LIPOXYGENASE PRODUCTS IN MARINE DIATOMS: A CONCISE ANALYTICAL METHOD TO EXPLORE THE FUNCTIONAL POTENTIAL OF OXYLIPINS1

Oxylipins are oxygenated derivatives of polyunsaturated fatty acids (PUFAs) that act as chemical mediators in many ecological and physiological processes in marine and freshwater diatoms. The occurrence and distribution of these molecules are relatively widespread within the lineage with considerable species‐specific differences due to the variability of both the fatty acids recognized as substrates and the enzymatic transformations. The present review provides a general introduction to recent studies on diatom oxylipins and describes an analytical method for the detection and assessment of these elusive molecules in laboratory and field samples. This methodology is based on selective enrichment of the oxylipin fraction by solvent extraction, followed by parallel acquisition of full‐scan UV and tandem mass spectra on reverse phase liquid chromatography (LC) peaks. The analytical procedure enables identification of potential genetic differences, enzymatic regulation, and ecophysiological conditions that result in different oxylipin signatures, thus providing an effective tool for probing the functional relevance of this class of lipids in plankton communities. Examples of oxylipin measurements in field samples are also provided as a demonstration of the analytical potential of the methodology.     

Cultivation of Microorganisms in the Cultural Medium Made from Squid Internal Organs and Accumulation of Polyunsaturated Fatty Acids in the Cells

The disposal and more efficient utilization of marine wastes is becoming increasingly serious. A culture media for microorganisms has been prepared from squid internal organs that are rich in polyunsaturated fatty acids (PUFAs). Both freshwater and marine bacteria grew well in this medium and some bacteria accumulated PUFAs in their lipids, suggesting uptake of exogenous PUFAs. Higher PUFA accumulations were observed in Escherichia coli mutant cells defective either in unsaturated fatty acid biosynthesis or fatty acid degradation, or both, compared to those without these mutations. Therefore, PUFA accumulation in cells can be improved by genetic modification of fatty acid metabolism in the bacteria. Squid internal organs would be a good source of medium, not only for marine bacteria but also for freshwater bacteria, and that this process may be advantageous to make efficient use of the fishery wastes and to produce PUFA-containing microbial cells and lipids.     

Climate change and freshwater biodiversity: detected patterns, future trends and adaptations in northern regions

Current rates of climate change are unprecedented, and biological responses to these changes have also been rapid at the levels of ecosystems, communities, and species. Most research on climate change effects on biodiversity has concentrated on the terrestrial realm, and considerable changes in terrestrial biodiversity and species’ distributions have already been detected in response to climate change. The studies that have considered organisms in the freshwater realm have also shown that freshwater biodiversity is highly vulnerable to climate change, with extinction rates and extirpations of freshwater species matching or exceeding those suggested for better‐known terrestrial taxa. There is some evidence that freshwater species have exhibited range shifts in response to climate change in the last millennia, centuries, and decades. However, the effects are typically species‐specific, with cold‐water organisms being generally negatively affected and warm‐water organisms positively affected. However, detected range shifts are based on findings from a relatively low number of taxonomic groups, samples from few freshwater ecosystems, and few regions. The lack of a wider knowledge hinders predictions of the responses of much of freshwater biodiversity to climate change and other major anthropogenic stressors. Due to the lack of detailed distributional information for most freshwater taxonomic groups and the absence of distribution‐climate models, future studies should aim at furthering our knowledge about these aspects of the ecology of freshwater organisms. Such information is not only important with regard to the basic ecological issue of predicting the responses of freshwater species to climate variables, but also when assessing the applied issue of the capacity of protected areas to accommodate future changes in the distributions of freshwater species. This is a huge challenge, because most current protected areas have not been delineated based on the requirements of freshwater organisms. Thus, the requirements of freshwater organisms should be taken into account in the future delineation of protected areas and in the estimation of the degree to which protected areas accommodate freshwater biodiversity in the changing climate and associated environmental changes.     

