Os fungos micorrízicos arbusculares (FMAs, filo Glomeromycota) formam associações simbióticas com a maioria das plantas vasculares. Normalmente, as hifas dos FMAs crescem no solo e colonizam o interior das raízes. No entanto, não se sabe se as espécies mais abundantes detectadas no solo, por meio da identificação com base na morfologia dos esporos assexuais, são também as mais abundantes no interior das raízes, devido às dificuldades para a identificação dos FMAs com base nas estruturas intrarradiculares. Assim, o objetivo do presente trabalho foi avaliar a estrutura da comunidade de FMAs em cana-de-açúcar sob dois manejos de colheita por meio da identificação das espécies que estão no solo na forma de esporos assexuais e aquelas que estão nas raízes usando o sequenciamento de clones do gene rRNA 18S. Amostras de solo e raízes de cana-de-açúcar de três variedades e dois manejos de colheita: SEM QUEIMA prévia e COM QUEIMA prévia à colheita, foram coletadas em um experimento localizado no município de Novo Horizonte, SP. Foram utilizadas três abordagens para a identificação dos FMAs no interior das raízes: emprego de (1) iniciador específico para fungos em geral, (2) iniciador específico para FMAs e (3) iniciadores específicos para grupos de FMAs. O número de esporos por 50 g de solo, a riqueza de espécies observada e estimada e a diversidade de esporos não diferiram significativamente entre os manejos SEM QUEIMA e COM QUEIMA. Efeitos significativos de variedades de cana-de-açúcar ou na interação dos fatores manejo e variedade não foram observados. A análise de ordenação com base nos esporos identificados também não indicou separação das amostras em função dos tratamentos. Entretanto, plantas do tratamento sob manejo SEM QUEIMA apresentaram as maiores taxas de colonização micorrízica arbuscular, quando comparadas às plantas do tratamento sob manejo COM QUEIMA. Esses dados indicam que a taxa de colonização micorrízica arbuscular é um indicador mais sensível à mudança de manejo de colheita da cana-de-açúcar do que os outros indicadores avaliados. Após a extração de DNA das raízes, o uso dos iniciadores específicos para fungos em geral, para FMAs e iniciadores específicos para grupo de FMAs não resultou em sequências de Glomeromycota. Mesmo assim, a comunidade de fungos associados às raízes detectada por sequenciamento do gene rRNA 18S foi avaliada. Os resultados indicam que a estrutra da comunidade fúngica associada às raízes de cana-de-açúcar diferiu significativamente entre os manejos de colheita SEM QUEIMA e COM QUEIMA prévia, apesar de não haver diferenças na riqueza e índices de diversidade de unidades taxonômicas operacionais observadas. Em geral, estudos adicionais devem ser feitos para otimizar as condições para amplificação do gene rRNA 18S de FMAs para melhor entender a ecologia dos mesmos. / Arbuscular mycorrhizal fungi (AMF, Glomeromycota) form mutualistic symbioses with most land plants. AMF hypha generally grow through the soil and colonize the cortical tissue of the plant roots. However, it is not known whether the most abundant species in the soil, determined based on the morphology of asexual spores are the most abundant inside the roots, due the difficulties in identifying AMF based on intraradical structures. Therefore, the aim of this study was to evaluate the AMF community structure in sugarcane rhizosphere and roots under two harvesting managements, based on spores in the soil and sequencing of 18S rRNA gene clones, respectively. Sugarcane rhizosphere soil and roots were sampled from three varieties, under two harvesting managements: without pre-harvesting burning and with pre-harvesting burning, at an experimental field located in Novo Horizonte (São Paulo, Brazil). Three approaches were used to identify AMF inside the roots: (1) using fungi-specific primers, (2) using AMF-specific primers and (3) using AMF group-specific primers. The number of spores in the soil, the observed and estimated species richness and the diversity of AMF spores in the treatments without and with pre-harvesting burning were not statistically different. Statistically significant effects of sugarcane varieties or the interaction of the factors Harvesting Management and Varieties were not observed. Ordination analysis based on the identified spores did not show clustering by treatments. However, intraradical root colonization rates were higher in the treatment without pre-harvesting burning, as compared to the treatment with pre-harvesting burning. These data indicate that intraradical colonization rate may be used as a more sensitive indicator of environmental changes due to harvesting management, as compared to the other indicators evaluated. The use of fungi-specific, AMF-specific and AMF group-specific primers did not allow the detection of Glomeromycota in the sugarcane roots sampled from the field experiment. Nonetheless, the fungal communities associated with sugarcane roots detected by 18S rRNA gene clone sequencing were evaluated. The results indicate that the fungal communities associated with sugarcane roots from the treatments without and with pre-harvesting burning were statistically different, even though no differences in operational taxonomic unit richness and diversity indices were observed. In general, additional studies are necessary to optimize AMF 18S rRNA gene amplification for a better understanding of their ecology.

