Filter-feeding in Colonial Protists.

Many protists form cell colonies. Among them several are filter-feeders depending on suspended food particles such as bacteria. It has been suggested that the formation of colonies enhances feeding efficiency and implied that - in the case of colonial choanoflagellates - it was an adaptive trait that led to the evolution of metazoans. Here it is shown experimentally - for a colonial peritrich ciliate and for a choanoflagellate - that colony-formation does not enhance the efficiency of filter-feeding relative to solitary cells and that the adaptive significance of cell colony-formation must have some other explanation.

Cosmopolitan Metapopulations?

A "metapopulation" is a group of populations of the same species separated by space but linked by dispersal and migration. Metapopulations of macroscopic organisms tend to have geographically-restricted distributions, but this does not seem to be the case in microbial eukaryotes due to their astronomical abundance. The term "metapopulation" was first applied to protists' biogeography in the article Finlay and Fenchel (2004), published in PROTIST, which contributed to the popularity of the paper. The article considered protist species as consisting of a single, cosmopolitan population. Here, we recall this paper, and assess developments during the last 15 years with respect to the question of protist species distribution on the surface of the earth.

CaCO3 precipitation in multilayered cyanobacterial mats: clues to explain the alternation of micrite and sparite layers in calcareous stromatolites.

Marine cyanobacterial mats were cultured on coastal sediments (Nivå Bay, Øresund, Denmark) for over three years in a closed system. Carbonate particles formed in two different modes in the mat: (i) through precipitation of submicrometer-sized grains of Mg calcite within the mucilage near the base of living cyanobacterial layers, and (ii) through precipitation of a variety of mixed Mg calcite/aragonite morphs in layers of degraded cyanobacteria dominated by purple sulfur bacteria. The d13C values were about 2‰ heavier in carbonates from the living cyanobacterial zones as compared to those generated in the purple bacterial zones. Saturation indices calculated with respect to calcite, aragonite, and dolomite inside the mats showed extremely high values across the mat profile. Such high values were caused by high pH and high carbonate alkalinity generated within the mats in conjunction with increased concentrations of calcium and magnesium that were presumably stored in sheaths and extracellular polymer substances (EPS) of the living cyanobacteria and liberated during their post-mortem degradation. The generated CaCO3 morphs were highly similar to morphs reported from heterotrophic bacterial cultures, and from bacterially decomposed cyanobacterial biomass emplaced in Ca-rich media. They are also similar to CaCO3 morphs precipitated from purely inorganic solutions. No metabolically (enzymatically) controlled formation of particular CaCO3 morphs by heterotrophic bacteria was observed in the studied mats. The apparent alternation of in vivo and post-mortem generated calcareous layers in the studied cyanobacterial mats may explain the alternation of fine-grained (micritic) and coarse-grained (sparitic) laminae observed in modern and fossil calcareous cyanobacterial microbialites as the result of a probably similar multilayered mat organization.

Respiration in heterotrophic unicellular eukaryotic organisms.

Surface:volume quotient, mitochondrial volume fraction, and their distribution within cells were investigated and oxygen gradients within and outside cells were modelled. Cell surface increases allometrically with cell size. Mitochondrial volume fraction is invariant with cell size and constitutes about 10% and mitochondria are predominantly found close to the outer membrane. The results predict that for small and medium sized protozoa maximum respiration rates should be proportional to cell volume (scaling exponent ≈1) and access to intracellular O2 is not limiting except at very low ambient O2-tensions. Available data do not contradict this and some evidence supports this interpretation. Cell size is ultimately limited because an increasing fraction of the mitochondria becomes exposed to near anoxic conditions with increasing cell size. The fact that mitochondria cluster close to the cell surface and the allometric change in cell shape with increasing cell size alleviates the limitation of aerobic life at low ambient O2-tension and for large cell size.

Studies on the genus Mesodinium I: ultrastructure and description of Mesodinium chamaeleon n. sp., a benthic marine species with green or red chloroplasts.

We provide here the description of a new marine species that harbors green or red chloroplasts. In contrast to certain other species of the genus, Mesodinium chamaeleon n. sp. can be maintained in culture for short periods only. It captures and ingests flagellates including cryptomonads. The prey is ingested very rapidly into a food vacuole without the cryptomonad flagella being shed and the trichocysts being discharged. The individual food vacuoles subsequently serve as photosynthetic units, each containing the cryptomonad chloroplast, a nucleus, and some mitochondria. The ingested cells are eventually digested. This type of symbiosis differs from other plastid-bearing Mesodinium spp. in retaining ingested cryptomonad cells almost intact. The food strategy of the new species appears to be intermediate between heterotrophic species, such as Mesodinium pulex and Mesodinium pupula, and species with red cryptomonad endosymbionts, such as Mesodinium rubrum.

Mixotrophy in ciliates.

