Publications by authors named "Sunil Mundra"

14 Publications

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Establishment of spruce plantations in native birch forests reduces soil fungal diversity.

FEMS Microbiol Ecol 2021 May 31. Epub 2021 May 31.

Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Blindernveien 31, 0316 Oslo, Norway.

Plantations of Norway spruce have been established well beyond its natural range in many parts of the world, potentially impacting native microbial ecosystems and the processes they mediate. In this study, we investigate how the establishment of spruce plantations in a landscape dominated by native birch forests in western Norway impacts soil properties and belowground fungal communities. Soil cores were collected from neighbouring stands of planted spruce and native birch forests. We used DNA metabarcoding of the rDNA ITS2 region and ergosterol measurements to survey the fungal community composition and its biomass, respectively. In the two investigated soil layers (litter and humus) fungal community composition, diversity and biomass were strongly affected by the tree species shift. Native birch stands hosted markedly richer fungal communities, including numerous fungi not present in planted spruce stands. By contrast, the spruce stands included higher relative abundance of ectomycorrhizal fungi as well as higher fungal biomass. Hence, establishing plantations of Norway spruce in native birch forests leads to significant losses in diversity, but increase in biomass of ectomycorrhizal fungi, which could potentially impact carbon sequestration processes and ecosystem functioning.
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http://dx.doi.org/10.1093/femsec/fiab074DOI Listing
May 2021

Complete Genome Sequences of Pseudomonas atacamensis Strain SM1 and Pseudomonas toyotomiensis Strain SM2, Isolated from the Date Palm Rhizosphere.

Microbiol Resour Announc 2021 May 6;10(18). Epub 2021 May 6.

Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates

Here, we announce the complete genome sequences of two phosphate-solubilizing rhizobacteria, strain SM1 (genome size, ∼5.9 Mb) and strain SM2 (genome size, ∼5.2 Mb), isolated from the rhizosphere of date palms growing in the oasis agroecosystem of the United Arab Emirates (UAE).
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http://dx.doi.org/10.1128/MRA.00253-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8103867PMC
May 2021

The airborne mycobiome and associations with mycotoxins and inflammatory markers in the Norwegian grain industry.

Sci Rep 2021 Apr 30;11(1):9357. Epub 2021 Apr 30.

Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.

Grain dust exposure is associated with respiratory symptoms among grain industry workers. However, the fungal assemblage that contribute to airborne grain dust has been poorly studied. We characterized the airborne fungal diversity at industrial grain- and animal feed mills, and identified differences in diversity, taxonomic compositions and community structural patterns between seasons and climatic zones. The fungal communities displayed strong variation between seasons and climatic zones, with 46% and 21% of OTUs shared between different seasons and climatic zones, respectively. The highest species richness was observed in the humid continental climate of the southeastern Norway, followed by the continental subarctic climate of the eastern inland with dryer, short summers and snowy winters, and the central coastal Norway with short growth season and lower temperature. The richness did not vary between seasons. The fungal diversity correlated with some specific mycotoxins in settled dust and with fibrinogen in the blood of exposed workers, but not with the personal exposure measurements of dust, glucans or spore counts. The study contributes to a better understanding of fungal exposures in the grain and animal feed industry. The differences in diversity suggest that the potential health effects of fungal inhalation may also be different.
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http://dx.doi.org/10.1038/s41598-021-88252-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8087811PMC
April 2021

Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils.

FEMS Microbiol Ecol 2021 03;97(3)

Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway.

Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0-5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.
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http://dx.doi.org/10.1093/femsec/fiab022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7948073PMC
March 2021

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies.

Sci Data 2020 07 13;7(1):228. Epub 2020 Jul 13.

Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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http://dx.doi.org/10.1038/s41597-020-0567-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359306PMC
July 2020

The Inhalable Mycobiome of Sawmill Workers: Exposure Characterization and Diversity.

Appl Environ Microbiol 2019 11 16;85(21). Epub 2019 Oct 16.

Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.