Der Einfluss unterschiedlich aggressiver Fusarium culmorum- und F. graminearum-Isolate auf die Schadbildausprägung bei Winterweizen sowie die Möglichkeit der Befallskontrolle mit Mykorrhiza Die durch Pilzarten der Gattung Fusarium spp. hervorgerufene partielle Taubährigkeit ist ein ernstes Problem im weltweiten Weizenanbau. Eine für die Schaderreger günstige feuchte Witterung zum Zeitpunkt der Weizenblüte in Kombination mit befallsfördernden agrotechnischen Maßnahmen löst immer wieder Epidemien aus. Hauptsächlich verursacht durch F. culmorum und F. graminearum führt eine Erkrankung zu Ertrags- und Qualitätseinbußen sowie zu einer Belastung des Ernteguts mit Mykotoxinen, die bereits in niedrigen Konzentrationen toxisch auf den tierischen und menschlichen Organismus wirken. Die am häufigsten vorkommenden Fusarium-Toxine in Weizen sind Deoxynivalenol (DON) und Zearalenon (ZEA). Isolate von F. graminearum- und F. culmorum können in ihrem DON- und ZEA-Bildungsvermögen und ihrem Potential, Nekrosen zu verursachen, stark variieren. In Laborversuchen (in vitro) wurden F. graminearum- und F. culmorum-Isolate hinsichtlich dieser Eigenschaften (hier als Aggressivität bezeichnet) charakterisiert und anschließend wurde im Feldversuch überprüft, ob die in vitro-ermittelte Aggressivität die Schadbildausprägung bei Weizenpflanzen beeinflusst. Nur im ersten Versuchsjahr, das durch hohe Niederschläge gekennzeichnet war, konnte ein Einfluss der Aggressivität und einer zusätzlichen Beregnung im Feldversuch nachgewiesen werden. Die als hoch-aggressiv eingestuften Fusarium-Isolate reduzierten unter dem Einfluss der Beregnung den Ertrag und das Tausendkorngewicht. Die Beregnung führte zu einer Erhöhung des Pilzwachstums und der DON- und ZEA-Produktion. Ein extrem trockener Sommer verhinderte die Infektion der Weizenpflanzen durch die beimpften Fusarium-Isolate und ein anschließendes Pilzwachstum in den Ähren im zweiten Versuchsjahr. Um den Befall von Weizenpflanzen mit Fusarium spp. vorzubeugen, stehen verschiedene pflanzenbauliche Maßnahmen zur Verfügung. Eine Möglichkeit stellen in diesem Zusammenhang die symbiotischen Mykorrhizapilze (MP) dar. Die Pilze sind in der Lage, Pflanzen zu stärken und antagonistisch auf pilzliche Schaderreger zu wirken. Um zu überprüfen, ob MP dazu beitragen könnten, den Befall von Weizenpflanzen mit Fusarium spp. niedrig zu halten, wurden Weizenpflanzen mit MP und Fusarium spp. beimpft und die Auswirkungen der Interaktionen auf die Weizenpflanzen in einem Klimakammer- und einem Feldversuch getestet. In der Klimakammer wurde eine Reduzierung des Fusarium-Befalls nachgewiesen. Die mykorrhizierten Weizenpflanzen wiesen außerdem höhere Photosyntheseraten, höhere Sprosstrockenmassen und mehr Ähren im Vergleich zu den nicht-mykorrhizierten und mit Fusarium-beimpften Weizenpflanzen auf. Insgesamt wurde durch die Mykorrhizierung der negative Einfluss von Fusarium spp. kompensiert. Im Freiland konnte kein Einfluss der MP auf Fusarium spp. beobachtet werden. Im ersten Versuchsjahr führte das Beimpfen der Weizenpflanzen mit MP zu höheren Wurzel- und Sprosstrockenmassen sowie zu höheren Tausendkorngewichten im Vergleich zu den mit Fusarium spp.