Community composition of root‐associated fungi in a Quercus‐dominated temperate forest: “codominance” of mycorrhizal and root‐endophytic fungi

In terrestrial ecosystems, plant roots are colonized by various clades of mycorrhizal and endophytic fungi. Focused on the root systems of an oak‐dominated temperate forest in Japan, we used 454 pyrosequencing to explore how phylogenetically diverse fungi constitute an ecological community of multiple ecotypes. In total, 345 operational taxonomic units (OTUs) of fungi were found from 159 terminal‐root samples from 12 plant species occurring in the forest. Due to the dominance of an oak species (Quercus serrata), diverse ectomycorrhizal clades such as Russula, Lactarius, Cortinarius, Tomentella, Amanita, Boletus, and Cenococcum were observed. Unexpectedly, the root‐associated fungal community was dominated by root‐endophytic ascomycetes in Helotiales, Chaetothyriales, and Rhytismatales. Overall, 55.3% of root samples were colonized by both the commonly observed ascomycetes and ectomycorrhizal fungi; 75.0% of the root samples of the dominant Q. serrata were so cocolonized. Overall, this study revealed that root‐associated fungal communities of oak‐dominated temperate forests were dominated not only by ectomycorrhizal fungi but also by diverse root endophytes and that potential ecological interactions between the two ecotypes may be important to understand the complex assembly processes of belowground fungal communities.     

The giant mycoheterotrophic orchid Erythrorchis altissima is associated mainly with a divergent set of wood‐decaying fungi

The climbing orchid Erythrorchis altissima is the largest mycoheterotroph in the world. Although previous in vitro work suggests that E. altissima has a unique symbiosis with wood‐decaying fungi, little is known about how this giant orchid meets its carbon and nutrient demands exclusively via mycorrhizal fungi. In this study, the mycorrhizal fungi of E. altissima were molecularly identified using root samples from 26 individuals. Furthermore, in vitro symbiotic germination with five fungi and stable isotope compositions in five E. altissima at one site were examined. In total, 37 fungal operational taxonomic units (OTUs) belonging to nine orders in Basidiomycota were identified from the orchid roots. Most of the fungal OTUs were wood‐decaying fungi, but underground roots had ectomycorrhizal Russula. Two fungal isolates from mycorrhizal roots induced seed germination and subsequent seedling development in vitro. Measurement of carbon and nitrogen stable isotope abundances revealed that E. altissima is a full mycoheterotroph whose carbon originates mainly from wood‐decaying fungi. All of the results show that E. altissima is associated with a wide range of wood‐ and soil‐inhabiting fungi, the majority of which are wood‐decaying taxa. This generalist association enables E. altissima to access a large carbon pool in woody debris and has been key to the evolution of such a large mycoheterotroph.     

Satellite chlorophyll fluorescence measurements reveal large‐scale decoupling of photosynthesis and greenness dynamics in boreal evergreen forests

Mid‐to‐high latitude forests play an important role in the terrestrial carbon cycle, but the representation of photosynthesis in boreal forests by current modelling and observational methods is still challenging. In particular, the applicability of existing satellite‐based proxies of greenness to indicate photosynthetic activity is hindered by small annual changes in green biomass of the often evergreen tree population and by the confounding effects of background materials such as snow. As an alternative, satellite measurements of sun‐induced chlorophyll fluorescence (SIF) can be used as a direct proxy of photosynthetic activity. In this study, the start and end of the photosynthetically active season of the main boreal forests are analysed using spaceborne SIF measurements retrieved from the GOME‐2 instrument and compared to that of green biomass, proxied by vegetation indices including the Enhanced Vegetation Index (EVI) derived from MODIS data. We find that photosynthesis and greenness show a similar seasonality in deciduous forests. In high‐latitude evergreen needleleaf forests, however, the length of the photosynthetically active period indicated by SIF is up to 6 weeks longer than the green biomass changing period proxied by EVI, with SIF showing a start‐of‐season of approximately 1 month earlier than EVI. On average, the photosynthetic spring recovery as signalled by SIF occurs as soon as air temperatures exceed the freezing point (2–3 °C) and when the snow on the ground has not yet completely melted. These findings are supported by model data of gross primary production and a number of other studies which evaluated in situ observations of CO₂ fluxes, meteorology and the physiological state of the needles. Our results demonstrate the sensitivity of space‐based SIF measurements to light‐use efficiency of boreal forests and their potential for an unbiased detection of photosynthetic activity even under the challenging conditions interposed by evergreen boreal ecosystems.     

