130,616 research outputs found
Molecular markers from the mitochondrial genome of arbuscular mycorrhizal fungi (Glomeromycota) : evolutionary dynamics and application
No full textThe arbuscular mycorrhizal fungi (AMF) are obligate biotrophic symbionts with a key role in ecosystem functioning by their main contribution to plant mineral nutrient uptake. A fragment of the mitochondrial large subunit gene of ribosomal RNA (mtLSU) has been established as a molecular marker for population studies in Glomus intraradices, based on its homogeneity within isolate though genetic variation among isolates.
The respective region of the mtLSU was analyzed in five species of Glomus (G. mosseae, G. geosporum, G. caledonium, G. clarum, G. coronatum) from the same major clade (Glomus group A), Glomus sp. ISCB 34 from the related Glomus group B and two species of Scutellospora. The nucleotide polymorphism was very low among related morphospecies and differences were mainly caused by the exon/intron structure, limiting the resolution to a species level. Phylogenetic analyses suggested vertical inheritance from common ancestors for some introns as well as horizontal transfer for others.
Four mitochondrial intergenic spacers (rns/nad5, atp6/nad2, nad3/nad6, and nad6/cox3) were assessed as potential intraspecific markers. Combined, they offer a resolution even higher than the mtLSU, with the highest polymorphism found in the rns/nad5 spacer, most likely caused by processes of evolutionary dynamics involving homing endonucleases.
A mtLSU PCR approach was applied to study the population structure of G. intraradices at geothermal sites in Europe and North America, revealing considerable newly-discovered mtLSU sequence types as well as previously-reported types from arable fields. The molecular survey showed strong biogeographical structure in the occurrence of G. intraradices.
Overall, this PhD thesis project showed that the genetic characteristics of the AMF mitochondrion are promising for development of molecular genetic markers and evolutionary sequence analyses, and will therefore be relevant for further studies of genetics, ecology and evolution of AMF
Molecular ecological analyses of specific interactions between symbionts in the arbuscular mycorrhizal symbiosis
No full textArbuscular mycorrhiza is an ancient symbiosis between the majority of land plants and fungi
from the phylum Glomeromycota. Arbuscular mycorrhizal fungi (AMF) colonize plant roots
and contribute to the mineral nutrient uptake of the hosts in exchange for carbohydrates. AMF
species diversity and identity was reported to have a decisive influence on the composition
and productivity of natural plant communities. Only around 200 glomeromycotan species
described so far were thought to colonize the majority of higher plant species and thus, their
host specificity was thought to be very low.
In this thesis, molecular methods were used to investigate ecological aspects of root
colonizing AMF. The community composition of these fungi was analyzed in two plant
species-rich grasslands facing different environmental conditions and harboring different
plant communities. One site consisting of two meadows located close to each other was
situated in the upper montane zone of the Swiss Alps. The other was located in the lowland in
France on the edge of the Jura mountains. The roots were analyzed using AMF-specific
nested PCR, RFLP screening and sequencing of rDNA small subunit and internal transcribed
spacer regions. AMF sequences were analyzed phylogenetically and used to define
monophyletic sequence types.
Overall, 27 different AMF sequence types were detected in the root samples from both
field sites. The overlap between the AMF communities in the alpine and lowland site was
relatively small - they shared just six sequence types. These results indicate strong
geographical differences in the AMF community composition, reflecting different
environmental conditions and plant species communities in each site.
The question was adressed, whether different host plant species co-occurring in the same
area host distinct or similar AMF communities. Gentiana verna, G. acaulis and Trifolium spp.
growing in two alpine species-rich meadows harbored significantly different AMF
communities, whereas the differences between the two sites were negligible. These results
indicate that within a relatively small area with similar soil and climatic conditions, the host
plant species can have a major influence on the AMF communities within the roots. In these
alpine sites, there was also a focus on green plants from the family Gentianaceae. In contrast
to their mycoheterotrophic relatives, the green gentians did not show a high level of
specificity towards AMF. The plants sampled harbored AMF communities comprising
multiple phylotypes from different fungal lineages.
In the lowland site – a calcareous grassland – different culturing methods and their
influence on the AMF community composition in the roots were adressed. Four plant species
were sampled i) directly in the field, ii) in a bait plant bioassay conducted directly in that
grassland and iii) in a greenhouse trap experiment using soil and a transplanted whole plant
from that grassland as inoculum. The community composition in their roots was strongly
influenced by the experimental approach, with additional influence of cultivation duration,
substrate and host plant species in some experiments.
Some fungal phylotypes, e.g. Glomus mosseae and several members of Glomus group B,
appeared predominantly in the greenhouse experiment or in bait plants. These phylotypes can
be considered r strategists, rapidly colonizing uncolonized ruderal habitats in early
successional stages of the fungal community. Other phylotypes as Glomus badium and
GLOM-A16 were detected almost exclusively in roots sampled from plants naturally growing
in the grassland or from bait plants exposed in the field, indicating that they preferentially
occur in late successional stages of fungal communities and thus represent the K strategy. The
only phylotype found with high frequency in all three experimental approaches as well as in
the alpine site was GLOM A-1 (Glomus intraradices), which is assumed to be a generalist.
