Protistan microbial observatory in the Cariaco Basin,Caribbean. II. Habitat specialization

This is the second paper in a series of three that investigates eukaryotic microbial diversity and taxon distribution in the Cariaco Basin, Venezuela, the ocean''s largest anoxic marine basin. Here, we use phylogenetic information, multivariate community analyses and statistical richness predictions to test whether protists exhibit habitat specialization within defined geochemical layers of the water column. We also analyze spatio-temporal distributions of protists across two seasons and two geographic sites within the basin. Non-metric multidimensional scaling indicates that these two basin sites are inhabited by distinct protistan assemblages, an observation that is supported by the minimal overlap in observed and predicted richness of sampled sites. A comparison of parametric richness estimations indicates that protistan communities in closely spaced—but geochemically different—habitats are very dissimilar, and may share as few as 5% of total operational taxonomic units (OTUs). This is supported by a canonical correspondence analysis, indicating that the empirically observed OTUs are organized along opposing gradients in oxidants and reductants. Our phylogenetic analyses identify many new clades at species to class levels, some of which appear restricted to specific layers of the water column and have a significantly nonrandom distribution. These findings suggest many pelagic protists are restricted to specific habitats, and likely diversify, at least in part due to separation by geochemical barriers.     

Diversity estimates of microeukaryotes below the chemocline of the anoxic Mariager Fjord, Denmark

Microbial communities of extreme environments have often been assumed to have low species richness. We analysed 18S rRNA gene signatures in a sample collected below the chemocline of the anoxic Mariager Fjord in Denmark, and from these data we computed novel parametric and standard nonparametric estimates of protistan phylotype richness. Our results indicate unexpectedly high richness in this environment: at the 99.5% phylotype definition, our most conservative estimate was 568 phylotypes (+/-114, standard error). Phylogenetic analyses revealed that the sequences collected cover the majority of described lineages in the eukaryotic domain. Out of 384 sequences analysed, 307 were identified as protistan targets, none of which was identical to known sequences. However, based on what is known about species that are phylogenetically related to the Mariager sequences, most of the latter seem to belong to strictly or facultative anaerobe organisms. We also found signatures that together with other environmental 18S rRNA gene sequences represent environmental clades of possibly high taxonomic levels (class to kingdom level). One of these clades, consisting exclusively of sequences from anoxic sampling sites, branches at the base of the eukaryotic evolutionary tree among the earliest eukaryotic lineages. Assuming eukaryotic evolution under oxygen-depleted conditions, these sequences may represent immediate descendants of early eukaryotic ancestors.     

A central Amazonian terra firme forest. I. High tree species richness on poor soils

Tree size, density, and species richness were established for three one-hectare plots of terra firme forest in central Amazonian Brazil. In the three hectares, 1916 individual trees with DBH 10 cm were sampled. A total of 58 families, 181 genera, and 513 species were determined. Hectare A had 285 species, 138 genera, and 47 families; hectare B 280 species, 123 genera, and 48 families; and hectare C 280 species, 125 genera, and 44 families. Comparably high species richness in Amazonia has heretofore only been reported from western Amazonia. This dispels the idea that high species richness can only develop in areas with rich soils and relatively high rainfall. It is suggested that such high species richness is the result of a combination of habitat heterogeneity and geological history. These high diversity forests, because they occur on nutrient poor soils, can be protected with little or no impact on development in the region because the soils are essentially useless for agriculture and for supporting long-term cattle pasture.     

Environmental correlates of vegetation patterns and species richness in the northern Grampians,Victoria

Abstract Plant species cover-abundance and density data were collected for 94 sample plots across a gradient from rocky uplands to sandy outwash plains in the northern part of Grampians (Gariwerd) National Park in western Victoria. Detrended correspondence analysis (DCA) was used to identify dominant gradients in species composition. A range of static (e.g. substrate type, soil depth, microclimate indicators) and dynamic (e.g. elapsed time since last fire) environmental variables were measured. Correlations were sought between these variables and vegetation patterns including those for richness (R) and Shannon-Weiner diversity (H′). The dominant gradient of vegetation change identified by DCA separated rocky sites and sites near ephemeral streams, from well-drained, sandy sites. Secondary gradients identified time since last fire as important for sandy sites, and altitude and aspect-related microclimate for rocky sites. Diversity was highest in the first 2 years after fire but showed no further decline in older sites. Overall, R and H' were negatively correlated with soil nutrient concentrations. On sandy sites R was high, but was low on rocky sites and near streams. Within the rocky sites, R was highest on cool, moist south and east slopes, and lowest on hot, dry north and west slopes. Explanations of diversity patterns based on inhibition of competitive exclusion due to stress and recurrent disturbance best fit the results presented here.     

