Biology subjects

Duenas, J. F.

Publications and source records attributed to Duenas, J. F..

4 recordsLinked to original sources

bioRxiv2025

Abrupt versus gradual application of pesticides: effects on soil bacterial and fungal communities

Pesticides are a major anthropogenic input to the environment and a factor in global change that puts pressure on soil microbial communities. However, the effects of different rates of pesticide application on soils remain poorly understood. This study investigates how abrupt versus gradual pesticide applications influence soil bacterial and fungal communities. Employing high-throughput sequencing, we examined the microbial diversity and community composition in response to ten commonly used pesticides. Bacterial communities exhibited minimal changes across treatments, whereas fungal communities responded strongly to pesticide exposure. Gradual applications reduced the relative abundance of dominant fungal taxa, resulting in an overall increase in community evenness. This effect was particularly pronounced for two herbicides and a triazole fungicide, which induced substantial shifts in fungal composition. Conversely, abrupt pesticide applications resulted in transient disruptions but did not promote the long-term proliferation of rare fungal variants. These findings suggest that prolonged exposure to pesticides exerts strong selective pressures on fungi, potentially altering fundamental soil functions such as nutrient cycling and decomposition. Future research should focus on the long-term responses of soil microbial communities to pesticide application and the cumulative effects of chronic low-dose exposure to provide a more comprehensive understanding of how they shape microbial communities. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/644867v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@8660a8org.highwire.dtl.DTLVardef@33ce7borg.highwire.dtl.DTLVardef@139113eorg.highwire.dtl.DTLVardef@19b388b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIFungal communities were more responsive to pesticides than bacterial communities C_LIO_LIHerbicides caused strong non-target effects, similar to those of fungicides C_LIO_LIGradual pesticide applications altered fungal diversity and community composition C_LIO_LIRare fungal taxa proliferated under gradual exposure, increasing evenness C_LIO_LIProlonged exposure exerted greater selective pressure than abrupt application C_LI

ecology↗

bioRxiv2023

Surfactant-mediated effects on hydrological and physical soil properties: a data synthesis

Soils are under threat of a multitude of anthropogenic factors affecting the complex interplay of various physical and hydrological soil processes and properties. One such factor is the group of surface-active compounds. Surfactants have a broad range of applications, and can reduce solid-liquid interfacial forces and increase wettability and dispersion of particles. Surfactant effects are context-dependent, giving rise to a wide range of reported effects on different soil processes and properties. Here, we evaluate the evidence base of surfactant research on 11 hydrological and physical soil variables. Our goal was to identify knowledge gaps and to test the robustness of proposed surfactant effects. We found that the current knowledge base is insufficient to reach strong data-backed conclusions about effects of surfactants in soils. We identified a unique case of bias in the data as a result of conflated patterns of lab and field studies. We could not support the hypothesis that surfactant charge determines soil effects for any of the tested soil variables. We believe that further experiments on surfactant mediated effects on soil properties and processes are urgently required, paying attention in particular to improving experimental design and data reporting standards. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=59 SRC="FIGDIR/small/547370v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@13e7953org.highwire.dtl.DTLVardef@8f5fc3org.highwire.dtl.DTLVardef@d81c52org.highwire.dtl.DTLVardef@2b4dfa_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

Deep learning image analysis for filamentous fungi taxonomic classification: Dealing with small data sets with class imbalance and hierarchical grouping

Deep learning applications in taxonomic classification for animals and plants from images have become popular, while those for microorganisms are still lagging behind. Our study investigated the potential of deep learning for the taxonomic classification of hundreds of filamentous fungi from colony images, which is typically a task that requires specialized knowledge. We isolated soil fungi, annotated their taxonomy using standard molecular barcode techniques, and took images of the fungal colonies grown in petri dishes (n = 606). We applied a convolutional neural network with multiple training approaches and model architectures to deal with some common issues in ecological datasets: small amounts of data, class imbalance, and hierarchically structured grouping. Model performance was overall low due mainly to the relatively small data set, class imbalance, and the high morphological plasticity exhibited by fungal colonies. However, our approach indicates that morphological features such as color, patchiness, and colony extension rate, could be used for the recognition of fungal colonies at higher taxonomic ranks (i.e., phylum, class, and order). Model explanation implies that image recognition characters appear at different positions within the colony (e.g., outer or inner hyphae), depending on the taxonomic resolution. Our study suggests the potential of deep learning applications for better understanding the taxonomy and ecology of filamentous fungi amenable to axenic culturing. Meanwhile, our study also highlights some technical challenges in deep learning image analysis in ecology, highlighting that the domain of applicability of these methods needs to be carefully considered.

microbiology↗

bioRxiv2021

Non-mycorrhizal root associated fungi of a tropical montane forest are relatively robust to the long-term addition of moderate rates of nitrogen and phosphorus

Andean forests are biodiversity hotspots and globally important carbon (C) repositories. This status might be at risk due to increasing rates of atmospheric nutrient deposition. As fungal communities are key in the recirculation of soil nutrients, assessing their responses to soil eutrophication can help establish a link between microbial biodiversity and the sustainability of the C sink status of this region. Beyond mycorrhizal fungi, which have been studied more frequently, a wide range of other fungi associate with the fine root fraction of trees. Monitoring these communities can offer insights into how communities composed of both facultative and obligate root associated fungi are responding to soil eutrophication. Here we document the response of non-mycorrhizal root associated fungal (RAF) communities to a long-term nutrient manipulation experiment. The stand level fine root fraction of an old growth tropical montane forest was sampled after seven years of nitrogen (N) and phosphorus (P) additions. RAF communities were characterized by a deep sequencing approach. As per the resource imbalance model, we expected that asymmetries in the availability of C, N and P elicited by fertilization will lead to mean richness reductions and alterations of the community structure. We recovered moderately diverse fungal assemblages composed by sequence variants classified within a wide set of trophic guilds. While mean richness remained stable, community composition shifted, particularly among Ascomycota and after the addition of P. Fertilization factors, however, only accounted for a minor proportion of the variance in community composition. These findings suggest that, unlike mycorrhizal fungi, RAF communities are less sensitive to shifts in soil nutrient availability. A plausible explanation is that non-mycorrhizal RAF have fundamentally different nutrient acquisition and life history traits, thus allowing them greater stoichiometric plasticity and an array of functional acclimation responses that collectively express as subtle shifts in community level attributes.

microbiology↗