Biology subjects

Mehrshad, M.

Publications and source records attributed to Mehrshad, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Eco-evolutionary dynamics of active virus-host interactions in a freshwater lake: revealed through metaHi-C

Detecting active phage-bacteria interactions in natural microbial communities remains a major limitation for understanding their ecological dynamics and associated co-evolutionary processes. Here, we applied metaHi-C, a chromosome conformation capture method, to resolve active virus-host associations in a freshwater microbial community. From >900 microbial and >33,000 viral Hi-C-assembled genomes, we identified 100 high-confidence phage-host linkages spanning major freshwater bacterial lineages, including Limnohabitans, Acidimicrobium, Synechococcus, Candidatus Nanopelagicus, Candidatus Planktophila, Candidatus Methylopumilus and Polynucleobacter. The inferred networks revealed diverse infection patterns, including broad-host-range phages, cellular-level co-infection, kill-the-winner dynamics and one-to-one interactions. These ecological patterns were associated with signatures of diversifying selection in host-interaction genes, consistent with host-range expansion, alongside conserved genomic regions in broad-host-range and co-infecting phages, indicating functional constraints on essential infection modules. Together, these results demonstrate that metaHi-C enables direct linking of community-level infection dynamics to underlying evolutionary processes, revealing how these forces shape bacterial population dynamics of freshwater bacteria.

microbiology↗

bioRxiv2025

The path to dependence: stepwise genome evolution from a facultative symbiont to an endosymbiont in the N2-fixing diatom-Richelia symbioses

A few genera of diatoms are widespread in the oceans and form stable partnerships with N2-fixing filamentous cyanobacteria Richelia spp. A unique feature of the diatom-Richelia symbioses is the symbiont cellular location spans a continuum of integration (epibiont, periplasmic, endobiont) that is reflected in the symbiont genome size and content. In this study we analyzed genomes derived from cultures and environmental metagenome-assembled genomes focusing on characters indicative of genome evolution. Our results show an enrichment of short length transposable elements (TEs) and pseudogenes in the periplasmic endosymbiont genomes, suggesting an active and transitionary period in genome evolution. In contrast, genomes of endobionts exhibited fewer TEs and pseudogenes, reflecting advanced stages of genome reduction and increased host dependency in the endobionts. Pangenome analyses identified that endobionts streamline their genomes and conserve a majority of their genes in the core, whereas periplasmic endobionts and epibionts maintain larger flexible genomes, suggesting increased genomic plasticity. Functional gene comparisons with other N2-fixing cyanobacteria revealed that Richelia endobionts have similar patterns of metabolic loss but are distinguished by absence of specific pathways (e.g. cytochrome bd ubiquinol oxidase, lipid-A) that increase dependency and direct interaction with their respective hosts. In conclusion, our findings underscore the dynamic nature of genome reduction in N2-fixing cyanobacterial symbionts and demonstrate the diatom-Richelia symbioses as a valuable and rare model to study genome evolution in the transitional stages from a free-living facultative symbiont to a host-dependent endobiont.

microbiology↗

bioRxiv2024

Niche and spatial partitioning restrain ecological equivalence among microbes along aquatic redox gradient

Microbial metabolic capabilities and interactions shape their niche hypervolume that in turn governs their ecological strategies and ecosystem services. In the context of functional redundancy or ecological equivalence, the focus has been on functional guilds in order to bypass the complex challenge faced by niche theory for disentangling the niche hypervolume. However, in some cases this simplification has been at the expense of ignoring the role of individual genotype of each microbe within a functional guild and fails to explain how the diversity within each functional guild is maintained. In this study, we inspect the metabolic profile of metagenome-assembled genomes along the pronounced redox gradient of the water column in an anchialine cave. Bridging neutral theory of biodiversity and biogeography and niche theory, our analysis uses focal metabolic capabilities while also incorporating individuality by looking into background metabolic capabilities of each individual and further includes spatial distribution of microbes to delineate their niche space. Our results emphasize that differences in background metabolic capabilities are critical for furnishing the niche hypervolume of microbes carrying the same focal metabolic capability and refute their ecological equivalence with their spatial distribution further enables niche partitioning among them.

ecology↗

bioRxiv2024

Cross-feeding options define eco-evolutionary dynamics of deep oligotrophic groundwater microbiome

Deep groundwaters populated by diverse and active microbes are among the most energy and nutrient-limited ecosystems. Characteristics of this ecosystem including nutrient and dispersal limitations, low cell densities, and episodic growth strategy interactively underpin the so far elusive eco-evolutionary dynamics of its microbiome. Here we applied a modular metabolic analyses on genome-resolved reconstructed community of disconnected deep groundwaters in the Fennoscandian Shield. In the community of deeper groundwaters despite their highly oligotrophic nature, lineages with larger genomes maintained larger populations which we hypothesize to be connected with their limited cross-feeding options. Thus providing an extension on the streamlining theory emphasizing the importance of ecological interactions in genome evolution which is further supported by the observed decrease in abundance of lineages with known metabolic dependencies, such as Patescibacteria and DPANN, with depth. The modular metabolic analyses showed that remarkably common niches based on same cross-feeding interactions are also available in different groundwaters, in addition to common niches for primary production. While these shared niches are critical for community assembly in this ecosystem, in different boreholes different lineages populated them. Our results provided new insights into the role of metabolic cross-feeding in genome evolution and community assembly of deep groundwater microbiome.

microbiology↗

bioRxiv2024

Niche-aware metagenomic screening for enzyme methioninase illuminates its contribution to metabolic syntrophy

AbstractThe single step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme is also a therapeutic target for its role in starving auxotrophic cancer cells. Applying our refined in-silico screening pipeline on 33,469 publicly available genome assemblies and 1878 MAGs/SAGs from brackish waters of the Caspian Sea and the Fennoscandian shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninsaes are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree we recovered 3 methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol.

microbiology↗

bioRxiv2022

Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity

The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as are molecular adaptations facilitating cross-biome transitions. Here, we conduct large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,276 MAGs). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. Distinct brackish basins co-hosted numerous species despite differences in salinity and geographic distance, the latter having stronger intra-species population structuring effects. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed towards the brackish biome. Transitions were accompanied by changes in isoelectric point distribution and amino acid composition of inferred proteomes, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content result in species-level separation between aquatic biomes.

microbiology↗

bioRxiv2022

Genome-resolved insight into the reservoir of antibiotic resistance genes in an aquatic microbial community

Aquatic microbial communities are an important reservoir of Antibiotic Resistance Genes. However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at a genome resolution. Detected ARGs were classified into five antibiotic resistance categories including Prevention of access to target (44%), Modification/protection of targets (30%), Direct modification of antibiotics (22%), Stress resistance (3%), and Metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotics target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with their ecological strategies.

microbiology↗

bioRxiv2022

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen. They mainly accumulate in oil reservoirs, but aromatic HCs can also have other sources and are widely distributed in the biosphere. Our perception of pathways for biotic degradation of major HCs and genetic information of key enzymes in these bioconversion processes have mainly been based on cultured microbes and are biased by uneven taxonomic representation. Here we use Annotree to provide a gene-centric view of aerobic degradation of aliphatic and aromatic HCs in a total of 23446 genomes from 123 bacterial and 14 archaeal phyla. Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. While genomes containing full pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota, other lineages capable of mediating such key steps could partner with representatives with truncated HC degradation pathways and collaboratively drive the process. Phylogeny reconstruction shows that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

