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The oxalate-carbonate pathway (OCP) involves degradation of soil oxalate to carbonate. To exploit and manage this natural mineralization of assimilated atmospheric CO 2 into stable carbonates, improved understanding of this complex biotransformation process is needed. A strain of oxalate-degrading bacteria, Azospirillum sp. OX-1, was isolated from soil, and its secondary products of calcium oxalate degradation were analyzed and characterized using SEM, XRD, TG/DTG-DTA and FTIR-spectroscopy. The molecular mechanism of calcium oxalate degradation was also analyzed using proteomics. The results showed, for the first time, that OX-1 could not only degrade calcium oxalate to calcium carbonate, but also that the process was accompanied by synthesis of methane. Proteomic analysis demonstrated that OX-1 has a dual enzyme system for calcium oxalate degradation, using formyl-CoA transferase (FRC) and thiamine pyrophosphate (ThDP)-dependent oxalyl-CoA decarboxylase (OXC) to form calcium carbonate. Up-regulated expression of enzymes related to methane synthesis was also detected during calcium oxalate degradation. Since methane is also a potent greenhouse gas, these new results suggest that the utility of exploiting the OCP to reduce atmospheric CO 2 must be re-evaluated and that further studies should be conducted to reveal how widespread the methane producing capacity of strain OX-1 is in other bacteria and soil environments., (© 2024. The Author(s).)

Tree growth in boreal forests is driven by ectomycorrhizal fungal mobilisation of organic nitrogen and mineral nutrients in soils with discrete organic and mineral horizons. However, there are no studies of how ectomycorrhizal mineral weathering and organic nitrogen mobilisation processes are integrated across the soil profile. We studied effects of organic matter (OM) availability on ectomycorrhizal functioning by altering the proportions of natural organic and mineral soil in reconstructed podzol profiles containing Pinus sylvestris plants, using 13 CO 2 pulse labelling, patterns of naturally occurring stable isotopes ( 26 Mg and 15 N) and high-throughput DNA sequencing of fungal amplicons. Reduction in OM resulted in nitrogen limitation of plant growth and decreased allocation of photosynthetically derived carbon and mycelial growth in mineral horizons. Fractionation patterns of 26 Mg indicated that magnesium mobilisation and uptake occurred primarily in the deeper mineral horizon and was driven by carbon allocation to ectomycorrhizal mycelium. In this horizon, relative abundance of ectomycorrhizal fungi, carbon allocation and base cation mobilisation all increased with increased OM availability. Allocation of carbon through ectomycorrhizal fungi integrates organic nitrogen mobilisation and mineral weathering across soil horizons, improving the efficiency of plant nutrient acquisition. Our findings have fundamental implications for sustainable forest management and belowground carbon sequestration., (© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation.)

Microbial mineralization is increasingly used in bioremediation of heavy metal pollution, but better mechanistic understanding of the processes involved and how they are regulated are required to improve the practical application of microorganisms in bioremediation. We used a combination of morphological (TEM) and analytical (XRD, XPS, FTIR) methods, together with novel proteomic analyses, to investigate the detoxification mechanisms, used by a range of bacteria, including the strains Bacillus velezensis LB002, Escherichia coli DH5α, B. subtilis 168, Pseudomonas putida KT2440, and B. licheniformis MT-1, exposed to elevated concentrations of Cd 2+ and combinations of Cd 2+ , Pb 2+ , Cu 2+ , and Zn 2+ , in the presence and absence of added CaCl 2 . Common features of detoxification included biomineralization, including the production of biological vaterite, up-regulation of proteins involved in flagellar movement and chemotaxis, biofilm synthesis, transmembrane transport of small molecules and organic matter decomposition. The putative roles of differentially expressed proteins in detoxification are discussed in relation to chemical and morphological data and together provide important tools to improve screening, selection, and practical application of bacterial isolates in bioremediation of polluted environments., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Nitrogen (N) fertilization is a routine practice in boreal forests but its effects on fungal functional guilds in Pinus sylvestris forests are still incompletely understood. Sampling is often restricted to the upper organic horizons and based on DNA extracted from mixtures of soil and roots without explicitly analysing different spatial niches. Fungal community structure in soil and roots of an 85-y-old Pinus sylvestris forest was investigated using high throughput sequencing. Fertilized plots had been treated with a single dose of N fertilizer, 15 months prior to sampling. Species richness of fungi colonizing roots was reduced in all horizons by N fertilization. In contrast, species richness of soil fungi in the organic horizon was increased by N fertilization, but unaffected in the mineral horizons. Community composition of fungi colonizing roots differed from that of soil fungi, and both communities were significantly influenced by soil horizon and N. The ectomycorrhizal community composition in both roots and soil was significantly affected by N fertilization but no significant effect was found on saprotrophic fungi. The results highlight the importance of analysing the rhizosphere soil and root compartments separately since the fungal communities in these two niches appear to respond differently to environmental perturbations involving the addition of nitrogen., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have influenced the work reported in this paper. Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020. Published by Elsevier B.V.)

Symbiotic ectomycorrhizal fungi have received increasing attention as regulators of below-ground organic matter storage. They are proposed to promote organic matter accumulation by suppressing saprotrophs, but have also been suggested to play an active role in decomposition themselves. Here we show that exclusion of tree roots and associated ectomycorrhizal fungi in a boreal forest increased decomposition of surface litter by 11% by alleviating nitrogen limitation of saprotrophs-a "Gadgil effect". At the same time, root exclusion decreased Mn-peroxidase activity in the deeper mor layer by 91%. Our results show that ectomycorrhizal fungi may hamper short-term litter decomposition, but also support a crucial role of ectomycorrhizal fungi in driving long-term organic matter oxidation. These observations stress the importance of ectomycorrhizal fungi in regulation of below-ground organic matter accumulation. By different mechanisms they may either hamper or stimulate decomposition, depending upon stage of decomposition and location in the soil profile.

The Fungal Kingdom is responsible for many ecosystem services as well as many industrial and agricultural products. Nevertheless, how these fungal species function and carry out these services is dependent on their capacity to grow under different stress conditions caused by a variety of abiotic factors such as ionizing radiation, UV radiation, extremes of temperature, acidity and alkalinity, and environments of low nutritional status, low water activity, or polluted with, e.g. toxic metals or xenobiotics. This article reviews some natural or synthetic environments where fungi thrive under stress and have important impacts in agriculture and forestry., (Copyright © 2018 British Mycological Society. Published by Elsevier Ltd. All rights reserved.)

Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonized by different fungi and analyzed differences in microbiome structure related to soils from distinct podzol horizons and effects of short-term additions of N, a growth-limiting nutrient commonly applied as a fertilizer, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonizing individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilized soil, but fertilization removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns., (© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Ectomycorrhizal (ECM) symbioses have evolved a minimum of 78 times independently from saprotrophic lineages, indicating the potential for functional overlap between ECM and saprotrophic fungi. ECM fungi have the capacity to decompose organic matter, and although there is increasing evidence that some saprotrophic fungi exhibit the capacity to enter into facultative biotrophic relationships with plant roots without causing disease symptoms, this subject is still not well studied. In order to determine the extent of biotrophic capacity in saprotrophic wood-decay fungi and which systems may be useful models, we investigated the colonization of conifer seedling roots in vitro using an array of 201 basidiomycete wood-decay fungi. Microtome sectioning, differential staining and fluorescence microscopy were used to visualize patterns of root colonization in microcosm systems containing Picea abies or Pinus sylvestris seedlings and each saprotrophic fungus. Thirty-four (16.9%) of the tested fungal species colonized the roots of at least one tree species. Two fungal species showed formation of a mantle and one showed Hartig net-like structures. These features suggest the possibility of an active functional symbiosis between fungus and plant. The data indicate that the capacity for facultative biotrophic relationships in free-living saprotrophic basidiomycetes may be greater than previously supposed., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)

In boreal forest soils, ectomycorrhizal fungi are fundamentally important for carbon (C) dynamics and nutrient cycling. Although their extraradical mycelium (ERM) is pivotal for processes such as soil organic matter build-up and nitrogen cycling, very little is known about its dynamics and regulation. In this study, we quantified ERM production and turnover, and examined how these two processes together regulated standing ERM biomass in seven sites forming a chronosequence of 12- to 100-yr-old managed Pinus sylvestris forests. This was done by determining ERM biomass, using ergosterol as a proxy, in sequentially harvested in-growth mesh bags and by applying mathematical models. Although ERM production declined with increasing forest age from 1.2 to 0.5 kg ha -1  d -1 , the standing biomass increased from 50 to 112 kg ha -1 . This was explained by a drastic decline in mycelial turnover from seven times to one time per year with increasing forest age, corresponding to mean residence times from 25 d up to 1 yr. Our results demonstrate that ERM turnover is the main factor regulating biomass across differently aged forest stands. Explicit inclusion of ERM parameters in forest ecosystem C models may significantly improve their capacity to predict responses of mycorrhiza-mediated processes to management and environmental changes., (© 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.)

Symbiotic ectomycorrhizal fungi mobilize nutrients from both organic and inorganic substrates and supply them to their host plants. Their role in mobilizing base cations and phosphorus from mineral substrates through weathering has received increasing attention in recent years but the processes involved remain to be elucidated. We grew selected ectomycorrhizal and nonmycorrhizal fungi in axenic systems containing mineral and organic substrates and examined their capacity to fractionate and assimilate stable isotopes of magnesium. The mycorrhizal fungi were significantly depleted in heavy isotopes with the lowest Δ 26 Mg values (the difference between δ 26 Mg in fungal tissue and δ 26 Mg in the substrate) compared with nonmycorrhizal fungi, when grown on mineral substrates containing granite particles. The ectomycorrhizal fungi accumulated significantly higher concentrations of Mg, K and P than the nonmycorrhizal fungi. There was a highly significant statistical relationship between δ 26 Mg tissue signature and mycelial concentration of Mg, with a clear separation between most ectomycorrhizal fungi and the nonmycorrhizal fungi. These results are consistent with the idea that ectomycorrhizal fungi have evolved efficient mechanisms to mobilize, transport and store Mg within their mycelia., (© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Symbiotic ectomycorrhizal tree roots represent an important niche for interaction with bacteria since the fungi colonizing them have a large surface area and receive a direct supply of photosynthetically derived carbon. We examined individual root tips of Pinus sylvestris at defined time points between 5 days and 24 weeks, identified the dominant fungi colonizing each root tip using Sanger sequencing and the bacterial communities colonizing individual root tips by 454 pyrosequencing. Bacterial colonization was extremely dynamic with statistically significant variation in time and increasing species richness until week 16 (3477 operational taxonomic units). Bacterial community structure of roots colonized by Russula sp. 6 GJ-2013b, Piloderma spp., Meliniomyces variabilis and Paxillus involutus differed significantly at weeks 8 and 16 but diversity declined and significant differences were no longer apparent at week 24. The most common genera were Burkholderia, Sphingopyxsis, Dyella, Pseudomonas, Acinetobacter, Actinospica, Aquaspirillum, Acidobacter Gp1, Sphingomonas, Terriglobus, Enhydrobacter, Herbaspirillum and Bradyrhizobium. Many genera had high initial abundance at week 8, declining with time but Dyella and Terriglobus increased in abundance at later time points. In roots colonized by Piloderma spp. several other bacterial genera, such as Actinospica, Bradyrhizobium, Acidobacter Gp1 and Rhizomicrobium appeared to increase in abundance at later sampling points., (© 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Background: Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq., Results: Approximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10% of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log2 fold-change > 3 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation., Conclusions: This RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.

