Effects of stump and slash removal on growth and mycorrhization of Picea abies seedlings outplanted on a forest clear-cut

The objectives of this study were to investigate impact of stump and slash removal on growth and mycorrhization of Picea abies seedlings outplanted on a forest clear-cut. Four non-replicated site preparation treatments included: (1) mounding (M), (2) removal of stumps (K), (3) mounding and removal of logging slash (HM) and (4) removal of logging slash and stumps (HK). Results showed that height increment of the seedlings was highest in K and lowest in M after the third growing season, and similar pattern remained after the fourth season. Ectomycorrhizal (ECM) colonisation of seedling roots was highest in M (96.6%) and lowest in K (72.3%), and even in HK (76.0%) and HM (76.3%). Morphotyping and sequencing of internal transcribed spacer of fungal ribosomal DNA revealed a total of 13 ECM species. Among those, Thelephora terrestris and Cenococcum geophilum were the most common, found on 27.4% and 26.3% of roots, respectively. The rest of species colonised 26.6% of roots. Richness of ECM species was highest in M (10 species) and lowest in K (three species). Consequently, stump and slash removal from clear-felled sites had a positive effect on growth of outplanted spruce seedlings, but negative effect on their mycorrhization. This suggests that altered soil conditions due to site disturbance by stump and slash removal might be more favourable for tree growth than more abundant mycorrhization of their root systems in less disturbed soil.     

Weak vertical canopy gradients of photosynthetic capacities and stomatal responses in a fertile Norway spruce stand

Wildfire severity in forests is projected to increase with warming and drying conditions associated with climate change. Our objective was to determine the impact of wildfire and clearcutting severity on the ectomycorrhizal fungal (EMF) community of Douglas-fir seedlings in the dry forests of interior British Columbia, Canada. We located our study within and surrounding the area of the McLure fire (August 2003). We hypothesized that disturbance would affect EMF community assembly due to reductions in fungal inoculum. Five treatments representing a range of disturbance severities were compared: high severity burn, low severity burn, screefed clearcut (manual removal of forest floor), clearcut, and undisturbed forest. EMF communities in the undisturbed forest were more complex than those in all disturbance treatments. However, aspects of community assembly varied with disturbance type, where the burn treatments had the simplest communities. After 4 months, regenerating seedlings in the burn treatments had the lowest colonization, but seedlings in all treatments were fully colonized within 1 year. EMF communities were similar among the four disturbance types, largely due to dominance of Wilcoxina throughout the study period. However, forest floor retention influenced community assembly as the EMF in the clearcut treatment, where forest floor was retained, had levels of diversity and richness comparable to the undisturbed forest. Overall, the results suggest that increasing forest floor disturbance can alter EMF community assembly in the first year of regeneration. A correlation between poorly colonized seedlings and seedling productivity also suggests a role for productivity in influencing community assembly.     

Population structure delineated with microsatellite markers in fragmented populations of a tropical tree, carapa guianensis (Meliaceae)

Deforestation and selective logging in the tropics may have serious consequences on genetic processes in tropical tree populations, affecting long-term survival of a given species as well as tropical forest communities. Because understanding the effects of human-induced changes on genetic processes is of utmost importance in formulating sound conservation and management plans for tropical forest communities, we developed microsatellite or simple sequence repeat (SSR) markers for the tropical tree Carapa guianensis (Meliaceae) and assessed the polymorphism of SSRs in adult and sapling populations in a large contiguous forest and in selectively logged and fragmented forests. The number of alleles in polymorphic loci ranged between 4 and 28. No inbreeding was detected in saplings or adult cohorts, but the allelic richness was lower in the sapling cohort of the isolated fragment. Genetic distances, Nei's D and (delta&mgr;)2, and RST values among saplings were greater than among adult cohorts, suggesting restriction of gene flow due to deforestation and habitat fragmentation. These SSR loci may be used to address many related questions regarding the population and conservation genetics of tropical trees.     

Diversity and species distribution of ectomycorrhizal fungi along productivity gradients of a southern boreal forest

Coniferous forests with diverse ectomycorrhizal fungus (EMF) communities are associated with nutrient-poor, acidic soils but there is some debate whether EMF can be equally adapted to more productive, nitrogen-rich sites. We compared EMF species distribution and diversity along a replicated productivity gradient in a southern boreal forest of British Columbia (Canada). Roots from subalpine fir (Abies lasiocarpa) saplings of the understory were sampled and EMF species were identified by morphotypes supplemented with ITS rDNA analysis. There were significant changes in the distribution and abundance of 74 EMF species along the productivity gradient, with as little as 24% community similarity among contrasting sites. Species richness per plot increased asymptotically with foliar nitrogen concentrations of subalpine fir, demonstrating that many EMF species were well suited to soils with high rates of nitrogen mineralization. EMF species abundance in relation to site productivity included parabolic, negative linear, and positive exponential curves. Both multi-site and more narrowly distributed EMF were documented, and a diverse mix of mantle exploration types was present across the entire productivity gradient. The results demonstrate strong associations of EMF fungal species with edaphic characteristics, especially nitrogen availability, and a specialization in EMF communities that may contribute to the successful exploitation of such contrasting extremes in soil fertility by a single tree host.     

The Effect of Logging on the Ground-Foraging Ant Community in Eastern Amazonia

In order to determine the suitability of ants as indicator organisms for habitat disruption in tropical forests, we studied the effects of both high and low impact logging on ant communities in northeastern Pará State, in the Brazilian Amazon. We collected ants from logged forests and unlogged forest sites with Winkler bags throughout the 1998 rainy season (January and April) and the following dry season (July and September). Both methods of timber harvesting showed impacts on ant community composition when compared with unlogged forest, although these impacts did not include modifications in total species richness or the relative contribution of each ant subfamily to the total number of species. Instead, logging induced alterations took place at the level of species and genera. A 2-fold reduction in the dominance of ants of the highly diverse genus Pheidole was associated with forest alterations in high-impact logging sites. Thus, logging in Amazonia can be seen to promote species shifts in ant communities, without, however, altering species richness. Ants of the genus Pheidole are potentially useful indicators for forest disturbances resulting from timber extraction.     

Norway Maple (Acer platanoides) Invasion of a Natural Forest Stand: Understory Consequence and Regeneration Pattern

Norway maple (Acer platanoidesis) is invasive in a natural stand in suburban Ithaca, NY. To determine the understory pattern and consequences of a Norway maple invasion, I compared density and species richness under Norway maples and sugar maples (Acer saccharum). Mean sapling density was significantly lower (P<0.0027) under Norway maples (3.64/100 m²±1.6 SE) than under sugar maples (19.4/100 m²±4.4 SE). Mean sapling species richness was significantly lower (P<0.0018) under Norway maples (0.7/32 m²±0.18 SE) than under sugar maples (2.6/32 m²±0.48 SE). Likewise, Norway maple regeneration is more frequent under sugar maples than sugar maple regeneration: 57% of sugar maple plots had Norway maple saplings while 0% of Norway maple plots had sugar maple saplings. Two significant plot effects were found for presence–absence: Norway maple saplings grow under Norway maples with a significantly lower frequency (P<0.03) than under sugar maples; sugar maple saplings grow under Norway maples with a significantly lower frequency (P<0.000) than under sugar maples. Across the site, Norway maple saplings were the most abundant (29 saplings for 480 m²). The success of Norway maple regeneration and the reductions in total stem density beneath Norway maples is most likely the result of its strong competitive abilities, notably its high shade tolerance and abundant seed crops.     

Macrofungal diversity and ecology in four Irish forest types

The macrofungal communities of Irish native tree species (ash and oak) and exotic tree species (Scots pine and Sitka spruce) forests were examined through the collection of sporocarps over 3 yr. Sampling of 27 plots revealed 186 species of macrofungi, including 10 species new to Ireland. The species richness of non-native Sitka spruce and Scots pine forests was similar to that of native oak forests. However, specific communities of macrofungi existed in each of the forest types as confirmed by non-metric multidimensional scaling and multi-response permutation procedure. Indicator species analysis was used to identify macrofungi which are indicative of the four forest types. The oak community lacked certain species/genera known to be distinctive of oak woods in Britain, possibly due to low inoculum availability as a result of historic removal of Ireland’s oak forests. Our results indicate that, while being similar to native forests in species richness, non-native forests of Sitka spruce and Scots pine in Ireland harbour many fungal species which are not typical of native forests, particularly members of the genus Cortinarius.     

