Diversity and geographic distribution of ciliates (Protista: Ciliophora)

About 4,500 free-living ciliate morphospecies have been described, applying an average synonymy rate of 20%. We estimate that 83–89% of the ciliate diversity is still undescribed, using the following probabilities: detailed habitat studies suggest that the described number of morphospecies must be doubled: 4,500 → 9,000; this figure has to be increased by about 50% due to species with similar interphase morphology but different resting cysts: 9,000 → 13,500; the genetic and molecular data suggest that this value must be doubled or trebled: 13,500 → 27,000 to 40,000 free-living, biological ciliate species. The knowledge on geographic distribution of ciliates heavily depends on flagship species and statistical analyses because reliable faunistic studies are rare and molecular data are still in its infancy. We present a list of 52 ciliate flagship species as a testable hypothesis, i.e., the hypothesis of restricted distribution of certain ciliate species must be refused when a considerable number of them is found in all or most biogeographic regions. Flagship species and statistical analyses consistently show Gondwanan and Laurasian ciliate communities, suggesting that the split of Pangaea deeply influenced ciliate distribution and rare species play a key role in geographic differentiation. However, there is also substantial evidence for continental, regional, and local endemism of free-living ciliates. The molecular studies usually show a high level of genetic diversity underlying ciliate morphospecies, suggesting that morphologic and molecular evolution may be decoupled in many ciliate species. Molecular studies on ciliate biogeography are at variance, possibly because most are still focusing on single molecular markers. In sum, the data indicate that ciliate biogeography is similar to that of plants and animals, but with an increased proportion of cosmopolites, favouring the moderate endemicity model. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Evidence for an active rare biosphere within freshwater protists community

Studies on the active rare biosphere at the RNA level are mainly focused on Bacteria and Archaea and fail to include the protists, which are involved in the main biogeochemical cycles of the earth. In this study, the richness, composition and activity of the rare protistan biosphere were determined from a temporal survey of two lakes by pyrosequencing. In these ecosystems, the always rare OTUs represented 77.2% of the total OTUs and 76.6% of the phylogenetic diversity. From the various phylogenetic indices computed, the phylogenetic units (PUs) constituted exclusively by always rare OTUs were discriminated from the other PUs. Therefore, the rare biosphere included mainly taxa that are distant from the reference databases compared to the dominant ones. In addition, the rarest OTUs represented 59.8% of the active biosphere depicted by rRNA and the activity (rRNA:rDNA ratio) increased with the rarity. The high rRNA:rDNA ratio determined in the rare fraction highlights that some protists were active at low abundances and contribute to ecosystem functioning. Interestingly, the always rare and active OTUs were characterized by seasonal changes in relation with the main environmental parameters measured. In conclusion, the rare eukaryotes represent an active, dynamic and overlooked fraction in the lacustrine ecosystems.     

Biodiversity of terrestrial protozoa appears homogeneous across local and global spatial scales

Free-living microbes are by far the most abundant group of organisms in the biosphere, yet estimates of global species richness remain nebulous, and there is no consensus regarding the likely geographical distribution of species. Both uncertainties are addressed by the suggestion that the vast abundance of microbes may drive their ubiquitous random dispersal; for this would also make it likely that global species richness is relatively low. Here we test the idea of ubiquitous dispersal of testate amoebae and ciliates living in soil. We analysed their abundance and species richness in 150 soil samples collected from the one-hectare grassland site at Sourhope in Scotland, and in comparable published data from 1500 soil samples collected worldwide. Following taxonomic revision and removal of synonyms, there remained a total of 186 taxa (91 testate and 95 ciliate) recorded from both Sourhope and other places in the world. A fundamental pattern of random spatial distribution of species was revealed in species that are relatively rare. This probably arises from random dispersal, for when localised population growth occurs, the distributions become aggregated, as in virtually all metazoan species. We find no evidence for geographically-restricted protozoan morphospecies at spatial scales of 4 m², 10,000 m², or worldwide. Species that are locally rare or abundant are similarly rare or abundant on a global scale. Approximately one third of the global diversity of soil protozoa was found at the one-hectare grassland site in Scotland, but this is a minimum figure, for recorded species richness is proportional to sampling effort, as shown here.     

Effects of Metazoan Predators on Ciliates in Freshwater Plankton Communities1

ABSTRACT. Ciliates are often important members of aquatic communities in terms of their biomass, productivity, trophic roles, or numerical abundance. The interaction of metazoan predators with ciliates will be mediated by a number of biotic factors, including the potential of ciliate populations for growth, the relative size of ciliates and metazooplankton, the species structure of the metazooplankton, and the defenses of ciliates. This paper reviews some of the recent laboratory an field data pertaining to these particular factor. Studies have generally shown that metazoans can reduce ciliate population growth rates, but this impact varies greatly with the ciliate and metazoans involved. Smaller ciliates are generally more vulnerable to metazoan predators than larger species, although this relationship will be affected by the defenses a ciliate may possess. The structure of the metazooplankton community itself will also affect ciliatemetazoan interactions. The suppression of ciliate populations by metazoans has important ecological consequences, and more study is needed to understand the interaction of these groups in aquatic systems.     

Sexual differences and sex ratios of dioecious plants under stressful environments

雌雄异株植物对环境胁迫响应的性别差异与性别比例 雌雄异株植物在性特征(繁殖器官)和次级性特征(植物的特征)均表现出性二态。形态、生理与生态特征等次级性特征的性别差异,通常在繁殖成本和其他功能性状之间存在着权衡。尽管有证据表明性二态对环境胁迫的响应不一定存在于所有植物中,但次级性特征的权衡可能受到环境胁迫的影响。当植物表现出性二态时,不同的物种与胁迫因子可以导致性别特异性的响应。因此,胁迫作用对雌雄异株植物影响的概括性研究是必须的。另外,性二态可能会影响雌雄异株植物沿着环境梯度的频率和分布,引起生态位分化与性别空间分异。目前,控制性别比例偏差的原因和机制还知之甚少。本综述旨在讨论不利环境下的性别特异性响应与性别比例偏差,有利于深入的理解性二态对环境胁迫的响应。     

Unexpected biodiversity of ciliates in marine samples from below the photic zone

Marine microbial eukaryotes play critical roles in planktonic food webs and have been described as most diverse in the photic zone where productivity is high. We used high‐throughput sequencing (HTS) to analyse the spatial distribution of planktonic ciliate diversity from shallow waters (<30 m depth) to beyond the continental shelf (>800 m depth) along a 163 km transect off the coast of New England, USA. We focus on ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), as these taxa are major components of marine food webs. We did not observe the decrease of diversity below the photic zone expected based on productivity and previous analyses. Instead, we saw an increase of diversity with depth. We also observed that the ciliate communities assessed by HTS cluster by depth layer and degree of water column stratification, suggesting that community assembly is driven by environmental factors. Across our samples, abundant OTUs tend to match previously characterized morphospecies while rare OTUs are more often undescribed, consistent with the idea that species in the rare biosphere remain to be characterized by microscopy. Finally, samples taken below the photic zone also reveal the prevalence of two uncharacterized (i.e. lacking sequenced morphospecies) clades – clusters X₁ and X₂ – that are enriched within the nano‐sized fraction (2–10 μm) and are defined by deletions within the region of the SSU‐rDNA analysed here. Together, these data reinforce that we still have much to learn about microbial diversity in marine ecosystems, especially in deep‐waters that may be a reservoir for rare species and uncharacterized taxa.     