There is currently an urgent need to increase global food security, reverse the trends of increasing cancer rates, protect environmental health, and mitigate climate change. Toward these ends, it is imperative to improve soil health and crop productivity, reduce food spoilage, reduce pesticide usage by increasing the use of biological control, optimize bioremediation of polluted sites, and generate energy from sustainable sources such as biofuels. This review focuses on fungi that can help provide solutions to such problems. We discuss key aspects of fungal stress biology in the context of the papers published in this Special Issue of Current Genetics. This area of biology has relevance to pure and applied research on fungal (and indeed other) systems, including biological control of insect pests, roles of saprotrophic fungi in agriculture and forestry, mycotoxin contamination of the food-supply chain, optimization of microbial fermentations including those used for bioethanol production, plant pathology, the limits of life on Earth, and astrobiology.

Boreal forest soils store a major proportion of the global terrestrial carbon (C) and below-ground inputs contribute as much as above-ground plant litter to the total C stored in the soil. A better understanding of the dynamics and drivers of root-associated fungal communities is essential to predict long-term soil C storage and climate feedbacks in northern ecosystems. We used 454-pyrosequencing to identify fungal communities across fine-scaled soil profiles in a 5000 yr fire-driven boreal forest chronosequence, with the aim of pinpointing shifts in fungal community composition that may underlie variation in below-ground C sequestration. In early successional-stage forests, higher abundance of cord-forming ectomycorrhizal fungi (such as Cortinarius and Suillus species) was linked to rapid turnover of mycelial biomass and necromass, efficient nitrogen (N) mobilization and low C sequestration. In late successional-stage forests, cord formers declined, while ericoid mycorrhizal ascomycetes continued to dominate, potentially facilitating long-term humus build-up through production of melanized hyphae that resist decomposition. Our results suggest that cord-forming ectomycorrhizal fungi and ericoid mycorrhizal fungi play opposing roles in below-ground C storage. We postulate that, by affecting turnover and decomposition of fungal tissues, mycorrhizal fungal identity and growth form are critical determinants of C and N sequestration in boreal forests., (© 2014 The Authors New Phytologist © 2014 New Phytologist Trust.)

Rhizobacteria with biocontrol ability exploit a range of mechanisms to compete successfully with other microorganisms and to ensure their growth and survival in the rhizosphere, ultimately promoting plant growth. The rhizobacterium Serratia plymuthica AS13 is able to promote oilseed rape growth and improve seedling survival in the presence of the fungal pathogen, Rhizoctonia solani AG 2-1; however, our understanding of the mechanisms underlying the antagonism of Serratia is limited. To elucidate possible mechanisms, genome-wide gene expression profiling of S. plymuthica AS13 was carried out in the presence or absence of R. solani. We used RNA sequencing methodology to obtain a comprehensive overview of Serratia gene expression in response to R. solani. The differential gene expression profiles of S. plymuthica AS13 revealed significantly increased expression of genes related to the biosynthesis of the antibiotic pyrrolnitrin (prnABCD), protease production and transporters. The results presented here provide evidence that antibiosis is a major functional mechanism underlying the antagonistic behaviour of S. plymuthica AS13., (© 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.

Boreal forests are characterized by spatially heterogeneous soils with low N availability. The decomposition of coniferous litter in these systems is primarily performed by basidiomycete fungi, which often form large mycelia with a well-developed capacity to reallocate resources spatially- an advantageous trait in heterogeneous environments. In axenic microcosm systems we tested whether fungi increase their biomass production by reallocating N between Pinus sylvestris (Scots pine) needles at different stages of decomposition. We estimated fungal biomass production by analysing the accumulation of the fungal cell wall compound chitin. Monospecific systems were compared with systems with interspecific interactions. We found that the fungi reallocated assimilated N and mycelial growth away from well-degraded litter towards fresh litter components. This redistribution was accompanied by reduced decomposition of older litter. Interconnection of substrates increased over-all fungal C use efficiency (i.e. the allocation of assimilated C to biomass rather than respiration), presumably by enabling fungal translocation of growth-limiting N to litter with higher C quality. Fungal connection between different substrates also restricted N-mineralization and production of dissolved organic N, suggesting that litter saprotrophs in boreal forest ecosystems primarily act to redistribute rather than release N. This spatial integration of different resource qualities was hindered by interspecific interactions, in which litters of contrasting quality were colonised by two different basidiomycete species. The experiments provide a detailed picture of how resource reallocation in two decomposer fungi leads to a more efficient utilisation of spatially separated resources under N-limitation. From an ecosystem point of view, such economic fungal behaviour could potentially contribute to organic matter accumulation in the litter layers of boreal forests.

Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild Equisetum sp., has the ability to stimulate plant growth and to suppress the growth of several soil-borne fungal pathogens of economically important crops. Here we present the non-contiguous, finished genome sequence of S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a 129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58 pseudogenes. This genome is a part of the project "Genomics of four rapeseed plant growth-promoting bacteria with antagonistic effect on plant pathogens" awarded through the 2010 DOE-JGI's Community Sequencing Program.

Serratia plymuthica AS13 is a plant-associated Gammaproteobacteria, isolated from rapeseed roots. It is of special interest because of its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The complete genome of S. plymuthica AS13 consists of a 5,442,549 bp circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced as part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens" within the 2010 DOE-JGI Community Sequencing Program (CSP2010).

