Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps

Distribution, assembly, and interactions of soil microorganisms in the bright coniferous forest area of China's cold temperate zone

The bright coniferous forest area in the cold temperate zone of China is a terrestrial ecosystem primarily dominated by low mountain Larix gmelinii trees. Limited information is available regarding the assembly mechanisms and interactions of microbial communities in the soil in this region. This study employed high-throughput techniques to obtain DNA from myxomycetes, bacteria, and fungi in the soil, evaluated their diversity in conjunction with environmental factors, associated them with the assembly process, and explored the potential interaction relationships between these microorganisms. The findings of our study showed that environmental factors had a more significant influence on the α and β diversity of bacteria compared to myxomycetes and fungi. Microbial communities were influenced by environmental selection and geographical diffusion, although environmental selection appeared to have a more significant impact than geographical diffusion. Our study suggested that different microorganisms exhibited unique evolutionary patterns and may have different assembly modes within phylogenetic groups. Myxomycetes and fungi exhibited a similar assembly process that was mainly influenced by stochastic dispersal limitation and drift. In contrast, bacteria's assembly process was primarily influenced by stochastic drift and deterministic homogeneous selection. The community of myxomycetes and fungi is greatly influenced by spatial distribution and random events, while bacteria have a relatively stable population composition in specific regions and may also be subject to environmental constraints. Finally, this study revealed that Humicolopsis cephalosporioides, a fungus that exclusively resided in cold environments, may play a critical role as a keystone species in maintaining molecular ecological networks and was considered a core member of the microbiome.

Biofilm-developed biomass residues as novel bulking agents and microbial carriers for synergistically enhanced bioevaporation: Degradation potential and contribution to metabolic heat

Economical and easily prepared bulking agents and microbial carriers are essential in the practical application of bioevaporation process. Biofilm-developed biomass residues not only provide structural support and microbial sources but also may contribute metabolic heat to the bioevaporation process, achieving the enhanced water evaporation and synergistic treatment of biomass residues. In this study, biofilm was cultivated on the rice straw, wheat straw, sawdust, corncob, luffa cylindrica and palm first, then those biofilm-developed biomass residues were successfully used as the bulking agents and microbial carriers in food waste bioevaporation. The degradation potential (volatile solid degradation ratio) of those biomass residues was in the order of corncob (23.96%), wheat straw (21.12%), rice straw (14.57%), luffa cylindrica (11.02%), sawdust (-2.87%) and palm (-9.24%). It's primarily the degradation of the major components, cellulose and hemicellulose, in corncob and wheat straw governed the metabolic heat contribution (91.73 and 79.61%) to the bioevaporation process. While the high lignin content in sawdust (14.57%) and palm (28.62%) caused negligible degradation of cellulose and hemicellulose, hence made them only function as structural supporter and did not contribute any metabolic heat. Moreover, though the metabolic heat contribution of rice straw and luffa cylindrica reached 58.19 and 37.84%, their lowest lignocellulose content (62.99 and 65.95%) and their lower density, as well as the dominated Xanthomonas (bacteria) and Mycothermus (fungi) led to their rapid collapse during the repeated cycles of bioevaporation. The greatest abundance of thermophilic bacteria (22.3-88.0%) and thermophilic fungi (82.0-99.3%) was observed in the corncob pile. Furthermore, considering the Staphylococcus (pathogenic bacteria) and Candida (animal pathogen) was effectively inhibited, the biofilm-developed corncob was the most favorable bulking agents and microbial carrier for the synergistic bioevaporation of highly concentrated organic wastewater and biomass residues.

