Consistent trade-offs in fungal trait expression across broad spatial scales

Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence

Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.

Effects of experimental canopy openness on wood-inhabiting fungal fruiting diversity across succession

While the succession of terrestrial plant communities is well studied, less is known about succession on dead wood, especially how it is affected by environmental factors. While temperate forests face increasing canopy mortality, which causes considerable changes in microclimates, it remains unclear how canopy openness affects fungal succession. Here, we used a large real-world experiment to study the effect of closed and opened canopy on treatment-based alpha and beta fungal fruiting diversity. We found increasing diversity in early and decreasing diversity at later stages of succession under both canopies, with a stronger decrease under open canopies. However, the slopes of the diversity versus time relationships did not differ significantly between canopy treatments. The community dissimilarity remained mainly stable between canopies at ca. 25% of species exclusively associated with either canopy treatment. Species exclusive in either canopy treatment showed very low number of occupied objects compared to species occurring in both treatments. Our study showed that canopy loss subtly affected fungal fruiting succession on dead wood, suggesting that most species in the local species pool are specialized or can tolerate variable conditions. Our study indicates that the fruiting of the fungal community on dead wood is resilient against the predicted increase in canopy loss in temperate forests.

A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.

Towards establishing a fungal economics spectrum in soil saprobic fungi

Trait-based frameworks are promising tools to understand the functional consequences of community shifts in response to environmental change. The applicability of these tools to soil microbes is limited by a lack of functional trait data and a focus on categorical traits. To address this gap for an important group of soil microorganisms, we identify trade-offs underlying a fungal economics spectrum based on a large trait collection in 28 saprobic fungal isolates, derived from a common grassland soil and grown in culture plates. In this dataset, ecologically relevant trait variation is best captured by a three-dimensional fungal economics space. The primary explanatory axis represents a dense-fast continuum, resembling dominant life-history trade-offs in other taxa. A second significant axis reflects mycelial flexibility, and a third one carbon acquisition traits. All three axes correlate with traits involved in soil carbon cycling. Since stress tolerance and fundamental niche gradients are primarily related to the dense-fast continuum, traits of the 2nd (carbon-use efficiency) and especially the 3rd (decomposition) orthogonal axes are independent of tested environmental stressors. These findings suggest a fungal economics space which can now be tested at broader scales.

Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales

The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.

Family matters inside the order Agaricales: systematic reorganization and classification of incertae sedis clitocyboid, pleurotoid and tricholomatoid taxa based on an updated 6-gene phylogeny

The phylogenetic position of several clitocyboid/pleurotoid/tricholomatoid genera previously considered incertae sedis is here resolved using an updated 6-gene dataset of Agaricales including newly sequenced lineages and more complete data from those already analyzed before. Results allowed to infer new phylogenetic relationships, and propose taxonomic novelties to accommodate them, including up to ten new families and a new suborder. Giacomia (for which a new species from China is here described) forms a monophyletic clade with Melanoleuca (Melanoleucaceae) nested inside suborder Pluteineae, together with the families Pluteaceae, Amanitaceae (including Leucocortinarius), Limnoperdaceae and Volvariellaceae. The recently described family Asproinocybaceae is shown to be a later synonym of Lyophyllaceae (which includes also Omphaliaster and Trichocybe) within suborder Tricholomatineae. The families Biannulariaceae, Callistosporiaceae, Clitocybaceae, Fayodiaceae, Macrocystidiaceae (which includes Pseudoclitopilus), Entolomataceae, Pseudoclitocybaceae (which includes Aspropaxillus), Omphalinaceae (Infundibulicybe and Omphalina) and the new families Paralepistaceae and Pseudoomphalinaceae belong also to Tricholomatineae. The delimitation of the suborder Pleurotineae (= Schizophyllineae) is discussed and revised, accepting five distinct families within it, viz. Pleurotaceae, Cyphellopsidaceae, Fistulinaceae, Resupinataceae and Schizophyllaceae. The recently proposed suborder Phyllotopsidineae (= Sarcomyxineae) is found to encompass the families Aphroditeolaceae, Pterulaceae, Phyllotopsidaceae, Radulomycetaceae, Sarcomyxaceae (which includes Tectella), and Stephanosporaceae, all of them unrelated to Pleurotaceae (suborder Pleurotineae) or Typhulaceae (suborder Typhulineae). The new family Xeromphalinaceae, encompassing the genera Xeromphalina and Heimiomyces, is proposed within Marasmiineae. The suborder Hygrophorineae is here reorganized into the families Hygrophoraceae, Cantharellulaceae, Cuphophyllaceae, Hygrocybaceae and Lichenomphaliaceae, to homogenize the taxonomic rank of the main clades inside all suborders of Agaricales. Finally, the genus Hygrophorocybe is shown to represent a distinct clade inside Cuphophyllaceae, and the new combination H. carolinensis is proposed. Taxonomic novelties: New suborder: Typhulineae Vizzini, Consiglio & P. Alvarado. New families: Aphroditeolaceae Vizzini, Consiglio & P. Alvarado, Melanoleucaceae Locq. ex Vizzini, Consiglio & P. Alvarado, Paralepistaceae Vizzini, Consiglio & P. Alvarado, Pseudoomphalinaceae Vizzini, Consiglio & P. Alvarado, Volvariellaceae Vizzini, Consiglio & P. Alvarado, Xeromphalinaceae Vizzini, Consiglio & P. Alvarado. New species: Giacomia sinensis J.Z. Xu. Stat. nov.: Cantharellulaceae (Lodge, Redhead, Norvell & Desjardin) Vizzini, Consiglio & P. Alvarado, Cuphophyllaceae (Z.M. He & Zhu L. Yang) Vizzini, Consiglio & P. Alvarado, Hygrocybaceae (Padamsee & Lodge) Vizzini, Consiglio & P. Alvarado, Lichenomphaliaceae (Lücking & Redhead) Vizzini, Consiglio & P. Alvarado. New combination: Hygrophorocybe carolinensis (H.E. Bigelow & Hesler) Vizzini, Consiglio & P. Alvarado. New synonyms: Sarcomyxineae Zhu L. Yang & G.S. Wang, Schizophyllineae Aime, Dentinger & Gaya, Asproinocybaceae T. Bau & G.F. Mou. Incertae sedis taxa placed at family level: Aphroditeola Redhead & Manfr. Binder, Giacomia Vizzini & Contu, Hygrophorocybe Vizzini & Contu, Leucocortinarius (J.E. Lange) Singer, Omphaliaster Lamoure, Pseudoclitopilus Vizzini & Contu, Resupinatus Nees ex Gray, Tectella Earle, Trichocybe Vizzini. New delimitations of taxa: Hygrophorineae Aime, Dentinger & Gaya, Phyllotopsidineae Zhu L. Yang & G.S. Wang, Pleurotineae Aime, Dentinger & Gaya, Pluteineae Aime, Dentinger & Gaya, Tricholomatineae Aime, Dentinger & Gaya. Resurrected taxa: Fayodiaceae Jülich, Resupinataceae Jülich. Citation: Vizzini A, Alvarado P, Consiglio G, Marchetti M, Xu J (2024). Family matters inside the order Agaricales: systematic reorganization and classification of incertae sedis clitocyboid, pleurotoid and tricholomatoid taxa based on an updated 6-gene phylogeny. Studies in Mycology 107: 67-148. doi: 10.3114/sim.2024.107.02.

