Microbial community analyses of three distinct, liquid cultures that degrade methyl tert-butyl ether using anaerobic metabolism

Methyl tert-butyl ether (MTBE) is a prevalent groundwater contaminant. In this study, three distinct MTBE-degrading, anaerobic cultures were derived from MTBE-contaminated aquifer material: cultures NW1, NW2 and NW3. The electron acceptors used are anthraquinone-2,6-disulfonate (AQDS; NW1), sulfate (NW2) and fumarate (NW3), respectively. About 1–2 mM MTBE is consistently degraded within 20–30 days in each culture. The 16S rDNA-based amplified ribosomal DNA restriction analysis (ARDRA) was used to analyze the microbial community in each culture. Results indicate novel microorganisms (i.e. no closely related known genera or species) catalyze anaerobic MTBE biodegradation, and microbial diversity varied with different electron acceptors. Tert-butyl alcohol (TBA) accumulated to nearly stoichiometric levels, and these cultures will be critical to understanding the factors that influence TBA accumulation versus degradation. The cultures presented here are the first stable anaerobic MTBE-degrading cultures that have been characterized with respect to taxonomy.     

Biotransformation products and mineralization potential for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in abiotic versus biological degradation pathways with anthraquinone-2,6-disulfonate (AQDS) and <Emphasis Type="Italic">Geobacter metallireducens</Emphasis>

This study investigated extracellular electron shuttle-mediated RDX biodegradation and the distribution of ring cleavage metabolites generated by biological degradation (cells) versus the products formed by abiotic degradation (reduced electron shuttles), and when the two pathways were acting simultaneously. All pathways were influenced by pH. Buffered suspensions (pH 6.8/7.9/9.2) were performed with cell-free anthrahydroquinone-2,6-disulfonate as the sole electron donor, cells (Geobacter metallireducens) + acetate, or cells/acetate + anthraquinone-2,6-disulfonate as an electron shuttle. The metabolites identified included methylenedinitramine, formaldehyde, nitrous oxide, nitrite, ammonium and carbon dioxide. As pH increased, the rates of RDX reduction by AH(2)QDS also increased. Cells alone reduced RDX faster at the lower pH values. However, at all pH the rates of the electron shuttle-mediated pathways were consistently the fastest, and the proportion of carbon present as formaldehyde, which is a precursor to mineralization, was highest in the presence of electron shuttles. Formaldehyde accounted for 45/51/54% of the carbon in electron shuttle amended cell suspensions as opposed to 13/42/45% of carbon without shuttles at the pH 6.8/7.9/9.2, respectively. Approximately 7-20% of RDX was mineralized to CO(2) in the presence of cells at all pH tested; AQDS increased the extent of (14)CO(2) produced. Nitrous oxide and nitrite were end products in the strictly abiotic pathway, but nitrite was depleted in the presence of cells to form ammonium. Understanding the different products formed in the abiotic versus biological pathways and the influence of pH is critical to developing mixed biotic-abiotic remediation strategies for RDX.     

Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments

Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe(III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe(III)-reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments.     

Solvent production from xylose

Xylose is the second most abundant sugar derived from lignocellulose; it is considered less desirable than glucose for fermentation, and strategies that specifically increase xylose utilization in wild type or engineered cells are goals for biofuel production. Issues arise with xylose utilization because of carbohydrate catabolite repression, which is the preferential utilization of glucose relative to xylose in fermentations with both pure and mixed cultures. Taken together the low substrate utilization rates and solvent yields with xylose compared to glucose, many industrial fermentations ignore the xylolytic portion of the reaction in lieu of methods to maintain high glucose. This is shortsighted given the massive potential for xylose generation from a number of sustainable biomass feedstocks, based on utilization of the hemicellulose fraction(s) that enter pretreatment. A number of strategies have been developed in recent years to address xylose utilization and solvent production from xylose in systems with just xylose, or in systems with mixtures of glucose plus xylose, which are more typical of pretreated lignocellulose. The approaches vary in terms of complexity, stability, and ease of introduction to existing fermentation infrastructure (i.e., so-called drop-in fermentation strategies). Some approaches can be considered traditional engineering approaches (e.g., change the reaction conditions), while others are more subtle cellular approaches to eliminate the impacts of catabolite repression. Finally, genetic engineering has been used to increase xylose utilization, although this can be considered a relatively nascent approach compared to manipulations completed to date for glucose utilization.

