scholarly journals Fungal communities associated with the eastern larch beetle: diversity and variation within developmental stages

2017 ◽  
Author(s):  
Audrey-Anne Durand ◽  
Jean-Philippe Buffet ◽  
Philippe Constant ◽  
Eric Déziel ◽  
Claude Guertin
Keyword(s):  
Filamentous Fungi ◽  
Bark Beetles ◽  
Developmental Stages ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Comprehensive Overview ◽  
Defense Compounds ◽  
Larval Stages ◽  
Dendroctonus Simplex

AbstractBacterial and fungal communities associated with bark beetles, especially some Dendroctonus species, mediate challenging aspects of the subcortical habitat for their hosts. Filamentous fungi and yeasts are important in various metabolic processes of certain bark beetles, with involvement in nutrition, protection and detoxification of plant defense compounds. The eastern larch beetle, Dendroctonus simplex, is recognized as a serious forest pest in the upper part of North America. Although D. simplex is well studied, the fungal communities and their ecological role remain to be investigated. Here, using 18S rRNA gene pyrosequencing, we provide a comprehensive overview of the yeasts and filamentous fungi associated with the eastern larch beetle and compare fungal communities between different developmental stages and microenvironments. Fungal mycobiome associated with the galleries was also investigated. Our study has unveiled an unexpected fungal diversity associated with the developmental stages. Significant differences in species richness between the developmental stages were determined. Yeasts were found to be predominant in the adult and larval stages, whereas filamentous fungi were most prevalent in the pupae. Our results indicate a possible implication of yeasts in the eastern larch beetle nutrition.

A new semi-nested PCR protocol to amplify large 18S rRNA gene fragments for PCR-DGGE analysis of soil fungal communities

2006 ◽  
Vol 65 (1) ◽  
pp. 63-75 ◽  
Author(s):  
Miruna Oros-Sichler ◽  
Newton C.M. Gomes ◽  
Gabriele Neuber ◽  
Kornelia Smalla
Keyword(s):  
Nested Pcr ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Dgge Analysis

scholarly journals Impact of Land Use on Arbuscular Mycorrhizal Fungal Communities in Rural Canada

2013 ◽  
Vol 79 (21) ◽  
pp. 6719-6729 ◽  
Author(s):  
Mulan Dai ◽  
Luke D. Bainard ◽  
Chantal Hamel ◽  
Yantai Gan ◽  
Derek Lynch
Keyword(s):  
Land Use ◽  
Species Richness ◽  
Diversity Index ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Canadian Prairie ◽  
Highly Correlated

ABSTRACTThe influence of land use on soil bio-resources is largely unknown. We examined the communities of arbuscular mycorrhizal (AM) fungi in wheat-growing cropland, natural areas, and seminatural areas along roads. We sampled the Canadian prairie extensively (317 sites) and sampled 20 sites in the Atlantic maritime ecozone for comparison. The proportions of the different AM fungal taxa in the communities found at these sites varied with land use type and ecozones, based on pyrosequencing of 18S rRNA gene (rDNA) amplicons, but the lists of AM fungal taxa obtained from the different land use types and ecozones were very similar. In the prairie, the Glomeraceae family was the most abundant and diverse family of Glomeromycota, followed by the Claroideoglomeraceae, but in the Atlantic maritime ecozone, the Claroideoglomeraceae family was most abundant. In the prairie, species richness and Shannon's diversity index were highest in roadsides, whereas cropland had a higher degree of species richness than roadsides in the Atlantic maritime ecozone. The frequencies of occurrence of the different AM fungal taxa in croplands in the prairie and Atlantic maritime ecozones were highly correlated, but the AM fungal communities in these ecozones had different structures. We conclude that the AM fungal resources of soils are resilient to disturbance and that the richness of AM fungi under cropland management has been maintained, despite evidence of a structural shift imposed by this type of land use. Roadsides in the Canadian prairie are a good repository for the conservation of AM fungal diversity.

scholarly journals Genotype-Specific Variation in the Structure of Root Fungal Communities Is Related to Chickpea Plant Productivity