Little evidence for niche partitioning among ectomycorrhizal fungi on spruce seedlings planted in decayed wood versus mineral soil microsites

Ectomycorrhizal fungal (EMF) communities vary among microhabitats, supporting a dominant role for deterministic processes in EMF community assemblage. EMF communities also differ between forest and clearcut environments, responding to this disturbance in a directional manner over time by returning to the species composition of the original forest. Accordingly, we examined EMF community composition on roots of spruce seedlings planted in three different microhabitats in forest and clearcut plots: decayed wood, mineral soil adjacent to downed wood, or control mineral soil, to determine the effect of retained downed wood on EMF communities over the medium and long term. If downed and decayed wood provide refuge habitat distinct from that of mineral soil, we would expect EMF communities on seedlings in woody habitats in clearcuts to be similar to those on seedlings planted in the adjacent forest. As expected, we found EMF species richness to be higher in forests than clearcuts (P ≤ 0.01), even though soil nutrient status did not differ greatly between the two plot types (P ≥ 0.05). Communities on forest seedlings were dominated by Tylospora spp., whereas those in clearcuts were dominated by Amphinema byssoides and Thelephora terrestris. Surprisingly, while substrate conditions varied among microsites (P ≤ 0.03), especially between decayed wood and mineral soil, EMF communities were not distinctly different among microhabitats. Our data suggest that niche partitioning by substrate does not occur among EMF species on very young seedlings in high elevation spruce-fir forests. Further, dispersal limitations shape EMF community assembly in clearcuts in these forests.     

Occurrence Patterns of Lichens on Stumps in Young Managed Forests

The increasing demand for forest-derived bio-fuel may decrease the amount of dead wood and hence also the amount of available substrate for saproxylic ( = dead-wood dependent) organisms. Cut stumps constitute a large portion of dead wood in managed boreal forests. The lichen flora of such stumps has received little interest. Therefore, we investigated which lichens that occur on stumps in young (4–19 years), managed forests and analyzed how species richness and occurrence of individual species were related to stump and stand characteristics. We performed lichen inventories of 576 Norway spruce stumps in 48 forest stands in two study areas in Central Sweden, recording in total 77 lichen species. Of these, 14 were obligately lignicolous, while the remaining were generalists that also grow on bark, soil or rocks. We tested the effect of characteristics reflecting successional stage, microclimate, substrate patch size, and the species pool in the surrounding area on (1) total lichen species richness, (2) species richness of obligately lignicolous lichens and (3) the occurrence of four obligately lignicolous lichen species. The most important variables were stump age, with more species on old stumps, and study area, with similar total species richness but differences in occupancy for individual species. Responses for total lichen species richness and species richness of obligately lignicolous lichens were overall similar, indicating similar ecological requirements of these two groups. Our results indicate that species richness measurements serve as poor proxies for the responses of individual, obligately lignicolous lichen species.     

The conservation value of South East Asia's highly degraded forests: evidence from leaf-litter ants

South East Asia is widely regarded as a centre of threatened biodiversity owing to extensive logging and forest conversion to agriculture. In particular, forests degraded by repeated rounds of intensive logging are viewed as having little conservation value and are afforded meagre protection from conversion to oil palm. Here, we determine the biological value of such heavily degraded forests by comparing leaf-litter ant communities in unlogged (natural) and twice-logged forests in Sabah, Borneo. We accounted for impacts of logging on habitat heterogeneity by comparing species richness and composition at four nested spatial scales, and examining how species richness was partitioned across the landscape in each habitat. We found that twice-logged forest had fewer species occurrences, lower species richness at small spatial scales and altered species composition compared with natural forests. However, over 80 per cent of species found in unlogged forest were detected within twice-logged forest. Moreover, greater species turnover among sites in twice-logged forest resulted in identical species richness between habitats at the largest spatial scale. While two intensive logging cycles have negative impacts on ant communities, these degraded forests clearly provide important habitat for numerous species and preventing their conversion to oil palm and other crops should be a conservation priority.     