The aim of this study was to assess belowground occurrence, persistence and possible impact of the biocontrol agent Phlebiopsis gigantea (Fr.) Jülich on soil fungi. Sampling of soil and roots of Picea abies (L.) H. Karst. was carried out at 12 P. gigantea-treated and five nontreated control sites representing 1- to 60-month-old clear-cuts and thinned forest sites in Finland and Latvia. The 454-sequencing of ITS rRNA from fine roots, humus and mineral soil resulted in 8626 high-quality fungal sequences. Phlebiopsis gigantea represented 1.3% of all fungal sequences and was found in 14 treated and nontreated sites and in all three substrates. In different substrates, the relative abundance of P. gigantea at stump treatment sites either did not differ significantly or was significantly lower than in nontreated controls. No significant correlation was found between the time elapsed since the tree harvesting and/or application of the biocontrol and abundance of P. gigantea in different substrates. In conclusion, the results demonstrate that P. gigantea occasionally occurs belowground in forest ecosystems but that stump treatment with the biocontrol agent has little or no impact on occurrence and persistence of P. gigantea belowground, and consequently no significant impact on soil fungi., (© 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest because it promotes plant growth and inhibits plant pathogens. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens".

The ecology and physiology of ectomycorrhizal (EcM) symbiosis with conifer trees are well documented. In comparison, however, very little is known about the molecular regulation of these associations. In an earlier study, we identified three EcM-regulated Pinus expressed sequence tags (EST), two of which were identified as homologous to the Medicago truncatula nodulin MtN21. The third EST was a homologue to the receptor-like kinase Clavata1. We have characterized the expression patterns of these genes and of auxin- and mycorrhiza-regulated genes after induction with indole-3-butyric acid in Pinus sylvestris and in a time course experiment during ectomycorrhizal initiation with the co-inoculation of 2,3,5-triiodobenzoic acid, an auxin transport inhibitor. Our results suggest that different P. sylvestris nodulin homologues are associated with diverse processes in the root. The results also suggest a potential role of the Clv1-like gene in lateral root initiation by the ectomycorrhizal fungus., (© The Author(s) 2011. This article is published with open access at Springerlink.com)

Serratia plymuthica are plant-associated, plant beneficial species belonging to the family Enterobacteriaceae. The members of the genus Serratia are ubiquitous in nature and their life style varies from endophytic to free-living. S. plymuthica AS9 is of special interest for its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The genome of S. plymuthica AS9 comprises a 5,442,880 bp long circular chromosome that consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome is part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens" awarded through the 2010 DOE-JGI Community Sequencing Program (CSP2010).

Arbuscular mycorrhizal fungi are widespread plant symbionts occurring in most agricultural crops, where they can play key roles in the growth and health of their plant hosts. Plant benefits can depend on the identity of the associated arbuscular mycorrhizal fungi (AMF), but little is known about the identity of the fungal partners in most agricultural systems. In this study, we describe the AMF assemblages associated with four cultivars of strawberry in an outdoor experiment using two field soils with different origin and management history. Assemblages were characterised by clone library sequencing of 18S rRNA gene fragments. Soil dramatically influenced the degree of mycorrhizal colonisation and AMF assemblage structure in the roots. No differences were observed between cultivars. Fungi belonging to the genus Acaulospora dominated the AMF assemblages in one soil, but they were not detected in the other. These results suggest that physicochemical soil characteristics and management can play a role in determining the identity and structure of microbial communities associated with particular hosts in agricultural systems.

Ectomycorrhizal (ECM) roots represent important niches for interactions with bacteria and ascomycete fungi, since they have a large surface area and receive a direct supply of plant assimilates from their tree hosts. We tested the hypothesis that the roots colonized by specific ECM fungi harbour distinct bacteria/ascomycete communities. Roots were collected from two different locations in a subarctic shrub forest dominated by Betula pubescens. Bacterial and ascomycete communities were analysed by PCR-DGGE and sequencing, in roots colonized by five frequently observed ECM fungi, Leccinum variicolor, Piloderma fallax, Tomentellopsis submollis, Lactarius torminosus and Pseudotomentella tristis. The bacterial communities associated with P. fallax- or P. tristis-colonized roots were distinct from those associated with roots colonized by three other ECM fungi at both sampling locations. Bacterial communities associated with T. submollis-, L. torminosus- and L. variicolor-colonized roots were more similar to each other. Lactarius- and Pseudotomentella-colonized roots hosted distinct ascomycete communities at one site while only the community associated with Lactarius was distinct at the second location. The results thus suggest that while the community structure of bacteria colonizing ECM roots can be influenced by the local soil environment, there can also be a strong selective effect of particular fungal symbionts., (© 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.)

Ectomycorrhizal fungi dominate the humus layers of boreal forests. They depend on carbohydrates that are translocated through roots, via fungal mycelium to microsites in the soil, wherein they forage for nutrients. Mycorrhizal fungi are therefore sensitive to disruptive disturbances that may restrict their carbon supply. By disrupting root connections, we induced a sudden decline in mycorrhizal mycelial abundance and studied the consequent effects on growth and activity of free living, saprotrophic fungi and bacteria in pine forest humus, using molecular community analyses in combination with enzyme activity measurements. Ectomycorrhizal fungi had decreased in abundance 14 days after root severing, but the abundance of certain free-living ascomycetes was three times higher within 5 days of the disturbance compared with undisturbed controls. Root disruption also increased laccase production by an order of magnitude and cellulase production by a factor of 5. In contrast, bacterial populations seemed little affected. The results indicate that access to an external carbon source enables mycorrhizal fungi to monopolise the humus, but disturbances may induce rapid growth of opportunistic saprotrophic fungi that presumably use the dying mycorrhizal mycelium. Studies of such functional shifts in fungal communities, induced by disturbance, may shed light on mechanisms behind nutrient retention and release in boreal forests. The results also highlight the fundamental problems associated with methods that study microbial processes in soil samples that have been isolated from living roots.

