Biology subjects

Tromas, N.

Publications and source records attributed to Tromas, N..

10 recordsLinked to original sources

bioRxiv2026

Linking Cyanobacterial Genomes to Toxin Dynamics Through Genome-Resolved Metagenomics

Global climate change and nutrient pollution from agricultural systems increase cyanobacterial bloom and toxin release events, and will pose a significant concern for public health and safety over the coming decades. Many in situ studies have focused on environmental, chemical, and microbial community changes and their impact on cyanobacterial bloom frequency and toxicity. However, fine-scale genetic differences in the genomes of bloom-forming cyanobacteria may also impact the quantity and types of toxins produced. Metagenomic approaches allow resolution of strain- and nucleotide-level changes within microbial communities and can improve our understanding of the factors that affect cyanobacterial bloom dynamics and toxicity. Here, we conduct a metagenomic analysis of the bloom-forming cyanobacterial genus Microcystis across a 10-month lake time series from the Valle de Bravo Reservoir, to assess how within-genus genotype-level changes are linked to intracellular toxin production and extracellular toxin release, as well as how single nucleotide variation may affect the types of microcystin toxins produced. Our results demonstrate that the abundances of both toxigenic and non-toxigenic Microcystis genotypes are significantly related to microcystin toxin concentrations. In addition to these genome-wide ("strain"-level) associations, specific single nucleotide variants show strong associations with chemical variants of microcystin in the environment. Our work highlights the importance of fine-scale analysis of microbial community composition for understanding cyanobacterial bloom dynamics and toxin production.

microbiology↗

bioRxiv2025

Co-occurrence drives horizontal gene transfer among marine prokaryotes

Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15,339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached bacteria and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine bacterial evolution through HGT.

evolutionary biology↗

bioRxiv2025

Deciphering the dynamics of Cyanobacteria-Phage in a natural lake: Insights from a decade-long investigation

Phages - viruses that infect bacteria - are often seen as key players in bacterial community dynamics and the ecosystem services those communities support. However, much of our understanding of phage-bacteria interactions comes from in vitro studies, which provide limited insights into how these interactions occur in natural environments. In this study, we used cyanobacterial blooms as a model microbial community to evaluate the potential role of phages in driving cyanobacterial populations. These blooms are characterized by massive and usually rapid accumulation of cyanobacterial biomass and occur worldwide, threatening aquatic systems. The frequency and intensity of cyanobacterial blooms are increasing over time, likely due to human activities, and, until now, the role of predators like phages has remained unclear. We used a deep amplicon sequencing approach targeting the g20 capsid gene to profile the cyanophage community in eutrophic Lake Champlain over time, comparing their dynamics and diversity with bacterial communities and examining their associations. We evaluated whether phages simply followed bacterial dynamics, with limited impact on bacterial composition, or instead whether they played an active role in drving bacterial community structure. We found that phages exhibited similar dynamics to their potential bacterial hosts and shared environmental niches. However, we also observed strong differences specific to the phage community, such as inter-annual variation and an increase in Shannon diversity over time. Phage-bacteria and phage-cyanobacteria co-variance uncovered potential interactions that resulted in strongly modular networks. However, while the network structure remained modular, the composition of the modules differed significantly between environmental and temporal conditions. Lastly, viral phylogeny partially explained phage-bacteria co-variance, but only for a small proportion of bacterial ASVs. Our results indicate that phage-bacterial interactions are partly genetically structured and vary within modules across environmental conditions.

ecology↗

bioRxiv2024

Cell-associated viral community composition and its functional potential in a dimictic lake on the Canadian Shield

The Turkey Lake Watershed (TLW), located in Northern Ontario, forms a cascading lake system that ultimately drains into Lake Superior. Historically, the TLW has served as a key research site for studies on acid rain and climate change. Despite its long-standing ecological importance, investigations into its microbial communities remain limited, and to date, no studies have explicitly examined the viral component of this watershed. A major obstacle to such research is the challenge of obtaining sufficient viral biomass from remote locations like the TLW for downstream sequencing and analysis. To address this, we focused on viral signatures associated with microbial cells, which require less biomass at the time of collection. Using this approach, we conducted a seasonal metagenomic survey of Big Turkey Lake (BTL)--one of the primary lakes within the TLW--from summer 2018 to winter 2020. Our study characterized the diversity and composition of cell-associated viral communities, predicted potential host relationships, and identified auxiliary metabolic genes (AMGs) to better understand the functional roles of these viruses. The results revealed a dynamic viral community that varied across seasons. Most viral contigs were classified within the class Caudoviricetes, while members of the Phycodnaviridae emerged as important non-bacteriophage contributors to the viral assemblage. We also reconstructed six draft viral metagenome-assembled genomes (vMAGs), ranging in size from 11 to 45 kbp, all identified as Caudoviricetes, with two being potential temperate phages, and a third containing ribosomal genes. Notably, AMGs associated with lipid metabolism were detected exclusively in a winter sample, suggesting a potential season- or niche-specific role for these genes in BTL, while AMGs related to phosphorus acquisition were present in all samples. Together, these findings provide the first insight into the viral ecology of the TLW and establish a foundation for future studies investigating the roles of viruses in shaping the microbial dynamics in this important habitat.

