Biology subjects

Kirchberger, P. C.

Publications and source records attributed to Kirchberger, P. C..

4 recordsLinked to original sources

bioRxiv2026

A beneficial megaplasmid transforms an opportunistic bacterial pathogen to benefit coral by extending their thermal range

Resilient turbid coral reefs, found 1{degrees} north of the equator, experience fewer and less intense bleaching events despite being situated within the worlds busiest shipping port in highly urbanised Singapore. We hypothesised that bacteria within the coral holobiont play a role in maintaining coral diversity within this extreme environment by conferring traits that enhance host tolerance. Eleven Pseudovibrio isolates, whose genomes differ by only four SNPs, were isolated from the scleractinian coral Pachyseris speciosa. A [~]490 kbp megaplasmid (pCJH) was found in 7 of the 11 Pseudovibrio isolates. This study identified an opportunistic Pseudovibrio sp. pathogen of P. speciosa, accelerating bleaching disease. However, presence of the megaplasmid alters the ecological strategy of Pseudovibrio sp. toward mutualism, delaying coral bleaching. The megaplasmid enhances Pseudovibrios host colonisation and establishment of symbiosis through increased attachment and extends its bioactive genetic potential, but reduces fecundity. The Pseudovibrio genomes and megaplasmid encode several diffusible antibiotic biosynthetic gene clusters and contact-dependent inhibition mechanisms, with both types of inhibitory activity shown against local (i.e. P. speciosa) and type-strain Vibrio spp. Interaction analyses in experimentally heat-stressed corals revealed negative associations between Pseudovibrio and Vibrio ASVs corresponding to these cultured isolates. They also showed increased coral thermal tolerance by a full degree (1{degrees}C) when it is associated with the megaplasmid-bearing strain. Together, these findings support the Coral Probiotic Hypothesis that bacteria enhance coral resilience through chemical defense and identifies additional aspects to this symbiosis by a mobile genetic element which could play an important role in coral reef resilience.

microbiology↗

bioRxiv2025

A novel mobile genetic element with virus-like characteristics is widespread in the world's oceans

While the majority of viruses falls within a handful of well-defined realms, many novel viruses and virus-like genetic elements remain to be discovered. Given the abundance and diversity of small, circular DNA genomes in animal gut viromes, we hypothesized that viruses of similar size might have been overlooked in other environments. Re-analyzing existing ocean virome datasets for small viruses, we discover a novel group of circular mobile genetic elements of [~]4.6kb in size, likely with double-stranded DNA, which we term Charybdis elements. Charybdis elements form a singular group based on cohesive gene content, encode around 10 hypothetical genes but apparently contain no virus, transposon or plasmid associated hallmark proteins. They are detected exclusively in marine datasets ranging from surface water to hydrothermal vents and sediments, from the Arctic to the Antarctic. Virome datasets separating virus-like particles by density gradients show that Charybdis elements accumulate in the fraction representing extracellular vesicles and small, tail-less viruses that are often associated with lipid membranes. One specific clade of Charybdis elements is shown to integrate into the genomes of the common marine group II archaeon candidate order Poseidoniales, the putative host of these elements. Analysis of thousands genomes shows a common genome architecture consisting of two modules: An accessory module containing a diverse range methyltransferases and other genes likely involved in host interactions, and a more conserved (putative) structural module. The structural module encodes proteins that are confidently predicted to form striking tri- or pentameric structures. These structures show stark resemblance and in some cases homology to protrusion or tail-elements on the capsids of viruses from the realms Varidnaviria and Duplodnaviria. Given these traits, Charybdis elements likely represent a hitherto undiscovered group of virus or virus-satellites, with at least one protein of a novel double-Greek-key fold serving as a potential capsid element. However, since their hosts remain unculturable, the true nature of these ubiquitous marine elements remains as of yet unresolvable.

genomics↗

bioRxiv2024

A stargate mechanism of Microviridae genome delivery unveiled by cryogenic electron tomography

