The soil microbiome is responsible for mediating key ecological processes, however little is known about its sensitivity to climate change. Observed increases in atmospheric [CO2] and alteration to rainfall patterns, due to anthropogenic release of greenhouse gases, will likely have a strong influence on soil microbial communities and ultimately the ecosystem services they provide. Therefore, it is vital to understand how soil microbial communities will respond to future climate change scenarios. In a large climate change experiment, we surveyed soil fungal community structure changes under Eucalyptus saligna exposed to a 3-year period of elevated [CO2] and one year of drought. Our results suggest that drought is a key factor in shaping soil fungal community composition and its interactive effect with elevated [CO2] appears to select for a fungal community that is more adapted to drought conditions. In-depth examination of fungal community composition showed that plant pathogenic strains, such as Fusarium sp. and Mycosphaerella sp., appear to be well adapted to climate change conditions, which may have significant implications for eucalypt plantation forest health under future climate conditions. Overall our results indicate that soil water availability regulates the abundance and diversity of the soil fungal community.

Spatial patterns in community structure are known to exist at a range of spatial scales. By understanding the relative importance of spatial and environmental variation in shaping community structure, it is possible to gain insight into the complexity of the underlying mechanisms driving community assembly. Here, we investigated how fungal community assembly is impacted by species sorting across a strong environmental filter in the same geographic space. Using a spatially explicit sampling design, root and soil associated fungal communities were sampled from eight study sites over a 500 km transect along the south-east coast of Australia. The relative importance of spatial and environmental factors in shaping fungal beta diversity was determined across a range of scales, along with the importance of deterministic and stochastic processes in shaping fungal beta diversity changes for each community type. Fungal community composition patterns were found to be generally similar in both root and soil associated communities, across the scales included in the sampling design (40 m-500 km). However, the mechanisms responsible for driving community assembly differed in the root and soil associated communities. Niche-based processes were found to be influential in shaping soil fungal community assembly, while the patterns in root-associated community structure were consistent with neutral assembly. This may be due to factors such as niche breadth, environmental heterogeneity, dispersal, and immigration differing in importance among the two environments. Our results indicate that both niche and neutral processes can be active in fungal community assembly and provide insight into the conditions under which each class of processes dominate. (C) 2014 Elsevier Ltd. All rights reserved.

A key component of biodiversity is the number and abundance of individuals (i.e. genotypes), and yet such intraspecific diversity is rarely considered when investigating the effects of biodiversity of mycorrhizal plants and fungi on ecosystem processes. Within a species, individuals vary considerably in important reproductive and functional attributes, including carbon fixation, mycelial growth and nutrient utilization, but this is driven by both genetic and environmental (including climatic) factors. The interactions between individual plants and mycorrhizal fungi can have important consequences for the maintenance of biodiversity and regulation of resource transfers in ecosystems. There is also emerging evidence that assemblages of genotypes may affect ecosystem processes to a similar extent as assemblages of species. The application of whole-genome sequencing and population genomics to mycorrhizal plants and fungi will be crucial to determine the extent to which individual variation in key functional attributes is genetically based. We argue the need to unravel the importance of the diversity (especially assemblages of different evenness and richness) of individuals of both mycorrhizal plants and fungi, and the need to take a 'community genetics' approach to better understand the functional significance of the biodiversity of mycorrhizal symbioses.

Soil microbial processes have a central role in global fluxes of the key biogenic greenhouse gases and are likely to respond rapidly to climate change. Whether climate change effects on microbial processes lead to a positive or negative feedback for terrestrial ecosystem resilience is unclear. In this study, we investigated the interactive effects of [CO(2)] and temperature on soil fungi associated with faster-growing Eucalyptus saligna and slower-growing Eucalyptus sideroxylon, and fungi that colonised hyphal in-growth bags. Plants were grown in native soil under controlled soil moisture conditions, while subjecting the above-ground compartment to defined atmospheric conditions differing in CO(2) concentrations (290, 400, 650 μL L(-1)) and temperature (26 and 30 °C). Terminal restriction fragment length polymorphism and sequencing methods were used to examine effects on the structure of the soil fungal communities. There was no significant effect of host plant or [CO(2)]/temperature treatment on fungal species richness (α diversity); however, there was a significant effect on soil fungal community composition (β diversity) which was strongly influenced by eucalypt species. Interestingly, β diversity of soil fungi associated with both eucalypt species was significantly influenced by the elevated [CO(2) ]/high temperature treatment, suggesting that the combination of future predicted levels of atmospheric [CO(2)] and projected increases in global temperature will significantly alter soil fungal community composition in eucalypt forest ecosystems, independent of eucalypt species composition. These changes may arise through direct effects of changes in [CO(2)] and temperature on soil fungi or through indirect effects, which is likely the case in this study given the plant-dependent nature of our observations. This study highlights the role of plant species in moderating below-ground responses to future predicted changes to [CO(2)] and temperature and the importance of considering integrated plant-soil system responses.

