Correlated evolution in an ectomycorrhizal host-symbiont system

Mechanisms of diversification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host-symbiont selection may be an important driver of fungal diversification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus. We use metabarcoding of ectomycorrhizal fungi collected with hyphal ingrowth bags from Nothofagus forests across southern New Zealand to investigate host-symbiont specialisation and correlated evolution. We examine how ectomycorrhizal communities differ between host species and look for patterns of host-symbiont cophylogeny. We found substantial differences in ectomycorrhizal communities associated with different host taxa, particularly between hosts from different subgenera (Lophozonia and Fuscospora), but also between more closely related hosts. Twenty-four per cent of fungal taxa tested showed affiliations to particular hosts, and tests for cophylogeny revealed significant correlations between host relatedness and the fungal phylogeny that extended to substantial evolutionary depth. These results provide new evidence of correlated evolution in ectomycorrhizal systems, indicating that preferences among closely related host species may represent an important evolutionary driver for local lineage diversification in ectomycorrhizal fungi.

Zeta diversity differentiates factors driving community assembly of rare and common ectomycorrhizal fungi

A fundamental goal in community ecology is to understand what factors drive community assembly processes. The factors affecting ectomycorrhizal fungal communities are unknown in many regions, particularly in the southern hemisphere. We investigate community assembly using ITS2 metabarcoding of ectomycorrhizal fungi sampled from 3943 hyphal ingrowth bags buried in 81 Nothofagus forests across New Zealand's South Island. By applying zeta diversity analysis and multisite generalized dissimilarity modelling (MS-GDM) we quantify the effects of 43 biotic and environmental variables on community turnover. Unlike traditional beta diversity analyses that are heavily influenced by rare species, the zeta diversity framework differentiates between factors driving turnover of rare and common species, providing a more complete picture of community dynamics. We found that community assembly was dominated by deterministic rather than stochastic processes and identified ecological factors affecting all taxa, as well as others that were specifically important to rare or common taxa. Soil variables were important drivers of turnover for all species, whereas ground cover variables, forest patch size, precipitation and host tree identity had greater effects on rarer species, and tree size and temperature effects were specific to more common species. Interestingly, the effect of temperature on common species is in line with recent evidence from other Kingdoms, pointing to possible generality, and highlighting the importance of considering common species. Applying these methods to fungi has allowed us to identify the distinct ecological processes that structure rare and common taxa during community assembly. This has important implications for understanding the functional effects of community responses to environmental change.

Purple haze: Cryptic purple sequestrate Cortinarius in New Zealand

CORTINARIUS

is a species-rich ectomycorrhizal genus containing taxa that exhibit agaricoid or sequestrate basidiome morphologies. In New Zealand, one of the most recognizable and common Cortinarius species is the purple sequestrate fungus, C. porphyroideus. We used genome skimming of the almost 100-y-old type specimen from C. porphyroideus to obtain the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and partial nuc rDNA 28S (28S) sequences. The phylogenetic position of C. porphyroideus was established, and we found that it represents a rarely collected species. Purple sequestrate Cortinarius comprise multiple cryptic species in several lineages. We describe four new species of Cortinarius with strong morphological similarity to C. porphyroideus: Cortinarius diaphorus, C. minorisporus, C. purpureocapitatus, and C. violaceocystidiatus. Based on molecular evidence, Thaxterogaster viola is recognized as Cortinarius violaceovolvatus var. viola. These species are associated with Nothofagus (southern beech) and have very similar morphology to C. porphyroideus but are all phylogenetically distinct based on molecular data.

Fungal diversity in canopy soil of silver beech, Nothofagus menziesii (Nothofagaceae)

Adventitious roots in canopy soils associated with silver beech (Nothofagus menziesii Hook.f. (Nothofagaceae)) form ectomycorrhizal associations. We investigated the extent to which canopy ectomycorrhizal communities contribute to overall diversity of ectomycorrhizal fungi associated with silver beech. Hyphal ingrowth bags were buried for 12 months in canopy and terrestrial soils of five trees at one site. We used amplicon sequencing of the nuclear ribosomal internal transcribed spacer 2 region (ITS2) to assess diversity of both ectomycorrhizal and non-ectomycorrhizal OTUs in hyphal ingrowth bags. There was a significant difference in ectomycorrhizal fungal community diversity between the terrestrial and canopy hyphal ingrowth bag communities. Ectomycorrhizal community composition of the terrestrial and canopy environments was also significantly different. Some ectomycorrhizal taxa were significantly differentially represented in either the terrestrial or canopy environment. The hyphal ingrowth bags also accumulated non-ectomycorrhizal species. The non-ectomycorrhizal fungi also had significantly different diversity and community composition between the canopy and terrestrial environments. Like the ectomycorrhizal community, some non-ectomycorrhizal taxa were significantly differentially represented in either the terrestrial or canopy environment. The canopy soil microhabitat provides a novel environment for growth of ectomycorrhizal adventitious roots and enables the spatial partitioning of ectomycorrhizal and non-ectomycorrhizal fungal diversity in the forest.

