| 1. |
- Marupakula, Srisailam, et al.
(författare)
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Analysis of single root tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi
- 2016
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 18, s. 1470-1483
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Tidskriftsartikel (refereegranskat)abstract
- Symbiotic ectomycorrhizal tree roots represent an important niche for interaction with bacteria since the fungi colonizing them have a large surface area and receive a direct supply of photosynthetically derived carbon. We examined individual root tips of Pinus sylvestris at defined time points between 5 days and 24 weeks, identified the dominant fungi colonizing each root tip using Sanger sequencing and the bacterial communities colonizing individual root tips by 454 pyrosequencing. Bacterial colonization was extremely dynamic with statistically significant variation in time and increasing species richness until week 16 (3477 operational taxonomic units). Bacterial community structure of roots colonized by Russula sp. 6 GJ-2013b, Piloderma spp., Meliniomyces variabilis and Paxillus involutus differed significantly at weeks 8 and 16 but diversity declined and significant differences were no longer apparent at week 24. The most common genera were Burkholderia, Sphingopyxsis, Dyella, Pseudomonas, Acinetobacter, Actinospica, Aquaspirillum, Acidobacter Gp1, Sphingomonas, Terriglobus, Enhydrobacter, Herbaspirillum and Bradyrhizobium. Many genera had high initial abundance at week 8, declining with time but Dyella and Terriglobus increased in abundance at later time points. In roots colonized by Piloderma spp. several other bacterial genera, such as Actinospica, Bradyrhizobium, Acidobacter Gp1 and Rhizomicrobium appeared to increase in abundance at later sampling points.
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| 2. |
- Marupakula, Srisailam, et al.
(författare)
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Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition
- 2017
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 19, s. 4736-4753
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Tidskriftsartikel (refereegranskat)abstract
- Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonized by different fungi and analyzed differences in microbiome structure related to soils from distinct podzol horizons and effects of short-term additions of N, a growth-limiting nutrient commonly applied as a fertilizer, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonizing individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilized soil, but fertilization removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns.
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| 3. |
- Marupakula, Srisailam
(författare)
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Interactions between ectomycorrhizal associations and bacteria
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Boreal forest podzol soils have vertically stratified horizons with different physico-chemical characteristics and high microbial diversity. Ectomycorrhizal fungi play key roles in accessing nutrients from both organic and mineral substrates. The role of associated bacteria in these processes is still poorly understood. The aim of the studies described in this thesis was to improve understanding of the distribution, diversity and community structure of fungi and bacteria on roots and in soil and their responses to environmental perturbations such as N-fertilisation. In two microcosm studies a single-root tip microbiome method was used to sample bacteria associated with different ectomycorrhizal roots at defined time-points, using high throughput sequencing of both fungi and bacteria The first study revealed highly dynamic patterns of assembly of bacterial communities associated with ectomycorrhizal roots at different time points in organic soil. Bacterial community structure differed between roots colonised by different species of ectomycorrhizal fungi from different genera. The second study extended these results to include both organic and mineral horizons, demonstrating significant differences between fungal and bacterial communities colonising soil from different horizons. Responses of both fungi and bacteria to short-term N additions were context dependent, influenced by both soil horizon and the dominant ectomycorrhizal fungi colonising the roots. Bacterial communities associated with roots colonised by pairs of closely related fungal species within the same fungal genera were also shown to be statistically distinct. Field studies of fungi and bacteria in a forest fertilised with 150 kg N ha⁻¹ 15 months previously, revealed 1017 unique fungal OTUs, (877 in the soil, 652 in the roots). N increased fungal diversity slightly in the O horizon soil but decreased it in the roots, particularly in the B horizon. Fungal community structure varied significantly between horizons and within each soil horizon the community structure of fungi colonising ectomycorrhizal roots was significantly different from that associated with the soil, suggesting that analyses of both soil and roots are necessary for accurate monitoring of environmental perturbations. 10925 unique bacterial OTUs were distinguished in total (8560 in the soil, 5512 in the roots). Bacteria displayed similar trends to the fungi but were less strongly influenced by N. These studies pave the way for more detailed functional studies of specific combinations of fungi and bacteria.
