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Switchgrass (Panicum virgatum L.) remains the preeminent American perennial (C4) bioenergy crop for cellulosic ethanol, that could help displace over a quarter of the US current petroleum consumption. Intriguingly, there is often little response to nitrogen fertilizer once stands are established. The rhizosphere microbiome plays a critical role in nitrogen cycling and overall plant nutrient uptake. We used high-throughput metagenomic sequencing to characterize the switchgrass rhizosphere microbial community before and after a nitrogen fertilization event for established stands on marginal land. We examined community structure and bulk metabolic potential, and resolved 29 individual bacteria genomes via metagenomic de novo assembly. Community structure and diversity were not significantly different before and after fertilization; however, the bulk metabolic potential of carbohydrate-active enzymes was depleted after fertilization. We resolved 29 metagenomic assembled genomes, including some from the ‘most wanted’ soil taxa such as Verrucomicrobia, Candidate phyla UBA10199, Acidobacteria (rare subgroup 23), Dormibacterota, and the very rare Candidatus Eisenbacteria. The Dormibacterota (formally candidate division AD3) we identified have the potential for autotrophic CO utilization, which may impact carbon partitioning and storage. Our study also suggests that the rhizosphere microbiome may be involved in providing associative nitrogen fixation (ANF) via the novel diazotroph Janthinobacterium to switchgrass. 

The exact role that cytochrome 579 plays in the aerobic iron respiratory chain of Leptospirillum ferriphilum is unclear. This paper presents genomic, structural, and kinetic data on the cytochrome 579 purified from cell-free extracts of L. ferriphilum cultured on soluble iron. Electrospray mass spectrometry of electrophoretically homogeneous cytochrome 579 yielded two principal peaks at 16,015 and 16,141 Daltons. N-terminal amino acid sequencing of the purified protein yielded data that were used to determine the following: there are seven homologs of cytochrome 579; each homolog possesses the CXXCH heme-binding motif found in c -type cytochromes; each of the seven sequenced strains of L. ferriphilum expresses only two of the seven homologs of the cytochrome; and each homolog contains an N-terminal signal peptide that directs the mature protein to an extra-cytoplasmic location. Static light scattering and macroion mobility measurements on native cytochrome 579 yielded masses of 125 and 135 kDaltons, respectively. The reduced alkaline pyridine hemochromogen spectrum of the purified cytochrome had an alpha absorbance maximum at 567 nm, a property not exhibited by any known heme group. The iron-dependent reduction and oxidation of the octameric cytochrome exhibited positively cooperative kinetic behavior with apparent Hill coefficients of 5.0 and 3.7, respectively, when the purified protein was mixed with mM concentrations of soluble iron. Consequently, the extrapolated rates of reduction at sub-mM iron concentrations were far too slow for cytochrome 579 to be the initial iron oxidase in the aerobic respiratory chain of L. ferriphilum . Rather, these observations support the hypothesis that the acid-stable cytochrome 579 is a periplasmic conduit of electrons from initial iron oxidation in the outer membrane of this Gram-negative bacterium to a terminal oxidase in the plasma membrane. 

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. 

ABSTRACT We present a new catalogue of radio sources in the face-on spiral galaxy M83. Radio observations taken in 2011, 2015, and 2017 with the Australia Telescope Compact Array at 5.5 and 9 GHz have detected 270 radio sources. Although a small number of these sources are background extragalactic sources, most are either H ii regions or supernova remnants (SNRs) within M83 itself. Three of the six historical supernovae are detected, as is the very young remnant that had been identified in a recent study, which is likely the result of a supernova that exploded in the last ∼100 yr but was missed. All of these objects are generally fading with time. Confusion limits our ability to measure the radio emission from a number of the SNRs in M83, but 64 were detected in unconfused regions, and these have the approximate power-law luminosity function that has been observed in other galaxies. The SNRs in M83 are systematically smaller in diameter and brighter than those that have been detected at radio wavelengths in M33. A number of the radio sources are coincident with X-ray sources in M83; most of these coincident sources turn out to be SNRs. Our dual frequency observations are among the most sensitive to date for a spiral galaxy outside the Local Group; despite this we were not able to place realistic constraints on the spectral indices, and as a result, it was not possible to search for SNRs based on their radio properties alone. 

Abstract The PHANGS program is building the first data set to enable the multiphase, multiscale study of star formation across the nearby spiral galaxy population. This effort is enabled by large survey programs with the Atacama Large Millimeter/submillimeter Array (ALMA), MUSE on the Very Large Telescope, and the Hubble Space Telescope (HST), with which we have obtained CO(2–1) imaging, optical spectroscopic mapping, and high-resolution UV–optical imaging, respectively. Here, we present PHANGS-HST, which has obtained NUV– U – B – V – I imaging of the disks of 38 spiral galaxies at distances of 4–23 Mpc, and parallel V - and I -band imaging of their halos, to provide a census of tens of thousands of compact star clusters and multiscale stellar associations. The combination of HST, ALMA, and VLT/MUSE observations will yield an unprecedented joint catalog of the observed and physical properties of ∼100,000 star clusters, associations, H ii regions, and molecular clouds. With these basic units of star formation, PHANGS will systematically chart the evolutionary cycling between gas and stars across a diversity of galactic environments found in nearby galaxies. We discuss the design of the PHANGS-HST survey and provide an overview of the HST data processing pipeline and first results. We highlight new methods for selecting star cluster candidates, morphological classification of candidates with convolutional neural networks, and identification of stellar associations over a range of physical scales with a watershed algorithm. We describe the cross-observatory imaging, catalogs, and software products to be released. The PHANGS high-level science products will seed a broad range of investigations, in particular, the study of embedded stellar populations and dust with the James Webb Space Telescope, for which a PHANGS Cycle 1 Treasury program to obtain eight-band 2–21 μ m imaging has been approved.