Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

Cystic fibrosis (CF) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. The need to maintain lung function in these patients means that characterising these infections is vital. Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known. Here, we applied ecological statistical tools to such culture-independent data, in a novel manner, to partition taxa within the metacommunity into core and satellite species. Sputa and clinical data were obtained from 14 clinically stable adult CF patients. Fourteen rRNA gene libraries were constructed with 35 genera and 82 taxa, identified in 2139 bacterial clones. Shannon–Wiener and taxa-richness analyses confirmed no undersampling of bacterial diversity. By decomposing the distribution using the ratio of variance to the mean taxon abundance, we partitioned objectively the species abundance distribution into core and satellite species. The satellite group comprised 67 bacterial taxa from 33 genera and the core group, 15 taxa from 7 genera (including Pseudomonas (1 taxon), Streptococcus (2), Neisseria (2), Catonella (1), Porphyromonas (1), Prevotella (5) and Veillonella (3)], the last four being anaerobes). The core group was dominated by Pseudomonas aeruginosa. Other recognised CF pathogens were rare. Mantel and partial Mantel tests assessed which clinical factors influenced the composition observed. CF transmembrane conductance regulator genotype and antibiotic treatment correlated with all core taxa. Lung function correlated with richness. The clinical significance of these core and satellite species findings in the CF lung is discussed.     

Reducing bias in bacterial community analysis of lower respiratory infections

High-throughput pyrosequencing and quantitative PCR (Q-PCR) analysis offer greatly improved accuracy and depth of characterisation of lower respiratory infections. However, such approaches suffer from an inability to distinguish between DNA derived from viable and non-viable bacteria. This discrimination represents an important step in characterising microbial communities, particularly in contexts with poor clearance of material or high antimicrobial stress, as non-viable bacteria and extracellular DNA can contribute significantly to analyses. Pre-treatment of samples with propidium monoazide (PMA) is an effective approach to non-viable cell exclusion (NVCE). However, the impact of NVCE on microbial community characteristics (abundance, diversity, composition and structure) is not known. Here, adult cystic fibrosis (CF) sputum samples were used as a paradigm. The effects of PMA treatment on CF sputum bacterial community characteristics, as analysed by pyrosequencing and enumeration by species-specific (Pseudomonas aeruginosa) and total bacterial Q-PCR, were assessed. At the local community level, abundances of both total bacteria and of P. aeruginosa were significantly lower in PMA-treated sample portions. Meta-analysis indicated no overall significant differences in diversity; however, PMA treatment resulted in a significant alteration in local community membership in all cases. In contrast, at the metacommunity level, PMA treatment resulted in an increase in community evenness, driven by an increase in diversity, predominately representing rare community members. Importantly, PMA treatment facilitated the detection of both recognised and emerging CF pathogens, significantly influencing ‘core'' and ‘satellite'' taxa group membership. Our findings suggest failure to implement NVCE may result in skewed bacterial community analyses.     

Shallow-soil endemics: adaptive advantages and constraints of a specialized root-system morphology

Worldwide, many rare plant species occur in shallow-soil, drought-prone environments. For most of these species, the adaptations required to be successful in their own habitats, as well as their possible consequences for establishment and persistence in others, are unknown. Here, two rare Hakea (Proteaceae) species confined to shallow-soil communities in mediterranean-climate south-western Australia were compared with four congeners commonly occurring on deeper soils. Seedlings were grown for 7 months in a glasshouse in individual 1.8 x 0.2-m containers, to allow for unconstrained root development. In addition, a reciprocal transplant experiment was carried out. The rare Hakea species differed consistently from their common congeners in their spatial root placement. They invested more in deep roots and explored the bottom of the containers much more quickly. In the reciprocal transplant experiment they showed increased survival in their own habitat, but not in others. This research suggests that shallow-soil endemics have a specialized root system that allows them to explore a large rock surface area, thereby presumably increasing their chance to locate cracks in the underlying rock. However, this root-system morphology may be maladaptive on deeper soils, providing a possible explanation for the restricted distribution of many shallow-soil endemics.     

