Article

Contrasting fungal responses to wildfire across different ecosystem types

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Abstract

Wildfire affects our planet's biogeochemistry both by burning biomass and by driving changes in ecological communities and landcover. Some plants and ecosystem types are threatened by increasing fire pressure while others respond positively to fire, growing in local and regional abundance when it occurs regularly. However, quantifying total ecosystem response to fire demands consideration of impacts not only on aboveground vegetation, but also on soil microbes like fungi, which influence decomposition and nutrient mineralization. If fire‐resistant soil fungal communities co‐occur with similarly adapted plants, these above‐ and belowground ecosystem components should shift and recover in relative synchrony after burning. If not, fire might decouple ecosystem processes governed by these different communities, affecting total functioning. Here, we use a natural experiment to test whether fire‐dependent ecosystems host unique, fire‐resistant fungal communities. We surveyed burned and unburned areas across two California ecosystem types with differing fire ecologies in the immediate aftermath of a wildfire, finding that the soil fungal communities of fire‐dependent oak woodlands differ from those of neighbouring mixed evergreen forests. We discovered furthermore that the latter are more strongly altered compositionally by fire than the former, suggesting that differences in fungal community structure support divergent community responses to fire across ecosystems. Our results thus indicate that fire‐dependent ecosystems may host fire‐resistant fungal communities.

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... Considering the negative effects of fire on fungal populations, the results are consistent with studies that have demonstrated that fungal diversity decreases in ecosystems exposed to fire [63]. Evidence suggests that this is due to both the lower thermal tolerance of fungi, mycorrhizal fungi, and the mortality of plant hosts during fires [101][102][103]. Fire did not affect abundance, diversity and evenness of microbes affirming the notion that microbes, as a whole, are resistant to fire effects. ...
... However, microbial biomass did decrease in response to fires, an aspect that has been documented by other researchers [104,105]. The changes in the nutrient supply due to the loss of plant residues is proposed as the reason for microbial biomass reductions following a fire [102,106]. These findings suggest that fire may affect biomass, while abundance and diversity and evenness may not be affected substantially following a fire. ...
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Globally, wildfires and prescribed fires are becoming more prevalent and are known to affect plant and animals in diverse ecosystems. Understanding the responses of animal communities to fire is a central issue in conservation and a panacea to predicting how fire regimes may affect communities and food webs. Here, a global meta-analysis of 2581 observations extracted from 208 empirical studies were used to investigate the effect of fire on aboveground and belowground fauna (e.g., bacteria, fungi, small mammals, arthropods). Overall, results revealed that fire had a negative effect on biomass, abundance, richness, evenness, and diversity of all faunas. Similarly, when considering wildfires and prescribed fires the data revealed that both fire regimes have negative effects on fauna. Similarly, fire had negative impacts on aboveground and aboveground fauna across most biomes and continents of the world. Moreover, there was little evidence of changes in pH, moisture and soil depth on soil organisms suggesting that other factors may drive community changes following a fire disturbance. Future research in fire ecology should consider the effects of fire across several species and across larger geospatial scales. In addition, fire effects on faunal community structure must be studied under contrasting global fire regimes and in light of the effects of climate change.
... There is growing evidence that a pulse of fire-responsive fungi appears quickly and proliferates across burned soil soon after fire in conifer forests. This phenomenon has been recently documented by new molecular probing techniques that detect mycelial and spore presence, so that evidence no longer depends solely on fruiting body occurrence, giving a broader picture of fungal distribution (Watts et al., 2018;Kauki and Salo, 2020;Smith et al., 2021). According to molecular results, pre-fire fungal communities dominated by basidiomycota are replaced by fireresponsive ascomycete fungi (including Pyronema and Morchella), as soon as one week after fire (Watts et al., 2018). ...
... According to molecular results, pre-fire fungal communities dominated by basidiomycota are replaced by fireresponsive ascomycete fungi (including Pyronema and Morchella), as soon as one week after fire (Watts et al., 2018). At least some of these fungi (Pyronema, Geopyxis, and Warcupia) may be restricted to burned conifer forests after fire (Smith et al., 2021). ...
Article
Forest fire is an important occurrence in western landscapes where it helps drive ecosystem processes, and prescribed fire is a common forest management strategy. An initial consequence of fire is burned ground with reduced biodiversity. Numerous studies have documented how forests recover after fire in terms of plant regeneration and animal colonization, but little is known of the ecological roles fungi play in this process. Pyrophilous (burn-loving) fungi are documented to reliably produce large fruitings and copious mycelium on burns after fire in North America, Europe, Asia, and Australia. We hypothesize that pyrophilous fungi help bind and stabilize soil after forest fires via their extensive mycelial network. Three pyrophilous fungi, Geopyxis carbonaria, Pyronema omphalodes, and Morchella septimelata were tested for their ability to aggregate burned soil. The fungi were isolated from burn sites, grown in vitro, and inoculated onto sterilized soil from a natural burn. The ability of each species to aggregate soil in comparison to non-inoculated controls was assessed after 10, 20, 30, and 40 days, using a wet sieve aggregate stability test. All three fungi increased soil aggregation after 10 days, and this increase was maintained for the 40-day period. The burned soil was up to 30% more aggregated when a fungus was present; results provide the first direct evidence that pyrophilous fungi aggregate burn soil. This further implies that these fungi play a role in reducing soil erosion and enhancing soil moisture soon after fire in burned forests. Pyrophilous fungi also decompose charred material, sequester carbon, and capture transient nitrogen pulses after fire. This overlooked group of fungi may be critical in enhancing conditions for plant regeneration after forest fire at an early stage in recovery. Consideration should be given to avoiding or delaying restoration activities that disturb this natural process, especially those that contribute to soil compaction, during early post-fire recovery when these fungi are proliferating.
... In most cases, fire severity appeared to favor microbial taxa that are resilient to heat stress and able to rapidly colonize and take advantage of increased nutrients in the young burnt area. For example, studies that evaluated the responses of fungi to fire (Chen and Cairney, 2002;Hansen et al., 2019) indicate that fungi have developed a variety of evolutionary adaptations to fire, including heat-resistant spores, where species with such adaptations might be less compositionally altered by fire (Smith et al., 2021) and thus shows a high level of species similarity (Anderson et al., 2006). Indeed, some evidence indicates that pyrogenic ecosystems might host distinct soil fungal communities that can resist fire-related change (Hansen et al., 2019;Oliver et al., 2015). ...
