Quantitative PCR enumeration of total/toxic Planktothrix rubescens and total cyanobacteria in preserved DNA isolated from lake sediments

The variability of spatial distribution and the determinism of cyanobacterial blooms, as well as their impact at the lake scale, are still not understood, partly due to the lack of long-term climatic and environmental monitoring data. The paucity of these data can be alleviated by the use of proxy data from high-resolution sampling of sediments. Coupling paleolimnological and molecular tools and using biomarkers such as preserved DNA are promising approaches, although they have not been performed often enough so far. In our study, a quantitative PCR (qPCR) technique was applied to enumerate total cyanobacterial and total and toxic Planktothrix communities in preserved DNA derived from sediments of three lakes located in the French Alps (Lake Geneva, Lake Bourget, and Lake Annecy), containing a wide range of cyanobacterial species. Preserved DNA from lake sediments was analyzed to assess its quality, quantity, and integrity, with further application for qPCR. We applied the qPCR assay to enumerate the total cyanobacterial community, and multiplex qPCR assays were applied to quantify total and microcystin-producing Planktothrix populations in a single reaction tube. These methods were optimized, calibrated, and applied to sediment samples, and the specificity and reproducibility of qPCR enumeration were tested. Accurate estimation of potential inhibition within sediment samples was performed to assess the sensitivity of such enumeration by qPCR. Some precautions needed for interpreting qPCR results in the context of paleolimnological approaches are discussed. We concluded that the qPCR assay can be used successfully for the analysis of lake sediments when DNA is well preserved in order to assess the presence and dominance of cyanobacterial and Planktothrix communities.     

Nutrient concentrations and fibre contents of plant community biomass reflect species richness patterns along a broad range of land-use intensities among agricultural grasslands

Understanding changes in biodiversity in agricultural landscapes in relation to land-use type and intensity is a major issue in current ecological research. In this context nutrient enrichment has been identified as a key mechanism inducing species loss in Central European grassland ecosystems. At the same time, insights into the linkage between agricultural land use and plant nutrient status are largely missing. So far, studies on the relationship between chemical composition of plant community biomass and biodiversity have mainly been restricted to wetlands and all these studies neglected the effects of land use. Therefore, we analyzed aboveground biomass of 145 grassland plots covering a gradient of land-use intensities in three regions across Germany. In particular, we explored relationships between vascular plant species richness and nutrient concentrations as well as fibre contents (neutral and acid detergent fibre and lignin) in the aboveground community biomass.We found the concentrations of several nutrients in the biomass to be closely linked to plant species richness and land use. Whereas phosphorus concentrations increased with land-use intensity and decreased with plant species richness, nitrogen and potassium concentrations showed less clear patterns. Fibre fractions were negatively related to nutrient concentrations in biomass, but hardly to land-use measures and species richness. Only high lignin contents were positively associated with species richness of grasslands. The N:P ratio was strongly positively related to species richness and even more so to the number of endangered plant species, indicating a higher persistence of endangered species under P (co-)limited conditions. Therefore, we stress the importance of low P supply for species-rich grasslands and suggest the N:P ratio in community biomass to be a useful proxy of the conservation value of agriculturally used grasslands.     

Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing

? Bryophytes are a dominant vegetation component of the boreal forest, but little is known about their associated fungal communities, including seasonal variation within them. ? Seasonal variation in the fungal biomass and composition of fungal communities associated with three widespread boreal bryophytes was investigated using HPLC assays of ergosterol and amplicon pyrosequencing of the internal transcribed spacer 2 (ITS2) region of rDNA. ? The bryophyte phyllosphere community was dominated by Ascomycota. Fungal biomass did not decline appreciably in winter (P?=?0.272). Significant host-specific patterns in seasonal variation of biomass were detected (P?=?0.003). Although seasonal effects were not the primary factors structuring community composition, collection date significantly explained (P?=?0.001) variation not attributed to locality, host, and tissue. Community homogenization and a reduction in turnover occurred with the onset of frost events and subzero air and soil temperatures. Fluctuations in the relative abundance of particular fungal groups seem to reflect the nature of their association with mosses, although conclusions are drawn with caution because of potential methodological bias. ? The moss-associated fungal community is dynamic, exhibiting seasonal turnover in composition and relative abundance of different fungal groups, and significant fungal biomass is present year-round, suggesting a winter-active fungal community.     

