Artículos de revista IMAB - IMAB aldizkari artikuluak

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Open Access
Pleurotus ostreatus as a model mushroom in genetics, cell biology, and material sciences
(Springer, 2024) Nakazawa, Takehito; Kawauchi, Moriyuki; Otsuka, Yuitsu; Han, Junxian; Koshi, Daishiro; Schiphof, Kim; Ramírez Nasto, Lucía; Pisabarro de Lucas, Gerardo; Honda, Yoichi; Institute for Multidisciplinary Research in Applied Biology - IMAB
Pleurotus ostreatus, also known as the oyster mushroom, is a popular edible mushroom cultivated worldwide. This review aims to survey recent progress in the molecular genetics of this fungus and demonstrate its potential as a model mushroom for future research. The development of modern molecular genetic techniques and genome sequencing technologies has resulted in breakthroughs in mushroom science. With efficient transformation protocols and multiple selection markers, a powerful toolbox, including techniques such as gene knockout and genome editing, has been developed, and numerous new findings are accumulating in P. ostreatus. These include molecular mechanisms of wood component degradation, sexual development, protein secretion systems, and cell wall structure. Furthermore, these techniques enable the identification of new horizons in enzymology, biochemistry, cell biology, and material science through protein engineering, fluorescence microscopy, and molecular breeding.
Open Access
Imipenem heteroresistance but not tolerance in Haemophilus influenzae during chronic lung infection associated with chronic obstructive pulmonary disease
(Frontiers Media, 2023) Gil Campillo, Celia; González-Díaz, Aida; Rapún Araiz, Beatriz; Iriarte-Elizaintzin, Oihane; Elizalde Gutiérrez, Iris; Fernández Calvet, Ariadna; Lázaro-Díez, María; Martí, Sara; Garmendia García, Juncal; Ciencias; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB
Antibiotic resistance is a major Public Health challenge worldwide. Mechanisms other than resistance are described as contributors to therapeutic failure. These include heteroresistance and tolerance, which escape the standardized procedures used for antibiotic treatment decision-making as they do not involve changes in minimal inhibitory concentration (MIC). Haemophilus influenzae causes chronic respiratory infection and is associated with exacerbations suffered by chronic obstructive pulmonary disease (COPD) patients. Although resistance to imipenem is rare in this bacterial species, heteroresistance has been reported, and antibiotic tolerance cannot be excluded. Moreover, development of antibiotic heteroresistance or tolerance during within-host H. influenzae pathoadaptive evolution is currently unknown. In this study, we assessed imipenem resistance, heteroresistance and tolerance in a previously sequenced longitudinal collection of H. influenzae COPD respiratory isolates. The use of Etest, disc diffusion, population analysis profiling, tolerance disc (TD)-test methods, and susceptibility breakpoint criteria when available, showed a significant proportion of imipenem heteroresistance with differences in terms of degree among strains, absence of imipenem tolerance, and no specific trends among serial and clonally related strains could be established. Analysis of allelic variation in the ftsI, acrA, acrB, and acrR genes rendered a panel of polymorphisms only found in heteroresistant strains, but gene expression and genome-wide analyses did not show clear genetic traits linked to heteroresistance. In summary, a significant proportion of imipenem heteroresistance was observed among H. influenzae strains isolated from COPD respiratory samples over time. These data should be useful for making more accurate clinical recommendations to COPD patients.
Open Access
Nature-based strategies to regenerate the functioning and biodiversity of vineyards
(Wiley, 2024) Ochoa‐Hueso, Raúl; Cantos‐Villar, Emma; Puertas, Belén; Aguiar del Río, Juan F.; Belda, Ignacio; Delgado-Baquerizo, Manuel; Fernández, Victoria; Gallardo, Antonio; García-Morales, José L.; Garde-Cerdán, Teresa; Santesteban García, Gonzaga; Lazcano, Cristina; Liberal, Isabel M.; Serrano-Grijalva, Lilia; Tortosa, Germán; Casimiro‐Soriguer, Ramón; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB
Grapevine is one of the most important perennial fruit crops worldwide. Historically, vineyards were compatible with soil conservation practices and multitrophic biodiversity, but vineyards are now generally eroded and biologically impoverished, making them more susceptible to pests and diseases. However, the idiosyncrasy of the wine sector places wine growers in a unique position to lead the adoption of a range of sustainable management strategies and, thus, to pioneer a wider transformation of the agricultural sector. In this article, we provide an overview of nature-based management strategies that may be used for the regeneration of the functioning and biodiversity of vineyards and that may also lead to improved plant nutrition, grape berry quality and the suppression of pathogens and pests. These strategies include the use of microbial and nonmicrobial biostimulants, fertilization with organic amendments as well as foliar fertilization with nature-based products, the use of cover crops and the reintegration of livestock in vineyards, especially sheep. We will also pay special attention to the implementation of circular economy in the vineyard in relation to the previously mentioned management strategies and will also discuss the importance of considering all these aspects from a holistic and integrative perspective, rather than taking them into account as single factors. Assuming the integral role of soils in the functioning of agroecosystems, soils will be considered transversally across all sections. Finally, we will argue that the time is now ripe for innovation from the public and private sectors to contribute to the sustainable management of vineyards while maintaining, or even improving, the profit margin for farmers and winemakers.