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Cistus scrublands are pyrophytic ecosystems and occur widely across Mediterranean regions. Management of these scrublands is critical to prevent major disturbances, such as recurring wildfires. This is because management appears to compromise the synergies necessary for forest health and the provision of ecosystem services. Furthermore, it supports high microbial diversity, opening questions of how forest management practices impact belowground associated diversity as research related to this issue is scarce. This study aims to investigate the effects of different fire prevention treatments and site history on bacterial and fungi co-response and co-occurrence patterns over a fire-risky scrubland ecosystem. Two different site histories were studied by applying three different fire prevention treatments and samples were analyzed by amplification and sequencing of ITS2 and 16S rDNA for fungi and bacteria, respectively. The data revealed that site history, especially regarding fire occurrence, strongly influenced the microbial community. Young burnt areas tended to have a more homogeneous and lower microbial diversity, suggesting environmental filtering to a heat-resistant community. In comparison, young clearing history also showed a significant impact on the fungal community but not on the bacteria. Some bacteria genera were efficient predictors of fungal diversity and richness. For instance, Ktedonobacter and Desertibacter were a predictor of the presence of the edible mycorrhizal bolete Boletus edulis. These results demonstrate fungal and bacterial community co-response to fire prevention treatments and provide new tools for forecasting forest management impacts on microbial communities.
... Thermotolerant fungi (Fergus 1964;Redman et al. 1999;Rippon et al. 1980;Suryanarayanan et al. 2011) parallel fire-resistant plants and include fireadapted plant-fungal associations (Baynes et al. 2011). Ecosystems defined by fire-adapted plants also appear to host fire-resistant fungi, likely representing parallel evolution (Pérez-Izquierdo et al. 2020;Smith et al. 2021). Thermotolerant fungi can also produce heat-resistant compounds (Sharkey et al. 2001;Singsaas 2000), including laccases (Hildén et al. 2007) and trehalose (Tereshina 2005). ...
Article
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Fires occur in most terrestrial ecosystems where they drive changes in the traits, composition, and diversity of fungal communities. Fires range from rare, stand-replacing wildfires to frequent, prescribed fires used to mimic natural fire regimes. Fire regime factors, including burn severity, fire intensity, and timing, vary widely and likely determine how fungi respond to fires. Despite the importance of fungi to post-fire plant communities and ecosystem functioning, attempts to identify common fungal responses and their major drivers are lacking. This synthesis addresses this knowledge gap and ranges from fire adaptations of specific fungi to succession and assembly fungal communities as they respond to spatially heterogenous burning within the landscape. Fires impact fungi directly and indirectly through their effects on fungal survival, substrate and habitat modifications , changes in environmental conditions, and/or physiological responses of the hosts with which fungi interact. Some specific pyrophilous, or "fire-loving," fungi often appear after fire. Our synthesis explores whether such taxa can be considered cosmopolitan, and whether they are truly fire-adapted or simply opportunists adapted to rapidly occupy substrates and habitats made available by fires. We also discuss the possible inoculum sources of post-fire fungi and explore existing conceptual models and ecological frameworks that may be useful in generalizing fungal fire responses. We conclude with identifying research gaps and areas that may best transform the current knowledge and understanding of fungal responses to fire.
... In this region, fire potentially affects the vegetation resources (Gassibe et al., 2011;Hernández-Rodríguez et al., 2013), including the biodiversity constituting the ecosystem. In addition, stand-replacing fires can alter the physical, chemical, and biochemical properties of the soil, mainly due to the intense heating of the soil and ash deposition (Peay et al., 2009;Smith et al., 2021). ...
Article
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In the context of global change, wildfires are not only a threat but are also increasing in their severity in forest ecosystems worldwide, affecting and modifying vegetation, wildlife, and fungal dynamics. Mediterranean ecosystems are frequently affected by fire and prescribed burning is being increasingly used as a tool to reduce the risk and severity of wildfires. Although some of the effects of prescribed burning have been studied, the best moment to perform a prescribed burn to reduce the impact of fire on fungal communities has not been fully investigated. In this study, we analysed the effect of prescribed burning in two different seasons (spring and autumn) on soil fungi associated with natural Pinus nigra forests. Four years after prescribed burning was applied, our analyses showed that the total fungal richness and the composition of fungal communities in spring-burned, autumn-burned, and unburned control plots did not differ significantly. However, analyses of specific phyla and functional trophic groups did reveal some significant differences between spring- or autumn-burned plots and unburned control plots. Valuable edible fungi, which were not affected by the prescribed burning, were also found in the study area. Thus, our results suggest that prescribed burning is not only an interesting tool that could be used to reduce the risk of wildfire but also is compatible with the conservation of fungal communities, and could even promote specific valuable edible species, generating complementary incomes for the rural population. Although further studies are needed, our analyses suggest that the season (spring or autumn) in which prescribed burning is performed does not affect fungal conservation and, therefore, does not need to be one of the factors taken into consideration when selecting the most appropriate time to perform a prescribed burning.
... Восстановление грибов-симбиотов напрямую связано с восстановлением деревьев. Маслята и рыжики растут через несколько лет после пожара там, где был самосев сосен (Smith et al., 2021). Плодовые тела грибовксилотрофов, собранные в том числе в местах, пройденных пожарами, используют в медицине. ...
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В связи с возрастающим антропогенным воздействием и глобальными климатическими изменениями, частота и интенсивность пожаров возрастают по всему миру. Пирогенный фактор становится всё более острой проблемой для лесных стран, требующей незамедлительных решений, так как происходят катастрофические сокращения площади лесных экосистем, невосполнимая утрата биоразнообразия — провайдера экосистемных функций и услуг лесов. Многие биологи рассматривают пожары как губительный для биоты фактор, приводящий к безвозвратной утере части видов и групп живых организмов, а если после действия пожаров восстановление и возможно, для этого требуется продолжительный период времени. Однако в настоящее время появляется время всё больше научных работ, авторы которых утверждают, что пожары не только не сокращают, но и повышают биоразнообразие лесных экосистем, а также способствуют сохранению видов и устойчивому функционированию лесов. Данная статья направлена на анализ результатов исследований влияния пожаров на основные компоненты лесных экосистем, их биоразнообразие и функции. Авторы дают ответ на вопрос, почему пожар как очевидно деструктивный фактор иногда рассматривается как фактор повышения биоразнообразия. Большинство «положительных» эффектов пожаров на биоразнообразие сводится к возникновению мозаичности, прорывов в пологе леса после пожара. Однако проведенный анализ литературы показывает, что устойчивое мнение в ряде работ о необходимости определенной периодичности пожаров для поддержания лесных сообществ связано с игнорированием или недопониманием роли биотических факторов в функционировании лесов. В современных лесных экосистемах утрачены или сильно сокращены популяции ключевых видов крупных млекопитающих, а следовательно, отсутствуют и формируемые ими микросайты, включая большие прорывы в пологе леса (окна, поляны), обеспечивающие возможности поддержания светолюбивой флоры, насекомых-опылителей и в целом поддержания условий для развития разновозрастных полидоминантных лесных экосистем с высоким биологическим разнообразием. В практике ведения лесного хозяйства известны подходы по поддержанию мозаичности (специальные виды рубок, поддержание популяций ключевых видов животных и др.), которые существенно менее катастрофичны в сравнении с пирогенным фактором и биологически обоснованы. Даны рекомендации по сохранению и поддержанию биоразнообразия и экосистемных функций лесов в современных лесах.
