Biology subjects

Cavicchioli, R.

Publications and source records attributed to Cavicchioli, R..

4 recordsLinked to original sources

bioRxiv2023

The intracellular lifestyle of an archaeal symbiont

DPANN Archaea are a diverse group of organisms typically characterised by small cells and reduced genomes. To date, all cultivated DPANN Archaea are ectosymbionts that require direct cell contact with an archaeal host species for proliferation. However, the dynamics of DPANN - host interactions and the impacts of these interactions on the host species are poorly understood. Here, we show that one DPANN archaeon (Candidatus Nanohaloarchaeum antarcticus) engages in parasitic interactions with its host (Halorubrum lacusprofundi) that result in host cell lysis. Our data also suggest that these interactions involve invasion of the host cell by the nanohaloarchaeon. This is the first reported instance of such a predatory-like lifestyle amongst Archaea and indicates that some DPANN Archaea may interact with host populations in a manner similar to viruses.

microbiology↗

bioRxiv2022

In depth characterization of an archaeal virus-host system reveals numerous virus exclusion mechanisms

Archaeal head-tailed viruses appear, at first sight, very closely related to head-tailed bacteriophages simply due to morphological similarities and similar life cycles. However, they encounter host cells that are very different from bacteria and share characteristics, that greatly influence virus life cycles, with eukaryotes. Here we present an in-depth characterization of the archaeal head-tailed virus, HRTV-Dl1, isolated from Deep Lake, Antarctica. The host Halorubrum lacusprofundi exhibits a large arsenal of virus exclusion mechanisms, indicating a long ongoing arms race with viruses. However, we uncover that the majority of this arsenal was lost spontaneously in a strain grown under non-challenging laboratory conditions. By challenging both the parental strain and the sensitive strain with HRTV-DL1, we discovered a number of putative virus exclusion mechanisms that are only activated in the sensitive strain upon the lack of defense systems present in the parental strain. We identify virus exclusion mechanisms that are also common in bacteria, mechanisms that are unique to archaea, and a potential mechanisms involving the archaeal homolog of the eukaryotic ORC1 and CDC6. We identify one of two S-layer proteins as primary receptor for HRTV-DL1, demonstrating that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. Our results clearly reflect the differences between bacterial and archaeal head-tailed viruses. Finally, we observed that our intention to isolate a clean and stable model virus-host system led to the generation of a virus-host pair with reduced genomes. This model system is great to study in the laboratory, but barely reflects the entire spectrum of virus-host interactions as they would occur in the environment, emphasizing the importance of combining wet lab data with environmental data.

microbiology↗

bioRxiv2022

Molecular hydrogen is an overlooked energy source for marine bacteria

Molecular hydrogen (H2) and carbon monoxide (CO) are supersaturated in seawater relative to the atmosphere and hence are readily accessible energy sources for marine microbial communities. Yet while marine CO oxidation is well-described, it is unknown whether seawater communities consume H2. Here we integrated genome-resolved metagenomics, biogeochemistry, thermodynamic modelling, and culture-based analysis to profile H2 and CO oxidation by marine bacteria. Based on analysis of 14 surface water samples, collected from three locations spanning tropical to subantarctic fronts, three uptake hydrogenase classes are prevalent in seawater and encoded by major marine families such as Rhodobacteraceae, Flavobacteriaceae, and Sphingomonadaceae. However, they are less abundant and widespread than carbon monoxide dehydrogenases. Consistently, microbial communities in surface waters slowly consumed H2 and rapidly consumed CO at environmentally relevant concentrations, with H2 oxidation most active in subantarctic waters. The cell-specific power from these processes exceed bacterial maintenance requirements and, for H2, can likely sustain growth of bacteria with low energy requirements. Concordantly, we show that the polar ultramicrobacterium Sphingopyxis alaskensis grows mixotrophically on H2 by expressing a group 2a [NiFe]-hydrogenase, providing the first demonstration of atmospheric H2 oxidation by a marine bacterium. Based on TARA Oceans metagenomes, genes for trace gas oxidation are globally distributed and are fourfold more abundant in deep compared to surface waters, highlighting that trace gases are important energy sources especially in energy-limited waters. Altogether, these findings show H2 is a significant energy source for marine communities and suggest that trace gases influence the ecology and biogeochemistry of oceans globally.

microbiology↗

bioRxiv2020

Ecology and molecular targets of hypermutation in the global microbiome.

Changes in the sequence of an organisms genome, i.e. mutations, are the raw material of evolution1. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as Diversity-generating retroelements (DGRs)2-4. DGRs introduce mutations in specific target genes, and were characterized from several cultivated bacteria and bacteriophages2. Whilst a larger diversity of DGR loci has been identified in genomic data from environmental samples, i.e. metagenomes, the ecological role of these DGRs and their associated evolutionary drivers remain poorly understood5-7. Here we built and analyzed an extensive dataset of >30,000 metagenome-derived DGRs, and determine that DGRs have a single evolutionary origin and a universal bias towards adenine mutations. We further identified six major lineages of DGRs, each associated with a specific ecological niche defined as a genome type, i.e. whether the DGR is encoded on a viral or cellular genome, a limited set of taxa and environments, and a distinct type of target. Finally, we leverage read mapping and metagenomic time series to demonstrate that DGRs are consistently and broadly active, and responsible for >10% of all amino acid changes in some organisms at a conservative estimate. Overall, these results highlight the strong constraints under which DGRs diversify and expand, and elucidate several distinct roles these elements play in natural communities and in shaping microbial community structure and function in our environment.

microbiology↗