Seed Density Significantly Affects Species Richness and Composition in Experimental Plant Communities

Studies on the importance of seed arrival for community richness and composition have not considered the number of seeds arriving and its effect on species richness and composition of natural communities is thus unknown. A series of experimental dry grassland communities were established. All communities were composed of the same 44 species in exactly the same proportions on two substrates using three different seed densities.The results showed that seed density had an effect on species richness only at the beginning of the experiment. In contrast, the effects on species composition persisted across the entire study period. The results do not support the prediction that due to higher competition for light in nutrient-rich soil, species richness will be the highest in the treatment with the lowest seed density. However, the prevalence of small plants in the lowest seed density supported the expectation that low seed density guarantees low competition under high soil nutrients. In the nutrient-poor soil, species richness was the highest at the medium seed density, indicating that species richness reflects the balance between competition and limitations caused by the availability of propagules or their ability to establish themselves. This medium seed density treatment also contained the smallest plants.The results demonstrate that future seed addition experiments need to consider the amount of seed added so that it reflects the amount of seed that is naturally found in the field. Differences in seed density, mimicking different intensity of the seed rain may also explain differences in the composition of natural communities that cannot be attributed to habitat conditions. The results also have important implications for studies regarding the consequences of habitat fragmentation suggesting that increasing fragmentation may change species compositions not only due to different dispersal abilities but also due to differential response of plants to overall seed density.     

Selection for Cu-Tolerant Bacterial Communities with Altered Composition,but Unaltered Richness,via Long-Term Cu Exposure

Toxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However, there is virtually no knowledge concerning the responses of members of specific bacterial taxa (e.g., phyla or classes) to metal toxicity, and contradictory results have been obtained regarding the impact of metals on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 to 3,537 μg g⁻¹) stemming from industrial contamination with CuSO₄ more than 85 years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [³H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu, as determined by the results seen with a Cu-specific bioluminescent biosensor strain, demonstrating a specific community response to Cu. The relative abundances of members of several phyla or candidate phyla, including the Proteobacteria, Bacteroidetes, Verrumicrobia, Chloroflexi, WS3, and Planctomycetes, decreased with increasing bioavailable Cu, while members of the dominant phylum, the Actinobacteria, showed no response and members of the Acidobacteria showed a marked increase in abundance. Interestingly, changes in the relative abundances of classes frequently deviated from the responses of the phyla to which they belong. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu levels did not show any correlation to bacterial OTU richness (97% similarity level). Our report highlights several bacterial taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for members of metal-responding taxa.     

Patterns of Species Richness and Composition in Re-Created Grassland

The success of many prairie restorations is not well documented. A restoration begun in 1975 at the Fermi National Accelerator Laboratory near Chicago, Illinois allows assessment of restoration efforts as well as changes through time. Data are presented on species richness and composition for 13 restorations planted in successive years between 1975 and 1990 and two remnant prairies. Presence of species was recorded using a stratified random design. Species richness at several scales and non‐metric multidimensional scaling ordination were used to assess trends in the vegetation. Species richness declined through time at all scales examined and was always less in the restored prairies than that found in the remnant prairies. Species composition changed with time but not in the direction of the composition found in the remnants. Our understanding of the maintenance of species richness is not sufficient to allow the re‐creation of patterns of species found in remnant grassland communities.     

Correlates of Viral Richness in Bats (Order Chiroptera)

Historic and contemporary host ecology and evolutionary dynamics have profound impacts on viral diversity, virulence, and associated disease emergence. Bats have been recognized as reservoirs for several emerging viral pathogens, and are unique among mammals in their vagility, potential for long-distance dispersal, and often very large, colonial populations. We investigate the relative influences of host ecology and population genetic structure for predictions of viral richness in relevant reservoir species. We test the hypothesis that host geographic range area, distribution, population genetic structure, migratory behavior, International Union for Conservation of Nature and Natural Resources (IUCN) threat status, body mass, and colony size, are associated with known viral richness in bats. We analyze host traits and viral richness in a generalized linear regression model framework, and include a correction for sampling effort and phylogeny. We find evidence that sampling effort, IUCN status, and population genetic structure correlate with observed viral species richness in bats, and that these associations are independent of phylogeny. This study is an important first step in understanding the mechanisms that promote viral richness in reservoir species, and may aid in predicting the emergence of viral zoonoses from bats.     

