Soil fungal communities respond compositionally to recurring frequent prescribed burning in a managed southeastern US forest ecosystem

Oliver, Alena K.; Callaham, Mac A.; Jumpponen, Ari

doi:10.1016/j.foreco.2015.02.020

Cited by 94 publications

(73 citation statements)

References 64 publications

(92 reference statements)

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“…For example, genes in subcluster 2 (135 genes) were observed at the 60y and 152y sites only. Genes in this subcluster mainly encode proteins in the following functional categories: iron transport (26 genes) and degradation of lignin (20), cellulose (18), pectin (14), and chitin (10). Genes in subcluster 4 (107 genes) that represent functions similar to those in subcluster 2 were absent at the 152y site only.…”

Section: Resultsmentioning

confidence: 99%

“…Fire can also lead to significant losses in fungal biomass in organic horizons (18). The microbial community responses to reoccurring low-intensity prescribed burning have been reported to be minimal unless fires are implemented at high frequency (2-to 3-year intervals) (19,20). However, only a few studies have investigated whether these changes in the microbial community persist over long periods of time.…”

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confidence: 99%

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Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

Sun

Santalahti

Pumpanen

et al. 2015

Appl Environ Microbiol

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129

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Forest fires are a common natural disturbance in forested ecosystems and have a large impact on the microbial communities in forest soils. The response of soil fungal communities to forest fire is poorly documented. Here, we investigated fungal community structure and function across a 152-year boreal forest fire chronosequence using high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region and a functional gene array (GeoChip). Our results demonstrate that the boreal forest soil fungal community was most diverse soon after a fire disturbance and declined over time. The differences in the fungal communities were explained by changes in the abundance of basidiomycetes and ascomycetes. Ectomycorrhizal (ECM) fungi contributed to the increase in basidiomycete abundance over time, with the operational taxonomic units (OTUs) representing the genera Cortinarius and Piloderma dominating in abundance. Hierarchical cluster analysis by using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting differences in the potential to maintain essential biogeochemical soil processes. The site with the greatest biological diversity had also the most diverse genes. The genes involved in organic matter degradation in the mature forest, in which ECM fungi were the most abundant, were as common in the youngest site, in which saprotrophic fungi had a relatively higher abundance. This study provides insight into the impact of fire disturbance on soil fungal community dynamics. Boreal forest soils play an important role in the global carbon cycle (1) and are a net sink for atmospheric CO 2 (2, 3). Approximately 16% of the terrestrial carbon (C) stock is estimated to be stored in the boreal forest ecosystem (1). Fire is a natural disturbance in most forest ecosystems (4), and about 1% of the boreal forest burns annually (5). The frequency of forest fires in the northern boreal zone is expected to increase because of rising temperatures and more frequent dry periods resulting from ongoing climate change (6).Soil microbes perform essential ecological functions in forested ecosystems via nutrient cycling and decomposition of organic matter. Microbial activities control the turnover of organic C in soil and thus contribute to global C cycling (7). Fungi are the predominant decomposers in boreal soils and play a central role in the turnover of carbon and nitrogen (8). Ectomycorrhizal fungi form symbioses with both trees and ground vegetation in boreal forests. Many species of ground vegetation can additionally form symbioses with ericoid mycorrhizal fungi. Boreal forest ecosystem productivity is linked to plant nutrient acquisition from the microbial community via soil organic matter (SOM) decomposition. Forest fires result in the loss of mycorrhizal host plants and may modify the SOM chemistry, leading to dramatic changes in soil microbial activity (9, 10). Fire disturbance often increases soil pH and causes changes in soil temperature due to loss of canopy cover, bo...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

Sun

Santalahti

Pumpanen

et al. 2015

Appl Environ Microbiol

Self Cite

129

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“…Based on our comparison of recently burned and unburned plots, we expect that significant postfire reorganization ( sensu Schmidt et al ., ) of fungal communities occurs within 1–2 yr after fire in pine savannas. By contrast, wildfire studies indicate that transitions of fungal communities from ‘burned’ to ‘unburned’ states can take more than a decade (Dooley & Treseder, ; Holden et al ., ; Oliver et al ., ). Decomposition data here indicate that fire effects on microbial decomposition may be important, albeit transient, compared with fire regime impacts through litter stoichiometry (Ficken & Wright, ; Butler et al ., ).…”

