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bioRxiv2023

Exploring the effects of ecological parameters on the spatial structure of genetic tree sequences

1Geographic space is a fundamental dimension of evolutionary change, determining how individuals disperse and interact with each other. Consequently, space has an important influence on the structure of genealogies and the distribution of genetic variants over time. Recently, the development of highly flexible simulation tools and computational methods for genealogical inference has greatly increased the potential for incorporating space into models of population genetic variation. It is now possible to explore how spatial ecological parameters can influence the distribution of genetic variation among individuals in unprecedented detail. In this study, we explore the effects of three specific parameters (the dispersal distance, competition distance and mate choice distance) on the spatial structure of genealogies. We carry out a series of in silico experiments using forwards-in-time simulations to determine how these parameters influence the distance between closely- and distantly-related individuals. We also assess the accuracy of the maximum likelihood estimation of the dispersal distance in a Gaussian model of dispersal from tree-sequence data, and highlight how it is affected by realistic factors such as finite habitat size and limited data. We find overall that the scale of mate choice in particular has marked patterns on short and long terms patterns of dispersal, as well as on the positions of individuals within a habitat. Our results showcase the potential for linking phylogeography, population genetics and ecology, in order to answer fundamental questions about the nature of spatial interactions across a landscape.

evolutionary biology↗

bioRxiv2023

An orphan protein drove the ecological expansion of nitrogen fixation

Nitrogenase metalloenzymes have catalyzed biological nitrogen fixation for billions of years and revolutionized planet Earth by supplying essential nitrogen to the biosphere. How these enzymes were built and distributed by microbial and evolutionary processes in a shifting geochemical landscape remains an open question. Here, we probe the birth and evolution of the G-subunit protein, an integral, Precambrian-age structural component of certain nitrogenase isozymes that makes its appearance midway through nitrogenase evolutionary history. We establish that the G-subunit is an orphan protein, with no homologs detected across wider protein diversity. We find that G-subunit emergence accompanied both the diversification of nitrogenase metal usage and an ecological expansion of nitrogen-fixing microbes during the transition in enviromental metal availabilities triggered by Earth surface oxygenation [~]2.5 billion years ago. Further, analyses of ancestral nitrogenase structures implicate a role for the G-subunit in novel metal incorporation, which would have primed nitrogenases and their hosts to exploit these newly diversified geochemical environments. However, permanent recruitment of the G-subunit into the nitrogenase complex was likely only enabled by tuning preexisting, protein interaction features that were selected prior to Earth oxygenation. Our results showcase how contingent evolutionary novelties shape microbial ecological responses and their global consequences.

evolutionary biology↗

bioRxiv2023

Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids

Chemosensory systems display exceptional variation between species, but little is known about how the evolution of gene expression and cell types contribute to this diversity. We have generated transcriptomes for five chemosensory tissues across six ecologically diverse Drosophila species and integrated their analyses with single-cell datasets to address these questions. The evolution of chemosensory transcriptomes has been predominantly shaped by stabilizing selection, but several thousand genes have nevertheless evolved expression changes in each tissue. Phylogenetic analyses of differentially expressed genes revealed strong evidence that their expression changes have been driven by a combination of cis-regulatory and cell composition evolution. We have also found that chemosensory-related gene families have undergone pervasive expression level changes and numerous species-specific expression gains/losses. Follow-up experiments revealed several chemoreceptors that evolved novel patterns of tissue and cellular expression that likely contribute to sensory differences. Finally, analyses of the genes that are differentially expressed between sexes uncovered extensive species-specific differences. Among these rapid changes, we discovered a D. melanogaster-specific excess of male-biased gene expression in its forelegs and identified sensory and muscle cells as the primary source of this dimorphism. Together, our analyses provide new insights for understanding evolutionary changes in ecologically key tissues at both global and individual gene levels.

evolutionary biology↗

bioRxiv2023

Annotating Metagenomically Assembled Bacteriophage from a Unique Ecological System using Protein Structure Prediction and Structure Homology Search

