Phylogenetic information from ribosomal RNA genes directly amplified from the environment changed our view of the biosphere, revealing an extraordinary diversity of previously undetected prokaryotic lineages. Using ribosomal RNA genes from marine picoplankton, several new groups of bacteria and archaea have been identified, some of which are abundant. Little is known, however, about the diversity of the smallest planktonic eukaryotes, and available information in general concerns the phytoplankton of the euphotic region. Here we recover eukaryotes in the size fraction 0.2-5 microm from the aphotic zone (250-3,000 m deep) in the Antarctic polar front. The most diverse and relatively abundant were two new groups of alveolate sequences, related to dinoflagellates that are found at all studied depths. These may be important components of the microbial community in the deep ocean. Their phylogenetic position suggests a radiation early in the evolution of alveolates.

The diversity and mode of life of microbial eukaryotes in hydrothermal systems is very poorly known. We carried out a molecular survey based on 18S ribosomal RNA genes of eukaryotes present in different hydrothermal niches at the Mid-Atlantic Ridge. These included metal-rich and rare-earth-element-rich hydrothermal sediments of the Rainbow site, fluid-seawater mixing regions, and colonization devices (microcolonizers) containing organic, ironrich, and porous mineral substrates that were exposed for 15 days to a fluid source. We identified considerable phylogenetic diversity, both at kingdom level and within kinetoplastids and alveolates. None of our sequences affiliates to photosynthesizing lineages, suggesting that we are targeting only autochthonous deep-sea communities. Although sediment harbored most phylogenetic diversity, microcolonizers predominantly contained bodonids and ciliates, indicating that these protists pioneer the colonization process. Given the large variety of divergent lineages detected within the alveolates in deep-sea plankton, hydrothermal sediments, and vents, alveolates seem to dominate the deep ocean in terms of diversity. Compared with data from the Pacific Guaymas basin, some protist lineages seem ubiquitous in hydrothermal areas, whereas others, notably kinetoplastid lineages, very abundant and diverse in our samples, so far have been detected only in Atlantic systems. Unexpectedly, although alvinellid polychaetes are considered endemic of Pacific vents, we detected alvinellidrelated sequences at the fluid-seawater interface and in microcolonizers. This finding can boost further studies on deep-sea vent animal biology and biogeography.C ompared with prokaryotes, microbial eukaryotes thriving in extreme environments have rarely been studied. This fact is partly because of the difficulties imposed by classical cultivation approaches. Recent eukaryotic diversity surveys based on 18S rRNA are revealing an unexpected variety of often divergent lineages in different biotopes, including some extreme environments (1-6). The only available molecular survey of microbial eukaryotes from deep-sea vents was recently carried out in hydrothermal sediments from the Pacific Guaymas basin and revealed an important diversity of hitherto unknown lineages (5). Surprisingly, many of these sequences affiliated to typical photosynthesizing groups (such as green algae or diatoms), leading to the conclusion that autochthonous eukaryotes cannot be distinguished from those deposited from the water column (5). There were two objectives in this study. First, we aimed at characterizing the diversity of autochthonous microbial eukaryotes from Mid-Atlantic Ridge hydrothermal systems. Thus, we have carried out a molecular survey of hydrothermal sediment and seawater-fluid interface. These results should constitute a first base for comparison with data from the Pacific systems. To date, whereas prokaryotes seem ubiquitous in different oceanic regions (7), possibly including vent areas, metazoans are subject to a defi...