Tree demography suggests multiple directions and drivers for species range shifts in mountains of Northeastern United States

Climate change is expected to lead to upslope shifts in tree species distributions, but the evidence is mixed partly due to land‐use effects and individualistic species responses to climate. We examined how individual tree species demography varies along elevational climatic gradients across four states in the northeastern United States to determine whether species elevational distributions and their potential upslope (or downslope) shifts were controlled by climate, land‐use legacies (past logging), or soils. We characterized tree demography, microclimate, land‐use legacies, and soils at 83 sites stratified by elevation (~500 to ~1200 m above sea level) across 12 mountains containing the transition from northern hardwood to spruce‐fir forests. We modeled elevational distributions of tree species saplings and adults using logistic regression to test whether sapling distributions suggest ongoing species range expansion upslope (or contraction downslope) relative to adults, and we used linear mixed models to determine the extent to which climate, land use, and soil variables explain these distributions. Tree demography varied with elevation by species, suggesting a potential upslope shift only for American beech, downslope shifts for red spruce (more so in cool regions) and sugar maple, and no change with elevation for balsam fir. While soils had relatively minor effects, climate was the dominant predictor for most species and more so for saplings than adults of red spruce, sugar maple, yellow birch, cordate birch, and striped maple. On the other hand, logging legacies were positively associated with American beech, sugar maple, and yellow birch, and negatively with red spruce and balsam fir – generally more so for adults than saplings. All species exhibited individualistic rather than synchronous demographic responses to climate and land use, and the return of red spruce to lower elevations where past logging originally benefited northern hardwood species indicates that land use may mask species range shifts caused by changing climate.     

Don’t miss the forest for the trees! Evidence for vertical differences in the response of plant diversity to disturbance in a tropical rain forest

Ecological studies in tropical rain forests traditionally focus on trees above a threshold diameter at breast height (dbh), since ignoring plant species of the other structural compartments is believed to be an acceptable tradeoff between exhaustiveness and effectiveness. However, the consequences of missing species below a threshold dbh value have been largely neglected so far. We evaluated whether the response of species diversity of ≥10-cm dbh trees was similar to the response of other structural ensembles (namely treelets, saplings, and terricolous herbs) in a lowland tropical rain forest, to three disturbance regimes: natural gap dynamics (control), and selective logging with and without additional thinning. We studied forest vegetation composition and diversity in a 20-yr replicated field experiment comprising nine 1 ha permanent plots established in a semi-deciduous rain forest of the Congo Basin and equally distributed among the three treatments. Once corrected by stem density, species richness was similar between logged (20 years since logging) and untouched old-growth forest stands with respect of trees, but higher with respect of treelets. As disturbance intensity increased, species richness increased within sapling layers but decreased within herb layers, while species spatial turnover (beta diversity) increased in both cases. Regarding the parameters of the partitioned rarefaction curves and relative abundance distribution curves, no correlation was found between trees and any of the other structural compartments. Whilst tree and treelet species composition was similar among treatments, the understories still reflected past disturbance intensity, with a strong response of the sapling and herb layers. These results show that ecological studies based solely on tree layers (dbh ≥ 10 cm) are misleading because their response to disturbance cannot be used as a surrogate for the response of other structural ensembles. Long-lasting effects of anthropogenic disturbance on the sapling bank and the herb layer may durably influence the long-term forest dynamics. Since overstory but not understory plant communities have recovered from human disturbances 20 years after silvicultural operations, African tropical rain forest ecosystems may not be as resilient to selective logging as previously thought.     

