Seasonal variability in microbial methanol utilisation in coastal waters of the western English Channel

© The authors 2016. Methanol is ubiquitous in seawater and is the most abundant oxygenated volatile organic compound (OVOC) in the atmosphere, where it influences oxidising capacity and ozone formation. Marine methylotrophic bacteria utilise methanol in seawater as an energy and/or growth substrate. This work represents the first fully resolved seasonal study of marine microbial methanol uptake dynamics. Rates of microbial methanol dissimilation in coastal surface waters of the UK varied between 0.7 and 11.2 nmol l-1 h-1 and reached a maximum in February. Rates of microbial methanol assimilation varied between 0.04 and 2.64 10-2 nmol l-1 h-1 and reached a maximum in August. Temporal variability in microbial methanol uptake rates shows that methanol assimilation and dissimilation display opposing seasonal cycles, although overall

A comparison of European eel Anguilla anguilla eDNA concentrations to fyke net catches in five Irish lakes

The European eel, Anguilla anguilla, is classified as critically endangered by the IUCN. To protect what remains of the European eel population, accurate monitoring methods for this species are important. Environmental DNA (eDNA) techniques are gaining popularity for ecological monitoring of aquatic organisms because they are sensitive and non-invasive. This study directly compared catch data from a standardised fyke-net fishing survey with a single species A. anguilla eDNA survey in five freshwater lakes in Ireland. The eDNA was recovered by the filtration of water samples and amplified by quantitative real-time Polymerase Chain Reaction (qPCR). European eel eDNA was reliably determined in 83 % (70/84) of surface water samples collected from lakes classified as having high, medium and low eel populations. In addition there was a positive association between the eDNA concentrations recovered and the eel population classification with lower eDNA concentrations in lakes classified as low eel population lakes. Similar amounts of A. anguilla eDNA were detected in water samples collected from open water and shore-side, suggesting shore sampling is an adequate method for eel detection. Together, the results demonstrate that eDNA sampling is more sensitive for detecting eel presence in low eel population environments than standard survey methods, and may be a useful non-invasive tool for monitoring A. anguilla species distribution

Combined cognitive and state-control training for children with and without AD/HD: Effects on behaviour, working memory and resting EEG

Abstract presented at the 23rd Australasian Society for Psychophysiology Conference, 20-22 Nov 2013, Wollongong, Australi

The in situ production of aquatic fluorescent organic matter in a simulated freshwater laboratory model

Dissolved organic matter (DOM) is ubiquitous throughout aquatic systems. Fluorescence techniques can be used to characterize the fluorescing proportion of DOM, aquatic fluorescent organic matter (AFOM). AFOM is conventionally named in association with specific fluorescence “peaks,” which fluoresce in similar optical regions as microbially-derived proteinaceous material (Peak T), and terrestrially-derived humic-like compounds (Peaks C/C+), with Peak T previously being investigated as a tool for bacterial enumeration within freshwaters. The impact of anthropogenic nutrient loading on the processing of DOM by microbial communities is largely unknown. Previous laboratory studies utilizing environmental freshwater have employed growth media with complex background fluorescence, or very high nutrient concentrations, preventing the investigation of AFOM production under a range of more representative nutrient concentrations within a matrix exhibiting very low background fluorescence. We describe a laboratory-based model with Pseudomonas aeruginosa that incorporates a low fluorescence growth matrix consisting of a simulated freshwater (SFW), representative of low-hardness freshwater systems allowing controlled nutrient conditions to be studied. The effects of microbial processing of DOM as a function of available nitrogen, phosphorous, and dissolved organic carbon (DOC) in the form of glucose were investigated over 48 h at highly resolved time increments. The model system demonstrates the production of a range of complex AFOM peaks in the presence and absence of DOC, revealing no linear relationship between cell numbers and any of the peaks for the bacterial species studied, with AFOM peaks increasing with microbial cell number, ranging from 55.2 quinine sulfate units (QSU) per 106 cells to 155 QSU per 106 cells (p < 0.05) for Peak T during the exponential growth phase of P. aeruginosa under high nutrient conditions with 5 mg L−1 DOC. Nutrient and DOC concentration was found to cause differential production of autochthonous- or allochthonous-like AFOM, with lower DOC concentrations resulting in higher Peak T production relative to Peaks C/C+ upon the addition of nutrients, and high DOC concentrations resulting in higher Peak C/C+ production relative to Peak T. Our results show the production of allochthonous-like AFOM from a simple and non-fluorescent carbon source, and provide uncertainty in the use of Peak T as a reliable surrogate for specific bacterial enumeration, particularly in dynamic or nutrient-impacted environments, pointing toward the use of fluorescence as an indicator for microbial metabolism

