Biology subjects

Whitman, T.

Publications and source records attributed to Whitman, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Persistent but variable effect of experimental laboratory burns on microbial community resistance, resilience, and function across contrasting boreal forest soils

Boreal forests stretch across vast swaths of the northern hemisphere, are shaped by wildfire, and play an important role in the global carbon cycle. Microorganisms play a critical role in soil nutrient cycling in these ecosystems, yet there are many open questions about the impacts of wildfire on microbially mediated soil biogeochemical cycles. In this study, we used laboratory burns and soil incubations of intact soil cores collected from two distinct soil types -- Histosols and Gleysols -- from boreal forest within Wood Buffalo National Park, Alberta, Canada, to assess burn effects on soil bacterial and fungal community composition and function. We compared resistance and resilience to burning for microbial communities vs. resistance and resilience to burning for soil pH and soil respiration to assess the relationships between burn-induced shifts in microbial community composition, the soil environment, and microbial activity. To link shifts in microbial community composition to potential community function, we measured glucose-specific carbon use efficiency (CUE) and assessed its relationship with weighted mean predicted 16S rRNA gene copy numbers for bacterial communities and FUNGuild-estimated relative abundance of putative symbiotrophic and saprotrophic fungi in burned and unburned soils. Microbial community resistance and resilience to burning varied across soil type with higher resistance of both bacterial and fungal communities from Histosols compared to the O horizons of Gleysols. This may be explained by a larger impact of burning on microbes in the thinner Gleysol O horizons. The relatively low resilience of bacterial and fungal communities to burning as well as the failure of resilience to increase with time since burning supports previous reports of post-burn microbial community recovery occurring over years rather than months. Burning caused a decrease in CUE with larger decreases following longer, hotter burns, which correlated with an increase in weighted mean predicted 16S rRNA gene copy number, raising the possibility that copy number could serve as a proxy for post-fire CUE in boreal forest soils, though more research is needed to constrain the effects of environmental conditions, substrates, and time since fire on this relationship. These findings suggest several ways in which burn-induced shifts in microbial community composition reflect altered microbial community function in meaningful ways for soil carbon cycling.

ecology↗

bioRxiv2025

Fire removes preexisting pyrogenic organic matter from the ecosystem through the mechanisms of both direct combustion and increasing mineralizability

Pyrogenic organic matter (PyOM) produced during fires plays an important role in the global carbon (C) cycle due to its low microbial availability and resulting high persistence. However, PyOM can be combusted or chemically altered in subsequent fires. To explore the effect of subsequent fire on PyOM, we used a mass loss calorimeter to deliver realistic heat fluxes to jack pine (Pinus banksiana Lamb.) PyOM produced at 350 {degrees}C, testing heat flux profiles (High, Low, and Control) and burial depths (Surface, 1 cm, and 5 cm) in a full-factorial design. We found that both variables significantly affected the C remaining after burns (p < 0.05), with greater C losses at higher heat fluxes and shallower exposure depths. Consistent with our predictions, treatments with high heat exposure (HFHigh+Surface, HFHigh+1cm, HFLow+Surface) showed increases in pH and decreases in total dissolved organic carbon (DOC) and mineralized C after the subsequent fire. Counter to our predictions, treatments with intermediate heat exposure (HFHigh+5cm and HFLow+1cm) caused significant decreases in pH and increases in DOC, mineralized C, modelled decomposable C, and modelled C decomposition rate (p < 0.05), compared to the unburned controls. These findings highlight that, despite its high persistence in fire-free conditions, PyOM is readily combusted and altered in subsequent fires, with important implications for changing fire regimes and the global C cycle. Synopsis StatementSubsequent fires not only consume PyOM produced in previous burns, but can also increase its susceptibility to microbial decomposition, which challenges the potential for PyOM to contribute to long-term carbon storage.

ecology↗

bioRxiv2025

Burn-induced decreases in soil microbial carbon use efficiency vary across soil types and substrates

