Diversity of Peronosporomycete (Oomycete) Communities Associated with the Rhizosphere of Different Plant Species

Peronosporomycete (oomycete) communities inhabiting the rhizospheres of three plant species were characterized and compared to determine whether communities obtained by direct soil DNA extractions (soil communities) differ from those obtained using baiting techniques (bait communities). Using two sets of Peronosporomycete-specific primers, a portion of the 5′ region of the large subunit (28S) rRNA gene was amplified from DNA extracted either directly from rhizosphere soil or from hempseed baits floated for 48 h over rhizosphere soil. Amplicons were cloned, sequenced, and then subjected to phylogenetic and diversity analyses. Both soil and bait communities arising from DNA amplified with a Peronosporomycetidae-biased primer set (Oom1) were dominated by Pythium species. In contrast, communities arising from DNA amplified with a Saprolegniomycetidae-biased primer set (Sap2) were dominated by Aphanomyces species. Neighbor-joining analyses revealed the presence of additional taxa that could not be identified with known Peronosporomycete species represented in GenBank. Sequence diversity and mean sequence divergence ( ) within bait communities were lower than the diversity within soil communities. Furthermore, the composition of Peronosporomycete communities differed among the three fields sampled and between bait and soil communities based on F_st and parsimony tests. The results of our study represent a significant advance in the study of Peronosporomycetes in terrestrial habitats. Our work has shown the utility of culture-independent approaches using 28S rRNA genes to assess the diversity of Peronosporomycete communities in association with plants. It also reveals the presence of potentially new species of Peronosporomycetes in soils and plant rhizospheres.     

Birds as marine–terrestrial linkages in sub-polar archipelagic systems: avian community composition, function and seasonal dynamics in the Cape Horn Biosphere Reserve (54–55°S), Chile

Marine environments are known to affect adjacent terrestrial biotic communities. In South America’s sub-Antarctic archipelago, birds are the most abundant and diverse terrestrial vertebrate assemblage. We hypothesized that birds would reflect a marine influence that would gradually decrease inland, expecting to find greater species richness, abundance, and biomass near the sea with decreases toward the island interior. We seasonally compared these parameters, with identified indicator species and assessed functional groups at 0, 150, and 300 m from the coast. Unexpectedly, we found a marked marine (0) and terrestrial (150–300) patterns for avian assemblages, rather than a gradient. In addition, seasonal patterns were warm (spring–summer) and cold (autumn–winter). The only parameter that displayed a true gradient was avian biomass in spring. During the cold season, higher values were observed in all variables for coastal assemblages, compared to inland sites. In the warm season, abundance and richness of coastal and terrestrial assemblages were similar, owing to migratory species. Milvago chimango was the only species abundant and frequent in both terrestrial and coastal systems, thereby indicating potential as a marine–terrestrial vector. Functionally, coastal assemblages were conformed of herbivores, carnivores, and scavengers, while terrestrial communities were made up of omnivores and insectivores. We conclude that the sea coast is a unique habitat in this archipelago, providing refuge for both marine and terrestrial sub-Antarctic birdlife particularly in the cold season. The relevance of the land/sea ecotone is poorly known, but important is given to high demand for the installation of salmon aquaculture facilities along the southern Chilean coastline.     

Disentangling the relative effects of ambient energy,water availability,and energy–water balance on pteridophyte species richness at a landscape scale in China

Understanding what factors generate geographic variation in species richness is a fundamental goal of ecology and biogeography. Water and energy are considered as the major environmental factors influencing large-scale patterns of species richness, but their roles vary among taxa and regions. Pteridophytes are an ideal group of organisms for examining the relationship between species richness and their environment because the distribution of pteridophytes is usually in equilibrium with contemporary climate to a greater degree than those of seed plants and most terrestrial vertebrates partly due to the lightness of their spores, which is highly capable of long-distance dispersal by wind, and partly due to their single-spore reproduction strategy. Using correlation and regression analyses and structural equation modeling technique, we examine the relationship of pteridophyte species richness in 151 localities from across China with environmental factors representing energy, water, and energy–water balance. We found that pteridophyte species richness is correlated to water availability more strongly than to ambient energy. Furthermore, we found that of all environmental variables considered, energy–water balance has played the most important role in regulating pteridophyte species richness gradients in China.     

