Open Access
Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems
(Blackwell Scientific Publications Ltd, 2023) Auer, Lucas; Buée, Marc; Fauchery, Laure; Lombard, Vincent; Barry, Kerrie; Clum, Alicia; Copeland, Alex; Daum, Chris; LaButti, Kurt; Singan, Vasanth; Yoshinaga, Yuko; Martineau, Christine; Castillo Martínez, Federico; Alfaro Sánchez, Manuel; Imbert Rodríguez, Bosco; Ramírez Nasto, Lucía; Castanera Andrés, Raúl; Pisabarro de Lucas, Gerardo; Finlay, Roger; Lindahl, Björn D.; Olson, Ake; Séguin, Armand; Kohler, Annegret; Henrissat, Bernard; Grigoriev, Igor V.; Martin, Francis; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB
Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
Open Access
Changes in long-term light properties of a mixed conifer–broadleaf forest in Southwestern Europe
(MDPI, 2021) Ruiz de la Cuesta Vela, Ignacio; Blanco Vaca, Juan Antonio; Imbert Rodríguez, Bosco; Peralta de Andrés, Francisco Javier; Rodríguez Pérez, Javier; Ciencias; Zientziak; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
Natural and anthropogenic factors affect forest structure worldwide, primarily affecting forest canopy and its light properties. However, not only stand-replacing events modify canopy structure, but disturbances of lower intensity can also have important ecological implications. To study such effects, we analyzed long-term changes in light properties of a conifer–broadleaf mixed forest in the Southwestern Pyrenees, placed in the fringe between the Mediterranean and Eurosi- berian biogeographical regions. At this site, a thinning trial with different intensities (0%, 20%, and 30–40% basal area removed) took place in 1999 and 2009, windstorms affected some plots in 2009 and droughts were recurrent during the sampling period (2003, 2005, 2011). We monitored light properties during 14 years (2005–2019) with hemispherical photographs. We applied partial autocorrelation functions to determine if changes between years could be attributed to internal canopy changes or to external disturbances. In addition, we mapped the broadleaf canopy in 2003, 2008, and 2016 to calculate broadleaf canopy cover and richness at the sampling points with different buffer areas of in- creasing surface. We applied generalized linear mixed models to evaluate the effects of light variables on canopy richness and cover. We found that light variables had the most important changes during the period 2008 to 2010, reacting to the changes caused that year by the combined effects of wind and forest management. In addition, we found that an area of 4.0 m radius around the sampling points was the best to explain the relationship between light properties and species richness, whereas a radius of 1.0 m was enough to estimate the relationship between light and canopy cover. In addition, light-related variables such as diffuse light and leaf area index were related to species richness, whereas structural variables such as canopy openness were related to canopy cover. In summary, our study demonstrates that non stand-replacing disturbances such as windstorms, thinning, or droughts can have an important role in modifying structural and light-related canopy properties, which in turn may inﬂuence natural processes of stand development and ecological succession.
Open Access
Under-vine cover crops: Impact on physical and biological soil proprieties in an irrigated Mediterranean vineyard
(Elsevier, 2023) Abad Zamora, Francisco Javier; Marín Ederra, Diana; Imbert Rodríguez, Bosco; Virto Quecedo, Íñigo; Garbisu Crespo, Carlos; Santesteban García, Gonzaga; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Ciencias; Zientziak; Gobierno de Navarra / Nafarroako Gobernua, 0011-1383-2022-000000
We present a novel approach to harmonic disturbance removal in single-channel wind turbine acceleration data by means of time-variant signal modeling. Harmonics are conceived as a set of quasi-stationary sinusoids whose instantaneous amplitude and phase vary slowly and continuously in a short-time analysis frame. These non-stationarities in the harmonics are modeled by low-degree time polynomials whose coefficients capture the instantaneous dynamics of the corresponding waveforms. The model is linear-in-parameters and is straightforwardly estimated by the linear least-squares algorithm. Estimates from contiguous analysis frames are further combined in the overlap-add fashion in order to yield overall harmonic disturbance waveform and its removal from the data. The algorithm performance analysis, in terms of input parameter sensitivity and comparison against three state-of-the-art methods, has been carried out with synthetic signals. Further model validation has been accomplished through real-world signals and stabilization diagrams, which are a standard tool for determining modal parameters in many timedomain modal identification algorithms. The results show that the proposed method exhibits a robust performance particularly when only the average rotational speed is known, as is often the case for stand-alone sensors which typically carry out data pre-processing for structural health monitoring. Moreover, for real-world analysis scenarios, we show that the proposed method delivers consistent vibration mode parameter estimates, which can straightforwardly be used for structural health monitoring.
