Hydrocarbon-degrading sulfate-reducing bacteria in marine hydrocarbon seep sediments

Microorganisms are key players in our biosphere because of their ability to degrade various organic compounds including a wide range of hydrocarbons. At marine hydrocarbon seeps, more than 90% of sulfate reduction (SR) is potentially coupled to non-methane hydrocarbon oxidation. Several hydrocarbon-degrading sulfate-reducing bacteria (SRB) were enriched or isolated from marine sediments. However, in situ active SRB remained largely unknown. In the present thesis, the global distribution and abundance of SRB at diverse gas and hydrocarbon seeps was investigated by catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH). The majority of Deltaproteobacteria was assigned to specific SRB groups, for instance on average 83% and 61% at gas and hydrocarbon seeps. Members of the Desulfosarcina/Desulfococcus (DSS) clade significantly dominated all sites, suggesting their important role in hydrocarbon degradation processes. Furthermore, butane- and dodecane-degrading SRB were identified from two contrasting marine hydrocarbon seeps using 13C-stable-isotope probing techniques. The identified key players affiliated with four distinct groups, of which three belonged to the DSS clade. Specific groups were, according to their ability to oxidize short-chain alkanes (SCA) or long-chain alkanes (LCA), denoted as SCA-SRB1 and SCA-SRB2 as well as LCA-SRB1 and LCA-SRB2 . Based on the obtained data it is assumed that diverse and highly specialized DSS organisms are involved in hydrocarbon degradation at marine seeps rather than generalists of one dominant subgroup. At marine hydrocarbon seeps, groups SCA-SRB1 and SCA-SRB2 constituted up to 31 and 9% of all Deltaproteobacteria, respectively. In addition, LCA-SRB2 comprised up to 6% of all detected Deltaproteobacteria. Furthermore, activities for these groups were analyzed on the cellular level by Nanometer-scale Secondary Ion Mass Spectrometry (NanoSIMS). Alkane oxidation rates for specific groups were determined to be on average between 45 and 58 amol butane and 1 amol dodecane per cell and per day. Extrapolated data indicate that specific alkane-degrading SRB groups have the potential to contribute up to 100% of the total SR rates at seeps from the Gulf of Mexico. Therefore, alkane-degrading SRB groups may significantly impact sulfur and carbon cycles at marine hydrocarbon seeps. In addition, based on the obtained data, members of the uncultured group SEEP-SRB2 are hypothesized to be involved in hydrocarbon degradation. SEEP-SRB2 were visualized for the first time using CARD-FISH and were detected either in association with methanotrophic archaea (ANME 2/SEEP2 and ANME-1/SEEP2 consortia) or as single cells. Furthermore, the high abundance of SEEP-SRB2 indicates their important ecological role at marine hydrocarbon seeps

Starvation-dependent inhibition of the hydrocarbon degrader marinobacter sp. TT1 by a chemical dispersant

During marine oil spills, chemical dispersants are used routinely to disperse surface slicks, transferring the hydrocarbon constituents of oil into the aqueous phase. Nonetheless, a comprehensive understanding of how dispersants affect natural populations of hydrocarbon-degrading bacteria, particularly under environmentally relevant conditions, is lacking. We investigated the impacts of the dispersant Corexit EC9500A on the marine hydrocarbon degrader Marinobacter sp. TT1 when pre-adapted to either low n-hexadecane concentrations (starved culture) or high n-hexadecane concentrations (well-fed culture). The growth of previously starved cells was inhibited when exposed to the dispersant, as evidenced by 55% lower cell numbers and 30% lower n-hexadecane biodegradation efficiency compared to cells grown on n-hexadecane alone. Cultures that were well-fed did not exhibit dispersant-induced inhibition of growth or n-hexadecane degradation. In addition, fluorescence microscopy revealed amorphous cell aggregate structures when the starved culture was exposed to dispersants, suggesting that Corexit affected the biofilm formation behavior of starved cells. Our findings indicate that (previous) substrate limitation, resembling oligotrophic open ocean conditions, can impact the response and hydrocarbon-degrading activities of oil-degrading organisms when exposed to Corexit, and highlight the need for further work to better understand the implications of environmental stressors on oil biodegradation and microbial community dynamics

