A mini-review of microbial consortia: Their roles in aquatic production and biogeochemical cycling

Molecular oxygen (O₂) is a potent inhibitor of key microbial processes, including photosynthesis, N₂ fixation, denitrification, sulfate reduction, methanogenesis, iron, and metal reduction reactions. Prokaryote survival and proliferation in aquatic environments is often controlled by the ability to tolerate exposure to oxic conditions. Many prokaryotes do not have subcellular organelles for isolating O₂-producing from O₂-consuming processes and have developed consortial associations with other prokaryotes and eukaryotes that alleviate metabolic constraints of high O₂. Nutrient transformations often rely on appropriate cellular and microenvironmental, or microzonal, redox conditions. The spatial and temporal requirements for microenvironmental overlap among microbial groups involved in nutrient transformations necessitates close proximity and diffusional exchange with other biogeochemically distinct, yet complementary, microbial groups. Microbial consortia exist at different levels of community and metabolic complexity, as shown for detrital, microbial mat, biofilm, and planktonic microalgal-bacterial assemblages. To assess the macroscale impacts of consortial interactions, studies should focus on the range of relevant temporal (minutes to hours) and spatial (microns to centimeters) scales controlling microbial production, nutrient exchange, and cycling. In this review, we discuss the utility and application of techniques suitable for determining microscale consortial activity, production, community composition, and interactions in the context of larger scale aquatic ecosystem structure and function. Correspondence to: Hans W. Paerl.     

Functional correlates of differences in bone density among terrestrial and aquatic genera in the family Mustelidae (Mammalia)

Summary Increasing body density by increasing bone density has been cited as a means by which semiaquatic mammals are able to control their buoyancy in water. In order to investigate the relationship of bone density to buoyancy and the degree of morphological adaptation to a semiaquatic existence, we examined limb-bone densities in a single mammalian family. Among genera within the Mustelidae, i.e., weasels and their relatives, there is an apparent trend toward increasing limb-bone density associated with a gradation from a terrestrial to an aquatic way of life. However, the association of increasing bone density with increasing adaptation to an aquatic environment is tempered by the realization that increasing body size may also influence bone density in larger, terrestrial mammals. These results are in accordance with previous data on bone density in other mammalian orders and suggest that a new hypothesis which encompasses historical, physiological, and behavioral information would be best suited to explaining differences in this morphological relationship.     

Current advances in engineering cyanobacteria and their applications for photosynthetic butanol production

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Lipids in photosynthetic reaction centres: structural roles and functional holes

Photosynthetic proteins power the biosphere. Reaction centres, light harvesting antenna proteins and cytochrome b(6)f (or bc(1)) complexes are expressed at high levels, have been subjected to an intensive spectroscopic, biochemical and mutagenic analysis, and several have been characterised to an informatively high resolution by X-ray crystallography. In addition to revealing the structural basis for the transduction of light energy, X-ray crystallography has brought molecular insights into the relationships between these multicomponent membrane proteins and their lipid environment. Lipids resolved in the X-ray crystal structures of photosynthetic proteins bind light harvesting cofactors, fill intra-protein cavities through which quinones can diffuse, form an important part of the monomer-monomer interface in multimeric structures and may facilitate structural flexibility in complexes that undergo partial disassembly and repair. It has been proposed that individual lipids influence the biophysical properties of reaction centre cofactors, and so affect the rate of electron transfer through the complex. Lipids have also been shown to be important for successful crystallisation of photosynthetic proteins. Comparison of the three types of reaction centre that have been structurally characterised reveals interesting similarities in the position of bound lipids that may point towards a generic requirement to reinforce the structure of the core electron transfer domain. The crystallographic data are also providing new opportunities to find molecular explanations for observed effects of different types of lipid on the structure, mechanism and organisation of reaction centres and other photosynthetic proteins.     

Cyanobacterial circadian clockwork: roles of KaiA,KaiB and the kaiBC promoter in regulating KaiC

Using model strains in which we ectopically express the cyanobacterial clock protein KaiC in cells from which the clock genes kaiA, kaiB and/or kaiC are deleted, we found that some features of circadian clocks in eukaryotic organisms are conserved in the clocks of prokaryotic cyanobacteria, but others are not. One unexpected difference is that the circadian autoregulatory feedback loop in cyanobacteria does not require specific clock gene promoters as it does in eukaryotes, because a heterologous promoter can functionally replace the kaiBC promoter. On the other hand, a similarity between eukaryotic clock proteins and the cyanobacterial KaiC protein is that KaiC is phosphorylated in vivo. The other essential clock proteins KaiA and KaiB modulate the status of KaiC phosphorylation; KaiA inhibits KaiC dephosphorylation and KaiB antagonizes this action of KaiA. Based upon an analysis of clock mutants, we conclude that the circadian period in cyanobacteria is determined by the phosphorylation status of KaiC and also by the degradation rate of KaiC. These observations are integrated into a model proposing rhythmic changes in chromosomal status.     

Wound-induced apoplastic peroxidase activities: their roles in the production and detoxification of reactive oxygen species

Production of reactive oxygen species (ROS) is a widely reported response of plants to wounding. However, the nature of enzymes responsible for ROS production and metabolism in the apoplast is still an open question. We identified and characterized the proteins responsible for the wound-induced production and detoxification of ROS in the apoplast of wheat roots ( Triticum aestivum L.). Compared to intact roots, excised roots and leachates derived from them produced twice the amount of superoxide (O₂^•−). Wounding also induced extracellular peroxidase (ECPOX) activity mainly caused by the release of soluble peroxidases with molecular masses of 37, 40 and 136 kD. Peptide mass analysis by electrospray ionization–quadrupole time-of-flight–tandem mass spectrometry (ESI–QTOF–MS/MS) following lectin affinity chromatography of leachates showed the presence of peroxidases in unbound (37 kD) and bound (40 kD) fractions. High sensitivity of O₂^•−-producing activity to peroxidase inhibitors and production of O₂^•− by purified peroxidases in vitro provided evidence for the involvement of ECPOXs in O₂^•− production in the apoplast. Our results present new insights into the rapid response of roots to wounding. An important component of this response is mediated by peroxidases that are released from the cell surface into the apoplast where they can display both oxidative and peroxidative activities.     

Organization in photosynthetic membranes of purple bacteria in vivo: The role of carotenoids

Photosynthesis in purple bacteria is performed by pigment–protein complexes that are closely packed within specialized intracytoplasmic membranes. Here we report on the influence of carotenoid composition on the organization of RC–LH1 pigment–protein complexes in intact membranes and cells of Rhodobacter sphaeroides. Mostly dimeric RC–LH1 complexes could be isolated from strains expressing native brown carotenoids when grown under illuminated/anaerobic conditions, or from strains expressing green carotenoids when grown under either illuminated/anaerobic or dark/semiaerobic conditions. However, mostly monomeric RC–LH1 complexes were isolated from strains expressing the native photoprotective red carotenoid spheroidenone, which is synthesized during phototrophic growth in the presence of oxygen. Despite this marked difference, linear dichroism (LD) and light-minus-dark LD spectra of oriented intact intracytoplasmic membranes indicated that RC–LH1 complexes are always assembled in ordered arrays, irrespective of variations in the relative amounts of isolated dimeric and monomeric RC–LH1 complexes. We propose that part of the photoprotective response to the presence of oxygen mediated by synthesis of spheroidenone may be a switch of the structure of the RC–LH1 complex from dimers to monomers, but that these monomers are still organized into the photosynthetic membrane in ordered arrays. When levels of the dimeric RC–LH1 complex were very high, and in the absence of LH2, LD and ?LD spectra from intact cells indicated an ordered arrangement of RC–LH1 complexes. Such a degree of ordering implies the presence of highly elongated, tubular membranes with dimensions requiring orientation along the length of the cell and in a proportion larger than previously observed.     

The ecology of chytrids in aquatic ecosystems: roles in food web dynamics

Chytrids are very important components of freshwater ecosystems, but the ecological significance of this group of fungi is not well understood. This review considers some of the significant environmental factors affecting growth and population composition of chytrids in aquatic habitats. The physical factors include primarily salinity, dissolved oxygen concentration and temperature. The biological factors include the role of chytrids as saprobes and parasites and methods of dispersal of propagules throughout the ecosystem. Dispersal depends upon both zoospores for short range and whole thalli for long range dispersal. Five roles for chytrids in food-web dynamics are proposed: (1) chytrid zoospores are a good food source for zooplankton, (2) chytrids decompose particulate organic matter, (3) chytrids are parasites of aquatic plants, (4) chytrids are parasites of aquatic animals and (5) chytrids convert inorganic compounds into organic compounds. New molecular methods for analysis of chytrid diversity in aquatic environments have the potential to provide accurate quantitative data necessary for better understanding of ecological processes in aquatic ecosystems.     

