Biology subjects

Oporto, C. I.

Publications and source records attributed to Oporto, C. I..

4 recordsLinked to original sources

bioRxiv2026

Strong habitat-associated differentiation of microbial communities across a fine-scale land-water interface

Microbial communities can remain strongly differentiated across environmental boundaries despite their potential for widespread dispersal. However, the extent to which habitat differences structure microbial communities at fine spatial scales remains poorly understood. Here, we investigated bacterial and fungal communities across a 350-m land-water interface in Lake Vanern, Sweden, including mainland soil, two small terrestrial islands and lake water. Using 16S and ITS amplicon sequencing, we compared microbial diversity and community composition across habitats and with increasing distance from the shoreline. Both bacterial and fungal communities showed pronounced habitat-associated differentiation, with the strongest contrasts between terrestrial and aquatic samples. Despite being surrounded by lake water, island communities were compositionally more similar to mainland soil communities, suggesting that geographic proximity alone does not necessarily lead to microbial community homogenization. Fungal, but not bacterial community composition varied significantly with shoreline position within both terrestrial and aquatic habitats, indicating contrasting spatial patterns between the two groups. Fungal genera also showed greater taxonomic overlap between terrestrial and aquatic habitats than bacterial genera, although overall community composition remained distinct. Taxonomically inferred functional profiles and ecological guilds further reflected habitat-associated differences. Together, our findings reveal strong microbial community differentiation across a fine-scale land-water interface and highlight how habitat identity and spatial context are associated with distinct patterns of bacterial and fungal community assembly.

microbiology↗

bioRxiv2026

Host-shift adaptation shapes genome architecture in S. eubayanus

The host environment can profoundly shape the genome architecture of microbial species, and Saccharomyces eubayanus, the wild progenitor of lager yeast, provides a natural system to study this process. Most populations are associated with Nothofagus trees across Patagonia, whereas related Holarctic strains occur in the Northern Hemisphere and are associated with non-Nothofagus hosts. The evolutionary events leading to the emergence of these northern populations on a novel host remain unclear. Here, we analyzed 471 genomes from eight countries and different hosts, Nothofagus in the Southern Hemisphere and non-Nothofagus tree species in the Northern Hemisphere. Phylogenomic analysis identified eight Patagonian lineages and revealed that Holarctic strains derived from recent admixture among Patagonian ancestors, generating the genomic background of the lager-yeast mother lineage. Long-read assemblies showed that non-Nothofagus-associated strains harbor an elevated burden of structural variants (SVs), particularly in subtelomeric MAL and IMA regions, involved in sugar metabolism. Phenotypic tests confirmed that Nothofagus isolates efficiently metabolize maltose, while non-Nothofagus strains do not, a pattern linked to recurrent SVs and loss-of-function mutations in MAL33. Consistently, bark-sugar profiling revealed that maltose is abundant in Nothofagus but absent in non-Nothofagus hosts, providing an ecological context for these genomic and phenotypic differences. These results support a model in which northward dispersal of Patagonian lineages into non-Nothofagus forests enriched admixed genotypes, generating genomic mosaics that accumulated structural changes and losses in maltose utilization. This interplay between gene flow and genome flexibility enabled host switching and global expansion, illustrating how ecological transitions reorder genomes and drive microbial diversification.

evolutionary biology↗

bioRxiv2025

Allelic variation in MAL33 drives ecological adaptation of maltose metabolism in Saccharomyces eubayanus

Maltose is one of the most abundant sugars in brewers wort, and its efficient utilization is critical for successful fermentation. However, maltose consumption varies naturally among Saccharomyces eubayanus strains isolated from different host trees, such as Quercus and Nothofagus. To identify the genetic determinants underlying these phenotypic differences, we performed bulk segregant analysis (BSA) and quantitative trait loci (QTL) mapping using an F2 offspring derived from QC18 (Quercus-associated) and CL467.1 (Nothofagus-associated) strains. QTL mapping identified two significant genomic regions on subtelomeric loci of chromosomes V-R and XVI-L, each containing complete MAL loci composed of MAL32 (encoding maltase), MAL31 (transporter), and MAL33 (transcriptional activator) genes. Comparative polymorphism analyses identified mutations in MAL32 and MAL33 of QC18, including frameshift mutations resulting in premature stop codons. Functional validation demonstrated that the heterologous expression of MAL33ChrV from CL467.1 fully restored maltose utilization in QC18, indicating the functional presence of MAL33 cis-regulatory sequences and MAL32 and MAL31 genes in QC18. While structural protein predictions identified truncation and impaired functionality in the maltose-responsive activation domain of Mal33p from QC18, overexpression of QC18s own MAL33ChrV allele also improved maltose metabolism, suggesting dosage-dependent transcriptional limitations rather than complete functional loss. These results indicate that allelic variations in the maltose-responsive activation domain of Mal33p lead to differences in maltose consumption between strains. We hypothesized that reduced maltose metabolism in QC18 is an adaptive response to the distinct sugar composition in Quercus robur bark, contrasting with the starch-rich environment of Nothofagus pumilio. These findings highlight subtelomeric MAL gene diversity as a reservoir of evolutionary plasticity, representing a key evolutionary mechanism that influences maltose adaptation among natural Saccharomyces isolates.

evolutionary biology↗

bioRxiv2019

An Out-of-Patagonia dispersal explains most of the worldwide genetic distribution in Saccharomyces eubayanus

Saccharomyces eubayanus represents missing cryotolerant ancestor of lager yeast hybrid and can be found in Patagonia in association with Nothofagus forests. The limited number of isolates and associated genomes available has prevented to resolve the S. eubayanus origin and evolution. Here, we present a sampling effort at an unprecedented scale and report the isolation of 160 strains from ten sampling sites along 2,000 km distance in South America. We sequenced the genome of 82 strains and, together with other 25 available genomes, performed comprehensive phylogenetic analysis. Our results revealed the presence of three main Patagonia-B lineages together with dozens of admixed strains distributed in three mosaic clusters. The PB-1 lineage isolated from Tierra del Fuego exhibited the highest genetic diversity, lowest LD blocks and highest Fis values compared to the other lineages, suggesting a successful adaptation to cold temperatures in extreme environments and greater inbreeding rates in Tierra del Fuego. Differences between lineages and strains were found in terms of aneuploidy and pangenome content, evidencing a lateral gene transfer event in PB-2 strains from an unknown donor species. Overall, the Patagonian lineages, particularly southern populations, showed a greater global genetic diversity compared to Holarctic and Chinese lineages, supporting the scenario of a S. eubayanus colonization from Patagonia and then spread towards northern and western regions, including the Holarctic (North America and China) and New Zealand. Interestingly, fermentative capacity and maltose consumption resulted negatively correlated with latitude, indicating a better fermentative performance in norther populations. Our genome analysis together with previous reports in the sister species S. uvarum strongly suggests that the S. eubayanus ancestor could have originated in Patagonia or the Southern Hemisphere, rather than China, yet further studies are needed to resolve this conflicting scenario. Understanding S. eubayanus evolutionary history is crucial to resolve the unknown origin of the lager yeast and might open new avenues for biotechnological applications.

genomics↗