Biology subjects

Eriksson, D.

Publications and source records attributed to Eriksson, D..

8 recordsLinked to original sources

bioRxiv2026

Genomically and ecologically cohesive subspecies as biologically meaningful units in the global ocean microbiome

Microbial diversity is organised into operationally defined species. However, it remains unclear whether these, or finer-scale groups represent biologically meaningful units in natural communities. Here, we implement a scalable, cultivation-independent framework to identify 724 genomically discrete and ecologically cohesive subspecies across 270 species in the global ocean microbiome. Their diversification is underpinned by gene-specific, nucleotide-level selection on the core genomic backbone and by variable restructuring of gene content, both of which proceed in a subspecies-specific manner. In over half of the species tested, subspecies were significantly associated with distinct environmental conditions, most frequently temperature. This coupling of genomic discreteness and ecological cohesiveness positions these subspecies as biologically meaningful units, a fundamental level at which ecological and evolutionary processes jointly drive divergence and structure microbial diversity in the oceans.

ecology↗

bioRxiv2026

Phytoplankton performance in the lab predicts occurrence in the field across a global temperature gradient

Biologists aim to predict where species will survive and thrive as the planet warms. To do so, we often rely on data-hungry species distribution models (SDMs) that use associations between species occurrences and environmental predictors to capture the realised niche. An alternative basis for predictions is to experimentally quantify the effect of environmental drivers on performance, which captures the fundamental niche. We presently do not know which of these approaches represents a better path towards accurate forecasts. SDMs may depend too strongly on present-day environmental covariation, which will change in the future. In contrast, a major shortcoming of experiments is that they ignore most environmental drivers to focus on one or two. Quantifying how well fundamental and realised niches agree today would help establish how useful both SDMs and experiments are likely to be. We therefore compared both niches in 39 relatively common marine phytoplankton species. The temperature-dependence of population growth rate was characterised with a thermal performance curve model applied to lab experimental data, and the temperature-dependence of species occurrence probability estimated with SDMs applied to a global compilation of marine presence records. We found a fairly strong, near 1:1 relationship between measures of thermal niche centre: the median growth temperature in the lab and the median occurrence temperature in the field (R2 = 0.49). We also found a modest positive relationship between measures of thermal niche width, the growth niche width and the occurrence niche width (R2 = 0.24). This agreement should increase our confidence in environmental preferences inferred with SDMs. It also suggests that simple experiments can reliably constrain species ranges and help forecast range shifts. This has important implications for forecasting community composition and ecosystem processes, as we ought to be able to predict range shifts in biogeochemically-important taxa such as diatoms and nitrogen-fixing cyanobacteria.

ecology↗

bioRxiv2025

Variations in the latitudinal diversity gradients of the ocean microbiome

Latitudinal diversity gradients (LDGs), typically declining from equator to poles, are a pervasive macroecological pattern, yet their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed layer microbiomes exhibited diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) showed no latitudinal diversity structuring. Taxonomic resolution revealed that the mixed layer LDG was underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibited distinct or contrasting LDGs. Diversity structuring also varied by seasons and regions, governed by temperature and nutrient availability. Together, these findings highlight that within the ocean microbiome, LDGs are not universal, but lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.

microbiology↗

bioRxiv2022

Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq

Phage Immunoprecipitation-Sequencing (PhIP-Seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-Seq for autoantigen discovery, including our previous work (Vazquez et al. 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki Disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), and finally, mild and severe forms of COVID19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as PDYN in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in 2 patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-Seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID19, including the endosomal protein EEA1. Together, scaled PhIP-Seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.

immunology↗

bioRxiv2021

Conserved structures of neural activity in sensorimotor cortex of freely moving rats allow cross-subject decoding

