Liang-Dong Guo

Global diversity and geography of soil fungi

Introduction The kingdom Fungi is one of the most diverse groups of organisms on Earth, and they are integral ecosystem agents that govern soil carbon cycling, plant nutrition, and pathology. Fungi are widely distributed in all terrestrial ecosystems, but the distribution of species, phyla, and functional groups has been poorly documented. On the basis of 365 global soil samples from natural ecosystems, we determined the main drivers and biogeographic patterns of fungal diversity and community composition. Direct and indirect effects of climatic and edaphic variables on plant and fungal richness. Line thickness corresponds to the relative strength of the relationships between the variables that affect species richness. Dashed lines indicate negative relationships. MAP, mean annual precipitation; Fire, time since last fire; Dist. equator, distance from the equator; Ca, soil calcium concentration; P, soil phosphorus concentration; pH, soil pH. Rationale We identified soil-inhabiting fungi using 454 Life Sciences (Branford, CN) pyrosequencing and through comparison against taxonomically and functionally annotated sequence databases. Multiple regression models were used to disentangle the roles of climatic, spatial, edaphic, and floristic parameters on fungal diversity and community composition. Structural equation models were used to determine the direct and indirect effects of climate on fungal diversity, soil chemistry, and vegetation. We also examined whether fungal biogeographic patterns matched paradigms derived from plants and animals—namely, that species’ latitudinal ranges increase toward the poles (Rapoport’s rule) and diversity increases toward the equator. Last, we sought group-specific global biogeographic links among major biogeographic regions and biomes using a network approach and area-based clustering. Results Metabarcoding analysis of global soils revealed fungal richness estimates approaching the number of species recorded to date. Distance from equator and mean annual precipitation had the strongest effects on richness of fungi, including most fungal taxonomic and functional groups. Diversity of most fungal groups peaked in tropical ecosystems, but ectomycorrhizal fungi and several fungal classes were most diverse in temperate or boreal ecosystems, and many fungal groups exhibited distinct preferences for specific edaphic conditions (such as pH, calcium, or phosphorus). Consistent with Rapoport’s rule, the geographic range of fungal taxa increased toward the poles. Fungal endemicity was particularly strong in tropical regions, but multiple fungal taxa had cosmopolitan distribution. Conclusions Climatic factors, followed by edaphic and spatial patterning, are the best predictors of soil fungal richness and community composition at the global scale. Richness of all fungi and functional groups is causally unrelated to plant diversity, with the exception of ectomycorrhizal root symbionts, suggesting that plant-soil feedbacks do not influence the diversity of soil fungi at the global scale. The plant-to-fungi richness ratio declined exponentially toward the poles, indicating that current predictions—assuming globally constant ratios—overestimate fungal richness by 1.5- to 2.5-fold. Fungi follow similar biogeographic patterns as plants and animals, with the exception of several major taxonomic and functional groups that run counter to overall patterns. Strong biogeographic links among distant continents reflect relatively efficient long-distance dispersal compared with macro-organisms. Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework. Global metagenomics detects hotspots of fungal diversity and macroecological patterns and indicates that plant and fungal diversity are uncoupled. [Also see Perspective by Wardle and Lindahl] Assessing fungal diversity worldwide Fungi are hyperdiverse but poorly known, despite their ecological and economic impacts. Tedersoo et al. collected nearly 15,000 topsoil samples from 365 sites worldwide and sequenced their genomes (see the Perspective by Wardle and Lindahl). Overall, they found a striking decline in fungal species richness with distance from the equator. For some specialist groups though, diversity depended more on the abundance of host plants than host diversity or geography. The findings reveal a huge gap between known and described species and the actual numbers of distinct fungi in the worlds soils. Science, this issue 10.1126/science.1256688; see also p. 1052

Community assembly during secondary forest succession in a Chinese subtropical forest

Subtropical broad-leaved forests in southeastern China support a high diversity of woody plants. Using a comparative study design with 30 × 30 m plots (n = 27) from five successional stages ( 1 m in height in each plot and counted all woody recruits (bank of all seedlings ≤1 m in height) in each central 10 × 10 m quadrant of each plot. In addition, we measured a number of environmen...

