Biogeochemical and historical drivers of microbial community composition and structure in sediments from Mercer Subglacial Lake, West Antarctica

Ice streams that flow into Ross Ice Shelf are underlain by water-saturated sediments, a dynamic hydrological system, and subglacial lakes that intermittently discharge water downstream across grounding zones of West Antarctic Ice Sheet (WAIS). A 2.06 m composite sediment profile was recently recovered from Mercer Subglacial Lake, a 15 m deep water cavity beneath a 1087 m thick portion of the Mercer Ice Stream. We examined microbial abundances, used 16S rRNA gene amplicon sequencing to assess community structures, and characterized extracellular polymeric substances (EPS) associated with distinct lithologic units in the sediments. Bacterial and archaeal communities in the surficial sediments are more abundant and diverse, with significantly different compositions from those found deeper in the sediment column. The most abundant taxa are related to chemolithoautotrophs capable of oxidizing reduced nitrogen, sulfur, and iron compounds with oxygen, nitrate, or iron. Concentrations of dissolved methane and total organic carbon together with water content in the sediments are the strongest predictors of taxon and community composition. δ¹³C values for EPS (−25 to −30‰) are consistent with the primary source of carbon for biosynthesis originating from legacy marine organic matter. Comparison of communities to those in lake sediments under an adjacent ice stream (Whillans Subglacial Lake) and near its grounding zone provide seminal evidence for a subglacial metacommunity that is biogeochemically and evolutionarily linked through ice sheet dynamics and the transport of microbes, water, and sediments beneath WAIS

A method for successful collection of multicores and gravity cores from Antarctic subglacial lakes

During the 2018–2019 Antarctic field season, the Subglacial Antarctic Lakes Scientific Access project team cleanly accessed Mercer Subglacial Lake, West Antarctica, to sample water and sediments beneath 1087 m of overlying ice. A multicorer was successful in sampling the sediment–water interface, with 4 deployments retrieving 10 cores between 0.3 and 0.4 m in length. Gravity coring was also successful, retrieving cores of 0.97 and 1.78 m in glacial diamict. However, sediment cores retrieved by the gravity cores were shorter than the core barrel penetration (as measured by mud streaks on the outside of the coring system), indicating that the system can likely be improved. This manuscript describes the design, implementation, successes, and lessons learned while coring sediments in a subglacial lake

Constraints on the Timing and Extent of Deglacial Grounding Line Retreat in West Antarctica

Projections of Antarctica\u27s contribution to future sea level rise are associated with significant uncertainty, in part because the observational record is too short to capture long-term processes necessary to estimate ice mass changes over societally relevant timescales. Records of grounding line retreat from the geologic past offer an opportunity to extend our observations of these processes beyond the modern record and to gain a more comprehensive understanding of ice-sheet change. Here, we present constraints on the timing and inland extent of deglacial grounding line retreat in the southern Ross Sea, Antarctica, obtained via direct sampling of a subglacial lake located 150 km inland from the modern grounding line and beneath \u3e1 km of ice. Isotopic measurements of water and sediment from the lake enabled us to evaluate how the subglacial microbial community accessed radiocarbon-bearing organic carbon for energy, as well as where it transferred carbon metabolically. Using radiocarbon as a natural tracer, we found that sedimentary organic carbon was microbially translocated to dissolved carbon pools in the subglacial hydrologic system during the 4.5-year period of water accumulation prior to our sampling. This finding indicates that the grounding line along the Siple Coast of West Antarctica retreated more than 250 km inland during the mid-Holocene (6.3 ± 1.0 ka), prior to re-advancing to its modern position

New 10Be exposure ages improve Holocene ice sheet thinning history near the grounding line of Pope Glacier, Antarctica

