Presented diploma thesis focuses on a new type of lightweight polyurethane foam (PUR), which has been manufactured with the intention of it being biodegradable within currently valid norms on biodegradation of plastic materials. The future use of said polyurethane foam is as carrier for odor repellent to avoid wildlife-vehicle collisions in agriculture landscape, where, after the end of its lifespan it could be left to biodegrade in soil the environment. The examined material, PUR BIO-10, was tested for biodegradability in laboratory microcosms according to standardized method ASTM D5988-03. Biodegradability was tested in two separate soil types - forest soil and agricultural soil, which have been selected with the future use of the material in mind. According to the method biodegradability was measured as mineralization of the material by capturing evolved carbon dioxide. Two trials with different treatments were executed. In the first trial the material was introduced directly into the soil and in the second trial the material was tested in a litterbag to avoid soil contamination which was problematic for further analysis. During the first trial, after 90 days, the mineralization of polyurethane foam was 10.65 ± 2.54 % in the forest soil and 20.48 ± 9.18 % in the agricultural soil. During the...

Microbial communities play important roles in human health and disease, are essential components of terrestrial and marine ecosystems, and are crucial for producing commercially valuable molecules in industrial processes. These communities consist of hundreds of species involved in complex interactions. Mapping the interrelationships between different species in a microbial community is vital for understanding and controlling ecosystem structure and function. Advances in sequencing and other omics technologies have led to thousands of datasets containing information about microbial composition, gene expression, and metabolism in microbial communities associated with human hosts and other environments. These provide valuable information in understanding how microbes interact with each other and how their interactions affect the health of their host (e.g., human or plant). Furthermore, understanding these interactions paves the way for the rational design and modulation of synthetic communities for producing antibiotics, biofuels, and pharmaceutical products. The first part of my thesis is focused on improving the workflow for the inference of microbial co-occurrence relationships from abundance data. Toward this goal, we developed Microbial Co-occurrence Network Explorer (MiCoNE), a pipeline that infers microbial co-occurrences from 16S ribosomal RNA (16S rRNA) amplicon data. This pipeline involves numerous complex steps that require specific tools and parameter choices, posing open questions about the robustness and uniqueness of the inferred networks. Through MiCoNE, we systematically analyzed how these choices of tools affect the final network and proposed guidelines on appropriate tool selection for a particular dataset. We envisage that this pipeline could be used to integrate multiple datasets and generate comparative analyses and consensus networks that can guide our understanding of microbial community assembly in different biomes. The second part of my thesis focuses on microbe-host interactions rather than microbe-microbe associations. In particular, we sought to predict the effects of microbial metabolites on human receptors and their associated regulatory pathways. We specifically focus on the Aryl hydrocarbon receptor (AHR), a ligand-mediated transcription factor involved in tumorigenesis. In this project, we aimed to systematically predict the binding of diverse microbial metabolites secreted from microorganisms found in the human oral microbiome to the AHR to identify links between the microbiome and cancer initiation. We further build a mathematical model of the AHR regulatory pathway and model the effects of ligand binding on downstream molecules. We envision that these methods could be used to predict the impact of microbial dysbioses on human regulatory pathways. In the final part of my thesis, we turn to the question of whether computational algorithms can help control microbial community growth to achieve specific objectives. In particular, we describe the development of a reinforcement learning algorithm to learn optimal environmental control strategies to steer a microbial community towards a certain goal, such as reaching a specific taxonomic distribution or producing desired metabolites. We train the reinforcement learning framework through community-level simulations of genome-scale metabolic models (GEMs) for different microbial species in bioreactor systems. In this project, we simulate a simple case study with two auxotrophic mutants to verify the algorithm's validity. Ultimately we aim to simulate the implementation of the algorithm in experimental bioreactor systems. Overall, the work presented in this thesis demonstrates how microbe-microbe and microbe-environment (including microbe-host) interactions represent plastic system-level properties whose understanding can help unravel the role of microbial communities in specific diseases. Correspondingly, manipulating these interactions, e.g., by appropriately modifying environmental conditions, can serve as a promising strategy for steering communities towards desired states, including producing valuable molecular products. / 2024-11-06T00:00:00Z

Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.