Common species have lower taxonomic diversity Evidence from the urban floras of Brussels and Rome

The species pool hypothesis claims that the large‐scale regional species pool is the chief parameter in determining small‐scale species richness through filtering of species that can persist within a community on the basis of their tolerance of the abiotic environment. Accordingly, different environmental conditions give rise to different species assemblages. From a taxonomic perspective, under the assumption of trait conservatism, co‐occurring species that experience similar environmental conditions are likely to be more taxonomically similar than ecologically distant species. The next step consists in understanding how commonness and rarity of individual species produce the observed taxonomic diversity. In this paper, the importance of environmental filtering in regulating the taxonomic structure of rare and common plant species in the urban floras of Brussels (Belgium) and Rome (Italy) is tested. First, we computed the taxonomic diversity of the rare and common species of Brussels and Rome based on the branching topology of the Linnaean taxonomic trees. Next, using a randomization procedure, we determined whether the taxonomic diversity of the rare species was significantly higher than the diversity of the common species. Results show that, for both urban floras, common species that shape the community matrix and experience similar environmental conditions have a taxonomic diversity that is significantly lower than that of the rare species that represent a relatively incidental set of species of more ‘disperse’ origin. Finally, from a conservation/management perspective our results imply that, given their high taxonomic heterogeneity, the protection of rare species is a central issue for preserving high levels of diversity in urban areas.     

Effects of Seasonality and Dispersal on the Ciliate Community Inhabiting Bromeliad Phytotelmata in Riparian Vegetation of a Large Tropical River

This study evaluated the influence of rainfall amount on the abundance, species richness, and species occurrence and abundance distribution of the ciliate community associated with the bromeliad Aechmea distichantha. The plants were collected from a rock wall of about 10‐km long at the left bank of Paraná River. We assessed the effects of both spatial and temporal variables on the community attributes, as well as whether plants geographically closer have a similar abundance distribution and species composition. The ciliate community was substantially distinct between both hydrological periods, with greater values of species richness and abundance in the rainy period. No spatial structuring (differences in the species occurrence and abundance distribution among strata) or geographical similarity (similarity in ciliate species composition among the plants) was found. Multiple regression analysis showed a positive relationship only between the ciliate abundances and water volumes for both periods. Although few of the formulated predictions were confirmed, our study provides valuable information on the ecological aspects of the ciliate community inhabiting bromeliad phytotelmata.     

Developmental variability and the limits of adaptation: Interactions with stress

1. Little evolutionary change may occur at species borders since the cost of accommodating environmental stresses is high. Extreme examples of such stasis include cave animals in stable stressed environments and ‘living fossils’ in widely fluctuating stressed environments. 2. Variability from the molecular to the organismic level tends to be high under extreme stress. At the developmental level, the fitness of such variants may be low. This means that much developmental variability in natural populations may have little evolutionary significance. 3. Rapid evolutionary change of morphological traits is most likely to be based upon genes acting late in a developmental pathway under conditions which are ecologically and energetically permissive. 4. Although some increases in resistance to temperature extremes have been recorded in laboratory selection experiments, major extensions of extremes in natural populations appear difficult to achieve. The energetic costs of surviving extremes at species borders implies that the evolution of major developmental and morphological shifts is more likely to be a feature of populations of more equable habitats.     

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China

Bacteria play key roles in the ecology of both aquatic and terrestrial ecosystems; however, little is known about their diversity and biogeography, especially in the rare microbial biosphere of inland freshwater ecosystems. Here we investigated aspects of the community ecology and geographical distribution of abundant and rare bacterioplankton using high-throughput sequencing and examined the relative influence of local environmental variables and regional (spatial) factors on their geographical distribution patterns in 42 lakes and reservoirs across China. Our results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance–decay relationship. This suggests that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa. However, we identified some differences between the abundant and rare groups as both groups of bacteria showed a significant positive relationship between sites occupancy and abundance, but the abundant bacteria exhibited a weaker distance–decay relationship than the rare bacteria. Our results implied that rare subcommunities were mostly governed by local environmental variables, whereas the abundant subcommunities were mainly affected by regional factors. In addition, both local and regional variables that were significantly related to the spatial variation of abundant bacterial community composition were different to those of rare ones, suggesting that abundant and rare bacteria may have discrepant ecological niches and may play different roles in natural ecosystems.     

