Bacterial community succession in a high‐altitude subarctic glacier foreland is a three‐stage process

Alpine glaciers are retreating rapidly, exposing foreland minerals, which develop into soils. Bacterial communities in glacier forelands exhibit high rates of turnover and undergo dramatic shifts in composition within the first 50 years after deglaciation, followed by relative stabilization and convergence. This period of microbial development occurs simultaneously with plant colonization in most systems; thus, it remains unclear whether the changes in the bacterial communities occur primarily as the result of edaphic, climatic or biotic factors. We examined bacterial community structure along two replicate chronosequences within the glacial foreland of Duke River Glacier, Yukon, Canada. This foreland is estimated to include >200 years of bare soils before an appreciable grassline, likely due to the high latitude and altitude of the glacier. This enabled us to examine bacterial community development prior to plant colonization over a longer period than previous studies. We observed three successional groups in the chronosequence: (i) an ‘early’ group in soils of less than approximately 50 years since deglaciation; (ii) an ‘intermediate’ group within bare soils, after the early period but before the grassline, containing communities with a relatively high degree of variability in composition; and (iii) a ‘grassline’ group in soils collected after plant colonization with higher diversity but lower age‐group variability in community composition. These findings suggest rapid replacement and addition of species better adapted to glacier foreland conditions followed by slower community shifts over the next 150 years and, finally, indications of a possible response to plant colonization.     

Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics

Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO₂ emissions. Short‐term atmospheric elevated CO₂ exposure has been shown to create major shifts in C flow routes and diversity of the active soil‐borne microbial community. Long‐term increases in CO₂ have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO₂ exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO₂ concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by ¹³C pulse‐chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA‐stable isotope probing (RNA‐SIP), in combination with real‐time PCR and PCR‐DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO₂ was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO₂ caused a continuous increase in the ¹³C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO₂ conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.     

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield

Spatial patterns of microbial communities have been extensively surveyed in well‐developed soils, but few studies investigated the vertical distribution of micro‐organisms in newly developed soils after glacier retreat. We used 454‐pyrosequencing to assess whether bacterial and fungal community structures differed between stages of soil development (SSD) characterized by an increasing vegetation cover from barren (vegetation cover: 0%/age: 10 years), sparsely vegetated (13%/60 years), transient (60%/80 years) to vegetated (95%/110 years) and depths (surface, 5 and 20 cm) along the Damma glacier forefield (Switzerland). The SSD significantly influenced the bacterial and fungal communities. Based on indicator species analyses, metabolically versatile bacteria (e.g. Geobacter) and psychrophilic yeasts (e.g. Mrakia) characterized the barren soils. Vegetated soils with higher C, N and root biomass consisted of bacteria able to degrade complex organic compounds (e.g. Candidatus Solibacter), lignocellulolytic Ascomycota (e.g. Geoglossum) and ectomycorrhizal Basidiomycota (e.g. Laccaria). Soil depth only influenced bacterial and fungal communities in barren and sparsely vegetated soils. These changes were partly due to more silt and higher soil moisture in the surface. In both soil ages, the surface was characterized by OTUs affiliated to Phormidium and Sphingobacteriales. In lower depths, however, bacterial and fungal communities differed between SSD. Lower depths of sparsely vegetated soils consisted of OTUs affiliated to Acidobacteria and Geoglossum, whereas depths of barren soils were characterized by OTUs related to Gemmatimonadetes. Overall, plant establishment drives the soil microbiota along the successional gradient but does not influence the vertical distribution of microbiota in recently deglaciated soils.     

Do bacterial and fungal communities assemble differently during primary succession?

High‐throughput sequencing technologies are now allowing us to study patterns of community assembly for diverse microbial assemblages across environmental gradients and during succession. Here we discuss potential explanations for similarities and differences in bacterial and fungal community assembly patterns along a soil chronosequence in the foreland of a receding glacier. Although the data are not entirely conclusive, they do indicate that successional trajectories for bacteria and fungi may be quite different. Recent empirical and theoretical studies indicate that smaller microbes (like most bacteria) are less likely to be dispersal limited than are larger microbes – which could result in a more deterministic community assembly pattern for bacteria during primary succession. Many bacteria are also better adapted (than are fungi) to life in barren, early‐successional sediments in that some can fix nitrogen and carbon from the atmosphere – traits not possessed by any fungi. Other differences between bacteria and fungi are discussed, but it is apparent from this and other recent studies of microbial succession that we are a long way from understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession. We especially need a better understanding of global and regional patterns of microbial dispersal and what environmental factors control the development of microbial communities in complex natural systems.     

