Andrew W. Stott

Changes in benthic denitrification, nitrate ammonification, and anammox process rates and nitrate and nitrite reductase gene abundances along an estuarine nutrient gradient (the Colne estuary, United Kingdom).

ABSTRACT Estuarine sediments are the location for significant bacterial removal of anthropogenically derived inorganic nitrogen, in particular nitrate, from the aquatic environment. In this study, rates of benthic denitrification (DN), dissimilatory nitrate reduction to ammonium (DNRA), and anammox (AN) at three sites along a nitrate concentration gradient in the Colne estuary, United Kingdom, were determined, and the numbers of functional genes (narG, napA, nirS, and nrfA) and corresponding transcripts encoding enzymes mediating nitrate reduction were determined by reverse transcription-quantitative PCR. In situ rates of DN and DNRA decreased toward the estuary mouth, with the findings from slurry experiments suggesting that the potential for DNRA increased while the DN potential decreased as nitrate concentrations declined. AN was detected only at the estuary head, accounting for ∼30% of N2 formation, with 16S rRNA genes from anammox-related bacteria also detected only at this site. Numbers of narG genes declined along the estuary, while napA gene numbers were stable, suggesting that NAP-mediated nitrate reduction remained important at low nitrate concentrations. nirS gene numbers (as indicators of DN) also decreased along the estuary, whereas nrfA (an indicator for DNRA) was detected only at the two uppermost sites. Similarly, nitrate and nitrite reductase gene transcripts were detected only at the top two sites. A regression analysis of log(n + 1) process rate data and log(n + 1) mean gene abundances showed significant relationships between DN and nirS and between DNRA and nrfA. Although these log-log relationships indicate an underlying relationship between the genetic potential for nitrate reduction and the corresponding process activity, fine-scale environmentally induced changes in rates of nitrate reduction are likely to be controlled at cellular and protein levels.

Priming and microbial nutrient limitation in lowland tropical forest soils of contrasting fertility

Priming is an increase in soil organic carbon decomposition following input of labile organic carbon. In temperate soils where biological activity is limited commonly by nitrogen availability, priming is expected to occur through microbial acquisition of nitrogen from organic matter or stimulated activity of recalcitrant-carbon degrading microorganisms. However, these priming mechanisms have not yet been assessed in strongly weathered tropical forest soils where biological activity is often limited by the availability of phosphorus. We examined whether microbial nutrient limitation or community dynamics drive priming in three lowland tropical forest soils of contrasting fertility (‘low’, ‘mid’ and ‘high’) by applying C4-sucrose (alone or in combination with nutrients; nitrogen, phosphorus and potassium) and measuring (1) the δ13C-signatures in respired CO2 and in phospholipid fatty acid (PLFA) biomarkers, and (2) the activities of enzymes involved in nitrogen (N-acetyl β-glucosaminidase), phosphorus (phosphomonoesterase) and carbon (β-glucosidase, cellobiohydrolase, xylanase, phenol oxidase) acquisition from organic compounds. Priming was constrained in part by nutrient availability, because priming was greater when sucrose was added alone compared to when added with nutrients. However, the greatest priming with sucrose addition alone was detected in the medium fertility soil. Priming occurred in parallel with stimulated activity of phosphomonoesterase and phenol oxidase (but not N-acetyl β-glucosaminidase); when sucrose was added with nutrients there were lower activities of phosphomonoesterase and phenol oxidase. There was no evidence according to PLFA δ13C-incorporation that priming was caused by specific groups of recalcitrant-carbon degrading microorganisms. We conclude that priming occurred in the intermediate fertility soil following microbial mineralization of organic nutrients (phosphorus in particular) and suggest that priming was constrained in the high fertility soil by high nutrient availability and in the low fertility soil by the low concentration of soil organic matter amenable to priming. This first study of priming mechanisms in tropical forest soils indicates that input of labile carbon can result in priming by microbial mineralization of organic nutrients, which has important implications for understanding the fate of organic carbon in tropical forest soils.

Studies of organic residues from ancient Egyptian mummies using high temperature-gas chromatography-mass spectrometry and sequential thermal desorption-gas chromatography-mass spectrometry and pyrolysis-gas chromatography-mass spectrometry.