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand

The cultivation of grasslands can modify both bacterial community structure and impact on nutrient cycling as well as the productivity and diversity of plant communities. In this study, two pristine New Zealand grassland sites dominated by indigenous tall tussocks (Chionochloa pallens or C. teretifolia) were examined to investigate the extent and predictability of variation of the bacterial community. The contribution of free-living bacteria to biological nitrogen fixation is predicted to be ecologically significant in these soils; therefore, the diazotrophic community was also examined. The C. teretifolia site had N-poor and poorly-drained peaty soils, and the C. pallens had N-rich and well-drained fertile soils. These soils also differ in the proportion of organic carbon (C), Olsen phosphorus (P) and soil pH. The nutrient-rich soils showed increased relative abundances of some copiotrophic bacterial taxa (including members of the Proteobacteria, Bacteroidetes and Firmicutes phyla). Other copiotrophs, Actinobacteria and the oliogotrophic Acidobacteria showed increased relative abundance in nutrient-poor soils. Greater diversity based on 16S rRNA gene sequences and the Tax4Fun prediction of enhanced spore formation associated with nutrient-rich soils could indicate increased resilience of the bacterial community. The two sites had distinct diazotrophic communities with higher diversity in C. teretifolia soils that had less available nitrate and ammonium, potentially indicating increased resilience of the diazotroph community at this site. The C. teretifolia soils had more 16S rRNA gene and nifH copies per g soil than the nutrient rich site. However, the proportion of the bacterial community that was diazotrophic was similar in the two soils. We suggest that edaphic and vegetation factors are contributing to major differences in the composition and diversity of total bacterial and diazotrophic communities at these sites. We predict the differences in the communities at the two sites will result in different responses to environmental change.

Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand

New Zealand ephemeral wetlands are ecologically important, containing up to 12% of threatened native plant species and frequently exhibiting conspicuous cyanobacterial growth. In such environments, cyanobacteria and associated heterotrophs can influence primary production and nutrient cycling. Wetland communities, including bacteria, can be altered by increased nitrate and phosphate due to agricultural practices. We have characterized cyanobacteria from the Wairepo Kettleholes Conservation Area and their associated bacteria. Use of 16S rRNA amplicon sequencing identified several operational taxonomic units (OTUs) representing filamentous heterocystous and non-heterocystous cyanobacterial taxa. One Nostoc OTU that formed macroscopic colonies dominated the cyanobacterial community. A diverse bacterial community was associated with the Nostoc colonies, including a core microbiome of 39 OTUs. Identity of the core microbiome associated with macroscopic Nostoc colonies was not changed by the addition of nutrients. One OTU was highly represented in all Nostoc colonies (27.6%-42.6% of reads) and phylogenetic analyses identified this OTU as belonging to the genus Sphingomonas. Scanning electron microscopy showed the absence of heterotrophic bacteria within the Nostoc colony but revealed a diverse community associated with the colonies on the external surface.

Morphological and molecular data for Australian Hebeloma species do not support the generic status of Anamika

The first collection of a macrofungal agaric species, with morphological features similar to already described Anamika species, has been found in association with animal bones in north Queensland, Australia. This species also shares features with several, commonly occurring and previously described Australian Hebeloma species. An integrated morphological and molecular study has resulted in the conclusion that all Anamika species belong in Hebeloma. As a result, already described species of Anamika are recombined as H. indicum (K.A. Thomas, Peintner, M.M. Moser and Manim.) B.J. Rees & Orlovich, H. angustilamellatum (Zhu L. Yang and Z.W. Ge) B.J. Rees & Orlovich and H. lactariolens (Clémençon and Hongo) B.J. Rees & Orlovich. A. phylogenetic tree based on ribosomal ITS sequences examines the relationship of these species with other Hebeloma species from both hemispheres. Four new species, Hebeloma youngii B.J. Rees, H. nothofagetorum B.J. Rees, H. subvictoriense B.J. Rees, H. lacteocoffeatum B.J. Rees, and one form, H. aminophilum f. hygrosarx B.J. Rees, are described as new from Australia.

