Biology subjects

Bowler, C.

Publications and source records attributed to Bowler, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2021

Contribution of genome scale metabolic modeling to niche theory

Standard niche modeling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome-scale descriptions of these organisms. This study over-comes this shortcoming by proposing a new conceptual niche that encompasses the whole metabolic capabilities of an organism. The so-called metabolic niche resumes well-known traits such as nutrient needs and their dependencies for survival. Despite the computational challenge, its implementation allows the detection of traits and the formal comparison of niches of different organisms, emphasizing that the presence-absence of functional genes is not enough to approximate the phenotype. Further statistical exploration of an organisms niche sheds light on genes essential for the metabolic niche and their role in understanding various biological experiments, such as transcriptomics, paving the way for incorporating better the genome-scale description in ecological studies.

ecology↗

bioRxiv2021

Evolutionary analysis of DNA methyltransferases in microeukaryotes: Insights from the model diatom Phaeodactylum tricornutum

Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes that include the main phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a pioneering view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.

genomics↗

bioRxiv2021

A robust approach to estimate relative phytoplankton cell abundance from metagenomic data

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Phytoplankton communities are generally studied by PCR amplification of bacterial (16S), nuclear (18S) or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. In addition, rRNA marker genes fail to capture both cyanobacteria and photosynthetic eukaryotes simultaneously. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the Tara Oceans datasets, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these organisms, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.

ecology↗

bioRxiv2021

Uncharted biosynthetic potential of the ocean microbiome

Microbes are phylogenetically and metabolically diverse. Yet capturing this diversity, assigning functions to host organisms and exploring the biosynthetic potential in natural environments remains challenging. We reconstructed >25,000 draft genomes, including from >2,500 uncharacterized species, from globally-distributed ocean microbial communities, and combined them with [~]10,000 genomes from cultivated and single cells. Mining this resource revealed [~]40,000 putative biosynthetic gene clusters (BGCs), many from unknown phylogenetic groups. Among these, we discovered Candidatus Eudoremicrobiaceae as one of the most biosynthetically diverse microbes detected to date. Discrete transcriptional states structuring natural populations were associated with a potentially niche-partitioning role for BGC products. Together with the characterization of the first Eudoremicrobiaceae natural product, this study demonstrates how microbiomics enables prospecting for candidate bioactive compounds in underexplored microbes and environments.

microbiology↗

bioRxiv2021

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

Biological nitrogen fixation is a major factor contributing to microbial primary productivity in the open ocean. The current view depicts a few cyanobacterial diazotrophs as the most relevant marine nitrogen fixers, whereas heterotrophic diazotrophs are more diverse and considered to have lower impacts on the nitrogen balance. Here, we used 891 Tara Oceans metagenomes to create a manually curated, non-redundant genomic database corresponding to free-living, as well as filamentous, colony-forming, particle-attached and symbiotic bacterial and archaeal populations occurring in the surface of five oceans and two seas. Notably, the database provided the genomic content of eight cyanobacterial diazotrophs including Trichodesmium populations and a newly discovered population similar to Richelia, as well as 40 heterotrophic bacterial diazotrophs organized into three main functional groups that considerably expand the known diversity of abundant marine nitrogen fixers compared to previous genomic surveys. Critically, these 48 populations may account for more than 90% of cells containing known nifH genes and occurring in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. The newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and co-occur under nitrate-depleted conditions in large size fractions where they might form aggregates providing the low-oxygen microenvironments required for nitrogen fixation. Most significantly, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas. This large-scale environmental genomic survey emphasizes the considerable potential of heterotrophs in the marine nitrogen balance.

microbiology↗

bioRxiv2021

Insights into biotic and abiotic modulation of ocean mesopelagic communities

For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO - and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.

ecology↗

bioRxiv2020

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we first report that in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study unveils a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/402172v5_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@13cf29dorg.highwire.dtl.DTLVardef@5c5c86org.highwire.dtl.DTLVardef@1be7516org.highwire.dtl.DTLVardef@f935cb_HPS_FORMAT_FIGEXP M_FIG Teano et al. report that that linker histone H1 and a group of H1-related telomeric proteins interplay to selectively influence the Polycomb repressive landscape at genes and telomeric repeats in Arabidopsis. These findings provide a mechanistic framework by which H1 influences the epigenome and nuclear organization in a sequence-specific manner. C_FIG HighlightsO_LIH1 promotes PRC2 activity and limits accessibility at a majority of genes C_LIO_LIH1 prevents PRC2 activity at telomeric DNA sequences C_LIO_LIPRC2 repression is achieved by restricting accessibility to TRB proteins C_LIO_LIH1 orchestrates the spatial organization of telomeres and interstitial telomeres (ITRs) C_LI

molecular biology↗

bioRxiv2020

Environmental vulnerability of the global ocean plankton community interactome

Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles, and help regulate climate. Though global surveys are starting to reveal ecological drivers underlying planktonic community structure, and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network - the community interactome - and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar), and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change, and forecasted most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios, while identifying plausible plankton bioindicators for ocean monitoring of climate change.