2015 ◽  
Vol 81 (7) ◽  
pp. 2368-2377 ◽  
Author(s):  
Navid Bazghaleh ◽  
Chantal Hamel ◽  
Yantai Gan ◽  
Bunyamin Tar'an ◽  
Joan Diane Knight
Keyword(s):  
Central Zone ◽  
Crop Productivity ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Canadian Prairie ◽  
Gene Markers ◽  
Content Type ◽  
Wide Range ◽  
Improvement Programs

ABSTRACTIncreasing evidence supports the existence of variations in the association of plant roots with symbiotic fungi that can improve plant growth and inhibit pathogens. However, it is unclear whether intraspecific variations in the symbiosis exist among plant cultivars and if they can be used to improve crop productivity. In this study, we determined genotype-specific variations in the association of chickpea roots with soil fungal communities and evaluated the effect of root mycota on crop productivity. A 2-year field experiment was conducted in southwestern Saskatchewan, the central zone of the chickpea growing region of the Canadian prairie. The effects of 13 cultivars of chickpea, comprising a wide range of phenotypes and genotypes, were tested on the structure of root-associated fungal communities based on internal transcribed spacer (ITS) and 18S rRNA gene markers using 454 amplicon pyrosequencing. Chickpea cultivar significantly influenced the structure of the root fungal community. The magnitude of the effect varied with the genotypes evaluated, and effects were consistent across years. For example, the roots of CDC Corrine, CDC Cory, and CDC Anna hosted the highest fungal diversity and CDC Alma and CDC Xena the lowest.Fusariumsp. was dominant in chickpea roots but was less abundant in CDC Corrine than the other cultivars. A bioassay showed that certain of these fungal taxa, includingFusariumspecies, can reduce the productivity of chickpea, whereasTrichoderma harzianumcan increase chickpea productivity. The large variation in the profile of chickpea root mycota, which included growth-promoting and -inhibiting species, supports the possibility of improving the productivity of chickpea by improving its root mycota in chickpea genetic improvement programs using traditional breeding techniques.

scholarly journals Fungal communities in sediments along a depth gradient in the Eastern Tropical Pacific

2020 ◽  
Author(s):  
Keilor Rojas-Jimenez ◽  
Hans Peter Grossart ◽  
Erik Cordes ◽  
Jorge Cortés
Keyword(s):  
Costa Rica ◽  
Marine Sediments ◽  
Sediment Cores ◽  
18S Rrna Gene ◽  
Tropical Pacific ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Eastern Tropical Pacific ◽  
Deep Waters

AbstractDeep waters represent the largest biome on Earth and the largest ecosystem of Costa Rica. Fungi play a fundamental role in global biogeochemical cycling in marine sediments, yet, they remain little explored. We studied fungal diversity and community composition in several marine sediments from 16 locations sampled along a bathymetric gradient (from a depth of 380 to 3474 m) in two transects of about 1500 km length in the Eastern Tropical Pacific (ETP) of Costa Rica. Sequence analysis of the V7-V8 region of the 18S rRNA gene obtained from sediment cores revealed the presence of 787 fungal amplicon sequence variants (ASVs). On average, we detected a richness of 75 fungal ASVs per sample. Ascomycota represented the most abundant phylum with Saccharomycetes constituting the dominant class. Three ASVs accounted for ca. 63% of all fungal sequences: the yeast Metschnikowia (49.4%), Rhizophydium (6.9%), and Cladosporium (6.7%). Although we distinguished a cluster dominated by yeasts and a second cluster dominated by filamentous fungi, we were unable to detect a strong effect of depth, temperature, salinity, dissolved oxygen, and pH on the composition of fungal communities. We highlight the need to understand further the ecological role of fungi in deep-sea ecosystems.

scholarly journals Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comté cheese area

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
N. Chemidlin Prévost-Bouré ◽  
B. Karimi ◽  
S. Sadet-Bourgeteau ◽  
C. Djemiel ◽  
M. Brie ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Dairy Farms ◽  
Raw Milk ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Farming Practices ◽  
Organic Fertilization ◽  
Grassland Ecosystems ◽  
Protected Designation Of Origin