Predictors of moss and liverwort species diversity of microsites in conifer‐dominated boreal forest

Patterns of moss and liverwort species diversity — species richness and species turnover (β‐diversity) — in three conifer‐dominated boreal forest stands of northern Alberta, Canada are described. We examined the relationship between bryophyte species diversity and micro‐environment at two sample grains, the microsite — substrate types for moss colonization: logs, stumps, tree bases, undisturbed patches of forest floor (dominated by feather moss species), and disturbed patches of forest floor — and the mesosite (25 m × 25 m plots). Microsite type and properties (e.g. decay class, hardwood vs softwood, pH) were the principal predictors of bryophyte species diversity and not micro‐environment variation among mesosites. Microsite type was the strongest predictor of microsite species richness and β‐diversity was higher among microsites and types and within microsites than among mesosites or stands. Microsite properties were significant predictors of species richness for all microsite types. Log and stump decay classes, influenced also by hardwood vs softwood predicted species richness of woody microsite types and soil pH and moisture predicted species richness of forest floor microsites. β‐diversity was highest for tree bases and disturbed patches of forest floor and lowest for logs. Mesosite β‐diversity was lower than that among microsites, and mesosite species richness was not well explained by measured environmental parameters. Results suggest that in conifer‐dominated boreal stands, species richness of microsites is only negligibly influenced by within‐stand variation at the mesosite grain and that substrate characteristics are the most important predictors of bryophyte species diversity in this ecosystem.     

Gut microbiomes of sympatric Amazonian wood‐eating catfishes (Loricariidae) reflect host identity and little role in wood digestion

Neotropical wood‐eating catfishes (family Loricariidae) can occur in diverse assemblages with multiple genera and species feeding on the same woody detritus. As such, they present an intriguing system in which to examine the influence of host species identity on the vertebrate gut microbiome as well as to determine the potential role of gut bacteria in wood digestion. We characterized the gut microbiome of two co‐occurring catfish genera and four species: Panaqolus albomaculatus, Panaqolus gnomus, Panaqolus nocturnus, and Panaque bathyphilus, as well as that of submerged wood on which they feed. The gut bacterial community did not significantly vary across three gut regions (proximal, mid, distal) for any catfish species, although interspecific variation in the gut microbiome was significant, with magnitude of interspecific difference generally reflecting host phylogenetic proximity. Further, the gut microbiome of each species was significantly different to that present on the submerged wood. Inferring the genomic potential of the gut microbiome revealed that the majority of wood digesting pathways were at best equivalent to and more often depleted or nonexistent within the catfish gut compared to the submerged wood, suggesting a minimal role for the gut microbiome in wood digestion. Rather, these fishes are more likely reliant on fiber degradation performed by microbes in the environment, with their gut microbiome determined more by host identity and phylogenetic history.     

Community structure of polypores (Basidiomycota) in Andean alder wood in Argentina: Functional groups among wood‐decay fungi?

Abstract The polypores (Aphyllophorales s.l., Basidiomycota) are very effective wood decayers. Different species differ in their capacity to decay wood; therefore, many functionally different species can be found decaying different substrate conditions (decay stages and log diameter). This study aimed to describe the structure of the wood‐decay polypore communities that occur on different states of wood of the Andean alder (Alnus acuminata) within Argentina and to identify groups of polypore species that share the same substrate condition, and thus might have a similar functional role in the decay processes. We found 16 polypore species, among which Trametes versicolor, Bjerkandera adusta and Trametes cubensis were dominant species, showing the highest relative frequency in alder wood. Species richness was lower on trunks of living trees and higher on dead branches. Based on preferential occurrence on different wood conditions, a cluster analysis distinguished three groups, each of them containing one of the three dominant species. This corresponds to the situation of other groups of organisms, where each functional type consists of a dominant species that accounts for most of the ‘function’ and several subordinate species with similar functions. Albeit preliminary, our results provide a formal classification of wood‐decay fungi into functional types.     