Exposure to fungal spores has been associated with respiratory symptoms and allergic alveolitis among sawmill workers, but the complexity of sawmill workers' fungal exposure has been poorly studied. We characterized the fungal diversity in air samples from sawmill workers' breathing zones and identified differences in the richness, diversity, and taxonomic composition between companies, departments, wood types, and seasons. Full-shift personal inhalable dust samples ( = 86) collected from 11 industrial sawmill, sorting mill, and planer mill companies processing spruce and/or pine were subjected to DNA metabarcoding using the fungal internal transcribed spacer (ITS) region 2. The workers were exposed to a higher total number of operational taxonomic units (OTUs) in summer than in winter and when processing spruce than when processing pine. Workers in the saw department had the richest fungal exposure, followed by workers in the planing department and sorting of dry timber department. Sawmills explained 11% of the variation in the fungal community composition of the exposure, followed by season (5%) and department (3%). The fungal compositions of the exposures also differed between seasons, sawmills, wood types, and departments at the taxonomic level, ranging from the phylum to the species level. The differences in exposure diversity suggest that the potential health effects of fungal inhalation may also be different; hence, a risk assessment based on the fungal diversity differences should be performed. This study may serve as a basis for establishing a fungal profile of signature species that are specific for sawmills and that can be measured quantitatively in future risk assessments of sawmill workers. To gain more knowledge about exposure-response relationships, it is important to improve exposure characterization by comprehensively identifying the temporal and spatial fungal composition and diversity of inhalable dust at workplaces. The variation in the diverse fungal communities to which individuals are exposed in different seasons and sawmills suggests that variations in exposure-related health effects between seasons and companies can be expected. More importantly, the distinct fungal profiles between departments across companies indicate that workers in different job groups are differently exposed and that health risks can be department specific. DNA metabarcoding provides insight into a broad spectrum of airborne fungi that may serve as a basis for obtaining important knowledge about the fungi to which workers are exposed.
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http://dx.doi.org/10.1128/AEM.01448-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6803317PMC
November 2019

Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil.

Front Microbiol 2018 8;9:3243. Epub 2019 Jan 8.

Department of Arctic Biology, The University Centre in Svalbard (UNIS), Longyearbyen, Norway.

Describing dynamics of belowground organisms, such as fungi, can be challenging. Results of studies based on environmental DNA (eDNA) may be biased as the template does not discriminate between metabolically active cells and dead biomass. We analyzed ribosomal DNA (rDNA) and ribosomal RNA (rRNA) coextracted from 48 soil samples collected from a manipulated snow depth experiment in two distinct vegetation types in Svalbard, in the High Arctic. Our main goal was to compare if the rDNA and rRNA metabarcoding templates produced congruent results that would lead to consistent ecological interpretation. Data derived from both rDNA and rRNA clustered according to vegetation types. Different sets of environmental variables explained the community composition based on the metabarcoding template. rDNA and rRNA-derived community composition of symbiotrophs and saprotrophs, unlike pathotrophs, clustered together in a similar way as when the community composition was analyzed using all OTUs in the study. Mean OTU richness was higher for rRNA, especially in symbiotrophs. The metabarcoding template was more important than vegetation type in explaining differences in richness. The proportion of symbiotrophic, saprotrophic and functionally unassigned reads differed between rDNA and rRNA, but showed similar trends. There was no evidence for increased snow depth influence on fungal community composition or richness. Our findings suggest that template choice may be especially important for estimating biodiversity, such as richness and relative abundances, especially in Helotiales and Agaricales, but not for inferring community composition. Differences in study results originating from rDNA or rRNA may directly impact the ecological conclusions of one's study, which could potentially lead to false conclusions on the dynamics of microbial communities in a rapidly changing Arctic.
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http://dx.doi.org/10.3389/fmicb.2018.03243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333106PMC
January 2019

Structure and function of the global topsoil microbiome.

Nature 2018 08 1;560(7717):233-237. Epub 2018 Aug 1.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.
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http://dx.doi.org/10.1038/s41586-018-0386-6DOI Listing
August 2018

Does warming by open-top chambers induce change in the root-associated fungal community of the arctic dwarf shrub Cassiope tetragona (Ericaceae)?

Mycorrhiza 2017 Jul 27;27(5):513-524. Epub 2017 Mar 27.

