Papers by Birgitte Ahring
Applied and Environmental Microbiology, Mar 1, 1992
The effects of Mg2+ on thermophilic (55°C) granules grown on acetate in 0.2-liter upflow anaerobi... more The effects of Mg2+ on thermophilic (55°C) granules grown on acetate in 0.2-liter upflow anaerobic sludge blanket reactors were studied. The methanogens in the granules were identified and counted by using antibody probes and the antigenic fingerprinting method. Packets of large coccoidal cells antigenically related to Methanosarcina thermophila TM-1 were scarce in the absence of Mg2' but increased with increasing Mg2+ concentrations up to 30 mM; Methanosarcina packets immunologically related to Methanosarcina barkeri R1M3 showed a similar trend, and their numbers increased up to 100 mM Mg2+. The number of single cells antigenically related to TM-1, R1M3, and Methanosarcina mazei S-6 were scarce at low Mg2+ concentrations but increased drastically at 30 and 100 mM Mg2+. The number of rod-shaped bacteria antigenically related to Methanobacterium thermoautotrophicum GC1 and AH was highest with no Mg2+ present, and their numbers decreased with increasing concentrations of the cation. These quantitative data, obtained by counting cells in suspensions made from disrupted granules, were confirmed by microscopic observation of the methanogenic subpopulations in thin histologic sections of the granules.
Applied and Environmental Microbiology, 1993
A thermophilic upflow anaerobic sludge blanket (UASB) reactor degrading acetate was started by ap... more A thermophilic upflow anaerobic sludge blanket (UASB) reactor degrading acetate was started by applying published methods (W. M. Wiegant and A. W. A. de Man, Biotechnol. Bioeng. 28:718-77, 1986) for production of granules dominated by Methanothrix spp. The reactor was inoculated with thermophilic digested sludge. No granules were observed during the first 7 months of start-up of the UASB reactor. However, after the concentrations of potassium, phosphate, ammonium, and magnesium in the medium were gradually increased, granules developed, indicating that there was a critical concentration of one or more of the ions required for production of granules from the starting material. After several years of stable operation, the effect of removing 60% of the granular sludge was investigated. Immunologic qualitative and quantitative studies showed that removal of the granular sludge resulted in an increase in the number of the predominant methanogens, antigenically related to Methanosarcina t...
Applied and Environmental Microbiology, 1992
Methanogenic upflow anaerobic granular-sludge blanket (UASB) reactors treat wastewaters at a high... more Methanogenic upflow anaerobic granular-sludge blanket (UASB) reactors treat wastewaters at a high rate while simultaneously producing a useful product, methane; however, recalcitrant environmental pollutants may not be degraded. To impart 3-chlorobenzoate (3-CB)-dechlorinating ability to UASB reactors, we inoculated granular sludge in UASB reactors with either a pure culture of Desulfomonile tiedjei (a 3-CB-dechlorinating anaerobe) or a three-member consortium consisting of D. tiejei, a benzoate degrader, and an H2-utilizing methanogen. No degradation occurred in an uninoculated control reactor which was started with the same granular sludge, but inoculated reactors and granules from the inoculated UASB systems rapidly transformed 3-CB (54 mumol/day/g of granule biomass). After several months at a hydraulic retention time of 0.5 day, much shorter than the generation time of D. tiedjei, the reactors still dechlorinated 3-CB. This indicated that the bacteria were immobilized in the re...
Applied and Environmental Microbiology, 1995
Granules from a mesophilic upflow anaerobic sludge blanket reactor were disintegrated, and bacter... more Granules from a mesophilic upflow anaerobic sludge blanket reactor were disintegrated, and bacteria utilizing only hydrogen or formate or both hydrogen and formate were added to investigate the role of interspecies electron transfer during degradation of propionate and butyrate. The data indicate that the major electron transfer occurred via interspecies hydrogen transfer, while interspecies formate transfer may not be essential for interspecies electron transfer in this system during degradation of propionate and butyrate.
