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Co‐existence theories fail to adequately explain observed community patterns (diversity and composition) because they mainly address local extinctions. For a more complete understanding, the regional processes responsible for species formation and geographic dispersal should also be considered. The species pool concept holds that local variation in community patterns is dependent primarily on the availability of species, which is driven by historical diversification and dispersal at continental and landscape scales. However, empirical evidence of historical effects is limited. This slow progress can be attributed to methodological difficulties in determining the characteristics of historical species pools and how they contributed to diversity patterns in contemporary landscapes. A role of landscape‐scale dispersal limitation in determining local community patterns has been demonstrated by numerous seed addition experiments. However, disentangling general patterns of dispersal limitation in communities still requires attention. Distinguishing habitat‐specific species pools can help to meet both applied and theoretical challenges. In conservation biology, the use of absolute richness may be uninformative because the size of species pools varies between habitats. For characterizing the dynamic state of individual communities, biodiversity relative to species pools provides a balanced way of assessing communities in different habitats. Information about species pools may also be useful when studying community assembly rules, because it enables a possible mechanism of trait convergence (habitat filtering) to be explicitly assessed. Empirical study of the role of historic effects and dispersal on local community patterns has often been restricted due to methodological difficulties in determining habitat‐specific species pools. However, accumulating distributional, ecological and phylogenetic information, as well as use of appropriate model systems (e.g. archipelagos with known biogeographic histories) will allow the species pool concept to be applied effectively in future research.

This article is a Commentary on Pither et al., 220: 1148–1160.

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.

Plant traits determine how individual plants cope with heterogeneous environments. Despite large variability in individual traits, trait coordination and trade-offs 1 , 2 result in some trait combinations being much more widespread than others, as revealed in the global spectrum of plant form and function (GSPFF 3 ) and the root economics space (RES 4 ) for aboveground and fine-root traits, respectively. Here we combine the traits that define both functional spaces. Our analysis confirms the major trends of the GSPFF and shows that the RES captures additional information. The four dimensions needed to explain the non-redundant information in the dataset can be summarized in an aboveground and a fine-root plane, corresponding to the GSPFF and the RES, respectively. Both planes display high levels of species aggregation, but the differentiation among growth forms, families and biomes is lower on the fine-root plane, which does not include any size-related trait, than on the aboveground plane. As a result, many species with similar fine-root syndromes display contrasting aboveground traits. This highlights the importance of including belowground organs to the GSPFF when exploring the interplay between different natural selection pressures and whole-plant trait integration. The authors analyse the coordination and trade-off of the aboveground and fine-root traits of vascular plants using global trait databases.

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. The wetland soil microbiome has a major impact on greenhouse gas emissions. Here the authors characterize how a group of archaea contribute to N 2 O emissions and find that climate and land use changes could promote these organisms.

Native biodiversity decline and non-native species spread are major features of the Anthropocene. Both processes can drive biotic homogenization by reducing trait and phylogenetic differences in species assemblages between regions, thus diminishing the regional distinctiveness of biotas and likely have negative impacts on key ecosystem functions. However, a global assessment of this phenomenon is lacking. Here, using a dataset of >200,000 plant species, we demonstrate widespread and temporal decreases in species and phylogenetic turnover across grain sizes and spatial extents. The extent of homogenization within major biomes is pronounced and is overwhelmingly explained by non-native species naturalizations. Asia and North America are major sources of non-native species; however, the species they export tend to be phylogenetically close to recipient floras. Australia, the Pacific and Europe, in contrast, contribute fewer species to the global pool of non-natives, but represent a disproportionate amount of phylogenetic diversity. The timeline of most naturalisations coincides with widespread human migration within the last ~500 years, and demonstrates the profound influence humans exert on regional biotas beyond changes in species richness. Human-driven movements and extinctions of species have made plant communities across biomes more homogenous. Here the authors quantify plant vascular species and phylogenetic homogenization across the globe, finding that non-native species naturalisations have been a major driver.