These ecological strategies of different AMF species or phylotypes should be considered
in AMF experimental work. In greenhouse trap experiments it is difficult to establish a rootcolonizing
AMF community reflecting the diversity of these fungi in the field roots, because
fungal succession in such artificial systems may bias the results. However, the field bait plant
approach might be a convenient way to study the influence of different environmental factors
on AMF community composition directly under the field conditions.
Finally, the co-existence of the Glomeromycota in the root samples with fungi from the
basidiomycotan order Sebacinales was addressed. These fungi are widely distributed and
known to form various types of presumable mycorrhizal associations of different morphology
(ecto-, ectendo-, orchid, ericoid, jungermannoid) with a broad range of host plant species.
However, their presence in plants forming arbuscular mycorrhiza has not been reported yet.
Therefore, the root samples originating from the two species-rich grasslands mentioned above
were analyzed with Sebacinales-specific primers for the D1/D2 region of the nuclear 28S
rDNA subunit. Fungi from the order Sebacinales were present in the majority of the root
samples from both sites, where they co-existed with the Glomeromycota. In agreement with
studies targeting the Sebacinales in ericoid plants, the phylogenetic analysis of sebacinoid
sequences from our samples did not reveal any patterns according to their host plant species
or geographical origin
Diversity of cultured isolates and field populations of the arbuscular mycorrhizal fungus "Glomus intraradices" : development and application of molecular detection methods for mitochondrial haplotypes
No full textToday’s plant communities have evolved together with arbuscular mycorrhizal fungi (AMF, Glomeromycota) for millions of years. In “arbuscular mycorrhiza”, a mutualistic symbiosis, plants provide carbohydrates to the fungi, which in turn make mineral nutrients like phosphate or nitrogen available to the plants. AMF species diversity is generally higher in natural sites than in agroecosystems, where it can be strongly reduced. The detection of AMF is either based on morphotyping of soil-borne spores or on molecular markers, which can be directly applied using colonized roots of the host plant.
Until recently, studies of AMF diversity on the population level were impossible, as no suitable marker genes were available. The first population studies on AMF had to rely on DNA from spores or root organ cultures (ROCs) and the molecular markers used could not be applied for the detection of AMF genotypes directly in colonized plant roots from the field. Previous work from our laboratory had shown that mitochondrial ribosomal RNA large subunit gene (mtLSU) sequences are homogeneous within several isolates of Glomus species and that the mitochondrial gene region is a promising marker for distinguishing strains of G. intraradices. The phylotype GLOM A-1 of this morphospecies which was defined in previous studies of our laboratory based on nuclear-encoded rDNA internal transcribed spacers (ITS) sequences seems to occur ubiquitously, showing a high ecological versatility. It is frequently used as model organism and its genome is being sequenced.
The aim of this thesis was to develop and apply detection methods based on the mtLSU in order to investigate the diversity of G. intraradices isolates and field populations. The main question was whether this marker is suitable to resolve the genetic structure of this morphospecies which might allow shedding light on the ecological role of strains within the species.
In the first part of this thesis, the diversity of the mtLSU was investigated in a set of 16 G. intraradices isolates originating from five continents, either obtained as soil inoculum or as ROC. Among these isolates, 12 different mtLSU haplotypes could be distinguished, whereas homogeneity of the marker within the isolates was confirmed. Several mtLSU haplotypes were already distinguishable by size differences of the PCR products, mainly based on the presence or absence of length-variable introns. The reliability of the marker is dependent on evolutionary intron stability, which was confirmed for some introns by comparisons of multiple culture lineages of the same isolate obtained from different culture collections. In phylogenetic analyses of mtLSU exon sequences from isolates and root-colonizing G. intraradices, several clades could be distinguished. Comparison with ITS sequences from the isolates showed a higher resolution of mtLSU exon sequences which was increased by intron sequences.
In order to increase the specificity for G. intraradices and to optimize amplification of the mtLSU fragment from colonized plant roots, a new nested PCR approach was developed and tested using field root samples from a semi-natural grassland and a mine spoil in Hungary. A RFLP approach was developed to reduce time-consuming and expensive cloning and sequencing procedures.
