Photodegraded Dissolved Organic Matter from Peak Freshet River Discharge as a Substrate for Bacterial Production in a Lake-rich Great Arctic Delta

Lake-rich Arctic river deltas are recharged with terrigenous dissolved organic matter (DOM) during the yearly peak water period corresponding with the solstice (24 h day−1 solar irradiance). Bacteria-free DOM collected during peak Mackenzie River discharge was exposed to sunlight for up to 14 days in June 2010. As solar exposure increased, carbon and lignin concentrations declined (10% and 42%, respectively, after 14 days), as did DOM absorptivity (62% after 14 days), aromaticity, and molecular weight. Photochemical changes were on par with those normally observed in Mackenzie Delta lakes over the entire open-water season. When irradiated freshet DOM was provided as a substrate, no significant differences were observed in community-level metabolism among five bacterial communities from representative delta habitats. However, bacterial abundance was significantly greater when nonirradiated (0 day) rather than irradiated DOM (7 or 14 days) was provided, while cell-specific metabolic measures revealed that per-cell bacterial production and growth efficiency were significantly greater when communities were provided irradiated substrate. This complex response to rapid DOM photodegradation may result from the production of inhibitory reactive oxygen species (ROS), along with shifts in bacterial community composition to species that are better able to tolerate ROS, or metabolize the labile photodegraded DOM

Photodegraded Dissolved Organic Matter from Peak Freshet River Discharge as a Substrate for Bacterial Production in a Lake-rich Great Arctic Delta

Lake-rich Arctic river deltas are recharged with terrigenous dissolved organic matter (DOM) during the yearly peak water period corresponding with the solstice (24 h day−1 solar irradiance). Bacteria-free DOM collected during peak Mackenzie River discharge was exposed to sunlight for up to 14 days in June 2010. As solar exposure increased, carbon and lignin concentrations declined (10% and 42%, respectively, after 14 days), as did DOM absorptivity (62% after 14 days), aromaticity, and molecular weight. Photochemical changes were on par with those normally observed in Mackenzie Delta lakes over the entire open-water season. When irradiated freshet DOM was provided as a substrate, no significant differences were observed in community-level metabolism among five bacterial communities from representative delta habitats. However, bacterial abundance was significantly greater when nonirradiated (0 day) rather than irradiated DOM (7 or 14 days) was provided, while cell-specific metabolic measures revealed that per-cell bacterial production and growth efficiency were significantly greater when communities were provided irradiated substrate. This complex response to rapid DOM photodegradation may result from the production of inhibitory reactive oxygen species (ROS), along with shifts in bacterial community composition to species that are better able to tolerate ROS, or metabolize the labile photodegraded DOM

Structural Variation in the Caenorhabditis elegans Genome: Challenges and Quality Assurance Strategies for Reliable Variant Calling

Obtaining an accurate and comprehensive representation of structural variation is crucial for understanding how large alterations in chromosome structure contribute to phenotype diversity and drive genome evolution. Despite continuous efforts into improving methods for identifying structural variation from whole genome sequencing data, accurate variant calling remains challenging. The barriers to progress in this area are complex and multifactorial but the technical limitations of short-read sequencing technologies and limited availability of suitable benchmarking resources for non-human species feature prominently. This thesis includes an in-depth evaluation of several commonly used tools for identifying structural variants from short- and long-read DNA sequencing data from natural Caenorhabditis elegans strains. The results of these comparisons revealed that popular tools yield considerably different results, which are described in detail in Chapter 2. A major aim of this project was to identify sources of error and variability that tool developers could address in the future. Surprisingly, the order of reads in PacBio FASTQ files were revealed to affect the predicted structural variants. Chapter 3 describes these results and demonstrates how alignment sorting algorithms contribute to the problem. In Chapter 4, an analysis of structural variation in 14 natural C. elegans strains is described. Importantly, this work demonstrates how long-read DNA sequencing data can be successfully used to identify structural variants at the population level

Ice-out and Freshet Fluxes of CO2 and CH4 Across the Air–water Interface of the Channel Network of a Great Arctic Delta, the Mackenzie

