Biology subjects

Villarreal, J. C.

Publications and source records attributed to Villarreal, J. C..

5 recordsLinked to original sources

bioRxiv2025

Decoding cryptic diversity of moss populations in a forest-tundra ecotone

Cryptic speciation is widespread among bryophytes, and it appears common in arctic and subarctic mosses where cryptic lineages may occur sympatrically in the environment. However, cryptic lineages are rarely considered in genetic diversity assessments. This situation poses a challenge, as the complex population structure resulting from cryptic speciation, along with factors like the predominance of clonality, can lead to inaccurate estimates of biodiversity. In this sense, we studied two populations of the subarctic moss Racomitrium lanuginosum in the forest-tundra ecotone to test the impact of accounting for differentiated genetic groups on moss genetic diversity estimates, clonal structure and microbial covariation. We performed genotyping-by-sequencing to infer genetic diversity and structure in the forest tundra and the shrub tundra. Genetic groups were identified using haplotype-based coancestry matrices and phylogenetic analyses. The clonal structure was explored by determining multilocus genotypes at the population and a finer scale (225 cm2). The covariation between genetic groups and microbial communities (bacterial and diazotrophic) was explored. The recognition of cryptic lineages in genetic diversity estimations revealed differences between habitats that remained undetected when treating R. lanuginosum as a single species. Clonal growth seemed to predominate and affect the genetic structure at the local scale. Finally, genetic groups did not host specific microbiomes, suggesting that moss microbial associations in the forest-tundra ecotone did strongly respond to a genetic component. This study highlights the importance of accounting for cryptic lineages in genetic diversity estimations for a precise biodiversity assessment in subarctic and arctic ecosystems.

ecology↗

bioRxiv2025

Antibiotic resistance genes detected in lichens: insights from Cladonia stellaris

Background and AimsAntibiotics are natural compounds produced by microorganisms that have long existed in ecosystems. However, the widespread clinical and agricultural use of antibiotics has intensified selective pressures on bacteria, leading to the proliferation of antibiotic resistance genes (ARGs). The increasing prevalence of these genetic elements now poses a major global health threat. While ARGs are well documented in anthropogenically influenced environments, their distribution and origins in remote ecosystems, such as the boreal forests, remain poorly understood. Here, we investigate the occurrence, diversity, and potential origins of ARGs in the boreal lichen Cladonia stellaris. MethodsWe conducted the first targeted assessment of ARGs in lichens by analyzing 42 C. stellaris samples from northern and southern lichen woodlands (LWs) in eastern Canada. Using high-throughput quantitative PCR, we screened for 33 ARGs and three mobile genetic elements (MGEs), quantifying their relative abundance. Bacterial community composition was characterized via 16S rRNA gene sequencing. Statistical analyses evaluated geographical patterns, ARGs-taxa association, and the influence of latitude on ARG distribution. Key ResultsTen ARGs conferring resistance to four antibiotic classes (aminoglycosides, beta-lactams, quinolones and sulfonamides), along with one MGE, were detected. Three ARGs, blaCTX-M-1, qnrB, and qepA, were highly prevalent, with qepA often surpassing 16S rRNA gene abundance. Latitude significantly influenced ARG profiles, whereas bacterial community composition did not. Network analysis identified Connexibacter, Granulicella, and Novosphingobium as potential hosts for qnrB, and Tundrisphaera and Terriglobus for qepA. To explain ARGs presence, we explored two hypotheses: bioaerosol dispersal from anthropogenic sources, and endogenous development through co-evolution between lichen-produced antimicrobial compounds and their associated bacterial communities. ConclusionsOur findings demonstrate that C. stellaris harbors diverse ARGs in remote boreal ecosystems, highlighting the ecological complexity of ARG persistence and the need to investigate not only ARG presence, but also the processes driving their distribution in natural environments.

plant biology↗

bioRxiv2024

Hornworts reveal a spatial model for pyrenoid-based CO2-concentrating mechanisms in land plants

Pyrenoid-based CO2-concentrating mechanisms (pCCMs) turbocharge photosynthesis by saturating CO2 around Rubisco. Hornworts are the only land plants with a pCCM. Owing to their closer relationship to crops, hornworts could offer greater translational potential compared to the green alga Chlamydomonas, the traditional model for studying pCCM. Here we report the first thorough investigation of a hornwort pCCM using the emerging model Anthoceros agrestis. The pyrenoids in A. agrestis exhibit liquid-like properties similar to Chlamydomonas, but differ by lacking starch sheaths and being enclosed by multiple thylakoids. We found that the core pCCM components in Chlamydomonas, including BST, LCIB, and CAH3, are conserved in A. agrestis and likely have similar functions based on their subcellular localizations. Therefore, the underlying chassis for concentrating CO2 might be shared between hornworts and Chlamydomonas, and ancestral to land plants. Our study presents the first spatial model for pCCM in a land plant, paving the way for future biochemical and genetic investigations.

plant biology↗

bioRxiv2021

Revisiting the early evolution of Cyanobacteria with a new thylakoid-less and deeply diverged isolate from a hornwort

Cyanobacteria have played pivotal roles in Earths geological history especially during the rise of atmospheric oxygen. However, our ability to infer the early transitions in Cyanobacteria evolution has been limited by their extremely lopsided tree of life--the vast majority of extant diversity belongs to Phycobacteria (or "crown Cyanobacteria"), while its sister lineage, Gloeobacteria, is depauperate and contains only two closely related species of Gloeobacter and a metagenome-assembled genome. Here we describe a new culturable member of Gloeobacteria, Anthocerobacter panamensis, isolated from a tropical hornwort. Anthocerobacter diverged from Gloeobacter over 1.4 billion years ago and has low 16S identities with environmental samples. Our ultrastructural, physiological, and genomic analyses revealed that this species possesses a unique combination of traits that are exclusively shared with either Gloeobacteria or Phycobacteria. For example, similar to Gloeobacter, it lacks thylakoids and circadian clock genes, but the carotenoid biosynthesis pathway is typical of Phycobacteria. Furthermore, Anthocerobacter has one of the most reduced gene sets for photosystems and phycobilisomes among Cyanobacteria. Despite this, Anthocerobacter is capable of oxygenic photosynthesis under a wide range of light intensities, albeit with much less efficiency. Given its key phylogenetic position, distinct trait combination, and availability as a culture, Anthocerobacter opens a new window to further illuminate the dawn of oxygenic photosynthesis.

evolutionary biology↗

bioRxiv2020

A target enrichment probe set for resolving the flagellate plant tree of life

Premise of the studyNew sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate plants, comprising hornworts, liverworts, mosses, lycophytes, ferns, and gymnosperms. Methods and ResultsWe leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target enrichment sequencing of 451 nuclear exons and non-coding flanking regions across flagellate plant lineages. We describe the performance of target enrichment using the probe set across flagellate plants and demonstrate the potential of the data to resolve relationships among both ancient and closely related taxa. ConclusionsA target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate plants.

evolutionary biology↗