AbstractThe specificity of dairy Protected Designation of Origin (PDO) products is related to their “terroir” of production. This relationship needs better understanding for efficient and sustainable productions preserving the agroecological equilibrium of agroecosystems, especially grasslands. Specificity of PDO Comté cheese was related to the diversity of natural raw milk bacterial communities, but their sources need to be determined. It is hypothesized that raw milk indigenous microbial communities may originate from permanent grazed grasslands by the intermediate of dairy cows according to the sequence soil–phyllosphere–teat–milk. This hypothesis was evaluated on a 44 dairy farms network across PDO Comté cheese area by characterizing prokaryotic and fungal communities of these compartments by metabarcoding analysis (16S rRNA gene: V3–V4 region, 18S rRNA gene: V7–V8 region). Strong and significant links were highlighted between the four compartments through a network analysis (0.34 < r < 0.58), and were modulated by soil pH, plant diversity and elevation; but also by farming practices: organic fertilization levels, cattle intensity and cow-teat care. This causal relationship suggests that microbial diversity of agroecosystems is a key player in relating a PDO product to its “terroir”; this under the dependency of farming practices. Altogether, this makes the “terroir” even more local and needs to be considered for production sustainability.

Identification ofBalanus amphitritelarvae from field zooplankton using species-specific primers

2014 ◽  
Vol 95 (3) ◽  
pp. 497-502
Author(s):  
Chetan C. Gaonkar ◽  
Lidita Khandeparker ◽  
Dattesh V. Desai ◽  
Arga Chandrashekar Anil
Keyword(s):  
18S Rrna ◽  
Developmental Stages ◽  
Marine Invertebrate ◽  
Pcr Primers ◽  
Morphological Characters ◽  
18S Rrna Gene ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Specific Pcr

Identification of marine invertebrate larvae using morphological characters is laborious and complicated by phenotypic plasticity.Balanus amphitriteis a dominant barnacle, important in the context of intertidal ecology and biofouling of manmade structures. Morphological identification of barnacle larval forms in a mixed population is difficult because of their intricacy and similarity in size, shape and developmental stages. We report the development and application of a nucleic acid-based Polymerase Chain Reaction (PCR) method for the specific identification of the barnacle,B. amphitrite, from the heterogeneous zooplankton sample. This method is reliable and accurate thereby overcoming taxonomic ambiguity. Sequence alignment of the 18S rRNA gene region of selected species of barnacles allowed the design ofB. amphitrite-specific PCR primers. Assay specificity was evaluated by screening DNA obtained from selected species of barnacles. The oligonucleotide primers used in the study flanked a 1600 bp region within the 18S rRNA gene. The primer is specific and can detect as few as 10 individuals ofB. amphitritelarvae spiked in a background of ~186 mg of zooplankton. This technique facilitates accurate identification and the primer can be used as a marker for enumeration ofB. amphitritelarvae in the plankton.

scholarly journals A High-Resolution Time Series Reveals Distinct Seasonal Patterns of Planktonic Fungi at a Temperate Coastal Ocean Site (Beaufort, North Carolina, USA)

2018 ◽  
Vol 84 (21) ◽  
Author(s):  
Yingbo Duan ◽  
Ningdong Xie ◽  
Zhiquan Song ◽  
Christopher S. Ward ◽  
Cheuk-Man Yung ◽  
...  
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Coastal Ocean ◽  
Fungal Communities ◽  
Seasonal Patterns ◽  
Rrna Gene ◽  
Resolution Time ◽  
Carbonate System ◽  
Content Type ◽  
Marine Systems

