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For soils in carbon balance, losses of soil carbon from biological activity are balanced by organic inputs from vegetation. Perturbations, such as climate or land use change, have the potential to disrupt this balance and alter soil-atmosphere carbon exchanges. As the quantification of soil organic matter stocks is an insensitive means of detecting changes, certainly over short timescales, there is a need to apply methods that facilitate a quantitative understanding of the biological processes underlying soil carbon balance. We outline the processes by which plant carbon enters the soil and critically evaluate isotopic methods to quantify them. Then, we consider the balancing CO(2) flux from soil and detail the importance of partitioning the sources of this flux into those from recent plant assimilate and those from native soil organic matter. Finally, we consider the interactions between the inputs of carbon to soil and the losses from soil mediated by biological activity. We emphasize the key functional role of the microbiota in the concurrent processing of carbon from recent plant inputs and native soil organic matter. We conclude that quantitative isotope labelling and partitioning methods, coupled to those for the quantification of microbial community substrate use, offer the potential to resolve the functioning of the microbial control point of soil carbon balance in unprecedented detail.

Summary: Cluster roots of white lupin are induced by low phosphorus (LP) to efficiently access unavailable P, but how soilborne microbes are associated with cluster root formation (CRF) is unclear.We investigated the roles of soilborne bacteria in CRF response to LP by high‐throughput sequencing and root–bacteria interactions.Cluster root number was significantly decreased in plants grown in sterilized soil compared with nonsterilized soil. Proteobacteria was enriched in CR, as shown by microbiome analysis of soil (bulk, rhizosphere, and rhizosheath) and roots (main, lateral, and CR). Large‐scale gene expression level implicated ethylene mediation in CRF. Klebsiella pneumoniae (P7), a soilborne bacterium belonging to Proteobacteria, was isolated from CR. Among 11 isolated strains, P7 exhibited the highest 1‐aminocyclopropane‐1‐carboxylate deaminase (ACCD) activity; this enzyme inhibits the biosynthesis of ethylene in plants by the cleavage of the ethylene precursor 1‐aminocyclopropane‐1‐carboxylic acid and promotes CRF under LP. We constructed an ACCD‐deficit mutant accd in the P7 genetic background. The loss‐of‐function mutation failed to promote CRF under LP conditions. Also, auxin responses may be involved in K. pneumoniae‐ethylene‐mediated CRF.Overall, we propose that the soilborne bacterium K. pneumoniae promotes CRF of white lupin in response to LP by ethylene mediation. [ABSTRACT FROM AUTHOR]

Summary: The discovery and characterization of plant species adapted to extreme environmental conditions have become increasingly important. Hoffmannseggia doellii is a perennial herb endemic to the Chilean Atacama Desert that grows in the western Andes between 2800 and 3600 m above sea level. Its growing habitat is characterized by high radiation and low water and nutrient availability. Under these conditions, H. doellii can grow, reproduce, and develop an edible tuberous root.We characterized the H. doellii soil‐associated microbiomes to understand the biotic factors that could influence their surprising ability to survive.We found an increased number of observed species and higher phylogenetic diversity of bacteria and fungi on H. doellii root soils compared with bare soil (BS) along different sites and to soil microbiomes of other plant species. Also, the H. doellii‐associated microbiome had a higher incidence of overall positive interactions and fungal within‐kingdom interactions than their corresponding BS network.These findings suggest a microbial diversity soil modulation mechanism that may be a characteristic of highly tolerant plants to diverse and extreme environments. Furthermore, since H. doellii is related to important cultivated crops, our results create an opportunity for future studies on climate change adaptation of crop plants. [ABSTRACT FROM AUTHOR]

Summary: Xylella fastidiosa is the causal agent of important crop diseases and is transmitted by xylem‐sap‐feeding insects. The bacterium colonizes xylem vessels and can persist with a commensal or pathogen lifestyle in more than 500 plant species. In the past decade, reports of X. fastidiosa across the globe have dramatically increased its known occurrence. This raises important questions: How does X. fastidiosa interact with the different host plants? How does the bacterium interact with the plant immune system? How does it influence the host's microbiome? We discuss recent strain genetic typing and plant transcriptome and microbiome analyses, which have advanced our understanding of factors that are important for X. fastidiosa plant infection. [ABSTRACT FROM AUTHOR]

