Biology subjects

Lopez-Perez, M.

Publications and source records attributed to Lopez-Perez, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Physics-aware measurement-supervised deep learning enables point spread function inversion in soft X-ray tomography

Soft X-ray tomography (SXT) is an emerging modality for whole-cell 3D imaging in near-native states. However, the effective spatial resolution is limited by optical artifacts characterized by the point spread function (PSF). Standard reconstruction methods force a compromise between structural sharpness and noise, failing to fully resolve these depth-dependent artifacts. By embedding experimentally measured, depth-variant PSFs into a differentiable forward model, we demonstrate a physics-aware computational optimization that bypasses these limitations to recover high-frequency cellular ultrastructure. The structural fidelity was validated using split-tilt Fourier ring correlation (FRC), alongside an experimental bead phantom tomogram, providing supporting evidence that the recovered high-frequency features reflect genuine specimen structure rather than fabricated artifacts. Our method effectively increases FRC spatial resolution and recovers cellular ultrastructure. Furthermore, under sparse-angular subsampling, the framework maintained spatial resolution using half the projection angles, a computational proxy pointing toward the potential for reduced radiation exposure in future acquisitions. This hardware-free, computational approach offers a route toward mitigating the optical and dosimetric constraints that currently limit nanoscale soft X-ray tomography.

Cell Biology↗

bioRxiv2025

Self-Supervised Missing Wedge Correction in Soft X-Ray Tomography: Towards Accurate Cellular Morphology and Volume Quantification

Soft X-Ray tomography (SXT) is a non-invasive bio-imaging technique that enables 3D imaging of cellular structures in large volume, with a unique resolution range that bridges the gap between fluorescence and transmission electron microscopy. However, a fundamental limitation, the missing wedge artefact caused by incomplete tilt-series acquisition, introduces systematic structural elongation in the reconstructed tomograms. This artifact compromises accurate quantitative biological analysis by overestimating cellular and organelle volumes. To overcome this persistent issue, we introduce a novel, self-supervised missing wedge correction model that learns key sine-wave patterns from existing SXT sinograms of the tilt series stacks. This model can be applied to recover the missing-angle region of the sinogram, reducing distortions and elongations in the reconstructed tomograms. We demonstrate a significant quantitative improvement in artifact removal, achieving faithful recovery of the spherical morphology of lipid droplets. We further applied this method to Plasmodium falciparum hemozoin crystals, a biomarker in antimalarial drug efficacy studies. Our model successfully reduced volume overestimation, achieving up to a 16% decrease in distorted volume. This level of precision is paramount for correctly interpreting the mode of action of antimalarial drugs.

cell biology↗

bioRxiv2025

Type IV pili increase phage encounter in marine cyanobacteria

Type IV pili are extracellular bacterial appendages with diverse functions, including biofilm formation, motility, conjugation, transformation, pathogenicity, and secretion. In planktonic marine cyanobacteria, they also enhance buoyancy and protect against grazing, yet their consequences for the oceanic carbon pump and microbial loop remain poorly understood. Pili production in dilute marine ecosystems entails ecological trade-offs, including high nutrient investment and, as we show here, increased vulnerability to phage infection. Using high-resolution electron microscopy, we observed cyanophages attaching along the entire length of extracellular pili, indicating that these filaments act as structural amplifiers of viral encounter in diffusion-limited environments. While piliated and non-piliated Synechococcus exhibited similar mortality in isolation, competition assays revealed a strong selective disadvantage for piliated cells, which were more rapidly depleted in mixed populations. This effect was most pronounced for cyanophage S-CAM7, which displayed higher pili-binding affinity and drove competitive exclusion of piliated hosts. To extend these findings to natural settings, we analysed single-cell amplified genomes (SAGs) observing pili genes encoded by 14.7% of total cyanobacterial SAGs. This proportion increased to 28.1% in virally infected SAGs (virocells; representing 3.8% of the total cyanobacterial SAGs), consistent with encounter-driven susceptibility of piliated cells in the environment. Together, our results identify type IV pili as double-edged structures: while conferring ecological advantages, they expose cells to viral attack by increasing encounter probability when pilus-attached phage are transport to the cell surface during pili retraction. This fitness cost may help explain the patchy distribution of pili in natural populations and the extreme sequence variability of pilins, reflecting an ongoing evolutionary arms race with phage.