ABSTRACTThere is a growing awareness of the ecological and biogeochemical importance of fungi in coastal marine systems. While highly diverse fungi have been discovered in these marine systems, still, little is known about their seasonality and associated drivers in coastal waters. Here, we examined fungal communities over 3 years of weekly sampling at a dynamic, temperate coastal site (Pivers Island Coastal Observatory [PICO], Beaufort, NC, USA). Fungal 18S rRNA gene abundance, operational taxonomic unit (OTU) richness, and Shannon's diversity index values exhibited prominent seasonality. Fungal 18S rRNA gene copies peaked in abundance during the summer and fall, with positive correlations with chlorophylla, SiO4, and oxygen saturation. Diversity (measured using internal transcribed spacer [ITS] libraries) was highest during winter and lowest during summer; it was linked to temperature, pH, chlorophylla, insolation, salinity, and dissolved inorganic carbon (DIC). Fungal communities derived from ITS libraries were dominated throughout the year byAscomycota, with contributions fromBasidiomycota,Chytridiomycota, andMucoromycotina, and their seasonal patterns linked to water temperature, light, and the carbonate system. Network analysis revealed that while cooccurrence and exclusion existed within fungus networks, exclusion dominated the fungus-and-phytoplankton network, in contrast with reported pathogenic and nutritional interactions between marine phytoplankton and fungi. Compared with the seasonality of bacterial communities in the same samples, the timing, extent, and associated environmental variables for fungi community are unique. These results highlight the fungal seasonal dynamics in coastal water and improve our understanding of the ecology of planktonic fungi.IMPORTANCECoastal fungal dynamics were long assumed to be due to terrestrial inputs; here, a high-resolution time series reveals strong, repeating annual patterns linked toin situenvironmental conditions, arguing for a resident coastal fungal community shaped by environmental factors. These seasonal patterns do, however, differ from those observed in the bacterioplankton at the same site; e.g., fungal diversity peaks in winter, whereas bacterial diversity maxima occur in the spring and fall. While the dynamics of these communities are linked to water temperature and insolation, fungi are also influenced by the carbonate system (pH and DIC). As both fungi and heterotrophic bacteria are thought to be key organic-material metabolizers, differences in their environmental drivers may offer clues as to which group dominates secondary production at this dynamic site. Overall, this study suggests the unique ecological roles of mycoplankton and their potentially broad niche complementarities to other microbial groups in the coastal ocean.

scholarly journals Fungal Diversity in the Phyllosphere of Pinus heldreichii H. Christ—An Endemic and High-Altitude Pine of the Mediterranean Region

Diversity ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 172 ◽  
Author(s):  
Jelena Lazarević ◽  
Audrius Menkis
Keyword(s):  
High Altitude ◽  
Bark Beetles ◽  
Fungal Pathogens ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
High Quality ◽  
The Balkans ◽  
Fungal Community Structure ◽  
Growing Conditions ◽  
Coniferous Tree Species

Pinus heldreichii is a high-altitude coniferous tree species naturaly occurring in small and disjuncted populations in the Balkans and southern Italy. The aim of this study was to assess diversity and composition of fungal communities in living needles of P. heldreichii specifically focusing on fungal pathogens. Sampling was carried out at six different sites in Montenegro, where 2-4 year-old living needles of P. heldreichii were collected. Following DNA isolation, it was amplified using ITS2 rDNA as a marker and subjected to high-throughput sequencing. Sequencing resulted in 31,831 high quality reads, which after assembly were found to represent 375 fungal taxa. The detected fungi were 295 (78.7%) Ascomycota, 79 (21.0%) Basidiomycota and 1 (0.2%) Mortierellomycotina. The most common fungi were Lophodermium pinastri (12.5% of all high-quality sequences), L. conigenum (10.9%), Sydowia polyspora (8.8%), Cyclaneusma niveum (5.5%), Unidentified sp. 2814_1 (5.4%) and Phaeosphaeria punctiformis (4.4%). The community composition varied among different sites, but in this respect two sites at higher altitudes (harsh growing conditions) were separated from three sites at lower altitudes (milder growing conditions), suggesting that environmental conditions were among major determinants of fungal communities associated with needles of P. heldreichii. Trees on one study site were attacked by bark beetles, leading to discolouration and frequent dieback of needles, thereby strongly affecting the fungal community structure. Among all functional groups of fungi, pathogens appeared to be an important component of fungal communities in the phyllosphere of P. heldreichii, especially in those trees under strong abiotic and biotic stress.

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