Use of Droplet Digital PCR for Estimation of Fish Abundance and Biomass in Environmental DNA Surveys

An environmental DNA (eDNA) analysis method has been recently developed to estimate the distribution of aquatic animals by quantifying the number of target DNA copies with quantitative real-time PCR (qPCR). A new quantitative PCR technology, droplet digital PCR (ddPCR), partitions PCR reactions into thousands of droplets and detects the amplification in each droplet, thereby allowing direct quantification of target DNA. We evaluated the quantification accuracy of qPCR and ddPCR to estimate species abundance and biomass by using eDNA in mesocosm experiments involving different numbers of common carp. We found that ddPCR quantified the concentration of carp eDNA along with carp abundance and biomass more accurately than qPCR, especially at low eDNA concentrations. In addition, errors in the analysis were smaller in ddPCR than in qPCR. Thus, ddPCR is better suited to measure eDNA concentration in water, and it provides more accurate results for the abundance and biomass of the target species than qPCR. We also found that the relationship between carp abundance and eDNA concentration was stronger than that between biomass and eDNA by using both ddPCR and qPCR; this suggests that abundance can be better estimated by the analysis of eDNA for species with fewer variations in body mass.     

Fungal biomass associated with the phyllosphere of bryophytes and vascular plants

Little is known about the amount of fungal biomass in the phyllosphere of bryophytes compared to higher plants. In this study, fungal biomass associated with the phyllosphere of three bryophytes (Hylocomium splendens, Pleurozium schreberi, Polytrichum commune) and three vascular plants (Avenella flexuosa, Gymnocarpium dryopteris, Vaccinium myrtillus) was investigated using ergosterol content as a proxy for fungal biomass. Phyllosphere fungi accounted for 0.2-4.0 % of the dry mass of moss gametophytes, representing the first estimation of fungal biomass associated with bryophytes. Significantly more fungal biomass was associated with the phyllosphere of bryophytes than co-occurring vascular plants. The ergosterol present in moss gametophytic tissues differed significantly between species, while the ergosterol present in vascular plant leaf tissues did not. The photosynthetic tissues of mosses had less associated fungal biomass than their senescent tissues, and the magnitude of this difference varied in a species-specific manner. The fungal biomass associated with the vascular plants studied varied significantly between localities, while that of mosses did not. The observed differences in phyllosphere community biomass suggest their size could be affected by host anatomical and physiological attributes, including micro-niche availability and chemical host defenses, in addition to abiotic factors like moisture and nutrient availability.     

Ergosterol-to-Biomass Conversion Factors for Aquatic Hyphomycetes

Fourteen strains of aquatic hyphomycete species that are common on decaying leaves in running waters were grown in liquid culture and analyzed for total ergosterol contents. Media included an aqueous extract from senescent alder leaves, a malt extract broth, and a glucose-mineral salt solution. Concentrations of ergosterol in fungal mycelium ranged from 2.3 to 11.5 mg/g of dry mass. The overall average was 5.5 mg/g. Differences among both species and growth media were highly significant but followed no systematic pattern. Stationary-phase mycelium had ergosterol contents 10 to 12% lower or higher than mycelium harvested during the growth phase, but these differences were only significant for one of four species examined. Availability of plant sterols in the growth medium had no clear effect on ergosterol concentrations in two species tested. To convert ergosterol contents determined in field samples to biomass values of aquatic hyphomycetes, a general multiplicative factor of 182 is proposed. More accurate estimates would be obtained with species-specific factors. Using these in combination with estimates of the proportion of the dominant species in a naturally established community on leaves resulted in biomass estimates that were typically 20% lower than those obtained with the general conversion factor. Improvements of estimates with species-specific factors may be limited, however, by intraspecific variability in fungal ergosterol content.     

