Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit ...multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6–38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.
The cultivation of short-rotation tree species on non-forest land is increasing due to the growing demand for woody biomass for the future bioeconomy and to mitigate climate change impacts. However, ...forest plantations are often seen as a trade-off between climate benefits and low biodiversity. The diversity and composition of soil fungal biota in plantations of hybrid aspen, one of the most planted tree species for short-rotation forestry in Northern Europe, are poorly studied.
The goal of this study was to obtain baseline knowledge about the soil fungal biota and the edaphic, floristic and management factors that drive fungal richness and communities in 18-year-old hybrid aspen plantations on former agricultural soils and compare the fungal biota with those of European aspen stands on native forest land in a 130-year chronosequence. Sites were categorized as hybrid aspen (17-18-year-old plantations) and native aspen stands of three age classes (8-29, 30-55, and 65-131-year-old stands). High-throughput sequencing was applied to soil samples to investigate fungal diversity and assemblages.
Native aspen forests showed a higher ectomycorrhizal (EcM) fungal OTU richness than plantations, regardless of forest age. Short-distance type EcM genera dominated in both plantations and forests. The richness of saprotrophic fungi was similar between native forest and plantation sites and was highest in the middle-aged class (30-55-year-old stands) in the native aspen stands. The fungal communities of native forests and plantations were significantly different. Community composition varied more, and the natural forest sites were more diverse than the relatively homogeneous plantations. Soil pH was the best explanatory variable to describe soil fungal communities in hybrid aspen stands. Soil fungal community composition did not show any clear patterns between the age classes of native aspen stands.
We conclude that edaphic factors are more important in describing fungal communities in both native aspen forest sites and hybrid aspen plantation sites than forest thinning, age, or former land use for plantations. Although first-generation hybrid aspen plantations and native forests are similar in overall fungal diversity, their taxonomic and functional composition is strikingly different. Therefore, hybrid aspen plantations can be used to reduce felling pressure on native forests; however, our knowledge is still insufficient to conclude that plantations could replace native aspen forests from the soil biodiversity perspective.
After the extensive spread of the African swine fever virus (ASFV) genotype II in Eastern Europe, the first case of African swine fever (ASF) in Estonia was diagnosed in September 2014. By the end of ...2019, 3971 ASFV-positive wild boars were found, and 27 domestic pig outbreaks were reported. A selection of ASFV isolates from wild boar and domestic pigs (during the period of September 2014–2019) was molecularly characterized using standardized genotyping procedures. One of the proven markers to characterize this virus is the central variable region (CVR) within the B602L gene. In summer 2015, a new ASFV genotype II CVR variant 2 (GII-CVR2) was confirmed in Estonia. The results suggest that the GII-CVR2 variant was only confirmed in wild boar from a limited area in southern Estonia in 2015 and 2016. In addition to GII-CVR2, a single nucleotide polymorphism (SNP) that resulted in amino acid change was identified within the genotype II CVR variant 1 (GII-CVR1). The GII-CVR1/SNP1 strain was isolated in Estonia in November 2016. Additional GII-CVR1/SNP1 cases were confirmed in two neighbouring counties, as well as in one outbreak farm in June 2017. Based on the available data, no GII-CVR2 and GII-CVR1/SNP1 have been reported by other affected European countries. The spread of variant strains in Estonia has been limited over time, and restricted to a relatively small area.
The European ash (Fraxinus excelsior L.) dieback is an acute forest pathology problem caused by the invasive ascomycete Hymenoscyphus fraxineus (T. Kowalski) Baral, Queloz, Hosoya. There are no ...practical solutions yet, but selection for resistant genotypes and intensive care have been highlighted as options. Our aim was to assess the disease mitigation potential of silvicultural harvests, which influence stress levels in retained trees. We annually monitored 577 retention trees on Estonian cut areas for 13 years, including 9 years impacted by the dieback. Sixty-five percent of the trees survived and 15% retained healthy crown, despite all sampled trees being infected. The damage was smallest in the trees retained near precut edges. Former forest-interior trees that were left in central parts of the cut areas suffered high initial damage but smaller disease progression than trees near postcut edges. Tree size and secondary infection by Armillaria spp. were not related to disease progression, but rapid decline was observed in the region with the highest density of ash trees retained. Our results indicate a significant silvicultural potential for tree resistance. Ash trees tend to be healthiest in open conditions, which probably inhibit the pathogen and provide better resources for the tree. Location near precut edges is an important tree retention criterion, which can mitigate initial harvest-induced stress.
Diplodia sapinea is a cosmopolitan endophyte and opportunistic pathogen having occurred on several conifer species in Europe for at least 200 years. In Europe, disease outbreaks have increased on ...several Pinus spp. in the last few decades. In this study, the genetic structure of the European and western Asian D. sapinea population were investigated using 13 microsatellite markers. In total, 425 isolates from 15 countries were analysed. A high clonal fraction and low genetic distance between most subpopulations was found. One single haplotype dominates the European population, being represented by 45.3% of all isolates and found in nearly all investigated countries. Three genetically distinct subpopulations were found: Central/North European, Italian and Georgian. The recently detected subpopulations of D. sapinea in northern Europe (Estonia) share several haplotypes with the German subpopulation. The northern European subpopulations (Latvia, Estonia and Finland) show relatively high genetic diversity compared to those in central Europe suggesting either that the fungus has existed in the North in an asymptomatic/endophytic mode for a long time or that it has spread recently by multiple introductions. Considerable genetic diversity was found even among isolates of a single tree as 16 isolates from a single tree resulted in lower clonal fraction index than most subpopulations in Europe, which might reflect cryptic sexual proliferation. According to currently published allelic patterns, D. sapinea most likely originates from North America or from some unsampled population in Asia or central America. In order to enable the detection of endophytic or latent infections of planting stock by D. sapinea, new species-specific PCR primers (DiSapi-F and Diplo-R) were designed. During the search for Diplodia isolates across the world for species specific primer development, we identified D. africana in California, USA, and in the Canary Islands, which are the first records of this species in North America and in Spain.
This study aimed to determine the differences and drivers of oomycete diversity and community composition in alder- and birch-dominated park and natural forest soils of the Fennoscandian and Baltic ...countries of Estonia, Finland, Lithuania, Norway, and Sweden. For this, we sequenced libraries of PCR products generated from the DNA of 111 soil samples collected across a climate gradient using oomycete-specific primers on a PacBio high-throughput sequencing platform. We found that oomycete communities are most affected by temperature seasonality, annual mean temperature, and mean temperature of the warmest quarter. Differences in composition were partly explained by the higher diversity of Saprolegniales in Sweden and Norway, as both total oomycete and Saprolegniales richness decreased significantly at higher longitudes, potentially indicating the preference of this group of oomycetes for a more temperate maritime climate. None of the evaluated climatic variables significantly affected the richness of Pythiales or Peronosporales. Interestingly, the relative abundance and richness of Pythiales was higher at urban sites compared to forest sites, whereas the opposite was true for Saprolegniales. Additionally, this is the first report of Phytophthora gallica and P. plurivora in Estonia. Our results indicate that the composition of oomycetes in soils is strongly influenced by climatic factors, and, therefore, changes in climate conditions associated with global warming may have the potential to significantly alter the distribution range of these microbes, which comprise many important pathogens of plants.
Inonotus obliquus, a well-known forest fungal pathogen, started gaining attention for its potential medicinal uses. Known as Chaga, the fungus has become prominent due to the bioactive compounds ...present in its conks. Forest owners are cultivating it to produce conks as a source of non-timber profit. However, not much is known about the natural occurrence of this pathogen, its formation of conks, the extent of decay in the infected trees, and the distribution of its basidiospores. Across 80 forest stands in Estonia dominated by Betula pendula, B. pubescens, Alnus incana, and A. glutinosa, the conks of I. obliquus were documented in 17 stands. The conks were more common in continental Estonia compared to the western islands. Among 800 randomly chosen trees, I. obliquus conks were documented on ten trees. Additionally, an asymptomatic I. obliquus infection was detected in one tree. After two years of spore trapping, I. obliquus basidiospores were detected only on four occasions, between the end of July and the beginning of September, and only at night. The proportion of rot damage in the total volume of model tree wood ranged from 8.6% to 58.5%. For fast and reliable detection of I. obliquus, TaqMan species-specific qPCR primers were developed and tested.
•The rot damage caused by I. obliquus ranged from 8.6% to 58.5% of the host tree volume.•obliquus propagates its basidiospores only at night.•The basidiospores were released from the end of July to the beginning of September.•The conks of I. obliquus are equally likely to be found in Betula and Alnus stands.•1.25% of host trees were having I. obliquus conks.
Global diversity and geography of soil fungi Tedersoo, Leho; Bahram, Mohammad; Põlme, Sergei ...
Science (American Association for the Advancement of Science),
11/2014, Letnik:
346, Številka:
6213
Journal Article
Recenzirano
Odprti dostop
Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally ...distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework. Assessing fungal diversity worldwideFungi are hyperdiverse but poorly known, despite their ecological and economic impacts. Tedersoo et al. collected nearly 15,000 topsoil samples from 365 sites worldwide and sequenced their genomes (see the Perspective by Wardle and Lindahl). Overall, they found a striking decline in fungal species richness with distance from the equator. For some specialist groups though, diversity depended more on the abundance of host plants than host diversity or geography. The findings reveal a huge gap between known and described species and the actual numbers of distinct fungi in the world's soils.Science, this issue 10.1126/science.1256688; see also p. 1052
The European ash (Fraxinus excelsior L.) dieback is an acute forest pathology problem caused by the invasive ascomycete Hymenoscyphus fraxineus (T. Kowalski) Baral, Queloz, Hosoya. There are no ...practical solutions yet, but selection for resistant genotypes and intensive care have been highlighted as options. Our aim was to assess the disease mitigation potential of silvicultural harvests, which influence stress levels in retained trees. We annually monitored 577 retention trees on Estonian cut areas for 13 years, including 9 years impacted by the dieback. Sixty-five percent of the trees survived and 15% retained healthy crown, despite all sampled trees being infected. The damage was smallest in the trees retained near precut edges. Former forest-interior trees that were left in central parts of the cut areas suffered high initial damage but smaller disease progression than trees near postcut edges. Tree size and secondary infection by Armillaria spp. were not related to disease progression, but rapid decline was observed in the region with the highest density of ash trees retained. Our results indicate a significant silvicultural potential for tree resistance. Ash trees tend to be healthiest in open conditions, which probably inhibit the pathogen and provide better resources for the tree. Location near precut edges is an important tree retention criterion, which can mitigate initial harvest-induced stress.
PDF
