Reconstructing the early evolution of Fungi using a six-gene phylogeny

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.     

Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the fungi

Pneumocystis carinii pneumonia is the most common opportunistic infection in AIDS, and accounts for significant morbidity and mortality in these and other immunocompromised patients. P. carinii is a eukaryotic microorganism of uncertain taxonomy that can infect numerous mammalian hosts. Developing from a small, unicellular 'trophozoite' into a 'cyst' containing eight 'sporozoites', its life cycle superficially resembles those seen both in the Protozoa and Fungi. Morphological and ultrastructural observations have lead some investigators to conclude that the organism is a protozoan, while others have felt that it more closely resembles a fungus. Phylogenetic relationships can be inferred from comparisons of macromolecular sequences. Small subunit ribosomal RNAs (16S-like rRNAs) are well-suited for this purpose because they have the same function in all organisms and contain sufficient information to estimate both close and distant evolutionary relationships. Phylogenetic frameworks based upon such comparisons reveal that the plant, animal and fungal lineages are distinct from the diverse spectrum of protozoan lineages. In this letter, phylogenetic analysis of Pneumocystis 16S-like rRNA demonstrates it to be a member of the Fungi.     

DNA条形码技术在菌物研究中的应用

生物DNA条形码是通过标准化的小片段DNA序列分析,进行物种快速鉴定的一项技术,目前已成为生物多样性和分类学研究的热点之一.尽管菌物在生物界中占据重要地位,但其DNA条形码研究明显滞后于动、植物.本文就生物DNA条形码的发展概况及其在菌物研究中的应用,特别是菌物DNA条形码标准序列选择、数据管理和分析、物种分化水平确定、新技术的应用等进行评述,并展望其研究和应用的前景,以期引起学术界和管理部门的关注,推进我国菌物DNA条形码的相关研究和应用领域的发展.     

The ring of life provides evidence for a genome fusion origin of eukaryotes

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteria.     

Cultivation of the ubiquitous SAR11 marine bacterioplankton clade

The alpha-proteobacterial lineage that contains SAR11 and related ribosomal RNA gene clones was among the first groups of organisms to be identified when cultivation-independent approaches based on rRNA gene cloning and sequencing were applied to survey microbial diversity in natural ecosystems. This group accounts for 26% of all ribosomal RNA genes that have been identified in sea water and has been found in nearly every pelagic marine bacterioplankton community studied by these methods. The SAR11 clade represents a pervasive problem in microbiology: despite its ubiquity, it has defied cultivation efforts. Genetic evidence suggests that diverse uncultivated microbial taxa dominate most natural ecosystems, which has prompted widespread efforts to elucidate the geochemical activities of these organisms without the benefit of cultures for study. Here we report the isolation of representatives of the SAR11 clade. Eighteen cultures were initially obtained by means of high-throughput procedures for isolating cell cultures through the dilution of natural microbial communities into very low nutrient media. Eleven of these cultures have been successfully passaged and cryopreserved for future study. The volume of these cells, about 0.01 micro m(3), places them among the smallest free-living cells in culture.     

Allometric degree distributions facilitate food-web stability

In natural ecosystems, species are linked by feeding interactions that determine energy fluxes and create complex food webs. The stability of these food webs enables many species to coexist and to form diverse ecosystems. Recent theory finds predator-prey body-mass ratios to be critically important for food-web stability. However, the mechanisms responsible for this stability are unclear. Here we use a bioenergetic consumer-resource model to explore how and why only particular predator-prey body-mass ratios promote stability in tri-trophic (three-species) food chains. We find that this 'persistence domain' of ratios is constrained by bottom-up energy availability when predators are much smaller than their prey and by enrichment-driven dynamics when predators are much larger. We also find that 97% of the tri-trophic food chains across five natural food webs exhibit body-mass ratios within the predicted persistence domain. Further analyses of randomly rewired food webs show that body mass and allometric degree distributions in natural food webs mediate this consistency. The allometric degree distributions hold that the diversity of species' predators and prey decreases and increases, respectively, with increasing species' body masses. Our results demonstrate how simple relationships between species' body masses and feeding interactions may promote the stability of complex food webs.     

