From morphological to molecular: studies of myxomycetes since the publication of the Martin and Alexopoulos (1969) monograph

Spatiotemporal patterns of soil myxomycetes in subtropical managed forests and their potential interactions with bacteria

Soil myxomycetes are crucial soil protists with important ecological functions. Yet, our understanding of their diversity patterns in managed forests and the interactions with their food is far behind other taxa. This study investigates the spatiotemporal patterns of soil myxomycetes in four northern subtropical managed forest types across seasons and aims to identify assembly processes, main predictors of myxomycete communities, and the potential interactions between myxomycetes and bacteria. Results showed that no significant difference in α diversity of myxomycete communities among forest types was observed, but a significant difference was observed in community structures. Significant differences were observed in α diversity and community structures of myxomycetes among seasons. Deterministic processes in each forest type and season dominated myxomycete community assemblies. Soil physicochemical properties and bacterial communities have a significant direct impact on the myxomycete community, while forest types, seasons, and enzyme activities have an indirect effect. There is a significant synergistic covariation between the soil myxomycete community and bacterial community. The genera of the phyla Acidobacteriota, Actinobacteriota, and Bacteroidota have a strong correlation with the richness of myxomycete genera. Overall, this study provides new insight into the diversity of soil myxomycetes and their influence by bacteria, crucial for myxomycetes ecology.IMPORTANCESoil myxomycetes are an important component of soil protists. Our study revealed for the first time the community structure of soil myxomycetes in managed forests of the northern subtropical regions and systematically investigated the seasonal variation patterns of soil myxomycetes. Meanwhile, we further investigated the potential interactions between soil myxomycetes and bacteria. This study will greatly enhance our understanding of the ecology of soil myxomycetes and their biological roles.

The Occurrence of Myxomycete Communities in Taxodium distichum Forests: Influence of Substrates and Seasons

Myxomycete communities in Taxodium distichum forests and the influence of substrates and seasons on myxomycete diversity were studied. In total, 80 substrates (40 living barks and 40 litters) were collected from the sample site in winter, spring, summer and autumn of 2023, followed by moist chamber cultures. A total of 733 records representing 34 myxomycete species in 21 genera were obtained. Arcyria cinerea and six other species were abundant (A). Six species were common (C), six species were occasional (O), and fifteen species were rare (R). Species diversity (H' = 2.04 ± 0.20) of corticolous communities was significantly higher than that (H' = 1.49 ± 0.31) of litter-inhabiting communities (p < 0.05). Nonmetric Multidimensional Scaling (NMDS) analyses showed significant differences between these two communities (p < 0.01). Species diversity was slightly higher in summer and autumn compared to winter and spring. NMDS analyses indicated no significant differences among seasonal communities. Redundancy Analysis showed that the corticolous species were closely related to wind speed (p < 0.05), while litter-inhabiting species were mainly determined by temperature (p < 0.05). The study revealed that substrates and seasons influenced myxomycete communities in T. distichum forests, with the communities being particularly affected by the substrates in which they live.

Myxomycetes on the bark of living Metasequoia glyptostroboides trees and their distribution along a rural-urban gradient

Myxomycete distribution along urban-rural gradients remains to be studied in detail. The ancient plant Metasequoia glyptostroboides has been mainly planted in urban parks and green areas in Japan, and it provides new habitats for myxomycetes on its growing tree bark. Here, we examined myxomycetes on bark along urbanization gradients, estimated by land-use coverage types. Survey sites were selected at 20 locations in western Japan, where the bark was sampled from 10 trees at each site. The bark samples were cultured in 10 Petri dishes per tree using the moist chamber technique. Myxomycete fruiting colonies occurred in 71% of cultures, and 44 species were identified across surveys. Diderma chondrioderma occurred at all sites, with the next most abundant species being Licea variabilis and Perichaena vermicularis. Twenty-two myxomycete communities ordinated using non-metric multidimensional scaling showed a significant negative correlation with building coverage and bark pH, increasing along the first axis. Relative abundances of Physarum crateriforme and Licea biforis positively correlated with increasing building coverage. Overall, urbanization causes alternation of the myxomycete community structure without diversity loss, and intermediate urbanization diversified species diversity on M. glyptostroboides tree bark.

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.

Diversity of bacterial communities in the plasmodia of myxomycetes

BACKGROUND

Myxomycetes are a group of eukaryotes belonging to Amoebozoa, which are characterized by a distinctive life cycle, including the plasmodium stage and fruit body stage. Plasmodia are all found to be associated with bacteria. However, the information about bacteria diversity and composition in different plasmodia was limited. Therefore, this study aimed to investigate the bacterial diversity of plasmodia from different myxomycetes species and reveal the potential function of plasmodia-associated bacterial communities.