In this study, we investigated the impact of organic and mineral fertilizers on the community composition of arbuscular mycorrhizal (AM) fungi and bacteria in the mycorrhizosphere of maize in a field experiment established in 1956, in south-east Sweden. Roots and root-associated soil aggregates were sampled four times during the growing season in 2005, in control plots and in plots amended with calcium nitrate, ammonium sulphate, green manure, farmyard manure or sewage sludge. Fungi in roots were identified by cloning and sequencing, and bacteria in soil aggregates were analysed by terminal-restriction fragment length polymorphism, cloning and sequencing. The community composition of AM fungi and bacteria was significantly influenced by the different fertilizers. Changes in microbial community composition were mainly correlated with changes in pH induced by the fertilization regime. However, other factors, including phosphate and soil carbon content, also contributed significantly to these changes. Changes in bacterial community composition and a reduction in bacterial taxon richness throughout the growing season were also manifest. The results of this study highlight the importance and significant effects of the long-term application of different fertilizers on edaphic factors and specific groups of fungi and bacteria playing a key role in arable soils.

Background: Symbiotic ectomycorrhizal associations of fungi with forest trees play important and economically significant roles in the nutrition, growth and health of boreal forest trees, as well as in nutrient cycling. The ecology and physiology of ectomycorrhizal associations with Pinus sp are very well documented but very little is known about the molecular mechanisms behind these mutualistic interactions with gymnosperms as compared to angiosperms., Results: Using a micro-array approach, the relative abundance of 2109 EST transcripts during interaction of Pinus sylvestris roots with the ectomycorrhizal fungus was profiled. The results reveal significant differential expression of a total of 236 ESTs, 96 transcripts differentially abundant after 1 day of physical contact with the fungus, 134 transcripts after 5 days and only 6 after 15 days at early stages of mantle formation on emerging lateral roots. A subset of cell wall modification and stress related genes was further assessed by quantitative reverse transcription PCR at late stages of mycorrhizal development coinciding with Hartig net formation. The results reveal down regulation of gene transcripts involved in general defence mechanism (e.g. antimicrobial peptide) as well as those involved in cell wall modification (e.g. glycine rich protein, xyloglucan endo transglycosylase)., Conclusion: This study constitutes the first attempt to characterize the transcriptome of the plant partner in the Pinus sylvestris - Laccaria bicolor model system. We identified 236 ESTs which are potentially important for molecular regulation of a functional symbiotic association in conifer host. The results highlight similarities with other studies based on angiosperm model systems, nevertheless some differences were found in the timing and spatial scale of gene regulation during ectomycorrhiza development in gymnosperms. The present study has identified a number of potentially important molecular events responsible for the initiation and regulation of biochemical, physiological and morphological changes during development of a fully functional symbiosis that are relevant for gymnosperm hosts.

Different symbiotic mycorrhizal associations between plants and fungi occur, almost ubiquitously, in a wide range of terrestrial ecosystems. Historically, these have mainly been considered within the rather narrow perspective of their effects on the uptake of dissolved mineral nutrients by individual plants. More recent research has placed emphasis on a wider, multifunctional perspective, including the effects of mycorrhizal symbiosis on plant and microbial communities, and on ecosystem processes. This includes mobilization of N and P from organic polymers, release of nutrients from mineral particles or rock surfaces via weathering, effects on carbon cycling, interactions with myco-heterotrophic plants, mediation of plant responses to stress factors such as drought, soil acidification, toxic metals, and plant pathogens, as well as a range of possible interactions with groups of other soil micro-organisms. Mycorrhizal fungi connect their plant hosts to the heterogeneously distributed nutrients required for their growth, enabling the flow of energy-rich compounds required for nutrient mobilization whilst simultaneously providing conduits for the translocation of mobilized products back to their hosts. In addition to increasing the nutrient absorptive surface area of their host plant root systems, the extraradical mycelium of mycorrhizal fungi provides a direct pathway for translocation of photosynthetically derived carbon to microsites in the soil and a large surface area for interaction with other micro-organisms. The detailed functioning and regulation of these mycorrhizosphere processes is still poorly understood but recent progress is reviewed and potential benefits of improved understanding of mycorrhizosphere interactions are discussed.

Symbiotic arbuscular mycorrhizal fungi (AMF) have been shown to influence both the diversity and productivity of grassland plant communities. These effects have been postulated to depend on the differential effects of individual mycorrhizal taxa on different plant species; however, so far there are few detailed studies of the dynamics of AMF colonization of different plant species. In this study, we characterized the communities of AMF colonizing the roots of two plant species, Prunella vulgaris and Antennaria dioica, in a Swedish seminatural grassland at different times of the year. The AMF small subunit rRNA genes were subjected to PCR, cloning, sequencing, and phylogenetic analysis. Nineteen discrete sequence types belonging to Glomus groups A and B and to the genus Acaulospora were distinguished. No significant seasonal changes in the species compositions of the AMF communities as a whole were observed. However, the two plant species hosted significantly different AMF communities. P. vulgaris hosted a rich AMF community throughout the entire growing season. The presence of AMF in A. dioica decreased dramatically in autumn, while an increased presence of Ascomycetes species was detected.

Plant root systems colonized by arbuscular mycorrhizal (AM) fungi have previously been shown to influence soil bacterial populations; however, the direct influence of the AM extraradical mycelium itself on bacterial growth and community composition is not well understood. In this study, we investigated the effects of exudates produced by AM extraradical mycelia on the growth and development of an extracted soil bacterial community in vitro. The chemical composition of the mycelial exudates was analysed using proton nuclear magnetic resonance spectrometry. Following the addition of exudates to a bacterial community extracted from soil, bacterial growth and vitality were determined using a bacterial vitality stain and fluorescence microscopy. Changes in community composition were also analysed at various times over the course of 3 days by terminal restriction fragment length polymorphism analysis, in combination with cloning and sequencing of 16S rRNA genes. Mycelial exudates increased bacterial growth and vitality and changed bacterial community composition. Several Gammaproteobacteria, including a taxon within the Enterobacteriaceae, increased in frequency of occurrence in response to AM mycelial exudates. This study is the first attempt to identify carbohydrates from the extraradical mycelium of an AM fungus, and demonstrates the direct effects of mycelial exudates on a soil bacterial community.

