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Soils and plant microbial communities are intricately linked to ecosystem functioning as they play important roles in nutrients dynamics as decomposers and feedback to plant communities as mutualists and pathogens. Numerous soil physicochemical factors as well as the land use management are shaping the composition and dynamics of microbial community. In addition, global warming and climate change are the most prominent of all environmental factors that influence all kinds of the living organisms including microbes associated to the plant soil systems. A better understanding of the environmental drivers shaping these microbial communities especially under future climate will help to understand and predict the expected changes of ecosystems functions and accordingly of the services they provide. In addition, such knowledge will help to detect potential ways on how soil microorganisms can be harnessed to help mitigating the negative consequences of climate change.The Global Change Experimental Facility (GCEF) is settled in the field research station of the Helmholtz Centre for Environmental Research (UFZ) in Bad Lauchstädt, Saxony-Anhalt, Germany (51_22’60 N, 11_50’60 E, 118 m a.s.l.). This facility has been designed to investigate the consequences of a predicted future climate scenario expected in 50-70 years in Central Germany on ecosystem processes under different land-use regimes applied on large field plots in comparison to similar sets of plots under the ambient climate. We performed our study using this research facility, with the aim to analyze the impact of future climate conditions, soil physicochemical factors, and/or land use type and intensity on microbial communities in different habitats (rhizosphere soil, plant endosphere, and plant residues) in grassland and cropland ecosystems. To assess the microbial communities, we used the highly sensitive and powerful highthroughput next generation sequencing, Illumina Miseq.This thesis constitutes the first assessment of microbial communities in the GCEF experimental facility. The samples were collected in 2015 for manuscript 4, while for manuscripts 1, 2, 3, 5, 6, the samples were collected in 2018-2019. Manuscript 1: (Sansupa, Wahdan, Hossen et al., 2021; Applied Science 2021, 11, 688) “Can we use functional annotation of prokaryotic taxa (FAPROTAX) to assign the ecological functions of investigated the potential use of FAPROTAX for bacterial functional annotation in non-aquatic ecosystems, specifically in soil. For this study, we used microbial datasets of soil systems including rhizosphere soil of Trifolium pratense from the extensively used meadow plots in the GCEF. We hypothesized that FAPROTAX can be used in terrestrial ecosystems. Our survey revealed that FAPROTAX tool can be used for screening or grouping of 16S derived bacterial data from terrestrial ecosystems and its performance could be enhanced through improving the taxonomic and functional reference databases. Manuscript 2: (Wahdan et al., 2021; Frontiers in Microbiology 12:629169) “Targeting the active rhizosphere microbiome of Trifolium pratense in grassland evidences a stronger-than-expected belowground biodiversity-ecosystem functioning link”. In this study, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to differentiate between total and active microbiomes (including both bacteria and fungi) in the rhizosphere of T. pratense. In the same rhizosphere soil samples, we also measured the activities of three microbial extracellular hydrolytic enzymes, (ß-glucosidase, N-acetylglucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We investigated the proportion of active and total rhizosphere microbiomes, and their responses to the manipulated future climate in the GCEF. In addition, we identified the possible links between total and active microbiomes and the soil ecosystem function (extracellular enzyme production). Our results revealed that the active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal operational taxonomic units (OTUs), respectively. Active and total microbial fractions were taxonomically and functionally diverse and displayed different responses to variations of soil physicochemical factors. We also showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Manuscript 3: (Wahdan et al., 2021; Microbiology Open 10:e1217) “Deciphering Trifolium pratense L. (red clover) holobiont reveals a resistant microbial community assembly to future climate changes predicted for the next 50–70 years”. We investigated the microbial communities of bacteria and fungi associated with four