microbiology↗

bioRxiv2022

Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity

Dissolved organic matter (DOM) is ubiquitous in aquatic ecosystems and fundamental for planetary processes and ecosystem functioning. While the link between microbial community composition and heterotrophic utilization of DOM has been recognized, the full diversity of organic compounds, their bioavailability, degradability and specific influences on the diversity and function of heterotrophs are still not clear. Here we experimentally investigate heterotrophic bacteria in thirty-three freshwater model communities. We identified 34 different heterotrophs growing in ambient lake DOM with taxonomic affiliations matching abundant freshwater bacterioplankton. We further describe 25 different heterotrophs growing in the phycosphere of M. Aeruginosa and 6 heterotrophs growing on the DOM produced by M. Aeruginosa with taxonomic affiliation in accord to phycosphere heterotrophs. In our experiment we observed that heterotrophs that live in the phycosphere remove more dissolved organic carbon than abundant freshwater heterotrophs. Moreover, phycosphere heterotrophs have bigger genomes than abundant lake bacteria. Altogether of the 4224 chemical features that were resolved by LC-MS, only 1229 were seen in all three treatments. None of the common/shared compounds were removed across all the model communities, suggesting contrasting niches of the studied taxa. Altogether our study highlights how each model community, with its unique taxonomic assemblages and organotroph functioning is upkept by the chemodiversity of DOM.

ecology↗

bioRxiv2021

mOTUpan: a robust Bayesian approach to leverage metagenome assembled genomes for core-genome estimation

Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome assembled genomes (MAGs) or single-cell assembled genomes (SAGs). While this expanded diversity can provide novel insights about microbial population structure, most tools available for core-genome estimation are overly sensitive to genome completeness. Consequently a major portion of the huge phylogenetic diversity uncovered by environmental genomics approaches remain excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core-genome for sets of genomes of highly diverse completeness range. The likelihood for each gene-cluster to belong to core- or accessory-genome is estimated by computing the probability of its presence/absence pattern in the target set of genomes. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates as state-of-the-art tools Roary and PPanGGoLiN for high-quality genomes and outperforms them at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.

bioinformatics↗

bioRxiv2021

A genomic perspective on genome size distribution across Earth's microbiomes reveals a tendency to gene loss

Our view of genome size in Archaea and Bacteria has remained skewed as the data used to paint its picture has been dominated by genomes of microorganisms that can be cultivated under laboratory settings. However, the continuous effort to catalog the genetic make-up of Earths microbiomes specifically propelled by recent extensive work on uncultivated microorganisms, provides a unique opportunity to revise our perspective on genome size distribution. Capitalizing on a recently released extensive catalog of tens of thousands of metagenome-assembled genomes, we provide a comprehensive overview of genome size distributions. We observe that the known phylogenetic diversity of environmental microorganisms possesses significantly smaller genomes than the collection of laboratory isolated microorganisms. Aquatic microorganisms average 3.1 Mb, host-associated microbial genomes average 3.0 Mb, terrestrial microorganism average 3.7 Mb and isolated microorganisms average 4.3 Mb. While the environment where the microorganisms live can certainly be linked to genome size, in some cases, evolutionary phylogenetic history can be a stronger predictor. Moreover, ecological strategies such as auxotrophies have a direct impact on genome size. To better understand the ecological drivers of genome size, we expand on the known and the overlooked factors that influence genome size in different environments, phylogenetic groups and trophic strategies.

microbiology↗

bioRxiv2020

Microbiome of the Black Sea water column analyzed by genome centric metagenomics

BackgroundThe Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former albeit with lower salinity and (mostly) temperature. In spite of its well-known hydrology and physico chemistry, this enormous water mass remains poorly studied at the microbial genomics level. ResultsWe have sampled its different water masses and analyzed the microbiome by classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has similarities to other similar aquatic environments of marine or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environments and includes Cyanobacteria (Synechococcus), photoheterotrophs (largely with marine relatives), facultative/microaerophilic microbes again largely marine, chemolithotrophs (N and S oxidizers) and a large number of anaerobes, mostly sulfate reducers but also a few methanogens and a large number of "dark matter" streamlined genomes of largely unpredictable ecology. ConclusionsThe Black Sea presents a mixture of similarities to other water bodies. The photic zone has many microbes in common with that of the Mediterranean with the relevant exception of the absence of Prochlorococcus. The chemocline already presents very different characteristics with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. Finally the euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy generating metabolism and a small but detectable methanogenesis.We are adding critical information about this unique and important ecosystem and its microbiome.