Piracy in the high trees: ectomycorrhizal fungi from an aerial 'canopy soil' microhabitat

The mantle of dead organic material ("canopy soil") associated with the mats of vascular and nonvascular epiphytes found on the branches of trees in the temperate rainforests along the southwestern coast of the South Island of New Zealand were examined for evidence of ectomycorrhizal fungi. DNA sequencing and cluster analysis were used to identify the taxa of fungi present in 74 root tips collected from the canopy soil microhabitat of three old growth Nothofagus menziesii trees in the South West New Zealand World Heritage Area. A diverse assemblage of ectomycorrhizal fungi was found to infect an extensive network of adventitious canopy roots of Nothofagus menziesii in this forest, including 14 phylotypes from nine genera of putative ectomycorrhizal fungi. Seven of the genera identified previously were known to form ectomycorrhizas with terrestrial roots of Nothofagus: Cortinarius, Russula, Cenococcum, Thelephora/Tomentella, Lactarius and Laccaria; two, Clavulina and Leotia, previously have not been reported forming ectomycorrhizas with Nothofagus. Canopy ectomycorrhizas provide an unexpected means for increased host nutrition that may have functional significance in some forest ecosystems. Presumably, canopy ectomycorrhizas on host adventitious roots circumvent the tree-ground-soil nutrient cycle by accessing a wider range of nutrients directly in the canopy than would be possible for non-mycorrhizal or arbuscular mycorrhizal canopy roots. In this system, both host and epiphytes would seem to be in competition for the same pool of nutrients in canopy soil.

The influence of probiotic treatment on sulfasalazine metabolism in rat

Probiotics are live microorganisms claimed to exert beneficial effects on the host. This study investigated their effect on the metabolism and pharmacokinetics of sulfasalazine (SSZ), a drug whose efficacy depends on metabolism by azoreductase (AR) in the gut microbiota to sulfapyridine (SP) and 5-acetylsalicylic acid (5-ASA). The probiotic strains Lactobacillus acidophilus L10, Bifidobacterium lactis B94 and Streptococcus salivarius K12 possessed AR activity and a corresponding ability to metabolize SSZ. Treatment of male Wistar rats (n = 5) with oral 2 g doses of a mixture of the three probiotics (total dose 1.8 × 10⁹ cfu) every 12 h for 3 days resulted in a significant increase (p < 0.05) in AR activity in ex vivo colon contents with a corresponding increase in SSZ metabolism. Similar probiotic treatment of male Wistar rats (n = 8) followed by an oral 100 mg/kg dose of SSZ produced high plasma levels of SP, but pharmacokinetic parameters of SSZ and SP were not significantly different from control rats given SSZ. These results indicate that probiotic strains possess AR activity and can metabolize SSZ. Treatment with probiotics increases AR activity in the gut microbiota but has no effect on plasma levels of SSZ and SP following a subsequent oral dose of SSZ.

Detection and analysis of endogenous badnaviruses in the New Zealand flora

BACKGROUND AND AIMS

Badnaviruses and their host-integrated DNA occur in tropical crops and a few northern temperate species. Following the discovery of a badnavirus on a subantarctic island with floristic links to New Zealand, we postulated that badnaviruses exist in the New Zealand flora. Badnavirus reverse transcriptase (RT) sequences consist of variable regions flanked by highly conserved regions. This study used RT sequences to detect and characterize badnavirus sequences in the New Zealand flora and to investigate their utility for the study of broader aspects of plant biology.

METHODOLOGY

Molecular diversity of RT sequences was analysed using polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). In a study of the genus Melicytus, internal transcribed spacer (ITS) sequences were compared with the RT data.

PRINCIPAL RESULTS

No freely replicating badnaviruses were detected but more than half of the species (37/60) contained RT sequences. Phylogenetic analysis of 21 RT sequences formed monophyletic groups distinct from other species and from badnaviruses. No frameshift mutations occurred in any of the sequences translated in silico. More detailed study of the genus Melicytus indicated broader applications for our approach. Analysis of RT sequences revealed the presence of a previously unrecognized species (confirmed using ITS). Inheritance of DGGE profiles by Melicytus ramiflorus seedlings suggested that this species may undergo apomixis.

