Evolution of the Set of Signal Transduction Proteins in 10 Species of \u3cem\u3eShewanella\u3c/em\u3e

The recent completion of the sequencing of several species of the Shewanella genus provides a unique opportunity for comparative genomics studies. We chose the first 10 fully sequenced Shewanella genomes to investigate the evolution of signal transduction proteins (ST). ST is a universal and highly regulated system, and as a very well-studied system provides an excellent starting point for investigation. Furthermore, Shewanella have been shown to have a large number of two-component systems and diguanylate cyclases relative to their genome size. In this study we investigate the evolution of signal transduction across several Shewanella strains by utilizing a domainlevel approach for determining homology and orthology of the parent proteins. Proteins were broken down into their constituent domains and domain sized sequences and compared using a reciprocal best BLAST hit approach to determine homology between all of the species. Analysis of homologous domains and proteins revealed several levels of conservation and a core group of signal transduction proteins common to all members. Further analysis of domain homology provided putative annotations of previously unrecognized sequences and highlighted deficiencies in specific Pfam domain models. Analysis of paralogous domains and proteins showed agreement with 16s rRNA based estimates of evolution, although the position of S. oneidensis MR-1 was novel

Flux dynamics at the groundwater-surface water interface in a tropical catchment

© 2017 Elsevier GmbH. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 12 month embargo from date of publication (July 2017) in accordance with the publisher’s archiving policySeasonal shifts between wet and dry seasons cause marked changes in river flow regimes and therefore exchanges with the streambed surface. This seasonal variation is particularly apparent in tropical climates, which are characterized by strong differences between wet and dry seasons. However, fluxes between surface water and groundwater and the impacts of these interactions on streambed dynamics are rarely investigated in tropical climates, where few surface water-groundwater field investigations have been performed. In this study, an intermittent river in south coastal Vietnam was investigated to better understand links between seasonal hydrologic shifts, human use of water resources, and streambed dynamics. Three transects along the main tributary were instrumented with water level and streambed temperature sensors to examine both spatial and temporal variability in stream-aquifer dynamics. Calibrated models estimated increasing streambed fluxes along the length of the river, with highly variable fluxes up to 1.6 m2 h−1 upstream and 0.2 m2 h−1 downstream during the rainy season (i.e. the rate of the total amount of water exchanged per meter of river length) decreasing to low fluxes of 1.0 m2 h−1 upstream and 0.15 m2 h−1 downstream in the dry season before flow ceased. During the wet and into the dry season the river was gaining (i.e. flux from the aquifer into the river) at all times and all locations with the notable exception of fluxes into the streambed only at the upstream and downstream sites during peak flow of the largest captured rain event (550 mm in 164 h). Based on 30 years of precipitation data, this suggests that water is pushed from the stream into the streambed approximately three times per year. Groundwater withdrawal by households near the cross-sections was found to have a comparatively small effect on streambed fluxes, reducing the flux by up to 3% during dry conditions, although this pumping did cause a reversal in the gradient to the stream for a short period (less than 12 h) on one occasion during the dry season

Error in hydraulic head and gradient time-series measurements: a quantitative appraisal