The alpha–beta–regional relationship: providing new insights into local–regional patterns of species richness and scale dependence of diversity components

Ecologists frequently regress local species richness on regional species richness to draw inferences about the processes that structure local communities. A more promising approach is to quantify the contributions of alpha and beta diversity to regional diversity (the ABR approach) using additive partitioning. We applied this approach to four local–regional relationships based on data from 583 arboreal beetle species collected in a hierarchically nested sampling design. All four local–regional relationships exhibited proportional sampling, yet the ABR approach indicated that each was produced by a different combination of alpha and beta richness. Using the results of the ABR analysis, we also analysed the scale dependence of alpha and beta using a hierarchical linear model. Alpha diversity contributed less than expected to regional diversity at the finest spatial scale and more than expected at the broadest spatial scale. A switch in relative dominance from beta to alpha diversity with increasing spatial scale suggested scale transitions in ecological processes. Analysing the scale dependence of diversity components using the ABR approach furthers our understanding about the additivity of species diversity in biological communities.     

Floral species richness,structural diversity and conservation value of vanilla agroecosystems in Madagascar

Agricultural landscapes provide financial livelihoods for farming communities in rural areas. However, such agroenvironments can significantly impact the local floral biodiversity and introduce harmful invasive species to the ecosystem. Despite the prominence of plantations throughout the tropics, their effects on local flora are limited to only a few specific cash crops and geographical regions. Here, we compared the species richness and structural diversity of vegetation in natural forest fragments and three types of vanilla plantation within the Sava region of north-east Madagascar ranging from those within or adjacent to existing forests, to intensively cultivated plantations. We recorded data on plant species abundance, diameter at breast height and canopy cover within multiple sites of each habitat. We used abundance data to calculate species richness indices, and we compared these metrics between habitats. Forested habitats contained a significantly higher floral species richness, structural diversity and more endemic and regionally native species than nonforested, anthropogenic vanilla plantations. However, our results suggest that the high floral species richness and structural diversity of natural forests can be partially achieved in vanilla plantations, depending on the site's management regime; traditionally managed vanilla plantations located close to natural forests can support diverse floral communities. These encouraging findings for plant conservation and sustainable agroforestry in Madagascar suggest that that newly created vanilla plantations and already existing nonforested plantations should endeavour to follow the more traditional forested approach to enhance the future sustainability and promote floristic diversity.     

喀斯特常绿落叶阔叶混交林物种多度与丰富度空间分布的尺度效应

物种多样性的空间分布格局及其尺度效应是生态学研究的重点,对于理解物种多样性的形成和维持机制以及生物多样性的管理和保护均具有重要意义。以贵州茂兰国家级自然保护区分布的亚热带原生性喀斯特常绿落叶阔叶混交林为研究对象,分析了2个1hm2(100m×100m)样地中物种多度和丰富度的空间分布特征及其与取样尺度的关系,采用方差和变异系数描述多度和丰富度在5个尺度(5m×5m,10m×10m,20m×20m,25m×25m,50m×50m)上的空间变异性。结果表明:(1)两个样地的物种多度和丰富度具有尺度依赖性特征;(2)由于多度具有叠加性,物种多度的方差随着尺度的增加呈线性增加,而变异系数呈线性下降;(3)丰富度的方差随尺度的增加表现出单峰分布的特征,在25 m×25 m尺度上达到最大值,变异系数则随取样尺度的增加而呈线性下降。研究表明,物种多度具有尺度推演规律,而丰富度却没有,因此,应慎重进行物种丰富度的尺度推演。在分析喀斯特森林物种多样性时,应注重尺度效应带来的影响。     

16S rRNA基因在微生物生态学中的应用

16S rRNA(Small subunit ribosomal RNA)基因是对原核微生物进行系统进化分类研究时最常用的分子标志物(Biomarker),广泛应用于微生物生态学研究中。近些年来随着高通量测序技术及数据分析方法等的不断进步,大量基于16S rRNA基因的研究使得微生物生态学得到了快速发展,然而使用16S rRNA基因作为分子标志物时也存在诸多问题,比如水平基因转移、多拷贝的异质性、基因扩增效率的差异、数据分析方法的选择等,这些问题影响了微生物群落组成和多样性分析时的准确性。对当前使用16S rRNA基因分析微生物群落组成和多样性的进展情况做一总结,重点讨论当前存在的主要问题以及各种分析方法的发展,尤其是与高通量测序技术有关的实验和数据处理问题。     

Patterns of ant species richness along elevational gradients in an arid ecosystem