The effects of plantation practice on soil properties based on the comparison between natural and planted forests: a meta‐analysis

Aim The effects of planted forests on soils are of great concern in the context of the increasing demands for timber production and atmospheric CO₂ sequestration. However, the effects of plantations on soil properties have not well been quantified. We determined the effects of plantation practice on soil properties based on a comparison between natural forests and plantations. Locations All the continents except for Antarctica. Methods The meta‐analysis approach was used to examine the differences in 14 soil variables in the mineral layer, including pH, bulk density, C, N, P, K, Ca, Mg, Na and Al concentrations, C/N ratio, cation exchangeable capacity, base saturation, and moisture between plantations and their adjacent natural forests from 73 published studies. Results Plantations did not differ from natural forests in soil pH or soil Na and Al concentrations. Soil bulk density below plantations increased by 12.5%, and soil C and N concentrations decreased by 36.0% and 26.5%, respectively, relative to natural forests. The other eight variables were 8.4–30.6% lower in plantations than in natural forests. The general patterns also held true for planted trees from the genus Pinus and for study regions in China. The patterns for soil bulk density and C and N concentrations were not different between the two groups in relation to various factors: stand age (< 25 years versus ≥ 25 years), leaf form (broadleaved versus coniferous) and leaf seasonality (deciduous versus evergreen), tree species origin (native versus exotic), land‐use history (afforestation versus reforestation) and site preparation for plantations (burnt versus un‐burnt treatment), and biogeographic zone (tropical versus temperate). Main conclusions Our results suggest that the level of soil fertility in plantations is unlikely to restore to the level in natural forests, implying that the replacement of natural forests by plantations may be a practice best avoided to maintain the ecosystem sustainability.     

Forest history and the development of old‐growth characteristics in fragmented boreal forests

Questions: Can small and isolated high‐conservation value forests (e.g. designated woodland key habitats) maintain old‐growth forest characteristics and functionality in fragmented landscapes? To what extent have past disturbances (natural and anthropogenic) influenced the development of old‐growth characteristics of these forests? How long does it take for selectively cut stands to attain conditions resembling old‐growth forests? Location: Southern boreal zone of central Sweden. Methods: We linked multiple lines of evidence from historical records, biological archives, and analyses of current forest structure to reconstruct the forest history of a boreal landscape, with special emphasis on six remaining core localities of high‐conservation value forest stands. Results: Our reconstructions revealed that several of these stands experienced wildfires up to the 1890s; all had been selectively harvested in the late 1800s; and all underwent substantial structural and compositional reorganization over the following 100‐150 years. This time interval was sufficient to recover considerable amounts of standing and downed dead wood (mean 60.3 m³ ha^?1), a range of tree ages and sizes (mean basal area 32.6 m² ha^?1), and dominance of shade‐tolerant spruce. It was insufficient to obtain clearly uneven tree age structures and large (>45 cm diameter) living and dead trees. Thus, these forests contain some, but not all, important compositional and structural attributes of old‐growth forests, their abundance being dependent on the timing and magnitude of past natural and anthropogenic disturbances. Our landscape‐level analysis showed marked compositional and structural differences between the historical forest landscape and the present landscape, with the latter having a greater proportion of young forests, introduction of non‐native species, and lack of large trees and dead wood. Conclusions: The remnant high‐conservation value stands were not true representatives of the pre‐industrial forests, but represent the last vestige of forests that have regenerated naturally and maintained a continuous tree cover. These traits, coupled with their capacity for old‐growth recovery, make them valuable focal areas for conservation.     

Silencing a key gene of the common symbiosis pathway in Nicotiana attenuata specifically impairs arbuscular mycorrhizal infection without influencing the root‐associated microbiome or plant growth

While the biochemical function of calcium and calmodulin‐dependent protein kinase (CCaMK) is well studied, and plants impaired in the expression of CCaMK are known not to be infected by arbuscular mycorrhizal fungi (AMF) in glasshouse studies, the whole‐plant and ecological consequences of CCaMK silencing are not well understood. Here we show that three independently transformed lines of Nicotiana attenuata plants silenced in CCaMK (irCCaMK) are neither infected by Rhizophagus irregularis in the glasshouse nor by native fungal inoculum in the field. The overall fungal community of field‐grown roots did not differ significantly among empty vector (EV) and the transgenic lines, and the bacterial communities only showed minor differences, as revealed by the alpha‐diversity parameters of bacterial OTUs, which were higher in EV plants compared with two of the three transformed lines, while beta‐diversity parameters did not differ. Furthermore, growth and fitness parameters were similar in the glasshouse and field. Herbivory‐inducible and basal levels of salicylic acid, jasmonic acid and abscisic acid did not differ among the genotypes, suggesting that activation of the classical defence pathways are not affected by CCaMK silencing. Based on these results, we conclude that silencing of CCaMK has few, if any, non‐target effects.     

