Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection.

Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity

Nondestructive Analysis of Astromaterials by Micro-CT and Micro-XRF Analysis for PET Examination

An integral part of any sample return mission is the initial description and classification of returned samples by the preliminary examination team (PET). The goal of the PET is to characterize and classify returned samples and make this information available to the larger research community who then conduct more in-depth studies on the samples. The PET tries to minimize the impact their work has on the sample suite, which has in the past limited the PET work to largely visual, nonquantitative measurements (e.g., optical microscopy). More modern techniques can also be utilized by a PET to nondestructively characterize astromaterials in much more rigorous way. Here we discuss our recent investigations into the applications of micro-CT and micro-XRF analyses with Apollo samples and ANSMET meteorites and assess the usefulness of these techniques in future PET. Results: The application of micro computerized tomography (micro-CT) to astromaterials is not a new concept. The technique involves scanning samples with high-energy x-rays and constructing 3-dimensional images of the density of materials within the sample. The technique can routinely measure large samples (up to approx. 2700 cu cm) with a small individual voxel size (approx. 30 cu m), and has the sensitivity to distinguish the major rock forming minerals and identify clast populations within brecciated samples. We have recently run a test sample of a terrestrial breccia with a carbonate matrix and multiple igneous clast lithologies. The test results are promising and we will soon analyze a approx. 600 g piece of Apollo sample 14321 to map out the clast population within the sample. Benchtop micro x-ray fluorescence (micro-XRF) instruments can rapidly scan large areas (approx. 100 sq cm) with a small pixel size (approx. 25 microns) and measure the (semi) quantitative composition of largely unprepared surfaces for all elements between Be and U, often with sensitivity on the order of a approx. 100 ppm. Our recent testing of meteorite and Apollo samples on micro-XRF instruments has shown that they can easily detect small zircons and phosphates (approx. 10 m), distinguish different clast lithologies within breccias, and identify different lithologies within small rock fragments (2-4 mm soil Apollo soil fragments)

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments

Theoretical Study of Electronic Structure and Superconductivity in Nb_(1-x)B_2 Alloys

Using the Korringa-Kohn-Rostoker coherent-potential approximation in the atomic-sphere approximation (KKR-ASA CPA) we have studied the changes in the electronic structure and the superconducting transition temperature T_{c} in Nb_{1-x}B_{2} alloys as a function of x. We find that the variation in the electronic structure of Nb_{1-x}B_{2} alloys as a function of x is consistent with the rigid-band model. However, the variation of T_{c}, obtained using the Allen-Dynes equation within the Gaspari-Gyorffy formalism to estimate the electron-phonon matrix elements, does not follow the expected trend. We associate this disagreement to the use of a constant \omega_{rms} in the Allen-Dynes equation over the whole range of vacancy concentration, thereby indicating the importance of lattice dynamical effects in these systems.Comment: 10 pages, 4 figure

Draft genome sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph isolated from a deep-sea hydrothermal vent

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Skoog, E. J., Huber, J. A., Serres, M. H., Levesque, A., & Zeigler Allen, L. Draft genome sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph isolated from a deep-sea hydrothermal vent. Microbiology Resource Announcements, 10(34), (2021): e0061521, https://doi.org/10.1128/MRA.00615-21.A thermophilic chemolithoautotrophic bacterium was isolated from vent fluids at Axial Seamount, an active deep-sea volcano in the northeast Pacific Ocean. We present the draft genome sequence of Desulfurobacterium sp. strain AV08.This research was supported by the National Aeronautics and Space Administration Exobiology Program (grant 80NSSC18K1076 to L.Z.A. and J.A.H.). This study was also partially supported by the NSF Center for Dark Energy Biosphere Investigations (C-DEBI) (grant OCE-0939564 to J.A.H.)

