Publications by authors named "Alberto Scoma"

34 Publications

Thin cell layer cultures of Chlamydomonas reinhardtii L159I-N230Y, pgrl1 and pgr5 mutants perform enhanced hydrogen production at sunlight intensity.

Bioresour Technol 2021 Aug 27;333:125217. Epub 2021 Apr 27.

Institute of Plant Biology, Biological Research Centre, Szeged, Temesvári krt. 62, H-6726 Szeged, Hungary. Electronic address:

Photobiological hydrogen (H) production is a promising renewable energy source. HydA hydrogenases of green algae are efficient but O-sensitive and compete for electrons with CO-fixation. Recently, we established a photoautotrophic H production system based on anaerobic induction, where the Calvin-Benson cycle is inactive and O scavenged by an absorbent. Here, we employed thin layer cultures, resulting in a three-fold increase in H production relative to bulk CC-124 cultures (50 µg chlorophyll/ml, 350 µmol photons m s). Productivity was maintained when increasing the light intensity to 1000 µmol photons ms and the cell density to 150 µg chlorophyll/ml. Remarkably, the L159I-N230Y photosystem II mutant and the pgrl1 photosystem I cyclic electron transport mutant produced 50% more H than CC-124, while the pgr5 mutant generated 250% more (1.2 ml H/ml culture in six days). The photosynthetic apparatus of the pgr5 mutant and its in vitro HydA activity remained remarkably stable.
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http://dx.doi.org/10.1016/j.biortech.2021.125217DOI Listing
August 2021

Functional groups in microbial ecology: updated definitions of piezophiles as suggested by hydrostatic pressure dependence on temperature.

Authors:
Alberto Scoma

ISME J 2021 Mar 29. Epub 2021 Mar 29.

Engineered Microbial Systems Laboratory (EMS-Lab), Department of Biological and Chemical Engineering (BCE), Aarhus University, Aarhus N, Denmark.

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http://dx.doi.org/10.1038/s41396-021-00930-0DOI Listing
March 2021

Mild hydrostatic-pressure (15 MPa) affects the assembly, but not the growth, of oil-degrading coastal microbial communities tested under limiting conditions (5°C, no added nutrients).

FEMS Microbiol Ecol 2020 11;96(11)

Department of Biology, Aarhus University, Ny munkegade 116, 8000, Aarhus C, Denmark.

Hydrostatic pressures (HP) <30-40 MPa are often considered mild, and their impact on petroleum biodegradation seldom considered. However, the frequent use of nutrient-rich media in lab-scale high-pressure reactors may exaggerate HP importance by resulting in a strong growth stimulation as compared to oligotrophic marine environments. Here, we tested coastal seawater microbial communities, presumably enriched in pressure-sensitive microorganisms. Limiting environmental conditions for growth were applied (i.e. low temperature [5°C], no added nutrients) and HP tested at 0.1 and 15 MPa, using crude oils from three different reservoirs. The cell number was not affected by HP contrary to the microbial community composition (based on 16S rRNA gene and 16S rRNA sequences). The most predominant genera were Zhongshania, Pseudomonas and Colwellia. The enrichment of Zhongshania was crude-oil dependent and comparable at 0.1 and 15 MPa, thus showing a piezotolerant phenotype under the present conditions; Pseudomonas' was crude-oil dependent at 0.1 MPa but unclear at 15 MPa. Colwellia was selectively enriched in the absence of crude oil and suppressed at 15 MPa. HP shaped the assemblage of oil-degrading communities even at mild levels (i.e. 15 MPa), and should thus be considered as a fundamental factor to assess oil bioremediation along the water column.
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http://dx.doi.org/10.1093/femsec/fiaa160DOI Listing
November 2020

Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders.

FEMS Microbiol Ecol 2020 09;96(9)

Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.

Deep-sea environments can become contaminated with petroleum hydrocarbons. The effects of hydrostatic pressure (HP) in the deep sea on microbial oil degradation are poorly understood. Here, we performed long-term enrichments (100 days) from a natural cold seep while providing optimal conditions to sustain high hydrocarbon degradation rates. Through enrichments performed at increased HP and ambient pressure (AP) and by using control enrichments with marine broth, we demonstrated that both pressure and carbon source can have a big impact on the community structure. In contrast to previous studies, hydrocarbonoclastic operational taxonomic units (OTUs) remained dominant at both AP and increased HP, suggesting piezotolerance of these OTUs over the tested pressure range. Twenty-three isolates were obtained after isolation and dereplication. After recultivation at increased HP, an Alcanivorax sp. showed promising piezotolerance in axenic culture. Furthermore, preliminary co-cultivation tests indicated synergistic growth between some isolates, which shows promise for future synthetic community construction. Overall, more insights into the effect of increased HP on oil-degrading communities were obtained as well as several interesting isolates, e.g. a piezotolerant hydrocarbonoclastic bacterium for future deep-sea bioaugmentation investigation.
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http://dx.doi.org/10.1093/femsec/fiaa097DOI Listing
September 2020

Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate.

Front Microbiol 2020 31;11:530. Epub 2020 Mar 31.

Center for Microbial Ecology and Technology, University of Ghent, Ghent, Belgium.

