Seasonal changes in microbial community structure and activity imply winter production is linked to summer hypoxia in a large lake

Carbon and nutrient cycles in large temperate lakes such as Lake Erie are primarily driven by phototrophic and heterotrophic microorganisms, although our understanding of these is often constrained to late spring through summer due to logistical constraints. During periods of \u3e 90% ice cover in February of 2008, 2009, and 2010, we collected samples from an icebreaker for an examination of bacterial production as well as microbial community structure. In comparison with summer months (August 2002 and 2010), we tested hypotheses concerning seasonal changes in microbial community diversity and production. Bacterial production estimates were c. 2 orders of magnitude higher (volume normalized) in summer relative to winter. Our observations further demonstrate that the microbial community, including single-celled phototrophs, varied in composition between August and February. Sediment traps deployed and collected over a 3 year period (2008-2011) confirmed that carbon export was ongoing and not limiting winter production. The results support the notion that active primary producers in winter months export carbon to the sediments that is not consumed until the warmer seasons. The establishment of this linkage is a critical observation in efforts to understand the extent and severity of annual summertime formations of a zone of regional hypoxia in Lake Erie. Seasonal changes in microbial community productivity and diversity suggest primary production in winter months may exacerbate summer hypoxia in Lake Eri. © 2014 Federation of European Microbiological Societies

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Construction and initial characterization of a luminescent Synechococcus sp. PCC 7942 Fe-dependent bioreporter

A Synechococcus sp. PCC 7942 bioreporter strain capable of sensing bioavailable Fe was constructed by fusing the Fe-responsive isiAB promoter to the Vibrio harveyi luxAB genes. Monitoring luxAB-dependent luminescence through the growth curve demonstrated that in Fe-replete media, transcription from the isiAB promoter was induced transiently in the mid-exponential phase of growth. The initiation of transcription was the functional response to a 10-fold depletion of intracellular Fe to ∼12 amol Fe per cell. Constitutive isiAB-dependent transcription was observed in Fe-depleted growth media. A dose-response relationship of the bioreporter was generated using trace metal-buffered Fraquil medium and was best represented by a sigmoidal curve having a linear component extending between pFe 21.1 (Fe3+=10-21.1 M) and pFe 20.6 (Fe3+=10-20.6 M). Initial field trials conducted using water sampled from Lake Erie demonstrate that the bioreporter can serve as a quantitative tool to assess Fe deficiency in natural freshwater environments. © 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved

An evaluation of iron bioavailability and speciation in western Lake Superior with the use of combined physical, chemical, and biological assessment

An iron-dependent cyanobacterial bioreporter (Synechococcus strain KAS101) was used in unison with size-fractionated iron content (>0.45, <0.45, <0.02 µm), and chemical characterization of iron complexation (C18 resin column) to elucidate the bioavailable forms of iron present in Lake Superior during periods of inverse thermal stratification (May) and strong thermal stratification (September) of the water column. The results provide evidence of organic complexation of iron in Lake Superior waters. Iron in most sampled water was complexed by organic compounds that behaved like fulvic acids, whereas some samples showed evidence for the presence of siderophore-like compounds. The presence of dissolved organic matter suppressed the cellular luminescence of the bioreporter, indicating an increased iron bioavailability. This effect could result either from the presence of siderophores forming iron complexes that are bioavailable to the bioreporter, or from more indirect effects because of the presence of other organic compounds, such as fulvic acids or polysaccharides. Model ligand additions, iron bioaccumulation, and photo-oxidation of dissolved organic matter were used to assess the bioavailability of organically complexed iron to the bioreporter. A significant fraction of the iron (40–100%) was bioavailable to the bioreporter. Iron bioavailability was high enough for the bioreporter not to be iron limited in the water collected from Lake Superior. This measure of bioavailability to picocyanobacteria is relevant because picoplankton accounted for the majority of chlorophyll a in Lake Superior during this study

Determination of bioavailable Fe in Lake Erie using a luminescent cyanobacterial bioreporter

