Investigation of hydrodynamic focusing in a microfluidic coulter counter device

The Coulter technique enables rapid analysis of particles or cells suspended in a fluid stream. In this technique, the cells are suspended in an electrically conductive solution, which is hydrodynamically focused by nonconducting sheath flows. The cells produce a characteristic voltage signal when they interrupt an electrical path. The population and size of the cells can be obtained through analyzing the voltage signal. In a microfluidic Coulter counter device, the hydrodynamic focusing technique is used to position the conducting sample stream and the cells and also to separate close cells to generate distinct signals for each cell and avoid signal jam. The performance of hydrodynamic focusing depends on the relative flow ratio between the sample stream and sheath stream. We use a numerical approach to study the hydrodynamic focusing in a microfluidic Coulter counter device. In this approach, the flow field is described by solving the incompressible Navier-Stokes equations. The sample stream concentration is modeled by an advection-diffusion equation. The motion of the cells is governed by the Newton-Euler equations of motion. Particle motion through the flow field is handled using an overlapping grid technique. A numerical model for studying a microfluidic Coulter counter has been validated. Using the model, the impact of relative flow rate on the performance of hydrodynamic focusing was studied. Our numerical results show that the position of the sample stream can be controlled by adjusting the relative flow rate. Our simulations also show that particles can be focused into the stream and initially close particles can be separated by the hydrodynamic focusing. From our study, we conclude that hydrodynamic focusing provides an effective way to control the position of the sample stream and cells and it also can be used to separate cells to avoid signal jam.     

A flow network model for animal movement on a landscape with application to invasion

Animal movement, whether for foraging, mate-seeking, predator avoidance, dispersal, or migration, is a fundamental aspect of ecology that shapes spatial abundance distributions, genetic compositions, and dynamics of populations. A variety of movement models have been used for predicting the effects of natural or human-caused landscape changes, invading species, or other disturbances on local ecology. Here we introduce the flow network—a general modeling framework for population dynamics and movement in a metapopulation representing a network of habitat sites (nodes). Based on the principles of physical transport phenomena such as fluid flow through pipes (Pouiselle’s Law) and analogously, the flow of electric current across a circuit (Ohm’s Law), the flow network provides a novel way of modeling movement, where flow rates are functions of relative node pressures and the resistance to movement between them. Flow networks offer the flexibility of incorporating abiotic and biotic conditions that affect either pressures, resistance, or both. To illustrate an application of the flow network, we present a theoretical invasion scenario. We consider the effects of spatial structure on the speed of invasion by varying the spatial regularity of node arrangement. In the context of invasion, we model management actions targeting nodes or edges, and consider the effects on speed of invasion, node occupation, and total abundance. The flow network approach offers the flexibility to incorporate spatial heterogeneity in both rates of flow and site pressures and offers an intuitive approach to connecting population dynamics and landscape features to model movement.     

Flow regime alteration effects on the organic C dynamics in semiarid stream ecosystems

There is evidence of an ongoing alteration of the flow regime owing to climate change forcing, which has resulted in substantial increases in the frequency and magnitude of extreme events such as floods and droughts. Such changes in the flow regime may have major implications in freshwater ecosystems and, in particular, in the organic carbon dynamics in semiarid stream ecosystems. Much is known about the role of extreme flow events on structuring stream ecosystems, but few studies explored the effects of extreme flow events magnitude, timing, and sequence on stream ecosystems. To assess the effect of extreme events on stream organic C dynamics, a simple and flexible modeling approach was applied to simulate the organic carbon dynamics in a simplified river reach. The river reach model was initially calibrated and tested using long-term data for stream water velocity and amount of organic carbon in sediment. After that, multiple scenarios differing in the extreme flow events (floods and droughts) sequence and magnitude were used to simulate the effects of possible flow regime changes on the stream organic carbon dynamics. Initial expectations were that: (i) an increase in the magnitude or frequency of extreme flow events would reduce the amount of organic carbon respired within the simulated river reach, and (ii) relationship between the timings of the extreme flow events and of the litterfall input would influence considerably the effects of the extreme flow events. Results pointed out that: (i) the amount of processed carbon respect the amount entering the ecosystem was affected by extreme events such floods and droughts, but the relevance of those events differed along the year, with a maximal effect during the litterfall period; (ii) extreme event timing rather than the magnitude was more relevant to the stream organic carbon dynamics; and (iii) the amount of respired carbon in the ecosystem could be amplified or reduced depending on event sequence. Increasing awareness of the role of inland waters in the global carbon cycle and the shaping role of hydrology on the stream organic carbon dynamics stress the need to better quantify carbon fluxes and the hydrological controls on these fluxes.     