Microbiology and Molecular Biology Reviews, 1999
SUMMARY The field covered in this review is new; the first sequence of a gene encoding the molecu... more SUMMARY The field covered in this review is new; the first sequence of a gene encoding the molecular chaperone Hsp70 and the first description of a chaperonin in the archaea were reported in 1991. These findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular biology and biochemistry of life in extreme environments, and stress tolerance at the cellular and molecular levels. In the last 8 years, archaeal stress genes and proteins belonging to the families Hsp70, Hsp60 (chaperonins), Hsp40(DnaJ), and small heat-shock proteins (sHsp) have been studied. The hsp70(dnaK), hsp40(dnaJ), and grpE genes (the chaperone machine) have been sequenced in seven, four, and two species, respectively, but their expression has been examined in detail only in ...
Journal of microbiological methods, Apr 1, 2017
In recent years, versatile genetic tools have been developed and applied to a number of filamento... more In recent years, versatile genetic tools have been developed and applied to a number of filamentous fungi of industrial importance. However, the existing techniques have limitations when it comes to achieve the desired genetic modifications, especially for efficient gene targeting. In this study, we used Aspergillus carbonarius as a host strain due to its potential as a cell factory, and compared three gene targeting techniques by disrupting the ayg1 gene involved in the biosynthesis of conidial pigment in A. carbonarius. The absence of the ayg1 gene leads to phenotypic change in conidia color, which facilitated the analysis on the gene targeting frequency. The examined transformation techniques included Agrobacterium-mediated transformation (AMT) and protoplast-mediated transformation (PMT). Furthermore, the PMT for the disruption of the ayg1 gene was carried out with bipartite gene targeting fragments and the recently adapted CRISPR-Cas9 system. All three techniques were successfu...
The Science of the total environment, Jan 10, 2015
Anaerobic digestate has valuable potential as organic fertilizer or soil amendment, given that it... more Anaerobic digestate has valuable potential as organic fertilizer or soil amendment, given that it typically contains high amounts of plant nutrients, such as nitrogen, phosphate and plant hormones. In this study, ammonia stripping and vacuum evaporation were tested to compare their technical feasibilities and their effects on plant nutrient properties in the liquid fraction of digestate. Results of the batch experiments showed that the nutrient characteristics of liquid digestate, including total ammonia nitrogen (TAN), soluble P, gibberellic acid (GA), indoleacetic acid (IAA) and abscisic acid (ABA), were strongly dependent on the initial pH in both ammonia stripping and vacuum evaporation processes. A low plant nutrient concentration (TAN 137mg·L(-1), soluble P 1.5mg·L(-1), GA3/ABA 0.04) in the liquid digestate was achieved in the ammonia stripping process with Ca(OH)2 addition of 12g·L(-1), whereas a high nutrient concentration (TAN 2998mg·L(-1), soluble P 178.3mg·L(-1), IAA 60.9...
Applied microbiology and biotechnology, Jan 31, 2015
Aspergillus saccharolyticus exhibits great potential as a cell factory for industrial production ... more Aspergillus saccharolyticus exhibits great potential as a cell factory for industrial production of dicarboxylic acids. In the analysis of the organic acid profile, A. saccharolyticus was cultivated in an acid production medium using two different pH conditions. The specific activities of the enzymes, pyruvate carboxylase (PYC), malate dehydrogenase (MDH), and fumarase (FUM), involved in the reductive tricarboxylic acid (rTCA) branch, were examined and compared in cells harvested from the acid production medium and a complete medium. The results showed that ambient pH had a significant impact on the pattern and the amount of organic acids produced by A. saccharolyticus. The wild-type strain produced higher amount of malic acid and succinic acid in the pH buffered condition (pH 6.5) compared with the pH non-buffered condition. The enzyme assays showed that the rTCA branch was active in the acid production medium as well as the complete medium, but the measured enzyme activities were ...
Water Research, 1996
Denitrification and methanogenesis of a synthetic wastewater containing volatile fatty acids and ... more Denitrification and methanogenesis of a synthetic wastewater containing volatile fatty acids and nitrate were obtained in a single-stage process using an upflow anaerobic sludge blanket (UASB) reactor. The reactor was initially inoculated with methanogenic granular sludge ...