Summary: Plants allocate resources to processes related to growth and enemy defence. Simultaneously, they interact with complex soil microbiomes that also affect plant performance. While the influence of individual microbial groups on single plants is increasingly studied, effects of microbial interactions on growth, defence and growth–defence relationships remain unknown, especially at the plant community level.We investigated how three microbial groups (bacteria, fungi, protists), alone and in full‐factorial combinations, affect plant performance and potential growth–defence relationships by measuring phenolics composition in early‐ and mid‐successional grass and forb communities in a glasshouse experiment.Microbial groups did not affect plant growth and only fungi increased defence compounds in early‐ and mid‐successional forbs, while grasses were not affected. Shoot biomass–defence relationships were negatively correlated in most microbial treatments in early‐successional forbs, but positively in several microbial treatments in mid‐successional forbs. The growth–defence relationship was generally negative in early‐successional but not in mid‐successional grasses. The presence of different microbiomes commonly removed the observed growth–defence relationships.We conclude that soil microorganisms and their interactions can shift growth–defence relationships differentially for plant functional groups and the relationships vary between successional stages. Microbial interaction‐induced growth–defence shifts might therefore underlie distinct plant strategies and fitness. See also the Commentary on this article by Bender, 233: 1015–1017. [ABSTRACT FROM AUTHOR]

This article is a Commentary on Scholz et al. (2021), 232: 2138–2151. [ABSTRACT FROM AUTHOR]

B Cover Legend b A seagrass ( I Zostera marina i ) patch in the Limfjord, Denmark, with big cable bacteria around the roots. Image courtesy of Vincent Valentin Scholz (Scholz I et al i ., pp. 2138-2151). [Extracted from the article]

Summary: A vast array of herbivorous arthropods live with symbiotic microorganisms. However, little is known about the nature and functional mechanism of bacterial effects on plant defense responses towards herbivores.We explored the role of microbes present in extracts of oral secretion (OS) isolated from larvae of Spodoptera litura, a generalist herbivore, in phytohormone signaling‐dependent defense responses in Arabidopsis thaliana (Arabidopsis).In response to mechanical damage (MD) with application of bacteria‐free OS (OS–) prepared by sterilization or filtration of OS, Arabidopsis leaves exhibited enhanced de novo synthesis of oxylipins, and induction of transcript abundance of the responsible genes, in comparison to those in leaves with MD + nonsterilized OS (OS+), indicating that OS bacteria serve as suppressors of these genes. By contrast, de novo synthesis/signaling of salicylic acid and signaling of abscisic acid were enhanced by OS bacteria. These signaling networks were cross‐regulated by each other.Meta‐analysis of OS bacteria identified 70 bacterial strains. Among them was Staphylococcus epidermidis, an anaerobic staphylococcus that was shown to contribute to the suppression/manipulation of phytohormone‐dependent plant defense signaling. The presence of OS bacteria was consequently beneficial for S. litura larvae hosted by Brassicaceae. [ABSTRACT FROM AUTHOR]

Summary: A host‐plant and its associated microbiota depend on one another. However, the assembly process and the functioning of host‐associated microbiota are poorly understood.Herein, rice was used as model plant to investigate the assemblage of bacterial microbiota, including those in the seed, root endosphere and rhizosphere. We also assessed the degree to which endosphere and rhizosphere communities were influenced by vertical transmission through seed and identified the core microbes that potentially associated with plant phenotypic properties.Plant microhabitat, rather than subspecies type, was the major driver shaping plant‐associated bacterial microbiota. Deterministic processes were primarily responsible for community assembly in all microhabitats. The influence of vertical transmission from seed to root‐associated bacterial communities appeared to be quite weak (endosphere) or even absent (rhizosphere). A core microbial community composed of 15 generalist species persisted across different microhabitats and represented key connectors in networks. Host‐plant functional traits were linked to the relative abundance of these generalist core microbes and could be predicted from them using machine learning algorithms.Overall, bacterial microbiota is assembled by host‐plant interactions in a deterministic‐based manner. This study enhances our understanding of the driving mechanisms and associations of microbiota in various plant microhabitats and provides new perspectives to improve plant performance. [ABSTRACT FROM AUTHOR]

Summary: Arbuscular mycorrhizal (AM) fungi gain access to nutrient patches outside the rhizosphere by producing an extensive network of fine hyphae. Here, we focused on establishing the mechanism by which AM fungal hyphae reach discrete organic patches with a cohort of functional bacteria transported in a biofilm on their surface.We investigated the mechanisms and impact of the translocation of phosphate solubilising bacteria (PSB) along AM fungal hyphae in bespoke microcosms. An in vitro culture experiment was also conducted to determine the direct impact of hyphal exudates of AM fungi upon the growth of PSB.The extraradical hyphae of AM fungi can transport PSB to organic phosphorus (P) patches and enhance organic P mineralisation both under in vitro culture and soil conditions. Bacteria move in a thick water film formed around fungal hyphae. However, the bacteria cannot be transferred to the organic P patch without an energy source in the form of hyphal exudates.Our results could be harnessed to better manage plant–microbe interactions and improve the ability of biological inocula involving AM fungi and bacteria to enhance the sustainability of agricultural crops in P limited conditions. See also the Commentary on this article by Jansa & Hodge, 230: 14–16. [ABSTRACT FROM AUTHOR]