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.

Niche types and community assembly

Studies of niche differentiation and biodiversity often focus on a few niche dimensions due to the methodological challenge of describing hyperdimensional niche space. However, this may limit our understanding of community assembly processes. We used the full spectrum of realized niche types to study arbuscular mycorrhizal fungal communities: distinguishing abiotic and biotic, and condition and resource, axes. Estimates of differentiation in relation to different niche types were only moderately correlated. However, coexisting taxon niches were consistently less differentiated than expected, based on a regional null model, indicating the importance of habitat filtering at that scale. Nonetheless, resource niches were relatively more differentiated than condition niches, which is consistent with the effect of a resource niche-based coexistence mechanism. Considering niche types, and in particular distinguishing resource and condition niches, provides a more complete understanding of community assembly, compared with studying individual niche axes or the full niche.

Above- and belowground fungal biodiversity of Populus trees on a continental scale

Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.

Temperate species underfill their tropical thermal potentials on land

Understanding how temperature determines the distribution of life is necessary to assess species' sensitivities to contemporary climate change. Here, we test the importance of temperature in limiting the geographic ranges of ectotherms by comparing the temperatures and areas that species occupy to the temperatures and areas species could potentially occupy on the basis of their physiological thermal tolerances. We find that marine species across all latitudes and terrestrial species from the tropics occupy temperatures that closely match their thermal tolerances. However, terrestrial species from temperate and polar latitudes are absent from warm, thermally tolerable areas that they could potentially occupy beyond their equatorward range limits, indicating that extreme temperature is often not the factor limiting their distributions at lower latitudes. This matches predictions from the hypothesis that adaptation to cold environments that facilitates survival in temperate and polar regions is associated with a performance trade-off that reduces species' abilities to contend in the tropics, possibly due to biotic exclusion. Our findings predict more direct responses to climate warming of marine ranges and cool range edges of terrestrial species.

Soil labile organic carbon fractions mediate microbial community assembly processes during long-term vegetation succession in a semiarid region

Conceptual diagram for the labile organic carbon (OC) fractions mediating microbial assembly processes during long-term vegetation succession.

Fungal Fight Club: phylogeny and growth rate predict competitive outcomes among ectomycorrhizal fungi

Ectomycorrhizal fungi are among the most prevalent fungal partners of plants and can constitute up to one-third of forest microbial biomass. As mutualistic partners that supply nutrients, water, and pathogen defense, these fungi impact host plant health and biogeochemical cycling. Ectomycorrhizal fungi are also extremely diverse, and the community of fungal partners on a single plant host can consist of dozens of individuals. However, the factors that govern competition and coexistence within these communities are still poorly understood. In this study, we used in vitro competitive assays between five ectomycorrhizal fungal strains to examine how competition and pH affect fungal growth. We also tested the ability of evolutionary history to predict the outcomes of fungal competition. We found that the effects of pH and competition on fungal performance varied extensively, with changes in growth media pH sometimes reversing competitive outcomes. Furthermore, when comparing the use of phylogenetic distance and growth rate in predicting competitive outcomes, we found that both methods worked equally well. Our study further highlights the complexity of ectomycorrhizal fungal competition and the importance of considering phylogenetic distance, ecologically relevant traits, and environmental conditions in predicting the outcomes of these interactions.

