Peat loss collocates with a threshold in plant-mycorrhizal associations in drained peatlands encroached by trees.

Drainage-induced encroachment by trees may have major effects on the carbon balance of northern peatlands, and responses of microbial communities are likely to play a central mechanistic role. We profiled the soil fungal community and estimated its genetic potential for the decay of lignin and phenolics (class II peroxidase potential) along peatland drainage gradients stretching from interior locations (undrained, open) to ditched locations (drained, forested). Mycorrhizal fungi dominated the community across the gradients. When moving towards ditches, the dominant type of mycorrhizal association abruptly shifted from ericoid mycorrhiza to ectomycorrhiza at c. 120 m from the ditches. This distance corresponded with increased peat loss, from which more than half may be attributed to oxidation. The ectomycorrhizal genus Cortinarius dominated at the drained end of the gradients and its relatively higher genetic potential to produce class II peroxidases (together with Mycena) was positively associated with peat humification and negatively with carbon-to-nitrogen ratio. Our study is consistent with a plant-soil feedback mechanism, driven by a shift in the mycorrhizal type of vegetation, that potentially mediates changes in aerobic decomposition during postdrainage succession. Such feedback may have long-term legacy effects upon postdrainage restoration efforts and implication for tree encroachment onto carbon-rich soils globally.

Woody invaders are more highly colonized by arbuscular mycorrhizal fungi than congeneric native species.

PREMISE: Invasive species tend to possess acquisitive plant traits that support fast growth and strong competitive ability. However, the relevance of symbioses with arbuscular mycorrhizal fungi (AMF) to the fast growing, acquisitive strategy of invasive species is still unclear. METHODS: We measured AMF colonization in roots of five congeneric pairs of invasive and native eastern North American woody species (10 species total; 4 lianas, 6 shrubs) that were grown in a monoculture common garden experiment in Syracuse, NY. We then examined the relationships of AMF colonization to above and belowground traits of these species. RESULTS: Total AMF colonization and arbuscule colonization were greater in invasive compared to native woody species, a pattern that was more distinct in congeneric shrubs than congeneric lianas. The level of AMF colonization was also positively correlated with traits indicative of rapid plant growth and nutrient uptake. CONCLUSIONS: The concordance of a resource-acquisitive strategy with higher AMF colonization suggests that symbioses with AMF may be part of the strategy by which invasive woody plants of eastern North America are able to maintain fast growth rates and outcompete their native counterparts.

The Rhizosphere Responds: Rich Fen Peat and Root Microbial Ecology after Long-Term Water Table Manipulation.

Hydrologic shifts due to climate change will affect the cycling of carbon (C) stored in boreal peatlands. Carbon cycling in these systems is carried out by microorganisms and plants in close association. This study investigated the effects of experimentally manipulated water tables (lowered and raised) and plant functional groups on the peat and root microbiomes in a boreal rich fen. All samples were sequenced and processed for bacterial, archaeal (16S DNA genes; V4), and fungal (internal transcribed spacer 2 [ITS2]) DNA. Depth had a strong effect on microbial and fungal communities across all water table treatments. Bacterial and archaeal communities were most sensitive to the water table treatments, particularly at the 10- to 20-cm depth; this area coincides with the rhizosphere or rooting zone. Iron cyclers, particularly members of the family Geobacteraceae, were enriched around the roots of sedges, horsetails, and grasses. The fungal community was affected largely by plant functional group, especially cinquefoils. Fungal endophytes (particularly Acephala spp.) were enriched in sedge and grass roots, which may have underappreciated implications for organic matter breakdown and cycling. Fungal lignocellulose degraders were enriched in the lowered water table treatment. Our results were indicative of two main methanogen communities, a rooting zone community dominated by the archaeal family Methanobacteriaceae and a deep peat community dominated by the family Methanomicrobiaceae. IMPORTANCE This study demonstrated that roots and the rooting zone in boreal fens support organisms likely capable of methanogenesis, iron cycling, and fungal endophytic association and are directly or indirectly affecting carbon cycling in these ecosystems. These taxa, which react to changes in the water table and associate with roots and, particularly, graminoids, may gain greater biogeochemical influence, as projected higher precipitation rates could lead to an increased abundance of sedges and grasses in boreal fens.