     

Continent‐scale phenotype mapping using citizen scientists’ photographs

Field investigations of phenotypic variation in free‐living organisms are often limited in scope owing to time and funding constraints. By collaborating with online communities of amateur naturalists, investigators can greatly increase the amount and diversity of phenotypic data in their analyses while simultaneously engaging with a public audience. Here, we present a method for quantifying phenotypes of individual organisms in citizen scientists’ photographs. We then show that our protocol for measuring wing phenotypes from photographs yields accurate measurements in two species of Calopterygid damselflies. Next, we show that, while most observations of our target species were made by members of the large and established community of amateur naturalists at iNaturalist.org , our efforts to increase recruitment through various outreach initiatives were successful. Finally, we present results from two case studies: 1) an analysis of wing pigmentation in male smoky rubyspots Hetaerina titia showing previously undocumented geographical variation in a seasonal polyphenism, and 2) an analysis of variation in the relative size of the wing spots of male banded demoiselles Calopteryx splendens in Great Britain questioning previously documented evidence for character displacement. Our results demonstrate that our protocol can be used to create high quality phenotypic datasets using citizen scientists’ photographs, and, when combined with metadata (e.g. date and location), can greatly broaden the scope of studies of geographical and temporal variation in phenotypes. Our analyses of the recruitment and engagement process also demonstrate that collaborating with an online community of amateur naturalists can be a powerful way to conduct hypothesis‐driven research aiming to elucidate the processes that impact trait evolution at landscape scales.     

Ferric iron and extracellular electron shuttling increase xylose utilization and butanol production during fermentation with multiple solventogenic bacteria

Xylose is the second most abundant sugar derived from lignocellulose; it is considered less desirable than glucose for fermentation, and strategies that specifically increase xylose utilization in wild-type cells are goals for biofuel production. Xylose consumption, butanol production, and hydrogen production increased in both Clostridium beijerinckii and a novel solventogenic bacterium (strain DC-1) when anthraquinone-2,6,-disulfonate (AQDS) or riboflavin were used as redox mediators to transfer electrons to poorly crystalline Fe(OH)₃ as an extracellular electron sink. Strain DC-1 was most closely related to Rhizobiales bacterium Mfc52 based on 95% 16S rRNA gene sequence similarity, which demonstrates that this response is not limited to a single genus of xylose-fermenting bacteria. Xylose utilization and butanol production were negligible in control incubations containing cells plus 3% (w/v) xylose alone during a 10-day batch fermentation, for both strains tested (n-butanol titers of 0.05 g L⁻¹). Micromolar concentrations of AQDS and riboflavin were added as electron shuttling compounds with poorly crystalline Fe(OH)₃ as an insoluble electron acceptor, and respective n-butanol titers increased to 6.35 and 7.46 g L⁻¹. Increases in xylose consumption for the iron treatments were relatively high, from less than 0.49 g L⁻¹ (xylose alone, no iron or electron shuttling molecules) to 25.98 and 29.15 g L⁻¹ for the AQDS and riboflavin treatments, respectively. Hydrogen production was also 3.68 times greater for the AQDS treatment and 5.27 greater for the riboflavin treatment relative to controls. Strain DC-1 data were similar, again indicating that the effects are not specific to the genus Clostridium.

     

Dolphins Can Maintain Vigilant Behavior through Echolocation for 15 Days without Interruption or Cognitive Impairment

In dolphins, natural selection has developed unihemispheric sleep where alternating hemispheres of their brain stay awake. This allows dolphins to maintain consciousness in response to respiratory demands of the ocean. Unihemispheric sleep may also allow dolphins to maintain vigilant states over long periods of time. Because of the relatively poor visibility in the ocean, dolphins use echolocation to interrogate their environment. During echolocation, dolphin produce clicks and listen to returning echoes to determine the location and identity of objects. The extent to which individual dolphins are able to maintain continuous vigilance through this active sense is unknown. Here we show that dolphins may continuously echolocate and accurately report the presence of targets for at least 15 days without interruption. During a total of three sessions, each lasting five days, two dolphins maintained echolocation behaviors while successfully detecting and reporting targets. Overall performance was between 75 to 86% correct for one dolphin and 97 to 99% correct for a second dolphin. Both animals demonstrated diel patterns in echolocation behavior. A 15-day testing session with one dolphin resulted in near perfect performance with no significant decrement over time. Our results demonstrate that dolphins can continuously monitor their environment and maintain long-term vigilant behavior through echolocation.     

Evoked potential audiometry of 13 Pacific bottlenose dolphins (Tursiops truncatus gilli)

Evoked potential audiograms were measured in 13 Pacific bottlenose dolphins (Tursiops truncatus gilli) to determine the variability in hearing sensitivity and range of hearing. The auditory evoked potential system used a transducer embedded in a suction cup to deliver sinusoidal amplitude modulated tones to each dolphin through the pan region of the lower right jaw. Evoked potentials were recorded noninvasively using surface electrodes, and hearing thresholds were estimated by tracking the amplitude of the envelope following response, an evoked potential that is phase‐locked to the stimulus modulation rate. Frequencies tested ranged from 10 to 180 kHz in each animal. Variability in the range of hearing and age‐related reductions in hearing sensitivity and range of hearing were consistent with those observed in Atlantic bottlenose dolphins. Comparison of audiograms to a captive population of Atlantic bottlenose dolphins demonstrated that the Pacific bottlenose dolphins tested in this study had significantly lower thresholds at frequencies of 40 and 60–115 kHz. Differences in thresholds between the groups are unlikely to be due to methodological factors.     

Anthrahydroquinone-2,6,-disulfonate (AH<Subscript>2</Subscript>QDS) increases hydrogen molar yield and xylose utilization in growing cultures of <Emphasis Type="Italic">Clostridium beijerinckii</Emphasis>

H₂ production and xylose utilization were investigated using the fermentative culture Clostridium beijerinckii NCIMB 8052. Adding anthrahydroquinone-2,6-disulfonate (AH₂QDS) increased the extent of xylose utilization by 56% and hydrogen molar yield by 24–37%. Enhanced hydrogen molar yield correlated with increased xylose utilization and increases in the acetate/butyrate product ratio. An electron balance indicated that AH₂QDS shifted the electrons from the butyric acid pathway (NADH-dependent pathway) to the acetic acid pathway (non-NADH-dependent pathway), putatively creating a surplus of reducing equivalents that were then available for hydrogen production. These data demonstrate that hydrogen yield and xylose utilization can be manipulated by amending redox active molecules into growing cultures. This will impact biohydrogen/biofuel production by allowing physiological manipulations of growing cells for increased (or decreased) output of selected metabolites using amendments that are not consumed during the reactions. Although the current yield increases are small, they suggest a target for cellular alterations. In addition, increased xylose utilization will be critical to the fermentation of pretreated lignocellulosic feedstocks, which may have higher xylose content.     

The IPV-GBM Scale: A New Scale to Measure Intimate Partner Violence among Gay and Bisexual Men

Objectives

The paper describes the creation of a new scale to measure intimate partner violence (IPV) among gay and bisexual men.

Methods

Seven focus group discussions were held with gay and bisexual men, focusing on defining intimate partner violence: 30 forms of IPV were identified. A venue-recruited sample of 912 gay and bisexual men was surveyed, examining definitional understanding and recent experiences of each of the 30 forms of IPV. Participants were also asked questions from the CDC definition of intimate partner violence and the short-form of the Conflicts Tactics Scale (CTS2S). Factor analysis of responses to the definitional questions was used to create the IPV-GBM scale, and the prevalence of intimate partner violence was compared with that identified by the CDC and CTS2S measures of intimate partner violence.

Results

A 23-item scale, with 5 unique domains, was created, with strong internal reliability (Cronbach Alpha >.90). The IPV-GBM scale mirrored both the CDC and CTS2S definitions of intimate partner violence, but contained additional domains such as controlling violence, monitoring behaviors, emotional violence, and HIV-related violence. The new scale identified a significantly higher prevalence of IPV than either of the more commonly used measures.

Conclusions

The results presented here provide encouraging evidence for a new, more accurate measure of intimate partner violence among gay and bisexual men in the U.S.