plant parts of T. pratense (the rhizosphere and the endopheres of the roots, whole shoot system (leaves and stems), and of the flower) and evaluated their potential ecological and metabolic functions in response to future climate conditions. This study was performed on the GCEF extensively managed grassland plots. Our analyses indicated that plant tissue/compartments differentiation enables the formation of a unique ecological niches that harbor specific microbial communities. Except for the fungal communities of the aboveground compartments, T. pratense microbiome diversity and community composition showed a resistance against the future climate changes. We also analyzed the predicted bacterial metabolic functional genes of red clover. Thereby, we detected microbial genes involved in plant growth processes, such as biofertilisation (nitrogen fixation, phosphorus solubilisation, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production), which were not influenced by the future climate. Manuscript 4: (Wahdan et al., 2021; Environmental Microbiology) “Organic agricultural practice enhances arbuscular mycorrhizal symbiosis in correspondence to soil warming and altered precipitation patterns”. This study was performed on the conventional and organic farming plots under both ambient and future climate conditions. We evaluated the effect of climate (ambient vs. future), agricultural practice (conventional vs. organic farming) and their interaction on Arbuscular Mycorrhizal Fungi (AMF) community composition and richness inside wheat roots. In addition, we evaluated the relationship between molecular richness of indigenous root AMF and wheat yield parameters. Future climate altered the total AMF community composition and a sub-community of Glomeraceae. Further, application of different agricultural practices altered both total AMF and Glomeraceae community, whereby organic farming appeared to enhance total AMF and Diversisporaceae richness. Under the future climate scenario, organic farming enhanced total AMF and Gigasporaceae richness in comparison with conventional farming. Our results revealed a positive correlation between AMF richness and wheat nutrient contents not only in organic farming system but also under conventionally managed fields. Manuscript 5: (Wahdan et al., 2020; Microorganisms 8, 908) “Future climate significantly alters fungal plant pathogen dynamics during the early phase of wheat litter decomposition”. This study was performed on the conventional farming plots. We investigated the structure and ecological functions of fungal communities colonizing wheat during the early phase of decomposition (0, 30, and 60 days) under current and future climate conditions. We found that plant pathogenic fungi dominated (~87% of the total sequences) within the wheat residue mycobiome. Destructive wheat fungal pathogens such as Fusarium graminearum, Fusarium tricinctum, and Zymoseptoria tritci were detected under ambient and future climates. Additionally, the future climate brought new pathogens to the system. Manuscript 6: (Wahdan et al., 2021; Microbial Ecology 10.1007/s00248-021-01840-6) “Life in the wheat litter: effects of future climate on microbiome and function during the early phase of decomposition”. This study was performed on the conventional farming plots. We assessed the effects of climate change on microbial richness, community compositions, interactions and their functions (production of extracellular enzymes) in decomposing residues of wheat. In addition, we investigated the effects of climate change on litter residues physicochemical factors as well as on mass loss during the early phase of decomposition. Future climate significantly accelerated litter mass loss as compared with ambient one. Our results indicated that future climate significantly increased fungal richness and altered fungal communities over time, while bacterial communities were more resistant in wheat residues. Fungi corresponded to different physicochemical elements of litter under ambient (C, Ca2+ and pH) and future (C/N, N, P, K+, Ca2+ and pH) climate conditions. Also, a highly correlative interactions between richness of bacteria and fungi were detected under future climate. Activities of microbial β-glucosidase and N-acetylglucosaminidase in wheat straw were significantly higher under future climate. Such high enzymatic activities were coupled with a significant positive correlation between microbial (both bacteria and fungi) richness and community compositions with these two enzymatic activities only under future climate.:CONTENTS BIBLIOGRAPHIC DESCRIPTION……………………………………………….......III ZUSAMMENFASSUNG………………………………………………………...........V SUMMARY……………………………………………………………………………..X GENERAL INTRODUCTION…………………………………………………………………...............1 I-1 Ecosystem functions carried out by soil and plant microbiomes…………………..2 I-2 Biodiversity and functional diversity and maintenance of ecosystem functions……………..3 I-3 Total vs. active microbial diversity for assessing ecosystem functions……………4 I-4 Factors influencing soil and plant microbiota…………………………………..……6 I-4.1 Elements of climate changes……………………………………………................7 I-4.2 Climate changes influence microbes in an interacting, complex manner………8 I-4.3 Environmental factors controlling the response of microorganisms to climate changes………………………………………………………………………………….....10 I-5 Interplay between climate and land use intensity in agroecosystems……………11 I-6 Study site, and overall objectives………………………………………………....…12 I-7 Methods used for the taxonomic and functional characterization of the microbiomes……...15 I-8 Presentation of aims and hypotheses of the publications/manuscripts in different chapters.................................................................................................................16 I-9References.........................................................................................................20 CHAPTER 1 Can we use functional annotation of prokaryotic taxa (FAPROTAX) to assign the ecological functions of soil bacteria? .....................................................................29 Publication…………………………………………………………………………...........31 Supplementary materials…………………………………………………………….......42 CHAPTER 2 Targeting the active rhizosphere microbiome of Trifolium pratense in grassland evidences a stronger-than-expected belowground biodiversity-ecosystem functioning link………………..........................................................................…49 Publication………………………………………………………………………………51 Supplementary materials……………………………………………………………..67 CHAPTER 3 Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes……………………………………………….…………………………..89 Publication………………………………………………………………………………….91 Supplementary materials……………………………………………………………….111 CHAPTER 4 Organic agricultural practice enhances arbuscular mycorrhizal symbiosis in correspondence to soil warming and altered precipitation patterns………………125 Publication……………………………………………………………………………….127 Supplementary materials………………………………………………………….......140 CHAPTER 5 Future climate significantly alters fungal plant pathogen dynamics during the early phase of wheat litter decomposition…...................………………….……………..156 Publication………………………………………………...…………….….…………...158 Supplementary materials………………………………………………….…....……..175 CHAPTER 6 Life in the wheat litter: effects of future climate on microbiome and function during the early phase of decomposition…………………………………….....……....…….181 Publication…………………………………..…………………………………….....…...183 Supplementary materials………………………………………………………………..199 GENERAL DISCUSSION…………………………………………………………….......210 D-I Approaches and main findings of the result chapters………………………..…211 D-2 Conclusion and implications of the study findings…………………………...…215 D-3 Technical limitation of the study……………………………………………......…217 D-4 Future prospects of the study field ...……………………………………………217 D-5 References…………………………………………………………………………..219 DATA AVAILABILITY……………………………………………………………………...223 ACKNOWLEDGEMENTS……………………………………………………………......224 CURRICULUM VITAE……………………………………………………………….....…225 LIST OF PUBLICATIONS………………………………………………………….........226 CONFERENCE PROCEEDINGS…………………………………………………….....227 STATUTORY DECLARATION………………………………………………................228 VERIFICATION OF AUTHOR PARTS……………………………………………........229

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Climate change resulting from emissions of fossil fuel combustion has sparked considerable interest in renewable energy and fuel production research, particularly energy derived from cellulosic ethanol, which is derived from biomass such as wood and grass. Cellulosic ethanol demonstrates a more promising future as a global energy source than corn-derived ethanol because it does not displace food crops, irrigation is not required, and chemical application rates are much lower than for annual crops, such as corn. Growing cellulosic biomass for energy can help reduce greenhouse gas emissions via carbon (C) sequestration and by reducing demand for fossil fuel production. The objective of this study was to investigate how land use change affects soil properties and selected soil C and nitrogen (N) dynamics among alternative cellulosic biofuel treatments at the Weyerhaeuser Alabama Cellulosic Biofuel Research site in west-central Alabama. Composite soils for characterization, along with forest floor, were collected at year 1 and year 2 after treatment establishment at 0-15cm and 15-30cm depths at six locations along three hillslope-riparian transects in five experimental watershed treatments. Decomposition of loblolly pine needles was assessed in each watershed using an in situ litter bag method. Seasonal in situ net nitrogen mineralization was measured using a sequential core method, and an anaerobic incubation for N mineralization potential of composite soils was performed in the laboratory. Results revealed high variability of soil properties and processes within these watersheds, along with no consistent treatment effects. This study provides baseline data for these watershed treatments for future studies. / Master of Science

Land-use change is the single most important global driver of changes in biodiversity. Such changes in biodiversity, in turn, are expected to influence the functioning of ecosystems and their resilience to environmental perturbations and disturbances. It is widely recognised that the use of functional traits and functional diversity is best for understanding the causes and functional consequences of changes in biodiversity, but conceptual development has outpaced empirical applications. This thesis explores these ideas in grazing systems, which are expected to undergo rapid intensification of fertiliser use and grazing pressure to meet the growing global demand for livestock products. First, a flexible framework for measuring different facets of functional diversity is described, and a new multidimensional functional diversity index, called functional dispersion (FDis), is presented. Second, two vegetation sampling methods are compared with regard to their ability to detect changes in vegetation composition. Third, shifts in plant trait distributions following land-use changes are quantified and compared to null models, and a maximum entropy approach is used to quantify the direction and strength of selection on each trait. Fourth, it is shown that these shifts in trait distributions have cascading effects on primary production, litter decomposition, soil respiration, and ultimately soil carbon sequestration. Finally, data from 18 land-use intensity gradients are used to show that land-use intensification reduces functional redundancy and response diversity, two components of biodiversity that are thought to influence ecosystem resilience to future disturbances. This study illustrates (i) the importance of considering species functional differences to understand how plant communities react to changes in soil resource availability and grazing pressure, and (ii) how such changes directly, indirectly, and interactively control ecosystem functioning, as well as (iii) increasing the vulnerability of ecosystems to future disturbances.

A diversidade da Mata Atlântica está constantemente ameaçada devido à perda de habitats provocada pela destruição e alteração dos ambientes naturais. Este fato é muito preocupante, pois os remanescentes florestais da Mata Atlântica encontram-se, em sua maior parte, em pequenos fragmentos altamente perturbados, acarretando em perda de biodiversidade da fauna existente. Muitos estudos demonstraram que mamíferos e aves especialistas (e. g. insetívoros) são muito sensíveis à fragmentação ambiental, tendendo a desaparecer em áreas abertas. A perda destes animais pode alterar a densidade de artrópodes e as taxas de herbivoria, ocasionando um efeito cascata (top- down), que causará influência até na decomposição e ciclagem de nutrientes. Entretanto o estudo de como esse efeito top-down ocorre em diferentes coberturas de solo ainda não foi testado, desta forma, objetivou-se investigar como as taxas de decomposição são modificadas pela exclusão experimental de vertebrados em áreas com diferentes coberturas vegetais na mata Atlântica. Parcelas de exclusão de vertebrados e parcelas controle foram alocadas em áreas com coberturas vegetais de pastagem e floresta, para verificar como ocorre o efeito top-down na decomposição. Utilizaram-se três tipos de serapilheira diferentes, uma gramínea (Brachiaria decumbens), uma espécie pioneira (Tibouchina sellowiana) e uma mistura de folhas de diferentes espécies da floresta primária adjacente. A técnica dos litter bags foi utilizada para avaliar as diferentes taxas de decomposição e foram coletados em intervalos de 16, 36, 71, 181 e 247 dias. O resíduo vegetal foi limpo, seco e pesado para obtenção das massas remanescentes (%) e taxa de decomposição, após isso o material foi triturado e pesado em subamostras para analises de nutrientes e compostos orgânicos (nitrogênio, carbono, fósforo, lignina, celulose e polifenóis). A taxa de decomposição não diferiu entre os tratamentos controle e exclusão de vertebrados, desta forma, não foi possível observar o efeito top-down da exclusão de vertebrados neste estudo, provavelmente devido à elevada biodiversidade da fauna do solo na área onde o experimento foi realizado e sugere-se repeti-lo em uma área menor e mais desconectada, com a finalidade de simular como o efeito cascata ocorre em pequenos fragmentos da mata Atlântica. Além disso, a decomposição foi mais rápida nos litter bags localizados na floresta do que na pastagem e as folhas de gramínea tiveram maior perda de massa do que as folhas de floresta primária e T. sellowiana, possivelmente devido às interações entre nitrogênio, lignina e a relação C:N dos resíduos vegetais. / The diversity of Atlantic forest is constantly threatened due to habitat loss caused by the destruction and alteration of natural environments, and most of the biome is now in small and fragmented areas. This fact is of a great concern, because the remaining areas in Atlantic forest are in small highly disturbed fragments, resulting in loss of biodiversity of the existing fauna, like mammals and birds. Many studies have shown that specialist mammals and birds (e.g. insectivores) are very sensitive to environment fragmentation and tend to disappear in open areas. The loss of these animals is likely to cause an increase in the density of arthropods and rates of herbivory, causing a top-down effect that may even influence the cycling of nutrients. We aimed to investigate how decomposition rates are modified by the experimental exclusion of vertebrates in an area with different land coverage in the Atlantic forest. Vertebrate exclusion plots and control plots were allocated in areas with different land coverage (pasture and forest) to evaluate the top-down effects in decomposition. We used three different kinds of leaves, being one grass (Brachiaria decumbens), one very common primary specie of the area (Tibouchina sellowiana) and a mix of primary forest leaves. Litterbags were used to evaluate the decomposition rate and it was collected during intervals of 16, 36, 71, 181 and 247 days. The vegetal residue was cleaned, dried and weighted to obtain the remaining mass (%) and decomposition rate, after that, the material was milled and weighted in subsamples for analyses of nutritional quality (N, C, P, lignin, cellulose and polyphenols). The decomposition rate was not different for the control and vertebrate exclusion plots, as a result, it was not possible to show the top-down effect in decomposition, possibly because of the high soil biodiversity in the area where the experiment was done. It would be very important to remake this experiment in a smaller and more disconnected area, in order to show how this cascade effect occur in Atlantic forest´s smaller fragments. Furthermore, the decomposition was faster at the forest plots than at the pastureland plots and the grass leaf litter presented the higher decomposition rate than the primary forest leaves and T. sellowiana and it was possibly caused by the interaction between nitrogen, lignin and C:N ratio.

Les essences de forêts tropicales sont caractérisées par une importante variabilité de la qualité et de la stœchiométrie des feuilles qui tombent au sol. Les microorganismes hétérotrophes à la base des réseaux trophiques de décomposeurs dépendent principalement de ces ressources organiques qui varient de façon substantielle à petite échelle quant à la quantité et la contribution relative de certains éléments clés tels que le carbone (C), l'azote (N) et le phosphore (P). J'ai évalué au cours de cette thèse comment les variations de qualité et de stœchiométrie C:N:P de la ressource influençaient l'activité, la biomasse, la stœchiométrie et la structure des communautés des décomposeurs microbiens. J'ai réalisé ce travail en forêt Amazonienne de Guyane française sur des sols extrêmement appauvris en nutriments où les microorganismes hétérotrophes sont supposés être particulièrement dépendants du C et des nutriments provenant des litières. J'ai d'abord démontré que la qualité du C et le contenu en P des feuilles de litières expliquaient plus de 50% de la variabilité observée du processus de respiration microbien (SIR) du sol sous-jacent. Lors d'une expérience de fertilisation factorielle avec du C (sous forme de cellulose), de l'N (sous forme d'urée) et du P (sous forme de phosphate) sur le terrain, j'ai ensuite confirmé que la SIR de la communauté du sol était co-limitée par C et P, alors la SIR dans la litière était co-limitée par N et P. Ces limitations différentielles dans les litières et le sol sous-jacent étaient reliées à des modifications de la structure des communautés microbiennes, et en particulier des changements du ratio champignon:bactérie et de la proportion de bactéries copiotrophes et oligotrophes. Finalement au cours d'une expérience d'incubation au laboratoire, j'ai montré que la biomasse, la stœchiométrie et la structure des communautés microbiennes de la litière différaient fortement entre six litières chimiquement contrastées variant dans leur stœchiométrie initiale C:N:P. Cependant, les variations des paramètres microbiens étaient mieux expliqués par les caractéristiques de la fraction soluble des litières (y compris sa stœchiométrie) que par la qualité de la litière dans son ensemble, entrainant des variations de la stœchiométrie de la biomasse microbienne et un shift vers une dominance fongique en réponse à une augmentation de la stœchiométrie C:N:P des lessivâts. Collectivement, ces résultats montrent que des qualités de litière distinctes produites par une importante diversité d'essences forestières contrôlent la structure, la stœchiométrie, l'abondance et l'activité des communautés microbiennes des litières à petites échelles spatiales en forêt tropicale d'Amazonie. Par ailleurs, les litières en décomposition stimulent également les communautés microbiennes du sol sous-jacent, qui apparaissent être limitées par l'accès combiné à une source de C (énergie) et de P. L'importance de la contrainte stœchiométrique pour les microorganismes hétérotrophes à la base des réseaux trophiques de décomposeurs suggère que des modifications de la composition des communautés végétales ou des dépositions atmosphériques de N et/ou P peuvent avoir des conséquences plus lointaines sur les cycles du C et des nutriments au sein des biomes tropicaux. / Tree species-rich tropical rainforests are characterized by a high variability in quality and stoichiometry of leaf litter input to the soil. Microbial heterotrophs in the decomposer food web depend primarily on these organic resources that can vary dramatically in quantity, quality and relative contribution in key elements such as carbon (C), nitrogen (N), and phosphorus (P). I evaluated during this thesis how differences in leaf litter resource quality and C:N:P stoichiometry influence the activity, biomass, stoichiometry and community structure of microbial decomposers. I did this work in the Amazonian rainforest of French Guiana, where the soils are highly nutrient-impoverished and microbial heterotrophs are assumed to be particularly dependent on litter-derived nutrients. I first showed that leaf litter C quality and P content explained more than 50% of the observed variability of the microbial respiration process in the underlying soil. Using a fertilization experiment with C (as cellulose), N (as urea), and P (as phosphate) in the field, I further showed that microbial respiration process in the litter layer was co-limited by N and P, while that in the soil was co-limited by C and P. Additionally, distinct nutritional limitations in litter and underlying soil were related to shifts in the microbial community structure, especially regarding the fungi:bacteria ratio and the proportion of copiotrophic versus oligotrophic bacteria. Finally, during a laboratory incubation experiment, I showed that litter microbial biomass, stoichiometry and community structure differed strongly among leaf litter from six different tree species varying in C:N:P stoichiometry. The variations in microbial parameters among substrate litters, however, were not related to bulk leaf litter quality, but rather driven by the stoichiometry of the soluble fraction, with larger microbial C:nutrients ratios and a shift towards fungal dominance with increasing litter leachate C:N:P stoichiometry. Collectively, these results showed that the distinct leaf litter quality produced by a diverse tree canopy controls the structure, stoichiometry, abundance and activity of microbial communities in the studied Amazonian rainforest at small spatial scales. Moreover, the decomposing leaf litter stimulates microbial communities in the underlying soil that appear to be under the combined control of energy (C) and P availability. The strong stoichiometric constraint on microbial heterotrophs in the decomposer food web suggests far-ranging consequences on ecosystem C and nutrient cycling with ongoing alteration of nutrient deposition and tree species diversity in tropical rainforests..