Structure of Desert Rodent Communities: A Critical Review of Questions and Approaches

Three attributes of communities—the number, relative abundances,and phenotypic attributes of coexisting species—togetherdefine their "structure," as the term has been used in the literature.Most ecologists have tried to uncover determinants of communitystructure by analyzing patterns of morphology or resource use,or by experimentally manipulating the species composition orenvironmental context of communities. Less often used is a mechanisticanalysis of processes operating at the level of individualsor populations. I discuss the logical basis for each of these approaches andillustrate their virtues and limitations with examples drawnfrom work on heteromyid rodents. While pattern analytic andexperimental approaches have provided an efficient means ofidentifying proximate determinants of species number and relativeabundance, a mechanistic approach holds more promise for answeringquestions about the ultimate determinants of phenotypic patternswithin communities     

Distribution of Extensive nifH Gene Diversity Across Physical Soil Microenvironments

The diversity of nitrogen-fixing bacteria is well described for aquatic environments; however, terrestrial analyses remain mostly biased to rhizobial plant–microbe associations. We maximized the level of resolution for this study through the use of nucleotide sequence information extracted from a series of soil microenvironments, ranging from macroaggregates at 2000 μm to the clay fraction at <75 μm in diameter. In addition, we attempted to create an overview of the distribution of terrestrial nitrogen fixers across such microenvironments by combining culture-independent techniques with a suite of natural soil environments from uniquely different origins. Soil diazotroph diversity was analyzed phylogenetically for 600 terrestrial nifH sequences from 12 midsized clone libraries based on microenvironments of three separate soils across a global scale. Statistical analyses of nifH gene clone libraries were used to estimate coverage, establish degrees of sequence overlap, and compare cluster distributions. These analyses revealed an extensive diversity in a tropical (19 phylotypes) and an arctic soil (17 phylotypes), and moderate diversity in a temperate soil (11 phylotypes). Within each soil, comparisons across aggregate size fractions delineated nifH gene cluster shifts within populations and degrees of sequence overlap that ranged from significantly different (arctic, tropical) to significantly similar (temperate). We suggest that this is due to population separation across aggregates of different size classes, which results from differences in the temporal stability of aggregates as niches for microbial communities. This study not only provides new knowledge of the arrangement of diazotrophic communities at the soil microscale, but it also contributes to the underrepresented knowledge of soil nifH sequences in the public databases.     

Plant Community Composition as a Predictor of Regional Soil Carbon Storage in Alaskan Boreal Black Spruce Ecosystems

The boreal forest is the largest terrestrial biome in North America and holds a large portion of the world’s reactive soil carbon. Therefore, understanding soil carbon accumulation on a landscape or regional scale across the boreal forest is useful for predicting future soil carbon storage. Here, we examined the relationship between floristic composition and ecosystem parameters, such as soil carbon pools, the carbon-to-nitrogen (C/N) ratio of live black spruce needles, and normalized basal area increment (NBAI) of trees in black spruce communities, the most widespread forest type in the boreal forest of Alaska. Variability in ecosystem properties among black spruce stands was as large as that which had previously been documented among all forest types in the central interior of Alaska; we found an eightfold range in NBAI and fivefold range in mineral soil carbon and nitrogen pools. Acidic black spruce communities had significantly more carbon in the organic soil horizon than did nonacidic black spruce communities, but did not differ in any other measured ecosystem parameter. We explained 48% of the variation in total soil carbon with a combination of plant community indices and abiotic and biotic factors. Plant community composition was at least as effective as any single environmental factor or stand characteristic in predicting soil C pools in Alaskan black spruce ecosystems. We conclude that among the community properties analyzed, the presence of key groups of species, overall species composition, and diversity of certain functional types, especially Sphagnum moss species, are important predictors of soil carbon sequestration in the black spruce forest type.     

