Taxonomic sufficiency in ecological studies of terrestrial invertebrates

The concept of taxonomic sufficiency (identifying organisms only to a level of taxonomic resolution sufficient to satisfy the objectives of a study) has received little attention in ecological studies of terrestrial invertebrate assemblages. Here we critically evaluate three approaches to taxonomic sufficiency: the use of morphospecies, genera and functional groups. The objective was to compare estimates of richness (α diversity) and turnover (β diversity) of ant assemblages generated by these data with estimates produced using data for ant species. Ground-active ants were sampled using pitfall trapping within three habitat types: a eucalypt plantation, woodland regrowth patches and the surrounding grassland at a study site in the upper Hunter Valley, New South Wales. Comparisons of assemblage richness and turnover among taxonomic data sets and habitats and after different data transformations used univariate (simple correlation and ANOVA ) and multivariate (Mantel tests, ANOSIM and SSHMDS ) techniques. Our study found: (i) morphospecies and genus richness was highly correlated with species richness over the study area; (ii) ordination scatterplots using species, morphospecies and genus data revealed similar patterns of site separation for the three habitats; (iii) the results were very similar using untransformed, log transformed and binary data; (iv) functional group ordinations separated all three habitat types for untransformed abundance data; and (v) estimates of species turnover were highly correlated with estimates of morphospecies and genus turnover. These results are discussed in relation to future monitoring of ant community structure.     

Abundance patterns and coexistence processes in communities of fleas parasitic on small mammals

The abundance of a given species in a community is likely to depend on both the total abundance and diversity of other species making up that community. A large number of co-occurring individuals or co-occurring species may decrease the abundance of any given species via diffuse competition; however, indirect interactions among many co-occurring species can have positive effects on a focal species. The existence of diffuse competition and facilitation remain difficult to demonstrate in natural communities. Here, we use data on communities of fleas ectoparasitic on small mammals from 27 distinct geographical regions to test whether the abundance of any given flea species in a community is affected by either the total abundance of all other co-occurring flea species, or the species richness and/or taxonomic diversity of the flea community. At all scales of analysis, i.e. whether we compared the same flea species on different host species, or different flea species, two consistent results emerged. First, the abundance of a given flea species correlates positively with the total abundance of all other co-occurring flea species in the community. Second, the abundance of any given flea species correlates negatively with either the species richness or taxonomic diversity of the flea community. The results do not support the existence of diffuse competition in these assemblages, because the more individuals of other flea species are present on a host population, the more individuals of the focal species are there as well. Instead, we propose explanations involving either apparent facilitation among flea species via suppression of host immune defenses, or niche filtering processes acting to restrict the taxonomic composition and abundance of flea assemblages.     

The influence of substrates and physicochemical factors on the composition of diatom assemblages in karst springs and their applicability in water-quality assessment

The methodological standards of monitoring programs recommend collecting material from stones, but this community is often absent in slow-flowing waters, whereas a great number of localities do offer bryophytic material for sampling. In order to investigate whether the kind of substrate (epilithic or bryophytic) influences the diatom-based biomonitoring results the structure of diatom assemblages from 13 anthropogenically altered springs were investigated. To examine differences between diatom assemblages, the species richness of diatom assemblages, H′ (Shannon-Wiener diversity index), Trophic Diatom Index (TDI) and Specific Pollution sensitivity Index (SPI) were compared. The TDI and SPI differed significantly (P = 0.002 and P = 0.004) between springs located in villages and springs away from villages, and did not differ significantly between epilithic and bryophytic samples (P > 0.05). No significant differences in species richness or the diversity index (H′) (P > 0.05) were found between the epilithic and bryophytic diatom assemblages. This study suggests that both the kinds of substrates can be successfully used for diatom-based water-quality biomonitoring in mesotrophic and eutrophic environments.     

Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability

Scleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean, Montastraea faveolata and Porites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here that M. faveolata and P. astreoides harbor distinct, host-specific bacteria but that specificity varies by species and site. P. astreoides generally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus, Endozoicomonas, within the order Oceanospirillales. The bacterial assemblages associated with M. faveolata are significantly more diverse and exhibit higher specificity at the family level than P. astreoides assemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude that the two coral species studied harbor distinct bacterial assemblages within the SML, but the degree to which each species maintains specific microbial associations varies both within each site and across large spatial scales. The taxonomic scale (i.e., phylum versus genus) at which scientists examine coral-microbe associations, in addition to host-elicited factors and environmental fluctuations, must be considered carefully in future studies of the coral holobiont.     