University of Oslo, P.O. Box 1072, Blindern, 0316, Oslo, Norway.

Climate change may alter mycorrhizal communities, which impact ecosystem characteristics such as carbon sequestration processes. These impacts occur at a greater magnitude in Arctic ecosystems, where the climate is warming faster than in lower latitudes. Cassiope tetragona (L.) D. Don is an Arctic plant species in the Ericaceae family with a circumpolar range. C. tetragona has been reported to form ericoid mycorrhizal (ErM) as well as ectomycorrhizal (ECM) symbioses. In this study, the fungal taxa present within roots of C. tetragona plants collected from Svalbard were investigated using DNA metabarcoding. In light of ongoing climate change in the Arctic, the effects of artificial warming by open-top chambers (OTCs) on the fungal root community of C. tetragona were evaluated. We detected only a weak effect of warming by OTCs on the root-associated fungal communities that was masked by the spatial variation between sampling sites. The root fungal community of C. tetragona was dominated by fungal groups in the Basidiomycota traditionally classified as either saprotrophic or ECM symbionts, including the orders Sebacinales and Agaricales and the genera Clavaria, Cortinarius, and Mycena. Only a minor proportion of the operational taxonomic units (OTUs) could be annotated as ErM-forming fungi. This indicates that C. tetragona may be forming mycorrhizal symbioses with typically ECM-forming fungi, although no characteristic ECM root tips were observed. Previous studies have indicated that some saprophytic fungi may also be involved in biotrophic associations, but whether the saprotrophic fungi in the roots of C. tetragona are involved in biotrophic associations remains unclear. The need for more experimental and microscopy-based studies to reveal the nature of the fungal associations in C. tetragona roots is emphasized.
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http://dx.doi.org/10.1007/s00572-017-0767-yDOI Listing
July 2017

Alpine bistort (Bistorta vivipara) in edge habitat associates with fewer but distinct ectomycorrhizal fungal species: a comparative study of three contrasting soil environments in Svalbard.

Mycorrhiza 2016 Nov 20;26(8):809-818. Epub 2016 Jun 20.

The University Centre in Svalbard, P.O. Box 156, Longyearbyen, NO-9171, Norway.

Bistorta vivipara is a widespread arctic-alpine ectomycorrhizal (ECM) plant species. Recent findings suggest that fungal communities associated with B. vivipara roots appear random over short distances, but at larger scales, environmental filtering structure fungal communities. Habitats in highly stressful environments where specialist species with narrower niches may have an advantage represent unique opportunity to test the effect of environmental filtering. We utilised high-throughput amplicon sequencing to identify ECM communities associated with B. vivipara in Svalbard. We compared ECM communities in a core habitat where B. vivipara is frequent (Dryas-heath) with edge habitats representing extremes in terms of nutrient availability where B. vivipara is less frequent (bird-manured meadow and a nutrient-depleted mine tilling). Our analysis revealed that soil conditions in edge habitats favour less diverse but more distinct ECM fungal communities with functional traits adapted to local conditions. ECM richness was overall lower in both edge habitats, and the taxonomic compositions of ECM fungi were in line with our functional expectations. Stress-tolerant genera such as Laccaria and Hebeloma were abundant in nutrient-poor mine site whereas functional competitors genera such as Lactarius and Russula were dominant in the nutrient-rich bird-cliff site. Our results suggest that ECM communities in rare edge habitats are most likely not subsets of the larger pool of ECM fungi found in natural tundra, and they may represent a significant contribution to the overall diversity of ECM fungi in the Arctic.
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http://dx.doi.org/10.1007/s00572-016-0716-1DOI Listing
November 2016

Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic.

Microbiologyopen 2016 Oct 2;5(5):856-869. Epub 2016 Jun 2.

The University Centre in Svalbard, P.O. Box 156, NO-9171, Longyearbyen, Norway.

