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Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic.

https://arctichealth.org/en/permalink/ahliterature289464
Source
Mol Ecol. 2017 Sep; 26(18):4798-4810
Publication Type
Journal Article
Date
Sep-2017
Author
Oriol Grau
József Geml
Aaron Pérez-Haase
Josep M Ninot
Tatiana A Semenova-Nelsen
Josep Peñuelas
Author Affiliation
CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Cerdanyola del Vallès, Catalonia, Spain.
Source
Mol Ecol. 2017 Sep; 26(18):4798-4810
Date
Sep-2017
Language
English
Publication Type
Journal Article
Keywords
Arctic Regions
DNA Barcoding, Taxonomic
DNA, Fungal - genetics
Ecosystem
Fungi - classification
Greenland
Mycobiome
Sequence Analysis, DNA
Soil Microbiology
Abstract
Fungi play a key role in soil-plant interactions, nutrient cycling and carbon flow and are essential for the functioning of arctic terrestrial ecosystems. Some studies have shown that the composition of fungal communities is highly sensitive to variations in environmental conditions, but little is known about how the conditions control the role of fungal communities (i.e., their ecosystem function). We used DNA metabarcoding to compare taxonomic and functional composition of fungal communities along a gradient of environmental severity in Northeast Greenland. We analysed soil samples from fell fields, heaths and snowbeds, three habitats with very contrasting abiotic conditions. We also assessed within-habitat differences by comparing three widespread microhabitats (patches with high cover of Dryas, Salix, or bare soil). The data suggest that, along the sampled mesotopographic gradient, the greatest differences in both fungal richness and community composition are observed amongst habitats, while the effect of microhabitat is weaker, although still significant. Furthermore, we found that richness and community composition of fungi are shaped primarily by abiotic factors and to a lesser, though still significant extent, by floristic composition. Along this mesotopographic gradient, environmental severity is strongly correlated with richness in all fungal functional groups: positively in saprotrophic, pathogenic and lichenised fungi, and negatively in ectomycorrhizal and root endophytic fungi. Our results suggest complex interactions amongst functional groups, possibly due to nutrient limitation or competitive exclusion, with potential implications on soil carbon stocks. These findings are important in the light of the environmental changes predicted for the Arctic.
PubMed ID
28664999 View in PubMed
Less detail

Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic.

https://arctichealth.org/en/permalink/ahliterature289622
Source
Mol Ecol. 2017 Sep; 26(18):4798-4810
Publication Type
Journal Article
Date
Sep-2017
Author
Oriol Grau
József Geml
Aaron Pérez-Haase
Josep M Ninot
Tatiana A Semenova-Nelsen
Josep Peñuelas
Author Affiliation
CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Cerdanyola del Vallès, Catalonia, Spain.
Source
Mol Ecol. 2017 Sep; 26(18):4798-4810
Date
Sep-2017
Language
English
Publication Type
Journal Article
Keywords
Arctic Regions
DNA Barcoding, Taxonomic
DNA, Fungal - genetics
Ecosystem
Fungi - classification
Greenland
Mycobiome
Sequence Analysis, DNA
Soil Microbiology
Abstract
Fungi play a key role in soil-plant interactions, nutrient cycling and carbon flow and are essential for the functioning of arctic terrestrial ecosystems. Some studies have shown that the composition of fungal communities is highly sensitive to variations in environmental conditions, but little is known about how the conditions control the role of fungal communities (i.e., their ecosystem function). We used DNA metabarcoding to compare taxonomic and functional composition of fungal communities along a gradient of environmental severity in Northeast Greenland. We analysed soil samples from fell fields, heaths and snowbeds, three habitats with very contrasting abiotic conditions. We also assessed within-habitat differences by comparing three widespread microhabitats (patches with high cover of Dryas, Salix, or bare soil). The data suggest that, along the sampled mesotopographic gradient, the greatest differences in both fungal richness and community composition are observed amongst habitats, while the effect of microhabitat is weaker, although still significant. Furthermore, we found that richness and community composition of fungi are shaped primarily by abiotic factors and to a lesser, though still significant extent, by floristic composition. Along this mesotopographic gradient, environmental severity is strongly correlated with richness in all fungal functional groups: positively in saprotrophic, pathogenic and lichenised fungi, and negatively in ectomycorrhizal and root endophytic fungi. Our results suggest complex interactions amongst functional groups, possibly due to nutrient limitation or competitive exclusion, with potential implications on soil carbon stocks. These findings are important in the light of the environmental changes predicted for the Arctic.
PubMed ID
28664999 View in PubMed
Less detail

An improved high throughput sequencing method for studying oomycete communities.