The techniques of gas chromatography-mass spectrometry (GC-MS) and sequential thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) and pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) have been utilised to characterise the constituents of tissue-derived or applied organic material from two Pharaonic Egyptian mummies with a view to identifying embalming practices/substances. The results obtained using TD-GC-MS revealed a series of monocarboxylic acids with the C16:0, C18:1 and C18:0 components dominating in both mummies. The thermal desorption products related to cholesterol, i.e., cholesta-3,5,7-triene and cholesta-3,5-diene (only in Khnum Nakht), were detected in both mummies. Khnum Nakht also contained a number of straight chain alkyl amides (C16-C18) and an alkyl nitrile (C18). Other products included the 2,5-diketopiperazine derivative (DKP) of proline-glycine (pro-gly) which was a major component (7.9%) in Khnum Nakht but only a very minor component in Horemkenesi. Py-GC-MS of samples of both specimens yielded a series of alkene/alkane doublets (Horemkenesi C6-C18, Khnum Nakht C6-C24) which dominated their chromatograms. Series of methyl ketones in the C9-C19 chain length range were also present, with C5-C7 cyclic ketones occurring in Horemkenesi only. These ketones are indicative of covalent bond cleavage, probably of polymerised acyl lipids. Nitrogenous products included nitriles (C9-C18) which were significant in both samples, and amides which were only detected in Khnum Nakht. Also present amongst the pyrolysis products were three steroidal hydrocarbons, cholest-(?)-ene, cholesta-3,5,7-triene and cholesta-3,5-diene. High temperature-GC-MS of trimethylsilylated lipid extracts yielded similar monocarboxylic acids to that obtained using TD-GC-MS, while a series of alpha, omega-dicarboxylic acids and a number of mono- and di-hydroxy carboxylic acids not seen in the thermal desorption or pyrolysis GC-MS analyses were significant constituents in both mummy samples. Overall, the use of GC-MS and sequential TD-GC-MS and Py-GC-MS has demonstrated in both mummies the presence of a complex suite of lipids and proteinaceous components whose compositions indicates extensive alteration via oxidative and hydrolytic processes during long-term interment. None of the classical embalming resins was detected but an exogenous origin for at least a proportion of these components cannot be discounted since fats, oils and gelatin have been proposed as embalming agents in mummification. The combined approach of sequential TD- and Py-GC-MS has potential for application to the characterisation of embalming materials in mummies. Most importantly these techniques virtually eliminate any destruction of the mummified bodies thereby allowing the scope of investigations of ancient Egyptian funerary practices to be significantly extended.

Variable source and age of different forms of carbon released from natural peatland pipes

We used the carbon isotope composition (14C and δ13C) to measure the source and age of DOC, POC, dissolved CO2 and CH4 (δ13C only) released from three natural peat pipes and the downstream catchment outlet of a small peatland in northern England. Sampling under different hydrological extremes (high flows associated with storm events and low flows before or after storms) was used to explore variability in C sources as flow paths change over short periods of time. The δ13C composition of organic C differed (δ13C-DOC −28.6‰ to −27.6‰; δ13C-POC −28.1‰ to −26.1‰) from that of the dissolved gases (δ13C-CO2 −20.5‰ to +1.1‰; δ13C-CH4 −67.7‰ to −42.0‰) and showed that C leaving the catchment was a mixture of shallow/deep pipe and non-pipe sources. The isotopic composition of the dissolved gases was more variable than DOC and POC, with individual pipes either showing 13C enrichment or depletion during a storm event. The 14C age of DOC was consistently modern at all sites; POC varied from modern to 653 years BP and evasion CO2 from modern to 996 years BP. Differences in the isotopic composition of evasion CO2 at pipe outlets do not explain the variability in δ13C and 14C at the catchment outlet and suggest that overland flow is likely to be an important source of CO2. Our results also show that the sources of CO2 and CH4 are significantly more variable and dynamic than DOC and POC and that natural pipes vent old, deep peat CO2 and POC (but not DOC) to the atmosphere.