Low Fe bioavailability has been suggested as a potential constraint on primary production In the Great Lakes. Here we report on the use of a cyanobacterlal bioreporter to assess available Fe In Lake Erie during summer and fall field seasons In 2001-02. Bioreporter luminescence was derived from a luclferase reporter controlled by Iron-responsive promoter element isiAB. Filtered (\u3c 0.2 μm) water sampled from the western basin during summer 2001-02 yielded low bioreporter response indicating Fe sufficient conditions [-log [free Fe3+] (pFe) \u3c 20.8]. Likewise, water collected from the eastern basin following autumnal mixing in November 2001 yielded a Fe sufficient bioreporter response. In contrast, surface water collected at pelagic stations located In central and eastern basins during summer 2002 indicated a seasonal depletion of bioavailable Fe. Whereas water sampled from these locations during July and August was characterized as Fe sufficient (pFe \u3c 20.8), samples collected during September elicited a high luminescent response from the bioreporter (pFe \u3e 21). Contrary to the characterization provided by the filtered samples, assay of bioreporter response in unfiltered water conducted during the September 2002 cruise indicated these samples to be Fe sufficient (pFe \u3c 20.6). Although this suggests that the dominant pool of bioavailable Fe is contained in the particulate fraction, we cannot discount the possibility that the bioreporter was rendered Fe sufficient by Fe regenerated predominantly from blore-porter cells themselves. Thus, while it is clear that regenerative processes contribute to the pool of bioavailable Fe, it is equally clear that future efforts using the bioreporter with unfiltered water samples must account for the potential influence of Fe introduced by the added reporter cells

Physiological characterization of a Synechococcus sp. (Cyanophyceae) strain PCC 7942 iron-dependent bioreporter for freshwater environments

The complex chemical speciation of Fe in aquatic systems and the uncertainties associated with biological assimilation of Fe species make it difficult to assess the bioavailability of Fe to phytoplankton in relation to total dissolved Fe concentrations in natural waters. We developed a cyanobacterial Fe-responsive bioreporter constructed in Synechococcus sp. strain PCC 7942 by fusing the Fe-responsive isiAB promoter to Vibrio harveyi luxAB reporter genes. A comprehensive physiological characterization of the bioreporter has been made in defined Fraquil medium at free ferric ion concentrations ranging from pFe 21.6 to pFe 19.5. Whereas growth and physiological parameters are largely constrained over this range of Fe bioavailability, the bioreporter elicits a luminescent signal that varies in response to Fe deficiency. A dose-response characterization of bioreporter luminescence made over this range of Fe3+ bioavailability demonstrates a sigmoidal response with a dynamic linear range extending between pFe 21.1 and pFe 20.6. The applicability of using this Fe bioreporter to assess Fe availability in the natural environment has been tested using water samples from Lake Huron (Laurentian Great Lakes). Parallel assessment of dissolved Fe and bioreporter response from these samples reinforces the idea that measures of dissolved Fe should not be considered alone when assessing Fe availability to phytoplankton communities

Consideration of the bioavailability of iron in the North American Great Lakes: Development of novel approaches toward understanding iron biogeochemistry

There is increasing recognition that iron distribution and availability is significant in terms of global oceanic production. Low availability of iron and other nutritive trace metals may also constrain productivity in the North American Great Lakes. Despite its importance, the biogeochemistry of iron in the water column of lacustrine systems remains poorly characterized. In addressing the current state of iron biogeochemistry, a workshop organized a decade ago at the Bermuda Biological Station for Research brought together a cross-disciplinary team of chemists and biologists who sought to synthesize current knowledge and identify research priorities in this field. Key among goals identified during the workshop, and one that remains today for the most part unfulfilled, was to \u27develop techniques to quantify those fractions of Fe that are accessible to phytoplankton.\u27 Here we review recent progress toward meeting this objective, drawing on specific examples from Lake Superior where these approaches have been applied