... Восстановление грибов-симбиотов напрямую связано с восстановлением деревьев. Маслята и рыжики растут через несколько лет после пожара там, где был самосев сосен (Smith et al., 2021). Плодовые тела грибовксилотрофов, собранные в том числе в местах, пройденных пожарами, используют в медицине. ...
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Due to ever-increasing anthropogenic impact and global climate change, wildfires are becoming more frequent and intense all over the world. The wildfire factor is turning into an acute problem for forested countries that requires prompt solutions as the areas of forest ecosystems are reducing catastrophically, which results in an irreparable loss of biodiversity that provides all ecosystem functions and forest services. Many biologists consider wildfires a factor destructive to biota that results in permanent loss of some species and groups of living organisms; even if it is possible for them to recover after a wildfire, they may need a lot of time to do so. However, some studies argue that not only do wildfires reduce the biodiversity in forest ecosystems, but they also increase it, thus contributing to species conservation and sustainable functioning of forests. This article is aimed at analyzing the works that study how wildfires impact the main components, biodiversity, and functions of forest ecosystems. The authors answer the question why wildfires, while being an obvious destruction factor, are sometimes considered a factor for increase in biodiversity. The “positive” influence wildfires have on biodiversity can mostly be reduced to mosaic patterns, that is, forest canopy gaps that occur after a wildfire. However, reference analysis shows that the persistent opinion found in a number of works that a certain frequency of wildfires is necessary to maintain forest communities may be associated with ignored or misunderstood importance of biotic factors in the functioning of forests. In contemporary forest ecosystems, populations of key large mammal species disappeared or are greatly reduced; therefore, there are no microsites they usually form, including large forest canopy leaps (gaps, glades) that provide both opportunities for photophilous flora and pollinating insects to develop and generally sufficient conditions for multi-aged polydominant forest ecosystems with high biodiversity. In the forestry practice, measures are known to maintain mosaics. They include special types of felling, supporting populations of key animal species, etc., and are both significantly less catastrophic in comparison with the wildfire factor and substantiated biologically. The authors provide recommendations for the conservation and maintenance of biodiversity and ecosystem functions in contemporary forests.
... Overall, these authors' findings also supported the notion that fungal communities had evolved within that fire-prone forest, and had somehow adapted to it. Such a notion is supported also by the findings of Smith et al. (2021), which also indicate the likely centrality of fireadapted soil fungal communities in restoring the structure and functions of fire-prone ecosystems. ...
Article
Fire has always been a driving factor of life on Earth. Now that mankind has definitely joined the other environmental forces in shaping the planet, lots of species are threatened by human-induced variation in fire regimes. Soil-dwelling organisms, i.e., those organisms that primarily live in soil, suffer the numerous and different consequences of fire occurrence that are, however, often overlooked compared to those on vegetation and wildlife. Most of these organisms live in the uppermost soil layer, where fire-imposed temperatures on the ground are the highest insofar as they are lethal or dangerously upset natural habitats. This contribution is a reasoned collation of findings from a number of works conducted worldwide that aims to gain insight into the immediate and longer-term impacts of single or repeated wild or prescribed fires on one group of soil-dwelling organisms or more. In fire-prone ecosystems, fire is a controlling factor of soil biota biodiversity and activity, but also where it is infrequent its ecological footprint can be substantial and lasting. Generally, the immediate fire impact on soil biota is strictly related to the peak temperatures reached on the ground and their duration, and on a set of soil properties and water content. Vertebrates can escape overheating death by running away, searching for wet niches or burrowing deep into soil. Invertebrates and microorganisms, which have little or no mobility, succumb more easily to fire, but make up for this intrinsic vulnerability thanks to their greater fecundity at the population level. Fire or burn severity, which can generally be defined as loss of organic matter aboveground and belowground, is the key factor of the indirect fire effects on soil-dwelling biota; whereas controlled burns do not often imply any substantial and lasting shift from the original situation, extreme and vast wildfires can have major consequences that may be severer than direct killing. In fact lairs are devastated, nutrient pools are heavily affected, food webs are upset, soil temperature and moisture regimes change, and toxic pyrogenic compounds remain in soil. All types of organisms can recolonise the burned area from their sanctuaries, provided that land use does not change, e.g., to pastures or arable fields, and prompt enough vegetation re-sprouting and/or encroachment prevent substantial soil erosion. Each major taxon has genera or species with useful traits and behaviours to resist fire or to recover from its unwelcome environmental legacy sooner than others. If burned soil does not undergo other fires that occur too closely together for the typical fire regime of that particular area, most of its living components are generally capable of returning to pre-fire levels in times that depend on a series of factors, such as fire severity and post-fire rainfall.
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Fire frequency is changing globally and is projected to affect the global carbon cycle and climate. However, uncertainty about how ecosystems respond to decadal changes in fire frequency makes it difficult to predict the effects of altered fire regimes on the carbon cycle; for instance, we do not fully understand the long-term effects of fire on soil carbon and nutrient storage, or whether fire-driven nutrient losses limit plant productivity. Here we analyse data from 48 sites in savanna grasslands, broadleaf forests and needleleaf forests spanning up to 65 years, during which time the frequency of fires was altered at each site. We find that frequently burned plots experienced a decline in surface soil carbon and nitrogen that was non-saturating through time, having 36 per cent (±13 per cent) less carbon and 38 per cent (±16 per cent) less nitrogen after 64 years than plots that were protected from fire. Fire-driven carbon and nitrogen losses were substantial in savanna grasslands and broadleaf forests, but not in temperate and boreal needleleaf forests. We also observe comparable soil carbon and nitrogen losses in an independent field dataset and in dynamic model simulations of global vegetation. The model study predicts that the long-term losses of soil nitrogen that result from more frequent burning may in turn decrease the carbon that is sequestered by net primary productivity by about 20 per cent of the total carbon that is emitted from burning biomass over the same period. Furthermore, we estimate that the effects of changes in fire frequency on ecosystem carbon storage may be 30 per cent too low if they do not include multidecadal changes in soil carbon, especially in drier savanna grasslands. Future changes in fire frequency may shift ecosystem carbon storage by changing soil carbon pools and nitrogen limitations on plant growth, altering the carbon sink capacity of frequently burning savanna grasslands and broadleaf forests.