microbiology↗

bioRxiv2024

Diversity of the O-chain biosynthetic cluster in the Pelagibacterales

We have used single-amplified genomes (SAGs) and long-read metagenomics to examine the diversity of the O-chain polysaccharide biosynthesis cluster (OBC) in marine bacteria of the Pelagibacterales order. OBCs are notorious for their diversity and have been used to type strains in pathogens and saprophytes, but their patterns of variation in free-living bacteria are little known. We found that, for these marine heterotrophic bacteria, the diversity is comparable to that of saprophytes, such as Enterobacteriales i.e. nearly each strain carries a different OBC. However, although OBC inheritance was largely vertical, the existence of some shared clusters allowed a comparative analysis. The OBCs diverge along with the genome, which is taken as indicative of old horizontal gene transfer (HGT) events. Only 14 cases of recent HGT were detected and they happened independently of taxonomy or location. Thus, although the O-chain is a major phage receptor in Gram-negative bacteria, the exchange of the complete cluster seems to play a minor role in the phage-bacterium arms-race. By long-read metagenomics, we could detect 380 different OBCs in a single sampling site in the Mediterranean. A single population (single species and sample) of the endemic Ia.3/VII genomospecies had a set of 158 OBCs of which 130 were different. This large diversity in clonal lineages might reflect the large amount of metabolic pathways required to deal with the enormous chemical diversity of dissolved organic matter in the ocean.

microbiology↗

bioRxiv2023

Impact of sickle cell trait hemoglobin in Plasmodium falciparum-infected erythrocytes

Sickle cell trait (HbAS) confers protection against severe Plasmodium falciparum malaria but has little effect on infection rates per se. The reason for this is not fully understood. However, it appears to involve impaired parasite survival at the low oxygen tensions prevailing in the postcapillary venules where P. falciparum-infected erythrocytes (IEs) often accumulate. This IE sequestration is mediated by parasite-encoded IE surface ligands, primarily PfEMP1. Different variants of this family of proteins bind to host receptors with different tissue distributions. We hypothesized that P. falciparum parasites modulate PfEMP1 expression to enhance their survival by altering IE tissue distribution in HbAS hosts. To test this, we studied PfEMP1 expression in parasites maintained in vitro in HbAS and HbAA erythrocytes. We found that parasite survival and PfEMP1 expression were reduced in HbAS IEs, particularly at low oxygen tensions, without obvious qualitative differences in PfEMP1 expression between HbAA and HbAS IEs. In contrast, parasites growing in HbAS erythrocytes increased their transcription of pfsa2, a parasite gene hypothesized to be under HbS-dependent selection. Taken together, our findings support the hypothesis of quantitative but not qualitative modulation of PfEMP1 expression as a parasite strategy for coping with HbAS-related host resistance. Moreover, it provides a hint at the role of Pfsa2 in parasite adaptation to HbAS and highlights the importance of further research.

microbiology↗

bioRxiv2023

Flotillin-Associated rhodopsin (FArhodopsin), a widespread paralog of proteorhodopsin in aquatic bacteria with streamlined genomes