Different responses of arbuscular mycorrhizal fungal community to day-time and night-time warming in a semiarid steppe

Arbuscular mycorrhizal （AM） fungi form mutualistic symbioses with most plant species and play important roles in ecosystems. Knowledge of the response of AM fungi to temperature change will improve our under- standing of the function of AM fungal community under global climate change scenarios in ecosystems. The effects of constant warming on AM fungal communities have been investigated previously, but responses to asymmetrical warming over 24-h periods have never been documented in natural ecosystems. In this study, we examined AM fungal communities in a full factorial design including day-time and night-time warming in a semiarid steppe in northern China. Day-time and 24-h warming, but not night-time warming, significantly increased AM fungal spore density. In contrast, none of the three warming regimes had a sig- nificant effect on AM fungal extra radical hyphal density. A total of 161 operational taxonomic units （OTUs） of AM fungi were recovered by 454 pyrosequencing of 18S rDNA. Day-time, night-time, and 24-h warming all significantly increased AM fungal OTU richness. Some AM fungal OTUs showed a significant bias toward day-time, night-time or 24-h warming. The AM fungal community composition was significantly affected by night-time warming, but not by day-time and 24-h warming. Our finding highlighted dif- ferent responses of AM fungal spore density and community composition to asymmetrical warming. This study might improve our understanding of ecosystem functioning of AM fungal community under global climate change scenarios in a semiarid steppe ecosystem.     

Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree

Although the relationship of angiosperms to other seed plants remains controversial, great progress has been made in identifying the earliest extant splits in flowering-plant phylogeny, with the discovery that the New Caledonian shrub Amborella trichopoda, the water lilies (Nymphaeales), and the woody Austrobaileyales constitute a basal grade of lines that diverged before the main radiation in the clade. By focusing attention on these ancient lines, this finding has re-written our understanding of angiosperm structural and reproductive biology, physiology, ecology and taxonomy. The discovery of a new basal lineage would lead to further re-evaluation of the initial angiosperm radiation, but would also be unexpected, as nearly all of the approximately 460 flowering-plant families have been surveyed in molecular studies. Here we show that Hydatellaceae, a small family of dwarf aquatics that were formerly interpreted as monocots, are instead a highly modified and previously unrecognized ancient lineage of angiosperms. Molecular phylogenetic analyses of multiple plastid genes and associated noncoding regions from the two genera of Hydatellaceae identify this overlooked family as the sister group of Nymphaeales. This surprising result is further corroborated by evidence from the nuclear gene phytochrome C (PHYC), and by numerous morphological characters. This indicates that water lilies are part of a larger lineage that evolved more extreme and diverse modifications for life in an aquatic habitat than previously recognized.     

真菌感染防控及真菌细胞壁靶标的研究进展

全球有超过10亿人患有真菌感染，每年有超过160万人因此而死亡，且真菌感染病例正呈激增趋势。此外，真菌病害不仅严重影响作物的生长，还会产生毒素影响农作物的质量，对农业生产带来严重影响。真菌的细胞壁结构在哺乳动物中不存在，且与植物细胞壁组分完全不同，因此成为开发抗真菌药物的理想靶标。本文详细阐述病原真菌对人类、动物和植物的风险，临床和农业上使用的抗真菌药物，以及真菌细胞壁不同组分在药物研发中的研究进展，并展望基于广西的天然资源在抗真菌药物研发中的潜在前景。     

A hydrogen-based subsurface microbial community dominated by methanogens.

The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16S ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.     