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Whether niche processes, like environmental filtering, or neutral processes, like dispersal limitation, are the primary forces driving community assembly is a central question in ecology. Here, we use a natural experimental system of isolated tree “islands” to test whether environment or geography primarily structures fungal community composition at fine spatial scales. This system consists of isolated pairs of two distantly-related, congeneric pine trees established at varying distances from each other and the forest edge, allowing us to disentangle the effects of geographic distance versus host and edaphic environment on associated fungal communities. We identified fungal community composition with Illumina sequencing of ITS amplicons, measured all relevant environmental parameters for each tree - including tree age, size, and soil chemistry - and calculated geographic distances from each tree to all others and to the nearest forest edge. We applied generalized dissimilarity modeling to test whether total and ectomycorrhizal fungal (EMF) communities were primarily structured by geographic or environmental filtering. Our results provide strong evidence that, as in many other organisms, niche and neutral processes both contribute significantly to turnover in community composition in fungi, but environmental filtering plays the dominant role in structuring both free-living and symbiotic fungal communities at fine spatial scales. In our study system, we found pH and organic matter primarily drive environmental filtering in total soil fungal communities and that pH and cation exchange capacity – and, surprisingly, not host species - were the largest factors affecting EMF community composition. These findings support an emerging paradigm that pH may play a central role in the assembly of all soil mediated systems. This article is protected by copyright. All rights reserved.
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Climate, land use, and other anthropogenic and natural drivers have the potential to influence fire dynamics in many regions. To develop a mechanistic understanding of the changing role of these drivers and their impact on atmospheric composition, long-term fire records are needed that fuse information from different satellite and in situ data streams. Here we describe the fourth version of the Global Fire Emissions Database (GFED) and quantify global fire emissions patterns during 1997–2016. The modeling system, based on the Carnegie–Ames–Stanford Approach (CASA) biogeochemical model, has several modifications from the previous version and uses higher quality input datasets. Significant upgrades include (1) new burned area estimates with contributions from small fires, (2) a revised fuel consumption parameterization optimized using field observations, (3) modifications that improve the representation of fuel consumption in frequently burning landscapes, and (4) fire severity estimates that better represent continental differences in burning processes across boreal regions of North America and Eurasia. The new version has a higher spatial resolution (0.25◦) and uses a different set of emission factors that separately resolves trace gas and aerosol emissions from temperate and boreal forest ecosystems. Global mean carbon emissions using the burned area dataset with small fires (GFED4s) were 2.2 × 1015 grams of carbon per year (Pg C yr−1) during 1997–2016, with a maximum in 1997 (3.0 Pg C yr−1) and minimum in 2013 (1.8 Pg C yr−1). These estimates were 11 % higher than our previous estimates (GFED3) during 1997–2011, when the two datasets overlapped. This net increase was the result of a substantial increase in burned area (37 %), mostly due to the inclusion of small fires, and a modest decrease in mean fuel consumption (−19 %) to better match estimates from field studies, primarily in savannas and grasslands. For trace gas and aerosol emissions, differences between GFED4s and GFED3 were often larger due to the use of revised emission factors. If small fire burned area was excluded (GFED4 without the “s” for small fires), average emissions were 1.5 Pg C yr−1. The addition of small fires had the largest impact on emissions in temperate North America, Central America, Europe, and temperate Asia. This small fire layer carries substantial uncertainties; improving these estimates will require use of new burned area products derived from high-resolution satellite imagery. Our revised dataset provides an internally consistent set of burned area and emissions that may contribute to a better understanding of multi-decadal changes in fire dynamics and their impact on the Earth system. GFED data are available from http://www.globalfiredata.org.
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Least-squares means are predictions from a linear model, or averages thereof. They are useful in the analysis of experimental data for summarizing the effects of factors, and for testing linear contrasts among predictions. The lsmeans package (Lenth 2016) provides a simple way of obtaining least-squares means and contrasts thereof. It supports many models fitted by R (R Core Team 2015) core packages (as well as a few key contributed ones) that fit linear or mixed models, and provides a simple way of extending it to cover more model classes.
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The recovery of forests following stand-replacing disturbance is of widespread interest; however, there is both a lack of definitional clarity for the term “recovery” and a dearth of empirical data on the rates of forest recovery associated with different disturbance types. We conducted a quantitative review of literature to determine recovery times following wildfire and timber harvest and to evaluate variation in recovery rates across Canada’s diverse forest ecosystems. Recovery was assessed according to the rate of change associated with certain forest structural attributes that have traditionally been used as indicators of forest growth and productivity. The recovery of forest canopy cover, tree height, and stand basal area varied at rates that depended on disturbance type, forest biome, and ecozone. We found that, on average, it took 5–10years, depending on factors such as location and species, for most forest ecosystems of Canada to attain a benchmark canopy cover of 10% after wildfire or harvest. Similarly, regenerating stands in Canada’s boreal forests were capable of attaining average heights of 5m within five to ten years after wildfire or harvest. Stands in the Boreal Plains ecozone post-harvest reached stand basal area, benchmarked at 10m2ha−1, faster than those in the Boreal Shield, attributable to differences in tree species composition and the rich mineral deposits of the Boreal Plains. Overall, recovery of canopy cover, tree height, and stand basal area was similar or more rapid following wildfire than harvest. Our review provides temporal benchmarks for gauging recovery times after disturbance. Building upon these temporal benchmarks, and conditioned by disturbance type, site conditions, and location, we present opportunities for using dense time series of remotely sensed data to inform on regional and national trends in forest recovery following disturbance.
