A Deep Hidden Diversity of Dictyostelia

Diversity of Dictyostelid Cellular Slime Molds, Including Two Species New to Science, in Forest Soils of Changbai Mountain, China

Dictyostelid cellular slime molds (dictyostelids) are protists that are common inhabitants of most soils, where they feed upon bacteria. Changbai Mountain is the highest mountain in northeast China. Soil samples collected on Changbai Mountain yielded 11 isolates representing six species of dictyostelid samples. Two of these species (Dictyostelium robusticaule and Heterostelium recretum) were found to be new to science, based on morphology, SSU rDNA sequences, and an ATPase subunit 1 gene (atp1) phylogeny. The present study also demonstrated that the increased accuracy and lower costs associated with the use of atp1 sequences make them a complement of SSU rDNA sequences for identifying dictyostelids. Changbai Mountain is characterized by a higher diversity of dictyostelids than indicated by the few previous reports. Moreover, the data for Changbai Mountain, compared with comparable data for Taiwan, suggest that differences in diversity at the family level are possibly related to latitude. Mixed broadleaf-conifer forests produced more isolates and species than broadleaf forests at the same elevation and also had the highest species richness, which indicates an effect of vegetation on dictyostelids. However, the pattern of slightly decreasing diversity with increasing elevation in dictyostelids was also apparent. IMPORTANCE Dictyostelium robusticaule and Heterostelium recretum are two new species of dictyostelids reported in this study. The potential use of atp1 sequences is a complement of SSU rDNA sequences for the identifying dictyostelids. A pattern of slightly decreasing diversity with increasing elevation in dictyostelids was observed, with the conditions that exist at lower elevations apparently more suitable for dictyostelids, whereas differences of diversity observed at the family level are possibly related to latitude.

Complexities of Inferring Symbiont Function: Paraburkholderia Symbiont Dynamics in Social Amoeba Populations and Their Impacts on the Amoeba Microbiota

The relationship between the social amoeba Dictyostelium discoideum and its endosymbiotic bacteria Paraburkholderia provides a model system for studying the development of symbiotic relationships. Laboratory experiments have shown that any of three species of the Paraburkholderia symbiont allow D. discoideum food bacteria to persist through the amoeba life cycle and survive in amoeba spores rather than being fully digested. This phenomenon is termed "farming," as it potentially allows spores dispersed to food-poor locations to grow their own. The occurrence and impact of farming in natural populations, however, have been a challenge to measure. Here, we surveyed natural D. discoideum populations and found that only one of the three symbiont species, Paraburkholderia agricolaris, remained prevalent. We then explored the effect of Paraburkholderia on the amoeba microbiota, expecting that by facilitating bacterial food carriage, it would diversify the microbiota. Contrary to our expectations, Paraburkholderia tended to infectiously dominate the D. discoideum microbiota, in some cases decreasing diversity. Similarly, we found little evidence for Paraburkholderia facilitating the carriage of particular food bacteria. These findings highlight the complexities of inferring symbiont function in nature and suggest the possibility that Paraburkholderia could be playing multiple roles for its host. IMPORTANCE The functions of symbionts in natural populations can be difficult to completely discern. The three Paraburkholderia bacterial farming symbionts of the social amoeba Dictyostelium discoideum have been shown in the laboratory environment to allow the amoebas to carry, rather than fully digest, food bacteria. This potentially provides a fitness benefit to the amoebas upon dispersal to food-poor environments, as they could grow their food. We expected that meaningful food carriage would manifest as a more diverse microbiota. Surprisingly, we found that Paraburkholderia tended to infectiously dominate the D. discoideum microbiota rather than diversifying it. We determined that only one of the three Paraburkholderia symbionts has increased in prevalence in natural populations in the past 20 years, suggesting that this symbiont may be beneficial, however. These findings suggest that Paraburkholderia may have an alternative function for its host, which drives its prevalence in natural populations.

Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids

Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these organisms solely relies on molecular phylogenetics of the SSU rDNA gene, which is not ideal for large-scale genetic diversity study. Here, we designed a set of PCR–single-strand conformation polymorphism (SSCP) primers and optimized the SSCP fingerprint method for the screening of dictyostelids. The optimized SSCP condition required gel purification of the SSCP amplicons followed by electrophoresis using a 9% polyacrylamide gel under 4°C. We also tested the optimized SSCP procedure with 73 Thai isolates of dictyostelid that had the SSU rDNA gene sequences published. The SSCP fingerprint patterns were related to the genus-level taxonomy of dictyostelids, but the fingerprint dendrogram did not reflect the deep phylogeny. This method is rapid, cost-effective, and suitable for large-scale sample screening as compared with the phylogenetic analysis of the SSU rDNA gene sequences.

Characterization of the bacterial microbiomes of social amoebae and exploration of the roles of host and environment on microbiome composition

As predators of bacteria, amoebae select for traits that allow bacteria to become symbionts by surviving phagocytosis and exploiting the eukaryotic intracellular environment. Soil-dwelling social amoebae can help us answer questions about the natural ecology of these amoeba-bacteria symbioses along the pathogen-mutualist spectrum. Our objective was to characterize the natural bacterial microbiome of phylogenetically and morphologically diverse social amoeba species using next-generation sequencing of 16S rRNA amplicons directly from amoeba fruiting bodies. We found six phyla of amoeba-associated bacteria: Proteobacteria, Bacteroidetes, Actinobacteria, Chlamydiae, Firmicutes, and Acidobacteria. The most common associates of amoebae were classified to order Chlamydiales and genus Burkholderia-Caballeronia-Paraburkholderia. These bacteria were present in multiple amoeba species across multiple locations. While there was substantial intraspecific variation, there was some evidence for host specificity and differentially abundant taxa between different amoeba hosts. Amoebae microbiomes were distinct from the microbiomes of their soil habitat, and soil pH affected amoeba microbiome diversity. Alpha-diversity was unsurprisingly lower in amoebae samples compared with soil, but beta-diversity between amoebae samples was higher than between soil samples. Further exploration of social amoebae microbiomes may help us understand the roles of bacteria, host, and environment on symbiotic interactions and microbiome formation in basal eukaryotic organisms.

Metatranscriptomics reveals unsuspected protistan diversity in leaf litter across temperate beech forests, with Amoebozoa the dominating lineage

Forest litter harbors complex networks of microorganisms whose major components are bacteria, fungi and protists. Protists, being highly selective consumers of bacteria and fungi could influence decomposition processes by shifting competitive microbial interactions. We investigated the eukaryotic diversity from 18 samples of one-year beech (Fagus sylvatica) leaf litter by RNA-based high-throughput sequencing of the small-subunit ribosomal RNA gene. By applying a metatranscriptomics approach, we avoided biases inherent to PCR-based methods, and could therefore focus on elusive protistan groups. We obtained 14 589 eukaryotic assembled sequences (contigs) representing 2223 unique taxa. Fungi dominated the eukaryotic assemblage, followed by an equal proportion of protists and plants. Among protists, the phylum Amoebozoa clearly dominated, representing more than twice the proportion of Alveolata (mostly ciliates) and Rhizaria (mostly Cercozoa), which are often retrieved as the dominant protistan groups in soils, revealing potential primer biases. By assigning functional traits to protists, we could assess that the proportion of free-living and heterotrophs was much higher than that of parasites and autotrophs, opening the way to a better understanding of the role played by the protistan communities and how biodiversity interacts with decomposition processes.