Peatland microbial community responses to plant functional group and drought are depth-dependent.

Peatlands store one-third of Earth's soil carbon, the stability of which is uncertain due to climate change-driven shifts in hydrology and vegetation, and consequent impacts on microbial communities that mediate decomposition. Peatland carbon cycling varies over steep physicochemical gradients characterizing vertical peat profiles. However, it is unclear how drought-mediated changes in plant functional groups (PFGs) and water table (WT) levels affect microbial communities at different depths. We combined a multiyear mesocosm experiment with community sequencing across a 70-cm depth gradient, to test the hypotheses that vascular PFGs (Ericaceae vs. sedges) and WT (high vs. low) structure peatland microbial communities in depth-dependent ways. Several key results emerged. (i) Both fungal and prokaryote (bacteria and archaea) community structure shifted with WT and PFG manipulation, but fungi were much more sensitive to PFG whereas prokaryotes were much more sensitive to WT. (ii) PFG effects were largely driven by Ericaceae, although sedge effects were evident in specific cases (e.g., methanotrophs). (iii) Treatment effects varied with depth: the influence of PFG was strongest in shallow peat (0-10, 10-20 cm), whereas WT effects were strongest at the surface and middle depths (0-10, 30-40 cm), and all treatment effects waned in the deepest peat (60-70 cm). Our results underline the depth-dependent and taxon-specific ways that plant communities and hydrologic variability shape peatland microbial communities, pointing to the importance of understanding how these factors integrate across soil profiles when examining peatland responses to climate change.

Accounting for local adaptation in ectomycorrhizas: a call to track geographical origin of plants, fungi, and soils in experiments.

Local adaptation, the differential success of genotypes in their native versus foreign environments, can influence ecological and evolutionary processes, yet its importance is difficult to estimate because it has not been widely studied, particularly in the context of interspecific interactions. Interactions between ectomycorrhizal (EM) fungi and their host plants could serve as model system for investigations of local adaptation because they are widespread and affect plant responses to both biotic and abiotic selection pressures. Furthermore, because EM fungi cycle nutrients and mediate energy flow into food webs, their local adaptation may be critical in sustaining ecological function. Despite their ecological importance and an extensive literature on their relationships with plants, the vast majority of experiments on EM symbioses fail to report critical information needed to assess local adaptation: the geographic origin of the plant, fungal inocula, and soil substrate used in the experiment. These omissions limit the utility of such studies and restrict our understanding of EM ecology and evolution. Here, we illustrate the potential importance of local adaptation in EM relationships and call for consistent reporting of the geographic origin of plant, soil, and fungi as an important step towards a better understanding of the ecology and evolution of EM symbioses.

Home-field advantage? evidence of local adaptation among plants, soil, and arbuscular mycorrhizal fungi through meta-analysis.

BACKGROUND: Local adaptation, the differential success of genotypes in their native versus foreign environment, arises from various evolutionary processes, but the importance of concurrent abiotic and biotic factors as drivers of local adaptation has only recently been investigated. Local adaptation to biotic interactions may be particularly important for plants, as they associate with microbial symbionts that can significantly affect their fitness and may enable rapid evolution. The arbuscular mycorrhizal (AM) symbiosis is ideal for investigations of local adaptation because it is globally widespread among most plant taxa and can significantly affect plant growth and fitness. Using meta-analysis on 1170 studies (from 139 papers), we investigated the potential for local adaptation to shape plant growth responses to arbuscular mycorrhizal inoculation. RESULTS: The magnitude and direction for mean effect size of mycorrhizal inoculation on host biomass depended on the geographic origin of the soil and symbiotic partners. Sympatric combinations of plants, AM fungi, and soil yielded large increases in host biomass compared to when all three components were allopatric. The origin of either the fungi or the plant relative to the soil was important for explaining the effect of AM inoculation on plant biomass. If plant and soil were sympatric but allopatric to the fungus, the positive effect of AM inoculation was much greater than when all three components were allopatric, suggesting potential local adaptation of the plant to the soil; however, if fungus and soil were sympatric (but allopatric to the plant) the effect of AM inoculation was indistinct from that of any allopatric combinations, indicating maladaptation of the fungus to the soil. CONCLUSIONS: This study underscores the potential to detect local adaptation for mycorrhizal relationships across a broad swath of the literature. Geographic origin of plants relative to the origin of AM fungal communities and soil is important for describing the effect of mycorrhizal inoculation on plant biomass, suggesting that local adaptation represents a powerful factor for the establishment of novel combinations of fungi, plants, and soils. These results highlight the need for subsequent investigations of local adaptation in the mycorrhizal symbiosis and emphasize the importance of routinely considering the origin of plant, soil, and fungal components.