Emergent long read sequencing technologies such as Oxfords Nanopore platform are invaluable in constructing high quality and complete genomes from a metagenome, and are needed investigate unique ecosystems on a genetic level. However, generating informative functional annotations from sequences which are highly divergent to existing nucleotide and protein sequence databases is a major challenge. In this study, we present wet and dry lab techniques which allowed us to generate 5432 high quality sub-genomic sized metagenomic circular contigs from 10 samples of microbial communities. This unique ecological system exists in an environment enriched with naphthenic acid (NA), which is a major toxic byproduct in crude oil refining and the major carbon source to this community. Annotation by sequence homology alone was insufficient to characterize the community, so as proof of principle we took a subset of 227 putative bacteriophage and greatly improved our existing annotations by predicting the structures of hypothetical proteins with ColabFold and using structural homology searching with Foldseek. The proportion of proteins for each bacteriophage that were highly similar to known proteins increased from approximately 10% to about 50%, while the number of annotations with KEGG or GO terms increased from essentially 0% to 15%. Therefore, protein structure prediction and homology searches can produce more informative annotations for microbes in unique ecological systems. The characterization of novel microbial ecosystems involved in the bioremediation of crude oil-process-affected wastewater can be greatly improved and this method opens the door to the discovery of novel NA degrading pathways. IMPORTANCEFunctional annotation of metagenomic assembled sequences from novel or unique microbial communities is challenging when the sequences are highly dissimilar to organisms or proteins in the known databases. This is a major obstacle for researchers attempting to characterize the functional capabilities of unique ecosystems. In this study, we demonstrate that including protein structure prediction and homology search based methods vastly improves the annotation of predicted genes identified in novel putative bacteriophage in a bacterial community that degrades naphthenic acids the major toxic component of oil refinery wastewater. This method can be extended to similar genomics studies of unique, uncharacterized ecosystems, to improve their annotations. Please read the Instructions to Authors carefully, or browse the FAQs for further details.

genomics↗

bioRxiv2023

Ecological Inducers of the Yeast Filamentous Growth Pathway Reveal Environment-Dependent Roles for Pathway Components

Signaling modules, such as MAPK pathways, are evolutionarily conserved drivers of cell differentiation and stress responses. In many fungal species including pathogens, MAPK pathways control filamentous growth, where cells differentiate into an elongated cell type. The convenient model budding yeast Saccharomyces cerevisiae undergoes filamentous growth by the filamentous growth (fMAPK) pathway; however, the inducers of the pathway remain unclear, perhaps because pathway activity has been mainly studied in laboratory conditions. To address this knowledge gap, an ecological framework was employed, which uncovered new fMAPK pathway inducers, including pectin, a material found in plants, and the metabolic byproduct ethanol. We also show that induction by a known inducer of the pathway, the non-preferred carbon source galactose, required galactose metabolism and induced the pathway differently than glucose limitation or other non-preferred carbon sources. By exploring fMAPK pathway function in fruit, we found induction of the pathway led to visible digestion of fruit rind through a known target, PGU1, which encodes a pectolytic enzyme. Different stimuli revealed different modes of pathway signaling. For example, combinations of inducers (galactose and ethanol) stimulated the pathway to near maximal levels, which showed dispensability of several fMAPK pathway components (e.g. mucin sensor, PAK), but not others (e.g. adaptor, MAPKKK) and required the Ras2-PKA pathway. This included a difference between the transcription factor binding partners for the pathway, as Tec1p, but not Ste12p, was partly dispensable for fMAPK pathway activity. Thus, by exploring ecologically-relevant stimuli, new modes of MAPK pathway signaling were uncovered, perhaps revealing how a pathway can respond differently to specific environments. Data Availability StatementAll data are in the manuscript and/or supporting information files.

microbiology↗

bioRxiv2023

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia

Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies. Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into 3 enterotypes, with one particularly enriched at high altitudes. We assembled 9,977 taxonomically and functionally diverse metagenome-assembled genomes, the vast majority of which were not found in a dataset of previously published chicken microbes, or in the Genome Taxonomy Database. The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argues for further discoveries in other agro-ecologies.

microbiology↗

bioRxiv2023

Assessment of the Effects of Environmental Perturbations on Soil Ecology in A Terrestrial Mesocosm.