Open Access
Source-sink manipulation does not mitigate the effects of grapevine red blotch virus (GRBV) infection on fruit sugar and flavonoid accumulation in Cabernet-Sauvignon
(International Viticulture and Enlogy Society, 2023) Kurtural, Sahap Kaan; Tanner, Justin D.; Mainos, Dimitirios; Yu, Runze; Torres Molina, Nazareth; Martínez-Lüscher, Johann; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB
Grapevine red blotch virus (GRBV) negatively affects the composition of grapevine (Vitis vinifera L.) berries by reducing total soluble solids and anthocyanins, leading to economic losses for grape producers. Negative effects of GRBV were suspected to be due to impeded carbon translocation from leaves to fruit which limits sugar and flavonoid accumulation in berries. A two-year trial was conducted to determine whether an increase in source: sink ratio may affect sugar allocation and mitigate the effects of GRBV on Cabernet-Sauvignon plants. Experimental design was factorial (2 by 2) with healthy plants that did not have the virus (GRBV (-)) and plants having GRBV (GRBV (+)) and plants were subjected either untreated (UNT) or cluster thinned down to 10 clusters (CT). Effects of cluster thinning and virus status on leaf and shoot total soluble sugars (TSS), plant water status, leaf gas exchange, berry primary and secondary metabolites, and yield components were measured. The TSS in leaves began to accumulate around véraison. In shoot sap, GRBV(-) plants had greater concentration in TSS than GRBV(+) plants. The presence of disease improved plant water status increasing the stem water potential and increasing berry mass. However, juice total soluble solids were consistently lower in GRBV(+) plants despite increasing source: sink ratio by 3× with cluster removal. Likewise, GRBV(+) plants produced berries with lower anthocyanin content at harvest regardless of CT in both years. Our results suggest that GRBV infection severally impeded carbohydrate translocation out of the leaves, and in contrast to healthy plants reducing the number of clusters does not induce a reconcentration of sugars in the remaining clusters.
Open Access
Vegetable waste extracts as enhancers of baculovirus infections
(Elsevier, 2023) Martínez Inda, Blanca; Simón de Goñi, Oihane; Jiménez Moreno, Nerea; Esparza Catalán, Irene; Moler Cuiral, José Antonio; Caballero Murillo, Primitivo; Ancín Azpilicueta, Carmen; Ciencias; Zientziak; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Multidisciplinary Research in Applied Biology - IMAB; Institute for Advanced Materials and Mathematics - INAMAT2
Vegetable waste extracts (VWE) contain a great variety of antioxidants such as polyphenols, which have shown to potentiate baculovirus infections, making them ingredients for pest control ingredients. In the present study, the mortality enhancement of different vegetable extracts obtained from food residues when combined with baculoviruses was evaluated. Extracts from spent coffee (E2), rosehip (E17), asparagus (E28), artichoke (E29), beet stalks (E32) and banana peel (E37) were selected as they increased mortality of Spodoptera littoralis nucleopolyhedrovirus (SpliNPV) in second instar S. littoralis larvae, when comparing with the virus inoculation alone. Extracts were assayed at 1 % w/v. In S. littoralis-SpliNPV system, the selected extracts reduced the median lethal concentration (LC50) of SpliNPV against second instar larvae. The E37 extract presented the highest potentiation, as it reduced the LC50 13.61 times, while the rest of the extracts presented LC50 reductions from 3.71 to 7.72-fold. In Spodoptera exigua-SeMNPV (Spodoptera exigua multiple nucleopolyhedrovirus) system, none of the extracts decreased the LC50 of SeMNPV. In contrast, in Spodoptera frugiperda-SfMNPV (Spodoptera frugiperda multiple nucleopolyhedrovirus) system, E2 showed the greatest potentiating effect. In the heterologous systems, none of the extracts tested increased the effective host range of SfMNPV, AcMNPV (Autographa californica multiple nucleopolyhedrovirus), and MbMNPV (Mamestra brassicae multiple nucleopolyhedrovirus) in second instar S. littoralis larvae. Thus, the viral enhancing effect of VWE was host-pathogen and instar dependent. However, the potentiation effect of the extracts could not be directly related with the antioxidants content of the extracts.