Evidence for the timing and pace of past grounding line retreat of the Thwaites Glacier system in the Amundsen Sea embayment (ASE) of Antarctica provides constraints for models that are used to predict the future trajectory of the West Antarctic Ice Sheet (WAIS). Existing cosmogenic nuclide surface exposure ages suggest that Pope Glacier, a former tributary of Thwaites Glacier, experienced rapid thinning in the early to mid-Holocene. There are relatively few exposure ages from the lower ice-free sections of Mt. Murphy (<300 m a.s.l.; metres above sea level) that are uncomplicated by either nuclide inheritance or scatter due to localised topographic complexities; this makes the trajectory for the latter stages of deglaciation uncertain. This paper presents 12 new 10Be exposure ages from erratic cobbles collected from the western flank of Mt. Murphy, within 160 m of the modern ice surface and 1 km from the present grounding line. The ages comprise two tightly clustered populations with mean deglaciation ages of 7.1 ± 0.1 and 6.4 ± 0.1 ka (1 SE). Linear regression analysis applied to the age–elevation array of all available exposure ages from Mt. Murphy indicates that the median rate of thinning of Pope Glacier was 0.27 m yr−1 between 8.1–6.3 ka, occurring 1.5 times faster than previously thought. Furthermore, this analysis better constrains the uncertainty (95 % confidence interval) in the timing of deglaciation at the base of the Mt. Murphy vertical profile (∼ 80 m above the modern ice surface), shifting it to earlier in the Holocene (from 5.2 ± 0.7 to 6.3 ± 0.4 ka). Taken together, the results presented here suggest that early- to mid-Holocene thinning of Pope Glacier occurred over a shorter interval than previously assumed and permit a longer duration over which subsequent late Holocene re-thickening could have occurred

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

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Investigating the Recent History of a Changing Planet with Innovative Isotopic Techniques and New Geologic Archives

Globally averaged Earth surface temperatures indicate a 0.8°C warming since 1880. Though this warming is a result of anthropogenic influence that has exceeded natural forcings, a thorough understanding of Earth\u27s climate system requires a knowledge of changes in global temperatures beyond the instrumental record. To achieve this, we must supplement the temporally limited observational record with proxy records of environmental conditions in the geologic past. Though the foundational questions underlying interrogations of the geologic past are seemingly simple (What happened? When?), the accuracy of their answers depend upon accessibility and availability of geologic materials as well as the capabilities of proxies applied to those materials. Because uncertainties in proxy reconstructions can propagate into projections of future conditions, it is important that we continuously work to expand the utility of geologic archives and the capabilities of proxies and preparatory techniques we apply to them. In this dissertation, I utilize the seldomly accessed sub-ice (subglacial and grounding-line-proximal) sediment record to address questions surrounding the deglacial history of the Ross Sea Embayment, Antarctica. I optimize ramped pyrolysis preparation of acid insoluble organic material in these sediments to assess the timing of past grounding line retreat, and use isotopic (Δ14C, δ¹³C) data to assess the origin, age, and cycling of carbon beneath the West Antarctic Ice Sheet. I demonstrate the utility of sub-ice archives for deglacial paleoglaciological reconstructions by investigating how Holocene-aged carbon is translocated to subglacial sediments. In the interest of addressing questions about past climate, I also present improvements to the mass spectrometry of multiply substituted isotopologues of CO2 (clumped isotopes; Δ47), a promising new isotopic paleothermometer

Investigating the Recent History of a Changing Planet with Innovative Isotopic Techniques and New Geologic Archives

Globally averaged Earth surface temperatures indicate a 0.8°C warming since 1880. Though this warming is a result of anthropogenic influence that has exceeded natural forcings, a thorough understanding of Earth\u27s climate system requires a knowledge of changes in global temperatures beyond the instrumental record. To achieve this, we must supplement the temporally limited observational record with proxy records of environmental conditions in the geologic past. Though the foundational questions underlying interrogations of the geologic past are seemingly simple (What happened? When?), the accuracy of their answers depend upon accessibility and availability of geologic materials as well as the capabilities of proxies applied to those materials. Because uncertainties in proxy reconstructions can propagate into projections of future conditions, it is important that we continuously work to expand the utility of geologic archives and the capabilities of proxies and preparatory techniques we apply to them. In this dissertation, I utilize the seldomly accessed sub-ice (subglacial and grounding-line-proximal) sediment record to address questions surrounding the deglacial history of the Ross Sea Embayment, Antarctica. I optimize ramped pyrolysis preparation of acid insoluble organic material in these sediments to assess the timing of past grounding line retreat, and use isotopic (Δ14C, δ¹³C) data to assess the origin, age, and cycling of carbon beneath the West Antarctic Ice Sheet. I demonstrate the utility of sub-ice archives for deglacial paleoglaciological reconstructions by investigating how Holocene-aged carbon is translocated to subglacial sediments. In the interest of addressing questions about past climate, I also present improvements to the mass spectrometry of multiply substituted isotopologues of CO2 (clumped isotopes; Δ47), a promising new isotopic paleothermometer