CONCLUSIONS

The presence of integrated badnavirus sequences in a wide range of taxa from this Southern Hemisphere flora indicates that these sequences may be common in many temperate regions. Potential to activate viruses from these sequences should be considered when placing these species in tissue culture or under other forms of abiotic or genomic stress. Analysis of endogenous RT sequences shows potential for the study of systematics, phylogenetics and plant reproductive biology.

The effects of an orally administered probiotic on sulfasalazine metabolism in individuals with rheumatoid arthritis: a preliminary study

AIM

To carry out a pilot study to investigate the effect of short-term oral probiotic administration on the metabolism of sulfasalazine (SSZ) in patients with rheumatoid arthritis (RA) stabilized on SSZ.

METHODS

Twelve subjects with RA taking stable doses of SSZ for a minimum of 3 months prior to the study, received a probiotic preparation contained three strains of bacteria (1.8 x 10(9) CFU/day) twice daily for 1 week. Single point blood and 12-h urine samples were taken before and after probiotic treatment and 3 weeks following discontinuation of probiotics, for determination of SSZ and its metabolites. The presence of the probiotic bacteria in the feces of patients was investigated by denaturing gradient gel electrophoresis (DGGE).

RESULTS

Adverse events recorded were three instances of gastrointestinal disturbance and one flare of RA. Plasma and urinary levels of SSZ and its metabolites showed no statistically significant changes after probiotic administration and the incidence of gastrointestinal disturbance did not appear to be ascribed to higher sulfapyridine plasma levels. Probiotic-specific DGGE bands were detected in the feces of some patients after the treatment period.

CONCLUSIONS

Short-term treatment of RA patients with a multi-strain probiotic did not significantly influence SSZ metabolism as has been demonstrated in animal models.

Detection and Specific Enumeration of Multi-Strain Probiotics in the Lumen Contents and Mucus Layers of the Rat Intestine After Oral Administration

Although the detection of viable probiotic bacteria following their ingestion and passage through the gastrointestinal tract (GIT) has been well documented, their mucosal attachment in vivo is more difficult to assess. In this study, we investigated the survival and mucosal attachment of multi-strain probiotics transiting the rat GIT. Rats were administered a commercial mixture of the intestinal probiotics Lactobacillus acidophilus LA742, Lactobacillus rhamnosus L2H and Bifidobacterium lactis HN019 and the oral probiotic Streptococcus salivarius K12 every 12 h for 3 days. Intestinal contents, mucus and faeces were tested 6 h, 3 days and 7 days after the last dose by strain-specific enumeration on selective media and by denaturing gradient gel electrophoresis. At 6 h, viable cells and DNA corresponding to all four probiotics were detected in the faeces and in both the lumen contents and mucus layers of the ileum and colon. Viable probiotic cells of B. lactis and L. rhamnosus were detected for 7 days and L. acidophilus for 3 days after the last dose. B. lactis and L. rhamnosus persisted in the ileal mucus and colon contents, whereas the retention of L. acidophilus appeared to be relatively higher in colonic mucus. No viable cells of S. salivarius K12 were detected in any of the samples at either day 3 or 7. The study demonstrates that probiotic strains of intestinal origin but not of oral origin exhibit temporary colonisation of the rat GIT and that these strains may have differing relative affinities for colonic and ileal mucosa.

Dispersed polyphosphate in fungal vacuoles in Eucalyptus pilularis/Pisolithus tinctorius ectomycorrhizas

Ectomycorrhizas produced between Pisolithus tinctorius and Eucalyptus pilularis under axenic conditions were rapidly frozen, freeze-substituted in tetrahydrofuran and embedded anhydrously, and dry-sectioned for X-ray microanalysis. The vacuoles of the sheath and Hartig net hyphae were rich in phosphorus and potassium. They also contained sulfur and variable amounts of chlorine. In anhydrously processed freeze-substituted mycorrhizas, dispersed electron-opaque material filled the fungal vacuoles. X-ray maps indicated that P was distributed evenly throughout the entire vacuole profile and was not concentrated in spherical bodies or subregions of the vacuole. There were no electron-opaque granules surrounded by electron-lucent areas, such as are commonly seen in chemically fixed material. The fungal vacuoles were also rich in K, which similarly gave a signal from the entire vacuolar profile. Such P-rich vacuoles occurred in both the mycorrhizal sheath and Hartig net hyphae. Stained sections of ether-acrolein freeze-substituted mycorrhizas also showed only dispersed material in the fungal vacuoles as, in most cases, did acetone-osmium freeze-substituted material. Precipitation of metachromatic granules by ethanol suggested that large amounts of polyphosphate are stored in these regions under the conditions of our experiments, as well as in the tips of actively growing hyphae of the same fungus. The higher plant vacuoles of ectomycorrhizas gave a much lower signal for K, and P was barely detectable. Much more K was located in the vacuoles of the root exodermal cells than in epidermal cells. The analysis of element distribution between the vacuole and cytoplasm in root cells agrees well with that found for other plant species using other techniques. We conclude that polyphosphate is indeed present in the vacuoles of the fungal cells of these ectomycorrhizas, but that in vivo it is in a dispersed form, not in granules.