Analytical and bioanalytical chemistry, 2014
Compared to traditional IR methods, Raman spectroscopy has the advantage of only minimal interfer... more Compared to traditional IR methods, Raman spectroscopy has the advantage of only minimal interference from water when measuring aqueous samples, which makes this method potentially useful for in situ monitoring of important industrial bioprocesses. This study demonstrates real-time monitoring of a Saccharomyces cerevisiae fermentation process using a Raman spectroscopy instrument equipped with a robust sapphire ball probe. A method was developed to correct the Raman signal for the attenuation caused by light scattering cell particulate, hence enabling quantification of reaction components and possibly measurement of yeast cell concentrations. Extinction of Raman intensities to more than 50 % during fermentation was normalized with approximated extinction expressions using Raman signal of water around 1,627 cm(-1) as internal standard to correct for the effect of scattering. Complicated standard multi-variant chemometric techniques, such as PLS, were avoided in the quantification mod...
PLoS ONE, 2013
The isoprenoid pathway converts pyruvate to isoprene and related isoprenoid compounds in plants a... more The isoprenoid pathway converts pyruvate to isoprene and related isoprenoid compounds in plants and some bacteria. Currently, this pathway is of great interest because of the critical role that isoprenoids play in basic cellular processes, as well as the industrial value of metabolites such as isoprene. Although the regulation of several pathway genes has been described, there is a paucity of information regarding system level regulation and control of the pathway. To address these limitations, we examined Bacillus subtilis grown under multiple conditions and determined the relationship between altered isoprene production and gene expression patterns. We found that with respect to the amount of isoprene produced, terpenoid genes fall into two distinct subsets with opposing correlations. The group whose expression levels positively correlated with isoprene production included dxs, which is responsible for the commitment step in the pathway, ispD, and two genes that participate in the mevalonate pathway, yhfS and pksG. The subset of terpenoid genes that inversely correlated with isoprene production included ispH, ispF, hepS, uppS, ispE, and dxr. A genome-wide partial least squares regression model was created to identify other genes or pathways that contribute to isoprene production. These analyses showed that a subset of 213 regulated genes was sufficient to create a predictive model of isoprene production under different conditions and showed correlations at the transcriptional level. We conclude that gene expression levels alone are sufficiently informative about the metabolic state of a cell that produces increased isoprene and can be used to build a model that accurately predicts production of this secondary metabolite across many simulated environmental conditions.
Water Research, 2003
Previous studies on the microbial degradation of individual phthalic acid esters (PAEs) have demo... more Previous studies on the microbial degradation of individual phthalic acid esters (PAEs) have demonstrated that the compounds with short ester hydrocarbon chains are easily biodegraded and mineralized, but PAEs with long ester chains are less susceptible to degradation and some of them are considered recalcitrant. Moreover, they inhibit methanogenesis. However, studies have not been made on the effect of feeding a combination of recalcitrant and biodegradable PAEs into anaerobic digesters treating wastewater sludge. The present study was conducted with wastewater sludge from the Los Angeles Bureau of Sanitation's Hyperion Treatment Plant. Di (2-ethylhexyl) phthalate (DEHP), the most common persistent PAE found in wastewater, and din -butyl phthalate (DBP), a common PAE with short ester chains, were sorbed into the sludge fed to a bench-scale digester for a period of 12 weeks. DEHP degradation was always poor, and accumulation of DEHP was correlated with inhibition of the microbial degradation of DBP and with process instability of the test digester. Inhibition of the DBP removal was completely reversed after DEHP addition was discontinued, but biogas production never recovered to the level observed in a control digester. Other process parameters of digester performance were not affected by DEHP accumulation. These results are similar to the toxic effects of long chain fatty acids on sludge digestion, suggesting that DEHP or its degradation products affect all the microbial populations in the anaerobic bioreactor. Our results imply that high levels of DEHP or other recalcitrant PAEs in wastewater sludge are likely to compromise methanogenesis and removal of biodegradable PAEs in sludge digesters.