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We review measured rates of soil respiration from terrestrial and wetland ecosystems to define the annual global CO 2 flux from soils, to identify uncertainties in the global flux estimate, and to investigate the influences of temperature, precipitation, and vegetation on soil respiration rates. The annual global CO 2 flux from soils is estimated to average (± S.D.) 68 ± 4 PgC/ yr, based on extrapolations from biome land areas. Relatively few measurements of soil respiration exist from arid, semi-arid, and tropical regions; these regions should be priorities for additional research. On a global scale, soil respiration rates are positively correlated with mean annual air temperatures and mean annual precipitation. There is a close correlation between mean annual net primary productivity (NPP) of different vegetation biomes and their mean annual soil respiration rates, with soil respiration averaging 24% higher than mean annual NPP. This difference represents a minimum estimate of the contribution of root respiration to the total soil CO 2 efflux. Estimates of soil C turnover rates range from 500 years in tundra and peaty wetlands to 10 years in tropical savannas. We also evaluate the potential impacts of human activities on soil respiration rates, with particular focus on land use changes, soil fertilization, irrigation and drainage, and climate changes. The impacts of human activities on soil respiration rates are poorly documented, and vary among sites. Of particular importance are potential changes in temperatures and precipitation. Based on a review of in situ measurements, the Q 10 value for total soil respiration has a median value of 2.4. Increased soil respiration with global warming is likely to provide a positive feedback to the greenhouse effect. DOI: 10.1034/j.1600-0889.1992.t01-1-00001.x
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After severe wildfires, pine recovery depends on ectomycorrhizal (ECM) fungal spores surviving and serving as partners for regenerating forest trees. We took advantage of a large, severe natural forest fire that burned our long-term study plots to test the response of ECM fungi to fire. We sampled the ECM spore bank using pine seedling bioassays and high-throughput sequencing before and after the California Rim Fire. We found that ECM spore bank fungi survived the fire and dominated the colonization of in situ and bioassay seedlings, but there were specific fire adapted fungi such as Rhizopogon olivaceotinctus that increased in abundance after the fire. The frequency of ECM fungal species colonizing pre-fire bioassay seedlings, post-fire bioassay seedlings and in situ seedlings were strongly positively correlated. However, fire reduced the ECM spore bank richness by eliminating some of the rare species, and the density of the spore bank was reduced as evidenced by a larger number of soil samples that yielded uncolonized seedlings. Our results show that although there is a reduction in ECM inoculum, the ECM spore bank community largely remains intact, even after a high-intensity fire. We used advanced techniques for data quality control with Illumina and found consistent results among varying methods. Furthermore, simple greenhouse bioassays can be used to determine which fungi will colonize after fires. Similar to plant seed banks, a specific suite of ruderal, spore bank fungi take advantage of open niche space after fires.The ISME Journal advance online publication, 16 October 2015; doi:10.1038/ismej.2015.182.
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Fungi typically live in highly diverse communities composed of multiple ecological guilds. Although high-throughput sequencing has greatly increased the ability to quantify the diversity of fungi in environmental samples, researchers currently lack a simple and consistent way to sort large sequence pools into ecologically meaningful categories. We address this issue by introducing FUNGuild, a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline. Using a database and an accompanying bioinformatics script, we demonstrate the application of FUNGuild to three high-throughput sequencing datasets from different habitats: forest soils, grassland soils, and decomposing wood. We found that guilds characteristic of each habitat (i.e., saprotrophic and ectomycorrhizal fungi in forest soils, saprotrophic and arbuscular mycorrhizal fungi in grassland soils, saprotrophic, wood decomposer, and plant pathogenic fungi in decomposing wood) were each well represented. The example datasets demonstrate that while we could quickly and efficiently assign a large portion of the data to guilds, another large portion could not be assigned, reflecting the need to expand and improve the database as well as to gain a better understanding of natural history for many described and undescribed fungal species. As a community resource, FUNGuild is dependent on third-party annotation, so we invite researchers to populate it with new categories and records as well as refine those already in existence.
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Plant species leave a chemical signature in the soils below them, generating fine-scale spatial variation that drives ecological processes. Since the publication of a seminal paper on plant-mediated soil heterogeneity by Paul Zinke in 1962, a robust literature has developed examining effects of individual plants on their local environments (individual plant effects). Here, we synthesize this work using meta-analysis to show that plant effects are strong and pervasive across ecosystems on six continents. Overall, soil properties beneath individual plants differ from those of neighbours by an average of 41%. Although the magnitudes of individual plant effects exhibit weak relationships with climate and latitude, they are significantly stronger in deserts and tundra than forests, and weaker in intensively managed ecosystems. The ubiquitous effects of plant individuals and species on local soil properties imply that individual plant effects have a role in plant-soil feedbacks, linking individual plants with biogeochemical processes at the ecosystem scale. © 2015 The Author(s).
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Decomposition of wood is an important component of global carbon cycling. Most wood decomposition models are based on tree characteristics and environmental conditions; however, they do not include community dynamics of fungi that are the major wood decomposers. We examined the factors explaining variation in sapwood decay in oak tree stumps two and five years after cutting. Wood moisture content was significantly correlated with sapwood decay in younger stumps, whereas ITS-based composition and species richness of the fungal community were the best predictors for mass loss in the older stumps. Co-occurrence analysis showed that, in freshly cut trees and in younger stumps, fungal communities were nonrandomly structured, whereas fungal communities in old stumps could not be separated from a randomly assembled community. These results indicate that the most important factors explaining variation in wood decay rates can change over time and that the strength of competitive interactions between fungi in decaying tree stumps may level off with increased wood decay. Our field analysis further suggests that ascomycetes may have a prominent role in wood decay, but their wood-degrading abilities need to be further tested under controlled conditions. The next challenging step will be to integrate fungal community assembly processes in wood decay models to improve carbon sequestration estimates of forests.
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Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework. Copyright © 2014, American Association for the Advancement of Science.
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Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R. As for most model-fitting functions in R, the model is described in an lmer call by a formula, in this case including both fixed- and random-effects terms. The formula and data together determine a numerical representation of the model from which the profiled deviance or the profiled REML criterion can be evaluated as a function of some of the model parameters. The appropriate criterion is optimized, using one of the constrained optimization functions in R, to provide the parameter estimates. We describe the structure of the model, the steps in evaluating the profiled deviance or REML criterion, and the structure of classes or types that represents such a model. Sufficient detail is included to allow specialization of these structures by users who wish to write functions to fit specialized linear mixed models, such as models incorporating pedigrees or smoothing splines, that are not easily expressible in the formula language used by lmer.
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Significance Microbes control vital ecosystem processes like carbon storage and nutrient recycling. Although megadiversity is a hallmark of microbial communities in nature, we still do not know how microbial diversity determines ecosystem function. We addressed this issue by isolating different geographic and local processes hypothesized to shape fungal community composition and activity in pine forests across the continental United States. Although soil enzyme activity varied across soils according to resource availability, enzyme activity was similar across different fungal communities. These observations indicate that much of fungal diversity plays an equal role in soil biogeochemical cycles. However, soil fungal communities vary dramatically in space, indicating that individual species are endemic to bioregions within the North American continent.