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Chloroplast structure and genome analyses support the hypothesis that three groups of organisms originated from the primary photosynthetic endosymbiosis between a cyanobacterium and a eukaryotic host: green plants (green algae + land plants), red algae and glaucophytes (for example, Cyanophora). Although phylogenies based on several mitochondrial genes support a specific green plants/red algae relationship, the phylogenetic analysis of nucleus-encoded genes yields inconclusive, sometimes contradictory results. To address this problem, we have analysed an alternative nuclear marker, elongation factor 2, and included new red algae and protist sequences. Here we provide significant support for a sisterhood of green plants and red algae. This sisterhood is also significantly supported by a multi-gene analysis of a fusion of 13 nuclear markers (5,171 amino acids). In addition, the analysis of an alternative fusion of 6 nuclear markers (1,938 amino acids) indicates that glaucophytes may be the closest relatives to the green plants/red algae group. Thus, our study provides evidence from nuclear markers for a single primary endosymbiosis at the origin of these groups, and supports a kingdom Plantae comprising green plants, red algae and glaucophytes.

When viruses were discovered, they were accepted as missing links between the inert world and living organisms. However, this idea was soon abandoned as information about their molecular parasitic nature accumulated. Recently, the notion that viruses are living organisms that have had a role in the evolution of some essential features of cells has experienced a renaissance owing to the discovery of unusually large and complex viruses that possess typical cellular genes. Here, we contend that there is strong evidence against the notion that viruses are alive and represent ancient lineages of the tree of life.

All cell membranes are composed of glycerol phosphate phospholipids, and this commonality argues for the presence of such phospholipids in the last common ancestor, or cenancestor. However, phospholipid biosynthesis is very different between bacteria and archaea, leading to the suggestion that the cenancestor was devoid of phospholipid membranes. Recent phylogenomic studies challenge this view, suggesting that the cenancestor did possess complex phospholipid membranes. Here, we discuss the implications of these recent findings for membrane evolution in archaea and bacteria, and for the origin of the eukaryotic cell.

Cyanobacteria have affected major geochemical cycles (carbon, nitrogen, and oxygen) on Earth for billions of years. In particular, they have played a major role in the formation of calcium carbonates (i.e., calcification), which has been considered to be an extracellular process. We identified a cyanobacterium in modern microbialites in Lake Alchichica (Mexico) that forms intracellular amorphous calcium-magnesium-strontium-barium carbonate inclusions about 270 nanometers in average diameter, revealing an unexplored pathway for calcification. Phylogenetic analyses place this cyanobacterium within the deeply divergent order Gloeobacterales. The chemical composition and structure of the intracellular precipitates suggest some level of cellular control on the biomineralization process. This discovery expands the diversity of organisms capable of forming amorphous calcium carbonates.

Isoprenoids are a very diverse family of organic compounds widespread in the three domains of life. Although they are produced from the condensation of the same precursors in all organisms (isopentenyl pyrophosphate and dimethylallyl diphosphate), the evolutionary origin of their biosynthesis remains controversial. Two independent nonhomologous metabolic pathways are known: the mevalonate (MVA) pathway in eukaryotes and archaea and the methylerythritol phosphate (MEP) pathway in bacteria and several photosynthetic eukaryotes. The MVA pathway is also found in a few bacteria, what has been explained in previous works by recent acquisition by horizontal gene transfer (HGT) from eukaryotic or archaeal donors. To reconsider the question of the evolutionary origin of the MVA pathway, we have studied the origin and the evolution of the enzymes of this pathway using phylogenomic analyses upon a taxon-rich sequence database. On the one hand, our results confirm the conservation in archaea of an MVA pathway partially different from eukaryotes. This implies that each domain of life possesses a characteristic major isoprenoid biosynthesis pathway: the classical MVA pathway in eukaryotes, a modified MVA pathway in archaea, and the MEP pathway in bacteria. On the other hand, despite the identification of several HGT events, our analyses support that the MVA pathway was ancestral not only in archaea and eukaryotes but also in bacteria, in contradiction with previous claims that the presence of this pathway in bacteria was due to HGT from other domains. Therefore, the MVA pathway is likely an ancestral metabolic route in all the three domains of life, and hence, it was probably present in the last common ancestor of all organisms (the cenancestor). These findings open the possibility that the cenancestor had membranes containing isoprenoids.