Assessing the impacts of oil contamination on microbial communities in a Niger Delta soil

Oil spills are a global challenge, contaminating the environment with organics and metals known to elicit toxic effects. Ecosystems within Nigeria's Niger Delta have suffered from prolonged severe spills for many decades but the level of impact on the soil microbial community structure and the potential for contaminant bioremediation remains unclear. Here, we assessed the extent/impact of an oil spill in this area 6 months after the accident on both the soil microbial community/diversity and the distribution of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHDGNα) genes, responsible for encoding enzymes involved in the degradation of PAHs, across the impacted area. Analyses confirmed the presence of oil contamination, including metals such as Cr and Ni, across the whole impacted area and at depth. The contamination impacted on the microbial community composition, resulting in a lower diversity in all contaminated soils. Gamma-, Delta-, Alpha- proteobacteria and Acidobacteriia dominated 16S rRNA gene sequences across the contaminated area, while Ktedonobacteria dominated the non-contaminated soils. The PAH-RHDαGN genes were only detected in the contaminated area, highlighting a clear relationship with the oil contamination/hydrocarbon metabolism. Correlation analysis indicated significant positive relationships between the oil contaminants (organics, Cr and Ni), PAH-RHDαGN gene, and the presence of bacteria/archaea such as Anaerolinea, Spirochaetia Bacteroidia Thermoplasmata, Methanomicrobia, and Methanobacteria indicating that the oil contamination not only impacted the microbial community/diversity present, but that the microbes across the impacted area and at depth were potentially playing an important role in degrading the oil contamination present. These findings provide new insights on the level of oil contamination remaining 6 months after an oil spill, its impacts on indigenous soil microbial communities and their potential for in situ bioremediation within a Niger Delta's ecosystem. It highlights the strength of using a cross-disciplinary approach to assess the extent of oil pollution in a single study.

Prolonged phenanthrene exposure reduces cardiac function but fails to mount a significant oxidative stress response in the signal crayfish (Pacifastacus leniusculus)

Crustaceans are important ecosystem bio-indicators but their response to pollutants such as polyaromatic hydrocarbons (PAHs) remains understudied, particularly in freshwater habitats. Here we investigated the effect of phenanthrene (at 0.5, 1.0 and 1.5 mg L^-1), a 3-ringed PAH associated with petroleum-based aquatic pollution on survival, in vivo and in situ cardiac performance, the oxidative stress response and the tissue burden in the signal crayfish (Pacifastacus leniusculus). Non-invasive sensors were used to monitor heart rate during exposure. Phenanthrene reduced maximum attainable heart rate in the latter half (days 8-15) of the exposure period but had no impact on routine heart rate. At the end of the 15-day exposure period, the electrical activity of the semi-isolated in situ crayfish heart was assessed and significant prolongation of the QT interval of the electrocardiogram was observed. Enzyme pathways associated with oxidative stress (superoxide dismutase and total oxyradical scavenging capacity) were also assessed after 15 days of phenanthrene exposure in gill, hepatopancreas and skeletal muscle; the results suggest limited induction of protective antioxidant pathways. Lastly, we report that 15 days exposure caused a dose-dependent increase in phenanthrene in hepatopancreas and heart tissues which was associated with reduced survivability. To our knowledge, this study is the first to provide such a thorough understanding of the impact of phenanthrene on a crustacean.

Root traits explain rhizosphere fungal community composition among temperate grassland plant species

While it is known that interactions between plants and soil fungi drive many essential ecosystem functions, considerable uncertainty exists over the drivers of fungal community composition in the rhizosphere. Here, we examined the roles of plant species identity, phylogeny and functional traits in shaping rhizosphere fungal communities and tested the robustness of these relationships to environmental change. We conducted a glasshouse experiment consisting of 21 temperate grassland species grown under three different environmental treatments and characterised the fungal communities within the rhizosphere of these plants. We found that plant species identity, plant phylogenetic relatedness and plant traits all affected rhizosphere fungal community composition. Trait relationships with fungal communities were primarily driven by interactions with arbuscular mycorrhizal fungi, and root traits were stronger predictors of fungal communities than leaf traits. These patterns were independent of the environmental treatments the plants were grown under. Our results showcase the key role of plant root traits, especially root diameter, root nitrogen and specific root length, in driving rhizosphere fungal community composition, demonstrating the potential for root traits to be used within predictive frameworks of plant-fungal relationships. Furthermore, we highlight how key limitations in our understanding of fungal function may obscure previously unmeasured plant-fungal interactions.