Climate, host and geography shape insect and fungal communities of trees

Non-native pests, climate change, and their interactions are likely to alter relationships between trees and tree-associated organisms with consequences for forest health. To understand and predict such changes, factors structuring tree-associated communities need to be determined. Here, we analysed the data consisting of records of insects and fungi collected from dormant twigs from 155 tree species at 51 botanical gardens or arboreta in 32 countries. Generalized dissimilarity models revealed similar relative importance of studied climatic, host-related and geographic factors on differences in tree-associated communities. Mean annual temperature, phylogenetic distance between hosts and geographic distance between locations were the major drivers of dissimilarities. The increasing importance of high temperatures on differences in studied communities indicate that climate change could affect tree-associated organisms directly and indirectly through host range shifts. Insect and fungal communities were more similar between closely related vs. distant hosts suggesting that host range shifts may facilitate the emergence of new pests. Moreover, dissimilarities among tree-associated communities increased with geographic distance indicating that human-mediated transport may serve as a pathway of the introductions of new pests. The results of this study highlight the need to limit the establishment of tree pests and increase the resilience of forest ecosystems to changes in climate.

Dispersal changes soil bacterial interactions with fungal wood decomposition

Although microbes are the major agent of wood decomposition - a key component of the carbon cycle - the degree to which microbial community dynamics affect this process is unclear. One key knowledge gap is the extent to which stochastic variation in community assembly, e.g. due to historical contingency, can substantively affect decomposition rates. To close this knowledge gap, we manipulated the pool of microbes dispersing into laboratory microcosms using rainwater sampled across a transition zone between two vegetation types with distinct microbial communities. Because the laboratory microcosms were initially identical this allowed us to isolate the effect of changing microbial dispersal directly on community structure, biogeochemical cycles and wood decomposition. Dispersal significantly affected soil fungal and bacterial community composition and diversity, resulting in distinct patterns of soil nitrogen reduction and wood mass loss. Correlation analysis showed that the relationship among soil fungal and bacterial community, soil nitrogen reduction and wood mass loss were tightly connected. These results give empirical support to the notion that dispersal can structure the soil microbial community and through it ecosystem functions. Future biogeochemical models including the links between soil microbial community and wood decomposition may improve their precision in predicting wood decomposition.

Eco-physiological Responses of Aquatic Fungi to Three Global Change Stressors Highlight the Importance of Intraspecific Trait Variability

Anthropogenic change at a global scale is affecting life on Earth with impacts on freshwaters. Aquatic hyphomycetes are fungi that drive organic matter decomposition in freshwaters and mediate energy transfer to higher trophic levels. Intraspecific trait variability affects ecological processes and can account for species adaptations to environmental change. To ascertain how aquatic hyphomycetes respond to global change related stressors, we selected 20 strains (7 species), based on their co-occurrence in streams and phylogenetic relatedness. We measured fungal growth rates at different temperatures (7 levels), nutrient concentrations (6 levels) and medium moisture (6 levels). Our results indicate that all stressors affected fungal growth, and responses to nutrient enrichment and moisture were strain specific. Fungal responses to the stressors were not explained by their phylogenetic relatedness. In the absence of stressors, interspecific diversity best explained the variance in fungal traits, while the increase in the stress gradient increased the importance of intraspecific diversity.

Foliar nutrient resorption stoichiometry and microbial phosphatase catalytic efficiency together alleviate the relative phosphorus limitation in forest ecosystems

Understanding how plants adapt to spatially heterogeneous phosphorus (P) supply is important to elucidate the effect of environmental changes on ecosystem productivity. Plant P supply is concurrently controlled by plant internal conservation and external acquisition. However, it is unclear how climate, soil, and microbes influence the contributions and interactions of the internal and external pathways for plant P supply. Here, we measured P and nitrogen (N) resorption efficiency, litter and soil acid phosphatase (AP) catalytic parameters (V_max(s) and K_m ), and soil physicochemical properties at four sites spanning from cold temperate to tropical forests. We found that the relative P limitation to plants was generally higher in tropical forests than temperate forests, but varied greatly among species and within sites. In P-impoverished habitats, plants resorbed more P than N during litterfall to maintain their N : P stoichiometric balance. In addition, once ecosystems shifted from N-limited to P-limited, litter- and soil-specific AP catalytic efficiency (V_max(s) /K_m ) increased rapidly, thereby enhancing organic P mineralization. Our findings suggested that ecosystems develop a coupled aboveground-belowground strategy to maintain P supply and N : P stoichiometric balance under P-limitation. We also highlighted that N cycle moderates P cycles and together shape plant P acquisition in forest ecosystems.

Genomic Diversity and Phenotypic Variation in Fungal Decomposers Involved in Bioremediation of Persistent Organic Pollutants

Fungi work as decomposers to break down organic carbon, deposit recalcitrant carbon, and transform other elements such as nitrogen. The decomposition of biomass is a key function of wood-decaying basidiomycetes and ascomycetes, which have the potential for the bioremediation of hazardous chemicals present in the environment. Due to their adaptation to different environments, fungal strains have a diverse set of phenotypic traits. This study evaluated 320 basidiomycetes isolates across 74 species for their rate and efficiency of degrading organic dye. We found that dye-decolorization capacity varies among and within species. Among the top rapid dye-decolorizing fungi isolates, we further performed genome-wide gene family analysis and investigated the genomic mechanism for their most capable dye-degradation capacity. Class II peroxidase and DyP-type peroxidase were enriched in the fast-decomposer genomes. Gene families including lignin decomposition genes, reduction-oxidation genes, hydrophobin, and secreted peptidases were expanded in the fast-decomposer species. This work provides new insights into persistent organic pollutant removal by fungal isolates at both phenotypic and genotypic levels.

