Effects of long-term benzene pollution on bacterial diversity and community structure in groundwater

In this study we analysed the relationship between bacterial community structures and geochemistry of groundwater in a sandstone aquifer (SIReN site) impacted mainly by BTEX hydrocarbons (benzene, toluene, ethylbenzene and xylenes), of which benzene is most abundant. The long-term presence of benzene reduced bacterial diversity: in groundwaters contaminated with more than 1.8 x 10(4) microg l(-1) of benzene, bacterial diversity was half of that in clean groundwaters. Terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rDNA revealed that the community structures were very similar in uncontaminated groundwaters, whereas communities subjected to long-term benzene contamination were different, not only from uncontaminated groundwater communities, but also from each other. Canonical correspondence analysis of the community profiles and the geochemical data showed that this divergence in community structure was not primarily caused by the direct toxic or stressful effects of benzene, but by the environmental changes brought about by benzene metabolism, in particular a decrease in redox potential.     

Species accumulation curves and incidence-based species richness estimators to appraise the diversity of cultivable yeasts from beech forest soils

Background

Yeast-like fungi inhabit soils throughout all climatic zones in a great abundance. While recent estimations predicted a plethora of prokaryotic taxa in one gram of soil, similar data are lacking for fungi, especially yeasts.

Methodology/Principal Findings

We assessed the diversity of soil yeasts in different forests of central Germany using cultivation-based techniques with subsequent identification based on rDNA sequence data. Based on experiments using various pre-cultivation sample treatment and different cultivation media we obtained the highest number of yeasts by analysing mixed soil samples with a single nutrient-rich medium. Additionally, several species richness estimators were applied to incidence-based data of 165 samples. All of them predicted a similar range of yeast diversity, namely 14 to 16 species. Randomized species richness curves reached saturation in all applied estimators, thus indicating that the majority of species is detected after approximately 30 to 50 samples analysed.

Conclusions/Significance

In this study we demonstrate that robust species identification as well as mathematical approaches are essential to reliably estimate the sampling effort needed to describe soil yeast communities. This approach has great potential for optimisation of cultivation techniques and allows high throughput analysis in the future.     

Plant and insect diversity along a pollution gradient: understanding species richness across trophic levels

We analysed species richness of plants and true bugs (Insecta, Heteroptera) along a pollution gradient in Scots pine stands in Central Germany. As a consequence of particulate deposition, pH-values of soils increased in the vicinity of the emission source. Therefore, emission increased productivity. Species richness of plants increased with decreasing distance from emission source, and thus with increasing productivity. Similarly, species richness of herbivorous Heteroptera increased with decreasing distance from emission source, whereas, surprisingly, abundance decreased. The proportion of specialised herbivorous bug species is largest in the vicinity of the emission source. Thus, the diversity pattern of herbivores may be explained by the specialisation hypothesis and not the consumer rarity hypothesis. Species richness and abundance of carnivorous Heteroptera showed no significant trend along the gradient. Overall our data favour the bottom-up control of species diversity in the analysed system.     

Negative relationships between species richness and evenness render common diversity indices inadequate for assessing long-term trends in butterfly diversity

Species richness and evenness, the two principle components of species diversity, are frequently used to describe variation in species assemblages in space and time. Compound indices, including variations of both the Shannon–Wiener index and Simpson’s index, are assumed to intelligibly integrate species richness and evenness into all-encompassing measures. However, the efficacy of compound indices is disputed by the possibility of inverse relationships between species richness and evenness. Past studies have assessed relationships between various diversity measures across survey locations for a variety of taxa, often finding species richness and evenness to be inversely related. Butterflies are one of the most intensively monitored taxa worldwide, but have been largely neglected in such studies. Long-term butterfly monitoring programs provide a unique opportunity for analyzing how trends in species diversity relate to habitat and environmental conditions. However, analyzing trends in butterfly diversity first requires an assessment of the applicability of common diversity measures to butterfly assemblages. To accomplish this, we quantified relationships between butterfly diversity measures estimated from 10 years of butterfly population data collected in the North Saskatchewan River Valley in Edmonton, Alberta, Canada. Species richness and evenness were inversely related within the butterfly assemblage. We conclude that species evenness may be used in conjunction with richness to deepen our understandings of assemblage organization, but combining these two components within compound indices does not produce measures that consistently align with our intuitive sense of species diversity.     