Comparison of survey methods for fungi using metabarcoding and fruit body inventories in an altitudinal gradient

Metabarcoding of environmental samples is nowadays an established method in biodiversity research. When it comes to studying fungal populations in various ecotypes, fruit body inventories are the traditional method to assess the diversity of fungal communities. In this study, both methods-metabarcoding of soil samples and a traditional fruit body inventory-were conducted on 144 sample plots in an altitudinal gradient in the Bavarian Forest (Germany) and the results were compared. Metabarcoding detected significantly more species than the traditional fruit body inventory. The majority of taxa recorded in the fruit body inventory belonged to the Basidiomycota, whereas in the metabarcoding data, the distribution of species between Basidiomycota and Ascomycota was approximately balanced. Species of several orders forming inconspicuous or hypogeous fruit bodies were detected only by metabarcoding, while several wood decomposers were recorded only in the fruit body inventory. The proportion of detected wood-colonising species with melanized spores was considerably higher with metabarcoding than with the fruit body inventory, where more than 70% of recorded wood-colonisers had hyaline spores. Based on the metabarcoding data, a decline of species richness with increasing altitude was evident, but this was not visible in the fruit body inventory data. Detrended correspondence analyses yielded similar results for relative species community similarities with both survey methods.

Warmer winters result in reshaping of the European beech forest soil microbiome (bacteria, archaea and fungi)-With potential implications for ecosystem functioning

In temperate regions, climate warming alters temperature and precipitation regimes. During winter, a decline in insulating snow cover changes the soil environment, where especially frost exposure can have severe implications for soil microorganisms and subsequently for soil nutrient dynamics. Here, we investigated winter climate change responses in European beech forests soil microbiome. Nine study sites with each three treatments (snow exclusion, insolation, and ambient) were investigated. Long-term adaptation to average climate was explored by comparing across sites. Triplicated treatment plots were used to evaluate short-term (one single winter) responses. Community profiles of bacteria, archaea and fungi were created using amplicon sequencing. Correlations between the microbiome, vegetation and soil physicochemical properties were found. We identify core members of the forest-microbiome and link them to key processes, for example, mycorrhizal symbiont and specialized beech wood degraders (fungi) and nitrogen cycling (bacteria, archaea). For bacteria, the shift of the microbiome composition due to short-term soil temperature manipulations in winter was similar to the community differences observed between long-term relatively cold to warm conditions. The results suggest a strong link between the changes in the microbiomes and changes in environmental processes, for example, nitrogen dynamics, driven by variations in winter climate.

Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing

Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1-3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes.

Local taxonomic spectra in plants, animals, fungi and terrestrial protists show common mathematical patterns

Taxonomic spectra, i.e. relations between supraspecific taxa by the number of included species, remain poorly understood in aspect of the mathematical properties. We studied taxonomic spectra of plants (Magnoliophyta, Bryophyta), animals (Coleoptera, Aves), fungi (Agaricomycetes) and terrestrial protists (Myxomycetes), found in the Homilsha Forests National Nature Park (North-East of Ukraine), and concluded that they correspond to the hollow-curve distribution at the level of genera, families and orders. The spectra of most taxa, as shown by the Akaike information criterion, are closely approximated by the log-series distribution model at all taxonomic levels. This type of distribution is typical for the species abundance curves, based on collections made from small areas. At the same time, in the genera–families–orders row the similarity to the lognormal distribution increases. The central values and variability vary considerably between different taxonomic groups and ranks, however, without affecting the type of distribution. The number of orders in all taxa except Bryophyta has reached the saturation and coincides with the curve of the estimated number of orders according to the Chao1 coefficient. For families and especially genera the correspondence with estimated number of species is much lower. Our results do not confirm the assumption that hollow-curve distributions of taxonomic spectra result from the artificial fragmentation of taxa. These distributions neither depend on the insufficient knowledge about the species composition at the locality, nor reflect the size of the studied area. The presence of such distributions in both local and global biota of different groups may be explained by the common features of their evolution, especially by the existence of relict orphan groups. The fact that in Homilsha Forests the kurtosis and skewness of distributions decreases in the genera–families–orders row can therefore be explained by the relatively low percentage of the high-rank orphan taxa in the local biota. This may be a common feature of communities studied at small geographical scale, since orphan taxa often demonstrate a high level of endemism. Comparative studies of local communities from different climate zones may help to understand how universal are the patterns, described herein.