Nitrogen and Iron Availability Drive Metabolic Remodeling and Natural Selection of Diverse Phytoplankton during Experimental Upwelling

Nearly half of carbon fixation and primary production originates from marine phytoplankton, and much of it occurs in episodic blooms in upwelling regimes. Here, we simulated blooms limited by nitrogen and iron by incubating Monterey Bay surface waters with subnutricline waters and inorganic nutrients and measured the wholecommunity transcriptomic response during mid- and late-bloom conditions. Cell counts revealed that centric and pennate diatoms (largely Pseudo-nitzschia and Chaetoceros spp.) were the major blooming taxa, but dinoflagellates, prasinophytes, and prymnesiophytes also increased. Viral mRNA significantly increased in late bloom and likely played a role in the bloom\u27s demise. We observed conserved shifts in the genetic similarity of phytoplankton populations to cultivated strains, indicating adaptive population-level changes in community composition. Additionally, the density of single nucleotide variants (SNVs) declined in late-bloom samples for most taxa, indicating a loss of intraspecific diversity as a result of competition and a selective sweep of adaptive alleles. We noted differences between mid- and late-bloom metabolism and differential regulation of light-harvesting complexes (LHCs) under nutrient stress. While most LHCs are diminished under nutrient stress, we showed that diverse taxa upregulated specialized, energy-dissipating LHCs in low iron. We also suggest the relative expression of NRT2 compared to the expression of GSII as a marker of cellular nitrogen status and the relative expression of iron starvationinduced protein genes (ISIP1, ISIP2, and ISIP3) compared to the expression of the thiamine biosynthesis gene (thiC) as a marker of iron status in natural diatom communities

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection

Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity

Reconstruction of a Bacterial Genome from DNA Cassettes

This basic research program comprised two major areas: (1) acquisition and analysis of marine microbial metagenomic data and development of genomic analysis tools for broad, external community use; (2) development of a minimal bacterial genome. Our Marine Metagenomic Diversity effort generated and analyzed shotgun sequencing data from microbial communities sampled from over 250 sites around the world. About 40% of the 26 Gbp of sequence data has been made publicly available to date with a complete release anticipated in six months. Our results and those mining the deposited data have revealed a vast diversity of genes coding for critical metabolic processes whose phylogenetic and geographic distributions will enable a deeper understanding of carbon and nutrient cycling, microbial ecology, and rapid rate evolutionary processes such as horizontal gene transfer by viruses and plasmids. A global assembly of the generated dataset resulted in a massive set (5Gbp) of genome fragments that provide context to the majority of the generated data that originated from uncultivated organisms. Our Synthetic Biology team has made significant progress towards the goal of synthesizing a minimal mycoplasma genome that will have all of the machinery for independent life. This project, once completed, will provide fundamentally new knowledge about requirements for microbial life and help to lay a basic research foundation for developing microbiological approaches to bioenergy

Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fortunato, C. S., Butterfield, D. A., Larson, B., Lawrence-Slavas, N., Algar, C. K., Zeigler Allen, L., Holden, J. F., Proskurowski, G., Reddington, E., Stewart, L. C., Topçuoğlu, B. D., Vallino, J. J., & Huber, J. A. Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities. Applied and Environmental Microbiology, 87, (2021): e00078-21, https://doi.org/10.1128/AEM.00078-21Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean.This work was funded by Gordon and Betty Moore Foundation grant GBMF3297; the NSF Center for Dark Energy Biosphere Investigations (C-DEBI) (OCE-0939564), contribution number 562; NOAA/PMEL, contribution number 5182; and the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA cooperative agreement NA15OAR4320063, contribution number 2020-1113. The RNA-SIP methodology used in this work was developed during cruise FK010-2013 aboard the R/V Falkor supported by the Schmidt Ocean Institute. The NOAA/PMEL supported this work with ship time in 2014 and through funding to the Earth Ocean Interactions group. NSF provided ship time for the 2015 expedition through OCE-1546695 to D.A.B. and OCE-1547004 to J.F.H