microbiology↗

bioRxiv2020

Freshwater Chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations

Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on their functional ecology and local adaptations came from isolates and merely 26 sequenced genomes that are poor representatives of natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-cell genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs) or "species". Of the 71 mOTUs, 57 were classified as genus Chlorobium and these mOTUs varied in relative abundance up to ~60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many were lacking genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian Chlorobium clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insights into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. ImportanceThe reconstruction of genomes from metagenomes has enabled unprecedented insights into the ecology and evolution of environmental microbiomes. We applied this powerful approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and pinpoint nutrients that likely fuel their electron chains. Being photoautotrophs, these Chlorobia organisms also have the potential to serve as carbon sources that support metalimnetic and hypolimnetic food webs.

ecology↗

bioRxiv2020

Distinct microbial communities along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents

Persian Gulf hosting ca. 48% of the worlds oil reserves; has been chronically exposed to natural oil seepage. Oil spill events have been studied over the last decade; however, the influence of chronic oil exposure on the microbial community of the Persian Gulf has remained unknown. We performed genome-resolved comparative analyses of the water and sediments prokaryotic community along the Gulfs pollution continuum (Strait of Hormuz, Asalouyeh and Khark Island). The continuous exposure to trace amounts of pollution has shifted the microbial profile toward the dominance of Oceanospirillales, Flavobacteriales, Alteromonadales, and Rhodobacterales in Asalouyeh and Khark samples. Intrinsic oil-degrading microbes present in low abundances in marine habitats; experience a bloom in response to oil pollution. Comparative analysis of the Persian Gulf samples with 106 oil-polluted marine samples reveals the pollutants hydrocarbon content, exposure time and sediment depth as main determinants of microbial response to pollution. High aliphatic content enriches for Oceanospirillales, Alteromonadales and Pseudomonadales whereas, Alteromonadales, Cellvibrionales, Flavobacteriales and Rhodobacterales dominate polyaromatic polluted samples. In sediment samples, Deltaproteobacteria and Gammaproteobacteria had the highest abundance. In chronic exposure and oil spill events, the community composition converges towards higher dominance of oil-degrading constituents while promoting the division of labor for successful bioremediation. Originality-Significance StatementThe impact of anthropogenic oil pollution on the microbial community has been studied for oil spill events; while the influence of long-term chronic exposure to oil derivatives on The microbes has remained unknown. Persian Gulf hosts ca. 48% of the worlds oil reserves and has been chronically exposed to natural and accidental oil pollutions. Different pollutant profilesin different locations and the recurrent pollution events; make Persian Gulf an ideal model system to analyse the impact of oil hydrocarbon on the microbial community and the recovery potential of marine ecosystems after pollution. In this study we perform an extensive analysis of thhe Persian Gulfs water and sediment samples along the water circulation and pollution continuum for the first time. Our results show that these long-standing trace exposure to oil has imposed a consistent selection pressure on the Gulfs microbes; developing unique and distinct communities along the pollution continuum. Our extensive genome-resolved analysis of the metabolic capabilities of the reconstructed MAGs shows an intricate division of labor among different microbes for oil degradation and determine the major drivers of each degradation step. Intrinsic oil-degrading microbes (e.g., Immundisolibacter, Roseovarius and Lutimaribacter) bloom along the Persian Gulfs pollution continuum and function as the main oil degraders. Comparative study of PG datasets with 106 oil-polluted marine samples (water and sediment) reveals similar community compositions in the Persian Gulfs water and sediment samples to those of oil spill events and suggests hydrocarbon type and exposure time as the main determinants of the microbial response to oil pollution.