Long-Term Monitoring and Evaluation of the Lower Red River Meadow Restoration Project, Idaho, U.S.A.

Although public and financial support for stream restoration projects is increasing, long‐term monitoring and reporting of project successes and failures are limited. We present the initial results of a long‐term monitoring program for the Lower Red River Meadow Restoration Project in north‐central Idaho, U.S.A. We evaluate a natural channel design’s effectiveness in shifting a degraded stream ecosystem onto a path of ecological recovery. Field monitoring and hydrodynamic modeling are used to quantify post‐restoration changes in 17 physical and biological performance indicators. Statistical and ecological significance are evaluated within a framework of clear objectives, expected responses (ecological hypotheses), and performance criteria (reference conditions) to assess post‐restoration changes away from pre‐restoration conditions. Compared to pre‐restoration conditions, we observed ecosystem improvements in channel sinuosity, slope, depth, and water surface elevation; quantity, quality, and diversity of in‐stream habitat and spawning substrate; and bird population numbers and diversity. Modeling documented the potential for enhanced river–floodplain connectivity. Failure to detect either statistically or ecologically significant change in groundwater depth, stream temperature, native riparian cover, and salmonid density is due to a combination of small sample sizes, high interannual variability, external influences, and the early stages of recovery. Unexpected decreases in native riparian cover led to implementation of adaptive management strategies. Challenges included those common to most project‐level monitoring—isolating restoration effects in complex ecosystems, securing long‐term funding, and implementing scientifically rigorous experimental designs. Continued monitoring and adaptive management that support the establishment of mature and dense riparian shrub communities are crucial to overall success of the project.     

A predictive model for water clarity following dreissenid invasion

Optical transparency, or water clarity, is a fundamental property of lake ecosystems which influences a wide range of physical, chemical and biological variables and processes. The establishment of non-native dreissenid mussels in lake and river ecosystems across North America and Europe has been associated with often dramatic, but highly variable, increases in water clarity. The objective of this study was to develop a predictive model for water clarity (Secchi depth, m) in lakes following the establishment of dreissenids. We compiled water clarity data before and after dreissenid invasion from North American lakes that varied in size and nutrient status. An AIC model averaging approach was used to generate post-invasion water clarity predictions based on pre-invasion water clarity and lake morphometric characteristics from a 53 lake dataset. The accuracy of the model was verified using cross-validation. We then extended this model to existing empirical models of lake mixing depth and Walleye (Sander vitreus) yield, to demonstrate that increased water clarity associated with dreissenid invasion may have far-reaching physical and ecological consequences in lakes, including deeper thermoclines and context-dependent changes in fish yields.     

提高生态位模型转移能力来模拟入侵物种 的潜在分布

生态位模型利用物种分布点所关联的环境变量去推算物种的生态需求, 模拟物种的分布。在模拟入侵物种分布时, 经典生态位模型包括模型构建于物种本土分布地, 然后将其转移并投射至另一地理区域, 来模拟入侵物种的潜在分布。然而在模型运用时, 出现了模型的转移能力较低、模拟的结果与物种的实际分布不相符的情况, 由此得出了生态位漂移等不恰当的结论。提高生态位模型的转移能力, 可以准确地模拟入侵物种的潜在分布, 为入侵种的风险评估提供参考。作者以入侵种茶翅蝽(Halyomorpha halys)和互花米草(Spartina alterniflora)为例, 从模型的构建材料(即物种分布点和环境变量)入手, 全面阐述提高模型转移能力的策略。在构建模型之前, 需要充分了解入侵物种的生物学特性、种群平衡状态、本土地理分布范围及物种的生物历史地理等方面的知识。在模型构建环节上, 物种分布点不仅要充分覆盖物种的地理分布和生态空间的范围, 同时要降低物种采样点偏差; 环境变量的选择要充分考虑其对物种分布的限制作用、各环境变量之间的空间相关性, 以及不同地理种群间生态空间是否一致, 同时要降低环境变量的空间维度; 模型构建区域要真实地反映物种的地理分布范围, 并考虑种群的平衡状态。作者认为, 在生态位保守的前提下, 如果模型是构建在一个合理方案的基础上, 生态位模型的转移能力是可以保证的, 在以模型转移能力较低的现象来阐述生态位分化时需要引起注意。     