Open Access
SilvAdapt.Net: a site-based network of adaptive forest management related to climate change in Spain
(MDPI, 2021) Molina, Antonio J.; Navarro Cerrillo, Rafael M.; Pérez-Romero, Javier; Alejano, Reyes; Bellot, Juan F.; Blanco Vaca, Juan Antonio; Camarero, Jesús Julio; Carrara, Arnaud; Castillo, Víctor M.; Cervera, Teresa; Barberá, Gonzalo G.; González-Sanchis, María; Hernández, Álvaro; Imbert Rodríguez, Bosco; Jiménez, María N.; Llorens, Pilar; Lucas Borja, Manuel Esteban; Moreno, Gerardo; Moreno de las Heras, Mariano; Navarro, Francisco B.; Palacios, Guillermo; Palero, Noemí; Ripoll, María A.; Regüés, D.; Ruiz Gómez, Francisco Javier; Vilagrosa, Alberto; Campo, Antonio D. del; Ciencias; Zientziak
Adaptive forest management (AFM) is an urgent need because of the uncertainty regarding how changes in the climate will affect the structure, composition and function of forests during the next decades. Current research initiatives for the long-term monitoring of impacts of silviculture are scattered and not integrated into research networks, with the consequent losses of opportunities and capacity for action. To increase the scientiﬁc and practical impacts of these experiences, it is necessary to establish logical frameworks that harmonize the information and help us to deﬁne the most appropriate treatments. In this context, a number of research groups in Spain have produced research achievements and know-how during the last decades that can allow for the improvement in AFM. These groups address the issue of AFM from different ﬁelds, such as ecophysiology, ecohydrology and forest ecology, thus resulting in valuable but dispersed expertise. The main objective of this work is to introduce a comprehensive strategy aimed to study the implementation of AFM in Spain. As a ﬁrst step, a network of 34 experimental sites managed by 14 different research groups is proposed and justiﬁed. As a second step, the most important AFM impacts on Mediterranean pines, as one of the most extended natural and planted forest types in Spain, are presented. Finally, open questions dealing with key aspects when attempting to implement an AFM framework are discussed. This study is expected to contribute to better outlining the procedures and steps needed to implement regional frameworks for AFM.
Open Access
Long-term carbon sequestration in pine forests under different silvicultural and climatic regimes in Spain
(MDPI, 2022) Navarro Cerrillo, Rafael M.; Ruiz Gómez, Francisco Javier; Camarero, Jesús Julio; Castillo, Víctor M.; Barberá, Gonzalo G.; Palacios Rodríguez, Guillermo; Navarro, Francisco B.; Blanco Vaca, Juan Antonio; Imbert Rodríguez, Bosco; Cachinero Vivar, Antonio M.; Molina, Antonio J.; Campo, Antonio D. del; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB; Ciencias
Proactive silviculture treatments (e.g., thinning) may increase C sequestration contributing to climate change mitigation, although, there are still questions about this effect in Mediterranean pine forests. The aim of this research was to quantify the storage of biomass and soil organic carbon in Pinus forests along a climatic gradient from North to South of the Iberian Peninsula. Nine experimental Pinus spp trials were selected along a latitudinal gradient from the pre-Pyrenees to southern Spain. At each location, a homogeneous area was used as the operational scale, and three thinning intensity treatments: unthinned or control (C), intermediate thinning (LT, removal of 30–40% of the initial basal area) and heavy thinning (HT, removal of 50–60%) were conducted. Growth per unit area (e.g., expressed as basal area increment-BAI), biomass, and Soil Organic Carbon (SOC) were measured as well as three sets of environmental variables (climate, soil water availability and soil chemical and physical characteristics). One-way ANOVA and Structural Equation Modelling (SEM) were used to study the effect of thinning and environmental variables on C sequestration. Biomass and growth per unit area were higher in the control than in the thinning treatments, although differences were only significant for P. halepensis. Radial growth recovered after thinning in all species, but it was faster in the HT treatments. Soil organic carbon (SOC10, 0–10 cm depth) was higher in the HT treatments for P. halepensis and P. sylvestris, but not for P. nigra. SEM showed that Pinus stands of the studied species were beneficed by HT thinning, recovering their growth quickly. The resulting model explained 72% of the variation in SOC10 content, and 89% of the variation in silvicultural condition (basal area and density) after thinning. SOC10 was better related to climate than to silvicultural treatments. On the other hand, soil chemical and physical characteristics did not show significant influence over SOC10- Soil water availability was the latent variable with the highest influence over SOC10. This work is a new contribution that shows the need for forest managers to integrate silviculture and C sequestration in Mediterranean pine plantations