A Novel "Microbial Bait" Technique for Capturing Fe(III)-Reducing Bacteria

Microbial reduction of Fe(III) is a key geochemical process in anoxic environments, controlling the degradation of organics and the mobility of metals and radionuclides. To further understand these processes, it is vital to develop a reliable means of capturing Fe(III)-reducing microorganisms from the field for analysis and lab-based investigations. In this study, a novel method of capturing Fe(III)-reducing bacteria using Fe(III)-coated pumice "microbe-baits" was demonstrated. The methodology involved the coating of pumice (approximately diameter 4 to 6 mm) with a bioavailable Fe(III) mineral (akaganeite), and was verified by deployment into a freshwater spring for 2 months. On retrieval, the coated pumice baits were incubated in a series of lab-based microcosms, amended with and without electron donors (lactate and acetate), and incubated at 20°C for 8 weeks. 16S rRNA gene sequencing using the Illumina MiSeq platform showed that the Fe(III)-coated pumice baits, when incubated in the presence of lactate and acetate, enriched for Deltaproteobacteria (relative abundance of 52% of the sequences detected corresponded to Geobacter species and 24% to Desulfovibrio species). In the absence of added electron donors, Betaproteobacteria were the most abundant class detected, most heavily represented by a close relative to Rhodoferax ferrireducens (15% of species detected), that most likely used organic matter sequestered from the spring waters to support Fe(III) reduction. In addition, TEM-EDS analysis of the Fe(III)-coated pumice slurries amended with electron donors revealed that a biogenic Fe(II) mineral, magnetite, was formed at the end of the incubation period. These results demonstrate that Fe(III)-coated pumice "microbe baits" can potentially help target metal-reducing bacteria for culture-dependent studies, to further our understanding of the nano-scale microbe-mineral interactions in aquifers.

Understanding the cardiac toxicity of the anthropogenic pollutant phenanthrene on the freshwater indicator species, the brown trout (Salmo trutta): From whole heart to cardiomyocytes

Freshwater systems are faced with a myriad of stressors including geomorphological alterations, nutrient overloading and pollution. Previous studies in marine fish showed polyaromatic hydrocarbons (PAHs) to be cardiotoxic. However, the cardiotoxicity of anthropogenic pollutants in freshwater fishes is unclear and has not been examined across multiple levels of cardiac organization. Here we investigated the effect of phenanthrene (Phe), a pervasive anthropogenic pollutant on a sentinel freshwater species, the brown trout (Salmo trutta). We first examined the electrical activity of the whole heart and found prolongation (∼8.6%) of the QT interval (time between ventricular depolarization and repolarization) of the electrocardiogram (ECG) and prolongation (∼13.2%) of the monophasic action potential duration (MAPD) following ascending doses of Phe. At the tissue level, Phe significantly reduced trabecular force generation by ∼24% at concentration 15 μM and above, suggesting Phe reduces cellular calcium cycling. This finding was supported by florescent microscopy showing a reduction (∼39%) in the intracellular calcium transient amplitude following Phe exposure in isolated brown trout ventricular myocytes. Single-cell electrophysiology was used to reveal the mechanism underlying contractile and electrical dysfunction following Phe exposure. A Phe-dependent reduction (∼38%) in the L-type Ca²⁺ current accounts, at least in part, for the lowered Ca²⁺ transient and force production. Prolongation of the MAPD and QT interval was explained by a reduction (∼70%) in the repolarising delayed rectifier K⁺ current following Phe exposure. Taken together, our study shows a direct impact of Phe across multiple levels of cardiac organization in a key freshwater salmonid.

