This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1550-7408.2012.00644.x

The revised classification of eukaryotes

Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated rapidly into glaucophytes, green plants and red algae. Secondary symbiogeneses subsequently transferred plastids laterally into different hosts, making yet more complex cell chimaeras--probably only thrice: from a red alga to the corticoflagellate ancestor of chromalveolates (Chromista plus Alveolata), from green algae to a secondarily uniciliate cercozoan to form chlorarachneans and independently to a biciliate excavate to yield photosynthetic euglenoids. Tertiary symbiogenesis involving eukaryotic algal symbionts replaced peridinin-containing plastids in two or three dinoflagellate lineages, but yielded no major novel groups. The origin and well-resolved primary bifurcation of eukaryotes probably occurred in the Cryogenian Period, about 850 million years ago, much more recently than suggested by unwarranted backward extrapolations of molecular 'clocks' or dubious interpretations as 'eukaryotic' of earlier large microbial fossils or still more ancient steranes. The origin of chloroplasts and the symbiogenetic incorporation of a red alga into a corticoflagellate to create chromalveolates may both have occurred in a big bang after the Varangerian snowball Earth melted about 580 million years ago, thereby stimulating the ensuing Cambrian explosion of animals and protists in the form of simultaneous, poorly resolved opisthokont and anterokont radiations.

The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.

In order to conduct experiments on interactions between animals and food organisms, it is necessary to develop a medium that adequately supports the growth of both algae and zooplankton without the need to alter the medium to accommodate either the algae or the animals. We devised a freshwater medium, named COMBO, that supports excellent growth of both algae and zooplankton. Two types of algae, Ankistrodesmus falcatus and Stephanodiscus hantzschii, were reared in COMBO and their growth rates were not significantly different from those of algae grown in a reference medium (WC). One of these algae, A. falcatus, was then fed to a cladoceran, Daphnia pulicaria, which was also cultured in COMBO, and the resulting fecundities of D. pulicaria were compared to those of animals reared in natural surface water. We also determined whether the value of COMBO as a medium for D. pulicaria was affected by modifications in nitrogen or phosphorus concentration to evaluate whether the new medium will be useful in nutritional research. Lowering the N or P content of COMBO did not affect the reproductive performance of D. pulicaria. Other researchers have also reported excellent growth and reproduction by numerous algae and zooplankton reared in COMBO. Our results suggest that COMBO is an effective artificial, defined culture medium capable of supporting robust growth and reproduction of both freshwater algae and zooplankton.

/pdf/combo-a-defined-freshwater-culture-medium-for-algae-and-3dmd1xk5l7.pdf

COMBO: a defined freshwater culture medium for algae and zooplankton

Iron and manganese in lakes

Although macroscopic plants, animals, and fungi are the most familiar eukaryotes, the bulk of eukaryotic diversity is microbial. Elucidating the timing of diversification among the more than 70 lineages is key to understanding the evolution of eukaryotes. Here, we use taxon-rich multigene data combined with diverse fossils and a relaxed molecular clock framework to estimate the timing of the last common ancestor of extant eukaryotes and the divergence of major clades. Overall, these analyses suggest that the last common ancestor lived between 1866 and 1679 Ma, consistent with the earliest microfossils interpreted with confidence as eukaryotic. During this interval, the Earth's surface differed markedly from today; for example, the oceans were incompletely ventilated, with ferruginous and, after about 1800 Ma, sulfidic water masses commonly lying beneath moderately oxygenated surface waters. Our time estimates also indicate that the major clades of eukaryotes diverged before 1000 Ma, with most or all probably diverging before 1200 Ma. Fossils, however, suggest that diversity within major extant clades expanded later, beginning about 800 Ma, when the oceans began their transition to a more modern chemical state. In combination, paleontological and molecular approaches indicate that long stems preceded diversification in the major eukaryotic lineages.

/pdf/estimating-the-timing-of-early-eukaryotic-diversification-10j7axrrzp.pdf

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

Rhodomonas lacustris (Pascher & Ruttner) Javornicky (Cryptomonadida): Ultrastructure of the Vegetative Cell

Hydrurus foetidus is a geographically widespread alga commonly detected as 2–10 cm thalli in mountain streams in early spring, and also in lowland rivers at latitudes where seasonal conditions are appropriate for this cold-water species. Reaching macroscopic dimensions but with a pronounced phenotypic plasticity, this species is not typical for the golden algae (Chrysophyceae) – they are almost exclusively microscopic organisms, best known as micro- or nanoplankton in fresh water. Other sessile multicellular members are less conspicuous in nature, and rarely detected and sampled for further investigation. Therefore, the phylogenetic position of Hydrurus within the Chrysophyceae is not clear and has been disputed. We determined the 18S and 28S rDNA subunit sequences from a typical H. foetidus sampled at Finse, Hardangervidda mountain plateau, in south Norway. Phylogenetic trees inferred from concatenated 18S and 28S sequences, including representatives of all known groups of heterokonts, safely confirmed H...