Open Access
Environment and density-dependency explain the fine-scale aggregation of tree recruits before and after thinning in a mixed forest of Southern Europe
(PeerJ, 2022) Rodríguez Pérez, Javier; Peralta de Andrés, Francisco Javier; Imbert Rodríguez, Bosco; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB; Ciencias
Thinning in forest management primarily reduces the density of trees and alters the patchiness and spatial complexity of environmental factors and individual interactions between plant recruits. At fine spatial scales, little is known about the relative weight of ecological processes affecting tree regeneration before and after thinning events. Here we studied the density and aggregation of tree recruits in fully-mapped plots located in mixed forests in Northern Iberian Peninsula (Southern Europe) for over four years, which comprises one year before and three years after a thinning event. We applied spatial point-pattern analyses to examine (a) the aggregation of recruits, and their association with trees and (b) the relative effect of both environmental (i.e., the patchiness of the local environment) and density-dependent factors (i.e., the aggregation of trees and/or recruits) to predict the density, aggregation, and survival of recruits. We found, in thinning plots, that recruits were less dense, their aggregation pattern was more heterogeneous, were distributed randomly in respect of trees and their survival was almost unaffected by the tree proximity. By contrast, recruits in control plots were denser, were only aggregated at distances lower than 1.0 m, were closer to trees, and such closer distance to trees affected negatively in their survival. Independently of the treatment, the aggregation of recruits was chiefly determined by the density-dependent factors at less than 1.0 m and environmental factors at distances beyond that proximity. Overall, our results suggest that thinning affected the aggregation of recruits at two spatial scales: (a) by favoring the tree-recruit and recruit-recruit facilitation at less than 1.0 m and (b) by modifying spatial heterogeneity of the environment at distances beyond that proximity.
Open Access
Drought limits tree growth more than greenness and reproduction: insights from five case studies in Spain
(KeAi Communications, 2025-08-01) Camarero, Jesús Julio; Rubio-Cuadrado, Álvaro; González de Andrés, Ester; Valeriano, Cristina; Pizarro, Manuel; Imbert Rodríguez, Bosco; Lo, Yueh-Hsin; Blanco Vaca, Juan Antonio; Ciencias; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB
Droughts impact forests by influencing various processes such as canopy greenness, tree growth, and reproduction, but most studies have only examined a few of these processes. More comprehensive assessments of forest responses to climate variability and water shortages are needed to improve forecasts of post-drought dynamics. Iberian forests are well-suited for evaluating these effects because they experience diverse climatic conditions and are dominated by various conifer and broadleaf species, many of which exhibit masting. We assessed how greenness, evaluated using the normalized difference vegetation index (NDVI), tree radial growth, and seed or cone production responded to drought in five tree species (three conifers: silver fir (Abies alba), Scots pine (Pinus sylvestris), and stone pine (Pinus pinea); two broadleaves: European beech (Fagus sylvatica) and holm oak (Quercus ilex) inhabiting sites with different aridity. We correlated these data with the standardized precipitation evapotranspiration index (SPEI) using the climate window analysis (climwin) package, which identifies the most relevant climate window. Drought constrained growth more than greenness and seed or cone production. Dry conditions led to high seed or cone production in species found in cool, moist sites (silver fir, beech, and Scots pine). We also found negative associations of cone production with summer SPEI in the drought-tolerant stone pine, which showed lagged growth−cone negative correlations. However, in the seasonally dry holm oak forests, severe droughts constrained both growth and acorn production, leading to a positive correlation between these variables. Drought impacts on greenness, growth, seed, and cone production depended on species phenology and site aridity. A negative correlation between growth and reproduction does not necessarily indicate trade-offs, as both may be influenced by similar climatic factors.
Open Access
8ª Edición de la Escuela de verano de Ecología de Navarra: ecólogas/os por un día
(Asociación Española de Ecología Terrestre, AEET, 2022) Imbert Rodríguez, Bosco; Blanco Vaca, Juan Antonio; Ciencias; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB
Durante los pasados 23 y 24 de junio tuvo lugar la 8ª edición de la Escuela de Verano de Ecología de Navarra de la Universidad Pública de Navarra (UPNA) con el título ‘Ecólogas/os por un día’. En la jornada se impartieron cuatro ponencias por parte de los miembros del grupo de investigación de Ecología y Medio Ambiente de la Universidad Pública de Navarra, pero la mayor parte del tiempo se dedicó al trabajo de campo en el parque. En dicho trabajo de campo los asistentes pudieron trabajar tres temas diferentes: el estudio de las comunidades vegetales en pastos, el estudio de la estructura de una comunidad arbórea y la observación y estimación de censos de aves. Los trabajos incluyeron la demostración y familiarización de los estudiantes con las distintas técnicas y aparatos para medir variables ambientales como luz ambiental, temperatura del suelo, humedad del suelo, diámetro y altura de árboles, así como las técnicas para realizar inventarios florísticos o de fauna.
Open Access
Cubierta vegetal bajo las cepas: una alternativa al control de las malas hierbas en los viñedos
(INTIA (Tecnologías e Infraestructuras Agroalimentarias), 2023) Abad Zamora, Francisco Javier; Cibriain Sabalza, Félix; Sagüés Sarasa, Ana; Santesteban García, Gonzaga; Lezáun San Martín, Juan Antonio; Fabo Boneta, Jesús María; Virto Quecedo, Íñigo; Imbert Rodríguez, Bosco; Marín Arroyo, Remedios; Garbisu Crespo, Carlos; Ciencias; Zientziak; Agronomía, Biotecnología y Alimentación; Agronomia, Bioteknologia eta Elikadura; Institute for Multidisciplinary Research in Applied Biology - IMAB; Institute on Innovation and Sustainable Development in Food Chain - ISFOOD
En este artículo se presentan los resultados obtenidos con una cubierta vegetal de trébol sembrada bajo las cepas para competir con las malas hierbas, de manera que no sea necesario recurrir al empleo de herbicidas o laboreos intercepas.
Open Access
Coarse woody debris' invertebrate community is affected directly by canopy type and indirectly by thinning in mixed scots pine-European beech forests
(MDPI, 2020) Herrera Álvarez, Ximena; Blanco Vaca, Juan Antonio; Imbert Rodríguez, Bosco; Álvarez, Willin; Rivadeneira Barba, Gabriela; Zientziak; Institute for Multidisciplinary Research in Applied Biology - IMAB; Ciencias
Research Highlights: Thinning and tree species alter the forest floor microclimate by modifying canopy cover, radiation, wind, and humidity. Thus, forest management can directly influence the edaphic mesofauna responsible for decomposing coarse woody debris (CWD). Background and Objectives: This research was carried out in the Southwestern Pyrenees Mountains (Northern Spain) and aimed to determine the influence of forest thinning and canopy type (pure Pinus sylvestris L. or a mix of P. sylvestris and Fagus sylvatica L.) on CWD colonization by edaphic fauna. Materials and Methods: CWD samples were collected belonging to intermediate and advanced decomposition stages, approximately 10 cm long and 5 cm in diameter. Using a design of three thinning intensities (0%, 20%, and 40% of basal area removed), with three replications per treatment (nine plots in total), four samples were taken per plot (two per canopy type) to reach 36 samples in total. Meso- and macrofauna were extracted from CWD samples with Berlese-Tullgren funnels, and individuals were counted and identified. Results: 19 taxonomic groups were recorded, the most abundant being the mesofauna (mites and Collembola). Mixed canopy type had a significant positive influence on richness, whereas advanced decay class had a positive significant influence on total abundance and richness. In addition, there were non-significant decreasing trends in richness and abundance with increasing thinning intensity. However, interactions among thinning intensity, canopy type, and decay class significantly affected mesofauna. Furthermore, some taxonomic groups showed differential responses to canopy type. CWD water content was positively correlated with total invertebrate abundance and some taxonomic groups. Our results suggest that stand composition has the potential to directly affect invertebrate communities in CWD, whereas stand density influence is indirect and mostly realized through changes in CWD moisture. As mesofauna is related to CWD decomposition rates, these effects should be accounted for when planning forest management transition from pure to mixed forests.