Section: Discussionmentioning

confidence: 97%

“…Locations near or away from pines and in litter or soil substrates may result in compositionally different fungal communities that, in turn, are differentially reorganized by fire. For example, fire intensity increases with greater density of pine needles (Ellair & Platt, ; Platt et al ., ), so fungal communities in the vicinity of pines may be altered by fire more than communities away from pines are. Postfire shifts in fungal communities should be tied to fire‐induced shifts in soil properties and vegetation, as suggested by prior studies in similar systems (Hart et al ., ; Ponder et al ., ; Oliver et al ., ). For example, fungal taxa associated with flammable plants favoured by fire ( sensu Gagnon et al ., ) might respond positively to fire, whereas fungi associated with less‐resistant plant hosts may decline ( sensu Platt et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Frequent fire reorganizes fungal communities and slows decomposition across a heterogeneous pine savanna landscape

et al. 2019

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Summary Pyrogenic savannas with a tree–grassland ‘matrix’ experience frequent fires (i.e. every 1–3 yr). Aboveground responses to frequent fires have been well studied, but responses of fungal litter decomposers, which directly affect fuels, remain poorly known. We hypothesized that each fire reorganizes belowground communities and slows litter decomposition, thereby influencing savanna fuel dynamics. In a pine savanna, we established patches near and away from pines that were either burned or unburned in that year. Within patches, we assessed fungal communities and microbial decomposition of newly deposited litter. Soil variables and plant communities were also assessed as proximate drivers of fungal communities. Fungal communities, but not soil variables or vegetation, differed substantially between burned and unburned patches. Saprotrophic fungi dominated in unburned patches but decreased in richness and relative abundance after fire. Differences in fungal communities with fire were greater in litter than in soils, but unaffected by pine proximity. Litter decomposed more slowly in burned than in unburned patches. Fires drive shifts between fire‐adapted and sensitive fungal taxa in pine savannas. Slower fuel decomposition in accordance with saprotroph declines should enhance fuel accumulation and could impact future fire characteristics. Thus, fire reorganization of fungal communities may enhance persistence of these fire‐adapted ecosystems.

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“…To do this, proofreading and non-proofreading thermostable hot start polymerases from the same manufacturer were compared, and whether the proofreading enzyme would minimize potentially erroneous sequences resulting from PCR errors in complex environmental templates was examined. 24 experimental units from a long-term experiment, that was designed to evaluate the effects of prescribed fires on ecosystem properties (see Brown et al, 2013;Oliver et al, 2015), were used. Each sample was amplified in triplicate with each of the two polymerases in a two-step PCR reaction (Berry et al, 2011) to generate comparable NGS data.…”

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

et al. 2015

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a b s t r a c tRare taxa overwhelm metabarcoding data generated using next-generation sequencing (NGS). Low frequency Operational Taxonomic Units (OTUs) may be artifacts generated by PCR-amplification errors resulting from polymerase mispairing. We analyzed two Internal Transcribed Spacer 2 (ITS2) MiSeq libraries generated with proofreading (ThermoScientific Phusion Ò ) and non-proofreading (ThermoScientific Phire Ò ) polymerases from the same MiSeq reaction, the same samples, using the same DNA tags, and with two different clustering methods to evaluate the effect of polymerase and clustering tool choices on the estimates of richness, diversity and community composition. Our data show that, while the overall communities are comparable, OTU richness is exaggerated by the use of the non-proofreading polymeraseeup to 15 % depending on the clustering method, and on the threshold of low frequency OTU removal. The overestimation of richness also consistently led to underestimation of community evenness, a result of increase in the low frequency OTUs. Stringent thresholds of eliminating the rare reads remedy this issue; exclusion of reads that occurred 10 times reduced overestimated OTU numbers to <0.3 %. As a result of these findings, we strongly recommend the use of proofreading polymerases to improve the data integrity as well as the use of stringent culling thresholds for rare sequences to minimize overestimation of community richness. ª

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Soil fungal communities respond compositionally to recurring frequent prescribed burning in a managed southeastern US forest ecosystem

Cited by 94 publications

References 64 publications

Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

Frequent fire reorganizes fungal communities and slows decomposition across a heterogeneous pine savanna landscape

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

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