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Dive into the research topics where Shawn P. Brown is active.

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Featured researches published by Shawn P. Brown.


Molecular Ecology | 2014

Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils

Shawn P. Brown; Ari Jumpponen

Early community assembly of soil microbial communities is essential for pedogenesis and development of organic legacies. We examined fungal and bacterial successions along a well‐established temperate glacier forefront chronosequence representing ~70 years of deglaciation to determine community assembly. As microbial communities may be heavily structured by establishing vegetation, we included nonvegetated soils as well as soils from underneath four plant species with differing mycorrhizal ecologies (Abies lasiocarpa, ectomycorrhizal; Luetkea pectinata, arbuscular mycorrhizal; Phyllodoce empetriformis, ericoid mycorrhizal; Saxifraga ferruginea, nonmycorrhizal). Our main objectives were to contrast fungal and bacterial successional dynamics and community assembly as well as to decouple the effects of plant establishment and time since deglaciation on microbial trajectories using high‐throughput sequencing. Our data indicate that distance from glacier terminus has large effects on biomass accumulation, community membership, and distribution for both fungi and bacteria. Surprisingly, presence of plants rather than their identity was more important in structuring bacterial communities along the chronosequence and played only a very minor role in structuring the fungal communities. Further, our analyses suggest that bacterial communities may converge during assembly supporting determinism, whereas fungal communities show no such patterns. Although fungal communities provided little evidence of convergence in community structure, many taxa were nonrandomly distributed across the glacier foreland; similar taxon‐level responses were observed in bacterial communities. Overall, our data highlight differing drivers for fungal and bacterial trajectories during early primary succession in recently deglaciated soils.


FEMS Microbiology Ecology | 2013

Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem

Shawn P. Brown; Mac A. Callaham; Alena K. Oliver; Ari Jumpponen

Prescribed burning is a common management tool to control fuel loads, ground vegetation, and facilitate desirable game species. We evaluated soil fungal community responses to long-term prescribed fire treatments in a loblolly pine forest on the Piedmont of Georgia and utilized deep Internal Transcribed Spacer Region 1 (ITS1) amplicon sequencing afforded by the recent Ion Torrent Personal Genome Machine (PGM). These deep sequence data (19,000 + reads per sample after subsampling) indicate that frequent fires (3-year fire interval) shift soil fungus communities, whereas infrequent fires (6-year fire interval) permit system resetting to a state similar to that without prescribed fire. Furthermore, in nonmetric multidimensional scaling analyses, primarily ectomycorrhizal taxa were correlated with axes associated with long fire intervals, whereas soil saprobes tended to be correlated with the frequent fire recurrence. We conclude that (1) multiplexed Ion Torrent PGM analyses allow deep cost effective sequencing of fungal communities but may suffer from short read lengths and inconsistent sequence quality adjacent to the sequencing adaptor; (2) frequent prescribed fires elicit a shift in soil fungal communities; and (3) such shifts do not occur when fire intervals are longer. Our results emphasize the general responsiveness of these forests to management, and the importance of fire return intervals in meeting management objectives.


Mycorrhiza | 2014

Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape

K. Lothamer; Shawn P. Brown; J. D. Mattox; Ari Jumpponen

Non-native tree species are often used as ornamentals in urban landscapes. However, their root-associated fungal communities remain yet to be examined in detail. Here, we compared richness, diversity and community composition of ectomycorrhizosphere fungi in general and ectomycorrhizal (EcM) fungi in particular between a non-native Pinus nigra and a native Quercus macrocarpa across a growing season in urban parks using 454-pyrosequencing. Our data show that, while the ectomycorrhizosphere community richness and diversity did not differ between the two host, the EcM communities associated with the native host were often more species rich and included more exclusive members than those of the non-native hosts. In contrast, the ectomycorrhizosphere communities of the two hosts were compositionally clearly distinct in nonmetric multidimensional ordination analyses, whereas the EcM communities were only marginally so. Taken together, our data suggest EcM communities with broad host compatibilities and with a limited numbers of taxa with preference to the non-native host. Furthermore, many common fungi in the non-native Pinus were not EcM taxa, suggesting that the fungal communities of the non-native host may be enriched in non-mycorrhizal fungi at the cost of the EcM taxa. Finally, while our colonization estimates did not suggest a shortage in EcM inoculum for either host in urban parks, the differences in the fungi associated with the two hosts emphasize the importance of using native hosts in urban environments as a tool to conserve endemic fungal diversity and richness in man-made systems.


