Single‐cell genomics of uncultivated deep‐branching magnetotactic bacteria reveals a conserved set of magnetosome genes

While magnetosome biosynthesis within the magnetotactic Proteobacteria is increasingly well understood, much less is known about the genetic control within deep‐branching phyla, which have a unique ultrastructure and biosynthesize up to several hundreds of bullet‐shaped magnetite magnetosomes arranged in multiple bundles of chains, but have no cultured representatives. Recent metagenomic analysis identified magnetosome genes in the genus ‘Candidatus Magnetobacterium’ homologous to those in Proteobacteria. However, metagenomic analysis has been limited to highly abundant members of the community, and therefore only little is known about the magnetosome biosynthesis, ecophysiology and metabolic capacity in deep‐branching MTB. Here we report the analysis of single‐cell derived draft genomes of three deep‐branching uncultivated MTB. Single‐cell sorting followed by whole genome amplification generated draft genomes of Candidatus Magnetobacterium bavaricum and Candidatus Magnetoovum chiemensis CS‐04 of the Nitrospirae phylum. Furthermore, we present the first, nearly complete draft genome of a magnetotactic representative from the candidate phylum Omnitrophica, tentatively named Candidatus Omnitrophus magneticus SKK‐01. Besides key metabolic features consistent with a common chemolithoautotrophic lifestyle, we identified numerous, partly novel genes most likely involved in magnetosome biosynthesis of bullet‐shaped magnetosomes and their arrangement in multiple bundles of chains.     

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate ‘switch'' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.     

Habitat constraints on carotenoid‐based coloration in a small euryhaline teleost

Display of bright and striking color patterns is a widespread way of communication in many animal species. Carotenoid‐based coloration accounts for most of the bright yellow, orange, and red displays in invertebrates, fish, amphibians, reptiles, and birds, being widely considered a signal of individual health. This type of coloration is under the influence of several factors, such as sexual selection, predator pressure, pigment availability, and light transmission. Fish offer numerous examples of visual communication by means of color patterns. We used a small cyprinodontid fish, Aphanius fasciatus (Valenciennes, 1821), as a model species to assess habitat constraints on the color display in male caudal fin. Populations from natural and open/closed artificial habitats were tested for differences in the pigmentation of caudal fins. The most important factors explaining the intensity of coloration were the habitat type and the chlorophyll concentration in the sediment, followed by water turbidity; yellow fins were observed in natural habitats with low chlorophyll concentration and high water turbidity, while orange fins occurred in artificial habitats with high chlorophyll concentration and low turbidity. Furthermore, A. fasciatus in artificial habitats showed a higher somatic and a lower reproductive allotment with respect to natural habitats, according to the existing literature on the species. Furthermore, in closed artificial habitats, where the most intense reddish coloration of caudal fins was observed, a trade‐off between somatic growth and the coloration intensity of a carotenoid‐based sexual ornament has been observed; in these populations, intensity of caudal fin coloration was negatively related to the somatic allotment. Results of this study suggested how both the pigmentation of male's caudal fin and the life history strategies of the species are constrained by habitat characteristics.     

Evolutionary innovation and diversification of carotenoid‐based pigmentation in finches

The ornaments used by animals to mediate social interactions are diverse, and by reconstructing their evolutionary pathways we can gain new insights into the mechanisms underlying ornamental innovation and variability. Here, we examine variation in plumage carotenoids among the true finches (Aves: Fringillidae) using biochemical and comparative phylogenetic analyses to reconstruct the evolutionary history of carotenoid states and evaluate competing models of carotenoid evolution. Our comparative analyses reveal that the most likely ancestor of finches used dietary carotenoids as yellow plumage colorants, and that the ability to metabolically modify dietary carotenoids into more complex pigments arose secondarily once finches began to use modified carotenoids to create red plumage. Following the evolutionary “innovation” that enabled modified red carotenoid pigments to be deposited as plumage colorants, many finch species subsequently modified carotenoid biochemical pathways to create yellow plumage. However, no reversions to dietary carotenoids were observed. The finding that ornaments and their underlying mechanisms may be operating under different selection regimes—where ornamental trait colors undergo frequent reversions (e.g., between red and yellow plumage) while carotenoid metabolization mechanisms are more conserved—supports a growing empirical framework suggesting different evolutionary patterns for ornaments and the mechanistic innovations that facilitate their diversification.     

Using comparative genomics to uncover new kinds of protein‐based metabolic organelles in bacteria

Bacterial microcompartment (MCP) organelles are cytosolic, polyhedral structures consisting of a thin protein shell and a series of encapsulated, sequentially acting enzymes. To date, different microcompartments carrying out three distinct types of metabolic processes have been characterized experimentally in various bacteria. In the present work, we use comparative genomics to explore the existence of yet uncharacterized microcompartments encapsulating a broader set of metabolic pathways. A clustering approach was used to group together enzymes that show a strong tendency to be encoded in chromosomal proximity to each other while also being near genes for microcompartment shell proteins. The results uncover new types of putative microcompartments, including one that appears to encapsulate B₁₂‐independent, glycyl radical‐based degradation of 1,2‐propanediol, and another potentially involved in amino alcohol metabolism in mycobacteria. Preliminary experiments show that an unusual shell protein encoded within the glycyl radical‐based microcompartment binds an iron‐sulfur cluster, hinting at complex mechanisms in this uncharacterized system. In addition, an examination of the computed microcompartment clusters suggests the existence of specific functional variations within certain types of MCPs, including the alpha carboxysome and the glycyl radical‐based microcompartment. The findings lead to a deeper understanding of bacterial microcompartments and the pathways they sequester.     