Bacterial,Archaeal and Fungal Succession in the Forefield of a Receding Glacier

Glacier forefield chronosequences, initially composed of barren substrate after glacier retreat, are ideal locations to study primary microbial colonization and succession in a natural environment. We characterized the structure and composition of bacterial, archaeal and fungal communities in exposed rock substrates along the Damma glacier forefield in central Switzerland. Soil samples were taken along the forefield from sites ranging from fine granite sand devoid of vegetation near the glacier terminus to well-developed soils covered with vegetation. The microbial communities were studied with genetic profiling (T-RFLP) and sequencing of clone libraries. According to the T-RFLP profiles, bacteria showed a high Shannon diversity index (H) (ranging from 2.3 to 3.4) with no trend along the forefield. The major bacterial lineages were Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Cyanobacteria. An interesting finding was that Euryarchaeota were predominantly colonizing young soils and Crenarchaeota mainly mature soils. Fungi shifted from an Ascomycota-dominated community in young soils to a more Basidiomycota-dominated community in old soils. Redundancy analysis indicated that base saturation, pH, soil C and N contents and plant coverage, all related to soil age, correlated with the microbial succession along the forefield.     

Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root‐associated fungi mirrors plant succession in two glacial chronosequences

Glacier chronosequences are important sites for primary succession studies and have yielded well‐defined primary succession models for plants that identify environmental resistance as an important determinant of the successional trajectory. Whether plant‐associated fungal communities follow those same successional trajectories and also respond to environmental resistance is an open question. In this study, 454 amplicon pyrosequencing was used to compare the root‐associated fungal communities of the ectomycorrhizal (ECM) herb Bistorta vivipara along two primary succession gradients with different environmental resistance (alpine versus arctic) and different successional trajectories in the vascular plant communities (directional replacement versus directional non‐replacement). At both sites, the root‐associated fungal communities were dominated by ECM basidiomycetes and community composition shifted with increasing time since deglaciation. However, the fungal community's successional trajectory mirrored the pattern observed in the surrounding plant community at both sites: the alpine site displayed a directional‐replacement successional trajectory, and the arctic site displayed a directional‐non‐replacement successional trajectory. This suggests that, like in plant communities, environmental resistance is key in determining succession patterns in root‐associated fungi. The need for further replicated study, including in other host species, is emphasized.     

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Microbial communities in plant roots provide critical links between above‐ and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities, we designed a trap‐plant bioassay experiment. Replicate Populus, Quercus and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of four loci (i.e., 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability.     

Plant–pollinator network assembly along the chronosequence of a glacier foreland

Forelands of retreating glaciers offer an ideal model system to study community assembly processes during primary succession. As plants colonize the area that is freed from ice they should be accompanied by their pollinators to successfully reproduce and spread. However, little is known about the assembly of plant–pollinator networks. We therefore used quantitative network analysis to study the structure of plant–pollinator interactions at seven sites representing a chronosequence from 8 to 130 years since deglaciation on the foreland of the Morteratsch glacier (southeastern Switzerland). At these sites, individual visits of plant flowers by insects were recorded throughout the flowering season. Species richness of insect‐pollinated plants and plant‐pollinating insects, together with measures of interaction diversity and evenness, increased along the chronosequence at least for the first 80 years after deglaciation. Bees were the most frequent flower visitors at the two youngest sites, whereas flies dominated in mature communities. Pollinator generalization (the number of visited plant species weighted by interaction strength), but not plant generalization, strongly increased during the primary succession. This was reflected in a pronounced decline in network level specialization (measured as Blüthgen's H₂’) and interaction strength asymmetry during the first 60 years along the chronosequence, while nestedness increased along the chronosequence. Thus, our findings contradict niche‐theoretical predictions of increasing specialization of pollination systems during succession, but are in agreement with expectations from optimal foraging theory, predicting an increase in pollinator generalization with higher plant diversity but similar flower abundance, and an increase in diet breadth at higher pollinator densities during primary succession.     

Influence of corn,switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side‐by‐side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipid analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.     