Microbial transformation of biogenic and abiogenic Fe minerals followed by in-situ incubations in an As-contaminated vs. non-contaminated aquifer

Contains fulltext : 234196.pdf (Publisher’s version ) (Open Access

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 112 (2015): 14900-14905, doi:10.1073/pnas.1507380112.During the Deepwater Horizon oil well blowout in the Gulf of Mexico, the application of 7 million liters of chemical dispersants aimed to stimulate microbial crude oil degradation by increasing the bioavailability of oil compounds. However, the effects of dispersants on oil biodegradation rates are debated. In laboratory experiments, we simulated environmental conditions comparable in the hydrocarbon-rich, 1100m deep, plume that formed during the Deepwater Horizon discharge. The presence of dispersant significantly altered the microbial community composition through selection for potential dispersant-degrading Colwellia, which also bloomed in situ in Gulf deep-waters during the discharge. In contrast, oil addition lacking dispersant stimulated growth of natural hydrocarbon-degrading Marinobacter. Dispersants did not enhance heterotrophic microbial activity or hydrocarbon oxidation rates. Extrapolating this comprehensive data set to real world scenarios questions whether dispersants stimulate microbial oil degradation in deep ocean waters and instead highlights that dispersants can exert a negative effect on microbial hydrocarbon degradation rates.This research was supported by a grant from BP/the Gulf of Mexico Research Initiative to support the "Ecosystem Impacts of Oil and Gas Inputs to the Gulf (ECOGIG)” consortium. PMM also acknowledges funding from the National Science Foundation (OCE-1057683)

Spatial and temporal evolution of groundwater arsenic contamination in the Red River delta, Vietnam: Interplay of mobilisation and retardation processes

Geogenic arsenic (As) contamination of groundwater poses a major threat to global health, particularly in Asia. To mitigate this exposure, groundwater is increasingly extracted from low-As Pleistocene aquifers. This, however, disturbs groundwater flow and potentially draws high-As groundwater into low-As aquifers. Here we report a detailed characterisation of the Van Phuc aquifer in the Red River Delta region, Vietnam, where high-As groundwater from a Holocene aquifer is being drawn into a low-As Pleistocene aquifer. This study includes data from eight years (2010–2017) of groundwater observations to develop an understanding of the spatial and temporal evolution of the redox status and groundwater hydrochemistry. Arsenic concentrations were highly variable (0.5–510 μg/L) over spatial scales of <200 m. Five hydro(geo)chemical zones (indicated as A to E) were identified in the aquifer, each associated with specific As mobilisation and retardation processes. At the riverbank (zone A), As is mobilised from freshly deposited sediments where Fe(III)-reducing conditions occur. Arsenic is then transported across the Holocene aquifer (zone B), where the vertical intrusion of evaporative water, likely enriched in dissolved organic matter, promotes methanogenic conditions and further release of As (zone C). In the redox transition zone at the boundary of the two aquifers (zone D), groundwater arsenic concentrations decrease by sorption and incorporations onto Fe(II) carbonates and Fe(II)/Fe(III) (oxyhydr)oxides under reducing conditions. The sorption/incorporation of As onto Fe(III) minerals at the redox transition and in the Mn(IV)-reducing Pleistocene aquifer (zone E) has consistently kept As concentrations below 10 μg/L for the studied period of 2010–2017, and the location of the redox transition zone does not appear to have propagated significantly. Yet, the largest temporal hydrochemical changes were found in the Pleistocene aquifer caused by groundwater advection from the Holocene aquifer. This is critical and calls for detailed investigations