Extramatrical mycelia (EMM) of ectomycorrhizal (ECM) fungi are potentially extensive in soil and receive significant allocations of plant-derived carbon. Although losses from living EMM occur via respiration and exudation, EMM represents a considerable biomass component and potential carbon sink in many forest soils. ECM root tips and rhizomorphs may persist in soil for many months, but interactions between grazing arthropods and decomposers probably facilitate more rapid turnover of diffuse EMM. Elevated atmospheric CO2 concentration [CO2] is likely to increase carbon allocation to ECM fungi by their tree hosts. This will probably increase root colonization by ECM fungi and drive changes in their communities in soil. The likely effects of elevated [CO2] and other climate change factors on the production and turnover of EMM production are difficult to predict from current evidence, and this hampers our understanding of their potential value as future carbon sinks. Responses of grazing soil arthropods to future climate change will have a strong influence on EMM turnover, along with the abilities of ECM fungi to store carbon in below-ground, and this should be seen as a priority area for future research.

The aim of this study has been to identify important processes that regulate early stages of embryo development in conifers. Somatic embryogenesis in Picea abies has become a model system for studying embryology in conifers, providing a well-characterized sequence of developmental stages, resembling zygotic embryogeny, which can be synchronized by specific treatments, making it possible to collect a large number of somatic embryos at specific developmental stages. We have used this model to analyze global changes in gene expression during early stages of embryo development by generating an expression profile of 12,536 complementary DNA clones. This has allowed us to identify molecular events regulating putative processes associated with pattern formation during the earliest stages of embryogenesis which have not been identified on the molecular level in conifers before. We recognize notable changes in the expression of genes involved in regulating auxin biosynthesis and auxin response, gibberellin-mediated signaling, signaling between the embryo and the female gametophyte, tissue specification including the formation of boundary regions, and the switch from embryonic to vegetative development. In addition, our results confirm the involvement of previously described processes, including stress, differentiation of a protoderm, and programmed cell death.

Many forest trees have evolved mutualistic symbioses with ectomycorrhizal (ECM) fungi that contribute to their phosphorus (P) nutrition. Forest productivity is frequently limited by P, a phenomenon that is likely to become more widespread under future conditions of elevated atmospheric CO 2 concentration [CO 2 ]. It is thus timely that this review considers current understanding of the key processes (absorption, translocation and transfer to the plant host) in ECM fungus-mediated P nutrition of forest trees. Solubilisation of inorganic P (P i ) and hydrolysis of organic P by ECM fungi in soil occurs largely at the growing mycelial front, where P i absorption is facilitated by high affinity transporters. While large gaps remain in our understanding of the physiological and molecular mechanisms that underpin movement of P in ECM mycelia in soil and P transfer to the plant, host P demand seems likely to be a key driver of these processes. ECM fungi may make considerable contributions to meeting the likely increased P demand of trees under elevated [CO 2 ] via increased colonization levels, shifts in ECM fungal community structure and changed patterns of EMM production. Further research into the spatial scale of ECM-mediated P movements in soil, along with the interplay between ECM fungi and other soil microflora is advocated.