Chemical interactions in diatoms: role of polyunsaturated aldehydes and precursors

Chemicals produced by aquatic organisms, and especially micro-organisms, have received increasing attention in the last decade for their role in shaping interactions and communities. Several cases emphasize the fact that chemical signals or defence may modulate interspecific interactions. Notably, it has been shown that diatoms, unicellular algae and key primary producers in aquatic ecosystems produce a wide range of bioactive metabolites. Among these compounds, polyunsaturated short-chain aldehydes in vitro strongly impair the reproduction of various potential grazers. In the field, the relationship between aldehyde production and reproductive failure in copepods remains unclear. Recent studies have suggested that these putative defence compounds may also be involved in intercellular communication and in interactions with competitors. Potential effects of the aldehyde precursors on various organisms have also been described. This review presents an overview of various results obtained in the last decade that could help us to understand the role of polyunsaturated aldehydes and their precursors in the ecology of diatoms. It is focused on the dichotomy between freshwater and marine environments. Indeed, most of the results on anti-proliferative aldehydes concern marine planktonic diatoms, whereas they are also known to be produced by benthic and freshwater species.     

Enzymes for transgenic biosynthesis of long-chain polyunsaturated fatty acids

Polyunsaturated fatty acids (PUFAs) are important for the normal development and function of all organisms, and are essential in maintaining human health. Impaired PUFA metabolism is thought to be associated with pathogenesis of many chronic diseases. Dietary supplementation of PUFAs, such as gamma-linolenic acid, arachidonic acid, eicosapentaenoic acid, and docosahexaenoic acid, which bypass the defective or dysfunctional steps of the biosynthetic pathway has been found to significantly alleviate the symptoms of the disease. These findings have drawn a great deal of interest from general public and food manufacturers. As the demand of these beneficial PUFAs has drastically increased in recent years, there are also increasing efforts in finding the alternate sources of PUFAs that are more economical and sustainable. One option is to modify the oil-seed crops to produce PUFAs through genetic engineering technique. This review examines the isolation, identification and expression of genes encoding the enzymes required for the biosynthesis of the above mentioned PUFAs in plants.     

Ultraviolet Insights: Attempting to Resolve Enigmatic Patterns in Pelagic Freshwaters – The Historical Context and a View to the Future

While great advances have been made in our understanding of pelagic freshwater communities and ecosystems in recent years, several unexplained patterns continue to evade our understanding. While no single factor can explain these enigmatic patterns, recent increases in our understanding of the ecology of ultraviolet radiation (UV) are consistent with UV playing an important role. Here we present a brief overview of why UV has historically received so little attention in pelagic freshwater ecosystems, review some of the important aspects of the ecology of UV that are important to these enigmatic patterns, and discuss how this new understanding of the ecology of UV may provide some insights into these previously unexplained patterns. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Microbial reductive dehalogenation.

A wide variety of compounds can be biodegraded via reductive removal of halogen substituents. This process can degrade toxic pollutants, some of which are not known to be biodegraded by any other means. Reductive dehalogenation of aromatic compounds has been found primarily in undefined, syntrophic anaerobic communities. We discuss ecological and physiological principles which appear to be important in these communities and evaluate how widely applicable these principles are. Anaerobic communities that catalyze reductive dehalogenation appear to differ in many respects. A large number of pure cultures which catalyze reductive dehalogenation of aliphatic compounds are known, in contrast to only a few organisms which catalyze reductive dehalogenation of aromatic compounds. Desulfomonile tiedjei DCB-1 is an anaerobe which dehalogenates aromatic compounds and is physiologically and morphologically unusual in a number of respects, including the ability to exploit reductive dehalogenation for energy metabolism. When possible, we use D. tiedjei as a model to understand dehalogenating organisms in the above-mentioned undefined systems. Aerobes use reductive dehalogenation for substrates which are resistant to known mechanisms of oxidative attack. Reductive dehalogenation, especially of aliphatic compounds, has recently been found in cell-free systems. These systems give us an insight into how and why microorganisms catalyze this activity. In some cases transition metal complexes serve as catalysts, whereas in other cases, particularly with aromatic substrates, the catalysts appear to be enzymes.     