Endophyte communities vary in the needles of Norway spruce clones

Endophytic fungi show no symptoms of their presence but can influence the performance and vitality of host trees. The potential use of endophytes to indicate vitality has been previously realized, but a standard protocol has yet to be developed due to an incomplete understanding of the factors that regulate endophyte communities. Using a culture-free molecular approach, we examined the extent to which host genotype influences the abundance, species richness, and community composition of endophytic fungi in Norway spruce needles. Briefly, total DNA was extracted from the surface-sterilized needles of 30 clones grown in a nursery field and the copy number of the fungal internal transcribed spacer (ITS) region of ribosomal DNA was estimated by quantitative PCR. Fungal species richness and community composition were determined by denaturing gradient gel electrophoresis and DNA sequencing. We found that community structure and ITS copy number varied among spruce clones, whereas species richness did not. Host traits interacting with endophyte communities included needle surface area and the location of cuttings in the experimental area. Although Lophodermium piceae is considered the dominant needle endophyte of Norway spruce, we detected this species in only 33 % of samples. The most frequently observed fungus (66 %) was the potentially pathogenic Phoma herbarum. Interestingly, ITS copy number of endophytic fungi correlated negatively with the richness of ectomycorrhizal fungi and thus potential interactions between fungal communities and their influence on the host tree are discussed. Our results suggest that in addition to environmental factors, endophyte communities of spruce needles are determined by host tree identity and needle surface area.     

Effectiveness of green-tree retention in the conservation of ectomycorrhizal fungi

Habitat fragmentation stresses may reduce the long-term effectiveness of green-tree retention as refugia for ectomycorrhizal fungal (EMF) species. We tested for a minimum retention patch size where EMF species abundance (morphotyping with molecular analysis), richness and reproduction (epigeous sporocarps) aligned with interior Pseudotsuga menziesii habitat on Vancouver Island (Canada). Ten years after logging, species richness was altered along the entire gradient of patch sizes (single trees to 0.12 ha), while % abundance and fruiting had significantly declined for some prevalent EMF species. Retention patches 20 m in diameter, on average, were therefore insufficient in size to ensure the continuity of mature-forest dependent EMF species. Refugia effectiveness would also correspond with habitat extent, and α and γ diversity estimates indicated retention patches approximately 0.2 ha in size, and culminating in at least 3 % of the cutblock area, would capture much of the spatial heterogeneity and species diversity of this EMF community.     

Response of fungal endophyte communities within Andropogon gerardii (Big bluestem) to nutrient addition and herbivore exclusion

Fungal endophytes may alter plant responses to the environment, but how does the environment affect the communities of fungal symbionts within plants? We examined the impact of nutrient addition and herbivore exclusion on endophyte communities of the prairie grass Andropogon gerardii in a full factorial field experiment. Fungi were cultured from stems, young leaves, and mature leaves, ITS sequences obtained, and endophyte incidence, community richness, and composition analyzed. Results indicate that in plots where nutrient addition and herbivore exclusion treatments had been applied separately, fungal endophyte incidence, community composition or evenness did not differ, but that greater species richness was observed in plots with nutrient addition and herbivore exclusion treatments applied in combination, compared to other treatments. Further, although fungal community composition was significantly different in stem and leaf tissues, OTU richness was greater in all endophyte communities in nutrient addition plus herbivore exclusion treatments, regardless of tissue type. Our results indicate the distinct fungal endophyte communities found in different plant tissues respond similarly to environmental factors.     

New Insights into the Consequences of Post-Windthrow Salvage Logging Revealed by Functional Structure of Saproxylic Beetles Assemblages

