Biology subjects

Jorgensen, S. L.

Publications and source records attributed to Jorgensen, S. L..

7 recordsLinked to original sources

bioRxiv2026

Asgard archaeal origin of microtubules

Eukaryotic cells change their shapes, actively segregate their DNA and contain membrane networks, facilitated by a complex cytoskeleton containing actin filaments, microtubules made from tubulin, and other components. These filaments have ancient evolutionary origins since actin- and tubulin-like proteins form prokaryotic cytoskeletons in archaea and bacteria. Bona fide eukaryotic F-actin can be traced back to crenarchaea and Asgard archaea, which are the closest known relatives of eukaryotes. A possible Asgard archaeal origin of microtubules was suggested recently with the discovery of a lokiarchaeon containing AtubAB mini microtubules that share architectural features with their eukaryotic counterparts. Using phylogenetic analyses of metagenomic data, here we report the broad occurrence of tubulins in Asgard archaea. Biochemical and structural analyses showed that one of our newly discovered heimdallarchaeial AtubAB tubulin pairs forms four-protofilament mini-microtubules that show dynamic instability and are inhibited by the tubulin drug maytansine. Our work raises the possibility that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis.

cell biology↗

bioRxiv2023

A new abundant nitrite-oxidizing phylum in oligotrophic marine sediments

Nitrite-oxidizing bacteria (NOB) are important nitrifiers whose activity regulates the availability of nitrite and links reduced ammonium and oxidized nitrate in ecosystems. In oxic marine sediments, ammonia-oxidizing archaea (AOA) and NOB together catalyze the oxidation of ammonium to nitrate, but the observed abundance ratios of AOA to canonical NOB are significantly higher than the theoretical ratio predicted from microbial physiology, indicating that many novel NOBs are yet to be discovered. Here we report a new bacterial phylum Candidatus Nitrosediminicolota, members of which are more abundant than canonical NOBs and are widespread across global oligotrophic sediments. Ca. Nitrosediminicolota members have the functional potential to oxidize nitrite, in addition to other accessory functions such as urea hydrolysis and thiosulfate reduction. While one recovered species (Ca. Nitrosediminicola aerophilis) is generally confined within the oxic zone, another (Ca. Nitrosediminicola anaerotolerans) can additionally thrive in anoxic sediments. Counting Ca. Nitrosediminicolota as a nitrite-oxidizer resolves the apparent abundance imbalance between AOA and NOB in oxic marine sediments, and thus its activity may exert a critical control on the nitrite budget.

microbiology↗

bioRxiv2022

Nitrite accumulation and the associated anammox bacteria niche partitioning in marine sediments

By consuming ammonium and nitrite, anammox bacteria form an important functional guild in nitrogen cycling in many environments including marine sediments. Recent studies have shown that anammox bacteria can consume most of the upwardly diffusing ammonium from deep anoxic sediments; however, their impact on the other important substrate nitrite has not been well characterized. Here we show niche partitioning of two anammox families emerges in a 2.4-m long mostly anoxic sediment core retrieved from the Nordic Seas. We document high abundances (~106 cells g-1) of anammox bacteria in most investigated sediment layers, with two distinct anammox abundance maxima in two nitrite consumption zones. Between the two anammox abundance maxima, nitrite accumulates as observed in other marine sediment sites and aquatic environments, indicating anammox bacteria play a fundamental role in modulating the nitrite distribution. Anammox bacteria in the upper nitrite consumption zone are dominated by the Candidatus Bathyanammoxibiaceae family, while Ca. Scalinduaceae family dominate at the lower zone. A high-quality representative Ca. Bathyanammoxibiaceae genome is recovered, which, comparing to Ca. Scalindua sediminis, the representative of Scalinduaceae in marine sediments, has fewer high-affinity ammonium transporters and lacks the capacity to access alternative substrates or energy sources such as urea and cyanate. These features may restrict Ca. Bathyanammoxibiaceae to conditions of higher ammonium concentrations or fluxes, and therefore drive the observed niche partitioning. These findings improve our understanding about nitrogen cycling in marine sediments by revealing the association between nitrite accumulation and niche partitioning of anammox bacteria.

microbiology↗

bioRxiv2020

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored inhabitants, that seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Ca. Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of gene repair systems that may allow to overcome challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy limiting and high-pressure environment.

microbiology↗

bioRxiv2020

Evaluation of a new probiotic concept for broilers

Probiotics were introduced as a spray directly in the hatcher when chickens started to leave the eggs which potentially could reduce the horizontal transmission and colonization with pathogenic bacteria. The single introduction of probiotics could limit the cost compared to multiple introductions with feed and/or water. A mixture of five probiotic strains belonging to Escherichia coli, Enterococcus faecalis, Lactobacillus agilis and Lactobacillus rhamnosus was tested with two independent flocks of broilers (Ross 308). For each experiment, a comparison was made to an untreated control flock on the same farm. At day 14 of production the probiotic strains were re-isolated from ileum of euthanized chickens. The first week mortality was slightly increased in the probiotic flock (0.42%) compared to the control (0.35%) in experiment 1, however, it was higher in the control flock (1.45%) compared to the probiotic flock (1.12%) in experiment 2. The average weight of chickens that could be slaughtered for consumption was increased by 3.5% in the probiotic flocks compared to the control flocks, resulting in a 1.9% higher total weight of slaughtered chickens in the probiotics treated flocks compared to the control as a mean of the two experiments. The number of condemned animals was within the normal range for the production system and could not directly be related to effects of probiotics. Although one probiotic strain of E. coli was isolated from dead animals, the probiotics did not affect the proportion of chickens which died due to E. coli during the first week compared to the control. Primary audienceplant managers, veterinarians, nutritionists

microbiology↗

bioRxiv2019

In situ growth of anammox bacteria in subseafloor sediments

The deep biosphere buried in marine sediments was estimated to host an equal number of microbes as found in the above oceans 1. It has been debated if these cells are alive and active 2, and their per cell energy availability does not seem to allow for net population growth 3. Here, we report the growth of anammox bacteria in [~]80,000 year old subsurface sediments indicated by their four orders of magnitude abundance increase in the nitrate-ammonia transition zone (NATZ). Their growth coincides with a local increase in anammox power supply. The genome of the dominant anammox bacterium from the NATZ was reconstructed and showed an increased index of replication confirming in situ active growth. The genome belongs to a new Scalindua species so far exclusively found in marine environments, which has the genetic capacity of urea and cyanate utilization and is enriched in genes allowing it to cope with external environmental stressors, such as energy limitation. Our results suggest that specific microbial groups are not only able to survive over geological timescales, but also thrive in the deep subsurface when encountering favorable conditions.

microbiology↗

bioRxiv2018

Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism

The Nucleocytoplasmic Large DNA Viruses (NCLDV) of eukaryotes (proposed order \"Megavirales\") include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified Pithoviruses, Pandoraviruses, Molliviruses and Faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep-sea sediments from the Lokis Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high quality genomic bins of novel NCLDV, 15 of which are closest related to Pithoviruses, 5 to Marseilleviruses, 1 to Iridoviruses, and 2 to Klosneuviruses. Some of the identified Pitho-like and Marseille-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses have a broad range of apparent genome sizes including putative giant members of the family Marseilleviridae, in agreement with multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the Pitho-Irido-Marseille branch of NCLDV. Similarly to other giant viruses, the Pitho-like viruses from Lokis Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than detected previously. Genome comparison suggests extensive gene exchange between members of the Pitho-like viruses and Mimiviridae. Further exploration of the genomic diversity of \"Megavirales\" in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.\n\nImportanceGenomics and evolution of giant viruses is one of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diveristy of the Nucleo-Cytoplasmic Large DNA Viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.

microbiology↗