Fluxes and fate of dissolved methane released at the seafloor at the landward limit of the gas hydrate stability zone offshore western Svalbard

Widespread seepage of methane from seafloor sediments offshore Svalbard close to the landward limit of the gas hydrate stability zone (GHSZ) may, in part, be driven by hydrate destabilization due to bottom water warming. To assess whether this methane reaches the atmosphere where it may contribute to further warming, we have undertaken comprehensive surveys of methane in seawater and air on the upper slope and shelf region. Near the GHSZ limit at ∼400 m water depth, methane concentrations are highest close to the seabed, reaching 825 nM. A simple box model of dissolved methane removal from bottom waters by horizontal and vertical mixing and microbially mediated oxidation indicates that ∼60% of methane released at the seafloor is oxidized at depth before it mixes with overlying surface waters. Deep waters are therefore not a significant source of methane to intermediate and surface waters; rather, relatively high methane concentrations in these waters (up to 50 nM) are attributed to isopycnal turbulent mixing with shelf waters. On the shelf, extensive seafloor seepage at <100 m water depth produces methane concentrations of up to 615 nM. The diffusive flux of methane from sea to air in the vicinity of the landward limit of the GHSZ is ∼4–20 μmol m−2 d−1, which is small relative to other Arctic sources. In support of this, analyses of mole fractions and the carbon isotope signature of atmospheric methane above the seeps do not indicate a significant local contribution from the seafloor source.

Root and arbuscular mycorrhizal mycelial interactions with soil microorganisms in lowland tropical forest

Tropical forests have high rates of soil carbon cycling, but little information is available on how roots, arbuscular mycorrhizal fungi (AMF), and free-living microorganisms interact and influence organic matter mineralization in these ecosystems. We used mesh ingrowth cores and isotopic tracers in phospholipid fatty acid biomarkers to investigate the effects of roots and AMF mycelia on (1) microbial community composition, microbial carbon utilization, and hydrolytic enzyme activities for large, potted tropical trees and (2) enzyme activities and litter mass loss in a lowland tropical forest. Under the tropical tree, plant-derived carbon was incorporated predominantly into bacterial groups in both rhizosphere and AMF-only soils. Gram-positive bacteria incorporated additional soil-derived carbon in rhizosphere soils, which also contained the highest microbial biomass. For hydrolytic enzymes, β-glucosidase and N-acetyl β-glucosaminidase activities were highest in rhizosphere soils, while phosphomonoesterase activity was highest in AMF-only soil. In the forest, leaf litter mass loss was increased by the presence of roots, but not by the presence of AMF mycelia only. Root-microbial interactions influenced organic matter cycling, with evidence for rhizosphere priming and accelerated leaf litter decomposition in the presence of roots. Although AMF mycelia alone did not stimulate organic matter mineralization, they were a conduit of carbon to other soil microorganisms.

Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient

This research investigated spatial-temporal variation in benthic bacterial community structure, rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) processes and abundances of corresponding genes and transcripts at three sites—the estuary-head, mid-estuary and the estuary mouth (EM) along the nitrate gradient of the Colne estuary over an annual cycle. Denitrification rates declined down the estuary, while DNRA rates were higher at the estuary head and middle than the EM. In four out of the six 2-monthly time-points, rates of DNRA were greater than denitrification at each site. Abundance of gene markers for nitrate-reduction (nitrate reductase narG and napA), denitrification (nitrite reductase nirS) and DNRA (DNRA nitrite reductase nrfA) declined along the estuary with significant relationships between denitrification and nirS abundance, and DNRA and nrfA abundance. Spatially, rates of denitrification, DNRA and corresponding functional gene abundances decreased along the estuary. However, temporal correlations between rate processes and functional gene and transcript abundances were not observed.

Adaptation by macrophytes to inorganic carbon down a river with naturally variable concentrations of CO2.

