The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth

Peer reviewedPublisher PD

Clay flocculation effect on microbial community composition in water and sediment

Clay-based flocculation techniques have been developed to mitigate harmful algal blooms; however, the potential ecological impacts on the microbial community are poorly understood. In this study, chemical measurements were combined with 16S rRNA sequencing to characterize the microbial community response to different flocculation techniques, including controls, clay flocculation, clay flocculation with zeolite, and clay flocculation with O2 added zeolite capping. Sediment bacterial biomass measured by PLFA were not significantly altered by the various flocculation techniques used. However, 16S rRNA sequencing revealed differences in water microbial community structure between treatments with and without zeolite capping. The differences were related to significant reductions of total nitrogen (TN), total phosphorus (TP) and ammonia (NH4+) concentration and increase of nitrate (NO3-) concentration in zeolite and O2 loaded zeolite capping. The relative abundance of ammonia oxidizing bacteria increased four-fold in zeolite capping microcosms, suggesting zeolite promoted absorbed ammonia removal in the benthic zone. Zeolite-capping promoted bacteria nitrogen cycling activities at the water-sediment interface. Potential pathogens that are usually adapted to eutrophic water bodies were reduced after clay flocculation. This study demonstrated clay flocculation did not decrease bacterial populations overall and may reduce regulatory indicators and pathogenic contaminants in water. Zeolite capping may also help prevent nutrients from being released back into the water thus preventing additional algal blooms

Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction.

Production of unconventional oil and gas continues to rise, but the effects of high-density hydraulic fracturing (HF) activity near aquatic ecosystems are not fully understood. A commonly used biocide in HF, 2,2-dibromo-3-nitrilopropionamide (DBNPA), was studied in microcosms of HF-impacted (HF+) versus HF-unimpacted (HF-) surface water streams to (i) compare the microbial community response, (ii) investigate DBNPA degradation products based on past HF exposure, and (iii) compare the microbial community response differences and similarities between the HF biocides DBNPA and glutaraldehyde. The microbial community responded to DBNPA differently in HF-impacted versus HF-unimpacted microcosms in terms of the number of 16S rRNA gene copies quantified, alpha and beta diversity, and differential abundance analyses of microbial community composition through time. The differences in microbial community changes affected degradation dynamics. HF-impacted microbial communities were more sensitive to DBNPA, causing the biocide and by-products of the degradation to persist for longer than in HF-unimpacted microcosms. A total of 17 DBNPA by-products were detected, many of them not widely known as DBNPA by-products. Many of the brominated by-products detected that are believed to be uncharacterized may pose environmental and health impacts. Similar taxa were able to tolerate glutaraldehyde and DBNPA; however, DBNPA was not as effective for microbial control, as indicated by a smaller overall decrease of 16S rRNA gene copies/ml after exposure to the biocide, and a more diverse set of taxa was able to tolerate it. These findings suggest that past HF activity in streams can affect the microbial community response to environmental perturbation such as that caused by the biocide DBNPA.IMPORTANCE Unconventional oil and gas activity can affect pH, total organic carbon, and microbial communities in surface water, altering their ability to respond to new environmental and/or anthropogenic perturbations. These findings demonstrate that 2,2-dibromo-3-nitrilopropionamide (DBNPA), a common hydraulic fracturing (HF) biocide, affects microbial communities differently as a consequence of past HF exposure, persisting longer in HF-impacted (HF+) waters. These findings also demonstrate that DBNPA has low efficacy in environmental microbial communities regardless of HF impact. These findings are of interest, as understanding microbial responses is key for formulating remediation strategies in unconventional oil and gas (UOG)-impacted environments. Moreover, some DBNPA degradation by-products are even more toxic and recalcitrant than DBNPA itself, and this work identifies novel brominated degradation by-products formed

Proteomic analysis of the hydrogen and carbon monoxide metabolism of Methanothermobacter marburgensis

Hydrogenotrophic methanogenic archaea are efficient H2 utilizers, but only a few are known to be able to utilize CO. Methanothermobacter thermoautotrophicus is one of the hydrogenotrophic methanogens able to grow on CO, albeit about 100 times slower than on H2 + CO2. In this study we show that the hydrogenotrophic methanogen Methanothermobacter marburgensis, is able to perform methanogenic growth on H2/CO2/CO and on CO as a sole substrate. To gain further insight in its carboxydotrophic metabolism, the proteome of M. marburgensis, grown on H2/CO2 and H2/CO2/CO, was analysed. Cultures grown with H2/CO2/CO showed relative higher abundance of enzymes involved in the reductive acetyl-CoA pathway and proteins involved in redox metabolism. The data suggest that the strong reducing capacity of CO negatively affects hydrogenotrophic methanogenesis, making growth on CO as a sole substrate difficult for this type of methanogens. M. marburgensis appears to partly deal with this by upregulating co-factor regenerating reactions and activating additional pathways allowing for formation of other products, like acetate.Research of AS is supported by an ERC grant (project 323009) and a Gravitation grant (project024.002.002)of the Netherlands Ministry of Education, Culture and Science and the Netherlands Science Foundation (NWO)