Nationwide tracing of two top freshwater fish invaders in Greece using environmental DNA sampling

Alien fish invasions are causing devastating impacts on native freshwater fauna; thus, rigorous, non-invasive and cost-effective biomonitoring of lotic and lentic freshwaters to design and implement appropriate prevention and control measures is now a priority. In this study, we used a species-specific qPCR eDNA assay to monitor two of the most invasive fish species (Gambusia holbrooki and Pseudorasbora parva) in 15 river basins of Greece and validated these results with conventional fish sampling as well as existing field sampling data. Our monitoring provided new records of invasive species indicating basins for rigorous future monitoring and possible eradication attempts. The eDNA proved more sensitive as a detection tool (56% detection rate) compared to conventional electrofishing (50% detection rate) for G. holbrooki. In contrast, it proved less sensitive for detecting P. parva (38% accuracy) compared to electrofishing (44% accuracy), as evident by the two locations where the eDNA failed to detect the target species. Our study illustrates the potential of the eDNA method for regular, standardised monitoring of riverine habitats for invasive fish species by local managers for early detection. Finally, we discuss the application of eDNA in management interventions for identifying invasive species’ hotspots for management prioritisation, for early detection of invaders and for the monitoring of eradication/control actions

New boundaries: Redefining the geographical range of a threatened fish through environmental DNA survey

Accurate data on the distribution and population status of threatened fish species are fundamental for effective conservation planning and management. In this work, in order to reassess the distribution of the globally threatened Evia barbel, Barbus euboicus, we undertook an environmental DNA (eDNA) survey coupled with conventional electrofishing, focusing on major river basins in Evia Island in proximity to its known occurrence in a single Evian basin (Manikiatiko stream). For comparison purposes, we conducted eDNA sampling in several locations in the geographically closest continental river basin, the Sperchios basin (Central Greece) which hosts the closely related Barbus sperchiensis. Our results expand the known range of the Evia barbel on Evia adding four new river basins, apart from its type locality (Manikiatiko stream (EV3)). In a single Evian River, where the species had never been located before, there was also a positive eDNA signal for Barbus sperchiensis within the same basin. The research confirms the occurrence of Evia barbel in a wider geographical area, highlighting however the sensitive conservation status of the species due to its still very narrow geographical distribution. The biogeographical implications of our study, as well as potential conservation interventions, are discussed

HIVToolbox, an Integrated Web Application for Investigating HIV

Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories. Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site. Weblink: [http://hivtoolbox.bio-toolkit.com

Microbial utilisation of methanol in seawater

Methylotrophs are aerobic bacteria that use methanol as a carbon and/or energy source. They are widespread but have not been extensively studied in marine environments. Seawater 14C tracer studies were combined with molecular biological cultivation- independent techniques (polymerase chain reactions using 16S rRNA and mxaF gene specific primers, 454 pyrosequencing) to investigate temporal and spatial variability in rates of microbial methanol utilisation and methylotrophic community composition in temperate coastal waters of the western English Channel, UK (WEC) and the Atlantic Ocean (Atlantic Meridional Transect 19). Microbial methanol dissimilation rates were, on average, thirteen times higher in waters of the WEC (0.65–11.2 nmol l-1h-1) than in open ocean waters of the Atlantic (0.01–1.7 nmol l-1h-1), with maximum rates found during winter months in the WEC. Highest methanol dissimilation rates in the Atlantic were measured in the north subtropical gyre of up to eight times higher than other Atlantic regions. Microbial methanol assimilation rates in the Atlantic Ocean (0.01–2.2 x10-2 nmol l-1h-1) were up to four times higher than those from the WEC (0.04–2.6 x10-2 nmol l-1h-1). Methanol assimilation rates from the WEC displayed seasonal maxima during summer, but showed methanol bacterial growth efficiency (BGEM) of <1% all year. Overall, assimilation rates were highest in the equatorial upwelling where BGEM reached 17%. Methanol assimilation rates showed a significant positive correlation with bacterial leucine incorporation in contrast to methanol dissimilation, which showed a negative relationship. Methanol dissimilation rates strongly correlated with the abundance of bacteria of the SAR11 clade, previously shown to utilise methanol as an energy source. The first basin scale approach using 454 pyrosequencing in the Atlantic revealed a remarkable increase in bacterial diversity in the nutrient limited southern gyre. Use of mxaF PCR primers also confirmed the ubiquitous presence of methylotrophic bacteria throughout the top 200m of the Atlantic Ocean