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Accounting for environmental variation in co-occurrence modelling reveals the importance of positive interactions in root-associated fungal communities.

https://arctichealth.org/en/permalink/ahliterature305463
Source
Mol Ecol. 2020 07; 29(14):2736-2746
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
07-2020
Author
Nerea Abrego
Tomas Roslin
Tea Huotari
Ayco J M Tack
Björn D Lindahl
Gleb Tikhonov
Panu Somervuo
Niels Martin Schmidt
Otso Ovaskainen
Author Affiliation
Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
Source
Mol Ecol. 2020 07; 29(14):2736-2746
Date
07-2020
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Abstract
Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. We generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more probably reflect interactive associations. Our results indicate that not only negative but also positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.
PubMed ID
32562300 View in PubMed
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Comparative genomic hybridization analysis shows different epidemiology of chromosomal and plasmid-borne cpe-carrying Clostridium perfringens type A.

https://arctichealth.org/en/permalink/ahliterature119535
Source
PLoS One. 2012;7(10):e46162
Publication Type
Article
Date
2012
Author
Päivi Lahti
Miia Lindström
Panu Somervuo
Annamari Heikinheimo
Hannu Korkeala
Author Affiliation
Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland. paivi.lahti@helsinki.fi
Source
PLoS One. 2012;7(10):e46162
Date
2012
Language
English
Publication Type
Article
Keywords
Animals
Cellobiose - genetics - metabolism
Chromosomes, Bacterial
Clostridium Infections - epidemiology - microbiology - transmission
Clostridium perfringens - classification - genetics - metabolism
Comparative Genomic Hybridization
Enterotoxins - genetics - metabolism
Ethanolamine - metabolism
Finland - epidemiology
Foodborne Diseases - epidemiology - microbiology
Genes, Bacterial
Genotype
Humans
Inositol - genetics - metabolism
Multigene Family
Phylogeny
Plasmids
Serotyping
Abstract
Clostridium perfringens, one of the most common causes of food poisonings, can carry the enterotoxin gene, cpe, in its chromosome or on a plasmid. C. perfringens food poisonings are more frequently caused by the chromosomal cpe-carrying strains, while the plasmid-borne cpe-positive genotypes are more commonly found in the human feces and environmental samples. Different tolerance to food processing conditions by the plasmid-borne and chromosomal cpe-carrying strains has been reported, but the reservoirs and contamination routes of enterotoxin-producing C. perfringens remain unknown. A comparative genomic hybridization (CGH) analysis with a DNA microarray based on three C. perfringens type A genomes was conducted to shed light on the epidemiology of C. perfringens food poisonings caused by plasmid-borne and chromosomal cpe-carrying strains by comparing chromosomal and plasmid-borne cpe-positive and cpe-negative C. perfringens isolates from human, animal, environmental, and food samples. The chromosomal and plasmid-borne cpe-positive C. perfringens genotypes formed two distinct clusters. Variable genes were involved with myo-inositol, ethanolamine and cellobiose metabolism, suggesting a new epidemiological model for C. perfringens food poisonings. The CGH results were complemented with growth studies, which demonstrated different myo-inositol, ethanolamine, and cellobiose metabolism between the chromosomal and plasmid-borne cpe-carrying strains. These findings support a ubiquitous occurrence of the plasmid-borne cpe-positive strains and their adaptation to the mammalian intestine, whereas the chromosomal cpe-positive strains appear to have a narrow niche in environments containing degrading plant material. Thus the epidemiology of the food poisonings caused by two populations appears different, the plasmid-borne cpe-positive strains probably contaminating foods via humans and the chromosomal strains being connected to plant material.
Notes
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PubMed ID
23094024 View in PubMed
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Flight-induced changes in gene expression in the Glanville fritillary butterfly.

https://arctichealth.org/en/permalink/ahliterature269219
Source
Mol Ecol. 2015 Oct;24(19):4886-900
Publication Type
Article
Date
Oct-2015
Author
Jouni Kvist
Anniina L K Mattila
Panu Somervuo
Virpi Ahola
Patrik Koskinen
Lars Paulin
Leena Salmela
Toby Fountain
Pasi Rastas
Annukka Ruokolainen
Minna Taipale
Liisa Holm
Petri Auvinen
Rainer Lehtonen
Mikko J Frilander
Ilkka Hanski
Source
Mol Ecol. 2015 Oct;24(19):4886-900
Date
Oct-2015
Language
English
Publication Type
Article
Keywords
Animals
Butterflies - genetics - physiology
Energy Metabolism - genetics
Female
Finland
Flight, Animal
Gene Expression
Male
Molecular Sequence Data
Polymorphism, Single Nucleotide
Sequence Analysis, RNA
Sex Characteristics
Transcriptome
Abstract
Insect flight is one of the most energetically demanding activities in the animal kingdom, yet for many insects flight is necessary for reproduction and foraging. Moreover, dispersal by flight is essential for the viability of species living in fragmented landscapes. Here, working on the Glanville fritillary butterfly (Melitaea cinxia), we use transcriptome sequencing to investigate gene expression changes caused by 15 min of flight in two contrasting populations and the two sexes. Male butterflies and individuals from a large metapopulation had significantly higher peak flight metabolic rate (FMR) than female butterflies and those from a small inbred population. In the pooled data, FMR was significantly positively correlated with genome-wide heterozygosity, a surrogate of individual inbreeding. The flight experiment changed the expression level of 1513 genes, including genes related to major energy metabolism pathways, ribosome biogenesis and RNA processing, and stress and immune responses. Males and butterflies from the population with high FMR had higher basal expression of genes related to energy metabolism, whereas females and butterflies from the small population with low FMR had higher expression of genes related to ribosome/RNA processing and immune response. Following the flight treatment, genes related to energy metabolism were generally down-regulated, while genes related to ribosome/RNA processing and immune response were up-regulated. These results suggest that common molecular mechanisms respond to flight and can influence differences in flight metabolic capacity between populations and sexes.
PubMed ID
26331775 View in PubMed
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Give me a sample of air and I will tell which species are found from your region: Molecular identification of fungi from airborne spore samples.