Spatial dynamics of invasion: the geometry of introduced species

Many exotic species combine low probability of establishment at each introduction with rapid population growth once introduction does succeed. To analyse this phenomenon, we note that invaders often cluster spatially when rare, and consequently an introduced exotic's population dynamics should depend on locally structured interactions. Ecological theory for spatially structured invasion relies on deterministic approximations, and determinism does not address the observed uncertainty of the exotic-introduction process. We take a new approach to the population dynamics of invasion and, by extension, to the general question of invasibility in any spatial ecology. We apply the physical theory for nucleation of spatial systems to a lattice-based model of competition between plant species, a resident and an invader, and the analysis reaches conclusions that differ qualitatively from the standard ecological theories. Nucleation theory distinguishes between dynamics of single- and multi-cluster invasion. Low introduction rates and small system size produce single-cluster dynamics, where success or failure of introduction is inherently stochastic. Single-cluster invasion occurs only if the cluster reaches a critical size, typically preceded by a number of failed attempts. For this case, we identify the functional form of the probability distribution of time elapsing until invasion succeeds. Although multi-cluster invasion for sufficiently large systems exhibits spatial averaging and almost-deterministic dynamics of the global densities, an analytical approximation from nucleation theory, known as Avrami's law, describes our simulation results far better than standard ecological approximations.     

Development and application of a hybrid model to analyze spatial distribution of macroinvertebrates under flow regulation in the Lijiang River

Alteration of natural flow regime due to reservoir operation imposes serious impacts on the aquatic ecosystem. To investigate the effects on the spatial distribution of macroinvertebrates, this study developed a hybrid ecohydraulics model which integrated a two-dimensional water quality module with an artificial neural network (ANN) based macroinvertebrate habitat module. The developed model was applied to a compound channel in the middle of the Lijiang River, where the flow in dry season has been largely modified by the Qingshitan Reservoir in the upstream. Semisulcospira amurensis (S. amurensis) which is the dominant macroinvertebrate species in the whole river basin was studied. The simulation and comparison results indicate that in general the flow regulation in dry season has negative impacts on the distribution of S. amurensis. The distribution area decreases, and in particular it becomes seriously fragmented. The model can be used through scenario analyses to adjust reservoir operation, so as to improve river management for ecological interest. In addition, the hybrid approach proposed in the paper has great potentials in studying this type of problems.     

Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference

1. The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously modeling true abundance, presence, and trajectories of ecological communities.
2. Simultaneous modeling of the population dynamics of multiple species provides an interesting mechanism to examine patterns in community processes and, as we emphasize herein, to improve species‐specific estimates by leveraging detection information among species. Here, we demonstrate a simple but effective approach to share information about observation parameters among species in hierarchical community abundance and occupancy models, where we use shared random effects among species to account for spatiotemporal heterogeneity in detection probability.
3. We demonstrate the efficacy of our modeling approach using simulated abundance data, where we recover well our simulated parameters using N‐mixture models. Our approach substantially increases precision in estimates of abundance compared with models that do not share detection information among species. We then expand this model and apply it to repeated detection/non‐detection data collected on six species of tits (Paridae) breeding at 119 1 km² sampling sites across a P. montanus hybrid zone in northern Switzerland (2004–2020). We find strong impacts of forest cover and elevation on population persistence and colonization in all species. We also demonstrate evidence for interspecific competition on population persistence and colonization probabilities, where the presence of marsh tits reduces population persistence and colonization probability of sympatric willow tits, potentially decreasing gene flow among willow tit subspecies.
4. While conceptually simple, our results have important implications for the future modeling of population abundance, colonization, persistence, and trajectories in community frameworks. We suggest potential extensions of our modeling in this paper and discuss how leveraging data from multiple species can improve model performance and sharpen ecological inference.

     

Long‐term mark‐and‐recapture study of a freshwater mussel reveals patterns of habitat use and an association between survival and river discharge

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Downstream flow and upstream movement determine the value of a stream reach for potadromous fish populations

Given that human activities often have negative impacts on biological populations, a common question is to find the location of greatest positive or least negative impact. Local habitat suitability is frequently used to evaluate viability of fish populations in river networks. Upper stream reaches are often undervalued, in particular when they are not navigable or do not contain commercially interesting fish. Since water flow transports certain local conditions downstream and individuals navigate river networks upstream and downstream, impacts of local perturbations can manifest elsewhere in the system, and overall effects of disturbances should be assessed on a network level. We study a model for a potadromous fish population in a system of connected stream reaches. We consider different geometries to evaluate how downstream transport and individual movement interact to determine the location of greatest and least impact of a single or two concurrent disturbances. Our results show how upper stream reaches can be highly significant for population persistence if downstream transport of abiotic conditions or upstream movement of individuals is strong.     