Dual in-aquifer and near surface processes drive arsenic mobilization in Cambodian groundwaters

Millions of people globally, and particularly in South and Southeast Asia, face chronic exposure to arsenic from reducing groundwaters in which. Arsenic release to is widely attributed largely to reductive dissolution of arsenic-bearing iron minerals, driven by metal reducing bacteria using bioavailable organic matter as an electron donor. However, the nature of the organic matter implicated in arsenic mobilization, and the location within the subsurface where these processes occur, remains debated. In a high resolution study of a largely pristine, shallow aquifer in Kandal Province, Cambodia, we have used a complementary suite of geochemical tracers (including ¹⁴C, ³H, ³He, ⁴He, Ne, δ¹⁸O, δD, CFCs and SF₆) to study the evolution in arsenic-prone shallow reducing groundwaters along dominant flow paths. The observation of widespread apparent ³H-³He ages of <55years fundamentally challenges some previous models which concluded that groundwater residence times were on the order of hundreds of years. Surface-derived organic matter is transported to depths of >30m, and the relationships between age-related tracers and arsenic suggest that this surface-derived organic matter is likely to contribute to in-aquifer arsenic mobilization. A strong relationship between ³H-³He age and depth suggests the dominance of a vertical hydrological control with an overall vertical flow velocity of ~0.4±0.1m·yr^-1 across the field area. A calculated overall groundwater arsenic accumulation rate of ~0.08±0.03μM·yr^-1 is broadly comparable to previous estimates from other researchers for similar reducing aquifers in Bangladesh. Although apparent arsenic groundwater accumulation rates varied significantly with site (e.g. between sand versus clay dominated sequences), rates are generally highest near the surface, perhaps reflecting the proximity to the redox cline and/or depth-dependent characteristics of the OM pool, and confounded by localized processes such as continued in-aquifer mobilization, sorption/desorption, and methanogenesis.

Biomarker-indicated extent of oxidation of plant-derived organic carbon (OC) in relation to geomorphology in an arsenic contaminated Holocene aquifer, Cambodia

The poisoning of rural populations in South and Southeast Asia due to high groundwater arsenic concentrations is one of the world’s largest ongoing natural disasters. It is important to consider environmental processes related to the release of geogenic arsenic, including geomorphological and organic geochemical processes. Arsenic is released from sediments when iron-oxide minerals, onto which arsenic is adsorbed or incorporated, react with organic carbon (OC) and the OC is oxidised. In this study we build a new geomorphological framework for Kandal Province, a highly studied arsenic affected region of Cambodia, and tie this into wider regional environmental change throughout the Holocene. Analyses shows that the concentration of OC in the sediments is strongly inversely correlated to grainsize. Furthermore, the type of OC is also related to grain size with the clay containing mostly (immature) plant derived OC and sand containing mostly thermally mature derived OC. Finally, analyses indicate that within the plant derived OC relative oxidation is strongly grouped by stratigraphy with the older bound OC more oxidised than younger OC.

High resolution profile of inorganic aqueous geochemistry and key redox zones in an arsenic bearing aquifer in Cambodia

Arsenic contamination of groundwaters in South and Southeast Asia is a major threat to public health. In order to better understand the geochemical controls on the mobility of arsenic in a heavily arsenic-affected aquifer in northern Kandal Province, Cambodia, key changes in inorganic aqueous geochemistry have been monitored at high vertical and lateral resolution along dominant groundwater flow paths along two distinct transects. The two transects are characterized by differing geochemical, hydrological and lithological conditions. Arsenic concentrations in groundwater are highly heterogenous, and are broadly positively associated with iron and negatively associated with sulfate and dissolved oxygen. The observed correlations are generally consistent with arsenic mobilization by reductive-dissolution of iron (hydr)oxides. Key redox zones, as identified using groupings of the PHREEQC model equilibrium electron activity of major redox couples (notably ammonium/nitrite; ammonium/nitrate; nitrite/nitrate; dissolved oxygen/water) have been identified and vary with depth, site and season. Mineral saturation is also characterized. Seasonal changes in groundwater chemistry were observed in areas which were (i) sandy and of high permeability; (ii) in close proximity to rivers; and/or (iii) in close proximity to ponds. Such changes are attributed to monsoonal-driven surface-groundwater interactions and are consistent with the separate provenance of recharge sources as identified using stable isotope mixing models.