Structure, function, and motility of vacuoles in filamentous fungi

Current information on the structure and function of motile tubular vacuoles in Pisolithus tinctorius and other fungi is reviewed. The use of fluorochromes to label the vacuole lumen is evaluated and observations on the structure and motility of vacuoles in P. tinctorius are differentiated from possible artifacts. The styryl dyes FM4-64 and MDY-64, used in yeast to demonstrate endocytosis, show little or no labeling of internal membranes in undamaged P. tinctorius cells. This agrees with our data showing that other probes for endocytosis such as Lucifer yellow CH are not taken up by hyphal tip cells. Overall, the observations do not support endocytosis in hyphal tips. It has been suggested that tubular vacuole systems carry out longitudinal transport, and evidence in favor of this hypothesis is evaluated. New data are presented to show that many of the large vacuoles in subapical cells are attached to the plasma membrane and are relatively immobile, while video sequences show movement of fluorochrome in pulses along a series of several large vacuoles, all interconnected via tubules. Tubular vacuoles from thick sections of hyphae processed under anhydrous conditions are shown by X-ray microanalysis to contain relatively high levels of P and K, as seen previously in the larger vacuoles. These results provide further evidence for a role of the tubular vacuoles in longitudinal transport of P. Copyright 1998 Academic Press.

Ion compartmentation in the red alga Caloglossa leprieurii in response to salinity changes: freeze-substitution and X-ray microanalysis

The elemental content of cell compartments in the euryhaline red macroalga Caloglossa leprieurii (Montague) J. Agardh subjected to different salinities, was determined by X-ray microanalysis of freeze-substituted thin sections. Duty are given for three compartments; cell wall, vacuole and cytoplasm. The most abundant elements detected were potassium, sodium and chlorine, with a Sulphur peak in the cell wall indicating the presence of sulphated polysaccharides. With salinity upshock the cytoplasm is maintained low in K, Na and Cl, whereas in the vacuoles they increased. High levels of K and Na located in the cell wall reflect cation binding to negatively charged polysaccharides. Hyposaline shock resulted in decreased K, Na and Cl levels in all compartments, though K was retained in the cytoplasm. Results are discussed with regard to the role of ion compartmentation in the salt tolerance of this alga, and the cation exchange properties of the cell wall are emphasized.

Cell-to-cell transport via motile tubules in growing hyphae of a fungus

The system of pleiomorphic, motile tubules and vacuoles in growing hyphal tips of Pisolithus tinctorius has been shown to play a role in intracellular transport. Here we show that the same system also exchanges material between adjacent cells. This exchange is most obvious between terminal and penultimate cells following nuclear division in the tip cell and just before dissolution of the cell wall between the clamp connection and penultimate cell. At this stage the two new dolipore septa are complete. The process was studied in living hyphae using confocal and conventional fluorescence microscopy. Tubules could move in either direction across the septum and often extended and retracted several times and penetrated for some distance (e.g. 40 microns) into the receiving cell. Movements appeared co-ordinated and during the exchange tubules transiently interconnected vacuoles in adjacent cells and by peristaltic movements appeared to transfer material between them. The fluorescent tubules occupied a specific plane in the vicinity of the septum and remained in this plane for the duration of their movement, suggesting that their orientation and direction of movement is controlled. In freeze-substituted hyphae, tubular cisternae of similar dimensions to fluorescent tubules passed through the parenthesome pores perpendicular to the septum and in some cases entered the mouth of the septal pore. This indicates that the septal pore is of an appropriate dimension to accommodate the tubules and that they can cross the septal pore to exchange material between vacuole systems of adjacent cells. This is the first direct demonstration of such intercellular transport via a sub-cellular compartment.