Drying Shapes Aquatic Fungal Community Assembly by Reducing Functional Diversity

Aquatic fungi are highly diverse organisms that play a critical role in global biogeochemical cycles. Yet it remains unclear which assembly processes determine their co-occurrence and assembly patterns over gradients of drying intensity, which is a common stressor in fluvial networks. Although aquatic fungi possess drying-specific adaptations, little is known about how functional similarity influences co-occurrence probability and which functional traits are sorted by drying. Using field data from 15 streams, we investigated how co-occurrence patterns and assembly processes responded to drying intensity. To do so, we determined fungal co-occurrence patterns, functional traits that best explain species co-occurrence likelihood, and community assembly mechanisms explaining changes in functional diversity over the drying gradient. Our results identified 24 species pairs with positive co-occurrence probabilities and 16 species pairs with negative associations. The co-occurrence probability was correlated with species differences in conidia shape and fungal endophytic capacity. Functional diversity reduction over the drying gradient is generally associated with non-random abiotic filtering. However, the assembly processes changed over the drying gradient, with random assembly prevailing at low drying intensity and abiotic filtering gaining more importance as drying intensifies. Collectively, our results can help anticipate the impacts of global change on fungal communities and ecosystem functioning.

Fungal growth response to recurring heating events is modulated by species interactions

An increasing frequency of heat events can affect key organisms related to ecosystem functions. Soil saprobic fungi have important roles in carbon and nutrient cycling in soils, and they are clearly affected by heat events. When tested individually, saprobic soil fungi showed a variety of growth responses to a series of two heat events. However, in nature, these fungi rarely grow alone. Coexistence theory predicts that diversity in the response to stressors can influence the outcome of species interactions and growth. This means that the co-cultivation of different fungi may affect their growth response to heat events. To test if recurring heat events affect fungal growth in small synthetic communities, we evaluated fungi previously known to respond to recurring heat events in experimental small communities composed of two and three species. For the fungi growing in pairs, surprisingly, most of the responses could not be predicted by how the isolates responded individually. In some cases, facilitation or increased competition was observed. For the three fungi growing together, results were also not predicted by the individual or pair responses. Both the heat events and the small communities influenced the growth of the fungi and growth properties emerged from the interactions among isolates and the heat stress. We show that not only do environmental conditions influence fungal interactions and growth rates but also that the co-cultivation of different fungi affects the fungal response to recurring heat events. These results indicate that more complex experimental designs are needed to better understand the effects of recurring heat events and climate change on soil fungi.

Global patterns in endemicity and vulnerability of soil fungi

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.

Environmental factors and stochasticity affect the fungal community structures in the water and sediments of Hulun Lake, China

Aquatic fungi form both morphologically and ecologically diverse communities. However, lake ecosystems are frequently overlooked as fungal habitats, despite the potentially important role of fungi in matter cycling and energy flow. Hulun Lake is a typical example of a seasonal glacial lake; however, previous studies have only focused on bacteria in this ecosystem. Therefore, in the current study, internal transcribed spacer ribosomal RNA (ITS rRNA) gene high-throughput sequencing was used to investigate the fungal communities in paired water and sediment samples from the Hulun Lake Basin in China. A significant difference was found between the fungal communities of the two sample types. Across all samples, we identified nine phyla, 30 classes, 78 orders, 177 families, and 307 genera. The dominant phyla in the lake were Ascomycota, Basidiomycota and Chytridiomycota. Our results show that both water and sediments have very high connectivity, are dominated by positive interactions, and have similar interaction patterns. The fungal community structures were found to be significantly affected by environmental factors (temperature, chemical oxygen demand, electrical conductivity, total phosphorus, and pH). In addition, the dispersal limitations of the fungi affected the structure of the fungal communities, and it was revealed that stochasticity is more important than deterministic mechanisms in influencing the structure and function of fungal communities. This study provides unique theoretical support for the study of seasonally frozen lake fungal communities and a scientific basis for the future management and protection of Hulun Lake.

Inter-annual Persistence of Canopy Fungi Driven by Abundance Despite High Spatial Turnover

While it is now well established that fungal community composition varies spatially at a variety of scales, temporal turnover of fungi is less well understood. Here we studied inter-annual community compositional changes of fungi in a rainforest tree canopy environment. We tracked fungal community shifts over 3 years in three substrate types (live bryophytes, dead bryophytes, and host tree bark) and compared these changes to amounts of community turnover seen at small spatial scales in the same system. The effect of substrate type on fungal community composition was stronger than that of sampling year, which was very small but significant. Although levels of temporal turnover varied among substrates, with greater turnover in live bryophytes than other substrates, the amount of turnover from year to year was comparable to what is seen at spatial distances between 5 and 9 cm for the same substrate. Stability of communities was largely driven by a few fungi with high relative abundances. A majority of fungal occurrences were at low relative abundances (≤ 0.1%). These fungi tended to be short lived and persisted to following years ≤ 50% of the time, depending on substrate. Their presence and persistence are likely impacted by stochastic processes like dispersal limitation and disturbance. Most samples contained only one or a few fungi at high relative abundance (≥ 10%) that persisted half or more of the time. These more abundant and persistent fungi are expected to have sustained functional interactions within the canopy ecosystem.