Our knowledge about neuronal activity in the sensorimotor cortex relies primarily on stereotyped movements that are strictly controlled in experimental settings. It remains unclear how results can be carried over to less constrained behavior like that of freely moving subjects. Toward this goal, we developed a self-paced behavioral paradigm that encouraged rats to engage in different movement types. We employed bilateral electrophysiological recordings across the entire sensorimotor cortex and simultaneous paw tracking. These techniques revealed behavioral coupling of neurons with lateralization and an anterior-posterior gradient from the premotor to the primary sensory cortex. The structure of population activity patterns was conserved across animals despite the severe under-sampling of the total number of neurons and variations in electrode positions across individuals. We demonstrated cross-subject and cross-session generalization in a decoding task through alignments of low-dimensional neural manifolds, providing evidence of a conserved neuronal code One-sentence summarySimilarities in neural population structures across the sensorimotor cortex enable generalization across animals in the decoding of unconstrained behavior. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/433869v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@4dffbborg.highwire.dtl.DTLVardef@d07d55org.highwire.dtl.DTLVardef@1d459eborg.highwire.dtl.DTLVardef@5b5d78_HPS_FORMAT_FIGEXP M_FIG Conserved structures of neural activity in freely moving rats allow for cross-subject decoding. (a) We conducted electrophysiological recordings across the bilateral sensorimotor cortex of six freely moving rats. Neural activities were projected into a low-dimensional space with LEMs (22). (b) In a decoding task, points in the aligned low-dimensional neural state space were used as input for a classifier that predicted behavioral labels. Importantly, training and testing data originated from different rats. (c) Our procedure led to successful cross-subject generalization for sessions with sufficient numbers of recorded units. The rat and brain drawings are adapted from scalablebrainatlas.incf.org and SciDraw. C_FIG

neuroscience↗

bioRxiv2021

Multichannel optogenetics combined with laminar recordings for ultra-controlled neuronal interrogation

Simultaneous large-scale recordings and optogenetic interventions hold the promise to decipher the fast-paced and multifaceted dialogue between neurons that sustains brain function. Here we developed unprecedentedly thin, cell-sized Lambertian side-emitting optical fibers and combined them with silicon probes to achieve high quality recordings and ultrafast multichannel optogenetic inhibition in freely moving animals. Our new framework paves the way for large-scale photo tagging and controlled interrogation of rapid neuronal communication in any combination of brain areas. HighlightsTo combine large-scale recordings with optical perturbation we have developed a number of new techniques such as thin optical side-emitting fibers, a fiber matrix connector for thin fibers, an electro-optical commutator for multiple thin fibers, an active patch cord, a flexible fiber bundle ribbon cable, and a modular multi-optrode implantation holder.

neuroscience↗

bioRxiv2019

Slow and fast cortical dynamics distinguish motor planning and execution

The smooth conduction of movements requires simultaneous motor planning and execution according to internal goals. So far it is not known how such movement plans can be modified without being distorted by ongoing movements. Previous studies have isolated planning and execution related neuronal activity by separating behavioral planning and movement periods in time by sensory cues1-7. Here, we introduced two novel tasks in which motor planning developed intrinsically. We separated this continuous self-paced motor planning statistically from motor execution by experimentally minimizing the repetitiveness of the movements. Thereby, we found that in the rat sensorimotor cortex, neuronal motor planning processes evolved with slower dynamics than movement related responses both on a sorted unit and population level. The fast evolving neuronal activity preceded skilled forelimb movements while it coincided with movements in a locomotor task. We captured this fast evolving movement related activity via a high-pass filter approach and confirmed the results with optogenetic stimulations. As biological mechanism underlying such a high pass filtering we suggest neuronal adaption. The differences in dynamics combined with a high pass filtering mechanism represents a simple principle for concurrent motor planning and execution in which planning will result in relatively slow dynamics that will not produce movements.

neuroscience↗

bioRxiv2019

Reconstruction of in-vivo subthreshold activity of single neurons from large-scale spiking recordings

Current developments in the manufacturing of silicon probes allow recording of spikes from large populations of neurons from several brain structures in freely moving animals. It is still, however, technically challenging to record the membrane potential from awake behaving animals. Routine access to the subthreshold activity of neurons would be of great value in order to understand the role of, for example, neuronal integration, oscillations, and excitability. Here we have developed a framework for reconstructing the subthreshold activity of single neurons using the spiking activity from large neuronal populations. The reconstruction accuracy and reliability have been evaluated with ground truth data provided from simultaneous patch clamp membrane potential recordings in-vivo. Given the abundance of large-scale spike recordings in the contemporary systems neuroscience society, this approach provides a general access to the subthreshold activity and hence could shed light on the intricate mechanisms of the genesis of spiking activity.

neuroscience↗