Rooting theories of plant community ecology in microbial interactions

Predominant frameworks for understanding plant ecology have an aboveground bias that neglects soil micro-organisms. This is inconsistent with recent work illustrating the importance of soil microbes in terrestrial ecology. Microbial effects have been incorporated into plant community dynamics using ideas of niche modification and plant–soil community feedbacks. Here, we expand and integrate qualitative conceptual models of plant niche and feedback to explore implications of microbial interactions for understanding plant community ecology. At the same time we review the empirical evidence for these processes. We also consider common mycorrhizal networks, and propose that these are best interpreted within the feedback framework. Finally, we apply our integrated model of niche and feedback to understanding plant coexistence, monodominance and invasion ecology.

Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.

Long-term response of the nematode community to elevated atmospheric CO2 in a temperate dry grassland soil

Long-term effects of the elevated atmospheric CO2 on biosphere have been in focus of research since the last few decades. In this experiment undisturbed soil monoliths of loess grassland were exposed to an elevated CO2 environment (two-times the ambient CO2 level) for a period of six years with the aid of the open top chamber method. Control without a chamber and CO2 elevation was applied as well. Elevated CO2 level had very little impact oil soil food web. It did not influence either root and microbial biomass or microbial and nematode community structure. The only significant response was that density of the bacterial feeder genus Heterocephalobus increased in the chamber with elevated CO2 concentration. Application of the open top chambers initiated more changes on nematodes than the elevated CO2 level. Open top chamber (OTC) method decreased nematode density (total and plant feeder as well) to less than half of the original level. Negative effect was found on the genus level in the case of fungal feeder Aphelenchoides, plant feeder Helicotylenchus and Paratylenchus. It is very likely that the significantly lower belowground root biomass and partly its decreased quality reflected by the increased C/N ratio are the main responsible factors for the lower density of the plant feeder nematodes in the plots of chambers. According to diversity profiles, MI and MI(2-15) parameters, nematode communities in the open top chambers (both on ambient and elevated CO2 level) seem to be more structured than those under normal circumstances six years after start of the experiment.

Macrophyte community structure and species occurrence in relation to environmental determinants in the ephemeral aquatic habitats of Gavdos, Greece

The aims of this study were to explore the environmental factors that determine the distribution of plant communities in temporary rock pools and provide a quantitative analysis of vegetation-environment relationships for five study sites on the island of Gavdos, southwest of Crete, Greece. Data from 99 rock pools were collected and analysed using Two-Way Indicator Species Analysis (TWINSPAN), Detrended Correspondence Analysis (DCA) and Canonical Correspondence Analysis (CCA) to identify the principal communities and environmental gradients that are linked to community distribution. A total of 46 species belonging to 21 families were recorded within the study area. The dominant families were Labiatae, Gramineae and Compositae while therophytes and chamaephytes were the most frequent life forms. The samples were classified into six community types using TWINSPAN, which were also corroborated by CCA analysis. The principal gradients for vegetation distribution, identified by CCA, were associated with water storage and water retention ability, as expressed by pool perimeter and water depth. Generalised Additive Models (GAMs) were employed to identify responses of four dominant rock pool species to water depth. The resulting species response curves showed niche differentiation in the cases of Callitriche pulchra and Tillaea vaillantii and revealed competition between Zannichellia pedunculata and Chara vulgaris. The use of classification in combination with ordination techniques resulted in a good discrimination between plant communities. Generalised Additive Models are a powerful tool in investigating species response curves to environmental gradients. The methodology adopted can be employed for improving baseline information on plant community ecology and distribution in Mediterranean ephemeral pools.

How to be a fig wasp down under: the diversity and structure of an Australian fig wasp community

Endophytic insects and their parasitoids provide valuable models for community ecology. The wasp communities in inflorescences of fig trees have great potential for comparative studies, but we must first describe individual communities. Here, we add to the few detailed studies of such communities by describing the one associated with Ficus rubiginosa in Australia. First, we describe community composition, using two different sampling procedures. Overall, we identified 14 species of non-pollinating fig wasp (NPFW) that fall into two size classes. Small wasps, including pollinators, gallers and their parasitoids, were more abundant than large wasps (both galler and parasitoid species). We show that in figs where wasps emerge naturally, the presence of large wasps may partly explain the low emergence of small wasps. During fig development, large gallers oviposit first, before and around the time of pollination, while parasitoids lay eggs after pollination. We further show that parasitoids in the subfamily Sycoryctinae, which comprise the majority of all individual NPFWs, segregate temporally by laying eggs at different stages of fig development. We discuss our results in terms of species co-existence and community structure and compare our findings to those from fig wasp communities on other continents.

Land degradation and vegetation distribution in Chott El Beida wetland, Algeria

The aim of this study is to explore the environmental factors that determine plant Community distribution in northeast Algeria. This paper provides a quantitative analysis of the vegetation-environment relationships for a study site in the Cholt El Beida wetland, a RAMSAR site in Setif, Algeria. Sixty vegetation plots were sampled and analysed using TWINSPAN and Detrended Correspondence Analysis (DCA) in order to identify the principal vegetation communities and determine the environmental gradients associated with these. 127 species belonging to 41 families and 114 genera were recorded. Six of the recorded species were endemic representing 4.7% of the total species. The richest families were Compositae, Gramineae, Cruciferae and Chenopodiaceae. Therophytes and hemicryptophytes were the most frequent life forms. the Mediterranean floristic element is dominant and is represented by 39 species. The samples were classified into four main community types. The principal DCA axes represent gradients of soil salinity, moisture and anthropogenic pressure. The use of classification in combination with ordination techniques resulted in a good discrimination between plant communities and a greater understanding of controlling environmental factors. The methodology adopted can be employed for improving baseline information on plant community ecology and distribution in often critically endangered Mediterranean wetland areas. (C) 2008 Elsevier Ltd. All rights reserved.

Environmental factors and vegetation composition, Lefka Ori Massif, Crete, S. Aegean

Aim The aim of this study was to explore the environmental factors that determine the spatial distribution of oro-mediterranean and alti-mediterranean plant communities in Crete. Location The paper provides a quantitative analysis of vegetation-environment relationships for two study areas within the Lefka Ori massif Crete, a proposed Natura 2000 site. Methods Eleven environmental variables were recorded: altitude, slope, aspect, percentage of bare rock, percentage of unvegetated ground, soil depth, pH, organic matter content and percentages of sand, silt and clay content. Classification of the vegetation was based on twinspan, while detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to identify environmental gradients linked to community distribution. Results One hundred and twenty-five species were recorded from 120 plots located within the two study areas. Forty-seven of the recorded species are endemic, belonging to 35 families. Hemicryptophytes and chamaephytes were the most frequent, suggesting a typical oro-mediterranean life form spectrum. The samples were classified into five main community types and one transitional. The main gradients, identified by CCA, were altitude and surface cover type in the North-west site, while in the Central site the gradients were soil formation-development and surface cover type. Main conclusions The use of classification in combination with ordination techniques resulted in a good discrimination between plant communities and a greater understanding of controlling environmental factors. The methodology adopted can be employed for improving baseline information on plant community ecology and distribution in Mediterranean mountain zones.

Land degradation and vegetation distribution in Chott El Beida wetland, Algeria

The aim of this study is to explore the environmental factors that determine plant Community distribution in northeast Algeria. This paper provides a quantitative analysis of the vegetation-environment relationships for a study site in the Cholt El Beida wetland, a RAMSAR site in Setif, Algeria. Sixty vegetation plots were sampled and analysed using TWINSPAN and Detrended Correspondence Analysis (DCA) in order to identify the principal vegetation communities and determine the environmental gradients associated with these. 127 species belonging to 41 families and 114 genera were recorded. Six of the recorded species were endemic representing 4.7% of the total species. The richest families were Compositae, Gramineae, Cruciferae and Chenopodiaceae. Therophytes and hemicryptophytes were the most frequent life forms. the Mediterranean floristic element is dominant and is represented by 39 species. The samples were classified into four main community types. The principal DCA axes represent gradients of soil salinity, moisture and anthropogenic pressure. The use of classification in combination with ordination techniques resulted in a good discrimination between plant communities and a greater understanding of controlling environmental factors. The methodology adopted can be employed for improving baseline information on plant community ecology and distribution in often critically endangered Mediterranean wetland areas. (C) 2008 Elsevier Ltd. All rights reserved.

