Estimating the growth potential of the soil protozoan community

We have developed a method for determining the potential abundance of free-living protozoa in soil. The method permits enumeration of four major functional groups (flagellates, naked amoebae, testate amoebae, and ciliates) and it overcomes some limitations and problems of the usual 'direct' and 'most probable number' methods. Potential abundance is determined using light microscopy, at specific time intervals, after quantitative re-wetting of air-dried soil with rain water. No exogenous carbon substrates or mineral nutrients are employed, so the protozoan community that develops is a function of the resources and inhibitors present in the original field sample. The method was applied to 100 soil samples (25 plots x 4 seasons) from an upland grassland (Sourhope, Southern Scotland) in the UK. Median abundances for all four functional groups lie close to those derived from the literature on protozoa living in diverse soil types. Flagellates are the most abundant group in soil, followed by the naked amoebae, then the testate amoebae and ciliates. This order is inversely related to typical organism size in each group. Moreover, preliminary evidence indicates that each functional group contains roughly the same number of species. All of these observations would be consistent with soil having fractal structure across the size-scale perceived by protozoa. The method described will be useful for comparing the effects on the soil protozoan community of different soil treatments (e.g. liming and biocides).     

Seed dispersal by changing frugivore assemblages: a mechanistic test of global change effects

In the face of global change it is important to understand how changes in species abundance and richness can affect ecosystem functions. Here we modelled seed dispersal by animals in a fragmented secondary forest of the Cantabrian Range (northwestern Iberian Peninsula), simulating the activity of six frugivorous bird species when dispersing three species of fleshy‐fruited trees. We calculated the density and richness of seeds deposited across a forested landscape, as well as the density of seeds arriving to open areas. We 1) study the complementarity of functional traits of each species with frugivore assemblages varying in species compositions (i.e. abundance and richness of bird assemblages), 2) identify those bird species whose functional roles are not redundant, and 3) explore the response of seed dispersal to random losses and to two non‐random bird loss scenarios (i.e. overhunting and fewer individuals from migrant species). We found that simulations with the avian composition observed in the field (i.e. with uneven abundances of six bird species) led to values of seed dispersal higher to those emerging from four bird species equally abundant. The selective removal of dominant bird species led to significant decays in seed dispersal, suggesting non‐redundant roles of abundant bird species. Seed dispersal decays were stronger under non‐random than random scenarios of bird loss. In terms of seed density, the functional decays also differed between the scenarios of overhunting and reduced arrival of migrant birds, notably beyond 50% changes in bird species composition. Our results illustrate the need to integrate species composition (controlling for bird abundance and richness) and their sensitivity to disturbances when predicting the impact of global change on ecosystem functions.     

Apparent global ubiquity of species in the protist genus Paraphysomonas

Evidence is presented for the ubiquity of protist species. Using the example of protists that leave traces (siliceous scales) of their recent population growth, we show that most - perhaps all species in the genus Paraphysomonas, are ubiquitous. Of the species recorded in surveys carried out worldwide, we have identified 78% of their number in 0.1 cm2 of sediment collected from a freshwater pond (total area 10(8) cm2) in England. Moreover, the pond appears to act like a microcosm of aquatic environments in general, for species that are globally rare or abundant, are likewise rare or abundant in the pond. We assume that the rate of neutral migration to the pond is greatest for the globally abundant species. As these species are probably capable of growth in a broad range of conditions, they will more frequently encounter the environment they require for population growth. Thus globally abundant species are also locally abundant in the pond - a pattern that will be amplified by periodic cyst production. Ubiquitous dispersal is probably driven by very high absolute abundance of individuals, and the water column of the pond was estimated to support >10(14) Paraphysomonas individuals. Ubiquity will dampen rates of speciation, and the evidence presented here indicates that global species richness of Paraphysomonas is indeed modest - perhaps close to what is already known.     

What is the upper size limit for cosmopolitan distribution in free‐living microorganisms?