A review on trade-offs at the warm and cold ends of geographical distributions

Species’ range limits are ubiquitous. This suggests that the evolution of the ecological niche is constrained in general and at the edges of distributions in particular. While there may be many ecological and genetic reasons for this phenomenon, here we focus on the potential role of trade-offs. We performed a literature search on evidence for trade-offs associated with geographical or elevational range limits. The majority of trade-offs were reported as relevant at either the cold end of species' distribution (n = 19), the warm or dry end (n = 19) or both together (n = 14). One common type of trade-off involved accelerating growth or development (27%), often at the cost of small size. Another common type involved resistance to or tolerance of climatic extremes that occur at certain periods of the year (64%), often at the cost of small size or reduced growth. Trade-offs overlapped with some of the classic trade-offs reported in life-history evolution or thermal adaptation. The results highlight several general insights about species' niches and ranges, and we outline how future research should better integrate the ecological context and test for the presence of microevolutionary trade-offs.

This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.

Legacies of invertebrate exclusion and tree secondary metabolites control fungal communities in dead wood

During decomposition of organic matter, microbial communities may follow different successional trajectories depending on the initial environment and colonizers. The timing and order of the species arrival (assembly history) can lead to divergent communities through priority effects. We explored how assembly history and resource quality affected fungal communities and decay rate of decomposing wood, 1.5 and 4.5 years after tree felling. Additionally, we investigated the effect of invertebrate exclusion during the first two summers. We measured initial resource quality of bark and wood of aspen (Populus tremula) logs and surveyed the fungal communities by DNA metabarcoding at different times during succession. We found that gradients in fungal community composition were related to resource quality and discuss how this may reflect different fungal life history strategies. As with previous studies, the initial amount of bark tannins was negatively correlated with wood decomposition rate over 4.5 years. The initial fungal community explained variation in community composition after 1.5, but not 4.5 years, of succession. Although the assembly history of initial colonizers may cause alternate trajectories in successional communities, our results indicate that the communities may converge with the arrival of secondary colonizers. We also identified a strong legacy of invertebrate exclusion on fungal communities, even after 4.5 years of succession, thereby adding crucial knowledge on the importance of invertebrates in affecting fungal community development. By measuring and manipulating aspects of assembly history and resource quality that have rarely been studied, we expand our understanding of the complexity of fungal community dynamics.

Linking soil fungi to bacterial community assembly in arid ecosystems

Revealing the roles of biotic factors in driving community assembly, which is crucial for the understanding of biodiversity and ecosystem functions, is a fundamental but infrequently investigated subject in microbial ecology. Here, combining a cross-biome observational study with an experimental microcosm study, we provided evidence to reveal the major roles of biotic factors (i.e., soil fungi and cross-kingdom species associations) in determining soil bacterial biogeography and community assembly in complex terrestrial ecosystems of the arid regions of northwest China. The results showed that the soil fungal richness mediates the balance of assembly processes of bacterial communities, and stochastic assembly processes decreased with increasing fungal richness. Our results further suggest that the predicted increase in aridity conditions due to climate change will reduce bacterial α-diversity, particularly in desert soils and subsurface layer, and induce more negative species associations. Together, our study represents a significant advance in linking soil fungi to the mechanisms underlying bacterial biogeographic patterns and community assembly in arid ecosystems under climate aridity and land-use change scenarios.

Evaluation and modeling of fungi towards wood degradation

Fungi play a significant role in wood fiber degradation since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The study aims to demonstrate the interactive fungal traits when they grow together and its development with total dead wood fiber degradation speed. A lab experiment was designed to describe decomposition rates and fungal properties using nonlinear fitting model and logistic equation from preliminary data sets. The degradation speed of five (A, B, C, D, and E) different types of fungi with different growth rates were calculated at various relative humidity’s (35, 50, 65, 80, and 95 g.kg⁻). Results showed that the mycelium length of fungus A, has faster ideal growth rate than that of fungus B, with ecological niche width A < B. Besides this the growth rate of fungus 1 was vg1 = 0.12 and the environmental-holding capacity k1 = 3000; vg2 = 0.15 and k2 = 2000 for fungus 2. Comparing the results of fiber decomposition with a single fungus, we were able to find that the overall efficiency of the two-fungal system decomposition model was higher in a defined environment. Besides this the successfully simulated the competitive relationship between different species of fungi and the effect of different environments on the decomposition rate of fungi, with a good fit and in accordance with the biological laws. Our model is well generalizable and can be extended to multiple environmental variables (light, temperature, and heat) with good accuracy.