https://arctichealth.org/en/permalink/ahliterature266900
Source
J Microbiol Methods. 2015 Mar;110:33-9
Publication Type
Article
Date
Mar-2015
Author
Rumakanta Sapkota
Mogens Nicolaisen
Source
J Microbiol Methods. 2015 Mar;110:33-9
Date
Mar-2015
Language
English
Publication Type
Article
Keywords
Aphanomyces - genetics
DNA Barcoding, Taxonomic
DNA Primers
DNA, Ribosomal Spacer - genetics
Daucus carota
Denmark
Genetic Variation
High-Throughput Nucleotide Sequencing - methods
Oomycetes - classification - genetics
Peronospora - genetics
Phytophthora - classification - genetics
Polymerase Chain Reaction - methods
Pythium - genetics
Saprolegnia - genetics
Sequence Analysis, DNA
Soil Microbiology
Species Specificity
Abstract
Culture-independent studies using next generation sequencing have revolutionized microbial ecology, however, oomycete ecology in soils is severely lagging behind. The aim of this study was to improve and validate standard techniques for using high throughput sequencing as a tool for studying oomycete communities. The well-known primer sets ITS4, ITS6 and ITS7 were used in the study in a semi-nested PCR approach to target the internal transcribed spacer (ITS) 1 of ribosomal DNA in a next generation sequencing protocol. These primers have been used in similar studies before, but with limited success. We were able to increase the proportion of retrieved oomycete sequences dramatically mainly by increasing the annealing temperature during PCR. The optimized protocol was validated using three mock communities and the method was further evaluated using total DNA from 26 soil samples collected from different agricultural fields in Denmark, and 11 samples from carrot tissue with symptoms of Pythium infection. Sequence data from the Pythium and Phytophthora mock communities showed that our strategy successfully detected all included species. Taxonomic assignments of OTUs from 26 soil sample showed that 95% of the sequences could be assigned to oomycetes including Pythium, Aphanomyces, Peronospora, Saprolegnia and Phytophthora. A high proportion of oomycete reads was consistently present in all 26 soil samples showing the versatility of the strategy. A large diversity of Pythium species including pathogenic and saprophytic species were dominating in cultivated soil. Finally, we analyzed amplicons from carrots with symptoms of cavity spot. This resulted in 94% of the reads belonging to oomycetes with a dominance of species of Pythium that are known to be involved in causing cavity spot, thus demonstrating the usefulness of the method not only in soil DNA but also in a plant DNA background. In conclusion, we demonstrate a successful approach for pyrosequencing of oomycete communities using ITS1 as the barcode sequence with well-known primers for oomycete DNA amplification.
PubMed ID
25602160 View in PubMed
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Barcoding the Collembola of Churchill: a molecular taxonomic reassessment of species diversity in a sub-Arctic area.

https://arctichealth.org/en/permalink/ahliterature262460
Source
Mol Ecol Resour. 2014 Mar;14(2):249-61
Publication Type
Article
Date
Mar-2014
Author
David Porco
Dariusz Skarzynski
Thibaud Decaëns
Paul D N Hebert
Louis Deharveng
Source
Mol Ecol Resour. 2014 Mar;14(2):249-61
Date
Mar-2014
Language
English
Publication Type
Article
Keywords
Animals
Arctic Regions
Arthropods - classification - genetics
DNA Barcoding, Taxonomic - methods
Entomology - methods
Genetic Variation
Genotyping Techniques - methods
Manitoba
Molecular Sequence Data
Abstract
Although their functional importance in ecosystems is increasingly recognized, soil-dwelling micro-arthropods are usually poorly known in comparison with their above-ground counterparts. Collembola constitute a significant and species-rich component of the soil biodiversity, but it remains a woefully understudied group because of the taxonomic impediment. The ever-increasing use of molecular taxonomic tools, such as DNA barcoding, provides a possible solution. Here, we test the use of this approach through a diversity survey of Collembola from the vicinity of Churchill, Manitoba, Canada, and compare the results with previous surveys in the same area and in other sub-Arctic regions. The systematic barcoding campaign at Churchill revealed a diverse collembolan fauna consisting of 97 species-level MOTUs in six types of habitats. If all these MOTUs are confirmed as species, this richness would be far higher than prior records for Arctic Canada and could lead to reconsider the actual diversity of the group in Arctic environments.
PubMed ID
24112538 View in PubMed
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Broader Geographic Sampling Increases Extent of Intermediate Host Specificity for a Trematode Parasite (Notocotylidae: Quinqueserialis quinqueserialis).