Active management to encourage the expansion of native pine woodland onto neighbouring moorland has been suggested as a tool to promote increases in forest area to combat climate change. Low intensity burning has previously been shown to increase pine seedling establishment, however the effect of this on below-ground diversity and functioning in these important terrestrial carbon stores is equivocal. Here, we assessed the effect of a single burn and grazing exclosures after a 6 year period on soil microbial respiratory activity and fungal community structure using terminal restriction fragment polymorphism (T-RFLP) analysis. The combined data suggest that the strategy of a single prescribed burn to facilitate Scots pine establishment had no lasting effect on either fungal taxonomic richness, fungal community composition or microbial activity. Thus, our findings support the proposed use of single, low intensity, prescribed burns in regenerating Scots pine forests as a low impact management tool.

Pisolithus are ectomycorrhizal fungi that associate with roots of numerous plant species in natural and plantation forests worldwide. Despite the fact that Pisolithus spp. are present in plantation forests in many countries, knowledge of the genetic population structure of Pisolithus spp. remains limited. In this study, we have tested the hypothesis that a propensity for long-distance spore dispersal in Pisolithus microcarpus, along with the widespread distribution of potential eucalypt and acacia plant hosts in south-eastern Australia facilitates gene flow that limits population differentiation. Five polymorphic simple sequence repeat markers were used to investigate the population structure of P. microcarpus. Isolates were grouped according to geographical origin and isolate genotypes were analysed among the geographical populations. Pairwise F (ST) estimates indicated limited genetic differentiation among the geographical populations. Analysis of molecular variance revealed that most of the genetic variation present was within geographical populations, with only 1.3% of the genetic variation among P. microcarpus geographical populations. This was particularly pronounced for four geographical populations within a ca 7,000 km(2) area New South Wales, which were each separated by < 100 km and appeared to be genetically homogeneous. The lack of population structure is suggested to be due to a high degree of gene flow, via basidiospores, between the New South Wales geographical populations.

Native rainforest tree plantations are increasingly viewed as potentially important for high value timber production and provision of a range of ecological services in tropical and subtropical areas. In order to determine the extent to which conversion of rainforest to native Araucariaceae plantation influences soil fungi, we compared soil fungal communities under native rainforest and 73–74 year-old Araucaria bidwillii, Araucaria cunninghamii and Agathis robusta plantations at Gadgarra State Forest, Queensland, Australia. Following direct extraction of DNA from soil, terminal restriction fragment length polymorphism (T-RFLP) analysis of rDNA internal transcribed spacer (ITS) regions was conducted. Ordination analysis of the T-RFLP data revealed significant separation of the fungal communities according to forest type along the first canonical axis, with the native rainforest samples separating from the three Araucariaceae plantations along the second axis. Overall, the most abundant ITS sequences in clone assemblages from the four forest types were Ascomycota, followed by Basidiomycota, Zygomycota and Chitridomycota, however their relative importance varied in individual forest types. The results indicate that conversion of tropical rainforest to monoculture plantations of native trees can significantly alter soil fungal diversity.

Purpose Commercial monoculture plantations of the native Australian Araucaria cunninghamii are common in subtropical and tropical Queensland and are generally established following clearing of native mixed forest. The consequences of such forest conversion for soil fungal communities, however, have not been assessed in detail.Materials and methods We utilised direct DNA extraction from soil coupled with terminal restriction fragment length polymorphism (T-RFLP) analysis of rDNA internal transcribed spacer (ITS) regions to investigate soil fungal community structure under native mixed forest and first and second rotation A. cunninghamii plantations at Yarraman State Forest, Queensland, Australia. We also investigated the influence of forest harvest residue windrows on soil fungi in a second rotation A. cunninghamii plantation and compared soil fungal communities in soil with those in sand-filled hyphal ingrowth bags buried at the site.Results and discussion Ordination analysis of the fungal community T-RFLP data indicated significant separation of native forest soil samples from the plantation forest soil samples along canonical axis 1, while with first rotation plantation forest soil samples separated from second rotation forest soil samples along canonical axis 2. Fungal communities in soil and hyphal ingrowth bag samples were also shown to differ significantly for the three forest types, suggesting that the hyphal ingrowth bags selected for certain fungi at the site. Windrow soil samples did not separate significantly from nonwindrow soil samples in the second rotation A. cunninghamii plantation. Mean terminal restriction fragment numbers were significantly lower in the A. cunninghamii plantation samples than in the native forest samples and lower in the second rotation than the first rotation plantations. Terminal restriction fragment numbers were also lower in the hyphal ingrowth bag samples than in the respective soil samples. Analysis of cloned ITS sequences indicated that Ascomycota were most abundant, followed by Basidiomycota and Zygomycota; however, their relative importance varied in the different forest types.Conclusions Overall, the data suggest that conversion of native mixed forest to A. cunninghamii plantations changes soil fungal community composition and that the effect is more pronounced in second rotation forests.