Open Access
Timing of defoliation affects anthocyanin and sugar decoupling in Grenache variety growing in warm seasons
(Elsevier, 2024) Fernández-Zurbano, Purificación; Santesteban García, Gonzaga; Villa Llop, Ana; Loidi Erviti, Maite; Peñalosa, Carlos; Músquiz, Sergio; Torres Molina, Nazareth; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
Warming trends over the winegrowing regions lead to an advance of grapevine phenology, decreased yield and increased sugar content with a lower polyphenol content. We hypothesized that different leaf removal timings may counteract these effects. A two-year experiment was conducted in La Rioja (Spain) with Vitis vinifera L. cv. Grenache trained in an open-vase system. Trial consisted in a complete block design with two leaf removal treatments differing in the moment of manipulation: i) severe leaf removal treatment conducted after fruit set (ELR); and ii) severe leaf removal at veraison (LLR) compared to an untreated control (Control). Both leaf removal treatments tended to decrease sugar content with no effect on yield, these effects being highly affected by the year. Defoliation accounted for a decreased flavanol and stilbene contents in berries at harvest. An ELR increased anthocyanin and phenolic acid contents at harvest, while warming during 2022 accounted for decreased contents of all the monitored groups of flavonols. ELR was only effective for delaying ripening by means of impairing the sugar:anthocyanin decoupling during the 2021 growing season which was related to lower % of kaempferol. Altogether, results suggested that defoliation should still be applied under currently warming trends in some viticulture regions.
Open Access
Conventional and newly bred rootstock effects on the ecophysiological response of Vitis vinifera L. cv. Tempranillo
(Elsevier, 2023) Buesa, Ignacio; Torres Molina, Nazareth; Tortosa, Ignacio; Marín Ederra, Diana; Villa Llop, Ana; Douthe, Cyril; Santesteban García, Gonzaga; Medrano, H.; Escalona, José M.; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB
Achieving more environmentally sustainable vineyards, particularly regarding efficient water use, is paramount in semi-arid grape-growing regions. Rootstocks may be a possible strategy to address these challenges, but require a comprehensive evaluation of their effect on the scion, including ecophysiological traits. The objectives of this study were 1) to characterize the physiological response of Tempranillo cultivar grafted onto five commercial (1103 P, 110 R, 140Ru, 420 A, and SO4), and seven recently bred (RG2, RG3, RG4, RG6, RG7, RG8 and RG9) rootstocks and 2) to elucidate the relationships between agronomic and physiological traits conferred by grapevine rootstocks. This was carried out over three seasons (2018–2020) in a typical Mediterranean vineyard by determining water relations, leaf gas exchange, carbon isotope ratios and vegetative development and yield components. The results highlighted the different behaviour of ‘Tempranillo’ vines due to the rootstock effects on vine water status, photosynthetic performance, hydraulic conductance, vegetative growth and yield parameters. Overall, rootstocks inducing vigour and yield in the scion, such as 140Ru and RG8, showed higher leaf gas exchange rates and hydraulic conductance at the whole-plant level due to less negative water potentials, suggesting a higher water uptake and transport capacity than RG2, RG7 and RG9. The RG rootstocks showed a very wide range of ecophysiological responses, but only RG8 outperformed compared to the most widely used commercial rootstocks. Moreover, this response was modulated by the season and the block soil type, suggesting the importance of rootstock selection according to the edaphoclimatic conditions. Therefore, this study highlights the high potential of rootstocks to adapt to water scarcity by improving crop water productivity in vineyards and provides physiological insights for future studies and breeding programmes.
Open Access
Effector-triggered susceptibility by the rice blast fungus Magnaporthe oryzae
(Wiley, 2024) Oliveira-Garcia, Ely; Yan, Xia; Osés Ruiz, Miriam; Paula, Samuel de; Talbot, Nicholas J.; Institute for Multidisciplinary Research in Applied Biology - IMAB
Rice blast, the most destructive disease of cultivated rice world-wide, is caused by the filamentous fungus Magnaporthe oryzae. To cause disease in plants, M. oryzae secretes a diverse range of effector proteins to suppress plant defense responses, modulate cellular processes, and support pathogen growth. Some effectors can be secreted by appressoria even before host penetration, while others accumulate in the apoplast, or enter living plant cells where they target specific plant subcellular compartments. During plant infection, the blast fungus induces the formation of a specialized plant structure known as the biotrophic interfacial complex (BIC), which appears to be crucial for effector delivery into plant cells. Here, we review recent advances in the cell biology of M. oryzae–host interactions and show how new breakthroughs in disease control have stemmed from an increased understanding of effector proteins of M. oryzae are deployed and delivered into plant cells to enable pathogen invasion and host susceptibility.