Microbial rhodopsins are often found more than once in a single genome (paralogs) that often have different functions. We screened a large dataset of open ocean single-amplified genomes (SAGs) for co-occurrences of multiple rhodopsin genes. Many such cases were found among Pelagibacterales (SAR11), HIMB59 and the Gammaproteobacteria Pseudothioglobus SAGs. These genomes always had a bona fide proteorhodopsin and a separate cluster of genes containing a second rhodopsin associated with a predicted flotillin coding gene and have thus been named flotillin-associated rhodopsins (FArhodopsins). They are quite divergent from the other proteorhodopsin paralog and contain either DTT, DTL or DNI motives in their key functional amino acids. FArhodopsins are mainly associated with the lower layers of the epipelagic zone. All marine FArhodopsins had the retinal binding lysine, but we found their relatives in freshwater metagenomes that lack this key amino acid. Alfa-fold predictions of marine FArhodopsins indicate that their retinal pocket might be very reduced or absent, hinting that they are retinal-less (blind). Freshwater FArhodopsins were more diverse than marine FArhodopsins, but we could not determine if they are present as paralogs of other rhodopsins, due to the lack of SAGs or isolates. Although the function of FArhodopsins could not be established, their conserved genomic context indicated involvement in the formation of membrane microdomains. The conservation of FArhodopsins in diverse and globally abundant microorganisms suggests that they may be important in the adaptation to the twilight zone of aquatic environments. IMPORTANCERhodopsins have been shown to play a key role in the ecology of aquatic microbes. Here we describe a group of widespread rhodopsins in aquatic microbes associated with dim light conditions. Their characteristic genomic context found in both marine and freshwater environments indicates a novel potential involvement in membrane microstructure that could be important for the function of the co-existing proteorhodopsin proton pumps. The absence or reduction of the retinal binding pocket points to drastically different physiology. In addition to their ecological importance, novel rhodopsins have biotechnological potential in the nascent field of optogenetics.

microbiology↗

bioRxiv2022

Allelic diversity uncovers protein domains contributing to the emergence of antimicrobial resistance

Antimicrobial resistance (AMR) remains a major threat to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here, we developed a framework that exploits genetic diversity from environmental bacterial populations to decode emergent phenotypes such as AMR. OmpU, is a porin that makes up to 60% of the outer membrane of Vibrio cholerae, the cholera pathogen. This porin is directly associated with the emergence of the bacterium and confers resistance to numerous host antimicrobials. In this study, we examined naturally occurring allelic variants of OmpU in environmental V. cholerae and established associations that connected genotypic variation with phenotypic outcome. We covered the landscape of gene variability and found that the porin forms two major phylogenetic clusters with striking genetic diversity. We generated 14 isogenic mutant strains, each encoding a unique ompU allele, and found that divergent genotypes lead to convergent antimicrobial resistance profiles. We identified and characterized functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Specifically, we identified four conserved domains that are linked with resistance to bile and host-derived antimicrobial peptides. Mutant strains for these domains exhibit differential susceptibility patterns to these and other antimicrobials. Interestingly, a mutant strain in which we exchanged the four domains of the clinical allele for those of a sensitive strain exhibits a resistance profile closer to a porin deletion mutant. Finally, using phenotypic microarrays, we uncovered novel functions of OmpU and their connection with allelic variability. Our findings highlight the suitability of our approach towards dissecting the specific protein domains associated with the emergence of AMR and can be naturally extended to other bacterial pathogens and biological processes. AUTHOR SUMMARYAntimicrobial resistance (AMR) is one of the major threats to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here we developed an approach that uses genetic diversity from environmental populations to decode emergent phenotypes such as AMR. Specifically, we examined naturally occurring allelic variants of an outer membrane porin, OmpU, in Vibrio cholerae and established associations between genotype and phenotype. Using this approach, we identified and characterized the functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Our perspective towards disentangling the emergence of AMR can be naturally extended to other proteins and bacterial pathogens.