Microservice Transition and its Granularity Problem: A Systematic Mapping Study

Microservices have gained wide recognition and acceptance in software industries as an emerging architectural style for autonomic, scalable, and more reliable computing. The transition to microservices has been highly motivated by the need for better alignment of technical design decisions with improving value potentials of architectures. Despite microservices' popularity, research still lacks disciplined understanding of transition and consensus on the principles and activities underlying "micro-ing" architectures. In this paper, we report on a systematic mapping study that consolidates various views, approaches and activities that commonly assist in the transition to microservices. The study aims to provide a better understanding of the transition; it also contributes a working definition of the transition and technical activities underlying it. We term the transition and technical activities leading to microservice architectures as microservitization. We then shed light on a fundamental problem of microservitization: microservice granularity and reasoning about its adaptation as first-class entities. This study reviews state-of-the-art and -practice related to reasoning about microservice granularity; it reviews modelling approaches, aspects considered, guidelines and processes used to reason about microservice granularity. This study identifies opportunities for future research and development related to reasoning about microservice granularity.Comment: 36 pages including references, 6 figures, and 3 table

Kohlenwasserstoffabauende sulfatreduzierende Bakterien in marinen Sedimenten von Kohlenwasserstoffquellen

Microorganisms are key players in our biosphere because of their ability to degrade various organic compounds including a wide range of hydrocarbons. At marine hydrocarbon seeps, more than 90% of sulfate reduction (SR) is potentially coupled to non-methane hydrocarbon oxidation. Several hydrocarbon-degrading sulfate-reducing bacteria (SRB) were enriched or isolated from marine sediments. However, in situ active SRB remained largely unknown. In the present thesis, the global distribution and abundance of SRB at diverse gas and hydrocarbon seeps was investigated by catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH). The majority of Deltaproteobacteria was assigned to specific SRB groups, for instance on average 83% and 61% at gas and hydrocarbon seeps. Members of the Desulfosarcina/Desulfococcus (DSS) clade significantly dominated all sites, suggesting their important role in hydrocarbon degradation processes. Furthermore, butane- and dodecane-degrading SRB were identified from two contrasting marine hydrocarbon seeps using 13C-stable-isotope probing techniques. The identified key players affiliated with four distinct groups, of which three belonged to the DSS clade. Specific groups were, according to their ability to oxidize short-chain alkanes (SCA) or long-chain alkanes (LCA), denoted as SCA-SRB1 and SCA-SRB2 as well as LCA-SRB1 and LCA-SRB2 . Based on the obtained data it is assumed that diverse and highly specialized DSS organisms are involved in hydrocarbon degradation at marine seeps rather than generalists of one dominant subgroup. At marine hydrocarbon seeps, groups SCA-SRB1 and SCA-SRB2 constituted up to 31 and 9% of all Deltaproteobacteria, respectively. In addition, LCA-SRB2 comprised up to 6% of all detected Deltaproteobacteria. Furthermore, activities for these groups were analyzed on the cellular level by Nanometer-scale Secondary Ion Mass Spectrometry (NanoSIMS). Alkane oxidation rates for specific groups were determined to be on average between 45 and 58 amol butane and 1 amol dodecane per cell and per day. Extrapolated data indicate that specific alkane-degrading SRB groups have the potential to contribute up to 100% of the total SR rates at seeps from the Gulf of Mexico. Therefore, alkane-degrading SRB groups may significantly impact sulfur and carbon cycles at marine hydrocarbon seeps. In addition, based on the obtained data, members of the uncultured group SEEP-SRB2 are hypothesized to be involved in hydrocarbon degradation. SEEP-SRB2 were visualized for the first time using CARD-FISH and were detected either in association with methanotrophic archaea (ANME 2/SEEP2 and ANME-1/SEEP2 consortia) or as single cells. Furthermore, the high abundance of SEEP-SRB2 indicates their important ecological role at marine hydrocarbon seeps