Biology subjects

Oldenburg, E.

Publications and source records attributed to Oldenburg, E..

7 recordsLinked to original sources

bioRxiv2026

Population dynamics of Arctic phytoplankton and mycoplankton reveal chytrid-mediated diatom bloom termination

Chytrids are unicellular fungi that infect and degrade phytoplankton as parasites or saprotrophs. They impact not only food availability and quality in surface waters but also carbon cycling and sequestration. So far, their ecological significance has mostly been investigated for freshwater environments, whereas observations for marine environments are scarce -- even though chytrids can be highly abundant there, too (as shown for the Arctic Ocean). To test the chytrids potential to control phytoplankton dynamics in the Arctic Ocean, we analysed metabarcoding and photosynthetic pigment data from two expeditions, Tara Polar Circle and MOSAiC; the latter providing a dense sampling transect across one year from the under-ice water column and sea ice samples. The phytoplankton communities of both environments were dominated by diatoms, with strong seasonal effects indicating blooms in the water column. Chytrids dominated fungal communities in both environments and revealed a strong cryo-pelagic coupling. They were especially abundant during the sea ice melt in water samples and in ice-associated (sympagic) samples, where they represented >2% and up to 61%, respectively, of all combined reads assigned to chytrids or phytoplankton. Co-occurrences of the two most abundant chytrid taxa with some of the most abundant diatom taxa and niche differentiation from other potential diatom parasites are consistent with the chytrids critical role in controlling diatom blooms, especially in sympagic habitats.

ecology↗

bioRxiv2026

Easy-to-use whole-genome sequencing workflows and standardized practices to uncover hidden genetic variation in Synechocystis PCC 6803 wild-type and knock-out strains

Knock-out mutants are often used to study gene function by disrupting a specific gene and comparing the mutant to a wild-type strain. Reliable interpretation, however, requires that the two strains differ only by the intended mutation and that the observed phenotype is caused specifically by the deleted gene. In the highly polyploid cyanobacterium Synechocystis sp. PCC 6803, this is particularly challenging because incomplete segregation can mask genetic heterogeneity or secondary suppressor mutations. The genetic variation among laboratory wild-type lines can further confound phenotypic analyses. We show that these challenges can be addressed by routine strain validation via whole-genome sequencing (WGS). To this end, we developed and tested user friendly workflows for short-read (Illumina), long-read (Oxford Nanopore Technologies; ONT), and hybrid data, providing standardized quality control, variant calling, and structural variant detection. We benchmarked their performance in detecting single-nucleotide polymorphisms (SNPs), small indels, and structural variants using simulated datasets across different coverages and mixed populations. Applying the workflows to three Synechocystis sp. PCC 6803 wild-type lines revealed multiple sequence and structural differences relative to the reference genome, including previously undescribed genetic variants, underscoring the importance of documenting the strain background and the value of long-read sequencing. Characterization of two independent 6-phosphogluconate dehydrogenase (gnd) knock-out mutants and their complemented strains highlighted how a failed rescue can reveal a phenotype unrelated to the intended knock-out. An automated literature analysis revealed that only a minority of the investigated Synechocystis studies that used knock-out mutants included complementation as a control (39%), whereas this practice is more common in studies involving Escherichia coli (63%) and Saccharomyces cerevisiae (55%). Based on these results, we propose a practical guide for standardizing knock-out phenotyping in Synechocystis PCC 6803. Combined with accessible workflows for routine whole-genome validation, this framework aims to support more robust and reproducible knock-out studies in the future.

microbiology↗

bioRxiv2024

Arctic Ocean virus communities: seasonality, bipolarity, and prokaryotic interactions

Viruses play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemical processes. However, we know little about the diversity, seasonality, and host interactions of viruses in polar waters. To address this, we studied dsDNA viruses in the Arctic Fram Strait across four years via 47 long-read metagenomes of the cellular size-fraction. Among 5,662 vOTUs, 69%, 30% and 1.4% were bacteriophages (Myoviridae, Podoviridae, and Siphoviridae), Unassigned, and Phycodnaviridae, respectively. Viral coverage was, on average, 5-fold higher than prokaryotic coverage, and 8-fold higher in summer. Viral community composition showed annual peaks in similarity and was strongly correlated with prokaryotic community composition. Using a Convergent Cross Mapping network, we identified putative virus-host interactions and six ecological modules, each associated with distinct environmental conditions. The network also revealed putative novel cyanophages with time-lagged correlations to their hosts (late summer) as well as diverse viruses correlated with Nitrososphaerales (winter). By comparison with global metagenomes, we found that 42% of Fram Strait vOTUs peaked in abundance in high latitude regions of both hemispheres (average 61{degrees}N and 51{degrees}S), and encoded proteins with biochemical signatures of cold adaptation. Our study reveals a rich diversity of polar viruses with pronounced seasonality, providing a foundation for understanding how they regulate and impact ecosystem functionality in changing polar oceans.