Summary: Recent research indicates that increased aridity linked to climate change will reduce the diversity of soil microbial communities and shift their community composition in drylands, Earth's largest biome. However, we lack both a theoretical framework and solid empirical evidence of how important biotic components from drylands, such as biocrust‐forming mosses, will regulate the responses of microbial communities to expected increases in aridity with climate change.Here we report results from a cross‐continental (North America, Europe and Australia) survey of 39 locations from arid to humid ecosystems, where we evaluated how biocrust‐forming mosses regulate the relationship between aridity and the community composition and diversity of soil bacteria and fungi in dryland ecosystems.Increasing aridity was negatively related to the richness of fungi, and either positively or negatively related to the relative abundance of selected microbial phyla, when biocrust‐forming mosses were absent. Conversely, we found an overall lack of relationship between aridity and the relative abundance and richness of microbial communities under biocrust‐forming mosses.Our results suggest that biocrust‐forming mosses mitigate the impact of aridity on the community composition of globally distributed microbial taxa, and the diversity of fungi. They emphasize the importance of maintaining biocrusts as a sanctuary for soil microbes in drylands. [ABSTRACT FROM AUTHOR]

• We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales. • Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities. • Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation. • Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres. [ABSTRACT FROM AUTHOR]

Producing and retaining leaves underlie the performance and survivorship of seedlings in deeply shaded tropical forests. These habitats are characterized by conditions ideal for foliar bacteria, which can be potent plant pathogens. Leaf production, retention and susceptibility to enemies may ultimately depend upon interactions among soil nutrients and foliar microbes, yet this has never been tested., We experimentally evaluated the degree that foliar bacteria and soil resource supply mediate leaf dynamics for five common tree species (five different families) in a Panamanian forest. We reduced foliar bacteria with antibiotics for 29 months and measured leaf production, retention and damage for seedlings nested within a replicated 15-yr factorial nutrient enrichment experiment (nitrogen, N; phosphorus, P; potassium, K)., Our results demonstrate that when we applied antibiotics, soil nutrients - particularly N - always regulated seedling leaf production (and to a lesser extent herbivore damage) for all five tree species. In addition, it was common for two macronutrients together to negate or completely reverse the impact of applying either one alone., Our findings of frequent plant-microbe-nutrient interactions are novel and suggest that these interactions may reinforce plant species-environment associations, thereby creating a fairly cryptic and fine-scale dimension of niche differentiation for coexisting tree species. [ABSTRACT FROM AUTHOR]

The current theoretical framework suggests that tripartite positive feedback relationships between soil biodiversity, fertility and plant productivity are universal. However, empirical evidence for these relationships at the continental scale and across different soil depths is lacking., We investigate the continental-scale relationships between the diversity of microbial and invertebrate-based soil food webs, fertility and above-ground plant productivity at 289 sites and two soil depths, that is 0-10 and 20-30 cm, across Australia., Soil biodiversity, fertility and plant productivity are strongly positively related in surface soils. Conversely, in the deeper soil layer, the relationships between soil biodiversity, fertility and plant productivity weaken considerably, probably as a result of a reduction in biodiversity and fertility with depth. Further modeling suggested that strong positive associations among soil biodiversity-fertility and fertility-plant productivity are limited to the upper soil layer (0-10 cm), after accounting for key factors, such as distance from the equator, altitude, climate and physicochemical soil properties., These findings highlight the importance of surface soil biodiversity for soil fertility, and suggest that any loss of surface soil could potentially break the links between soil biodiversity-fertility and/or fertility-plant productivity, which can negatively impact nutrient cycling and food production, upon which future generations depend. [ABSTRACT FROM AUTHOR]

Root and rhizosphere microbial communities can affect plant health, but it remains undetermined how plant domestication may influence these bacterial and fungal communities., We grew 33 sunflower ( Helianthus annuus) strains ( n = 5) that varied in their extent of domestication and assessed rhizosphere and root endosphere bacterial and fungal communities. We also assessed fungal communities in the sunflower seeds to investigate the degree to which root and rhizosphere communities were influenced by vertical transmission of the microbiome through seeds., Neither root nor rhizosphere bacterial communities were affected by the extent of sunflower domestication, but domestication did affect the composition of rhizosphere fungal communities. In particular, more modern sunflower strains had lower relative abundances of putative fungal pathogens. Seed-associated fungal communities strongly differed across strains, but several lines of evidence suggest that there is minimal vertical transmission of fungi from seeds to the adult plants., Our results indicate that plant-associated fungal communities are more strongly influenced by host genetic factors and plant breeding than bacterial communities, a finding that could influence strategies for optimizing microbial communities to improve crop yields. [ABSTRACT FROM AUTHOR]

