Holocene environmental changes in the lower Thames Valley, London, UK: implications for our understanding of the history of Taxus woodland

A radiocarbon-dated multiproxy palaeoenvironmental record from the Lower Thames Valley at Hornchurch Marshes has provided a reconstruction of the timing and nature of vegetation succession against a background of Holocene climate change, relative sea level movement and human activities. The investigation recorded widespread peat formation between c. 6300 and 3900 cal. yr BP (marine ‘regression’), succeeded by evidence for marine incursion. The multiproxy analyses of these sediments, comprising pollen, Coleoptera, diatoms, and plant and wood macrofossils, have indicated significant changes in both the wetland and dryland environment, including the establishment of Alnus (Alder) carr woodland, and the decline of both Ulmus (Elm; c. 5740 cal. yr BP) and Tilia (Lime; c. 5600 cal. yr BP, and 4160–3710 cal. yr BP). The beetle faunas from the peat also suggest a thermal climate similar to that of the present day. At c. 4900 cal. yr BP, Taxus (L.; Yew) woodland colonised the peatland forming a plant community that has no known modern analogue in the UK. The precise reason, or reasons, for this event remain unclear, although changes in peatland hydrology seem most likely. The growth of Taxus on peatland not only has considerable importance for our knowledge of the vegetation history of southeast England, and NW Europe generally, but also has wider implications for the interpretation of Holocene palaeobotanical records. At c. 3900 cal. yr BP, Taxus declined on the peatland surface during a period of major hydrological change (marine incursion), an event also strongly associated with the decline of dryland woodland taxa, including Tilia and Quercus, and the appearance of anthropogenic indicators.

The monitoring of ecological quality and the classification of standing waters in temperate regions: a review and proposal based on a worked scheme for British waters

This paper reviews the ways that quality can be assessed in standing waters, a subject that has hitherto attracted little attention but which is now a legal requirement in Europe. It describes a scheme for the assessment and monitoring of water and ecological quality in standing waters greater than about I ha in area in England & Wales although it is generally relevant to North-west Europe. Thirteen hydrological, chemical and biological variables are used to characterise the standing water body in any current sampling. These are lake volume, maximum depth, onductivity, Secchi disc transparency, pH, total alkalinity, calcium ion concentration, total N concentration,winter total oxidised inorganic nitrogen (effectively nitrate) concentration, total P concentration, potential maximum chlorophyll a concentration, a score based on the nature of the submerged and emergent plant community, and the presence or absence of a fish community. Inter alia these variables are key indicators of the state of eutrophication, acidification, salinisation and infilling of a water body.

The global distribution of phytoplankton size spectrum and size classes from their light-absorption spectra derived from satellite data

The absorption spectra of phytoplankton in the visible domain hold implicit information on the phytoplankton community structure. Here we use this information to retrieve quantitative information on phytoplankton size structure by developing a novel method to compute the exponent of an assumed power-law for their particle-size spectrum. This quantity, in combination with total chlorophyll-a concentration, can be used to estimate the fractional concentration of chlorophyll in any arbitrarily-defined size class of phytoplankton. We further define and derive expressions for two distinct measures of cell size of mixed populations, namely, the average spherical diameter of a bio-optically equivalent homogeneous population of cells of equal size, and the average equivalent spherical diameter of a population of cells that follow a power-law particle-size distribution. The method relies on measurements of two quantities of a phytoplankton sample: the concentration of chlorophyll-a, which is an operational index of phytoplankton biomass, and the total absorption coefficient of phytoplankton in the red peak of visible spectrum at 676 nm. A sensitivity analysis confirms that the relative errors in the estimates of the exponent of particle size spectra are reasonably low. The exponents of phytoplankton size spectra, estimated for a large set of in situ data from a variety of oceanic environments (~ 2400 samples), are within a reasonable range; and the estimated fractions of chlorophyll in pico-, nano- and micro-phytoplankton are generally consistent with those obtained by an independent, indirect method based on diagnostic pigments determined using high-performance liquid chromatography. The estimates of cell size for in situ samples dominated by different phytoplankton types (diatoms, prymnesiophytes, Prochlorococcus, other cyanobacteria and green algae) yield nominal sizes consistent with the taxonomic classification. To estimate the same quantities from satellite-derived ocean-colour data, we combine our method with algorithms for obtaining inherent optical properties from remote sensing. The spatial distribution of the size-spectrum exponent and the chlorophyll fractions of pico-, nano- and micro-phytoplankton estimated from satellite remote sensing are in agreement with the current understanding of the biogeography of phytoplankton functional types in the global oceans. This study contributes to our understanding of the distribution and time evolution of phytoplankton size structure in the global oceans.