The giant panda is known worldwide for having successfully moved to a diet almost exclusively based on bamboo. Provided that no lignocellulose-degrading enzyme was detected in panda's genome, bamboo digestion is believed to depend on its gut microbiome. However, pandas retain the digestive system of a carnivore, with retention times of maximum 12 h. Cultivation of their unique gut microbiome under controlled laboratory conditions may be a valid tool to understand giant pandas' dietary habits, and provide valuable insights about what component of lignocellulose may be metabolized. Here, we collected gut microbiomes from fresh fecal samples of a giant panda (either entirely green or yellow stools) and supplied them with green leaves or yellow pith (i.e., the peeled stem). Microbial community composition was substrate dependent, and resulted in markedly different fermentation profiles, with yellow pith fermented to lactate and green leaves to lactate, acetate and ethanol, the latter to strikingly high concentrations (∼3%, v:v, within 3.5 h). Microbial metaproteins pointed to hemicellulose rather than cellulose degradation. The alpha-amylase from the giant panda (E.C. 3.2.1.1) was the predominant identified metaprotein, particularly in reactors inoculated with pellets derived from fecal samples (up to 60%). Gut microbiomes assemblage was most prominently impacted by the change in substrate (either leaf or pith). Removal of soluble organics from inocula to force lignocellulose degradation significantly enriched (in green leaf) and / (in yellow pith). Overall, different substrates (either leaf or pith) markedly shaped gut microbiome assemblies and fermentation profiles. The biochemical profile of fermentation products may be an underestimated factor contributing to explain the peculiar dietary behavior of giant pandas, and should be implemented in large scale studies together with short-term lab-scale cultivation of gut microbiomes.
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http://dx.doi.org/10.3389/fmicb.2020.00530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145396PMC
March 2020

Parallel artificial and biological electric circuits power petroleum decontamination: The case of snorkel and cable bacteria.

Water Res 2020 Apr 22;173:115520. Epub 2020 Jan 22.

Section of Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark; Biological and Chemical Engineering (BCE), Department of Engineering, Aarhus University, Aarhus, Denmark.

Degradation of petroleum hydrocarbons (HC) in sediments is often limited by the availability of electron acceptors. By allowing long-distance electron transport (LDET) between anoxic sediments and oxic overlying water, bioelectrochemical snorkels may stimulate the regeneration of sulphate in the anoxic sediment thereby accelerating petroleum HC degradation. Cable bacteria can also mediate LDET between anoxic and oxic sediment layers and thus theoretically stimulate petroleum HC degradation. Here, we quantitatively assessed the impact of cable bacteria and snorkels on the degradation of alkanes in marine sediment from Aarhus Bay (Denmark). After seven weeks, cable bacteria and snorkels accelerated alkanes degradation by +24 and +25%, respectively, compared to control sediment with no cable bacteria nor snorkel. The combination of snorkels and cable bacteria further enhanced alkanes degradation (+46%). Higher degradation rates were sustained by LDET-induced sulphide removal rather than, as initially hypothesized, sulphate regeneration. Cable bacteria are thus overlooked players in the self-healing capacity of crude-oil contaminated sediments, and may inspire novel remediation treatments upon hydrocarbon spillage.
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http://dx.doi.org/10.1016/j.watres.2020.115520DOI Listing
April 2020

Constraints on CaCO precipitation in superabsorbent polymer by aerobic bacteria.

Appl Microbiol Biotechnol 2020 Jan 25;104(1):365-375. Epub 2019 Nov 25.

Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.

Microbially induced CaCO precipitation (MICP) can give concrete self-healing properties. MICP agents are typically bacterial endospores which are coated into shelled granules, infused into expanded clay, or embedded into superabsorbent polymer (SAP). When small cracks appear in the cured concrete, the encapsulation is broken and the metabolic CO production from the germinated bacteria causes healing of the cracks by precipitation of CaCO. Such systems are being tested empirically at large scales, but survival of endospores through preparation and application, as well as germination and growth kinetics of the germinated vegetative cells, remains poorly resolved. We encapsulated endospores of Bacillus subtilis and Bacillus alkalinitrilicus in crosslinked acrylamide-based SAP and quantified their germination, growth, and, in the case of B. alkalinitrilicus, CaCO precipitation potential. The endospores survived crosslinking and desiccation inside the polymer matrix. Microcalorimetry and microscopy showed that ~ 80% of the encapsulated endospores of both strains readily germinated after rehydration of freeze-dried SAP. Germinated cells grew into dense colonies of cells inside the SAP, and those of B. alkalinitrilicus calcified with up to 0.3 g CaCO produced per g desiccated SAP when incubated aerobically. Measurements by planar optodes indicated that the precipitation rates were inherently oxygen limited due to diffusional constraints, rather than limited by electron donor or Ca availability. Such oxygen limitation will limit MICP in all water-saturated and oxygen-dependent systems, and MICP agents based on anaerobic bacteria, e.g., nitrate reducers, should be developed to broaden the applicability of bioactive self-healing concretes to wet and waterlogged environments.
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http://dx.doi.org/10.1007/s00253-019-10215-4DOI Listing
January 2020

The Polyextremophilic Bacterium Clostridium paradoxum Attains Piezophilic Traits by Modulating Its Energy Metabolism and Cell Membrane Composition.

Appl Environ Microbiol 2019 08 18;85(15). Epub 2019 Jul 18.

Department of Bioscience, Section of Microbiology, Aarhus University, Aarhus, Denmark.