Arsenic (As) contamination in a paddy environment can cause phytotoxicity and elevated As accumulation in rice ( Oryza sativa). The mechanism of As detoxification in rice is still poorly understood., We isolated an arsenate (As(V))-sensitive mutant of rice. Genomic resequencing and complementation identified OsCLT1, encoding a CRT-like transporter, as the causal gene for the mutant phenotype., OsCLT1 is localized to the envelope membrane of plastids. The glutathione and γ-glutamylcysteine contents in roots of Osclt1 and RNA interference lines were decreased markedly compared with the wild-type (WT). The concentrations of phytochelatin PC2 in Osclt1 roots were only 32% and 12% of that in WT after As(V) and As(III) treatments, respectively. OsCLT1 mutation resulted in lower As accumulation in roots but higher As accumulation in shoots when exposed to As(V). Under As(III) treatment, Osclt1 accumulated a lower As concentration in roots but similar As concentration in shoots to WT. Further analysis showed that the reduction of As(V) to As(III) was decreased in Osclt1. Osclt1 was also hypersensitive to cadmium (Cd)., These results indicate that OsCLT1 plays an important role in glutathione homeostasis, probably by mediating the export of γ-glutamylcysteine and glutathione from plastids to the cytoplasm, which in turn affects As and Cd detoxification in rice. [ABSTRACT FROM AUTHOR]

Turnover of fungal biomass in forest litter and soil represents an important process in the environment. To date, knowledge of mycelial decomposition has been derived primarily from short-term studies, and the guild of mycelium decomposers has been poorly defined., Here, we followed the fate of the fruiting bodies of an ectomycorrhizal fungus in litter and soil of a temperate forest over 21 wk. The community of associated microbes and enzymatic processes in this specific substrate were described., The decomposition of fungal fruiting bodies exhibited biphasic kinetics. The rapid initial phase, which included the disappearance of DNA, was followed by a slower turnover of the recalcitrant fraction. Compared with the surrounding litter and soil, the mycelium represented a hotspot of activity of several biopolymer-degrading enzymes and high bacterial biomass. Specific communities of bacteria and fungi were associated with decomposing mycelium. These communities differed between the initial and late phases of decomposition. The bacterial community associated with decomposing mycelia typically contained the genera Pedobacter, Pseudomonas, Variovorax, Chitinophaga, Ewingella and Stenotrophomonas, whereas the fungi were mostly nonbasidiomycetous r-strategists of the genera Aspergillus, Penicillium, Mortierella, Cladosporium and several others., Decomposing ectomycorrhizal fungal mycelium exhibits high rates of decomposition and represents a specific habitat supporting a specific microbial community. [ABSTRACT FROM AUTHOR]

The increase in aridity predicted with climate change will have a negative impact on the multiple functions and services (multifunctionality) provided by dryland ecosystems worldwide. In these ecosystems, soil communities dominated by mosses, lichens and cyanobacteria (biocrusts) play a key role in supporting multifunctionality. However, whether biocrusts can buffer the negative impacts of aridity on important biogeochemical processes controlling carbon (C), nitrogen (N), and phosphorus (P) pools and fluxes remains largely unknown., Here, we conducted an empirical study, using samples from three continents (North America, Europe and Australia), to evaluate how the increase in aridity predicted by climate change will alter the capacity of biocrust-forming mosses to modulate multiple ecosystem processes related to C, N and P cycles., Compared with soil surfaces lacking biocrusts, biocrust-forming mosses enhanced multiple functions related to C, N and P cycling and storage in semiarid and arid, but not in humid and dry-subhumid, environments. Most importantly, we found that the relative positive effects of biocrust-forming mosses on multifunctionality compared with bare soil increased with increasing aridity. These results were mediated by plant cover and the positive effects exerted by biocrust-forming mosses on the abundance of soil bacteria and fungi., Our findings provide strong evidence that the maintenance of biocrusts is crucial to buffer negative effects of climate change on multifunctionality in global drylands. [ABSTRACT FROM AUTHOR]

I.II.III.IV.V.References Summary: Interactions between trees and microorganisms are tremendously complex and the multispecies networks resulting from these associations have consequences for plant growth and productivity. However, a more holistic view is needed to better understand trees as ecosystems and superorganisms, where many interacting species contribute to the overall stability of the system. While much progress has been made on microbial communities associated with individual tree niches and the molecular interactions between model symbiotic partners, there is still a lack of knowledge of the multi‐component interactions necessary for holistic ecosystem‐level understanding. We review recent studies in Populus to emphasize the importance of such holistic efforts across the leaf, stem and rooting zones, and discuss prospects for future research in these important ecosystems. [ABSTRACT FROM AUTHOR]

The ongoing expansion of shrub cover in response to climate change represents a unique opportunity to explore the link between soil microbial communities and vegetation changes. This link is particularly important in peatlands where shrub expansion is expected to feed back negatively on the carbon sink capacity of these ecosystems., Microbial community structure and function were measured seasonally in four peatlands located along an altitude gradient representing a natural gradient of climate and associated vascular plant abundance., We show that increased soil temperature and reduced water content are associated with greater vascular plant biomass, in particular that of ericoids, and that this, in turn, is correlated with greater microbial biomass. More specifically, microbial community structure is characterized by an increasing dominance of fungi over bacteria with improved soil oxygenation. We also found that the carbon and nitrogen stoichiometry of microbial biomass differs in relation to soil microbial community structure and that this is ultimately associated with a different investment in extracellular enzymatic activity., Our findings highlight the fact that the determination of the structural identity of microbial communities can help to explain the biogeochemical dynamics of organic matter and provide a better understanding of ecosystem response to environmental changes. [ABSTRACT FROM AUTHOR]