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To test the direct regeneration hypothesis and support natural disturbancebased forest management we characterized the structure and composition of boreal mixedwood forests regenerating after large wildfires and examined the influence of pre-fire stand composition and post-fire competing vegetation. In stands which had been deciduous (Populus sp.)-dominated, conifer (white spruce)-dominated, or mixed pre-fire we measured regeneration stocking (presence in 10 m2 plots), density and height 10–20 years post-burn in five wildfires in Alberta, Canada. Most plots regenerated to the deciduous or mixed stocking types; plots in the older fire and in stands that were pure conifer pre-fire had higher amounts of conifer regeneration. Surprisingly, regeneration in pre-fire ‘pure’ white spruce stands was most often to pine, although these had not been recorded in the pre-fire inventory. Pre-fire deciduous stands were the most resilient in that poplar species dominated their post-fire regeneration in terms of stocking, density and height. Pre-fire pure spruce stands also had the highest diversity of regenerating tree species and the most unstocked plots. High grass cover negatively affected regeneration density of both deciduous and conifer trees. Our results demonstrate the natural occurrence of regeneration gaps, pre- to post-fire changes in forest composition, and high variation in post-fire regeneration composition. These should be taken into consideration when developing goals for post-harvest regeneration mimicking natural disturbance.
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1. Fuels in the groundcover of frequently burned south-eastern pine savannas include shed leaves of trees. Flammable needles of longleaf pine (Pinus palustris) potentially increase maximum fire tem-peratures and durations of heating, negatively affecting other trees within the groundcover. Less flammable leaves that accumulate around the bases of understorey stems of hardwood trees such as mockernut hickories (Carya alba) in the fall potentially depress maximum fire temperatures and durations of heating, enhancing post-fire recovery. 2. We experimentally manipulated amounts of pine and hickory leaves beneath understorey hickory stems in a pine savanna, measured temperatures during prescribed fires and assessed combustion of fuels and survival and regrowth of hickory stems. 3. Pine needles increased fire temperatures and durations of heating relative to herbaceous fuels and increased combustion of hickory leaves. Hickory leaves, however, neither increased nor decreased fire characteristics relative to herbaceous fuels. 4. All hickories survived fire by resprouting. When pine needles were absent, most hickories respro-uted from buds located above-ground along the stem at heights inversely related to temperature increase. In contrast, resprouting occurred only from underground root crowns when pine needles were present. Such differences in locations of resprouts influenced sizes of stems at the end of the growing season. 5. Synthesis. Groundcover fuels containing flammable leaves shed by pyrogenic species of savanna trees affect local fire characteristics and resprouting of non-pyrogenic understorey trees. Thus, local variation in flammable fuels produced by pyrogenic species can engineer landscape dynamics of other trees in savannas.
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Wildfires are a pervasive disturbance in boreal forests, and the frequency and intensity of boreal wildfires is expected to increase with climate warming. Boreal forests store a large fraction of global soil organic carbon (C), but relatively few studies have documented how wildfires affect soil microbial communities and soil C dynamics. We used a fire chronosequence in upland boreal forests of interior Alaska with sites that were 1, 7, 12, 24, 55, ~90, and ~100 years post-fire to examine the short- and long-term responses of fungal community composition, fungal abundance, extracellular enzyme activity, and litter decomposition to wildfires. We hypothesized that post-fire changes in fungal abundance and community composition would constrain decomposition following fires. We found that wildfires altered the composition of soil fungal communities. The relative abundance of ascomycetes significantly increased following fire whereas basidiomycetes decreased. Post-fire decreases in basidiomycete fungi were likely attributable to declines in ectomycorrhizal fungi. Fungal hyphal lengths in the organic horizon significantly declined in response to wildfire, and they required at least 24 years to return to pre-fire levels. Post-fire reductions in fungal hyphal length were associated with decreased activities of hydrolytic extracellular enzymes. In support of our hypothesis, the decomposition rate of aspen and black spruce litter significantly increased as forests recovered from fire. Our results indicate that post-fire reductions in soil fungal abundance and activity likely inhibit litter decomposition following boreal wildfires. Slower rates of litter decay may lead to decreased heterotrophic respiration from soil following fires and contribute to a negative feedback to climate warming.
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The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference dataset, and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g., Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term “species hypothesis” (SH) for the taxa discovered in clustering on different similarity tresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such species hypothesis. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, e.g., local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new web-based sequence management system in UNITE.This article is protected by copyright. All rights reserved.
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Rationale: Pyrogenic savannas with a tree-grassland "matrix" experience frequent fires (i.e. every 1-3 years). 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 below-ground communities and slows litter decomposition, thereby influencing savanna fuel dynamics. Methods: 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. Results: 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 soils, but unaffected by pine proximity. Litter decomposed more slowly in burned than unburned patches. Conclusions: 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. This article is protected by copyright. All rights reserved.
Article
Fungal communities associated with plants and soil influence plant fitness and ecosystem functioning. They are frequently studied by metabarcoding approaches targeting the ribosomal internal transcribed spacer (ITS), but there is no consensus concerning the most appropriate bioinformatic approach for the analysis of these data. We sequenced an artificial fungal community composed of 189 strains covering a wide range of Ascomycota and Basidiomycota, to compare the performance of 360 software and parameter combinations. The most sensitive approaches, based on the USEARCH and VSEARCH clustering algorithms, detected almost all fungal strains but greatly overestimated the total number of strains. By contrast, approaches using DADA2 to detect amplicon sequence variants were the most effective for recovering the richness and composition of the fungal community. Our results suggest that analyzing single forward (R1) sequences with DADA2 and no filter other than the removal of low-quality and chimeric sequences is a good option for fungal community characterization.
Book
This book provides a foundation for modern applied ecology. Much of current ecology research and conservation addresses problems across landscapes and regions, focusing on spatial patterns and processes. This book is aimed at teaching fundamental concepts and focuses on learning-by-doing through the use of examples with the software R. It is intended to provide an entry-level, easily accessible foundation for students and practitioners interested in spatial ecology and conservation.
Article
Laboratory incubation of soil samples from burned prairie stands demonstrated the presence of both coprophilous and carbonicolous ascomycetes. These fungi did not appear on soils collected from unburned prairie stands or from spring-burned stands that were sampled in July. Evidence is presented which suggests that prairie fires bring about a reduction in microbial competition at the soil surface, thereby permitting the successful development of these post-fire fungal colonists. Several of the coprophilous ascomycetes appearing on burned soil were also found on deer and rabbit feces collected from unburned prairie stands. It is suggested that grassland fires provide an additional mechanism by which the coprophilous forms can complete their life cycle. Furthermore, these fires may provide the principle means of initiating growth and development of several noncoprophilous ascomycetes.
