Monophyly is essential prerequisite for species delimitation. In protists, molecular phylogenetic studies revealed, in recent years, many polyphyletic groups at all taxonomic levels, which afterwards led to their revisions for getting closer to natural classification. Above all, species-level polyphyly not only causes revisions of species, but also forces taxonomists to face species problems, especially species delimitation. Technological advancement in molecular biology represented by next-generation sequencing enables to develop various new methods for species delimitation, which open up a new way of taxonomy. Morphologically indistinct groups such as small flagellates or amoebas have been out of search for intraspecific polyphyly because of inability of delimiting their species boundaries. However, a new approach called "reverse taxonomy" including increased taxon sampling shed light on their species delimitation.
The aquatic food linkage between heterotrophic bacteria and protists is so-called “microbial loop”, functioning as important matter cycling in pelagic food webs of marine and freshwater systems. Organic matter transfer from heterotrophic bacteria to protists has been intensively studied by numerous researchers all over the world. The ecological roles of planktonic protists, such as heterotrophic nanoflagellates and ciliates, in microbial loop are to consume bacteria that are too small to serve directly as major prey items for most zooplankters, and to be consumed by the zooplankton. There is the consensus that food linkages between bacteria and protists are substantial in many lakes and oceans. The present review provides the overview on the trend and future stage of microbial loop research. A review on unique microbial loop developed in the hypolimnion of Lake Biwa is also provided.
Horizontal gene transfer (HGT) plays an important role in bacterial evolution and the exchange of genetic material between different species and genera. Recently, whole genome analysis demonstrated that HGT also played an important role in the diversification of all three domains of organisms. Bacterial HGTs are mediated by one of three mechanisms: transformation, conjugation, or transduction. In addition to these distinct mechanisms, gene transfer agent (GTA) or membrane vesicles (MV) mediate a transduction-like process that has been reported as an alternative HGT process. The occurrence of HGT has been confirmed by both laboratory and field studies. Both biotic and abiotic parameters affect the success of gene transfer events in natural environments. However, the frequency and the role of HGT in natural environments are currently not well understood due to the difficult nature of defining the experimental conditions required in order to elucidate this important parameter in HGT events. This knowledge will help in the estimation of the emergence of antibiotic resistance genes among bacteria and the potential consequences of the environmental usage of genetically modified bacteria for bioremediation purposes. The aim of this review was to summarize the brief history of HGT and the biotic factors that may affect the frequency of HGT in the ecosystem.
Mitochondria are ubiquitous organelles in all eukaryotes that are essential for a range of cellular processes and cellular signaling. Nearly all mitochondria have their own DNA or mitochondrial genome, which varies considerably in size, structure and organization. The phylum Apicomplexa includes a variety of unicellular eukaryotes, some of which are parasites of clinical or economic importance. Recent studies have demonstrated that apicomplexan mitochondrial genomes, which include the smallest 6-kb genome of the malaria parasites, exhibit remarkably diverse structures. Apicomplexan parasites are interesting model organisms in order to understand the evolution of mitochondrial genomes. This review summarizes the structure of apicomplexan mitochondrial genomes and highlights the unique features and the evolution of the mitochondrial genome.
Plastids (chloroplasts) have been evolved by multiple endosymbiotic events between a non-photosynthetic protist and a photosynthetic organism. Plants and a part of algae (green and red algae) acquired plastids from a cyanobacterium through a primary endosymbiosis, and many other algal groups have more complex plastids originated from green or red algal endosymbionts via secondary endosymbioses. In these events, many genes residing in the endosymbiont genomes have been transferred to the host nuclear genomes, and bulk of which encode proteins that are targeted back to plastids across multiple membranes. Plastid targeting of nucleus-encoded proteins is essential to maintain and control an endosymbiont as a photosynthetic organelle. Chlorarachniophytes are an algal group possessing extremely complex plastids acquired by the uptake of green algal endosymbiont. Four membrane surround the plastids and a relict nucleus, called the nucleomorph, of the endosymbiont exists in the periplastidal compartment. This review summarizes current studies on protein targeting into complex plastids of chlorarachniophytes and reductive evolution of the endosymbiotically-derived nucleomorph genomes.