-beimpften Weizenpflanzen. Im zweiten Versuchsjahr konnte dieses Ergebnis nicht wiederholt werden. / Impact of aggressiveness of Fusarium culmorum and Fusarium graminearum isolates on the degree of symptoms as well as the possibility to control Fusarium spp. with mycorrhiza Fusarium Head Blight (FHB) is a serious problem worldwide and is mainly caused by Fusarium (F). culmorum and F. graminearum. Humid weather conditions, especially at anthesis and agricultural measures forcing pathogen attack cause epidemics repeatedly. FHB leads to yield and quality losses and also to contamination of harvest with mycotoxins that are toxic to humans and animals already in low concentrations. The most frequently occurring Fusarium toxins in wheat are deoxynivalenol (DON) and zearalenone (ZEA). F. culmorum and F. graminearum isolates can differ in their potential to produce mycotoxins and to cause necrosis. Isolates of these two species were assigned to three different groups of aggressiveness on the basis of mycotoxin production and necrotic activity. Afterwards these isolates were inoculated on wheat in fields to ascertain their aggressiveness on the degree of symptoms. Only in the first year of the trial that was characterized by high precipitation amounts an influence of the aggressiveness and of an additional irrigation could be determined. Influenced by irrigation isolates of high aggressiveness reduced yield and 1000-kernel-weight. Besides, irrigation led to an increase of fungal growth and DON and ZEA production. An extremely dry summer in the second year of the trial prevented wheat infection by Fusarium isolates and subsequent colonization of the ears. Various agricultural measures are available to prevent Fusarium infection. The release of mycorrhizal fungi is one possibility. These fungi are able to strengthen plants and affect fungal pathogens antagonistically. Mycorrhizal fungi and Fusarium isolates were inoculated on wheat plants in climate chamber and fields to determine their potential for pest management. The impact of the interactions of these two organisms on wheat plants was analyzed. In climate chamber a reduction of Fusarium colonization was observed. Furthermore a higher rate of photosynthesis, a higher shoot dry weight and a higher number of ears were detected for the mycorrhizal plants compared to the non-mycorrhizal Fusarium inoculated plants. Altogether the negative effects of Fusarium spp. on the wheat plants were compensated by mycorrhizal colonization. In fields no influence of mycorrhizal colonization on Fusarium spp. could be determined. In the first year of the trial inoculation of wheat plants with mycorrhiza led to higher root and shoot dry weight as well as to higher 1000-kernel-weight in comparison to the wheat plants inoculated with Fusarium spp. These results could not be reproduced in the second year of the trial.

Green roof design has proceeded without integration of arbuscular mycorrhizal fungi (AMF). A literature survey was therefore conducted in order to determine which aspects of green roof functioning might be enhanced by AMF, and subsequently levels of AMF and endophyte colonization were determined for seven plant species used in green roofs. Plants were sampled from an experimental green roof and from the field. A commercial growing medium was also tested for AMF inoculum potential. Colonization was poor in both field and rooftop samples of the commercially popular succulent, Sedum acre, but significantly higher in Solidago bicolor, a proposed green roof species. The commercial growing medium was found to contain extremely low levels of viable AMF propagules. Although the apparent lack of mycorrhizal dependency of S. acre helps to explain its popularity as a green roof plant, its overuse precludes the important ecosystem services potentially provided by AMF symbioses.

