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Ghost-dune hollows on the eastern Snake River Plain (ESRP), Idaho, USA, are topographically inverted, crescent-shaped depressions that record the partial encasement of sand dunes by ca. 61 ka basalt lava flows. Deflation of these “ghost” sand dunes produced approximately two dozen, 5–10-m-deep ghost-dune hollows now incompletely filled with pedogenically altered eolian and colluvial sediment. Optically stimulated luminescence (OSL) and 40Ar/39Ar ages constrain a ghost-dune hollow model that illuminates the late Pleistocene to Holocene environmental and climate history of the ESRP. Detrital zircon analyses indicate sand-dune supply routes changed following the burial of Pleistocene Henrys Fork (tributary of the Snake River) alluvium by ca. 70 ka basalt flows. Removal of Henrys Fork alluvium from the eolian supply system made Lake Terreton sediment the primary source for later ESRP sand dunes. Such sediment supply changes highlight the potential impacts of effusive volcanism on sand-dune histories and landscapes. Our results support stratigraphic and sedimentary modeling of comparable ghost-dune 舠pit舡 deposits older than ca. 2 Ga on Mars that may have served as refugia for early life on that planet. Analogous ancient ghost-dune hollow deposits on Earth may also have served as early life refugia.

Approximately 2 km2 of sand- and gravel-rich Pleistocene glacial-outburst megaflood sediment has accumulated in a series of five subparallel paleochannels that are an important component of a basalt-dominated aquifer system on the semiarid, ~450-km2 West Plains area. Located near Spokane, Washington (USA), the West Plains paleochannel deposits have been used for artificial storage and recovery wells and for planned and passive stormwater disposal in this rapidly growing area. Recent recognition of perfluorooctanoic acid contamination and excessive drawdowns have led to the closure of multiple municipal wells on the West Plains, highlighting the challenges of developing a sustainable groundwater supply in this complex aquifer system. Geologic and hydrogeologic data, from more than 1,400 water-well reports, surface exposures, existing groundwater geochemistry reports, and modeling, reveal the interconnections between the paleochannel deposits and surrounding basalt flows in three dimensions (3D). Initially incised into the Miocene Columbia River Basalt and excavated by Pleistocene glacial-outburst megaflooding, the West Plains paleochannels are projected in unprecedented 3D. This study’s modeled interactions between the more highly hydraulically conductive (100×) paleochannel sedimentary deposits and surrounding basalt beds provide insight into 14C ages and tritium values that had been measured previously. Sediment-filled closed depressions at the bases of the paleochannels, which are features likely formed by turbulent bursts (‘kolks’) during peak megaflood flows, are potentially promising groundwater storage sites. However, because of the relatively higher permeability of the unconfined paleochannel deposits, the closed depressions also are potential conduits for infiltration of contamination to deeper parts of the aquifer system.

Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and in regulating cellular processes. Investigation of marine microbial proteins by metaproteomics methods enables the discovery of numerous aspects of microbial biogeochemistry processes. However, these datasets present big-data challenges as they often involve many samples collected across broad geospatial and temporal scales, resulting in thousands of protein identifications, abundances, and corresponding annotation information. The Ocean Protein Portal (OPP) was created to enable data sharing and discovery among multiple scientific domains and serve both research and education functions. The portal focuses on three use case questions: “Where is my protein of interest?”, “Who makes it?”, and “How much is there?”, and provides profile and section visualizations, real-time taxonomic analysis, and links to metadata, sequence analysis, and other external resources to enabling connections to be made between biogeochemical and proteomics datasets.

We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the least common ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https://metatryp.whoi.edu). Major expansion of the marine METATRYP database with predicted proteomes from environmental sequencing confirms a low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed to facilitate ocean metaproteomics and has been integrated into the Ocean Protein Portal (https://oceanproteinportal.org); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal (https://metatryp-coronavirus.whoi.edu/) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa analyzed, sharing

We present METATRYP version-2 software that identifies shared peptides across organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include: ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the Least Common Ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https://metatryp.whoi.edu). Major expansion of the marine database confirms low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed for ocean metaproteomics and has been integrated into the Ocean Protein Portal (https://oceanproteinportal.org); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal (https://metatryp-coronavirus.whoi.edu/) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A Coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa, sharing 0.1% peptides or less (1 peptide) with the Influenza A & B pan-proteomes, establishing that taxonomic specificity is achievable using tryptic peptide-based proteomic diagnostic approaches.Statement of significanceWhen assigning taxonomic attribution in bottom-up metaproteomics, the potential for shared tryptic peptides among organisms in mixed communities should be considered. The software program METATRYP v 2 and associated interactive web portals enables users to identify the frequency of shared tryptic peptides among taxonomic groups and evaluate the occurrence of specific tryptic peptides within complex communities. METATRYP facilitates phyloproteomic studies of taxonomic groups and supports the identification and evaluation of potential metaproteomic biomarkers.

Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, colimitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries. Yet challenges remain for ocean metaproteomics due to the great biological diversity that produces highly complex mass spectra, as well as the difficulty in obtaining and working with environmental samples. This review summarizes the progress and challenges facing ocean metaproteomic scientists and proposes best practices for data sharing of ocean metaproteomic data sets, including the data types and metadata needed to enable intercomparisons of protein distributions and annotations that could foster global ocean metaproteomic capabilities.

The St. Anthony Dune Field (SADF) is a ~300 km2 expanse of active to stabilized transverse, barchan, barchanoid, and parabolic sand dunes located in a semi-arid climate in southeastern Idaho. The northeastern portion of the SADF, ~16 km2, was investigated to examine meteorological influences on dune mobility. Understanding meteorological predictors of sand-dune migration for the SADF informs landscape evolution and impacts assessment of eolian activity on sensitive agricultural lands in the western United States, with implications for semi-arid environments globally. Archival aerial photos from 1954 to 2011 were used to calculate dune migration rates which were subsequently compared to regional meteorological data, including temperature, precipitation and wind speed. Observational analyses based on aerial photo imagery and meteorological data indicate that dune migration is influenced by weather for up to 5–10 years and therefore decadal weather patterns should be taken into account when using dune migration rates as proxies from climate fluctuation. Statistical examination of meteorological variables in this study indicates that 24% of the variation of sand dune migration rates is attributed to temperature, precipitation and wind speed, which is increased to 45% when incorporating lag time.

The Kulshan caldera formed at ∼1.15 Ma on the present-day site of Mt. Baker, Washington State, northwest USA and erupted a compositionally zoned (dacite-rhyolite) magma and a correlative eruptive, the Lake Tapps tephra. This tephra has previously been described, but only from the Puget Lowland of NW Washington. Here an occurrence of a Kulshan caldera correlative tephra is described from the Quaternary Palouse loess at the Washtucna site (WA-3). Site WA-3 is located in east-central Washington, ∼340 km southeast of the Kulshan caldera and ∼300 km east-southeast of the Lake Tapps occurrence in the Puget Lowland. Major- and trace element chemistry and location of the deposit at Washtucna within reversed polarity sediments indicates that it is not correlative with the Mesa Falls, Rockland, Bishop Ash, Lava Creek B or Huckleberry Ridge tephras. Instead the Washtucna deposit is related to the Lake Tapps tephra by fractional crystallisation, but is chemically distinct, a consequence of its eruption from a compositionally zoned magma chamber. The correlation of the Washtucna occurrence to the Kulshan caldera-forming eruption indicates that it had an eruptive volume exceeding 100 km3, and that its tephra could provide a valuable early-Pleistocene chronostratigraphic marker in the Pacific Northwest.