Fossilization of melanosomes via sulfurization

Fossil melanin granules (melanosomes) are an important resource for inferring the evolutionary history of colour and its functions in animals. The taphonomy of melanin and melanosomes, however, is incompletely understood. In particular, the chemical processes responsible for melanosome preservation have not been investigated. As a result, the origins of sulfur-bearing compounds in fossil melanosomes are difficult to resolve. This has implications for interpretations of original colour in fossils based on potential sulfur-rich phaeomelanosomes. Here we use pyrolysis gas chromatography mass spectrometry (Py-GCMS), fourier transform infrared spectroscopy (FTIR) and time of flight secondary ion mass spectrometry (ToF-SIMS) to assess the mode of preservation of fossil microstructures, confirmed as melanosomes based on the presence of melanin, preserved in frogs from the Late Miocene Libros biota (NE Spain). Our results reveal a high abundance of organosulfur compounds and non-sulfurized fatty acid methyl esters in both the fossil tissues and host sediment; chemical signatures in the fossil tissues are inconsistent with preservation of phaeomelanin. Our results reflect preservation via the diagenetic incorporation of sulfur, i.e. sulfurization (natural vulcanization), and other polymerization processes. Organosulfur compounds and/or elevated concentrations of sulfur have been reported from melanosomes preserved in various invertebrate and vertebrate fossils and depositional settings, suggesting that preservation through sulfurization is likely to be widespread. Future studies of sulfur-rich fossil melanosomes require that the geochemistry of the host sediment is tested for evidence of sulfurization in order to constrain interpretations of potential phaeomelanosomes and thus of original integumentary colour in fossils.

Characterisation of organic matter associated with groundwater arsenic in reducing aquifers of southwestern Taiwan

Arsenic (As) in groundwaters extensively used by people across the world constitutes a serious public health threat. The importance of organic matter (OM) as an electron donor in microbially-mediated reduction of As(V) or Fe(III)-bearing As-host minerals leading to mobilisation of solid-phase arsenic is widely recognised. Notwithstanding this, there are few studies characterising OM in such aquifers and, in particular, there is a dearth of data from the classic arsenic bearing aquifers in southwestern Taiwan. Organic geochemical analyses of sediments from a known groundwater arsenic hot-spot in southwestern Taiwan revealed contributions of thermally mature and plant derived origin, consistent with OM sources in all other Asian groundwater aquifer sediments analysed to date, indicating comparable sources and routes of OM transfer. The combined results of amended As(V) reduction assays with the organic geochemical analysis revealed that the microbiological process of dissimilatory As(V) reduction is active in this aquifer, but it is not controlled by a specific source of analysed OM. These indicate that (i) part of the OM that was considered to be less bio-available could still be used as an electron donor or (ii) other electron donors, not analysed in present study, could be controlling the rate of As release.

Organic geochemical analysis of archaeological medicine pots from Northern Ghana. The multi-functionality of pottery

Sherds from pots found layered under a granite boulder in the Tong Hills of the Upper East Region of Northern Ghana seem, based on their deposition context to have been used for the preparation of medicines. Organic geochemical and isotopic analyses of these sherds and a modern day analogue reveal an n-alkanoic acid composition that is consistent with their being used in the preparation of plant derived substances. Isotopic analyses of the modern medicine pot indicate a contribution of n-alkanoic acids derived from plants that use C₄ carbon fixation, most likely maize, sorghum and/or millet suggesting that this pot was used for cooking C₄ based plant substances, perhaps, based on current analogy, staple porridge type food. The modern medicine pot could thus have had a prior use. The absence of C₄ plant residues in the archaeological sherds suggests that either staple foodstuffs differed radically to today, or, more likely, were not prepared in vessels that were to be used for medicinal purposes.

Morphological and geochemical evidence of eumelanin preservation in the feathers of the Early Cretaceous bird, Gansus yumenensis

Recent studies have shown evidence for the preservation of colour in fossilized soft tissues by imaging melanosomes, melanin pigment containing organelles. This study combines geochemical analyses with morphological observations to investigate the preservation of melanosomes and melanin within feathers of the Early Cretaceous bird, Gansus yumenensis. Scanning electron microscopy reveals structures concordant with those previously identified as eumelanosomes within visually dark areas of the feathers but not in lighter areas or sedimentary matrices. Fourier transform infrared analyses show different spectra for the feathers and their matrices; melanic functional groups appear in the feather including carboxylic acid and ketone groups that are not seen in the matrix. When mapped, the carboxylic acid group absorption faithfully replicates the visually dark areas of the feathers. Electron Paramagnetic Resonance spectroscopy of one specimen demonstrates the presence of organic signals but proved too insensitive to resolve melanin. Pyrolysis gas chromatography mass spectrometry shows a similar distribution of aliphatic material within both feathers that are different from those of their respective matrices. In combination, these techniques strongly suggest that not only do the feathers contain endogenous organic material, but that both geochemical and morphological evidence supports the preservation of original eumelanic pigment residue.