Testing the interactive effects of testosterone and parasites on carotenoid‐based ornamentation in a wild bird

Abstract Testosterone underlies the expression of most secondary sexual traits, playing a key role in sexual selection. However, high levels might be associated with physiological costs, such as immunosuppression. Immunostimulant carotenoids underpin the expression of many red‐yellow ornaments, but are regulated by testosterone and constrained by parasites. We manipulated testosterone and nematode burdens in red grouse (Lagopus lagopus scoticus) in two populations to tease apart their effects on carotenoid levels, ornament size and colouration in three time‐step periods. We found no evidence for interactive effects of testosterone and parasites on ornament size and colouration. We showed that ornament colouration was testosterone‐driven. However, parasites decreased comb size with a time delay and testosterone increased carotenoid levels in one of the populations. This suggests that environmental context plays a key role in determining how individuals resolve the trade‐off between allocating carotenoids for ornamental coloration or for self‐maintenance needs. Our study advocates that adequately testing the mechanisms behind the production or maintenance of secondary sexual characters has to take into account the dynamics of sexual trait expression and their environmental context.     

Single‐cell sequencing reveals the heterogeneity and intratumoral crosstalk in human endometrial cancer

BackgroundEndometrial cancer (EC) is one of the most common gynecologic malignancies with increasing morbidity. Cell–cell and cell‐matrix interactions within the tumour microenvironment (TME) exert a powerful influence over the progression of EC. Therefore, a comprehensive exploration of heterogeneity and intratumoral crosstalk is essential to elucidate the mechanisms driving EC progression and develop novel therapeutic approaches.Methods4 EC and 2 normal endometrium samples were applied for single‐cell RNA sequencing (scRNA‐seq) analysis. In addition, we also included the public database to explore the clinical benefits of the single cell analysis.Results9 types of cells were identified with specific expression of maker genes. Both the malignant epithelial cells and cells comprising the immune microenvironment displayed a high degree of intertumoral heterogeneity. Notably, the proliferation T cells also showed an exhausted feature. Moreover, the malignant cells may induce an immunosuppressive microenvironment through TNF‐ICOS pair. Cancer‐associated fibroblasts (CAFs) were divided into four subsets with distinct characteristics and they maintained frequent communications with malignant cells which facilitating the progression of EC. We also found that the existence of vascular CAF (vCAF) may indicate a worse prognosis for EC patients through integrating TCGA database.ConclusionThe TME of human EC remains highly heterogeneous. Out finding that malignant cells interact closely with immune cells and vCAFs identifies potential therapeutic targets.

In order to comprehensively explore the heterogeneity and intra‐tumoral crosstalk of human endometrial cancer, we profiled 41,358 single cells of human endometrial cancer and normal endometrial tissues. The results showed that the tumour microenvironment of human ECs remains highly heterogeneity. Malignant cells interact closely with immune cells and vCAFs which may indicate potential therapeutic targets.     

Single‐cell functional analysis of parathyroid adenomas reveals distinct classes of calcium sensing behaviour in primary hyperparathyroidism

Primary hyperparathyroidism (PHPT) is a common endocrine neoplastic disorder caused by a failure of calcium sensing secondary to tumour development in one or more of the parathyroid glands. Parathyroid adenomas are comprised of distinct cellular subpopulations of variable clonal status that exhibit differing degrees of calcium responsiveness. To gain a clearer understanding of the relationship among cellular identity, tumour composition and clinical biochemistry in PHPT, we developed a novel single cell platform for quantitative evaluation of calcium sensing behaviour in freshly resected human parathyroid tumour cells. Live‐cell intracellular calcium flux was visualized through Fluo‐4‐AM epifluorescence, followed by in situ immunofluorescence detection of the calcium sensing receptor (CASR), a central component in the extracellular calcium signalling pathway. The reactivity of individual parathyroid tumour cells to extracellular calcium stimulus was highly variable, with discrete kinetic response patterns observed both between and among parathyroid tumour samples. CASR abundance was not an obligate determinant of calcium responsiveness. Calcium EC50 values from a series of parathyroid adenomas revealed that the tumours segregated into two distinct categories. One group manifested a mean EC50 of 2.40 mM (95% CI: 2.37–2.41), closely aligned to the established normal range. The second group was less responsive to calcium stimulus, with a mean EC50 of 3.61 mM (95% CI: 3.45–3.95). This binary distribution indicates the existence of a previously unappreciated biochemical sub‐classification of PHPT tumours, possibly reflecting distinct etiological mechanisms. Recognition of quantitative differences in calcium sensing could have important implications for the clinical management of PHPT.     

