Endophytic fungal entomopathogens with activity against plant pathogens: ecology and evolution

Dual biological control, of both insect pests and plant pathogens, has been reported for the fungal entomopathogens, Beauveria bassiana (Bals.-Criv.) Vuill. (Ascomycota: Hypocreales) and Lecanicillium spp. (Ascomycota: Hypocreales). However, the primary mechanisms of plant disease suppression are different for these fungi. Beauveria spp. produce an array of bioactive metabolites, and have been reported to limit growth of fungal plant pathogens in vitro. In plant assays, B. bassiana has been reported to reduce diseases caused by soilborne plant pathogens, such as Pythium, Rhizoctonia, and Fusarium. Evidence has accumulated that B. bassiana can endophytically colonize a wide array of plant species, both monocots and dicots. B. bassiana also induced systemic resistance when endophytically colonized cotton seedlings were challenged with a bacterial plant pathogen on foliage. Species of Lecanicillium are known to reduce disease caused by powdery mildew as well as various rust fungi. Endophytic colonization has been reported for Lecanicillium spp., and it has been suggested that induced systemic resistance may be active against powdery mildew. However, mycoparasitism is the primary mechanism employed by Lecanicillium spp. against plant pathogens. Comparisons of Beauveria and Lecanicillium are made with Trichoderma, a fungus used for biological control of plant pathogens and insects. For T. harzianum Rifai (Ascomycota: Hypocreales), it has been shown that some fungal traits that are important for insect pathogenicity are also involved in biocontrol of phytopathogens.     

Deep space and hidden depths: understanding the evolution and ecology of fungal entomopathogens

Entomopathogens are important natural enemies of many insect and mite species and as such have been recognised as providing an important ecosystem service. Indeed, fungal entomopathogens have been widely investigated as biological control agents of pest insects in attempts to improve the sustainability of crop protection. However, even though our understanding of the ecology of fungal entomopathogens has vastly increased since the early 1800s, we still require in-depth ecological research that can expand our scientific horizons in a manner that facilitates widespread adoption of these organisms as efficient biological control agents. Fungal entomopathogens have evolved some intricate interactions with arthropods, plants and other microorganisms. The full importance and complexity of these relationships is only just becoming apparent. It is important to shift our thinking from conventional biological control, to an understanding of an as yet unknown “deep space”. The use of molecular techniques and phylogenetic analyses have helped us move in this direction, and have provided important insights on fungal relationships. Nevertheless, new techniques such as the PhyloChip and pyrosequencing might help us see beyond the familiar fields, into areas that could help us forge a new understanding of the ecology of fungal entomopathogens.     

Fungal entomopathogens: new insights on their ecology

An important mechanism for insect pest control should be the use of fungal entomopathogens. Even though these organisms have been studied for more than 100 y, their effective use in the field remains elusive. Recently, however, it has been discovered that many of these entomopathogenic fungi play additional roles in nature. They are endophytes, antagonists of plant pathogens, associates with the rhizosphere, and possibly even plant growth promoting agents. These findings indicate that the ecological role of these fungi in the environment is not fully understood and limits our ability to employ them successfully for pest management. In this paper, we review the recently discovered roles played by many entomopathogenic fungi and propose new research strategies focused on alternate uses for these fungi. It seems likely that these agents can be used in multiple roles in protecting plants from pests and diseases and at the same time promoting plant growth.     

Molecular ecology of fungal entomopathogens: molecular genetic tools and their applications in population and fate studies

The power of molecular genetic techniques to address ecological research questions has opened a distinct interdisciplinary research area collectively referred to as molecular ecology. Molecular ecology combines aspects of diverse research fields like population and evolutionary genetics, as well as biodiversity, conservation biology, behavioural ecology, or species-habitat interactions. Molecular techniques detect specific DNA sequence characteristics that are used as genetic markers to discriminate individuals or taxonomic groups, for instance in analyses of population and community structures, for elucidation of phylogenetic relationships, or for the characterization and monitoring of specific strains in the environment. Here, we summarize the PCR-based molecular techniques used in molecular ecological research on fungal entomopathogens and discuss novel techniques that may have relevance to the studies of entomopathogenic fungi in the future. We discuss the flow chart of the molecular ecology approaches and we highlight some of the critical steps involved. There are still many unresolved questions in the understanding of the ecology of fungal entomopathogens. These include population characteristics and relations of genotypes and habitats as well as host-pathogen interactions. Molecular tools can provide substantial support for ecological research and offer insight into this far inaccessible systems. Application of molecular ecology approaches will stimulate and accelerate new research in the field of entomophathogen ecology.     

Molecular approaches for AM fungal community ecology: A primer

Molecular techniques are no longer optional for ecologists interested in arbuscular mycorrhizal (AM) communities. Understanding the role of these soil fungi in natural systems requires knowledge of their abundance and identity but this is impossible to achieve without a molecular approach. Adapting molecular tools to AM fungi can be challenging because of the unique biology of the fungi. Moreover, many recruits in the field of mycorrhizal ecology have little or no experience with molecular biology. Here, we outline a conceptual framework for designing robust ecological experiments with AM fungi using molecular approaches.     

Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology

Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log-normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant-associated fungal communities - phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log-normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log-normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data - a log-normal model for the core group and a log-series model for the satellite group. The prominent log-series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.     

Population proteomics: an emerging discipline to study metapopulation ecology

Proteomics research has developed until recently in a relative isolation from other fast-moving disciplines such as ecology and evolution. This is unfortunate since applying proteomics to these disciplines has apparently the potential to open new perspectives. The huge majority of species indeed exhibit over their entire geographic range a metapopulation structure, occupying habitats that are fragmented and heterogeneous in space and/or through time. Traditionally, population genetics is the main tool used to studying metatopulations, as it describes the spatial structure of populations and the level of gene flow between them. In this Viewpoint, we present the reasons why we think that proteomics, because of the level of integration it promotes, has the potential to resolve interesting issues specific to metapopulation biology and adaptive processes.     

Insights from paleoecology to community ecology

Ecologists and paleoecologists have become increasingly aware that the temporal and spatial scales of the two disciplines overlap considerably and provide complementary information. Pollen and macrofossil evidence from thousands of radiocarbon-dated sites worldwide indicate that species respond to environmental change independently, that communities are relatively open assemblages, and that instability and change characterize Quaternary environments and biotas. The extended temporal view provided by paleoecology also enables detection of the occurrence, intensity and changing frequency of periodic and unique events such as disturbances and environmental fluctuations. As these insights contribute to our understanding of a dynamic environment and biota, they may help to increase our ability to anticipate future changes in communities.     

Levels of understanding in ecology: interspecific competition and community ecology

Abstract Ecological interpretation has been subject to several divisive controversies, involving, for example, the significance of density dependence and interspecific competition as ecological processes. Generally, resolution has been obtained through compromise and concensus or calls for yet more data. Essentially, both sides in the discussion are seen to have been correct to some extent. As a consequence the debates have been portrayed widely as having been sterile. We agree, but only because they have been conducted at a level so superficial that the relevance of the original criticisms to the theoretical structure of ecology has not been widely appreciated, nor resolved. Debate that deals with ecological generalizations must be conducted at a level appropriate to such aims.     

Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques

Fungi fulfil a range of important ecological functions, yet current understanding of fungal biodiversity in soil is limited. Direct DNA extraction from soil, coupled with polymerase chain reaction amplification and community profiling techniques, has proved successful in investigations of bacterial ecology and shows great promise for elucidating the taxonomic and functional characteristics of soil fungal communities. These community profiling techniques include denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism (SSCP), terminal restriction fragment length polymorphism (T-RFLP), amplified rDNA restriction analysis (ARDRA), amplified ribosomal intergenic spacer analysis (ARISA) and cloning, and are generally coupled with DNA sequencing. The techniques and their potential limitations are discussed, along with recent advances that have been made possible through their application in soil fungal ecology. It is unlikely that a single approach will be universally applicable for assessing fungal diversity in all soils or circumstances. However, judicious selection of the methodology, keeping the experimental aims in mind, and the exploitation of emerging technologies will undoubtedly increase our understanding of soil fungal communities in the future.     