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| 4. |
- Marupakula, Srisailam, et al.
(författare)
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Root associated fungi respond more strongly than rhizosphere soil fungi to N fertilization in a boreal forest
- 2021
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 766
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogen (N) fertilization is a routine practice in boreal forests but its effects on fungal functional guilds in Pinus sylvestris forests are still incompletely understood. Sampling is often restricted to the upper organic horizons and based on DNA extracted from mixtures of soil and roots without explicitly analysing different spatial niches. Fungal community structure in soil and roots of an 85-y-old Pinus sylvestris forest was investigated using high throughput sequencing. Fertilized plots had been treated with a single dose of N fertilizer, 15 months prior to sampling. Species richness of fungi colonizing roots was reduced in all horizons by N fertilization. In contrast, species richness of soil fungi in the organic horizon was increased by N fertilization, but unaffected in the mineral horizons. Community composition of fungi colonizing roots differed from that of soil fungi, and both communities were significantly influenced by soil horizon and N. The ectomycorrhizal community composition in both roots and soil was significantly affected by N fertilization but no significant effect was found on saprotrophic fungi. The results highlight the importance of analysing the rhizosphere soil and root compartments separately since the fungal communities in these two niches appear to respond differently to environmental perturbations involving the addition of nitrogen. (C) 2020 Published by Elsevier B.V.
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| 5. |
- Nallanchakravarthula, Srivathsa, et al.
(författare)
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Changes in the root fungal microbiome of strawberry following application of residues of the biofumigant oilseed radish
- 2021
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Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 168
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Tidskriftsartikel (refereegranskat)abstract
- Biofumigation has been proposed as an environmentally friendly method of plant protection against soil-borne pathogens, but its effects on microbial communities are still incompletely understood. Using high throughput DNA sequencing, we investigated the effects of oilseed radish residues on the root fungal microbiome of strawberry in the presence of a soil-borne fungal pathogen, Verticillium dahliae. Results of our greenhouse study show that early flowering occurred in response to residue addition, suggesting a plant stress-response and there was a significant decrease in berry yield. The fungal microbiome of roots was significantly restructured by both biofumigation and inoculation with Verticillium. In particular, the abundance of root endophyte- and arbuscular mycorrhizal functional guilds was reduced significantly as a result of biofumigant and V. dahliae addition, whereas the abundance of saprotrophs increased significantly when both treatments were applied together. Alpha diversity analyses of fungi associated with roots indicated a significant increase in species richness following Verticillium inoculation, whereas the biofumigant alone or in the presence of V. dahliae resulted in no significant effect, suggesting that apparently some rare taxa may have been enriched/stimulated in the presence of the pathogen. Further investigations should reveal whether negative effects of biofumigation on potentially beneficial root associated endophytes and arbuscular mycorrhizal fungi are host genotype- or soil-dependent.
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| 6. |
- Thaduri, Srinivas, et al.
(författare)
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Global similarity, and some key differences, in the metagenomes of Swedish varroa-surviving and varroa-susceptible honeybees
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- There is increasing evidence that honeybees (Apis mellifera L.) can adapt naturally to survive Varroa destructor, the primary cause of colony mortality world-wide. Most of the adaptive traits of naturally varroa-surviving honeybees concern varroa reproduction. Here we investigate whether factors in the honeybee metagenome also contribute to this survival. The quantitative and qualitative composition of the bacterial and viral metagenome fluctuated greatly during the active season, but with little overall difference between varroa-surviving and varroa-susceptible colonies. The main exceptions were Bartonella apis and sacbrood virus, particularly during early spring and autumn. Bombella apis was also strongly associated with early and late season, though equally for all colonies. All three affect colony protein management and metabolism. Lake Sinai virus was more abundant in varroa-surviving colonies during the summer. Lake Sinai virus and deformed wing virus also showed a tendency towards seasonal genetic change, but without any distinction between varroa-surviving and varroa-susceptible colonies. Whether the changes in these taxa contribute to survival or reflect demographic differences between the colonies (or both) remains unclear.
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