Environmental filtering and community delineation in the streambed ecotone

Abstract A current controversy in ecology is whether biological communities are discrete biological entities or simply study units created for convenience; a debate that becomes even more heated when delimiting communities along ecotones. Here, we report an interdisciplinary study designed to address the interplay between environmental drivers and community ecology in a typical ecotone ecosystem: the streambed. Environmental filtering at a micro-scale determined how diversity, productivity and composition of the whole streambed assemblage varied with depth and with the direction of vertical water exchange. Biomass and production decreased with increasing depth, and were lower under upwelling than downwelling conditions. However, the rate at which biomass and production decreased with increasing depth differed significantly for different taxonomic groups. Using quantitative biocenosis analysis, we also showed that benthic and hyporheic zone assemblages (assemblages in close juxtaposition) could be clearly distinguished as discrete communities with individual integrity. Vertical hydrodynamic conditions also influenced the demarcation between both communities; the benthic community reached greater depths in downwelling than in upwelling zones

Seasonal Differences in the Attenuation of Polar Trace Organics in the Hyporheic Zone of an Urban Stream

Attenuation of trace organic compounds (TrOCs) in a river occurs to a large extent in its hyporheic zone. A major part of the attenuation of polar TrOCs is of microbial origin. As microbial activity depends on temperature and redox conditions, seasonal differences in TrOC attenuation are likely. We investigated TrOC attenuation at a river influenced by treated wastewater during two sampling campaigns, one in summer and one in winter. In addition to redox conditions and temperature, we also determined residence times of porewater in sediment using three methods: (a) non‐parametric deconvolution of electrical conductivity time series, (b) the model VFLUX 2.0 based on temperature time series (only summer), and (c) applying Darcy's law to differences in hydraulic heads (only summer). Contrary to our expectations, we found higher attenuation for 12 out of 18 TrOCs in winter, while three TrOCs were better attenuated in summer. Sediment conditions varied between seasons as more of the top sandy layer with a higher hydraulic permeability accumulated on the river bed in summer. As a result, residence times in the sediment were shorter in summer. In winter, longer residence times, lower temperatures, and a steeper oxygen gradient in sediment coincided with higher TrOC attenuation. Further research is needed to understand our unexpected findings and underlying mechanisms.DFG, 248198858, GRK 2032: Grenzzonen in urbanen WassersystemenEC/H2020/765553/EU/A EUROpean training and research network for environmental FLOW management in river basins/EUROFLO

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles

Gathering at the top? Environmental controls of microplastic uptake and biomagnification in freshwater food webs

Microplastics are ubiquitous in the environment, with high concentrations being detected now also in river corridors and sediments globally. Whilst there has been increasing field evidence of microplastics accumulation in the guts and tissues of freshwater and marine aquatic species, the uptake mechanisms of microplastics into freshwater food webs, and the physical and geological controls on pathway-specific exposures to microplastics, are not well understood. This knowledge gap is hampering the assessment of exposure risks, and potential ecotoxicological and public health impacts from microplastics. This review provides a comprehensive synthesis of key research challenges in analysing the environmental fate and transport of microplastics in freshwater ecosystems, including the identification of hydrological, sedimentological and particle property controls on microplastic accumulation in aquatic ecosystems. This mechanistic analysis outlines the dominant pathways for exposure to microplastics in freshwater ecosystems and identifies potentially critical uptake mechanisms and entry pathways for microplastics and associated contaminants into aquatic food webs as well as their risk to accumulate and biomagnify. We identify seven key research challenges that, if overcome, will permit the advancement beyond current conceptual limitations and provide the mechanistic process understanding required to assess microplastic exposure, uptake, hazard, and overall risk to aquatic systems and humans, and provide key insights into the priority impact pathways in freshwater ecosystems to support environmental management decision making

Breeding progress and preparedness for mass‐scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar

UK: The UK‐led miscanthus research and breeding was mainly supported by the Biotechnology and Biological Sciences Research Council (BBSRC), Department for Environment, Food and Rural Affairs (Defra), the BBSRC CSP strategic funding grant BB/CSP1730/1, Innovate UK/BBSRC “MUST” BB/N016149/1, CERES Inc. and Terravesta Ltd. through the GIANT‐LINK project (LK0863). Genomic selection and genomewide association study activities were supported by BBSRC grant BB/K01711X/1, the BBSRC strategic programme grant on Energy Grasses & Bio‐refining BBS/E/W/10963A01. The UK‐led willow R&D work reported here was supported by BBSRC (BBS/E/C/00005199, BBS/E/C/00005201, BB/G016216/1, BB/E006833/1, BB/G00580X/1 and BBS/E/C/000I0410), Defra (NF0424) and the Department of Trade and Industry (DTI) (B/W6/00599/00/00). IT: The Brain Gain Program (Rientro dei cervelli) of the Italian Ministry of Education, University, and Research supports Antoine Harfouche. US: Contributions by Gerald Tuskan to this manuscript were supported by the Center for Bioenergy Innovation, a US Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science, under contract number DE‐AC05‐00OR22725. Willow breeding efforts at Cornell University have been supported by grants from the US Department of Agriculture National Institute of Food and Agriculture. Contributions by the University of Illinois were supported primarily by the DOE Office of Science; Office of Biological and Environmental Research (BER); grant nos. DE‐SC0006634, DE‐SC0012379 and DE‐SC0018420 (Center for Advanced Bioenergy and Bioproducts Innovation); and the Energy Biosciences Institute. EU: We would like to further acknowledge contributions from the EU projects “OPTIMISC” FP7‐289159 on miscanthus and “WATBIO” FP7‐311929 on poplar and miscanthus as well as “GRACE” H2020‐EU.3.2.6. Bio‐based Industries Joint Technology Initiative (BBI‐JTI) Project ID 745012 on miscanthus.Peer reviewedPostprintPublisher PD

Relationship between the Clinical Frailty Scale and short-term mortality in patients ≥ 80 years old acutely admitted to the ICU: a prospective cohort study.

BACKGROUND: The Clinical Frailty Scale (CFS) is frequently used to measure frailty in critically ill adults. There is wide variation in the approach to analysing the relationship between the CFS score and mortality after admission to the ICU. This study aimed to evaluate the influence of modelling approach on the association between the CFS score and short-term mortality and quantify the prognostic value of frailty in this context. METHODS: We analysed data from two multicentre prospective cohort studies which enrolled intensive care unit patients ≥ 80 years old in 26 countries. The primary outcome was mortality within 30-days from admission to the ICU. Logistic regression models for both ICU and 30-day mortality included the CFS score as either a categorical, continuous or dichotomous variable and were adjusted for patient's age, sex, reason for admission to the ICU, and admission Sequential Organ Failure Assessment score. RESULTS: The median age in the sample of 7487 consecutive patients was 84 years (IQR 81-87). The highest fraction of new prognostic information from frailty in the context of 30-day mortality was observed when the CFS score was treated as either a categorical variable using all original levels of frailty or a nonlinear continuous variable and was equal to 9% using these modelling approaches (p < 0.001). The relationship between the CFS score and mortality was nonlinear (p < 0.01). CONCLUSION: Knowledge about a patient's frailty status adds a substantial amount of new prognostic information at the moment of admission to the ICU. Arbitrary simplification of the CFS score into fewer groups than originally intended leads to a loss of information and should be avoided. Trial registration NCT03134807 (VIP1), NCT03370692 (VIP2)

Seasonal Differences in the Attenuation of Polar Trace Organics in the Hyporheic Zone of an Urban Stream

Attenuation of trace organic compounds (TrOCs) in a river occurs to a large extent in its hyporheic zone. A major part of the attenuation of polar TrOCs is of microbial origin. As microbial activity depends on temperature and redox conditions, seasonal differences in TrOC attenuation are likely. We investigated TrOC attenuation at a river influenced by treated wastewater during two sampling campaigns, one in summer and one in winter. In addition to redox conditions and temperature, we also determined residence times of porewater in sediment using three methods: (a) non‐parametric deconvolution of electrical conductivity time series, (b) the model VFLUX 2.0 based on temperature time series (only summer), and (c) applying Darcy's law to differences in hydraulic heads (only summer). Contrary to our expectations, we found higher attenuation for 12 out of 18 TrOCs in winter, while three TrOCs were better attenuated in summer. Sediment conditions varied between seasons as more of the top sandy layer with a higher hydraulic permeability accumulated on the river bed in summer. As a result, residence times in the sediment were shorter in summer. In winter, longer residence times, lower temperatures, and a steeper oxygen gradient in sediment coincided with higher TrOC attenuation. Further research is needed to understand our unexpected findings and underlying mechanisms.Key Points: The attenuation of 12 out of 18 trace organic compounds (TrOCs) in the hyporheic zone was higher in winter while three TrOCs were attenuated better in summer. Residence times in sediment were longer and more diverse in winter. The extent of the oxic sediment was similar between seasons but the gradient from the oxic to anoxic zone was steeper in winter.Deutsche Forschungsgemeinschaft (DFG) http://dx.doi.org/10.13039/501100001659EC | H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska‐Curie Actions (MSCA) http://dx.doi.org/10.13039/100010665University of Western Australia ‐ University Postgraduate AwardAustralian Government Research Training Program ScholarshipBundesministerium für Bildung und Forschung (BMBF) http://dx.doi.org/10.13039/501100002347https://doi.org/10.18728/igb-fred-578.