Host niches and defensive extended phenotypes structure parasitoid wasp communities

Oak galls are spectacular extended phenotypes of gallwasp genes in host oak tissues and have evolved complex morphologies that serve, in part, to exclude parasitoid natural enemies. Parasitoids and their insect herbivore hosts have coevolved to produce diverse communities comprising about a third of all animal species. The factors structuring these communities, however, remain poorly understood. An emerging theme in community ecology is the need to consider the effects of host traits, shaped by both natural selection and phylogenetic history, on associated communities of natural enemies. Here we examine the impact of host traits and phylogenetic relatedness on 48 ecologically closed and species-rich communities of parasitoids attacking gall-inducing wasps on oaks. Gallwasps induce the development of spectacular and structurally complex galls whose species- and generation-specific morphologies are the extended phenotypes of gallwasp genes. All the associated natural enemies attack their concealed hosts through gall tissues, and several structural gall traits have been shown to enhance defence against parasitoid attack. Here we explore the significance of these and other host traits in predicting variation in parasitoid community structure across gallwasp species. In particular, we test the "Enemy Hypothesis,'' which predicts that galls with similar morphology will exclude similar sets of parasitoids and therefore have similar parasitoid communities. Having controlled for phylogenetic patterning in host traits and communities, we found significant correlations between parasitoid community structure and several gall structural traits (toughness, hairiness, stickiness), supporting the Enemy Hypothesis. Parasitoid community structure was also consistently predicted by components of the hosts' spatiotemporal niche, particularly host oak taxonomy and gall location (e.g., leaf versus bud versus seed). The combined explanatory power of structural and spatiotemporal traits on community structure can be high, reaching 62% in one analysis. The observed patterns derive mainly from partial niche specialisation of highly generalist parasitoids with broad host ranges (>20 hosts), rather than strict separation of enemies with narrower host ranges, and so may contribute to maintenance of the richness of generalist parasitoids in gallwasp communities. Though evolutionary escape from parasitoids might most effectively be achieved via changes in host oak taxon, extreme conservatism in this trait for gallwasps suggests that selection is more likely to have acted on gall morphology and location. Any escape from parasitoids associated with evolutionary shifts in these traits has probably only been transient, however, due to subsequent recruitment of parasitoid species already attacking other host galls with similar trait combinations.

Phylogenies reveal predictive power of traditional medicine in bioprospecting

There is controversy about whether traditional medicine can guide drug discovery, and investment in ethnobotanically led research has fluctuated. One view is that traditionally used plants are not necessarily efficacious and there are no robust methods for distinguishing the ones that are most likely to be bioactive when selecting species for further testing. Here, we reconstruct a genus-level molecular phylogeny representing the 20,000 species found in the floras of three disparate biodiversity hotspots: Nepal, New Zealand and the Cape of South Africa. Borrowing phylogenetic methods from community ecology, we reveal significant clustering of the 1,500 traditionally used species, and provide a direct measure of the relatedness of the three medicinal floras. We demonstrate shared phylogenetic patterns across the floras: related plants from these regions are used to treat medical conditions in the same therapeutic areas. This strongly suggests independent discovery of plant efficacy, an interpretation corroborated by the presence of a significantly greater proportion of known bioactive species in these plant groups than in a random sample. Phylogenetic cross-cultural comparison can focus screening efforts on a subset of traditionally used plants that are richer in bioactive compounds, and could revitalise the use of traditional knowledge in bioprospecting.

Detecting local adaptation in widespread grassland species - the importance of scale and local plant community

1 Adaptation of plant populations to local environments has been shown in many species but local adaptation is not always apparent and spatial scales of differentiation are not well known. In a reciprocal transplant experiment we tested whether: (i) three widespread grassland species are locally adapted at a European scale; (ii) detection of local adaptation depends on competition with the local plant community; and (iii) local differentiation between neighbouring populations from contrasting habitats can be stronger than differentiation at a European scale. 2 Seeds of Holcus lanatus, Lotus corniculatus and Plantago lanceolata from a Swiss, Czech and UK population were sown in a reciprocal transplant experiment at fields that exhibit environmental conditions similar to the source sites. Seedling emergence, survival, growth and reproduction were recorded for two consecutive years. 3 The effect of competition was tested by comparing individuals in weeded monocultures with plants sown together with species from the local grassland community. To compare large-scale vs. small-scale differentiation, a neighbouring population from a contrasting habitat (wet-dry contrast) was compared with the 'home' and 'foreign' populations. 4 In P. lanceolata and H. lanatus, a significant home-site advantage was detected in fitness-related traits, thus indicating local adaptation. In L. corniculatus, an overall superiority of one provenance was found. 5 The detection of local adaptation depended on competition with the local plant community. In the absence of competition the home-site advantage was underestimated in P. lanceolata and overestimated in H. lanatus. 6 A significant population differentiation between contrasting local habitats was found. In some traits, this small-scale was greater than large-scale differentiation between countries. 7 Our results indicate that local adaptation in real plant communities cannot necessarily be predicted from plants grown in weeded monocultures and that tests on the relationship between fitness and geographical distance have to account for habitat-dependent small-scale differentiation. Considering the strong small-scale differentiation, a local provenance from a different habitat may not be the best choice in ecological restoration if distant populations from a more similar habitat are available.