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles

Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO₂ pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO₂ emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO₂ production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.

Ecological assemblages of corticulous myxomycetes in forest communities of the North-East Ukraine

Corticulous myxomycetes remain one of the least surveyed ecological groups of terrestrial protists. These organisms develop on the bark of trees, mostly feeding on bacteria and microalgae. Their microscopic size and fast developmental cycle (3–5 days) complicate the study of these organisms, and therefore data their on ecological relationships and patterns of biodiversity corticulous myxomycetes remain controversial. On the territory of the southwest spurs of the Central Russian Upland (Northeast Ukraine), no special studies on these organisms have been conducted. During 2017–2020, in nine forest sites located in this territory, we collected samples of bark of 16 species of tree plants, on which sporulating myxomycetes were then identified using the moist chamber technique in laboratory conditions. A total of 434 moist chambers was prepared, and 267 (61.5%) of which were found to contain myxomycete fruiting bodies. In total, we made 535 observations, finding 20,211 sporocarps. As a result, in the surveyed territory, we found 38 species of corticulous myxomycetes, belonging to 18 genera, 10 families, 7 orders, and 2 subclasses of Myxomycetes. Among the species of corticulous myxomycetes, the most abundant were Echinostelium minutum, Arcyria pomiformis, Macbrideola cornea, Perichaena chrysosperma, Licea kleistobolus, Paradiacheopsis fimbriata, Cribraria violacea, Enerthenema papillatum, A. cinerea, and L. operculata. The greatest species richness in the examined biota was observed for genera Comatricha, Licea, Paradiacheopsis and Perichaena, families Amaurochaetaceae and Trichiaceae, orders Stemonitidales, Trichiales and Physarales. By species diversity, dark-spored myxomycetes (Collumellomycetidae) somewhat exceeded bright-spored myxomycetes (Lucisporomycetidae). Badhamia versicolor, Didymium dubium, D. sturgisii, Macbrideola decapillata, and Perichaena luteola are new species for the surveyed area. Four species of myxomycetes were collected in Ukraine for the first time: Hemitrichia pardina, Licea floriformis, L. pygmea, and Macbrideola argentea. Quantitative and qualitative structure of myxomycete consortia developing on different species of substrate-forming plants demonstrated significant differences. The highest level of similarity was demonstrated by Fraxinus excelsior and Acer platanoides, and a relatively strong relationship was seen between Pinus sylvestris and Tilia cordata. The central cluster comprised F. excelsior, A. platanoides and P. sylvestris. By the sum of values of Bray-Curtis coefficient, Quercus robur appeared to be most distinctive plant species by quantitative composition of myxomycete consortia. F. excelsior and T. cordata are the most favourable for the development of corticulous myxomycetes. In all the analyzed consortia, the dominant species belonged to the Stemonitidales and Trichiales orders, while the remaining orders were represented by notably fewer species. Relative species richness of Stemonitidales was the highest in consortia of P. sylvestris, the contribution of Liceales was the greatest in A. platanoides and P. sylvestris, the percentage of Echinosteliales and Physarales was the highest on F. excelsior, the share of Cribrariales was especially large on A. platanoides. Trichiales were represented on all the analyzed substrates to almost the same extent. Representatives of Cribrariales and Physarales were completely absent on P. sylvestris, the species of Clastodermatales – on all species of plants, except Q. robur. Prevalence of bright-spored myxomycetes was determined for consortia of Acer platanoides, the dominance of dark-spored myxomycetes – for F. excelsior, P. sylvestris and Q. robur. The obtained data indicate the presence of stable complexes of corticulous myxomycetes, associated with different species of trees in the forest ecosystems of Northeast Ukraine. This encourages further study of the structure of myxomycete consortia with tree species that were not included in this study and determining the influence of physical-chemical properties of the bark of different plant species on the discovered peculiarities of myxomycete communities.