Assemblages of fungi associated with roots of cooccurring Epacris pulchella (Ericaceae) and Leptospermum polygalifolium (Myrtaceae) seedlings at a sclerophyll forest site in New South Wales, Australia, were investigated by direct DNA extraction and analysis of rRNA gene internal transcribed spacer (ITS) products by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analyses. While ordination of the DGGE data suggested that the assemblages did not differ significantly between the two plant taxa, T-RFLP data provided marginal statistical support for the presence of different assemblages. Fungi isolated from roots of both plants were identified by ITS sequence comparisons largely as ascomycetes, several of which had close sequence identity to Helotiales ericoid mycorrhizal (ERM) fungi. One isolate morphotype from E. pulchella had close sequence similarity to ectomycorrhizal fungi in the Cenococcum geophilum complex, and neighbour-joining analysis grouped this strongly with other Australian C. geophilum-like sequences. Distribution of genotypes of an ERM Helotiales ascomycete in root systems of the two plant taxa was also investigated using inter-simple sequence repeat (ISSR)-PCR. Nineteen ISSR genotypes were identified, two of which were present in roots of both plant taxa. The results are discussed in the context of potential mycelial connections between Ericaceae and non-Ericaceae plants.

Repeated prescribed burning alters the biologically labile fraction of nutrients and carbon of soil organic matter (SOM). Using a long-term (30 years) repeated burning experiment where burning has been carried out at a 2- or 4-year frequency, we analysed the effect of prescribed burning on gross potential C turnover rates and phenol oxidase activity in relation to shifts in SOM composition as observed using Fourier-transform infrared spectroscopy. In tandem, we assessed the genetic diversity of basidiomycete laccases. While the overall effect of burning was a decline in phenol oxidase activity, Shannon diversity and evenness of laccases was significantly higher in burned sites. Co-correspondence analysis of SOM composition and laccase operational taxonomic unit frequency data also suggested a strong correlation. While this correlation could indicate that the observed increase in laccase genetic diversity due to burning is due to increased resource diversity, a temporal replacement of the most abundant members of the assembly by an otherwise dormant pool of fungi cannot be excluded. As such, our results fit the intermediate disturbance hypothesis. Effects were stronger in plots burned in 2-year rotations, suggesting that the 4-year burn frequency may be a more sustainable practice to ensure the long-term stability of C cycling in such ecosystems.

Fungi were isolated from the roots of 17 plant species from the families Apiaceae, Cunoniaceae, Cyperaceae, Droseraceae, Fabaceae-Mimosoideae, Lomandraceae, Myrtaceae, Pittosporaceae, Proteaceae and Stylidiaceae at a sclerophyll forest site in New South Wales, Australia. Internal transcribed spacer (ITS) restriction fragment length polymorphism (RFLP) and sequence comparisons indicated that the isolated fungi had affinities to a range of ascomycetes, basidiomycetes and zygomycetes. Four RFLP types had closest affinities to previously identified Helotiales ericoid mycorrhizal (ERM) or Oidiodendron spp. Isolates representing six RFLP types, which were variously isolated from all 17 plant species, formed ERM coils in hair root epidermal cells of Woollsia pungens (Ericaceae) under gnotobiotic conditions. Three of these isolates formed intercellular hyphae, intracellular hyphae and/or microsclerotia, which are typical of dark septate endophyte infection, in roots of Stylidium productum (Stylidiaceae), indicating an ability to form different types of association with roots of different hosts. Overall the data indicate that a broad range of plant taxa may act as repositories for ERM fungi in sclerophyll forest soil.