Open Access
Constrained trait variation by water availability modulates radial growth in evergreen and deciduous mediterranean oaks
(Elsevier, 2024) González de Andrés, Ester; Serra-Maluquer, Xavier; Gazol, Antonio; Olano, José Miguel; García Plazaola, José Ignacio; Fernández Marín, Beatriz; Imbert Rodríguez, Bosco; Coll, Lluís; Ameztegui, Aitor; Espelta, Josep Maria; Alla, Arben Q.; Camarero, Jesús Julio; Ciencias; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB
Spatial and temporal variation in functional traits allows trees to adjust to shifting environmental conditions such as water stress. However, the change of traits, both mean and variances, along water availability gradients and across growing seasons, as well as their covariation with tree performance, have been rarely assessed. We examined intraspecific trait variation in coexisting evergreen (Quercus ilex ssp. ilex and Q. ilex ssp. ballota) and deciduous (Quercus faginea and Quercus humilis) Mediterranean oaks along a wide water availability gradient in northeastern Spain during six years. We measured leaf area (LA), shoot twig mass (Sm), leaf mass per area (LMA) and the ratio of shoot twig to leaf biomass (Sm:Lm). We characterized tree performance through basal area increment (BAI) and drought resilience indices. Higher variation was found within individuals than between individuals across populations and years. Within species, we found trait adjustments toward more conservative water-use (low LA and Sm and high LMA) with increasing drier conditions. Intraspecific trait variation was constrained by water availability, particularly on the deciduous species. In Q. ilex, trait variance of LMA positively covaried with annual BAI, whereas variance of LA, Sm and Sm:Lm was positively related to resistance and resilience against the severe 2012 drought in deciduous oaks. Our results support a tradeoff between the ability to tolerate drought and the capacity to cope with unpredictable changes in the environment through increased intraspecific trait variation, which may have implications on tree performance in the face of increased extreme events.
Open Access
Municipal solid waste management in a decentralized composting scenario: assessment of the process reproducibility and quality of the obtained composts
(MDPI, 2024) Álvarez-Alonso, Cristina; Pérez-Murcia, María Dolores; Sánchez-Méndez, Silvia; Martínez-Sabater, Encarnación; Irigoyen Iriarte, Ignacio; López, Marga; Nogués, Isabel; Paredes, Concepción; Orden, Luciano; García-Rández, Ana; Bustamante, María Ángeles; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB
Over the last several years, the models for organic waste management have changed to implement circular economy in the productive cycle. In this context, new scenarios have emerged, where the management of different organic waste streams by composting is conducted with decentralized models that manage organic wastes in a more local way. However, in these new models, the standardization of the process control and of the end-product characteristics is necessary to guarantee the quality and agronomic value of the compost obtained, avoiding potential risks for human health and the environment. Thus, the aim of this work was to study two different scenarios of community composting of the organic fraction of municipal solid waste separately collected in order to guarantee the effectiveness and reproducibility of the composting processes and the quality of the composts obtained. For this, the development of the process and the characteristics of the composts at agronomic, hygienic–sanitary and environmental levels were assessed in real conditions and during three cycles of the process. The results obtained show high similarity among the different composting cycles, indicating an important degree of reproducibility among the processes. In addition, the composts obtained showed a good sanitary quality, absence of phytotoxicity and low contents of potentially toxic elements, which guarantee their use in agriculture without posing any risk to human health and to the environment.
Open Access
Sensitivity of long-term productivity estimations in mixed forests to uncertain parameters related to fine roots.
(Elsevier, 2024) Yeste Yeste, Antonio; Seely, Brad; Imbert Rodríguez, Bosco; Blanco Vaca, Juan Antonio; Ciencias; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB
Forest growth models are increasingly being used in forestry and ecology research as predictive tools to help developing practical guidelines and to improve understanding of the drivers of forest ecosystem functioning. Models are usually calibrated using parameters directly obtained or estimated from empirical field observation, and hence are subject to uncertainty. Thus, output accuracy depends on input parameters precision and on how influential is each parameter on model behaviour. Hence, it is important to analyse parameter-related uncertainty and its effects on model outputs. This can be done by performing sensitivity analyses, which allow to explore the influence of one or several calibration parameters on model outputs. As studies on tree root parameters are particularly scarce, the aim of the present work was to evaluate the influence of parameters related to fine roots on estimations of long-term forest growth patterns in pure and mixed forests, using FORECAST (a hybrid forest growth model) as a virtual lab. The fine root parameters assessed were biomass, turnover rate, and nitrogen content. The analysis was performed by simulating monospecific stands of two contrasting species (Pinus sylvestris L. and Fagus sylvatica L.), and mixed stands formed by both species. In all cases, FORECAST showed good capability to contain uncertainty propagation during the first and middle stages of stand development (<40 years). After that moment, model output uncertainty steadily increased, but it reached different maximum uncertainty levels depending on stand type. Simulations of the less nutrient demanding P. sylvestris manifested very little sensitivity when growing in monospecific stands. However, F. sylvatica monospecific stands showed intermediate sensitivity, but significant species interactions occurred in mixed stands that determined the biggest impact detected of uncertainty related to fine root parameters over model outputs. All things considered, FORECAST displayed an interesting capability to capture some of the interspecific interactions that are key in mixed forests functioning. Our results suggest an acceptable model performance under uncertain parameterization but also caution against expecting accurate quantitative estimations of forest growth, especially when considering long-term scenarios in complex mixed stands.