Carbon dioxide (CO2) and methane (CH4) were monitored at five sites spanning the upstream–downstream extent of the Mackenzie Delta channel network during May 2010, capturing the historically under-sampled ice-out period that includes the rising freshet, peak water levels and the early falling freshet (flood recession). Unexpectedly, partial pressures of CO2 in the Mackenzie River were undersaturated during the rising freshet before water levels peaked, indicating net CO2 invasion at instantaneous CO2 flux rates (F-CO2) ranging from –112 to –258 mg-C m-2 d-1. Net CO2 invasion was also observed around the time of peak water levels at sites in the middle and outer delta. Following peak water levels, the Mackenzie River switched to saturation and net CO2 evasion (F-CO2 from 74 to 177 mg-C m-2 d-1). Although the Peel River (which flows into the west side of the Mackenzie Delta) was a strong emitter of CO2 (F-CO2 from 373 to 871 mg-C m-2 d-1), overall, the Mackenzie River and Delta were weak emitters of CO2 during the 2010 ice-out period. All sites were strong emitters of CH4 during ice-out, however, with the highest evasive fluxes observed in the outer delta when the extent of flooded delta landscape was greatest. Estimated aerial fluxes from Mackenzie Delta channel surfaces during May 2010 ranged from 2.1 to 4.8 Gg-C as CO2, and 186 to 433 Mg-C as CH4. These results provide critical information that can be used to refine gas flux estimates in high-latitude circumpolar river deltas during the relatively under-studied ice-out period

Multiple tracers demonstrate distinct sources of dissolved organic matter to lakes of the Mackenzie Delta, western Canadian Arctic

Author Posting. © American Society of Limnology and Oceanography, 2011. This article is posted here by permission of American Society of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 56 (2011): 1297-1309, doi:10.4319/lo.2011.56.4.1297.Lakes of the Mackenzie Delta occur across a gradient that contains three clear end members: those that remain connected to river-water channels throughout the summer; those that receive only brief inputs of river water during an annual spring flood but contain dense macrophyte stands; and those that experience significant permafrost thaw along their margins. We measured dissolved organic carbon (DOC) concentration, dissolved organic matter (DOM) absorption and fluorescence, and stable isotopes of DOM, DOM precursor materials, and bacteria to elucidate the importance of river water, macrophytes, and thermokarst as DOM sources to Mackenzie Delta lakes. Despite standing stocks of macrophyte C that are sevenfold to 12-fold greater than those of total DOC, stable isotopes indicated that autochthonous sources contributed less than 15% to overall DOM in macrophyte-rich lakes. Instead, fluorescence and absorption indicated that the moderate summertime increase in DOC concentration in macrophyte-rich lakes was the result of infrequent flushing, while bacterial δ13C indicated rapid bacterial removal of autochthonous DOC from the water column. In thermokarst lakes, summertime increases in DOC concentration were substantial, and stable isotopes indicated that much of this increase came from C released as a result of thermokarst-related processes. Our results indicate that these distinct sources of DOM to neighboring arctic Delta lakes may drive between-lake differences in C cycling and energy flow. Rapidly assimilated macrophyte DOM should be an important contributor to microbial food webs in our study lakes. In contrast, the accumulation of thermokarst-origin DOM allows for a significant role in physico-chemistry but indicates a lesser contribution of this DOM to higher trophic levels.This study was supported by a Discovery Grant and Northern Research Supplement from the Natural Sciences and Engineering Research Council of Canada (NSERC) to L.F.W.L.; funds from the Science Horizons Youth Internship Program, Northern Scientific Training Program, and NSERC Northern Research Internship. Personal financial support to S.E.T. was provided by a Simon Fraser University CD Nelson Memorial Graduate Scholarship, an NSERC Canada Graduate Scholarship-Doctoral, and a Garfield Weston Award for Northern Research

WETMETH 1.0: A New Wetland Methane Model for Implementation in Earth System Models

Wetlands are the single largest natural source of methane (CH4), a powerful greenhouse gas affecting the global climate. In turn, wetland CH4 emissions are sensitive to changes in climate conditions such as temperature and precipitation shifts. However, biogeochemical processes regulating wetland CH4 emissions (namely microbial production and oxidation of CH4) are not routinely included in fully coupled Earth system models that simulate feedbacks between the physical climate, the carbon cycle, and other biogeochemical cycles. This paper introduces a process-based wetland CH4 model (WETMETH) developed for implementation in Earth system models and currently embedded in an Earth system model of intermediate complexity. Here, we (i) describe the wetland CH4 model, (ii) evaluate the model performance against available datasets and estimates from the literature, and (iii) analyze the model sensitivity to perturbations of poorly constrained parameters. Historical simulations show that WETMETH is capable of reproducing mean annual emissions consistent with present-day estimates across spatial scales. For the 2008–2017 decade, the model simulates global mean wetland emissions of 158.6 Tg CH4 yr−1, of which 33.1 Tg CH4 yr−1 is from wetlands north of 45∘ N. WETMETH is highly sensitive to parameters for the microbial oxidation of CH4, which is the least constrained process in the literature