Conservation strategies for poorly surveyed taxa: a dung beetle (Coleoptera, Scarabaeidae) case study from southern Africa

Despite being the focus of an international research effort spanning decades, the spatial distribution of southern African scarab beetles remains poorly documented. As well as reinforcing the magnitude of the challenge facing biodiversity scientists, this raises real concerns about best practice conservation strategies in the absence of detailed distribution information. However, dung beetles appear to be well represented in established conservation areas. This apparent contradiction could be ascribed to anthropogenic transformation, successful conservation efforts, the presence of dung generalists and reserve-biased or mesic-biased dung beetle collection efforts. It is suggested that all of the above contribute to the observed pattern to varying degrees. The implications of selecting areas that are either rich in species, contain rare species or contain taxonomically distinct species from a group whose taxonomy is well known but for which inadequate distribution data exist are explored. Best practice, in the face of inadequate data, appears to revolve around a subtle interplay between advantages and disadvantages associated with data interpolation techniques, reserve selection algorithms that use criteria more robust than database rarity (such as taxonomic distinctiveness) and the long-term economic costs of proceeding with the data at hand versus investing in biological surveys.     

Vascular plant species richness and rarity across a minerotrophic gradient in wetlands of St. Lawrence County,New York,USA

Thirteen wetlands in St. Lawrence County, NY were sampled to examine the effect of a minerotrophic gradient on vascular plant species richness and rarity. Wetlands ranged from organic soil based poor fens (average conductivity 46.40 microsemens, average Ca 3.55 ppm) to mineral soil based rich fens (average conductivity 342.10 microsemens, Ca 23.00 ppm). Vascular plant species richness was sampled during 1990 in randomly located 1.0 m² quadrats. Specific conductivity, presence or absence of hummocks, and water depth predicted 62% of the variation in richness. Richness increased as conductivity increased until 413 microsemens at which a down trend became obvious. The negative curvilinear relation between conductivity and richness is in accordance with the hump-backed model of Grime but occurs at high rather than intermediate conductivity values. State-listed rare species were found in species-rich wetlands only and had a mean associated richness value of 14.50 species m^-2. This relationship should be taken into consideration when selecting wetlands for protection or managing wetlands for maximum plant diversity.     

Continental scale patterns of biodiversity: can higher taxa accurately predict African plant distributions?

The distribution maps of a total of 3563 species, which represent 8.9% of the known African angiosperm flora, were entered into cells representing a one-degree latitude–longitude grid of Sub-Saharan Africa. The computer programme WORLDMAP was used to explore continental scale patterns of biodiversity. The maps were used to assess the use of higher taxa as a surrogate measure for predicting patterns of species richness. Genera were found to predict species richness distributions most closely, with higher taxa (families, orders, subclasses) exhibiting progressively worse correlations. However in two areas, the Cape Region of South Africa and coastal Cameroon, there was a higher species to genus ratio than in other areas of Africa. In the Cape Region this meant that generic richness failed to predict species richness. Hotspots, defined as the 5% of grid cells with the highest scores for richness and range-size rarity, were identified for species and higher taxa. Whilst a high percentage of species richness hotspots were predicted by higher taxa, there were important exceptions like the Cape Region. Species range-size rarity hotspots were not well predicted by higher taxa. Hotspots of higher taxa (families and orders) do not therefore accurately predict the location of species hotspots. Higher taxa appear to provide a powerful and accurate tool that can be used to predict large scale patterns of species biodiversity in Sub-Saharan Africa. However care must be taken when using taxa higher than genera, especially if selecting areas of highest conservation priority. The special case of the Cape Region indicates the danger of extending predictive generalizations as the ecological mechanisms that promote and retain species may not be the same in all places. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 138 , 225–235.     

Annotated checklist of marine fishes from the Sanctuary of Bahía Chamela,Mexico with occurrence and biogeographic data

An annotated checklist of marine fishes of the Sanctuary of Islands and Islets of Bahía Chamela in the central Mexican Pacific is presented. Records of fish species were obtained by different methods including visual census, sampling with anesthetics, fisherman-nets, and trawling with a biological dredge. Additional records were obtained from natural history collections and publications. The list comprises 196 species in 64 families and 141 genera. The Carangidae is the most speciose family with 11 species, followed by the Labridae with 10 and the Pomacentridae with nine. Fourteen species are endemic in Mexican Pacific waters, but none is restricted to Bahía Chamela. The most dominant species recorded during underwater surveys were Epinepheluslabriformis, Stegastesflavilatus, and Halichoeresdispilus. Most species are of tropical affinities distributed throughout the tropical eastern Pacific (123), eastern Pacific (23), and Mexican Pacific (14). Other species are known from the eastern and Indo-Pacific regions (18), eastern Pacific and western Atlantic oceans (2), and some are circumtropical (9). A new record of the Gulf Brotula Ogilbiaventralis is provided for the Bahía Chamela and its geographical distribution is extended to Mexican central Pacific.