Wildfires cause immediate changes in above and belowground carbon (C) stocks in boreal forest ecosystems with long-term repercussions for C cycling. Understanding the role of soil microbes in mediating post-fire C cycling and recovery is an important step to predicting how these ecosystems will respond to novel wildfire regimes caused by climate change. Wildfires can cause large shifts in soil bacterial and fungal community composition that can persist for years post-fire. Less is known about the effects of fire on soil microbial community function, such as C use efficiency (CUE). In this study, we measured the effects of burning on substrate-specific CUE using a laboratory incubation of boreal forest soils. We amended burned and unburned soils with either 13C-labelled ground pine roots or glucose and measured the amount of added substrate C that was incorporated into microbial biomass C versus respired as CO2 in order to calculate CUE. Burning caused a decrease in the amount of soil microbial biomass and respiration derived from soil organic C. Glucose-specific CUE declined with burning, driven by a decrease in glucose-derived microbial biomass. This decrease in glucose-specific CUE following burning correlated with an increase in weighted mean predicted 16S rRNA gene copy number, raising the possibility of using copy number as a proxy for post-fire CUE in boreal forest soils. Overall, pine-specific CUE was lower than glucose-specific CUE, likely reflecting the difference in chemical complexity between the two substrates; burning had a much smaller effect on pine-specific CUE, highlighting the variability of CUE between substrates in burned soils.

ecology↗

bioRxiv2025

Resilience not yet apparent in soil fungal communities of the boreal forest from one to five years after wildfire across a severity gradient

Wildfires are natural disturbances characteristic of boreal forests. However, fire regimes around the world are changing, with effects on fire frequency and fire severity. Here, we present data from one and five years post-fire across 40 different sites from the boreal forest of the Northwest Territories and Alberta, Canada, asking the following questions: (1) Do the factors that structure post-fire soil fungal communities change over time? (2) Is there evidence for resilience in fungal community composition across different burn severities? (3) Do fire-enriched taxa change one vs. five years post-fire? Factors correlated with fungal community composition remain largely the same five years post-fire, with a declining correlation with burned/unburned, and an increasing association with vegetation community composition. This suggests that the immediate effects of fire on fungal community composition wane or diverge with time, while the influence of longer-term effects of fire, such as changes in vegetation, increases. Fungal communities failed to demonstrate resilience in community composition five years post-fire, in contrast to our findings for bacterial communities, and suggesting that fungal communities may be more closely tied to soil properties and vegetation communities that take longer to recover post-fire. Finally, we identify and classify fire-responsive fungi into different response types, based on their enrichment or depletion one vs. five years post fire. Persistent fire responders include taxa from the genera Penicillium, Coniochaeta, and Calyptrozyma, and the family Venturiaceae, but different taxa within a single genus respond differently to fires, underscoring that generalizations even at relatively fine taxonomic levels may be inappropriate, and that the mere presence of traits that may be relevant to post-fire success are insufficient alone to guarantee post-fire abundance. Future manipulative and observational studies will help us continue to dissect the multiple factors and traits structuring fungal responses to fires.

microbiology↗

bioRxiv2024

A laboratory method for simulating the effects of subsequent fires on pyrogenic organic matter at different exposure depths in a sand matrix

BackgroundAcross a variety of anthropogenic and natural contexts, fire can reoccur in a previously burned location. However, effects of subsequent fire on preexisting pyrogenic organic matter (PyOM) stocks are difficult to discern. Laboratory experiments offer a powerful approach to investigating how subsequent fire impacts the preexisting PyOM. AimsWe aimed to design a highly repeatable laboratory method to effectively measure the impacts of subsequent fires on PyOM at different soil depths while addressing key limitations of previous methods. MethodsJack pine (Pinus banksiana Lamb.) log burns were used to parameterize realistic heat flux profiles. Using a cone calorimeter, these profiles were applied to buried jack pine PyOM to simulate variable reburn fire intensities. Key resultsIn general, higher heat flux and shallower depths led to more mass loss of PyOM from combustion and more heat exposure. ConclusionsOur reburn method offers a highly replicable way to simulate specific fire scenarios. Conditions that result in more heat exposure (higher heat fluxes, shallower depths) are likely to lead to more loss of PyOM in subsequent fires. ImplicationsThe customizable method could simulate different fire scenarios to investigate spatial variability within a given fire event, or to study the effects of fire on different types of biomass or organisms, such as microbes. Summary textOur paper illustrates a laboratory method to better quantify loss of preexisting PyOM in soil after a fire. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/605814v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@10e9104org.highwire.dtl.DTLVardef@152cb49org.highwire.dtl.DTLVardef@a04c41org.highwire.dtl.DTLVardef@1ee543d_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2024