Single-stranded DNA bacteriophages of the Microviridae family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection. Here, we have characterized an exceptionally large microvirus, Ebor, and provide crucial insights into long-standing mechanistic questions. Cryogenic electron microscopy of Ebor revealed a capsid with trimeric protrusions that recognise lipopolysaccharides on the host surface. Cryogenic electron tomography of the host cell colonized with virus particles demonstrated that the virus initially attaches to the cell via five such protrusions, located at the corners of a single pentamer. This interaction triggers a stargate mechanism of capsid opening along the 5-fold symmetry axis, enabling delivery of the virus genome. Despite variations in specific virus-host interactions among different Microviridae family viruses, structural data indicate that the stargate mechanism of infection is universally employed by all members of the family. Startlingly, our data reveal a mechanistic link for the opening of relatively small capsids made out of a single jelly-roll fold with the structurally unrelated giant viruses.

microbiology↗

bioRxiv2019

Simultaneous quantification of Vibrio metoecus and Vibrio cholerae with its O1 serogroup and toxigenic subpopulations in environmental reservoirs

Vibrio metoecus is a recently described and little studied causative agent of opportunistic infections in humans, often coexisting with V. cholerae in aquatic environments. However, the relative abundance of V. metoecus with V. cholerae and their population dynamics in aquatic reservoirs is still unknown. We developed a multiplex qPCR assay with a limit of detection of three copies per reaction to simultaneously quantify total V. metoecus and V. cholerae abundance, as well as the toxigenic and O1 serogroup subpopulations of V. cholerae from environmental samples. Four different genes were targeted as specific markers for individual Vibrio species or subpopulations; viuB, a gene encoding a vibriobactin utilization protein, was used to quantify the total V. cholerae population. The cholera toxin gene ctxA provided an estimation of toxigenic V. cholerae abundance, while the rfbO1 gene specifically detected and quantified V. cholerae belonging to the O1 serogroup, which includes almost all lineages of the species responsible for the majority of past and ongoing cholera pandemics. To measure V. metoecus abundance, the gene mcp, encoding methyl accepting chemotaxis protein, was used. Marker specificity was confirmed by testing several isolates of V. cholerae and V. metoecus alongside negative controls of isolates within and outside of the Vibrio genus. Analysis of environmental water samples collected from four different geographic locations including cholera-endemic (Dhaka, Kuakata and Mathbaria in Bangladesh) and non-endemic (Oyster Pond in Falmouth, Massachusetts, USA) regions showed that V. metoecus was only present in the USA site, recurring seasonally. Within the coastal USA site, the non-toxigenic O1 serogroup represented up to [~]18% of the total V. cholerae population. V. cholerae toxigenic O1 serogroup was absent or present in low abundance in coastal Bangladesh (Kuakata and Mathbaria) but constituted a relatively high proportion of the total V. cholerae population sustained throughout the year in inland Bangladesh (Dhaka). A preference for host/particle attachment was observed, as the majority of cells from both Vibrio species (>90%) were identified in the largest water size fraction sampled, composed of particles or organisms >63 m and their attached bacteria. This is the first study to apply a culture-independent method to quantify V. cholerae or V. metoecus directly in environmental reservoirs of areas endemic and non-endemic for cholera on significant temporal and spatial scales.\n\nSIGNIFICANCECholera is a life-threatening disease that requires immediate intervention; it is of prime importance to have fast, accurate and sensitive means to detect V. cholerae. Consistent environmental monitoring of the abundance of V. cholerae along with its toxigenic and O1 serogroup subpopulations could facilitate the determination of the actual distribution of this organism in aquatic reservoirs and thus help to predict an outbreak before it strikes. The lack of substantial temporal and spatial environmental sampling, along with specific quantitative measures, has made this goal elusive so far. The same is true for V. metoecus, a close relative of V. cholerae which has been associated with several clinical infections and could likely pose an emerging threat, readily exchanging genetic material with its more famous relative.

microbiology↗