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Soil microorganisms are primarily limited by carbon (C) availability. The majority of C entering belowground food webs comes directly from local flora. Plant derived labile C compounds affect microbial community structure and function, which in turn drive ecosystem function. Research has focused on dissolved organic C (DOC) from litter leachates and root exudates. These compounds are often readily assimilable by soil microorganisms and are precursors for stable soil organic matter formation. Due to diffusion limitation DOC rarely travels far beyond its origin, meaning most soil microorganisms are unable to access these compounds unless they are located near the C source. However, recent studies have illuminated the importance of volatile organic compounds (VOCs) in soil ecosystems. VOCs are produced in abundance and, as vapors, they are able to travel through soil more rapidly than DOC. This dissertation aims to investigate the importance of VOCs commonly produced during the decomposition of leaf litter. We used three separate microcosm experiments to answer the following questions. 1) How do abundant VOCs affect microbial activity in soil? 2) How do VOCs affect nitrogen (N) transformations and the microbes associated with N transformations? 3) How do VOCs affect microbial community composition? 4) Are VOCs from decomposing litter incorporated into soil C pools? In chapter 2, we show that methanol and acetone – common litter derived VOCs – increase microbial activity and labile soil C, while also decreasing available nitrate, and ammonia oxidizing archaea. Interestingly, this decrease in nitrifiers did not affect nitrification rate after VOC addition was ceased. In chapter 3, we demonstrate that soil microbial taxa respond differently to DOC and VOCs at different soil moisture levels. Specifically, DOC primarily affected taxa abundance in wetter soils, while the insoluble VOC α-pinene had the largest impact at lower moisture levels, and methanol affected abundance at all moisture levels. Finally, in chapter 4, we demonstrate that VOCs from decomposing leaf litter altered soil bacterial and fungal communities, and VOC derived C entered all measured soil organic matter pools without direct contact between decomposing litters and the soil. This work demonstrates the importance of VOCs on soil microbial communities and ecosystem function. The VOC induced increase in microbial activity, and the effects of VOCs at low moisture levels suggest that VOCs may function in the bulk soil in a manner similar to DOC in rhizosphere soil. Additionally, the incorporation of VOC-C into soil organic matter pools identifies a hitherto unrecognized mechanism for soil organic matter formation. / Doctor of Philosophy / Soil microorganisms live in an environment where their access to carbon containing compounds limits their growth. In these belowground environments most of the carbon flows from aboveground plant matter through soil microbes into the organisms that consume those microbes. The carbon from plants not only feeds the soil microbes but also changes the type of microbes and how those microbes process important chemicals in the environment – e.g., carbon and nitrogen. Previously, research has focused on carbon compounds that are able to dissolve in water. Often, these compounds originate from liquids that plants release from their roots, or dissolve like tea when leaves are soaked in water. Soil microorganisms can often use these dissolved carbon compounds and directly incorporate them into their biomass. Additionally, these compounds can be stored in soil - sequestering that carbon in the soil, potentially long term. However, dissolved compounds are unable to move very quickly through soil, and the soil microorganisms that live far from the source of these compounds do not have access to them. However, recent studies have found that another form of carbon, volatile organic compounds, are also produced in abundance in the soil environment. These compounds can travel through the air in the soil, as well as in the soil water. When in the air, VOCs travel very quickly and can also travel farther than dissolved compounds. This dissertation aims to investigate the importance of volatile organic compounds that are produced during the decomposition of leaves. We carried out three experiments using small volumes of soil under controlled conditions in the laboratory. We aimed to answer the following questions. 1) How do abundant volatile organic compounds affect microbial activity in soil? 2) How do volatile organic compounds affect microbial processing of nitrogen containing compounds, and the populations of microorganisms that process those compounds? 3) How do volatile organic compounds affect the composition of microorganism in the soil? 4) Are volatile organic compounds from decomposing leaves able to be stabilized in the soil. In chapter 1, we show that methanol and acetone – common volatile compounds produced during the decomposition of leaves– increase microbial activity, and microbial available carbon in soil. Methanol and acetone also decreased available nitrate (an important N containing compound) and a group of organisms that produce nitrate called ammonia oxidizing archaea. Interestingly, once we stopped adding methanol and acetone to the soil the production of nitrate did not differ, meaning that the nitrate producing community was able to recover from the reduction in ammonia oxidizing archaea. In chapter 2, we demonstrated that soil microbial taxa respond differently to dissolved carbon and volatile organic compounds across a gradient of soil moisture. Specifically, dissolved carbon primarily affected taxa abundance in wetter soils, while the insoluble volatile α-pinene had the largest impact at lower moisture levels, and the volatile compound methanol affected abundance of microbial taxa at all moisture levels. Finally, in chapter 3, we demonstrate that volatile organic compounds produced during the decomposition of leaves altered the composition of both bacterial and fungal communities in the soil. Also, and possibly most interestingly, carbon from those volatile organic compounds was stored in all of the pools of carbon that we measured. Together these chapters demonstrate the importance of volatile organic compounds on soil microbial communities and ecosystem function. Since volatile organic compounds induced an increase in microbial activity we are able to infer that soil microorganisms are using these compounds; paired with our observation that volatile organic compounds affected microbial taxa at lower moisture levels than the dissolved compounds did, we can infer that volatile compounds may function as a carbon source in parts of the soil that do not have access to dissolved carbon. Additionally, the incorporation of carbon from volatile organic compounds into soil identified a hitherto unrecognized mechanism for soil carbon sequestration.