A granular view of the traits controlling soil bacterial community reconstruction following a prescribed burn

Prescribed burns and wildfires both cause transient reduction of soil microbiome diversity, which has wide-ranging functions in soil and plant health. However, a genetic basis for understanding the mechanisms behind post-fire microbiome recovery is not well-established. Here, we conducted prescribed burns in multiple plots with paired unburned controls, at two prairie locations, sampling each over 5 months. We assembled >300 bacterial genomes that were conserved in both time and space, then identified genomes that were either enriched or depleted post-fire compared to timepoint controls. On a metagenome level, burned and unburned samples were functionally equivalent, but on a species level we determined that post- fire survival is more nuanced than possession of previously hypothesized pyrophilous traits. Our study therefore advances the understanding of how both function and taxonomy contribute to success during the reconstruction of a complex soil microbiome.

microbiology↗

bioRxiv2024

Effects of fire and fire-induced changes in soil properties on post-burn soil respiration

BackgroundBoreal forests cover vast areas of land in the northern hemisphere and store large amounts of carbon (C) both aboveground and belowground. Wildfires, which are a primary ecosystem disturbance of boreal forests, affect soil C via combustion and transformation of organic matter during the fire itself, and via changes in plant growth and microbial activity post-fire. Wildfire regimes in many areas of the boreal forests of North America are shifting towards more frequent and severe fires driven by changing climate. As wildfire regimes shift and the effects of fire on belowground microbial community composition are becoming clearer, there is a need to link fire-induced changes in soil properties to changes in microbial functions such as respiration in order to better predict the impact of future fires on C cycling. ResultsWe used laboratory burns to simulate boreal crown fires on both organic-rich and sandy soil cores collected from Wood Buffalo National Park, Alberta, Canada, to measure the effects of burning on soil properties including pH, total C, and total nitrogen (N). We used 70-day soil incubations and two-pool exponential decay models to characterize the impacts of burning and its resulting changes in soil properties on soil respiration. Laboratory burns successfully captured a range of soil temperatures that were realistic for natural wildfire events. We found that burning increased pH and caused small decreases in C:N in organic soil. Overall, respiration per gram total (post-burn) C in burned soil cores was 16% lower than in corresponding unburned control cores, indicating that soil C lost during a burn may be partially offset by burn-induced decreases in respiration rates. Simultaneously, burning altered how remaining C cycled, causing an increase in the proportion of C represented in the modelled slow-cycling vs. fast-cycling C pool as well as an increase in fast-cycling C decomposition rates. ConclusionsTogether, our findings imply that C storage in boreal forests following wildfires will be driven by the combination of C losses during the fire itself as well as fire-induced changes to the soil C pool that modulate post-fire respiration rates. Moving forward, we will pair these results with soil microbial community data to understand how fire-induced changes in microbial community composition may influence respiration.

ecology↗

bioRxiv2023

Soil carbon mineralization and microbial community dynamics in response to PyOM addition

Wildfires can either negatively impact soil carbon (C) stocks through combustion or increase soil carbon stocks through the production of pyrogenic organic matter (PyOM), which is highly persistent and can affect non-pyrogenic soil organic carbon (SOC) mineralization rates. In this study, we used fine-resolution 13CO2 flux tracing to investigate PyOM-C mineralization, soil priming effects, and their impacts on soil microbial communities in a Californian mixed conifer forest Xerumbrept soil burned in the 2014 King Fire. We added PyOM produced from pine biomass at 350 {degrees}C and 550 {degrees}C to the soil and separately traced the mineralization of 13C-labeled water-extractable and non-water-extractable PyOM-C fractions in a short-term incubation. Our results indicate that the water-extractable fraction is 10-50x more mineralizable in both 350 {degrees}C and 550 {degrees}C PyOM treatments than the SOC or non-water-extractable PyOM fraction. 350 {degrees}C PyOM addition led to a short-term positive priming effect, likely due to co-metabolism of easily mineralizable PyOM-C and the SOC, whereas 550 {degrees}C PyOM addition induced negative priming, potentially due to physical protection of SOC. We observed significant shifts in bacterial community composition in response to both 350 {degrees}C and 550 {degrees}C PyOM, with positive PyOM responders belonging to the genera Noviherbaspirillum, Pseudonocardia, and Gemmatimonas. In contrast, fungal communities were less responsive to PyOM additions. Our findings expand our understanding of the post-fire cycling of PyOM and SOC, providing insights into the microbial mineralization of different PyOM-C fractions and their influence on soil C dynamics in fire-affected ecosystems.