Hydropower-related pulsed-flow impacts on stream fishes: a brief review,conceptual model,knowledge gaps,and research needs

The societal benefits of hydropower systems (e.g., relatively clean electrical power, water supply, flood control, and recreation) come with a cost to native stream fishes. We reviewed and synthesized the literature on hydropower-related pulsed flows to guide resource managers in addressing significant impacts while avoiding unnecessary curtailment of hydropower operations. Dams may release pulsed flows in response to needs for peaking power, recreational flows, reservoir storage adjustment for flood control, or to mimic natural peaks in the hydrograph. Depending on timing, frequency, duration, and magnitude, pulsed flows can have adverse or beneficial short and long-term effects on resident or migratory stream fishes. Adverse effects include direct impacts to fish populations due to (1) stranding of fishes along the changing channel margins, (2) downstream displacement of fishes, and (3) reduced spawning and rearing success due to redd/nest dewatering and untimely or obstructed migration. Beneficial effects include: (1) maintenance of habitat for spawning and rearing, and (2) biological cues to trigger spawning, hatching, and migration. We developed a basic conceptual model to predict the effects of different types of pulsed flow, identified gaps in knowledge, and identified research activities to address these gaps. There is a clear need for a quantitative framework incorporating mathematical representations of field and laboratory results on flow, temperature, habitat structure, fish life stages by season, fish population dynamics, and multiple fish species, which can be used to predict outcomes and design mitigation strategies in other regulated streams experiencing pulsed flows.     

Fish recruitment in rivers with modified discharge depends on the interacting effects of flow and thermal regimes

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Influence of groundwater exploitation on the ecological status of streams in a Mediterranean system (Selva Basin,NE Spain)

The ecological status of streams depends on an equilibrium between hydrological processes and biological dynamics. Water discharge is the main requisite for a wealthy riparian habitat. Nevertheless, human practices severely affect water availability through stream water derivation and groundwater withdrawal. In this sense, impacts upon aquifer water storage and its effects on base flow generation have a significant effect on stream biology. Consequently, biological indicators will point out poor conditions resulting from such human impacts. In this paper, the effects of groundwater exploitation on stream discharge and surface water quality are evaluated and compared to biological indicators in a Mediterranean catchment.The stream–aquifer relationship is investigated by considering the hydrological context of each river reach, including human pressures, and the hydraulic head in the contiguous alluvial aquifer, where it exists. These data allow us to differentiate distinct types of reaches that are defined according to a “Stream–Aquifer relationship and chemical Pressure” (SAP) classification, which is used later on to standardize the different hydrochemical and biological features of the sampling points.Stream water and groundwater hydrochemistry are compared to depict the hydraulic behavior of the sampled watercourses during wet and dry periods. Specific elements are used as tracers of groundwater inputs, wastewater influence, or even stagnant conditions during the dry season. This dataset defines a framework to interpret the biological status of each reach based on the Iberian biological monitoring working party indicator (IBMWP). Affinities between hydrological and hydrochemical conditions with biological indicator values allow the causal effects of groundwater exploitation on stream ecology to be defined.The use of multivariate principal component analysis shows that the dataset variance is distributed according to the SAP classification, and that variable grouping is in agreement with the observed hydrological processes and their effects on biological indicator values.This work provides evidence of the importance of groundwater dynamics on biological indicators in a human-modified environment. When using the SAP classification, biological indicators acquire a broader meaning as they reveal the status of biological processes and the causal references. Such information is relevant for water management assessment within the context of the European Water Framework Directive, as it emphasizes the control of groundwater exploitation as a key parameter in the preservation of stream ecological status and the achievement of the objectives of the directive.     

The nature of the fluid boundary layer and the selection of parameters for benthic ecology

1. The nature of flow structure close to a river bed is reviewed and suggestions made as to appropriate equations to apply to given hydrodynamic regimes. 2. It is emphasized that in natural rivers the laminar sublayer observed immediately above the bed in some experimental studies is completely disrupted for flows characterized by high turbulence levels. 3. Instead of resorting to direct topographical measurement of bed undulations, the roughness of the river bed also can be quantified using hydraulic data obtained from velocity profiles. 4. Ambuhl's experimental findings of 1959 underpin modern ecological research into the nature of the benthic boundary layer. Common misconceptions concerning Ambuhl's contribution are corrected and it is shown that his results only apply to certain prescribed hydrodynamic conditions. 5. The adoption of a consistent approach to describing the benthic boundary layer is to be preferred, so that diverse studies can be usefully compared.     