In the second part of this thesis, the population structure of an AMF in roots from the environment was analyzed for the first time. Two agricultural field experiments in Switzerland, including different tillage treatments, and two semi-natural grasslands in Switzerland and France were chosen for the investigation of the genetic structure of G. intraradices phylotype GLOM A-1 using the PCR-RFLP approach. Each field site was dominated by one or two frequently found RFLP patterns of G. intraradices GLOM A-1, which were defined as Intra types. The composition of Intra types differed strongly between the agricultural sites and the semi-natural grasslands, but also between the two agricultural sites. In contrast to the situation often found in AMF species community studies, RFLP type richness was higher in the agricultural sites compared to the grasslands. Four Intra types, shared by different sites, were further resolved by sequence analyses, but only the two grasslands were found to share mtLSU sequence haplotypes. In phylogenetic analyses of completely sequenced examples of each Intra type, almost all haplotypes from the grassland sites fell within a separate “grassland clade”.
If a single mtLSU haplotype could be specifically detected in a pool of others, such a molecular tool could be used for tracing single strains inoculated in a field site. Nested PCR primers were developed specifically for one single mtLSU haplotype, which dominated one of the agricultural sites and was known from previous studies analyzing ROCs. By applying this approach to all samples from the four study sites, it could be shown that the respective haplotype was only detected in samples previously tested positive for this type using the general approach. In other words, both methods confirmed each other.
Two further specific nested PCR approaches were developed for two mtLSU haplotypes representing the G. intraradices isolate BEG140. These approaches were designed to be applied for tracing this isolate inoculated in a field experiment performed in a mine spoil bank of the Czech Republic in the context of a reclamation project.
Besides the considerable genetic structure of this fungus among the isolates studied and in the roots of the field sites, evidence of specialized mtLSU haplotypes was reported, which might represent ecotypes or even different (“cryptic”) species. It could be shown that world-wide mtLSU haplotype diversity of G. intraradices is considerably higher than previously assumed. More investigations of different ecosystems are required for the determination of adapted ecotypes.
The approaches developed here will be furthermore useful for instance in inoculation experiments and functional tests, e.g. in greenhouse experiments. By presenting first insights into the genetic structure of the most widespread species of arbuscular mycorrhizal fungi, the findings presented here will have major implications on our views of processes of adaptation and specialization in these plant ⁄ fungus associations
MeSH term explosion and author rank improve expert recommendations
No full textInformation overload is an often-cited phenomenon that reduces the productivity, efficiency and efficacy of scientists. One challenge for scientists is to find appropriate collaborators in their research. The literature describes various solutions to the problem of expertise location, but most current approaches do not appear to be very suitable for expert recommendations in biomedical research. In this study, we present the development and initial evaluation of a vector space model-based algorithm to calculate researcher similarity using four inputs: 1) MeSH terms of publications; 2) MeSH terms and author rank; 3) exploded MeSH terms; and 4) exploded MeSH terms and author rank. We developed and evaluated the algorithm using a data set of 17,525 authors and their 22,542 papers. On average, our algorithms correctly predicted 2.5 of the top 5/10 coauthors of individual scientists. Exploded MeSH and author rank outperformed all other algorithms in accuracy, followed closely by MeSH and author rank. Our results show that the accuracy of MeSH term-based matching can be enhanced with other metadata such as author rank
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
"Closing the R&D Gap, Evaluating the Sources of R&D Spending"
No full textBoth spending and tax policies have been implemented in the United States with the goal of stimulating private sector research and development (R&D). Karier questions whether current R&D policy, especially the research and experimentation tax credit, can contribute to closing the gap between nondefense expenditures on R&D in the United States and such expenditures in other countries, such as Japan and Germany. He also explores possible changes to our current R&D policy to make it more effective.
Development of new molecular markers for phylogeny and molecular identification of arbuscular mycorrhizal fungi (glomeromycota)
No full textThe RPB1 gene was analyzed as a possible new nuclear-encoded molecular marker for the Glomeromycota. New Glomus group A-specific primers were designed and successfully tested on several members of this group. No evidence for genetic variability was found within the isolates. Based on the new RPB1 sequences, phylogenetic analyses were performed. The phylum-level phylogeny of the fungi was very well resolved by protein sequence analyses. The Glomeromycota were recovered as a monophyletic group, with the Mortierellales (Zygomycota) as closest relatives. A symbiomycotan clade (Asco-, Basidio and Glomeromycota) was not supported in the RPB1 phylogeny whereas the "Dicaryomycota" (Asco- and Basidiomycota) were supported in the trees. The morphospecies-level RPB1 phylogeny of Glomus group A performed best using nucleotide sequences. Interestingly, Geosiphon pyriformis was determined to be the most deeply-diverging lineage of the Glomeromycota. However, RPB1 sequences of representatives of the remaining families are needed for for a comprehensive phylogeny of glomeromycotan fungi. All members of the Glomeromycota contained an intron at the same location in their RPB1 gene. This sequence region seems to be ideal for molecular species identification using restriction analysis in community studies of the AMF in the future
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Scholarly Communication and Publishing Lunch and Learn Talk #11: The ULS Open Access Author Fee Fund
No full textAt the May 2014 talk, you will learn about the ULS Open Access Author Fee Fund--what it is, why we do it, how it works, and how the program is going so far
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