Yes / A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term ‘community’ is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of ‘Who is there?’ and ‘What are they doing?’ to the mechanistically driven question of ‘How will they respond?’

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Master of Science / Department of Plant Pathology / Karen A. Garrett / Ari Jumpponen / Traditional fallow periods in the Bolivian highlands are being shortened in an effort to increase short-term crop yields, with potential long-term impacts on soil communities. Using 454-pyrosequencing, we characterized fungal and bacterial community responses to (1) the length of fallow period and (2) the presence of the plants Parasthrephia sp. or Baccharis sp. (both locally known as ‘thola’). Thola is widely considered by farmers as beneficial to soil health, although it is also frequently harvested as a source of fuel by farmers. Soils in one study area, Ancoraimes, had higher levels of organic matter, nitrogen and other macronutrients compared to the other study area, Umala. In our analyses, Ancoraimes soils supported more diverse fungal communities, whereas Umala had more diverse bacterial communities. Unexpectedly, the longer fallow periods were associated with lower fungal diversity in Umala and lower bacterial diversity in Ancoraimes. Fungi assigned to genera Verticillium, Didymella, and Alternaria, and bacteria assigned to genera Paenibacillus, Segetibacter, and Bacillariophyta decreased in abundance with longer fallow period. The presence of thola did not significantly affect overall soil fungal or bacterial diversity, but did increase the frequency of some genera such as Fusarium and Bradyrhizobium. Our results suggest that fallow period has a range of effects on microbial communities, and that the removal of thola from the fields impacts the dynamics of the soil microbial communities.

Atividades humanas podem causar degradação e impedir que serviços ambientais cheguem á sociedade. Evitá-la demanda constante monitoramento, que pode ser realizado com indicadores ambientais. Buscamos selecionar indicadores da exploração de petróleo nas comunidades microbianas de riachos da Amazônia, Mata Atlântica, Cerrado e Caatinga. Avaliamos as diversidades taxonômica (Sequenciamento 16S) e funcional (GeoChip 5.0M) e comparamos os resultados de amostras de água, sedimento, biofilme e solo das margens de riachos influenciados por campos de petróleo com áreas de referência. Todas as estações apresentaram alta riqueza, baixa similaridade taxonômica e alta similaridade funcional. Impactos da atividade de exploração de petróleo foram relacionados ao uso do solo e não à contaminação por hidrocarbonetos, já que as estações não tinham histórico de vazamentos. Os indicadores identificados não foram atreldos a grupos taxonômicos ou atividades metabólicas específicas, sendo mais promissora a utilização de um conceito baseado em sequencias genéticas indicadoras. / Human activities can cause degradation and prevent environmental services from reaching society. Avoid it demand constant monitoring, which can be carried out with environmental indicators. We sought to select indicators of oil exploration in the microbial communities of streams in the Amazon, Atlantic Forest, Cerrado and Caatinga morphoclimatic domains. We evaluated taxonomic (16S Sequencing) and functional (GeoChip 5.0M) diversity and compared the results from water, sediment, biofilm and soil (from the margins of streams) samples influenced by oil fields with reference areas. All of them presented high richness, low taxonomic similarity and high functional similarity. Impacts of the oil exploration activity are related to the use of soil and not to hydrocarbon contamination, since the sampling stations we choose are historically not affected by oil spills. The indicators we identified are not related to taxonomic groups or specific metabolic activities, and the use of a concept based on indicator sequences is more promising.