Invasive aquarium fish transform ecosystem nutrient dynamics

Trade of ornamental aquatic species is a multi-billion dollar industry responsible for the introduction of myriad fishes into novel ecosystems. Although aquarium invaders have the potential to alter ecosystem function, regulation of the trade is minimal and little is known about the ecosystem-level consequences of invasion for all but a small number of aquarium species. Here, we demonstrate how ecological stoichiometry can be used as a framework to identify aquarium invaders with the potential to modify ecosystem processes. We show that explosive growth of an introduced population of stoichiometrically unique, phosphorus (P)-rich catfish in a river in southern Mexico significantly transformed stream nutrient dynamics by altering nutrient storage and remineralization rates. Notably, changes varied between elements; the P-rich fish acted as net sinks of P and net remineralizers of nitrogen. Results from this study suggest species-specific stoichiometry may be insightful for understanding how invasive species modify nutrient dynamics when their population densities and elemental composition differ substantially from native organisms. Risk analysis for potential aquarium imports should consider species traits such as body stoichiometry, which may increase the likelihood that an invasion will alter the structure and function of ecosystems.     

Population Dynamics of Intermediate-Host Snails in the White Nile River,Sudan: A Year-Round Observational Descriptive Study

We aimed to explore the population dynamics of snail in 3 sites of the White Nile in Sudan. More specifically, we aimed to investigate the annual patterns of snail populations that act as intermediate hosts of schistosomes and monthly snail infection rates and ecological characteristics presumably related to snail populations. We collected snails for 1 year monthly at 3 different shore sites in the vicinity of El Shajara along the White Nile river in Khartoum State, Sudan. In addition, we measured air and water temperatures, water turbidities, vegetation coverages, and water depths and current speeds. Most of the collected snails were Biomphalaria pfeifferi and Bulinus truncatus. The population densities of snails and their infection rates varied across survey sites. The collected snails liberated S. mansoni and S. haematobium cercariae as well as Amphistome and Echinostome cercariae. Infected snails were found during March–June. The ecological characteristics found to be associated with the absence of snails population were: high turbidity, deep water, low vegetation coverage (near absence of vegetation), high water temperature, and high current speed. To our knowledge, this is the first longitudinal study of the snail population and ecological characteristics in the main basin of the White Nile river.     

Allee effect makes possible patchy invasion in a predator–prey system

The dynamics of interacting ecological populations results from the interplay between various deterministic and stochastic factors and this is particularly the case for the phenomenon of biological invasion. Whereas the spread of invasive species via propagation of a population front was shown to appear as a result of deterministic processes, the spread via formation, interaction and movement of separate patches has been recently attributed to the influence of environmental stochasticity. An appropriate understanding of the comparative importance of deterministic and stochastic mechanisms is still lacking, however. In this paper, we show that the patchy invasion appears to be possible also in a fully deterministic predator–prey model as a result of the Allee effect.     

The dynamics of fish populations in the Palancar stream,a small tributary of the river Guadalquivir,Spain

The relationship between flooding and changes in the size distribution of fish populations in the Palancar stream confirms observations in other rivers. On average, density decreased by 36.2 % and biomass increased by 14.5 %, passing from a period of severe drought to one of heavier than normal rains. Precipitation is the most important of the many factors affecting the populations of the Palancar stream; the most evident changes all occurred after the drought. During the drought period, the marked seasonal fluctuation in flow was the most important factor regulating the population dynamics. Fish density and biomass varied in proportion to the water volume. During the rainy period, the studied section of the river was found to be an important reproduction and nursery area, with juveniles and individuals of reproduction age dominating. The presence of Micropterus salmoides, an introduced piscivorous species, is another factor affecting the population dynamics in the Palancar stream. The observed absence of age 0+ individuals of the dominant populations is considered a direct effect of predation.     

The effects of land use changes on streams and rivers in mediterranean climates

We reviewed the literature on the effects of land use changes on mediterranean river ecosystems (med-rivers) to provide a foundation and directions for future research on catchment management during times of rapid human population growth and climate change. Seasonal human demand for water in mediterranean climate regions (med-regions) is high, leading to intense competition for water with riverine communities often containing many endemic species. The responses of river communities to human alterations of land use, vegetation, hydrological, and hydrochemical conditions are similar in mediterranean and other climatic regions. High variation in hydrological regimes in med-regions, however, tends to exacerbate the magnitude of these responses. For example, land use changes promote longer dry season flows, concentrating contaminants, allowing the accumulation of detritus, algae, and plants, and fostering higher temperatures and lower dissolved oxygen levels, all of which may extirpate sensitive native species. Exotic species often thrive in med-rivers altered by human activity, further homogenizing river communities worldwide. We recommend that future research rigorously evaluate the effects of management and restoration practices on river ecosystems, delineate the cause–effect pathways leading from human perturbations to stream biological communities, and incorporate analyses of the effects of scale, land use heterogeneity, and high temporal hydrological variability on stream communities.