Fifty‐seven years of composition change in the eastern boreal forest of Canada

Question: In the boreal forest of eastern Canada, how does forest vegetation change in the sustained absence of fire? Location: Eastern boreal forest in Quebec's North Shore region, Canada (49°30′–50°00′N; 67°30′–68°35′W). Methods: Aerial photos from three different periods (1930, 1965 and 1987) were used to characterize changes in vegetation composition in 23 scenes of 200 ha. Time since fire, presence of secondary disturbances and data on soil and topographic variables were obtained. Ordination and clustering techniques were used to define compositional trajectories of change over the 57‐yr period. These trajectories were further grouped into pathways based on compositional changes, time since fire and preferential deposit‐drainage types. Results: Among the 26 compositional trajectories, three successional pathways were distinguished. Two start post‐fire succession with a dominance of intolerant hardwood. In one of these, this is followed by an increase in Abies balsamea, while in the second the importance of Picea mariana increases with time. In the third pathway P. mariana is an important component from the outset. In this pathway, we observed modest fluctuation in the relative dominance of P. mariana and A. balsamea and variation in stand structure. Conclusion: The boreal forest vegetation of Eastern Canada is diverse and dynamic even in the absence of fire, notably under the influence of partial disturbances. Such disturbances can be associated with changes in composition or stand structure. The development of management strategies aimed at maintaining stand diversity by emulating a broader variety of partial and secondary disturbances should be encouraged.     

The role of amoeboid protists and the microbial community in moss-rich terrestrial ecosystems: biogeochemical implications for the carbon budget and carbon cycle, especially at higher latitudes

Moss-rich terrestrial communities are widely distributed in low- and high-latitude environments, covering vast surface areas in the boreal forests and tundra. The microbial biota in these organic-rich communities may contribute substantially to the carbon budget of terrestrial communities and the carbon cycle on a global scale. Recent research is reported on the carbon content of microbial communities in some temperate and high-latitude moss communities. The total carbon content and potential respiratory carbon dioxide (CO(2)) efflux is reported for bacteria, microflagellates, naked amoebae, and testate amoebae within sampling sites at a northeastern forest and the tundra at Toolik, Alaska. Quantitative models of the predicted total CO(2) efflux from the microbes, based on microscopic observations and enumeration of the microbiota in samples from the research sites, are described and predictions are compared with published field-based data of CO(2) efflux. The significance of the predictions for climate change and global warming are discussed.     

Tree species compositional change and conservation implications in the white‐water flooded forests of the Brazilian Amazon

Aim The aim of this study was to use compositional changes in tree species along the Amazon River floodplain in Brazil to identify and characterize biogeographic regions that would serve as broad surrogates for conservation planning. Location The main course of the Amazon River in Brazil, covering a river distance of approximately 2800 km. Methods Two sampling methods were employed at specific sites: standardized transects and/or individual‐based samples. Seventy‐three samples were collected from 26 sites at approximately 100‐km intervals along the floodplain. Biogeographic regions were identified by non‐metric multidimensional scaling (NMDS) ordination and by a hierarchical cluster analysis. The relative influence of environmental components (flood depths, annual rainfall, and length of the dry season) on tree species composition and one spatial component (longitude) were analysed by multiple regressions against a one‐dimensional NMDS ordination axis. Results Based on tree species composition, three main biogeographic regions were identified: a western region between Tabatinga and the Negro River confluence; a central region from the Negro River confluence to the Xingu confluence; and an estuarine region from the Xingu confluence to Santana. The regions identified were consistent using different data sets and analytical techniques. Mixed environmental and spatial effects explained most of the variation, but the spatial effect alone had a greater influence on species composition than environmental effects alone. Main conclusions The regions delimited in the analyses differed from those based on geomorphology or World Wildlife Fund (WWF) ecoregions. These results reinforce the need for surrogates to be tested against biological data before they are used to shape approaches to conservation planning. Although a protected area coverage of 25% gives the impression of extensive conservation management on the floodplain, less than 1% of the Amazon’s floodplain in Brazil is strictly protected. The significant compositional differences between regions and the strong spatial variation along the Amazon indicate that strict protection areas should be distributed much more evenly within and between regions.