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Metallosphaera sedulais a thermoacidophilic archaeon that obtains all of its energy for growth from aerobic respiration and oxidative phosphorylation at the expense of selected organic and inorganic sources of electrons. Initial velocities for the oxidation of soluble ferrous ions by intact cells at 60 °C and pH 1.5 were determined using an integrating cavity absorption meter that permitted accurate absorbance measurements to quantify the increase in soluble ferric iron in the presence of turbid suspensions of the live organisms.M. sedulathat was cultured on yeast extract either in the absence or the presence of 20 mM soluble ferrous iron exhibited turnover numbers for soluble iron oxidation of 304 ± 26 and 333 ± 31 attamoles/cell/min, respectively. These functional data were consistent with the transcriptomic evidence presented by others, that the proteins presumably responsible for aerobic respiration on soluble iron are expressed constitutively inM. sedula. Intact cells ofM. sedulawere characterized by electrical impedance, laser light diffraction, and transmission electron microscopic measurements. All three types of measurements were consistent with the surprising observation that cells cultured on yeast extract in the presence of soluble iron bifurcated into approximately equal numbers of coccoidal cells of two sizes, smaller cells with an average diameter of 0.6 μm and larger cells with an average diameter of 1.35 μm. Cells cultured on the same concentration of yeast extract but in the absence of soluble iron comprised a single cell size with an intermediate average diameter of 1.06 μm. This unexpected bifurcation of a clonal cell population into two demonstrably different sizes when the extracellular nutrient environment changes has not previously been reported forM. sedula, or any other single-celled archaeon or eubacterium. 

Abstract Motivation Viruses infect, reprogram, and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Results Here we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240,311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from “conservative” to “eXtremely Conservative” resulted in 37,841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ∼24% on average (up to ∼42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem. Availability The resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143). Supplementary information Supplementary data are available at Bioinformatics online.