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Article ; Online: Evaluation of non-destructive DNA extraction protocols for insect metabarcoding

Daniel Marquina / Tomas Roslin / Piotr Łukasik / Fredrik Ronquist

Metabarcoding and Metagenomics, Vol 6, Iss , Pp 187-

gentler and shorter is better

2022 Volume 201

Abstract: DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specimens. Mild ... ...

Abstract	DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specimens. Mild digestion of the tissue by incubation in a lysis buffer has been proposed as an alternative, and, although some mild lysis protocols have already been presented, they have so far not been evaluated against each other. Here, we analyse how two mild lysis buffers (one more aggressive, one gentler in terms of tissue degradation), two different incubation times, and two DNA purification methods (a manual precipitation and an automated protocol) affect the accuracy of retrieving the true composition of mock communities using two mitochondrial markers (COI and 16S). We found that protocol-specific variation in concentration and purity of the DNA extracts produced had little effect on the recovery of species. However, the two lysis treatments differed in quantification of species abundances. Digestion in the gentler buffer and for a shorter time yielded better representation of original sample composition. Digestion in a more aggressive buffer or longer incubation time yielded lower alpha diversity values and increased differences between metabarcoding results and the true species-abundance distribution. We conclude that the details of non-destructive protocols can have a significant effect on metabarcoding performance. A short and mild lysis treatment appears the best choice for recovering the true composition of the sample. This not only improves accuracy, but also comes with a faster processing time than the other treatments.
Keywords	Ecology ; QH540-549.5
Subject code	621
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Pensoft Publishers
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Herbivory in a changing climate—Effects of plant genotype and experimentally induced variation in plant phenology on two summer‐active lepidopteran herbivores and one fungal pathogen

Adam Ekholm / Maria Faticov / Ayco J. M. Tack / Tomas Roslin

Ecology and Evolution, Vol 12, Iss 1, Pp n/a-n/a (2022)

2022

Abstract: Abstract With climate change, spring warming tends to advance plant leaf‐out. While the timing of leaf‐out has been shown to affect the quality of leaves for herbivores in spring, it is unclear whether such effects extend to herbivores active in summer. ... ...

Abstract	Abstract With climate change, spring warming tends to advance plant leaf‐out. While the timing of leaf‐out has been shown to affect the quality of leaves for herbivores in spring, it is unclear whether such effects extend to herbivores active in summer. In this study, we first examined how spring and autumn phenology of seven Quercus robur genotypes responded to elevated temperatures in spring. We then tested whether the performance of two summer‐active insect herbivores (Orthosia gothica and Polia nebulosa) and infection by a pathogen (Erysiphe alphitoides) were influenced by plant phenology, traits associated with genotype or the interaction between these two. Warm spring temperatures advanced both bud development and leaf senescence in Q. robur. Plants of different genotype differed in terms of both spring and autumn phenology. Plant phenology did not influence the performance of two insect herbivores and a pathogen, while traits associated with oak genotype had an effect on herbivore performance. Weight gain for O. gothica and ingestion for P. nebulosa differed by a factor of 4.38 and 2.23 among genotypes, respectively. Herbivore species active in summer were influenced by traits associated with plant genotype but not by phenology. This suggest that plant attackers active in summer may prove tolerant to shifts in host plant phenology—a pattern contrasting with previously documented effects on plant attackers active in spring and autumn.
Keywords	Climate change ; Community ecology ; Mismatch ; Phenology ; Trophic interactions ; Ecology ; QH540-549.5
Subject code	580 ; 550
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Different spatial structure of plant‐associated fungal communities above‐ and belowground

Maria Faticov / Ahmed Abdelfattah / Peter Hambäck / Tomas Roslin / Ayco J. M. Tack

Ecology and Evolution, Vol 13, Iss 5, Pp n/a-n/a (2023)

2023

Abstract: Abstract The distribution and community assembly of above‐ and belowground microbial communities associated with individual plants remain poorly understood, despite its consequences for plant–microbe interactions and plant health. Depending on how ... ...

Abstract	Abstract The distribution and community assembly of above‐ and belowground microbial communities associated with individual plants remain poorly understood, despite its consequences for plant–microbe interactions and plant health. Depending on how microbial communities are structured, we can expect different effects of the microbial community on the health of individual plants and on ecosystem processes. Importantly, the relative role of different factors will likely differ with the scale examined. Here, we address the driving factors at a landscape level, where each individual unit (oak trees) is accessible to a joint species pool. This allowed to quantify the relative effect of environmental factors and dispersal on the distribution of two types of fungal communities: those associated with the leaves and those associated with the soil of Quercus robur trees in a landscape in southwestern Finland. Within each community type, we compared the role of microclimatic, phenological, and spatial variables, and across community types, we examined the degree of association between the respective communities. Most of the variation in the foliar fungal community was found within trees, whereas soil fungal community composition showed positive spatial autocorrelation up to 50 m. Microclimate, tree phenology, and tree spatial connectivity explained little variation in the foliar and soil fungal communities. Foliar and soil fungal communities differed strongly in community structure, with no significant concordance detected between them. We provide evidence that foliar and soil fungal communities assemble independent of each other and are structured by different ecological processes.
Keywords	community ecology ; dispersal ; metacommunity ; microclimate ; phenology ; phyllosphere microorganisms ; Ecology ; QH540-549.5
Subject code	580
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: DNA traces the origin of honey by identifying plants, bacteria and fungi

