Site properties have a stronger influence than fire severity on ectomycorrhizal fungi and associated N-cycling bacteria in regenerating post-beetle-killed lodgepole pine forests

Following a pine beetle epidemic in British Columbia, Canada, we investigated the effect of fire severity on rhizosphere soil chemistry and ectomycorrhizal fungi (ECM) and associated denitrifying and nitrogen (N)-fixing bacteria in the root systems of regenerating lodgepole pine seedlings at two site types (wet and dry) and three fire severities (low, moderate, and high). The site type was found to have a much larger impact on all measurements than fire severity. Wet and dry sites differed significantly for almost all soil properties measured, with higher values identified from wet types, except for pH and percent sand that were greater on dry sites. Fire severity caused few changes in soil chemical status. Generally, bacterial communities differed little, whereas ECM morphotype analysis revealed ectomycorrhizal diversity was lower on dry sites, with a corresponding division in community structure between wet and dry sites. Molecular profiling of the fungal ITS region confirmed these results, with a clear difference in community structure seen between wet and dry sites. The ability of ECM fungi to colonize seedlings growing in both wet and dry soils may positively contribute to subsequent regeneration. We conclude that despite consecutive landscape disturbances (mountain pine beetle infestation followed by wildfire), the “signature” of moisture on chemistry and ECM community structure remained pronounced

Soil Bacterial and Fungal Community Structure Across a Range of Unimproved and Semi-Improved Upland Grasslands

Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects

Impact of wildfire intensity and logging on fungal and nitrogen-cycling bacterial communities in British Columbia forest soils

Wildfire and logging are common disturbances in the forests of northwestern North America, causing changes in soil chemistry and microbiology, including fungal and nitrogen-cycling bacterial communities. These organisms play key roles in nutrient cycling, and affect the regeneration of tree seedlings after disturbance. We studied the effects of wildfire and logging on fungal and nitrogen-cycling communities in the rhizosphere of 16 month-old Douglas-fir seedlings as they regenerated in burned and logged soils. Seeds were planted against root windows that were set up vertically in the soil, with a removable front panel used to access the seedling rhizosphere soil surface. Windows were established in control, lightly burned, and severely burned plots, as well as two types of logged plots (clearcut and screefed clearcut). Soil scrapings from the root window–soil interface were taken and the structure of fungal and nitrogen-cycling communities was resolved using length-heterogeneity PCR (LH-PCR) of fungal nuclear ribosomal RNA genes, and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and nosZ genes. We found striking differences in the community structure of fungal, denitrifying, and N-fixing communities in response to burning and logging. With the exception of clearcut and screefed clearcut, which were generally similar, each treatment had a unique impact on community structure for these genes. Burning and logging also impacted the relative richness and evenness of these communities. Fungal relative richness and evenness increased in response to logging and severe burning, while denitrifier relative richness and evenness increased in all disturbance treatments, and N-fixing bacterial relative richness and evenness decreased in response to burning. The greatest differences in microbial community structure, relative richness, and evenness were found in the comparisons of lightly burned and logged treatments. The results suggest that the presence of an intact forest floor influences soil microbial communities less than the presence of living trees

Fingerprinting the fungal community

Fungi can be found in almost any environment, and play important roles in ecosystem processes such as nutrient cycling and degradation. Despite their importance, the vast majority of fungi have not yet been isolated and identified. Due to the difficulties inherent in culture-based methods, fungal ecologists have turned to community fingerprinting techniques, which utilise signal molecules to profile the fungal members of an environmental sample without culturing. Commonly used signal molecules include chitin, ergosterol, membrane lipids, and nucleic acids. Several DNA-based fingerprinting methods have been successfully applied to fungal communities, including D/TGGE (denaturing/temperature gradient gel electrophoresis), SSCP (single-stranded conformational polymorphism), RISA (ribosomal intergenic spacer analysis), and T-RFLP (terminal restriction length fragment polymorphism). These techniques allow the fungal ecologist to rapidly profile fungal populations in an ecosystem, without the need for laborious culturing or cloning

Impact of lime, nitrogen and plant species on fungal community structure in grassland microcosms

A microcosm-based approach was used to study impacts of plant and chemical factors on the fungal community structure of an upland acidic grassland soil. Seven plant species typical of both unimproved and fertilized grasslands were either left unamended or treated with lime, nitrogen or lime plus nitrogen. Fungal community structure was assessed by a molecular approach, fungal automated ribosomal intergenic spacer analysis (FARISA), while fungal biomass was estimated by measuring soil ergosterol content. Addition of nitrogen (with or without lime) had the largest effect, decreasing soil pH, fungal biomass and fungal ribotype number, but there was little corresponding change in fungal community structure. Although different plant species were associated with some changes in fungal biomass, this did not result in significant differences in fungal community structure between plant species. Addition of lime alone caused no changes in fungal biomass, ribotype number or community structure. Overall, fungal community structure appeared to be more significantly affected through interactions between plant species and chemical treatments, as opposed to being directly affected by changes in individual improvement factors. These results were in contrast to those found for the bacterial communities of the same soils, which changed substantially in response to chemical (lime and nitrogen) additions

Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms

A microcosm-based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved ( Nardus stricta , Agrostis capillaris , Festuca ovina and F. rubra ) and fertilized, improved ( Holcus lanatus, Lolium perenne and Trifolium repens ) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75-day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects

Seasonal influences on fungal community structure in unimproved and improved upland grassland soils

Seasonal and management influences on the fungal community structure of two upland grassland soils were investigated. An upland site containing both unimproved, floristically-diverse (U4a) and mesotrophic, improved (MG7b) grassland types was selected, and samples from both grassland types were taken at five times in one year. Soil fungal community structure was assessed using fungal automated ribosomal intergenic spacer analysis (ARISA), a DNA-profiling approach. Grassland management regime was found to strongly affect fungal community structure, with fungal ARISA profiles from unimproved and improved grassland soils differing significantly. The number of fungal ribotypes found was higher in unimproved than improved grassland soils, providing evidence that improvement may reduce the suitability of upland soil as a habitat for specific groups of fungi. Seasonal influences on fungal community structure were also noted, with samples taken in autumn (October) more correlated with change in ribotype profiles than samples from other seasons. However, seasonal variation did not obscure the measurement of differences in fungal community structure that were due to agricultural improvement, with canonical correspondence analysis (CCA) indicating grassland type had a stronger influence on fungal profiles than season

Seasonal and management influences on bacterial community structure in an upland grassland soil

Floristically diverse Nardo–Galion upland grasslands are common in Ireland and the UK and are valuable in agricultural, environmental and ecological terms. Under improvement (inputs of lime, fertiliser and re-seeding), they convert to mesotrophic grassland containing very few plant species. The effects of upland grassland improvement and seasonality on soil microbial communities were investigated at an upland site. Samples were taken at five times in one year in order to observe seasonal trends, and bacterial community structure was monitored using automated ribosomal intergenic spacer analysis (ARISA), a DNA-fingerprinting approach. Differences in soil chemistry and bacterial community structure between unimproved and improved grassland soils were noted. Season was also found to cause mild fluctuations in bacterial community structure, with soil samples from colder months (October and December) more correlated with change in ribotype profiles than samples from warmer months. However, for the majority of seasons clear differences in bacterial community structures from unimproved and improved soils could be seen, indicating seasonal influences did not obscure effects associated with improvement

Assessment of post-beetle impacts on natural regeneration of Lodgepole Pine

The ecological disturbance from wildfire (2004) on ~ 10,000 hectares of forests near the Kenny Dam presented a unique opportunity to study the natural and artificial regeneration in burned mountain pine beetle (Dendroctonus ponderosae Hopkins) infested stands in north-central British Columbia. Mountain pine beetle (MPB) has been documented as a natural disturbance agent that may precede wildfire in lodgepole pine forests (Pinus contorta var. latifolia). The objectives of this study were to i) characterize lodgepole pine regeneration and related micro-site conditions associated with wildfire, ii) identify limitations for germination, survival and recruitment of natural and artificial regeneration in relation to site moisture, fire severity, and vegetative competition, iii) determine if regeneration was limited by belowground factors (soil characteristics, ectomycorrhizal inoculum, nitrogen-cycling bacterial communities), and iv) provide guidance on local operational management of MPB-killed stands. The germination, survival and recruitment of lodgepole pine seedlings over two growing seasons were compared on 18 disturbance plots (replicated three times) with three fire severity classes (high, moderate, low), two moisture regimes (dry and wet), two seed provenances (wild and improved Class-A), and two seedbed types (disturbed and undisturbed). In the growing seasons following the fire (2005 and 2006), seeded plots experienced bursts of spring germination followed by continuous minor waves of new germination (that ended by August 2006). Results showed that natural regeneration was highest on wet sites and seedling density increased with declining fire severity. On dry sites, new germinants were rare and limited by microsite conditions associated with high and moderate fire severity, with highest germination rates experienced on low fire severity. Seed provenance did not influence germination and survival rates. In contrast to the germination, survival and recruitment results, growth rates were highest on the dry sites and increased with increasing fire severity. Thus, although recruitment on dry sites is unlikely to sufficiently restock these stands with lodgepole pine, the recruits show the highest growth rates. Conversely, recruitment on the wet sites will fully sufficient to fully restock these stands, but the growth rates of the seedlings will likely be impeded by competition with other vegetation. Although we documented adverse impacts of MPB and burning on soil properties, and lower diversity of ectomycorrhizal communities and nitrogen-cycling bacterial communities on the dry sites, there is no evidence that these factors are limiting growth of recruits on these dry sites. We are reviewing these results and preparing publications, and will make final management recommendations once the data are completely analyzed

Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2–5 m scale (P < 0.05), whereas AOA communities were dependent at the �1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases