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
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:76136 |
| Date | 04 October 2021 |
| Creators | Fareed Mohamed Wahdan, Sara |
| Contributors | Universität Leipzig |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/updatedVersion, doc-type:doctoralThesis, info:eu-repo/semantics/doctoralThesis, doc-type:Text |
| Rights | info:eu-repo/semantics/openAccess |
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