Biology subjects

Bidartondo, M.

Publications and source records attributed to Bidartondo, M..

3 recordsLinked to original sources

bioRxiv2026

MycorrhizaTracer: A BIOINFORMATIC PIPELINE FOR FUNGI AND PLANT CLASSIFICATION OF SANGER DNA SEQUENCES

Processing Sanger DNA sequences remains a routine yet technically demanding step in many biodiversity and ecological studies, particularly when barcoding large numbers of environmental samples. Manual inspection and editing of trace files, DNA sequence alignment, and classification using taxonomic reference databases is time-consuming, inconsistent, and prone to error. These challenges are compounded in studies involving degraded samples, in-house DNA sequencing, under-described taxa, or when investigators have limited access to computational tools. We present MycorrhizaTracer, an open-source, fully automated pipeline for processing and taxonomically classifying large batches of Sanger sequencing chromatograms. We have optimized it for fungal and plant taxa, but it is adaptable across the tree of life. The pipeline performs quality trimming, consensus generation from bidirectional reads, taxonomic classification via BLAST, clustering, optional salvaging of low-quality sequences, and functional annotation of fungal taxa. Designed for scalability and ease of use, MycorrhizaTracer can process thousands of DNA chromatograms in a matter of hours without the need for an HPC. Accuracy and ecological relevance are ensured by features such as gene region-specific taxonomic filtering and sequence-based clustering of unclassified reads. By streamlining trace-to-taxon workflows, MycorrhizaTracer reduces the burden of manual curation, supports reproducibility, and enables efficient recovery of biodiversity data from Sanger sequences - particularly in field-based or resource-limited research contexts.

bioinformatics↗

bioRxiv2023

Assessing above and belowground recovery from ammonium sulfate addition and wildfire in a lowland heath: mycorrhizal fungi as potential indicators

Atmospheric pollution containing soil-nitrifying ammonium sulphate is affecting semi-natural ecosystems worldwide. Long-term additions of ammonium sulphate on nitrogen (N)-limited habitats such as heathlands increase climate stress affecting recovery from wildfires. Yet although heathland vegetation largely depends on ericoid mycorrhizal fungi (ErM) to access soil N, we lack a detailed understanding of how prolonged exposure to ammonium sulphate may alter ErM community composition and host plants reliance on fungal partners following wildfire and substantial reductions in ammonium sulphate pollution. Effects on ecosystem processes, particularly carbon stores, also remain uncertain. Ammonium sulphate additions occurred bi-weekly for five years after a 2006 wildfire burnt a UK heathland. Ten years after the treatments ceased (2021), we measured vegetation structure, lichen and lichen photobiont composition, soil characteristics, ErM colonisation, ErM diversity in roots and soil, and assessed their potential as recovery indicators. We found heather height and density, and moss groundcover, were greater in N-enriched plots. Lichen community indices showed significant treatment effects without photobiont differences. Soil pH and Mg, and the proportion of putative ErM fungi in soil were significantly lower in treated plots while soil cation exchange capacity was significantly higher. Increases in soil pH were positively correlated to soil ErM abundance. Soil carbon stock measures were variable and negatively related with soil ErM. Our results indicate that atmospheric pollution following fire can have significant lingering effects and mycorrhizal fungi diversity are a novel and effective ecological tool to assess ecosystem recovery on heathlands. IMPLICATIONS FOR PRACTICEO_LIRecovery of heathlands from wildfire and atmospheric pollution may require decadal scales. Conventional restoration assessment tools lack critical understanding of belowground soil and mycorrhizal fungi interactions and nutritional feedback loops with aboveground hosts. C_LIO_LIGiven that ericoid mycorrhizal fungi (ErM) communities are key nutrient regulators of resilient heathlands, we recommend baseline measurements of ErM diversity and abundance in both soil and dominant plant roots be added to the recovery assessment toolkit prior to commencing restoration or management plans. C_LIO_LIWhat defines ErM recovery, and disentangling effects of ammonium sulphate pollution and fire, remain open questions which only long-term field experiments across pollution gradients will address. C_LI

ecology↗

bioRxiv2020

Prevalence and phenology of mycorrhizal colonization across populations of Lycopodiella inundata.

Mycorrhizal fungi are critical components of terrestrial habitats and agroecosystems. Recently, Mucoromycotina fine root endophyte (MucFRE) fungi were found to engage in nutritional mutualism with the rare plant Lycopodiella inundata ( marsh clubmoss), one of the earliest vascular plant lineages known to associate with MucFRE. The extent to which this mutualism plays a role in resilient plant populations can only be understood by examining its occurrence rate and phenological patterns. To test for prevalence and seasonality in colonization, we examined 1,297 individual L. inundata roots collected during spring and autumn 2019 from 11 semi-natural heathlands in Britain and the Netherlands. We quantified presence/absence of MucFRE-like hyphae and vesicles and explored possible relationships between temperature and precipitation in the months immediately before sampling. MucFRE-like hyphae were the dominant mycorrhizal fungi observed in all of the examined heathlands. However, we found significant differences in colonization between the two seasons at every site. Overall, 14% of L. inundata roots were colonised in spring (2.4% with vesicles) compared with 86% in autumn (7.6% with vesicles). Colonization levels between populations were also significantly different, and correlated with temperature and precipitation, suggesting some local environments may be more conducive to hyphal growth. These marked seasonal differences in host-plant colonization suggest that results about mycorrhizal status - typically drawn from single time point collections - should be carefully interpreted. Our findings are directly relevant to habitat restoration, species conservation plans, agricultural bio-inoculation nutrient enhancement treatments, microbial diversity and functional studies of host plants and symbionts.

ecology↗