Changing climate is expected to alter precipitation patterns in the Arctic, with consequences for subsurface temperature and moisture conditions, community structure, and nutrient mobilization through microbial belowground processes. Here, we address the effect of increased snow depth on the variation in species richness and community structure of ectomycorrhizal (ECM) and saprotrophic fungi. Soil samples were collected weekly from mid-July to mid-September in both control and deep snow plots. Richness of ECM fungi was lower, while saprotrophic fungi was higher in increased snow depth plots relative to controls. [Correction added on 23 September 2016 after first online publication: In the preceding sentence, the richness of ECM and saprotrophic fungi were wrongly interchanged and have been fixed in this current version.] ECM fungal richness was related to soil NO -N, NH -N, and K; and saprotrophic fungi to NO -N and pH. Small but significant changes in the composition of saprotrophic fungi could be attributed to snow treatment and sampling time, but not so for the ECM fungi. Delayed snow melt did not influence the temporal variation in fungal communities between the treatments. Results suggest that some fungal species are favored, while others are disfavored resulting in their local extinction due to long-term changes in snow amount. Shifts in species composition of fungal functional groups are likely to affect nutrient cycling, ecosystem respiration, and stored permafrost carbon.
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http://dx.doi.org/10.1002/mbo3.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5061721PMC
October 2016

Temporal variation of Bistorta vivipara-associated ectomycorrhizal fungal communities in the High Arctic.

Mol Ecol 2015 12 7;24(24):6289-302. Epub 2015 Dec 7.

The University Centre in Svalbard, P.O. Box 156, Longyearbyen, NO-9171, Norway.

Ectomycorrhizal (ECM) fungi are important for efficient nutrient uptake of several widespread arctic plant species. Knowledge of temporal variation of ECM fungi, and the relationship of these patterns to environmental variables, is essential to understand energy and nutrient cycling in Arctic ecosystems. We sampled roots of Bistorta vivipara ten times over two years; three times during the growing-season (June, July and September) and twice during winter (November and April) of both years. We found 668 ECM OTUs belonging to 25 different ECM lineages, whereof 157 OTUs persisted throughout all sampling time-points. Overall, ECM fungal richness peaked in winter and species belonging to Cortinarius, Serendipita and Sebacina were more frequent in winter than during summer. Structure of ECM fungal communities was primarily affected by spatial factors. However, after accounting for spatial effects, significant seasonal variation was evident revealing correspondence with seasonal changes in environmental conditions. We demonstrate that arctic ECM richness and community structure differ between summer (growing-season) and winter, possibly due to reduced activity of the core community, and addition of fungi adapted for winter conditions forming a winter-active fungal community. Significant month × year interactions were observed both for fungal richness and community composition, indicating unpredictable between-year variation. Our study indicates that addressing seasonal changes requires replication over several years.
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http://dx.doi.org/10.1111/mec.13458DOI Listing
December 2015

Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation.

New Phytol 2015 Mar 5;205(4):1587-1597. Epub 2014 Dec 5.

The University Centre in Svalbard (UNIS), PO Box 156, N-9171, Longyearbyen (Svalbard), Norway.

Soil conditions and microclimate are important determinants of the fine-scale distribution of plant species in the Arctic, creating locally heterogeneous vegetation. We hypothesize that root-associated fungal (RAF) communities respond to the same fine-scale environmental gradients as the aboveground vegetation, creating a coherent pattern between aboveground vegetation and RAF. We explored how RAF communities of the ectomycorrhizal (ECM) plant Bistorta vivipara and aboveground vegetation structure of arctic plants were affected by biotic and abiotic variables at 0.3-3.0-m scales. RAF communities were determined using pyrosequencing. Composition and spatial structure of RAF and aboveground vegetation in relation to collected biotic and abiotic variables were analysed by ordination and semi-variance analyses. The vegetation was spatially structured along soil C and N gradients, whereas RAF lacked significant spatial structure. A weak relationship between RAF community composition and the cover of two ECM plants, B. vivipara and S. polaris, was found, and RAF richness increased with host root length and root weight. Results suggest that the fine-scale spatial structure of RAF communities of B. vivipara and the aboveground vegetation are driven by different factors. At fine spatial scales, neighbouring ECM plants may affect RAF community composition, whereas soil nutrients gradients structure the vegetation.
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http://dx.doi.org/10.1111/nph.13216DOI Listing
March 2015