Climate and Species Richness Predict the Phylogenetic Structure of African Mammal Communities

We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change.     

Viral Communities Among Sympatric Vampire Bats and Cattle

Vampire bats are the only mammals known to feed exclusively on blood from other animals, often from domestic cattle. We tested the hypothesis that the adaptation of vampire bats to hematophagy would have resulted in shared viral communities among vampire bats and cattle, as a direct result of historic spillover events occurring due to hematophagy. We analyzed the presence of different viruses in sample populations of sympatric bat and prey populations and searched for shared viruses between taxa. A limited number of DNA viral groups were detected within each species. However, there was no evidence for a shared viral community among the vampire bat and cattle populations tested.     

Species Richness of Yeast Communities in Floral Nectar of Southern Spanish Plants

Floral nectar of insect-pollinated plants often contains dense yeast populations, yet little quantitative information exists on patterns and magnitude of species richness of nectar-dwelling yeasts in natural plant communities. This study evaluates yeast species richness at both the plant community and plant species levels in a montane forest area in southern Spain, and also explores possible correlations between the incidence of different yeast species in nectar and their reported tolerance to high sugar concentrations, and between yeast diversity and pollinator composition. Yeast species occurring in a total of 128 field-collected nectar samples from 24 plant species were identified by sequencing the D1/D2 domain of the large subunit rDNA, and rarefaction-based analyses were used to estimate yeast species richness at the plant community and plant species levels, using nectar drops as elemental sampling units. Individual nectar samples were generally characterized by very low species richness (1.2 yeast species/sample, on average), with the ascomycetous Metschnikowia reukaufii and Metschnikowia gruessii accounting altogether for 84.7% of the 216 isolates identified. Other yeasts recorded included species in the genera Aureobasidium, Rhodotorula, Cryptococcus, Sporobolomyces, and Lecythophora. The shapes and slopes of observed richness accumulation curves were quite similar for the nectar drop and plant species approaches, but the two approaches yielded different expected richness estimates. Expected richness was higher for plant species-based than for nectar drop-based analyses, showing that the coverage of nectar yeast species occurring in the region would be improved by sampling additional host plant species. A significant correlation was found between incidence of yeast species in nectar and their reported ability to grow in a medium containing 50% glucose. Neither diversity nor incidence of yeasts was correlated with pollinator composition across plant species.     

Relationship between Degree of Dominance and Species Richness in Grass Communities with Different Productivities

The aim of this study is to test the assumption that the relationship between the degree of dominance and local species richness may be different in grass communities with different productivities. Alpine, subalpine, and low-mountain grasslands, as well as subalpine mires, alpine communities of low-snow habitats and those with long-term snow cover, steppe communities, and the grass layer of low-mountain forest communities of the Western Caucasus and Ciscaucasia, are used as objects of research. The data on the phytomass of 419 plots with an area of 0.25 m² are studied. The results show that, the higher the mean productivity of communities is, the closer the relationship between the degree of dominance and species richness is, and the closest relationship is observed in meadow communities. Possible causes of these relationships are considered. It is reasonably suggested that this may be due to the features of the organization of plant communities with high and low productivity (in particular, high or low intensity of interspecific competition).     