749I.749II.750III.754IV.758V.759760References761 Summary: Ant–plant symbioses involve plants that provide hollow structures specialized for housing ants and often food to ants. In return, the inhabiting ants protect plants against herbivores and sometimes provide them with nutrients. Here, we review recent advances in ant–plant symbioses, focusing on three areas. First, the nutritional ecology of plant‐ants, which is based not only on plant‐derived food rewards, but also on inputs from other symbiotic partners, in particular fungi and possibly bacteria. Food and protection are the most important ‘currencies’ exchanged between partners and they drive the nature and evolution of the relationships. Secondly, studies of conflict and cooperation in ant–plant symbioses have contributed key insights into the evolution and maintenance of mutualism, particularly how partner‐mediated feedbacks affect the specificity and stability of mutualisms. There is little evidence that mutualistic ants or plants are under selection to cheat, but the costs and benefits of ant–plant interactions do vary with environmental factors, making them vulnerable to natural or anthropogenic environmental change. Thus, thirdly, ant–plant symbioses should be considered good models for investigating the effects of global change on the outcome of mutualistic interactions. [ABSTRACT FROM AUTHOR]

Mutualistic ants are commonly considered as an efficient indirect defence against herbivores. Nevertheless, their indirect protective role against plant pathogens has been scarcely investigated., We compared the protective role against pathogens of two different ant partners, a mutualistic and a parasitic ant, on the host plant Acacia hindsii (Fabaceae). The epiphytic bacterial community on leaves was evaluated in the presence and absence of both ant partners by cultivation and by 454 pyrosequencing of the 16S rRNA gene., Pathogen-inflicted leaf damage, epiphytic bacterial abundance (colony-forming units) and number of operational taxonomic units ( OTUs) were significantly higher in plants inhabited by parasitic ants than in plants inhabited by mutualistic ants. Unifrac unweighted and weighted principal component analyses showed that the bacterial community composition on leaves changed significantly when mutualistic ants were removed from plants or when plants were inhabited by parasitic ants. Direct mechanisms provided by ant-associated bacteria would contribute to the protective role against pathogens., The results suggest that the indirect defence of mutualistic ants also covers the protection from bacterial plant pathogens. Our findings highlight the importance of considering bacterial partners in ant-plant defensive mutualisms, which can contribute significantly to ant-mediated protection from plant pathogens. [ABSTRACT FROM AUTHOR]

Invaders can gain ecological advantages because of their evolutionary novelty, but little is known about how these novel advantages will change over time as the invader and invaded community evolve in response to each other. Invasive plants often gain such an advantage through alteration of soil microbial communities. In soil communities sampled from sites along a gradient of invasion history with Alliaria petiolata, microbial richness tended to decline, but the community's resistance to A. petiolata's effects generally increased with increasing history of invasion. However, sensitive microbial taxa appeared to recover in the two oldest sites, leading to an increase in richness, but consequent decrease in resistance. This may be because of evolutionary changes in the A. petiolata populations, which tend to reduce their investment to allelopathic compounds over time. These results show that, over time, microbial communities can develop resistance to an invasive plant but at the cost of lower richness. However, over longer time-scales evolution in the invasive species may allow for the recovery of soil microbial communities. [ABSTRACT FROM AUTHOR]

• In arbuscular mycorrhizas (AM), the supply of phosphorus from the fungi is one of the most important benefits to the host plant. Here we describe for the first time the ultrastructure and polyphosphate (poly P) distribution in rapidly frozen and freeze-substituted germ tubes of the AM fungus Gigaspora margarita. • At the ultrastructural level, phosphorus distribution was analysed using energy-filtering transmission electron microscopy, and poly P was detected using an enzyme-affinity method. Semithin sections and live cells were also stained with 4′,6-diamidino-2-phenylindole, which is not specific but fluoresces yellow when viewed under UV irradiation by binding with poly P. • The cryotechnique method showed that extensive elongate ellipsoid vacuoles containing a uniform electron-opaque material occupied most of the cell volume. Combining the results of multiple methods revealed that poly P was localized in a dispersed form in vacuoles and in the outer fungal cell wall. • These results show the significant potential of AM fungi for phosphorus storage based on its localization in the extensive complement of vacuoles in thick hyphae. The mechanism of translocation of poly P in tubular vacuoles, and the role of poly P in the cell wall, need to be elucidated. [ABSTRACT FROM AUTHOR]