宁波地区蝴蝶种类调查及区系分析

宁波地区蝶类164种,尿属于11科106属,其中,东洋种81个,占总数的49．39％,古北种15个,占总数的9．14％,东洋古北共有种65个,占39．63％,广布种3个,占1．82％,区系分析表明,本地区蝶类资源属于东洋区系范畴,并具有东洋区向古北区过渡的特性,蝶类分布型有24个,仅限于华中,华南,西南3区分布的种类有49个,占总数的近1／3,调查发现浙江省新纪录3种。     

Rarity and genetic diversity in Indo-Pacific Acropora corals

Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo-Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome.     

Evidence for cryptic speciation in Carchesium polypinum Linnaeus, 1758 (Ciliophora: Peritrichia) inferred from mitochondrial, nuclear, and morphological markers

Protist diversity is currently a much debated issue in eukaryotic microbiology. Recent evidence suggests that morphological and genetic diversity might be decoupled in some groups of protists, including ciliates, and that these organisms might be much more diverse than their morphology implies. We sought to assess the genetic and morphological diversity of Carchesium polypinum, a widely distributed peritrich ciliate. The mitochondrial marker cytochrome c oxidase subunit I and the nuclear small subunit ribosomal RNA were used to examine genetic diversity. For the morphological assessment, live microscopy and Protargol staining were used. The mitochondrial marker revealed six robust, deeply diverging, and strongly supported clades, while the nuclear gene was congruent for three of these clades. There were no major differences among individuals from the different clades in any of the morphological features examined. Thus, the underlying genetic diversity in C. polypinum is greater than what its morphology suggests, indicating that morphology and genetics are not congruent in this organism. Furthermore, because the clades identified by the mitochondrial marker are so genetically diverse and are confirmed by a conserved nuclear marker in at least three cases, we propose that C. polypinum be designated as a "cryptic species complex." Our results provide another example where species diversity can be underestimated in microbial eukaryotes when using only morphological criteria to estimate species richness.     

Stream diatoms exhibit weak niche conservation along global environmental and climatic gradients

Niche conservatism (NC) describes the scenario in which species retain similar characteristics or traits over time and space, and thus has potentially important implications for understanding their biogeographic distributions. Evidence consistent with NC includes similar niche properties across geographically distant regions. We investigated whether NC was evident in stream diatom morphospecies by modeling species responses to environmental and climatic variables in a set of calibration sites (from the US) and then evaluated the models with test sets (from France, Finland, New Zealand, Antilles and La Réunion). We also examined whether diatom species showed congruency in environmental niche optima and niche breadths between the study regions, and whether species occupancy and functional traits influenced the observed patterns. We used boosted regression tree models with local environmental variables and climatic variables as predictors. We detected low NC in both environmental and climate models and a lack of consistent differences in NC between widely distributed and regionally rare species and among functional groups. For all species, diatom environmental and climatic optima varied clearly between the regions but showed some positive relationships especially for pH and total phosphorus. Diatom niche breadths were only weakly correlated between the US and the other regions. We demonstrated that diatoms showed overall relatively little NC globally, and NC was especially low for climatic variables. Collectively, these findings suggest that there may exist locally adapted lineages within the diatom morphospecies or diatoms possess some adaptation potential for differences in temperature. We argue that in diatoms, environmental and especially climate models may not be transferrable in space globally but need regional diatom data for calibration because species niches seem to differ among geographical regions.     

拉萨河中下游纤毛虫群落时空分布模式及其驱动机制

为了探究拉萨河中下游纤毛虫群落的组成模式、时空多样性格局及其维持机制, 本文于2015年5月和8月以及2016年10月在拉萨河中下游17个样点进行采样, 采用活体观察、鲁哥氏碘液固定染色以及Wilbert蛋白银法相结合的物种鉴定方法, 对纤毛虫群落结构进行了研究。通过Shannon多样性指数、Margalef丰富度指数、物种数分析群落结构时空上的差异性; 通过共现网络分析纤毛虫类群之间的相互作用; 通过冗余分析(redundancy analysis, RDA)探讨水体理化因子对纤毛虫群落结构的影响。结果表明, Shannon多样性指数在季节和河段间没有显著性差异; Margalef丰富度指数、物种数在河段间存在极显著性差异; 中游和下游河段共现网络节点间的相关关系均以正相关为主; 溶解氧(DO)、总氮(TN)、总磷(TP)、总溶解盐(TDS)是影响纤毛虫群落结构的关键因子。综上所述, 拉萨河中下游纤毛虫群落结构在季节间没有显著差异, 在空间上具有显著差异; 纤毛虫在纲级水平上类群间的相互作用以协同作用为主导, 不同类群间存在复杂的相互作用, 整体上互作关系在春季较为复杂、夏季较为简单; 影响拉萨河中下游纤毛虫群落结构是多个环境因子共同作用的结果。     