Adaptive radiation of multituberculate mammals before the extinction of dinosaurs

The Cretaceous-Paleogene mass extinction approximately 66 million years ago is conventionally thought to have been a turning point in mammalian evolution. Prior to that event and for the first two-thirds of their evolutionary history, mammals were mostly confined to roles as generalized, small-bodied, nocturnal insectivores, presumably under selection pressures from dinosaurs. Release from these pressures, by extinction of non-avian dinosaurs at the Cretaceous-Paleogene boundary, triggered ecological diversification of mammals. Although recent individual fossil discoveries have shown that some mammalian lineages diversified ecologically during the Mesozoic era, comprehensive ecological analyses of mammalian groups crossing the Cretaceous-Paleogene boundary are lacking. Such analyses are needed because diversification analyses of living taxa allow only indirect inferences of past ecosystems. Here we show that in arguably the most evolutionarily successful clade of Mesozoic mammals, the Multituberculata, an adaptive radiation began at least 20 million years before the extinction of non-avian dinosaurs and continued across the Cretaceous-Paleogene boundary. Disparity in dental complexity, which relates to the range of diets, rose sharply in step with generic richness and disparity in body size. Moreover, maximum dental complexity and body size demonstrate an adaptive shift towards increased herbivory. This dietary expansion tracked the ecological rise of angiosperms and suggests that the resources that were available to multituberculates were relatively unaffected by the Cretaceous-Paleogene mass extinction. Taken together, our results indicate that mammals were able to take advantage of new ecological opportunities in the Mesozoic and that at least some of these opportunities persisted through the Cretaceous-Paleogene mass extinction. Similar broad-scale ecomorphological inventories of other radiations may help to constrain the possible causes of mass extinctions.     

真菌细胞壁水解物对大豆幼苗生长的影响

制备了 3种真菌细胞壁水解物 ,分别对大豆种子进行诱导发芽处理。大豆幼苗上胚轴长、苗重较对照有明显增加 ,子叶状态较对照为好 ,真菌细胞壁水解物表现出对大豆幼苗促生长的作用     

烟曲霉细胞壁作为药物靶标的鉴定研究

烟曲霉(Aspergillus fumigatus)作为侵袭性真菌感染的三大机会病原真菌之一,因其高致病率和高致死率而成为威胁人类健康的重大隐患。有限的抗真菌类药物以及近年来耐药性菌株的涌现使得寻找新的药物靶标并开发新型抗真菌药物迫在眉睫。真菌细胞壁作为真菌所特有的结构一直以来被认为是理想的药物靶标。本文概述了烟曲霉细胞壁结构及合成过程的相关研究进展,并分析了参与细胞壁各组分合成的酶作为药靶的可行性。     

Articulated Palaeozoic fossil with 17 plates greatly expands disparity of early chitons

Modern chitons (Mollusca: Polyplacophora) possess a highly conserved skeleton of eight shell plates (valves) surrounded by spicules or scales, and fossil evidence suggests that the chiton skeleton has changed little since the first appearance of the class in the Late Cambrian period (about 500 million years before present, Myr bp). However, the Palaeozoic problematic taxon Multiplacophora, in spite of having a more complex skeleton, shares several derived characters with chitons. The enigmatic status of the Multiplacophora is due in part to the fact that its members had an exoskeleton of numerous calcium carbonate valves that usually separated after death. A new articulated specimen from the Carboniferous period (about 335 Myr bp) of Indiana reveals that multiplacophorans had a dorsal protective surface composed of head and tail valves, left and right columns of overlapping valves (five on each side), and a central zone of five smaller valves, all surrounded by an annulus of large spines. Here we describe and name the articulated specimen and present evidence that multiplacophorans were chitons. Thus the highly conserved body plan of living chitons belies the broad disparity of this clade during the Palaeozoic era.     