Contents Summary 22 I. Introduction 23 II. Evidence for the occurrence of MHB 23 III. Ecological and evolutionary implications of MHB 23 IV. The question of MHB specificity 27 V. Mechanisms of the MHB effect 28 VI. Role of MHB in mycorrhizal functions 31 VII. Conclusions and research priorities 32 References 33 In natural conditions, mycorrhizal fungi are surrounded by complex microbial communities, which modulate the mycorrhizal symbiosis. Here, the focus is on the so-called ‘mycorrhiza helper bacteria’ (MHB). This concept is revisited, and the distinction is made between the helper bacteria, which assist mycorrhiza formation, and those that interact positively with the functioning of the symbiosis. After considering some examples of MHB from the literature, the ecological and evolutionary implications of the relationships of MHB with mycorrhizal fungi are discussed. The question of the specificity of the MHB effect is addressed, and an assessment is made of progress in understanding the mechanisms of the MHB effect, which has been made possible through the development of genomics. Finally, clear evidence is presented suggesting that some MHB promote the functioning of the mycorrhizal symbiosis. This is illustrated for three critical functions of practical significance: nutrient mobilization from soil minerals, fixation of atmospheric nitrogen, and protection of plants against root pathogens. The review concludes with discussion of future research priorities regarding the potentially very fruitful concept of MHB. [ABSTRACT FROM AUTHOR]

The article explores the mechanisms and specificity of mycorrhization helper bacteria (MHB). It provides discussions on the mycorrhizosphere, mycorrhizal fungi, the capacity of bacterial strains to enhance fungus growth, inoculation of MHB with low specificity into a nonsterile environment and root colonization. The author notes that the capacity of bacterial strains to enhance fungus growth in vitro is not a useful indicator of MHB activity. Some MHB appear to have specificity for certain strains of mycorrhizal fungus.

• Despite their ecological relevance, field studies of the extraradical mycelia of ectomycorrhizal (ECM) fungi are rare. Here we examined in situ interactions between ECM mycelia and host vigour. • Ectomycorrhizal mycelia were harvested with in-growth mesh bags buried under Norway spruce ( Picea abies) clones planted in 1994 in a randomized block design. Mycelial biomass was determined and fungal species were identified by denaturing gradient gel electrophoresis (DGGE) and sequencing of the internal transcribed spacer 1 (ITS1) region. Microbial community structure in the mycelium was investigated by phospholipid fatty acid (PLFA) profiling. • Compared to slow-growing spruce clones, fast-growing clones tended to support denser mycelia where the relative proportions of Atheliaceae fungi and PLFAs indicative of Gram-positive bacteria were higher. Ascomycetes and PLFAs representative of Gram-negative bacteria were more common with slow-growing clones. In general, the ECM mycelial community was similar to the ECM root-tip community. • Growth rate of the hosts, the ECM mycelial community and the microbes associated with the mycelium were related, suggesting multitrophic interactions between trees, fungi and bacteria. [ABSTRACT FROM AUTHOR]

This article comments on an article by Mougel C. et al on the composition of the rhizosphere decomposer communities. The importance of the microorganisms for the functioning of plants is explained. The role of decomposer fungi is compared with that of decomposer bacteria. The effects of mycorrhization on the composition is discussed.

• Here we characterized the effect of the ectomycorrhizal symbiosis on the genotypic and functional diversity of soilPseudomonas fluorescenspopulations and analysed its possible consequences in terms of plant nutrition, development and health.• Sixty strains ofP. fluorescenswere isolated from the bulk soil of a forest nursery, the ectomycorrhizosphere and the ectomycorrhizas of the Douglas fir (Pseudostuga menziesii) seedlings-Laccaria bicolorS238N. They were characterizedin vitrowith the following criteria: ARDRA, phosphate solubilization, siderophore, HCN and AIA production, genes of N2-fixation and antibiotic synthesis,in vitroconfrontation with a range of phytopathogenic and ectomycorrhizal fungi, effect on the Douglas fir– L. bicolorsymbiosis.• For most of these criteria, we demonstrated that the ectomycorrhizosphere significantly structures theP. fluorescenspopulations and selects strains potentially beneficial to the symbiosis and to the plant.• This prompts us to propose the ectomycorrhizal symbiosis as a true microbial complex where multitrophic interactions take place. Moreover it underlines the fact that this symbiosis has an indirect positive effect on plant growth, via its selective pressure on bacterial communities, in addition to its known direct positive effect.New Phytologist(2004)doi: 10.1111/j.1469-8137.2004.01212.x© New Phytologist(2004) [ABSTRACT FROM AUTHOR]

In studies with a laboratory isolate of the fungal pathogen Stagonospora (Septoria) nodorum three different isolates of bacteria were closely associated with the fungus. Bacteria were also closely associated with fresh isolates of S. nodorum obtained from artificially and naturally infected field material. Although a range of bacteria was isolated, only one type of bacterium was found to be associated with each isolate of S. nodorum. In co-inoculation studies with pycnidiospores of the fungus on detached leaves, some of the bacterial isolates significantly increased the pathogenicity of the fungus, particularly Xanthomonas maltophilia, Sphingobacterium multivorum, Enterobacter agglomerans and Erwinia amylovora. Evidence is presented indicating that one of the ways that the 'helper bacteria' may assist in the establishment of infections is by the production of lipases that were not detected in germinating fungal spores. [ABSTRACT FROM AUTHOR]

