Determining trophic niche width: An experimental test of the stable isotope approach

Determining the trophic niche width of an animal population and the relative degree to which a generalist population consists of dietary specialists are long-standing problems of ecology. It has been proposed that the variance of stable isotope values in consumer tissues could be used to quantify trophic niche width of consumer populations. However, this promising idea has not yet been rigorously tested. By conducting controlled laboratory experiments using model consumer populations (Daphnia sp., Crustacea) with controlled diets, we investigated the effect of individual- and population-level specialisation and generalism on consumer d C mean and variance values. While our experimental data follow general expectations, we extend current qualitative models to quantitative predictions of the dependence of isotopic variance on dietary correlation time, a measure for the typical time over which a consumer changes its diet. This quantitative approach allows us to pinpoint possible procedural pitfalls and critical sources of measurement uncertainty. Our results show that the stable isotope approach represents a powerful method for estimating trophic niche widths, especially when taking the quantitative concept of dietary correlation time into account. © 2012 The Authors.

Levels and patterns of population genetic diversity in the red seaweed Chondrus crispus (Florideophyceae): a direct comparison of single nucleotide polymorphisms and microsatellites

Single nucleotide polymorphisms (SNPs) are predicted to supersede microsatellites as the marker of choice for population genetic studies in the near future. To date, however, very few studies have directly compared both marker systems in natural populations, particularly in non-model organisms. In the present study, we compared the utility of SNPs and microsatellites for population genetic analysis of the red seaweed Chondrus crispus (Florideophyceae). Six SNP loci yielded very different patterns of intrapopulation genetic diversity compared to those obtained using seven moderately (mean 5.2 alleles) polymorphic microsatellite loci, although Bayesian clustering analysis gave largely congruent results between the two marker classes. A weak but significant pattern of isolation-by-distance was observed across scales from a few hundred metres to approximately 200?km using the combined SNP and microsatellite data set of 13 loci. Over larger scales, however, there was little correlation between genetic divergence and geographical distance. Our findings suggest that even a moderate number of SNPs is sufficient to determine patterns of genetic diversity across natural populations, and also highlight the fact that patterns of genetic variation in seaweeds arise through a complex interplay of short- and long-term natural processes, as well as anthropogenic influence.

The effects of past, present and future climate change on range-wide genetic diversity in northern North Atlantic marine species

It is now accepted that changes in the Earth’s climate are having a profound effect on the distributions of a wide variety of species. One aspect of these changes that has only recently received any attention, however, is their potential effect on levels of within-species genetic diversity. Theoretical, empirical and modelling studies suggest that the impact of trailing-edge population extirpation on range-wide intraspecific diversity will be most pronounced in species that harbour the majority of their genetic variation at low latitudes as a result of changes during the Quaternary glaciations. In the present review, I describe the historical factors that have determined current patterns of genetic variation across the ranges of Northern North Atlantic species, highlight the fact that the majority of these species do indeed harbour a disproportionate level of genetic diversity in rear-edge populations, and outline how combined species distribution modelling and genetic analyses can provide insights into the potential effects of climate change on their overall genetic diversity.

Identifying trophic variation in a marine suspension feeder:DNA- and stable isotope-based dietary analysis in Mytilus spp.

Accurate field data on trophic interactions for suspension feeders are lacking, and new approaches to dietary analysis are necessary. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was integrated with stable isotope analysis to examine dietary patterns in suspension-feeding Mytilus spp. from seven spatially discrete locations within a semi-enclosed marine bay (Strangford Lough, Northern Ireland) during June 2009. Results of the two methods were highly correlated, reflecting dietary variation in a similar manner. Variation in PCR-DGGE data was more strongly correlated with the principal environmental gradient (distance from the opening to the Irish Sea), while values of dC and dN became progressively enriched, suggesting a greater dependence on animal tissue and benthic microalgae. Diatoms and crustaceans were the most frequently observed phylotypes identified by sequencing, but specific DNA results provided little support for the trophic trends observed in the stable isotope data. This combined approach offers an increased level of trophic insight for suspension feeders and could be applied to other organisms. © 2012 Springer-Verlag Berlin Heidelberg.

Microbiota of De-Novo Pediatric IBD: Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis

OBJECTIVES: The gastrointestinal microbiota is considered important in inflammatory bowel disease (IBD) pathogenesis. Discoveries from established disease cohorts report reduced bacterial diversity, changes in bacterial composition, and a protective role for Faecalibacterium prausnitzii in Crohn's disease (CD). The majority of studies to date are however potentially confounded by the effect of treatment and a reliance on established rather than de-novo disease.

METHODS: Microbial changes at diagnosis were examined by biopsying the colonic mucosa of 37 children: 25 with newly presenting, untreated IBD with active colitis (13 CD and 12 ulcerative colitis (UC)), and 12 pediatric controls with a macroscopically and microscopically normal colon. We utilized a dual-methodology approach with pyrosequencing (threshold >10,000 reads) and confirmatory real-time PCR (RT-PCR).

RESULTS: Threshold pyrosequencing output was obtained on 34 subjects (11 CD, 11 UC, 12 controls). No significant changes were noted at phylum level among the Bacteroidetes, Firmicutes, or Proteobacteria. A significant reduction in bacterial alpha-diversity was noted in CD vs. controls by three methods (Shannon, Simpson, and phylogenetic diversity) but not in UC vs. controls. An increase in Faecalibacterium was observed in CD compared with controls by pyrosequencing (mean 16.7% vs. 9.1% of reads, P = 0.02) and replicated by specific F. prausnitzii RT-PCR (36.0% vs. 19.0% of total bacteria, P = 0.02). No disease-specific clustering was evident on principal components analysis.

CONCLUSIONS: Our results offer a comprehensive examination of the IBD mucosal microbiota at diagnosis, unaffected by therapeutic confounders or changes over time. Our results challenge the current model of a protective role for F. prausnitzii in CD, suggesting a more dynamic role for this organism than previously described.

Genotypic and phenotypic diversity of the noncapsulated Haemophilus influenzae:Adaptation and pathogenesis in the human airways

The human respiratory tract contains a highly adapted microbiota including commensal and opportunistic pathogens. Noncapsulated or nontypable Haemophilus influenzae (NTHi) is a human-restricted member of the normal airway microbiota in healthy carriers and an opportunistic pathogen in immunocompromised individuals. The duality of NTHi as a colonizer and as a symptomatic infectious agent is closely related to its adaptation to the host, which in turn greatly relies on the genetic plasticity of the bacterium and is facilitated by its condition as a natural competent. The variable genotype of NTHi accounts for its heterogeneous gene expression and variable phenotype, leading to differential host-pathogen interplay among isolates. Here we review our current knowledge of NTHi diversity in terms of genotype, gene expression, antigenic variation, and the phenotypes associated with colonization and pathogenesis. The potential benefits of NTHi diversity studies discussed herein include the unraveling of pathogenicity clues, the generation of tools to predict virulence from genomic data, and the exploitation of a unique natural system for the continuous monitoring of long-term bacterial evolution in human airways exposed to noxious agents. Finally, we highlight the challenge of monitoring both the pathogen and the host in longitudinal studies, and of applying comparative genomics to clarify the meaning of the vast NTHi genetic diversity and its translation to virulence phenotypes.

Relative role of deterministic and stochastic determinants of soil animal community: a spatially explicit analysis of oribatid mites

1. Ecologists are debating the relative role of deterministic and stochastic determinants of community structure. Although the high diversity and strong spatial structure of soil animal assemblages could provide ecologists with an ideal ecological scenario, surprisingly little information is available on these assemblages.
2. We studied species-rich soil oribatid mite assemblages from a Mediterranean beech forest and a grassland. We applied multivariate regression approaches and analysed spatial autocorrelation at multiple spatial scales using Moran's eigenvectors. Results were used to partition community variance in terms of the amount of variation uniquely accounted for by environmental correlates (e.g. organic matter) and geographical position. Estimated neutral diversity and immigration parameters were also applied to a soil animal group for the first time to simulate patterns of community dissimilarity expected under neutrality, thereby testing neutral predictions.
3. After accounting for spatial autocorrelation, the correlation between community structure and key environmental parameters disappeared: about 40% of community variation consisted of spatial patterns independent of measured environmental variables such as organic matter. Environmentally independent spatial patterns encompassed the entire range of scales accounted for by the sampling design (from tens of cm to 100 m). This spatial variation could be due to either unmeasured but spatially structured variables or stochastic drift mediated by dispersal. Observed levels of community dissimilarity were significantly different from those predicted by neutral models.
4. Oribatid mite assemblages are dominated by processes involving both deterministic and stochastic components and operating at multiple scales. Spatial patterns independent of the measured environmental variables are a prominent feature of the targeted assemblages, but patterns of community dissimilarity do not match neutral predictions. This suggests that either niche-mediated competition or environmental filtering or both are contributing to the core structure of the community. This study indicates new lines of investigation for understanding the mechanisms that determine the signature of the deterministic component of animal community assembly.

Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

Extreme arid regions in the worlds' major deserts are typified by quartz pavement terrain. Cryptic hypolithic communities colonize the ventral surface of quartz rocks and this habitat is characterized by a relative lack of environmental and trophic complexity. Combined with readily identifiable major environmental stressors this provides a tractable model system for determining the relative role of stochastic and deterministic drivers in community assembly. Through analyzing an original, worldwide data set of 16S rRNA-gene defined bacterial communities from the most extreme deserts on the Earth, we show that functional assemblages within the communities were subject to different assembly influences. Null models applied to the photosynthetic assemblage revealed that stochastic processes exerted most effect on the assemblage, although the level of community dissimilarity varied between continents in a manner not always consistent with neutral models. The heterotrophic assemblages displayed signatures of niche processes across four continents, whereas in other cases they conformed to neutral predictions. Importantly, for continents where neutrality was either rejected or accepted, assembly drivers differed between the two functional groups. This study demonstrates that multi-trophic microbial systems may not be fully described by a single set of niche or neutral assembly rules and that stochasticity is likely a major determinant of such systems, with significant variation in the influence of these determinants on a global scale.

Identifying appropriate sampling and modelling approaches for analysing distributional patterns of Antarctic terrestrial arthropods along the Victoria Land latitudinal gradient

Biotic communities in Antarctic terrestrial ecosystems are relatively simple and often lack higher trophic levels (e. g. predators); thus, it is often assumed that species' distributions are mainly affected by abiotic factors such as climatic conditions, which change with increasing latitude, altitude and/or distance from the coast. However, it is becoming increasingly apparent that factors other than geographical gradients affect the distribution of organisms with low dispersal capability such as the terrestrial arthropods. In Victoria Land (East Antarctica) the distribution of springtail (Collembola) and mite (Acari) species vary at scales that range from a few square centimetres to regional and continental. Different species show different scales of variation that relate to factors such as local geological and glaciological history, and biotic interactions, but only weakly with latitudinal/altitudinal gradients. Here, we review the relevant literature and outline more appropriate sampling designs as well as suitable modelling techniques (e. g. linear mixed models and eigenvector mapping), that will more adequately address and identify the range of factors responsible for the distribution of terrestrial arthropods in Antarctica.