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Many ectomycorrhizal fungi (EMF) are generalists, but most plant genera that form ectomycorrhizas have at least some fungal partners that are specific to that host genus. Because shared mycorrhizal fungi mediate plant community interactions, host preference has implications for plant succession and competition. We studied the EMF of oaks (Quercus spp.) and pines (Pinus spp.) in a forest in northern Florida, USA, focusing on symbionts shared with longleaf pine (Pinus palustris Mill.). Longleaf pine is an important species in the southeastern USA, both for timber plantations and for restoring savanna and woodland habitat. However, we found no research on the composition of naturally occurring EMF on longleaf pine roots. A lower proportion of EMF operational taxonomic units (OTUs) were found colonizing both oaks and pines than expected, providing evidence of host preference within the community. Although most EMF were detected only on either oaks or pines, the OTUs found on both tended to be frequently occurring and abundant. Cenococcum OTUs were found to be significantly associated with oaks, an unexpected finding as this genus is widespread, with a broad host range. These results suggest that host preference of EMF may structure EMF communities and therefore influence ecosystem effects of mycorrhizal networks.
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The roots of most plants are colonized by symbiotic fungi to form mycorrhiza, which play a critical role in the capture of nutrients from the soil and therefore in plant nutrition. Mycorrhizal Symbiosis is recognized as the definitive work in this area. Since the last edition was published there have been major advances in the field, particularly in the area of molecular biology, and the new edition has been fully revised and updated to incorporate these exciting new developments. . Over 50% new material . Includes expanded color plate section . Covers all aspects of mycorrhiza . Presents new taxonomy . Discusses the impact of proteomics and genomics on research in this area.
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This new edition to the classic book by ggplot2 creator Hadley Wickham highlights compatibility with knitr and RStudio. ggplot2 is a data visualization package for R that helps users create data graphics, including those that are multi-layered, with ease. With ggplot2, it's easy to: • produce handsome, publication-quality plots with automatic legends created from the plot specification • superimpose multiple layers (points, lines, maps, tiles, box plots) from different data sources with automatically adjusted common scales • add customizable smoothers that use powerful modeling capabilities of R, such as loess, linear models, generalized additive models, and robust regression • save any ggplot2 plot (or part thereof) for later modification or reuse • create custom themes that capture in-house or journal style requirements and that can easily be applied to multiple plots • approach a graph from a visual perspective, thinking about how each component of the data is represented on the final plot This book will be useful to everyone who has struggled with displaying data in an informative and attractive way. Some basic knowledge of R is necessary (e.g., importing data into R). ggplot2 is a mini-language specifically tailored for producing graphics, and you'll learn everything you need in the book. After reading this book you'll be able to produce graphics customized precisely for your problems, and you'll find it easy to get graphics out of your head and on to the screen or page. New to this edition:< • Brings the book up-to-date with ggplot2 1.0, including major updates to the theme system • New scales, stats and geoms added throughout • Additional practice exercises • A revised introduction that focuses on ggplot() instead of qplot() • Updated chapters on data and modeling using tidyr, dplyr and broom
Article
We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
Article
Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/ survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population. Illumina sequencing of root-associated fungi in a monodominant south beech forest revealed that the network representing symbiont-symbiont co-occurrence patterns was compartmentalized into clear modules, which consisted of diverse functional groups of mycorrhizal and endophytic fungi. Consequently, terminal roots of the plantwere colonized by either of the two largest fungal species sets (represented by Oidiodendron or Cenococcum). Thus, species-rich root microbiomes can have alternative community structures, as recently shown in the relationships between human gut microbiome type (i.e. 'enterotype') and host individual health. This study also shows an analytical framework for pinpointing network hubs in symbiont-symbiont networks, leading to the working hypothesis that a small number of microbial species organize the overall root-microbiome dynamics. © 2016 The Author(s) Published by the Royal Society. All rights reserved.
Article
Northwestern California has amassed its diverse flora over a long period of time, and from many sources. This chapter focuses on the classification and ecological dynamics of Northwestern forests. Northwestern California's forests are comprised of 100 tree species, 39 conifers, 22 oaks, and 26 currents and gooseberries among a vascular flora of 3,540 taxa. The chapter discusses conifer forests and reasons why they have limited ranges; forests in low-elevation, montane, and subalpine belts; and terrain and forests of the Klamath Mountains and the North Coast. It also looks at conservation and restoration efforts, and areas for future research.
Article
Although it is well known that fire can exert strong control on stand structure, composition, and dynamics in savannas and woodlands, the relationship between fire frequency and stand structure has been characterized in few of the world's savanna and woodland ecosystems. To address this issue in temperate oak-dominated ecosystems, we studied the effects of fire frequency on stand structure and dynamics in oak savanna and woodland stands that had been burned 0-26 times in 32 yr, in the Anoka Sand Plain region of Minnesota (USA). Seedling densities declined with increasing fire frequency, but differentially, for northern pin oak (Quercus ellipsoidalis), black cherry (Prunus serotina), serviceberry (Amelanchier sp.), and red maple (Acer rubrum). Bur oak (Q. macrocarpa) seedling density was not sensitive to fire frequency. Frequent burning (at least three fires per decade) prevented development of a sapling layer and canopy ingrowth. Low-frequency burning (fewer than two fires per decade) produced stands with dense sapling thickets. Reductions in overstory density and basal area from 1984 to 1995 were observed for all stands burned two or more times during that period. Basal area declined by 4-7% per year, and density declined by 6-8% per year in stands burned four or more times. Mortality rates in burned stands were higher for northern pin oak (50%) than for bur oak (8%). Northern pin oak mortality was highest for small trees (< 20 cm dbh) and lowest for mature trees (30-40 cm dbh); mortality increased with fire frequency. Bur oak mortality declined with increasing fire frequency. Attempts to preserve and maintain savannas as a viable ecosystem type in this region will require a long-term commitment to restoration-based management, with prescribed fire as a central tool. Burn frequency treatments with four or more fires per decade produce similar reductions in stem density and stand basal area but may lead to unsustainable oak tree populations. Within this general range, fire frequencies at a decadal scale should be chosen to address other management objectives, including suppressing shrubs and promoting increased cover of grasses and other herbaceous species. Fire management with a long-term view may also require periodic respites to allow for new cohorts of mature oak trees.
Article
Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.