Mixotrophy is the occurrence of phagotrophy and phototrophy in the same organism. In ciliates the intracellular phototroph can be unicellular green algae (zoochlorellae), dinoflagellates (zooxanthellae), cryptomonads or sequestered chloroplasts from ingested algae. An intermediate mixotrophic mechanism is that where the phagotroph ingests algal cells, maintains them intact and functional in the cytoplasm for some time, but the algae are afterwards digested. This seems to occur in some species of Mesodinium. Ciliates with phototrophic endosymbionts have evolved independently in marine and freshwater habitats. The enslaved algal cells or chloroplasts provide host cells with organic matter. Mixotrophs flourish in oxygen-rich, but also in micro-aerobic waters and in the complete absence of oxygen. In the latter case, the aerobic host retains aerobic metabolism, sustained by the oxygen produced by the phototrophic endosymbionts or the sequestered chloroplasts. Mixotrophic ciliates can attain spectacular abundances in some habitats, and entirely dominate the ciliate community.

The life history of Flabellula baltica Smirnov (Gymnamoebae, Rhizopoda): adaptations to a spatially and temporally heterogeneous environment.

The polymorphic life history of the marine naked amoeba Flabellula baltica was studied. It can be interpreted in terms of adaptations to an environment that is patchy in time and space and it represents trade-off between longevity during starvation and the ability to initiate multiplication soon after food resource become available. The life history also represents bet hedging in that different cells within a clonal culture may respond in different ways when food is depleted.

Oxygen and the spatial structure of microbial communities.

Oxygen has two faces. On one side it is the terminal electron acceptor of aerobic respiration - the most efficient engine of energy metabolism. On the other hand, oxygen is toxic because the reduction of molecular O2 creates reactive oxygen species such as the superoxide anion, peroxide, and the hydroxyl radical. Probably most prokaryotes, and virtually all eukaryotes, depend on oxygen respiration, and we show that the ambiguous relation to oxygen is both an evolutionary force and a dominating factor driving functional interactions and the spatial structure of microbial communities.We focus on microbial communities that are specialised for life in concentration gradients of oxygen, where they acquire the full panoply of specific requirements from limited ranges of PO2, which also support the spatial organisation of microbial communities. Marine and lake sediments provide examples of steep O2 gradients, which arise because consumption or production of oxygen exceeds transport rates of molecular diffusion. Deep lakes undergo thermal stratification in warm waters, resulting in seasonal anaerobiosis below the thermocline, and lakes with a permanent pycnocline often have permanent anoxic deep water. The oxycline is here biologically similar to sediments, and it harbours similar microbial biota, the main difference being the spatial scale. In sediments, transport is dominated by molecular diffusion, and in the water column, turbulent mixing dominates vertical transport. Cell size determines the minimum requirement of aerobic organisms. For bacteria (and mitochondria), the half-saturation constant for oxygen uptake ranges within 0.05-0.1% atmospheric saturation; for the amoeba Acanthamoeba castellanii it is 0.2%, and for two ciliate species measuring around 150 microm, it is 1-2 % atmospheric saturation. Protection against O2 toxicity has an energetic cost that increases with increasing ambient O2 tension. Oxygen sensing seems universal in aquatic organisms. Many aspects of oxygen sensing are incompletely understood, but the mechanisms seem to be evolutionarily conserved. A simple method of studying oxygen preference in microbes is to identify the preferred oxygen tension accumulating in O2 gradients. Microorganisms cannot sense the direction of a chemical gradient directly, so they use other devices to orient themselves. Different mechanisms in different prokaryotic and eukaryotic microbes are described. In O2 gradients, many bacteria and protozoa are vertically distributed according to oxygen tension and they show a very limited range of preferred PO2. In some pigmented protists the required PO2 is contingent on light due to photochemically generated reactive oxygen species. In protists that harbour endosymbiotic phototrophs, orientation towards light is mediated through the oxygen production of their photosynthetic symbionts. Oxygen plays a similar role for the distribution of small metazoans (meiofauna) in sediments, but there is little experimental evidence for this. Thus the oxygenated sediments surrounding ventilated animal burrows provide a special habitat for metazoan meiofauna as well as unicellular organisms.

The microbial engines that drive Earth's biogeochemical cycles.

Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet's history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.

The diversity of microbes: resurgence of the phenotype.

The introduction of molecular genetic methods has caused confusion about the nature of microbial species. Environmental DNA extraction has indicated the existence of a vast diversity of genotypes, but how this relates to functional and phenotypic diversity has not been sufficiently explored. It has been implied that genetic distance per se correlates with phenotypic differentiation and thus reflects subtle (but undiscovered) adaptive fine-tuning to the environment, and that microbes may show biogeographic patterns at the genetic level. Here, we argue that no theoretically based species concept exists; species represent only the basic unit in the taxonomic hierarchy. The significance of naming species is that it organizes biological information. The reason why microbial species collectively represent large genetic differences is owing to huge absolute population sizes, absence of allopatric speciation and low extinction rates. Microbial phenotypes are, therefore, ancient in terms of the geological time-scale and have been maintained through stabilizing selection. These problems are discussed with special reference to eukaryotic micro-organisms.

