ORCID Profile
0000-0002-9392-6544
Current Organisation
Research Alliance Ruhr, University of Duisburg-Essen
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Publisher: Springer Science and Business Media LLC
Date: 12-2011
Publisher: Public Library of Science (PLoS)
Date: 26-05-2015
Publisher: Public Library of Science (PLoS)
Date: 21-04-2016
Publisher: Springer Science and Business Media LLC
Date: 30-07-2021
DOI: 10.1038/S41467-021-24803-4
Abstract: The continental subsurface houses a major portion of life’s abundance and ersity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca . Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 s les from one subsurface ecosystem suggest a sophisticated interplay of viral ersification and adapting CRISPR-mediated resistances of Ca . Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.
Publisher: Springer Science and Business Media LLC
Date: 12-11-2020
DOI: 10.1038/S41564-020-00827-2
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher: Springer Science and Business Media LLC
Date: 08-06-2020
DOI: 10.1038/S41564-020-0733-X
Abstract: The assembly of single- lified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial ersity.
Publisher: Springer Science and Business Media LLC
Date: 28-04-2015
Publisher: Elsevier BV
Date: 09-2022
Publisher: Cold Spring Harbor Laboratory
Date: 22-07-2020
DOI: 10.1101/2020.07.22.215848
Abstract: The continental subsurface houses a major portion of life’s abundance and ersity, yet little is known about viruses infecting microbes that reside there. Here, we used a combination of metagenomics and genome-informed microscopy to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches displayed resistances of Ca. Altiarchaea against eight predicted viral clades, which showed genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tagged and imaged a putatively viral genome rich in protospacers using fluorescence microscopy. Virus-targeted genomeFISH revealed a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 s les from one subsurface ecosystem suggest a sophisticated interplay of viral ersification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.
Publisher: Environmental Health Perspectives
Date: 12-2016
DOI: 10.1289/EHP158
Publisher: Springer Science and Business Media LLC
Date: 19-09-2022
DOI: 10.1038/S41564-022-01214-9
Abstract: Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single- lified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry ( seqco.de/ ), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide ex les for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.
Location: United States of America
Location: Germany
No related grants have been discovered for Alexander J. Probst.