Aim In this study, we examine patterns of local and regional ant species richness along three elevational gradients in an arid ecosystem. In addition, we test the hypothesis that changes in ant species richness with elevation are related to elevation‐dependent changes in climate and available area. Location Spring Mountains, Nevada, U.S.A. Methods We used pitfall traps placed at each 100‐m elevational band in three canyons in the Spring Mountains. We compiled climate data from 68 nearby weather stations. We used multiple regression analysis to examine the effects of annual precipitation, average July precipitation, and maximum and minimum July temperature on ant species richness at each elevational band. Results We found that patterns of local ant species richness differed among the three gradients we sampled. Ant species richness increased linearly with elevation along two transects and peaked at mid‐elevation along a third transect. This suggests that patterns of species richness based on data from single transects may not generalize to larger spatial scales. Cluster analysis of community similarity revealed a high‐elevation species assemblage largely distinct from that of lower elevations. Major changes in the identity of ant species present along elevational gradients tended to coincide with changes in the dominant vegetation. Regional species richness, defined here as the total number of unique species within an elevational band in all three gradients combined, tended to increase with increasing elevation. Available area decreased with increasing elevation. Area was therefore correlated negatively with ant species richness and did not explain elevational patterns of ant species richness in the Spring Mountains. Mean July maximum and minimum temperature, July precipitation and annual precipitation combined to explain 80% of the variation in ant species richness. Main conclusions Our results suggest that in arid ecosystems, species richness for some taxa may be highest at high elevations, where lower temperatures and higher precipitation may support higher levels of primary production and cause lower levels of physiological stress.     

Mammalian species richness and morphological complexity along an elevational gradient in the arid south-west

Aim We examined the relationship between species richness and morphological complexity of terrestrial mammal communities along an elevational gradient. Location The gradient is in the Sonoran Desert in Southern California and extends from a sand dune habitat near sea level to coniferous forest ending at >2600 m. Methods Morphological diversity, characterized by both size and shape of coexisting mammal species, was estimated within and between sites from projections of variables on principal components axes. Similarities among species were calculated as Euclidean distances. To tease apart size and shape, we constructed two principal component analyses: one based on log-transformed original measurements, the other on log-transformed proportional shape variables. To test whether species number accounted for the morphological diversity at each site we designed two null models. The models generated were random communities generated from the forty-two-species pool. Indices of morphological diversity for real communities were compared with the results of 500 simulations of each null model. Results Species richness varied along the gradient, peaking in the mid-elevation agave-ocotillo habitat. Morphological diversity of shapes and sizes correlated strongly with species richness. Locomotor, tooth, and skull traits were all important in distinguishing among species. Main conclusions Two important patterns emerged: (1) diversity of both sizes and of shapes of species within communities correlated positively with species number, and both sets of variables behaved similarly across this gradient; (2) the most species rich sites were not composed of specialists on these best places, but rather, a community of species derived from overlapping faunal groups.     

Patterns of tree species richness in relation to environment in southeastern New South Wales,Australia

Abstract We present regression models of species richness for total tree species, two growth forms, rainforest trees (broadleaf evergreens) and eucalypts (sclerophylls), and two large subgenera of Eucalyptus. The correlative models are based on a data set of 166 tree species from 7208 plots in an area of southeastern New South Wales, Australia. Eight environmental variables are used to model the patterns of species richness, four continuous variables (mean annual temperature, rainfall, radiation and plot size), plus four categorical factors (topographic position, lithology, soil nutrient level and rainfall seasonality). Generalized linear modelling with curvilinear and interaction terms, is used to derive the models. Each model shows a significant and differing response to the environmental predictors. Maximum species richness of eucalypts occurs at high temperatures, and intermediate rainfall and radiation conditions on ridges with aseasonal rainfall and intermediate nutrient levels. Maximum richness of rainforest species occurs at high temperatures, intermediate rainfall and low radiation in gullies with summer rainfall and high nutrient levels. The eucalypt subgenera models differ in ways consistent with experimental studies of habitat preferences of the subgenera. Curvilinear and interaction terms are necessary for adequate modelling. Patterns of richness vary widely with taxonomic rank and growth form. Any theories of species diversity should be consistent with these correlative models. The models are consistent with an available energy hypothesis based on actual evapotranspiration. We conclude that studies of species richness patterns should include local (e.g. soil nutrients, topographic position) and regional (e.g. mean annual temperature, annual rainfall) environmental variables before invoking concepts such as niche saturation.     

Two Urosoma species (Ciliophora,Hypotrichia): A multidisciplinary approach provides new insights into their ultrastructure and systematics

The general morphology and ultrastructure of two soil hypotrichous ciliates, Urosoma emarginata and U. salmastra, were investigated using light microscopy, scanning electron microscopy and transmission electron microscopy. Phylogenetic analyses, based on the newly sequenced small subunit ribosomal (SSU) rRNA genes, were conducted on three U. emarginata populations and one U. salmastra population. Our findings support for the validity of Perilemmaphora Berger, 2008, a rankless taxon comprising spirotrich ciliates having a perilemma. The cortical granules of both species are extrusomes representing a new type of mucocyst in U. emarginata and possibly a new type of pigmentocyst in U. salmastra. Additionally, the lithosomes were revealed as subglobose structures composed of a low electron-dense, homogeneous inner part and an electron-dense outer part. The ultrastructural features of the cortical granules, together with ontogenetic and molecular phylogenetic data, suggest that the genus Urosoma might need to be divided. It is posited that ultrastructural features of hypotrichous ciliates in general may have important taxonomic value warranting further investigation.     