Changes in species richness of vascular plants under the impact of air pollution: a global perspective

Aim To investigate the general pattern of changes in species richness and diversity of vascular plants due to environmental contamination and associated habitat changes imposed by point polluters, and identify the sources of variation in the response of plant communities to industrial pollution. Location Global. Methods We collected species richness and diversity data from 86 studies that were conducted around 60 atmospheric point polluters worldwide and reported in 95 papers (published in 1953–2007). We used meta‐analysis to search for a general effect and to compare between polluter types and plant groups, and linear regression to describe the latitudinal gradient and to quantify relationships between pollution and effect size. Results Although the species richness of vascular plants generally decreased with pollution, the effects were not uniform across the studies. Polluters that cause soil acidification imposed a stronger detrimental effect on plant diversity than industries whose emissions increased soil pH. An overall adverse effect was primarily due to the contribution of non‐ferrous smelters and aluminium plants; the effects of other SO₂‐emitting industries were less detrimental, albeit negative, and the effects of chemical plants, fertilizer factories and cement industries did not differ from zero. Longevity of the pollution impact only made a slight contribution to the detected variation, while adverse effects increased with increase in pollution load. Main conclusions This study is the first demonstration of geographical variation in the responses of plant communities to aerial emissions: adverse effects increased from high to low latitudes, and this pattern was explained primarily by increases in both the diversity of original (undisturbed) communities and mean summer temperatures. The latter result suggests that under a future warmer climate the existing pollution loads may become more harmful. Model calculations indicate that a detectable depauperation of plant communities is unlikely if the polluter emits < 1500 t of SO₂ annually.     

Plant species richness and diversity of the serpentine areas on the Witwatersrand

Soil chemistry can play an important role in determining plant diversity. Serpentine soils are usually toxic to many plant taxa, which limits plant diversity compared to that on adjacent non-serpentine soils. The usually high concentrations of toxic metals in serpentine soils are considered to be the edaphic factors that cause low diversity and high endemism. This paper aimed primarily to determine whether there is a relationship between serpentine soil chemistry and species richness on the Witwatersrand and to compare species richness of the serpentine areas with that of adjacent non-serpentine areas as well as with the species richness of the serpentine areas in the Barberton Greenstone Belt. The alpha- and beta-diversity of the Witwatersrand serpentine and non-serpentine areas was also investigated. A secondary aim of this study was to determine which of the non-serpentine taxa were more common on the serpentine than off the serpentine, which taxa were more common off the serpentine than on the serpentine and which taxa were equally common on and off serpentine soils. There was no significant difference in alpha-diversity between the serpentine and the adjacent non-serpentine areas, but beta-diversity is higher between serpentine plots than between non-serpentine plots. Although soil factors do affect species richness and diversity of plants on the Witwatersrand to a limited extent, the concentrations of soil chemicals in serpentine soils are not sufficiently different from those in non-serpentine soils to significantly influence the species richness and diversity of the serpentine soils. The high, but similar, diversity on serpentine and non-serpentine soils on the Witwatersrand indicates that soil factors do not play a significant role in determining diversity on potentially toxic soils in the area.     

Interactive effects of species richness and species traits on functional diversity and redundancy

The importance of species diversity for ecosystem function has emerged as a key question for conservation biology. Recently, there has been a shift from examining the role of species richness in isolation towards understanding how species interact to effect ecosystem function. Here, we briefly review theoretical predictions regarding species contributions to functional diversity and redundancy and further use simulated data to test combined effects of species richness, number of functional traits, and species differences within these traits on unique species contributions to functional diversity and redundancy, as well as on the overall functional diversity and redundancy within species assemblages. Our results highlighted that species richness and species functional attributes interact in their effects on functional diversity. Moreover, our simulations suggested that functional differences among species have limited effects on the proportion of redundancy of species contributions as well as on the overall redundancy within species assemblages, but that redundancy rather was determined by number of traits and species richness. Our simulations finally indicated scale dependence in the relative effects of species richness and functional attributes, which suggest that the relative influence of these factors may affect individual contributions differently compared to the overall ecosystem function of species assemblages. We suggest that studies on the relationship between biological diversity and ecosystem function will benefit from focusing on multiple processes and ecological interactions, and that the relative functional attributes of species will have pivotal roles for the ecosystem function of a given species assembly.     