ecology↗

bioRxiv2020

Mitotic interhomolog recombination drives genomic diversity in diatoms

Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific variability in natural populations. However, the process generating such diversity is unknown. Here we estimated the variability within a natural diatom population and subsequently mapped the genomic changes arising within cultures clonally propagated from single diatom cells. We demonstrate that genome rearrangements and mitotic recombination between homologous chromosomes underlie clonal variability, resulting in haplotype diversity accompanied by the appearance of novel protein variants and loss of heterozygosity resulting in the fixation of alleles. The frequency of interhomolog mitotic recombination exceeds 4 out of 100 cell divisions and increases under environmental stress. We propose that this plastic response in the interhomolog mitotic recombination rate increases the evolutionary potential of diatoms, contributing to their ecological success. One Sentence SummaryRecombination between homologous chromosomes in diatom vegetative cells leads to extensive genomic diversity in clonal populations.

genomics↗

bioRxiv2020

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Biological nitrogen fixation plays a critical role in marine primary production, yet, our understanding of marine N2-fixers (diazotrophs) is hindered by limited observations. Here, we developed a quantitative image analysis pipeline in concert with mapping of molecular markers for mining >2,000,000 images and >1,300 metagenomes in surface, deep chlorophyll maximum and mesopelagic samples across 6 size fractions (<0.2-2000 m). Imaging and PCR-free molecular data were remarkably congruent. Sequences from diazotrophs were detected from the ultrasmall bacterioplankton (<0.2 m) to mesoplankton (180-2000 m), while images predicted symbiotic and colonial-forming diazotrophs (>20 {micro}m). Imaging and molecular data estimated that polyploidy can significantly impact gene abundances of symbiotic vs colonial-forming diazotrophs. In general our results support the canonical view that larger sized diazotrophs (>10 m) dominate the tropical belts, while sequences from unicellular cyanobacterial and non-cyanobacterial diazotrophs were globally distributed in surface and the mesopelagic. Co-occurring diazotrophic lineages of different lifestyles were frequently encountered, and several new high density regions of diazotrophs were identified in the global ocean. Overall, this work provides an update of marine diazotroph biogeographical diversity and contributes a new bio-imaging-informatic workflow.

microbiology↗

bioRxiv2020

Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics

Marine planktonic eukaryotes play a critical role in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years. CoverNavigating on the map of plankton genomics with Tara Oceans and anvio: a comprehensive genome-resolved metagenomic survey dedicated to eukaryotic plankton. O_FIG O_LINKSMALLFIG WIDTH=153 HEIGHT=200 SRC="FIGDIR/small/341214v2_ufig1.gif" ALT="Figure 1"> View larger version (82K): org.highwire.dtl.DTLVardef@536fe5org.highwire.dtl.DTLVardef@1d72cc9org.highwire.dtl.DTLVardef@1bd5281org.highwire.dtl.DTLVardef@739512_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Global drivers of eukaryotic plankton biogeography in the sunlit ocean

Eukaryotic plankton are a core component of marine ecosystems with exceptional taxonomic and ecological diversity. Yet how their ecology interacts with the environment to drive global distribution patterns is poorly understood. Here, we use Tara Oceans metabarcoding data covering all the major ocean basins combined with a probabilistic model of taxon co-occurrence to compare the biogeography of 70 major groups of eukaryotic plankton. We uncover two main axes of biogeographic variation. First, more diverse groups display stronger biogeographic structure. Second, large-bodied consumers are structured by oceanic basins, mostly via the main currents, while small-bodied phototrophs are structured by latitude, with a comparatively stronger influence of environmental conditions. Our study highlights striking differences in biogeographies across plankton groups and investigates their determinants at the global scale. One-sentence summaryEukaryotic plankton biogeography and its determinants at global scale reflect differences in ecology and body size.

