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Geochemical analyses of sedimentary barites (barium sulfates) in the geological record have yielded fundamental insights into the chemistry of the Archean environment and evolutionary origin of microbial metabolisms. However, the question of how barites were able to precipitate from a contemporary ocean that contained only trace amounts of sulfate remains controversial. Here we report dissolved and particulate multi-element and barium-isotopic data from Lake Superior that evidence pelagic barite precipitation at micromolar ambient sulfate. These pelagic barites likely precipitate within particle-associated microenvironments supplied with additional barium and sulfate ions derived from heterotrophic remineralization of organic matter. If active during the Archean, pelagic precipitation and subsequent sedimentation may account for the genesis of enigmatic barite deposits. Indeed, barium-isotopic analyses of barites from the Paleoarchean Dresser Formation are consistent with a pelagic mechanism of precipitation, which altogether offers a new paradigm for interpreting the temporal occurrence of barites in the geological record. The question of how significant barite deposits were able to form from early Earth’s low-sulfate seas remains controversial. Here, the authors show pelagic barite precipitation within a strongly barite-undersaturated ecosystem, highlighting the importance of particle-associated microenvironments.

Unicellular nitrogen fixer Crocosphaera contributes substantially to nitrogen fixation in oligotrophic subtropical gyres. They fix nitrogen even when significant amounts of ammonium are available. This has been puzzling since fixing nitrogen is energetically inefficient compared with using available ammonium. Here we show that by fixing nitrogen, Crocosphaera can increase their population and expand their niche despite the presence of ammonium. We have developed a simple but mechanistic model of Crocosphaera based on their growth in steady state culture. The model shows that the growth of Crocosphaera can become nitrogen limited despite their capability to fix nitrogen. When they fix nitrogen, the population increases by up to 78% relative to the case without nitrogen fixation. When we simulate a simple ecological situation where Crocosphaera exists with non-nitrogen-fixing phytoplankton, the relative abundance of Crocosphaera increases with nitrogen fixation, while the population of non-nitrogen-fixing phytoplankton decreases since a larger fraction of fixed nitrogen is consumed by Crocosphaera . Our study quantitatively supports the benefit of nitrogen fixation despite the high electron/energy costs, even when an energetically efficient alternative is available. It demonstrates a competitive aspect of Crocosphaera , permitting them to be regionally significant nitrogen fixers.

Whole-genome sequencing of Plasmodium is becoming an increasingly important tool for genomic surveillance of malaria. Due to the predominance of human DNA in a patient blood sample, time-consuming laboratory procedures are required to deplete human DNA or enrich Plasmodium DNA. Here, we investigated the potential of nanopore adaptive sampling to enrich Plasmodium falciparum reads while sequencing unenriched patient blood samples. To compare adaptive sampling versus regular sequencing on a MinION device, a dilution series consisting of 0%–84% P . falciparum DNA in human DNA was sequenced. Half of the flow cell channels were run in adaptive sampling mode, enriching for the P. falciparum reference genome, resulting in a three- to five-fold enrichment of P. falciparum bases in samples containing 0.1%–8.4% P. falciparum DNA. This finding was confirmed by sequencing three P. falciparum patient blood samples with common levels of parasitemia, that is, 0.1%, 0.2%, and 0.6% in adaptive mode. Their estimated enrichment was 5.8, 3.9, and 2.7, respectively, which was sufficient to cover at least 97% of the P. falciparum reference genome at a median depth of 5 (lowest parasitemia) or 355 (highest parasitemia). In all, 38 drug resistance loci were compared to Sanger sequencing results, showing high concordance, which suggests that the obtained sequencing data are of sufficient quality to address common clinical research questions for patients with parasitemias of 0.1% and higher. Overall, our results indicate that adaptive nanopore sequencing has the potential to replace more time-consuming Plasmodium enrichment protocols in the future. Malaria is caused by parasites of the genus Plasmodium , and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich Plasmodium DNA. We used the Oxford Nanopore Technologies’ adaptive sampling feature to circumvent this problem and enrich Plasmodium reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches Plasmodium reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.

Elective transjugular intrahepatic portosystemic shunt (TIPS) placement can worsen cognitive dysfunction in hepatic encephalopathy (HE) patients due to toxins, including possible microbial metabolites, entering the systemic circulation. We conducted untargeted metabolomics on a prospective cohort of 22 patients with cirrhosis undergoing elective TIPS placement and followed them up to one year post TIPS for HE development. Here we suggest that pre-existing intrahepatic shunting predicts HE severity post-TIPS. Bile acid levels decrease in the peripheral vein post-TIPS, and the abundances of three specific conjugated di- and tri-hydroxylated bile acids are inversely correlated with HE grade. Bilirubins and glycerophosphocholines undergo chemical modifications pre- to post-TIPS and based on HE grade. Our results suggest that TIPS-induced metabolome changes can impact HE development, and that pre-existing intrahepatic shunting could be used to predict HE severity post-TIPS. Patients with liver disease undergoing transjugular intrahepatic portosystemic shunt (TIPS) are at a higher risk of hepatic encephalopathy (HE). Here, the authors show intrahepatic shunting and specific metabolites, especially bile acids, as potential biomarkers and treatment targets for HE.

There is a growing interest in unraveling the chemical complexity of our diets. To help the scientific community gain insight into the molecules present in foods and beverages that we ingest, we created foodMASST, a search tool for MS/MS spectra (of both known and unknown molecules) against a growing metabolomics food and beverage reference database. We envision foodMASST will become valuable for nutrition research and to assess the potential uniqueness of dietary biomarkers to represent specific foods or food classes.