International Journal of Plant Sciences | 2016

A community of clones: Snow algae are diverse communities of spatially structured clones

Shawn P. Brown; Mark C. Ungerer; Ari Jumpponen

Premise of research. Snow algae are cosmopolitan and often colonize late-season snowpacks. These snow algae do not occur in isolation; rather, visible algal blooms consist of multispecies communities. Although several of these common snow algae have been characterized taxonomically, their inter- and intraspecific diversity remains unknown. Further, the phylogeographic and biogeographic structuring of snow algal species is poorly understood. Methodology. Algal communities were censused by sequencing the variable internal transcribed spacer 2 locus using Illumina MiSeq. We further analyzed two of the most common and abundant algal operational taxonomic units (OTUs) for biogeographic haplotype diversity. Pivotal results. Our data show that the communities are diverse and taxonomically broad (orders: Chlamydomonadales [74% of OTUs], Microthamniales [20% OTUs], and Chlorellales [6% OTUs]). We demonstrate that the two most common species (best nucleotide basic local alignment search tool match to Coenochloris sp. and Chlamydomonas sp.) have distinct haplotype distributions locally and regionally. Each sampled algal colony was dominated by one and only one haplotype, with negligible intraspecific haplotype diversity. Conclusions. Our results suggest that snow algae are communities of clones within a discrete patch yet are heterogeneous across the landscape. Thus, these communities are likely structured via strong priority effects, intense kin competition, and dispersal limitations.


Molecular Ecology | 2016

Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem.

Allison M. Veach; James C. Stegen; Shawn P. Brown; Walter K. Dodds; Ari Jumpponen

Biofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third‐order stream at Konza Prairie over a 2‐ to 64‐day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations) increased and never plateaued during the experiment. Net primary productivity (net balance of oxygen consumption and production) of the developing biofilms did not differ statistically from zero until 64 days suggesting a balance of the use of autochthonous and allochthonous energy sources until late succession. Bacterial communities (MiSeq analyses of the V4 region of 16S rRNA) established quickly. Bacterial richness, diversity and evenness were high after 2 days and increased over time. Several dominant bacterial phyla (Beta‐, Alphaproteobacteria, Bacteroidetes, Gemmatimonadetes, Acidobacteria, Chloroflexi) and genera (Luteolibacter, Flavobacterium, Gemmatimonas, Hydrogenophaga) differed in relative abundance over space and time. Bacterial community composition differed across both space and successional time. Pairwise comparisons of phylogenetic turnover in bacterial community composition indicated that early‐stage succession (≤16 days) was driven by stochastic processes, whereas later stages were driven by deterministic selection regardless of site. Our data suggest that microbial biofilms predictably develop both functionally and structurally indicating distinct successional trajectories of bacterial communities in this ecosystem.


Molecular Ecology | 2014

The rich and the sensitive: diverse fungal communities change functionally with the warming Arctic

Ari Jumpponen; Shawn P. Brown

Fungi are very abundant and functionally pivotal in Arctic terrestrial ecosystems. Yet, our understanding of their community composition, diversity and particularly their environmental drivers is superficial at the very best. In this issue of Molecular Ecology, Timling et al. ( ) describe perhaps one of the most comprehensive and geographically ambitious molecular studies on Arctic fungal communities to date. The results highlight the potential sensitivity of the fungal communities to plant communities, environmental conditions and therefore to environmental change. Thus, these studies lay a foundation to educated speculation on the fungal community migration northwards as a result of predicted climate change.


Molecular Ecology Resources | 2016

Don't put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array

Shawn P. Brown; Astrid Ferrer; James W. Dalling; Katy D. Heath

With the increasing democratization of high‐throughput sequencing (HTS) technologies, along with the concomitant increase in sequence yield per dollar, many researchers are exploring HTS for microbial community ecology. Many elements of experimental design can drastically affect the final observed community structure, notably the choice of primers for amplification prior to sequencing. Some targeted microbes can fail to amplify due to primer‐targeted sequence divergence and be omitted from obtained sequences, leading to differences among primer pairs in the sequenced organisms even when targeting the same community. This potential source of taxonomic bias in HTS makes it prudent to investigate how primer choice will affect the sequenced community prior to investing in a costly community‐wide sequencing effort. Here, we use Fluidigms microfluidic Access Arrays (IFC) followed by Illumina® MiSeq Nano sequencing on a culture‐derived local mock community to demonstrate how this approach allows for a low‐cost combinatorial investigation of primer pairs and experimental samples (up to 48 primer pairs and 48 samples) to determine the most effective primers that maximize obtained communities whilst minimizing taxonomic biases.


Fungal Ecology | 2015

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

Shawn P. Brown; Allison M. Veach; Anne R. Rigdon-Huss; Kirsten Grond; Spencer K. Lickteig; Kale M. Lothamer; Alena K. Oliver; Ari Jumpponen


Fungal Ecology | 2012

Twenty years of research on fungus-microbe-plant interactions on Lyman Glacier forefront – lessons learned and questions yet unanswered

Ari Jumpponen; Shawn P. Brown; James M. Trappe; Efrén Cázares; Rauni Strömmer


Fungal Ecology | 2015

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

Alena K. Oliver; Shawn P. Brown; Mac A. Callaham; Ari Jumpponen

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Allison M. Veach

Oak Ridge National Laboratory

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Mac A. Callaham

United States Forest Service

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James C. Stegen

Pacific Northwest National Laboratory

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K. Lothamer

Kansas State University

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