Although experiments show a positive association between vascular plant and arbuscular mycorrhizal fungal (AMF) species richness, evidence from natural ecosystems is scarce. Furthermore, there is little knowledge about how AMF richness varies with belowground plant richness and biomass. We examined relationships among AMF richness, above‐ and belowground plant richness, and plant root and shoot biomass in a native North American grassland. Root‐colonizing AMF richness and belowground plant richness were detected from the same bulk root samples by 454‐sequencing of the AMF SSU rRNA and plant trnL genes. In total we detected 63 AMF taxa. Plant richness was 1.5 times greater belowground than aboveground. AMF richness was significantly positively correlated with plant species richness, and more strongly with below‐ than aboveground plant richness. Belowground plant richness was positively correlated with belowground plant biomass and total plant biomass, whereas aboveground plant richness was positively correlated only with belowground plant biomass. By contrast, AMF richness was negatively correlated with belowground and total plant biomass. Our results indicate that AMF richness and plant belowground richness are more strongly related with each other and with plant community biomass than with the plant aboveground richness measures that have been almost exclusively considered to date.

Despite the important ecosystem role played by arbuscular mycorrhizal fungi (AMF), little is known about spatial and temporal variation in soil AMF communities. We used pyrosequencing to characterise AMF communities in soil samples (n = 44) from a natural forest ecosystem. Fungal taxa were identified by BLAST matching of reads against the MaarjAM database of AMF SSU rRNA gene diversity. Sub-sampling within our dataset and experimental shortening of a set of long reads indicated that our approaches to taxonomic identification and diversity analysis were robust to variations in pyrosequencing read length and numbers of reads per sample. Different forest plots (each 10 × 10 m and separated from one another by 30 m) contained significantly different soil AMF communities, and the pairwise similarity of communities decreased with distance up to 50 m. However, there were no significant changes in community composition between different time points in the growing season (May-September). Spatial structure in soil AMF communities may be related to the heterogeneous vegetation of the natural forest study system, while the temporal stability of communities suggests that AMF in soil represent a fairly constant local species pool from which mycorrhizae form and disband during the season.

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.

Functional trait differences among species are increasingly used to infer the effects of biotic and abiotic processes on species coexistence. Commonly, the trait diversity observed within communities is compared to patterns simulated in randomly generated communities based on sampling within a region. The resulting patterns of trait convergence and divergence are assumed to reveal abiotic and biotic processes, respectively. However, biotic processes such as competition can produce both trait divergence and convergence, through either excluding similar species (niche differences, divergence) or excluding dissimilar species (weaker competitor exclusion, convergence). Hence, separating biotic and abiotic processes that can produce identical patterns of trait diversity, or even patterns that neutralize each other, is not feasible with previous methods. We propose an operational framework in which the functional trait dissimilarity within communities (FDcomm) is compared to the corresponding trait dissimilarity expected from the species pool (i.e., functional species pool diversity, FDpool). FDpool includes the set of potential species for a site delimited by the operating environmental and dispersal limitation filters. By applying these filters, the resulting pattern of trait diversity is consistent with biotic processes, i.e., trait divergence (FDcomm > FDpool) indicates niche differentiation, while trait convergence (FDcomm < FDpool) indicates weaker competitor exclusion. To illustrate this framework, with its potential application and constraints, we analyzed both simulated and field data. The functional species pool framework more consistently detected the simulated trait diversity patterns than previous approaches. In the field, using data from plant communities of typical Northern European habitats in Estonia, we found that both niche-based and weaker competitor exclusion influenced community assembly, depending on the traits and community considered. In both simulated and field data, we demonstrated that only by estimating the species pool of a site is it possible to differentiate the patterns of trait dissimilarity produced by operating biotic processes. The framework, which can be applied with both functional and phylogenetic diversity, enables a reinterpretation of community assembly processes. Solving the challenge of defining an appropriate reference species pool for a site can provide a better understanding of community assembly.