Multiple beta-fructofuranosidases by Aureobasidium pullulans DSM2404 and their roles in fructooligosaccharide production

At least five types of beta-fructofuranosidases (FFases I, II, III, IV and V) were found in the cell wall of Aureobasidium pullulans DSM2404 grown in a sucrose medium. The fungus first catalyzed the transfructosylation of sucrose, and produced fructooligosaccharide (FOS) and glucose in the culture. FOS was then consumed together with glucose, and finally fructose was produced. In the FOS-producing period, the fungus expressed FFase I as a dominant FFase. However, in the FOS-degrading period, the levels of FFases II, III, IV and V increased. The ratios of transfructosylating activity to hydrolyzing activity by FFases I-V were 14.3, 12.1, 11.7, 1.28 and 8.11, respectively. When glucose was used as a carbon source, only FFase I showed significant activity. On the other hand, the activities of all five FFases were detected when FOS or fructose was used as a carbon source. These results suggested that the expression of FFase I was not repressed by glucose, but those of FFases II-V were strongly inhibited in the presence of glucose. It is considered that FFase I plays a key role in FOS production by this fungus, whereas FFase IV may function as a FOS-degrading enzyme with its strong hydrolyzing activity.     

Relationships among four genera of mojarras (Teleostei: Perciformes: Gerreidae) from the western Atlantic and their tentative placement among percomorph fishes

A phylogenetic study of the percoid family Gerreidae at both lower and higher taxonomic levels is presented based on DNA sequence data of four genes: mitochondrial 12S and 16S, and nuclear genes rhodopsin and recombination activating gene 1 (RAG1). The taxonomic sampling includes four genera of Gerreidae from the western Atlantic, 39 additional percomorph representatives and two outgroups. Phylogenetic results confirm the monophyly of the Gerreidae and suggest that the family is divided into two sub-groups ( Diapterus auratus plus Eugerres plumieri and Eucinostomus gula plus Gerres cinereus ), which correspond to two previously defined taxonomic assemblages characterized by the shape of the preoperculum. Gerreids are placed at an intermediate position in the percomorph tree between two basal clades (L and Q) and a terminal clade N (grouping tetraodontiforms, acanthuroids, lophiiforms, caproids and several percoids). In addition, topology tests indicate that two traditional assemblages, Labroidei (seven representatives sampled) and Percoidei (22 representatives sampled) are not natural groups. Labrids and scarids appear to be more closely related to gerreids and to the members of clade N than to any other basal percomorphs, including their labroid 'allies' sampled in this study, Embiotocidae, Pomacentridae and Cichlidae, which are all nested within clade Q that also includes atherinomorphs, mugiliforms and Chandidae. The percoid taxa included in this study are widely distributed among various percomorph lineages. The percomorph phylogeny obtained is highly congruent with results from recent molecular studies.     

Ecological impacts of photosynthetic light harvesting in changing aquatic environments: A systematic literature map

Underwater light is spatially as well as temporally variable and directly affects phytoplankton growth and competition. Here we systematically (following the guidelines of PRISMA‐EcoEvo) searched and screened the published literature resulting in 640 individual articles. We mapped the conducted research for the objectives of (1) phytoplankton fundamental responses to light, (2) effects of light on the competition between phytoplankton species, and (3) effects of climate‐change‐induced changes in the light availability in aquatic ecosystems. Among the fundamental responses of phytoplankton to light, the effects of light intensity (quantity, as measure of total photon or energy flux) were investigated in most identified studies. The effects of the light spectrum (quality) that via species‐specific light absorbance result in direct consequences on species competition emerged more recently. Complexity in competition arises due to variability and fluctuations in light which effects are sparsely investigated on community level. Predictions regarding future climate change scenarios included changes in in stratification and mixing, lake and coastal ocean darkening, UV radiation, ice melting as well as light pollution which affect the underwater light‐climate. Generalization of consequences is difficult due to a high variability, interactions of consequences as well as a lack in sustained timeseries and holistic approaches. Nevertheless, our systematic literature map, and the identified articles within, provide a comprehensive overview and shall guide prospective research.     

Characterization of human mitochondrial PDSS and COQ proteins and their roles in maintaining coenzyme Q10 levels and each other's stability

Mutations of many PDSS and COQ genes are associated with primary coenzyme Q₁₀ (CoQ₁₀) deficiency, whereas mitochondrial DNA (mtDNA) mutations might cause secondary CoQ₁₀ deficiency. Previously, we found that COQ5 and COQ9 proteins are present in different protein complexes in the mitochondria in human 143B cells and demonstrated that COQ5 and COQ9 knockdown suppresses CoQ₁₀ levels. In the present study, we characterized other PDSS and COQ proteins and examined possible crosstalk among various PDSS and COQ proteins. Specific antibodies and mitochondrial localization of mature proteins for these proteins, except PDSS1 and COQ2, were identified. Multiple isoforms of PDSS2 and COQ3 were observed. Moreover, PDSS1, PDSS2, and COQ3 played more important roles in maintaining the stability of the other proteins. Protein complexes containing PDSS2, COQ3, COQ4, COQ6, or COQ7 protein in the mitochondria were detected. Two distinct PDSS2-containing protein complexes could be identified. Transient knockdown of these genes, except COQ6 and COQ8, decreased CoQ₁₀ levels, but only COQ7 knockdown hampered mitochondrial respiration and caused increased ubiquinol:ubiquinone ratios and accumulation of a putative biosynthetic intermediate with reversible redox property as CoQ₁₀. Furthermore, suppressed levels of PDSS2 and various COQ proteins (except COQ3 and COQ8A) were found in cybrids containing the pathogenic mtDNA A8344G mutation or in FCCP-treated 143B cells, which was similar to our previous findings for COQ5. These novel findings may prompt the elucidation of the putative CoQ synthome in human cells and the understanding of these PDSS and COQ protein under physiological and pathological conditions.     