A comparison of testate amoebae assemblages from the Arctic and Antarctic (areas of similar habitat a maximum distance apart) is used to try and answer the question ‘What is the upper size limit for cosmopolitan distribution in free‐living microbes?’ Species restricted to either the Arctic or Antarctic exhibited sizes up to 230 μm while the largest cosmopolitan species was 135 μm in size. Comparison of the testate assemblages using a multivariate classificatory technique (TWINSPAN ) also suggested more restricted distribution for the larger species. There was a negative relationship between species size and number of sites at which it was recorded (r_s=?0.261, P < 0.05), with all the more widespread species having a size of below 100 μm. It is suggested that for testate amoebae cosmopolitan distributions become common below 100–150 μm. This suggests that most species of testate (indeed most free‐living microbes) have low species richness because of lack of opportunities for allopatric speciation as most are below 100 μm and so geographical isolation is unlikely. It is suggested that if this is correct, only the largest free‐living microbes (> 150 μm) are likely to be of conservation concern because of their smaller ranges. However, I point out that currently different studies are giving very different answers to the question, how ubiquitous and species rich are free‐living microbes? The subject requires further work to try and reconcile these different results.     

Does microhabitat influence the testate amoebae communities in the Nameri National Park,northeastern India? A tropical forest perspective

The community structure of testate amoebae inhabiting different microhabitats (soil and tree-moss) within a tropical forest biome in Nameri National Park, northeastern India, was investigated. A total of 33 testate amoebae species belonging to 13 genera were identified. Species belonging to the class Lobosea constituted 73% of total testate amoebae density in the soil habitat, whereas the class Filosea constituted the most dominant forms (58%) in the moist tree-moss habitat. The relative abundance of species was higher in the tree-moss habitat compared to the soil habitats of the forest. Although multivariate analysis suggested a significant difference in assemblage patterns between the habitats, the turnover in species (i.e., beta diversity) was insignificant. Species accumulation curves (SAC) constructed using both parametric and non-parametric species richness estimators revealed that the asymptote of species richness was achieved by a low number of sample replicates in both habitats. The temperature and pH of the substratum on testate amoebae distribution patterns suggest the importance of additional background factors on testate amoebae community structure. Further studies involving more biotopes, seasons, and trophic interactions are recommended to document a complete record of testate amoebae diversity and their interactions with environmental gradients in the tropical forest biomes of northeastern India.     

Cochliopodium barki n. sp. (Rhizopoda, Himatismenida) re-isolated from soil 30 years after its initial description

A strain of Cochliopodium isolated from grassland soil at Sourhope Research Station (Scotland, UK) was found to be identical to the strain “Cochliopodium sp.2” studied by Bark in 1973. We name it Cochliopodium barki. It belongs to a group of species (comprising also C. minus and Cochliopodium sp. “NYS strain”) with very similar scale pattern.     

Influence of habitat characteristics on small mammals in a Mexican high-altitude grassland

Small mammals in a high-altitude grassland area close to Mexico City were studied. Populations of 10 species were censused using live traps in 48 sample quadrats. Within each quadrat, vegetation characterization, including complete floristic listings, cover values for species and layers and values of habitat modification, were assessed. Habitats were described according to plant communities identified using ordination and classification methods. Nine different plant communities were obtained. Densities and abundance of all small mammal species were calculated for each of the habitats classified. Peromyscus alsloni was the most abundant species in all habitats, reaching maximum densities of 55 ha⁻¹ in pine forest with dense ground and herb layer. Peromyscus melanotis also occurred in all habitats but at lower densities (maximum 29 ha⁻¹). Reithrodontomys megalotis was found in all habitats except in tall dense grassland. Densities for this species were generally low (1-9 ha⁻¹) but reached 19 ha⁻¹ in short dense grassland. All other species were largely absent from 4–8 habitats and showed very low densities (0.75–4 ha⁻¹). The densities of the more abundant species were largely correlated with more open habitats and higher indices of habitat modification. Lower altitude grassland habitats have a greater abundance of small mammals and a higher species richness than the medium and higher altitude, physiognomically more complex habitats. Species richness was highest in tall pine-alder forest with a species-rich, dense herb layer and lowest in pine forest with dense ground and herb layers. Species richness was positively correlated with overall small mammal density.     

Plant species richness,identity and productivity differentially influence key groups of microbes in grassland soils of contrasting fertility

The abundance of microbes in soil is thought to be strongly influenced by plant productivity rather than by plant species richness per se. However, whether this holds true for different microbial groups and under different soil conditions is unresolved. We tested how plant species richness, identity and biomass influence the abundances of arbuscular mycorrhizal fungi (AMF), saprophytic bacteria and fungi, and actinomycetes, in model plant communities in soil of low and high fertility using phospholipid fatty acid analysis. Abundances of saprophytic fungi and bacteria were driven by larger plant biomass in high diversity treatments. In contrast, increased AMF abundance with larger plant species richness was not explained by plant biomass, but responded to plant species identity and was stimulated by Anthoxantum odoratum. Our results indicate that the abundance of saprophytic soil microbes is influenced more by resource quantity, as driven by plant production, while AMF respond more strongly to resource composition, driven by variation in plant species richness and identity. This suggests that AMF abundance in soil is more sensitive to changes in plant species diversity per se and plant species composition than are abundances of saprophytic microbes.     

