Biology subjects

Anton, J.

Publications and source records attributed to Anton, J..

11 recordsLinked to original sources

bioRxiv2026

Coupled effects of salinity and host phylogeny on niche breadth and viral evolution from seawater to salt saturation

Virus-host interactions are fundamental drivers of microbial community structure, yet whether viral ecological niches are confined within individual host niches (nested host niche scenario) or span multiple hosts and exceed any single host niche (expanded host niche scenario) remains poorly understood. To explore these patterns, we characterized prokaryotic and viral distributions and predicted virus-host interactions along a salinity gradient at Bras del Port salterns (Spain), ranging from seawater (3.6% salinity) to salt saturation (39.0%). We analyzed metagenomes and viromes from six ponds supplemented by 27 additional published viromes from the same hypersaline system, recovering 170 metagenome-assembled genomes (MAGs) dereplicated at the genomospecies level (MAGs clustered at 95 % average nucleotide identity), approximately 55,000 viral operational taxonomic units (vOTUs), and nearly 4,000 predicted virus-host pairs. Viruses exhibited broader niches than their putative hosts at the highest salinities, while at lower salinities the pattern was reversed or inconsistent depending on the site, and niche breadths of both viruses and hosts increased steadily toward higher salinities. Host taxonomy at the class level and below was the primary driver of viral genomic clustering, explaining more variance than salinity provenance (approximately 30% vs. approximately 19%), while the contribution of salinity to viral genomic composition appeared indirect, mediated through the salinity-driven distribution of distinct host classes rather than direct environmental filtering of viral sequences. Together, these findings support the expanded host niche scenario as the predominant virus-host interaction strategy, with evolutionary and ecological dynamics jointly shaped by salinity and host identity.

microbiology↗

bioRxiv2026

Aerobic Exercise Preserves Capillary Oxygen Homeostasis and Neurovascular Function in a Mouse Model of Alzheimer's Disease

Age-related cerebrovascular dysfunction is increasingly recognized as a critical contributor to cognitive decline and Alzheimers disease (AD) progression. Aerobic physical activity (PA) and other modifiable lifestyle interventions can substantially reduce the likelihood of dementia; however, their ability to mitigate cerebrovascular alterations remains poorly defined. PA reportedly improves systemic vascular health and cognitive function in aging humans, but its impact on cerebrovascular function during aging and amyloid {beta} (A{beta}) pathology is unclear. Here, we longitudinally quantified microvascular oxygen tension and stimulus-evoked oxygen dynamics in awake APP/PS1dE9 mice and wild-type littermates using two-photon phosphorescence lifetime microscopy. Routine aerobic PA initiated in early adulthood preserved basal arteriolar, capillary, and venular oxygenation, prevented age-dependent increases in microvascular heterogeneity, and mitigated excessive oxygen extraction in preclinical AD mice. While amyloid pathology impaired stimulus-evoked oxygen responses across vascular compartments, PA selectively enhanced capillary dilation and accelerated hyperemic kinetics without altering vascular density or architecture. Notably, sedentary AD mice developed lower, widely-dispersed distributions in capillary oxygenation, hallmarks of malignant microvascular dysfunction, which were largely absent in physically active animals. These findings demonstrate that routine aerobic PA preserves basal capillary oxygenation and stimulus-evoked hyperemia during aging and A{beta}, supporting a capillary-centric mechanism through which exercise confers neurovascular resilience in preclinical AD.

neuroscience↗

bioRxiv2026

Metagenomic insights into microbial mediation of Caulerpa prolifera invasion in a coastal lagoon

Opportunistic seaweeds of the genus Caulerpa have benefited from human-driven environmental change to expand within coastal lagoons, frequently displacing native seagrasses. In the Mar Menor lagoon (southeastern Spain), Caulerpa prolifera has progressively expanded since the 1970s, coinciding with the decline of the native seagrass Cymodocea nodosa. Sediments colonized by Ca. prolifera are characterized by elevated sulfide concentrations, which are toxic to seagrasses. Because sulfide is microbially produced, these sediment communities likely shape the competition between Ca. prolifera and Cy. nodosa. However, their metabolic potential and activity remain poorly understood. Here, we examined the taxonomic composition and functional capabilities of sediment microbial communities using 12 paired metagenomes and metatranscriptomes from areas dominated by either Ca. prolifera or Cy. nodosa. Caulerpa-associated sediments displayed a higher potential for organic matter degradation and sulfate reduction. Several metagenome-assembled genomes (MAGs) encoded enzymes putatively involved in the degradation of pectin-like polysaccharides characteristic of the Caulerpa cell wall. Comparison of metagenomic and metatranscriptomic data further revealed that the most abundant MAGs were not necessarily the most transcriptionally active. This finding challenges the common assumption that ecological importance is primarily determined by abundance and highlights the potential contribution of less abundant microorganisms to biogeochemical cycling. Further, 97 of the 100 most highly expressed genes lacked functional annotation. Recombinant production and functional characterization of the protein encoded by the most highly expressed gene in the analyzed sediments revealed that it is an enzyme able to breakdown endogenous bacterial peptidoglycan. Collectively, these results underscore the importance of integrating metagenomics and metatranscriptomics with experimental validation to achieve a more comprehensive understanding of microbial functional capabilities, an integration that is still uncommon in the microbial ecology field.

microbiology↗

bioRxiv2025

Metagenomics reveal allopatric speciation and higher connectivity among coastal vs. inland hypersaline lakes and solar salterns

Hypersaline environments, due to their discrete and geographically isolated nature, constitute ideal systems for studying evolutionary patterns and microbial diversification, and especially here when contrasting coastal with inland systems. Based on metagenomic comparisons of 25 hypersaline sites across 11 countries, we explored the influence of environmental factors, ionic composition, and geographic distance on their microbial community structures and taxa diversification. Our results revealed that microbial communities from coastal environments were taxonomically and functionally more similar to each other than to those from inland sites. A distance-decay relationship in the genetic relatedness, significantly more pronounced for the coastal sites, was observed among reconstructed metagenome-assembled genomes (MAGs), clearer at distances below 400 km, but still detectable across global scales up to 20,000 km. The 484 MAGs recovered, representing 284 distinct species, revealed a striking global ubiquity, with 62.5% of the species showed cosmopolitanism as were detected across multiple sites. The higher taxonomic and genetic similarity of coastal environments over the inland sites seems to reflect an environmental connection that may be related to the ocean current dynamics. Most cosmopolitan species showed clear allopatric differentiation, although few cases of a single globally dominant genomovar (average nucleotide identity, ANI > 99.8%) were also observed, especially for some Haloquadratum species. The findings suggest that coastal hypersaline systems are loosely constrained by geographic isolation, with clear signals of allopatric speciation at the mesoscale (tenths to hundreds of kilometers) that become blurrier at larger scales.

microbiology↗

bioRxiv2025

Biological context modulates virus-host dynamics and diversification

Virus-host interactions are fundamental to microbial ecology and evolution, yet they are often studied in simplified systems. To assess the impact of biological complexity, we examined the halophilic bacterium Salinibacter ruber strain M1 and the EM1 virus, a bacteriophage that infects M1, in the presence of additional strains and viruses. In the short term, the presence of a biotic background delayed population-level lysis and reduced EM1 production. In the long term, both M1 and EM1 persisted across all conditions, but their evolutionary trajectories diverged. The virus accumulated many mutations, showed reduced infectivity against its native host, and expanded its host range in the presence of other viruses, highlighting a role of virus-virus interactions in promoting diversification. In contrast, the host accumulated more mutations when evolving with other bacterial strains. Taken together, these findings demonstrate that biological complexity shapes both the ecological dynamics and evolutionary trajectories of virus-host interactions.

microbiology↗

bioRxiv2025

Systemic inflammation reduces astrocyte Ca2+ and neurovascular coupling in a mouse model of Alzheimers disease

Chronic neuroinflammation in Alzheimers disease (AD) activates astrocytes--key regulators of both brain immunity and neurovascular coupling. The primed immune environment in AD brain also renders it highly susceptible to secondary systemic inflammatory challenges. Inflammatory activation drives phenotypic shifts in astrocytes that may compromise their ability to regulate cerebral blood flow. The capacity for inflammation-activated astrocytes to retain this regulatory function, however, remains unknown. To investigate astrocyte regulation of cerebral blood flow in AD brain and under systemic inflammation, we investigated astrocytic Ca2+ dynamics and functional hyperemia at rest and during brief and prolonged sensory stimulation in 12-month-old female APP/PS1dE9 mice. We further examined how a secondary systemic inflammatory challenge induced by low-dose, repeated injection of LPS modulates astrocytic signaling and neurovascular function. AD mice exhibited elevated spontaneous but diminished stimulation-evoked astrocytic Ca2+ activity, accompanied by impaired sustained functional hyperemia, particularly within the capillary network. LPS-induced systemic inflammation further suppressed both spontaneous and evoked astrocytic Ca2+ responses and attenuated functional hyperemia. Together, these findings reveal that inflammation disrupts astrocyte-dependent regulation of sustained neurovascular responses in the AD brain. HIGHLIGHTSO_LIAstrocytes in AD mice exhibit increased spontaneous Ca2+ signaling but cannot sustain stimulus-evoked Ca2+ release. C_LIO_LIReduced astrocyte Ca2+ release during 30s functional brain activation correlates with impaired neurovascular coupling in both penetrating arterioles and capillaries of AD mice C_LIO_LIA secondary, 14-day systemic inflammatory challenge further suppressed functional hyperemia of 30 s stimulus-evoked astrocytic Ca2+ release in AD mice. C_LIO_LIA secondary inflammatory insult lasting 14 days reduced amyloid deposition in the AD brain. C_LI

bioengineering↗

bioRxiv2024

Aerolysin nanopore structure revealed at high resolution in lipid environment

Aerolysin is a {beta}-pore-forming toxin produced by most Aeromonas bacteria which has attracted large attention in the field of nanopore sensing due to its narrow and charged pore lumen. Structurally similar proteins, belonging to the aerolysin-like family, are present throughout all kingdoms of life, but very few of them have been structurally characterized in a lipid environment. Here we present the first high-resolution atomic cryo-EM structures of aerolysin pre-pore and pore in a membrane-like environment. These structures allow the identification of key interactions, which are relevant for the pore formation and for positioning the pore barrel into the membrane with the anchoring {beta}-turn motif now finally observed. Moreover, we elucidate at high resolution the architecture of key mutations and precisely identify four constriction rings in the pore lumen that are highly relevant for nanopore sensing experiments.

biochemistry↗

bioRxiv2024

Episomal virus maintenance enables bacterial population recovery from infection and virus-bacterial coexistence

Hypersaline environments harbor the highest concentrations of virus-like particles (VLPs) reported for aquatic ecosystems. The substantial densities of both microbial populations and VLPs challenge traditional explanations of top-down control exerted by viruses. At close to saturation salinities, prokaryotic populations are dominated by Archaea and the bacterial clade Salinibacter. In this work we examine the episomal maintenance of a virus within a Salinibacter ruber host. We found that infected cultures of Sal. ruber M1 developed a population-level resistance and underwent systematic and reproducible recovery post infection that was counter-intuitively dependent on the multiplicity of infection (MOI), where higher MOI led to better host outcomes. Furthermore, we developed a nonlinear population dynamics model that successfully reproduced the qualitative features of the recovery. This suggests that the maintenance of the virus episomally, often referred to as pseudolysogeny, and lysis inhibition allow for host-virus co-existence under high MOI infections. Our results emphasize the ecological importance of exploring a spectrum of viral infection strategies beyond the conventional binary of lysis or lysogeny.

microbiology↗

bioRxiv2024

A natural ANI gap that can define intra-species units of bacteriophages and other viruses

Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A 95% whole-genome average nucleotide identity (ANI) gap is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage species revealed a region of low frequency of pairs around 99.2-99.8% ANI, showing 3-fold or fewer pairs than expected for an even or normal distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts, and from a variety of environments, although a few exceptions to this pattern were also observed ([~]3.7% of the total species evaluated) and are likely attributed to cultivation biases. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled including SARS-CoV-2, whose ANI-based clusters matched well the WHO-defined Variants of Concern, indicating that they represent functionally and/or ecologically distinct units. The existence of sequence-discrete units appears to be predominantly driven by (high) ecological cohesiveness coupled to either recombination frequency for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2. These results indicate that fundamentally different underlying mechanisms could lead to similar diversity patterns. Based on these results, we propose the 99.5% ANI as a practical, standardized, and data-supported threshold for defining viral intra-species units of bacteriophages, for which we propose the term genomovars. ImportanceViral species are composed of an ensemble of intra-species variants whose dynamic may have major implications for human and animal health and/or ecosystem functioning. However, the lack of universally-accepted standards to define these intra-species variants has led researchers to use different approaches for this task, creating inconsistent intra-species units across different viral families and confusion in communication. By comparing hundreds of viral bacteriophage genomes, we show that there is a nearly universal natural gap in whole-genome average nucleotide identities (ANI) among genomes at around 99.5%, which can be used to define intra-species units. Therefore, these results advance the molecular toolbox for tracking viral intra-species units and should facilitate future epidemiological and environmental studies.

microbiology↗

bioRxiv2021

Shifts in marine invertebrate bacterial assemblages associated with tissue necrosis during a heatwave

Marine heatwaves (MHWs) are periods of extremely high seawater temperature that affect marine ecosystems in several ways. Anthozoans (corals and gorgonians) and Porifera (sponges) are usually among the taxa most affected by MHWs. Both are holobiont entities that form complex interactions with a wide range of microbes, which are an essential part of these organisms and play key roles in their health status. Here, we determine microbial community changes suffered in two corals (Cladocora caespitosa and Oculina patagonica), one gorgonian (Leptogorgia sarmentosa), and one sponge (Sarcotragus fasciculatus) during the 2015 MHW. The microbial communities were different among hosts and displayed shifts related to host health status, with a higher abundance in necrosed tissues of Ruegeria species or of potential pathogens like Vibrio. We also carry out a meta-analysis using 93 publicly accessible 16S rRNA gene libraries from O. patagonica, C. caespitosa and L. sarmentosa to establish a Mediterranean core microbiome in these species. We have identified one Ruegeria OTU that maintained a stable and consistent association with these species, which was also related with tissue necrosis in their hosts. Therefore, Ruegeria sp. could play an important and still underexplored role in the health status of its hosts.

microbiology↗

bioRxiv2019

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments. Here we investigate the origin, evolution, and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboratory, we obtained DNA sequences of crAssphage from over one-third of the worlds countries, and showed that its phylogeography is locally clustered within countries, cities, and individuals. We also found colinear crAssphage-like genomes in both Old-World and New-World primates, challenging genomic mosaicism and suggesting that the association of crAssphage with primates may be millions of years old. We conclude that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.

microbiology↗