AM plants acquire Pi via two pathways; the direct uptake pathway via plant roots and the AM pathway via external fungal hyphae and colonised cortical cells. It has been assumed that these two pathways are additive and therefore in non-responsive plants the AM pathway is often considered to be non-functional. However, data from ³²P uptake studies indicates that the AM pathway is functional in many non-responsive symbioses and in some instances supplies the majority of plant P. In recent years the high-affinity Pi transporters involved in both direct and AM Pi uptake pathways have been identified. They are expressed at the root epidermis and the symbiotic interface of colonised cortical cells and respond to the P and AM status of the plant. The overall objective of the work described in this thesis was to characterise Pi uptake via the AM pathway in barley, a non-responsive AM host, using an approach which integrated physiological measurements of plant responsiveness and AM contribution with investigations of gene expression and functional characterisation of the plant Pi transporters. A preliminary survey of field-grown barley demonstrated the persistence of AM colonisation under commercial cropping regimes in southern Australia and highlighted the relevance of AM studies to commercial agriculture. Under glasshouse conditions AM colonisation of barley induced depressions in growth and P uptake compared to NM controls. Growth depressions were unrelated to percent colonisation by two AM fungal species and could not readily be explained by fungal C demand; the strong correlation between growth and P content suggested that P was the limiting factor in these experiments. However, a compartmented pot system incorporating ³²P-labelling demonstrated that the AM pathway is functional in colonised barley and, in the interaction with G. intraradices, contributed 48% of total P. This suggested that P flux via the direct uptake pathway is decreased in AM barley. The expression of three Pi transporters, HvPT1, HvPT2 and HvPT8 was investigated in colonised roots. HvPT1 and HvPT2 have previously been localised to the root epidermis and root hairs and are involved in Pi uptake via the direct pathway whilst HvPT8 is an AM-inducible Pi transporter which was localised by in-situ hybridisation to colonised cortical cells. Using promoter::GFP gene fusions the localisation of HvPT8 to arbuscule-containing cortical cells was confirmed in living roots from transgenic barley. Quantitative real-time PCR analysis of the expression of these three Pi transporters indicated that HvPT1 and HvPT2 were expressed constantly, under all conditions regardless of AM colonisation status and indicated that decreased P flux via the direct pathway is not related to expression of these transporters. HvPT8 was induced in AM colonised roots. However, the level of expression was not related to flux via the AM pathway or arbuscular colonisation. The HvPT8 transporter was further characterised by constitutive over-expression in transgenic barley. ³²P uptake assays in excised roots demonstrated increased Pi uptake from low P solution compared to wild-type roots and confirmed that HvPT8 is a functional Pi transporter with high-affinity transport properties. This is the first report of characterisation of an AM-inducible Pi transporter in planta. When these transgenic plants were grown in solution culture there was no increase in growth or P uptake relative to wild-type or transgenic controls and growth in soil and AM colonisation were also unaffected in these transgenic lines. The data presented in this thesis highlights the importance of combined physiological and molecular approaches to characterising plant AM interactions. The persistence of AM colonisation in barley in the field indicates the importance of improving our understanding of symbiotic function in non-responsive plants. Future efforts should be directed towards understanding the signals which regulate P flux via both the direct and AM pathways with the ultimate aim of enhancing AM responsiveness of non-responsive species. Making the direct and AM pathways additive in nonresponsive species should be a key aim of future research. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1313311 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2008

AM plants acquire Pi via two pathways; the direct uptake pathway via plant roots and the AM pathway via external fungal hyphae and colonised cortical cells. It has been assumed that these two pathways are additive and therefore in non-responsive plants the AM pathway is often considered to be non-functional. However, data from ³²P uptake studies indicates that the AM pathway is functional in many non-responsive symbioses and in some instances supplies the majority of plant P. In recent years the high-affinity Pi transporters involved in both direct and AM Pi uptake pathways have been identified. They are expressed at the root epidermis and the symbiotic interface of colonised cortical cells and respond to the P and AM status of the plant. The overall objective of the work described in this thesis was to characterise Pi uptake via the AM pathway in barley, a non-responsive AM host, using an approach which integrated physiological measurements of plant responsiveness and AM contribution with investigations of gene expression and functional characterisation of the plant Pi transporters. A preliminary survey of field-grown barley demonstrated the persistence of AM colonisation under commercial cropping regimes in southern Australia and highlighted the relevance of AM studies to commercial agriculture. Under glasshouse conditions AM colonisation of barley induced depressions in growth and P uptake compared to NM controls. Growth