Identification of a chemoreceptor that specifically mediates chemotaxis toward metabolizable purine derivatives

Chemotaxis is an essential mechanism that enables bacteria to move toward favorable ecological niches. Escherichia coli, the historical model organism for studying chemotaxis, has five well‐studied chemoreceptors. However, many bacteria with different lifestyle have more chemoreceptors, most of unknown function. Using a high throughput screening approach, we identified a chemoreceptor from Pseudomonas putida KT2440, named McpH, which specifically recognizes purine and its derivatives, adenine, guanine, xanthine, hypoxanthine and uric acid. The latter five compounds form part of the purine degradation pathway, permitting their use as sole nitrogen sources. Isothermal titration calorimetry studies show that these six compounds bind McpH‐Ligand Binding Domain (LBD) with very similar affinity. In contrast, non‐metabolizable purine derivatives (caffeine, theophylline, theobromine), nucleotides, nucleosides or pyrimidines are unable to bind McpH‐LBD. Mutation of mcpH abolished chemotaxis toward the McpH ligands identified – a phenotype that is restored by complementation. This is the first report on bacterial chemotaxis to purine derivatives and McpH the first chemoreceptor described that responds exclusively to intermediates of a catabolic pathway, illustrating a clear link between metabolism and chemotaxis. The evolution of McpH may reflect a saprophytic lifestyle, which would have exposed the studied bacterium to high concentrations of purines produced by nucleic acid degradation.     

129 Cryptoendolithic Photosynthetic Communities Within Recent and Ancient Travertine in Yellowstone National Park

Travertine terraces have been deposited by calcareous hot springs in Yellowstone from as early as 365,000 years to the present. Most of these porous and non‐porous CaCO3 rocks (old or new) contain a 1–2 mm thick greenish band about 1–3 mm below the upper surface. These bands are composed of cyanobacteria and, sometimes, unicellular green algae. Although some moisture may be retained for much of the year, all undergo freezing in winter and desiccation in summer. DGGE (denaturing gradient gel electrophoresis), with subsequent 16S rDNA sequence analyses of bands, has shown that relatively few phylotypes of cyanobacteria are present, but some occur in travertine of very different ages, indicating secondary establishment of the communities. Clonal cultures of predominant types have also been established and sequenced. All those tested are able to survive extreme desiccation. Preliminary sequence analyses of cultures show that some strains are nearly identical to known cyanobacterial strains while others show little similarity. One sequence is 100% identical to the cyanobacterium Cyanobium gracile. This cyanobacterium is known to be distributed worldwide in lakes and brackish seas, but not in a cryptoendolithic environment. Another sequence shows 99% identity to two cyanobacteria isolated from Antarctic freshwater ponds. Both Antarctic ponds and Yellowstone travertine are environments in which adaptations for desiccation and/or freezing tolerance could be crucial. The lack of ecological similarity among some of these strains indicates that genes other than 16S rDNA must be used for differentiation. These results will be discussed along with the ecology of travertine habitats.     

A macroecological perspective of diversity patterns in the freshwater realm

1. The aim of this paper is to review literature on species diversity patterns of freshwater organisms and underlying mechanisms at large spatial scales. 2. Some freshwater taxa (e.g. dragonflies, fish and frogs) follow the classical latitudinal decline in regional species richness (RSR), supporting the patterns found for major terrestrial and marine organism groups. However, the mechanisms causing this cline in most freshwater taxa are inadequately understood, although research on fish suggests that energy and history are major factors underlying the patterns in total species and endemic species richness. Recent research also suggests that not all freshwater taxa comply with the decline of species richness with latitude (e.g. stoneflies, caddisflies and salamanders), but many taxa show more complex geographical patterns in across‐regions analyses. These complexities are even more profound when studies of global, continental and regional extents are compared. For example, clear latitudinal gradients may be present in regional studies but absent in global studies (e.g. macrophytes). 3. Latitudinal gradients are often especially weak in the across‐ecosystems analyses, which may be attributed to local factors overriding the effects of large‐scale factors on local communities. Nevertheless, local species richness (LSR) is typically linearly related to RSR (suggesting regional effects on local diversity), although saturating relationships have also been found in some occasions (suggesting strong local effects on diversity). Nestedness has often been found to be significant in freshwater studies, yet this pattern is highly variable and generally weak, suggesting also a strong beta diversity component in freshwater systems. 4. Both geographical location and local environmental factors contribute to variation in alpha diversity, nestedness and beta diversity in the freshwater realm, although the relative importance of these two groups of explanatory variables may be contingent on the spatial extent of the study. The mechanisms associated with spatial and environmental control of community structure have also been inferred in a number of studies, and most support has been found for species sorting (possibly because many freshwater studies have species sorting as their starting point), although also dispersal limitation and mass effects may be contributing to the patterns found. 5. The lack of latitudinal gradients in some freshwater taxa begs for further explanations. Such explanations may not be gained for most freshwater taxa in the near future, however, because we lack species‐level information, floristic and faunistic knowledge, and standardised surveys along extensive latitudinal gradients. A challenge for macroecology is thus to use the best possible species‐level information on well‐understood groups (e.g. fish) or use surrogates for species‐level patterns (e.g. families) and then develop hypotheses for further testing in the freshwater realm. An additional research challenge concerns understanding patterns and mechanisms associated with the relationships between alpha, beta and gamma components of species diversity. 6. Understanding the mechanistic basis of species diversity patterns should preferably be based on a combination of large‐scale macroecological and landscape‐scale metacommunity research. Such a research approach will help in elucidating patterns of species diversity across regional and local scales in the freshwater realm.     

