John Dearnaley

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

Further advances in orchid mycorrhizal research

Orchid mycorrhizas are mutualistic interactions between fungi and members of the Orchidaceae, the world’s largest plant family. The majority of the world’s orchids are photosynthetic, a small number of species are myco-heterotrophic throughout their lifetime, and recent research indicates a third mode (mixotrophy) whereby green orchids supplement their photosynthetically fixed carbon with carbon derived from their mycorrhizal fungus. Molecular identification studies of orchid-associated fungi indicate a wide range of fungi might be orchid mycobionts, show common fungal taxa across the globe and support the view that some orchids have specific fungal interactions. Confirmation of mycorrhizal status requires isolation of the fungi and restoration of functional mycorrhizas. New methods may now be used to store orchid-associated fungi and store and germinate seed, leading to more efficient culture of orchid species. However, many orchid mycorrhizas must be synthesised before conservation of these associations can be attempted in the field. Further gene expression studies of orchid mycorrhizas are needed to better understand the establishment and maintenance of the interaction. These data will add to efforts to conserve this diverse and valuable association.

ITS-RFLP and sequence analysis of endophytes from Acianthus, Caladenia and Pterostylis (orchidaceae) in southeastern Queensland

We used ITS-RFLP and sequence analysis to determine the identities of the fungal endophytes of six terrestrial orchid species from southeastern Queensland, a region previously unexplored in this context. Pure cultures of orchid--colonising fungi were obtained and fungal identities were assessed by means of ITS-PCR, RFLP analysis, sequence comparison, and protocorm colonisation tests. ITS-PCR and RFLP analysis resulted in five main groupings. Sequencing and GenBank comparison of these five groups showed that the fungal endophytes isolated from the three Pterostylis species were probably Thanatephorus species. There was close sequence identity (90%) of the fungus isolated from Acianthus spp. to Epulorhiza repens, suggesting these may be the same fungal species. However, that only E. repens succeeded in colonising protocorms of Thelymitra pauciflora suggests these may be different species of Epulorhiza. Analysis of the ITS and LSU sequences of the fungus isolated from Caladenia carnea showed high identities with a sequence from a Sebacina vermifera originally isolated from Caladenia dilatata. These results show that there is specificity for fungal partners within the orchid genera Acianthus, Caladenia and Pterostylis.

Expression of a polygalacturonase enzyme in germinating pollen of Brassica napus

Abstract Penetration of pollen tubes through stigmatic tissues in Brassica napus L. may involve the release of cell wall modifying enzymes from the pollen tube tip. We examined the expression of a pectin-degrading polygalacturonase (PG) enzyme in unpollinated and early and late pollinated stigmas via immunoblotting and immuno-light microscopy using a PG polyclonal antibody. Immunoblotting analysis indicated that PG enzyme was present at low levels in unpollinated stigmas and at high levels in pollinated stigmas. The level of PG did not detectably increase between early and late pollinated stigmas. Immuno-light microscopy demonstrated that PG enzyme was present in ungerminated pollen grains, stigmatic papillae and in the tip of pollen tubes growing into the papillar wall. This latter evidence suggests that PG enzyme may play an important role in papillar cell wall penetration during pollination although other interpretations of the role of pollen PG should not be discounted.

Caelestines A-D, brominated quinolinecarboxylic acids from the Australian ascidian Aplidium caelestis.

Four new brominated natural products, caelestines A-D (1-4), have been isolated from the Australian ascidian Aplidium caelestis. The structures of 1-4 were determined by analysis of their NMR and MS data. This is the first report of brominated quinolinecarboxylic acids from nature. Compound 1 has been previously synthesized but not spectroscopically characterized. Compounds 1-4 were tested against three mammalian cell lines (MCF-7, NFF, and MM96L) and a panel of microbial strains and showed only minor cytotoxicity.

