Soil organic matter and the extracellular microbial matrix show contrasting responses to C and N availability

AbstractAn emerging paradigm in soil science suggests microbes can perform ‘N mining’ from recalcitrant soil organic matter (SOM) in conditions of low N availability. However, this requires the production of extracellular structures rich in N (including enzymes and structural components) and thus defies stoichiometric expectation. We set out to extract newly synthesised peptides from the extracellular matrix in soil and compare the amino acid (AA) profiles, N incorporation and AA dynamics in response to labile inputs of contrasting C/N ratio. Glycerol was added both with and without an inorganic source of N (10% 15N labelled NH4NO3) to a soil already containing a large pool of refractory SOM and incubated for 10 days. The resulting total soil peptide (TSP) and extracellular pools were compared using colorimetric methods, gas chromatography, and isotope ratio mass spectrometry. N isotope compositions showed that the extracellular polymeric substance (EPS) contained a greater proportion of products formed de novo than did TSP, with hydrophobic EPS-AAs (leucine, isoleucine, phenylalanine, hydroxyproline and tyrosine) deriving substantially more N from the inorganic source provided. Quantitative comparison between extracts showed that the EPS contained greater relative proportions of alanine, glycine, proline, phenylalanine and tyrosine. The greatest increases in EPS-peptide and EPS-polysaccharide concentrations occurred at the highest C/N ratios. All EPS-AAs responded similarly to treatment whereas the responses of TSP were more complex. The results suggest that extracellular investment of N (as EPS peptides) is a microbial survival mechanism in conditions of low N/high C which, from an evolutionary perspective, must ultimately lead to the tendency for increased N returns to the microbial biomass. A conceptual model is proposed that describes the dynamics of the extracellular matrix in response to the C/N ratio of labile inputs

Determining patterns in the composition of dissolved organic matter in fresh waters according to land use and management

In fresh waters, the origins of dissolved organic matter (DOM) have been found to exert a fundamental control on its reactivity, and ultimately, its ecosystem functional role. A detailed understanding of landscape scale factors that control the export of DOM to aquatic ecosystems is, therefore, pivotal if the effects of DOM flux to fresh waters are to be fully understood. In this study we present data from a national sampling campaign across the United Kingdom in which we explore the variability in DOM composition in three broad landscape types defined by similar precipitation, geology, land use and management, hydrology, and nutrient enrichment status. We characterised samples from fifty-one sites, grouping them into one of three major underlying classifications: circumneutral streams underlain by clay and mudstone (referred to as ‘clay’), alkaline streams underlain by Cretaceous Chalk or by Carboniferous or Jurassic Limestone (‘limestone’), and acidic streams in peatland catchments underlain by a range of low permeability lithologies (‘peat’). DOM composition was assessed through organic matter stoichiometry (organic carbon: organic nitrogen; organic carbon: organic phosphorus; C/N(P)DOM) and metrics derived from ultra-violet (UV)/visible spectroscopic analysis of DOM such as specific UV absorption (a254 nm; SUVA254). We found similar SUVA254, C/NDOM and DOM/a254 relationships within classifications, demonstrating that despite a large degree of heterogeneity within environments, catchments with shared environmental character and anthropogenic disturbance export DOM with a similar composition and character. Improving our understanding of DOM characterisation is important to help predict shifts in stream ecosystem function, and ecological responses to enrichment or mitigation efforts and how these may result in species composition shifts and biodiversity loss in freshwater ecosystems

Characterisation of riverine dissolved organic matter using a complementary suite of chromatographic and mass spectrometric methods

Dissolved organic matter (DOM) plays a fundamental role in nutrient cycling dynamics in riverine systems. Recent research has confirmed that the concentration of riverine DOM is not the only factor regulating its functional significance; the need to define the chemical composition of DOM is a priority. Past studies of riverine DOM rested on bulk quantification, however technological advancements have meant there has been a shift towards analytical methods which allow the characterisation of DOM either at compound class or more recently molecular level. However, it is important to consider that all analytical methods only consider a defined analytical window. Thus, herein, we explore the use of a hierarchy of methods which can be used in combination for the investigation of a wide range of DOM chemistries. By using these methods to investigate the DOM composition of a range of streams draining catchments of contrasting environmental character, a wide range of compounds were identified across a range of polarities and molecular weight, thereby extending the analytical window. Through the elucidation of the DOM character in stream samples, information can be collected about likely the sources of DOM. The identification of individual key compounds within the DOM pool is a key step in the design of robust and informative bioassay experiments, used to understand in-stream ecosystem responses. This is critical if we are to assess the role of DOM as a bioavailable nutrient resource and/or ecotoxicological factor in freshwater

Refining human palaeodietary reconstruction using amino acid delta N-15 values of plants, animals and humans.