Ecological considerations in producing and formulating fungal entomopathogens for use in insect biocontrol

Insect pests persist in a wide-variety of agricultural, arboreal and urban environments. Effective control with fungal entomopathogens using inundation biocontrol requires an understanding of the ecology of the target insect, fungal pathogen, and the insect-pathogen interaction. Historically, the development of production and formulation processes for biocontrol fungi has primarily focused on reducing costs by maximizing the yield of infective propagules, increasing storage stability, and improving product form for ease of application. These goals are critical for commercialization but are often in conflict with environmental and ecological considerations. Critical parameters for selecting a fungal pathogen for use in inundation biocontrol include the cost-effective production of a stable, infective propagule that is suited for use in the environment where the insect must be controlled. Production processes can be manipulated nutritionally and environmentally to produce efficacious propagules or to direct fungal differentiation to propagule forms that may be better suited for use in specific environments. Formulation development must also consider ecological and environmental factors to maximize biocontrol efficacy. A basic understanding of the surface chemistries of the fungal propagule and insect, the interactions between a fungal propagule and the insect cuticle that lead to infection, and the impact of the environment on this interaction can aid in the development of effective formulations.     

Occurrence and diversity of fungal entomopathogens in soils of low and high Arctic Greenland

Knowledge of the occurrence, distribution and diversity of pathogens of insects and arachnids (entomopathogens) in the Arctic is very limited. Climate change is expected to affect Arctic terrestrial arthropod communities and therefore also host–pathogen interactions, given that entomopathogens are present. We conducted a survey of fungal entomopathogens in soil samples collected at four localities in Greenland; two at low Arctic sites (Ritenbenk and Disko Island) and two at sites in the high Arctic (Zackenberg and Danmarkshavn). Fungi were isolated from soil samples using larvae of the insect species Galleria mellonella (Lepidoptera) and Tenebrio molitor (Coleoptera) as baits providing evidence that the fungal isolates were indeed entomopathogenic. Five fungal species (Ascomycota; Hypocreales) were found: Isaria fumosorosea Wize, Isaria farinosa (Holmsk.) Fr., Beauveria bassiana (Bals.) Vuill., Beauveria pseudobassiana Rehner and Humber and Tolypocladium inflatum W. Gams (syn.?=?T. niveum). I. farinosa was found at all four localities, while I. fumosorosea was detected in single samples at each of three localities including both high Arctic sites. Only the locality on Disko Island revealed B. bassiana, whereas B. pseudobassiana was isolated at the three other sites. T. inflatum was only found on Disko Island and only isolated with T. molitor as a bait insect. The results document that fungal entomopathogens are widely distributed in the soil environment in Greenland. Entomopathogens should therefore be included in future studies of arthropod ecology in the Arctic.     

Neutral theory and community ecology

I review the mathematical and biological aspects of Hubbell's (2001) neutral theory of species abundance for ecological communities, and clarify its historical connections with closely related approaches in population genetics. A selective overview of the empirical evidence for and against this theory is provided, with a special emphasis on tropical plant communities. The neutral theory predicts many of the basic patterns of biodiversity, confirming its heuristic power. The strict assumption of equivalence that defines neutrality, equivalence among individuals, finds little empirical support in general. However, a weaker assumption holds for stable communities, the equivalence of average fitness among species. One reason for the surprising success of the neutral theory is that all the theories of species coexistence satisfying the fitness equivalence assumption, including many theories of niche differentiation, generate exactly the same patterns as the neutral theory. Hubbell's neutral theory represents an important synthesis and a much needed demonstration of the pivotal role of intraspecific variability in ecology. Further improvements should lead to an explicit linking to niche‐based processes. This research programme will depend crucially on forthcoming theoretical and empirical achievements.     

Implications of empirical data quality to metapopulation model parameter estimation and application

Parameter estimation is a critical step in the use of any metapopulation model for predictive purposes. Typically metapopulation studies assume that empirical data are of good quality and any errors are so insignificant that they can be ignored. However, three types of errors occur commonly in metapopulation data sets. First, patch areas can be mis-estimated. Second, unknown habitat patches may be located within or around the study area. Third, there may be false zeros in the data set, that is, some patches were observed to be empty while there truly was a population in the patch. This study investigates biases induced into metapopulation model parameter estimates by these three types of errors. It was found that mis-estimated areas influence the scaling of extinction risk with patch area; extinction probabilities for large patches become overestimated. Missing patches cause overestimation of migration distances and colonization ability of the species. False zeros can affect very strongly all model components, the extinction risk in large patches, intrinsic extinction rates in general, migration distances and colonization ability may become all overestimated. Biases in parameter estimates translate into corresponding biases in model predictions, which are serious particularly if metapopulation persistence becomes overestimated. This happens for example when the migration capability of the species is overestimated. Awareness of these biases helps in understanding seemingly anomalous parameter estimation results. There are also implications for field work: it may be reasonable to allocate effort so that serious errors in data are minimized. It is particularly important to avoid observing false zeros for large and/or isolated patches.     