&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Abstract.&amp;lt;/strong&amp;gt; Hydraulic head and gradient measurements underpin practically all investigations in hydro(geo)logy. There is sufficient information in the literature to suggest that head measurement errors may be so large that flow directions can not be inferred reliably, and that their magnitude can have as great an effect on the uncertainty of flow rates as the hydraulic conductivity. Yet, educational text books contain limited content regarding measurement techniques and studies rarely report on measurement errors. The objective of our study is to review currently-accepted standard operating procedures in hydrological research and to determine the smallest head gradients that can be resolved. To this aim, we first systematically investigate the systematic and random measurements errors involved in collecting time series information on hydraulic head at a given location: (1) geospatial position, (2) point of head, (3) depth to water, and (4) water level time series. Then, by propagating the random errors, we find that with current standard practice, horizontal head gradients&amp;amp;#8201;&amp;lt;&amp;amp;#8201;10&amp;lt;sup&amp;gt;&amp;amp;#8722;4&amp;lt;/sup&amp;gt; are resolvable at distances&amp;amp;#8201;&amp;amp;#10886;&amp;amp;#8201;170&amp;amp;#8201;m. Further, it takes extraordinary effort to measure hydraulic head gradients&amp;amp;#8201;&amp;lt;&amp;amp;#8201;10&amp;lt;sup&amp;gt;&amp;amp;#8722;3&amp;lt;/sup&amp;gt; over distances&amp;amp;#8201;&amp;lt;&amp;amp;#8201;10&amp;amp;#8201;m. In reality, accuracy will be worse than our theoretical estimates because of the many possible systematic errors. Regional flow on a scale of kilometres or more can be inferred with current best-practice methods, but processes such as vertical flow within an aquifer cannot be determined until more accurate and precise measurement methods are developed. Finally, we offer a concise set of recommendations for water level, hydraulic head and gradient time series measurements. We anticipate that our work contributes to progressing the quality of head time series data in the hydro(geo)logical sciences, and provides a starting point for the development of universal measurement protocols for water level data collection.&amp;lt;/p&amp;gt; </jats:p

LPMLE3 : a novel 1-D approach to study water flow in streambeds using heat as a tracer

We introduce LPMLE3, a new 1-D approach to quantify vertical water flow components at streambeds using temperature data collected in different depths. LPMLE3 solves the partial differential equation for coupled water flow and heat transport in the frequency domain. Unlike other 1-D approaches it does not assume a semi-infinite halfspace with the location of the lower boundary condition approaching infinity. Instead, it uses local upper and lower boundary conditions. As such, the streambed can be divided into finite subdomains bound at the top and bottom by a temperature-time series. Information from a third temperature sensor within each subdomain is then used for parameter estimation. LPMLE3 applies a low order local polynomial to separate periodic and transient parts (including the noise contributions) of a temperature-time series and calculates the frequency response of each subdomain to a known temperature input at the streambed top. A maximum-likelihood estimator is used to estimate the vertical component of water flow, thermal diffusivity, and their uncertainties for each streambed subdomain and provides information regarding model quality. We tested the method on synthetic temperature data generated with the numerical model STRIVE and demonstrate how the vertical flow component can be quantified for field data collected in a Belgian stream. We show that by using the results in additional analyses, nonvertical flow components could be identified and by making certain assumptions they could be quantified for each subdomain. LPMLE3 performed well on both simulated and field data and can be considered a valuable addition to the existing 1-D methods

The interaction of flow regimes and nutrient fluxes on the water quality and ecosystem health of a clear, freshwater wetland

Across the globe, the hydrology and ecology of wetland systems have been altered by anthropogenic activities, sometimes leading to regime shift or even ecosystem collapse. Often, it is not only the impact of one stressor, but the combination of multiple stressors interacting that ultimately leads to adverse ecological impact in wetland systems. However, because of the difficulty in measuring the combined, dynamic effects of multiple stressors, relatively few studies estimate the relative importance of multiple stressors on wetland ecosystems. We combined controlled laboratory and field experiments with a modeling exercise to examine the relative importance of flow and nutrient loads on the resilience of a clear, groundwater-fed wetland dominated by macrophytes. We examined the potential for a combination of lower inflow and higher nutrient loads to increase phytoplankton growth and reduce light availability, culminating in a reduction in macrophyte growth due to the shading of the phytoplankton. This combination of events could result in a collapse of this endemic ecosystem, including local extinction of several endangered species. We found that the resilience of the macrophyte-dominated wetlands is maintained by preserving high flow even under increasing phosphorus concentrations. Nutrient availability increases as flow decreases, favoring pelagic algal development and inducing a shift in the ecosystem conditions. This shows that focusing only on input nutrient levels, as is often done in open waters of concern, is not sufficient to preserve the native ecosystem and highlights the need to consider multiple factors when assessing anthropogenic impacts on wetlands.Margaret Shanafield, Anna Rigosi, Yang Liu and Justin Brooke