Helena Wirta / Nerea Abrego / Kirsten Miller / Tomas Roslin / Eero Vesterinen

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 14

Abstract: Abstract The regional origin of a food product commonly affects its value. To this, DNA-based identification of tissue remains could offer fine resolution. For honey, this would allow the usage of not only pollen but all plant tissue, and also that of ... ...

Abstract	Abstract The regional origin of a food product commonly affects its value. To this, DNA-based identification of tissue remains could offer fine resolution. For honey, this would allow the usage of not only pollen but all plant tissue, and also that of microbes in the product, for discerning the origin. Here we examined how plant, bacterial and fungal taxa identified by DNA metabarcoding and metagenomics differentiate between honey samples from three neighbouring countries. To establish how the taxonomic contents of honey reflect the country of origin, we used joint species distribution modelling. At the lowest taxonomic level by metabarcoding, with operational taxonomic units, the country of origin explained the majority of variation in the data (70–79%), with plant and fungal gene regions providing the clearest distinction between countries. At the taxonomic level of genera, plants provided the most separation between countries with both metabarcoding and metagenomics. The DNA-based methods distinguish the countries more than the morphological pollen identification and the removal of pollen has only a minor effect on taxonomic recovery by DNA. As we find good resolution among honeys from regions with similar biota, DNA-based methods hold great promise for resolving honey origins among more different regions.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Site-specific length-biomass relationships of arctic arthropod families are critical for accurate ecological inferences

Tom S. L. Versluijs / Mikhail K. Zhemchuzhnikov / Dmitry Kutcherov / Tomas Roslin / Niels Martin Schmidt / Jan A. van Gils / Jeroen Reneerkens

PeerJ, Vol 11, p e

2023 Volume 15943

Abstract: Arthropods play a crucial role in terrestrial ecosystems, for instance in mediating energy fluxes and in forming the food base for many organisms. To better understand their functional role in such ecosystem processes, monitoring of trends in arthropod ... ...

Abstract	Arthropods play a crucial role in terrestrial ecosystems, for instance in mediating energy fluxes and in forming the food base for many organisms. To better understand their functional role in such ecosystem processes, monitoring of trends in arthropod biomass is essential. Obtaining direct measurements of the body mass of individual specimens is laborious. Therefore, these data are often indirectly acquired by utilizing allometric length-biomass relationships based on a correlative parameter, such as body length. Previous studies have often used such relationships with a low taxonomic resolution and/or small sample size and/or adopted regressions calibrated in different biomes. Despite the scientific interest in the ecology of arctic arthropods, no site-specific family-level length-biomass relationships have hitherto been published. Here we present 27 family-specific length-biomass relationships from two sites in the High Arctic: Zackenberg in northeast Greenland and Knipovich in north Taimyr, Russia. We show that length-biomass regressions from different sites within the same biome did not affect estimates of phenology but did result in substantially different estimates of arthropod biomass. Estimates of daily biomass at Zackenberg were on average 24% higher when calculated using regressions for Knipovich compared to using regressions for Zackenberg. In addition, calculations of daily arthropod biomass at Zackenberg based on order-level regressions from frequently cited studies in literature revealed overestimations of arthropod biomass ranging from 69.7% to 130% compared to estimates based on regressions for Zackenberg. Our results illustrate that the use of allometric relationships from different sites can significantly alter the biological interpretation of, for instance, the interaction between insectivorous birds and their arthropod prey. We conclude that length-biomass relationships should be locally established rather than being based on global relationships.
Keywords	Allometry ; Arctic ; Insects ; Invertebrate Biomass ; Trophic Interactions ; Medicine ; R ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ecological signals of arctic plant-microbe associations are consistent across eDNA and vegetation surveys

Bastien Parisy / Niels M. Schmidt / Helena Wirta / Laerke Stewart / Loic Pellissier / William E. Holben / Sam Pannoni / Panu Somervuo / Mirkka M. Jones / Jukka Siren / Eero Vesterinen / Otso Ovaskainen / Tomas Roslin

Metabarcoding and Metagenomics, Vol 7, Iss , Pp 155-

2023 Volume 193

Abstract: Understanding how different taxa respond to abiotic characteristics of the environment is of key interest for understanding the assembly of communities. Yet, whether eDNA data will suffice to accurately capture environmental imprints has been the topic ... ...

