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There is remarkable potential for research at the interface between the earth sciences and environmental microbiology that may lead to advances in our understanding of the role of bacterial communities in the surface or subsurface environment of our planet. One mainstay of sedimentary classification is the concept of differential soil and/or paleosol horizons being the result of primarily physical and chemical weathering, with relatively little understanding of how microbial communities between these stratified horizons differ, if at all. In this study we evaluate the differences in microbial community taxonomy and biogeochemical functional potential between stratified soil horizons in an alpine paleosol environment using next-generation sequencing (NGS) shotgun sequencing. Paleosols represent a unique environment to study the effect of differences soil horizon environments on the microbial community due to their relative isolation, and the fact that three distinct stratified soil horizons can be identified within the top 30 cm of the soil. This enables us to assess variation in microbial community composition that will be relatively distinct from variation due to distance alone. We test the hypothesis that variation in soil community composition is linked to variation in the physical and chemical parameters that define stratigraphy. Multivariate statistical analysis of sequencing reads from soil horizons across five sampling sites revealed that 1223 microbial genera vary significantly and consistently in abundance across stratified soil horizons at class level. Specifically Ktedonobacter, Bacilli and Betaproteobacteria responded most strongly to soil depth. Alpha diversity showed a positive correlation with soil depth. Beta diversity, however, did not differ significantly between horizons. Genes involved in carbohydrate and nitrogen metabolism were found to be more abundant in Ah horizon samples. Closer inspection of carbohydrate metabolism genes revealed that genes involved in CO2 fixation, fermentation and saccharide metabolism decreased in abundance with depth while one‑carbon metabolism increased down profile.

The formation, fate, and toxicology of oxy-, hydroxy-, and carboxy- substituted PAH (OPAH, OHPAH, COOHPAH, respectively) alongside PAH in contaminated soils have received increasing attention over the past two decades; however, there are still to date no standardized methods available for their identification and quantitation in soil. Here we investigated and developed the first method using aminopropylsilica solid phase extraction (SPE) for these compounds. We further investigated the efficacy of the developed method for three soils representing a range of contamination levels and soil textural characteristics and evaluated the impact of different sample preparation steps on the recovery of targeted compounds. Average recovery of PAH, OPAH, and OHPAH standards were 99%, 84%, and 86%, respectively for the SPE method. In contrast, COOHPAH exhibited the lowest recovery (0–82%) and poor inter-batch reproducibility. Soil texture and contamination levels influenced full method efficiency. Specifically, soils with higher proportion of clay contributed to the loss of the higher molecular weight OHPAH prior to SPE. Soil with the highest contamination showed enhanced recovery of some lower-concentration mid weight PAH and OPAH, while the least contaminated soil showed greater sensitivity to evaporative losses during sample preparation. Recommendations for reducing matrix effects as well as the practice of using deuterated PAH surrogate standards for OPAH analysis are further discussed. Quantitation of recovered PAH and oxygenated PAH across the three soils showed high reproducibility (

Bacterial laccases are now known to be abundant in soil and to function outside of the cell facilitating the bacterial degradation of lignin. In this study we wanted to test the hypotheses that: i) Such enzymes can be identified readily in stratified paleosols using metagenomics approaches, ii) The distribution of these genes as potential ‘public good’ proteins in soil is a function of the soil environment, iii) Such laccase genes can be readily retrieved and expressed in E. coli cloning systems to demonstrate that de novo assembly processes can be used to obtain similar metagenome-derived enzyme activities. To test these hypotheses, in silico gene-targeted assembly was employed to identify genes encoding novel type B two-domain bacterial laccases from alpine soil metagenomes sequenced on an Illumina MiSeq sequencer. The genes obtained from different strata were heterologously cloned, expressed and the gene products were shown to be active against two classical laccase substrates. The use of a metagenome-driven pipeline to obtain such active biocatalysts has demonstrated the potential for gene mining to be applied systematically for the discovery of such enzymes. These data ultimately further demonstrate the application of soil pedology methods to environmental enzyme discovery. As an interdisciplinary effort, we can now establish that paleosols can serve as a useful source of novel biocatalytic enzymes for various applications. We also, for the first time, link soil stratigraphy to enzyme profiling for widespread functional gene activity in paleosols.

