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Polyporous fungi, a morphologically delineated group of Agaricomycetes ( Basidiomycota ), are considered well studied in Europe and used as model group in ecological studies and for conservation. Such broad interest, including widespread sampling and DNA based taxonomic revisions, is rapidly transforming our basic understanding of polypore diversity and natural history. We integrated over 40,000 historical and modern records of polypores in Estonia (hemiboreal Europe), revealing 227 species, and including Polyporus submelanopus and P. ulleungus as novelties for Europe. Taxonomic and conservation problems were distinguished for 13 unresolved subgroups. The estimated species pool exceeds 260 species in Estonia, including at least 20 likely undescribed species (here documented as distinct DNA lineages related to accepted species in, e.g., Ceriporia, Coltricia , Physisporinus , Sidera and Sistotrema ). Four broad ecological patterns are described: (1) polypore assemblage organization in natural forests follows major soil and tree-composition gradients; (2) landscape-scale polypore diversity homogenizes due to draining of peatland forests and reduction of nemoral broad-leaved trees (wooded meadows and parks buffer the latter); (3) species having parasitic or brown-rot life-strategies are more substrate-specific; and (4) assemblage differences among woody substrates reveal habitat management priorities. Our update reveals extensive overlap of polypore biota throughout North Europe. We estimate that in Estonia, the biota experienced ca. 3–5% species turnover during the twentieth century, but exotic species remain rare and have not attained key functions in natural ecosystems. We encourage new regional syntheses on long studied fungal groups to obtain landscape-scale understanding of species pools, and for elaborating fungal indicators for biodiversity assessments.

The aim of this work was to summarize the data on the ecological, biological, and morphological features of Calcipostia guttulata (Polyporales, Basidiomycota) by using the original materials, revised herba-rium specimens, data on molecular barcoding of original collections, the available literature, and iconography and information stored on the GBIF portal. It was shown that C. guttulata is a widespread, but rare polypore in the Holarctic; is confined to the early stages of drying of coniferous stands, primarily spruce forests; and is a poorly studied headwood pathogen and a saprotroph that colonizes coniferous deadwood and, less often, fallen trees. The morphological diagnosis of C. guttulata was clarified. Its substrate spectrum, distribution, and relationships with insects, which are important for forest pathology, have been identified most fully to date. The conservation status of the species and the prospects for its use in biotechnology are discussed.

Diversity of secondary lichen metabolites was studied in epiphytic lichens on six phorophytes—spruce, pine, birch, alder, aspen and poplar in the Middle Urals of Russia. Atranorin, usnic, fumarprotocetraric acid, zeorin, and gyrophoric acid were found in 31, 24, 23, 18, and 14 species, respectively, of 237 taxa collected. Seventy-seven species (i.e., 32% of total species documented) contained no secondary metabolites. Spectra of secondary metabolites of fruticose and foliose lichens varied on different phorophytes, while in crustose species the strong dependence on the tree species was not detected. This is different to the pH dependence of saxicolous lichens where crustose lichens were more susceptible to the rock chemistry. The results of Canonical Correspondence Analysis reveal the affinity of species containing depsides, depsidones or usnic acid to acidic substrata and those lacking secondary metabolites or containing terpenes and antraquinones to the pH-neutral bark. We suppose that phenolic compounds and flavonoids, as chemical constituents of bark, may interact with lichen symbioses and elements in phellem, and similarly to the lichen acids shape the affinity of species to the substrata.

The serpentine-substrate effect is well documented for vascular plants, but the literature for bryophytes is limited. The majority of literature on bryophytes in extreme geoedaphic habitats focuses on the use of species as bioindicators of industrial pollution. Few attempts have been made to characterize bryophyte floras on serpentine soils derived from peridotite and other ultramafic rocks. This paper compares the bryophyte floras of both a peridotite and a granite outcrop from the Deer Isles, Hancock County, Maine, and examines tissue elemental concentrations for select species from both sites. Fifty-five species were found, 43 on serpentine, 26 on granite. Fourteen species were shared in common. Twelve species are reported for the first time from serpentine soils. Tissue analyses indicated significantly higher Mg, Ni, and Cr concentrations and significantly lower Ca∶Mg ratios for serpentine mosses compared to those from granite. Soil analyses demonstrated significant differences between the two substrates.

A comparison between lime (Tilia platyphyllos) and holly oak (Quercus ilex) as substrate trees for epiphytic lichens was carried out in Siena (central Italy). The purpose of this study was to investigate the influence of these phorophytes on the diversity of epiphytic lichens, at a similar climatic regime and at the same air pollution status. The diversity values measured on Tilia were on the average 1.5 times higher than those on Quercus. No difference between the two tree species appeared for bark pH and bark concentrations of NO3−, SO42−, NH4+, Cu, and Pb. Bark concentrations of Mn were higher for Quercus. The water-holding capacity of the bark of Tilia was higher than that of Quercus. The amount of incident light radiation was similar for the two trees in summer, when both species have leaves, but was higher on deciduous lime in winter, when only the evergreen Q. ilex has leaves. Influx light in winter is the most important factor for determining differences in the biodiversity of epiphytic lichens on Tilia and Q. ilex.