The composition and origin of Ghana medicine clays

The mineral, organic and elemental composition of medicine clays from three shrines in the Tong Hills in northern Ghana (Gbankil, Kusanaab, and Yaane) are assessed to ascertain what additives they might contain and the implications for their recognition, for example in archaeological contexts. These are clays that are widely used for healing purposes being perceived efficacious in curing multiple ailments and which are given a divine provenance, but their collection is ascribed human agency. The Yaane clay is also supplied as part of the process of obtaining the right to operate the shrine elsewhere making it widely dispersed. Organic geochemical analyses revealed a predominance of plant-derived material with a substantial contribution of microbial origin. Based on these (supported by elemental and mineral analyses), no unnatural organic material could be detected, making an exogenous contribution to these clays unlikely. The implications are that these are wholly natural medicinal substances with no anthropogenic input into their preparation, as the traditions suggest. The very similar mineralogy of all the clays, including a non-medicine clay sampled, suggests that, unless the geology radically differed, differentiating between them analytically in an archaeological contexts would be doubtful.

Mineralized soft-tissue structure and chemistry in a mummified hadrosaur from the Hell Creek Formation, North Dakota (USA)

An extremely well-preserved dinosaur (Cf. Edmontosaurus sp.) found in the Hell Creek Formation (Upper Cretaceous, North Dakota) retains soft-tissue replacement structures and associated organic compounds. Mineral cements precipitated in the skin apparently follow original cell boundaries, partially preserving epidermis microstructure. Infrared and electron microprobe images of ossified tendon clearly show preserved mineral zonation, with silica and trapped carbon dioxide forming thin linings on Haversian canals within apatite. Furthermore, Fourier transform infrared spectroscopy (FTIR) of materials recovered from the skin and terminal ungual phalanx suggests the presence of compounds containing amide groups. Amino acid composition analyses of the mineralized skin envelope clearly differ from the surrounding matrix; however, intact proteins could not be obtained using protein mass spectrometry. The presence of endogenously derived organics from the skin was further demonstrated by pyrolysis gas chromatography mass spectrometry (Py-GCMS), indicating survival and presence of macromolecules that were in part aliphatic (see the electronic supplementary material).

Off-line pyrolysis and compound-specific stable carbon isotope analysis of lignin moieties: a new method for determining the fate of lignin residues in soil

Off-line pyrolysis was used to liberate lignin moieties from dung and soil and, after trimethylsilylation, the delta(13)C values of these derivatives were determined by gas chromatography-combustion-isotope ratio mass spectrometry. Initial delta(13)C values determined for 4-vinylphenol, syringol, 4-vinylguaiacol, 4-acetylsyringol, 4-vinylsyringol, 4-(2-Z-propenyl)syringol, 4-(2-E-propenyl)syringol and 4-(2-propenone)syringol pyrolysis products of the lignin polyphenol structure from C(4) (delta(13)C(bulk) = -12.6%) and C(3) (delta(13)C(bulk) = -30.1 per thousand) dung confirmed the robust and reproducible nature of the off-line preparation technique. C(4) dung was used as a treatment in a randomised field experiment to assess the short-term sequestration of dung carbon in managed grasslands. Since lignin was on average 3.5 per thousand depleted in (13)C compared with bulk dung delta(13)C values, this may have resulted in an under-estimation of dung C incorporation based on bulk delta(13)C values. Therefore, an investigation of the compound-specific delta(13)C values of dung-derived lignin moieties extracted from soils sampled up to 372 days was undertaken. Delta(13)C values between lignin moieties extracted from treated and untreated soils showed that dung-derived lignin was not especially resistant to degradation and suggested that individual moieties of the lignin macromolecule must: (i) move into soil, (ii) be degraded, or (iii) be transformed diagenetically at different rates. This adds to a gathering body of evidence that lignin is not particularly stable in soils, which has considerable significance for the perceived role of different biochemical components in the cycling of C in soils.