How many species of flowering plants are there?

We estimate the probable number of flowering plants. First, we apply a model that explicitly incorporates taxonomic effort over time to estimate the number of as-yet-unknown species. Second, we ask taxonomic experts their opinions on how many species are likely to be missing, on a family-by-family basis. The results are broadly comparable. We show that the current number of species should grow by between 10 and 20 per cent. There are, however, interesting discrepancies between expert and model estimates for some families, suggesting that our model does not always completely capture patterns of taxonomic activity. The as-yet-unknown species are probably similar to those taxonomists have described recently—overwhelmingly rare and local, and disproportionately in biodiversity hotspots, where there are high levels of habitat destruction.     

Community history affects the predictability of microbial ecosystem development

Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community''s previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications.     

A molecular survey of protist diversity through the central Arctic Ocean

The protist assemblage in the central Arctic Ocean is scarcely surveyed despite them being the major primary producers. Elucidating their response to changing environmental variables requires an a priori analysis of their current diversity, including abundant and rare species. In late summer 2011, samples were collected during the ARK-XXVI/3 expedition (RV Polarstern) to study Arctic protist community structures, by implementation of automated ribosomal intergenic spacer analysis (ARISA) and 454-pyrosequencing. Protist assemblages were related to the hydrology and environmental variables (temperature, salinity, ice coverage, nitrate, phosphate, and silicate). The abundant (≥1 %) biosphere and rare (<1 %) biosphere were considered separately in the diversity analysis in order to reveal their mutual relationships. A relation between hydrology and protist community structure was highly supported by ARISA and partially by 454-pyrosequencing. Sea ice showed a stronger influence on the local community structure than nutrient availability, making statements on the water mass influence more difficult. Dinoflagellates (Syndiniales), chlorophytes (Micromonas spp.), and haptophytes (Phaeocystis spp.) were important contributors to the abundant biosphere, while other dinoflagellates and stramenopiles dominated the rare biosphere. No significant correlation was found between the abundant and rare biosphere. However, relative contributions of major taxonomic groups revealed an unexpected stable community structure within the rare biosphere, indicating a potential constant protist reservoir. This study provides a first molecular survey of protist diversity in the central Arctic Ocean, focusing on the diversity and distribution of abundant and rare protists according to the environmental conditions, and can serve as baseline for future analysis.     

Sibling species of bean bruchids: a morphological and phylogenetic study of Acanthoscelides obtectus Say and Acanthoscelides obvelatus Bridwell

Acanthoscelides Schilsky is a large genus of neotropical bruchid beetles, in which most species show host plant specialization. Acanthoscelides obtectus and Acanthoscelides obvelatus are two sibling species specialized on Phaseolus beans, and are therefore considered pests. Up to now, the status of these two taxa has remained unclear, the few studies conducted having failed to elucidate whether these are two differentiated species or a single morphologically variable species. In addition, A. obvelatus has not been taken into account in the great majority of studies of bean bruchids. In this morphological and genetic study, we show that A. obtectus and A. obvelatus are two 'true' non-hybridizing species, which diverged about 22 Mya. Although the two species demonstrate only few morphological differences, we point out some diagnostic characters that enable their identification in the field. We also address a genetic method of differentiation of the two species, based on species-specific microsatellite loci. The strong morphological resemblance of these two species, despite their ancient divergence, may be the result of evolutionary stasis, which could be the consequence of stabilizing selection. Niche differentiation could enable the two species to coexist indefinitely.