microbiology↗

bioRxiv2020

Single-colony sequencing reveals phylosymbiosis, co-phylogeny, and horizontal gene transfer between the cyanobacterium Microcystis and its microbiome

Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria - their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies - including cyanobacteria and associated bacterial genomes - isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil. We found 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely-related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter, suggesting long-term evolutionary associations. Roseomonas and Rhodobacter genomes encode functions which could complement the metabolic repertoire of Microcystis, such as cobalamin and carotenoid biosynthesis, and nitrogen fixation. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting.

microbiology↗

bioRxiv2019

The evolution of biotic and abiotic realized niches within freshwater Synechococcus

Understanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely-related organisms share similar ecological preferences due to phylogenetic conservation - or if they are forced apart by competition - is still debated. Here we explored the co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether more closely-related taxa share more similar niches, and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely-related Synechococcus (in the continuous range of 93-100% nucleotide identity in 16S) had an increased tendency to co-occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co-occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub-genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation. Originality-Significance StatementWe address a fundamental question in ecology and evolution: how do niche preferences change over evolutionary time? Using time-series analysis of 16S rRNA gene amplicon sequencing data, we develop an approach to highlight the importance of biotic factors in defining realized niches, and show how niche preferences change proportionally with the 16S gene molecular clock within the genus Synechococcus. Ours is also one of few studies on the ecology of freshwater Synechococcus, adding significantly to our knowledge about this abundant and widespread lineage of Cyanobacteria.

ecology↗

bioRxiv2019

Two cases of type-a Haemophilus influenzae meningitis within the same week in the same hospital are phylogenetically unrelated but recently exchanged capsule genes

H. influenzae causes common and sometimes severe pediatric disease including chronic obstructive respiratory disease, otitis media, and infections of the central nervous system. Serotype b strains, with a b-type capsule, have been the historical cause of invasive disease, and the introduction of a serotype b-specific vaccine has led to their decline. However, unencapsulated or non-b-type H. influenzae infections are not prevented by the vaccine and appear to be increasing in frequency. Here we report two pediatric cases of severe central nervous system H. influenzae infection presenting to the same hospital in San Diego, California during the same week in January 2016. Due to good vaccine coverage in this part of the world, H. influenzae cases are normally rare and seeing two cases in the same week was unexpected. We thus suspected a recent transmission chain, and possible local outbreak. To test this hypothesis, we isolated and sequenced whole genomes from each patient and placed them in a phylogenetic tree spanning the known diversity of H. influenzae. Surprisingly, we found that the two isolates (H1 and H2) belonged to distantly related lineages, suggesting two independent transmission events and ruling out a local outbreak. Despite being distantly related, H1 and H2 belong to two different lineages that appear to engage in frequent horizontal gene transfer (HGT), suggesting overlapping ecological niches. Together, our comparative genomic analysis supports a scenario in which an f-type ancestor of H2 arrived in North America around 2011 and acquired an a-type capsule by recombination (HGT) with a recent ancestor of H1. Therefore, as in other bacterial pathogens, capsule switching by HGT may be an important evolutionary mechanism of vaccine evasion in H. influenzae.\n\nOUTCOMETwo cases of severe central nervous system H. influenzae infection occurred during the same week in the same hospital in San Diego, California - a region where such infections are usually very rare due to vaccine coverage. We thus suspected a local outbreak of an H. influenzae clone not covered by the vaccine. Using whole genome sequencing and phylogenetic analysis of two isolates (H1 and H2, one from each patient), we found that they were distantly related, rapidly ruling out a local outbreak and suggesting independent transmission events. This result highlights the potential for rapid global spread of non-vaccine H. influenzae strains. In this case, both H1 and H2 both encoded a-type capsules, whereas the vaccine targets b-type capsules. We also present comparative genomic evidence that a recent f-type ancestor of H2 acquired an a-type capsule locus from a recent ancestor of H1, and that this horizontal gene transfer (HGT) event likely happened in the past decade in North America, but probably not in the San Diego hospital. These results highlight the potential importance of HGT in the capsule locus in allowing H. influenzae to escape vaccine coverage.\n\nDATA SUMMARYH. influenzae H1 and H2 genome sequences have been deposited in NCBI under BioProject PRJNA534512.\n\nCONFLICT OF INTEREST STATEMENTThe authors declare that they have no conflict of interest to report.

microbiology↗

bioRxiv2019

Coherence of Microcystis species revealed through population genomics

Microcystis is a genus of freshwater cyanobacteria which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into morphospecies. However, colony morphology is a plastic trait which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes (of which 19 were resequenced to check for mutation in culture) mainly from Canada and Brazil. We identified eight Microcystis clusters of genomic similarity, only four of which correspond to named morphospecies and monophyletic groups. Notably, M. aeruginosa is paraphyletic, distributed across four genomic clusters, suggesting it is not a coherent species. Most monophyletic groups are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clusters further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes - including some involved in microcystin and micropeptin biosynthesis - are recombined between monophyletic groups in the same geographic location, suggesting local adaptation. Together, our results show the importance of using genomic criteria for Microcystis species delimitation and suggest the existence of locally adapted lineages and genes. ImportanceThe genus Microcystis is responsible for harmful and often toxic cyanobacterial blooms across the world, yet it is unclear how and if the genus should be divided into ecologically and genomically distinct species. To resolve the controversy and uncertainty surrounding Microcystis species, we performed a population genomic analysis of Microcystis genome from public databases, along with new isolates from Canada and Brazil. We inferred that significant genetic substructure exists within Microcystis, with several species being maintained by barriers to gene flow. Thus, Microcystis appears to be among a growing number of bacteria that adhere to a Biological Species-like Concept (BSC). Barriers to gene flow are permeable, however, and we find evidence for relatively frequent cross-species horizontal gene transfer (HGT) of genes that may be involved in local adaptation. Distinct clades of Microcystis (putative species) tend to have distinct profiles of toxin biosynthesis genes, and yet toxin genes are also subject to cross-species HGT and local adaptation. Our results thus pave the way for more informed classification, monitoring and understanding of harmful Microcystis blooms.

microbiology↗

bioRxiv2017

Niche separation increases with genetic distance among bloom-forming cyanobacteria

Bacterial communities are composed of distinct groups of potentially interacting lineages, each thought to occupy a distinct ecological niche. It remains unclear, however, how quickly niche preference evolves and whether more closely related lineages are more likely to share ecological niches. We addressed these questions by following the dynamics of two bloom-forming cyanobacterial genera over an 8-year time-course in Lake Champlain, Canada, using 16S amplicon sequencing and measurements of several environmental parameters. The two genera, Microcystis (M) and Dolichospermum (D), are frequently observed simultaneously during bloom events and thus have partially overlapping niches. However, the extent of their niche overlap is debated, and it is also unclear to what extent niche partitioning occurs among strains within each genus. To identify strains within each genus, we applied minimum entropy decomposition (MED) to 16S rRNA gene sequences. We confirmed that at a genus level, M and D have different preferences for nitrogen and phosphorus concentrations. Within each genus, we also identified strains differentially associated with temperature, precipitation, and concentrations of nutrients and toxins. In general, niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering - in which closely-related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. In contrast with this general pattern, similarity in certain niche dimensions (notably particulate nitrogen and phosphorus) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering - such as competition between closely-related taxa, or convergent trait evolution in distantly-related taxa - in shaping particular traits in microbial communities.

ecology↗

bioRxiv2017

Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination

Some microbial public goods can provide both individual and community-wide benefits, and are open to exploitation by non-producing species. One such example is the production of metal-detoxifying siderophores. Here, we investigate whether heavy metals select for increased siderophore production in natural microbial communities, or whether exploitation of this detoxifying effect reduces siderophore production. We show that the proportion of siderophore-producing taxa increases along a natural heavy metal gradient. A causal link between metal contamination and siderophore production was subsequently demonstrated in a microcosm experiment in compost, in which we observed changes in community composition towards taxa that produce relatively more siderophores following copper contamination. We confirmed the selective benefit of siderophores by showing that taxa producing large amount of siderophores suffered less growth inhibition in toxic copper. Our results suggest that ecological selection will favour siderophore-mediated decontamination, with important consequences for potential remediation strategies.\n\nAuthorshipEH, SOB, AL, DJH, EvV, AB conceived and designed the experiment. DJH provided new perspectives. EH, SOB, FB, AL collected the data. EH, FB, NT, DJH carried out the data analyses. EH & AB wrote the first draft of the manuscript, and all authors contributed substantially to revisions.\n\nData accessibilityUpon acceptance, data presented in the manuscript will be made available on Dryad.

ecology↗