| 1. |
- Bugge Harder, Christoffer, et al.
(author)
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Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks' rapid sand filters
- 2019
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In: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 95:11
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Journal article (peer-reviewed)abstract
- As groundwater-fed waterworks clean their raw inlet water with sand filters, a variety of pro-and eukaryotic microbial communities develop on these filters. While several studies have targeted the prokaryotic sand filter communities, little is known about the eukaryotic communities, despite the obvious need for knowledge of microorganisms that get in contact with human drinking water. With a new general eukaryotic primer set (18S, V1-V3 region), we performed FLX-454 sequencing of material from 21 waterworks' sand filters varying in age (3-40 years) and geographical location on a 250 km east-west axis in Denmark, and put the data in context of their previously published prokaryotic communities. We find that filters vary highly in trophic complexity depending on age, from simple systems with bacteria and protozoa (3-6 years) to complex, mature systems with nematodes, rotifers and turbellarians as apex predators (40 years). Unlike the bacterial communities, the eukaryotic communities display a clear distance-decay relationship that predominates over environmental variations, indicating that the underlying aquifers feeding the filters harbor distinct eukaryotic communities with limited dispersal in between. Our findings have implications for waterworks' filter management, and offer a window down to the largely unexplored eukaryotic microbiology of groundwater aquifers.
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| 2. |
- Eshghi Sahraei, Shadi, et al.
(author)
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Bringing uncultured arbuscular mycorrhizal fungi to the genomic era – a case study with field spores of Funneliformis geosporum
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Other publication (other academic/artistic)abstract
- Arbuscular mycorrhizal (AM) fungi are ubiquitous microorganisms, forming symbiosis with most terrestrial plants. The fungal partner improves host performance by providing nutrients like P and N and increase tolerance of host plants against biotic and abiotic stresses. Most studies on AM fungi have focused on species and strains maintained on a single plant host under controlled conditions for several years. There is some evidence suggesting this cultivation system can render phenotypic and genotypic variations in AM fungi. In this study, we isolated spores of AM fungi from a field, the spores were identified as Funneliformis geosporum based on morphology and phylogenetic analyses. We assembled the genomes of two spores using individually amplified and sequenced nuclei. The genomes were compared with other members of Glomeraceae including two strains of F. mosseae, which have been maintained in culture for more than 20 years. No significant differences were observed among them in terms of gene content, while the SNP density was higher in the strains of F. geosporum when compared to the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble the genomes from AM fungal spores sampled in the field, which opens up the possibility to study genomic variation in natural populations of this important plant symbionts.
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| 3. |
- Lindahl, Björn, et al.
(author)
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Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide
- 2013
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 199:1, s. 288-299
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Research review (peer-reviewed)abstract
- * Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. * Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. * Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. * Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.
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| 4. |
- Nielsen, Knud Brian, et al.
(author)
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Colonization of new land by arbuscular mycorrhizal fungi
- 2016
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In: Fungal Ecology. - : Elsevier BV. - 1754-5048. ; 20, s. 22-29
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Journal article (peer-reviewed)abstract
- The study describes the primary assembly of arbuscular mycorrhizal communities on a newly constructed island Peberholm between Denmark and Sweden. The AM fungal community on Peberholm was compared with the neighboring natural island Saltholm. The structure of arbuscular mycorrhizal communities was assessed through 454 pyrosequencing. Internal community structure was investigated through fitting the rank-abundance of Operational Taxonomic Units to different models. Heterogeneity of communities within islands was assessed by analysis of group dispersion. The mean OTU richness per sample was significantly lower on the artificial island than on the neighboring natural island, indicating that richness of the colonizing AM fungal community is restricted by limited dispersal. The AM fungal communities colonizing the new island appeared to be a non-random subset of communities on the natural and much older neighboring island, which points to high colonization potential of certain - probably early successional - mycorrhizal fungi, likely assisted by migratory birds.
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| 5. |
- Schnoor, Tim Krone, et al.
(author)
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Mechanical soil disturbance as a determinant of arbuscular mycorrhizal fungal communities in semi-natural grassland.
- 2011
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In: Mycorrhiza. - : Springer Science and Business Media LLC. - 1432-1890 .- 0940-6360. ; 21:3, s. 211-220
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Journal article (peer-reviewed)abstract
- While the effect of disturbance on overall abundance and community composition of arbuscular mycorrhizal (AM) fungi has been researched in agricultural fields, less is known about the impact in semi-natural grasslands. We sampled two AM plant species, Festuca brevipila and Plantago lanceolata, from an ongoing grassland restoration experiment that contained replicated plowed and control plots. The AM fungal community in roots was determined using nested PCR and LSU rDNA primers. We identified 38 phylotypes within the Glomeromycota, of which 29 belonged to Glomus A, six to Glomus B, and three to Diversisporaceae. Only three phylotypes were closely related to known morphospecies. Soil disturbance significantly reduced phylotype richness and changed the AM fungal community composition. Most phylotypes, even closely related ones, showed little or no overlap in their distribution and occurred in either the control or disturbed plots. We found no evidence of host preference in this system, except for one phylotype that preferentially seemed to colonize Festuca. Our results show that disturbance imposed a stronger structuring force for AM fungal communities than did host plants in this semi-natural grassland.
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| 6. |
- Wang, Yutao, et al.
(author)
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Community dynamics of arbuscular mycorrhizal fungi in high-input and intensively irrigated rice cultivation systems.
- 2015
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In: Applied and Environmental Microbiology. - 0099-2240. ; 81:8, s. 2958-2965
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Journal article (peer-reviewed)abstract
- Application of mycorrhizal inoculum could be one way to increase the yield of rice plants, and reduce the application of fertilizer. We therefore studied arbuscular mycorrhizal fungi (AMF) in the roots of wetland rice (Oryza sativa L.) collected at the seedling, tillering, heading and ripening stages in four paddy wetlands that had been under a high-input and intensively irrigated rice cultivation system for more than 20 years. It was found that AMF colonization was mainly established in the heading and ripening stages. The AMF community structure was characterized in rhizosphere soil and root from two of the studied paddy wetlands. A fragment covering partial SSU, the whole ITS and partial LSU rRNA operon region of AMF was amplified, cloned and sequenced from roots and soils. A total of 639 AMF sequences were obtained, and these were finally assigned to 16 phylotypes based on a phylogenetic analysis, including 12 phylotypes from Glomeraceae, one phylotype from Claroideoglomeraceae, two phylotypes from Paraglomeraceae and one unidentified phylotype. The AMF phylotype compositions in the soils were similar between the two surveyed sites, but there was a clear discrepancy between the communities obtained from root and soil. The relatively high number of AMF phylotypes at the surveyed sites suggests that the conditions are suitable for some species of AMF and that they may have an important function in conventional rice cultivation systems. The species richness of root-colonizing AMF increased with growth of rice, and future studies should consider the developmental stages of this crop in the exploration of AMF function in paddy wetlands.
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