Ectomycorrhizal fungal decay traits along a soil nitrogen gradient

The extent to which ectomycorrhizal (ECM) fungi decay soil organic matter (SOM) has implications for accurately predicting forest ecosystem response to climate change. Investigating the distribution of gene traits associated with SOM decay among ectomycorrhizal fungal communities could improve understanding of SOM dynamics and plant nutrition. We hypothesized that soil inorganic nitrogen (N) availability structures the distribution of ECM fungal genes associated with SOM decay and, specifically, that ECM fungal communities occurring in inorganic N-poor soils have greater SOM decay potential. To test this hypothesis, we paired amplicon and shotgun metagenomic sequencing of 60 ECM fungal communities associating with Quercus rubra along a natural soil inorganic N gradient. Ectomycorrhizal fungal communities occurring in low inorganic N soils were enriched in gene families involved in the decay of lignin, cellulose, and chitin. Ectomycorrhizal fungal community composition was the strongest driver of shifts in metagenomic estimates of fungal decay potential. Our study simultaneously illuminates the identity of key ECM fungal taxa and gene families potentially involved in the decay of SOM, and we link rhizomorphic and medium-distance hyphal morphologies with enhanced SOM decay potential. Coupled shifts in ECM fungal community composition and community-level decay gene frequencies are consistent with outcomes of trait-mediated community assembly processes.

Timing of Resource Addition Affects the Migration Behavior of Wood Decomposer Fungal Mycelia

Studies of fungal behavior are essential for a better understanding of fungal-driven ecological processes. Here, we evaluated the effects of timing of resource (bait) addition on the behavior of fungal mycelia when it remains in the inoculum and when it migrates from it towards a bait, using cord-forming basidiomycetes. Experiments allowed mycelium to grow from an inoculum wood across the surface of a soil microcosm, where it encountered a new wood bait 14 or 98 d after the start of growth. After the 42-d colonization of the bait, inoculum and bait were individually moved to a dish containing fresh soil to determine whether the mycelia were able to grow out. When the inoculum and bait of mycelia baited after 14 d were transferred to new soil, there was 100% regrowth from both inoculum and bait in Pholiota brunnescens and Phanerochaete velutina, indicating that no migration occurred. However, when mycelium was baited after 98 d, 3 and 4 out of 10 replicates of P. brunnescens and P. velutina, respectively, regrew only from bait and not from inoculum, indicating migration. These results suggest that prolonged periods without new resources alter the behavior of mycelium, probably due to the exhaustion of resources.

Belowground community turnover accelerates the decomposition of standing dead wood

Standing dead trees (snags) decompose more slowly than downed dead wood and provide critical habitat for many species. The rate at which snags fall therefore influences forest carbon dynamics and biodiversity. Fall rates correlate strongly with mean annual temperature, presumably because warmer climates facilitate faster wood decomposition and hence degradation of the structural stability of standing wood. These faster decomposition rates coincide with turnover from fungal-dominated wood decomposer communities in cooler forests to co-domination by fungi and termites in warmer regions. A key question for projecting forest dynamics is therefore whether temperature effects on wood decomposition arise primarily because warmer conditions facilitate faster decomposer metabolism, or are also influenced indirectly by belowground community turnover (e.g. termites exert additional influence beyond fungal-plus-bacterial mediated decomposition). To test between these possibilities, we simulate standing dead trees with untreated, wooden posts and follow them in the field across five years at 12 sites, before measuring buried, soil-air interface and aerial post sections to quantify wood decomposition and organism activities. High termite activities at the warmer sites are associated with rates of post fall that are 3-times higher than at the cooler sites. Termites primarily consume buried wood, with decomposition rates greatest where termite activities are highest. However, where higher microbial and termite activities co-occur, they appear to first compensate for one another and then slow decomposition rates at their highest activities, suggestive of interference competition. If the range of microbial- and termite co-domination of wood decomposer communities expands under climate warming, our data suggest that expansion will accelerate snag fall with consequent effects on forest carbon cycling and biodiversity in forests previously dominated by microbial decomposers.

What can intraspecific trait variability tell us about fungal communities and adaptations?

Analyses of species functional traits are suitable to better understand the coexistence of species in a given environment. Trait information can be applied to investigate diversity patterns along environmental gradients and subsequently to predict and mitigate threats associated with climate change and land use. Species traits are used to calculate community trait means, which can be related to environmental gradients. However, while species traits can provide insights into the mechanisms underlying community assembly, they can lead to erroneous inferences if mean trait values are used. An alternative is to incorporate intraspecific trait variability (ITV) into calculating the community trait means. This approach gains increasing acceptance in plant studies. For macrofungi, functional traits have recently been applied to examine their community ecology but, to our knowledge, ITV has yet to be incorporated within the framework of community trait means. Here, we present a conceptual summary of the use of ITV to investigate the community ecology of macrofungi, including the underlying ecological theory. Inferences regarding community trait means with or without the inclusion of ITV along environmental gradients are compared. Finally, an existing study is reconsidered to highlight the variety of possible outcomes when ITV is considered. We hope this Opinion will increase awareness of the potential for within-species trait variability and its importance for statistical inferences, interpretations, and predictions of the mechanisms structuring communities of macro- and other fungi.

Linking Genes to Traits in Fungi

Fungi are mediators of the nitrogen and carbon cycles in terrestrial ecosystems. Examining how nitrogen uptake and organic matter decomposition potential differs in fungi can provide insight into the underlying mechanisms driving fungal ecological processes and ecosystem functioning. In this study, we assessed the frequency of genes encoding for specific enzymes that facilitate nitrogen uptake and organic matter decomposition in 879 fungal genomes with fungal taxa grouped into trait-based categories. Our linked gene-trait data approach revealed that gene frequencies vary across and within trait-based groups and that trait-based categories differ in trait space. We present two examples of how this linked gene-trait approach can be used to address ecological questions. First, we show that this type of approach can help us better understand, and potentially predict, how fungi will respond to environmental stress. Specifically, we found that trait-based categories with high nitrogen uptake gene frequency increased in relative abundance when exposed to high soil nitrogen enrichment. Second, by comparing frequencies of nitrogen uptake and organic matter decomposition genes, we found that most ectomycorrhizal fungi in our dataset have similar gene frequencies to brown rot fungi. This demonstrates that gene-trait data approaches can shed light on potential evolutionary trajectories of life history traits in fungi. We present a framework for exploring nitrogen uptake and organic matter decomposition gene frequencies in fungal trait-based groups and provide two concise examples on how to use our framework to address ecological questions from a mechanistic perspective.