Climate change is altering ecosystems in unprecedented ways and necessitates the development of strategies that model ecosystems and allow for the evaluation of environmental impacts of perturbations: including climate events, novel approaches to agronomy or ecosystem management, and impacts of bio-industry and biotechnology innovations. Mesocosms present a platform to model some of the complexity of an ecosystem, while still being controlled and reproducible enough that they can be used to ask targeted questions and systematically assess the impacts of perturbation events. Herein, we established a methodological pipeline to assess the impact of three perturbation events (hydration, nutrification, contamination) upon plant-associated microbial communities using a terrestrial mesocosm. Mesocosms were assessed over a 30-day time-course following environmental perturbations, including modeling contamination with a foreign microbe via the introduction of Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a perturbation event in a system that models a terrestrial ecosystem. The resultant data show that our mesocosms are dynamic yet reproducible, and that the analysis pipeline presented here allowed for a longitudinal assessment of microbial population dynamics and abiotic soil characteristics following perturbations, as well as the fate of yeast in the soil. Notably, our data indicate that a single perturbation event can have long-lasting impact upon soil composition and underlying microbial populations. Thus, this approach can be used to ask targeted questions as well as gain insights on broader ecological trends of soil perturbation events. ImportanceSoils are key to a healthy environment, but the impact of human activities and climate change upon soil microbiomes remains unclear. It is challenging to model the complexity of an ecosystem in a laboratory; however, to gain insight on how ecosystems are impacted by outside perturbations it is valuable to develop approaches that mimic an environmental system. Here, we developed a mesocosm that uses readily accessible components that come together to model a terrestrial ecosystem which is coupled with an analysis pipeline to assess how various perturbations impact the soil. We demonstrate the utility of this approach by tracking the effects of three perturbations (water, nutrition, contamination with yeast) on the soil over the course of 30 days. Our results demonstrate that these treatments can have lasting impacts on the soil. These findings and the methods presented here could be useful to other researchers assessing how ecosystems respond to perturbations. HighlightsO_LIWe developed a pipeline using terrestrial mesocosms that allow for the analysis of how perturbations impact soil systems and demonstrate that it is effective for targeted detection of a microbe of interest as well as global phylogenomic observation of ecological changes due to external perturbation events. C_LIO_LIdigital droplet PCR was adapted to track a low abundance, non-native microbe in soil mesocosms. C_LIO_LITemporal sampling allowed for the longitudinal observation of soil response to a one-time perturbance. C_LIO_LIIntroduction of yeast and its associated growth media conferred an expansion of total biomass and increase in alpha-diversity and shifts in the beta-diversity of the soil microbiome. C_LIO_LITreatment with media or yeast resulted in the expansion in the relative contribution of fungal biomass and an increase in the relative abundances of Saccharomycetes and Trellomycetes, with decreases in Sordariomycetes, Leotiomycetes, and Eurotomycetes C_LIO_LIMedia or yeast introduction also resulted in an expansion of the relative abundances of Gammaproteobacteria, Bacilli, and Bacteroidia, and decreases in Actinomycetia and Acidobacteria. C_LI

microbiology↗

bioRxiv2023

Evidence for ecological tuning of novel anuran biofluorescent signals

Our study assesses the variability of amphibian biofluorescence and provides insight into its potential functions and role in anuran evolution. Via a field survey across South America, we discovered and documented patterns of biofluorescence in tropical amphibians. We more than tripled the number of species that have been tested for this trait and added representatives from previously untested anuran families. We found evidence for ecological tuning (i.e., the specific adaptation of a signal to the environment in which it is received) of the novel anuran biofluorescent signals. Across groups, the fluorescence excitation peak matches the wavelengths most available at twilight, the light environment in which most frog species are active. Additionally, biofluorescence emission spans both wavelengths of low availability in twilight and the peak sensitivity of green-sensitive rods in the anuran eye, likely increasing contrast of this signal for a conspecific receiver. With evidence of tuning to the ecology and sensory systems of frogs, our results suggest frog biofluorescence is likely functioning in anuran communication.

evolutionary biology↗

bioRxiv2023

Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios

The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages).We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics. Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers. Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism. We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.

microbiology↗

bioRxiv2023

Community ecology of phages on a clonal bacterial host

Bacteriophages are the most abundant and diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. Here, we have discovered a general mechanism that allows phage diversity to outstrip the diversity of their bacterial hosts. We assembled and passaged dozens of diverse phage communities on a single, non-coevolving strain of Escherichia coli until the phage communities reached equilibrium. In all cases, we found multiple phage species coexisted stably, despite competition for a single, clonal host population. Coexistence within these communities was supported through host phenotypic heterogeneity, whereby phages specialized on cells adopting different growth phenotypes. Our experiments reveal a rich community ecology of bacteriophages where multiple phage species coexist and interact at the scale of a single bacterial host. One-Sentence SummaryDiverse communities of phages emerge stably and consistently on a clonal bacterial host, enabled by phenotypic heterogeneity.

microbiology↗

bioRxiv2023

Unravelling species demographic responses to local and global past ecological disruptions using whole-genome sequencing in volcanic oceanic island organisms

Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of past ecological disruptions operating at local and regional scales on population demographic histories. We investigate potential drivers of past population dynamics for three closely related species of passerine birds from two volcanic oceanic islands, Reunion and Mauritius (Mascarene archipelago), with distinct volcanic history. Using ABC and PSMC inferences from complete genomes, we reconstructed the demographic history of the Reunion Grey White-eye (Zosterops borbonicus (Pennant, 1781)), the Reunion Olive White-eye (Z. olivaceus (Linnaeus, 1766)), and the Mauritius Grey White-eye (Z. mauritianus (Gmelin, 1789)), and searched for possible causes underlying similarities or differences between species living on the same or different islands. Both demographic inferences strongly support ancient and long-term expansions in all species. They also reveal different trajectories between species inhabiting different islands, but consistent demographic trajectories in species or populations from the same island. Species from Reunion appear to have experienced synchronous reductions in population size during the Last Glacial Maximum, a trend not seen in the Mauritian species. Overall, this study suggests that local events may have played a role in shaping population trajectories of these island species. It also highlights the potential of our conceptual framework to disentangle the effects of local and regional drivers on past species demography and long-term population processes.

evolutionary biology↗

bioRxiv2023

Species-specific epigenetic responses to drought stress of two sympatric oak species reflect their ecological preferences.

O_LIIn a context of climate change, it is necessary to decipher the strategies established by plants to cope with limited water supply. C_LIO_LITranscriptome, methylome and small RNA data were generated for two oak species with contrasting levels of drought tolerance (Quercus robur and Quercus petraea), under control and drought stress conditions C_LIO_LIAll data are in line with a species-specific response to drought stress consistent with their ecological preferences. The biological processes associated with genomic regions identified in all datasets were mainly associated with parietal processes in Q. petraea, which may explain in part its better tolerance to water deprivation. C_LIO_LIA significant proportion of DNA methylation differences observed in control conditions between the two oak species were maintained during DS which may constitute a pool of epigenetic markers discriminating these two oak species. These markers were enriched in highly differentiated SNPs suggesting that some of them may be associated both with the ecological differences or intrinsic barriers to reproduction between the two species. C_LIO_LIAn integrative approach of the three datasets revealed genomic co-locations of potential importance for forest three adaptation to drought stress. C_LI

genomics↗

bioRxiv2023

Exploring the genetic architecture of ecophysiological traits in microbial ecology using statistical analysis of the properties of protein sequences: application to the glycogen accumulating organism (GAO) phenotype

Nearly 50 years ago, King and Wilson introduced a key distinction between two types of genetic variation-named structural and regulatory variation-for exploring the molecular basis for phenotypic traits. Structural variation is genetic variation that will influence gene product structure via changes in coding sequence, whereas regulatory variation will influence the control of gene product expression. Here we repurpose these concepts to study the molecular basis of eco-physiological traits observed in microbial ecology, focusing on a specialized glycogen accumulating phenotype, known to be exhibited by a phylogenetically diverse group of microbes. We analyse the statistical properties of the protein sequence of the 1,4--glucan branching enzyme (glgB), a key enzyme responsible for formation of glycogen from linear glucans. We show that the glgB proteins in a subgroup of these organisms show unusual statistical properties of protein sequence length, sequence similarity and patterning of functional domains, compared to organisms that do not exhibit this phenotype. These findings suggest a role for structural genetic variation in determining this phenotype in some species. Our analysis holds implications for dissecting the genetic/genomic architecture of complex traits exhibited by microbial communities and also provides a complementary framework to presence-absence level analyses that are ubiquitous in microbial ecology.

genomics↗

bioRxiv2023

Quantifying and mitigating recorder-induced variability in ecological acoustic indices

Due to the complexity of soundscapes, Ecological Acoustic indices (EAI) are frequently used as metrics to summarize ecologically meaningful information from audio recordings. Recent technological advances have allowed the rapid development of many audio recording devices with significant hardware/firmware variations among brands, whose effects in calculating EAI have not yet be determined. In this work, we show how recordings of the same landscape with different devices effectively hinder reproducibility and produce contradictory results. To address these issues, we propose a preprocessing pipeline to reduce EAI variability resulting from different hardware without altering the target information in the audio. To this end, we tested eight EAI commonly used in soundscape analyses. We targeted three common cases of variability caused by recorder characteristics: sampling frequency, microphone gain variation, and frequency response. We quantified the difference in the probability density functions of each index among recorders according to the Kullback-Leibler divergence. As a result, our approach reduced up to 75% variations among recorders from different brands (AudioMoth and SongMeter) and identified the conditions in which these devices are comparable. In conclusion, we demonstrated that different devices effectively affect EAI and show how these variations can be mitigated. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/562620v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@13defb9org.highwire.dtl.DTLVardef@14597d8org.highwire.dtl.DTLVardef@1f3e795org.highwire.dtl.DTLVardef@1e90f2e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAddressing recorder-induced biases in acoustic indices for improved reproducibility. C_LIO_LIProposing an effective method to mitigate recorder-related biases. C_LIO_LIEvaluating pipeline proposed performance via acoustic index distribution analysis. C_LI