Multiple cosmopolitan ecotypes within a microbial eukaryote morphospecies.

Microbial eukaryotes that are morphologically indistinguishable (i.e. 'morphospecies') tend to be genetically diverse. While most protist morphospecies have cosmopolitan distribution, it has been suggested that ribotypes (unique rRNA gene sequences) or rRNA sequence clusters do have biogeography and such clusters may correlate with particular (non-morphological) adaptations. We have studied this in the ciliated protozoan morphospecies Cyclidium glaucoma. Fifty-four isolates collected worldwide represented 31 distinct ribotypes. There was no evidence of biogeographic distribution patterns. For example, identical ribotypes occurred in samples from Argentina, Peru, Morocco, Russia and Ukraine; in samples from Denmark and Australia; and in samples from Great Salt Lake and hyperhaline ponds in Spain. The morphospecies Cyclidium glaucoma is euryhaline and occurs in freshwater, brackish water, seawater, and hyperhaline waters. Evidence suggests that one ribotype cluster occurs only in marine or brackish habitats, and another one has so far been found only in hyperhaline habitats. Two clades seem to occur only in freshwater, but one clade includes ribotypes that were found in freshwater as well as in brackish water.

Self-similar patterns of nature: insect diversity at local to global scales.

The insects are probably the most hyperdiverse and economically important metazoans on the planet, but there is no consensus on the best way to model the dimensions of their diversity at multiple spatial scales, and the huge amount of information involved hinders data synthesis and the revelation of 'patterns of nature'. Using a sample of more than 600k insect species in the size range 1-100mm, we analysed insect body sizes and revealed self-similar patterns persisting across spatial scales from several hectares to the World. The same patterns were found in both Northern and Southern Hemispheres. The patterns include: parallel rank-abundance distributions; flatter species-area curves in smaller insects-indicating their wider geographical distribution; the recurrence of the same species-rich family in the same body-size class at all spatial scales-which generates self-similar size-frequency distributions (SFDs)-and the discovery that with decreasing mean body size, local species richness represents an increasing fraction of global species richness. We describe how these 'rationalizing' patterns can be translated into methods for monitoring and predicting species diversity and community structure at all spatial scales.

Survey of motile microaerophilic bacterial morphotypes in the oxygen gradient above a marine sulfidic sediment.

Enrichment cultures for free-swimming microaerophilic bacteria were prepared from marine sulfidic sediment samples (Nivå Bay, Denmark). We observed nine different morphotypes; three of these morphotypes represented already-described species, i.e., Thiovulum majus, "Candidatus Ovobacter propellens," and an as-yet-unnamed large vibrioid bacterium. In addition, we observed several morphotypes of spirilla and one vibrioid morphotype. A common feature of all investigated bacteria was that they aggregated chemotactically at the oxic-anoxic interface, whereas preferred oxygen concentration were in the range of 1 to 10 muM. The motile behavior and flagellar dynamics are analyzed in detail with an emphasis on spirilla.

Cosmopolitan metapopulations of free-living microbial eukaryotes.

Metapopulations of macroscopic organisms tend to be geographically restricted, but free-living protists and other microbial eukaryotes present a different picture. Here we show that most organisms smaller than 1 mm occur worldwide wherever their required habitats are realised. This is a consequence of ubiquitous dispersal driven by huge population sizes, and the consequently low probability of local extinction. Organisms larger than 10 mm are much less abundant, and rarely cosmopolitan. The supporting data, together with the discovery that the 1-10 mm size range accommodates a transition from cosmopolitan to regionally-restricted distribution, were derived from extensive inventories of eukaryotic species in a freshwater pond (1278 species), and a shallow marine bay (785 species). All accessible records were examined to establish the extent of global coverage by these species. Some groups of microbial eukaryotes are severely undersampled (e.g. naked amoebae; marine meiofauna in the southern hemisphere) but this fails to weaken evidence that metapopulations of microbial eukaryotes are cosmopolitan.

Complex flagellar motions and swimming patterns of the flagellates Paraphysomonas vestita and Pteridomonas danica.

Most flagellates with hispid flagella, that is, flagella with rigid filamentous hairs (mastigonemes), swim in the direction of the flagellar wave propagation with an anterior position of the flagellum. Previous analysis was based on planar wave propagation showing that the mastigonemes pull fluid along the flagellar axis. In the present study, we investigate the flagellar motions and swimming patterns for two flagellates with hispid flagella: Paraphysomonas vestita and Pteridomonas danica. Studies were carried out using normal and high-speed video recording, and particles were added to visualize flow around cells generating feeding currents. When swimming or generating flow, P. vestita was able to pull fluid normal to, and not just along, the flagellum, implying the use of the mastigonemes in an as yet un-described way. When the flagellum made contact with food particles, it changed the flagellar waveform so that the particle was fanned towards the ingestion area, suggesting mechano-sensitivity of the mastigonemes. Pteridomonas danica was capable of more complex swimming than previously described for flagellated protists. This was associated with control of the flagellar beat as well as an ability to bend the plane of the flagellar waveform.