Biology subjects

Rossello-Mora, R.

Publications and source records attributed to Rossello-Mora, R..

8 recordsLinked to original sources

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↗

bioRxiv2024

Promiscuous and unbiased recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean

Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species usually show >95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria), which play a major role in carbon cycling, are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, we analyzed high-quality, single-cell amplified genomes (SAGs) and companion metagenomes from an oxygen minimum zone (OMZ) in the Eastern Tropical Pacific Ocean, where the SAR11 make up [~]20% of the total microbial community. Our results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86-91%, with intra-species ANI ranging between 91-100%. Measuring recent gene exchange among these genomes based on a newly developed methodology revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR-11 appears to be more promiscuous compared to other prokaryotic species and has facilitated the spreading of adaptive mutations within the species, further promoting the high intra-species diversity observed. These results implicate rampant, genome-wide homologous recombination as the mechanism that underlies the evolution of SAR11 into discrete species. SignificanceDistinguishing "species" is a pressing issue in microbiology, partly because the mechanisms that create and maintain clusters of genetically similar microbes are sparsely documented for natural populations. By leveraging high quality single-cell genomic data and a novel method for assessing homologous recombination, we show that rampant homologous recombination maintains species-level clusters of genomes for the most abundant order of marine bacteria, suggesting that these genomes may be evolving sexually to a much greater extent than previously thought. Therefore, our results identify a mechanism explaining the evolution of species in a major microbial group and have implications for understanding microbial diversity and the species concept more broadly.

microbiology↗

bioRxiv2024

Microbial species exist and are maintained by ecological cohesiveness coupled to high homologous recombination.

Recent analyses of metagenomes and genomes have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars). To advance the species concept the underlying genetic or ecological mechanisms that maintain these discrete units need to be elucidated. By analyzing closely related isolate genomes from the same or related samples we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on higher similarity in abundance patterns of genomes of the same vs. different units, while recombination frequency was shown to have two times or more impact on sequence evolution than point mutation. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or selection-driven recombination, but not their synergistic effect, as the mechanism of unit cohesion. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results have strong implications for how to identify and regulate microbial species and genomovars of clinical or environmental importance and answer an important question for microbiology: what a species is. SIGNIFICANCEA highly pressing issue to resolve toward advancing the species concept for microbes (i.e., "what a species is") is to elucidate the underlying mechanisms for creating and maintaining species- and intraspecies-level gaps in diversity, or simply "clusters". In this study, we provide a novel methodology and the appropriate data to elucidate these mechanisms, and thus provide a mechanistic explanation of how the evolution of species- and strain-level clusters takes place. Specifically, our results show that several bacteria may be evolving and speciating much more sexually than previously thought, even under conditions of no strong positive selection for DNA exchange (i.e., neutral conditions). These results have major implications for better understanding and modeling microbial diversity on the planet.

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↗

bioRxiv2023

Towards estimating the number of strains that make up a natural bacterial population

What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with significantly lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. Preliminary analyses of available genomes revealed that the thresholds used for defining strains and distinct intra-species units (genomovars) may be broadly applicable to additional bacterial species. Significance StatementStrains are the smallest distinguishable units within a microbial species. Strains that carry unique gene content often underly the emergence of disease outbreaks and the response of the species to environmental perturbations. Therefore, a major challenge in microbiome research across environmental and clinical settings is to evaluate how many strains of the same species coexist in nature and how dominant strains emerge from this diversity. Unfortunately, the available theoretical concept of strain is not directly applicable to culture-independent surveys. Here, we provide such a practical definition for strain and use it to show that that the number of strains making up a natural bacterial population may be large, in the order of a few thousands, but not infinite.

microbiology↗

bioRxiv2022

A natural definition for a bacterial strain and clonal complex

Large-scale surveys of prokaryotic communities (metagenomes) as well as isolate genomes have revealed that their diversity is predominantly organized in sequence-discrete units that may be equated to species. Specifically, genomes of the same species commonly show genome-aggregate average nucleotide identity (ANI) >95% among themselves and ANI <90% to members of other species, while genomes showing ANI 90-95% are comparatively rare. However, it remains unclear if such "discontinuities" or gaps in ANI values can be observed within species and thus, used to advance and standardize intra-species units such as strains and sequence types. By analyzing 18,123 complete isolate genomes from 330 bacterial species with at least ten genome representatives each as well as available long-read metagenomes, we show that such a discontinuity exists between 99.2-99.8% (mean 99.5%) ANI. The 99.5% ANI threshold is largely consistent with how sequence types have been defined in previous epidemiological studies but provides clusters with [~]20% higher accuracy in terms of evolutionary and gene-content relatedness of the grouped genomes, while strains should be consequently defined at higher ANI values (>99.99% proposed). Collectively, our results should facilitate future micro-diversity studies across clinical or environmental settings because they provide a more natural definition of intra-species units of diversity.

microbiology↗

bioRxiv2021

Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations

Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological mechanisms that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to environmental perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes recovered from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of these ecosystems. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size ([~]15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (non-core) genes showed low in situ coverage based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or ephemeral, 3.49% of them became abundant when salinity (but not light intensity) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results revealed a possible mechanism for how this immense gene diversity is maintained, which has implications for the prokaryotic species concept. Significance StatementThe pangenomes of bacterial species, i.e., the number of non-redundant genes carried by members of the species, can be enormous based on the genome sequencing of isolates from various sites around the globe and different years. However, to what extent this pattern of gene diversity applies to natural bacterial populations, i.e., strains co-occurring in the same site, and the value of this diversity for population adaptation during environmental transition remains unclear. This study showed that while the pangenome of a natural population can be similarly large, only a small fraction of the pangenome appears to be functionally important when conditions change. Taken together, these results provided quantitative insights into the extent and functional significance of the accessory pangenome of a natural, species-like population.

microbiology↗

bioRxiv2021

Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease

Inflammatory bowel diseases (IBD), which include ulcerative colitis (UC) and Crohns disease (CD), cause chronic inflammation of the gut, affecting millions of people worldwide. IBD have been frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is generally characterized by an increase in abundance of Proteobacteria such as Escherichia coli, and a decrease in abundance of Firmicutes such as Faecalibacterium prausnitzii (an indicator of a healthy colonic microbiota). The mechanisms behind the development of the IBD and the dysbiosis are incompletely understood. Using samples from colonic biopsies, we studied the mucosa-associated intestinal microbiota in Chilean and Spanish patients with IBD. In agreement with previous studies, microbiome comparison between IBD patients and non-IBD controls indicated that dysbiosis in these patients is characterized by an increase of pro-inflammatory bacteria (mostly Proteobacteria) and a decrease of commensal beneficial bacteria (mostly Firmicutes). Notably, bacteria typically residing on the mucosa of healthy individuals were mostly obligate anaerobes, whereas in the inflamed mucosa an increase of facultative anaerobe and aerobic bacteria was observed. We also identify potential co-occurring and mutually exclusive interactions between bacteria associated with the healthy and inflamed mucosa, which appear to be determined by the oxygen availability and the type of respiration. Finally, we identify a panel of bacterial biomarkers that allow the discrimination between eubiosis from dysbiosis with a high diagnostic performance (96% accurately), which could be used for the development of non-invasive diagnostic methods. Thus, this study is a step forward toward understanding the landscapes and alterations of mucosa-associated intestinal microbiota in patients with IBD.

microbiology↗