The mycorrhizal basidiomycetes are known to have multiple, independent evolutionary origins from saprotrophic ancestors. To date, a number of studies have revealed functional resemblance of mycorrhizal fungi to free-living saprotrophs, but information on the ability of saprotrophic fungi to perform as mycorrhizal symbionts is scarce. Here, the objective was to investigate the ability of three wood-decay fungi, Phlebiopsis gigantea, Phlebia centrifuga and Hypholoma fasciculare, to colonize fine roots of conifer seedlings. For each fungus, mycorrhizal syntheses were attempted with Picea abies and Pinus sylvestris. After 24 wk, isolation of fungi and direct sequencing of fungal internal transcribed spacer (ITS) rDNA were carried out from healthy-looking surface-sterilized root tips that yielded both pure cultures and ITS sequences of each inoculated strain. Mycelial mantle of P. gigantea was frequently formed on root tips of P. abies, and microscopical examination has shown the presence of intercellular hyphae inside the roots. The results provide evidence of the ability of certain wood-decay fungi to colonise fine roots of tree seedlings.

Our understanding of how saprotrophic and mycorrhizal fungi interact to re-circulate carbon and nutrients from plant litter and soil organic matter is limited by poor understanding of their spatiotemporal dynamics. In order to investigate how different functional groups of fungi contribute to carbon and nitrogen cycling at different stages of decomposition, we studied changes in fungal community composition along vertical profiles through a Pinus sylvestris forest soil. We combined molecular identification methods with 14C dating of the organic matter, analyses of carbon:nitrogen (C:N) ratios and 15N natural abundance measurements. Saprotrophic fungi were primarily confined to relatively recently (< 4 yr) shed litter components on the surface of the forest floor, where organic carbon was mineralized while nitrogen was retained. Mycorrhizal fungi dominated in the underlying, more decomposed litter and humus, where they apparently mobilized N and made it available to their host plants. Our observations show that the degrading and nutrient-mobilizing components of the fungal community are spatially separated. This has important implications for biogeochemical studies of boreal forest ecosystems.

Attachment of certain bacteria to living arbuscular mycorrhizal fungal extraradical hyphae may be an important prerequisite for interactions between these microorganisms, with implications for nutrient supply and plant health. The attachment of five different strains of gfp-tagged soil bacteria (Paenibacillus brasilensis PB177 (pnf8), Bacillus cereus VA1 (pnf8), Pseudomonas fluorescens SBW25 :: gfp/lux, Arthrobacter chlorophenolicus A6G, and Paenibacillus peoriae BD62 (pnf8)) to vital and nonvital extraradical hyphae of the arbuscular mycorrhizal fungi Glomus sp. MUCL 43205 and Glomus intraradices MUCL 43194 was examined. Arthrobacter chlorophenolicus did not attach to hyphae, whereas the other bacterial strains did to a varying degree. Only P. brasilensis showed greater attachment to vital hyphae than nonvital hyphae of both Glomus species tested. Pseudomonas fluorescens showed a higher attachment to vital compared with nonvital Glomus sp. MUCL 43205 hyphae, whereas this relationship was opposite for attachment to G. intraradices. Both B. cereus and P. peoriae showed higher attachment to nonvital hyphae. This study provides novel evidence that under laboratory conditions soil bacteria differ in their ability to colonize vital and nonvital hyphae and that this can also be influenced by the arbuscular mycorrhizal fungal species involved. The significance of bacterial attachment to mycorrhizal fungal extraradical hyphae is discussed.

Accurate estimates of mycelial exudation in time and space are crucial for the assessment of ectomycorrhizal involvement in biogeochemical processes. Knowledge of exudation from mycelia of ectomycorrhizal fungi is still limited, especially for fungi in symbiosis with a host. Pinus sylvestris seedlings colonized by Hebeloma crustuliniforme were grown in aseptic multicompartment dishes. This novel system enabled identification of exudates originating only from extramatrical mycelium. At harvest, hyphal density and numbers were estimated using microscopic imaging. A fractal geometric approach was adopted for calculation of exudation rates. The main compounds identified were oxalate and ferricrocin. The exudation rate for oxalate was 19 +/- 3 fmol per hyphal tip h(-1) (mean +/- standard error of the mean) or 488 +/- 95 fmol hyphal mm(-2) h(-1). Ferricrocin rates were approx. 10 000 times lower. The fractal dimension (D) of the mycelia was 1.4 +/- 0.1, suggesting an explorative growth. Potassium nutrition was a significant regulatory factor for ferricrocin but not oxalate. The results suggest that hyphal exudation may alter the chemical conditions of soil microsites and affect mineral dissolution. Calculations also indicated that oxalate exudation may be a significant carbon sink.

The community of arbuscular mycorrhizal fungi (AMF) colonizing the roots of Festuca pratensis and Achillea millefolium was characterized in a Swedish pasture at different times, along a gradient of fertilization. The small subunit ribosomal RNA gene was subjected to PCR and denaturing gradient gel electrophoresis (DGGE), sequencing and phylogenetic analysis. The sequences found in this study clustered in 10 discrete sequence groups, seven belonging to Glomus, two to Scutellospora and one to Diversispora. A negative correlation was observed between soil mineral nitrogen and the number of AMF sequence groups in the roots. The frequency of occurrence of AMF in roots decreased dramatically between June and September. No plant-host specificity could be detected.