Initial colonization, nutrient supply, and fungal activity on leaves decaying in streams

Aquatic hyphomycetes dominate leaf decomposition in streams, and their biomass is an important component in the diet of leaf-eating invertebrates. After 2 weeks of exposure in a first-order stream, maple leaf disks had low levels of fungal biomass and species diversity. Spore production by aquatic hyphomycetes also was low. Subsets of these disks were left in the stream for another 3 weeks or incubated in defined mineral solutions with one of three levels of nitrate and phosphate. Stream disks lost mass, increased ergosterol levels and spore production, and were colonized by additional fungal species. External N and P significantly stimulated mass loss, ergosterol accumulation, and spore production of laboratory disks. On disks incubated without added N and P, ergosterol levels declined while conidium production continued, suggesting conversion of existing hyphal biomass to propagules. In all other treatments, approximately equal amounts of newly synthesized biomass were invested in hyphae and conidia. Net yield (fungal biomass per leaf mass lost) varied between 1% (in the laboratory, without added N or P) and 31% (decay in stream). In most treatments, the three aquatic hyphomycete species that dominated spore production during the first 2 weeks in the stream also produced the largest numbers of conidia in the following 3 weeks. Principal-component analysis suggested two divergent trends from the initial fungal community established after 2 weeks in the stream. One culminated in the community of the second phase of stream exposure, and the other culminated in the laboratory treatment with the highest levels of N and P. The results suggest that fungal production in streams, and, by extension, production of invertebrates and higher tropic levels, is stimulated by inorganic N and P.     

Initial Colonization, Nutrient Supply, and Fungal Activity on Leaves Decaying in Streams

Aquatic hyphomycetes dominate leaf decomposition in streams, and their biomass is an important component in the diet of leaf-eating invertebrates. After 2 weeks of exposure in a first-order stream, maple leaf disks had low levels of fungal biomass and species diversity. Spore production by aquatic hyphomycetes also was low. Subsets of these disks were left in the stream for another 3 weeks or incubated in defined mineral solutions with one of three levels of nitrate and phosphate. Stream disks lost mass, increased ergosterol levels and spore production, and were colonized by additional fungal species. External N and P significantly stimulated mass loss, ergosterol accumulation, and spore production of laboratory disks. On disks incubated without added N and P, ergosterol levels declined while conidium production continued, suggesting conversion of existing hyphal biomass to propagules. In all other treatments, approximately equal amounts of newly synthesized biomass were invested in hyphae and conidia. Net yield (fungal biomass per leaf mass lost) varied between 1% (in the laboratory, without added N or P) and 31% (decay in stream). In most treatments, the three aquatic hyphomycete species that dominated spore production during the first 2 weeks in the stream also produced the largest numbers of conidia in the following 3 weeks. Principal-component analysis suggested two divergent trends from the initial fungal community established after 2 weeks in the stream. One culminated in the community of the second phase of stream exposure, and the other culminated in the laboratory treatment with the highest levels of N and P. The results suggest that fungal production in streams, and, by extension, production of invertebrates and higher tropic levels, is stimulated by inorganic N and P.     

Amplicon‐pyrosequencing‐based detection of compositional shifts in bryophyte‐associated fungal communities along an elevation gradient

Although bryophytes are a dominant vegetation component of boreal and alpine ecosystems, little is known about their associated fungal communities. HPLC assays of ergosterol (fungal biomass) and amplicon pyrosequencing of the ITS2 region of rDNA were used to investigate how the fungal communities associated with four bryophyte species changed across an elevational gradient transitioning from conifer forest to the low‐alpine. Fungal biomass and OTU richness associated with the four moss hosts did not vary significantly across the gradient (P > 0.05), and both were more strongly affected by host and tissue type. Despite largely constant levels of fungal biomass, distinct shifts in community composition of fungi associated with Hylocomium, Pleurozium and Polytrichum occurred between the elevation zones of the gradient. This likely is a result of influence on fungal communities by major environmental factors such as temperature, directly or indirectly mediated by, or interacting with, the response of other components of the vegetation (i.e. the dominant trees). Fungal communities associated with Dicranum were an exception, exhibiting spatial autocorrelation between plots, and no significant structuring by elevation. Nevertheless, the detection of distinct fungal assemblages associated with a single host growing in different elevation zones along an elevational gradient is of particular relevance in the light of the ongoing changes in vegetation patterns in boreal and alpine systems due to global climate warming.     