Abstract	Understanding how different taxa respond to abiotic characteristics of the environment is of key interest for understanding the assembly of communities. Yet, whether eDNA data will suffice to accurately capture environmental imprints has been the topic of some debate. In this study, we characterised patterns of species occurrences and co-occurrences in Zackenberg in northeast Greenland using environmental DNA. To explore the potential for extracting ecological signals from eDNA data alone, we compared two approaches (visual vegetation surveys and soil eDNA metabarcoding) to describing plant communities and their responses to abiotic conditions. We then examined plant associations with microbes using a joint species distribution model. We found that most (68%) of plant genera were detectable by both vegetation surveys and eDNA signatures. Species-specific occurrence data revealed how plants, bacteria and fungi responded to their abiotic environment – with plants, bacteria and fungi all responding similarly to soil moisture. Nonetheless, a large proportion of fungi decreased in occurrences with increasing soil temperature. Regarding biotic associations, the nature and proportion of the plant-microbe associations detected were consistent between plant data identified via vegetation surveys and eDNA. Of pairs of plants and microbe genera showing statistically supported associations (while accounting for joint responses to the environment), plants and bacteria mainly showed negative associations, whereas plants and fungi mainly showed positive associations. Ample ecological signals detected by both vegetation surveys and by eDNA-based methods and a general correspondence in biotic associations inferred by both methods, suggested that purely eDNA-based approaches constitute a promising and easily applicable tool for studying plant-soil microbial associations in the Arctic and elsewhere.
Keywords	Ecology ; QH540-549.5
Subject code	580
Language	English
Publishing date	2023-08-01T00:00:00Z
Publisher	Pensoft Publishers
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Research data: (with research data) Dung beetle species interactions and multifunctionality are affected by an experimentally warmed climate

Slade, Eleanor M / Tomas Roslin

Oikos. 2016 Nov., v. 125, no. 11

2016

Abstract: While substantial effort has been invested in modelling changes in species distribution with climate change, less attention has been given to how climate warming will affect interactions among coâoccurring species, and the cascading functional ... ...

Abstract	While substantial effort has been invested in modelling changes in species distribution with climate change, less attention has been given to how climate warming will affect interactions among coâoccurring species, and the cascading functional consequences. In this study, realistic dung beetle communities were subjected to an experimental warming treatment and the net effect on the functions of dung decomposition (in terms of dung mass) and plant productivity (in terms of biomass production of ryegrass grown on soil from underneath the dung pats) were examined. A priori, we hypothesized that the largest tunneling species would be functionally dominant, and be differently affected by experimental warming compared to patâdwelling, smaller species. In terms of dung decomposition, the largest beetles did prove to be the functionally most important, with the qualitative pattern unaffected by experimental warming. In contrast, for plant productivity all species appeared equally important under ambient conditions. However, the effects of single species on plant productivity were reduced as temperature increased: In a warmed climate, a combination of both tunneling and patâdwelling species came the closest to returning ecosystem functioning to levels found in the ambient treatment. These results suggest different roles for different species, and highlight the importance of maintaining multiple species within an ecosystem â particularly when systems are perturbed.
Keywords	biogeography ; climate ; Coleoptera ; dung beetles ; ecosystems ; feces ; global warming ; insect communities ; Lolium ; models ; soil ; temperature
Language	English
Dates of publication	2016-11
Size	p. 1607-1616.
Publishing place	Blackwell Publishing Ltd
Document type	Article ; Research data
Note	JOURNAL ARTICLE
ZDB-ID	207359-6
ISSN	0030-1299 ; 0030-1299
ISSN	0030-1299
DOI	10.1111/oik.03207
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Community phenology of insects on oak

Adam Ekholm / Maria Faticov / Ayco J. M. Tack / Josef Berger / Graham N. Stone / Eero Vesterinen / Tomas Roslin

Ecosphere, Vol 12, Iss 11, Pp n/a-n/a (2021)

local differentiation along a climatic gradient

2021

Abstract: Abstract Climate change is advancing the onset of phenological events, with the rate of advance varying among species and trophic levels. In addition, local populations of the same species may show genetic differences in their response to seasonal cues. ... ...