How to get more out of molecular fingerprints: practical tools for microbial ecology

Community-level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), single-strand conformation polymorphism (SSCP), length heterogeneity-PCR (LH-PCR), terminal-restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a setting-independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness (Rr) reflecting the carrying capacity of the system, (ii) the dynamics (Dy) reflecting the specific rate of species coming to significance, and (iii) functional organization (Fo), defined through a relation between the structure of a microbial community and its functionality. These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern.     

Functional diversity is positively associated with biomass for lake diatoms

1. Recent work has emphasised the benefit of using functional measures when relating biodiversity to ecosystem functioning. In this study, we investigated the extent to which functional and taxonomic diversity might be related to summed biovolume in community assemblages of 212 species of diatoms collected from 65 temperate lakes in western and central Quebec, Canada. 2. We quantified functional diversity as both the total path‐length of a functional dendrogram (FD) and the variance in species traits (TV) for a given community. Selected traits included both size and responses to a set of environmental variables known to be influential for diatom communities. 3. Species richness, as well as both FD and TV, was positively associated with total diatom biovolume at the level of the entire diatom community, suggesting that diversity in response types (particularly to total phosphorus and pH) is important for diatom community production. 4. Although functional measures of diversity did not provide enhanced explanatory power over species richness, we argue that an exploration of functional traits potentially allows greater insight into the mechanisms underlying biodiversity–ecosystem functioning relations, indicating which traits might be most influential in driving community biomass production.     

Is coarse taxonomy sufficient for detecting macroinvertebrate patterns in floodplain lakes?

Taxonomic sufficiency (TS) — defined as the minimum taxonomic detail required to discern some ecological pattern of interest — has been used extensively in bioassessment and biodiversity studies as a way of avoiding a portion of the time and monetary costs associated with species diagnoses. The taxonomic sufficiency for detecting species-level patterns among floodplain-lake benthic-invertebrate assemblages remains unexplored. We examined cross-taxonomic-level congruence in assemblage-environment relationships among 23 Chinese floodplain lakes. Our objectives were: (1) to compare the correlation between species richness and density and those at coarser taxonomic resolution; (2) to identify whether assemblage-environment relationships depend on taxonomic scale; and (3) to test whether the proportion of between-lake variability accounted for by environmental variables was independent of taxonomic scale. When taxonomic structure was described using sequentially coarser taxonomic aggregations, species-level patterns of richness and abundance were sequentially obscured (i.e., genus-level taxonomy best preserved patterns in species composition, order- and class-level taxonomy poorly represented species composition). Similar environmental variables were important for distinguishing lake species assemblages and genus assemblages; however, different environmental variables were important for describing family-, order-, and class-level assemblage patters. Moreover, environmental variables accounted for a similar amount of biological variability, regardless of taxonomic scale. Our results suggest genus taxonomy as sufficient for rapid assessments of lake diversity. Numerical dominance of the species- and genus-rich Chironomidae, Tubificidae, and Naididae, may account for the marked loss of information that occurs when lake invertebrates are assigned only to their families. In summary, we describe taxonomic sufficiency to detecting patterns of richness and abundance among subtropical lake macroinvertebrate faunas. This study will interest Chinese benthologists concerned with conservation and bioassessment.     

Contributions of habitat sampling and alkalinity to diatom diversity and distributional patterns in streams: implications for conservation

Diatoms, microscopic unicellular algae, have been widely sampled from streams around the world because of their use in biological assessments, but as a result they are often only collected from epilithic habitats in riffles, which may lead to a substantial underreporting of their diversity and distributional patterns. The goals of this study were to identify how sampling methods and water chemistry affect the characterization of local and regional diversity and distributions. Species richness, Shannon diversity, and evenness were significantly greater in multiple habitat (MH) than epilithic habitat (EH) samples (paired t-test; P < 0.01). At the local scale, MH sampling yielded 76% of the total species collected (42% unique), EH sampling captured 58% (24% unique), and 34% were shared. From MH samples, 3, 28, and 60 regionally rare species were collected from >75, >50, and >25% of sites, respectively, whereas 1, 14, and 34 were collected from EH samples, respectively. Regional abundance more strongly predicted site frequency than mean local abundance. Smaller drainage basins tended to have fewer species, likely because of species-area relationships, but local factors (% EH and alkalinity) influenced the taxonomic complexity of assemblages. Diversity was greatest at intermediate % EH, but low alkalinity reduced diversity, which is potentially important for ecosystems affected by anthropogenic acidification, as in our study. Multiple habitats need to be sampled for better documenting diatom diversity and distributions, which could improve conservation efforts at local and regional scales along with the characterization of ecological patterns and processes.     

