Root of Dictyostelia based on 213 universal proteins.

Dictyostelia are common soil microbes that can aggregate when starved to form multicellular fruiting bodies, a characteristic that has also led to their long history of study and widespread use as model systems. Ribosomal RNA phylogeny of Dictyostelia identified four major divisions (Groups 1-4), none of which correspond to traditional genera. Group 1 was also tentatively identified as sister lineage to the other three Groups, although not consistently or with strong support. We tested the dictyostelid root using universal protein-coding genes identified by exhaustive comparison of six completely sequenced dictyostelid genomes, which include representatives of all four major molecular Groups. A set of 213 genes are low-copy number in all genomes, present in at least one amoebozoan outgroup taxon (Acanthamoeba castellanii or Physarum polycephalum), and phylogenetically congruent. Phylogenetic analysis of a concatenation of the deduced protein sequences produces a single topology dividing Dictyostelia into two major divisions: Groups 1+2 and Groups 3+4. All clades in the tree are fully supported by maximum likelihood and Bayesian inference, and all alternative roots are unambiguously rejected by the approximately unbiased (AU) test. The 1+2, 3+4 root is also fully supported even after deleting clusters with strong individual support for this root, or concatenating all clusters with low support for alternative roots. The 213 putatively ancestral amoebozoan proteins encode a wide variety of functions including 21 KOG categories out of a total of 25. These comprehensive analyses and consistent results indicate that it is time for full taxonomic revision of Dictyostelia, which will also enable more effective exploitation of its unique potential as an evolutionary model system.

DNA metabarcoding reveals the impact of Cu2+ on soil cercozoan diversity.

Although copper (Cu2+) is a micronutrient, the metal may be toxic if present in high concentrations in soil ecosystems and subsequently affect various organisms, ranging from microorganisms to earthworms. We performed a microcosm study with an array of Cu2+ concentrations, with a specific focus on Cercozoa, an important protozoan group in most soil food webs. Research on Cercozoa is still scarce in terms of both diversity and ecology; hence, to explore this group in more depth, we used high-throughput sequencing to detect Cu2+ induced community changes. Increased levels of Cu2+ caused a shift in the cercozoan community, and we observed decreased cercozoan relative abundance across the majority of orders, families and genera. Due to their key role in soil food webs, especially as bacterial predators and providers of nutrients to plants, the reduction of cercozoan abundance and diversity may seriously affect soil functionality. Our results indicate that the increase of Cu2+ concentrations in the soil could potentially have this effect and the consequences need exploration.

Impact of model assumptions on the inference of the evolution of ectomycorrhizal symbiosis in fungi.

Ectomycorrhiza (ECM) is a symbiotic relation between plant and fungi that is essential for nutrient uptake of many stand forming trees. There are two conflicting views about the evolution of ECM in fungi suggesting (1) relatively few transitions to ECM followed by reversals to non-ECM, or (2) many independent origins of ECM and no reversals. In this study, we compare these, and other, hypotheses and test the impact of different models on inference. We assembled a dataset of five marker gene sequences (nuc58, nucLSU, nucSSU, rpb1, and rpb2) and 2,174 fungal taxa covering the three subphyla: Agaricomycotina, Mucoromycotina and Pezizomycotina. The fit of different models, including models with variable rates in clades or through time, to the pattern of ECM fungal taxa was tested in a Bayesian framework, and using AIC and simulations. We find that models implementing variable rates are a better fit than models without rate shift, and that the conclusion about the relative rate between ECM and non-ECM depend largely on whether rate shifts are allowed or not. We conclude that standard constant-rate ancestral state reconstruction models are not adequate for the analysis of the evolution of ECM fungi, and may give contradictory results to more extensive analyses.

A New Classification of the Dictyostelids.

Traditional morphology-based taxonomy of dictyostelids is rejected by molecular phylogeny. A new classification is presented based on monophyletic entities with consistent and strong molecular phylogenetic support and that are, as far as possible, morphologically recognizable. All newly named clades are diagnosed with small subunit ribosomal RNA (18S rRNA) sequence signatures plus morphological synapomorphies where possible. The two major molecular clades are given the rank of order, as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders are recognized and given the rank of family as, respectively, Acytosteliaceae and Cavenderiaceae fam. nov. in Acytosteliales, and Dictyosteliaceae and Raperosteliaceae fam. nov. in Dictyosteliales. Twelve genera are recognized: Cavenderia gen. nov. in Cavenderiaceae, Acytostelium, Rostrostelium gen. nov. and Heterostelium gen. nov. in Acytosteliaceae, Tieghemostelium gen. nov., Hagiwaraea gen. nov., Raperostelium gen. nov. and Speleostelium gen. nov. in Raperosteliaceae, and Dictyostelium and Polysphondylium in Dictyosteliaceae. The "polycephalum" complex is treated as Coremiostelium gen. nov. (not assigned to family) and the "polycarpum" complex as Synstelium gen. nov. (not assigned to order and family). Coenonia, which may not be a dictyostelid, is treated as a genus incertae sedis. Eighty-eight new combinations are made at species and variety level, and Dictyostelium ammophilum is validated.

Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.

Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity. Unlike the other major divisions of Discoba (Jakobida and Euglenozoa), little is known about the mitochondrial DNAs (mtDNAs) of Heterolobosea. We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly AT-rich (83.3%) molecule of 51.5 kb. Unexpectedly, A. kona mtDNA is missing roughly 40% of the protein-coding genes and nearly half of the transfer RNAs found in the only other sequenced heterolobosean mtDNAs, those of Naegleria spp. Instead, over a quarter of A. kona mtDNA consists of novel open reading frames. Eleven of the 16 protein-coding genes missing from A. kona mtDNA were identified in its nuclear DNA and polyA RNA, and phylogenetic analyses indicate that at least 10 of these 11 putative nuclear-encoded mitochondrial (NcMt) proteins arose by direct transfer from the mitochondrion. Acrasis kona mtDNA also employs C-to-U type RNA editing, and 12 homologs of DYW-type pentatricopeptide repeat (PPR) proteins implicated in plant organellar RNA editing are found in A. kona nuclear DNA. A mapping of mitochondrial gene content onto a consensus phylogeny reveals a sporadic pattern of relative stasis and rampant gene loss in Discoba. Rampant loss occurred independently in the unique common lineage leading to Heterolobosea + Tsukubamonadida and later in the unique lineage leading to Acrasis. Meanwhile, mtDNA gene content appears to be remarkably stable in the Acrasis sister lineage leading to Naegleria and in their distant relatives Jakobida.