Embargo
Downed woody debris carbon emissions in a European temperate virgin forest as driven by species, decay classes, diameter and microclimate
(Elsevier, 2024) Buezo Bravo, Javier; Medina, Nagore G.; Hereş, Ana-Maria; Petritan, Ion C.; Cornelissen, Johannes H.C.; Petritan, Any Mary; Esteban Terradillos, Raquel; Ilinca, Elisabeth; Stoian, R.; Curiel Yuste, Jorge; Ciencias; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB
Downed woody debris (DWD) plays an important role as regulator of nutrient and carbon (C) cycling in forests, accounting for up to the 20 % of the total C stocks in primary forests. DWD persistence is highly influenced by microbial decomposition, which is determined by various environmental factors, including fluctuations in temperature and moisture, as well as in intrinsic DWD properties determined by species, diameter, or decay classes (DCs). The relative importance of these different drivers, as well as their interactions, remains largely unknown. Moreover, the importance of DWD for C cycling in virgin forests remains poorly understood, due to their scarcity and poor accessibility. To address this research gap, we conducted a study on DWD respiration (RDWD), in a temperate virgin forest dominated by European beech and silver fir. Our investigation analysed the correlation between RDWD of these two dominant tree species and the seasonal changes in climate (temperature and moisture), considering other intrinsic DWD traits such as DCs (1, 2 and 4) and diameters (1, 10 and 25 cm). As anticipated, RDWD (normalized per gram of dry DWD) increased with air temperature. Surprisingly, DWD diameter also had a strong positive correlation with R DWD. Nonetheless, the sensitivity to both variables and other intrinsic traits (DC and density) was greatly modulated by the species. On the contrary, water content, which exhibited a considerable spatial variation, had an overall negative effect on R DWD. Virgin forests are generally seen as ineffective C sinks due to their lack of net productivity and high respiration and nutrient turnover. However, the rates of R DWD in this virgin forest were significantly lower than those previously estimated for managed forests. This suggests that DWD in virgin forests may be bufferingforest CO2 emissions to the atmosphere more than previously thought.
Embargo
A new oxidative pathway of nitric oxide production from oximes in plants
(Cell Press, 2024) López Gómez, Pedro; Buezo Bravo, Javier; Urra Rodríguez, Marina; Cornejo Ibergallartu, Alfonso; Esteban Terradillos, Raquel; Fernández de los Reyes, Jorge; Urarte Rodríguez, Estíbaliz; Rodríguez-Dobreva, Estefanía; Chamizo Ampudia, Alejandro; Eguaras, Alejandro; Wolf, Sebastian; Marino Bilbao, Daniel; Martínez Merino, Víctor; Morán Juez, José Fernando; Ciencias; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB; Institute for Advanced Materials and Mathematics - INAMAT2
Nitric oxide (NO) is an essential reactive oxygen species and a signal molecule in plants. Although several studies have proposed the occurrence of oxidative NO production, only reductive routes for NO production, such as the nitrate (NO-3) -upper-reductase pathway, have been evidenced to date in land plants. However, plants grown axenically with ammonium as the sole source of nitrogen exhibit contents of nitrite and NO3, evidencing the existence of a metabolic pathway for oxidative production of NO. We hypothesized that ox- imes, such as indole-3-acetaldoxime (IAOx), a precursor to indole-3-acetic acid, are intermediate oxidation products in NO synthesis. We detected the production of NO from IAOx and other oximes catalyzed by peroxidase (POD) enzyme using both 4-amino-5-methylamino-20,70-difluorescein fluorescence and chem- iluminescence. Flavins stimulated the reaction, while superoxide dismutase inhibited it. Interestingly, mouse NO synthase can also use IAOx to produce NO at a lower rate than POD. We provided a full mech- anism for POD-dependent NO production from IAOx consistent with the experimental data and supported by density functional theory calculations. We showed that the addition of IAOx to extracts from Medicago truncatula increased the in vitro production of NO, while in vivo supplementation of IAOx and other oximes increased the number of lateral roots, as shown for NO donors, and a more than 10-fold increase in IAOx dehydratase expression. Furthermore, we found that in vivo supplementation of IAOx increased NO pro- duction in Arabidopsis thaliana wild-type plants, while prx33-34 mutant plants, defective in POD33-34, had reduced production. Our data show that the release of NO by IAOx, as well as its auxinic effect, explain the superroot phenotype. Collectively, our study reveals that plants produce NO utilizing diverse molecules such as oximes, POD, and flavins, which are widely distributed in the plant kingdom, thus intro- ducing a long-awaited oxidative pathway to NO production in plants. This knowledge has essential impli- cations for understanding signaling in biological systems.