Windstorms, bark beetle outbreaks and fires are important natural disturbances in coniferous forests worldwide. Wind-thrown trees promote biodiversity and restoration within production forests, but also cause large economic losses due to bark beetle infestation and accelerated fungal decomposition. Such damaged trees are often removed by salvage logging, which leads to decreased biodiversity and thus increasingly evokes discussions between economists and ecologists about appropriate strategies. To reveal the reasons behind species loss after salvage logging, we used a functional approach based on four habitat-related ecological traits and focused on saproxylic beetles. We predicted that salvage logging would decrease functional diversity (measured as effect sizes of mean pairwise distances using null models) as well as mean values of beetle body size, wood diameter niche and canopy cover niche, but would increase decay stage niche. As expected, salvage logging caused a decrease in species richness, but led to an increase in functional diversity by altering the species composition from habitat-filtered assemblages toward random assemblages. Even though salvage logging removes tree trunks, the most negative effects were found for small and heliophilous species and for species specialized on wood of small diameter. Our results suggested that salvage logging disrupts the natural assembly process on windthrown trees and that negative ecological impacts are caused more by microclimate alteration of the dead-wood objects than by loss of resource amount. These insights underline the power of functional approaches to detect ecosystem responses to anthropogenic disturbance and form a basis for management decisions in conservation. To mitigate negative effects on saproxylic beetle diversity after windthrows, we recommend preserving single windthrown trees or at least their tops with exposed branches during salvage logging. Such an extension of the green-tree retention approach to windthrown trees will preserve natural succession and associated communities of disturbed spruce forests.     

Do foliar fungal communities of Norway spruce shift along a tree species diversity gradient in mature European forests?

Foliar fungal species are diverse and colonize all plants, though whether forest tree species composition influences the distribution of these fungal communities remains unclear. Fungal communities include quiescent taxa and the functionally important and metabolically active taxa that respond to changes in the environment. To determine fungal community shifts along a tree species diversity gradient, needles of Norway spruce were sampled from trees from four mature European forests. We hypothesized that the fungal communities and specific fungal taxa would correlate with tree species diversity. Furthermore, the active fungal community, and not the total community, would shift along the tree diversity gradient. High-throughput sequencing showed significant differences in the fungal communities in the different forests, and in one forest, tree diversity effects were observed, though this was not a general phenomenon. Our study also suggests that studying the metabolically active community may not provide additional information about community composition or diversity.     

Ectomycorrhizal community composition and function in a spruce forest transitioning between nitrogen and phosphorus limitation

Nitrogen is the main limiting nutrient in boreal ecosystems, but studies in southwest Sweden suggest that certain forests approach phosphorus (P) limitation driven by nitrogen (N) deposition. We added N, P or N + P to a Norway spruce forest in this region, to push the system to N or P limitation. Tree growth and needle nutrient concentrations indicated that the trees are P limited. EMF biomass was reduced only by N + P additions. Soil EMF communities responded more strongly to P than to N. Addition of apatite to ingrowth meshbags altered EMF community composition and enhanced the abundance of Imleria badia in the control and N plots, but not when P was added. The ecological significance of this species is discussed. Effects on tree growth, needle chemistry, and EMF communities indicate a dynamic interaction between EMF fungi and the nutrient status of trees and soils.     

Epigeous fruiting bodies of ectomycorrhizal fungi as indicators of soil fertility and associated nitrogen status of boreal forests

Soil fertility and associated nitrogen (N) status was a key ecosystem attribute, and surveys of ectomycorrhizal fungal (EMF) communities via epigeous fruiting bodies could provide an effective biotic indicator of forest soil productivity. We explored the utility of aboveground EMF communities in this regard by surveying sporocarps over a 3-year period from contrasting plant associations of southern old-growth boreal forests of British Columbia (Canada). Cumulative richness ranged from 39 to 89 EMF species per plot (0.15 ha) and followed a skewed parabolic correlation with foliar N concentrations and soil N availability. EMF species composition was consistently distinct in ordinations and strongly correlated to the increasing rates of N mineralization aligned with soil productivity. Approximately 40 EMF species were specialists, as they collectively indicated oligotrophic, mesotrophic, and eutrophic nutrient regimes, while the remaining species were categorized as broadly tolerant (distributed over 100% of the N gradient), partially intolerant (approximately 70%), or satellites (rare). The functional organization of EMF communities reflected by distribution classes could help define the ecological integrity of forests, which was characterized in this boreal landscape by an average allotment of 20 broadly tolerant, 25 partially intolerant, 15 specialist, and ten satellite species per plot. Epigeous fruiting bodies provided a disparate yet complementary view to the belowground assessment of EMF communities that was valuable in identifying indicators for ecosystem monitoring.     

Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil

Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.