depressions were unrelated to percent colonisation by two AM fungal species and could not readily be explained by fungal C demand; the strong correlation between growth and P content suggested that P was the limiting factor in these experiments. However, a compartmented pot system incorporating ³²P-labelling demonstrated that the AM pathway is functional in colonised barley and, in the interaction with G. intraradices, contributed 48% of total P. This suggested that P flux via the direct uptake pathway is decreased in AM barley. The expression of three Pi transporters, HvPT1, HvPT2 and HvPT8 was investigated in colonised roots. HvPT1 and HvPT2 have previously been localised to the root epidermis and root hairs and are involved in Pi uptake via the direct pathway whilst HvPT8 is an AM-inducible Pi transporter which was localised by in-situ hybridisation to colonised cortical cells. Using promoter::GFP gene fusions the localisation of HvPT8 to arbuscule-containing cortical cells was confirmed in living roots from transgenic barley. Quantitative real-time PCR analysis of the expression of these three Pi transporters indicated that HvPT1 and HvPT2 were expressed constantly, under all conditions regardless of AM colonisation status and indicated that decreased P flux via the direct pathway is not related to expression of these transporters. HvPT8 was induced in AM colonised roots. However, the level of expression was not related to flux via the AM pathway or arbuscular colonisation. The HvPT8 transporter was further characterised by constitutive over-expression in transgenic barley. ³²P uptake assays in excised roots demonstrated increased Pi uptake from low P solution compared to wild-type roots and confirmed that HvPT8 is a functional Pi transporter with high-affinity transport properties. This is the first report of characterisation of an AM-inducible Pi transporter in planta. When these transgenic plants were grown in solution culture there was no increase in growth or P uptake relative to wild-type or transgenic controls and growth in soil and AM colonisation were also unaffected in these transgenic lines. The data presented in this thesis highlights the importance of combined physiological and molecular approaches to characterising plant AM interactions. The persistence of AM colonisation in barley in the field indicates the importance of improving our understanding of symbiotic function in non-responsive plants. Future efforts should be directed towards understanding the signals which regulate P flux via both the direct and AM pathways with the ultimate aim of enhancing AM responsiveness of non-responsive species. Making the direct and AM pathways additive in nonresponsive species should be a key aim of future research. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1313311 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2008

I have studied arbuscular mycorrhizal symbiosis of 44 herbaceous invasive neophytes occuring in the Czech Republic. My results show that about 70% of the examined species are capable to form symbiotic association with arbuscular mycorrhizal fungi (AMF) in the field. To my knowledge, mycorrhizal status of 23 invasive species is reported here for the first time. I predicted, based on the hypothesis of Urcelay & Díaz (2003), that the intensity of AMF in the roots of invasive species will be correlated with that of the native dominant species of invaded plant community, but collected data did not support this hypothesis. In addition, the effects of habitat and community characteristics on the intensity of AMF colonization of the invasive species{\crq} roots were tested. My results show that, at the within-species level, plants in the habitats with higher light and temperature conditions have less colonized roots whereas intensity of mycorrhizal colonization increases with habitat moisture. At the among-species level, invasive species occurring in the habitats with elevated nitrogen availability have higher mycorrhizal colonization of their roots. The effect of nitrogen availability is revealed at the among-species level and stays significant even after phylogenetic correction, suggesting this is an evolutionary adaptation rather than a phenotypic plasticity.

Os fungos representam cerca de 75% da biomassa microbiana em áreas florestais, desempenhando funções importantes, desde a mineralização dos resíduos orgânicos até a disponibilização de nutrientes para plantas por meio das associações micorrízicas, o que influencia a ciclagem de nutrientes e, consequentemente, o crescimento das árvores. O objetivo desse trabalho foi avaliar a comunidade de fungos do solo, da rizosfera e do sistema radicular de Eucalyptus grandis e Acacia mangium plantados em monocultivos e em consórcio, e encontrar respostas para os padrões observados por meio da correlação com os atributos físicos, químicos, biológicos e a profundidade do solo. A coleta das amostras foi realizada na Estação Experimental de Ciências Florestais de Itatinga, em 2016, quando as plantas estavam com 2 anos de idade. Foram coletadas amostras em quatro tratamentos: monoculturas de E. grandis e de A. mangium e consórcios de E. grandis e de A. mangium, nos quais foram construídas trincheiras para coleta das amostras nas camadas de 0-10, 10-20, 20-50 e 50-100 cm de profundidade. Foram caracterizados os atributos físicos e biológicos do solo e os atributos químicos do solo, da rizosfera e das raízes. Para a avaliação micorrízica, foi quantificado o número de esporos de fungos micorrízicos arbusculares (FMA) e as taxas de colonização radicular por FMA e por fungos ectomicorrízicos. Foi avaliada a morfologia das estruturas das micorrizas arbusculares e ectomicorriza (ECM). A estrutura da comunidade de fungos do