An established method of estimating the trophic level of an organism is through stable isotope analysis of its tissues and those of its diet. This method has been used in archaeology to reconstruct past human diet from the stable nitrogen isotope (d15N) values of human and herbivore bone collagen. However, this approach, using the 15N-enrichment of human bone collagen d15N values over associated herbivore bone collagen d15N values to predict the relative importance of animal protein, relies on the assumptions that: (i) the d15N values of plants consumed by humans and herbivores are identical, and (ii) the 15Nenrichment between diet and consumer is consistent. Bone collagen amino acid d15N values have the potential to tackle these uncertainties, as they constrain the factors influencing bone collagen d15N values. In this study, the d15N values of glutamic acid and phenylalanine in human and herbivore bone collagen isolates from Neolithic sites in Germany, Greece and Turkey were determined by gas chromatography-combustion-isotope ratio mass spectrometry. The fraction of animal protein in total dietary protein consumed by the humans was estimated by: (i) comparing bulk human and herbivore collagen d15N values, (ii) comparing bulk human and herbivore collagen and ancient charred cereal grain d15N values, (iii) comparing human bone collagen d15NGlutamic acid and d15NPhenylalanine values, and (iv) comparing d15NGlutamic acid values of human and herbivore bone collagen and estimated d15NGlutamic acid values of ancient charred cereal grains. Where determined cereal grain d15N values are higher than estimated herbivore forage values, estimates of animal protein consumption are significantly lower, emphasising the importance of the plant nitrogen contribution to human bone collagen. This study also highlights the need for further investigation into: (i) the D15NConsumer-Diet values of glutamic acid and phenylalanine in terrestrial ecosystems, and (ii) D15NGlutamic acid-Phenylalanine values of common plant foods in order to improve the accuracy and more widespread applicability of amino acid-based methods for palaeodietary reconstruction

Strontium isotope evidence for human mobility in the Neolithic of northern Greece

Strontium isotope ratios are widely used in archaeology to differentiate between local and non-local populations. Herein, strontium isotope ratios of 36 human tooth enamels from seven archaeological sites spanning the Early to Late Neolithic of northern Greece (7th–5th millennia B.C.E.) were analysed with the aim of providing new information relating to the movement of humans across the region. Local bioavailable 87Sr/86Sr signals were established using tooth enamel from 26 domestic animals from the same Neolithic sites. 87Sr/86Sr values of faunal enamel correlate well with predicted strontium isotope ratios of the local geology. This is consistent with animal management occurring at a local level, although at Late Neolithic sites strontium isotope values became more varied, potentially indicating changing herding practices. The strontium isotope analysis of human tooth enamel likewise suggests limited population movement within the Neolithic of northern Greece. Almost all individuals sampled exhibited 87Sr/86Sr values consistent with having spent their early life (during the period of tooth mineralisation) in the local area, although movement could have occurred between isotopically homo- geneous areas. The strontium isotope ratios of only three individuals lay outside of the local bioavailable 87Sr/86Sr range and these individuals are interpreted as having spent their early lives in a region with a more radiogenic biologically available 87Sr/86Sr. Mobility patterns determined using Sr isotope analysis supports the current evidence for movement and exchange observed through studies of pottery circulation. Suggesting limited movement in the Early and Middle Neolithic and greater movement in the Late Neolithic

Finding Oxford’s medieval Jewry using organic residue analysis, faunal records and historical documents

Food is often one of the most distinctive expressions of social, religious, cultural or ethnic groups. However, the archaeological identification of specific religious dietary practices, including the Jewish tradition of keeping kosher, associated with ritual food practices and taboos, is very rare. This is arguably one of the oldest known diets across the world and, for an observant Jew, maintaining dietary laws (known as Kashruth) is a fundamental part of everyday life. Recent excavations in the early medieval Oxford Jewish quarter yielded a remarkable assemblage of animal bones, marked by a complete absence of pig specimens and a dominance of kosher (permitted) birds, domestic fowl and goose. To our knowledge, this is the first identification of a Jewish dietary signature in British zooarchaeology, which contrasted markedly with the previous Saxon phase where pig bones were present in quantity and bird bones were barely seen. Lipid residue analysis of pottery from St Aldates showed that vessels from the possible Jewish houses were solely used to process ruminant carcass products, with an avoidance of pig product processing, correlating well with the faunal data. In contrast, lipid analysis of pottery from comparative assemblages from the previous Saxon phase at the site and a contemporaneous site in the city, The Queen’s College, shows that the majority of these vessels appear to have been used to process mixtures of both ruminant and non-ruminant (pig) products. Here, the combination of organic residue analysis, site excavation and animal and fish bone evidence was consistent with the presence of Jewish houses in eleventh- and twelfth-century St Aldates, Oxford, hitherto only suspected through documentary information. This is the first identification of specific religious dietary practices using lipid residue analysis, verifying that, at least 800 years ago, medieval Jewish Oxford communities practised dietary laws known as Kashruth