Functional Richness and Relative Resilience of Bird Communities in Regions with Different Land Use Intensities

Abstract Empirical estimates of the function and resilience of communities under different management regimes can provide valuable information for sustainable natural resource management, but such estimates are scarce to date. We quantified the functional richness and relative resilience of bird communities inhabiting five regions in southeastern Australia that represented different management regimes. First, we show that functional richness and relative resilience were reduced at species-poor sites in all regions. Second, we show that bird communities in agricultural regions had fewer body mass groups and fewer functional groups than expected by chance. This suggests that both the function and the resilience of bird communities in agricultural regions were reduced. The likely mechanisms for the observed loss of function and relative resilience are: (1) the simplification of landscape texture resulting in selective extinction of certain body mass groups; and (2) the selective extinction of certain functional groups that are particularly sensitive to intensive land use. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

一株引起普通棉耳狨猴死亡病毒的分离与鉴定

1999年6月,天津医科大学动物中心饲养的珍贵灵长类实验动物——普通棉耳狨猴群体中暴发急性呼吸道传染病,病死率高达33％。在排除细菌感染的基础上,通过死亡狨猴肺组织匀浆接种鸡胚和MDCK细胞的分离培养,分离出一株具有高血凝效价的病毒株。经双份血清试验及动物接种试验,确认该病毒是本次疾病流行的病原体。又进一步通过与常见呼吸道病毒标准毒株及血清进行交叉血凝抑制试验、电镜观察、RT—PCR技术并结合生物信息学方法对该毒株进行鉴定,确认本次疾病流行的病原体是副流感1型病毒中的仙台病毒。     

一株引起普通棉耳狨猴死亡病毒的分离与鉴定

1999年6月,天津医科大学动物中心饲养的珍贵灵长类实验动物--普通棉耳狨猴群体中暴发急性呼吸道传染病,病死率高达33%.在排除细菌感染的基础上,通过死亡狨猴肺组织匀浆接种鸡胚和MDCK细胞的分离培养,分离出一株具有高血凝效价的病毒株.经双份血清试验及动物接种试验,确认该病毒是本次疾病流行的病原体.又进一步通过与常见呼吸道病毒标准毒株及血清进行交叉血凝抑制试验、电镜观察、RT-PCR技术并结合生物信息学方法对该毒株进行鉴定,确认本次疾病流行的病原体是副流感1型病毒中的仙台病毒.     

Sampling Natural Viral Communities from Soil for Culture-Independent Analyses

An essential first step in investigations of viruses in soil is the evaluation of viral recovery methods suitable for subsequent culture-independent analyses. In this study, four elution buffers (10% beef extract, 250 mM glycine buffer, 10 mM sodium pyrophosphate, and 1% potassium citrate) and three enumeration techniques (plaque assay, epifluorescence microscopy [EFM], and transmission electron microscopy [TEM]) were compared to determine the best method of extracting autochthonous bacteriophages from two Delaware agricultural soils. Beef extract and glycine buffer were the most effective in eluting viable phages inoculated into soils (up to 29% recovery); however, extraction efficiency varied significantly with phage strain. Potassium citrate eluted the highest numbers of virus-like particles from both soils based on enumerations by EFM (mean, 5.3 × 10⁸ g of dry soil⁻¹), but specific soil-eluant combinations posed significant problems to enumeration by EFM. Observations of virus-like particles under TEM gave confidence that the particles were, in fact, phages, but TEM enumerations yielded measurements of phage abundance (mean, 1.5×10⁸ g of dry soil⁻¹) that were about five times lower. Clearly, the measurement of phage abundance in soils varies with both the extraction and enumeration methodology; thus, it is important to assess multiple extraction and enumeration approaches prior to undertaking ecological studies of phages in a particular soil.     

pH Shaping the Composition of sqhC-Containing Bacterial Communities

Sediment and tailings samples were collected from sites with a contrasting physicochemical gradient to investigate microbial squalene-hopene cyclase (sqhC) composition and distribution in terrestrial environments. Acidobacteria (66%), Alphaproteobacteria (96%) and Gammaproteobacteria (55%) were found to dominate sqhC communities, respectively, at the acidic Dajiuhu Peatland, the alkaline Heshang Cave and strongly acidic tailings of Tongling copper mine in China. Statistical analysis confirmed that pH was the important factor impacting the geographical distribution of sqhC at phylum level. sqhC gene abundance is comparable at the three sites. However, the total amount of hopanoids in per gram total organic matter content (TOC) is 1.75 times higher in the acidic peatland than that in the alkaline Cave and it is below the detecting limit in tailings of Tongling copper mine, inferring the potential impact of pH in regulating the hopanoid production.     