Characterization of a carbohydrate transporter from symbiotic glomeromycotan fungi

The symbiotic relationships between mycorrhizal fungi and plants have an enormous impact on terrestrial ecosystems. Most common are the arbuscular mycorrhizas, formed by fungi belonging to the phylum Glomeromycota. Arbuscular mycorrhizal fungi facilitate the uptake of soil nutrients by plants and in exchange obtain carbohydrates, thus representing a large sink for atmospheric plant-fixed CO(2). However, how carbohydrates are transported through the symbiotic interface is still unknown. Here we report the characterization of the first known glomeromycotan monosaccharide transporter, GpMST1, by exploiting the unique symbiosis of a glomeromycotan fungus (Geosiphon pyriformis) with cyanobacteria. The GpMST1 gene has a very low GC content and contains six introns with unusual boundaries. GpMST1 possesses twelve predicted transmembrane domains and functions as a proton co-transporter with highest affinity for glucose, then mannose, galactose and fructose. It belongs to an as yet uncharacterized phylogenetic monosaccharide transporter clade. This initial characterization of a new transporter family involved in fungal symbiosis will lead to a better understanding of carbon flows in terrestrial environments.     

Patterns of predation in a diverse predator-prey system

There are many cases where animal populations are affected by predators and resources in terrestrial ecosystems, but the factors that determine when one or the other predominates remain poorly understood. Here we show, using 40 years of data from the highly diverse mammal community of the Serengeti ecosystem, East Africa, that the primary cause of mortality for adults of a particular species is determined by two factors--the species diversity of both the predators and prey and the body size of that prey species relative to other prey and predators. Small ungulates in Serengeti are exposed to more predators, owing to opportunistic predation, than are larger ungulates; they also suffer greater predation rates, and experience strong predation pressure. A threshold occurs at prey body sizes of approximately 150 kg, above which ungulate species have few natural predators and exhibit food limitation. Thus, biodiversity allows both predation (top-down) and resource limitation (bottom-up) to act simultaneously to affect herbivore populations. This result may apply generally in systems where there is a diversity of predators and prey.     

Affinities of 'hyopsodontids' to elephant shrews and a Holarctic origin of Afrotheria

Macroscelideans (elephant shrews or sengis) are small-bodied (25-540 g), cursorial (running) and saltatorial (jumping), insectivorous and omnivorous placental mammals represented by at least 15 extant African species classified in four genera. Macroscelidea is one of several morphologically diverse but predominantly African placental orders classified in the superorder Afrotheria by molecular phylogeneticists. The distribution of modern afrotheres, in combination with a basal position for Afrotheria within Placentalia and molecular divergence-time estimates, has been used to link placental diversification with the mid-Cretaceous separation of South America and Africa. Morphological phylogenetic analyses do not support Afrotheria and the fossil record favours a northern origin of Placentalia. Here we describe fossil postcrania that provide evidence for a close relationship between North American Palaeocene-Eocene apheliscine 'hyopsodontid' 'condylarths' (early ungulates or hoofed mammals) and extant Macroscelidea. Apheliscine postcranial morphology is consistent with a relationship to other ungulate-like afrotheres (Hyracoidea, Proboscidea) but does not provide support for a monophyletic Afrotheria. As the oldest record of an afrothere clade, identification of macroscelidean relatives in the North American Palaeocene argues against an African origin for Afrotheria, weakening support for linking placental diversification to the break-up of Gondwana.     

AMF对间套作体系中植物-土壤-微生物相互作用的影响及机制

丛枝菌根真菌（AMF）能与自然环境中的多数陆生植物互利共生。间套作种植作为增加农田生态系统生物多样性的重要措施，能显著提高植物对农田环境中多种资源的利用率。在间套作体系中，AMF通过对农作物和土壤环境的影响，提高农田生态系统的经济产量并促进其可持续发展。本文从AMF对宿主植物根系特征的影响、AMF对宿主植物根际微生物群落结构功能的影响、AMF在改善土壤结构提高土壤肥力方面的作用、菌根植物间共生菌丝网络的养分资源传递分配等方面，阐述AMF对间套作体系中植物-土壤-微生物相互作用的影响及其机制，为AMF在农业方面的进一步应用提供理论基础。