Volatile organic compound patterns predict fungal trophic mode and lifestyle

Fungi produce a wide variety of volatile organic compounds (VOCs), which play central roles in the initiation and regulation of fungal interactions. Here we introduce a global overview of fungal VOC patterns and chemical diversity across phylogenetic clades and trophic modes. The analysis is based on measurements of comprehensive VOC profiles of forty-three fungal species. Our data show that the VOC patterns can describe the phyla and the trophic mode of fungi. We show different levels of phenotypic integration (PI) for different chemical classes of VOCs within distinct functional guilds. Further computational analyses reveal that distinct VOC patterns can predict trophic modes, (non)symbiotic lifestyle, substrate-use and host-type of fungi. Thus, depending on trophic mode, either individual VOCs or more complex VOC patterns (i.e., chemical communication displays) may be ecologically important. Present results stress the ecological importance of VOCs and serve as prerequisite for more comprehensive VOCs-involving ecological studies.

Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips

How do fungi navigate through the complex microscopic maze-like structures found in the soil? Fungal behaviour, especially at the hyphal scale, is largely unknown and challenging to study in natural habitats such as the opaque soil matrix. We monitored hyphal growth behaviour and strategies of seven Basidiomycete litter decomposing species in a micro-fabricated "Soil Chip" system that simulates principal aspects of the soil pore space and its micro-spatial heterogeneity. The hyphae were faced with micrometre constrictions, sharp turns and protruding obstacles, and the species examined were found to have profoundly different responses in terms of foraging range and persistence, spatial exploration and ability to pass obstacles. Hyphal behaviour was not predictable solely based on ecological assumptions, and our results obtained a level of trait information at the hyphal scale that cannot be fully explained using classical concepts of space exploration and exploitation such as the phalanx/guerrilla strategies. Instead, we propose a multivariate trait analysis, acknowledging the complex trade-offs and microscale strategies that fungal mycelia exhibit. Our results provide novel insights about hyphal behaviour, as well as an additional understanding of fungal habitat colonisation, their foraging strategies and niche partitioning in the soil environment.

Decay stages of wood and associated fungal communities characterise diversity-decomposition relationships

The biodiversity–ecosystem function relationship is a central topic in ecology. Fungi are the dominant decomposers of organic plant material in terrestrial ecosystems and display tremendous species diversity. However, little is known about the fungal diversity–decomposition relationship. We evaluated fungal community assemblies and substrate quality in different stages of wood decay to assess the relationships between fungal species richness and weight loss of wood substrate under laboratory conditions. Wood-inhabiting fungal communities in the early and late stages of pine log decomposition were used as a model. Colonisation with certain species prior to inoculation with other species resulted in four-fold differences in fungal species richness and up to tenfold differences in the rate of wood substrate decomposition in both early- and late-decaying fungal communities. Differences in wood substrate quality had a significant impact on species richness and weight loss of wood and the relationships between the two, which were negative or neutral. Late communities showed significantly negative species richness–decay relationships in wood at all decay stages, whereas negative relationships in early communities were significant only in the intermediate decay stage. Our results suggest that changes in fungal communities and wood quality during wood decomposition affect the fungal diversity–decomposition relationship.

Multiple distinct, scale-dependent links between fungi and decomposition

Decomposition has historically been considered a function of climate and substrate but new research highlights the significant role of specific micro-organisms and their interactions. In particular, wood decay is better predicted by variation in fungal communities than in climate. Multiple links exist: interspecific competition slows decomposition in more diverse fungal communities, whereas trait variation between different communities also affects process rates. Here, we paired field and laboratory experiments using a dispersal gradient at a forest-shrubland ecotone to examine how fungi affect wood decomposition across scales. We observed that while fungal communities closer to forests were capable of faster decomposition, wood containing diverse fungal communities decomposed more slowly, independent of location. Dispersal-driven stochasticity in small-scale community assembly was nested within large-scale turnover in the regional species pool, decoupling the two patterns. We thus find multiple distinct links between microbes and ecosystem function that manifest across different spatial scales.

Exploring Trait Trade-Offs for Fungal Decomposers in a Southern California Grassland

Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed “YAS” framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland.

Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling

Biodiversity is important for supporting ecosystem functioning. To evaluate the factors contributing to the strength of microbial diversity-function relationships in complex terrestrial ecosystems, we conducted a soil survey over different habitats, including an agricultural field, forest, wetland, grassland, and desert. Soil microbial multidiversity was estimated by the combination of bacterial and fungal diversity. Soil ecosystem functions were evaluated using a multinutrient cycling index (MNC) in relation to carbon, nitrate, phosphorus, and potassium cycling. Significant positive relationships between soil multidiversity and multinutrient cycling were observed in all habitats, except the grassland and desert. Specifically, community compositions showed stronger correlations with multinutrient cycling than α-diversity, indicating the crucial role of microbial community composition differences on soil nutrient cycling. Importantly, we revealed that changes in both the neutral processes (Sloan neutral modeling) and the proportion of negative bacterial-fungal associations were linked to the magnitude and direction of the diversity-MNC relationships. The habitats less governed by neutral processes and dominated by negative bacterial-fungal associations exhibited stronger negative microbial α-diversity-MNC relationships. Our findings suggested that the balance between positive and negative bacterial-fungal associations was connected to the link between soil biodiversity and ecosystem function in complex terrestrial ecosystems. This study elucidates the potential factors influencing diversity-function relationships, thereby enabling future studies to forecast the effects of belowground biodiversity on ecosystem function.IMPORTANCE The relationships between soil biodiversity and ecosystem functions are an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the factors driving the relationships between microbial diversity and potential soil nutrient cycling in complex terrestrial ecosystems. Our structural equation modeling and random forest analysis revealed that the balance between positive and negative bacterial-fungal associations was clearly linked to the strength of the relationships between soil microbial diversity and multiple nutrients cycling across different habitats. This study revealed the potential factors underpinning diversity-function relationships in terrestrial ecosystems and thus helps us to manage soil microbial communities for better provisioning of key ecosystem services.

Ciprofloxacin increased abundance of antibiotic resistance genes and shaped microbial community in epiphytic biofilm on Vallisneria spiralis in mesocosmic wetland

This study investigated the fate of ciprofloxacin (CIP) in wetlands dominated by Vallisneria spiralis. About 99% of CIP was degraded from overlaying water within 4 days of treatment but significantly inhibited the nutrient removal capacity (TN, TP, and COD) by causing a drastic reduction in microbial aggregation in epiphytic biofilm and bacterial biodiversity. CIP triggered resistance mechanisms among dominant bacteria phyla such as Proteobacteria, Actinobacteria, and Planctomycetes causing their increased relative abundance. Additionally, the relative abundances of eukaryotic microorganisms (including; Chloroplastida, Metazoa, and Rhizaria) and 13 ARGs subtypes (including; Efflux pump, Tetracycline, Multi-drug, Rifampin, Beta-lactam, Peptide, Trimethoprim) were significantly increased. While dominant metabolic pathways such as Carbohydrate, amino acid, energy and nucleotide metabolism were inhibited. This study revealed that V. spiralis has great sorption capacity for CIP than sediment and though CIP was effectively removed from the overlying water, it caused a prolonged effect on the epiphytic biofilm microbial communities.

Variation in hyphal production rather than turnover regulates standing fungal biomass in temperate hardwood forests

Soil fungi link above- and belowground carbon (C) fluxes through their interactions with plants and contribute to C and nutrient dynamics through the production, turnover, and activity of fungal hyphae. Despite their importance to ecosystem processes, estimates of hyphal production and turnover rates are relatively uncommon, especially in temperate hardwood forests. We sequentially harvested hyphal ingrowth bags to quantify the rates of Dikarya (Ascomycota and Basidiomycota) hyphal production and turnover in three hardwood forests in the Midwestern United States, where plots differed in their abundance of arbuscular (AM)- vs. ectomycorrhizal (ECM)-associated trees. Hyphal production rates increased linearly with the percentage of ECM trees and annual production rates were 66% higher in ECM- than AM-dominated plots. Hyphal turnover rates did not differ across the mycorrhizal gradient (plots varying in their abundance of AM vs. ECM trees), suggesting that the greater fungal biomass in ECM-dominated plots relates to greater fungal production rather than slower fungal turnover. Differences in hyphal production across the gradient aligned with distinctly different fungal communities and activities. As ECM trees increased in dominance, fungi inside ingrowth bags produced more extracellular enzymes involved in degrading nitrogen (N)-bearing relative to C-bearing compounds, suggesting greater fungal (and possibly plant) N demand in ECM-dominated soils. Collectively, our results demonstrate that shifts in temperate tree species composition that result in changes in the dominant type of mycorrhizal association may have strong impacts on Dikarya hyphal production, fungal community composition and extracellular enzyme activity, with important consequences for soil C and N cycling.

Sniffing fungi - phenotyping of volatile chemical diversity in Trichoderma species

Volatile organic compounds (VOCs) play vital roles in the interaction of fungi with plants and other organisms. A systematic study of the global fungal VOC profiles is still lacking, though it is a prerequisite for elucidating the mechanisms of VOC-mediated interactions. Here we present a versatile system enabling a high-throughput screening of fungal VOCs under controlled temperature. In a proof-of-principle experiment, we characterized the volatile metabolic fingerprints of four Trichoderma spp. over a 48 h growth period. The developed platform allows automated and fast detection of VOCs from up to 14 simultaneously growing fungal cultures in real time. The comprehensive analysis of fungal odors is achieved by employing proton transfer reaction-time of flight-MS and GC-MS. The data-mining strategy based on multivariate data analysis and machine learning allows the volatile metabolic fingerprints to be uncovered. Our data revealed dynamic, development-dependent and extremely species-specific VOC profiles from the biocontrol genus Trichoderma. The two mass spectrometric approaches were highly complementary to each other, together revealing a novel, dynamic view to the fungal VOC release. This analytical system could be used for VOC-based chemotyping of diverse small organisms, or more generally, for any in vivo and in vitro real-time headspace analysis.