Taxonomic Composition of Hymenopteran Parasitoid Assemblages from Agromyzid Leaf-miners Sampled in Central Argentina

This paper deals with the taxonomic composition of parasitoid assemblages reared from agromyzid leaf-miners of 28 species collected in Cordoba, Central Argentina. The relative representation of each parasitic family was estimated, taking into consideration their species richness and abundance. Sample size affected the total species richness in each complex, and also that of Eulophidae and Pteromalidae, indicating that not only size but also taxonomic structure of parasitic assemblages are influenced by sampling effort. 3 superfamilies and 5 families of Hymenoptera Parasitica were represented, with Eulophidae (Chalcidoidea) specifically and numerically dominant both in the total community of parasitoids and in the parasitic assemblages of individual hosts. Chrysonotomyia, Chrysocharis (Eulophidae), Halticoptera (Pteromalidae) and Phaedrotoma (Braconidae) were the most relevant genera in terms of number of species and number of specimens reared. The parasitoids obtained from samples taken in agroecosystems differed from the global spectrum of taxa mainly by showing a numerical dominance of Braconidae, despite a noticeable specific impoverishment of this family.     

在种与属两个级别评价太子河硅藻群落与环境因子的关系

2009年8—9月,对辽宁省太子河流域67个点位进行采样调查,以硅藻群落为研究对象,比较硅藻属级水平与种级水平相对多度、物种丰富度以及生物多样性指数间的相关性,并比较硅藻属级与种级属性与环境因子的相关性。实验结果表明,太子河流域硅藻属级水平的相对多度、丰富度和多样性指数与硅藻种级水平都极显著相关。Pearson相关性分析表明,硅藻属级水平的丰富度与环境显著相关的因子与种级水平丰富度与环境显著相关的因子相一致。Mantel-Test相关性分析表明,硅藻属级水平的相对多度与环境因子的相关性弱于种级水平与环境因子相关性。典范对应分析结果显示,影响硅藻属级和种级群落结构分布的主要环境因子均为悬浮物。基于硅藻生物评价指数的流域健康评价结果表明,应用硅藻属级和种级属性对太子河流域进行健康评价,其评价结果相一致。     

小兴安岭阔叶红松林地表甲虫Beta多样性

Beta多样性用来衡量集群内物种组成的变异性,可以被分解为空间物种转换和物种集群镶嵌两个组分,是揭示群落构建机制的重要基础。目前开展了较多的地上生态系统beta多样性研究,然而地下生态系统beta多样性进展缓慢。以小兴安岭凉水和丰林自然保护区为研究地区,于2015年8、10月采用陷阱法对阔叶红松林进行调查,揭示地表甲虫(步甲科、隐翅虫科、葬甲科)的beta多样性。结果表明:(1)凉水共发现39种、856只地表甲虫,丰林共发现43种、1182只地表甲虫。8月凉水明显具有较高的全部甲虫(三个科的总和)物种多样性和丰富度,10月正好相反。(2)凉水和丰林之间地表甲虫beta多样性的差异仅发现于8月的步甲科和葬甲科之间。(3)凉水和丰林地表甲虫的beta多样性主要由空间物种转换组成,物种集群镶嵌对beta多样性的贡献很小,说明地表甲虫物种组成变异主要由本地物种之间较高的转换引起。研究表明小兴安岭阔叶红松林地表甲虫的beta多样性主要由空间物种转换组成,在揭示群落构建机制过程中,其内部物种交换和环境调控不容忽视。     

The role of habitat and daily activity patterns in explaining the diversity of mountain Neotropical dung beetle assemblages

The interaction between land use and climate change is expected to strongly affect species distributions along high elevation landscapes. We aimed to test the effect of climatic variables on community metrics among five types of land use in a high elevation landscape. We described dung beetle spatial and temporal taxonomic and functional diversity patterns, and partitioned β‐diversity into turnover and nestedness components. The interaction between land use and daily period of activity mostly drives abundance, functional richness and functional diversity, but not dung beetle species richness. Unlike Neotropical lowlands, species richness and abundance in open environments are similar to those existing in forests. Temperature is an important predictor of abundance and functional divergence. There is a higher spatial component of the taxonomic β‐diversity, which is highly driven by species turnover. The temporal component of the taxonomic β‐diversity was strongly driven by nestedness, where night assemblages are sub‐sets, although not entirely, of diurnal assemblages. For functional diversity, the temporal β‐diversity was much higher than the spatial β‐diversity, but both were similarly represented by functional group turnover and nestedness. The composition of nocturnal and diurnal assemblages is clearly different, even more than the differences observed between habitats. However, taxonomic turnover is the dominant force between sampling sites while nestedness dominates the daily pattern. This means that forest habitats are unlikely to act as shelters for grassland species under a scenario of rising temperature.     