Changes in the structure and heterogeneity of vegetation and microsite environments with the chronosequence of primary succession on a glacier foreland in Ellesmere Island, high arctic Canada

Primary plant succession was investigated on a well-vegetated glacier foreland on Ellesmere Island in high arctic Canada. A field survey was carried out on four glacier moraines differing in time after deglaciation to assess vegetation development and microsite modification in the chronosequence of succession. The results showed evidence of directional succession without species replacement, which is atypical in the high arctic, reflecting the exceptionally long time vegetation development. During this successional process, Salix arctica dominated throughout all moraines. The population structures of S. arctica on these moraines implied the population growth of this species with progressing succession. The population density of S. arctica reflected the abundance of vascular plants, suggesting that development of the plant community might be related to structural changes and the growth of constituting populations. Through such growths of the population and the whole community with progressing succession, the spatial heterogeneity of vegetation gradually declines. Moreover, this vegetation homogenization is accompanied by changes in the spatial heterogeneity of microsite environments, suggesting significant plant effects on the modification of microsite environments. Accordingly, it was concluded that the directional primary succession observed on this glacier foreland is characterized by the initial sporadic colonization of plants, subsequent population growths, and the community assembly of vascular plants, accompanied by microsite modification.     

Microbial Community Succession in an Unvegetated,Recently Deglaciated Soil

Primary succession is a fundamental process in macroecosystems; however, if and how soil development influences microbial community structure is poorly understood. Thus, we investigated changes in the bacterial community along a chronosequence of three unvegetated, early successional soils (∼20-year age gradient) from a receding glacier in southeastern Peru using molecular phylogenetic techniques. We found that evenness, phylogenetic diversity, and the number of phylotypes were lowest in the youngest soils, increased in the intermediate aged soils, and plateaued in the oldest soils. This increase in diversity was commensurate with an increase in the number of sequences related to common soil bacteria in the older soils, including members of the divisions Acidobacteria, Bacteroidetes, and Verrucomicrobia. Sequences related to the Comamonadaceae clade of the Betaproteobacteria were dominant in the youngest soil, decreased in abundance in the intermediate age soil, and were not detected in the oldest soil. These sequences are closely related to culturable heterotrophs from rock and ice environments, suggesting that they originated from organisms living within or below the glacier. Sequences related to a variety of nitrogen (N)-fixing clades within the Cyanobacteria were abundant along the chronosequence, comprising 6–40% of phylotypes along the age gradient. Although there was no obvious change in the overall abundance of cyanobacterial sequences along the chronosequence, there was a dramatic shift in the abundance of specific cyanobacterial phylotypes, with the intermediate aged soils containing the greatest diversity of these sequences. Most soil biogeochemical characteristics showed little change along this ∼20-year soil age gradient; however, soil N pools significantly increased with soil age, perhaps as a result of the activity of the N-fixing Cyanobacteria. Our results suggest that, like macrobial communities, soil microbial communities are structured by substrate age, and that they, too, undergo predictable changes through time.     

Influences of Plant Species Composition,Fertilisation and <Emphasis Type="Italic">Lolium perenne</Emphasis> Ingression on Soil Microbial Community Structure in Three Irish Grasslands

Semi-natural grassland soils are frequently fertilised for agricultural improvement. This practice often comes at a loss of the indigenous flora while fast-growing nitrogen-responsive species, such as Lolium perenne, take over. Since soil microbial communities depend on plant root exudates for carbon and nitrogen sources, this shift in vegetation is thought to influence soil microbial community structure. In this study, we investigated the influence of different plant species, fertilisation and L. perenne ingression on microbial communities in soils from three semi-natural Irish grasslands. Bacterial and fungal community compositions were determined by automated ribosomal intergenic spacer analysis, and community changes were linked to environmental factors by multivariate statistical analysis. Soil type had a strong effect on bacterial and fungal communities, mainly correlated to soil pH, as well as soil carbon and nitrogen status. Within each soil type, plant species composition was the main influencing factor followed by nitrogen fertilisation and finally Lolium ingression in the acidic upland and mesotrophic grassland. In the alkaline grassland, however, Lolium ingression had a stronger effect than fertilisation. Our results suggest that a change in plant species diversity strongly influences the microbial community structure, which may subsequently lead to significant changes in ecosystem functioning.     

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities

Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near‐pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near‐pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near‐pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near‐pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near‐pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche‐based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β‐diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.     

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands?

Invasive plants are often associated with greater productivity and soil nutrient availabilities, but whether invasive plants with dissimilar traits change decomposer communities and decomposition rates in consistent ways is little known. We compared decomposition rates and the fungal and bacterial communities associated with the litter of three problematic invaders in intermountain grasslands; cheatgrass (Bromus tectorum), spotted knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula), as well as the native bluebunch wheatgrass (Pseudoroegneria spicata). Shoot and root litter from each plant was placed in cheatgrass, spotted knapweed, and leafy spurge invasions as well as remnant native communities in a fully reciprocal design for 6 months to see whether decomposer communities were species‐specific, and whether litter decomposed fastest when placed in a community composed of its own species (referred to hereafter as home‐field advantage–HFA). Overall, litter from the two invasive forbs, spotted knapweed and leafy spurge, decomposed faster than the native and invasive grasses, regardless of the plant community of incubation. Thus, we found no evidence of HFA. T‐RFLP profiles indicated that both fungal and bacterial communities differed between roots and shoots and among plant species, and that fungal communities also differed among plant community types. Synthesis. These results show that litter from three common invaders to intermountain grasslands decomposes at different rates and cultures microbial communities that are species‐specific, widespread, and persistent through the dramatic shifts in plant communities associated with invasions.     

Co-occurring grass species differ in their associated microbial community composition in a temperate native grassland

Background and aims

Specific associations exist between plant species and the soil microbial community and these associations vary between habitat types and different plant groups. However, there is evidence that the associations are highly specific. Hence, we aimed to determine the specificity of plant-microbe relationships amongst co-occurring grass species in a temperate grassland.

Methods and results

We examined the broad microbial groups of bacteria and fungi as well as a specific fungal group, the arbuscular mycorrhizal community amongst two dominant C₃ and C₄ species and one sub-dominant C₃ species using terminal restriction fragment length polymorphism (T-RFLP) analysis. We found that the two dominant species were more similar to each other in their bacterial and arbuscular mycorrhizal community composition than either was to the sub-dominant species, but not in their fungal community composition. We also found no clear evidence that those differences were directly linked to soil chemical properties.

Conclusions

Our results demonstrate that co-occurring grass species have a distinct soil microbial community and T-RFLP analysis is able to detect plant species effect on the microbial community composition on an extremely local scale, providing an insight into the differences in the response of bacterial, fungal and arbuscular mycorrhizal communities to different, but similar and co-occurring, plant species.     

内蒙古草原典型植物对土壤微生物群落的影响

为了分析内蒙古草原不同植物物种对土壤微生物群落的影响, 采用实时荧光定量PCR (real-time PCR)以及末端限制性片段长度多态性分析(terminal restriction fragment length polymorphism, T-RFLP)等分子生物学技术, 测定了退化-恢复样地上几种典型植物的根际土壤和非根际土壤中细菌和真菌的数量及群落结构。结果表明, 不同植物物种对根际和非根际细菌及根际真菌数量均有显著影响。根际土壤中的细菌和真菌数量普遍高于非根际土壤, 尤其以真菌更为明显。对T-RFLP数据进行多响应置换过程(multi-response permutation procedures, MRPP)分析和主成分分析(principal component analysis, PCA), 结果表明, 大多数物种的根际细菌及真菌的群落结构与非根际有明显差异, 并且所有物种的真菌群落可以按根际和非根际明显分为两大类群。此外, 细菌和真菌群落结构在一定程度上存在按物种聚类的现象, 以细菌较为明显。这些结果揭示了不同植物对土壤微生物群落的影响特征, 对理解内蒙古草原地区退化及恢复过程中植被演替引起的土壤性质和功能的变化有一定的帮助。     

Proportion of mycorrhiza-associated trees mediates community assemblages of soil fungi but not of bacteria

Recent studies have shown that mycorrhizal trees can greatly influence soil microbial communities, which in turn play important roles in the function offorest ecosystems. However, there is lack of understanding how the composition of trees with different mycorrhizal types affects soil microbial communities. Here, we collected 1606 soil samples from a 25-ha subtropical forest plot to investigate how the proportion of arbuscular mycorrhizal (AM) versus ectomycorrhizal (EcM) trees mediated soil microbial assemblages. Results showed the alpha diversities of both soil fungal and bacterial communities were significantly positively correlated with the ratio of AM/EcM trees. The AM/EcM tree ratio was important to the fungal community assembly, whereas soil pH was key to the bacterial communities. The increase in the AM/EcM tree ratio decreased the importance of stochastic forces in assembling fungal communities, while it had no significant effect on the bacterial communities. The differential importance of the AM/EcM tree ratio to fungal and bacterial communities highlights the role of mycorrhiza-associated tree composition in regulating soil microbial communities. This finding suggests that forests with different AM/EcM tree ratios would have different soil microbial communities, potentially leading to differences in soil nutrient cycling and in return different tree diversity and forest productivity.     