放牧干扰下高寒草甸物种和生活型丰富度与地上及地下生物量的关系

明晰放牧干扰下高寒草甸植物丰富度与生物量的相关关系,为草地植物不同生长时期生物量的预测提供依据。设置6个放牧强度样地,连续3a放牧,2014年进行3个季节(6月、8月、10月)的植物丰富度和地上、地下生物量调查,对比分析放牧干扰下物种和生活型丰富度(生活型的种类)分别与地上、地下生物量的相关关系。结果表明:(1)物种和生活型丰富度与地上生物量均受放牧强度的显著影响,物种丰富度仅在8月与放牧强度显著负相关,生活型丰富度在10月随放牧强度单峰变化,地上生物量在不同季节均与放牧强度显著负相关,而地下生物量与放牧强度无关。(2)物种丰富度与地上和地下生物量均受季节的显著影响,物种丰富度和地上生物量仅在低强度放牧区随季节呈单峰变化,地下生物量在中等强度放牧区随季节呈单峰变化;生活型丰富度与季节无关。(3)放牧干扰前物种和生活型丰富度与地上和地下生物量均显著正相关。3a放牧后仅在8月,物种丰富度只与地上生物量显著正相关,生活型丰富度与地上和地下生物量均显著正相关。(4)对于不同放牧强度,物种丰富度仅在低强度放牧区与地上生物量显著正相关,而生活型丰富度在所有放牧强度区均与地上生物量显著正相关。综上所述,放牧干扰扰乱了高寒草甸丰富度与生物量之间的关系,尤其影响了物种丰富度与地下生物量之间的相关关系。生活型丰富度与地上生物量之间的显著关系不受放牧强度干扰,使生活型丰富度在预测生物量方面表现出优势。     

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre

Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0–1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology‐based studies in the region (4,024 OTUs, 10‐fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic–upper mesopelagic depths (100–300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth‐stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2–0.5 mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones.     

Spatial and environmental determinants of vascular plant species richness distribution in the Iberian Peninsula and Balearic Islands

Using an exhaustive data compilation, Iberian vascular plant species richness in 50 times 50 UTM grid cells was regressed against 24 explanatory variables (spatial, geographical, topographical, geological, climatic, land use and environmental diversity variables) using Generalized Linear Models and partial regression analysis in order to ascertain the relative contribution of primary, heterogeneous and spatially structured variables. The species richness variation accounted for by these variables is reasonably high (65% of total deviance). Little less than half of this variation is accounted for spatially structured variables. A purely spatial component of variation is hardly significant. The most significant variables are those related to altitude, and particularly maximum altitude, whose cubic response reflects the occurrence of the maximum number of species at the highest altitudes. This result highlighted the importance of Iberian mountains as hotspots of diversity and the relevance of large and small scale historical factors in contemporary plant distribution patterns. Climatic or energy-related variables contributed little, whereas geological (calcareous and acid rocks) and, to a lesser extent, environmental heterogeneity variables (land use diversity and altitude range) seem to be more important.     

Water-energy dynamics, climate, and prediction of woody plant species richness: an interim general model

Predictable geographic patterns in the distribution of species richness, especially the latitudinal gradient, are intriguing because they suggest that if we knew what the controlling factors were we could predict species richness where empirical data is lacking (e.g. tropics). Based on analyses of the macro-scale distribution of woody plant species richness in Southern Africa, one controlling factor appears to be climate-based water-energy dynamics. Using the regression models of climate's relationship to species richness in Southern Africa, I was able to describe an Interim General Model (IGM) and to predict first-order macro-scale geographic variations in woody plant species richness for the continent of Africa, as well as elsewhere in the world—exemplified using South America, the United States and China.
In all cases, the geographic pattern of variation in species richness is in accord with geographic variations in vegetation (visual comparison with vegetation maps) and net primary productivity. What validation was possible (Africa and U.S.A.) suggests that the IGM provides 'reasonable' estimates for actual woody plant species richness where species richness is in relative equilibrium with climate. Areas of over- or under-prediction support the contention of earlier workers that edaphic, topographic, historical, and dispersal factors need to be considered in a more complete explanation for spatio-temporal variations in species richness.
In addition to providing a means for systematically estimating woody plant species richness where present-day empirical data is lacking, the Interim General Model may prove useful for modelling the effects of climate change (past/future) on species richness (and, by association, the vegetation).     

Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus

Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life‐history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life‐history traits, such as age, sex, and reproductive success. Using PCR‐TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts.