Response of fungal and actinobacterial communities to water-level drawdown in boreal peatland sites

We used PCR-DGGE fingerprinting and direct sequencing to analyse the response of fungal and actinobacterial communities to changing hydrological conditions at 3 different sites in a boreal peatland complex in Finland. The experimental design involved a short-term (3 years; STD) and a long-term (43 years; LTD) water-level drawdown. Correspondence analyses of DGGE bands revealed differences in the communities between natural sites representing the nutrient-rich mesotrophic fen, the nutrient-poorer oligotrophic fen, and the nutrient-poor ombrotrophic bog. Still, most fungi and actinobacteria found in the pristine peatland seemed robust to the environmental variables. Both fungal and actinobacterial diversity was higher in the fens than in the bog. Fungal diversity increased significantly after STD whereas actinobacterial diversity did not respond to hydrology. Both fungal and actinobacterial communities became more similar between peatland types after LTD, which was not apparent after STD. Most sequences clustered equally between the two main fungal phyla Ascomycota and Basidiomycota. Sequencing revealed that basidiomycetes may respond more (either positively or negatively) to hydrological changes than ascomycetes. Overall, our results suggest that fungal responses to water-level drawdown depend on peatland type. Actinobacteria seem to be less sensitive to hydrological changes, although the response of some may similarly depend on peatland type.     

中国北方森林坡向对土壤细菌和从枝菌根真菌群落的影响

The effects of slope aspects on soil biogeochemical properties and plant communities in forested environments have been studied extensively; however, slope aspect influence on soil microbial communities remains largely unexamined, despite the central role of soil biota in ecosystem functioning. In this study, the communities of both soil bacteria and arbuscular mycorrhizal fungi (AMF) were investigated using tagged pyrosequencing for three types of slope aspects (south-facing aspect, north-facing aspect and flat area) in a boreal forest of the Greater Khingan Mountains, China. The bacterial and AMF community composition differed with slope aspects. Bacterial diversity was the lowest on the north-facing aspect, and AMF diversity was the lowest on the flat area. Aspects also had a significant impact on soil pH and available phosphorus (P) and shrubby biomass. Soil pH and understory shrub biomass were significantly correlated with bacterial communities, and soil available P and shrub biomass showed significant correlations with AMF communities. Our results suggested that slope aspects affected bacterial and AMF communities, mediated by aspect-induced changes in plant community and soil chemical properties (e.g., pH and available P), which improved the knowledge on the effects of forest slope aspects on aboveground and belowground communities.     

Nested plant and fungal communities; the importance of area and habitat quality in maximizing species capture in boreal old-growth forests

Knowledge of the distribution of rare species is crucial for species conservation in fragmented habitats. Species communities often exhibit nestedness, i.e. species in species-poor sites comprise a subset of richer ones. Thus, rare species are confined to species-rich sites. We evaluate whether plant and fungal communities in 46 old-growth spruce forest patches (0.17-12 ha) exhibit nestedness. The question whether a single large patch or several small patches capture most species (i.e. the SLOSS-issue) is evaluated in combination with species saturation analyses. All species groups exhibited significant nestedness. Area was generally related to nestedness, i.e. rare species were over-represented in the largest patches. Species saturation analysis indicated that large patches accumulated more Red-list species in patch interiors than small patches. Thus, rare and Red-list species were best captured in large patches. However, nestedness also emerged in equal sized sample plots, i.e. rare species were over-represented in high quality habitats. Thus, small habitats of high quality should not be neglected in a conservation perspective.     

No evidence that nitrogen enrichment affect fungal communities of Vaccinium roots in two contrasting boreal forest types

In boreal forests ericaceous shrubs often dominate the forest floor vegetation. Nitrogen enrichment has been shown to decrease shrub abundance and in this study we explored whether it also affects the root associated fungal communities. Fine roots of Vaccinium myrtillus were collected in a Norway spruce dominated forest and of Vaccinium vitis-idaea in a Scots pine dominated forest. In both forests, nitrogen enrichment was experimentally induced by adding 12.5 and 50 kg N ha⁻¹ yr⁻¹ for 12 (spruce forest) and four (pine forest) years. Based on terminal restriction fragment length polymorphisms, subcloning and sequencing analyses, the root associated fungal communities were examined. We found 93 fungal species including Asco-, Basidio- and Zygo-mycota. In general, the Rhizoscyphus ericae aggregate was the most dominant and this was followed by Herpotrichiellaceae and Sebacina. Ordination analysis revealed that nitrogen enrichment did not change species composition of the fungal communities in neither the spruce nor the pine forest, while fungal community structures were clearly discriminated between the dominant shrub species in each forest. Similarly, no fungal species showed a significant response to nitrogen enrichment. Therefore, nitrogen enrichment appears to have no effect on root associated fungi of understorey dwarf shrubs in boreal forests, while it is clear that spruce and pine forests harbor distinctive communities of these fungi.     