Ant community succession within eucalypt plantations on used pasture and implications for taxonomic sufficiency in biomonitoring

Abstract Ground‐active ants were sampled from three habitats: (i) a 10‐year‐old Eucalyptus punctata plantation, (ii) native woodland regrowth, and (iii) the surrounding pasture, at a study site in the Hunter Valley, New South Wales, Australia. A previous study, undertaken 6 years earlier at the same study sites, revealed no difference in species richness or composition between the eucalypt plantation and pasture. The aims of the present study were: (i) to investigate the successional change in ant community structure within the plantations; and (ii) to evaluate what levels of taxonomic identification were sufficient to indicate a change had taken place. Univariate statistics (anova ) were used to compare estimates of assemblage richness between habitats using data classified at five levels of taxonomic resolution: species, morphospecies, easily recognisable taxonomic units, genus and functional group. Multivariate statistics (anosim and non‐metric multidimensional scaling) were used to compare ant assemblages between habitats and between sampling events at a range of taxonomic resolutions from species to functional group. This study found: (i) a significant temporal change in community composition was evident using species, genus and functional group level data, but no change was detected in the pasture or woodland; (ii) mean ant species, morphospecies and easily recognisable taxonomic units richness were significantly greater within the plantations than the pasture; (iii) compositional differences between the plantation and pasture assemblages were evident at all levels of taxonomic resolution; (iv) mean ant species and genus richness were significantly higher in the woodland than in the plantation, and these two habitats were compositionally distinct at all levels of taxonomic resolution. This is the first case study to have documented a successional response from ants to the revegetation of agricultural land with eucalypt plantations. Reasons for the temporal and interhabitat differences in community structure are discussed, as well as the implications for taxonomic sufficiency in monitoring ant community successions.     

Paleoecology of the Greater Phyllopod Bed community,Burgess Shale

To better understand temporal variations in species diversity and composition, ecological attributes, and environmental influences for the Middle Cambrian Burgess Shale community, we studied 50,900 fossil specimens belonging to 158 genera (mostly monospecific and non-biomineralized) representing 17 major taxonomic groups and 17 ecological categories. Fossils were collected in situ from within 26 massive siliciclastic mudstone beds of the Greater Phyllopod Bed (Walcott Quarry — Fossil Ridge). Previous taphonomic studies have demonstrated that each bed represents a single obrution event capturing a predominantly benthic community represented by census- and time-averaged assemblages, preserved within habitat. The Greater Phyllopod Bed (GPB) corresponds to an estimated depositional interval of 10 to 100 KA and thus potentially preserves community patterns in ecological and short-term evolutionary time.The community is dominated by epibenthic vagile deposit feeders and sessile suspension feeders, represented primarily by arthropods and sponges. Most species are characterized by low abundance and short stratigraphic range and usually do not recur through the section. It is likely that these are stenotopic forms (i.e., tolerant of a narrow range of habitats, or having a narrow geographical distribution). The few recurrent species tend to be numerically abundant and may represent eurytopic organisms (i.e., tolerant of a wide range of habitats, or having a wide geographical distribution). Rarefaction curves demonstrate variation in species richness through the GPB and suggest that more stenotopic species could still be discovered with additional sampling. Comparisons between richness and evenness trends suggest that the community is relatively stable overall, despite gradual species turnover through time, especially in assemblages from younger beds. Less diverse assemblages with low species evenness possibly represent the onset of less favourable environmental conditions.Fossil occurrences in individual beds were analysed using a range of statistical techniques (Correspondence Analysis, Canonical Correspondence Analysis, Minimum Spanning Tree, Indicator Species Analysis, Mantel Test) to extract community patterns. Results suggest the presence of four fossil assemblages based on distinct species associations. The different assemblages presumably reflect variations in environmental and ecological conditions, some acting through time, leading to species turnover. “Disturbances” (e.g., changes in paleo-redox conditions), differences in substrate firmness, and limited taphonomic biases are probably the main factors contributing to community structure. The influence of ecological factors, however, is also predicted from non-random patterns of species recurrences in successive events. Preliminary comparisons with Lower Cambrian Chengjiang-type assemblages of southern China suggest that the overall structure and ecology of Cambrian communities remained relatively stable until at least the Middle Cambrian in subtidal siliciclastic soft substrate environments.Comparisons with modern marine benthic ecosystems further suggest the Burgess Shale community was probably highly dependent on immigration from a regional pool of species after each burial event. This could support the view that species availability, habitat characteristics, and recolonisation processes were more important in structuring the community in the long-term than species interactions or environmental variations at a local scale.     