The productivity and ecological distribution of freshwater plants can be controlled by the availability of inorganic carbon in water despite the existence of different mechanisms to ameliorate this, such as the ability to use bicarbonate. Here we took advantage of a short, natural gradient of CO2 concentration, against a background of very high and relatively constant concentration of bicarbonate, in a spring-fed river, to study the effect of variable concentration of CO2 on the ability of freshwater plants to use bicarbonate. Plants close to the source, where the concentration of CO2 was up to 24 times air equilibrium, were dominated by Berula erecta. pH-drift results and discrimination against (13)C were consistent with this and the other species being restricted to CO2 and unable to use the high concentration of bicarbonate. There was some indication from stable (13)C data that B. erecta may have had access to atmospheric CO2 at low water levels. In contrast, species downstream, where concentrations of CO2 were only about 5 times air-equilibrium were almost exclusively able to use bicarbonate, based on pH-drift results. Discrimination against (13)C was also consistent with bicarbonate being the main source of inorganic carbon for photosynthesis in these species. There was, therefore, a transect downstream from the source of increasing ability to use bicarbonate that closely matched the decreasing concentration of CO2. This was produced largely by altered species composition, but partly by phenotypic changes in individual species.

Olive oil or lard?: Distinguishing plant oils from animal fats in the archeological record of the eastern Mediterranean using gas chromatography/combustion/isotope ratio mass spectrometry

Distinguishing animal fats from plant oils in archaeological residues is not straightforward. Characteristic plant sterols, such as β-sitosterol, are often missing in archaeological samples and specific biomarkers do not exist for most plant fats. Identification is usually based on a range of characteristics such as fatty acid ratios, all of which indicate that a plant oil may be present, none of which uniquely distinguish plant oils from other fats. Degradation and dissolution during burial alter fatty acid ratios and remove short-chain fatty acids, resulting in degraded plant oils with similar fatty acid profiles to other degraded fats. Compound-specific stable isotope analysis of δ(13)C(18:0) and δ(13)C(16:0), carried out by gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS), has provided a means of distinguishing fish oils, dairy fats, ruminant and non-ruminant adipose fats, but plant oils are rarely included in these analyses. For modern plant oils where C(18:1) is abundant, δ(13)C(18:1) and δ(13)C(16:0) are usually measured. These results cannot be compared with archaeological data or data from other modern reference fats where δ(13)C(18:0) and δ(13)C(16:0) are measured, as C(18:0) and C(18:1) are formed by different processes resulting in different isotopic values. Eight samples of six modern plant oils were saponified, releasing sufficient C(18:0) to measure the isotopic values, which were plotted against δ(13)C(16:0). The isotopic values for these oils, with one exception, formed a tight cluster between ruminant and non-ruminant animal fats. This result complicates the interpretation of mixed fatty residues in geographical areas where both animal fats and plant oils were in use.

Stable isotope switching (SIS): a new stable isotope probing (SIP) approach to determine carbon flow in the soil food web and dynamics in organic matter pools

RATIONALE Recent advances in stable isotope probing (SIP) have allowed direct linkage of microbial population structure and function. This paper details a new development of SIP, Stable Isotope Switching (SIS), which allows the simultaneous assessment of carbon (C) uptake, turnover and decay, and the elucidation of soil food webs within complex soils or sedimentary matrices. METHODS SIS utilises a stable isotope labelling approach whereby the (13)C-labelled substrate is switched part way through the incubation to a natural abundance substrate. A (13)CH(4) SIS study of landfill cover soils from Odcombe (Somerset, UK) was conducted. Carbon assimilation and dissimilation processes were monitored through bulk elemental analysis isotope ratio mass spectrometry and compound-specific gas chromatography/combustion/isotope ratio mass spectrometry, targeting a wide range of biomolecular components including: lipids, proteins and carbohydrates. RESULTS Carbon assimilation by primary consumers (methanotrophs) and sequential assimilation into secondary (Gram-negative and -positive bacteria) and tertiary consumers (Eukaryotes) was observed. Up to 45% of the bacterial membrane lipid C was determined to be directly derived from CH(4) and at the conclusion of the experiment ca. 50% of the bulk soil C derived directly from CH(4) was retained within the soil. CONCLUSIONS This is the first estimate of soil organic carbon derived from CH(4) and it is comparable with levels observed in lakes that have high levels of benthic methanogenesis. SIS opens the way for a new generation of SIP studies aimed at elucidating total C dynamics (incorporation, turnover and decay) at the molecular level in a wide range of complex environmental and biological matrices.