长期石油和重金属污染对农田土壤假单胞菌种群多样性及结构的影响

采用PCR—DGGE方法,对我国东北地区长期石油和重金属污染农田土壤中的假单胞菌多样性及其种群结构进行研究．结果表明：石油污染区土壤中假单胞菌多样性指数显著高于重金属污染区;石油污染区旱田土壤假单胞菌多样性接近于对照清洁土壤,但低于相似污染程度的石油污染区水田土壤,表明污染物类型与耕作管理方式是影响土壤中假单胞菌多样性的主要因素．经16SrRNA的V6／V7区测序,Pseudomonas mendocina、P．stutzeri和P．aeruginosa是该石油和重金属污染区土壤中的优势类群,说明在长期污染胁迫下,这3种假单胞菌分别得到了不同程度的富集,推测与石油烃的自然降解及假单胞菌的重金属抗性有关．     

Exotic species richness and native species endemism increase the impact of exotic species on islands

Aim Exotic species pose one of the most significant threats to biodiversity, especially on islands. The impacts of exotic species vary in severity among islands, yet little is known about what makes some islands more susceptible than others. Here we determine which characteristics of an island influence how severely exotic species affect its native biota. Location We studied 65 islands and archipelagos from around the world, ranging from latitude 65° N to 54° S. Methods We compiled a global database of 10 island characteristics for 65 islands and determined the relative importance of each characteristic in predicting the impact of exotic species using multivariate modelling and hierarchical partitioning. We defined the impact of exotic species as the number of bird, amphibian and mammal (BAM) species listed by the International Union for Conservation of Nature (IUCN) as threatened by exotics, relative to the total number of BAM species on that island. Results We found that the impact of exotic species is more severe on islands with more exotic species and a greater proportion of native species that are endemic. Unexpectedly, the level of anthropogenic disturbance did not influence an island's susceptibility to the impacts of exotic species. Main conclusions By coupling our results with studies on the introduction and establishment of exotic species, we conclude that colonization pressure, or invasion opportunities, influences all stages of the invasion process. However, species endemism, the other important factor determining the impact of exotic species, is not known to contribute to introduction and establishment success on islands. This demonstrates that different factors correlate with the initial stages of the invasion process and the subsequent impacts of those invaders, highlighting the importance of studying the impacts of exotic species directly. Our study helps identify islands that are at risk of impact by exotics and where investment should focus on preventing further invasions.     

Short-term plant species impact on microbial community structure in soils with long-term agricultural history

The goal of our study was to capture the short-term effects of individual plant species on an established microbial community in a soil with a well-defined agricultural history. Using biochemical and molecular techniques we quantified the effects of plant species on changes in the soil microbial community over an 8-week time-course. We conducted a greenhouse experiment using field soil from a site that was managed as a Zea mays monoculture for over 50 years. The conditioned soil provided a baseline from which changes in microbial community composition through the effects of newly introduced plants could be determined. Within a short time frame (8 weeks), introduced plants influenced the soil microbial community in ways unique to each plant. Some species (Fagopyrm esculentum and xTriticosecale spp.) resulted in an increase of total microbial community richness, diversity and the stimulation of new microbial species not associated with the legacy vegetation. Other plants (Vicia villosa and Lolium multiflorum) tended to reduce community diversity. We suggest root surface area is good general predictor of rhizosphere microbial community diversity, but in some cases other plant traits may have dominant influence on plant-induced changes in microbial community composition.     

长期施肥对稻田土壤细菌、古菌多样性和群落结构的影响

稻田土壤是“迷失碳”的重要吸纳场所之一,也是温室气体(CH4和N2O等)的重要排放源.大气温室气体的动态变化与土壤碳氮转化的微生物过程紧密相关.以湖南桃江国家级稻田肥力变化长期定位试验点为平台,采用PCR-克隆测序和实时荧光定量PCR技术,研究不施肥(CK)、施氮磷钾肥(NPK)和氮磷钾肥+秸秆还田(NPKS)3种长期施肥制度(＞25 a)对稻田土壤细菌和古菌群落结构及数量的影响.细菌和古菌16S rRNA基因文库分析结果表明:稻田土壤细菌主要类群为变形菌、酸杆菌、绿弯菌,而古菌主要为泉古菌和广古菌.长期施肥导致土壤细菌和古菌种群结构产生明显差异,与CK相比,NPK和NPKS处理稻田土壤的变形菌、酸杆菌和泉古菌相对丰度增加.LIBSHUFF软件分析结果也表明,16S rRNA基因文库在CK、NPK及NPKS处理间存在显著差异.3种施肥处理的稻田土壤细菌16S rRNA基因拷贝数为每克干土0.58× 1010～1.06×1010个,古菌为每克干土1.16×106 ～ 1.72×106个.施肥(NPK和NPKS)后,细菌和古菌的多样性和数量增加,且NPKS＞NPK.说明长期施肥显著影响土壤细菌和古菌群落结构、多样性及数量.     

Modelling species richness and diversity in grassland communities of the Central Caucasus

In this study I used small squares (4 cm×4 cm) as a sampling technique within plots (128 cm×128 cm) of different elevation, aspect and slope angle in grassland communities (20 plots examined). Then I used a rectangular hyperbole equation (the Michaelis-Menten model) to describe species richness and the Inverse of Simpson Concentration (ISC) as functions of sample size. I checked robustness and precision of the model both by interpolation and extrapolation. Interpolation was similarly good in both cases, while extrapolation produced reliable predictions of ISC but underestimated species richness. Dominance analysis indicated that the underestimation of richness depends on the proportion of bottom species, and that the predicted values of richness roughly coincide with the numbers of dominant species found in plots. Therefore, the model may be used to assess number of dominant species when precision is less important than saving time during a survey. However, the rectangular hyperbole equation appears to be precise and robust in the prediction of ISC, at least in grassland communities. This property may also be employed for extrapolation of diversity indices with a limited sampling effort.     

Effects of foundation species genotypic diversity on subordinate species richness in an assembling community

Foundation (dominant or matrix) species play a key role in structuring plant communities, influencing processes from population to ecosystem scales. However, the effects of genotypic diversity of foundation species on these processes have not been thoroughly assessed in the context of assembling plant communities. We modified the classical filter model of community assembly to include genotypic diversity as part of the biotic filter. We hypothesized that the proportion of fit genotypes (i.e. competitively superior and dominant) affects niche space availability for subordinate species to establish with consequence for species diversity. To test this hypothesis, we used an individual‐based simulation model where a foundation species of varying genotypic diversity (number of genotypes and variability among genotypes) competes for space with subordinate species on a spatially heterogeneous lattice. Our model addresses a real and practical problem in restoration ecology: choosing the level of genetic diversity of re‐introduced foundation and subordinate species. Genotypic diversity of foundation species significantly affected equilibrium community diversity, measured as species richness, either positively or negatively, depending upon environmental heterogeneity. Increases in genotypic diversity gave the foundation species a wider niche breadth. Under conditions of high environmental heterogeneity, this wider niche breadth decreased niche space for other species, lowering species richness with increased genotypic diversity until the genotypes of the foundation species saturated the landscape. With a low level of environmental heterogeneity, increasing genotypic diversity caused the foundation species niche breadth to be overdispersed, resulting in a weak positive relationship with species richness. Under these conditions, some genotypes are maladapted to the environment lowering fitness of the foundation species. These effects of genotypic diversity were secondary to the larger effects of overall foundation species fitness and environmental heterogeneity. The novel aspect of incorporating genotype diversity in combination with environmental heterogeneity in community assembly models include predictions of either positive or negative relationships between species diversity and genotypic diversity depending on environmental heterogeneity, and the conditions under which these factors are potentially relevant. Mechanistically, differential niche availability is imposed by the foundation species.     

Vascular plant species richness in relation to habitat diversity and island area in the Finnish Archipelago

Aim The aim of this study is to explore the interrelationships between island area, species number and habitat diversity in two archipelago areas. Location The study areas, Brunskär and Getskär, are located in an archipelago in south‐western Finland. Methods The study areas, 82 islands in Brunskär and 78 in Getskär, were classified into nine habitat types based on land cover. In the Brunskär area, the flora (351 species) was surveyed separately for each individual habitat on the islands. In the Getskär area, the flora (302 species) was surveyed on a whole‐island basis. We used standard techniques to analyse the species–area relationship on a whole‐island and a habitat level. We also tested our data for the small island effect (SIE) using breakpoint and path analysis models. Results Species richness was significantly associated with both island area and habitat diversity. Vegetated area in particular, defined as island area with the rock habitat subtracted, proved to be a strong predictor of species richness. Species number had a greater association with island area multiplied by the number of habitats than with island area or habitat number separately. The tests for a SIE in the species–area relationship showed the existence of a SIE in one of the island groups. No SIE could be detected for the species–vegetated area relationship in either of the island groups. The strength of the species–area relationship differed considerably between the habitats. Main conclusions The general principles of island biogeography apply well to the 160 islands in this study. Vascular plant diversity for small islands is strongly influenced by physiographic factors. For the small islands with thin and varying soil cover, vegetated area was the most powerful predictor of species richness. The species–area curves of various habitats showed large variations, suggesting that the measurement of habitat areas and establishment of habitat‐based species lists are needed to better understand species richness on islands. We found some evidence of a SIE, but it is debatable whether this is a ‘true’ SIE or a soil cover/habitat characteristics feature.     