Effects of Pitfall Trap Spacing on the Abundance, Richness and Composition of Invertebrate Catches

Pitfall trapping is one of the most commonly used methods to survey surface-active invertebrates, but has many potential biases that may affect the catch of invertebrates. The distance between pitfall traps (inter-trap spacing) is one such factor. The abundance, richness and composition of invertebrate orders, and species of ants and beetles was examined for three commonly used inter-trap spacings (1, 5, 10m) in a grassy-woodland ecosystem in Victoria, Australia. Abundance and composition was not significantly different between treatments for any taxa. A significant difference in richness between treatments was found only for beetles. The 5 and 10m treatments had a significantly higher number of beetle morphospecies than the 1m treatment. Knowledge of such biases, and how subtle variations in trap design affect efficiency, is important for designing invertebrate surveys.     

Bryophyte Species Richness and Composition along an Altitudinal Gradient in Gongga Mountain,China

An investigation of terrestrial bryophyte species diversity and community structure along an altitudinal gradient from 2,001 to 4,221 m a.s.l. in Gongga Mountain in Sichuan, China was carried out in June 2010. Factors which might affect bryophyte species composition and diversity, including climate, elevation, slope, depth of litter, vegetation type, soil pH and soil Eh, were examined to understand the altitudinal feature of bryophyte distribution. A total of 14 representative elevations were chosen along an altitudinal gradient, with study sites at each elevation chosen according to habitat type (forests, grasslands) and accessibility. At each elevation, three 100 m × 2 m transects that are 50 m apart were set along the contour line, and three 50 cm × 50 cm quadrats were set along each transect at an interval of 30 m. Species diversity, cover, biomass, and thickness of terrestrial bryophytes were examined. A total of 165 species, including 42 liverworts and 123 mosses, are recorded in Gongga mountain. Ground bryophyte species richness does not show any clear elevation trend. The terrestrial bryophyte cover increases with elevation. The terrestrial bryophyte biomass and thickness display a clear humped relationship with the elevation, with the maximum around 3,758 m. At this altitude, biomass is 700.3 g m⁻² and the maximum thickness is 8 cm. Bryophyte distribution is primarily associated with the depth of litter, the air temperature and the precipitation. Further studies are necessary to include other epiphytes types and vascular vegetation in a larger altitudinal range.     

Environmental Factors as Predictors of Aquatic Macrophyte Richness and Composition in Wetlands of Southern Brazil

The main goal of this study was to determine how much variation in macrophyte richness and composition is explained by wetland area, altitude, water conductivity, and nitrate and total phosphorus concentrations in wetlands in southern Brazil, and to compare these variations in two wetland subsystems (palustrine and lacustrine). A total of 126 wetlands were sampled distributed in two subsystems: 87 palustrine and 39 lacustrine wetlands. A total of 153 species of aquatic macrophytes was found in wetlands of southern Brazil and the mean number of macrophyte species per site was 8.7 (range 1–23). From the variables tested, the altitude and area were the only predictor of macrophyte richness and explained 23.1% of variation in richness. The two first axes generated by CCA explained only 4.4% of the variation in the aquatic macrophytes distribution. The macrophyte richness was similar across lacustrine and palustrine subsystems. While altitude, area and conductivity explained 33.2% of variation in macrophyte richness in the palustrine subsystem, none of the variables were associated with macrophyte richness in the studied lacustrine wetlands.     