In polyextremophiles, i.e., microorganisms growing preferentially under multiple extremes, synergistic effects may allow growth when application of the same extremes alone would not. High hydrostatic pressure (HP) is rarely considered in studies of polyextremophiles, and its role in potentially enhancing tolerance to other extremes remains unclear. Here, we investigated the HP-temperature response in , a haloalkaliphilic moderately thermophilic endospore-forming bacterium, in the range of 50 to 70°C and 0.1 to 30 MPa. At ambient pressure, growth limits were extended from the previously reported 63°C to 70°C, defining as an actual thermophile. Concomitant application of high HP and temperature compared to standard conditions (i.e., ambient pressure and 50°C) remarkably enhanced growth, with an optimum growth rate observed at 22 MPa and 60°C. HP distinctively defined physiology, as at 22 MPa biomass, production increased by 75% and the release of fermentation products per cell decreased by >50% compared to ambient pressure. This metabolic modulation was apparently linked to an energy-preserving mechanism triggered by HP, involving a shift toward pyruvate as the preferred energy and carbon source. High HPs decreased cell damage, as determined by Syto9 and propidium iodide staining, despite no organic solute being accumulated intracellularly. A distinct reduction in carbon chain length of phospholipid fatty acids (PLFAs) and an increase in the amount of branched-chain PLFAs occurred at high HP. Our results describe a multifaceted, cause-and-effect relationship between HP and cell metabolism, stressing the importance of applying HP to define the boundaries for life under polyextreme conditions. Hydrostatic pressure (HP) is a fundamental parameter influencing biochemical reactions and cell physiology; however, it is less frequently applied than other factors, such as pH, temperature, and salinity, when studying polyextremophilic microorganisms. In particular, how HP affects microbial tolerance to other and multiple extremes remains unclear. Here, we show that under polyextreme conditions of high pH and temperature, demonstrates a moderately piezophilic nature as cultures grow to highest cell densities and most efficiently at a specific combination of temperature and HP. Our results highlight the importance of considering HP when exploring microbial physiology under extreme conditions and thus have implications for defining the limits for microbial life in nature and for optimizing industrial bioprocesses occurring under multiple extremes.
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http://dx.doi.org/10.1128/AEM.00802-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643245PMC
August 2019

Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities.

ISME J 2019 04 12;13(4):1004-1018. Epub 2018 Dec 12.

Center for Microbial Ecology and Technology (CMET), Gent University, Coupure Links 653, Gent, B 9000, Belgium.

Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure. In long-term enrichments, increased HP selectively inhibited obligate hydrocarbon-degraders and downregulated the expression of beta-oxidation-related proteins (i.e., the main hydrocarbon-degradation pathway) resulting in low cell growth and CO production. Short-term experiments with HP-adapted synthetic communities confirmed this data, revealing a HP-dependent accumulation of citrate and dihydroxyacetone. Citrate accumulation suggests rates of aerobic oxidation of fatty acids in the TCA cycle were reduced. Dihydroxyacetone is connected to citrate through glycerol metabolism and glycolysis, both upregulated with increased HP. High degradation rates by obligate hydrocarbon-degraders may thus be unfavourable at increased HP, explaining their selective suppression. Through lab-scale cultivation, the present study is the first to highlight a link between impaired cell metabolism and microbial community assembly in hydrocarbon degradation at high HP. Overall, this data indicate that hydrocarbons fate differs substantially in surface waters as compared to deep-sea environments, with in situ low temperature and limited nutrients availability expected to further prolong hydrocarbons persistence at deep sea.
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http://dx.doi.org/10.1038/s41396-018-0324-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461773PMC
April 2019

Editorial overview: Environmental microbiology: Environmental and engineered microbiomes.

Curr Opin Microbiol 2018 06;43:v-vii

Institute of Microbiology, ETH Zurich, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.mib.2018.05.004DOI Listing
June 2018

Corrigendum: The Effect of Hydrostatic Pressure on Enrichments of Hydrocarbon Degrading Microbes From the Gulf of Mexico Following the Deepwater Horizon Oil Spill.

Front Microbiol 2018 23;9:1050. Epub 2018 May 23.

Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.

[This corrects the article DOI: 10.3389/fmicb.2018.00808.].
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http://dx.doi.org/10.3389/fmicb.2018.01050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5974540PMC
May 2018

The Effect of Hydrostatic Pressure on Enrichments of Hydrocarbon Degrading Microbes From the Gulf of Mexico Following the Deepwater Horizon Oil Spill.

Front Microbiol 2018 26;9:808. Epub 2018 Apr 26.

Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.

The Deepwater Horizon oil spill was one of the largest and deepest oil spills recorded. The wellhead was located at approximately 1500 m below the sea where low temperature and high pressure are key environmental characteristics. Using cells collected 4 months following the Deepwater Horizon oil spill at the Gulf of Mexico, we set up Macondo crude oil enrichments at wellhead temperature and different pressures to determine the effect of increasing depth/pressure to the microbial community and their ability to degrade oil. We observed oil degradation under all pressure conditions tested [0.1, 15, and 30 megapascals (MPa)], although oil degradation profiles, cell numbers, and hydrocarbon degradation gene abundances indicated greatest activity at atmospheric pressure. Under all incubations the growth of psychrophilic bacteria was promoted. Bacteria closely related to RB-8 dominated the communities at all pressures. At 30 MPa we observed a shift toward , a genus that includes piezophiles. Alphaproteobacterial members of the , previously associated with oil-degradation, were also highly abundant at 0.1 MPa. Our results suggest that pressure acts synergistically with low temperature to slow microbial growth and thus oil degradation in deep-sea environments.
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http://dx.doi.org/10.3389/fmicb.2018.00808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932198PMC
April 2018

Water-splitting-based, sustainable and efficient H production in green algae as achieved by substrate limitation of the Calvin-Benson-Bassham cycle.