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

Microbes are the unseen majority in soil and comprise a large portion of life's genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogen-fixing bacteria are responsible for c. 5–20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.     

Testate amoebae communities in the southern tundra and forest-tundra of Western Siberia

The species composition and community structure of soil-inhabiting testate amoebae communities have been studied in biotopes of different types in the southern tundra and forest-tundra of the Tazovskaya Lowland, Western Siberia. A total of 93 species and forms have been identified. It has been found that the species richness of testate amoebae is much lower in dry than in moist biotopes due to a lower level of beta-diversity, with alpha diversity being the same (on average, 16.9 and 17.1 species per sample, respectively). Factors acting at the microbiotope level (biotope type and moisture) play the most important role in the formation of species richness; biotope features (soils and vegetation) are second in importance. In moist habitats, local communities of testate amoebae from different microbiotopes (mosses, lichens, or litter) are fairly similar in species structure, and communities from different moist biotopes are heterogeneous. In dry areas, the opposite situation is observed: local communities differ at the microbiotope level but are similar at the biotope level. The abundance of testate amoebae in moist biotopes reaches 200 × 10³ ind./g dry soil, being an order of magnitude lower in dry biotopes.     

2013年夏威夷东南部海区表层砂壳纤毛虫的群落结构和分布特征

鉴于东太平洋热带海区表层砂壳纤毛虫和其他微型浮游动物的群落结构资料几乎空白, 我们于2013年8月14日至9月18日在夏威夷东南部海区的23个站位采样调查了表层砂壳纤毛虫群落。23个站位共采集到砂壳纤毛虫22属36种, 均为透明壳种类。各站砂壳纤毛虫种丰富度范围为15-21种, 总丰度范围为4,730-23,693个/m³, 生物量范围为9.60-88.61 μg C/m³。本海区主要优势种为镯形囊坎虫(Ascampbelliella armilla)、斯廷细瓮虫(Steenstrupiella steenstrupii)、薄壳真铃虫(Eutintinnus tenuis)和纤弱细瓮虫(Steenstrupiella gracilis), 这4种主要优势种的口径范围不同。     

Species traits and environmental characteristics together regulate ant‐associated biodiversity

Host‐associated organisms (e.g., parasites, commensals, and mutualists) may rely on their hosts for only a portion of their life cycle. The life‐history traits and physiology of hosts are well‐known determinants of the biodiversity of their associated organisms. The environmental context may strongly influence this interaction, but the relative roles of host traits and the environment are poorly known for host‐associated communities. We studied the roles of host traits and environmental characteristics affecting ant‐associated mites in semi‐natural constructed grasslands in agricultural landscapes of the Midwest USA. Mites are frequently found in ant nests and also riding on ants in a commensal dispersal relationship known as phoresy. During nonphoretic stages of their development, ant‐associated mites rely on soil or nest resources, which may vary depending on host traits and the environmental context of the colony. We hypothesized that mite diversity is determined by availability of suitable host ant species, soil detrital resources and texture, and habitat disturbance. Results showed that that large‐bodied and widely distributed ant species within grasslands support the most diverse mite assemblages. Mite richness and abundance were predicted by overall ant richness and grassland area, but host traits and environmental predictors varied among ant hosts: mites associated with Aphaenogaster rudis depended on litter depth, while Myrmica americana associates were predicted by host frequency and grassland age. Multivariate ordinations of mite community composition constructed with host ant species as predictors demonstrated host specialization at both the ant species and genus levels, while ordinations with environmental variables showed that ant richness, soil texture, and grassland age also contributed to mite community structure. Our results demonstrate that large‐bodied, locally abundant, and cosmopolitan ant species are especially important regulators of phoretic mite diversity and that their role as hosts is also dependent on the context of the interaction, especially soil resources, texture, site age, and area.     