Variations in the mode of stolon growth among different genera of colonial hydroids,and their evolutionary implications

Stolonic growth has been compared among several genera of calyptoblastic (Campanularia flexuosa, C. calceolifera, Gonothyraea and Sertularia) and gymnoblastic (Pennaria, Bougainvillia, Eudendrium and Cordylophora) hydroids with respect to such features as the (1) complexity and uniformity of the tip movements, (2) constancy of growth cycle duration, (3) variability in growth among cycles, (4) growth rate, and (5) variability of retractions among cycles. The “growth cycle,” previously described in C. flexuosa, is the basis for elongation in all species observed. Its pattern is indistinguishable between the Campanularia species; however, at the generic level the tip movements show peculiarities which delineate each genus from all others. In addition, the movements in all calyptoblasts are uniform from cycle to cycle and comparatively simple, whereas those of the gymnoblasts are complicated by the variable appearance of one or more secondary forward thrusts between crests. A dichotomy is seen between the calyptoblasts and most gymnoblasts in other respects as well. Cycle time is very predictable and cycle-to-cycle variability in growth is relatively narrow in all calyptoblasts. However, in most gymnoblasts both features are much more loosely regulated: only Pennaria shows some degree of control to its timing mechanism, and only in Bougainvillia and Eudendrium does the uniformity of growth per cycle reach the calyptoblast level. On the premise that calyptoblasts are evolutionarily the more advanced group, simplicity and regularity of growth movements are concluded to be the evolved, and complexity and variability the primitive, conditions. On this basis the evolutionary relations among the four gymnoblasts, as deduced from their stolonic growth behavior alone, are consistent in many but not all respects with those interpreted from morphological considerations.     

Sulfur and primary production in aquatic environments: an ecological perspective

Sulfur is one of the critical elements in living matter, as it participates in several structural, metabolic and catalytic activities. Photosynthesis is an important process that entails the use of sulfur during both the light and carbon reactions. Nearly half of global photosynthetic carbon fixation is carried out by phytoplankton in the aquatic environment. Aquatic environments are very different from one another with respect to sulfur content: while in the oceans sulfate concentration is constantly high, freshwaters are characterized by daily and seasonal variations and by a wide range of sulfur concentration. The strategies that algal cells adopt for energy and resource allocation often reflect these differences. In the oceans, the amount and chemical form of sulfur has changed substantially during the course of the Earth's history; it is possible that sulfur availability played a role in the evolution of marine phytoplankton communities and it may continue to have appreciable effects on global biogeochemistry and ecology. Phytoplankton is also the main biogenic source of sulfur; sulfur can be released into the atmosphere by algal cells as dimethylsulfide, with possibly important repercussions on global climate. These and related matters are discussed in this review.     

Beyond aerodynamics: The critical roles of the circulatory and tracheal systems in maintaining insect wing functionality

Insect wings consist almost entirely of lifeless cuticle; yet their veins host a complex multimodal sensory apparatus and other tissues that require a continuous supply of water, nutrients and oxygen. This review provides a survey of the various living components in insect wings, as well as the specific contribution of the circulatory and tracheal systems to provide all essential substances. In most insects, hemolymph circulates through the veinal network in a loop flow caused by the contraction of accessory pulsatile organs in the thorax. In other insects, hemolymph oscillates into and out of the wings due to the complex interaction of several factors, such as heartbeat reversal, intermittent pumping of the accessory pulsatile organs in the thorax, and the elasticity of the wall of a special type of tracheae. A practically unexplored subject is the need for continuous hydration of the wing cuticle to retain its flexibility and toughness, including the associated problem of water loss due to evaporation. Also, widely neglected is the influence of the hemolymph mass and the circulating flow in the veins on the aerodynamic properties of insect wings during flight. Ventilation of the extraordinarily long wing tracheae is probably accomplished by intricate interactions with the circulatory system, and by the exchange of oxygen via cutaneous respiration.