Biology subjects

Sjoqvist, C.

Publications and source records attributed to Sjoqvist, C..

3 recordsLinked to original sources

bioRxiv2023

Local adaptation of a marine diatom is governed by genome-wide changes in diverse metabolic processes

Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics data with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experiment that has played out over the past 8,000 years in one of the worlds largest brackish water bodies: the colonization of the Baltic Sea by the marine diatom Skeletonema marinoi. To this end, we used a novel approach for protist population genomics, combining target capture of the entire nuclear genome with pooled sequencing, and showed that the method performs well on both cultures and single cells. Genotype-environment association analyses identified >3,000 genes with signals of selection in response to major environmental gradients in the Baltic Sea, which apart from salinity, include marked differences in temperature and nutrient availability. Locally adapted genes were related to diverse metabolic processes, including signal transduction, cell cycle, DNA methylation, and maintenance of homeostasis. The locally adapted genes showed significant overlap with salinity-responsive genes identified in a laboratory common garden experiment, suggesting the Baltic salinity gradient is a major factor driving local adaptation of S. marinoi. Altogether, our data show that local adaptation of phytoplankton to complex coastal environments, which are characterized by a multitude of environmental gradients, is driven by intricate changes in diverse metabolic pathways and functions.

microbiology↗

bioRxiv2021

Genotype-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline

The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of S. marinoi grown in a common garden. Our experiment included eight genotypes from source populations spanning the Baltic Sea salinity cline. Changes in gene expression revealed a shared response to salinity across genotypes, where low salinities induced profound changes in cellular metabolism, including upregulation of carbon fixation and storage compound biosynthesis, and increased nutrient demand and oxidative stress. Nevertheless, the genotype effect overshadowed the salinity effect, as genotypes differed significantly in their response, both in the magnitude and direction of gene expression. Intraspecific differences included regulation of transcription and translation, nitrogen metabolism, cell signaling, and aerobic respiration. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond and adapt to environmental change.

microbiology↗

bioRxiv2020

Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

BackgroundBacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. However, difficulties in culturing the majority of aquatic prokaryotic species have complicated the study of their microdiversity. Here, we present POGENOM, a software that quantifies population genomic indices from metagenome data, enabling comparative analysis of genomic diversity and differentiation in multiple species in parallel. We demonstrate POGENOM on metagenome-assembled genomes from the Baltic Sea and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. ResultsThe majority of the investigated species, representing several major bacterioplankton clades, displayed population structure correlating significantly with environmental factors such as salinity, temperature, nutrients and oxygen, both over horizontal and vertical dimensions. Population differentiation was more pronounced over spatial than temporal scales, although some species displayed population structure correlating with season. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations existence along the salinity range. ConclusionsWe provide a new tool for high-throughput population genomics analysis based on metagenomics data. From an evolutionary point of view, our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species, despite their seemingly unlimited dispersal potential. This is of central importance when learning about how species have adapted to new environmental conditions and what their adaptive potential is in the face of Global Change.

genomics↗