Soil drying procedure affects the DNA quantification of <Emphasis Type="Italic">Lactarius vinosus</Emphasis> but does not change the fungal community composition

Drying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different drying procedures (freeze-drying, oven-drying, and room temperature) on 12 different soil samples to determine (a) the soil mycelium biomass of the ectomycorrhizal species Lactarius vinosus using qPCR with a specifically designed TaqMan® probe and (b) the fungal community composition and diversity using the PacBio® RS II sequencing platform. Mycelium biomass of L. vinosus was significantly greater in the freeze-dried soil samples than in samples dried at oven and room temperature. However, drying procedures had no effect on fungal community composition or on fungal diversity. In addition, there were no significant differences in the proportions of fungi according to their functional roles (moulds vs. mycorrhizal species) in response to drying procedures. Only six out of 1139 operational taxonomic units (OTUs) had increased their relative proportions after soil drying at room temperature, with five of these OTUs classified as mould or yeast species. However, the magnitude of these changes was small, with an overall increase in relative abundance of these OTUs of approximately 2 %. These results suggest that DNA degradation may occur especially after drying soil samples at room temperature, but affecting equally nearly all fungi and therefore causing no significant differences in diversity and community composition. Despite the minimal effects caused by the drying procedures at the fungal community composition, freeze-drying resulted in higher concentrations of L. vinosus DNA and prevented potential colonization from opportunistic species.     

Upstream trophic structure modulates downstream community dynamics via resource subsidies

In many natural systems, the physical structure of the landscape dictates the flow of resources. Despite mounting evidence that communities’ dynamics can be indirectly coupled by reciprocal among ecosystem resource flows, our understanding of how directional resource flows might indirectly link biological communities is limited. We here propose that differences in community structure upstream should lead to different downstream dynamics, even in the absence of dispersal of organisms. We report an experimental test of the effect of upstream community structure on downstream community dynamics in a simplified but highly controlled setting, using protist microcosms. We implemented directional flows of resources, without dispersal, from a standard resource pool into upstream communities of contrasting interaction structure and then to further downstream communities of either one or two trophic levels. Our results demonstrate that different types of species interactions in upstream habitats may lead to different population sizes and levels of biomass in these upstream habitats. This, in turn, leads to varying levels of detritus transfer (dead biomass) to the downstream communities, thus influencing their population densities and trophic interactions in predictable ways. Our results suggest that the structure of species interactions in directionally structured ecosystems can be a key mediator of alterations to downstream habitats. Alterations to upstream habitats can thus cascade down to downstream communities, even without dispersal.     

A metagenetic approach for revealing community structure of marine planktonic copepods

Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species‐level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species‐level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field‐collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass‐dominant species in each field‐collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.     

Fungal Growth and Biomass Development is Boosted by Plants in Snow-Covered Soil

Soil microbial communities follow distinct seasonal cycles which result in drastic changes in processes involving soil nutrient availability. The biomass of fungi has been reported to be highest during winter, but is fungal growth really occurring in frozen soil? And what is the effect of plant cover on biomass formation and on the composition of fungal communities? To answer these questions, we monitored microbial biomass N, ergosterol, and the amount of fungal hyphae during summer and winter in vegetated and unvegetated soils of an alpine primary successional habitat. The winter fungal communities were identified by rDNA ITS clone libraries. Winter soil temperatures ranged between -0.6°C and -0.1°C in snow-covered soil. We found distinct seasonal patterns for all biomass parameters, with highest biomass concentrations during winter in snow-covered soil. The presence of plant cover had a significant positive effect on the amount of biomass in the soil, but the type of plant cover (plant species) was not a significant factor. A mean hyphal ingrowth of 5.6 m g(-1) soil was detected in snow-covered soil during winter, thus clearly proving fungal growth during winter in snow-covered soil. Winter fungal communities had a typical species composition: saprobial fungi were dominating, among them many basidiomycete yeasts. Plant cover had no influence on the composition of winter fungal communities.     