Species divergence and trait convergence in experimental plant community assembly

Despite decades of research, it remains controversial whether ecological communities converge towards a common structure determined by environmental conditions irrespective of assembly history. Here, we show experimentally that the answer depends on the level of community organization considered. In a 9-year grassland experiment, we manipulated initial plant composition on abandoned arable land and subsequently allowed natural colonization. Initial compositional variation caused plant communities to remain divergent in species identities, even though these same communities converged strongly in species traits. This contrast between species divergence and trait convergence could not be explained by dispersal limitation or community neutrality alone. Our results show that the simultaneous operation of trait-based assembly rules and species-level priority effects drives community assembly, making it both deterministic and historically contingent, but at different levels of community organization.

Changing precipitation patterns alter plant community dynamics and succession in an ex-arable grassland

1. Changes in the frequency of extreme events, such as droughts, may be one of the most significant impacts of climate change for ecosystems. Models predict more frequent summer droughts in much of England: this paper investigates the impact on different types of plants in an ex-arable grassland community. 2. A long-term experiment simulated increased and decreased summer precipitation. Substantial interannual variation allowed the effects of summer drought to be tested in combination with wet and dry weather in other seasons. This is important, as climate models predict increased winter precipitation. 3. Total cover abundance in early summer increased with increasing water supply in the previous summer; there was no effect of winter precipitation. Productivity is therefore likely to decrease with more frequent summer droughts, with no mitigating effect of wetter winters. 4. The percentage cover of perennial grasses declined during a natural drought in 1995-97; this was exacerbated by the experimental drought treatment and reduced by supplemented rainfall. Simultaneously, short-lived ruderal species increased; this was greatest in drought treatments and least with supplemented rainfall. 4. These trends were subsequently reversed during several years of unusually wet weather, with perennial grasses increasing and short-lived forbs decreasing. This occurred even in experimentally droughted plots, and we propose that it resulted from rapid coverage of gaps during wet autumns and winters. 6. Deep-rooted species generally proved to be more drought resistant, but there were exceptions. 7. We conclude that increased frequency of summer droughts could have serious implications for the establishment and successional development of ex-arable grasslands. Increased winter precipitation would moderate the impact on species composition, but not on productivity.

Modulation of the microbial ecology of the human colon by probiotics, prebiotics and synbiotics to enhance human health: an overview of enabling science and potential applications

The application of probiotics and prebiotics to the manipulation of the microbial ecology of the human colon has recently seen many scientific advances. The sequencing of probiotic genomes is providing a wealth of new information on the biology of these microorganisms. In addition, we are learning more about the interactions of probiotics with human cells and with pathogenic bacteria. An alternative means of modulating the colonic microbial community is by the use of prebiotic oligosaccharides. Increasing knowledge of the metabolism of prebiotics by probiotics is allowing us to consider specifically targeting such dietary intervention tools at specific populatiori groups and specific disease states. (c) 2005 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

Coping with multiple enemies - the evolution of resistance and host-parasitoid community structure

Recent work has shown that the evolution of Drosophila melanogaster resistance to attack by the parasitoid Asobara tabida is constrained by a trade-off with larval competitive ability. However, there are two very important questions that need to be answered. First, is this a general cost, or is it parasitoid specific? Second, does a selected increase in immune response against one parasitoid species result in a correlated change in resistance to other parasitoid species? The answers to both questions will influence the coevolutionary dynamics of these species, and also may have a previously unconsidered, yet important, influence on community structure.