Patterns of ferns community assemblages in some Malaysian and Nigerian tropical forests

Research on fern ecology has gained attention in the last decade, yet there is a paucity of information on the comparison of ferns communities across continents. This study focused on comparing the ferns community assemblages in some tropical forests of Malaysia and Nigeria, thereby assessing the patterns of species richness (SR) and phylogenetic diversity (PD) in relation to the bioclimatic drivers across the continents. The diversity and taxonomic compositions of ferns were assessed using 180 plots of 10 m × 10 m in each country. The species richness and other diversity indices were determined using the combined forests data for each country and for the individual forests. Also, the phylogenetic diversity of the ferns was assessed using the genus‐based molecular sequences downloaded from the GeneBank. The patterns of the ferns SR and PD in the two countries as driven by some bioclimatic factors were evaluated using the regression analysis. The observed and rarefied–extrapolated fern species richness is significantly higher in Malaysian forests than in Nigerian forests. Also, the other diversity indices are significantly higher in Malaysian forests except for the Shannon index which showed no significant difference between the two biogeographic regions. There is a very low similarity (7.41%) in the taxonomic composition of ferns between the two biogeographic areas, although the similarity in composition increased with increasing taxonomic levels (species: 7.41%, genus: 12.77%, family: 70.96%). Terrestrial and epiphytic ferns are more dominant than the other life forms in the two countries. The precipitation variables drive the phylogenetic structure of ferns in Nigeria, whereas both precipitation and temperature variables drive the phylogenetic structure of ferns in Malaysia. This indicates that ferns assemblages in Nigeria and Malaysia are driven by both climatic variables. Besides, we also hypothesize that these observed differences could be due to other historical and evolutionary processes.     

Global patterns of guild composition and functional diversity of spiders

The objectives of this work are: (1) to define spider guilds for all extant families worldwide; (2) test if guilds defined at family level are good surrogates of species guilds; (3) compare the taxonomic and guild composition of spider assemblages from different parts of the world; (4) compare the taxonomic and functional diversity of spider assemblages and; (5) relate functional diversity with habitat structure. Data on foraging strategy, prey range, vertical stratification and circadian activity was collected for 108 families. Spider guilds were defined by hierarchical clustering. We searched for inconsistencies between family guild placement and the known guild of each species. Richness and abundance per guild before and after correcting guild placement were compared, as were the proportions of each guild and family between all possible pairs of sites. Functional diversity per site was calculated based on hierarchical clustering. Eight guilds were discriminated: (1) sensing, (2) sheet, (3) space, and (4) orb web weavers; (5) specialists; (6) ambush, (7) ground, and (8) other hunters. Sixteen percent of the species richness corresponding to 11% of all captured individuals was incorrectly attributed to a guild by family surrogacy; however, the correlation of uncorrected vs. corrected guilds was invariably high. The correlation of guild richness or abundances was generally higher than the correlation of family richness or abundances. Functional diversity was not always higher in the tropics than in temperate regions. Families may potentially serve as ecological surrogates for species. Different families may present similar roles in the ecosystems, with replacement of some taxa by other within the same guild. Spiders in tropical regions seem to have higher redundancy of functional roles and/or finer resource partitioning than in temperate regions. Although species and family diversity were higher in the tropics, functional diversity seems to be also influenced by altitude and habitat structure.     

Methanogenic profiles by denaturing gradient gel electrophoresis using order-specific primers in anaerobic sludge digestion

In the present study, the diversity of methanogenic populations was monitored for 25 days, together with the process data for an anaerobic batch reactor treating waste-activated sludge. To understand this microbial diversity and dynamics, 16S rRNA-gene-targeted denaturing gradient gel electrophoresis (DGGE) fingerprinting was conducted at two different taxonomic levels: the domain and order levels. The DGGE profiles of the domain Archaea and the three orders Methanosarcinales, Methanomicrobiales, and Methanobacteriales were comparatively analyzed after each DGGE band was sequenced to enable identification. The DGGE profiles of the three orders showed methanogens belonging to each order that were not detected in the DGGE profile of the Archaea. This discrepancy may have resulted from PCR bias or differences in the abundances of the three microbial orders in the anaerobic bioreactor. In conclusion, to fully understand the detailed methanogenic diversity and dynamics in an anaerobic bioreactor, it is necessary to conduct DGGE analysis with 16S rRNA gene primers that target lower taxonomic groups.     

