Earth’s oceans are predominantly cold, with nearly 90% of their volume having temperatures below 5 °C. Microorganisms commonly referred to as psychrophiles have adapted to the temperatures of these cold waters. The most extreme psychrophiles are found inside the sea ice of polar oceans, where bacterial growth can be observed down to -20 °C. Sea ice consists of a matrix of ice and high-saline water (brine) that provide a unique habitat for microbial communities. Microscopic algae and bacteria dominate these extreme environments, which are considered very stressful as they are characterised by large variations in salinity, low temperatures, and low radiation levels. However, the brine-filled channels also provide a platform from which microscopic algae remain in the euphotic zone and refugees from significant grazing, thereby enabling net autotrophic growth. As a result, sea ice hosts some of the highest chlorophyll a concentrations on the planet, and is one of the most important factors controlling primary production and bloom dynamics in polar areas. In this thesis, I focus on the ecophysiology of psychrophiles adapted to the sea ice environment. Physiological acclimation to environmental change needs to be studied in order to address how different stressors may influence organisms’ capacity to tolerate both naturally- and climatically-driven changes. Extremophiles growing close to their physiological limits may be especially susceptible to environmental stressors, such as rapid climate change. Therefore, a series of studies has been performed to investigate how environmental stressors, such as increased temperature and elevated CO2, affect microbial physiology and community structure in polar areas. The ecophysiology of sea ice microorganisms has been addressed in laboratory experiments (Papers I, II, and IV) and in field measurements (Paper III). In brief, relatively small changes in temperature had considerable effects on the physiology of sea ice diatoms, and indirectly affected the structure of sea ice bacterial communities. Increasing temperature (on both climatic and seasonal scales) positively affected the growth and primary productivity of two sea ice diatom species, and negatively affected the taxonomic richness and diversity of sea ice bacterial communities, probably by the subsequent changes in salinity. On the other hand, sea ice diatoms seem quite tolerant to changes in pH and partial pressure of CO2 (pCO2) in terms of growth, probably due to the fact that they grow in an environment with large seasonal variations in the carbonate system. However, increased pCO2 resulted in other cellular changes that may have important ecological consequences, such as cellular stoichiometry. This includes changes in fatty acid composition and dissolved organic carbon exudation, which are important components in food webs and biogeochemistry in many marine ecosystems. Although most studies on marine organisms have focused on short-term responses to increased pCO2, acclimation and adaptation are key components in order to identify the consequences of climate change in biological systems. In Paper IV, the physiological responses to long-term acclimation to high pCO2 were investigated in the psychrophilic sea ice diatom Nitzschia lecointei. After long-term acclimation (194 days), a small reduction in growth was detected at high pCO2. Previous short-term experiments have failed to detect altered growth in N. lecointei at high pCO2, which illustrates the importance of experimental duration in ocean acidification studies.

Predicting the growth of key microorganisms is essential to improve the efficiency of wastewater treatment of recirculating aquaculture systems (RAS). We have developed a stochastic model to assess quantitatively the microbial populations in RAS. This stochastic model encompassed the growth model into the Monte Carlo simulation and was constructed with risk analysis software. A modified logistic model combined with the saturation growth-rate model was successfully developed to regress the growth curves of six microorganisms. Monte Carlo simulation was employed to model the effects of chemical oxygen demand (COD) on the maximum specific growth rate. Probabilistic distributions and predictions under the different COD ranges were generated for each simulated scenario. The coefficient of determination (R²) and bias factor (Bf) were used to assess the performance of an established model. Logistic model produced a good fit to the growth curve of Flavobacterium sp. (R² = 0.9511), Acinetobacter baumannii (R² = 0.9970), Sphingomonas paucimobilis (R² = 0.9086), Vibrio natriegens (R² = 0.9993), Lutimonas sp. (R² = 0.9872) and Bacillus pumilus (R² = 0.9816). Bacterial population structure was determined by the construction of 16S rRNA gene libraries. A regular variation trend was observed for the dominant groups during the entire process, with a decrease of Cytophaga–Flavobacterium–Bacteroidetes from 37.6 to 18.7 % and an increase in Gammaproteobacteria from 8.5 to 30.6 %. The predicted model agreed well with observed values except for Flavobacterium sp., and the results can be applied to predict key microorganisms in actual environments. The results of this study provide a method to monitor the dynamics of key microorganisms, which can also help to evaluate the impacts of microorganisms on the operations of RAS.

Food webs include complex ecological interactions that define the flow of matter and energy, and are fundamental in understanding the functioning of an ecosystem. Temporal variations in the densities of communities belonging to the planktonic food web (i.e., microbial: bacteria, flagellate, and ciliate; and grazing: zooplankton and phytoplankton) were investigated, aiming to clarify the interactions between these organisms and the dynamics of the planktonic food web in a floodplain lake. We hypothesized that hydrological pulse determines the path of matter and energy flow through the planktonic food web of this floodplain lake. Data were collected monthly from March 2007 to February 2008 at three different sites in Guaraná Lake (Mato Grosso do Sul State, Brazil). The path analysis provided evidence that the dynamics of the planktonic food web was strongly influenced by the hydrological pulse. The high-water period favored interactions among the organisms of the microbial loop, rather than their relationships with zooplankton and phytoplankton. Therefore, in this period, the strong interaction among the organisms of the grazing food chain suggests that the microbial loop functions as a sink of matter and energy. In turn, in the low-water period, higher primary productivity appeared to favor different interactions between the components of the grazing food chain and microorganisms, which would function as a link to the higher trophic levels.