Viral Communities Associated with Human Pericardial Fluids in Idiopathic Pericarditis

Pericarditis is a common human disease defined by inflammation of the pericardium. Currently, 40% to 85% of pericarditis cases have no identified etiology. Most of these cases are thought to be caused by an infection of undetected, unsuspected or unknown viruses. In this work, we used a culture- and sequence-independent approach to investigate the viral DNA communities present in human pericardial fluids. Seven viral metagenomes were generated from the pericardial fluid of patients affected by pericarditis of unknown etiology and one metagenome was generated from the pericardial fluid of a sudden infant death case. As a positive control we generated one metagenome from the pericardial fluid of a patient affected by pericarditis caused by herpesvirus type 3. Furthermore, we used as negative controls a total of 6 pericardial fluids from 6 different individuals affected by pericarditis of non-infectious origin: 5 of them were sequenced as a unique pool and the remaining one was sequenced separately. The results showed a significant presence of torque teno viruses especially in one patient, while herpesviruses and papillomaviruses were present in the positive control. Co-infections by different genotypes of the same viral type (torque teno viruses) or different viruses (herpesviruses and papillomaviruses) were observed. Sequences related to bacteriophages infecting Staphylococcus, Enterobacteria, Streptococcus, Burkholderia and Pseudomonas were also detected in three patients. This study detected torque teno viruses and papillomaviruses, for the first time, in human pericardial fluids.     

Influence of Forest Management on the Species Richness and Composition of Wood-inhabiting Basidiomycetes in Swiss Forests

In order to investigate the diversity of wood-inhabiting aphyllophoroid basidiomycetes in Swiss forests, 86 plots of 50 m ² were established. They harboured a total of 3339 samples of woody debris, classified according to three categories (coarse, fine, and very fine woody debris), yielding 238 species of wood-inhabiting fungi. The selected sites cover the main forest types of Switzerland and various degrees of management intensity. A multiple linear regression analysis showed that substrate variation, i.e. differences in the quality of dead wood, including volume, age, degree of decomposition and host tree species, are the most important factors influencing diversity of wood-inhabiting fungi. In addition, a Principle Coordinate Analysis highlighted differences in the fungal communities in the different forest types. The greatest fungal species richness is found on thermophilic deciduous tree and woody shrub species. Fine and very fine woody debris, even present in intensively managed forests, often serve as important refuges for many species. Forests with a recent management intervention were found to be either species poor or species rich. Possible reasons for these differences may lay in forest size and landscape fragmentation, the distance to the nearest species pool or microclimatic factors. In Switzerland intensively managed forests harbour significantly less wood-inhabiting, aphyllophoroid fungi than non-managed or extensively managed forests. This is the case in both deciduous forests and in conifer forests. However, occasionally intensively managed forest will also harbour rare and endangered species.     

An Exploration of Hypotheses that Explain Herbivore and Pathogen Attack in Restored Plant Communities

Many hypotheses address the associations of plant community composition with natural enemies, including: (i) plant species diversity may reduce enemy attack, (ii) attack may increase as host abundance increases, (iii) enemy spillover may lead to increased attack on one host species due to transmission from another host species, or enemy dilution may lead to reduced attack on a host that would otherwise have more attack, (iv) physical characteristics of the plant community may influence attack, and (v) plant vigor may affect attack. Restoration experiments with replicated plant communities provide an exceptional opportunity to explore these hypotheses. To explore the relative predictive strengths of these related hypotheses and to investigate the potential effect of several restoration site preparation techniques, we surveyed arthropod herbivore and fungal pathogen attack on the six most common native plant species in a restoration experiment. Multi-model inference revealed a weak but consistent negative correlation with pathogen attack and host diversity across the plant community, and no correlation between herbivory and host diversity. Our analyses also revealed host species-specific relationships between attack and abundance of the target host species, other native plant species, introduced plant species, and physical community characteristics. We found no relationship between enemy attack and plant vigor. We found minimal differences in plant community composition among several diverse site preparation techniques, and limited effects of site preparation techniques on attack. The strongest associations of community characteristics with attack varied among plant species with no community-wide patterns, suggesting that no single hypothesis successfully predicts the dominant community-wide trends in enemy attack.