More than a decade ago, the Driver (arbuscular mycorrhizal fungal partners drive plant communities) and Passenger (AMF community dynamics follows changes in the host plant community) hypotheses were ...suggested to explain the mutual relationships of plant and AMF communities. We propose one more hypothesis: the Habitat hypothesis, which postulates that both plant and AMF communities follow changes in abiotic conditions. The null hypothesis for all three working hypotheses can be called the Independence hypothesis, which proposes that plant and AMF communities are unrelated. We investigate the assumptions of these hypotheses and the available evidence in support of them. We suggest that community dynamics during secondary succession, including those related to land‐use changes, may be explained by the Driver hypothesis, while the dynamics of plant and AMF communities during primary succession may be explained by the Passenger hypothesis. Within‐region co‐variation of successionally stable plant and AMF communities may be explained by the Habitat hypothesis, while the Independence hypothesis may explain global patterns of plant and AMF communities. These suggestions are tentative, and more evidence from both descriptive and experimental studies is required to assess them. In particular, comparative information is needed about dispersal limitation of plant and AMF communities in dynamic landscapes.
Abstract
Wetland soils are the greatest source of nitrous oxide (N
2
O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N
2
O ...emissions from wetland soils are poorly understood. Using in situ N
2
O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N
2
O emissions. We show that N
2
O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N
2
O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N
2
O.
Arbuscular mycorrhizal fungi (AMF) occur in the majority of terrestrial, and some aquatic, habitats worldwide. They are important for the functioning of individual plants and of entire ecosystems. ...Here, we review trends in research on species- (species recognition, phylogenetic relationships, autecology) and community-level AMF diversity patterns and aim to identify ways of improving the complementarity of these approaches. Research into many aspects of AMF diversity has flourished in parallel with the increasing availability of molecular biology techniques. However, despite their shared goal of understanding AMF biodiversity, species- and community-level perspectives, and the morphological and molecular approaches that underpin them, currently have limited capacity for information exchange. We indicate critical research gaps in AMF species and community characterisation and outline important research directions. We propose steps that could link research using different methods and targeting different aspects of diversity, in order to maximise our understanding of AMF.
•We briefly review research trends in AMF species and community characterisation.•We provide a Glomeromycota species list, with data on marker sequence availability.•We propose developments in AMF species characterisation.•We show the importance of regional and local processes in AMF community ecology.•We outline research directions to improve our understanding of AMF diversity.
Arbuscular mycorrhizal fungi (AMF) can benefit growth and yield of agriculturally significant crops by increasing mineral nutrient uptake, disease resistance and drought tolerance of plants. We ...conducted a meta-analysis of 38 published field trials with 333 observations to determine the effects of inoculation and root colonization by inoculated and non-inoculated (resident) AMF on P, N and Zn uptake, growth and grain yield of wheat. Field AMF inoculation increased aboveground biomass, grain yield, harvest index, aboveground biomass P concentration and content, straw P content, aboveground biomass N concentration and content, grain N content and grain Zn concentration. Grain yield was positively correlated with root AMF colonization rate, whereas straw biomass was negatively correlated. The most important drivers of wheat growth response to AMF were organic matter concentration, pH, total N and available P concentration, and texture of soil, as well as climate and the AMF species inoculated. Analysis showed that AMF inoculation of wheat in field conditions can be an effective agronomic practice, although its economic profitability should still be addressed for large-scale applications in sustainable cropping systems.
•AMF field inoculation increased wheat dry weight, P, N and Zn uptake.•AMF inoculation increased wheat grain yield by 20% and harvest index by 25%.•Grain yield of wheat was positively related to root colonization (RC) by AMF.•P and Zn concentration in grain were positively correlated to RC by indigenous AMF.•Soil organic matter and soil pH were the most important parameters affecting wheat response to AMF.
1 Arbuscular mycorrhizal (AM) fungi are obligate root symbionts that are present in most terrestrial ecosystems and have roles in plant mineral nutrition, carbon cycling and biotic interactions. In ...this work, 26 publications were surveyed that report on the occurrence of natural root-colonizing AM fungi identified using rDNA region sequences. A total of 52 host plant species were investigated. Sixteen publications provided data enabling a comparison to be made of AM fungal taxon richness and community composition across 36 host plant species and 25 locations. Ninety-five fungal taxa (small subunit rRNA gene sequence types) were involved, 49 of which were recorded from at least two study sites, and 65 from more than one host plant species. 2 The number of AM fungal taxa per host plant species differed between habitat types: a significantly higher richness was found in tropical forests (18.2 fungal taxa per plant species), followed by grasslands (8.3), temperate forests (5.6) and habitats under anthropogenic influence (arable fields and polluted sites, 5.2). 3 AM fungal communities exhibit differing compositions in broadly defined habitat types: tropical forests, temperate forests and habitats under anthropogenic influence. Grassland locations around the world host heterogeneous AM fungal communities. 4 A number of AM fungi had a global distribution, including sequence types related to the Glomus intraradiceslfasciculatum group, G. mosseae, G. sp. UY1225 and G. hoi, as well as the Glomus and Scutellospora types of unknown taxonomic affiliation. Widespread taxa occur in both natural and anthropogenic (disturbed) habitats, and may show high local abundance. However, about 50% of taxa have been recorded from only a single site. 5 The current global analysis of AM fungal communities suggests that soil microorganisms may exhibit different distribution patterns, resulting in a high variability of taxon richness and composition between particular ecosystems.