Pestalotiopsis—morphology, phylogeny, biochemistry and diversity

The genus Pestalotiopsis has received considerable attention in recent years, not only because of its role as a plant pathogen but also as a commonly isolated endophyte which has been shown to produce a wide range of chemically novel diverse metabolites. Classification in the genus has been previously based on morphology, with conidial characters being considered as important in distinguishing species and closely related genera. In this review, Pestalotia, Pestalotiopsis and some related genera are evaluated; it is concluded that the large number of described species has resulted from introductions based on host association. We suspect that many of these are probably not good biological species. Recent molecular data have shown that conidial characters can be used to distinguish taxa; however, host association and geographical location is less informative. The taxonomy of the genera complex remains confused. There are only a few type cultures and, therefore, it is impossible to use gene sequences in GenBank to clarify species names reliably. It has not even been established whether Pestalotia and Pestalotiopsis are distinct genera, as no isolates of the type species of Pestalotia have been sequenced, and they are morphologically somewhat similar. When selected GenBank ITS accessions of Pestalotiopsis clavispora, P. disseminata, P. microspora, P. neglecta, P. photiniae, P. theae, P. virgatula and P. vismiae are aligned, most species cluster throughout any phylogram generated. Since there appears to be no living type strain for any of these species, it is unwise to use GenBank sequences to represent any of these names. Type cultures and sequences are available for the recently described species P. hainanensis, P. jesteri, P. kunmingensis and P. pallidotheae. It is clear that the important species in Pestalotia and Pestalotiopsis need to be epitypified so that we can begin to understand the genus/genera. There are numerous reports in the literature that various species produce taxol, while others produce newly discovered compounds with medicinal potential and still others cause disease. The names assigned to these novel compound-producing taxa lack an accurate taxonomic basis, since the taxonomy of the genus is markedly confused. Until the important species have been epitypified with living strains that have been sequenced and deposited in public databases, researchers should refrain from providing the exact name of species.

Antifungal Metabolites from the Plant Endophytic Fungus Pestalotiopsis foedan

Pestafolide A ( 1), a new reduced spiro azaphilone derivative, and pestaphthalides A ( 2) and B ( 3), two new isobenzofuranones, have been isolated form solid cultures of an isolate of Pestalotiopsis foedan. The structures of these compounds were determined mainly by analysis of their NMR spectroscopic data. The relative configuration of 1- 3 was assigned by analysis of (1)H NMR J-values and NOESY data, and the absolute configuration was determined by application of the CD excitation chirality and modified Mosher method. Compounds 1- 3 showed modest antifungal activity.

Designing forest biodiversity experiments: general considerations illustrated by a new large experiment in subtropical China

Summary 1. Biodiversity–ecosystem functioning (BEF) experiments address ecosystem-level consequences of species loss by comparing communities of high species richness with communities from which species have been gradually eliminated. BEF experiments originally started with microcosms in the laboratory and with grassland ecosystems. A new frontier in experimental BEF research is manipulating tree diversity in forest ecosystems, compelling researchers to think big and comprehensively. 2. We present and discuss some of the major issues to be considered in the design of BEF experiments with trees and illustrate these with a new forest biodiversity experiment established in subtropical China (Xingangshan, Jiangxi Province) in 2009/2010. Using a pool of 40 tree species, extinction scenarios were simulated with tree richness levels of 1, 2, 4, 8 and 16 species on a total of 566 plots of 25� 8 9 25� 8m each. 3. The goal of this experiment is to estimate effects of tree and shrub species richness on carbon storage and soil erosion; therefore, the experiment was established on sloped terrain. The following important design choices were made: (i) establishing many small rather than fewer larger plots, (ii) using high planting density and random mixing of species rather than lower planting density and patchwise mixing of species, (iii) establishing a map of the initial ‘ecoscape’ to characterize site heterogeneity before the onset of biodiversity effects and (iv) manipulating tree species richness not only in random but also in trait-oriented extinction scenarios. 4. Data management and analysis are particularly challenging in BEF experiments with their hierarchical designs nesting individuals within-species populations within plots within-species compositions. Statistical analysis best proceeds by partitioning these random terms into fixed-term contrasts, for example, species composition into contrasts for species richness and the presence of particular functional groups, which can then be tested against the remaining random variation among compositions. 5. We conclude that forest BEF experiments provide exciting and timely research options. They especially require careful thinking to allow multiple disciplines to measure and analyse data jointly and effectively. Achiev