The application of an organic amendment modifies the arbuscular mycorrhizal fungal communities colonizing native seedlings grown in a heavy-metal-polluted soil

A mesocosm experiment was conducted to investigate whether communities of arbuscular mycorrhizal (AM) fungi associated with roots of native (Piptatherum miliaceum, Retama sphaerocarpa, Psoralea bituminosa, Coronilla juncea, and Anthyllis cytisoides) and for comparison (Lolium perenne) seedlings in a heavy-metal-contaminated, semiarid soil were affected by the application of composted sugar beet waste. We also investigated whether there were relation between AMF diversity and metal concentration (Al, Cd, Cu, Fe, Mn, Pb and Zn) and total P in shoot as well as some soil parameters (total organic carbon and total N) when the SB waste was added to the soil. We analyzed a portion of approximately 795 base pairs of the small-subunit (SSU) rRNA gene by nested PCR, cloning, sequencing, and phylogenetic analyses. Twelve different AMF sequence types were distinguished: seven of these belonged to Glomus group A, one to Glomus group B, one to Diversispora, one to Archaeospora, and two to Paraglomus. The AM fungal populations colonizing roots in a heavy-metal-polluted soil were quite dependent on the host plant, the highest diversity values being obtained in authochtonous plants recognized as metallophytes, such as P. bituminosa, and in an allochtonous, invasive species (L. perenne). No significant correlation was found between AMF diversity and plant metal concentration and soil parameters. Excepting P. bituminosa, when sugar beet waste was added to soil, the populations of AM fungi in roots increased and the shoot metal concentrations decreased in all host plant species studied. Therefore, the addition of sugar beet waste can be considered a good strategy for the remediation and/or phytostabilization of mine tailing sites.     

Temporal dynamics of fungal communities in soybean rhizosphere

Purpose

Many biotic and abiotic factors influence the structural and functional diversity of microbial communities in the rhizosphere. This study aimed to understand the dynamics of fungal community in the soybean rhizosphere during soybean growth and directly compare the influence of abiotic and biotic factors in shaping the fungal communities across different growth periods.

Materials and methods

High-throughput sequencing based on internal transcribed spacer (ITS) region, quantitative PCR, and statistical analysis approaches were used to measure the fungal community structure, abundance, and dynamic changes of 63 rhizosphere soil samples which were taken from different fertilization regimes and rhizobium inoculation treatments during three soybean growth stages.

Results and discussion

Among the taxa examined, more than 16 fungal classes were detected from the 21 soil samples. Sordariomycetes was the most abundant class, followed by Dothideomycetes, Agaricomycetes, and Eurotiomycetes. Soybean growth stage was the most important factor determining the diversity patterns of the fungal communities. Fungal community diversity was closely related to the base-fertilizer application, and fungal community richness was associated with rhizobium inoculation. Beta diversity of the fungal community based on the Bray-Curtis distance was significantly related to plant growth stage. Network analysis showed that mutual cooperation among fungal taxa became more intimate during the plant growth.

Conclusions

Compared with edaphic properties, plant growth stage was the dominant factor in determining soil fungal community dynamics. Base-fertilizer and rhizobium inoculation affected the alpha diversity of the soil fungi.

     

Moisture effects on microbial communities in boreal forest floors are stand-dependent

Landscape level factors such as overstory canopy composition can have a profound effect on the ecology of microbial communities in boreal forest floors. However, factors influencing community composition at the microsite scale are still poorly described and understood. Here we explored moisture effects on microbial communities in forest floor derived from undisturbed trembling aspen and white spruce stands, two of the dominant trees in the boreal forest of western Canada. Forest floor samples were incubated in a laboratory experiment for a period of one month under a moisture regime ranging from moist to dry (field capacity, 60% of field capacity and wilting point). As in previous studies we found that the origin of the forest floor material had a strong effect on the microbial community. Additionally, we found that moisture manipulation did not alter the microbial communities of the white spruce forest floor. On the other hand, the moisture had a profound effect on the aspen forest floor, and resulted in structurally and functionally distinct microbial communities. This different response to moisture could be linked to the adaptation of microbial groups to the physical environment inherent to the aspen and spruce forest floors and provides an avenue to further work into microbial mediated biogeochemical processes in the boreal forest.     

乙草胺、甲胺磷及其复合污染对黑土土壤真菌的影响

Using plate counting and ergosterol assay, single and joint effects of acetochlor and methamidophos on the dynamics of soil fungal population and total fungal biomass in the black soil zone of Northeast China were investigated. The results demonstrated that acetochlor at high concentration levels （150 and 250 mg kg^-1） had an acute and mostly chronic toxicity on both the soil fungal population and total fungal biomass, but at a low concentration （50 mg kg^-1） generally had a stimulating effect that was stronger with total fungal biomass than with the soil fungal population. Methamidophos at a high concentration level （250 mg kg^-1） alone and almost all of its combinations with various dosages of acetochlor increased the soil fungal population, whereas at most sampling dates with 250 mg methamidophos kg^-1 soil, total fungal biomass increased, but in combination with acetochlor it was decreased in the early period of incubation and then increased 28 days after incubation. Thus, through measuring the number of colony forming unit of the soil fungal population along with the total fungal biomass, a better understanding on effects of agrochemicals on soil fungi could be made.     

Spatial distribution of fungal communities in a coastal grassland soil

In grasslands, saprotrophic fungi, including basidiomycetes, are major decomposers of dead organic matter, although spatial distributions of their mycelial assemblages are little described. The aim of this study was to characterise the scale and distribution of saprotrophic fungal communities in a coastal grassland soil using terminal restriction fragment length polymorphism (T-RFLP).Soil fungi were sampled at Point Reyes, California, USA, by taking forty-five 26 mm diam. cores in a spatially defined manner. Within each sampled core, complete core sections at 1-2 cm and 14-15 cm depths were removed and sub-sampled for DNA extraction and amplification using the primer pairs ITS1F-FAM/ITS4 (general fungi) or ITS1F-FAM/ITS4B (basidiomycete-specific).Nonmetric Multidimensional Scaling showed that general fungal communities could be clearly separated by depth, although basidiomycete communities could not. There were no strong patterns of community similarity or dissimilarity for general or basidiomycete fungal communities at horizontal geographical distances from 25 cm to 96 m in the upper horizon. These results show considerable vertical, but little horizontal, variability in fungal community structure in a semi-natural grassland at the spatial scales measured here.     

Plant genotype strongly modifies the structure and growth of maize rhizosphere microbial communities

We studied the microbial communities in maize (Zea mays) rhizosphere to determine the extent to which their structure, biomass, activity and growth were influenced by plant genotype (su1 and sh2 genes) and the addition of standard and high doses of different types of fertilizer (inorganic, raw manure and vermicompost). For this purpose, we sampled the rhizosphere of maize plants at harvest, and analyzed the microbial community structure (PLFA analysis) and activity (basal respiration and bacterial and fungal growth rates). Discriminant analysis clearly differentiated rhizosphere microbial communities in relation to plant genotype. Although microorganisms clearly responded to dose of fertilization, the three fertilizers also contributed to differentiate rhizosphere microbial communities. Moreover, larger plants did not promoted higher biomass or microbial growth rates suggesting complex interactions between plants and fertilizers, probably as a result of the different performance of plant genotypes within fertilizer treatments, i.e. differences in the quality and/or composition of root exudates.     

Assessing the extinction vulnerability of wood-inhabiting fungal species in fragmented northern Swedish boreal forests

Fragmentation of old-growth forests and greatly reduced amounts of coarse dead wood in managed forests threat the persistence of many saproxylic species in boreal Fennoscandia. Individual old-growth forest remnants may lose species over time as they pay off their extinction debt. We tested this by comparing the observed site occupancy of individual wood-inhabiting fungal species in isolated old-growth stands (i.e. woodland key habitats; WKHs) with statistical predictions of their occupancy assuming potential extinction debt had already been paid off. The occupancy of species was analysed in two sets of WKHs differing in time since isolation (i.e. recent and old isolates).Few species occurred more frequently than expected in WKHs. However, patterns across species and across all WKHs masked important differences among species in their risk of facing future extinction. The site occupancy decreased significantly between recent and old isolates for a group of annual, red-listed specialist fungal species, suggesting that an extinction debt in WKHs may exist among specific species confined to coarse dead wood and old-growth forest habitat. Generalist species that also occur in the surrounding matrix showed no negative trends, or actually increased in site occupancy, making future extinctions less likely. Thus, continuing loss of threatened species are likely if not preservation of WKHs are combined with other conservation efforts in managed forest landscapes. Natural forest landscapes may serve as important references when aiming to identify species in risk of future extinction but more detailed knowledge about the biology of the most vulnerable species is also required.     