Interactions between communities of plants and arbuscular mycorrhizal (AM) fungi shape fundamental ecosystem properties. Experimental evidence suggests that compositional changes in plant and AM ...fungal communities should be correlated, but empirical data from natural ecosystems are scarce. We investigated the dynamics of covariation between plant and AM fungal communities during three stages of grassland succession, and the biotic and abiotic factors shaping these dynamics.
Plant communities were characterised using vegetation surveys. AM fungal communities were characterised by 454-sequencing of the small subunit rRNA gene and identification against the AM fungal reference database MaarjAM. AM fungal abundance was estimated using neutral-lipid fatty acids (NLFAs).
Multivariate correlation analysis (Procrustes) revealed a significant relationship between plant and AM fungal community composition. The strength of plant–AM fungal correlation weakened during succession following cessation of grassland management, reflecting changes in the proportion of plants exhibiting different AM status. Plant–AM fungal correlation was strong when the abundance of obligate AM plants was high, and declined as the proportion of facultative AM plants increased.
We conclude that the extent to which plants rely on AM symbiosis can determine how tightly communities of plants and AM fungi are interlinked, regulating community assembly of both symbiotic partners.
Processes controlling the assembly of microorganism communities are poorly understood. In taxonomic groups where many organisms are only described from environmental DNA, phylogenetic relationships ...may provide a proxy for functional attributes. We used a null model approach to compare the phylogenetic diversity of arbuscular mycorrhizal (AM) fungal communities coexisting within the roots of plant individuals sampled worldwide. Parallel null models were constructed using taxon pools that were filtered according to some or all of spatial scale, ecosystem type and host plant identity. This allowed us to assess the importance of individual ecological gradients in shaping phylogenetic diversity and to identify potential mechanisms. In general, coexisting fungi were more phylogenetically clustered than the random communities defined by null models. However, clustering increased when null models incorporated large spatial scales, indicating that communities are assembled according to the dispersal ability of fungal taxa. Clustering also increased when null models incorporated a variety of ecosystems or host plant species, indicating effects of habitat filtering and mutualist partner selection at wide and local scales, respectively. We did not record phylogenetic overdispersion among coexisting fungi, providing no support for a role of limiting similarity in structuring AM fungal communities. However, the existence of significant clustering even in comparison with the finest-scale null model indicates that, in addition to larger-scale deterministic and neutral processes, the symbiosis may be further influenced by genotypic selectivity or stochastic processes at very small scales.
•Phylogenetic relationships may represent functional attributes in soil microbes.•Here, phylogenetic diversity is used to assess community assembly in AMF.•Nested null models are used to identify individual processes influencing assembly.•Dispersal limitation, habitat filtering and mutualist selection all play roles.•However, very small scale deterministic or stochastic processes are also important.
An increasing number of case studies are reporting Glomeromycota molecular diversity from ecosystems worldwide. Typically, phylogroups that can be related to morphospecies and those that remain ...unidentified ("environmental") are recorded. To compare such data and generalise observed patterns, the principles underlying sequence identification should be unified. Data from case studies are collected and systematized in a public database MaarjAM (http://www.maarjam.botany.ut.ee), which applies a unique molecular operational taxonomic unit (MOTU) nomenclature: virtual taxa (VT) are phylogenetically defined sequence groups roughly corresponding to species-level taxa. VT are based on type sequences, making them consistent in time, but they also evolve: they can be split or merged, when necessary. This system allows standardisation of original MOTU designations and, much like binomial taxonomic nomenclature, comparison and consistency between studies. Refinement ofVT delimitation principles and comparability with traditional Glomeromycota taxonomy will benefit from more information about intra- vs. inter-specific nucleotide variation in Glomeromycota, sequencing of morphospecies, and resolution of issues in Glomeromycota taxonomy. As the recorded number of VT already exceeds the number of Glomeromycota morphospecies, designation of species based on DNA alone appears a necessity in the near future. Application of VT is becoming widespread, and MaarjAM database is increasingly used as a reference for environmental sequence identification. The current status and future prospects of arbuscular mycorrhizal fungi (AMF) DNA-based identification and community description are presented.
Abstract
Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use ...intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status.
By analysing AM fungal DNA in soil from different habitats, its shown that forested and open habitats harbour different fungal communities, while disturbance changes the phylogenetic structure of fungal communities.
By analysing AM fungal DNA in soil from different habitats, its shown that forested and open habitats harbour different fungal communities, while disturbance changes the phylogenetic structure of fungal communities.
Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 ...previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant-associated fungal interaction networks.
We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds. We also assessed how plant–fungal network structure was related to host phylogeny, environmental and sampling properties.
Orchid mycorrhizal fungal communities responded most strongly to host identity, but the effect of host was similar among all other fungal guilds. Community nestedness, which did not differ among fungal guilds, declined significantly with increasing mean annual precipitation on a global scale. Orchid and ericoid mycorrhizal fungal communities were more modular than ectomycorrhizal and root endophytic communities, with arbuscular mycorrhizal fungi in an intermediate position.
Network properties among a broad suite of plant-associated fungi were largely comparable and generally unrelated to phylogenetic distance among hosts. Instead, network metrics were predominantly affected by sampling and matrix properties, indicating the importance of study design in properly inferring ecological patterns.
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