The nitrogen (N) content of wood is usually suboptimal for fungal colonization. During decomposition of wood, an increasing fraction of the N becomes incorporated into fungal mycelium. Between 5 and 50% of the N in wood-degrading mycelium may be incorporated into chitin. Chitinolytic enzymes render this N available for re-utilization. Here, the activities of chitinolytic enzymes produced by wood-rotting fungi during degradation of spruce (Picea abies) wood were quantified in situ using fluorogenic 4-methylumbelliferyl substrates. A new method was developed that enables spatial quantification of enzyme activities on solid surfaces. All of the three tested fungi produced endochitinases, chitobiosidases and N-acetylhexosaminidases during colonization of wood. N-acetylhexosaminidase activity, and in some cases also chitobiosidase and endochitinase activities, were higher during secondary overgrowth of another fungus than during primary colonization of noncolonized wood. The results suggest that wood-degrading fungi degrade their own cell walls as well as the hyphae of earlier colonizers. Recycling of cell wall material within single mycelia and between fungal individuals during succession may lead to retention of N within woody debris.

Arbuscular mycorrhizal (AM) fungi and bacteria can interact synergistically to stimulate plant growth through a range of mechanisms that include improved nutrient acquisition and inhibition of fungal plant pathogens. These interactions may be of crucial importance within sustainable, low-input agricultural cropping systems that rely on biological processes rather than agrochemicals to maintain soil fertility and plant health. Although there are many studies concerning interactions between AM fungi and bacteria, the underlying mechanisms behind these associations are in general not very well understood, and their functional properties still require further experimental confirmation. Future mycorrhizal research should therefore strive towards an improved understanding of the functional mechanisms behind such microbial interactions, so that optimized combinations of microorganisms can be applied as effective inoculants within sustainable crop production systems. In this context, the present article seeks to review and discuss the current knowledge concerning interactions between AM fungi and plant growth-promoting rhizobacteria, the physical interactions between AM fungi and bacteria, enhancement of phosphorus and nitrogen bioavailability through such interactions, and finally the associations between AM fungi and their bacterial endosymbionts. Overall, this review summarizes what is known to date within the present field, and attempts to identify promising lines of future research.

High numbers of bacteria are associated with arbuscular mycorrhizal (AM) fungi, but their functions and in situ activities are largely unknown and most have never been characterized. The aim of the present study was to study the impact of Glomus mosseae inoculation and plant type on the active bacterial communities in soil by using a molecular approach, bromodeoxyuridine (BrdU) immunocapture in combination with terminal-restriction fragment length polymorphism (T-RFLP). This approach combined with sequence information from clone libraries, enabled the identification of actively growing populations, within the total bacterial community. Distinct differences in active bacterial community compositions were found according to G. mosseae inoculation, treatment with an antifungal compound (Benomyl) and plant type. The putative identities of the dominant bacterial species that were activated as a result of G. mosseae inoculation were found to be mostly uncultured bacteria and Paenibacillus species. These populations may represent novel bacterial groups that are able to influence the AM relationship and its subsequent effect on plant growth.

Effects of elevated atmospheric carbon dioxide (CO2) levels on the production and spread of ectomycorrhizal fungal mycelium from colonised Scots pine roots were investigated. Pinus sylvestris (L.) Karst. seedlings inoculated with either Hebeloma crustuliniforme (Bull:Fr.) Quel. or Paxillus involutus (Fr.) Fr. were grown at either ambient (350 ppm) or elevated (700 ppm) levels of CO2. Mycelial production was measured after 6 weeks in pots, and mycelial spread from inoculated seedlings was studied after 4 months growth in perlite in shallow boxes containing uncolonised bait seedlings. Plant and fungal biomass were analysed, as well as carbon and nitrogen content of seedling shoots. Mycelial biomass production by H. crustuliniforme was significantly greater under elevated CO2 (up to a 3-fold increase was observed). Significantly lower concentrations and total amounts of N were found in plants exposed to elevated CO2.

•  Ectomycorrhizal fungi occur abundantly in the mineral horizons of forest soils, but their interactions with mineral substrates are largely unknown. We have examined the proliferation of ectomycorrhizal roots and mycelium colonising different mineral substrates. •  By exposing the shoots of Pinus sylvestris seedlings to air containing 14 CO 2 , the carbon allocation patterns in intact ectomycorrhizal associations could be monitored using electronic autoradiography. •  In plants colonised by either Hebeloma crustuliniforme or Piloderma fallax, a larger fraction of the photosynthetically derived carbon was allocated to a mineral soil substrate compared with a Sphagnum peat. In mycorrhizal seedlings colonised by H. crustuliniforme, carbon allocation was significantly greater to roots and mycelia colonising patches of pure potassium feldspar than to those in patches of quartz. •  These results suggest that ectomycorrhizal mycelia may respond to the presence of different mineral substrates by regulating their growth and activity.

In sustainable, low-input cropping systems the natural roles of microorganisms in maintaining soil fertility and biocontrol of plant pathogens may be more important than in conventional agriculture where their significance has been marginalised by high inputs of agrochemicals. Better understanding of the interactions between arbuscular mycorrhizal fungi and other microorganisms is necessary for the development of sustainable management of soil fertility and crop production. Many studies of the influence of mycorrhizal colonisation on associated bacterial communities have been conducted, however, the mechanisms of interaction are still poorly understood. Novel approaches including PCR-based methods, stable isotope profiling, and molecular markers have begun to shed light on the activity, identity and spatiotemporal location of bacteria in the mycorrhizosphere. This paper reviews current knowledge concerning the interactions between arbuscular mycorrhizal fungi and other microorganisms, particularly bacteria, and discusses the implications these interactions may have in sustainable agriculture.