Human milk is the optimal infant nutrition. However, although human‐derived metabolites (such as lipids and oligosaccharides) in human milk are regularly reported, the presence of exogenous chemicals (such as drugs, food, and synthetic compounds) are often not addressed. To understand the types of exogenous compounds that might be present, human milk (n = 996) was analyzed by untargeted metabolomics. This analysis revealed that lifestyle molecules, such as medications and their metabolites, and industrial sources, such as plasticizers, cosmetics, and other personal care products, are found in human milk. We provide further evidence that some of these lifestyle molecules are also detectable in the newborn's stool. Thus, this study gives important insight into the types of exposures infants receiving human milk might ingest due to the lifestyle choices, exposure, or medical status of the lactating parent.

Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research. Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality—including ordination integration and animations—alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of ‘omic data. IMPORTANCE Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research. The ever-growing scale of modern microbiome surveys has led to numerous challenges in visualizing these data. In this paper we used five diverse data sets to showcase the versatility and scalability of EMPress, an interactive web visualization tool. EMPress addresses the growing need for exploratory analysis tools that can accommodate large, complex multi-omic data sets.

Characterization of dissolved organic matter in terms of its composition and optical properties, with an eye toward ultimately understanding its deep ocean dynamics, is the currently active frontier in DOM research. We used UV-visible absorption spectroscopy and fluorescence excitation-emission matrix (EEM) spectroscopy to characterize dissolved organic matter in the open ocean along sections of the U.S. CO2/CLIVAR Repeat Hydrography Project located in all the major ocean basins outside the Arctic. Despite large differences in fluorescence intensity between ocean basins, some variability patterns were similar throughout the global ocean, suggesting similar processes controlling the composition of the DOM. We find that commercially available single channel CDOM sensors are sensitive to the fluorescence of humic materials in the deep ocean and thermocline but not to the UVA-fluorescing and absorbing materials that characterize freshly produced CDOM in surface waters, revealing fundamental diversity in the DOM profile. In surface waters, UVA fluorescence and absorption signatures indicate the presence of freshly produced material and the process of bleaching removal, but in the upper mesopelagic and in the main thermocline these optical signatures are replaced by those of humic materials, with distribution patterns correlated to apparent oxygen utilization and other signatures of remineralization. Empirical orthogonal analysis (EOF) of the EEM data suggests the presence of two (unidentified) processes which convert “fresh” DOM to humic materials: one located in the surface ocean (shallower than 500m) and one located in the main thermocline. These hypothetical humification processes represent less than 5% of the overall variability in oceanic humic DOM fluorescence, which appears to be dominated by terrestrial input and solar bleaching of humic materials.

Crocosphaera is one of the major N 2 -fixing microorganisms in the open ocean. On a global scale, the process of N 2 fixation is important in balancing the N budget, but the factors governing the rate of N 2 fixation remain poorly resolved. Here, we combine a mechanistic model and both previous and present laboratory studies of Crocosphaera to quantify how chemical factors such as C, N, Fe, and O 2 and physical factors such as temperature and light affect N 2 fixation. Our study shows that Crocosphaera combines multiple mechanisms to reduce intracellular O 2 to protect the O 2 -sensitive N 2 -fixing enzyme. Our model, however, indicates that these protections are insufficient at low temperature due to reduced respiration and the rate of N 2 fixation becomes severely limited. This provides a physiological explanation for why the geographic distribution of Crocosphaera is confined to the warm low-latitude ocean. Crocosphaera is a major dinitrogen (N 2 )-fixing microorganism, providing bioavailable nitrogen (N) to marine ecosystems. The N 2 -fixing enzyme nitrogenase is deactivated by oxygen (O 2 ), which is abundant in marine environments. Using a cellular scale model of Crocosphaera sp. and laboratory data, we quantify the role of three O 2 management strategies by Crocosphaera sp.: size adjustment, reduced O 2 diffusivity, and respiratory protection. Our model predicts that Crocosphaera cells increase their size under high O 2 . Using transmission electron microscopy, we show that starch granules and thylakoid membranes are located near the cytoplasmic membranes, forming a barrier for O 2 . The model indicates a critical role for respiration in protecting the rate of N 2 fixation. Moreover, the rise in respiration rates and the decline in ambient O 2 with temperature strengthen this mechanism in warmer water, providing a physiological rationale for the observed niche of Crocosphaera at temperatures exceeding 20°C. Our new measurements of the sensitivity to light intensity show that the rate of N 2 fixation reaches saturation at a lower light intensity (∼100 μmol m −2 s −1 ) than photosynthesis and that both are similarly inhibited by light intensities of >500 μmol m −2 s −1 . This suggests an explanation for the maximum population of Crocosphaera occurring slightly below the ocean surface. IMPORTANCE Crocosphaera is one of the major N 2 -fixing microorganisms in the open ocean. On a global scale, the process of N 2 fixation is important in balancing the N budget, but the factors governing the rate of N 2 fixation remain poorly resolved. Here, we combine a mechanistic model and both previous and present laboratory studies of Crocosphaera to quantify how chemical factors such as C, N, Fe, and O 2 and physical factors such as temperature and light affect N 2 fixation. Our study shows that Crocosphaera combines multiple mechanisms to reduce intracellular O 2 to protect the O 2 -sensitive N 2 -fixing enzyme. Our model, however, indicates that these protections are insufficient at low temperature due to reduced respiration and the rate of N 2 fixation becomes severely limited. This provides a physiological explanation for why the geographic distribution of Crocosphaera is confined to the warm low-latitude ocean.

The original version of this Article contained an error in the barite saturation state equation in the fourth paragraph of the Introduction and incorrectly read ‘Ω barite =({ 134 Ba 2+ }⋅{SO 4 2− })/ K sp )’. The correct version removes the superscript 134 next to ‘Ba 2+ ’. This error has now been corrected in both the PDF and HTML versions of the Article.