On May 5-6, 2011, the Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP... more On May 5-6, 2011, the Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP) met to discuss future directions of the BID Science Theme and how to best align EMSL processes with the more proactive model for user engagement outlined in the EMSL 2.0 research plan. Overall, the STAP thought that EMSL operated well as a user facility, but there were areas that could be improved, especially if the objective is to increase its overall scientific impact. For example, the current Science Theme proposal process, with its yearly calls and funding cycles, is perhaps reasonable for a typical, reactive user facility. However, it is less suited for the new, proactive "EMSL 2.0-style" research paradigm. Because of the rapid pace of modern genomics and systems biology research, it is necessary to respond rapidly and flexibly to science opportunities as they arise. The current system is too slow. The STAP felt that to attract the best users, it is important to reduce the "barriers to entry" for EMSL. There are many of these barriers, including difficulty in understanding the useful information that an instrument can provide, a rigid proposal process, and lack of seed money to support students/scientists in performing EMSL studies. Biologists are particularly unfamiliar with the usefulness of advanced technologies. The panel suggested that EMSL create a series of "I Didn't Know You Could Do That!" educational videos to educate the biology community. Also, capabilities descriptions on the website should be in a form understandable and accessible to biologists. Instrument lists are useless to most biologists. Another important outreach effort is the presentation of research by EMSL staff, where they demonstrate the power of the EMSL facility. However, the focus should be on engaging specific users who could deliver the most impactful science, not simply bringing in more users. Forming partnerships with communities of scientists will be essential for achieving the vision of the higher-impact science of EMSL 2.0. Communities tend to self-assemble around funding sources or attend common topical scientific meetings. Broadly, scientific communities can be classified as "mission-oriented" or "basic-science oriented." Mission-oriented communities are most likely to be identified by funding source, while basic science areas tend to self-assemble around meetings, such as Gordon or Keystone Conferences. The organizers of these conferences usually are community leaders. Funding agencies, both public and private, also would know the leaders of the communities. The STAP suggests making lists of community leaders and areas of research that would be potential targets of research. Once potential "fits" are identified, the STAP suggests we simply contact several of these leaders and start a dialogue. Successful conversations eventually could evolve into workshops that would serve to define EMSL 2.0 projects. With respect to U.S. Department of Energy (DOE) mission areas, the obvious communities are those focused on bioenergy research or groups working on systems microbiology. The most organized are the bioenergy research centers (BRCs), and they would be relatively easy to engage because of their well-defined sets of deliverables. One important aspect to consider when engaging DOE community scientists is to also engage the Joint Genome Institute (JGI). Proposing a specific project to JGI in which an important objective of the BRCs was achieved could be a significant winwin situation for both EMSL and JGI and could help win endorsement of the EMSL 2.0 concept from DOE's Office of Biological and Environmental Research (BER). A good focus of this joint project could be the large-scale characterization of genes of unknown function.
FEMS Microbiology Letters, 2005
A hot spring in the solfataric field of Pisciarelli (Naples-Italy) was analysed for Archaeal dive... more A hot spring in the solfataric field of Pisciarelli (Naples-Italy) was analysed for Archaeal diversity. Total DNA was extracted from the environment, archaeal 16S rRNA genes were amplified with Archaea specific primers, and a clone library consisting of 201 clones was established. The clones were grouped in 10 different groups each representing a specific band pattern using restriction fragment length polymorphism (RFLP). Members of all 10 groups were sequenced and phylogenetically analyzed. Surprisingly, a high abundance of clones belonging to non-thermophilic Crenarchaeal clusters were detected together with the thermophilic archaeon Acidianus infernus in this thermophilic environment. Neither Sulfolobus species nor other hyperthermophilic Crenarchaeota were detected in the clone library. The relative abundance of the sequenced clones was confirmed by terminal restriction fragment analyses. Amplification of 16S rRNA genes from Archaea transferred from the surrounding environment was considered negligible because DNA from non-thermophilic Crenarchaeota incubated under conditions similar to the solfatara could not be PCR amplified after 5 min.
FEBS Letters, 1998
The membrane‐bound 3‐chloro‐4‐hydroxyphenylacetate (Cl‐OHPA) reductive dehalogenase from the chlo... more The membrane‐bound 3‐chloro‐4‐hydroxyphenylacetate (Cl‐OHPA) reductive dehalogenase from the chlorophenol‐reducing anaerobe Desulfitobacterium hafniense was purified 11.3‐fold to apparent homogeneity in the presence of the detergent CHAPS. The purified dehalogenase catalyzed the reductive dechlorination of Cl‐OHPA to 4‐hydroxyphenylacetate with reduced methyl viologen as the electron donor at a specific activity of 103.2 nkat/mg protein. SDS‐PAGE revealed a single protein band with an apparent molecular mass of 46.5 kDa. The enzyme contained 0.68±0.2 mol corrinoid, 12.0±0.7 mol iron, and 13.0±0.7 mol acid‐labile sulfur per mol subunit. The N‐terminal amino acid sequence of the enzyme was determined and no significant similarity was found to any protein present in the gene bank.