不同生境黑果枸杞根际与非根际土壤微生物群落多样性

研究典型生境黑果枸杞根际与非根际土壤微生物群落多样性及其与土壤理化性质间的关系,为进一步研究黑果枸杞抗逆性提供理论数据。采集新疆精河县艾比湖地区(EB)盐碱地、乌苏市(WS)路旁荒地、五家渠市(WQ)人工林带的黑果枸杞根际与非根际土壤,利用Illumina-MiSeq高通量测序技术分析细菌和真菌群落组成和多样性。结果表明:根际土壤细菌多样性高于非根际土壤(WQ除外),而根际真菌多样性低于非根际土壤。WQ非根际土壤细菌和真菌多样性均高于EB和WS;根际细菌多样性排序为EBWSWQ,根际真菌多样性排序为WSEBWQ。根际土壤优势细菌门依次是变形菌门、拟杆菌门、放线菌门、酸杆菌门,真菌优势门为子囊菌门、担子菌门。根际土壤细菌变形菌门、拟杆菌门、酸杆菌门的相对丰度高于非根际土壤,而厚壁菌在根际土壤中的丰度显著降低,真菌优势门丰度在根际土和非根际土中的变化趋势因地区而异; Haliea、Gp10、Pelagibius、Microbulbifer、假单胞菌属、Thioprofundum、Deferrisoma是根际土壤细菌优势属;多孢子菌属、支顶孢属、Corollospora、Cochlonema是根际真菌优势属。细菌、真菌优势类群(门、属)的组成以及丰富度存在地区间差异,厚壁菌门在EB地区的丰富度显著高于含盐量较低的WS、WQ;盐碱生境EB中根际土壤嗜盐细菌的丰度高于非盐碱生境(WQ、WS),如盐单胞菌属、动性球菌属、Geminicoccu、Pelagibius、Gracilimonas、Salinimicrobium等。小囊菌属是EB根际真菌的最优势属,Melanoleuca是WQ和WS的最优势属,地孔菌属、Xenobotrytis、Brachyconidiellopsis、多孢子菌属等在EB根际土壤中的丰度显著高于WQ和WS。非盐碱生境(WS和WQ)的微生物群落之间的相似性较高,并且高于与盐碱环境(EB)之间的相似性,表明土壤含盐量对微生物群落组成丰度具有重要的影响。     

Availability and function of arbuscular mycorrhizal and ectomycorrhizal fungi during revegetation of dewatered reservoirs left after dam removal

Revegetation following dam removal projects may depend on recovery of arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungal communities, which perform valuable ecosystem functions. This study assessed the availability and function of AM and EM fungi for plants colonizing dewatered reservoirs following a dam removal project on the Elwha River, Olympic Peninsula, Washington, United States. Availability was assessed via AM fungal spore density in soils and EM root tip colonization of Salix sitchensis (Sitka willow) in an observational field study. The effect of mycorrhizal fungi from 4 sources (reservoir soils, commercial inoculum, and 2 mature plant community soils) on growth and nutrient status of S. sitchensis was quantified in a greenhouse study. AM fungal spores and EM root tips were present in all field samples. In the greenhouse, plants receiving reservoir soil inoculum had only incipient mantle formation, while plants receiving inoculum from mature plant communities had fully formed EM root tips. EM formation corresponded with alleviation of phosphorus stress in plants (lower shoot nitrogen:phosphorus). Thus, revegetating plants have access to AM and EM fungi following dam removal, and EM formation may be especially important for plant P uptake in reservoir soils. However, availability of mycorrhizal fungi declines with distance from established plant communities. Furthermore, EM fungal communities in recently dewatered reservoirs may not be as effective at forming beneficial mycorrhizae as those from mature plant communities. Whole soil inoculum from mature plant communities may be important for the success of revegetating plants and recovery of mycorrhizal fungal communities.     

Meta‐barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO‐11063, GnS‐GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico‐chemical characteristics and land use. A meta‐barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS‐GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO‐11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO‐11063 standard.