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      Genomic sequence analysis of Dissulfurirhabdus thermomarina SH388 and proposed reassignment to Dissulfurirhabdaceae fam. nov.

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          Abstract

          Here, we report the draft genome sequence of Dissulfurirhabdus thermomarina SH388. Improved phylogenetic and taxonomic analysis of this organism using genome-level analyses supports assignment of this organism to a novel family within the phylum Desulfobacterota. Additionally, comparative genomic and phylogenetic analyses contextualize the convergent evolution of sulfur disproportionation and potential extracellular electron transfer in this organism relative to other members of the Desulfobacterota.

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          Extracellular electron transfer mechanisms between microorganisms and minerals.

          Liang Shi, Hailiang Dong, Gemma Reguera … (2016)
          Electrons can be transferred from microorganisms to multivalent metal ions that are associated with minerals and vice versa. As the microbial cell envelope is neither physically permeable to minerals nor electrically conductive, microorganisms have evolved strategies to exchange electrons with extracellular minerals. In this Review, we discuss the molecular mechanisms that underlie the ability of microorganisms to exchange electrons, such as c-type cytochromes and microbial nanowires, with extracellular minerals and with microorganisms of the same or different species. Microorganisms that have extracellular electron transfer capability can be used for biotechnological applications, including bioremediation, biomining and the production of biofuels and nanomaterials.
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            Single cell activity reveals direct electron transfer in methanotrophic consortia.

            Shawn E. McGlynn, Grayson L Chadwick, Christopher Kempes … (2015)
            Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling mechanisms between these paired organisms is not well understood, despite the attention given them because of the global significance of anaerobic methane oxidation. Here we examined the influence of interspecies spatial positioning as it relates to biosynthetic activity within structurally diverse uncultured methane-oxidizing consortia by measuring stable isotope incorporation for individual archaeal and bacterial cells to constrain their potential metabolic interactions. In contrast to conventional models of syntrophy based on the passage of molecular intermediates, cellular activities were found to be independent of both species intermixing and distance between syntrophic partners within consortia. A generalized model of electric conductivity between co-associated archaea and bacteria best fit the empirical data. Combined with the detection of large multi-haem cytochromes in the genomes of methanotrophic archaea and the demonstration of redox-dependent staining of the matrix between cells in consortia, these results provide evidence for syntrophic coupling through direct electron transfer.
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              Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data

              F. Lemoine, J.-B. Domelevo Entfellner, E. Wilkinson … (2018)
              Felsenstein’s article describing the application of the bootstrap to evolutionary trees is one of the most cited papers of all time. The bootstrap method, based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now available for a wide variety of species, and phylogenies with hundreds or thousands of taxa are becoming routine. In that framework, Felsenstein’s bootstrap tends to yield very low supports, especially on deep branches. We propose a new version of phylogenetic bootstrap, in which the presence of inferred branches in replications is measured using a gradual “transfer” distance, as opposed to the original version using a binary presence/absence index. The resulting supports are higher, while not inducing falsely supported branches. Our method is applied to large mammal, HIV, and simulated datasets, for which it reveals the phylogenetic signal, while Felsenstein’s bootstrap fails to do so.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Microb Genom
                Journal ID (iso-abbrev): Microb Genom
                Journal ID (hwp): mgen
                Journal ID (publisher-id): mgen
                Title: Microbial Genomics
                Publisher: Microbiology Society
                ISSN (Electronic): 2057-5858
                Publication date Collection: July 2020
                Publication date (Electronic): 17 June 2020
                Publication date PMC-release: 17 June 2020
                Volume: 6
                Issue: 7
                Affiliations
                [ 1​ ] departmentDepartment of Earth and Planetary Sciences , Harvard University , Cambridge, MA, USA
                [ 2​ ] departmentEarth-Life Science Institute , Tokyo Institute of Technology , Tokyo, Japan
                [ 3​ ] departmentDepartment of Geosciences , Princeton University , Princeton, NJ, USA
                Author notes
                *Correspondence: Lewis M. Ward, lewis_ward@ 123456fas.harvard.edu
                Article
                Publisher ID: 000390
                DOI: 10.1099/mgen.0.000390
                PMC ID: 7478628
                SO-VID: 58f76921-2668-4380-9f08-5e3a3ba8006d
                Copyright statement: © 2020 The Authors
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License.

                History
                Date received : 12 March 2020
                Date accepted : 20 May 2020
                Product
                Funding
                Funded by: National Aeronautics and Space Administration
                Award ID: NNX15AP58G
                Award Recipient : David T. Johnston
                Funded by: National Science Foundation
                Award ID: EAR-1149555
                Award Recipient : Emma Bertran
                Funded by: Simons Foundation
                Award Recipient : Lewis M Ward
                Funded by: Agouron Institute
                Award Recipient : Lewis M Ward
                Categories
                Subject: Short Communication
                Subject: Systems Microbiology: Genome annotation, metabolic reconstructions
                Custom metadata
                OpenAccessEmbargo 0

                Keywords: deltaproteobacteria,sulfate reduction,comparative genomics,eet
                Data availability:
                Keywords: deltaproteobacteria, sulfate reduction, comparative genomics, eet

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