ecology↗

bioRxiv2023

Soil microaggregate bacterial communities following Amynthas tokioensis and Amynthas agrestis earthworm co-invasion

Earthworms restructure the soil environment through burrowing, consumption, and casting behaviors. Though non-native European Lumbricid earthworms are well-studied in North American soils, the Asian pheretimoid Amynthas tokioensis and Amynthas agrestis earthworms exhibit distinct ecological patterns that alter invaded habitats. In particular, bioturbation may affect soil aggregation and microbial community assembly processes, such as dispersal and selection. We aimed to determine the effects of A. tokioensis and A. agrestis co-invasions in woodlands in Madison, WI, U.S. on soil bacterial communities and edaphic characteristics. Using 16S rRNA gene sequencing, we found that the presence and activity of these Amynthas species earthworms significantly affected bacterial community composition. At one site, there was a decrease in sample-to-sample dissimilarity (i.e., decreased beta diversity), with concomitant increases in homogenizing community assembly processes. However, at the other site, we found opposite trends, with evidence for increased compositional dissimilarity between samples and decreased evidence for homogenizing community assembly processes. Overall, inconclusive support for the hypothesized homogenization of bacterial community composition driven by homogenizing community assembly processes indicates that the effects of Amynthas pressure in these systems represent a departure from previously established soil disturbance paradigms. Instead, we conclude that aggregate formation via A. tokioensis and A. agrestis casting activity does not consistently impose a strong selective filter on soil bacterial communities, nor does the heightened earthworm activity necessarily act to meaningfully homogenize soil communities via dispersal. Overall increases in soil C and N under Amynthas spp. activity support previous work indicating enhanced decomposition and incorporation of soil litter, but future work could focus on long-term fate of microaggregate-protected C.

ecology↗

bioRxiv2023

Tillage homogenizes soil bacterial communities in microaggregate fractions by facilitating dispersal

Soil aggregation physically protects soil organic matter and promotes soil carbon persistence through microaggregate formation and organo-mineral associations. Tillage is a ubiquitous disturbance to arable soil that disrupts aggregation, thus affecting microbial resource availability, soil microhabitat conditions, and microbial interactions. We investigated how tillage affects bacterial community composition of soil microaggregate fractions (53-250 {micro}m), specifically the free microaggregate fraction in bulk soil, and the occluded microaggregate fraction from within macroaggregates, using two long-term tillage vs. no-tillage experiments in southern WI, U.S., that represent two different silt loam soils (Alfisol and Mollisol). We applied 16S rRNA gene amplicon sequencing to characterize the effects of tillage on microaggregate bacterial communities by relating compositional changes and ecological community assembly patterns to various tillage-driven changes in the soil environment, including aggregate size distribution and carbon content. Tillage homogenized soil bacterial communities, as quantified by increased compositional similarity at both within-plot and between-plot scales, and community assembly was increasingly influenced by homogenizing dispersal with tillage. We did not identify major distinctions between bacterial communities of the free and occluded microaggregate fractions, thus highlighting how soil microaggregates readily shift between these operationally defined fractions in temperate annual cropping systems, where the soil environment is subject to drastic seasonal changes that are exacerbated by tillage. With this study, we improve our understanding of the microbial response to soil disturbance, and thus the potential mechanisms through which disturbances like tillage affect soil carbon persistence. HighlightsO_LITillage homogenized soil bacterial communities, within and between plots C_LIO_LIHomogenizing dispersal drove community assembly under tillage C_LIO_LIFree and occluded microaggregate fractions hosted similar communities C_LI

ecology↗

bioRxiv2022

An empirical approach to developing and testing a traits-based fire ecology framework for bacterial response to wildfires