Testate amoebae community pattern in different types of boundary structures at the water-land contact zone

The patterns of changes in the species richness, abundance, species composition, and species structure of the testate amoebae community along six different types of water-land boundaries in the Medveditsa River (Don river Basin) were studied, namely, a new boundary, terrigenous and reogeneous edges, reogeneous and terrigenous hemiecotones, and the full ecotone. The testate amoebae communities are divided into terrestrial and aquatic variants for all types of boundaries. Hydrophilic species of the genera Arcella, Diffugia, Cyphoderia, and Pseudodifflugia dominate in the aquatic types of communities while pedobiont and eurybiont groups from the genera Centropyxis, Euglypha, Plagiopyxis, and Trinema are characteristic of the terrestrial communities. A decrease in the abundance and species richness of testate amoebae in the boundary zones was detected.     

Hypothesis: the rate and scale of dispersal of freshwater diatom species is a function of their global abundance

We have analysed the geographical records of a representative selection of extant diatom species from a freshwater pond. The more often a species is recorded in the ecological literature, the greater is its apparent global distribution. One explanation is that the frequently recorded species are globally abundant, whereas species that are infrequently recorded are globally rare. We suggest a model in which random dispersal is the dominant force driving large-scale distribution of species, with the rate and scale of dispersal largely determined by global population size. Thus species that are locally rare or abundant are likewise rare or abundant worldwide. It is predicted that many of the rarer diatom species will, with additional sampling effort, be shown to have wide geographical distribution, but this requires intensive studies focused on revealing species that are normally cryptic. The argument in favour of endemic diatom species is untenable, because it is not possible to disprove their existence elsewhere in the biosphere.     

Have we underestimated the importance of humans in the biogeography of free‐living terrestrial microorganisms?

The role of humans in the global dispersal of free‐living terrestrial microorganisms has received surprisingly little attention in the literature, compared with the frequent discussions of human dispersal for aquatic microbes. Here I argue that this area needs more study, using examples from the ecology of testate amoebae to illustrate the nature of the problem. The techniques of molecular ecology now make these ideas open to investigation in a way that would have been difficult in the past, and, in the case of testate amoebae, palaeoecological approaches may also be valuable.     

Ants and plants as indicators of biodiversity,ecosystem services,and conservation value in constructed grasslands

Grasslands are constructed for soil and wildlife conservation in agricultural landscapes across Europe and North America. Constructed grasslands may mitigate habitat loss for grassland-dependent animals and enhance ecosystem services that are important to agriculture. The responses of animal species richness and abundance to grassland habitat quality are often highly variable, however, and monitoring of multiple taxa is often not feasible. We evaluated whether multiple animal taxa responded to variation in constructed grassland habitats of southwest Ohio, USA, in ways that could be predicted from indicators based on quality assessment indices, Simpson diversity, and the species richness of ants and plants. The quality assessment indices included a widely used Floristic Quality Assessment (FQA) index, and a new Ant Quality Assessment (AntQA) index, both based on habitat specificity and species traits. The ant and plant indicators were used as predictor variables in separate general linear models of four target taxa—bees, beetles, butterflies and birds—with response variables of overall species richness and abundance, and subsets of taxa that included the abundance of ecosystem-service providers and grassland-associated species. Plant Simpson diversity was the best-fitting predictor variable in models of overall bee and beetle abundance, and the abundance of bees classified as ecosystem-service (ES) providers. FQA and plant richness were the best predictors of overall butterfly species richness and abundance. Ant species richness was the best predictor of overall bird species richness and abundance as well as the abundance of ES birds, while the AntQA index was the best predictor for the abundance of grassland bird and butterfly species. Thus, plant Simpson diversity and ant species richness were the most effective indicators for complementary components of grassland animal communities, whereas quality assessment indices were less robust as indicators and require more knowledge on the habitat specificity of individual ant and plant species.     

Sphagnum-dwelling testate amoebae in subarctic bogs are more sensitive to soil warming in the growing season than in winter: the results of eight-year field climate manipulations

Sphagnum-dwelling testate amoebae are widely used in paleoclimate reconstructions as a proxy for climate-induced changes in bogs. However, the sensitivity of proxies to seasonal climate components is an important issue when interpreting proxy records. Here, we studied the effects of summer warming, winter snow addition solely and winter snow addition together with spring warming on testate amoeba assemblages after eight years of experimental field climate manipulations. All manipulations were accomplished using open top chambers in a dry blanket bog located in the sub-Arctic (Abisko, Sweden). We estimated sensitivity of abundance, diversity and assemblage structure of living and empty shell assemblages of testate amoebae in the living and decaying layers of Sphagnum. Our results show that, in a sub-arctic climate, testate amoebae are more sensitive to climate changes in the growing season than in winter. Summer warming reduced species richness and shifted assemblage composition towards predominance of xerophilous species for the living and empty shell assemblages in both layers. The higher soil temperatures during the growing season also decreased abundance of empty shells in both layers hinting at a possible increase in their decomposition rates. Thus, although possible effects of climate changes on preservation of empty shells should always be taken into account, species diversity and structure of testate amoeba assemblages in dry subarctic bogs are sensitive proxies for climatic changes during the growing season.     

