Microbial ecology

Microbial ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine, nose, and mouth. As a consequence of the quantitative magnitude of microbial life (calculated as 5.0e30 cells; eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, consti

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Metagenomics

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomi

Microbiome

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 microbi

Microbiology

Microbiology () is the scientific study of microorganisms, those being of unicellular (single-celled), multicellular (consisting of complex cells), or acellular (lacking cells). Microbiology encomp

Microbial diversity of aerobic granular sludge: Is it different from activated sludge?

David Gregory Weissbrodt

This common presentation was given within the Aerobic Granular Sludge Workshop organized during the IWA Biofilm Conference 2011 (Shanghai, China). The aim was to bring the state-of-the-art knowledge on the microbial diversity present in aerobic granular sludge (AGS) biofilms in comparison with the composition of flocculent activated sludge. Three main parts have been discussed. The first part focused on the bacterial ecology and dynamics during the formation of early-stage granules and then of mature granules, after start-up with flocculent activated sludge and under artificial laboratory conditions. The second part focused on the microbial community comparison of flocculent and granular sludge systems operated under real conditions and fed with raw municipal wastewater. The third part consisted in bringing knowledge on the granule formation mechanisms within an aerobic wastewater system designed for phosphorus removal. The presentation served as support for generating a discussion with the microbial ecology, biochemistry and process engineering scientists present on the following topics. From fundamental to application: To which extent is specific AGS microbial ecology knowledge required? Are there more options for microbial population engineering? Is microbial diversity the defining characteristic for granulation or are there universal microbial triggers?

2011

The porous surface model, a novel experimental system for online quantitative observation of microbial processes under unsaturated conditions

Gamze Gülez, Dani Or

Water is arguably the most important constituent of microbial microhabitats due to its control of physical and physiological processes critical to microbial activity. In natural environments, bacteria often live on unsaturated surfaces, in thin (micrometric) liquid films. Nevertheless, no experimental systems are available that allow real-time observation of bacterial processes in liquid films of controlled thickness. We propose a novel, inexpensive, easily operated experimental platform, termed the porous surface model (PSM) that enables quantitative real-time microscopic observations of bacterial growth and activity under controlled unsaturated conditions. Bacteria are inoculated on a porous ceramic plate, wetted by a liquid medium. The thickness of the liquid film at the surface of the plate is set by imposing suction, corresponding to soil matric potential, to the liquid medium. The utility of the PSM was demonstrated using Pseudomonas putida KT2440 tagged with gfp as a model bacterium. Single cells were inoculated at the surface of the PSM, and the rate at which colonies expanded laterally was measured for three matric potentials (-0.5, -1.2, and -3.6 kPa). The matric potential exerted significant influence on colony expansion rates, with a faster rate of spreading at -0.5 than at -1.2 or -3.6 kPa (diameter increase rate, ca. 1,000, 200, and 17 mu m h(-1), respectively). These differences can be attributed to cell motility, strongly limited under the most negative matric potential. The PSM constitutes a tool uniquely adapted to study the influence of liquid film geometry on microbial processes. It should therefore contribute to uncovering mechanisms of microbial adaptation to unsaturated environments.

2008

Linking bacterial population dynamics and nutrient removal in the granular sludge biofilm ecosystem engineered for wastewater treatment

Christof Holliger, Noam Shani, David Gregory Weissbrodt

Intensive nutrient removal from wastewater in anaerobic–aerobic systems using granular sludge should rely on optimal balances at biofilm and microbial ecology levels. This study targets the impacts of reactor characteristics and fluctuations in operation conditions on nutrient removal and bacterial community structures by means of microbial and numerical ecology methods. The dynamics of both predominant and accompanying populations were investigated with high resolution on temporal and phylogenetic scales in two reactors operated during 5 months with synthetic wastewater. Multivariate analyses highlighted significant correlations from process to microbial scales in the first reactor, whereas nitrification and phosphorus removal might have been affected by oxygen mass transfer limitations with no impact at population level in the second system. The bacterial community continuum of the first reactor was composed of two major antagonistic Accumulibacter-Nitrosomonas-Nitrospira and Competibacter-Cytophaga-Intrasporangiaceae clusters that prevailed under conditions leading to efficient P- (> 95%) and N-removal (> 65%) and altered P- (< 90%) and N-removal (< 60%), respectively. A third cluster independent of performances was dominated by Xanthomonadaceae affiliates that were on average more abundant at 25 °C (31 ± 5%) than at 20 °C (22 ± 4%). Starting from the physiological traits of the numerous phylotypes identified, a conceptual model is proposed as a base for functional analysis in the granular sludge microbiome and for future investigations with complex real wastewater.

Blackwell Publishing Ltd, Oxford2014

ENV-202: Microbiology for engineers

Le cours "Microbiologie pour l'ingénieur" couvre les processus microbiens principaux qui ont lieu dans l'environnement et dans des systèmes de traitement. Il présente les cycles des éléments qui sont catalysés par des microorganismes et qui ont un impact important sur la planète Terre.

ENV-103: Biology

Diversité du monde vivant, rôle et action des Procaryotes dans la biosphère. Fonctionnement biochimique des êtres vivants comprenant les voies métaboliques centrales et les fonctions des biomolécules majeures. Rôle central joué par l'information génétique, des mécanismes évolutifs et de régulation.

ENV-426: Fluvial biogeosciences

Stream and river ecosystems are increasingly deteriorated owing to global change and climate change. Students will understand basic physical, chemical and biological processes in streams and rivers, and how they relate to ecosystem health and integrity .