Relatively little is known about the factors controlling ectomycorrhizal fungal communities. One possible factor is forest litter chemistry. In a series of experiments we demonstrated that the growth of ectomycorrhizal fungi able to colonize red pine (Pinus resinosa Ait.) are differentially affected by red pine needles and needle chemical components. For example, water extracts of pine needles stimulated the growth of Suillus intermedius (Smith & Thiers) Smith & Theirs and inhibited the growth of Amanita rubescens Pers. Catechin and epicatechin gallate, components of the water extract, acted similarly to the extract. The volatile compounds α- and β-pinene also had differential effects on the growth of the various species of ectomycorrhizal fungi. Our results suggest that forest litter chemistry has the potential differentially to affect the growth of ectomycorrhizal fungal species and so could affect the structure of ectomycorrhizal fungal communities. [ABSTRACT FROM AUTHOR]

Thioredoxins are ubiquitous small-molecular-weight proteins (typically 100-120 amino-acid residues) containing an extremely reactive disulphide bridge with a highly conserved sequence -CYs-Gly(Ala/Pro)-Pro-Cys-. In bacteria and animal cells, thioredoxins participate in multiple reactions which require reduction of disulphide bonds on selected target proteins/enzymes. There is now ample biochemical evidence that thioredoxins exert very specific functions in plants, the best documented being the redox regulation of chloroplast enzymes. Another area in which thioredoxins are believed to play a prominent role is in reserve protein mobilization during the process of germination. It has been discovered that thioredoxins constitute a large multigene family in plants with different subcellular localizations, a unique feature in living cells so far. Evolutionary studies based on these molecules will be discussed, as well as the available biochemical and genetic evidence related to their functions in plant cells. Eukaryotic photosynthetic plant cells are also unique in that they possess two different reducing systems, one extrachloroplastic dependent on NADPH as an electron donor, and the other one chloroplastic, dependent on photoreduced ferredoxin. This review will examine in detail the latest progresses in the area of thioredoxin structural biology in plants, this protein being an excellent model for this purpose. The structural features of the reducing enzymes ferredoxin thioredoxin reductase and NADPH thioredoxin reductase will also he described. The properties of the target enzymes known so far in plants will be detailed with special emphasis on the structural features which make them redox regulatory. Based on sequence analysis, evidence will be presented that redox regulation of enzymes of the biosynthetic pathways first appeared in cyanobacteria possibly as a way to cope with the oxidants produced by oxygenic photosynthesis. It became more elaborate in the chloroplasts of higher plants where a coordinated functioning of the chloroplastic and extra chloroplastic metabolisms is required. [ABSTRACT FROM AUTHOR]

In contrast to that of Anabaena sp. PCC 7120, the fdxN gene in Anabaena variabilis ATCC 29413 is not interrupted by a 55-kb DNA element, making this strain more suitable for genetic analysis of fdxN independent of the developmentally regulated excision during heterocyst formation. As a basis for mutational analysis, the fdxN gene of A. variabilis was cloned and sequenced. The deduced FdxN protein sequence was highly homologous to the Anabaena 7120 fdxN gene product including eight cysteine residues that are known to he conserved among ferredoxins containing two [4Fe-4S] clusters. The fdxN gene of A. variabilis was disrupted by insertion of an interposon within the fdxN coding region resulting in mutant strain KG29. Diazotrophic growth and in vivo nitrogenase activity of KG29 were similar to those of the wild-type, indicating that FdxN was not essential for N2 fixation in A. variabilis. [ABSTRACT FROM AUTHOR]

Bacteria isolated from proteoid roots and non-proteoid lateral roots of Telopea speciosissima (Sm.) R. Br. seedlings were able to acidify the medium and solubilize calcium phosphates when grown in culture in the presence of ammonium salts and an appropriate carbon source. In general this activity was not detected when NO3- was substituted for NH4+, and it is proposed that protons were secreted in exchange for ammonium ions. Canon exchange between these protons and calcium in the medium is a possible cause of the calcium phosphate solubilizing activity. The relevance of these data to phosphate-solubilizing activity in natural environments is discussed. [ABSTRACT FROM AUTHOR]

Endotrophic bacteria were isolated from the mycorrhizal tissues of 12 out ut 13 tested species of Western Australian terrestrial orchids. The bacteria were placed into eight groups based on u.v. light fluorescence, Gram staining and colony characteristics. The most commonly isolated bacteria from 9 out of the 12 orchid species sampled were strains within the Pseudomonas fluorescens-putida group. The abundance of bacteria followed a seasonal pattern that differed between orchid genera especially on the basis of the morphology of fungus infected tissue. There was little evidence of specificity of bacterial groups to orchid taxa or part of the plant infected by the fungus. Symbiotic germination of Pterostylis vittata seed in association with seven bacterial isolates showed a significant promotion of germination and seedling development with three bacterial strains. The influence of a fourth strain was no different to the control while the remaining three strains significantly suppressed seedling development. [ABSTRACT FROM AUTHOR]

Individual legumes may be infectible by one or more of the three bacterial genera (collectively known as rhizobia) Rhizobium, Bradyrhizobium, or Azorhizobium. The type of infection process by which rhizobia gain entry is largely governed by the host genotype. In addition to the widely studies roothair pathway, infections maybe associated with lateral root emergence or occur between root epidermal cells. Rhizobial features essential for infection include particular surface polysaccharides and the induction of nodulation genes by plant root exudates.