Subsidies of long‐chain polyunsaturated fatty acids from aquatic to terrestrial environments via amphibian emergence

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Local context and connectivity determine the response of zooplankton communities to salt contamination

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More than meets the eye: The barrier effect of the Yangtze River outflow

The Yangtze (Changjiang) River enters the East China Sea with huge annual freshwater and sediment deposits. This outflow, known as the Changjiang diluted water (CDW), causes striking ecological gradients that potentially shape coastal species’ distribution and differentiation. The CDW has long been rendered as a marine biogeographic boundary separating cold‐temperature and warm‐water faunas, but it remains unclear whether and to what extent it acts as an intraspecific barrier. Here, we synthesize published phylogeographic studies related to the CDW to address these issues. We find that the influence of the CDW on population differentiation is taxonomically variable, and even congeneric species may respond differently. In studies that claim the CDW is a phylogeographic barrier, the underlying assumptions explaining observed genetic breaks are sometimes incorrect, and some may have misinterpreted results due to conceptual confusion or insufficient geographic sampling. After excluding these studies, the remaining ones generally show shallow genetic divergence but significant population structure for coastal species across the CDW, suggesting that the CDW has not been a historically persistent barrier, but rather has acted as a filter within some species recently, probably after the last glacial maximum.     

Nestedness patterns and the dual nature of community reassembly in California streams: a multivariate permutation‐based approach

Many factors contribute to the nonrandom processes of extinctions and invasions that are changing the structure of ecological communities worldwide. These factors include the attributes of the species, their abiotic environment, and the interactions and feedbacks between them. The relative importance of these factors has been difficult to quantify. We used nested subset theory and a novel permutation‐based extension of gradient analysis to disentangle the direct and indirect pathways by which these factors affect the metacommunity structure of freshwater fishes inhabiting the streams tributary to the San Francisco Bay. Our analyses provide quantitative measures of how species and stream attributes may influence extinction vulnerability and invasion risk, highlight the need for considering the multiple interacting drivers of community change concurrently, and indicate that the ongoing disassembly and assembly of Bay Area freshwater fish communities are not fully symmetric processes. Fish communities are being taken apart and put back together in only partially analogous trajectories of extinction and invasion for which no single explanatory hypothesis is sufficient. Our study thereby contributes to the forecasting of continued community change and its effects on the functioning of freshwater ecosystems.     

Natural production of fluorinated compounds and biotechnological prospects of the fluorinase enzyme

Fluorinated compounds are finding increasing uses in several applications. They are employed in almost all areas of modern society. These compounds are all produced by chemical synthesis and their abundance highly contrasts with fluorinated molecules of natural origin. To date, only some plants and a handful of actinomycetes species are known to produce a small number of fluorinated compounds that include fluoroacetate (FA), some ω-fluorinated fatty acids, nucleocidin, 4-fluorothreonine (4-FT), and the more recently identified (2R3S4S)-5-fluoro-2,3,4-trihydroxypentanoic acid. This largely differs from other naturally produced halogenated compounds, which totals more than 5000. The mechanisms underlying biological fluorination have been uncovered after discovering the first actinomycete species, Streptomyces cattleya, that is capable of producing FA and 4-FT, and a fluorinase has been identified as the enzyme responsible for the formation of the C–F bond. The discovery of this enzyme has opened new perspectives for the biotechnological production of fluorinated compounds and many advancements have been achieved in its application mainly as a biocatalyst for the synthesis of [¹⁸F]-labeled radiotracers for medical imaging. Natural fluorinated compounds may also be derived from abiogenic sources, such as volcanoes and rocks, though their concentrations and production mechanisms are not well known. This review provides an outlook of what is currently known about fluorinated compounds with natural origin. The paucity of these compounds and the biological mechanisms responsible for their production are addressed. Due to its relevance, special emphasis is given to the discovery, characterization and biotechnological potential of the unique fluorinase enzyme.     