microbiology↗

bioRxiv2024

Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome

Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. Thus far, we know little about the structuring of community functionality and the coupling between taxonomy and function over seasonal environmental gradients. To address this, we employed autonomous sampling devices and in situ sensors to investigate the taxonomic and functional dynamics of a pelagic Arctic Ocean microbiome over a four-year period. We demonstrate that the dominant prokaryotic and microeukaryotic populations exhibit recurrent, unimodal fluctuations each year, with community gene content following the same trend. The recurrent dynamics within the prokaryotic microbiome are structured into five temporal modules that represent distinct ecological states, characterised by unique taxonomic and metabolic signatures and connections to specific microeukaryotic populations and oceanographic conditions. For instance, Cand. Nitrosopumilus and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, along with Radiolarians. In contrast, late summer is characterised by Amylibacter, sulfur compound metabolism and diverse Haptophyta lineages. Exploring the composition of modules further along with their degree of functional redundancy and the structuring of genetic diversity within functions over time revealed seasonal heterogeneity in environmental selection processes. In particular, we observe strong selection pressure on a functional level in spring while late polar night features weaker selection pressure that likely acts on an organismal level. By integrating taxonomic, functional, and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced environmental variability in understudied, yet rapidly changing polar marine ecosystems.

microbiology↗

bioRxiv2024

Beyond blooms: A novel time series analysis framework predicts seasonal keystone species and sheds light on ecosystem stability in the Fram strait

A thorough understanding of ecosystem functioning in the Arctic Ocean, a region under severe threat by climate change, requires detailed studies on linkages between biodiversity and ecosystem stability. The identification of keystone species with special relevance for ecosystem stability is of great importance, yet difficult to achieve with established community assessments. In the case of microbes, metabarcoding and metagenomics offer fundamental insights into community structure and function, yet remain limited regarding the ecological relevance of individual taxa. To overcome this limitation, we have developed an analytical approach based on three different methods: Co-Occurrence Networks, Convergent Cross Mapping, and Energy Landscape Analysis. These methods enable the identification of seasonal communities in microbial ecosystems, elucidate their interactions, and predict potential stable community configurations under varying environmental conditions. Combining the outcomes of these three methods allowed us to define 38 keystone species in the Arctic Fram Strait that represent different trophic modes within the food web, and might signify indicator for ecosystem functionality under the impact of environmental change. Our research reveals a clear seasonal pattern in phytoplankton composition, with distinct assemblages characterizing the phases of carbon fixation (polar day) and consumption (polar night). Species interactions exhibited strong seasonality, with significant influence of summer communities on winter communities but not vice versa. Spring harbored two distinct groups: consumers (heterotrophs), strongly linked to polar night, and photoautotrophs (mainly Bacillariophyta). These groups are not causally related, suggesting a "winter reset" with selective effects that facilitates a new blooming period, allowing survivors of the dark phase to emerge. Energy Landscape Analysis showed that winter communities are more stable than summer communities. In summary, the ecological landscape of the Fram Strait can be categorized into two distinct phases: a production phase governed by specialized organisms that are highly responsive to environmental variability, and a heterotrophic phase dominated by generalist species with enhanced resilience.

bioinformatics↗

bioRxiv2023

Sea-ice melt determines seasonal phytoplankton dynamics and delimits the habitat of temperate Atlantic taxa as the Arctic Ocean atlantifies

The Arctic Ocean is one of the regions where anthropogenic environmental change is progressing most rapidly and drastically. The impact of rising temperatures and decreasing sea ice on Arctic marine microbial communities is yet not well understood. Microbes form the basis of food webs in the Arctic Ocean, providing energy for larger organisms. Previous studies have shown that Atlantic taxa associated with low light are robust to more polar conditions. In this study, we compared to which extent sea ice melt influences light-associated phytoplankton dynamics and biodiversity over two years at two mooring locations in the Fram Strait. One mooring is deployed in pure Atlantic water, and the second in the intermittently ice-covered Marginal Ice Zone. Time-series analysis of amplicon sequence variants abundance over a two-year period, allowed us to identify communities of co-occurring taxa that exhibit similar patterns throughout the annual cycle. We then examined how alterations in environmental conditions affect the prevalence of species. During high abundance periods of diatoms, polar phytoplankton populations dominated, while temperate taxa were weakly represented. Generally, polar pelagic and ice-associated taxa (such as Fragilariopsis cylindrus or Melosira arctica) were more prevalent in Atlantic conditions whereas temperate taxa (such as Odontella aurita or Proboscia alata) have limited potential to persist in colder ice-impacted waters. In contrast to previous assumptions, we think that sea-ice melt acts as a barrier to the horizontal extent of temperate diatoms by preventing their succession at places strongly influenced by polar conditions such as the melting sea ice.

ecology↗

bioRxiv2022

Variations in Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

The Arctic Ocean is experiencing unprecedented changes as a result of climate warming, necessitating detailed analyses on the ecology and dynamics of biological communities to understand current and future ecosystem shifts. Here we show the pronounced impact that variations in Atlantic water influx and sea-ice cover have on bacterial communities in the East Greenland Current (Fram Strait) using two, 2-year high-resolution amplicon datasets and an annual cycle of long-read metagenomes. Densely ice-covered polar waters harboured a temporally stable, resident microbiome. In contrast, low-ice cover and Atlantic water influx shifted community dominance to seasonally fluctuating populations enriched in genes for phytoplankton-derived organic matter degradation. We identified signature populations associated with distinct oceanographic conditions and predicted their ecological niches. Our study indicates progressing "Biological Atlantification" in the Arctic Ocean, where the niche space of Arctic bacterial populations will diminish, while communities that taxonomically and functionally resemble those in temperate oceans will become more widespread.

microbiology↗