THE ECOLOGY OF SUBARCTIC MOLLUSCS IN THE LOWER NELSON RIVER SYSTEM, MANITOBA, CANADA

A total of 18 stream habitats were sampled on the Lower NelsonRiver system within the area bounded by 56°10'—50'Nand 93°50'—94°50'W, where discontinuous permafrostis present. Thirteen gastropod species were found, with a meancommunity species richness of 3.4. Gastropod richness was adverselyaffected by hydroelectric dams, but was positively correlatedwith macrophyte richness and proportion of clay in the sediments.Some interspecific associations were evident. Species proportionsin communities were related to sediment particle size, whichreflected amount of turbulence. Young were recruited into thepopulations until mid-September. (Received 22 April 1991; accepted 23 September 1991)     

Salmon subsidize an escape from a size spectrum

A general rule in ecology is that the abundance of species or individuals in communities sharing a common energy source decreases with increasing body size. However, external energy inputs in the form of resource subsidies can modify this size spectrum relationship. Here, we provide the first test of how a marine resource subsidy can affect size spectra of terrestrial communities, based on energy derived from Pacific salmon carcasses affecting a forest soil community beside streams in western Canada. Using both species-based and individual approaches, we found size structuring in this forest soil community, and transient community-wide doubling of standing biomass in response to energy pulses from Pacific salmon carcasses. One group of species were clear outliers in the middle of the size spectrum relationship: larval calliphorid and dryomyzid flies, which specialize on salmon carcasses, and which showed a tenfold increase in biomass in their size class when salmon were available. Thus, salmon subsidize their escape from the size spectrum. These results suggest that using a size-based perspective of resource subsidies can provide new insights into the structure and functioning of food webs.     

Evolution of Social Behavior in Spiders (Araneae; Eresidae and Theridiidae)

Whereas most spiders are asocial, species in eight familiesare known to live all their life in communities and are thus"permanent-social." Their special attributes are: tolerance,interattraction, and cooperation. These peculiarities must havebeen achieved step by step several times independently. Periodic-socialspiders have been studied as a link between asocial and permanent-socialspiders. In two families—the cribellate Eresidae and ecribellateTheridiidae—different steps of periodic sociality havebeen discovered, from brood-care to feeding by regurgitation.The comparative study of the phylogeny of social behavior inboth families uncovers remarkable convergences of patterns fromasocial to permanent-social via periodical-social species ofspiders.     

The species-pool hypothesis from a bryological perspective

Bryophytes form one-layered communities, which provide good opportunities to test predictions of the species pool hypothesis. The prediction that competitive exclusion occurs rarely, if at all, in established communities seems to hold for many types of bryophyte vegetation, but the drastic effects on local diversity of some invading exotic species suggests, that this may be partly due to the “ghost of competition past”. In a survey of bryophyte communities on earth banks, variation in species number per stand was rather larger than predicted by the species-pool hypothesis. Large differences in accessibility of the stands may have played an important role in this respect. Small-scale repeated chartings and permanent grid studies suggest, that competitive exclusion hardly ever occurs in a range of terrestrial bryophyte communities. Evidence for interspecific competition (as derived from small-scale association between behaviour — increase or decrease in grid cells — of species pairs) was equally rare, but this may have been due to interaction with positively density-dependent facilitation effects. However, a rigorous proof of the hypothesis that facilitation may prevent competitive exclusion is still lacking.     