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Limitations of linear regression applied on ecological data. - Things are not always linear additive modelling. - Dealing with hetergeneity. - Mixed modelling for nested data. - Violation of independence - temporal data. - Violation of independence spatial data. - Generalised linear modelling and generalised additive modelling. - Generalised estimation equations. - GLMM and GAMM. - Estimating trends for Antarctic birds in relation to climate change. - Large-scale impacts of land-use change in a Scottish farming catchment. - Negative binomial GAM and GAMM to analyse amphibian road killings. - Additive mixed modelling applied on deep-sea plagic bioluminescent organisms. - Additive mixed modelling applied on phyoplankton time series data. - Mixed modelling applied on American Fouldbrood affecting honey bees larvae. - Three-way nested data for age determination techniques applied to small cetaceans. - GLMM applied on the spatial distribution of koalas in a fragmented landscape. - GEE and GLMM applied on binomial Badger activity data.
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Spores and sclerotia are the main propagules that allow fungi to persist through unfavorable conditions and disperse into new environments. Despite their importance, very little is known about their longevity and dormancy, especially in ectomycorrhizal fungi. To assess the viability of ectomycorrhizal fungal spores in forest soil, we collected and buried non-sterile forest soil, in pots, in the field distant from an inoculum source. After 6 yr, a subset of this soil was assayed for viable spores by baiting the fungi with Bishop pine (Pinus muricata) seedlings. Our results show that the three most frequent colonizers in year 1 continued to colonize significant percentages of seedlings in year 6: Wilcoxina mikolae (77 %), Rhizopogon vulgaris (13 %) and Suillus brevipes (9 %). While three species that colonized low percentages of seedlings in year 1, Suillus pungens (1 %), Rhizopogon salebrosus (2 %), and Thelephora terrestris (5 %) were not recovered in year 6. Laccaria proxima, a species not seen in year 1, was recovered on a single seedling in year 6. This is the first report of long-term survival of S. brevipes and W. mikolae. Our results reveal a more complete picture of ectomycorrhizal fungal spore longevity in soil spore banks.
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Group-level variance estimates of zero often arise when fitting multilevel or hierarchical linear models, especially when the number of groups is small. For situations where zero variances are implausible a priori, we propose a maximum penalized likelihood approach to avoid such boundary estimates. This approach is equivalent to estimating variance parameters by their posterior mode, given a weakly informative prior distribution. By choosing the penalty from the log-gamma family with shape parameter greater than 1, we ensure that the estimated variance will be positive. We suggest a default log-gamma(2,λ) penalty with λ→0, which ensures that the maximum penalized likelihood estimate is approximately one standard error from zero when the maximum likelihood estimate is zero, thus remaining consistent with the data while being nondegenerate. We also show that the maximum penalized likelihood estimator with this default penalty is a good approximation to the posterior median obtained under a noninformative prior. Our default method provides better estimates of model parameters and standard errors than the maximum likelihood or the restricted maximum likelihood estimators. The log-gamma family can also be used to convey substantive prior information. In either case—pure penalization or prior information—our recommended procedure gives nondegenerate estimates and in the limit coincides with maximum likelihood as the number of groups increases.
Article
Temperatures at the soil surface and at several soil depths were measured during, and at intervals, for 33 months after a low-intensity prescribed burn in a subalpine Eucalyptus pauciflora forest. The high organic matter content, low bulk density, and low moisture content of the surface soil caused steep soil temperature gradients to be generated during the fire. Mean maximum temperatures during the fire were 600 ± 50, 450 ± 52, 54 ± 5 and 42 ± 5°C in the litter and at 0, 2 and 5 cm soil depths respectively. The highest temperatures recorded at 0, 2 and 5 cm depths were 703, 94 and 44°C. Temperatures exceeding 200°C, which result in volatilization of N from soil organic matter, were estimated to have occurred in the upper 3 mm of the soil. Byram fire intensity tended to be negatively correlated with the maximum temperature measured at the soil surface, but was not correlated with the amount of heat absorbed by black cans (thermal integrators) or the increase in the heat content of the soil. After the burn, the mean daily maximum temperatures in the soil were markedly higher on burnt than on unburnt sites. For example, soon after burning increases were 6, 10, 4 and 4°C at 0, 2, 5 and 10 cm depths, respectively, during a 5-day summer period. Mean daily minimum temperatures on recently burnt plots were similar to or slightly lower than those on unburnt areas. Average day-time temperature in recently burnt forest in summer was elevated by up to 8 and 4°C at 0 and 10 cm soil depths.
Article
SUMMARY A study was conducted to determine if ectomycorrhizal fungi in an age sequence of jack pine (Pinus banksiana Lamb.) stands which had regenerated following wildfire disturbance followed a successional pattern. Ectomycorrhizal development and number of symbionts were assessed in the forest floor and 0-20 cm deep mineral soil in 6, 41, 65 and 122-yr-old stands by conducting a macrofungal fruit body survey and examining pine root tips microscopically for mycorrhizal status and types of fungi forming the symbiosis. The majority of roots were located in the mineral soil with no substantial invasion of the forest floor except in the 122-yr-old stand. Over 90 % of the jack pine root tips were mycorrhizal and the majority of fruit bodies were produced by ectomycorrhizal species, regardless of stand age. There was no decrease in ectomycorrhizal colonization of roots with stand age. Both fruit body and root assessments revealed a distinct sequence of mycorrhizal fungi with stand age consisting of early-stage fungi (Coltricia perennis (L:Fr.) Murr., Thelephora spp., E-strain); multi-stage fungi (Suillus brevipes (Pk.) Kuntze, Inocybe spp., Cenococcum geophilum Fr., lClycelium radicis atrovirens Melin) and late-stage fungi (Cortinariusspp., Lactarius spp., Russula spp., Tricholoma spp., Hygrophorus spp., Hydnellum peckii Banker, Suillus tomentosus (Kauff.) Sing., Snell & Dick, Piloderma byssinum (Karst.) Jiil. and Sarcodon scabrosus (Fr.) Karst.). Many of the basidiomycete species fruiting above ground were detected also on the roots below ground. Fruit bodies of 50 species of ectomycorrhizal fungi were recorded while 39 distinct mycorrhizal types were identified on the roots. There was a significant increase in mycorrhizal species richness between the 6 and 41-yr-old stands and this was primarily the result of partial replacement of Suillus brevipes on the 6-yr-old trees by late-stage fungi in the older stands. Very few species present in the 6-yr-old stand were completely replaced in the older stands; rather, the multi-stage species present in the young stand were joined by late-stage species in the mature stands. The species abundance distribution of fungi on the roots in the 6-yr-old stand was best described by a geometric series which is typical of an early successional community while the distributions in the three oldest stands conformed to a lognormal series which is indicative of a stable, species rich community. Both the composition and structure of the ectomycorrhizal community had stabilized 41 yr after wildfire.