Open Access
Expansion of the global RNA virome reveals diverse clades of bacteriophages
(Elsevier, 2022) Neri, Uri; Wolf, Yuri I.; Roux, Simon; Camargo, Antonio Pedro; Lee, Benjamin; Kazlauskas, Darius; Chen, I. Min; Ivanova, Natalia; Zeigler Allen, Lisa; Paez-Espino, David; Bryant, Donald A.; Bhaya, Devaki; Krupovic, Mart; Dolja, Valerian V.; Kyrpides, Nikos C.; Koonin, Eugene V.; Gophna, Uri; RNA Virus Discovery Consortium; Narrowe, Adrienne B.; Ramírez Nasto, Lucía; Wang, Zhong; Nusslein, Klaus; Meredith, Laura K.; Buée, Marc; Huntemann, Marcel; Kalyuzhnaya, Marina G.; Waldrop, Mark P.; Sullivan, Matthew B.; Schrenk, Matthew O.; Hess, Matthias; Vega, Michael A.; O’Malley, Michelle A.; Medina, Mónica; Gilbert, Naomi E.; Delherbe, Nathalie; Mason, Olivia U.; Probst, Alexander J.; Sczyrba, Alexander; Kohler, Annegret; Séguin, Armand; Shade, Ashley; Campbell, Barbara J.; Lindahl, Björn D.; Reese, Brandi Kiel; Roque, Breanna M.; DeRito, Christopher; Averill, Colin; Cullen, Daniel; Beck, David A.C.; Walsh, David A.; Ward, David M.; Wu, Dongying; Eloe-Fadrosh, Emiley; Brodie, Eoin L.; Dijkstra, Paul; Chuckran, Peter F.; Baldrian, Petr; Constant, Philippe; Stepanauskas, Ramunas; Daly, Rebecca A.; Lamendella, Regina; Gruninger, Robert J.; McKay, Robert M.; Hylander, Samuel; Lebeis, Sarah L.; Esser, Sarah P.; Acinas, Silvia G.; Young, Erica B.; Lilleskov, Erik A.; Castillo, Federico J.; Martin, Francis; LeCleir, Gary R.; Attwood, Graeme T.; Cadillo-Quiroz, Hinsby; Simon, Holly M.; Hewson, Ian; Grigoriev, Igor V.; Tiedje, James M.; Jansson, Janet K.; Lee, Janey; VanderGheynst, Jean S.; Dangl, Jeff; Bowman, Jeff S.; Blanchard, Jeffrey L.; Bowen, Jennifer L.; Xu, Jiangbing; Banfield, Jillian F.; Deming, Jody W.; Kostka, Joel E.; Gladden, John M.; Rapp, Josephine Z.; Sharpe, Joshua; McMahon, Katherine D.; Treseder, Kathleen K.; Bidle, Kay D.; Wrighton, Kelly C.; Thamatrakoln, Kimberlee; Wilhelm, Steven S.; Singer, Steven W.; Tringe, Susannah S.; Woyke, Tanja; Reddy, T.B.K.; Bell, Terrence H.; Mock, Thomas; McAllister, Tim; Thiel, Vera; Denef, Vincent J.; Liu, Wen-Tso; Martens-Habbena, Willm; Liu, Xiao-Jun Allen; Cooper, Zachary S.; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.
Open Access
Antifungal activity of chitosan/poly (ethylene oxide) blend electrospun polymeric fiber mat doped with metallic silver nanoparticles
(MDPI, 2023) Murillo Larrey, Leire; Rivero Fuente, Pedro J.; Sandúa Fernández, Xabier; Pérez Garrido, Gumersinda; Palacio, José F.; Rodríguez Trías, Rafael; Ingeniería; Ingeniaritza; Institute for Multidisciplinary Research in Applied Biology - IMAB; Institute for Advanced Materials and Mathematics - INAMAT2
In this work, the implementation of advanced functional coatings based on the combination of two compatible nanofabrication techniques such as electrospinning and dip-coating technology have been successfully obtained for the design of antifungal surfaces. In a first step, uniform and beadless electrospun nanofibers of both polyethylene oxide (PEO) and polyethylene (PEO)/chitosan (CS) blend samples have been obtained. In a second step, the dip-coating process has been gradually performed in order to ensure an adequate distribution of silver nanoparticles (AgNPs) within the electrospun polymeric matrix (PEO/CS/AgNPs) by using a chemical reduction synthetic process, denoted as in situ synthesis (ISS). Scanning electron microscopy (SEM) has been used to evaluate the surface morphology of the samples, showing an evolution in average fiber diameter from 157 ± 43 nm (PEO), 124 ± 36 nm (PEO/CS) and 330 ± 106 nm (PEO/CS/AgNPs). Atomic force microscopy (AFM) has been used to evaluate the roughness profile of the samples, indicating that the ISS process induced a smooth roughness surface because a change in the average roughness Ra from 84.5 nm (PEO/CS) up to 38.9 nm (PEO/CS/AgNPs) was observed. The presence of AgNPs within the electrospun fiber mat has been corroborated by UV-Vis spectroscopy thanks to their characteristic optical properties (orange film coloration) associated to the Localized Surface Plasmon Resonance (LSPR) phenomenon by showing an intense absorption band in the visible region at 436 nm. Energy dispersive X-ray (EDX) profile also indicates the existence of a peak located at 3 keV associated to silver. In addition, after doping the electrospun nanofibers with AgNPs, an important change in the wettability with an intrinsic hydrophobic behavior was observed by showing an evolution in the water contact angle value from 23.4° ± 1.3 (PEO/CS) up to 97.7° ± 5.3 (PEO/CS/AgNPs). The evaluation of the antifungal activity of the nanofibrous mats against Pleurotus ostreatus clearly indicates that the presence of AgNPs in the outer surface of the nanofibers produced an important enhancement in the inhibition zone during mycelium growth as well as a better antifungal efficacy after a longer exposure time. Finally, these fabricated electrospun nanofibrous membranes can offer a wide range of potential uses in fields as diverse as biomedicine (antimicrobial against human or plant pathogen fungi) or even in the design of innovative packaging materials for food preservation.
