Biodiversity and emerging biogeography of the neutrophilic iron-oxidizing Zetaproteobacteria

Members of the neutrophilic iron-oxidizing candidate class Zetaproteobacteria have predominantly been found at sites of microbially mediated iron oxidation in marine environments around the Pacific Ocean. Eighty-four full-length (\u3e1,400 bp) and forty-eight partial-length Zetaproteobacteria small subunit ribosomal RNA (SSU rRNA) gene sequences from five novel clone libraries, one novel Zetaproteobacteria isolate, and the GenBank database were analyzed to assess the biodiversity of this burgeoning class of the Proteobacteria and to investigate its biogeography between three major sampling regions in the Pacific Ocean: Loihi Seamount, the Southern Mariana Trough, and the Tonga Arc. Sequences were grouped into operational taxonomic units (OTUs) based on a 97% minimum similarity. Of the 28 OTUs detected, 13 were found to be endemic to one of the three main sampling regions, and 2 were ubiquitous throughout the Pacific Ocean. Additionally, two deeply-rooted OTUs were identified that potentially dominate communities of iron-oxidizers originating in the deep subsurface. Spatial autocorrelation analysis and analysis of molecular variance (AMOVA) showed that geographic distance played a significant role in the distribution of Zetaproteobacteria biodiversity, whereas environmental parameters, such as temperature, pH, or total Fe concentration, did not have a significant effect. These results, detected using the coarse resolution of the SSU rRNA gene, indicate that the Zetaproteobacteria have a strong biogeographic signal

Quantum Circuit Cosmology: The Expansion of the Universe Since the First Qubit

We consider cosmological evolution from the perspective of quantum information. We present a quantum circuit model for the expansion of a comoving region of space, in which initially-unentangled ancilla qubits become entangled as expansion proceeds. We apply this model to the comoving region that now coincides with our Hubble volume, taking the number of entangled degrees of freedom in this region to be proportional to the de Sitter entropy. The quantum circuit model is applicable for at most 140 $e$-folds of inflationary and post-inflationary expansion: we argue that no geometric description was possible before the time $t_1$ when our comoving region was one Planck length across, and contained one pair of entangled degrees of freedom. This approach could provide a framework for modeling the initial state of inflationary perturbations.Comment: v2, minor correction

Cryptic metabolisms in anoxic subseafloor sediment

Microbial gene expression in anoxic subseafloor sediment was recently explored in the Baltic Sea and the Peru Margin. Our analysis of these data reveals diverse transcripts encoding proteins associated with neutralization of reactive oxygen species, including catalase, which may provide an in situ source of oxygen. We also detect transcripts associated with oxidation of iron and sulfur, and with reduction of arsenate, selenate and nitrate. Given limited input of electron acceptors from outside the system, these results suggest that the microbial communities use an unexpectedly diverse variety of electron acceptors. Products of water radiolysis and their interactions with sediment continuously provide diverse electron acceptors and hydrogen. Cryptic microbial utilization of these oxidized substrates and H2 may be an important mechanism for multi-million-year survival under the extreme energy limitation in subseafloor sediment

Hidden Diversity Revealed by Genome-resolved Metagenomics of Iron-oxidizing Microbial Mats from Lō’ihi Seamount, Hawai’i

The Zetaproteobacteria are ubiquitous in marine environments, yet this class of Proteobacteria is only represented by a few closely-related cultured isolates. In high-iron environments, such as diffuse hydrothermal vents, the Zetaproteobacteria are important members of the community driving its structure. Biogeography of Zetaproteobacteria has shown two ubiquitous operational taxonomic units (OTUs), yet much is unknown about their genomic diversity. Genome-resolved metagenomics allows for the specific binning of microbial genomes based on genomic signatures present in composite metagenome assemblies. This resulted in the recovery of 93 genome bins, of which 34 were classified as Zetaproteobacteria. Form II ribulose 1,5-bisphosphate carboxylase genes were recovered from nearly all the Zetaproteobacteria genome bins. In addition, the Zetaproteobacteria genome bins contain genes for uptake and utilization of bioavailable nitrogen, detoxification of arsenic, and a terminal electron acceptor adapted for low oxygen concentration. Our results also support the hypothesis of a Cyc2-like protein as the site for iron oxidation, now detected across a majority of the Zetaproteobacteria genome bins. Whole genome comparisons showed a high genomic diversity across the Zetaproteobacteria OTUs and genome bins that were previously unidentified by SSU rRNA gene analysis. A single lineage of cosmopolitan Zetaproteobacteria (zOTU 2) was found to be monophyletic, based on cluster analysis of average nucleotide identity and average amino acid identity comparisons. From these data, we can begin to pinpoint genomic adaptations of the more ecologically ubiquitous Zetaproteobacteria, and further understand their environmental constraints and metabolic potential

Iroki: automatic customization and visualization of phylogenetic trees

Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki

Silica Biomineralization of Calothrix-Dominated Biofacies from Queen\u27s Laundry Hot-Spring, Yellowstone National Park, USA

Experiments on microorganisms capable of surviving silicification are often conducted to gain a better understanding of the process of silica biomineralization and to gain insights into microbially influenced rock formations and biofabrics like those found in ancient deposits such as the Early Archean Apex Chert formation (Schopf, 1993; House et al., 2000). An ideal microorganism for studying silicification is the large sheathed cyanobacterium Calothrix, which form distinctive organo-sedimentary structures in the low to moderate temperature regions of hydrothermal springs or columnar stromatolitic structures in aquatic systems. Our ability to identify and characterize microfossils from ancient deposits allows us to gain a better understanding of environmental conditions on early Earth. Here we characterized Calothrix-dominated biofacies along the outflow apron of Queen\u27s Laundry Hot-Spring in Yellowstone National Park using microscopy and molecular techniques to examine biofacies morphology and phylogenetic diversity. We found that flow regime and temperature had a profound effect on community composition as identified by the observation of five distinct Calothrix-dominated communities and on biofacies architecture along the outflow apron

Silica Biomineralization of Calothrix-Dominated Biofacies from Queen\u27s Laundry Hot-Spring, Yellowstone National Park, USA

Experiments on microorganisms capable of surviving silicification are often conducted to gain a better understanding of the process of silica biomineralization and to gain insights into microbially influenced rock formations and biofabrics like those found in ancient deposits such as the Early Archean Apex Chert formation (Schopf, 1993; House et al., 2000). An ideal microorganism for studying silicification is the large sheathed cyanobacterium Calothrix, which form distinctive organo-sedimentary structures in the low to moderate temperature regions of hydrothermal springs or columnar stromatolitic structures in aquatic systems. Our ability to identify and characterize microfossils from ancient deposits allows us to gain a better understanding of environmental conditions on early Earth. Here we characterized Calothrix-dominated biofacies along the outflow apron of Queen\u27s Laundry Hot-Spring in Yellowstone National Park using microscopy and molecular techniques to examine biofacies morphology and phylogenetic diversity. We found that flow regime and temperature had a profound effect on community composition as identified by the observation of five distinct Calothrix-dominated communities and on biofacies architecture along the outflow apron

Cryogenic Memory Architecture Integrating Spin Hall Effect based Magnetic Memory and Superconductive Cryotron Devices

One of the most challenging obstacles to realizing exascale computing is minimizing the energy consumption of L2 cache, main memory, and interconnects to that memory. For promising cryogenic computing schemes utilizing Josephson junction superconducting logic, this obstacle is exacerbated by the cryogenic system requirements that expose the technology's lack of high-density, high-speed and power-efficient memory. Here we demonstrate an array of cryogenic memory cells consisting of a non-volatile three-terminal magnetic tunnel junction element driven by the spin Hall effect, combined with a superconducting heater-cryotron bit-select element. The write energy of these memory elements is roughly 8 pJ with a bit-select element, designed to achieve a minimum overhead power consumption of about 30%. Individual magnetic memory cells measured at 4 K show reliable switching with write error rates below $10^{-6}$, and a 4x4 array can be fully addressed with bit select error rates of $10^{-6}$. This demonstration is a first step towards a full cryogenic memory architecture targeting energy and performance specifications appropriate for applications in superconducting high performance and quantum computing control systems, which require significant memory resources operating at 4 K.Comment: 10 pages, 6 figures, submitte