https://arctichealth.org/en/permalink/ahliterature308152
Source
J Parasitol. 2019 12; 105(6):874-877
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
12-2019
Author
D K Gagnon
J T Detwiler
Author Affiliation
Department of Biological Sciences, University of Manitoba, Winnipeg, Canada, R3T 2N2.
Source
J Parasitol. 2019 12; 105(6):874-877
Date
12-2019
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Arctic Regions
DNA Barcoding, Taxonomic
Host Specificity
Manitoba
Northwest Territories
Southeastern United States
Trematoda - physiology
Trematode Infections - parasitology - transmission
Abstract
Knowledge of helminth life cycles is essential to understanding their host specificity, geographic distribution, and transmission. Many helminth life cycle descriptions are based on field collections in a limited part of the parasite's range. However, it is important to determine whether helminth life cycles and host specificity remain consistent across their geographic range so that we may better understand their life history and transmission ecology. Here, we investigated whether the life cycle of a widespread trematode, Quinqueserialis quinqueserialis (Notocotylidae) varies across its geographic range. Four species of planorbid snails; Gyraulus circumstriatus, Gyraulus crista, Planorbula sp., and Promenetus exacuous, were collected at 5 locations in Canada (3 in Manitoba, 2 in Northwest Territories). Snails and parasite larvae were morphologically and genetically identified to species. The total prevalence of Q. quinqueserialis infections in snail hosts among the 5 locations was 2.3% (n = 1,017). Three species of snails were infected with Q. quinqueserialis rediae: G. circumstriatus, G. crista, and P. exacuous. Two of the 3 species of snails were infected in central (Manitoba) and northern locations (Northwest Territories) within Canada, which indicates limited life cycle variation across a large geographic range. This is the first report of snails naturally infected with Q. quinqueserialis in Canada. These novel host records demonstrate that this trematode species is not as host-specific for first intermediate host species as previously described.
PubMed ID
31730391 View in PubMed
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Building a DNA barcode library of Alaska's non-marine arthropods.

https://arctichealth.org/en/permalink/ahliterature281301
Source
Genome. 2017 Mar;60(3):248-259
Publication Type
Article
Date
Mar-2017
Author
Derek S Sikes
Matthew Bowser
John M Morton
Casey Bickford
Sarah Meierotto
Kyndall Hildebrandt
Source
Genome. 2017 Mar;60(3):248-259
Date
Mar-2017
Language
English
Publication Type
Article
Keywords
Alaska
Animals
Arthropods - genetics
Biodiversity
Canada
DNA - analysis
DNA Barcoding, Taxonomic - methods
Ecology
Gene Library
Genetic Variation
Geography
Insects - genetics
Models, Genetic
Phylogeny
Sequence Analysis, DNA
Species Specificity
Temperature
Abstract
Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection. We submitted tissues from 4776 specimens, of which 81% yielded DNA barcodes representing 1662 species and 1788 Barcode Index Numbers (BINs), of primarily terrestrial, large-bodied arthropods. This represents 84% of the species available for DNA barcoding in the UAM Insect Collection. There are now 4020 Alaskan arthropod species represented by DNA barcodes, after including all records in Barcode of Life Data Systems (BOLD) of species that occur in Alaska - i.e., 48.5% of the 8277 Alaskan, non-marine-arthropod, named species have associated DNA barcodes. An assessment of the identification power of the library in its current state yielded fewer species-level identifications than expected, but the results were not discouraging. We believe we are the first to deliberately begin development of a DNA barcode library of the entire arthropod fauna for a North American state or province. Although far from complete, this library will become increasingly valuable as more species are added and costs to obtain DNA sequences fall.
PubMed ID
28106469 View in PubMed
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Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak.

https://arctichealth.org/en/permalink/ahliterature285508
Source
PLoS One. 2017;12(4):e0175808
Publication Type
Article
Date
2017
Author
Julia A F Langer
Rahul Sharma
Susanne I Schmidt
Sebastian Bahrdt
Henriette G Horn
María Algueró-Muñiz
Bora Nam
Eric P Achterberg
Ulf Riebesell
Maarten Boersma
Marco Thines
Klaus Schwenk
Source
PLoS One. 2017;12(4):e0175808
Date
2017
Language
English
Publication Type
Article
Keywords
Alveolata - genetics - growth & development - metabolism
Carbon Dioxide - analysis
Chlorophyll - analysis
Cryptophyta - genetics - growth & development - metabolism
DNA - chemistry - isolation & purification - metabolism
DNA Barcoding, Taxonomic
Fungi - genetics - growth & development - metabolism
High-Throughput Nucleotide Sequencing
Hydrogen-Ion Concentration
Oceans and Seas
Plankton - genetics - growth & development - metabolism
RNA, Ribosomal, 18S - chemistry - isolation & purification - metabolism
Sequence Analysis, DNA
Sweden
Abstract
The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 µatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.
Notes
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PubMed ID
28445483 View in PubMed
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A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline.