Abstract	Abstract Climate change is advancing the onset of phenological events, with the rate of advance varying among species and trophic levels. In addition, local populations of the same species may show genetic differences in their response to seasonal cues. If populations of interacting species differ in their response, then climate change may result in geographically varying shifts in the community‐level distribution of interaction strength. We explored the magnitude of trophic‐ and species‐level responses to temperature in a tritrophic system comprising pedunculate oak, insect herbivores, and their associated parasitoids. We sampled local realizations of this community at five sites along a transect spanning fifteen degrees of latitude. Samples from each trophic level at each site were exposed to the same set of five climatic regimes during overwintering in climate chambers. We then recorded the number of days and degree‐days required for oak acorns to develop and insects to emerge. In terms of dates of events, phenology differed among populations. In terms of degree‐days, we found that for two species pairs, the heat sum required to develop in spring differed by an additional ˜500 degree‐days between trophic levels when overwintering at the highest temperature. For three species, within‐population variation in the number of degree‐days required for emergence was higher at warmer temperatures. Our findings suggest that changing temperatures can modify interactions within a community by altering the relative phenology of interacting species and that some interactions are more vulnerable than others to a shift in temperature. The geographic variation in the phenological response of a species suggests that there is a genetic component in determining the phenology of local populations. Such local variation blended with interspecific differences in responses makes it complex to understand how communities will respond to warmer temperatures.
Keywords	climate change ; community ecology ; mismatch ; phenology ; Ecology ; QH540-549.5
Subject code	590
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Woody encroachment in grassland elicits complex changes in the functional structure of above‐ and belowground biota

Siim‐Kaarel Sepp / John Davison / Mari Moora / Lena Neuenkamp / Jane Oja / Tomas Roslin / Martti Vasar / Maarja Öpik / Martin Zobel

Ecosphere, Vol 12, Iss 5, Pp n/a-n/a (2021)

2021

Abstract: Abstract Woody plant encroachment affects dry grasslands globally. To predict changes in biodiversity and ecosystem processes, it is important to understand how this process affects the functional composition of grassland organism groups. In this context, ...

Abstract	Abstract Woody plant encroachment affects dry grasslands globally. To predict changes in biodiversity and ecosystem processes, it is important to understand how this process affects the functional composition of grassland organism groups. In this context, seminatural wooded meadows represent a form of experimental manipulation—where open grassland and woody patches co‐occur in homogeneous environmental conditions due to human management decisions—which provides an opportunity to address the effect of woody plant encroachment on vegetation and soil biota. We used environmental DNA metabarcoding to address variation in plant, soil fungal, and soil animal communities in parallel. We also addressed functional groups of fungi—animal and plant pathogens, saprotrophs, decomposers, arbuscular mycorrhizal, ectomycorrhizal, endophytic, and other symbiotrophic fungi—and of soil animals—fungivores, bacterivores, litter feeders, root feeders, macro plant feeders, algal/lichen feeders, predators, and parasites. Co‐variation between communities was detected from aboveground vegetation plots and metabarcoding of soil DNA, in terms of estimated richness and compositional patterns. Differences between open and wooded patches were most pronounced among plants and symbiotic fungi, whereas soil animals exhibited less marked differences. For most organisms, mean richness, as well as total richness per habitat type, was higher in open than wooded patches, but ectomycorrhizal fungi exhibited the opposite pattern. The functional structure of the soil biotic community, as characterized by the proportion of DNA sequences attributed to different functional groups, differed significantly between open and wooded grassland patches, with symbiotic fungi (arbuscular mycorrhizal, ectomycorrhizal, and other symbiotrophic [mostly orchid mycorrhizal] fungi) contributing most to the difference. This study supports the notion that a soil DNA‐based metabarcoding approach can provide insights into the diversity and composition of multiple taxonomic ...
Keywords	co‐variation ; ecosystem engineers ; environmental DNA ; plant–fungal interactions ; plant–soil interactions ; seminatural ecosystem ; Ecology ; QH540-549.5
Subject code	580 ; 630
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An ecosystem-wide reproductive failure with more snow in the Arctic.

Niels Martin Schmidt / Jeroen Reneerkens / Jens Hesselbjerg Christensen / Martin Olesen / Tomas Roslin

PLoS Biology, Vol 17, Iss 10, p e

2019 Volume 3000392

Abstract: 2018: Arctic researchers have just witnessed another extreme summer-but in a new sense of the word. Although public interest has long been focused on general warming trends and trends towards a lower sea ice cover in the Arctic Ocean, this summer saw the ...

Abstract	2018: Arctic researchers have just witnessed another extreme summer-but in a new sense of the word. Although public interest has long been focused on general warming trends and trends towards a lower sea ice cover in the Arctic Ocean, this summer saw the realization of another predicted trend: that of increasing precipitation during the winter months and of increased year-to-year variability. In a well-studied ecosystem in Northeast Greenland, this resulted in the most complete reproductive failure encountered in the terrestrial ecosystem during more than two decades of monitoring: only a few animals and plants were able to reproduce because of abundant and late melting snow. These observations, we suggest, should open our eyes to potentially drastic consequences of predicted changes in both the mean and the variability of arctic climate.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2019-10-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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