Fungal diversity increases soil fungistasis and resistance to microbial invasion by a non resident species

Biodiversity decline is a major concern for ecosystem functioning. Recent research efforts have been mostly focused on terrestrial plants, while, despite their importance in both natural and artificial ecosystems, little is known about soil microbial communities. This work aims at investigating the effects of fungal species richness on soil invasion by non resident microbes. Synthetic fungal communities with a species diversity ranging from 1 to 8 were assembled in laboratory microcosms and used in three factorial experiments to assess the effect of diversity on soil fungistasis, microbial invasion of soil amended with plant litter and of plant rhizosphere. The capability of different microbes to colonize environments characterized by different resident microbial communities was measured. The number of microbial species in the microcosms positively affected soil fungistasis that was also induced more rapidly in presence of synthetic communities with more species. Moreover, the increase of resident fungal diversity dramatically reduced the invasibility of both soil and plant rhizosphere. We found lower variability of soil fungistasis and invasibility in microcosms with higher species richness of microbial communities. Our study pointed out the existence of negative relationships between fungal diversity and soil invasibility by non resident microbes. Therefore, the loss of microbial species may adversely affect ecosystem functionality under specific environmental conditions.     

Assessing abundance and diversity patterns of soil microarthropod assemblages in northern Victoria Land (Antarctica)

This study aimed to: (1) assess differences between two quantitative sampling methods of soil microarthropods (visual census vs. stone washing) in ice-free areas located along a latitudinal gradient (from 72°37′S to 74°42′S) in northern Victoria Land (Antarctica); (2) furnish preliminary results on the abundance and diversity of mites and springtails in the studied areas. Visual census yielded reliable density estimates for adult collembolans and larger prostigmatic mites but did not detect small species. The study updates the distribution of several mites, including the southernmost record of an Oribatida species at global scale. Species composition was correlated with latitude but the uneven abundance distribution and local high beta-diversity probably reflect habitat fragmentation and population isolation. Under this circumstance nested sampling design should be usefully employed. Priorities and suitable methods for studying terrestrial microarthropod communities in continental Antarctica are discussed.     

Development of a diverse epiphyte community in response to phosphorus fertilization

The role of terrestrial soil nutrient supply in determining the composition and productivity of epiphyte communities has been little investigated. In a montane Hawaiian rainforest, we documented dramatic increases in the abundance and species richness of canopy epiphytes in a forest that had been fertilized annually with phosphorus (P) for 15 years; there was no response in forest that had been fertilized with nitrogen (N) or other nutrients. The response of N-fixing lichens to P fertilization was particularly strong, although mosses and non-N-fixing lichens also increased in abundance and diversity. We show that enhancement of canopy P availability is the most likely factor driving the bloom in epiphytes. These results provide strong evidence that terrestrial soil fertility may structure epiphyte communities, and in particular that the abundance of N-fixing lichens – a functionally important epiphyte group – may be particularly sensitive to ecosystem P availability.     

Environmental and plant community determinants of species loss following nitrogen enrichment

Global energy use and food production have increased nitrogen inputs to ecosystems worldwide, impacting plant community diversity, composition, and function. Previous studies show considerable variation across terrestrial herbaceous ecosystems in the magnitude of species loss following nitrogen (N) enrichment. What controls this variation remains unknown. We present results from 23 N-addition experiments across North America, representing a range of climatic, soil and plant community properties, to determine conditions that lead to greater diversity decline. Species loss in these communities ranged from 0 to 65% of control richness. Using hierarchical structural equation modelling, we found greater species loss in communities with a lower soil cation exchange capacity, colder regional temperature, and larger production increase following N addition, independent of initial species richness, plant productivity, and the relative abundance of most plant functional groups. Our results indicate sensitivity to N addition is co-determined by environmental conditions and production responsiveness, which overwhelm the effects of initial community structure and composition.     