The bacterial community composition and biomass abundance from a depositional mud belt in the western Irish Sea and regional sands were investigated by phospholipid ester-linked fatty acid profiling, denaturing gradient gel electrophoresis and barcoded pyrosequencing of 16S rRNA genes. The study area varied by water depth (12–111 m), organic carbon content (0.09–1.57% TOC), grain size, hydrographic regime (well-mixed vs. stratified), and water column phytodetrital input (represented by algal polyunsaturated PLFA). The relative abundance of bacterial-derived PLFA (sum of methyl-branched, cyclopropyl and odd-carbon number PLFA) was positively correlated with fine-grained sediment, and was highest in the depositional mud belt. A strong association between bacterial biomass and eukaryote primary production was suggested based on observed positive correlations with total nitrogen and algal polyunsaturated fatty acids. In addition, 16S rRNA genes affiliated to the classes Clostridia and Flavobacteria represented a major proportion of total 16S rRNA gene sequences. This suggests that benthic bacterial communities are also important degraders of phytodetrital organic matter and closely coupled to water column productivity in the western Irish Sea.

Following a period of unusually strong winds and high seas in the spring of 2014, a blanket peat bog formerly covered by a beach comprised of fine sand and large rocks was uncovered at a coastal site in Spiddal, Co. Galway, Ireland. The surface of the bog was littered with standing tree stumps, the remnants of a Holocene forest that had succumbed to a relatively sudden drowning. A combination of inorganic and organic geochemical techniques was applied to determine the cause of this rapid submersion and to glean palaeoclimatic information from the preserved record within the peat. The study represents the first use of a multiproxy lipid biomarker approach to investigate palaeoclimate conditions from a peat bog in Ireland. The results provide evidence of climatic variation throughout a ca. 3400 yr timeframe during the mid-Holocene. Biomarker proxies displaying the relative contribution of Sphagnum spp. vs. higher plants were used to show changes in precipitation and temperature during peat formation. The data correlate with described events, including the 4.2 ka event and the Subboreal-Subatlantic transition and show the benefit of a lipid biomarker method for investigating Ireland’s peatland resources. In particular, the indication of colder/wetter conditions coinciding with the 4.2 ka event implies the possibility that its effects were felt in Ireland, contrary to some reports. The results suggest that a combination of warm and dry conditions followed by a rapid rise in sea level led to the growth and subsequent drowning of the ancient forest landscape.

A suite of lipid biomarkers were investigated from surface sediments and particulate matter across hydrographically distinct zones associated with the western Irish Sea gyre and the seasonal bloom. The aim was to assess the variation of organic matter (OM) composition, production, distribution and fate associated with coastal and southern mixed regions and also the summer stratified region. Based on the distribution of a suite of diagnostic biomarkers, including phospholipid fatty acids, source-specific sterols, wax esters and C25 highly branched isoprenoids, diatoms, dinoflagellates and green algae were identified as major contributors of marine organic matter (MOM) in this setting. The distribution of cholesterol, wax esters and C20 and C22 polyunsaturated fatty acids indicate that copepod grazing represents an important process for mineralising this primary production. Net tow data from 2010 revealed much greater phytoplankton and zooplankton biomass in well-mixed waters compared to stratified waters. This appears to be largely reflected in MOM input to surface sediments. Terrestrial organic matter (TOM), derived from higher plants, was identified as a major source of OM regionally, but was concentrated in proximity to major riverine input at the Boyne Estuary and Dundalk Bay. Near-bottom residual circulation and the seasonal gyre also likely play a role in the fate of TOM in the western Irish Sea.

A marine sediment core obtained from a methane seepage site off the northern coast of Irelandwas analysed, at 3 depths, for catabolic genes associated with the aerobic and anaerobic degradation of aromatic compounds. Catabolic gene copy numbers varied through the core peaking at 2.1 meters below sediment surface (mbsf)-just above the sulphate boundary. Beyond the sulphate boundary gene copy numbers fell considerably, suggesting the boundary may be a critical factor in the degradation of aromatic compounds within marine sediments. At the 2.1 mbsf depth our data also suggest that known benzoyl CoA reductase utilizing bacteria are readily detectable.

Living (LM) and non-living maerl (NLM) rhodoliths of the species Lithothamnion coral- lioides (Crouan & Crouan, 1867) from Kingstown Bay, Galway, were sampled and compared in rela- tion to their physical structure and lipid and low molecular weight carbohydrate (LMWC) composi- tion. Saturated (SATFA) and polyunsaturated fatty acids (PUFA) were dominant, in particular 16:0, 20:4n-6 and 20:5n-3, but a diverse range of fatty acids were identified. The abundance of n-alkanals was high, and sterol composition was simple, with cholesterol accounting for over 90% of the total sterols. Mono-, di-, and trisaccharides, with galactose units being dominant, and floridoside were present in high abundance. Notably, the fatty acid and LMWC profiles varied little between NLM and LM. The relatively high abundance of PUFA and floridoside, in particular, suggests that NLM may have further potential for research and commercial purposes in a variety of food, biomedical and industrial applications. Previously reported unidentified 'globular inclusions' were more abundant in NLM and exhibited a crystalline morphology. Together with the bacterial fatty acid composition of LM and NLM, the results indicate that these structures are not bacterial in nature.

The Dry Valleys of Antarctica are one of the coldest and driest environments on Earth with paleosols in selected areas that date to the emplacement of tills by warm-based ice during the Early Miocene. Cited as an analogue to the martian surface, the ability of the Antarctic environment to support microbial life-forms is a matter of special interest, particularly with the upcoming NASA/ESA 2018 ExoMars mission. Lipid biomarkers were extracted and analyzed by gas chromatography--mass spectrometry to assess sources of organic carbon and evaluate the contribution of microbial species to the organic matter of the paleosols. Paleosol samples from the ice-free Dry Valleys were also subsampled and cultivated in a growth medium from which DNA was extracted with the explicit purpose of the positive identification of bacteria. Several species of bacteria were grown in solution and the genus identified. A similar match of the data to sequenced DNA showed that Alphaproteobacteria, Gammaproteobacteria, Bacteriodetes, and Actinobacteridae species were cultivated. The results confirm the presence of bacteria within some paleosols, but no assumptions have been made with regard to in situ activity at present. These results underscore the need not only to further investigate Dry Valley cryosols but also to develop reconnaissance strategies to determine whether such likely Earth-like environments on the Red Planet also contain life.

The influence of montmorillonite intercalated with representatives of three major classes of biological molecules-lysine (amino acid), α–glucose (carbohydrate) and rhamnolipid (lipid) on the catalytic activity of acid phosphatase was investigated. In comparison to pure clay, the presence of the organic intercalates preserves residual activity at extreme pH values of 3 and 11 and temperatures as low as 10 °C. Thermodynamic parameters of free energy, enthalpy and entropy, suggest that catalytic activity on the lysine and rhamnolipid intercalated surfaces is more spontaneous and favorable than that of pure clay. Michaelis-constants (Km values) and maximum reaction velocities (Vmax values) were determined and confirmed the enhancement of activity on the organo-mineral surfaces. The catalytic reaction product was measured as a function of time and the data fitted to equations describing the behavior of first and second order rates of reaction. All processes apart from the glucose-intercalated clay (second order) could be described by first order reactions. Catalytic activity was generally less on the glucose-mineral surface compared to the other organo-mineral surfaces and the pure clay. However, when all surfaces were saturated with acid phosphatase the glucose complex exhibited the highest level of catalytic activity.

Reports concerning the quantitative analysis of pharmaceuticals in marine ecosystems are somewhat limited. It is necessary to determine pharmaceutical fate and assess any potential risk of exposure to aquatic species and ultimately, seafood consumers. In the work presented herein, analytical methods were optimised and validated for the quantification of pharmaceutical residues in wastewater effluent, receiving marine waters and marine mussels ( Mytilus spp.). Selected pharmaceuticals included two non-steroidal anti-inflammatory drugs (NSAIDs) (diclofenac and mefenamic acid), an antibiotic (trimethoprim), an antiepileptic (carbamazepine) and a lipid regulator (gemfibrozil). This paper also presents the results of an in situ study in which caged Mytilus spp. were deployed at three sites on the Irish coastline over a 1-year period. In water samples, pharmaceutical residues were determined using solid phase extraction (SPE) and liquid chromatography–tandem mass spectrometry (LC–MS/MS). The extraction of pharmaceuticals from mussel tissues used an additional pressurised liquid extraction (PLE) step prior to SPE and LC–MS/MS. Limits of quantification between 15 and 225 ng·L − 1 were achieved in wastewater effluent, between 3 and 38 ng·L − 1 in marine surface water and between 4 and 29 ng·g − 1 dry weight in marine mussels. Method linearity was achieved for pharmaceuticals in each matrix with correlation coefficients of R 2 ≥ 0.976. All five selected pharmaceuticals were quantified in wastewater effluent and marine surface waters. This work has demonstrated the susceptibility of the Mytilus spp. to pharmaceutical exposure following the detection of pharmaceutical residues in the tissues of this mussel species at measurable concentrations.