microbiology↗

bioRxiv2020

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

Extremely oligotrophic deep groundwaters host organisms attuned to the low-end of the bioenergetics spectrum. While all domains of life along with viruses are active in this habitat, the evolutionary and ecological constraints on colonization and niche shifts and their consequences for the microbiome convergence are unknown. Here we provide a comparative genome-resolved analysis of the prokaryotic community in disconnected fracture fluids of the Fennoscandian Shield. The data show that the oligotrophic deep groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common deep groundwater core microbiome. Based on this high resolution "multi-omics" enabled understanding of the underlying mechanisms via functional expression analysis, we conclude that deep groundwater ecosystems foster highly diverse, yet cooperative microbial communities adapted to this setting. The fitness of primary energy producers is increased by ecological traits such as aggregate or biofilm formation. This also facilitates reciprocal promiscuous partnerships with diverse and prevalent epi-bionts, alleviating the "tragedy of common goods". Hence, instead of a lifestyle where microbes predominantly invest in functions related to maintenance and survival, an episodic and cooperative lifestyle ensures the subsistence of the deep groundwater microbiome. We suggest the name "halt and catch fire" for this way of life.

microbiology↗

bioRxiv2019

Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics

The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain obscure. Here, using ultra-deep metagenomic sequencing from freshwater habitats we recovered complete genomes of >2000 phages, including small \"miniphages\" and large \"megaphages\" infecting iconic prokaryotic lineages. We also show that many phages encode genes that likely enhance survival of infected microbes during strong eukaryotic grazing pressure. For instance, we describe genes that afford protection to their host from reactive oxygen species (ROS) in the environment and from the oxidative burst in protist phagolysosomes (phage-mediated ROS defense) or those that directly effect targeted killing of the predators upon ingestion of a phage-infected microbe (Trojan horse). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.

microbiology↗

bioRxiv2018

A Swiftian Voyage from Brobdingnag to Lilliput: Freshwater Planctomycetes drifting towards the poles of the genome size spectrum

Freshwater environments teem with microbes. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from Planctomycetes phylum. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments were, through processes mostly associated with reductive genome evolution, gave rise to new freshwater-specific clades. The most successful lineage was found to simultaneously have the most specialized lifestyle (increased regulatory genetic circuits; metabolism tuned for mineralization of proteinaceous sinking aggregates; psychrotrophic behavior) and to harbor the smallest genomes, highlighting a genomic architecture shaped by niche-directed evolution.

microbiology↗

bioRxiv2018

The sunlit microoxic niche of the archaeal eukaryotic ancestor comes to light

Recent advances in phylogenomic analyses and increased genomic sampling of uncultured prokaryotic lineages brought compelling evidence in support of the emergence of eukaryotes from within the Archaea domain of life. The discovery of Asgardaeota archaea and their recognition as the closest extant relative of eukaryotes fuelled the revival of a decades-old debate regarding the topology of the tree of life. While it is apparent that Asgardaeota encode a plethora of eukaryotic-specific proteins (the highest number identified to date in prokaryotes), the lack of genomic information and metabolic characterization has precluded inferences about their lifestyles and the metabolic landscape that may have favoured the emergence of the hallmark eukaryotic subcellular architecture. Here, we use advanced phylogenetic analyses to infer the deep ancestry of eukaryotes and genome-scale metabolic reconstructions to shed light on the metabolic milieu of the closest archaeal eukaryotic ancestors discovered till date. In doing so, we: i) generate the largest Asgardaeota genomic dataset available so far, ii) describe a new clade of rhodopsins encoded within the recovered genomes, iii) provide unprecedented evidence for mixotrophy within Asgardaeota, iv) present first-ever proofs that the closest extant archaeal relatives to all eukaryotes (Heimdallarchaeia) have microoxic lifestyles with aerobic metabolic pathways unique among Archaea (i.e. kynurenine pathway) and v) generate the first images of Asgardaeota.

microbiology↗