Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Limnology and Oceanography 62 (2017): 1984–2003, doi:10.1002/lno.10547.Thaumarchaea are among the most abundant microbial groups in the ocean, but controls on their abundance and the distribution and metabolic potential of different subpopulations are poorly constrained. Here, two ecotypes of ammonia-oxidizing thaumarchaea were quantified using ammonia monooxygenase (amoA) genes across the equatorial Pacific Ocean. The shallow, or water column “A” (WCA), ecotype was the most abundant ecotype at the depths of maximum nitrification rates, and its abundance correlated with other biogeochemical indicators of remineralization such as NO3 : Si and total Hg. Metagenomes contained thaumarchaeal genes encoding for the catalytic subunit of the urease enzyme (ureC) at all depths, suggesting that members of both WCA and the deep, water column “B” (WCB) ecotypes may contain ureC. Coupled urea hydrolysis-ammonia oxidation rates were similar to ammonia oxidation rates alone, suggesting that urea could be an important source of ammonia for mesopelagic ammonia oxidizers. Potential inducement of metal limitation of both ammonia oxidation and urea hydrolysis was demonstrated via additions of a strong metal chelator. The water column inventory of WCA was correlated with the depth-integrated abundance of WCB, with both likely controlled by the flux of sinking particulate organic matter, providing strong evidence of vertical connectivity between the ecotypes. Further, depth-integrated amoA gene abundance and nitrification rates were correlated with particulate organic nitrogen flux measured by contemporaneously deployed sediment traps. Together, the results refine our understanding of the controls on thaumarchaeal distributions in the ocean, and provide new insights on the relationship between material flux and microbial communities in the mesopelagic.United States National Science Foundation (NSF) Grant Numbers: OCE-1260006, OCE-1031271, OCE-1337780, OCE-1259994; University of Maryland Center for Environmental Science (UMCES); JGI Community Sequencing Project 133

Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cohen, N. R., Noble, A. E., Moran, D. M., McIlvin, M. R., Goepfert, T. J., Hawco, N. J., German, C. R., Horner, T. J., Lamborg, C. H., McCrow, J. P., Allen, A. E., & Saito, M. A. Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean. Biogeosciences, 18(19), (2021): 5397–5422, https://doi.org/10.5194/bg-18-5397-2021.Bioactive trace metals are critical micronutrients for marine microorganisms due to their role in mediating biological redox reactions, and complex biogeochemical processes control their distributions. Hydrothermal vents may represent an important source of metals to microorganisms, especially those inhabiting low-iron waters, such as in the southwest Pacific Ocean. Previous measurements of primordial 3He indicate a significant hydrothermal source originating in the northeastern (NE) Lau Basin, with the plume advecting into the southwest Pacific Ocean at 1500–2000 m depth (Lupton et al., 2004). Studies investigating the long-range transport of trace metals associated with such dispersing plumes are rare, and the biogeochemical impacts on local microbial physiology have not yet been described. Here we quantified dissolved metals and assessed microbial metaproteomes across a transect spanning the tropical and equatorial Pacific with a focus on the hydrothermally active NE Lau Basin and report elevated iron and manganese concentrations across 441 km of the southwest Pacific. The most intense signal was detected near the Mangatolo Triple Junction (MTJ) and Northeast Lau Spreading Center (NELSC), in close proximity to the previously reported 3He signature. Protein content in distal-plume-influenced seawater, which was high in metals, was overall similar to background locations, though key prokaryotic proteins involved in metal and organic uptake, protein degradation, and chemoautotrophy were abundant compared to deep waters outside of the distal plume. Our results demonstrate that trace metals derived from the NE Lau Basin are transported over appreciable distances into the southwest Pacific Ocean and that bioactive chemical resources released from submarine vent systems are utilized by surrounding deep-sea microbes, influencing both their physiology and their contributions to ocean biogeochemical cycling.This research has been supported by the National Science Foundation (grant nos. 1031271, 1924554, 1850719, 1736599, and 1851007); the Gordon and Betty Moore Foundation (grant no. 3782); and the Simons Foundation (grant no. 544236)

Improved data acquisition efficiency for respiratory motion correction in coronary MRI

To investigate the performance of a novel algorithm for correcting respiratory-induced heart motion for whole-heart coronary MRI

Guiding neutral atoms around curves with lithographically patterned current-carrying wires

Laser-cooled neutral atoms from a low-velocity atomic source are guided via a magnetic field generated between two parallel wires on a glass substrate. The atoms bend around three curves, each with a 15-cm radius of curvature, while traveling along a 10-cm-long track. A maximum flux of 2*10^6 atoms/sec is achieved with a current density of 3*10^4 A/cm^2 in the 100x100-micrometer-cross-section wires. The kinetic energy of the guided atoms in one transverse dimension is measured to be 42 microKelvin.Comment: 9 page

Free-breathing late gadolinium enhancement CMR with a fixed short scan time using CosMo

To evaluate the performance of compressed sensing for motion correction (CosMo) [1] in compensating the respiratory motion of the heart in 3D late gadolinium enhancement (LGE) CMR

Basin-scale inputs of cobalt, iron, and manganese from the Benguela-Angola front to the South Atlantic Ocean

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2012. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 57 (2012): 989-1010, doi:10.4319/lo.2012.57.4.0989.We present full-depth zonal sections of total dissolved cobalt, iron, manganese, and labile cobalt from the South Atlantic Ocean. A basin-scale plume from the African coast appeared to be a major source of dissolved metals to this region, with high cobalt concentrations in the oxygen minimum zone of the Angola Dome and extending 2500 km into the subtropical gyre. Metal concentrations were elevated along the coastal shelf, likely due to reductive dissolution and resuspension of particulate matter. Linear relationships between cobalt, N2O, and O2, as well as low surface aluminum supported a coastal rather than atmospheric cobalt source. Lateral advection coupled with upwelling, biological uptake, and remineralization delivered these metals to the basin, as evident in two zonal transects with distinct physical processes that exhibited different metal distributions. Scavenging rates within the coastal plume differed for the three metals; iron was removed fastest, manganese removal was 2.5 times slower, and cobalt scavenging could not be discerned from water mass mixing. Because scavenging, biological utilization, and export constantly deplete the oceanic inventories of these three hybrid-type metals, point sources of the scale observed here likely serve as vital drivers of their oceanic cycles. Manganese concentrations were elevated in surface waters across the basin, likely due to coupled redox processes acting to concentrate the dissolved species there. These observations of basin-scale hybrid metal plumes combined with the recent projections of expanding oxygen minimum zones suggest a potential mechanism for effects on ocean primary production and nitrogen fixation via increases in trace metal source inputs.This research was supported US National Science Foundation Chemical Oceanography (Division of Ocean Sciences OCE-0452883, OCE-0752291, OCE-0928414, OCE-1031271), the Center for Microbial Research and Education, the Gordon and Betty Moore Foundation, the WHOI Coastal Ocean Institute, and the WHOI Ocean Life Institute

Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing

A precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures