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Master of Science / Department of Biology / Lydia H. Zeglin / Anthropogenic actions have significantly increased biological nitrogen (N) availability on a global scale. In tallgrass prairies, this phenomenon is exacerbated by land management changes, such as fire suppression. Historically, tallgrass prairie fire removed N through volatilization, but fire suppression has contributed to increased soil N availability as well as woody encroachment. Because soil microbes respond to N availability and plant growth, these changes may alter microbial composition and important microbially-mediated functions. Grassland management affects the soil environment on multiple time scales including short (fertilization or fire event), seasonal (growing vs. non-growing season), and long-term (decadal plant turnover and nutrient accumulation), therefore my goal was to understand community variability at different time scales affecting the population and community dynamics of soil microbes. I predicted soil microbes would be sensitive to environmental changes at all time scales, seasonal variation would reflect increased plant rhizodeposit-supported populations during summer and decomposers during winter, and long-term fire suppression and chronic fertilization would drive soil microbial community turnover associated with accumulation of plant litter and N. To address these predictions, soils were collected from the Belowground Plot Experiment (BGPE) at Konza Prairie Biological Station: a 30-y factorial field manipulation of N fertilization and burning. Surface soils (0-15 cm) were sampled monthly between Nov 2014 – Dec 2015, including one week post-fire (April) and post-fertilization (June). Genomic DNA was extracted from each sample for qPCR and PCR for Illumina MiSeq library sequencing of the prokaryotic 16S rRNA gene and fungal ITS, to estimate population and community dynamics of soil microbes. Soil environmental characteristics and plant communities were measured in July 2015 to evaluate correlations between plant and microbial communities, and environmental variability. Soil microbial responses to short-term fire/fertilization events were minimal, while microbial population sizes fluctuate seasonally and synchronously, and microbial community composition varied more with management history than at shorter time scales. Bacterial populations increased 10x during growing-season plant rhizodeposition, while fungal populations were less dynamic, but decreased in fall, possibly reflecting a shift to subsistence on soil organic matter. In contrast, microbial community composition was seasonally stable, but distinct between long-term management treatments, which may indicate accumulation of niche-defining plant or soil properties over decades. Prokaryotic communities responded to altered N availability via both fertilization and loss due to fire, with the highest abundance of "copiotrophic" (r-selected) taxa in unburned, fertilized soils. Fungal communities responded to N fertilization with higher abundance of arbuscular mycorrhizal fungi, pathogens, and saprotrophs, possibly due to changes in nutrient stoichiometry and litter availability in fertilized plots. However, fungal response to fire was largely independent of N availability, and plant community differences were correlated with fungal, but not bacterial, community composition, highlighting the likely nutritional codependence of fungi and plants, and fungal competitive advantages for plant litter substrates. The timing of changes in soil microbial communities is critical for plant nutrition and nutrient cycling in prairies, and this novel dataset on the temporal resolution of microbial responses to environmental variability contributes to the broader understanding of ecosystem responses to global change.

Indiana University-Purdue University Indianapolis (IUPUI) / Nitrous oxide (N2O) is an atmospheric constituent that contributes to climate warming and stratospheric ozone depletion. A large fraction of the anthropogenic N2O emission originates from agricultural soils suggesting therefore a strong connection between N2O accumulation in the atmosphere and agricultural land management. During the last 2-3 decades, no-till (NT) farming and integration of cover crops into crop rotation represent two major developments in agriculture, but much remains to be learned about the impact of these management approaches on N2O emission and underlying biological soil factors. This dissertation focuses on the contribution of different components of the soil microflora to N2O production, and how different types of cover crops (legume vs grass) affect the soil microbial community composition, mineral N availability, and N2O emission in plowed (PT) and NT soils. To address these questions, several laboratory and greenhouse experiments were conducted. Results of these experiments documented soil microbial community responses to cover crop addition and could inform the selection of cover crops most suitable to soils under different tillage practices.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol) / The Succulent Karoo Biome (SKB) in South Africa is widely reputed to house Earth’s greatest diversity of succulent plants. It is also famous for spectacular displays of annual flowers after good rains. The area experiences winter rainfall which infrequently exceeds 100 mm per annum but certain parts of the SKB can get 250 mm. Irrigated agriculture on a large scale was therefore not a viable option when European farmers began colonizing the land. The land was conquered from the indigenous Khoekhoe herders and San hunter-gatherers, South Africa’s first peoples. The biome underwent extreme transformation in the last 200 years following colonisation which resulted in homogenization of the landscape and extinction of many succulents thus reducing biodiversity.

Yes / The mechanisms regulating community composition and local dominance of trees in species-rich forests are poorly resolved, but the importance of interactions with soil microbes is increasingly acknowledged. Here, we show that tree seedlings that interact via root-associated fungal hyphae with soils beneath neighbouring adult trees grow faster and have greater survival than seedlings that are isolated from external fungal mycelia, but these effects are observed for species possessing ectomycorrhizas (ECM) and not arbuscular mycorrhizal (AM) fungi. Moreover, survival of naturally-regenerating AM seedlings over ten years is negatively related to the density of surrounding conspecific plants, while survival of ECM tree seedlings displays positive density dependence over this interval, and AM seedling roots contain greater abundance of pathogenic fungi than roots of ECM seedlings. Our findings show that neighbourhood interactions mediated by beneficial and pathogenic soil fungi regulate plant demography and community structure in hyperdiverse forests. / This research was funded by the National Key Research and Development Program of China (Project No. 2017YFA0605100) and the National Natural Science Foundation of China (NSFC 31770466 to X.L. and 31870403 to M.L.), and partly supported by awards from the UK Natural Environment Research Council (NERC NE/M004848/1 and NE/R004986/1). D.J. is also supported by the N8 AgriFood programme.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: see item for full text / AFRIKAANSE OPSOMMING: sien item vir volteks

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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[pt] A contaminação de solos por hidrocarbonetos é uma real preocupação ambiental em muitas partes do mundo devido a crescente dependência econômica dos derivados do petróleo, principalmente os combustíveis fósseis que estão frequentemente sujeitos a vazamentos e derramamentos acidentais. Estudos capazes de entender os mecanismos de biodegradação dos componentes da gasolina no solo não saturado se fazem necessários, pois auxiliam no processo de tomada de decisões em relação ao gerenciamento e controle da propagação em subsuperfície. No Brasil, o etanol é utilizado como aditivo oxigenado à gasolina e alguns autores sugerem para solo saturado que, por ser mais degradável, ele atrasa a degradação dos outros componentes mais tóxicos desse combustível. O trabalho anterior realizado por esse grupo de pesquisa para solo não saturado obteve conclusões semelhantes às já constatadas para solo saturado. No entanto, os mecanismos de degradação na zona não saturada ainda foram pouco estudados e compreendidos. Este estudo tem como objetivo analisar a degradação do contaminante em blocos não saturados indeformados de solo arenoso e siltoso, oriundos do município de Duque de Caxias – RJ, submetidos a um pulso de contaminante. Dois blocos, um arenoso (BA) e outro argiloso (BS), foram contaminados pela solução de dois porcento de Benzeno, quatro porcento de Tolueno em Heptano (BT); outros dois blocos, também um arenoso (EA) e outro argiloso (ES), foram submetidos à mesma solução adicionados etanol a vinte porcento (BTE). Foram realizados ensaios com a finalidade de monitorar a atividade degradadora total do meio, carbono disponível, perfil metabólico da microbiota, concentração dos contaminantes, além de medições da umidade volumétrica através do uso do Time Domain Reflectometer (TDR). A atividade microbiana inicial, antes da contaminação, apresentou valores baixos. Logo após a contaminação dos blocos, àqueles sujeitos a etanol apresentaram ausência de atividade enquanto os sujeitos apenas à mistura BT mostraram um aumento, contrariando as expectativas. As atividades microbianas oscilaram ao longo de todo o experimento o que pode indicar uma adaptação da microbiota às novas condições do meio. Com base nos resultados dos ensaios e monitoramentos realizados, podemos sugerir que o principal fator determinante para alteração da atividade foi à composição do solo. O contaminante não exerceu a influência esperada e vista nos estudos anteriores. / [en] The soil contamination by hydrocarbons is a real environmental concern in many parts of the world due to growing economic dependence on petroleum, mostly fossil fuels are often subject to leaks and accidental spills. Studies able to understand the mechanisms of biodegradation of gasoline components in unsaturated soil are necessary because they help in making decisions regarding the management and control of the propagation process in the subsurface. In Brazil, ethanol is used as an oxygenate gasoline additive and some authors suggest that for saturated soils, being more degradable, it delays the degradation of other more toxic components of this fuel. The previous study by this research group to unsaturated soil obtained similar results to those already observed for saturated soil. However, the mechanism of degradation in the unsaturated zone have few studies. This study aims to analyze the degradation mechanisms of the contaminant in unsaturated blocks of sand and silt soil from the city of Duque de Caxias - RJ, subjected to a pulse of contaminant. Two blocks, one sandy (BA) and silty (BS), were contaminated by two percent solution of benzene, four percent toluene in heptane (BT); other two blocks, also sandy (EA) and silty (ES), underwent the same solution added to twenty percent ethanol (BTE). Analyzes were performed to monitor the overall activity of the degrading medium, available carbon, the microbiota metabolic profile, concentration of the contaminants were performed as well as measurements of the water content through the use of Time Domain Reflectometer (TDR). The initial microbial activity before the contamination, showed low values. Soon after contamination of the blocks, those subjected to ethanol showed no activity while subject to BT mixture showed an increase, contrary to expectations. Microbial activities ranged throughout the experiment which may indicate an adaptation of microbes to new environmental conditions. Based on the results of testing and monitoring conducted, we suggest that the main determinant for changing the activity factor was the composition of the soil. The contaminant did not exert the expected influence and seen in previous studies