Timing and pace of dairying inception and animal husbandry practices across Holocene North Africa

The timing and extent of the adoption and exploitation of domesticates and their secondary products, across Holocene North Africa, has long been the subject of debate. The three distinct areas within the region, Mediterranean north Africa, the Nile Valley and the Sahara, each with extremely diverse environments and ecologies, demonstrate differing trajectories to pastoralism. Here, we address this question using a combination of faunal evidence and organic residue analyses of c. 300 archaeological vessels from sites in Algeria, Libya and Sudan. This synthesis of new and published data provides a broad regional and chronological perspective on the scale and intensity of domestic animal exploitation and the inception of dairying practices in Holocene North Africa. Following the introduction of domesticated animals into the region our results confirm a hiatus of around one thousand years before the adoption of a full pastoral economy, which appears first in the Libyan Sahara, at c. 5200 BCE, subsequently appearing at c. 4600 BCE in the Nile Valley and at 4400–3900 BCE in Mediterranean north Africa

The organic chemistry of embalming agents in Pharaonic and Graeco-Roman mummies

Chemical treatments were an essential element of ancient Egyptian mummification. Although the inorganic salt natron is recognized as having a central role as a desiccant, without the application of organic preservatives the bodies would have decomposed in the humid environment of the tombs. The nature of the organic treatments remains obscure, because the ancient Egyptians left no written record of the process. Secondary textual evidence for mummification is provided by Herodotus, Diodorus Siculus4, Strabo and Pliny. The most important account is that of Herodotus3 (about 450 yr bc), although archaeological evidence shows that by this time the process had declined significantly and the best results had been achieved centuries before. His account mentions myrrh, cassia, palm wine, 'cedar oil' (still widely disputed) and 'gum'; however, it is vague with respect to the specific natural products used. Here we report the results of chemical investigations of a substantial collection of samples of tissues, wrappings and 'resinous/bituminous' materials from provenanced and dated Egyptian mummies. We focused on examples of the 'classic' mummy-making culture of the Pharaonic or dynastic period, from which we can begin to track the development of mummification chronologically

Palaeoenvironmental modelling of δ13C and δ15N values in the North Atlantic Islands: understanding past marine resource use

RATIONALE Carbon (δ13C) and nitrogen (δ15N) analysis has been extensively used to investigate the importance of marine foods in the diet of archaeological populations in the North Atlantic Islands; however, few faunal studies exist to aid the interpretation of results. Palaeoenvironmental modelling of δ13C and δ15N values is crucial in determining whether changes in the stable isotope values are a result of dietary change, rather than temporal or geographical fluctuations in carbon and nitrogen. Investigating faunal dietary behaviour can provide an insight into past foddering and land management strategies. METHODS Detailed sampling of wild and domestic species for bulk collagen analysis was undertaken in order to characterise geographical variations in δ13C and δ15N values in the Outer Hebrides and Orkney. Samples from the Neolithic to the Norse period were analysed to assess temporal and geographical variations in δ13C and δ15N values, in addition to determining the contribution of marine foods to the diet of local fauna. RESULTS A δ15N shift of 1‰ was observed between the Outer Hebrides and Orkney in the Neolithic and Iron Age. A geographical variation in δ13C values was observed in the Norse period between Orkney and the Outer Hebrides. Temporal fluctuations in δ13C and δ15N values demonstrate variations in foddering practices of sheep in the Outer Hebrides. Pig specimens from the Outer Hebrides demonstrated evidence of marine food consumption in the Iron Age. CONCLUSIONS Faunal dietary behaviour can act as a vital indicator of the importance of marine resources in the past. Characterisation of faunal δ13C and δ15N values geographically and temporally is crucial in our interpretation of human dietary behaviour