https://arctichealth.org/en/permalink/ahliterature295286
Source
Mol Ecol Resour. 2018 May; 18(3):511-524
Publication Type
Journal Article
Date
May-2018
Author
Nerea Abrego
Veera Norros
Panu Halme
Panu Somervuo
Heini Ali-Kovero
Otso Ovaskainen
Author Affiliation
Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
Source
Mol Ecol Resour. 2018 May; 18(3):511-524
Date
May-2018
Language
English
Publication Type
Journal Article
Keywords
Air Microbiology
Biodiversity
DNA Barcoding, Taxonomic
Finland
Fungi - classification - genetics
Seasons
Species Specificity
Spores, Fungal - genetics - isolation & purification
Abstract
Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning and are important for human health, food production and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise. The method consists of using a cyclone sampler to acquire fungal spores directly from the air to an Eppendorf tube, and applying DNA barcoding with probabilistic species identification to generate a list of species from the sample. We tested the feasibility of the method by acquiring replicate air samples from different geographical regions within Finland. Our results show that air sampling is adequate for regional-level surveys, with samples collected >100 km apart varying but samples collected
PubMed ID
29330936 View in PubMed
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Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient.

https://arctichealth.org/en/permalink/ahliterature304907
Source
Ecol Evol. 2020 Aug; 10(16):8989-9002
Publication Type
Journal Article
Date
Aug-2020
Author
Nerea Abrego
Tea Huotari
Ayco J M Tack
Björn D Lindahl
Gleb Tikhonov
Panu Somervuo
Niels Martin Schmidt
Otso Ovaskainen
Tomas Roslin
Author Affiliation
Department of Agricultural Sciences University of Helsinki Helsinki Finland.
Source
Ecol Evol. 2020 Aug; 10(16):8989-9002
Date
Aug-2020
Language
English
Publication Type
Journal Article
Abstract
How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.
PubMed ID
32884673 View in PubMed
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Scaling up the effects of inbreeding depression from individuals to metapopulations.

https://arctichealth.org/en/permalink/ahliterature310558
Source
J Anim Ecol. 2019 08; 88(8):1202-1214
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
08-2019
Author
Etsuko Nonaka
Jukka Sirén
Panu Somervuo
Lasse Ruokolainen
Otso Ovaskainen
Ilkka Hanski
Author Affiliation
Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland.
Source
J Anim Ecol. 2019 08; 88(8):1202-1214
Date
08-2019
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Bayes Theorem
Butterflies
Ecosystem
Finland
Inbreeding Depression
Population Dynamics
Abstract
Inbreeding is common in nature, and many laboratory studies have documented that inbreeding depression can reduce the fitness of individuals. Demonstrating the consequences of inbreeding depression on the growth and persistence of populations is more challenging because populations are often regulated by density- or frequency-dependent selection and influenced by demographic and environmental stochasticity. A few empirical studies have shown that inbreeding depression can increase extinction risk of local populations. The importance of inbreeding depression at the metapopulation level has been conjectured based on population-level studies but has not been evaluated. We quantified the impact of inbreeding depression affecting the fitness of individuals on metapopulation persistence in heterogeneous habitat networks of different sizes and habitat configuration in a context of natural butterfly metapopulations. We developed a spatial individual-based simulation model of metapopulations with explicit genetics. We used Approximate Bayesian Computation to fit the model to extensive demographic, genetic and life-history data available for the well-studied Glanville fritillary butterfly (Melitaea cinxia) metapopulations in the Åland islands in SW Finland. We compared 18 semi-independent habitat networks differing in size and fragmentation. The results show that inbreeding is more frequent in small habitat networks, and consequently, inbreeding depression elevates extinction risks in small metapopulations. Metapopulation persistence and neutral genetic diversity maintained in the metapopulations increase with the total habitat amount in and mean patch size of habitat networks. Dispersal and mating behaviour interact with landscape structure to determine how likely it is to encounter kin while looking for mates. Inbreeding depression can decrease the viability of small metapopulations even when they are strongly influenced by stochastic extinction-colonization dynamics and density-dependent selection. The findings from this study support that genetic factors, in addition to demographic factors, can contribute to extinctions of small local populations and also of metapopulations.
PubMed ID
31077598 View in PubMed
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6 records – page 1 of 1.