https://arctichealth.org/en/permalink/ahliterature292509
Source
Mol Ecol Resour. 2017 Nov; 17(6):e46-e62
Publication Type
Comparative Study
Evaluation Studies
Journal Article
Date
Nov-2017
Author
Bastian Niemeyer
Laura S Epp
Kathleen R Stoof-Leichsenring
Luidmila A Pestryakova
Ulrike Herzschuh
Author Affiliation
Periglacial Research Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany.
Source
Mol Ecol Resour. 2017 Nov; 17(6):e46-e62
Date
Nov-2017
Language
English
Publication Type
Comparative Study
Evaluation Studies
Journal Article
Keywords
Biodiversity
DNA Barcoding, Taxonomic - methods
DNA, Plant - genetics - isolation & purification
Geologic sediments
Lakes
Metagenomics - methods
Plants - classification - genetics
Pollen - classification
Siberia
Abstract
Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single-tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition.
PubMed ID
28488798 View in PubMed
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Confirming Hypoderma tarandi (Diptera: Oestridae) human ophthalmomyiasis by larval DNA barcoding.

https://arctichealth.org/en/permalink/ahliterature259344
Source
Acta Parasitol. 2014 Jun;59(2):301-4
Publication Type
Article
Date
Jun-2014
Author
Bjørn Arne Rukke
Symira Cholidis
Arild Johnsen
Preben Ottesen
Source
Acta Parasitol. 2014 Jun;59(2):301-4
Date
Jun-2014
Language
English
Publication Type
Article
Keywords
Animals
Child
DNA Barcoding, Taxonomic
Diptera - classification - genetics - growth & development
Electron Transport Complex IV - genetics
Eye Diseases - diagnosis - parasitology
Humans
Male
Molecular Sequence Data
Myiasis - diagnosis - parasitology
Norway
Sequence Analysis, DNA
Abstract
DNA barcoding is a practical tool for species identification, when morphological classification of an organism is difficult. Herein we describe the utilisation of this technique in a case of ophthalmomyiasis interna. A 12-year-old boy was infested during a summer holiday in northern Norway, while visiting an area populated with reindeer. Following medical examination, a Diptera larva was surgically removed from the boy's eye and tentatively identified from its morphological traits as Hypoderma tarandi (L.) (Diptera: Oestridae). Ultimately, DNA barcoding confirmed this impression. The larval cytochrome c oxidase subunit 1 (COI) DNA sequence was matched with both profiles of five adult H. tarandi from the same region where the boy was infested, and other established profiles of H. tarandi in the Barcode of Life Data Systems (BOLD) identification engine.
PubMed ID
24827102 View in PubMed
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Cyanobacterial gardens: the liverwort Frullania asagrayana acts as a reservoir of lichen photobionts.

https://arctichealth.org/en/permalink/ahliterature285451
Source
Environ Microbiol Rep. 2016 Jun;8(3):352-7
Publication Type
Article
Date
Jun-2016
Author
Carolina Cornejo
Christoph Scheidegger
Source
Environ Microbiol Rep. 2016 Jun;8(3):352-7
Date
Jun-2016
Language
English
Publication Type
Article
Keywords
Bacterial Proteins - genetics
Biodiversity
Cluster analysis
Cyanobacteria - classification - genetics - isolation & purification
DNA Barcoding, Taxonomic
Frullania - microbiology
Lichens - microbiology
Newfoundland and Labrador
Phylogeny
RNA, Ribosomal, 16S - genetics
Abstract
Cyanobacteria are important mediators of unrelated lichen species, which form epiphytic communities that share the same cyanobiont. No study to date, however, has considered the role of cyanobacteria as mediator between lichens and bryophytes. In the present study, DNA barcoding (16S rDNA, rbcLX) was used to identify filamentous cyanobacteria living in close association with members of an epiphytic liverwort-lichen community on balsam fir in Newfoundland. This study is the first to confirm the presence of Rhizonema strains in boreal forests where they are associated with the liverwort Frullania asagrayana and several lichen species. The majority of cyanobacterial haplotypes can associate with the liverwort, however, some lichen species appear to be more selective for single or closely related haplotypes. Some Rhizonema strains were found exclusively in association with boreal lichens, while others seem to be globally distributed and involved in different lichen symbioses of unrelated fungal lineages and of varying ecological traits. Complex biological interactions in a cyanobacteria-mediated guild are proposed here, which explains composition and dynamics in bryophyte and lichen-dominated epiphytic communities.
PubMed ID
26929112 View in PubMed
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51 records – page 1 of 6.