microbiology↗

bioRxiv2022

Cluster-driven evolution and modularity uncover paths of cholera emergence

Cholera, an acute secretory diarrhea, is caused by strains from a phylogenetically confined group within the Vibrio cholerae species, the pandemic cholera group (PCG). To date, the molecular and evolutionary factors that enable the isolated emergence of toxigenic V. cholerae from environmental populations remain mostly enigmatic. Comprehensive analyses of over 1,100 V. cholerae genomes, including novel environmental isolates from this study, reveal that the species consists of four major clades and several minor ones. PCG belongs to a large clade located within a lineage shared with environmental strains, the pandemic cholera lineage. This hierarchical classification provided us with a framework to unravel the eco-evolutionary dynamics of the genetic determinants associated with the emergence of toxigenic V. cholerae. Our analyses indicate that this phenomenon is largely dependent on the acquisition of unique modular gene clusters and allelic variations that confer a competitive advantage during intestinal colonization. We determined that certain PCG-associated alleles are essential for successful colonization whereas others provide a non-linear competitive advantage, acting as a critical bottleneck that elucidates the isolated emergence of PCG. For instance, toxigenic strains encoding non-PCG alleles of a) tcpF or b) a sextuple allelic exchange mutant for genes tcpA, toxT, VC0176, VC1791, rfbT and ompU, lose their ability to colonize the intestine. Interestingly, these alleles do not play a role in the colonization of model environmental reservoirs. Our study uncovers the evolutionary roots of toxigenic V. cholerae and offers a tractable approach for investigating the emergence of pathogenic clones within an environmental population. SIGNIFICANCEThe underlying factors that lead to specific strains within a species to emerge as human pathogens remain mostly enigmatic. Toxigenic clones of the cholera agent, Vibrio cholerae, are encompassed within one phylogenomic clade, the pandemic cholera group (PCG). Here, we investigate the molecular and evolutionary factors that explain the confined nature of this group. Our analyses determined that the emergence of PCG is largely dependent on the acquisition of unique modular gene clusters and allelic variations that confer a competitive advantage during intestinal colonization. These allelic variations act as a critical bottleneck that elucidates the isolated emergence of PCG and provides a tractable blueprint for the study of the emergence of pathogenic clones within an environmental population.

microbiology↗

bioRxiv2021

Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients: a retrospective cohort study in a Mediterranean area.

BackgroundThere is mounting evidence suggesting that the microbiome composition could be different in COVID-19 patients. However, the relationship between microbiota and COVID-19 severity progression is still being assessed. This study aimed to analyse the diversity and taxonomic composition of the nasopharyngeal microbiota, to determine its association with COVID-19 clinical outcome. Methods and FindingsSamples came from a retrospective cohort of adult patients with COVID-19, hospitalised in a tertiary centre. To study the nasopharyngeal microbiota, we utilized 16S rRNA sequencing. Raw sequences were processed by QIIME2. The associations between the microbiota, invasive mechanical ventilation (IMV), and all-cause mortality were analysed by multiple logistic regression (OR; 95%CI), adjusted for age, gender, and comorbidity. 177 patients were included: median age 68.0 years, 57.6% males, 59.3% had a Charlson comorbidity index [≥]3, and 89.2% with pneumonia. The microbiota diversity indexes were lower in patients with a fatal outcome, and this association persisted after adjustment for the main confounders; whereas the {beta} diversity analysis showed a significant clustering, grouping the patients with a fatal outcome. After multivariate adjustment, the presence of Selenomonas spp., Filifactor spp., Actinobacillus spp., or Chroococcidiopsis spp., was associated with a reduced risk of IMV (adjusted OR 0.06[95%CI 0.01-0.0.47], p = 0.007). ConclusionsThe microbiota diversity and taxonomic composition are related to COVID-19 severity. Higher diversity and the presence of certain genera in the nasopharyngeal microbiota seem to be early biomarkers of a favourable clinical evolution in hospitalised patients with moderate to severe SARS-CoV-2 infections.

microbiology↗

bioRxiv2021

Phylogenomics of SAR116 clade reveals two subclades with different evolutionary trajectories and important role in the ocean sulfur cycle

The SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship between genome diversity and its role in the marine environment. In this study, we use all publicly available genomes to provide a genomic overview of the phylogeny, metabolism and biogeography within the SAR116 clade. This increased genomic diversity revealed has led to the discovery of two subclades of SAR116 that, despite having similar genome size (ca. 2.4 Mb) and coexist in the same environment, display different properties in their genomic make up. One represents a novel subclade for which no pure cultures have been isolated and is composed mainly of single-amplified genomes (SAGs). Genomes within this subclade showed convergent evolutionary trajectories with more streamlining features, such as low GC content (ca. 30%), short intergenic spacers (<22 bp) and strong purifying selection (low dN/dS). Besides, they were more abundant in metagenomic databases recruiting also at the deep chlorophyll maximum. Less abundant and restricted to the upper photic layers of the global ocean, the other subclade of SAR116, enriched in MAGs, accommodated the only two pure cultures. Genomic analysis suggested that both clades have a significant role in the sulfur cycle with differences in the way in which both clades can metabolize the dimethylsulfoniopropionate (DMSP). IMPORTANCESAR116 clade of Alphaproteobacteria is an ubiquitous group of heterotrophic bacteria inhabiting the surface of the ocean, but the information about their ecology and population genomic diversity is scarce due to the difficulty of getting pure culture isolates. The combination of single-cell genomics and metagenomics has become an alternative approach to study this kind of microbes. Our results expand the understanding of the genomic diversity, distribution, and lifestyles within this clade and provide evidence of different evolutionary trajectories in the genome make-up of the two subclades that could serve to understand how evolutionary pressure can drive different adaptations to the same environment. Therefore, the SAR116 clade represents an ideal model organism for the study of the evolutionary streamlining of genomes in microbes that have relatively close relatedness to each other.

microbiology↗

bioRxiv2021

Afucosylated Plasmodium falciparum-specific IgG is induced by infection but not by subunit vaccination

IgG specific for members of the Plasmodium falciparum erythrocyte membrane protein 1(PfEMP1) family, which mediates receptor- and tissue-specific sequestration of infected erythrocytes (IEs), is a central component of naturally acquired malaria immunity. PfEMP1-specific IgG is thought to protect via inhibition of IE sequestration, and through IgG-Fc Receptor (Fc{gamma}R) mediated phagocytosis and killing of antibody-opsonized IEs. The affinity of afucosylated IgG to Fc{gamma}RIIIa is elevated up to 40-fold compared to fucosylated IgG, resulting in enhanced antibody-dependent cellular cytotoxicity. Most IgG in plasma is fully fucosylated, but afucosylated IgG is elicited in response to enveloped viruses and to paternal alloantigens during pregnancy. Here we show that naturally acquired PfEMP1-specific IgG is likewise markedly afucosylated in a stable and exposure-dependent manner, and efficiently induces Fc{gamma}RIIIa-dependent natural killer (NK) cell degranulation. In contrast, immunization with a soluble subunit vaccine based on VAR2CSA-type PfEMP1 resulted in fully fucosylated specific IgG. These results have implications for understanding natural and vaccine-induced antibody-mediated protective immunity to malaria. SummaryAfucosylated IgG has enhanced Fc-receptor affinity and functionality, and is formed specifically against membrane proteins of enveloped viruses. We show that this also applies to Plasmodium falciparum erythrocyte membrane-specific IgG induced by natural infection, but not by soluble PfEMP1 vaccination.

immunology↗

bioRxiv2021

Viral and parasitic cell ratios per free-living microbe across ecosystems

It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 {micro}m size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by [~]13 fold and in plankton from marine and saline waters by [~]2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.

microbiology↗

bioRxiv2020

Nasopharyngeal microbial communities of patients infected with SARS-COV-2 that developed COVID-19.

BackgroundSARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however studies focused on the patients microbiota are still lacking. In this study, we investigated the nasopharyngeal microbiome composition of patients who developed different severity levels of COVID-19. We performed Rdna-SSU (16S) sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization) and severe (admission to ICU). We compared the microbiome diversity and OTU composition among severity groups using Similarity Percentage (SIMPER) analysis and Maaslin2. We also built bacterial co-abundance networks for each group using Fastpar. ResultsStatistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidetes (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthemore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms. ConclusionsOur preliminary study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. These microbes with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results. IMPORTANCEThis work has studied the microbiota of the nasopharyngeal tract in COVID19 patients using advanced techniques of molecular microbiology. Diverse microorganisms, most of which are harmless or even beneficial to the host, colonize the nasopharyngeal tract. These microorganisms are the microbiota, and they are present in every people. However, changes in this microbiota could be related to different diseases as cancer, gastrointestinal pathologies or even COVID19. This study has been performed to investigate the microbiota from patients with COVID19, in order to determinate its implication in the pathology severity. The results obtained showed that it is possible that several specific microorganisms are present only in patients with severe COVID19. These data, could be used as a prognostic biomarker to early detect whose patients will develop a severe COVID19 and improve their clinical management.

microbiology↗

bioRxiv2020

Long read metagenomics, the next step?

BackgroundThird-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, 2nd generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in allowing assembly of microbes with high microdiversity or retrieving the flexible (adaptive) compartment of prokaryotic genomes. ResultsHere we have used different 3rd generation techniques to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared Oxford Nanopore and PacBio last generation technologies with the classical approach using Illumina short reads followed by assembly. PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. Long reads allow efficient direct retrieval of complete genes (473M/Tb) and operons before assembly, facilitating annotation and compensates the limitations of short reads or short-read assemblies. MetaSPAdes was the most appropriate assembly program when used in combination with short reads. The assemblies of the long reads allow also the reconstruction of much more complete metagenome-assembled genomes, even from microbes with high microdiversity. The flexible genome of reconstructed MAGs is much more complete and allows rescuing more adaptive genes. ConclusionsFor most applications of metagenomics, from community structure analysis to ecosystem functioning, long-reads should be applied whenever possible. Particularly for in-silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be used from raw reads, before a computing-demanding (and potentially artefactual) assembly step.

microbiology↗

bioRxiv2020

Staphylococcus sciuri C2865 from a distinct subspecies cluster as reservoir of the novel transferable trimethoprim resistance gene, dfrE, and adaptation driving mobile elements

Four methicillin-resistant Staphylococcus sciuri (MRSS) strains isolated from stranded dogs showed trimethoprim (TMP) resistance, while all staphylococcal TMP resistant dihydrofolate reductase genes (dfr) were negative. An in-depth whole-genome-sequencing approach on strain C2865 was followed for resistome and mobilome profiling, and for comparative genomics with S. sciuri group available genomes. Lack of species host tropism was observed, with MRSS C2865 placed at a separate sub-branch within S. sciuri species, close to the average nucleotide identity to be considered a different species (95-96%). S. sciuri proved a pronounced accessory genome (73% of genes), while MRSS C2865 distinctively harboured the highest total gene number and highest number of unique genes, with 75% associated to the recognised mobilome. A novel multidrug resistance mosaic plasmid (pUR2865-34) with several adaptive, mobilization (oriT mimic) and segregational stability (Type Ib par system) traits and two small single resistance plasmids were identified. Plasmid pUR2865-34 enclosed a novel staphylococcal TMP resistance gene, named dfrE, which shared highest identity with dfr of soil-related Paenibacillus anaericanus (68%). DfrE conferred high-level TMP resistance in S. aureus and Escherichia coli. Database searches revealed that dfrE was formerly denoted (dfr_like) in an Exiguobacterium spp. from a fish-farm sediment and that was present but unnoticed in several staphylococcal and onemacrococcal genomes with different epidemiological backgrounds. Novel chromosomal site-specific mobile islands with resourceful traits were identified, including a multidrug-resistant SCCmec cassette lacking cassette chromosome recombinase (Ccr) genes, a staphylococcal pathogenicity island of the SaPI4 family, and three unrelated siphoviridae prophages, two of which enclosed recombinases with the conserved Ccr-motif. We reveal a novel staphylococcal TMP resistance dfrE gene already present in diverse bacterial backgrounds. We confirm the ubiquity, high genome plasticity and low host tropism of S. sciuri highlighting its role as a resourceful reservoir for evolutionary novel features contributing to its extraordinary versatility and adaptability. Author summaryStaphylococcus spp. are ubiquitous bacteria present in diverse ecological niches, including humans, animals and the environment. They are clinically relevant opportunistic pathogens and are notorious for their ability to acquire antimicrobial resistance (AMR) and virulence properties, resulting in a significant impact for Public Health. Mobile genetic elements (MGEs) play a central role in this adaptation process and are a means to transfer genetic information across bacterial species. Staphylococcus sciuri represents one of the most ancestral species in the genus and has been suggested a reservoir for AMR genes. Here, following a refined whole genome sequencing approach we determined the entire genome of an animal and environment-associated multidrug resistant (MDR) S. sciuri strain uncovering a novel acquired staphylococcal TMP resistance gene already spread among different bacterial species from different epidemiological backgrounds. We also reveal several additional MGEs, including a novel MDR mobilizable plasmid that encloses several adaptive and stabilization features, and novel mobilizable chromosomal islands with resourceful traits, including three unrelated prophages. Together with comparative genomics, we confirm the ubiquity, high intraspecies heterogenicity, genome plasticity and low host tropism of this species, highlighting its role as resourceful reservoir for evolutionary novel features contributing to its extraordinary versatility and adaptability.