The cyanobacterial community of polygon soils at an inland Antarctic nunatak

Inland Antarctic terrestrial ecosystems and biodiversity are poorly understood in comparison with Antarctic coastal regions. Microorganisms, as primary colonists, are integral to Antarctic soil ecosystem development, essential for pedogenesis and structuring the soil, and providing the nutrients necessary for the subsequent establishment of macroorganisms. This study analysed the microbial communities present in polygon soils of Coal Nunatak (Alexander Island, at the southern limit of the maritime Antarctic). Soils were analysed across three polygons (centre and margins) and at three depths (0–1, 1–2, 2–5 cm). Cyanobacterial communities were characterised using two complementary molecular biological approaches, temperature gradient gel electrophoresis and clone library analysis. The three polygons exhibited conspicuous differences in community composition, both between different polygons and spatially (horizontally and vertically) within a single polygon. Comparison of our data with that from previous studies using classical culture and morphological identification techniques clearly shows the need for more intensive research on patterns of microbial diversity in terrestrial habitats throughout the Antarctic. The majority of the 17 cyanobacterial genera identified at Coal Nunatak are thought to have ubiquitous distributions, while none are known only from the Antarctic. Three of the genera present are also known to be capable of being lichen photobionts.     

三江平原农田地表和地下土壤螨类丰富度与环境因子的空间关联性

地表和地下土壤动物群落空间格局及其与环境因子的空间作用关系,是揭示地表-地下生态系统格局与过程及生物多样性维持机制的重要基础。于2011年在三江平原农田生态系统,在50m×50m的空间尺度内,基于地统计空间分析方法,揭示地表和地下土壤螨群落及不同螨类物种丰富度的空间格局,并分析这种空间格局与土壤含水量、土壤p H值及大豆株高空间格局的空间关联性。半方差函数和普通克里格插值表明,8月份地表、地下和10月份地下螨群落及这些群落内大部分螨类物种在特定空间尺度内形成集群,表现为空间异质性特征,且这种空间分异多由结构性因素或结构性因素和随机性因素共同调控。交叉方差函数表明,土壤螨群落和不同螨类物种的空间格局与环境因子的空间格局在多种尺度上表现出复杂的空间关联性(正的或负的)。但简单Mantel检验仅发现8月份地表中气门亚目未定种1(Mesostigmata unidentified sp.1)和大豆株高存在明显的正的空间关联性。研究结果表明地下螨群落和生长季节的地表螨群落具有明显的空间异质性结构,地表和地下螨群落及大多数螨类物种丰富度与土壤含水量、土壤p H值及大豆株高的空间关联性并不显著。促进地表-地下生态系统土壤动物群落空间格局研究,为地表-地下格局与过程研究奠定基础。     

Does the Existence of Bird's Nest Ferns Enhance the Diversity of Oribatid (Acari: Oribatida) Communities in a Subtropical Forest?

We examined the effects of the presence of bird's nest ferns on the species diversity of oribatid mites in the whole forest in terms of the three categories of species diversity (α-, β-, and γ-diversity) in a subtropical forest in south-western Japan. The species diversity (1 − D) of oribatid communities in the ferns was significantly lower than those in bark of trees and the forest-floor litter and soil, and was similar to that in the branches. The oribatid faunas in the litter in and the roots of the fern were more similar to those in both the forest-floor litter and soil than to the faunas in the other arboreal habitats. However, the ferns can be colonized by endemic oribatid species specialized to such environments. The number of oribatid species estimated for a hypothetical stand with no ferns was about 180 species from 80 samples; this value did not differ significantly from that in another hypothetical stand with ferns (ca. 190 species). Thus, the species richness of oribatid communities estimated for the whole forest (the γ-diversity) was not affected by the presence or absence of bird's nest ferns. The α- and β-diversities of oribatid communities on bird's nest ferns were lower than those in other habitats, and they might not dramatically raise the overall γ-diversity of invertebrate communities in the whole forest. The bird's nest ferns, however, can generate a unique habitat for specialized species, and this would help to maintain species diversities of invertebrates at the whole-forest scale in subtropical forests.     