An optimised and validated method for the determination of pharmaceutical residues in blue mussels (Mytilus spp.) is presented herein, as well as an investigation of the effect of cooking (by steaming) on any potential difference in human exposure risk. Selected pharmaceuticals included two non-steroidal anti-inflammatory drugs (diclofenac and mefenamic acid), an antibiotic (trimethoprim), an anti-epileptic (carbamazepine) and a lipid regulator (gemfibrozil). An in vivo exposure experiment was set up in the laboratory in which mussels were exposed either directly by injection (10 ng) or daily through spiked artificial seawater (ASW) over 96 h. In liquid matrices, pharmaceutical residues were either determined using liquid chromatography-tandem mass spectrometry (LC-MS/MS) directly, or in combination with solid-phase extraction (SPE) for analyte concentration purposes. The extraction of pharmaceuticals from mussel tissues used an additional pressurised liquid extraction step prior to SPE and LC-MS/MS. Limits of quantification of between 2 and 46 ng L(-1) were achieved for extracted cooking water and ASW, between 2 and 64 μg L(-1) for ASW in exposure tanks, and between 4 and 29 ng g(-1) for mussel tissue. Method linearities were achieved for pharmaceuticals in each matrix with correlation coefficients of R (2) 0.975. A selection of exposed mussels was also cooked (via steaming) and analysed using the optimised method to observe any effect on detectable concentrations of parent pharmaceuticals present. An overall increase in pharmaceutical residues in the contaminated mussel tissue and cooking water was observed after cooking.

Sequestration of CO2 via biological sinks is a matter of great scientific importance due to their potential to lower atmospheric CO2 levels. In this study a custom built incubation chamber was used to cultivate a soil microbial community, under ideal conditions, to investigate soil chemoautotrophy. The internal atmospheric CO2 concentrations were monitored and used to estimate the mass of CO2 uptake. It was found after careful background corrections that 256.4 μg CO2 kg−1 dry soil was removed from the chamber atmosphere over 16 h. Comparisons were made to photosynthetic controls (i.e. grass and soil algae) whereupon it was observed that the chemoautotrophic fraction sequestered 2.6 and 5.4 % of that taken up by grass and soil algae respectively. Using isotopically labelled 13CO2 and GCMS-IRMS it was also possible to extract and identify labelled fatty acids after a short incubation time, hence confirming the CO2 uptake potential of the soil slurry. Provided with favourable conditions, chemoautotrophic soil bacteria have the potential to make a significant impact on inorganic carbon sequestration within the environment. The results of this in vivo study have provided ground work for future studies intending to mimic the in situ environment by providing a reliable method for investigating CO2 uptake by soil microorganisms.

Erythrocyte folates are commonly extracted for assay by 10-fold dilution of EDTA-anticoagulated blood (EDTA-WB) in 10 g/L ascorbic acid. It is assumed that this procedure achieves two goals: the complete lysis of erythrocytes and the exposure of intracellular folate polyglutamates to plasma conjugase enzyme (γ-glutamyl hydrolase) at a pH near 4.5, which favors their conversion to assayable folate. These EDTA-WB hemolysates require a further 20-fold (or more) dilution before analysis by microbiological assay with Lactobacillus rhamnosus . A recent study of red cell folate extraction (1), using a microbiological assay, challenged these assumptions. The authors noted that adjusting the pH of a 10 g/L ascorbic acid diluent from pH 2.7 to pH 4 or 4.25 with 1 mol/L NaOH before EDTA-WB dilution (1 in 10) and incubation produced significantly increased whole-blood folate (WBF) yields (>10%) from fresh, unfrozen hemolysates. They also recommended the inclusion of a cell-lysing agent in extraction diluents, noting that saponin (100 mg/L) could substantially increase WBF yields, depending on hemolysate pH (1). We evaluated these findings using our “in house” microbiological assay …