Globally, wildfires represent major disturbances, burning millions of hectares annually. Wildfires can restructure soil microbial communities via changes in soil properties and microbial mortality. Fire-induced changes in bacterial communities may influence soil carbon cycling, and recovery to pre-burn community composition and function may take years. We investigated carbon cycling, soil properties, and the importance of three fire-adaptive strategies - fire survival, fast growth, and affinity for post-fire soil environmental conditions - in structuring soil bacterial communities following burns of varying temperatures in boreal forest soils. To identify taxa with each strategy, we simulated burns and incubated soils, tracking respiration and sequencing DNA and rRNA. We then quantified their abundances in the field following wildfires of varying burn severities. The importance of these strategies varies over time and with burn severity. Fire survival has a small but persistent effect on structuring burned soil communities. Fast growing bacteria rapidly colonize the post-fire soil but return to pre-burn relative abundances between one and five years post-fire. Taxa with an affinity for the post-fire environment thrive post-fire, but the effect of this strategy declines by five years post-fire, suggesting that other factors such as vegetation recovery or bacterial dispersal may influence community composition over decadal timescales. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/495025v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@f6cf22org.highwire.dtl.DTLVardef@198f5fdorg.highwire.dtl.DTLVardef@13de0f2org.highwire.dtl.DTLVardef@17b4712_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2022

Resilience in soil bacterial communities of the boreal forest from one to five years after wildfire across a severity gradient

Wildfires can represent a major disturbance to ecosystems, including soil microbial communities belowground. Furthermore, fire regimes are changing in many parts of the world, altering and often increasing fire severity, frequency, and size. The boreal forest and taiga plains ecoregions of northern Canada are characterized by naturally-occurring stand-replacing wildfires on a 40-350 year basis. We previously studied the effects of wildfire on soil microbial communities one year post-fire across 40 sites, spanning a range of burn severity. Here, we return to the same sites five years post-fire to test a series of hypotheses about the effects of fire on bacterial community composition. We ask the following questions: (1a) Do the fundamental factors structuring bacterial community composition remain the same five years post-fire? (1b) Do the effects of fire on bacterial community composition decrease between one and five years post-fire? (1c) Do shifts in bacterial community composition between one and five years post-fire suggest resilience? (2a) Does the importance of fast growth diminish between one and five years post-fire? (2b) Do short-term post-fire responders continue to dominate the community five years post-fire? We find the following: (1a) Five years post-fire, vegetation community, moisture regime, pH, total carbon, texture, and burned/unburned all remained significant predictors of bacterial community composition with similar predictive value (R2). (1b and 1c) Bacterial communities became more similar to unburned sites five years post-fire, across the range of severity, suggesting resilience, while general structure of co-occurrence networks remained similar one and five years post-fire. (2a) Fast growth potential, as estimated using predicted 16S rRNA copy numbers, was no longer significantly correlated with burn severity five years post-fire, indicating the importance of this trait for structuring bacterial community composition may be limited to relatively short timescales. (2b) Many taxa that were enriched in burned sites one year post-fire remained enriched five years post-fire, although the degree to which they were enriched generally decreased. Specific taxa of interest from the genera Massilia, Blastococcus, and Arthrobacter all remained significantly enriched, suggesting that they may have traits that allow them to continue to flourish in the post-fire environment, such as tolerance to increased pH or ability to degrade pyrogenic organic matter. This hypothesis-based work expands our understanding of the post-fire recovery of soil bacterial communities and raises new hypotheses to test in future studies.

ecology↗

bioRxiv2022

Disturbance by soil mixing decreases microbial richness and supports homogenizing community assembly processes

The spatial heterogeneity of soils microhabitats warrants the study of ecological patterns and community assembly processes in the context of community coalescence, or the combining and restructuring of communities and their environment. By mixing soil at various frequencies in a 16-week lab incubation, we explored the effects of mixing disturbance on soil bacterial richness, community composition, and community assembly processes. We hypothesized that well-mixed soil would harbor less richness, dominated by homogenizing dispersal and homogeneous selection. Using 16S rRNA gene sequencing, we inferred ecological processes, estimated richness and differential abundance, calculated compositional dissimilarity, and constructed co-occurrence networks. Findings supported our hypotheses, with >20% decrease in soil bacterial richness in well-mixed soil. While soil mixing resulted in increasingly dissimilar communities compared to unmixed soil (Bray-Curtis dissimilarity; 0.75 vs. 0.25), well-mixed soil communities were increasingly self-similar. Our results imply that vast soil diversity may be attributed to the unmixed and spatially heterogeneous nature of soil, and also provide insight into soil communities following coalescence events. By isolating and better understanding the effect of spatial heterogeneity and dysconnectivity on soil microbial communities, we may better extrapolate how anthropogenic disturbances, such as climate change or land use change, may affect broad soil functions. One sentence summarySoil mixing decreases bacterial richness as several taxa dominate the community, providing evidence for homogenizing community assembly processes.

ecology↗

bioRxiv2021

Short-interval reburns in the boreal forest alter soil bacterial communities, reflecting increased pH and poor conifer seedling establishment

Increasing burn rates (percentage area burned annually) in some biomes are leading to fires burning in close succession, triggering rapid vegetation change as well as altering soil properties. Despite the importance of soil microbes for nutrient cycling and as plant symbionts, the effects of increased fire frequency on belowground microbial communities remain largely unknown. We present a study of the effects of short interval reburns (defined here as <20 years between fires) on soil bacterial communities in the boreal forest of northwestern Canada, using a paired site design that spans wetlands and uplands, with 50 sites total. We asked whether short interval reburns significantly alter soil bacterial community composition and richness, and which bacterial taxa are associated with greater or lower fire frequency. We found that, while short interval reburns had no significant effect on bacterial richness, there were significant changes in overall community composition. We did not find correlations between understory vegetation community dissimilarities and bacterial community dissimilarities, suggesting the primary drivers of changes induced by short interval reburns may differ between plants and microbes. We identified an abundant Blastococcus sp. that was consistently enriched in short interval reburns, in both wetlands and uplands, indicating its role as a strongly "pyrophilous" bacterium. We also identified an abundant Callaberonia sordidicola taxon as being consistently depleted in short interval reburns. This endophytic diazotrophic organism is a robust colonizer of pine and spruce seedlings and has the ability to increase seedling growth, due in part to large contributions of fixed nitrogen. Its depletion in short-interval reburn sites raises questions about whether this is contributing to - or merely reflects - poor conifer seedling recolonization post-fire at short-interval reburns.

ecology↗

bioRxiv2021

Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues

1.Minerals preserve the oldest most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that carbon source and soil microorganisms also influence mineral-SOM associations, we incubated permeable minerals bags in soil microcosms with and without plants, in a 13CO2 labeling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or native soil minerals isolated via density separation. Using 13C-NMR, FTICR-MS, and lipidomics, we traced plant-derived carbon onto minerals harvested from microcosms at three plant growth stages, characterizing total carbon, 13C enrichment, and SOM chemistry. While C accumulation was rapid and mineral-dependent, the accumulated amount was not significantly affected by the presence of plant roots. However, the rhizosphere did shape the chemistry of mineral-associated SOM. Minerals incubated in the rhizosphere were associated with a more diverse array of compounds with different C functional groups (carbonyl, aromatics, carbohydrates, lipids) than minerals incubated in a bulk soil control. These diverse rhizosphere-derived compounds may represent a "transient fraction" of mineral SOM, rapidly exchanging with mineral surfaces. Our results also suggest that many of the lipids which persist on minerals are microbially-derived with a large fraction of fungal lipids. SynopsisThis study explores the interaction of rhizosphere carbon, minerals, and microbial influence on the fate of soil carbon. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/436628v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@17ce1bborg.highwire.dtl.DTLVardef@1c7c2e8org.highwire.dtl.DTLVardef@1cd0e41org.highwire.dtl.DTLVardef@162ff90_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2021

Pyrolyzed substrates induce aromatic compound metabolism in the post-fire fungus, Pyronema domesticum