Open Access
Activity of ammonia-oxidizing bacteria in enriched cultures exposed to 3,4-dimethyl-1H-pyrazole dihydrogen phosphate nitrification inhibitor
(Elsevier, 2023) Rodrigues dos Santos, Janaina Maria; Cruz, Cristina; Tenreiro, Rogerio; Gouveia, Catarina; Lasa Larrea, Berta; Institute for Multidisciplinary Research in Applied Biology - IMAB; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
The use of nitrification inhibitors is an interesting tool to achieve a higher N efficiency in plants while decreasing the environmental impact of N fertilization. However, an integrated evaluation of the efficiency of nitrification inhibitors over time, understood as the period in which the nitrifying activity is inhibited or slows down, is necessary to assess whether their use is ecofriendly and sustainable. To test the direct efficiency of 3,4-dimethyl-1H-pyrazole dihydrogen phosphate (DMPP) on nitrification, a study has been carried out in two cultures enriched with ammonia-oxidizing bacteria (AOB) obtained from a soil with continuous N fertilization (80 kg N ha−1 year−1 as NH4NO3) and from soil without N fertilization. In addition, Cu has been evaluated as a cofactor of ammonia monoxygenase, a key enzyme in the nitrifying activity of AOBs. On the other hand, the stability of DMP has been studied both in the cultivation system enriched in AOBs and in soil to assess the efficiency of the inhibitor due to its persistence over time. Our work reveals that nitrification rates observed in cultures enriched in AOBs from genus Nitrosospira isolated from soils with continuous N fertilization were not higher than those of cultures without N fertilization. In AOB cultures, DMPP was a very efficient inhibitor of nitrification (> 50 % inhibition of integrated AMO activity), mainly due to the stability of DMP (3,4-dimethyl-1 H-pyrazole) in the cultures. However, DMP stability was significantly lower under soil conditions (> 90 % of DMP was degraded in the first 30 days of incubation). Other metals are suggested as cofactors of the enzyme ammonia monooxygenase alternatively to Cu.
Open Access
Characterization of an accessory plasmid of Sinorhizobium meliloti and its two replication-modules
(Public Library of Science, 2023) Luchetti, Abril; Castellani, Lucas Gabriel; Toscani, Andrés Martín; Lagares, Antonio; Del Papa, María Florencia; Torres Tejerizo, Gonzalo; Pistorio, Mariano; Institute for Multidisciplinary Research in Applied Biology - IMAB
Rhizobia are Gram-negative bacteria known for their ability to fix atmospheric N-2 in symbiosis with leguminous plants. Current evidence shows that rhizobia carry in most cases a variable number of plasmids, containing genes necessary for symbiosis or free-living, a common feature being the presence of several plasmid replicons within the same strain. For many years, we have been studying the mobilization properties of pSmeLPU88b from the strain Sinorhizobium meliloti LPU88, an isolate from Argentina. To advance in the characterization of pSmeLPU88b plasmid, the full sequence was obtained. pSmeLPU88b is 35.9 kb in size, had an average GC % of 58.6 and 31 CDS. Two replication modules were identified in silico: one belonging to the repABC type, and the other to the repC. The replication modules presented high DNA identity to the replication modules from plasmid pMBA9a present in an S. meliloti isolate from Canada. In addition, three CDS presenting identity with recombinases and with toxin-antitoxin systems were found downstream of the repABC system. It is noteworthy that these CDS present the same genetic structure in pSmeLPU88b and in other rhizobial plasmids. Moreover, in all cases they are found downstream of the repABC operon. By cloning each replication system in suicide plasmids, we demonstrated that each of them can support plasmid replication in the S. meliloti genetic background, but with different stability behavior. Interestingly, while incompatibility analysis of the cloned rep systems results in the loss of the parental module, both obtained plasmids can coexist together.