Biotechnol Biofuels 2018 19;11:69. Epub 2018 Mar 19.

1Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Temesvári krt. 62, 6726 Szeged, Hungary.

Background: Photobiological H production has the potential of becoming a carbon-free renewable energy source, because upon the combustion of H, only water is produced. The [Fe-Fe]-type hydrogenases of green algae are highly active, although extremely O-sensitive. Sulphur deprivation is a common way to induce H production, which, however, relies substantially on organic substrates and imposes a severe stress effect resulting in the degradation of the photosynthetic apparatus.

Results: We report on the establishment of an alternative H production method by green algae that is based on a short anaerobic induction, keeping the Calvin-Benson-Bassham cycle inactive by substrate limitation and preserving hydrogenase activity by applying a simple catalyst to remove the evolved O. Cultures remain photosynthetically active for several days, with the electrons feeding the hydrogenases mostly derived from water. The amount of H produced is higher as compared to the sulphur-deprivation procedure and the process is photoautotrophic.

Conclusion: Our protocol demonstrates that it is possible to sustainably use algal cells as whole-cell catalysts for H production, which enables industrial application of algal biohydrogen production.
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http://dx.doi.org/10.1186/s13068-018-1069-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5858145PMC
March 2018

Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms.

Trends Biotechnol 2017 09 13;35(9):860-870. Epub 2017 May 13.

King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division, 23955-6900 Thuwal, Saudi Arabia. Electronic address:

The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.
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http://dx.doi.org/10.1016/j.tibtech.2017.04.003DOI Listing
September 2017

On the pathways feeding the H production process in nutrient-replete, hypoxic conditions. Commentary on the article "Low oxygen levels contribute to improve photohydrogen production in mixotrophic non-stressed ", by Jurado-Oller et al., Biotechnology for Biofuels, published September 7, 2015; 8:149.

Biotechnol Biofuels 2017 4;10:116. Epub 2017 May 4.

Biological Research Centre Szeged, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726 Hungary.

Background: Under low O concentration (hypoxia) and low light, cells can produce H gas in nutrient-replete conditions. This process is hindered by the presence of O, which inactivates the [FeFe]-hydrogenase enzyme responsible for H gas production shifting algal cultures back to normal growth. The main pathways accounting for H production in hypoxia are not entirely understood, as much as culture conditions setting the optimal redox state in the chloroplast supporting long-lasting H production. The reducing power for H production can be provided by photosystem II (PSII) and photofermentative processes during which proteins are degraded via yet unknown pathways. In hetero- or mixotrophic conditions, acetate respiration was proposed to indirectly contribute to H evolution, although this pathway has not been described in detail.

Main Body: Recently, Jurado-Oller et al. (Biotechnol Biofuels 8: 149, 7) proposed that acetate respiration may substantially support H production in nutrient-replete hypoxic conditions. Addition of low amounts of O enhanced acetate respiration rate, particularly in the light, resulting in improved H production. The authors surmised that acetate oxidation through the glyoxylate pathway generates intermediates such as succinate and malate, which would be in turn oxidized in the chloroplast generating FADH and NADH. The latter would enter a PSII-independent pathway at the level of the plastoquinone pool, consistent with the light dependence of H production. The authors concluded that the water-splitting activity of PSII has a minor role in H evolution in nutrient-replete, mixotrophic cultures under hypoxia. However, their results with the PSII inhibitor DCMU also reveal that O or acetate additions promoted acetate respiration over the usually dominant PSII-dependent pathway. The more oxidized state experienced by these cultures in combination with the relatively short experimental time prevented acclimation to hypoxia, thus precluding the PSII-dependent pathway from contributing to H production.

Conclusions: In , continuous H gas evolution is expected once low O partial pressure and optimal reducing conditions are set. Under nutrient-replete conditions, the electrogenic processes involved in H photoproduction may rely on various electron transport pathways. Understanding how physiological conditions select for specific metabolic routes is key to achieve economic viability of this renewable energy source.
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http://dx.doi.org/10.1186/s13068-017-0800-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5418857PMC
May 2017

Efficient molasses fermentation under high salinity by inocula of marine and terrestrial origin.

Biotechnol Biofuels 2017 31;10:23. Epub 2017 Jan 31.

Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, 9000 Ghent, Belgium.

Background: Molasses is a dense and saline by-product of the sugar agroindustry. Its high organic content potentially fuels a myriad of renewable products of industrial interest. However, the biotechnological exploitation of molasses is mainly hampered by the high concentration of salts, an issue that is nowadays tackled through dilution. In the present study, the performance of microbial communities derived from marine sediment was compared to that of communities from a terrestrial environment (anaerobic digester sludge). The aim was to test whether adaptation to salinity represented an advantage for fermenting molasses into renewable chemicals such as volatile fatty acids (VFAs) although high sugar concentrations are uncommon to marine sediment, contrary to anaerobic digesters.