bioengineering↗

bioRxiv2023

Phenology and ecological role of Aerobic Anoxygenic Phototrophs in fresh waters

Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centres. Despite their substantial contribution to bacterial biomass, microbial food webs and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across three years in a temperate, meso-oligotrophic freshwater lake. AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM gene, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource we demonstrated recurrent and dynamic seasonal succession of the AAP community. The majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. Our results document the indigenous freshwater nature of the AAP community, characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom, contributing significantly to the ecological dynamics of lakes.

microbiology↗

bioRxiv2017

Two SecA/SecY Systems with Distinct Roles in the Ecological Adaptations of Bacteria

Bacteria interact with their environment through the secretion of a specific set of proteins (known as secretome) through various secretion systems. Molecular modifications of these secretion systems may lead to the emergence of new bacterial-environment interactions, although this remains unexplored. In this study we investigate the possible link between molecular and functional changes in secretion proteins and the ecological diversity of bacteria. We studied functional modifications in secretion proteins by identifying events of functional evolutionary divergence--that is, changes at the molecular level that have driven changes of proteins function. We present data supporting that these functional diversifications occurred in essential secretion proteins in bacteria. In particular, functional divergence of the two most important secretion proteins SecA and SecY in pathogenic bacteria suggests that molecular changes at these proteins are responsible for their adaptations to the host. Functional divergence has mainly occurred at protein domains involved in ATP hydrolysis in SecA and membrane pore formation in SecY. This divergence is stronger in pathogenic bacteria for protein copies resulting from the duplication of SecA/SecY, known as SecA2/SecY2. In concert with these results, we find that the secretome of bacteria with the strongest functional divergence is enriched for proteins specialized in the interaction with specific environments. We unravel evolutionary signatures that link mutations at secretion proteins to the ecological diversification of bacteria.

microbiology↗

bioRxiv2024

An ecological investigation of the effect of background noise on speech processing in a Virtual Classroom

Many real-life situations can be extremely noisy. Psychoacoustic studies have shown that background noise can have a detrimental effect on the ability to process and understand speech. However, most studies use stimuli and task designs that are highly artificial, limiting their generalization to more realistic contexts. Moreover, to date, we do not fully understand the neurophysiological consequences of trying to pay attention to speech in a noisy place. To address this lab to real-life gap and increase the ecological validity of speech in noise research, here we introduce a novel audiovisual Virtual Reality (VR) experimental platform. Combined with neurophysiological measurements of neural activity (EEG), eye-gaze and skin conductance (GSR) we studied the effects of background noise in a realistic context where the ability to process and understand continuous speech is especially important: A VR Classroom. Participants (n=32) sat in a VR Classroom and were told to pay attention to mini-lecture segments by a virtual teacher. Trials were either Quiet or contained background construction noise, emitted from outside the classroom window, which was either Continuous (drilling) or Intermittent (air hammers). Result show that background noise had a detrimental effect on learning outcomes, which was also accompanied by reduced neural tracking of the teachers speech. Comparison of the two noise types showed that the intermittent construction noise was more disruptive than continuous noise, as index by both behavioral and neural measures, and it also elicited higher skin-conductance levels, reflecting heightened arousal. Interesting, eye-gaze dynamics were not affected by the presence of noise. This study advances our understanding of the neurophysiological effects of background noise and extends it to more ecologically relevant contexts. It also emphasizes the role that temporal dynamics play for processing speech in noise, highlighting the need to consider the features of realistic noises, as we expand speech in noise research to increasingly realistic circumstances.

neuroscience↗

bioRxiv2024

Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.

Microbiomes are generally characterized by high diversity of coexisting microbial species and strains that remains stable within a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis obtained, namely, pure competition, host-parasite relationship and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environments. These findings show that basic phenomena that are universal in microbial communities, environmental variation and HGT, provide for stabilization of microbial diversity and ecological complexity.

evolutionary biology↗