Forage crops alter soil bacterial and fungal communities in an apple orchard

In this study, we investigated the effects of planting three types of forage crops in an apple orchard on the soil microbial community structure. The apple orchard was intercropped with native grasses (NG), red clover (RC; Trifolium pratense L.), ryegrass (RE; Trifolium repens L.), and no vegetation (CT control; clean tillage). We obtained soil samples from depths of 0–20, 20–40, and 40–60?cm from the different treatment plots in the orchard and analysed them using a high-throughput DNA sequencing technique. The three forage crops had affected the soil bacterial and fungal community structures. Compared with CT control, intercropping with NG increased the proportion of Acidobacteria and reduced those of Nitrospirae and Verrucomicrobia, whereas intercropping with RC increased the proportions of Nitrospirae and Verrucomicrobia and reduced that of Planctomycetes. Intercropping with RE increased the proportions of Nitrospirae and Chloroflexi, whereas reduced that of Acidobacteria. Furthermore, unlike in the other treatments, intercropping with NG increased the proportion of Zygomycota in the 0–20-cm soil layer. Intercropping with RC increased the proportion of Chytridiomycota in all the three soil layers, whereas intercropping with RE increased the proportion of Basidiomycota in the 20–40-cm soil layer. Collectively, these findings suggest that intercropping with forage crops, especially RC, in an apple orchard, could alter soil microbial community structure. In our previous study, we showed that microbial sole-carbon-source utilisation is changed by intercropping with forage crops; thus, it can be considered as an effective approach to improve the efficiency of soil C cycling in the apple orchard by altering the microbial community structure.     

Functional diversity of microbial communities in the mixed boreal plain forest of central Canada

This study was designed to examine whether or not specific tree species (Picea glauca, Picea mariana, Pinus banksiana, Populus tremuloides), their post-fire stand age, or their position in a successional pathway had any significant effect on the functional diversity of associated soil microbial communities in a typical mixed boreal forest ecosystem (Duck Mountain Provincial Forest, Manitoba, Canada). Multivariate analyses designed to identify significant biotic and/or abiotic variables associated with patterns of organic substrate utilization (assessed using the BIOLOG™ System) revealed the overall similarity in substrate utilization by the soil microbial communities. The five clusters identified differed mainly by their substrate-utilization value rather than by specific substrate utilization. Variability in community functional diversity was not strongly associated to tree species or post-fire stand age; however, redundancy analysis indicated a stronger association between substrate utilization and successional pathway and soil pH. For example, microbial communities associated with the relatively high pH soils of the P. tremuloides-P. glauca successional pathway, exhibited a greater degree of substrate utilization than those associated with the P. banksiana-P. mariana successional pathway and more acidic soils. Differences in functional diversity specific to tree species were not observed and this may have reflected the mixed nature of the forest stands and of their heterogeneous forest floor. In a densely treed, mixed boreal forest ecosystem, great overlap in tree and understory species occur making it difficult to assign a definitive microbial community to any particular tree species. The presence of P. tremuloides in all stand types and post fire stand ages has probably contributed to the large amount of overlap in utilization profiles among soil samples.     

Metagenetics of fairy rings reveals complex and variable soil fungal communities

Although fairy rings are widely observed, little is known about the community processes associated with them. Here, we studied fairy rings in a natural grassland in northern Mongolia by sampling soils outside (future stage), directly under (present stage), and within (past stage) the rings, to represent different time stages during the expansion of fairy rings. Soil DNA was extracted for amplicon sequencing of the fungal ITS1 region. The present stage had reduced fungal diversity and different fungal communities toward the other stages. Most strikingly, there was an increase in the pathogenic fungus Gibberella baccata in the present stage of most rings and the saprotrophic fairy ring fungus Lepista luscina in several. However, no mushrooms of Lepista had been recorded from any of these rings during several years of observation. Known fairy ring fungi were not found in the present stage of every ring, even in some known rings to have previously displayed mushrooms of such species. It is possible that these fungi occurred or were more abundant at the unsampled leading edge of the ring. The increase in G. baccata is intriguing, but its importance, if any, is unclear. It is also unclear whether consortia of fungi or other microbes might be present in these rings. The absence or low abundance of the previously reported fairy ring fungal species suggests that their presence is transient, with rapid replacement by other fungi. No differences in soil parameters were found between the fairy ring stages, except for aluminum. There is a need for broader sampling, including analysis of non-fungal biota, to understand the functional diversity of fairy ring fungi and the consequences for plant communities.     

The impact of increasing heavy metal stress on the diversity and structure of the bacterial and actinobacterial communities of metallophytic grassland soil

A study was undertaken to investigate the bacterial community found in metallophytic grassland soil contaminated with Zn and Pb. We hypothesised that such communities would be tolerant of additional heavy metal stress due to phylogenetic and functional adaptation. In microcosm experiments, lasting 51 days, denaturing gradient gel electrophoresis (DGGE) analyses was used to compare the total bacterial and actinobacterial communities in non-amended soils and those to which additional Pb and Zn concentrations were added. There was a decrease in total bacterial diversity with each addition of Pb and Zn; in contrast, the actinobacterial community diversity remained unaffected. The community structures were analysed using multivariate analyses of the DGGE profiles. Total bacterial community profiles showed two distinct groups sharing less than 80% similarity, irrespective of Pb and Zn addition. The first contained profiles sampled during the first 7 days of the experiment; the second contained those sampled from day 10 onwards. Actinobacterial profiles from those that were non-amended showed a similar distribution to those of the total bacterial community. However, in soil amended with fivefold additional Pb and Zn, all the profiles shared more than 80% similarity. Raup and Crick analyses suggested that total bacterial soil communities were subject deterministic selection becoming significantly similar as the experiment progressed, but this was inhibited by the highest concentration of additional Pb and Zn. Actinobacterial communities showed a similar response but were less affected by elevated Pb and Zn concentrations. These data indicate that the diversity of the actinobacterial community was not negatively affected by additional heavy metal stress in contrast to total bacterial community diversity.     

Precipitation modifies the effects of warming and nitrogen addition on soil microbial communities in northern Chinese grasslands

Terrestrial ecosystems experience simultaneous shifts in multiple drivers of global change, which can interactively affect various resources. The concept that different resources co-limit plant productivity has been well studied. However, co-limitation of soil microbial communities by multiple resources has not been as thoroughly investigated. Specifically, it is not clearly understood how microbial communities respond to shifts in multiple interacting resources such as water, temperature, and nitrogen (N), in the context of global change. To test the effects of these various resources on soil microorganisms, we established a field experiment with temperature and N manipulation in three grasslands of northern China, where there is a decrease in precipitation from east to west across the region. We found that microbial responses to temperature depended upon seasonal water regimes in these temperate steppes. When there was sufficient water present, warming had positive effects on soil microorganisms, suggesting an interaction between water and increases in temperature enhanced local microbial communities. When drought or alternating wet–dry stress occurred, warming had detrimental effects on soil microbial communities. Our results also provide clear evidence for serial co-limitation of microorganisms by water and N at the functional group and community levels, where water is a primary limiting factor and N addition positively affects soil microorganisms only when water is sufficient. We predict that future microbial responses to changes in temperature and N availability could be seasonal or exist only in non-drought years, and will strongly rely on future precipitation regimes.     

Effect of chemical fumigation on soil fungal communities in Spanish strawberry nurseries

Strawberry runners are a high-value cash crop in Spain that requires vigorous transplants free of pathogens. Pre-plant soil fumigation with methyl bromide (MB), or with mixtures of MB and chloropicrin (Pic), are standard practices for controlling soil-borne diseases. However, use of MB will be forbidden in European Union countries by the year 2005; for this reason several soil fumigants have been tested as chemical alternatives to MB in Spanish strawberry nurseries. Because of the known broad activity of these compounds, their effects on strawberry soil fungal communities were studied. Experiments were conducted over a 5-year period, with pre-plant applications at two different locations each year. Soil fungal populations were estimated in each plot before and after treatments on potato-dextrose agar amended with 0.5 g l⁻¹ streptomycin sulphate and selective media for Fusarium spp., Pythium spp., Verticillium spp., Phytophthora spp., and Rhizoctonia spp. Soil fungal populations in Spanish strawberry nurseries were clearly reduced in number and composition after pre-plant soil fumigation. Differences in the level of reduction was obtained with some treatments. Penicillium sp., following by Alternaria sp., Fusarium sp., Morteriella sp., Cladosporium sp., Pythium sp., and Verticillium spp. were usually presented in Spanish nursery soils from March to April, whereas Phytophthora spp. and Rhizoctonia spp. were only sporadically isolated. All the fumigants reduced the soil fungal population quantitatively, but only MB:Pic and dazomet caused a clear change in their fungal genera composition. A total reduction was observed on Pythium and Morteriella populations after application of all the fumigants, except for DMDS. Populations of Verticillium spp. were also reduced by the applied fumigants in the strawberry nursery soils tested; the lowest reductions were obtained with 1,3-D:Pic + Virtually Impermeable Film, metam sodium, metam potassium and DMDS.