Results: Terrestrial and marine microbial communities were enriched in consecutive batches at different initial pH values (pH; either 6 or 7) and molasses dilutions (equivalent to organic loading rates (OLRs) of 1 or 5 g L d) to determine the best VFA production conditions. Marine communities were supplied with NaCl to maintain their native salinity. Due to molasses inherent salinity, terrestrial communities experienced conditions comparable to brackish or saline waters (20-47 mS cm), while marine conditions resembled brine waters (>47 mS cm). Enrichments at optimal conditions of OLR 5 g L d and pH 7 were transferred into packed-bed biofilm reactors operated continuously. The reactors were first operated at 5 g L d, which was later increased to OLR 10 g L d. Terrestrial and marine reactors had different gas production and community structures but identical, remarkably high VFA bioconversion yields (above 85%) which were obtained with conductivities up to 90 mS cm. COD-to-VFA conversion rates were comparable to the highest reported in literature while processing other organic leftovers at much lower salinities.

Conclusions: Although salinity represents a major driver for microbial community structure, proper acclimation yielded highly efficient systems treating molasses, irrespective of the inoculum origin. Selection of equivalent pathways in communities derived from different environments suggests that culture conditions select for specific functionalities rather than microbial representatives. Mass balances, microbial community composition, and biochemical analysis indicate that biomass turnover rather than methanogenesis represents the main limitation to further increasing VFA production with molasses. This information is relevant to moving towards molasses fermentation to industrial application.
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http://dx.doi.org/10.1186/s13068-017-0701-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282813PMC
January 2017

Hydrocarbonoclastic Isolates Exhibit Different Physiological and Expression Responses to -dodecane.

Front Microbiol 2016 21;7:2056. Epub 2016 Dec 21.

Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy.

Autochthonous microorganisms inhabiting hydrocarbon polluted marine environments play a fundamental role in natural attenuation and constitute promising resources for bioremediation approaches. spp. members are ubiquitous in contaminated surface waters and are the first to flourish on a wide range of alkanes after an oil-spill. Following oil contamination, a transient community of different spp. develop, but whether they use a similar physiological, cellular and transcriptomic response to hydrocarbon substrates is unknown. In order to identify which cellular mechanisms are implicated in alkane degradation, we investigated the response of two isolates belonging to different species, KS 293 and SK2 growing on -dodecane (C12) or on pyruvate. Both strains were equally able to grow on C12 but they activated different strategies to exploit it as carbon and energy source. The membrane morphology and hydrophobicity of SK2 changed remarkably, from neat and hydrophilic on pyruvate to indented and hydrophobic on C12, while no changes were observed in KS 293. In addition, SK2 accumulated a massive amount of intracellular grains when growing on pyruvate, which might constitute a carbon reservoir. Furthermore, SK2 significantly decreased medium surface tension with respect to KS 293 when growing on C12, as a putative result of higher production of biosurfactants. The transcriptomic responses of the two isolates were also highly different. KS 293 changes were relatively balanced when growing on C12 with respect to pyruvate, giving almost the same amount of upregulated (28%), downregulated (37%) and equally regulated (36%) genes, while SK2 transcription was upregulated for most of the genes (81%) when growing on pyruvate when compared to C12. While both strains, having similar genomic background in genes related to hydrocarbon metabolism, retained the same capability to grow on C12, they nevertheless presented very different physiological, cellular and transcriptomic landscapes.
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http://dx.doi.org/10.3389/fmicb.2016.02056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174103PMC
December 2016

Challenging Oil Bioremediation at Deep-Sea Hydrostatic Pressure.

Front Microbiol 2016 3;7:1203. Epub 2016 Aug 3.

Center of Microbial Ecology and Technology, University of Gent Gent, Belgium.

The Deepwater Horizon accident has brought oil contamination of deep-sea environments to worldwide attention. The risk for new deep-sea spills is not expected to decrease in the future, as political pressure mounts to access deep-water fossil reserves, and poorly tested technologies are used to access oil. This also applies to the response to oil-contamination events, with bioremediation the only (bio)technology presently available to combat deep-sea spills. Many questions about the fate of petroleum-hydrocarbons within deep-sea environments remain unanswered, as well as the main constraints limiting bioremediation under increased hydrostatic pressures and low temperatures. The microbial pathways fueling oil bioassimilation are unclear, and the mild upregulation observed for beta-oxidation-related genes in both water and sediments contrasts with the high amount of alkanes present in the spilled oil. The fate of solid alkanes (tar), hydrocarbon degradation rates and the reason why the most predominant hydrocarbonoclastic genera were not enriched at deep-sea despite being present at hydrocarbon seeps at the Gulf of Mexico have been largely overlooked. This mini-review aims at highlighting the missing information in the field, proposing a holistic approach where in situ and ex situ studies are integrated to reveal the principal mechanisms accounting for deep-sea oil bioremediation.
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http://dx.doi.org/10.3389/fmicb.2016.01203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971052PMC
August 2016

An impaired metabolic response to hydrostatic pressure explains Alcanivorax borkumensis recorded distribution in the deep marine water column.

Sci Rep 2016 08 12;6:31316. Epub 2016 Aug 12.

Center of Microbial Ecology and Technology (CMET), University of Gent, Coupure Links 653, B 9000 Gent, Belgium.

Alcanivorax borkumensis is an ubiquitous model organism for hydrocarbonoclastic bacteria, which dominates polluted surface waters. Its negligible presence in oil-contaminated deep waters (as observed during the Deepwater Horizon accident) raises the hypothesis that it may lack adaptive mechanisms to hydrostatic pressure (HP). The type strain SK2 was tested under 0.1, 5 and 10 MPa (corresponding to surface water, 500 and 1000 m depth, respectively). While 5 MPa essentially inactivated SK2, further increase to 10 MPa triggered some resistance mechanism, as indicated by higher total and intact cell numbers. Under 10 MPa, SK2 upregulated the synthetic pathway of the osmolyte ectoine, whose concentration increased from 0.45 to 4.71 fmoles cell(-1). Central biosynthetic pathways such as cell replication, glyoxylate and Krebs cycles, amino acids metabolism and fatty acids biosynthesis, but not β-oxidation, were upregulated or unaffected at 10 MPa, although total cell number was remarkably lower with respect to 0.1 MPa. Concomitantly, expression of more than 50% of SK2 genes was downregulated, including genes related to ATP generation, respiration and protein translation. Thus, A. borkumensis lacks proper adaptation to HP but activates resistance mechanisms. These consist in poorly efficient biosynthetic rather than energy-yielding degradation-related pathways, and suggest that HP does represent a major driver for its distribution at deep-sea.
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http://dx.doi.org/10.1038/srep31316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981847PMC
August 2016

Osmotic Stress Confers Enhanced Cell Integrity to Hydrostatic Pressure but Impairs Growth in Alcanivorax borkumensis SK2.

Front Microbiol 2016 18;7:729. Epub 2016 May 18.

Center for Microbial Ecology and Technology, Department of Biochemical and Microbial Technology, University of Ghent Ghent, Belgium.

Alcanivorax is a hydrocarbonoclastic genus dominating oil spills worldwide. While its presence has been detected in oil-polluted seawaters, marine sediment and salt marshes under ambient pressure, its presence in deep-sea oil-contaminated environments is negligible. Recent laboratory studies highlighted the piezosensitive nature of some Alcanivorax species, whose growth yields are highly impacted by mild hydrostatic pressures (HPs). In the present study, osmotic stress was used as a tool to increase HP resistance in the type strain Alcanivorax borkumensis SK2. Control cultures grown under standard conditions of salinity and osmotic pressure with respect to seawater (35.6 ppt or 1136 mOsm kg(-1), respectively) were compared with cultures subjected to hypo- and hyperosmosis (330 and 1720 mOsm kg(-1), or 18 and 62 ppt in salinity, equivalent to brackish and brine waters, respectively), under atmospheric or increased HP (0.1 and 10 MPa). Osmotic stress had a remarkably positive impact on cell metabolic activity in terms of CO2 production (thus, oil bioremediation) and O2 respiration under hyperosmosis, as acclimation to high salinity enhanced cell activity under 10 MPa by a factor of 10. Both osmotic shocks significantly enhanced cell protection by reducing membrane damage under HP, with cell integrities close to 100% under hyposmosis. The latter was likely due to intracellular water-reclamation as no trace of the piezolyte ectoine was found, contrary to hyperosmosis. Notably, ectoine production was equivalent at 0.1 MPa in hyperosmosis-acclimated cells and at 10 MPa under isosmotic conditions. While stimulating cell metabolism and enhancing cell integrity, osmotic stress had always a negative impact on culture growth and performance. No net growth was observed during 4-days incubation tests, and CO2:O2 ratios and pH values indicated that culture performance in terms of hydrocarbon degradation was lowered by the effects of osmotic stress alone or combined with increased HP. These findings confirm the piezosensitive nature of A. borkumensis, which lacks proper resistance mechanisms to improve its metabolic efficiency under increased HP, thus explaining its limited role in oil-polluted deep-sea environments.
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http://dx.doi.org/10.3389/fmicb.2016.00729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870253PMC
May 2016

Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria?

Sci Rep 2016 Mar 29;6:23526. Epub 2016 Mar 29.

Laboratory of Microbial Ecology and Technology (LabMET), University of Gent, Coupure Links 653, B 9000 Gent, Belgium.

Oil spills represent an overwhelming carbon input to the marine environment that immediately impacts the sea surface ecosystem. Microbial communities degrading the oil fraction that eventually sinks to the seafloor must also deal with hydrostatic pressure, which linearly increases with depth. Piezosensitive hydrocarbonoclastic bacteria are ideal candidates to elucidate impaired pathways following oil spills at low depth. In the present paper, we tested two strains of the ubiquitous Alcanivorax genus, namely A. jadensis KS_339 and A. dieselolei KS_293, which is known to rapidly grow after oil spills. Strains were subjected to atmospheric and mild pressure (0.1, 5 and 10 MPa, corresponding to a depth of 0, 500 and 1000 m, respectively) providing n-dodecane as sole carbon source. Pressures equal to 5 and 10 MPa significantly lowered growth yields of both strains. However, in strain KS_293 grown at 10 MPa CO2 production per cell was not affected, cell integrity was preserved and PO4(3-) uptake increased. Analysis of its transcriptome revealed that 95% of its genes were downregulated. Increased transcription involved protein synthesis, energy generation and respiration pathways. Interplay between these factors may play a key role in shaping the structure of microbial communities developed after oil spills at low depth and limit their bioremediation potential.
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http://dx.doi.org/10.1038/srep23526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810429PMC
March 2016

Multipurpose, Integrated 2nd Generation Biorefineries.

Biomed Res Int 2016 19;2016:4327575. Epub 2016 Jan 19.

Centre for Sustainable Chemical Technologies (CSCT), University of Bath, Bath BA2 7AY, UK.

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http://dx.doi.org/10.1155/2016/4327575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4745271PMC
November 2016

High impact biowastes from South European agro-industries as feedstock for second-generation biorefineries.

Crit Rev Biotechnol 2016 6;36(1):175-89. Epub 2014 Nov 6.

a Department of Civil , Chemical, Environmental and Materials Engineering (DICAM), Alma Mater Studiorum, University of Bologna , Bologna , Italy.

Availability of bio-based chemicals, materials and energy at reasonable cost will be one of the forthcoming issues for the EU economy. In particular, the development of technologies making use of alternative resources to fossil fuels is encouraged by the current European research and innovation strategy to face the societal challenge of natural resource scarcity, fossil resource dependence and sustainable economic growth. In this respect, second- generation biorefineries, i.e. biorefineries fed with biowastes, appear to be good candidates to substitute and replace the present downstream processing scheme. Contrary to first-generation biorefineries, which make use of dedicated crops or primary cultivations to achieve such a goal, the former employ agricultural, industrial, zootechnical, fishery and forestry biowastes as the main feedstock. This leaves aside any ethical and social issue generated by first-generation approaches, and concomitantly prevents environmental and economical issues associated with the disposal of the aforementioned leftovers. Unfortunately, to date, a comprehensive and updated mapping of the availability and potential use of bioresources for second-generation biorefineries in Europe is missing. This is a lack that severely limits R&D and industrial applications in the sector. On the other hand, attempts at valorizing the most diverse biowastes dates back to the nineteenth century and plenty of information in the literature on their sustainable exploitation is available. However, the large majority of these investigations have been focused on single fractions of biowastes or single steps of biowaste processing, preventing considerations on an integrated and modular (cascade) approach for the whole valorization of organic leftovers. This review aims at addressing these issues by gathering recent data on (a) some of the main high-impact biowastes located in Europe and in particular in its Southern part, and (b) the bio-based chemicals, materials and fuels that can be produced from such residues. In particular, we focused on those key compounds referred to as "chemical platforms", which have been indicated as fundamental to generate the large majority of the industrially relevant goods to date.
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http://dx.doi.org/10.3109/07388551.2014.947238DOI Listing
September 2016

Uncoupled hydrogen and volatile fatty acids generation in a two-step biotechnological anaerobic process fed with actual site wastewater.

N Biotechnol 2015 May 29;32(3):341-6. Epub 2014 Aug 29.

Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, via Terracini 28, 40131 Bologna, Italy.

Among agro-wastes, olive mill wastewater (OMW) truly qualifies as a high impact organic residue due to its biochemical-rich composition and high annual production. In the present investigation, dephenolized OMW (OMWdeph) was employed as the feedstock for a biotechnological two-stage anaerobic process dedicated to the production of biohydrogen and volatile fatty acids (VFAs), respectively. To this end, two identically configured packed-bed biofilm reactors were operated sequentially. In the first, the hydraulic retention time was set to 1 day, whereas in the second it was equal to 5 days. The rationale was to decouple the hydrolysis of the organic macronutrients held by the OMWdeph, so as to quantitatively generate a biogas enriched in H2 (first stage aim), for the acidogenesis of the residual components left after hydrolysis, to then produce a highly concentrated mixture of VFAs (second stage aim). Results showed that the generation of H2 and VFAs was effectively split, with carbohydrates and lipids, respectively, being the main substrates of the two processes. About 250 ml H2 L(-1) day(-1) was produced, corresponding to a yield of 0.36 mol mol(-1) of consumed carbohydrates (expressed as glucose equivalents). The overall concentration of VFAs in the acidogenic process was 13.80 g COD L(-1), so that 2.76 g COD L(-1) day(-1) was obtained. Second generation biorefineries use a selected fraction of an organic waste to conduct a microbiologically-driven pathway towards the generation of one target molecule. With the proposed approach, a greater value of the waste was attained, since the multi-purpose two-stage process did not entail competition for substrates between the first and the second steps.
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http://dx.doi.org/10.1016/j.nbt.2014.08.002DOI Listing
May 2015

Acclimation to hypoxia in Chlamydomonas reinhardtii: can biophotolysis be the major trigger for long-term H2 production?

New Phytol 2014 Dec 8;204(4):890-900. Epub 2014 Aug 8.

Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), School of Engineering and Architecture, Alma Mater Studiorum, University of Bologna, Via U. Terracini 28, I-40131, Bologna, Italy.

In anaerobiosis, the microalga Chlamydomonas reinhardtii is able to produce H2 gas. Electrons mainly derive from mobilization of internal reserves or from water through biophotolysis. However, the exact mechanisms triggering this process are still unclear. Our hypothesis was that, once a proper redox state has been achieved, H2 production is eventually observed. To avoid nutrient depletion, which would result in enhanced fermentative pathways, we aimed to induce long-lasting H2 production solely through a photosynthesis : respiration equilibrium. Thus, growing cells were incubated in Tris Acetate Phosphate (TAP) medium under low light and high chlorophyll content. After a 250-h acclimation phase, a 350-h H2 production phase was observed. The light-to-H2 conversion efficiency was comparable to that given in some reports operating under sulphur starvation. Electron sources were found to be water, through biophotolysis, and proteins, particularly through photofermentation. Nonetheless, a substantial contribution from acetate could not be ruled out. In addition, photosystem II (PSII) inhibition by 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) showed that it actively contributed to maintaining a redox balance during cell acclimation. In appropriate conditions, PSII may represent the major source of reducing power to feed the H2 evolution process, by inducing and maintaining an ideal excess of reducing power.
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http://dx.doi.org/10.1111/nph.12964DOI Listing
December 2014

Advances in the biotechnology of hydrogen production with the microalga Chlamydomonas reinhardtii.

Crit Rev Biotechnol 2015 22;35(4):485-96. Epub 2014 Apr 22.

a Sede di Firenze, Via Madonna del Piano, Istituto per lo Studio degli Ecosistemi , Sesto Fiorentino , Italy .

Biological hydrogen production is being evaluated for use as a fuel, since it is a promising substitute for carbonaceous fuels owing to its high conversion efficiency and high specific energy content. The basic advantages of biological hydrogen production over other "green" energy sources are that it does not compete for agricultural land use, and it does not pollute, as water is the only by-product of the combustion. These characteristics make hydrogen a suitable fuel for the future. Among several biotechnological approaches, photobiological hydrogen production carried out by green microalgae has been intensively investigated in recent years. A select group of photosynthetic organisms has evolved the ability to harness light energy to drive hydrogen gas production from water. Of these, the microalga Chlamydomonas reinhardtii is considered one of the most promising eukaryotic H2 producers. In this model microorganism, light energy, H2O and H2 are linked by two excellent catalysts, the photosystem 2 (PSII) and the [FeFe]-hydrogenase, in a pathway usually referred to as direct biophotolysis. This review summarizes the main advances made over the past decade as an outcome of the discovery of the sulfur-deprivation process. Both the scientific and technical barriers that need to be overcome before H2 photoproduction can be scaled up to an industrial level are examined. Actual and theoretical limits of the efficiency of the process are also discussed. Particular emphasis is placed on algal biohydrogen production outdoors, and guidelines for an optimal photobioreactor design are suggested.
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http://dx.doi.org/10.3109/07388551.2014.900734DOI Listing
September 2016

Recovery of amorphous polyhydroxybutyrate granules from Cupriavidus necator cells grown on used cooking oil.

Int J Biol Macromol 2014 Nov 19;71:117-23. Epub 2014 Apr 19.

REQUIMTE/CQFB, Chemistry Department, FCT/Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.

Used cooking oil (UCO) was employed as the sole carbon source for the production of polyhydroxybutyrate (PHB) by cultivation in batch mode of Cupriavidus necator DSM 428. The produced biomass was used for extraction of the PHB granules with a solvent-free approach using sodium dodecyl sulfate (SDS), ethylenediaminetetraacetic acid (EDTA), and the enzyme Alcalase in an aqueous medium. The recovered PHB granules showed a degree of purity higher than 90% and no crystallization (i.e., granules were recovered in their 'native' amorphous state) as demonstrated by wide angle X-ray diffraction (WAXS). Granules were characterized according to their thermal properties and stability by differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). Results show that UCO can be used as a renewable resource to produce amorphous PHB granules with excellent properties in a biocompatible manner.
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http://dx.doi.org/10.1016/j.ijbiomac.2014.04.016DOI Listing
November 2014

Biotechnology for the bio- and green economy.

N Biotechnol 2013 Sep;30(6):581-4

Laboratory of Bioengineering, Earth & Life Institute, Université Catholique de Louvain (UCL), Building Boltzmann/Mendel (c.025), 2 Croix du Sud (Box L7.05.19), B-1348 Louvain-la-Neuve, Belgium.

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http://dx.doi.org/10.1016/j.nbt.2013.08.009DOI Listing
September 2013

A physicochemical-biotechnological approach for an integrated valorization of olive mill wastewater.

Bioresour Technol 2011 Nov 28;102(22):10273-9. Epub 2011 Aug 28.

Department of Civil, Environmental and Materials Engineering (DICAM), Unit of Environmental Biotechnology and Biorefineries, Faculty of Engineering, University of Bologna, via Terracini 28, 40131 Bologna, Italy.

An integrated physicochemical-biotechnological approach for a multipurpose valorization of olive mill wastewaters was studied. More than 60% of the wastewater natural polyphenols were recovered through a solid phase extraction procedure, by employing Amberlite XAD16 resin as the adsorbent and ethanol as the biocompatible desorbing phase. Thereafter, the dephenolized effluent was fed to a mesophilic anaerobic acidogenic packed-bed biofilm reactor for the bioconversion of the organic leftover into volatile fatty acids (VFAs). A VFAs concentration of 19 gCODL(-1) was obtained, representing more than 70% of the COD occurring in the anaerobic effluent. The biotechnological process was assessed by means of bio-molecular analyses, which showed that the reactor packed bed was mostly colonized by bacteria of the Firmicutes phylogenetic group. The biorefinery scheme developed in this study allowed the obtainment of 1.59 g of polyphenols per liter of wastewater treated and 2.72 gCODL(-1) day(-1) of VFAs.
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http://dx.doi.org/10.1016/j.biortech.2011.08.080DOI Listing
November 2011