群落构建研究的新进展:进化和生态相结合的群落谱系结构研究

群落如何构建足群落生态学中的重要问题.群落谱系结构研究将物种间的亲缘进化关系运用到群落生态学研究中,利用物种的系统发育状况推测历史因素对现有群落的影响,为推断影响群落组成的生态学机制提供了有效方法.群落谱系结构的研究方法是首先建立可代表群落物种库的超级系统进化树,然后计算群落内物种间的谱系距离,最后通过统计方法检测其与随机模型下的谱系距离是否有显著差异来获得谱系结构(如谱系聚集、谱系发散),从而揭示群落构建中的关键生态过程(如生境过滤、竞争作用).群落谱系结构与空间尺度、分类群尺度、时间尺度等不同研究尺度有关.在小的空间尺度下,随着分类群尺度降低、树木年龄级增大,群落谱系结构从聚集逐渐转为发散;而随群落空间尺度的增大,谱系趋向于聚集.谱系结构受到环境因素影响,因此分析集合群落下的谱系可以揭示区域生态过程的影响.另外,群落谱系结构研究还有助于探讨中性理论、密度制约假说等生态学理论,并预测干扰作用下的群落演化趋势.在利用谱系结构深入探讨群落构建成因时,需要基于生态特征和环境变量共同分析,同时考虑小尺度局域过程(群落的微环境或群落内种间相互作用等)和大尺度区域过程(地史过程和物种形成等),并可结合生态控制实验,以确认群落构建的关键因素.在研究方法和手段上,今后需要注重通过选择合适的基因片段建立系统树,然后通过生态特征来加以校正,以更准确地反映物种间的亲缘距离.另外,获得谱系树后还需要寻找更加合理的统计模型和指数,增加统计分析和解决问题的能力.     

Dispersal and the metapopulation paradigm in amphibian ecology and conservation: are all amphibian populations metapopulations?

Amphibians are frequently characterized as having limited dispersal abilities, strong site fidelity and spatially disjunct breeding habitat. As such, pond‐breeding species are often alleged to form metapopulations. Amphibian species worldwide appear to be suffering population level declines caused, at least in part, by the degradation and fragmentation of habitat and the intervening areas between habitat patches. If the simplification of amphibians occupying metapopulations is accurate, then a regionally based conservation strategy, informed by metapopulation theory, is a powerful tool to estimate the isolation and extinction risk of ponds or populations. However, to date no attempt to assess the class‐wide generalization of amphibian populations as metapopulations has been made. We reviewed the literature on amphibians as metapopulations (53 journal articles or theses) and amphibian dispersal (166 journal articles or theses for 53 anuran species and 37 salamander species) to evaluate whether the conditions for metapopulation structure had been tested, whether pond isolation was based only on the assumption of limited dispersal, and whether amphibian dispersal was uniformly limited. We found that in the majority of cases (74%) the assumptions of the metapopulation paradigm were not tested. Breeding patch isolation via limited dispersal and/or strong site fidelity was the most frequently implicated or tested metapopulation condition, however we found strong evidence that amphibian dispersal is not as uniformly limited as is often thought. The frequency distribution of maximum movements for anurans and salamanders was well described by an inverse power law. This relationship predicts that distances beneath 11–13 and 8–9 km, respectively, are in a range that they may receive one emigrating individual. Populations isolated by distances approaching this range are perhaps more likely to exhibit metapopulation structure than less isolated populations. Those studies that covered larger areas also tended to report longer maximum movement distances – a pattern with implications for the design of mark‐recapture studies. Caution should be exercised in the application of the metapopulation approach to amphibian population conservation. Some amphibian populations are structured as metapopulations – but not all.