Biology subjects

John, U.

Publications and source records attributed to John, U..

6 recordsLinked to original sources

bioRxiv2026

Microbial priming controls terrestrial carbon burial in marine sediments

Marine sediments are a globally important sink for organic carbon of both marine and terrestrial origin, yet far less terrestrial carbon is ultimately buried than rivers deliver to the ocean margins. This long-standing "terrestrial carbon conundrum" has resisted explanation, largely because conventional bulk proxies cannot distinguish marine, terrestrial and microbial-degrader carbon pools. Here we use sedimentary ancient DNA from five records spanning the Bering Sea to the Sea of Okhotsk over the past 30,000 years to reconstruct organic carbon resolved simultaneously by taxonomy and habitat. Integrating these taxon-resolved carbon estimates with environmental proxies across the last glacial-interglacial cycle, we find that terrestrial carbon burial is governed not only by supply but by biogeochemical interactions previously documented only in soils. Microbial processing splits into two competing pathways: under priming, marine organic matter fuels the degradation of terrestrial organic matter, whereas under preferential substrate utilization microbes consume marine organic matter and spare terrestrial carbon. Both pathways are triggered only once marine organic-matter availability crosses a critical, temperature-governed threshold. This temperature-sensitive cascade reveals a previously unrecognized vulnerability of the ocean's carbon sink to global warming.

biochemistry↗

bioRxiv2025

Ontogenetic sequence of differential gene expression in predator-induced Daphnia pulex

As a reaction to the presence of predators, many Daphnia species develop morphological defenses. These defenses are phenotypically plastic traits as their production is switched off in the absence of the predator. Previous studies identified some neurohumoral factors and candidate genes that are involved in the development of the defenses. However, there is still significant uncertainty regarding the involvement of certain genes and factors, and minimal information is available about the timing of gene expression changes throughout this development. In the current study, we thus performed a candidate-independent gene expression analysis of defense development over juvenile developmental stages in D. pulex. We analyzed transcriptome responses of the microcrustaceans to the natural mix of predator-emitted compounds and also to the pure kairomone which had been identified recently and which we synthesized. With the data obtained we show that the main factor correlating with the global gene expression patterns in Daphnia is molt cycle. Influence of kairomone treatment on the level of global gene expression is evident only in certain stages. The stages generally show unique patterns of kairomone-induced gene expression. However, expression profiles are highly similar for the naturally released and the chemically synthesized kairomone in each one of the stages. A number of genes with regulatory, structural and detoxification roles are differentially expressed as a reaction to the kairomone treatment. The most consistent response was found in the expression levels of ilp-3 coding for an insulin-like peptide. Gene knockdown experiments suggest that this hormone plays a role in the production of the defense. Many of the genes responding to the kairomone treatment have no predicted function stressing the need to investigate gene functions in Daphnia.

genetics↗

bioRxiv2024

A CRISPR-Cas9 assisted analysis of single-cell microbiomes for identifying rare bacterial taxa in phycospheres of diatoms

Primary production in aquatic systems is governed by interactions between microalgae and their associated bacteria. Most of our knowledge about algal microbiomes stems from natural mixed communities or isolated algal monocultures, which therefore does neither address the role of genotypic diversity among the algal host cells nor do they reveal how this host diversity impacts the assembly process of associated bacteria. To overcome this knowledge gap, we developed a single-cell 16S sequencing approach in combination with CRISPR-Cas9 guided depletion of host 16S contaminations from the chloroplast. The validity of this novel method was tested by comparing bacterial communities of 144 single-cells across three genotypes of the Arctic marine diatom Thalassiosira gravida grown under different environmental conditions. From these, 62 single-cells were additionally sequenced after CRISPR-Cas9 treatment. Due to the improved sequencing depth, bacterial richness associated with individual diatom cells was increased by up to 56%. By applying this CRISPR-Cas9 treatment we not only revealed intraspecific host-genotype associations but also rare bacterial taxa that were not detected by standard 16S rRNA gene metabarcoding. Thus, the CRISPR-Cas9 assisted single-cell approach developed in this study advances our understanding on how the intraspecific diversity among algal hosts impacts the assembly process of their associated bacteria. This knowledge is essential to understand the co-evolution and adaptation of species in algal microbiomes.

microbiology↗

bioRxiv2022

Evolution of resilience against heat stress in a red-tide dinoflagellate

"Red tides" are harmful algal blooms (HABs) caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. Increasingly frequent, HABs are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters. Here, we present the de novo assembled genome (~4.75 Gbp), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we studied the molecular mechanisms that underpin response to temperature stress, which is relevant to current ocean warming trends. We discovered a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. Our multi-omics analyses uncover the molecular response to heat stress in an important HAB species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation.

genomics↗

bioRxiv2021

An 18S V4 rDNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth.

Arctic marine protist communities have been understudied due to challenging sampling conditions, in particular during winter and in deep waters. The aim of this study was to improve our knowledge on Arctic protist diversity through the year, both in the epipelagic (< 200 m depth) and mesopelagic zones (200-1000 m depth). Sampling campaigns were performed in 2014, during five different months, to capture the various phases of the Arctic primary production: January (winter), March (pre-bloom), May (spring bloom), August (post-bloom) and November (early winter). The cruises were undertaken west and north of the Svalbard archipelago, where warmer Atlantic waters from the West Spitsbergen Current meets cold Arctic waters from the Arctic Ocean. From each cruise, station, and depth, 50 L of sea water were collected and the plankton was size-fractionated by serial filtration into four size fractions between 0.45-200 {micro}m, representing the picoplankton, nanoplankton and microplankton. In addition vertical net hauls were taken from 50 m depth to the surface at selected stations. From the plankton samples DNA was extracted, the V4 region of the 18S rRNA-gene was amplified by PCR with universal eukaryote primers and the amplicons were sequenced by Illumina high-throughput sequencing. Sequences were clustered into Amplicon Sequence Variants (ASVs), representing protist genotypes, with the dada2 pipeline. Taxonomic classification was made against the curated Protist Ribosomal Reference database (PR2). Altogether 6,536 protist ASVs were obtained (including 54 fungal ASVs). Both ASV richness and taxonomic composition were strongly dependent on size-fraction, season, and depth. ASV richness was generally higher in the smaller fractions, and higher in winter and the mesopelagic samples than in samples from the well-lit epipelagic zone during summer. During spring and summer, the phytoplankton groups diatoms, chlorophytes and haptophytes dominated in the epipelagic zone. Parasitic and heterotrophic groups such as Syndiniales and certain dinoflagel-lates dominated in the mesopelagic zone all year, as well as in the epipelagic zone during the winter. The dataset is available at https://doi.org/10.17882/79823, (Egge et al., 2014).

ecology↗

bioRxiv2020

Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum

The marine ciliate Mesodinium rubrum is famous for its ability to acquire and exploit chloroplasts and other cell organelles from some cryptophyte algal species. We sequenced genomes and transcriptomes of free-swimming Teleaulax amphioxeia, as well as well-fed and starved M. rubrum in order to understand cellular processes upon sequestration under different prey and light conditions. From its prey, the ciliate acquires the ability to photosynthesize as well as the potential to metabolize several essential compounds including lysine, glycan, and vitamins that elucidate its specific prey dependency. M. rubrum does not express photosynthesis related genes itself, but elicits considerable transcriptional control of the acquired cryptophyte organelles. This control is limited as light dependent transcriptional changes found in free-swimming T. amphioxeia got lost after sequestration. We found strong transcriptional rewiring of the cryptophyte nucleus upon sequestration, where 35% of the T. amphioxeia genes were significantly differentially expressed within well-fed M. rubrum. Qualitatively, 68% of all genes expressed within well-fed M. rubrum originated from T. amphioxeia. Quantitatively, these genes contributed up to 48% to the global transcriptome in well-fed M. rubrum and down to 11% in starved M. rubrum. This tertiary endosymbiosis system functions for several weeks, when deprived of prey. After this point in time, the ciliate dies if not supplied with fresh prey cells. M. rubrum represents one evolutionary way of acquiring photosystems from its algal prey, and might represent a step on the evolutionary way towards a permanent tertiary endosymbiosis.

evolutionary biology↗