Open Access
A novel use of Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae) as inoculative agent of baculoviruses
(Wiley, 2023) Gutiérrez-Cárdenas, Oscar Giovanni; Adán, Ángeles; Medina, Pilar; Muñoz, Delia; Caballero Murillo, Primitivo; Garzón, Agustín; Institute for Multidisciplinary Research in Applied Biology - IMAB
Background: Alphabaculoviruses are Lepidoptera-specific virulent pathogens that infect numerous pests, including the Spodoptera complex. Due to their low environmental persistence, the traditional use of Alphabaculoviruses as bioinsecticides consist in high-rate spray applications with repeated treatments. Several abiotic and biotic factors can foster its dispersion, promoting their persistence in the agroecosystem. Amongst biotic factors, predatory arthropods can disperse the viruses by excretion after preying on infected individuals. Therefore, this study focused on promoting predator's ingestion of nucleopolyhedrovirus (NPV)-treated diets, and the later exposition of the insect host to leaf surfaces contaminated with predator excreta. The virus–host–predator system studied was Spodoptera littoralis nucleopolyhedrovirus (SpliNPV), Spodoptera littoralis (Boisduval) and Nesidiocoris tenuis (Reuter). The infective potential of N. tenuis feces and the retention time of SpliNPV were assessed under laboratory conditions after feeding on treated diets (sucrose solution and Ephestia kuehniella eggs). Results: Mortality of S. littoralis larvae was lower via N. tenuis excretion than in positive control (spray application) in the first infection cycle, together with a delay in host death. In the second infection cycle, both SpliNPV-treated diets triggered 100% mortality. Both diets allowed the transmission of SpliNPV, with a faster excretion via sucrose solution compared to E. kuehniella eggs. SpliNPV remained in N. tenuis digestive tract and was viable after excretion at least for 9 days for both diets. Conclusions: This study demonstrated the potential of the predator N. tenuis as inoculative agent of baculoviruses, representing a new alternative that, along with inundative applications, might contribute to improve pest management strategies.
Open Access
Insecticidal traits of variants in a genotypically diverse natural isolate of anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV)
(MDPI, 2023) Parras-Jurado, Ana; Muñoz Labiano, Delia; Beperet Arive, Inés; Williams, Trevor; Caballero Murillo, Primitivo; Institute for Multidisciplinary Research in Applied Biology - IMAB
Outbreaks of Anticarsia gemmatalis (Hübner, 1818) (Lepidoptera: Erebidae), a major pest of soybean, can be controlled below economic thresholds with methods that do not involve the application of synthetic insecticides. Formulations based on natural isolates of the Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) (Baculoviridae: Alphabaculovirus) played a significant role in integrated pest management programs in the early 2000s, but a new generation of chemical insecticides and transgenic soybean have displaced AgMNPV-based products over the past decade. However, the marked genotypic variability present among and within alphabaculovirus isolates suggests that highly insecticidal genotypic variants can be isolated and used to reduce virus production costs or overcome isolate-dependent host resistance. This study aimed to select novel variants of AgMNPV with suitable insecticidal traits that could complement the existing AgMNPV active ingredients. Three distinct AgMNPV isolates were compared using their restriction endonuclease profile and in terms of their occlusion body (OB) pathogenicity. One isolate was selected (AgABB51) from which eighteen genotypic variants were plaque purified and characterized in terms of their insecticidal properties. The five most pathogenic variants varied in OB pathogenicity, although none of them was faster-killing or had higher OB production characteristics than the wild-type isolate. We conclude that the AgABB51 wild-type isolates appear to be genotypically structured for fast speed of kill and high OB production, both of which would favor horizontal transmission. Interactions among the component variants are likely to influence this insecticidal phenotype.
Open Access
Cysteine proteases are activated in sensitive Amaranthus palmeri populations upon treatment with herbicides inhibiting amino acid biosynthesis
(Wiley, 2023) Barco Antoñanzas, María; Font Farre, María; Eceiza, Mikel Vicente; Gil Monreal, Miriam; Van der Hoorn, Reiner; Royuela Hernando, Mercedes; Zabalza Aznárez, Ana; Institute for Multidisciplinary Research in Applied Biology - IMAB; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
The herbicides glyphosate and pyrithiobac inhibit the enzyme 5-enolpyruvylshikimate3-phosphate synthase (EPSPS) in the aromatic amino acid biosynthetic pathway and acetolactate synthase (ALS) in the branched-chain amino acid biosynthetic pathway, respectively. Here we characterise the protease activity profiles of a sensitive (S), a glyphosate-resistant (GR) and a multiple-resistant (MR) population of Amaranthus palmeri in response to glyphosate and pyrithiobac. Amino acid accumulation and cysteine protease activities were induced with both herbicides in the S population and with pyrithiobac in the GR population, suggesting that the increase in cysteine proteases is responsible for the increased degradation of the available proteins and the observed increase in free amino acids. Herbicides did not induce any changes in the proteolytic activities in the populations with target-site resistance, indicating that this effect was only induced in sensitive plants.

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