Active heat pulse sensing of 3-D-flow fields in streambeds

© Author(s) 2018. This work is distributed under the Creative Commons Attribution 4.0 License.Profiles of temperature time series are commonly used to determine hyporheic flow patterns and hydraulic dynamics in the streambed sediments. Although hyporheic flows are 3-D, past research has focused on determining the magnitude of the vertical flow component and how this varies spatially. This study used a portable 56-sensor, 3-D temperature array with three heat pulse sources to measure the flow direction and magnitude up to 200 mm below the water–sediment interface. Short, 1 min heat pulses were injected at one of the three heat sources and the temperature response was monitored over a period of 30 min. Breakthrough curves from each of the sensors were analysed using a heat transport equation. Parameter estimation and uncertainty analysis was undertaken using the differential evolution adaptive metropolis (DREAM) algorithm, an adaption of the Markov chain Monte Carlo method, to estimate the flux and its orientation. Measurements were conducted in the field and in a sand tank under an extensive range of controlled hydraulic conditions to validate the method. The use of short-duration heat pulses provided a rapid, accurate assessment technique for determining dynamic and multi-directional flow patterns in the hyporheic zone and is a basis for improved understanding of biogeochemical processes at the water–streambed interface

How Low Can You Go?: Widespread Challenges in Measuring Low Stream Discharge and a Path Forward

Low flows pose unique challenges for accurately quantifying streamflow. Current field methods are not optimized to measure these conditions, which in turn, limits research and management. In this essay, we argue that the lack of methods for measuring low streamflow is a fundamental challenge that must be addressed to ensure sustainable water management now and into the future, particularly as climate change shifts more streams to increasingly frequent low flows. We demonstrate the pervasive challenge of measuring low flows, present a decision support tool (DST) for navigating best practices in measuring low flows, and highlight important method developmental needs

Emerging Themes and Future Directions of Multi-Sector Nexus Research and Implementation

Water, energy, and food are all essential components of human societies. Collectively, their respective resource systems are interconnected in what is called the “nexus”. There is growing consensus that a holistic understanding of the interdependencies and trade-offs between these sectors and other related systems is critical to solving many of the global challenges they present. While nexus research has grown exponentially since 2011, there is no unified, overarching approach, and the implementation of concepts remains hampered by the lack of clear case studies. Here, we present the results of a collaborative thought exercise involving 75 scientists and summarize them into 10 key recommendations covering: the most critical nexus issues of today, emerging themes, and where future efforts should be directed. We conclude that a nexus community of practice to promote open communication among researchers, to maintain and share standardized datasets, and to develop applied case studies will facilitate transparent comparisons of models and encourage the adoption of nexus approaches in practice

Surface Energy Budgets of Arctic Tundra During Growing Season

This study analyzed summer observations of diurnal and seasonal surface energy budgets across several monitoring sites within the Arctic tundra underlain by permafrost. In these areas, latent and sensible heat fluxes have comparable magnitudes, and ground heat flux enters the subsurface during short summer intervals of the growing period, leading to seasonal thaw. The maximum entropy production (MEP) model was tested as an input and parameter parsimonious model of surface heat fluxes for the simulation of energy budgets of these permafrost‐underlain environments. Using net radiation, surface temperature, and a single parameter characterizing the thermal inertia of the heat exchanging surface, the MEP model estimates latent, sensible, and ground heat fluxes that agree closely with observations at five sites for which detailed flux data are available. The MEP potential evapotranspiration model reproduces estimates of the Penman‐Monteith potential evapotranspiration model that requires at least five input meteorological variables (net radiation, ground heat flux, air temperature, air humidity, and wind speed) and empirical parameters of surface resistance. The potential and challenges of MEP model application in sparsely monitored areas of the Arctic are discussed, highlighting the need for accurate measurements and constraints of ground heat flux.Plain Language SummaryGrowing season latent and sensible heat fluxes are nearly equal over the Arctic permafrost tundra regions. Persistent ground heat flux into the subsurface layer leads to seasonal thaw of the top permafrost layer. The maximum energy production model accurately estimates the latent, sensible, and ground heat flux of the surface energy budget of the Arctic permafrost regions.Key PointThe MEP model is parsimonious and well suited to modeling surface energy budget in data‐sparse permafrost environmentsPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150560/1/jgrd55584.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150560/2/jgrd55584_am.pd