Aspects of in vitro and in vivo research approaches directed towards identifying probiotics and prebiotics for human use

The microbiota of the human gastrointestinal tract plays a key role in nutrition and health. Through the process of fermentation, gut bacteria metabolize various substrates (principally dietary components) to end products such as short-chain fatty acids and gases. This anaerobic metabolism is thought to contribute positively toward host daily energy requirements. However, under certain circumstances, the fermentative process may produce undesirable metabolites. This may cause the onset of gut disorders that can be manifest through both acute and chronic conditions. Moreover, the gut flora may become contaminated by transient pathogens that serve further to upset the normal community structure. There has been a recent increase in the use of dietary components that help to maintain, or even improve, the gut microflora "balance." Probiotics are live microbial feed supplements added to appropriate food vehicles (usually fermented milks), whereas prebiotics are dietary carbohydrates that have a selective metabolism in the colon and serve to increase numbers of bacteria seen as desirable. Because of their purported health-promoting properties, lactic acid-producing bacteria, including bifidobacteria, are the usual target organisms. The market value and biological potential of both approaches are enormous. This article will summarize how efficacious types can be identified.

Age and microenvironment outweigh genetic influence on the Zucker rat microbiome

Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n = 6; heterozygous n = 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?

Probiotics, prebiotics, and the host microbiome: the science of translation

Recent advances in our understanding of the community structure and function of the human microbiome have implications for the potential role of probiotics and prebiotics in promoting human health. A group of experts recently met to review the latest advances in microbiota/microbiome research and discuss the implications for development of probiotics and prebiotics, primarily as they relate to effects mediated via the intestine. The goals of the meeting were to share recent advances in research on the microbiota, microbiome, probiotics, and prebiotics, and to discuss these findings in the contexts of regulatory barriers, evolving healthcare environments, and potential effects on a variety of health topics, including the development of obesity and diabetes; the long-term consequences of exposure to antibiotics early in life to the gastrointestinal (GI) microbiota; lactose intolerance; and the relationship between the GI microbiota and the central nervous system, with implications for depression, cognition, satiety, and mental health for people living in developed and developing countries. This report provides an overview of these discussions.

The development of soil organic matter in restored biodiverse Jarrah forests of South-Western Australia as determined by ASE and GCMS

Background, aim and scope Soil organic matter (SOM) is known to increase with time as landscapes recover after a major disturbance; however, little is known about the evolution of the chemistry of SOM in reconstructed ecosystems. In this study, we assessed the development of SOM chemistry in a chronosequence (space for time substitution) of restored Jarrah forest sites in Western Australia. Materials and methods Replicated samples were taken at the surface of the mineral soil as well as deeper in the profile at sites of 1, 3, 6, 9, 12, and 17 years of age. A molecular approach was developed to distinguish and quantify numerous individual compounds in SOM. This used accelerated solvent extraction in conjunction with gas chromatography mass spectrometry. A novel multivariate statistical approach was used to assess changes in accelerated solvent extraction (ASE)-gas chromatography-mass spectrometry (GCMS) spectra. This enabled us to track SOM developmental trajectories with restoration time. Results Results showed total carbon concentrations approached that of native forests soils by 17 years of restoration. Using the relate protocol in PRIMER, we demonstrated an overall linear relationship with site age at both depths, indicating that changes in SOM chemistry were occurring. Conclusions The surface soils were seen to approach native molecular compositions while the deeper soil retained a more stable chemical signature, suggesting litter from the developing diverse plant community has altered SOM near the surface. Our new approach for assessing SOM development, combining ASE-GCMS with illuminating multivariate statistical analysis, holds great promise to more fully develop ASE for the characterisation of SOM.

Re-creation of heathland on improved pasture using topsoil removal and sulphur amendments: edaphic drivers and impacts on ericoid mycorrhizas

Understanding the factors that drive successful re-creation and restoration of lowland heaths is crucially important for achieving the long-term conservation of this threatened habitat type. In this study we investigated the changes in soil chemistry, plant community and interactions between Calluna vulgaris and symbiotic ericoid mycorrhizas (ERM) that occurred when improved pasture was subjected to one of three treatments (i) acidification with elemental sulphur (ii) acidification with ferrous sulphur (iii) removal of the topsoil. We found that the soil stripping treatment produced the greatest reduction in available phosphate but did not decrease soil pH. Conversely, acidification with elemental sulphur decreased pH but increased availability of phosphate and potentially toxic cations. The elemental sulphur treatment produced plant communities that most closely resembled those on surrounding heaths and acid grasslands. The most important driver was low pH and concomitant increased availability of potentially toxic cations. Plant community development was found to be little related to levels of available soil phosphate, particularly at low pH. The elemental sulphur treatment also produced the best germination and growth of C. vulgaris over 4–5 years. However, this treatment was found to inhibit the development of symbiotic relationships between C. vulgaris and ERM. This may affect the long-term persistence of re-created vegetation and its interactions with other components of heathland communities.

The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons

Despite the accumulating knowledge on the development and establishment of the gut microbiota, its role as a reservoir for multidrug resistance is not well understood. This study investigated the prevalence and persistence patterns of an integrase gene (int1), used as a proxy for integrons (which often carry multiple antimicrobial resistance genes), in the fecal microbiota of 147 mothers and their children sampled longitudinally from birth to 2 years. The study showed the int1 gene was detected in 15% of the study population, and apparently more persistent than the microbial community structure itself. We found int1 to be persistent throughout the first two years of life, as well as between mothers and their 2-year-old children. Metagenome sequencing revealed integrons in the gut meta-mobilome that were associated with plasmids and multidrug resistance. In conclusion, the persistent nature of integrons in the infant gut microbiota makes it a potential reservoir of mobile multidrug resistance.

High-throughput monitoring of wild bee diversity and abundance via mitogenomics

1. Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline. 2. We show that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees. We assembled the mitogenomes of 48 UK bee species and then shotgun-sequenced total DNA extracted from 204 whole bees that had been collected in 10 pan-trap samples from farms in England and been identified morphologically to 33 species. Each sample data set was mapped against the 48 reference mitogenomes. 3. The morphological and mitogenomic data sets were highly congruent. Out of 63 total species detections in the morphological data set, the mitogenomic data set made 59 correct detections (93�7% detection rate) and detected six more species (putative false positives). Direct inspection and an analysis with species-specific primers suggested that these putative false positives were most likely due to incorrect morphological IDs. Read frequency significantly predicted species biomass frequency (R2 = 24�9%). Species lists, biomass frequencies, extrapolated species richness and community structure were recovered with less error than in a metabarcoding pipeline. 4. Mitogenomics automates the onerous task of taxonomic identification, even for cryptic species, allowing the tracking of changes in species richness and istributions. A mitogenomic pipeline should thus be able to contain costs, maintain consistently high-quality data over long time series, incorporate retrospective taxonomic revisions and provide an auditable evidence trail. Mitogenomic data sets also provide estimates of species counts within samples and thus have potential for tracking population trajectories.

Size matters: body size determines functional responses of ground beetle interactions

Understanding patterns in predator:prey systems and the mechanisms that underlie trophic interactions provides a basis for predicting community structure and the delivery of natural pest control services. The functional response of predators to prey density is a fundamental measure of interaction strength and its characterisation is essential to understanding these processes. We used mesocosm experiments to quantify the functional responses of five ground beetle species that represent common generalist predators of north-west European arable agriculture. We investigated two mechanisms predicted to be key drivers of trophic interactions in natural communities: predator:prey body size ratio and multiple predator effects. Our results show regularities in foraging patterns characteristic of similarly sized predators. Ground beetle attack rates increased and handling times decreased as the predator:prey body-mass ratio rose. Multiple predator effects on total prey consumption rates were sensitive to the identity of the interacting species but not prey density. The extent of interspecific interactions may be a result of differences in body mass between competing beetle species. Overall these results add to the growing evidence for the importance of size in determining trophic interactions and suggest that body mass could offer a focus on which to base the management of natural enemy assemblages.