Blood parasite infection differentially relates to carotenoid‐based plumage and bill color in the American goldfinch

Male and female American goldfinches (Spinus tristis) express condition‐dependent carotenoid‐based plumage and bill coloration. Plumage color is relatively static, as pigments incorporated into feathers during the spring molt cannot be mobilized thereafter. In contrast, bill color is dynamic, reflecting changes in condition over short time periods. Previous studies have shown that male and female ornaments, though similar in expression, are differentially related to measures of immunocompetence, suggesting that the relationship between ornamentation and parasite infection may differ between the sexes. In this study, we evaluate the relationship between condition‐dependent ornamentation (plumage and bill color) and blood parasite infection in male and female American goldfinches. We captured goldfinches after completion of the pre‐alternate molt and prior to the onset of nesting and assessed prevalence of Trypanosoma parasites via blood smears. Plumage color strongly predicted trypanosome infection: Birds with more colorful plumage were less likely to present infections. In contrast, we detected no relationship between infection and bill color, which in other studies has been shown to dynamically reflect current condition. Sex did not affect the relationship between infection status and either ornament. Together, these results suggest that physiological pathways linking carotenoid ornamentation and infection may vary even within a single species.     

Population genomics reveals multiple drivers of population differentiation in a sex‐role‐reversed pipefish

A major goal of molecular ecology is to identify the causes of genetic and phenotypic differentiation among populations. Population genomics is suitably poised to tackle these key questions by diagnosing the evolutionary mechanisms driving divergence in nature. Here, we set out to investigate the evolutionary processes underlying population differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled approximately 50 fish from each of 12 populations distributed from the Gulf coast of Texas to the Atlantic coast of Florida and performed restriction‐site‐associated DNA sequencing to identify SNPs throughout the genome. After imposing quality and stringency filters, we selected a panel of 6348 SNPs present in all 12 populations, 1753 of which were not physically linked. We identified a genome‐wide pattern of isolation by distance, in addition to a more substantial genetic break separating populations in the Gulf of Mexico from those in the Atlantic. We also used several divergence outlier approaches and tests for genotype–environment correlations to identify 400 SNPs putatively involved in local adaptation. Patterns of phenotypic differentiation and variation diverged from the overall genomic pattern, suggesting that selection, phenotypic plasticity or demographic factors may be shaping phenotypes in distinct populations. Overall, our results suggest that population divergence is driven by a variety of factors in S. scovelli, including neutral processes and selection on multiple traits.     

Bare laser‐synthesized Au‐based nanoparticles as nondisturbing surface‐enhanced Raman scattering probes for bacteria identification

The ability of noble metal‐based nanoparticles (NPs) (Au, Ag) to drastically enhance Raman scattering from molecules placed near metal surface, termed as surface‐enhanced Raman scattering (SERS), is widely used for identification of trace amounts of biological materials in biomedical, food safety and security applications. However, conventional NPs synthesized by colloidal chemistry are typically contaminated by nonbiocompatible by‐products (surfactants, anions), which can have negative impacts on many live objects under examination (cells, bacteria) and thus decrease the precision of bioidentification. In this article, we explore novel ultrapure laser‐synthesized Au‐based nanomaterials, including Au NPs and AuSi hybrid nanostructures, as mobile SERS probes in tasks of bacteria detection. We show that these Au‐based nanomaterials can efficiently enhance Raman signals from model R6G molecules, while the enhancement factor depends on the content of Au in NP composition. Profiting from the observed enhancement and purity of laser‐synthesized nanomaterials, we demonstrate successful identification of 2 types of bacteria (Listeria innocua and Escherichia coli). The obtained results promise less disturbing studies of biological systems based on good biocompatibility of contamination‐free laser‐synthesized nanomaterials.

     

Changes in carotenoid‐based plumage colour in relation to age in European Serins Serinus serinus

Yearling birds generally display duller colours than adults. This may be due to selection favouring birds with more intensely coloured plumage or to an increase in colour after the first complete moult. Most research to date on the topic has been carried out on species with structural plumage coloration or with carotenoid‐based coloration that is produced by the unmodified deposition of pigments. However, no study has been carried out on species whose carotenoids are metabolically modified before deposition. In this study, we assess age‐related changes in the carotenoid‐based coloration of European Serins, a species that metabolically processes carotenoids before they can be deposited into feathers. Birds were captured over consecutive years and we carried out both cross‐sectional and longitudinal analysis. Adults had significantly greater values of lightness and chroma than yearling birds. However, there were no changes in plumage colour when analysing the same individuals captured in subsequent seasons. Plumage lightness and chroma of adult males after moult were related to body mass, suggesting a role of body condition on plumage coloration. Our results suggest that changes in plumage coloration with age in European Serins are due to a selection process that favours more intensely coloured individuals.