Moorella stamsii sp. nov., a new anaerobic thermophilic hydrogenogenic carboxydotroph isolated from digester sludge

A novel anaerobic, thermophilic, carbon monoxide-utilizing bacterium, strain E3-O, was isolated from anaerobic sludge of a municipal solid waste digester. Cells were straight rods, 0.6 to 1μm in diameter and 2 to 3 μm in length, growing as single cells or in pairs. Cells formed round terminal endospores. The temperature range for growth was 50 to 70°C, with an optimum at 65°C. The pH range for growth was 5.7 to 8.0, with an optimum at 7.5. Strain E3-O had the capability to ferment various sugars, such as fructose, galactose, glucose, mannose, raffinose, ribose, sucrose and xylose, producing mainly H2 and acetate. In addition, the isolate was able to grow with CO as the sole carbon and energy source. CO oxidation was coupled to H2 and CO2 formation. The G+C content of the genomic DNA was 54.6 mol %. Based on 16S rRNA gene sequence analysis, this bacterium is most closely related to Moorella glycerini (97% sequence identity). Based on the physiological features and phylogenetic analysis, it is proposed that strain E3-O should be classified in the genus Moorella as a new species, Moorella stamsii. The type strain of Moorella stamsii is E3-OT (=DMS 26271T=CGMCC 1.5181T).This work was possible through the financial support provided by the Portuguese Science Foundation (FCT) and the European Social Fund (POPH-QREN) through a PhD grant SFRH/BD/48965/2008 to J.I.A

Die Verbesserung der Situation demenziell erkrankter Menschen auf dem Prüfstand:Eine Vergleichsstudie zu Therapieansätzen und Versorgungsstrukturen auf der Grundlage internationaler Forschungsergebnisse

Anliegen dieser Dissertation ist es, auf der Grundlage von internationalen empirischen Studien sowohl nichtmedizinische Therapieansätze als auch neuere Versorgungssettings für demenziell erkrankte Menschen einer Bewertung zu unterziehen. Eine solche scheint angesichts der Brisanz des Themas „Demenz“ gegenwärtig dringend geboten. Die hier durchgeführte Wirksamkeitsanalyse ist dabei gleichermaßen erforderlich und wichtig, für die Therapieansätze, die sich in schneller Folge entwickeln und die Versorgungssettings, von denen nach heutigem Stand am ehesten eine Verbesserung der Lebenssituation von demenzerkrankten Menschen zu erwarten ist. Die Zielsetzung der Arbeit ist auch eine sozialpolitische: durch die Evaluation der Therapieansätze und der neueren stationären Wohnumwelten soll ein Beitrag zur Implementierung und zum Aufbau adäquater, das heißt insbesondere dem Anspruch der Lebensqualität verpflichteter Versorgungs- und Betreuungsstrukturen geleistet werden

Impacts of Nutrients on Alkene Biodegradation Rates and Microbial Community Composition in Enriched Consortia from Natural Inocula

