Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches.

PREMISE OF THE STUDY: Heterokont algae of the class Synurophyceae, characterized by distinctive siliceous scales that cover the surface of the cell, are ecologically important in inland waters, yet their evolutionary history remains enigmatic. We explore phylogenetic relationships within this group of algae relative to geologic time, with a focus on evolution of siliceous components. METHODS: We combined an expansive five-gene and time-calibrated molecular phylogeny of synurophyte algae with an extensive array of fossil specimens from the middle Eocene to infer evolutionary trends within the group. KEY RESULTS: The group originated in the Jurassic approximately 157 million years ago (Ma), with the keystone genera Mallomonas and Synura diverging during the Early Cretaceous at 130 Ma. Mallomonas further splits into two major subclades, signaling the evolution of the V-rib believed to aid in the spacing and organization of scales on the cell covering. Synura also diverges into two primary subclades, separating taxa with forward-projecting spines on the scale from those with a keel positioned on the scale proper. Approximately one third of the fossil species are extinct, whereas the remaining taxa are linked to modern congeners. CONCLUSIONS: The taxonomy of synurophytes, which relies extensively on the morphology of the siliceous components, is largely congruent with molecular analyses. Scales of extinct synurophytes were significantly larger than those of modern taxa and may have played a role in their demise. In contrast, many fossil species linked to modern lineages were smaller in the middle Eocene, possibly reflecting growth in the greenhouse climatic state that characterized this geologic interval.

Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes.

The Raphidophyceae is an ecologically important eukaryotic lineage of primary producers and predators that inhabit marine and freshwater environments worldwide. These organisms are of great evolutionary interest because their plastids are the product of eukaryote-eukaryote endosymbiosis. To obtain deeper insight into the evolutionary history of raphidophycean plastids, we sequenced and analyzed the plastid genomes of three freshwater and three marine species. Our comparison of these genomes, together with the previously reported plastid genome of Heterosigma akashiwo, revealed unexpected variability in genome structure. Unlike the genomes of other analyzed species, the plastid genome of Gonyostomum semen was found to contain only a single rRNA operon, presumably due to the loss of genes from the inverted repeat (IR) region found in most plastid genomes. In contrast, the marine species Fibrocapsa japonica contains the largest IR region and overall plastid genome for any raphidophyte examined thus far, mainly due to the presence of four large gene-poor regions and foreign DNA. Two plastid genes, tyrC in F. japonica and He. akashiwo and serC in F. japonica, appear to have arisen via lateral gene transfer (LGT) from diatoms, and several raphidophyte open reading frames are demonstrably homologous to sequences in diatom plasmids and plastid genomes. A group II intron in the F. japonica psbB gene also appears to be derived by LGT. Our results provide important insights into the evolutionary history of raphidophyte plastid genomes via LGT from the plastids and plasmid DNAs of diatoms.

Complete Genome Sequence of Bisphenol A-Degrading Bacterium Sphingobium sp. Strain A3, Isolated from Contaminated Soil.

This study reports the complete genome sequence of bisphenol A-degrading bacterium Sphingobium sp. strain A3, which was isolated from a contaminated soil sample from the site of a factory fire in South Korea. The genome consists of a 6.53-Mbp chromosome and eight plasmid contigs (532,947 bp), with 6,406 protein-coding sequences and a GC content of 63.82%.

Complex phylogeographic patterns in the freshwater alga Synura provide new insights into ubiquity vs. endemism in microbial eukaryotes.

The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multigene data set, we study the phylogeography of the freshwater heterokont alga Synura petersenii sensu lato. Our results suggest that this Synura morphotaxon contains both cosmopolitan and regionally endemic cryptic species, co-occurring in some cases, and masked by a common ultrastructural morphology. Phylogenies based on both proteins (seven protein-coding plastid and mitochondrial genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced biogeographic delineations within phylotypes of this cryptic species complex while retaining one clade that is globally distributed. Relaxed molecular clock calculations, constrained by fossil records, suggest that the genus Synura is considerably older than currently proposed. The availability of tectonically relevant geological time (107-108 years) has enabled the development of the observed, complex biogeographic patterns. Our comprehensive analysis of freshwater algal biogeography suggests that neither ubiquity nor endemism wholly explains global patterns of microbial eukaryote distribution and that processes of dispersal remain poorly understood.

Complete Genome Sequence of Gordonia rubripertincta SD5, a Soil Bacterium Isolated from a Di-(2-Ethylhexyl) Phthalate-Degrading Enrichment Culture.

We report the complete genome sequence of Gordonia rubripertincta SD5, isolated from a soil-derived di-(2-ethylhexyl) phthalate-degrading enrichment culture. The final genome assembly consists of a 5.10-Mbp chromosome and a plasmid (159 kbp). A total of 4,814 coding sequences were predicted, including 4,741 protein-coding sequences.

STUDIES ON ULTRASTRUCTURE AND THREE-GENE PHYLOGENY OF THE GENUS MALLOMONAS (SYNUROPHYCEAE)(1).

The genus Mallomonas, a common and often abundant member of the planktic community in many freshwater habitats worldwide, consists of 180 species divided into 19 sections and 23 series. Classification of species is based largely on ultrastructural characteristics of the siliceous scales and bristles that collectively form a highly organized covering over the cell. However, the relative importance of the different siliceous features of the scales, such as the dome, V rib, and secondary structures, as well as the different types of scales, in understanding the evolution and phylogeny of the genus is little known. In this study, we investigated the scale and bristle ultrastructure, along with sequences of three genes, for 19 isolates (18 species) of Mallomonas (18 isolates were from Korean habitats). The isolates represented nine of the 19 sections. Sequences for both the nuclear SSU and LSU rDNA and plastid LSU of RUBISCO (rbcL) genes for each of the 19 Mallomonas isolates and four outgroups were determined. Bayesian and maximum-likelihood (ML) analyses of the data revealed that Mallomonas consists of two strongly supported clades. Mallomonas bangladeshica (E. Takah. et T. Hayak.) Siver et A. P. Wolfe was at the base of the first clade that included taxa from the sections Planae and Heterospinae, both of which lack a V rib on the shield of the scales. Our results indicated that the sections Planae and Heterospinae should be combined. The second clade, with Mallomonas insignis Penard and Mallomonas punctifera Korshikov at the base, contained taxa from the sections Mallomonas, Striatae, Akrokomae, Annulatae, Torquatae, Punctiferae, and Insignes, all of which have V ribs or well-developed marginal ribs on the scales. Sister relationships between Mallomonas and Striatae were strongly supported, but interrelations among the remaining sections were not resolved, probably due to inclusion of too few species. Our results suggest that the current classification of the genus Mallomonas at the section level will require some revision. Additional species will need to be added in future analyses.