Repeated prescribed burning is frequently used as a forest management tool and can influence soil microbial diversity and activity. Soil fungi play key roles in carbon and nutrient cycling processes and soil fungal community structure has been shown to alter with increasing burning frequency. Such changes are accompanied by changes to soil carbon and nitrogen pools, however, we know little regarding how repeated prescribed burning alters functional diversity in soil fungal communities. We amended soil with 13C-cellulose and used RNA stable isotope probing to investigate the effect of biennial repeated prescribed burning over a 34-year period on cellulolytic soil fungi. Results indicated that repeated burning altered fungal community structure. Moreover, fungal community structure and diversity in 12C and 13C fractions from the unburned soil were not significantly different from each other, while those from the biennial burned soils differed from each other. The data indicate that fewer active fungi in the biennially burned soil incorporated 13C from the labelled cellulose and that repeated prescribed burning had a significant impact on the diversity of an important functional group of soil fungi (cellulolytic fungi) that are key drivers of forest soil decomposition and carbon cycling processes.

Bacterial communities associated with ectomycorrhizal and uncolonized roots of Pinus elliottii (slash pine) collected from a plantation in south-east Queensland, Australia, were investigated, using cultivation-dependent and -independent methods. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene PCR products obtained using a cultivation-independent approach revealed that bacterial communities associated with ectomycorrhizal root tips differed significantly from those associated with roots uncolonized by ectomycorrhizal fungi. DGGE analysis of cultivable bacterial communities revealed no significant difference between ectomycorrhizal and uncolonized roots. Neither analytical approach revealed significant differences between the bacterial communities associated with ectomycorrhizal roots colonized by a Suillus sp. or an Atheliaceae taxon. Cloned bacterial 16S rRNA genes revealed sequence types closely related with that of Burkholderia phenazinium, common in both ectomycorrhizal-colonized and -uncolonized roots, while sequence types most similar to the potentially phyopathogenic bacteria Burkholderia andropogonis and Pantoea ananatis were only detected in ectomycorrhizal roots. These results highlight the possibility of global movement of microorganisms, including putative pathogens, as a result of the introduction of exotic pine plantations.

MicroRNAs (miRNAs) are known to regulate plant development, but have not been studied in gymnosperm seed tissues. The presence and characteristics of several miRNAs were examined in zygotic embryos (ZEs) and female gametophytes (FGs) of Pinus taeda (loblolly pine). Evidence for miRNAs was obtained using northern analyses and quantitative reverse transcription polymerase chain reaction (qRT-PCR) mediated with poly(A) polymerase. Partial sequences of two miRNAs were verified. Three regions of putative mRNA targets were analyzed by qRT-PCR to monitor the occurrence of stage-dependent miRNA-mediated cleavage. Five miRNAs were identified in ZEs and FGs along with partial sequences of Pta-miR166 and Pta-miR167. Both miRNAs showed differing degrees of tissue-specific and stage-specific modulation. Analysis of HB15L mRNA (a potential Pta-miR166 target) suggested miRNA-guided cleavage in ZEs and FGs. Analysis of ARF8L mRNA (a potential Pta-miR167 target) implied cleavage in ZEs but not in FGs. Argonaute9-like mRNA (ptAGO9L) showed stage-specific modulation of expression in ZEs that appeared to be inverted in the corresponding FGs. MicroRNAs and argonaute genes varied spatiotemporally during seed development. The peak levels of Pta-miR166 in FGs and ptAGO9L in embryos occurred at stage 9.1, a critical transition point during embryo development and a point where somatic embryo maturation often stops. MicroRNAs identified in FG tissue may play a role in embryogenesis.

Soils from a long term experiment, established in 1972, incorporating replicated treatments of burning every 2 and 4years with control plots were sampled in 2005 to determine the changes in microbial community structure, measured using phospholipid fatty acids (PLFAs) and functional diversity measured using multiple substrate induced respiration (SIR) tests (MicroResp™). Microbial biomass (total PLFA) in the 2year burn treatments was 50% less than both the control and 4-year burn treatments. There was also concomitantly less respiratory activity which mirrored the known changes in soil C and substrate quality. Contrary to other studies soil bacterial PLFAs were reduced as much as fungal PLFAs in the 2-year burn and the short term (6h) SIR of arginine, lysine, galactose and trehalose were significantly inhibited in the 2-year burn soils. The data suggest that a 4-year burn is a more sustainable practice for maintaining the original structure and function of the forest belowground ecosystem.