Differing assemblage composition and dynamics in T4‐like myophages of two neighbouring sub‐alpine lakes

相似文献   

Patterns in freshwater diatom taxonomic distinctness along an eutrophication gradient

1. A variety of species richness measures have been used to assess the effects of environmental degradation on biodiversity. Such measures can be highly influenced by sample size, sampling effort, habitat type or complexity, however, and typically do not show monotonic responses to human impact. In addition to being independent of the degree of sampling effort involved in data acquisition, effective measures of biodiversity should reflect the degree of taxonomical relatedness among species within ecological assemblages and provide a basis for understanding observed diversity for a particular habitat type. Taxonomic diversity or distinctness indices emphasize the average taxonomic relatedness (i.e. degree of taxonomical closeness) between species in a community. 2. Eutrophication of freshwater ecosystems, mainly due to the increased availability of nutrients, notably phosphorus, has become a major environmental problem. Two measures of taxonomic distinctness (Average Taxonomic Distinctness and Variation in Taxonomic Distinctness) were applied to surface sediment diatoms from 45 lakes across the island of Ireland to examine whether taxonomic distinctness and nutrient enrichment were significantly related at a regional scale. The lakes span a range of concentrations of epilimnic total phosphorus (TP) and were grouped into six different types, based on depth and alkalinity levels, and three different categories according to trophic state (ultra‐oligotrophic and oligotrophic; mesotrophic; and eutrophic and hyper‐eutrophic). 3. The taxonomic distinctness measures revealed significant differences among lakes in the three different classes of trophic state, with nutrient‐rich lakes generally more taxonomically diverse than nutrient‐poor lakes. This implies that enrichment of oligotrophic lakes does not necessarily lead to a reduction in taxonomic diversity, at least as expressed by the indices used here. Furthermore, taxonomic distinctness was highly variable across the six different lake types regardless of nutrient level. 4. Results indicate that habitat availability and physical structure within the study lakes also exert a strong influence on the pattern of taxonomic diversity. Overall the results highlight problems with the use of taxonomic diversity measures for detecting impacts of freshwater eutrophication based on diatom assemblages.     

Improvements for comparative analysis of changes in diversity of microbial communities using internal standards in PCR-DGGE

The use of internal standards both during DNA extraction and PCR-DGGE procedure gives the opportunity to analyse the relative abundance of individual species back to the original sample, thereby facilitating relative comparative analysis of diversity. Internal standards were used throughout the DNA extraction and PCR-DGGE to compensate for experimental variability. Such variability causes decreased reproducibility among replicate samples as well as compromise comparisons between samples, since experimental errors cannot be differentiated from actual changes in the community abundance and structure. The use of internal standards during DNA extraction and PCR-DGGE is suitable for ecological and ecotoxicological experiments with microbial communities, where relative changes in the community abundance and structure are studied. We have developed a protocol Internal Standards in Molecular Analysis of Diversity (ISMAD) that is simple to use, inexpensive, rapid to perform and it does not require additional samples to be processed. The internal standard for DNA extraction (ExtrIS) is a fluorescent 510-basepair PCR product which is added to the samples prior to DNA extraction, recovered together with the extracted DNA from the samples and analysed with fluorescence spectrophotometry. The use of ExtrIS during isolation of sample DNA significantly reduced variation among replicate samples. The PCR internal standard (PCR(IS)) originates from the Drosophila melanogaster genome and is a 140-basepair long PCR product, which is amplified by non-competitive primers in the same PCR reaction tubes as the target DNA and analysed together with the target PCR product on the same DGGE gel. The use of PCR(IS) during PCR significantly reduced variation among replicate samples both when assessing total PCR product and when comparing bands representing species on a DGGE gel. The entire ISMAD protocol was shown to accurately describe changes in relative abundance in an environmental sample using PCR-DGGE. It should, however, be mentioned that despite the use of ISMAD some inherent biases still exist in DNA extraction and PCR-DGGE and these should be taken into consideration when interpreting the diversity in a sample based on a DGGE gel.