Molecular evidence for widespread occurrence of Foraminifera in soils

Environmental SSU rDNA‐based surveys are contributing to the dramatic revision of eukaryotic high‐level diversity and phylogeny as the number of sequence data increases. This ongoing revolution gives the opportunity to test for the presence of some eukaryotic taxa in environments where they have not been found using classical microscopic observations. Here, we test whether the foraminifera, a group of single‐celled eukaryotes, considered generally as typical for the marine ecosystems are present in soil. We performed foraminiferal‐specific nested PCR on 20 soil DNA samples collected in contrasted environments. Unexpectedly, we found that the majority of the samples contain foraminiferal SSU rDNA sequences. In total, we obtained 49 sequences from 17 localities. Phylogenetic analysis clusters them in four groups branching among the radiation of early foraminiferal lineages. Three of these groups also include sequences originated from previous freshwater surveys, suggesting that there were up to four independent colonization events of terrestrial and/or freshwater ecosystems by ancestral foraminifera. As shown by our data, foraminifera are a widespread and diverse component of soil microbial communities. Yet, identification of terrestrial foraminiferal species and understanding of their ecological role represent an exciting challenge for future research.     

BIOACTIVE PROTEINS,PEPTIDES, AND AMINO ACIDS FROM MACROALGAE1

Macroalgae are a diverse group of marine organisms that have developed complex and unique metabolic pathways to ensure survival in highly competitive marine environments. As a result, these organisms have been targeted for mining of natural biologically active components. The exploration of marine organisms has revealed numerous bioactive compounds that are proteinaceous in nature. These include proteins, linear peptides, cyclic peptides and depsipeptides, peptide derivatives, amino acids, and amino acid–like components. Furthermore, some species of macroalgae have been shown to contain significant levels of protein. While some protein‐derived bioactive peptides have been characterized from macroalgae, macroalgal proteins currently still represent good candidate raw materials for biofunctional peptide mining. This review will provide an overview of the important bioactive amino‐acid‐containing compounds that have been identified in macroalgae. Moreover, the potential of macroalgal proteins as substrates for the generation of biofunctional peptides for utilization as functional foods to provide specific health benefits will be discussed.     

Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

The diversity of freshwater bacterioplankton communities has not been extensively studied despite their key role in foodwebs and the cycling of carbon and associated major elements. In order to explore and characterize the composition of bacterioplankton associated with cyanobacterial blooms, large 16S rRNA clone libraries from four lakes experiencing such blooms were analysed. The four libraries contained 1461 clones, of which 559 were prokaryotic sequences of non-cyanobacterial origin. These clones were classified into 158 operational taxonomic units affiliated mainly with bacterial divisions commonly found in freshwater systems, e.g. Proteobacteria, Bacteriodetes, Actinobacteria, Verrucomicrobia and Planctomycetes. Richness and evenness of non-cyanobacterial clones were similar to other clone libraries obtained for freshwater bacterioplankton, suggesting that bacterial communities accompanying cyanobacterial blooms are as diverse as non-bloom communities. Many of the identified operational taxonomic units grouped with known freshwater clusters but the libraries also contained novel clusters of bacterial sequences that may be characteristic for cyanobacterial blooms. About 25% of the operational taxonomic units were detected in more than one lake. Even so, 16S rRNA heterogeneity analysis demonstrated large differences in community composition between lakes regardless of their similar characteristics and close proximity. Hence even the similar environmental conditions created by different cyanobacterial blooms may foster very dissimilar bacterial communities, which could indicate that the genetic diversity in lake bacteria have been underestimated in the past.