Conversion to soy on the Amazonian agricultural frontier increases streamflow without affecting stormflow dynamics

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Global Change Biology 17 (2011): 1821–1833, doi:10.1111/j.1365-2486.2011.02392.x.Large-scale soy agriculture in the southern Brazilian Amazon now rivals deforestation for pasture as the region’s predominant form of land use change. Such landscape level change can have substantial consequences for local and regional hydrology, which remain relatively unstudied. We examined how the conversion to soy agriculture influences water balances and stormflows using stream discharge (water yields) and the timing of discharge (stream hydrographs) in small (2.5 to 13.5 km2) forested and soy headwater watersheds in the Upper Xingu Watershed in the state of Mato Grosso, Brazil. We monitored water yield for one year in three forested and four soy watersheds. Mean daily water yields were approximately four times higher in soy than forested watersheds, and soy watersheds showed greater seasonal variability in discharge. The contribution of stormflows to annual streamflow in all streams was low (< 13% of annual streamflow), and the contribution of stormflow to streamflow did not differ between land uses. If the increases in water yield observed in this study are typical, landscape-scale conversion to soy substantially alters water-balance, potentially altering the regional hydrology over large areas of the southern Amazon.This project was supported by grants from NSF (DEB-0640661) and the Fundaçao de Amparo à Pesquisa do Estado de São Paulo (FAPESP 03/13172-2)

Band-edge absorption characteristics of semi-insulating indium phosphide under unified Franz-Keldysh and Einstein models

The foundational Franz-Keldysh effect and Einstein model are applied in this work to characterize semiconductor band-edge absorption—and its departures from ideality. We unify the Franz-Keldysh and Einstein models to fully characterize the field-induced tunneling of photoexcited electrons from degenerate valence bands into the conduction band, with encroachment into the band gap arising as an Urbach tail. Our unified model is implemented for semi-insulating indium phosphide (SI-InP) with strong agreement seen between the theoretical and experimental results for varied photon energies and electric fields

Morphometric characteristics of basal cell carcinoma peritumoral stroma varies among basal cell carcinoma subtypes

<p>Abstract</p> <p>Background</p> <p>The role that the peritumoral stroma plays in the growth of tumours is currently poorly understood. In this manuscript the morphometric characteristics of basal cell carcinoma subtypes and their associated peritumoral stromas are presented.</p> <p>Methods</p> <p>Ninety eight digitized basal cell carcinoma histology slides were categorized as infiltrative, nodular, or superficial subtypes, and were analysed using a combination of manual and computer-assisted approaches. The morphometric characteristics of the tumour nests and their associated peritumoral stroma were quantified, and the presence of a marked immune reaction or elastosis was noted.</p> <p>Results</p> <p>The tumour to stroma ratio was different among each tumour subtype. Elastosis was identified in a greater proportion of the infiltrative tumours.</p> <p>Conclusions</p> <p>Quantitative differences exist between the peritumoral stroma of basal cell carcinoma subtypes. Future work exploring the relation between these morphometric differences and biochemical variations in peritumoral stroma may further our understanding of the biology of carcinoma development.</p> <p>Trial Registration</p> <p>Not applicable.</p

Niche construction by non-diazotrophs for N2 fixers in the eastern tropical North Atlantic Ocean

Diazotrophic dinitrogen (N2) fixation contributes ~76% to "new" nitrogen inputs to the sunlit open ocean, but environmental factors determining N2 fixation rates are not well constrained. Excess phosphate (phosphate-nitrate/16 > 0) and iron availability control N2 fixation rates in the eastern tropical North Atlantic (ETNA), but it remains an open question how excess phosphate is generated within or supplied to the phosphate-depleted sunlit layer. Our observations in the ETNA region (8°N-15°N, 19°W-23°W) suggest that Prochlorococcus and Synechococcus, the two ubiquitous non-diazotrophic cyanobacteria with cellular N:P ratios higher than the Redfield ratio, create an environment of excess phosphate, which cannot be explained by diapycnal mixing, atmospheric, and riverine inputs. Thus, our results unveil a new biogeochemical niche construction mechanism by non-diazotrophic cyanobacteria for their diazotrophic phylum group members (N2 fixers). Our observations may help to understand the prevalence of diazotrophy in low-phosphate, oligotrophic regions