Bacterium-like organelles (BLOs) were found by electron microscopy in the vesicular-arhuscular (VA) mycorrhizal fungus Glomus caledonius. They were morphologically similar to those found by others in other VA mycorrhizal fungi, in the ectendomycorrhizal fungus Endogone flammicorona and in the Discomycete Scutellinia. They occurred free in the cytoplasm of Glomus caledonius reproductive spores and in the intercellular hyphae and thick arbuscule branches in infected roots. They were irregularly coccal with diameters of 0.3 ±0.6 μm and had a conspicuous cell membrane and simple cell wall and appeared to divide by median constriction and separation. The fungal cytoplasm did not show any cytopathic effects in the vicinity of the BLOs. A competely different type of bacterium colonized and eroded the walls of reproductive spores of Glomus caledonius. These bacteria did not enter the fungal cytoplasm and had a thick complex wall and peripheral membranes. In contrast to BLOs, their cytoplasm was clearly differentiated into electron-dense and transparent areas. [ABSTRACT FROM AUTHOR]

Light and electron microscopy have been used to study the emergence through the spore wall and subsequent growth and development of the germ-tube of Gigaspora margarita. Spore-wall penetration by the germ-tube is unusual as two different mechanisms seem to be operating, one for the inner spore-wall layers and another for the outer layer. As the germ-tube develops a primary wall layer is formed, and this can be traced back to its origin as a layer continuous with the thickened region of the innermost spore-wall layer. In the maturing germ-tube a highly osmiophilic secondary wall is deposited and this may be the wall layer that persists when the fungus penetrates a host root and sets up a mycorrhizal association. In common with other fungi that have been studied, the ultrastructural organization found in G. margarita can be categorized into approximately three zones: the apical zone, the subapical zone and the zone of vacuolation. Other features of the cytoplasmic organization are also discussed including the possible significance of bacteria-like organisms, membrane-bound crystals, osmiophilic granules and glycogen particles. Features of the culture-grown germ-tubes are also compared with those of host-associated stages of the fungus reported in the literature. [ABSTRACT FROM AUTHOR]

In a series of experiments, aqueous washings of the leaves of Camelina sativa (L.) Crantz consistently stimulated the growth in length of radicles of germinating seeds of Linum usitatissimum L. The presence of free-living nitrogen-fixing bacteria in the Camelina phyllosphere was necessary for the production of the stimulation. [ABSTRACT FROM AUTHOR]

The primitive giant amoeba, Pelomyxa palustris, contains a population of endosymbiotic bacteria. The distinctive ultrastructure of one of the species of bacteria is described in detail. A particularly close relationship exists between these bacteria and the nuclei of Pelomyxa. The significance of some aspects of this relationship is discussed with reference to the endosymbiotic theory of the origin of mitochondria from bacterial precursors. [ABSTRACT FROM AUTHOR]

Populations of viable bacteria and fungi were shown to exist in various strata of peat formed in the Florida Everglades. The populations present were quantitatively and qualitatively different in three distinct peat-forming habitats and at various depths in the peat profiles. Relatively few pieces of peat taken from horizons below the surface were colonized by actively growing fungi or actinomycetes. Direct observation of peat confirmed some features of the cultural studies. Bacteria were mostly present in small groups of two to six cells and most of the hyphae recorded were apparently formed by Actinomycetales rather than the fungi. The significance of these data in relation to possible long-term changes in the peats is discussed. [ABSTRACT FROM AUTHOR]

In assays of acid phosphatase activity with p-nitrophenyl phosphate as substrate, the low activity found in fluids removed from around roots in liquid medium was not affected by the presence of micro-organisms. Most phosphatase activity of intact seedling roots was associated with the root surface and was not increased by micro-organisms in the rhizoplane; in some experiments activity was significantly reduced by soil micro-organisms. Inoculation of roots with pure cultures of bacteria and a fungus known to have phosphatase activity did not increase this activity of the roots. These results are contrasted with those of other workers. Possible application to the soil situation is discussed. [ABSTRACT FROM AUTHOR]

The article discusses various reports published within the issue, including one by Chen and colleagues on the evolution of effectors, one by Szczesny and colleagues on type III secretion (T3S) system, and one by Kale and colleagues on phosphoinositol-3-phosphate (PI3P).