Does the growth rate hypothesis apply to aquatic hyphomycetes?

The growth rate hypothesis states that in many organisms or tissues, the specific growth rate μ correlates with RNA concentrations. Since RNA often accounts for much of the phosphorus content of cells, μ may also correlate positively with P concentrations and negatively with C:P and N:P ratios. We tested this hypothesis with broth cultures of five aquatic hyphomycete species. Samples were harvested on eight occasions after 3–56 d of incubation. Accumulation of biomass was fitted to a rectangular hyperbola, whose parameters were used to estimate μ. There were no consistent trends related to culture age or μ for C, N, P or ergosterol concentrations. RNA and DNA concentrations and RNA:DNA ratios were significantly and negatively correlated with culture age. Only RNA concentrations were positively and linearly correlated with μ. While RNA or DNA concentrations are unsuitable as indicators for total biomass, levels of fungal RNA combined with markers for fungal biomass may allow estimates of the extent to which the mycelia are metabolically active.     

Shotgun metagenomics of soil invertebrate communities reflects taxonomy,biomass, and reference genome properties

• Metagenomics – shotgun sequencing of all DNA fragments from a community DNA extract – is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene‐based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.
• We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.
• We recovered over 95% of the species, and observed relatively high false‐positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon‐specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass–read relationships. Results were similar among different sequencing efforts.
• The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low‐ and high‐sequencing efforts yield similar results, suggesting high cost‐efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics‐based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.

     

Punching above their weight: low-biomass non-native plant species alter soil properties during primary succession

Non‐native invasive plants can greatly alter community and ecosystem properties, but efforts to predict which invasive species have the greatest impacts on these properties have been generally unsuccessful. An hypothesis that has considerable promise for predicting the effects of invasive non‐native plant species is the mass ratio hypothesis (i.e. that dominant species exert the strongest effects). We tested this hypothesis using data from a four year removal experiment in which the presence of two dominant shrub species (one native and the other not), and subordinate plant species, were manipulated in factorial combinations over four years in a primary successional floodplain system. We measured the effects of these manipulations on the plant community, soil nutrient status and soil biota in different trophic levels of the soil food web. Our experiment showed that after four years, low‐biomass non‐native plant species exerted disproportionate belowground effects relative to their contribution to total biomass in the plant community, most notably by increasing soil C, soil microbial biomass, altering soil microbial community structure and increasing the abundance of microbial‐feeding and predatory nematodes. Low‐biomass, non‐native plant species had distinct life history strategies and foliar traits (higher foliar N concentrations and higher leaf area per unit mass) compared with the two dominant shrub species (97% of total plant mass). Our results have several implications for understanding species’ effects in communities and on soil properties. First, high‐biomass species do not necessarily exert the largest impacts on community or soil properties. Second, low‐biomass, inconspicuous non‐native species can influence community composition and have important trophic consequences belowground through effects on soil nutrient status or resource availability to soil biota. Our finding that low‐biomass non‐native species influence belowground community structure and soil properties more profoundly than dominant species demonstrates that the mass ratio hypothesis does not accurately predict the relative effects of different coexisting species on community‐ and ecosystem‐level properties.     

Development of environmental DNA (eDNA) methods for detecting high-risk freshwater fishes in live trade in Canada

Preventing the arrival, establishment, and spread of aquatic invasive species is an important step in protecting our aquatic environments. The use of detection tools, like DNA barcoding technologies, high-throughput sequencing and environmental DNA (eDNA) monitoring, is becoming increasingly important in preventing the introduction of potential invasive species. The combination of eDNA with realtime PCR (qPCR) provide the opportunity to have a rapid and specific detection. In this study, we developed a DNA sequence library that has sufficient depth and species coverage such that high-risk species can be confidently discriminated from legitimately imported and native species. A total of 12 species-specific qPCR assays were developed for the detection of 13 potential invasive species (pAIS) in bulk water samples. Detection of these species was also compared with a HTS approach. We have demonstrated the high sensitivity of qPCR assays using eDNA at very low densities, suggesting we could detect a low number of individuals mixed with non-target species in a simulated live shipment. For the detection of a targeted list of species, qPCR is advantageous. The mini-barcodes developed in this project offered a good sensitivity of detection, and HTS is a discovery tool that can be desirable when unlisted or numerous species need to be identified.     