Are soil biota buffered against climatic extremes? An experimental test on testate amoebae in arctic tundra (Qeqertarsuaq,West Greenland)

Climate warming is likely to have pronounced impacts on soil biota in arctic ecosystems. In a warmer climate, heatwaves are more frequent and intense, but it is unclear to what extent soil communities are buffered against this. We studied the effects of an artificially induced heatwave on the structure of testate amoebae communities in dry heath tundra in Qeqertarsuaq (Disko Island, West Greenland) during the summer of 2003. While the heatwave was severe enough to induce significant leaf mortality in the aboveground vegetation, overall testate amoebae abundance did not react to the difference in temperature. However, in the heated plots transient shifts in species populations occurred during the exposure, followed by increases in species richness weeks after the heatwave had ended. The most important taxa appearing after the heating period belonged to bacterivorous genera, in agreement with a transient peak in bacterial colony forming units, caused by the heatwave. Lobose testate amoebae resisted the heating and its associated desiccation better than their filose counterparts.     

Diversity of Antarctic terrestrial protozoa

Heterotrophic protozoa have a global distribution in terrestrial habitats. The functional groups significantly represented are zooflagellates, cillates, gymnamoebae and testate amoebae. Their range extends into the Antarctic zone, but the species richness of the communities is rarely of the same order of magnitude as those in temperate latitudes. Species diversity is usually very low owing to dominance of the communities by single, or a few, species which are best adapted to the Antarctic terrestrial environment. This is characterized by seasonal, diurnal or unpredictable fluctuations in moisture, temperature and bacterial food supply of high amplitude. The fauna shows pauperization with latitude and climatic severity. Nearly all records of species distribution are consistent with the model that community composition is determined by local conditions. An important exception is the distribution of the testate amoeba genus Nebela whose species distribution is influenced by biogeographical factors. Successional changes in community composition in fellfield habitats are characterized by the sequence: pioneer microflagellate colonizers, larger flagellates and small ciliates, and finally testate amoebae. The succession is most closely correlated with the accumulation of organic matter. A model of the strategies of dominant microflagellate species can be constructed by ordinating them on a two-dimensional habitat template of A-r-K selection continuum. The globally ubiquitous microflagellate Heteromita globosa emerges as the most strongly A-selected and K-selected. The occurrence of terrestrial protozoa near their latitudinal limits of distribution can serve as sensitive indicators of the biological effects of climatic change. Having short generation times and effective means of cyst dispersal, changes in the gross distribution can provide rapid warning of critical changes in thermal regimes.     

Environmental factors influencing soil testate amoebae in herbaceous and shrubby vegetation along an altitudinal gradient in subarctic tundra (Abisko,Sweden)

Shifts in community composition of soil protozoa in response to climate change may substantially influence microbial activity and thereby decomposition processes. However, effects of climate and vegetation on soil protozoa remain poorly understood. We studied the distribution of soil testate amoebae in herbaceous and shrubby vegetation along an altitudinal gradient (from below the treeline at 500 m to the mid-alpine region at 900 m a.s.l.) in subarctic tundra. To explain patterns in abundance, species diversity and assemblage composition of testate amoebae, a data set of microclimate and soil chemical characteristics was collected. Both elevation and vegetation influenced the assemblage composition of testate amoebae. The variation was regulated by interactive effects of summer soil moisture, winter soil temperature, soil pH and nitrate ion concentrations. Besides, soil moisture regulated non-linear patterns in species richness across the gradient. This is the first study showing the effects of winter soil temperatures on species composition of soil protozoa. The effects could be explained by specific adaptations of testate amoebae such as frost-resistant cysts allowing them to survive low winter temperatures. We conclude that the microclimate and soil chemical characteristics are the main drivers of changes in protozoan assemblage composition in response to elevation and vegetation.