solo e da rizosfera foi avaliada por meio da técnica de Terminal restriction fragment length polymorphism (T-RFLP). Para isso, o DNA foi amplificado utilizando os primers ITS1f-FAM e ITS4 e a restrição dos fragmentos foi realizada com a enzima HaeIII. A abundância de cópias do gene ITS do solo e da rizosfera foi quantificada por PCR quantitativo (qPCR), utilizando os primers ITS1f e 5.8s. Os atributos físicos, químicos e biológicos tiveram poucas variações entre os tratamentos avaliados, sendo as maiores diferenças encontradas entre as profundidades. O número de esporos (<29) e as taxas de colonização micorrízica (<48%) foram baixos em todos os tratamentos, e se reduziram com o aumento da profundidade. As plantas de A. mangium não formaram micorrizas arbusculares. Nas raízes de E. grandis, não houve a formação de arbúsculos, mas foi verificada a presença de hifas enroladas (hyphal coils), estrutura de micorriza do tipo Paris. A anatomia das ECM confirmou a colonização destes fungos nas raízes das plantas estudadas. O qPCR mostrou maior abundância de genes ITS na rizosfera em relação ao solo, assim como nas camadas superficiais (0-10 cm) em relação às mais profundas (10 cm abaixo). A Análise de Coordenadas Principais revelou diferenças na estrutura das comunidades de fungos nos tratamentos estudados, principalmente para a região da rizosfera, diferenciando o perfil de fungos do monocultivo de E. grandis dos demais tratamentos, assim como a influência da A. mangium na estruturação da comunidade. A análise de redundância mostrou a influência de alguns atributos químicos nas taxas de colonização e estruturação da comunidade. Dessa forma, conclui-se que em sistema de consórcio, uma espécie de planta parece ser mais influente do que a outra na estruturação da comunidade de fungos e essa influência é mais evidente na rizosfera. Além disso, os atributos químicos são fatores importantes na organização da comunidade fúngica. / The fungi represent about 75% of the microbial biomass in forest areas, performing important functions, from the mineralization of the organic residues to the availability of nutrients to plants through mycorrhizal associations, which influences the nutrient cycling and, consequently, the growth of trees. The objective of this work was to evaluate the community of fungi of the soil, rhizosphere and root system of Eucalyptus grandis and Acacia mangium planted in monocultures and consortium, and to find explanations for the observed patterns through the correlation with physical and chemical soil attributes and soil depth. The samples were collected at the Experimental Station of Forest Sciences of Itatinga in 2016, when the plants were 2 years old. Samples were collected in four treatments: monocultures of E. grandis and A. mangium and consortia of E. grandis and A. mangium, in which trenches were constructed to collect samples in the 0-10, 10-20, 20 -50 and 50-100 cm deep. The physical and biological attributes of the soil and the chemical attributes of soil, rhizosphere and roots were characterized. For the mycorrhizal evaluation, the number of spores of arbuscular mycorrhizal fungi (AMF) and the rates of root colonization by AMF and ectomycorrhizal fungi were quantified. The morphology of arbuscular mycorrhizal and ectomycorrhizal (ECM) structures was evaluated. The structure of the soil and rhizosphere fungi community by was evaluated by the technique of Terminal restriction fragment length polymorphism (T-RFLP). For this, the DNA was amplified using primers ITS1f-FAM and ITS4 and restriction of the fragments was performed with the enzyme HaeIII. The abundance of ITS gene copies of soil and rhizosphere was quantified by quantitative PCR (qPCR), using primers ITS1f and 5.8s. The physical, chemical and biological attributes had few variations among the evaluated treatments, being the greatest differences found between the depths. The number of spores (<29) and mycorrhizal colonization rates (<48%) were low in all treatments, and reduced with increasing depth. A. mangium plants did not form FMA. In the roots of E. grandis, there was no formation of arbuscules, but we found the presence of hyphal coils, mycorrhizal structures of the Paris type. The anatomy of the ECM confirmed the colonization of these fungi in the roots of the studied plants. The qPCR showed higher abundance of ITS genes in the rhizosphere in relation to the soil, as well as in the superficial layers (0-10 cm) in relation to the deeper ones (10 cm below). The Principal Coordinates Analysis revealed differences in the structure of the fungal communities in the treatments studied, especially for the rhizosphere region, differentiating the fungal profile of the E. grandis monoculture from the other treatments, as well as the influence of A. mangium on the structure of the community. The redundancy analysis showed the influence of some chemical soil attributes on the rates of colonization and community structuring. Thus, it is concluded that in a consortium system, one plant species seems to be more influential than the other in structuring the fungal community, and this influence is more evident in the rhizosphere. In addition, chemical attributes are important factors in the organization of the fungal community.

Thesis (M.Sc. (Horticulture)) -- University of Limpopo, 2017 / Refer to document / National Research Foundation of South Africa, and Agricultural Research Council-Universities Collaboration Centreꞌ for scholarship and research

京都大学 / 0048 / 新制・課程博士 / 博士(地球環境学) / 甲第22022号 / 地環博第186号 / 新制||地||96(附属図書館) / 京都大学大学院地球環境学舎地球環境学専攻 / (主査)准教授 岡田 直紀, 教授 舟川 晋也, 准教授 真常 仁志 / 学位規則第4条第1項該当 / Doctor of Global Environmental Studies / Kyoto University / DGAM

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