A colorimetric method was developed to permit semi-quantitative measurement of substrate acidification by different ectomycorrhizal and one saprotrophic fungus growing on media containing one of five different minerals. Overall, substrate acidification differed between fungal species and the degree of variation in acidification in response to different minerals was highly species-dependent. Mycena galopus and Cortinarius glaucopus produced the least biomass of all tested species and produced the highest amount of acidification per unit mycelial density. Substrate acidification by C. glaucopus was inversely related to mycelial density, with particularly high acidification at low mycelial density on medium enriched with tri-calcium phosphate. Substrate acidification by M. galopus was constant irrespective of mycelial density and varied only according to mineral treatment, with higher substrate acidification on tri-calcium phosphate compared to the other minerals.

Models of the effects of elevated concentrations of aluminum (Al) on growth and nutrient uptake of forest trees frequently ignore the effects of mycorrhizal fungi. In this study, we present novel data indicating that ectomycorrhizal mycelia may prevent leaching of base cations and Al. Mycorrhizal and non-mycorrhizal Pinus sylvestris L. seedlings were grown in sand obtained from the B-horizon of a local forest. In Experiment 1, non-mycorrhizal seedlings and seedlings inoculated with Hebeloma cf. longicaudum (Pers.: Fr.) Kumm. ss. Lange or Laccaria bicolor (Maire) Orton were provided with nutrient solution containing 2.5 mM Al. Aluminum did not affect growth of non-mycorrhizal seedlings or seedlings inoculated with L. bicolor. Seedlings colonized by H. cf. longicaudum had the highest biomass production of all seedlings grown without added Al, but the fungus did not tolerate Al. Shoots of seedlings colonized by L. bicolor had the lowest nitrogen (N) concentrations but the highest phosphorus (P) concentrations of all seedlings. The treatments had small but significant effects on shoot and root Al concentrations. In Experiment 2, inoculation with L. bicolor was factorially combined with the addition of a complete nutrient solution, or a solution lacking the base cations K, Ca and Mg, and solutions containing 0 or 0.74 mM Al. Seedling growth decreased in response to 0.74 mM Al, but the effect was significant only for non-mycorrhizal seedlings. Mycorrhizal seedlings generally had higher P concentrations than non-mycorrhizal seedlings. Aluminum reduced P uptake in non-mycorrhizal plants but had no effect on P uptake in mycorrhizal plants. Mycorrhizal colonization increased the pH of the soil solution by about 0.5 units and addition of Al decreased the pH by the same amount. We conclude that the presence of ectomycorrhizal mycelia decreased leaching of base cations and Al from the soil.

Abstract Plant growth, nutrient uptake, microbial biomass and activity were studied in pot systems containing spruce seedlings colonised with different ectomycorrhizal fungi from an ash-fertilised forest. The seedling root systems were enclosed in mesh bags inside an outer compartment containing crushed, hardened wood ash. Three different species of mycorrhizal fungi and a non-mycorrhizal control were exposed to factorial combinations of ash and N addition. Ash treatment had a highly significant, positive effect on plant growth and on shoot and root concentrations of K, Ca and P, irrespective of mycorrhizal status. Mycorrhizal inoculation had a significant effect on plant growth, which was proportionally greater in the absence of ash. N addition had a significant positive effect on plant biomass in mycorrhizal treatments with ash, but no effect in non-mycorrhizal treatments or most of the mycorrhizal treatments without ash. Piloderma sp. 1, which was earlier found to colonise wood ash granules in field studies, appeared to accumulate Ca from ash in the mycorrhizal roots. 5-6.7% of the total P in the ash was solubilised, with 0.9-1.5% in solution, 3.6-4.6% in the plants and 0.5-1.5% in microbial biomass. Bacterial activity as determined by [(3)H]-thymidine and [(14)C]-leucine incorporation was significantly greater in ash treatments than in controls with no ash addition. Principal component analysis (PCA) of phospholipid fatty acids (PLFAs) showed a clear difference in bacterial community structure between samples collected from ash-treated pots and controls without ash.

•  Changes in below-ground ectomycorrhizal (ECM) community structure in response to elevated CO 2 and balanced nutrient addition were investigated in a 37-yr-old Picea abies forest. • Trees in whole-tree chambers were exposed to factorial combinations of ambient/elevated CO 2 (700 ppm) and fertilization (+/-). ECM fungal community structure was determined in 1997 and 2000 using a combination of morphotyping and molecular analyses. Samples were taken both from chambers and from reference trees receiving the same fertilization treatments but without chambers. • Significant effects on ECM community structure were found in response to elevated CO 2 . Neither elevated CO 2 nor fertilization altered species richness; however, there was considerable variation among samples, which may have masked treatment effects on individual species. After 3 yr, the effects of elevated CO 2 on community composition were of the same magnitude as those seen after 15 yr of fertilization treatment. • Our results show that increasing atmospheric CO 2 concentrations affect the community structure of root symbionts colonizing forest trees. The potential effects of altered ECM community structure on allocation and turnover of carbon and nutrients within forest ecosystems are discussed.

Studies of effects of fertilizer treatment on ectomycorrhizal fungal community structure have predominantly been based on large, single additions of nitrogen. Studies involving chronic additions of nutrients in combination with irrigation are much less common. We used morphotyping to study effects of balanced additions of a nutrient solution on ectomycorrhizal fungal community structure in a 36-year-old stand of Picea abies (L.) Karst. Despite high variability among individual samples, principal components analysis revealed a clear shift in community structure in response to fertilization. Irrigated plots receiving only water did not differ significantly from untreated control plots. Mycorrhizal root tips colonized by Cenococcum geophilum Fr. were significantly more common in fertilized plots than in control plots. Possible responses by other ectomycorrhizal species were masked by high variability. Over sixty morphotypes were distinguished, but there was no measurable effect of either fertilizer or irrigation treatment on morphotype richness or total number of root tips.