Fermentation products can chaotropically disorder macromolecular systems and induce oxidative stress, thus inhibiting biofuel production. Recently, the chaotropic activities of ethanol, butanol and vanillin have been quantified (5.93, 37.4, 174kJkg−1m−1 respectively). Use of low temperatures and/or stabilizing (kosmotropic) substances, and other approaches, can reduce, neutralize or circumvent product-chaotropicity. However, there may be limits to the alcohol concentrations that cells can tolerate; e.g. for ethanol tolerance in the most robust Saccharomyces cerevisiae strains, these are close to both the solubility limit (<25%, w/v ethanol) and the water-activity limit of the most xerotolerant strains (0.880). Nevertheless, knowledge-based strategies to mitigate or neutralize chaotropicity could lead to major improvements in rates of product formation and yields, and also therefore in the economics of biofuel production.

A flea preserved in Dominican amber is described as Atopopsyllus cionus, n. gen., n. sp. (Atopopsyllini n. tribe, Spilopsyllinae, Pulicidae). The male specimen has two unique characters that have not been noted in previous extant or extinct fleas, thus warranting its tribal status. These characters are five-segmented maxillary palps and cerci-like organs on abdominal tergite X. Additional characters are the absence of ctenidia, very small eyes, a lanceolate terminal segment of the maxillary palps, legs with six notches on the dorsal margin of the tibiae, five pairs of lateral plantar bristles on the distitarsomeres, and nearly straight ungues with a wide space between the basal lobe and tarsal claw. Trypanosomes and coccobacilli in the rectum and coccobacilli on the tip of the epipharynx of the fossil are depicted and briefly characterized.

The commonly employed screening test for detection of cervical carcinoma is Pap smear examination. However, it can also be used for screening cervico-vaginal infections. Several microorganisms are encountered in Pap smears such as bacteria, fungi, parasites etc. The occurrence of few such organisms may be rare and when encountered should be reported with caution for several reasons such as to avoid unnecessary toxic anti-fungal therapy. Chlamydia is a sexually transmitted disease. The infection with Chlamydia and trichomonas may show changes in cells which mimic malignancy. So in our case report, we present three such cases and discuss the importance of reporting them.

Microbial cell immobilization has long been considered as a potential bioprocessing strategy to increase both microorganisms’ tolerance and fitness in fermentation systems. To date, little emphasis has been put on how the entrapped cells respond to the bioprocessing stresses encountered during the cultivation. The present work presents for the first time a methodology to decipher the real health status of the entrapped microorganisms by combining multiparameter flow cytometry with confocal fluorescence microscopy as monitoring tools. Comparison between resting free and immobilized cell-based systems enabled to characterize the spatial-temporal physiological response of entrapped Pseudomonas taetrolens cells during lactobionic acid production in submerged cultivation. Whereas cellular leakage from beads led to planktonic cells that faced a progressive loss of membrane integrity, immobilized cells underwent a prompt stress-induced physiological response featured by the predominance of cellular damaging. Moreover, visualization without matrix de-entrapment through confocal fluorescence microscopy revealed the overtime formation of cellular micro-colonies inside the beads. These micro-colonies comprised a shell made of dead cells, whereas the inward cells remained metabolically active. The proposed approach herein raises the possibility of using flow cytometry and confocal fluorescence microscopy as indicators of microbial cell immobilization, providing further key information on the health status and robustness of entrapped microorganisms.

The benefits of high pressure processing (HPP) for microbial inactivation in food production include reduced thermal treatment and minimized effects on sensory and nutritional profiles. These benefits have resulted in increasing commercial production of high pressure pasteurized foods. In this review, the current state of the art in terms of vegetative cell and bacterial spore inactivation by HPP in complex food matrices is assessed with an emphasis on mechanisms of inactivation and treatment of products that have low or non-uniform water activity (aw) profiles. Low aw can be the result of a high concentration in solutes, the presence of oils/fats, or the physical removal of water through dehydration. Microbial inactivation in low aw environments remains a particular challenge for HPP and studies on microbial inactivation observed in the different types of low aw food matrices are reviewed in detail.HPP-treated food products with low aw have been on the market since the nineties, but the mechanisms of microbial inactivation at low aw are still not well understood, which hinders the development of new applications in low or inhomogeneous aw food. This review summarizes the state of the art in terms of HPP microbial inactivation mechanisms in model systems and various low aw food environments. Thereby, it identifies existing and potential new applications as well as the current gaps and future research needs.

The performance of a novel reverse membrane bioreactor (RMBR) with encased microorganisms for syngas bio-methanation as well as a co-digestion process of syngas and organic substances was examined. The sachets were placed in the reactors and examined in repeated batch mode. Different temperatures and short retention time were studied. The digesting sludge encased in the PVDF membranes was able to convert syngas into methane at a retention time of 1day and displayed a similar performance as the free cells in batch fermentation. The co-digestion of syngas and organic substances by the RMBR (the encased cells) showed a good performance without any observed negative effects. At thermophilic conditions, there was a higher conversion of pure syngas and co-digestion using the encased cells compared to at mesophilic conditions.