from resting egg banks can be advantageous for the monopolization of small-sized ephemeral habitats.     

A note on the role of the lichen collema auriforma in solution basin development on a carboniferous limestone substrate

A study carried out on Carboniferous limestone in the north and west of Ireland supports the idea that rock substrate is removed by the direct mechanical action of lichens. An experiment in which the lichen Collema auriforma was subjected to a number of wetting-drying cycles, showed, using scanning electron microscopy, that contraction of the lichen thallus during the drying phase plucked rock fragments from the substrate surface. This process could contribute to the formation of karstic features including solution basins.     

An analytical solution to study substrate-microbial dynamics in soils

We provide an approximate analytical solution for the substrate-microbial dynamics of the organic carbon cycle in natural soils under hydro-climatic variable forcing conditions. The model involves mass balance in two carbon pools: substrate and biomass. The analytical solution is based on a perturbative solution of concentrations, and can properly reproduce the numerical solutions for the full non-linear problem in a system evolving towards a steady state regime governed by the amount of labile carbon supplied to the system. The substrate and the biomass pools exhibit two distinct behaviors depending on whether the amount of carbon supplied is below or above a given threshold. In the latter case, the concentration versus time curves are always monotonic. Contrarily, in the former case the C-pool concentrations present oscillations, allowing the reproduction of non-monotonic small-scale biomass concentration data in a natural soil, observed so far only in short-term experiments in the rhizosphere. Our results illustrate the theoretical dependence of oscillations from soil moisture and temperature and how they may be masked at intermediate scales due to the superposition of solutions with spatially variable parameters.     

Simulation of green roof test bed runoff

Low Impact Development (LID) aims to mitigate the hydrological impacts of urbanization by replication of processes in natural catchments. Green roofs covered with vegetation and pervious substrate are one alternative among a wide range of LID tools. Water retention of green roofs depends on many factors (e.g. local climate), and measurements remain crucial in evaluating their performance. The simulation of green roof retention by a hydrological model is one option to evaluate their potential benefits before implementation. In this paper, we evaluated the ability of the recently introduced LID green roof module of the stormwater management model to replicate runoff from monitored green roof test beds under Nordic climate conditions. A parameter sensitivity analysis was conducted to identify calibration parameters. The model showed an overall acceptable performance, and the results indicated the importance of accurately estimating potential evapotranspiration rates for inter‐event periods, which is essential in representing the retention capacity regeneration. Copyright © 2015 John Wiley & Sons, Ltd.     

Analysis of biodegradation in a 3-D heterogeneous porous medium using nonlinear stochastic finite element method

Probabilistic analysis by Monte Carlo Simulation method (MCSM) is a computationally prohibitive task for a reactive solute transport involving coupled PDEs with nonlinear source/sink terms in 3-D heterogeneous porous media. The perturbation based stochastic finite element method (SFEM) is an attractive alternative method to MCSM as it is computationally efficient and accurate. In the present study SFEM is developed for solving nonlinear reactive solute transport problem in a 3-D heterogeneous medium. Here the solution of the biodegradation problem involving a single solute by a single class of microorganisms coupled with dynamic microbial growth is attempted using this method. The SFEM here produces a second-order accurate solution for the mean and a first-order accurate solution for the standard deviation of concentrations. In this study both the physical parameters (hydraulic conductivity, porosity, dispersivity and diffusion coefficient) and the biological parameters (maximum substrate utilization rate and the coefficient of cell decay) are considered as spatially varying random fields. A comparison between the MCSM and SFEM for the mean and standard deviation of concentration is made for 1-D and 3-D problem. The effects of heterogeneity on the degradation of substrate and growth of biomass concentrations for a range of variances of input parameters are discussed for both 1-D and 3-D problems.