Microbiome | EPFL Graph Search

A microbiome () is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al., but supplemented with two explanatory paragraphs. The first explanatory paragraph pronounces the dynamic character of the microbiome, and the second explanatory paragraph clearly separates the term microbiota from the term microbiome. The microbiota consists of all living members forming t

Improved framework to estimate travel time and derived distributions in hydrological control volumes

Mitra Asadollahi

Crossing properties of soil saturation, defined as the duration and excursion of soil saturation below and above certain thresholds, are key variables to ecosystem functioning and evolution by primarily influencing the plant and soil microbes physiological dynamics. Under climate change, the variability in the precipitation patterns is expected to be more ubiquitous and directly translate to a shift in soil saturation levels. This, in turn, will influence crossing properties of soil saturation and thus be expected to leave a mark on ecosystems. However, the lack of a deep understanding of the links between biological processes and the change in soil saturation patterns hinders foretelling the impact of climate variability on ecohydrological systems even at the smallest scale, that is, the level of a single plant.To that end, this thesis presents experimental results from laboratory soil column experiments and extensive computational studies on the interactions between soil saturation and biological activities, that is, plants and microbes. To this aim, the depth-time soil saturation patterns are mapped by means of modeling the transport processes of relevance and experimental tools at a minimal hydrological control volume in search for upscaling methods. In this context, two modeling approaches can be employed. Physically based models that explicitly represent transport processes with high costs of application at larger scales. Age-based models that rely on generic functions with a focus on time past since arrival, that is, the age of event water in the storage. This thesis work combines models (HYDRUS-1D as physically based and tran-SAS as age-based) with soil column experimental data and Bayesian inference methods to explore the links between age characteristics and transport processes. In this thesis, data from four different experimental designs on monthly to yearly timescale under varied environmental conditions are examined in terms of tracer type, precipitation pattern, vegetation, soil type, resolution and type of collected data. Of the modeled data, two sets of results from specific experiments were carried out within the framework of this thesis.This thesis addresses also the role of the balance between dispersive and convective forces, known as Péclet number, in controlling the shape of age functions in drainage. While sole reliance on drainage flow and tracer data (reflective of Péclet number) suffice to capture age dynamics in drainage, un- certainties may arise for predictions on (evapo)transpiration. This thesis deals also with the role of root distributions as controls in determining the age to root uptake and shows plants with similar uniform-equivalent root distribution render very similar age dynamics. It was shown in this thesis that nitrate consumption by microbes can be linked to age characteristics of a conservative tracer and that the relation between microbial respiration and soil saturation may bear more complexity than is currently integrated in most models. Overall, this thesis lays steps to the development of modeling tools with high predictive power for soil saturation by originating upscaling methods and bridging the gaps between physically based and age-based models with a view on the consequences of (possi- bly changing) variable soil saturation on adaptations of microbial communities and their metabolic product.

EPFL2022

Influence of Microplastics on Microbial Structure, Function, and Mechanical Properties of Stream Periphyton

Renata Behra, Kristin Schirmer, Ahmed Tlili

Periphyton is a freshwater biofilm composed of prokaryotic and eukaryotic communities that occupy rocks and sediments, forming the base of the food web and playing a key role in nutrient cycling. Given the large surface that periphyton comprises, it may also act as a sink for a diverse range of man-made pollutants, including microplastics (MP). Here we investigated the effect of 1-4 mu m and 63-75 mu m sized, spherical polyethylene MP with native and ultraviolet (UV)-weathered surface on developing natural stream periphyton communities over 28 days. In order to ensure proper particle exposure, we first tested MP suspension in water or in water containing either Tween 80, extracellular polymeric substances - EPS, fulvic acids, or protein. We found the extract of EPS from natural periphyton to be most suitable to create MP suspensions in preparation of exposure. Upon exposure, all tested types of MP were found to be associated with the periphyton, independent of their size and other properties. While biomass accrual and phenotypic community structure of the photoautotrophs remained unchanged, the prokaryotic and eukaryotic communities experienced a significant change in composition and relative abundances. Moreover, alpha diversity was affected in eukaryotes, but not in prokaryotes. The observed changes were more prominent in periphyton exposed to UV-treated as compared with native surface MP. Mechanical properties, as assessed by compression rheology, showed that MP-exposed periphyton had longer filamentous streamers, higher stiffness, lower force recovery and a higher viscoelasticity than control periphyton. Despite the observed structural and mechanical changes of periphyton, functional parameters (i.e., photosynthetic yield, respiration and nutrient uptake efficiencies) were not altered by MP, indicating the absence of MP toxicity, and suggesting functional redundancy in the communities. Together, our results provide further proof that periphyton is a sink for MP and demonstrate that MP can impact local microbial community composition and mechanical properties of the biofilms. Consequences of these findings might be a change in dislodgement behavior of periphyton, a propagation through the food chains and impacts on nutrient cycling and energy transfer. Hence, taking the omnipresence, high persistence and material and size diversity of MP in the aquatic environment into account, their ecological consequences need further investigation.

FRONTIERS MEDIA SA2022

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the known biochemistry based on different sets of enzymatic reaction rules. To address the complexity of the metabolic networks, elaborate methods were developed to transform them into computable graphs, navigate them, and construct the best possible pathways. However, the recent experimental research points to the new challenges and opportunities for the computational pathway design. Here, we review the most recent advances, especially in the last two years, in computational discovery of new pathways and their prospects for expanding metabolic capabilities. We draw attention to the potential ways of improvement for pathway design algorithms, including the expansion of Design-Build-Test-Learn cycle to novel compounds and reactions and the standardization for the reaction rules and metabolic reaction databases.