Energy & Fuels, 2014
ABSTRACT Various organics with quite different oxygen-containing functional groups mixing togethe... more ABSTRACT Various organics with quite different oxygen-containing functional groups mixing together in bio-oil lead to the high instability of bio-oils. A liquid-liquid extraction method was developed to separate the bio-oil into different chemical groups by their polarities to stabilize bio-oils and improve the quality. The separated bio-oil had similar oxygen-containing functional groups in different phases. Biomass pyrolysis using Douglas fir pellet and characterization of the bio-oil chemical compounds were conducted, followed by bio-oil liquid-liquid extractions with several solvents (e.g., hexane, petroleum ether, and chloroform). In comparison to the raw bio-oil, the solvent phase had high concentrations (85%) of phenols and guaiacols, while no sugar and very low acid and alcohol contents were detected, which were left in the water phases.
Biotechnology and Bioengineering, 2005
A novel reactor configuration was investigated for anaerobic digestion (AD) of the organic fracti... more A novel reactor configuration was investigated for anaerobic digestion (AD) of the organic fraction of municipal solid waste (OFMSW). An anaerobic hyper‐thermophilic (68°C) reactor R68 was implemented as a post‐treatment step for the effluent of a thermophilic reactor R1 (55°C) in order to enhance hydrolysis of recalcitrant organic matter, improve sanitation and ease the stripping of ammonia from the reactor. The efficiency of the combined system was studied in terms of methane yield, volatile solids (VS) reduction, and volatile fatty acid (VFA) production at different hydraulic retention times (HRT). A single‐stage thermophilic (55°C) reactor R2 was used as control. VS reduction and biogas yield of the combined system was 78–89% and 640–790 mL/g VS, respectively. While the VS reduction in the combined system was up to 7% higher than in the single‐stage treatment, no increase in methane yield was observed. Shifting the HRT of the hyper‐thermophilic reactor from 5 days to 3 days resu...
Bioresource Technology, 2002
Alkaline wet oxidation pre-treatment (water, sodium carbonate, oxygen, high temperature and press... more Alkaline wet oxidation pre-treatment (water, sodium carbonate, oxygen, high temperature and pressure) of wheat straw was performed as a 2 4À1 fractional factorial design with the process parameters: temperature, reaction time, sodium carbonate and oxygen. Alkaline wet oxidation was an ecient pre-treatment of wheat straw that resulted in solid fractions with high cellulose recovery (96%) and high enzymatic convertibility to glucose (67%). Carbonate and temperature were the most important factors for fractionation of wheat straw by wet oxidation. Optimal conditions were 10 min at 195°C with addition of 12 bar oxygen and 6:5 g l À1 Na 2 CO 3. At these conditions the hemicellulose fraction from 100 g straw consisted of soluble hemicellulose (16 g), low molecular weight carboxylic acids (11 g), monomeric phenols (0.48 g) and 2-furoic acid (0.01 g). Formic acid and acetic acid constituted the majority of degradation products (8.5 g). The main phenol monomers were 4-hydroxybenzaldehyde, vanillin, syringaldehyde, acetosyringone (4-hydroxy-3,5-dimethoxy-acetophenone), vanillic acid and syringic acid, occurring in 0.04±0.12 g per 100 g straw concentrations. High lignin removal from the solid fraction (62%) did not provide a corresponding increase in the phenol monomer content but was correlated to high carboxylic acid concentrations. The degradation products in the hemicellulose fractions co-varied with the pre-treatment conditions in the principal component analysis according to their chemical structure, e.g. diacids (oxalic and succinic acids), furan aldehydes, phenol aldehydes, phenol ketones and phenol acids. Aromatic aldehyde formation was correlated to severe conditions with high temperatures and low pH. Apart from CO 2 and water, carboxylic acids were the main degradation products from hemicellulose and lignin.
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Papers by Birgitte Ahring