ecology↗

bioRxiv2020

Ecogenomics of key prokaryotes in the Arctic Ocean

The Arctic Ocean is a key player in the regulation of climate and at the same time is under increasing pressure as a result of climate change. Predicting the future of this ecosystem requires understanding of the responses of Arctic microorganisms to environmental change, as they are the main drivers of global biogeochemical cycles. However, little is known about the ecology and metabolic potential of active Arctic microbes. Here, we reconstructed a total of 3,550 metagenomic bins from 41 seawater metagenomes collected as part of the Tara Oceans expedition, covering five different Arctic Ocean regions as well as the sub-Arctic North Atlantic Ocean and including various depths and different seasons (spring to autumn). Of these bins, 530 could be classified as Metagenome Assembled Genomes (MAGs) and over 75% of them represented novel species. We describe their habitat range and environmental preferences, as well as their metabolic capabilities, building the most comprehensive dataset of uncultured bacterial and archaeal genomes from the Arctic Ocean to date. We found a prevalence of mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic Arctic Ocean during spring and autumn. Finally, the catalogue of Arctic MAGs was complemented with metagenomes and metatranscriptomes from the global ocean to identify the most active MAGs present exclusively in polar metagenomes. These polar MAGs, which display a range of metabolic strategies, might represent Arctic sentinels of climate change and should be considered in prospective studies of the future state of the Arctic Ocean.

ecology↗

bioRxiv2019

H3K27me3 natural variation selectively marks genes predicted to be important for differentiation in unicellular algae

O_LIIn multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit H3K27me3 to establish and maintain gene silencing, critical for developmentally regulated processes. PRC2 complex is absent in both widely studied model yeasts which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. C_LIO_LIHere, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di and tri-methylation of lysine 27 of histone H3. C_LIO_LIH3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. C_LIO_LIThese results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species and highlight their ancestral function in a broader evolutionary context than is currently appreciated. C_LI

cell biology↗

bioRxiv2019

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical and physical context of the ocean (the seascape) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

ecology↗

bioRxiv2019

Diatoms structure the plankton community based on selective segregation in the world’s ocean

Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of the plankton. Through analysis of co-occurrence networks derived from the Tara Oceans expedition that take into account the importance of both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions, whereas the vast majority are independent of abiotic factors. In contrast to most other plankton groups, at a global scale diatoms display a much higher proportion of negative correlations with other organisms, particularly towards potential predators and parasites, suggesting that their biogeography is constrained by top down pressure. Genus level analyses indicate that abundant diatoms are not necessarily the most connected, and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of co-occurrence networks, an open access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best known organismal groups.\n\nImportanceDiatoms are key phytoplankton in the modern ocean involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open access database, we propose an eco-systems level understanding of diatom interactions in the ocean.

ecology↗

bioRxiv2019

Metabolic Architecture of the Deep Ocean Microbiome

The deep sea, the largest compartment of the ocean, is an essential component of the Earth system, but the functional exploration of its microbial communities lags far behind that of other marine realms. Here we analyze 58 bathypelagic microbial metagenomes from the Atlantic, Indian, and Pacific Oceans in an unprecedented sampling effort from the Malaspina Global Expedition, to resolve the metabolic architecture of the deep ocean microbiome. The Malaspina Deep-Sea Gene Collection, 71% of which consists of novel genes, reveals a strong dichotomy between the functional traits of free-living and particle-attached microorganisms, and shows relatively patchy composition challenging the paradigm of a uniform dark ocean ecosystem. Metagenome Assembled Genomes uncovered 11 potential new phyla, establishing references for deep ocean microbial taxa, and revealed mixotrophy to be a widespread trophic strategy in the deep ocean. These results expand our understanding of the functional diversity, metabolic versatility, and carbon cycling in the largest ecosystem on Earth.\n\nOne Sentence SummaryA whole community genomic survey of the deep microbiome sheds light on the microbial and functional diversity of the dark ocean.

microbiology↗

bioRxiv2019

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in histone H3 Lys-4 trimethylation independently from histone H2B monoubiquitination

The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in S. cerevisiae, where a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with Set1), in Arabidopsis thaliana this activity involves multiple histone methyltransferases (HMTs). Among these, the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. S2Lb co-purifies with the AtCOMPASS core subunit WDR5 from a high-molecular weight complex, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. Notwithstanding, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2 or H3 Lys-4 trimethylation, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been coopted by the plant-specific SDG2 HMT and mediates H3K4me3 deposition through an H2Bub-independent pathway in Arabidopsis.

plant biology↗