There is a growing need for biological and chemical methods for upcycling plastic waste streams. Pyrolysis processes can accelerate plastic depolymerization by breaking polyethylene into smaller alkene components which may be more biodegradable than the initial polymer. While the biodegradation of alkanes has been extensively studied, the role microorganisms play in alkene breakdown is not well understood. Alkene biodegradation holds the potential to contribute to the coupling of chemical and biological processing of polyethylene plastics. In addition, nutrient levels are known to impact rates of hydrocarbon degradation. Model alkenes were used (C6, C10, C16, and C20) to follow the breakdown capability of microbial communities from three environmental inocula in three nutrient levels over the course of 5 days. Higher-nutrient cultures were anticipated to exhibit enhanced biodegradation capabilities. Alkene mineralization was assessed by measuring CO production in the culture headspace using GC-FID (gas chromatography-flame ionization detection), and alkene breakdown was directly quantified by measuring extracted residual hydrocarbons using gas chromatography-mass spectrometry (GC/MS). Here, the efficacy of enriched consortia derived from the microbial communities of three inoculum sources (farm compost, Caspian Sea sediment, and an iron-rich sediment) at alkene breakdown was investigated over the course of 5 days across three nutrient treatments. No significant differences in CO production across nutrient levels or inoculum types were found. A high extent of biodegradation was observed in all sample types, with most samples achieving 60% to 95% biodegradation of all quantified compounds. Here, our findings indicate that alkene biodegradation is a common metabolic process in diverse environments and that nutrient levels common to culture media can support the growth of alkene-biodegrading consortia, primarily from the families , , and . Excess plastic waste poses a major environmental problem. Microorganisms can metabolize many of the breakdown products (alkenes) of plastics. While microbial degradation of plastics is typically slow, coupling chemical and biological processing of plastics has the potential to lead to novel methods for the upcycling of plastic wastes. Here, we explored how microbial consortia derived from diverse environments metabolize alkenes, which are produced by the pyrolysis of polyolefin plastics such as HDPE, and PP. We found that microbial consortia from diverse environments can rapidly metabolize alkenes of different chain lengths. We also explored how nutrients affect the rates of alkene breakdown and the microbial diversity of the consortia. Here, the findings indicate that alkene biodegradation is a common metabolism in diverse environments (farm compost, Caspian sediment, and iron-rich sediment) and that nutrient levels common to culture medium can support growth of alkene-biodegrading consortia, primarily from the families Xanthamonadaceae, Nocardiaceae, and Beijerinkiaceae

Open source vacuum oven design for low-temperature drying: Performance evaluation for recycled pet and biomass

Vacuum drying can dehydrate materials further than dry heat methods, while protecting sensitive materials from thermal degradation. Many industries have shifted to vacuum drying as cost-or time-saving measures. Small-scale vacuum drying, however, has been limited by the high costs of specialty scientific tools. To make vacuum drying more accessible, this study provides design and performance information for a small-scale open source vacuum oven, which can be fabricated from off-the-shelf and 3-D printed components. The oven is tested for drying speed and effectiveness on both waste plastic polyethylene terephthalate (PET) and a consortium of bacteria developed for bioprocessing of terephthalate wastes to assist in distributed recycling of PET for both additive manufacturing as well as potential food. Both materials can be damaged when exposed to high temperatures, making vacuum drying a desirable solution. The results showed that the open source vacuum oven was effective at drying both plastic and biomaterials, drying at a higher rate than a hot-air dryer for small samples or for low volumes of water. The system can be constructed for less than 20% of commercial vacuum dryer costs for several laboratory-scale applications, including dehydration of bio-organisms, drying plastic for distributed recycling and additive manufacturing, and chemical processing

Unconventional oil and gas energy systems: An unidentified hotspot of antimicrobial resistance?

Biocides used in unconventional oil and gas (UOG) practices, such as hydraulic fracturing, control microbial growth. Unwanted microbial growth can cause gas souring, pipeline clogging, and microbial-induced corrosion of equipment and transportation pipes. However, optimizing biocide use has not been a priority. Moreover, biocide efficacy has been questioned because microbial surveys show an active microbial community in hydraulic fracturing produced and flowback water. Hydraulic fracturing produced and flowback water increases risks to surface aquifers and rivers/lakes near the UOG operations compared with conventional oil and gas operations. While some biocides and biocide degradation products have been highlighted as chemicals of concern because of their toxicity to humans and the environment, the selective antimicrobial pressure they cause has not been considered seriously. This perspective article aims to promote research to determine if antimicrobial pressure in these systems is cause for concern. UOG practices could potentially create antimicrobial resistance hotspots under-appreciated in the literature, practice, and regulation arena, hotspots that should not be ignored. The article is distinctive in discussing antimicrobial resistance risks associated with UOG biocides from

Production of medium-chain fatty acids and higher alcohols by a synthetic co-culture grown on carbon monoxide or syngas

Synthesis gas, a mixture of CO, H2, and CO2, is a promising renewable feedstock for bio-based production of organic chemicals. Production of medium-chain fatty acids can be performed via chain elongation, utilizing acetate and ethanol as main substrates. Acetate and ethanol are main products of syngas fermentation by acetogens. Therefore, syngas can be indirectly used as a substrate for the chain elongation process.ERC Grant (Project 323009) and the Gravitation Grant (Project 024.002.002) of the Netherlands Ministry of Education, Culture and Science, and the Netherlands Science Foundation (NWO