Molecular identification of the primary root fungal endophytes of Dipodium hamiltonianum (Orchidaceae)

We have identified the primary root fungal endophytes of Dipodium hamiltonianum F.M.Bailey, a species of orchid endangered in Victoria and uncommon in New South Wales and Queensland. Genomic DNA was extracted from whole colonised root portions from four orchid individuals and PCR amplified with ITS1F and ITS4 primers. Cloning and sequencing of the main amplicons produced from the PCR analysis revealed that the primary root fungal endophytes were Gymnomyces and Russula spp., both members of the Russulaceae. The implications of these findings are discussed in terms of conservation of the orchid species.

The rare Australian epiphytic orchid Sarcochilus weinthalii associates with a single species of Ceratobasidium

Sarcochilus weinthalii is a rare, epiphytic orchid largely restricted to the dry rainforests of eastern Australia. Part of the conservation procedures for the orchid includes isolation and identification of the associated mycorrhizal fungus. In this study the mycorrhizal fungal partner of the species was determined through extraction and sequencing of DNA from both colonised orchid roots and pure fungal cultures grown out from orchid roots. A single species of Ceratobasidium predominated in the orchid suggesting that the orchid displays narrow fungal specificity. This mycorrhizal fungus can now be used in conservation procedures involving ex situ growth and the reintroduction of plants to the natural state.

Nitrogen transport in the orchid mycorrhizal symbiosis – further evidence for a mutualistic association

Mycorrhizas are symbioses integral to the health of plant-based ecosystems (Smith & Read, 2008). In a typical mycorrhizal association, fungi in, or on, plant roots pass soil-acquired inorganic nutrients and water to the plant host. In return, the host transfers excess photosynthate to the fungus.

Australian cultures of Botryosphaeriaceae held in Queensland and Victoria plant pathology herbaria revisited

The Botryosphaeriaceae is one of the most widespread and cosmopolitan endophytic group of fungi. However, the species of this group can cause severe disease when the hosts are under stressful conditions. The aim of this study was to identify living cultures from the Botryosphaeriaceae family preserved in the Queensland and Victorian Plant Pathology Herbaria using DNA sequence analyses. The 51 isolates were collected between 1971 and 2017, from 35 different host genera, with the dominant host genera being Mangifera (11 isolates), Acacia (10), and Persea (5). Multilocus sequence analyses resulted in the re-identification of 41 isolates to the genera Botryosphaeria (2 isolates), Diplodia (4), Dothiorella (1), Lasiodiplodia (19), and Neofusicoccum (15), as well as some that belonged to genera outside of the Botryosphaeriaceae (10). New records for Australia were Botryosphaeria sinensis, Diplodia alatafructa, Lasiodiplodia gonubiensis, Neofusicoccum cryptoaustrale, and N. mangroviorum. These were identified as a result of a workshop organised by the Subcommittee on Plant Health Diagnostics. The results of this study provide the fundamental information regarding the diversity of Botryosphaeriaceae species present in Australian.

First Report of Powdery Mildew on Goji Berry (Lycium barbarum) Caused by Arthrocladiella mougeotii in Queensland, Australia

Goji berry (Lycium barbarum) is mainly cultivated in China for its fruit which is considered by consumers as a ‘superfood’ (Amagase and Farnsworth 2011). In Australia, this solanaceous shrub is known as a naturalized environmental weed, and has long been available for cultivation in nurseries (Haegi 1976). In April 2017, heavy powdery mildew infection was observed on roadside L. barbarum shrubs in Killarney, Queensland, Australia. Abundant sporulating mycelium covered both leaf surfaces and calyces of most plants. Conidiophores were erect, with straight, cylindrical foot-cells, 23 to 35 x 7 to 10 μm, followed by 1 to 3 shorter cells, and producing conidia in chains. Conidia were mostly cylindrical or ellipsoid-ovoid, 22 to 34 x 10 to 18 μm, and produced germ tubes apically or sub-apically, with simple ends. Hyphal appressoria were nipple-shaped. Based on these patterns, the pathogen was identified as Arthrocladiella mougeotii, the only powdery mildew species known to infect L. barbarum worldwide (Braun an...