| 1. |
- Banas, Indra, et al.
(author)
-
Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere
- 2023
-
In: The ISME Journal. - : Springer Nature. - 1751-7362 .- 1751-7370. ; 17, s. 1789-1792
-
Journal article (peer-reviewed)abstract
- Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.
|
|
| 2. |
- Noardo, Francesca, et al.
(author)
-
Reference study of CityGML software support : The GeoBIM benchmark 2019—Part II
- 2021
-
In: Transactions in GIS. - : Wiley. - 1361-1682 .- 1467-9671. ; 25:2, s. 842-868
-
Journal article (peer-reviewed)abstract
- OGC CityGML is an open standard for 3D city models intended to foster interoperability and support various applications. However, through our practical experience and discussions with practitioners, we have noticed several problems related to the implementation of the standard and the use of standardized data. Nevertheless, a systematic investigation of these issues has never been carried out, and there is thus insufficient evidence for tackling the problems. The GeoBIM benchmark project is aimed at finding such evidence by involving external volunteers, reporting on various aspects of the behavior of tools (geometry, semantics, georeferencing, functionalities), analyzed and described in this article. This study explicitly pointed out the critical points embedded in the format as an evidence base for future development. A companion article (Part I) describes the results of the benchmark related to IFC, the counterpart of CityGML within building information modeling.
|
|
| 3. |
- Rahlff, Janina, et al.
(author)
-
Lytic archaeal viruses infect abundant primary producers in Earth's crust
- 2021
-
In: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
-
Journal article (peer-reviewed)abstract
- The continental subsurface houses a major portion of life's abundance and diversity, 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 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification 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. Little is known about viral-host interactions in the continental subsurface. Here, the authors use a combination of metagenomics, fluorescence in situ hybridization, and electron microscopy to show infections of abundant C-fixing subsurface archaea by lytic viruses.
|
|
| 4. |
- Turzynski, Victoria, et al.
(author)
-
Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition
- 2023
-
In: Viruses. - : MDPI. - 1999-4915. ; 15:4
-
Journal article (peer-reviewed)abstract
- Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.
|
|
