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1. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

   https://doi.org/10.1186/s12859-022-04973-8  

   Espinoza, Josh L. ; Dupont, Chris L. ( October 2022 , BMC Bioinformatics)

   With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth’s natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ,however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes.

   In this study, we introduce theViral Eukaryotic Bacterial Archaeal(VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge,VEBAis the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes.VEBAimplements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone.VEBAincludes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification.VEBAalso provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally,VEBAis the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genomemore »quality assessments.VEBA’s capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives.

   TheVEBAsoftware suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways.VEBAfully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions ofVEBAto the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks.VEBAallows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.

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2. Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

   https://doi.org/10.1038/s41396-020-00843-4  

   Seyler, Lauren M. ; Trembath-Reichert, Elizabeth ; Tully, Benjamin J. ; Huber, Julie A. ( December 2020 , The ISME Journal)

   The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.
3. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

   https://doi.org/10.1038/s41396-020-00825-6  

   Gazitúa, M. Consuelo ; Vik, Dean R. ; Roux, Simon ; Gregory, Ann C. ; Bolduc, Benjamin ; Widner, Brittany ; Mulholland, Margaret R. ; Hallam, Steven J. ; Ulloa, Osvaldo ; Sullivan, Matthew B. ( November 2020 , The ISME Journal)

   Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-likeMyoviridaephages, predicted to infectCyanobacteriaandProteobacteria, or in unclassified archaeal viruses predicted to infectThaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.
4. Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria)

   https://doi.org/10.1128/mbio.00302-23  

   Macher, Jan-Niklas ; Coots, Nicole L. ; Poh, Yu-Ping ; Girard, Elsa B. ; Langerak, Anouk ; Muñoz-Gómez, Sergio A. ; Sinha, Savar D. ; Jirsová, Dagmar ; Vos, Rutger ; Wissels, Richard ; et al ( April 2023 , mBio)

   Xu, Jianping (Ed.)

   ABSTRACT Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria—the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we determined two complete mitochondrial genomes of Foraminifera and two nearly complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes contain a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and contain only 14 or 15 protein-coding genes, including nad1 , - 3 ,more »- 4 , - 4L , - 5 , and - 7 , cob , cox1 , - 2 , and - 3 , and atp1 , - 6 , and - 9 , with forams and radiolarians additionally carrying nad2 and nad6 , respectively. In radiolarian mitogenomes, a noncanonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases. IMPORTANCE We present the reduced mitochondrial genomes of Retaria, the rhizarian lineage comprising the phyla Foraminifera and Radiolaria. By applying single-cell genomic approaches, we found that foraminiferan and radiolarian mitochondrial genomes contain an overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. An alternative genetic code was identified in radiolarian mitogenomes in which all three stop codons encode amino acids. Collectively, these results shed light on the divergent nature of the mitochondrial genomes from an ecologically important group, warranting further questions into the biological underpinnings of gene content variability and genetic code variation between mitochondrial genomes.« less
5. Random transposon mutagenesis identifies genes essential for transformation in Methanococcus maripaludis

   https://doi.org/10.1007/s00438-023-01994-7  

   Fonseca, Dallas R. ; Loppnow, Madison B. ; Day, Leslie A. ; Kelsey, Elisa L. ; Abdul Halim, Mohd Farid ; Costa, Kyle C. ( February 2023 , Molecular Genetics and Genomics)

   Natural transformation, the process whereby a cell acquires DNA directly from the environment, is an important driver of evolution in microbial populations, yet the mechanism of DNA uptake is only characterized in bacteria. To expand our understanding of natural transformation in archaea, we undertook a genetic approach to identify a catalog of genes necessary for transformation inMethanococcus maripaludis. Using an optimized method to generate random transposon mutants, we screened 6144 mutant strains for defects in natural transformation and identified 25 transformation-associated candidate genes. Among these are genes encoding components of the type IV-like pilus, transcription/translation associated genes, genes encoding putative membrane bound transport proteins, and genes of unknown function. Interestingly, similar genes were identified regardless of whether replicating or integrating plasmids were provided as a substrate for transformation. Using allelic replacement mutagenesis, we confirmed that several genes identified in these screens are essential for transformation. Finally, we identified a homolog of a membrane bound substrate transporter inMethanoculleus thermophilusand verified its importance for transformation using allelic replacement mutagenesis, suggesting a conserved mechanism for DNA transfer in multiple archaea. These data represent an initial characterization of the genes important for transformation which will inform efforts to understand gene flow in naturalmore »populations. Additionally, knowledge of the genes necessary for natural transformation may assist in identifying signatures of transformation machinery in archaeal genomes and aid the establishment of new model genetic systems for studying archaea.

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