Wildfires represent a fundamental and profound disturbance in many ecosystems, and their frequency and severity are increasing in many regions of the world. Fire affects soil by removing carbon in the form of CO2 and transforming remaining surface carbon into pyrolyzed organic material (PyOM). Fires also generate substantial necromass at depths where the heat kills soil organisms but does not catalyze the formation of PyOM. Pyronema species strongly dominate soil fungal communities within weeks to months after fire. However, the carbon pool (i.e. necromass or PyOM) that fuels their rise in abundance is unknown. We used a Pyronema domesticum isolate from the catastrophic 2013 Rim Fire (CA, USA) to ask if P. domesticum is capable of metabolizing PyOM. P. domesticum grew readily on agar media where the sole carbon source was PyOM (specifically, pine wood PyOM produced at 750 {degrees}C). Using RNAseq, we investigated the response of P. domesticum to PyOM and observed a comprehensive induction of genes involved in the metabolism and mineralization of aromatic compounds, typical of those found in PyOM. Lastly, we used 13C-labeled 750 {degrees}C PyOM to demonstrate that P. domesticum is capable of mineralizing PyOM to CO2. Collectively, our results indicate a robust potential for P. domesticum to liberate carbon from PyOM in post-fire ecosystems and return it to the bioavailable carbon pool. IMPORTANCEFires are increasing in frequency and severity in many regions across the world. Thus, its critically important to understand how our ecosystems respond to inform restoration and recovery efforts. Fire transforms the soil, removing many nutrients while leaving behind both nutritious necromass and complex pyrolyzed organic matter, which is often recalcitrant. Filamentous fungi of the genus Pyronema strongly dominate soil fungal communities soon after fire. While Pyronema are key pioneer species in post-fire environments, the nutrient source that fuels their rise in abundance is unknown. In this manuscript, we used a P. domesticum isolate from the catastrophic 2013 Rim Fire (CA, USA) to demonstrate that P. domesticum metabolizes pyrolyzed organic material, effectively liberating this complex pyrolyzed carbon and returning it to the bioavailable carbon pool. The success of Pyronema in post-fire ecosystems has the potential to kick-start growth of other organisms and influence the entire trajectory of post-fire recovery.

microbiology↗

bioRxiv2021

Effects of physical, chemical, and biological ageing on the mineralization of pine wood biochar by a Streptomyces isolate

If biochar is to be used for carbon (C) management, we must understand how ageing affects biochar C mineralization. Here, we incubated aged and unaged eastern white pine wood biochar produced at 350 and 550 {degrees}C with a Streptomyces isolate, a putative biochar-decomposing microbe. Ageing was simulated via exposure to (a) alternating freeze-thaw and wet-dry cycles (physical ageing), (b) concentrated hydrogen peroxide (chemical ageing) and (c) nutrients and microorganisms (biological ageing). Elemental composition and surface chemistry (Fourier Transform Infrared spectroscopy) of biochar samples were compared before and after ageing. Ageing significantly increased biochar C mineralization in the case of physically aged 350 {degrees}C biochar (p < 0.001). Among 350 {degrees}C biochars, biochar C mineralization was positively correlated with an increase in O/C ratio (R2 = 0.78) and O-containing functional groups (R2 = 0.73) post-ageing, suggesting that surface oxidation during ageing enhanced biochar degradation by the isolate. However, in the case of 550 {degrees}C biochar, ageing did not result in a significant change in biochar C mineralization (p > 0.05), likely due to lower surface oxidation and high condensed aromatic C content. These results have implications for the use of biochar for long term C storage in soils. SynopsisThis study highlights the impact of ageing on the microbial mineralization of biochar, which can affect its long-term C storage capacity. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/430652v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@14f3d6dorg.highwire.dtl.DTLVardef@149ebe3org.highwire.dtl.DTLVardef@1d8df9org.highwire.dtl.DTLVardef@5404a7_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2020

Standard and Non-Standard Measurements of Acidity and the Bacterial Ecology of Northern Temperate Mineral Soils

Databases of soil pH values today guide the decisions of land managers and the experimental designs of microbiologists and biogeochemists. Soil acidity underpins fundamental properties and functions in the soil, such as the solubilities of exchangeable ions and nutrients, or bacterial use of gradients of internal and external acidity to generate ATP and turn flagellar motors. Therefore, it is perhaps unsurprising that soil pH has emerged as the strongest predictor of soil bacterial community composition. However, the measurement of these particular values today does not address whether soil pH accurately represents the in situ acidity of soil microhabitats where microorganisms survive and reproduce. This study analyzes and compares soils of a large-scale natural soil pH gradient and a long-term experimental soil pH gradient for the purposes of testing new methods of measuring and interpreting soil acidity when applied to soil ecology. We extracted and prepared soil solutions using laboratory simulation of levels of carbon dioxide and soil moisture more typical of soil conditions while also miniaturizing extraction methods using a centrifuge for extractions. The simulation of in situ soil conditions resulted in significantly different estimates of soil pH. Furthermore, for soils from the long-term experimental soil pH gradient trial, the simulated soil pH values substantially improved predictions of bacterial community composition (from R2 = 0.09 to R2 = 0.16). We offer suggestions and cautions for researchers considering how to better represent soil pH as it exists in situ.

ecology↗