RESULTS

The bacterial communities associated with the plasmodia of six myxomycetes (Didymium iridis, Didymium squamulosum, Diderma hemisphaericum, Lepidoderma tigrinum, Fuligo leviderma, and Physarum melleum) were identified by 16S rRNA amplicon sequencing. The six plasmodia harbored 38 to 52 bacterial operational taxonomic units (OTUs) that belonged to 7 phyla, 16 classes, 23 orders, 40 families, and 53 genera. The dominant phyla were Bacteroidetes, Firmicutes, and Proteobacteria. Most OTUs were shared among the six myxomycetes, while unique bacteria in each species only accounted for a tiny proportion of the total OTUs.

CONCLUSIONS

Although each of the six myxomycetes plasmodia had different bacterial community compositions, a high similarity was observed in the plasmodia-associated bacterial communities' functional composition. The high enrichment for gram-negative (> 90%) and aerobic (> 99%) bacteria in plasmodia suggest that myxomycetes may positively recruit certain kinds of bacteria from the surrounding environment.

Cribraria lepida, Physarum dictyosporum, P. diderma, and P. spectabile newly recorded from Turkey

The moist chamber technique was used to obtain Cribraria lepida, Physarum dictyosporum, and P. diderma from wood or bark at different outdoor localities in Karaman Province and P. spectabile in Konya Province. These taxa are reported for the first time from Turkey.

The Response of Litter-Associated Myxomycetes to Long-Term Nutrient Addition in a Lowland Tropical Forest

Myxomycetes (plasmodial slime molds) are abundant protist predators that feed on bacteria and other microorganisms, thereby playing important roles in terrestrial nutrient cycling. Despite their significance, little is known about myxomycete communities and the extent to which they are affected by nutrient availability. We studied the influence of long-term addition of N, P, and K on the myxomycete community in a lowland forest in the Republic of Panama. In a previous study, microbial biomass increased with P but not N or K addition at this site. We hypothesized that myxomycetes would increase in abundance in response to P but that they would not respond to the sole addition of N or K. Moist chamber cultures of leaf litter and small woody debris were used to quantify myxomycete abundance. We generated the largest myxomycete dataset (3,381 records) for any single locality in the tropics comprised by 91 morphospecies. In line with our hypothesis, myxomycete abundance increased in response to P addition but did not respond to N or K. Community composition was unaffected by nutrient treatments. This work represents one of very few large-scale and long-term field studies to include a heterotrophic protist highlighting the feasibility and value in doing so.

Is Myxomycetes (Amoebozoa) a Truly Ambiregnal Group? A Major Issue in Protist Nomenclature

Myxomycetes is one of the largest groups of protists belonging to Amoebozoa, with ca 1,000 species recognised and more than 4,000 names in use. Historically, myxomycetes were considered fungi or protozoans which, however, fell under the provisions of the former International Code of Botanical Nomenclature (ICBN), currently the International Code of Nomenclature for algae, fungi, and plants (ICN). Attempts to apply the International Code of Zoological Nomenclature (ICZN) to myxomycetes were rare and inconsistent; thus, we argue that Myxomycetes is not a truly ambiregnal group (i.e. one falling under both Codes). Recently, nomenclatural novelties within Myxomycetes have been proposed using ICZN rules, and the application of zoological orthography to myxomycete higher-level taxa in the recent amoebozoan phylogenies is increasingly common. We summarise the consequences of application of either ICN or ICZN to Myxomycetes. In our opinion, nomenclatural stability within Myxomycetes is best served by strict application of ICN. Either treating myxomycetes as falling under ICZN or considering them an ambiregnal group would cause serious nomenclatural instability, mainly owing to the incompatibility of the two Codes as to the date of the starting point of nomenclature and to the appearance of numerous homonyms.

Genetic barcoding of dark-spored myxomycetes (Amoebozoa)-Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.

Speciation in progress? A phylogeographic study among populations of Hemitrichia serpula (Myxomycetes)

Myxomycetes (plasmodial slime molds, Amoebozoa) are often perceived as widely distributed, confounding to the “everything is everywhere” hypothesis. To test if gene flow within these spore-dispersed protists is restricted by geographical barriers, we chose the widespread but morphologically unmistakable species Hemitrichia serpula for a phylogeographic study. Partial sequences from nuclear ribosomal RNA genes (SSU) revealed 40 ribotypes among 135 specimens, belonging to three major clades. Each clade is dominated by specimens from a certain region and by one of two morphological varieties which can be differentiated by SEM micrographs. Partial sequences of the protein elongation factor 1 alpha (EF1A) showed each clade to possess a unique combination of SSU and EF1A genotypes. This pattern is best explained assuming the existence of several putative biospecies dominating in a particular geographical region. However, occasional mismatches between molecular data and morphological characters, but as well heterogeneous SSU and heterozygous EF1A sequences, point to ongoing speciation. Environmental niche models suggest that the putative biospecies are rather restricted by geographical barriers than by macroecological conditions. Like other protists, myxomycetes seem to follow the moderate endemicity hypothesis and are in active speciation, which is most likely shaped by limited gene flow and reproductive isolation.