The Andes are predicted to warm by 3–5 °C this century with the potential to alter the processes regulating carbon (C) cycling in these tropical forest soils. This rapid warming is expected to stimulate soil microbial respiration and change plant species distributions, thereby affecting the quantity and quality of C inputs to the soil and influencing the quantity of soil‐derived CO₂ released to the atmosphere. We studied tropical lowland, premontane and montane forest soils taken from along a 3200‐m elevation gradient located in south‐east Andean Peru. We determined how soil microbial communities and abiotic soil properties differed with elevation. We then examined how these differences in microbial composition and soil abiotic properties affected soil C‐cycling processes, by amending soils with C substrates varying in complexity and measuring soil heterotrophic respiration (RH). Our results show that there were consistent patterns of change in soil biotic and abiotic properties with elevation. Microbial biomass and the abundance of fungi relative to bacteria increased significantly with elevation, and these differences in microbial community composition were strongly correlated with greater soil C content and C:N (nitrogen) ratios. We also found that RH increased with added C substrate quality and quantity and was positively related to microbial biomass and fungal abundance. Statistical modelling revealed that RH responses to changing C inputs were best predicted by soil pH and microbial community composition, with the abundance of fungi relative to bacteria, and abundance of gram‐positive relative to gram‐negative bacteria explaining much of the model variance. Synthesis. Our results show that the relative abundance of microbial functional groups is an important determinant of RH responses to changing C inputs along an extensive tropical elevation gradient in Andean Peru. Although we do not make an experimental test of the effects of climate change on soil, these results challenge the assumption that different soil microbial communities will be ‘functionally equivalent’ as climate change progresses, and they emphasize the need for better ecological metrics of soil microbial communities to help predict C cycle responses to climate change in tropical biomes.

Abstract Niche Theory is a central framework in ecology based on the recognition that most interactions between organisms are indirect, mediated by the biotic and abiotic dynamical environment these organisms live in. Despite its potential generality, the theory still mostly focuses on how resource–consumer dynamics mediate competition in ecological communities. However, it is being increasingly recognized that positive interactions between organisms also play an important role in driving the structure and functioning of ecological communities, from plants to microbes. In this paper, we present a unified theory of the niche that applies to both positive and negative interactions between organisms, mediated by one or two environmental factors. We show that classical concepts such as niche differences and fundamental and realized niches can naturally be expanded to facilitative and mutualistic interactions. In addition, we introduce and formalize new general niche concepts that appear exclusively in the presence of positive interactions: (1) the Allee niche, a region of environmental conditions for which a species can persist but not invade from low densities and (2) niche facilitation, when the presence of a species expands the set of environmental conditions under which a second species can invade and/or persist. To show the broad applicability of this theory, we illustrate these concepts using a diverse set of theoretical examples, from bacteria feeding on an inhibiting substrate, to nitrogen‐fixing plants and the indirect mutualism between a plant and a carnivore species. In sum, our work shows how Niche Theory provides a natural framework for positive interactions in ecology, bringing a unified perspective and new conceptual tools to study ecological systems where these positive interactions occur.

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that—like for AOB—ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

Elemental stoichiometry constitutes an inherent link between biogeochemistry and the structure and processes within food webs, and thus is at the core of ecosystem functioning. Stoichiometry allows for spanning different levels of biological organization, from cellular metabolism to ecosystem structure and nutrient cycling, and is therefore particularly useful for establishing links between different ecosystem compartments. We review elemental carbon : nitrogen : phosphorus (C:N:P) ratios in terrestrial ecosystems (from vegetation, leaf litter, woody debris, and dead roots, to soil microbes and organic matter). While the stoichiometry of the plant, litter, and soil compartments of ecosystems is well understood, heterotrophic microbial communities, which dominate the soil food web and drive nutrient cycling, have received increasing interest in recent years. This review highlights the effects of resource stoichiometry on soil microorganisms and decomposition, specifically on the structure and function of heterotrophic microbial communities and suggests several general patterns. First, latitudinal gradients of soil and litter stoichiometry are reflected in microbial community structure and function. Second, resource stoichiometry may cause changes in microbial interactions and community dynamics that lead to feedbacks in nutrient availability. Third, global change alters the C:N, C:P, and N:P ratios of primary producers, with repercussions for microbial decomposer communities and critical ecosystem services such as soil fertility. We argue that ecological stoichiometry provides a framework to analyze and predict such global change effects at various scales.

Ferns have been considered ecological indicators of soil nutrient composition and can be adapted to limestone (calcicole), volcanic substrates (calcifuge), or both (generalists). However, how many species exhibit substrate preferences and how these substrates affect their leaf nutrient composition remains unclear. We studied the occurrence of fern species across 37 sites in Veracruz and Puebla, Mexico, identifying their possible soil preferences (limestone vs volcanic), and performing an elemental analysis (C, N, P, K, Na, Ca, Mg, S, Fe, Al, and Mn) of leaf tissues and underlying substrates. We found 13 species confined to limestone, five to volcanic substrates, and one generalist species on both substrates. Limestone substrates had higher Ca but lower Fe, Mn, and P concentrations than igneous substrates, and calcicole ferns had higher Ca, Mg, and N concentrations than calcifuge ferns, each independent from elevation. A further ordination based on nutrient composition split calcicole ferns into two groups. Group I had lower nutrient concentrations except for higher Al, Fe, and Mn concentrations, and group II showed the opposite nutrient pattern. Additionally, group I consisted of species growing mainly at higher elevations than group II. The soil generalist had higher Ca and Al concentrations on limestone than on volcanic substrates. Fern species differed considerably in nutrient composition even within calcicole and calcifuge groups and most leaf nutrients decreased with elevation. Calcium concentrations, however, were consistently higher in calcicole than in calcifuge ferns regardless of elevation and may serve as a nutrient indicator for limestone specialists.