Strong associations between plant genotypes and bacterial communities in a natural salt marsh

Although microbial communities have been shown to vary among plant genotypes in a number of experiments in terrestrial ecosystems, relatively little is known about this relationship under natural conditions and outside of select model systems. We reasoned that a salt marsh ecosystem, which is characterized by twice‐daily flooding by tides, would serve as a particularly conservative test of the strength of plant–microbial associations, given the high degree of abiotic regulation of microbial community assembly resulting from alternating periods of inundation and exposure. Within a salt marsh in the northeastern United States, we characterized genotypes of the foundational plant Spartina alterniflora using microsatellite markers, and bacterial metagenomes within marsh soil based on pyrosequencing. We found significant differences in bacterial community composition and diversity between bulk and rhizosphere soil, and that the structure of rhizosphere communities varied depending on the growth form of, and genetic variation within, the foundational plant S. alterniflora. Our results indicate that there are strong plant–microbial associations within a natural salt marsh, thereby contributing to a growing body of evidence for a relationship between plant genotypes and microbial communities from terrestrial ecosystems and suggest that principles of community genetics apply to this wetland type.     

Interpreting co-variation in species richness and productivity in terrestrial vegetation: Making sense of causations and correlations at multiple scales

This commentary examines conventional and recent ideas regarding the interpretation of species richness-productivity relationships (SRPR) in terrestrial vegetation. A new conceptual modelling approach — cascading graph diagrams — is used to search for maximum parsimony by distilling and clarifying synthetic linkages between several potential causes of variation and co-variation in these two vegetation attributes at three distinctly different spatial scales: global/continental scale (variation between climatic/geographic regions within a continent, or across latitudes); regional scale (variation between local communities representing different habitat (soil) fertility types or different habitat disturbance levels within a climatic/geographic region); and local community scale (variation between neighbourhood plots within a particular plant community/habitat). In contrast with a number of interpretations in recent literature, the approach developed here emphases that SRPR at each scale in terrestrial vegetation involve a “cascade” of several intermediary causational variables that have not been generally accounted for in previous studies of SRPR. Accordingly, SRPR are expected usually to be correlational, sometimes indirectly causational, but never directly causational, at any scale. Rather than suggesting that causational mechanisms “scale up”, the analysis here illustrates that several mechanistic features may be shared across scales and that in some cases, mechanisms may “scale down”. This has crucial implications for identifying testable and un-confounded hypotheses for future research and for selecting effective experimental designs and appropriate methods of data analyses for the interpretation of SRPR in natural vegetation.     

Variation between freshwater and terrestrial fungal communities on decaying bamboo culms

Fungal communities on decaying culms of a bamboo host (Phyllostachys bambusoides) from freshwater and adjacent terrestrial habitats were identified. Collections were made at Xiao Bai Long Mountain, Yiliang, Yunnan, China in the winter and summer. In each collection, 100 similar-sized bamboo culms were collected, comprising 50 submerged samples from a stream and 50 terrestrial samples from adjacent riparian vegetation. A total of 82 fungal taxa were recorded from the samples, including 30 ascomycetes and 52 anamorphic fungi. The frequency of occurrence of these fungi were recorded and the Shannon–Weiner indices (H′) were applied to evaluate fungal diversity. The results showed that variation of the fungal diversity between the summer and winter collections was insignificant (0.2<p<0.5). Fungal diversity on submerged bamboo however, was significantly higher than that on terrestrial bamboo (p<0.001). Further findings were that: (1) some commonly recorded freshwater and terrestrial taxa were found in both habitats, but overall there were only 15 overlapping species between the two habitats; (2) the dominant species in each habitat were considerably different, and (3) only a few fungi were dominant, while most species were rare, being recorded only once or twice. Factors responsible for the distribution patterns and variations in composition of the fungal communities are discussed.