Anthropogenic noise reduces bird species richness and diversity in urban parks

Anthropogenic noise is becoming more prevalent in the world and has been shown to affect many animal species, including birds. The impact of such noise was measured in Neotropical urban parks to assess how the noise affects avifauna diversity and species richness. We sampled bird species, and concurrently measured sound pressure (noise) levels (L_eq, equivalent noise levels) in eight urban green areas or parks located in a large city (Belo Horizonte) in south‐eastern Brazil over a 1‐year period. The diversity of sampled points was measured by means of total species richness, Fisher's alpha and Shannon–Wiener diversity indices. Noise levels within all parks were greater than those in natural areas. We found that an increase in noise levels and the area of open habitats surrounding sampling points were negatively related to species richness. Social factors reflecting increased urbanization, such as higher incomes, were also negatively correlated with bird species richness. However, noise was the factor that explained most of the variance. These results suggest that anthropogenic noise can have a significant negative impact on the conservation value of urban parks for bird species.     

Pyramids of species richness: the determinants and distribution of species diversity across trophic levels

How species richness is distributed across trophic levels determines several dimensions of ecosystem functioning, including herbivory, predation, and decomposition rates. We perform a meta‐analysis of 72 large published food webs to investigate their trophic diversity structure and possible endogenous, exogenous, and methodological causal variables. Consistent with classic theory, we found that published food webs can generally be described as ‘pyramids of species richness’. The food webs were more predator‐poor, prey‐rich and hierarchical than is expected by chance or by the niche or cascade models. The trophic species richness distribution also depended on centrality, latitude, ecosystem‐type and methodological bias. Although trophic diversity structure is generally pyramidal, under many conditions the structure is consistently uniform or inverse‐pyramidal. Our meta‐analysis adds nuance to classic assumptions about food web structure: diversity decreases with trophic level, but not under all conditions, and the decrease may be scale‐dependent. Synthesis The distribution of species richness across trophic levels has not been evaluated in recent decades, despite improvement in food web resolution and the relevance of biodiversity distribution to ecosystem function. Our meta‐analysis of 72 large, recent food webs, illustrates that published food webs can generally be described as basal‐rich, top‐poor ‘pyramids of species richness’, consistent with classic theory. Although trophic diversity structure is generally pyramidal, under some environmental and ecological conditions the structure is uniform or inverse‐pyramidal. Our meta‐analysis confirms classic theory about food web structure, while adding nuance by describing conditions under which classic pyramid structure is not observed.     

南海陆坡沉积物细菌丰度预测

分别利用参数模型和无参数估计法预测南海陆坡沉积物柱MD05-2896中的细菌丰度.基于非培养的PCR-RFLP的16SrRNA基因分子技术,扩增了沉积物柱中的细菌16S rRNA基因序列,并构建16S rRNA基因文库.系统发育分析表明16S rRNA基因文库中,大多数序列属于17个已知的“门”.分别以99％、97％、90％和80％序列一致性作为分类单元分界点,将16SrRNA基因序列组群为分类单元.使用逆高斯分布模型、对数正态分布模型、负二项式分布模型、帕雷托分布模型、双指数分布模型以及ACE、ACE-1等估计方法预测不同分类单元分类水平下的细菌丰度.结果表明在“种”级分类水平上,负二项式分布为最优估计模型,估计细菌丰度为244±10(SE).不过,受实验条件的限制,该估计值可能偏低.     

Microhabitat effects on bryophyte species richness and community distribution on exposed rock outcrops in Portugal

Background: Rock outcrops have been shown to provide specific conditions for bryophyte communities, but no studies have focused on the importance of microhabitats on such communities.

Aim: To analyse the distribution pattern of bryophyte species from granite and schist outcrops in three microhabitats (rock surfaces, fissures and cavities) in Portugal.

Methods: Sample plots were established in fissures, cavities and on rock surfaces of rock outcrops in north and central Portugal. Micro-scale variables, such as exposure and slope were assessed for each microhabitat.

Results: The microhabitats most different in species composition were surfaces versus cavities and surfaces versus fissures, both on granite and schist. Short-lived shuttle species tended to be associated with surfaces, and perennial species were more frequent in cavities and fissures. Both on granite and schist, the number of species found in each microhabitat was highest in cavities, followed by fissures and rock surfaces. The most relevant predictors of bryophyte richness were microhabitat type, exposure and rock type.

Conclusions: This investigation confirmed that rock microhabitats play an important role in bryophyte diversity by promoting habitat heterogeneity. In addition, our results clearly suggest local explanations for variation in bryophyte species richness and communities.