Genetics-based interactions among plants, pathogens, and herbivores define arthropod community structure.

Plant resistance to pathogens or insect herbivores is common, but its potential for indirectly influencing plant-associated communities is poorly known. Here, we test whether pathogens' indirect effects on arthropod communities and herbivory depend on plant resistance to pathogens and/or herbivores, and address the overarching interacting foundation species hypothesis that genetics-based interactions among a few highly interactive species can structure a much larger community. In a manipulative field experiment using replicated genotypes of two Populus species and their interspecific hybrids, we found that genetic variation in plant resistance to both pathogens and insect herbivores modulated the strength of pathogens' indirect effects on arthropod communities and insect herbivory. First, due in part to the pathogens' differential impacts on leaf biomass among the two Populus species and the hybrids, the pathogen most strongly impacted arthropod community composition, richness, and abundance on the pathogen-susceptible tree species. Second, we found similar patterns comparing pathogen-susceptible and pathogen-resistant genotypes within species. Third, within a plant species, pathogens caused a fivefold greater reduction in herbivory on insect-herbivore-susceptible plant genotypes than on herbivore-resistant genotypes, demonstrating that the pathogen-herbivore interaction is genotype dependent. We conclude that interactions among plants, pathogens, and herbivores can structure multitrophic communities, supporting the interacting foundation species hypothesis. Because these interactions are genetically based, evolutionary changes in genetic resistance could result in ecological changes in associated communities, which may in turn feed back to affect plant fitness.

Tree genotype and genetically based growth traits structure twig endophyte communities.

PREMISE OF THE STUDY: Fungal endophytes asymptomatically inhabit plant tissues where they have mutualistic, parasitic, or commensal relationships with their hosts. Although plant-fungal interactions at the genotype scale have broad ecological and evolutionary implications, the sensitivity of endophytes in woody tissues to differences among plant genotypes is poorly understood. We hypothesize that (1) endophyte communities in Populus angustifolia (Salicaceae) twigs vary among tree genotypes, (2) endophyte variation is linked to quantitative tree traits, and (3) tree genotype influences interspecific fungal interactions. METHODS: Endophytes were isolated from twigs of replicated P. angustifolia genotypes in a common garden and characterized with PCR-RFLP and DNA sequencing. Twig length and diameter, aboveground tree biomass, and condensed tannins were also quantified. KEY RESULTS: (1) Aspects of fungal community structure, including composition and total isolation frequency (i.e., abundance), varied among genotypes. (2) Aboveground biomass and twig diameter were positively associated with isolation frequency and covaried with composition, whereas twig length and condensed tannin concentration were not significantly correlated to endophytes. (3) Fungal co-occurrence patterns suggested negative species interactions, but the presence of significant co-occurrences was genotype dependent. CONCLUSIONS: The species is often assumed to be the most important ecological unit; however, these results indicate that genetically based trait variation within a species can influence an important community of associated organisms. Given the dominance of plants as primary producers and the ubiquity of endophytes, the effect of host genetic variation on endophytes has fundamental implications for our understanding of terrestrial ecosystems.

Plant genetic identity of foundation tree species and their hybrids affects a litter-dwelling generalist predator.

The effects of plant genetics on predators, especially those not living on the plant itself, are rarely studied and poorly understood. Therefore, we investigated the effect of plant hybridization and genotype on litter-dwelling spiders. Using an 18-year-old cottonwood common garden, we recorded agelenid sheet-web density associated with the litter layers of replicated genotypes of three tree cross types: Populus fremontii, Populus angustifolia, and their F1 hybrids. We surveyed 118 trees for agelenid litter webs at two distances from the trees (0-100 and 100-200 cm from trunk) and measured litter depth as a potential mechanism of web density patterns. Five major results emerged: web density within a 1-m radius of P. angustifolia was approximately three times higher than within a 1-m radius of P. fremontii, with F1 hybrids having intermediate densities; web density responded to P. angustifolia and F1 hybrid genotypes as indicated by a significant genotype × distance interaction, with some genotypes exhibiting a strong decline in web density with distance, while others did not; P. angustifolia litter layers were deeper than those of P. fremontii at both distance classes, and litter depth among P. angustifolia genotypes differed up to 300%; cross type and genotype influenced web density via their effects on litter depth, and these effects were influenced by distance; web density was more sensitive to the effects of tree cross type than genotype. By influencing generalist predators, plant hybridization and genotype may indirectly impact trophic interactions such as intraguild predation, possibly affecting trophic cascades and ecosystem processes.

An elusive ectomycorrhizal fungus reveals itself: a new species of Geopora (Pyronemataceae) associated with Pinus edulis.

Species of the genus Geopora are important ectomycorrhizal associates that can dominate the communities of some plant taxa, such as pinyon pine (Pinus edulis), a widespread tree of the western United States. Several members of the genus Geopora are known only from ectomycorrhizal root tips and thus have not been described formally. The sporocarps of some Geopora species occur infrequently because they depend on wet years for sporulation. In addition, Geopora sporocarps can be small and may be hypogeous at some developmental stage, limiting the opportunities for describing their morphology. Using molecular and morphological data, we have described a new species of fungus, Geopora pinyonensis, which produced ascocarps after unusually high precipitation at a northern Arizona site in summer 2012. Based on analysis of the ITS and nuLSU regions of the rDNA, G pinyonensis is a new species of Geopora. It has small sporocarps and ascospores relative to other members of the genus; however, these morphological features overlap with other species. Using rDNA data from sporocarps and ectomycorrhizal root tips, we show that the sporocarps correspond to an abundant species of ectomycorrhizal fungus associated with pinyon pines that is increasing in abundance in drought-affected landscapes and may promote drought tolerance.

FungiQuant: a broad-coverage fungal quantitative real-time PCR assay.

BACKGROUND: Fungal load quantification is a critical component of fungal community analyses. Limitation of current approaches for quantifying the fungal component in the human microbiome suggests the need for new broad-coverage techniques. METHODS: We analyzed 2,085 18S rRNA gene sequences from the SILVA database for assay design. We generated and quantified plasmid standards using a qPCR-based approach. We evaluated assay coverage against 4,968 sequences and performed assay validation following the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. RESULTS: We designed FungiQuant, a TaqMan® qPCR assay targeting a 351 bp region in the fungal 18S rRNA gene. Our in silico analysis showed that FungiQuant is a perfect sequence match to 90.0% of the 2,617 fungal species analyzed. We showed that FungiQuant's is 100% sensitive and its amplification efficiencies ranged from 76.3% to 114.5%, with r(2)-values of >0.99 against the 69 fungal species tested. Additionally, FungiQuant inter- and intra-run coefficients of variance ranged from <10% and <20%, respectively. We further showed that FungiQuant has a limit of quantification 25 copies and a limit of detection at 5 copies. Lastly, by comparing results from human-only background DNA with low-level fungal DNA, we showed that amplification in two or three of a FungiQuant performed in triplicate is statistically significant for true positive fungal detection. CONCLUSIONS: FungiQuant has comprehensive coverage against diverse fungi and is a robust quantification and detection tool for delineating between true fungal detection and non-target human DNA.

Variation in carbon and nitrogen concentrations among peatland categories at the global scale.

