49 research outputs found

    Cross-kingdom interactions shape soil biogeochemistry in natural and agricultural ecosystems

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    Microorganisms influence life on earth in innumerable ways, including in medical, industrial, environmental, and agricultural contexts. Given the increasingly apparent consequences of climate warming, interest in how to better predict and manage Earth’s carbon sinks has never been greater. Soil, the largest terrestrial carbon sink, harbors an incredibly taxonomically and functionally diverse microbial community. These soil-dwelling microbes govern the fate of soil carbon and nutrients by cycling organic matter as they live, grow, and die. It has only been relatively recently that technological advancement has allowed for in-depth surveys of the vast diversity of soil microbes. High throughput analytical capabilities like next-generation DNA sequencing have resulted in an explosion of data confirming the importance of microbial communities in biogeochemical cycles. Nevertheless, many questions remain regarding microbially-mediated biogeochemical cycling in different environmental contexts (e.g., forest soil versus agricultural soil) and under changing environmental conditions (e.g., warming, agricultural intensification). In this dissertation, I examine the role of cross-kingdom interactions in shaping soil biogeochemistry under two different scenarios: 1) in a manipulated forest soil food web (animal-microbe interactions) and 2) early Miscanthus x giganteus cultivation on lands of varying disturbance histories using a suite of management strategies (plant-microbe interactions). I was broadly interested in how manipulating these interactions impacted soil carbon and nitrogen cycling and storage

    Remote sensing tools for monitoring grassland plant leaf traits and biodiversity

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    Rocchini, Duccio1This project has received funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie SkƂodowska-Curie Grant No. 721995 (project Trustee).openGrasslands are one of the most important ecosystems on Earth, covering approximately onethird of the Earth’s surface. Grassland biodiversity is important as many services provided by such ecosystems are crucial for the human economy and well-being. Given the importance of grasslands ecosystems, in recent years research has been carried out on the potential to monitor them with novel remote sensing techniques. Improved detectors technology and novel sensors providing finescale hyperspectral imagery have been enabling new methods to monitor plant traits (PTs) and biodiversity. The aims of the work were to study different approaches to monitor key grassland PTs such as Leaf Area Index (LAI) and biodiversity-related traits. The thesis consists of 3 parts: 1) Evaluating the performance of remote sensing methods to estimate LAI in grassland ecosystems, 2) Estimating plant biodiversity by using the optical diversity approach in grassland ecosystems, and 3) Investigating the relationship between PTs variability with alpha and beta diversity for the applicability of the optical diversity approach in a subalpine grassland of the Italian Alps To evaluate the performance of remote sensing methods to estimate LAI, temporal and spatial observations of hyperspectral reflectance and LAI were analyzed at a grassland site in Monte Bondone, Italy (IT-MBo). In 2018, ground temporal observations of hyperspectral reflectance and LAI were carried out at a grassland site in Neustift, Austria (AT-NEU). To estimate biodiversity, in 2018 and 2019 a floristics survey was conducted to determine species composition and hyperspectral data were acquired at two grassland sites: IT-MBo and University of Padova’s Experimental Farm, Legnaro, Padua, Italy (IT-PD) respectively. Furthermore, in 2018, biochemistry analysis of the biomass samples collected from the grassland site IT-MBo was carried out to determine the foliar biochemical PTs variability. The results of the thesis demonstrated that the grassland spectral response across different spectral regions (Visible: VIS, red-edge: RE, Near-infrared: NIR) showed to be both site-specific and scale-dependent. In the first part of the thesis, the performance of spectral vegetation indices (SVIs) based on visible, red-edge (RE), and NIR bands alongside SVIs solely based or NIRshoulder bands (wavelengths 750 - 900 nm) was evaluated. A strong correlation (R2 > 0.8) was observed between grassland LAI and both RE and NIR-shoulder SVIs on a temporal basis, but not on a spatial basis. Using the PROSAIL Radiative Transfer Model (RTM), it was demonstrated that grassland structural heterogeneity strongly affects the ability to retrieve LAI, with high uncertainties due to structural and biochemical PTs co-variation. In the second part, the applicability of the spectral variability hypothesis (SVH) was questioned and highlighted the challenges to use high-resolution hyperspectral images to estimate biodiversity in complex grassland ecosystems. It was reported that the relationship between biodiversity (Shannon, Richness, Simpson, and Evenness) and optical diversity metrics (Coefficient of variation (CV) and Standard deviation (SD)) is not consistent across plant communities. The results of the second part suggested that biodiversity in terms of species richness could be estimated by optical diversity metrics with an R2 = 0.4 at the IT-PD site where the grassland plots were artificially established and are showing a lower structure and complexity from the natural grassland plant communities. On the other hand, in the natural ecosystems at IT-MBo, it was more difficult to estimate biodiversity indices, probably due to structural and biochemical PTs co-variation. The 18 effects of canopy non-vegetative elements (flowers and dead material), shadow pixels, and overexposed pixels on the relationship between optical diversity metrics and biodiversity indices were highlighted. In the third part, we examined the relationship between PTs variability (at both local and community scales, measured by standard deviation and by the Euclidean distances of the biochemical and biophysical PTs respectively) and taxonomic diversity (both α-diversity and ÎČdiversity, measured by Shannon’s index and by Jaccard dissimilarity index of the species, families, and functional groups percent cover respectively) in Monte Bondone, Trentino province, Italy. The results of the study showed that the PTs variability metrics at alpha scale were not correlated with α-diversity. However, the results at the community scale (ÎČ-diversity) showed that some of the investigated biochemical and biophysical PTs variations metrics were associated with ÎČ-diversity. The SVH approach was also tested to estimate ÎČ-diversity and we found that spectral diversity calculated by spectral angular mapper (SAM) showed to be a better proxy of biodiversity in the same ecosystem where the spectral diversity failed to estimate alpha diversity, this leading to the conclusion that the link between functional and species diversity may be an indicator of the applicability of optical sampling methods to estimate biodiversity. The findings of the thesis highlighted that grassland structural heterogeneity strongly affects the ability to retrieve both LAI and biodiversity, with high uncertainties due to structural and biochemical PTs co-variation at complex grassland ecosystems. In this context, the uncertainties of satellite-based products (e.g., LAI) in monitoring grassland canopies characterized by either spatially or temporally varying structure need to be carefully taken into account. The results of the study highlighted that the poor performance of optical diversity proxies in estimating biodiversity in structurally heterogeneous grasslands might be due to the complex relationships between functional diversity and biodiversity, rather than the impossibility to detect functional diversity with spectral proxiesopenImran, H.A

    Carbon fluxes in a mature deciduous forest under elevated CO₂

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    This PhD thesis addressed several major aspects of the carbon (C) cycle in a c. 100-year-old, mixed deciduous forest under elevated CO₂ with an emphasis on below-ground processes. The aim was to assess the responses of tree fine roots and soil respiration to canopy CO₂ enrichment (? 550 ppm) in this tallest forest studied to date. Furthermore, leaf gas-exchange of the five study species was examined to ascertain the long-term response of photosynthetic carbon uptake to elevated atmospheric CO₂. Investigations at the Swiss Canopy Crane (SCC) experimental site were guided by the following key questions: (1) Does below-ground C allocation to fine root production increase in response to CO₂ enrichment in order to acquire more nutrients to match the enhanced C supply in the forest canopy? (2) Is below-ground metabolism enhanced and therefore forest soil respiration stimulated by canopy CO₂ enrichment? (3) Is leaf-level photosynthesis persistently stimulated by elevated CO₂ in this stand or had these mature broad-leaved trees reduced their carbon up- take by photosynthetic down-regulation under long-term CO₂ enrichment? Findings from earlier studies at the SCC site, including 13C isotope tracing, all point towards an in- creased flux of C through CO₂-enriched trees to the soil but neither fine root biomass nor soil respiration were stimulated by elevated CO₂. Surprisingly, fine root biomass in bulk soil and ingrowth cores showed strong reductions by ? 30% in year five and six but were unaffected in the following seventh year of CO₂ enrichment. Given the absence of a positive biomass response of fine roots, we assumed that the extra C assimilated in the CO₂-enriched forest canopy was largely respired back to the atmosphere via increases in fine root and rhizosphere respiration and the metabolization of increased root derived exudates by soil microbes. Indeed, 52% higher soil air CO₂ concentration during the growing season and 14% greater soil microbial biomass both in- dicated enhanced below-ground metabolism in soil under CO₂-enriched trees. However, this did not translate into a persistent stimulation of soil respiration. At times of high or continuous precipitation soil water savings under CO₂-exposed trees (resulting from reduced sapflow) led to excessive soil moisture (> 45 vol.-%) impeding soil gas-exchange and thus soil respiration. Depending on the interplay between soil temperature and the consistently high soil water content in this stand, instantaneous rates of soil respiration were periodically reduced or increased under elevated CO₂ but on a diel scale and integrated over the growing season soil CO₂ emissions were similar under CO₂-enriched and control trees. Soil respiration could therefore not explain the fate of the extra C. The lacking sink capacity for additional assimilates led us to assume downward adjustment of photosynthetic capacity in CO₂-enriched trees thereby reducing carbon uptake in the forest canopy. Photosynthetic acclimation cannot completely eliminate the CO₂-driven stimulation in carbon uptake, but a reduction could hamper the detection of a CO₂ effect considering the low statistical power inevitably involved with such large-scale experiments. However, after eight years of CO₂ enrichment we found sustained stimulation in leaf photosynthesis (42-49%) indicating a lack of closure in the carbon budget for this stand under elevated atmospheric CO₂

    Response of root associated fungal communities to increased atmospheric deposition of nitrogen and phosphorus in tropical montane forests

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    Primary tropical montane forests along the eastern Andes contribute significantly to the storage of carbon and to the designation of the tropical Andes as a biodiversity hotspot. Despite their remoteness, these unique ecosystems are increasingly experiencing the effects of different global change factors. Of particular concern, given the adaptation of eastern Andean forests to infertile soils, is the increased deposition rate of nitrogen and phosphorus resulting from the intensification of human activities in neighboring regions. Tropical montane forest trees rely on arbuscular mycorrhizal fungi (AMF) to obtain nutrients from the scarcely available pool found in eastern Andean soils. In addition to AMF, it is believed that tropical trees interact with a broad range of fungal taxa that range from facultative saprobes to specialized plant pathogens. Given root associated fungi stand at the interphase of soil and plants and are directly involved in the flow of nutrients, studying their response to an increased availability of N and P can give insight into the response of the ecosystem to this disturbance. The work presented in this dissertation is a compendium of three scientific contributions. Two of them document the response of root associated fungal communities to increased availability of nitrogen and phosphorus and one is a methodological viewpoint that critically assesses the suitability of current sampling strategies to study soil microbial communities. The empirical studies collected mixed root samples from a fertilization experiment seven years after the manipulation started. This experiment simulated the atmospheric deposition rates expected for the eastern Andes, by fertilizing the forest floor at a rate of 50 kg N ha-1 yr-1 and 10 kg P ha-1 yr-1. To increase the external validity of the manipulation, the experiment was deployed in forests occurring along an elevation gradient (1000–3000 m above sea level) that represents the typical transition from pre-montane to upper montane forests observed in the eastern Andes. High-throughput sequencing was employed to characterize AM and non-AM fungal communities recovered from DNA extracted from mixed root samples. Based on previous studies, it was hypothesized that chronic fertilization will decrease AMF diversity and community composition given plants will invest less C in the symbiosis. As the ambient N and P availabilities shift with elevation and it is likely that AMF clades have distinct nutritional niches, it was further hypothesized that site and clade specific responses will be observed. Regarding additional clades of root associated fungi, it was expected that fertilization will reduce diversity and alter community composition. It was assumed that the pool of soil fungi available to interact with roots decreases, since it is unlikely all fungal taxa are able to regulate their elemental stoichiometry to maintain homeostasis with the altered soil stoichiometry elicited by fertilization. AMF alpha diversity decreased with elevation and there was a strong turnover of operational taxonomic units (OTUs) across sites, which indicates AMF taxa have narrow environmental niches. Non-AM fungal communities were taxonomically rich, mostly including phylotypes within Ascomycota, Basidiomycota and Mortierellomycota. Guild structure was also diverse, and mostly included fungal saprobes and plant pathogens. Fertilization consistently altered AMF community composition along the elevation gradient, but only reduced Glomeraceae richness. Compositional changes were mainly driven by increases in P supply while richness reductions were observed only after combined N and P additions. Taxonomic richness of non-AM fungal communities was not affected by fertilization, neither at the kingdom nor at the phylum level. In contrast, community composition shifted, particularly among Ascomycota and after the addition of P. These findings suggest that, unlike AMF, non-AM fungal communities are less sensitive to shifts in soil nutrient availability. Overall the findings reported in this dissertation expand our understanding about the response of root associated fungi to increased nutrient availability in tropical systems. Sensitivity of AMF communities to P fertilization is in line with previous literature and causes concern in light of the current trends of atmospheric deposition. We confirmed that tropical montane trees interact with diverse fungal communities, and these appear to be robust to the addition of nutrients. Despite the fact that we characterized root associated fungal communities at a resolution that has never been achieved before in this region, we are still lacking the most basic understanding of the functional roles and trophic modes of most members of these communities. Hence, we hope the patterns revealed in these studies inspire further exploration of tropical montane fungi

    Effects of woody weeds on fuels and fire behaviour in Eastern Australian forests and woodlands.

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    Fire is a common feature in most ecosystems in Australia. Much of the native flora is well adapted to occasional fire and recovers over time in a variety of ways. Invasive species or ‘weeds’ are also a common feature in most Australian ecosystems, particularly in forests and woodlands close to urban settlements. Many invasive species have the potential to recover or recolonise more rapidly following disturbance than native species and may change the fuel load and structure of invaded areas. Invasive species can alter the fuel load and structure providing the fine fuel necessary for initiation and propagation of fire. Woody weeds can also provide elevated biomass to sustain fire and ‘ladder fuels’ allowing fire to reach the canopy. When both of these elements are considered there is the likelihood of alteration of fire behaviour in weed-infested areas of forests and woodlands. The research described in this thesis aims to investigate the effect of invasive species on fire in woodlands of eastern Australia. The fuel load, fuel structure and flammability of pristine (non-invaded) Cumberland Plain Woodland (Australian Botanical Garden, Mount Annan, New South Wales, Australia) and adjacent areas invaded with the woody weed, African Olive (Olea europaea subsp. cuspidata), was assessed and compared. Heavily-invaded areas are comprised of mature trees of African Olive present for more than 15 years, with a continuous canopy and a limited number of species in the understorey were contrasted with areas of ‘intermediate’ invasion, where immature trees of African Olive were interspersed among a grassy/shrubby matrix, and areas of pristine woodland

    Remote Sensing for Precision Nitrogen Management

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    This book focuses on the fundamental and applied research of the non-destructive estimation and diagnosis of crop leaf and plant nitrogen status and in-season nitrogen management strategies based on leaf sensors, proximal canopy sensors, unmanned aerial vehicle remote sensing, manned aerial remote sensing and satellite remote sensing technologies. Statistical and machine learning methods are used to predict plant-nitrogen-related parameters with sensor data or sensor data together with soil, landscape, weather and/or management information. Different sensing technologies or different modelling approaches are compared and evaluated. Strategies are developed to use crop sensing data for in-season nitrogen recommendations to improve nitrogen use efficiency and protect the environment

    From trees to soil: microbial and spatial mediation of tree diversity effects on carbon cycling in subtropical Chinese forests

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    The loss of biodiversity is affecting all ecosystems on Earth, one of the greatest threats to biodiversity being climate change. Forests have been highlighted for the potential to mitigate climate change by storing carbon above- and belowground in soils. In this thesis, I studied the effects of tree diversity on carbon cycling in subtropical Chinese forests. I aimed to explore the mechanisms behind tree diversity effects on carbon cycling by focusing on microbial-based processes and the consequences of tree diversity-induced spatial heterogeneity. First, my colleagues and I tested the effects of tree diversity on litterfall spatial patterns and the consequences for litter decomposition and quantified the importance of microbial community in decomposition processes. Second, we explored the effects of tree diversity on relationships between soil microbial facets and soil microbial functions. Third, we tested the effects of tree diversity on soil microbial biomass and carbon concentrations, and their mediation by biotic and abiotic conditions. Finally, we explored the consequences of diversifying forests for re-/afforestation initiatives and plantations to reduce atmospheric carbon levels, and the benefits of diversity for mitigating the effects of climate change on ecosystems and human well-being. We highlighted the positive effects of tree diversity on tree productivity. By increasing the amount and diversity of litterfall, tree diversity increased litter decomposition and subsequently the assimilation of tree products into the forest soils. Our investigation has shown the key role of microbial communities for forests carbon dynamics by carrying out litter decomposition, soil heterotrophic respiration, and soil carbon stabilization. Most notably, tree diversity effects on soil microbial respiration were mainly mediated by soil microbial biomass rather than soil microbial community taxonomic or functional diversity. The effects of tree diversity on microbial biomass were mediated by biotic and abiotic conditions. Taken together, we revealed the importance of considering space to understand biodiversity-ecosystem functioning relationships. Finally, we argued that tree diversity is a promising avenue to maximize the potential of re-/afforestation projects to mitigate increasing atmospheric carbon. Moreover, we highlighted that diversifying forests in re-/afforestation initiatives can help to reduce climate change effects on ecosystems: first, by increasing resistance and resilience to extreme climatic events, and second, by buffering microclimatic conditions in natural and urban areas. My investigation highlighted that tree diversity effects on ecosystem functioning could be explained by both mass and diversity effects on higher trophic levels and their functions. In addition, I showed the key role of tree diversity-induced spatial heterogeneity and the need to consider space and time in further research. Moreover, these results need to be combined with practitioner constraints to enable feasible restoration projects.:Summary table Bibliographic information .................................................................................... I ~ XV Main body ......................................................................................................... 1 ~ 212 Supplementary materials ..................................................................................... i ~ xv Scientific supplementary materials ............................................................. -1- ~ - 154- Table of Contents Table of figures .......................................................................................................... XI Table of scientific supplementary materials ............................................................. XIII Glossary ................................................................................................................... XV Introduction ................................................................................................................. 3 Chapter I - Tree diversity effects on litter decomposition are mediated by litterfall and microbial processes .................................................................................................. 35 Transition I - II ........................................................................................................... 67 Chapter II - Tree diversity and soil chemical properties drive the linkages between soil microbial community and ecosystem functioning................................................ 71 Transition II - III ....................................................................................................... 107 Chapter III - Abiotic and biotic drivers of scale-dependent tree trait effects on soil microbial biomass and soil carbon concentration ................................................... 111 Transition III - IV ..................................................................................................... 155 Chapter IV – Diverse forests are cool: promoting diverse forests to mitigate carbon emissions and climate change ............................................................................... 159 General discussion ................................................................................................. 173 Abstract .................................................................................................................. 195 General acknowledgments ..................................................................................... 209 Supplementary materials ..............................................................................................

    Déterminisme et stochasticité dans l'assemblage des communautés mycorhiziennes

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    La vaste majoritĂ© des plantes terrestres sont impliquĂ©es dans des interactions symbiotiques avec des champignons du sol. Ces interactions, appelĂ©es mycorhizes, jouent un rĂŽle clĂ© dans l’écologie des plantes en influençant plusieurs facettes de leur croissance ou de leur reproduction (e.g., nutrition, protection contre les pathogĂšnes, activation du systĂšme immunitaire). Toutefois, nous connaissons encore trĂšs peu de choses sur l’assemblage des communautĂ©s mycorhiziennes en milieu naturel : existe-t-il de la spĂ©cificitĂ© entre certaines espĂšces de plantes et de champignons, ou ces associations sont-elles le fruit du hasard et des conditions locales seulement? Cette question pose un dĂ©fi tant sur le plan fondamental, oĂč nous cherchons Ă  comprendre comment les mutualismes persistent Ă©volutivement, que sur la plan appliquĂ©, oĂč nous aimerions connaĂźtre comment les Ă©cosystĂšmes naturels s’assemblent pour guider nos pratiques de restauration Ă©cologique. Ainsi, mon doctorat a gravitĂ© autour de cette question : quels sont les mĂ©canismes responsables de l’assemblage des communautĂ©s mycorhiziennes? En d’autres termes, qu’est-ce qui dĂ©termine qu’une plante s’associera avec certains champignons, et ne s’associera pas avec d’autres, en milieu naturel. En premier lieu, j’ai approchĂ© cette question sur le plan thĂ©orique en utilisant la thĂ©orie des rĂ©seaux comme outil pour dĂ©tecter les associations prĂ©fĂ©rentielles entre plantes et champignons. J’ai aussi dĂ©veloppĂ©, pour prĂ©dire ces associations prĂ©fĂ©rentielles, un cadre thĂ©orique basĂ© sur les traits fonctionnels des organismes, en adaptant le triangle CSR de J.P. Grime. Finalement, j’ai pu tester mes hypothĂšses par des observations en milieu naturel et des expĂ©riences en milieu contrĂŽlĂ©. L’ensemble de mes travaux ont contribuĂ© Ă  mettre en lumiĂšre deux Ă©lĂ©ments clĂ©s de l’assemblage des communautĂ©s mycorhiziennes. PremiĂšrement, l’assemblage semble se faire de maniĂšre hiĂ©rarchique, oĂč d’abord des contraintes neutres comme l’abondance et la distribution spatiale dĂ©terminent quelles espĂšces auront l’opportunitĂ© d’interagir entre elles et ensuite, une sĂ©lection dĂ©terministe des partenaires s’opĂšre, oĂč les ii plantes ayant des traits fonctionnels similaires tendent Ă  interagir avec un pool similaire de champignons mycorhiziens. DeuxiĂšmement, bien qu’il semble y avoir de la sĂ©lection dĂ©terministe de partenaires, tant en milieu naturel qu’en milieu contrĂŽlĂ©, ce choix de partenaires demeure extrĂȘmement flexible et dĂ©pend probablement des conditions locales et de phĂ©nomĂšnes stochastiques (e.g., conditions du sol, luminositĂ©, effets de prioritĂ© par les plantes voisines, etc.). Ces rĂ©sultats permettent de mieux comprendre la spĂ©cificitĂ© dans la symbiose mycorhizienne. Ils suggĂšrent aussi que ces communautĂ©s symbiotiques seront fortement rĂ©silientes aux perturbations (e.g., extinction locale d’une espĂšce), car la spĂ©cificitĂ© dans le choix de partenaires que l’on observe sur le terrain ne semble pas rĂ©sulter d’évĂšnements de coĂ©volution rĂ©ciproque et de spĂ©cialisation
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