Crown fire and surface fire: effects on myxomycetes inhabiting pine plantations

Myxomycetes are heterotrophic eukaryote organisms that have three life stages, none of which are known to be resistant to fire. The response of myxobiota to different severity of fire is not well known either. We examined myxomycetes in Pinus mugo plantations following a crown fire and in Pinus sylvestris plantations following a surface fire during the first three years after the wildfire event in forested coastal sand dunes in western Lithuania. Additionally, we investigated myxomycetes in corresponding unburned stands. All studied sites (unburned and burned) bore rather different myxomycete assemblages but the disparities of the species compositions between both burn types were more pronounced showing that fire severity had stronger impact on myxomycete species composition than the pre-fire stand type. Analysis of myxomycete assemblages (including the results from field collections, bark and litter cultures) showed that surface fire sites bore the highest number of post-fire species compared to crown fire and unburned sites. Dynamic annual changes in species composition were observed in all studied sites but only crown fire plots showed a clear chronosequence of post-fire myxomycete assemblages. Fire impact promoted establishment and/or sporulation of myxomycete species that are rare in similar unburned stands, or are usually confined to other types of forests and substrata. In addition, individual myxomycete species tended to switch substratum usage during the course of vegetation succession, with a final return to their usual substrata. This possibly signaled the end of early stage of post-fire succession.

Additions to the myxobiota of the Åland Islands

Six myxomycete species new to the Åland Islands are presented: Comatrichaelegans, Cribrariaintricata, Didymiumminus, Hemitrichiaclavata, Liceavariabilis and Trichiafavoginea. The record of Cribrariaintricata is the third in Finland. Specimens were collected in September 2014. Altogether the number of myxomycete species found from the Åland Islands is now 55.

Species-specific cell mobility of bacteria-feeding myxamoebae in plasmodial slime molds

On decaying wood or litter in forests, plasmodial slime molds (myxomycetes) represent a large fraction of eukaryotic protists that feed on bacteria. In his seminal book Experimental Physiology of Plants (1865), Julius Sachs referred to the multinucleate plasmodium of myxomycetes, which were considered at that time as primitive plants (or fungi). Today it is well established that myxomycetes are members of the Amoebozoa (Protista). In this study we compare the mobility of myxamoebae of 3 European species, Lycogala epidendrum (order Liceales), Tubulifera arachnoidea, and Trichia decipiens (order Trichiales). Using agar plates, on which 3 separate bacterial species were cultivated as prey organisms (Methylobacterium mesophilicum, Escherichia coli, Agrobacterium tumefaciens), we document large differences in cell motility between the myxomycetes investigated. In addition, we show that the 3 species of myxamoebae can be distinguished based on their average cell size. These data shed light on the mode of co-occurrence via differential substrate utilization in these members of the Amoebozoa.

Species diversity of corticolous myxomycetes in Tianmu Mountain National Nature Reserve, China

The species diversity of corticolous myxomycetes on 4 vegetation types in the Tianmu Mountain National Natural Reserve, eastern China, was examined from 2011 to 2012. A total of 1440 moist chamber cultures were prepared with bark samples, which yielded several hundred collections representing 42 species in 20 genera. It was found that 79% of cultures produced some evidence (either plasmodia or fruiting bodies) of myxomycetes. Eight species (Comatricha elegans, Cribraria confusa, Licea pusilla, Cribraria microcarpa, Collaria arcyrionema, Licea biforis, Arcyria cinerea, and Clastoderma debaryanum) were abundant (exceeding 3% of all records), but about a third of all species were classified as rare. Species richness (S = 33) and diversity (exp[H'] = 16.60, S/G = 1.74) of corticolous myxomycetes were the most diverse in the deciduous broadleaf forest. The species recorded from coniferous forest showed the lowest species richness (S = 21) but the highest evenness (J' = 0.91). The cluster analyses were based on the Bray-Curtis similarity matrix, and the results indicated that corticolous myxomycete assemblages were distributed by a seasonal and annual pattern. Canonical correspondence analysis showed that season and pH were key factors in determining species distribution.