Peatlands account for 15 to 30% of the world's soil carbon (C) stock and are important controls over global nitrogen (N) cycles. However, C and N concentrations are known to vary among peatlands contributing to the uncertainty of global C inventories, but there are few global studies that relate peatland classification to peat chemistry. We analyzed 436 peat cores sampled in 24 countries across six continents and measured C, N, and organic matter (OM) content at three depths down to 70 cm. Sites were distinguished between northern (387) and tropical (49) peatlands and assigned to one of six distinct broadly recognized peatland categories that vary primarily along a pH gradient. Peat C and N concentrations, OM content, and C:N ratios differed significantly among peatland categories, but few differences in chemistry with depth were found within each category. Across all peatlands C and N concentrations in the 10-20 cm layer, were 440 ± 85.1 g kg-1 and 13.9 ± 7.4 g kg-1, with an average C:N ratio of 30.1 ± 20.8. Among peatland categories, median C concentrations were highest in bogs, poor fens and tropical swamps (446-532 g kg-1) and lowest in intermediate and extremely rich fens (375-414 g kg-1). The C:OM ratio in peat was similar across most peatland categories, except in deeper samples from ombrotrophic tropical peat swamps that were higher than other peatlands categories. Peat N concentrations and C:N ratios varied approximately two-fold among peatland categories and N concentrations tended to be higher (and C:N lower) in intermediate fens compared with other peatland types. This study reports on a unique data set and demonstrates that differences in peat C and OM concentrations among broadly classified peatland categories are predictable, which can aid future studies that use land cover assessments to refine global peatland C and N stocks.

Patterns and drivers of fungal community depth stratification in Sphagnum peat.

Peatlands store an immense pool of soil carbon vulnerable to microbial oxidation due to drought and intentional draining. We used amplicon sequencing and quantitative PCR to (i) examine how fungi are influenced by depth in the peat profile, water table and plant functional group at the onset of a multiyear mesocosm experiment, and (ii) test if fungi are correlated with abiotic variables of peat and pore water. We hypothesized that each factor influenced fungi, but that depth would have the strongest effect early in the experiment. We found that (i) communities were strongly depth stratified; fungi were four times more abundant in the upper (10-20 cm) than the lower (30-40 cm) depth, and dominance shifted from ericoid mycorrhizal fungi to saprotrophs and endophytes with increasing depth; (ii) the influence of plant functional group was depth dependent, with Ericaceae structuring the community in the upper peat only; (iii) water table had minor influences; and (iv) communities strongly covaried with abiotic variables, including indices of peat and pore water carbon quality. Our results highlight the importance of vertical stratification to peatland fungi, and the depth dependency of plant functional group effects, which must be considered when elucidating the role of fungi in peatland carbon dynamics.

A novel isolate and widespread abundance of the candidate alphaproteobacterial order (Ellin 329), in southern Appalachian peatlands.

Peatlands of all latitudes play an integral role in global climate change by serving as a carbon sink and a primary source of atmospheric methane; however, the microbial ecology of mid-latitude peatlands is vastly understudied. Herein, next generation Illumina amplicon sequencing of small subunit rRNA genes was utilized to elucidate the microbial communities in three southern Appalachian peatlands. In contrast to northern peatlands, Proteobacteria dominated over Acidobacteria in all three sites. An average of 11 bacterial phyla was detected at relative abundance values >1%, with three candidate divisions (OP3, WS3 and NC10) represented, indicating high phylogenetic diversity. Physiological traits of isolates within the candidate alphaproteobacterial order, Ellin 329, obtained here and in previous studies indicate that bacteria of this order may be involved in hydrolysis of poly-, di- and monosaccharides. Community analyses indicate that Ellin 329 is the third most abundant order and is most abundant near the surface layers where plant litter decomposition should be primarily occurring. In sum, members of Ellin 329 likely play important roles in organic matter decomposition, in southern Appalachian peatlands and should be investigated further in other peatlands and ecosystem types.

MycoDB, a global database of plant response to mycorrhizal fungi.

Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems.

Community specificity: life and afterlife effects of genes.

Community-level genetic specificity results when individual genotypes or populations of the same species support different communities. Our review of the literature shows that genetic specificity exhibits both life and afterlife effects; it is a widespread phenomenon occurring in diverse taxonomic groups, aquatic to terrestrial ecosystems, and species-poor to species-rich systems. Such specificity affects species interactions, evolution, ecosystem processes and leads to community feedbacks on the performance of the individuals expressing the traits. Thus, genetic specificity by communities appears to be fundamentally important, suggesting that specificity is a major driver of the biodiversity and stability of the world's ecosystems.