The genome of the protist parasite Entamoeba histolytica

Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which is a significant source of morbidity and mortality in developing countries. Here we present the genome of E. histolytica, which reveals a variety of metabolic adaptations shared with two other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis. These adaptations include reduction or elimination of most mitochondrial metabolic pathways and the use of oxidative stress enzymes generally associated with anaerobic prokaryotes. Phylogenomic analysis identifies evidence for lateral gene transfer of bacterial genes into the E. histolytica genome, the effects of which centre on expanding aspects of E. histolytica's metabolic repertoire. The presence of these genes and the potential for novel metabolic pathways in E. histolytica may allow for the development of new chemotherapeutic agents. The genome encodes a large number of novel receptor kinases and contains expansions of a variety of gene families, including those associated with virulence. Additional genome features include an abundance of tandemly repeated transfer-RNA-containing arrays, which may have a structural function in the genome. Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen.     

Microbiology: eukaryotic diversity in Spain's River of Fire

The Rio Tinto, known by the Phoenicians as 'Ur-yero', or 'River of Fire', because of its deep red colour and high acidity, flows through the world's largest pyritic belt in southwestern Spain. Surprisingly, eukaryotic microbes are the principal contributors of biomass in this hostile river, which has a pH of 2 and contains much higher concentrations of heavy metals than are typically found in fresh waters. Here we show that the Rio Tinto shows an unexpected degree of eukaryotic diversity and includes new lineages that we have identified by sequence analysis of genes encoding small-subunit ribosomal RNAs. The diversity of these eukaryotes is much greater than that of prokaryotes, whose metabolism is responsible for the extreme environment.     

Evidence against dust-mediated control of glacial-interglacial changes in atmospheric CO2

The low concentration of atmospheric CO2 inferred to have been present during glacial periods is thought to have been partly caused by an increased supply of iron-bearing dust to the ocean surface. This is supported by a recent model that attributes half of the CO2 reduction during past glacial stages to iron-stimulated uptake of CO2 by phytoplankton in the Southern Ocean. But atmospheric dust fluxes to the Southern Ocean, even in glacial periods, are thought to be relatively low and therefore it has been proposed that Southern Ocean productivity might be influenced by iron deposited elsewhere-for example, in the Northern Hemisphere-which is then transported south via ocean circulation (similar to the distal supply of iron to the equatorial Pacific Ocean). Here we examine the timing of dust fluxes to the North Atlantic Ocean, in relation to climate records from the Vostok ice core in Antarctica around the time of the penultimate deglaciation (about 130 kyr ago). Two main dust peaks occurred 155 kyr and 130 kyr ago, but neither was associated with the CO2 rise recorded in the Vostok ice core. This mismatch, together with the low dust flux supplied to the Southern Ocean, suggests that dust-mediated iron fertilization of the Southern Ocean did not significantly influence atmospheric CO2 at the termination of the penultimate glaciation.     

Comparative genomics of the neglected human malaria parasite Plasmodium vivax

The human malaria parasite Plasmodium vivax is responsible for 25-40% of the approximately 515 million annual cases of malaria worldwide. Although seldom fatal, the parasite elicits severe and incapacitating clinical symptoms and often causes relapses months after a primary infection has cleared. Despite its importance as a major human pathogen, P. vivax is little studied because it cannot be propagated continuously in the laboratory except in non-human primates. We sequenced the genome of P. vivax to shed light on its distinctive biological features, and as a means to drive development of new drugs and vaccines. Here we describe the synteny and isochore structure of P. vivax chromosomes, and show that the parasite resembles other malaria parasites in gene content and metabolic potential, but possesses novel gene families and potential alternative invasion pathways not recognized previously. Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species.