Pestalazines and Pestalamides, Bioactive Metabolites from the Plant Pathogenic Fungus Pestalotiopsis theae

Pestalazines A (1) and B (2), two new diketopiperazine heterodimers, and pestalamides A-C (3-5), three new amides, have been isolated from cultures of the plant pathogenic fungus Pestalotiopsis theae. The structures of these compounds were elucidated mainly by NMR spectroscopy. The absolute configurations of 1 and 2 were determined using Marfeys method on their acid hydrolysates and by comparison of their CD spectra with that of a model compound. Compounds 1, 3, and 6 displayed inhibitory effects on HIV-1 replication in C8166 cells. Compound 3 also showed potent antifungal activity against Aspergillus fumigatus.

A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species

Pestalotiopsis is a taxonomically confused, pathogenic and chemically creative genus requiring a critical re-examination using a multi-gene phylogeny based on ex-type and ex-epitype cultures. In this study 40 isolates of Pestalotiopsis, comprised of 28 strains collected from living and dead plant material of various host plants from China were studied by means of morphology and analysis of ITS, β–tubulin and tef1 gene sequence data. Based on molecular and morphological data we describe 14 new species (Pestalotiopsis asiatica, P. chinensis, P. chrysea, P. clavata, P. diversiseta, P. ellipsospora, P. inflexa, P. intermedia, P. linearis, P. rosea, P. saprophyta, P. umberspora, P. unicolor and P. verruculosa) and three species are epitypified (P. adusta, P. clavispora and P. foedans). Of the 10 gene regions (ACT, β-tubulin, CAL, GPDH, GS, ITS, LSU, RPB 1, SSU and tef1) utilized to resolve cryptic Pestalotiopsis species, ITS, β–tubulin and tef1 proved to be the better markers. The other gene regions were less useful due to poor success in PCR amplification and/or in their ability to resolve species boundaries. As a single gene tef1 met the requirements for an ideal candidate and functions well for species delimitation due to its better species resolution and PCR success. Although β-tubulin showed fairly good differences among species, a combination of ITS, β-tubulin and tef1 gene data gave the best resolution as compared to single gene analysis. This work provides a backbone tree for 22 ex-type/epitypified species of Pestalotiopsis and can be used in future studies of the genus.

Chloropupukeananin, the First Chlorinated Pupukeanane Derivative, and Its Precursors from Pestalotiopsis fici

Chloropupukeananin (1), the first pupukeanane chloride with highly functionalized tricyclo-[4.3.1.03,7]-decane skeleton and its possible biosynthetic precursors iso-A82775C (2) and pestheic acid (3), have been isolated from the plant endophyte Pestalotiopsis fici. The structure of 1 was determined by NMR spectroscopy and X-ray crystallography. Biogenetically, 1 could be derived from the Diels-Alder adduct of 2 and 3.

Chloropestolide A, an Antitumor Metabolite with an Unprecedented Spiroketal Skeleton from Pestalotiopsis fici

Chloropestolide A (1), a highly functionalized spiroketal with an unprecedented skeleton derived from a chlorinated bicyclo-[2.2.2]-oct-2-en-5-one ring and a 2,6-dihydroxy-4-methylbenzoic acid unit, has been isolated from the scale-up fermentation extract of Pestalotiopsis fici. The structure of 1 was elucidated by NMR spectroscopy and X-ray crystallography. 1 could be derived from the same Diels-Alder precursors as 2 and showed significant inhibitory effects on growth of two human cancer cell lines, HeLa and HT29, with GI(50) values of 0.7 and 4.2 microM, respectively.

Pestalofones A-E, bioactive cyclohexanone derivatives from the plant endophytic fungus Pestalotiopsis fici

Pestalofones A-E (1-5), five new cyclohexanone derivatives, have been isolated from cultures of the plant endophytic fungus Pestalotiopsis fici, along with the known compounds, isosulochrin (6), isosulochrin dehydrate (7), and iso-A82775C (8). The structures of 1-5 were determined by NMR spectroscopy, and the absolute configuration of 1 was assigned using the modified Mosher method. Compounds 1, 2, and 5 displayed inhibitory effects on HIV-1 replication in C8166 cells, whereas 3 and 5 showed significant antifungal activity against Aspergillus fumigatus.