Active-distributed temperature sensing to continuously quantify vertical flow in boreholes

We show how a distributed borehole flowmeter can be created from armored Fiber Optic cables with the Active-Distributed Temperature Sensing (A-DTS) method. The principle is that in a flowing fluid, the difference in temperature between a heated and unheated cable is a function of the fluid velocity. We outline the physical basis of the methodology and report on the deployment of a prototype A-DTS flowmeter in a fractured rock aquifer. With this design, an increase in flow velocity from 0.01 to 0.3 m s−1 elicited a 2.5°C cooling effect. It is envisaged that with further development this method will have applications where point measurements of borehole vertical flow do not fully capture combined spatiotemporal dynamics

Controls on the composition and lability of dissolved organic matter in Siberia's Kolyma River basin

High-latitude northern rivers export globally significant quantities of dissolved organic carbon (DOC) to the Arctic Ocean. Climate change, and its associated impacts on hydrology and potential mobilization of ancient organic matter from permafrost, is likely to modify the flux, composition, and thus biogeochemical cycling and fate of exported DOC in the Arctic. This study examined DOC concentration and the composition of dissolved organic matter (DOM) across the hydrograph in Siberia's Kolyma River, with a particular focus on the spring freshet period when the majority of the annual DOC load is exported. The composition of DOM within the Kolyma basin was characterized using absorbance-derived measurements (absorbance coefficienta330, specific UV absorbance (SUVA254), and spectral slope ratio SR) and fluorescence spectroscopy (fluorescence index and excitation-emission matrices (EEMs)), including parallel factor analyses of EEMs. Increased surface runoff during the spring freshet led to DOM optical properties indicative of terrestrial soil inputs with high humic-like fluorescence, SUVA254, and low SRand fluorescence index (FI). Under-ice waters, in contrast, displayed opposing trends in optical properties representing less aromatic, lower molecular weight DOM. We demonstrate that substantial losses of DOC can occur via biological (∼30% over 28 days) and photochemical pathways (>29% over 14 days), particularly in samples collected during the spring freshet. The emerging view is therefore that of a more dynamic and labile carbon pool than previously thought, where DOM composition plays a fundamental role in controlling the fate and removal of DOC at a pan-Arctic scale

Permafrost Landscape History Shapes Fluvial Chemistry, Ecosystem Carbon Balance, and Potential Trajectories of Future Change

Intensifying permafrost thaw alters carbon cycling by mobilizing large amounts of terrestrial substrate into aquatic ecosystems. Yet, few studies have measured aquatic carbon fluxes and constrained drivers of ecosystem carbon balance across heterogeneous Arctic landscapes. Here, we characterized hydrochemical and landscape controls on fluvial carbon cycling, quantified fluvial carbon fluxes, and estimated fluvial contributions to ecosystem carbon balance across 33 watersheds in four ecoregions in the continuous permafrost zone of the western Canadian Arctic: unglaciated uplands, ice-rich moraine, and organic-rich lowlands and till plains. Major ions, stable isotopes, and carbon speciation and fluxes revealed patterns in carbon cycling across ecoregions defined by terrain relief and accumulation of organics. In previously unglaciated mountainous watersheds, bicarbonate dominated carbon export (70% of total) due to chemical weathering of bedrock. In lowland watersheds, where soil organic carbon stores were largest, lateral transport of dissolved organic carbon (50%) and efflux of biotic CO2 (25%) dominated. In watersheds affected by thaw-induced mass wasting, erosion of ice-rich tills enhanced chemical weathering and increased particulate carbon fluxes by two orders of magnitude. From an ecosystem carbon balance perspective, fluvial carbon export in watersheds not affected by thaw-induced wasting was, on average, equivalent to 6%–16% of estimated net ecosystem exchange (NEE). In watersheds affected by thaw-induced wasting, fluvial carbon export approached 60% of NEE. Because future intensification of thermokarst activity will amplify fluvial carbon export, determining the fate of carbon across diverse northern landscapes is a priority for constraining trajectories of permafrost region ecosystem carbon balance

Flow-weighted values of runoff tracers (δ18O, DOC, Ba, alkalinity) from the six largest Arctic rivers

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 35 (2008): L18606, doi:10.1029/2008GL035007.We present new flow-weighted data for δ 18OH2O, dissolved organic carbon (DOC), dissolved barium and total alkalinity from the six largest Arctic rivers: the Ob', Yenisey, Lena, Kolyma, Yukon and Mackenzie. These data, which can be used to trace runoff, are based upon coordinated collections between 2003 and 2006 that were temporally distributed to capture linked seasonal dynamics of river flow and tracer values. Individual samples indicate significant variation in the contributions each river makes to the Arctic Ocean. Use of these new flow-weighted estimates should reduce uncertainties in the analysis of freshwater transport and fate in the upper Arctic Ocean, including the links to North Atlantic thermohaline circulation, as well as regional water mass analysis. Additional improvements should also be possible for assessing the mineralization rate of the globally significant flux of terrigenous DOC contributed to the Arctic Ocean by these major rivers.Supported by the U.S. National Science Foundation (OPP-0229302), the U.S. Geological Survey and the Water Resources Division of Canada’s Department of Indian Affairs and Northern Development

Geographically widespread C-13-depletion of grazing caddis larvae:a third way of fuelling stream food webs?

Stream ecosystems are supported by both green (i.e. based on grazing) and brown (i.e. detritus) food webs, whereas methane-derived carbon is not considered generally to be important; here, we add circumstantial evidence for this potential third way. Grazing cased-caddis (Trichoptera) larvae in the family Glossosomatidae can be very abundant in springs and headwaters and frequently have much lower stable carbon isotope ratios (i.e. they are depleted in the heavier C-13 stable isotope) than the biofilm (epilithon) on the upper surfaces of the stones on which they live, and which is their presumed diet. Evidence for similar isotopic depletion in other lotic invertebrates is currently limited, however; even for glossosomatids it has been observed so far only in some streams draining the southern English cretaceous chalk and in a few headwaters in northern California. If this phenomenon proves to be more widespread, among streams or taxa, it could imply a more general underpinning of stream food webs by isotopically light carbon derived from methane and accessed via consumers feeding on methanotrophic bacteria. Here, we sampled 58 stream sites to examine whether caddis larvae are also C-13-depleted in streams draining other geologies. We focused mainly on carboniferous limestone and sandstone, as well as on further chalk streams representative of most of the British chalk aquifer: together, these new sites covered an area of almost 90,000 km(2), around three times greater than that surveyed previously. At all 58 sites methane gas was supersaturated relative to the atmospheric equilibrium, and at 49 of them larvae were conspicuously C-13-depleted (from -17.5 parts per thousand to -3.6 parts per thousand) relative to the bulk epilithon (components of which we know can oxidise methane). Although still most pronounced on chalk, this phenomenon was geographically and geologically much more widespread than shown previously and suggests methane-derived carbon could indeed play a prominent role in stream food webs (i.e. the third way)

Highly Sensitive Detection of Individual HEAT and ARM Repeats with HHpred and COACH

BACKGROUND:HEAT and ARM repeats occur in a large number of eukaryotic proteins. As these repeats are often highly diverged, the prediction of HEAT or ARM domains can be challenging. Except for the most clear-cut cases, identification at the individual repeat level is indispensable, in particular for determining domain boundaries. However, methods using single sequence queries do not have the sensitivity required to deal with more divergent repeats and, when applied to proteins with known structures, in some cases failed to detect a single repeat. METHODOLOGY AND PRINCIPAL FINDINGS:Testing algorithms which use multiple sequence alignments as queries, we found two of them, HHpred and COACH, to detect HEAT and ARM repeats with greatly enhanced sensitivity. Calibration against experimentally determined structures suggests the use of three score classes with increasing confidence in the prediction, and prediction thresholds for each method. When we applied a new protocol using both HHpred and COACH to these structures, it detected 82% of HEAT repeats and 90% of ARM repeats, with the minimum for a given protein of 57% for HEAT repeats and 60% for ARM repeats. Application to bona fide HEAT and ARM proteins or domains indicated that similar numbers can be expected for the full complement of HEAT/ARM proteins. A systematic screen of the Protein Data Bank for false positive hits revealed their number to be low, in particular for ARM repeats. Double false positive hits for a given protein were rare for HEAT and not at all observed for ARM repeats. In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries. SIGNIFICANCE:A protocol is presented for the identification of individual HEAT or ARM repeats which is straightforward to implement. It provides high sensitivity at a low false positive rate and will therefore greatly enhance the accuracy of predictions of HEAT and ARM domains

The LRRK2 signalling system

The LRRK2 gene is a major contributor to genetic risk for Parkinson's disease and understanding the biology of the leucine-rich repeat kinase 2 (LRRK2, the protein product of this gene) is an important goal in Parkinson's research. LRRK2 is a multi-domain, multi-activity enzyme and has been implicated in a wide range of signalling events within the cell. Because of the complexities of the signal transduction pathways in which LRRK2 is involved, it has been challenging to generate a clear idea as to how mutations and disease associated variants in this gene are altered in disease. Understanding the events in which LRRK2 is involved at a systems level is therefore critical to fully understand the biology and pathobiology of this protein and is the subject of this review

Boreal forest soil carbon fluxes one year after a wildfire: Effects of burn severity and management

The extreme 2018 hot drought that affected central and northern Europe led to the worst wildfire season in Sweden in over a century. The Ljusdal fire complex, the largest area burnt that year (8995 ha), offered a rare opportunity to quantify the combined impacts of wildfire and post-fire management on Scandinavian boreal forests. We present chamber measurements of soil CO2 and CH4 fluxes, soil microclimate and nutrient content from five Pinus sylvestris sites for the first growing season after the fire. We analysed the effects of three factors on forest soils: burn severity, salvage-logging and stand age. None of these caused significant differences in soil CH4 uptake. Soil respiration, however, declined significantly after a high-severity fire (complete tree mortality) but not after a low-severity fire (no tree mortality), despite substantial losses of the organic layer. Tree root respiration is thus key in determining post-fire soil CO2 emissions and may benefit, along with heterotrophic respiration, from the nutrient pulse after a low-severity fire. Salvage-logging after a high-severity fire had no significant effects on soil carbon fluxes, microclimate or nutrient content compared with leaving the dead trees standing, although differences are expected to emerge in the long term. In contrast, the impact of stand age was substantial: a young burnt stand experienced more extreme microclimate, lower soil nutrient supply and significantly lower soil respiration than a mature burnt stand, due to a thinner organic layer and the decade-long effects of a previous clear-cut and soil scarification. Disturbance history and burn severity are, therefore, important factors for predicting changes in the boreal forest carbon sink after wildfires. The presented short-term effects and ongoing monitoring will provide essential information for sustainable management strategies in response to the increasing risk of wildfire