https://www.tandfonline.com/doi/pdf/10.1080/09670262.2011.598950

The 18S and 28S rDNA identity and phylogeny of the common lotic chrysophyte Hydrurus foetidus

The Haptophyta is a common algal group in many marine environments, but only a few species have been observed in freshwaters, with DNA sequences available from just a single species, Crysochromulina parva Lackey, 1939. Here we investigate the haptophyte diversity in a high mountain lake, Lake Finsevatn, Norway, targeting the variable V4 region of the 18S rDNA gene with PCR and 454 pyrosequencing. In addition, the freshwater diversity of Pavlovophyceae was investigated by lineage-specific PCR-primers and clone library sequencing from another Norwegian lake, Lake Svaersvann. We present new freshwater phylotypes belonging to the classes Prymnesiophyceae and Pavlovophyceae, as well as a distinct group here named HAP-1. This is the first molecular evidence of a freshwater species belonging to the class Pavlovophyceae. The HAP-1 and another recently detected marine group (i.e. HAP-2) are separated from both Pavlovophyceae and Prymnesiophyceae and may constitute new higher order taxonomic lineages. As all obtained freshwater sequences of haptophytes are distantly related to the freshwater species C. parva, the phylogeny demonstrates that haptophytes colonized freshwater on multiple independent occasions. One of these colonizations, which gave rise to HAP-1, took place very early in the history of haptophytes, before the radiation of the Prymnesiophyceae.

Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences.

High Arctic lakes are among the most sensitive ecosystems and climate change strongly affects their physical properties, especially water temperature, and mixing processes. To study the effect of recent climate change on such a lake in the Arctic environment, we measured water chemistry and temperature from 2005 to 2010 in Kongressvatn, a crenogenic meromictic lake in Spitsbergen (Svalbard). In addition, we monitored water column temperatures during two consecutive years and compared them to regional air temperature data and physicochemical lake data from 1962 and 1968, two relatively cold years. Summer surface water temperature was highly correlated to air temperature, and both have increased by approximately 2°C since 1962. Temperature monitoring during 2 years showed that the warm summer of 2007 resulted in increased water temperatures even in the stratified, denser hypolimnion. Our water chemistry measurements showed that the chemocline position in 2005–2010 was ca 12 m deeper than in 1962–1968, and a second, weaker, chemocline appeared at metalimnetic depths of 7–15 m. During the study period, the water level decreased by 4 m, and this change accelerated between 2008 and 2010. Our data support the hypothesis that water temperatures and stratification patterns are changing rapidly with air temperature, but changes in the catchment, such as glacial retreat and permafrost melting, may have an even stronger impact on lake properties.

Rapid physicochemical changes in the high Arctic Lake Kongressvatn caused by recent climate change

The Hindak strain of a Cryptomonas species (Cryptophyceae) produces extracellular polysaccharides. Because there is no information on the structure of these compounds in the Cryptophyceae we conducted structural studies. Gas–liquid chromatographic analyses showed that the polysaccharide is composed of fucose, rhamnose, xylose, mannose, glucose, galactose, galacturonic acid, glucuronic acid, and traces of 3-O-methyl galactose. The polysaccharide was separated into two subtractions by ion-exchange chromatography. Fraction A consisted mainly of 1,3-linked galactose units and 1,4-linked galacturonic acid. Unlike fraction B, fraction A did not have xylose, 3-O-methyl galactose, or glucuronic acid. Also, its degree of branching was low compared to that of fraction B. Only traces of sulfate were present infraction A, but fraction B was 10–15% sulfated. Protein was approximately 1% in both fractions. These polysaccharides appear to be a novel type of polymer in algae.

Dag Klaveness

Papers

Rhodomonas lacustris (Pascher & Ruttner) Javornicky (Cryptomonadida): Ultrastructure of the Vegetative Cell

The 18S and 28S rDNA identity and phylogeny of the common lotic chrysophyte Hydrurus foetidus

Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences.

Rapid physicochemical changes in the high Arctic Lake Kongressvatn caused by recent climate change

Structure of extracellular polysaccharides produced by a soil cryptomonas sp. (cryptophyceae)1