Effect of (a)synchronous light fluctuation on diversity,functional and structural stability of a marine phytoplankton metacommunity

Disentangling the mechanisms that maintain the stability of communities and ecosystem properties has become a major research focus in ecology in the face of anthropogenic environmental change. Dispersal plays a pivotal role in maintaining diversity in spatially subdivided communities, but only a few experiments have simultaneously investigated how dispersal and environmental fluctuation affect community dynamics and ecosystem stability. We performed an experimental study using marine phytoplankton species as model organisms to test these mechanisms in a metacommunity context. We established three levels of dispersal and exposed the phytoplankton to fluctuating light levels, where fluctuations were either spatially asynchronous or synchronous across patches of the metacommunity. Dispersal had no effect on diversity and ecosystem function (biomass), while light fluctuations affected both evenness and community biomass. The temporal variability of community biomass was reduced by fluctuating light and temporal beta diversity was influenced interactively by dispersal and fluctuation, whereas spatial variability in community biomass and beta diversity were barely affected by treatments. Along the establishing gradient of species richness and dominance, community biomass increased but temporal variability of biomass decreased, thus highest stability was associated with species-rich but highly uneven communities and less influenced by compensatory dynamics. In conclusion, both specific traits (dominance) and diversity (richness) affected the stability of metacommunities under fluctuating conditions.     

Bottom-up effects of species diversity on the functioning and stability of food webs

1. The importance of species diversity for the stability of populations, communities and ecosystem functions is a central question in ecology. 2. Biodiversity experiments have shown that diversity can impact both the average and variability of stocks and rates at these levels of ecological organization in single trophic-level ecosystems. Whether these impacts hold in food webs and across trophic levels is still unclear. 3. We asked whether resource species diversity, community composition and consumer feeding selectivity in planktonic food webs impact the stability of resource or consumer populations, community biomass and ecosystem functions. We also tested the relative importance of resource diversity and community composition. 4. We found that resource diversity negatively affected resource population stability, but had no effect on consumer population stability, regardless of the consumer's feeding selectivity. Resource diversity had positive effects on most ecosystem functions and their stability, including primary production, resource biomass and particulate carbon, nitrogen and phosphorus concentrations. 5. Community composition, however, generally explained more variance in population, community and ecosystem properties than species diversity per se. This result points to the importance of the outcomes of particular species interactions and individual species' effect traits in determining food web properties and stability. 6. Among the stabilizing mechanisms tested, an increase in the average resource community biomass with increasing resource diversity had the greatest positive impact on stability. 7. Our results indicate that resource diversity and composition are generally important for the functioning and stability of whole food webs, but do not have straightforward impacts on consumer populations.     

Comparative mitochondrial and nuclear quantitative PCR of historical marine mammal tissue,bone, baleen,and tooth samples

The use of historical and ancient tissue samples for genetic analysis is increasing, with ever greater numbers of samples proving to contain sufficient mitochondrial and even nuclear DNA for multilocus analysis. DNA yield, however, remains highly variable and largely unpredictable based solely on sample morphology or age. Quantification of DNA from historical and degraded samples can greatly improve efficiency of screening DNA extracts prior to attempting sequencing or genotyping, but requires sequence‐specific quantitative polymerase chain reaction (qPCR) based assays to detect such minute quantities of degraded DNA. We present two qPCR assays for marine mammal DNA quantification, and results from analysis of DNA extracted from preserved soft tissues, bone, baleen, and tooth from several cetacean species. These two assays have been shown to amplify DNA from 26 marine mammal species representing 12 families of pinnipeds and cetaceans. Our results indicate that different tissues retain different ratios of mitochondrial to nuclear DNA, and may be more or less suitable for analysis of nuclear loci. Specifically, historical bone and tooth samples average 60‐fold higher ratio of mitochondrial DNA to nuclear DNA than preserved fresh soft tissue, and the ratio is almost 8000‐fold higher in baleen.