microbiology↗

bioRxiv2020

RaFAH: A superior method for virus-host prediction

Viruses of prokaryotes are extremely abundant and diverse. Culture-independent approaches have recently shed light on the biodiversity these biological entities1,2. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), based on the analysis of nearly 200,000 viral genomes. RaFAH outperformed other methods for virus-host prediction (F1-score = 0.97 at the level of phylum). RaFAH was applied to diverse datasets encompassing genomes of uncultured viruses derived from eight different biomes of medical, biotechnological, and environmental relevance, and was capable of accurately describing these viromes. This led to the discovery of 537 genomic sequences of archaeal viruses. These viruses represent previously unknown lineages and their genomes encode novel auxiliary metabolic genes, which shed light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.

bioinformatics↗

bioRxiv2020

New Viral Biogeochemical Roles Revealed Through Metagenomic Analysis of Lake Baikal

Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat but the viral communities from this ecosystem have not been characterized in detail. Here we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance.

microbiology↗

bioRxiv2017

Varying water deficit stress (WDS) tolerance in grain amaranths involves multifactorial shifts in WDS-related responses

In this study, water deficit stress (WDS)-tolerance in several cultivars of grain amaranth species (Amaranthus hypochondriacus [Ahypo], A. cruentus [Acru] and A. caudatus [Acau]), in addition to A. hybridus (Ahyb), an ancestral amaranth, was examined. Ahypo was the most WDS-tolerant species, whereas Acau and Ahyb were WDS-sensitive. Data revealed that the differential WDS tolerance observed was multifactorial. It involved increased proline and raffinose (Raf) in leaves and/ or roots. Higher foliar Raf coincided with induced Galactinol synthase 1 (AhGolS1) and Raffinose synthase (AhRafS) expression. Unknown compounds, possibly larger RFOs, also accumulated in leaves of WDS-tolerant amaranths, which had high Raf/ Verbascose ratios. Distinct nonstructural carbohydrate (NSC) accumulation patterns were observed in tolerant species under WDS and recovery, such as: i) high Hex/ Suc ratios in roots coupled to increased cell wall and vacuolar invertase and sucrose synthase activities; ii) a severer depletion of starch reserves; iii) lower NSC content in leaves, and iv) higher basal hexose levels in roots which further increased under WDS. WDS-marker gene expression patterns proposed a link between amaranths WDS tolerance and abscisic acid-dependent signaling. Results obtained also suggest that AhTRE, AhTPS9, AhTPS11, AhGolS1 and AhRafS are reliable gene markers of WDS tolerance in amaranth.\n\nHighlightDifferential water deficit stress tolerance in grain amaranths and their ancestor, Amaranthus hybridus, is a multifactorial process involving various biochemical changes and modified expression patterns of key stress-related genes.

plant biology↗