http://www.aquaticbiosystems.org The latest research articles published by Aquatic Biosystems 2012-05-18T00:00:00Z Background: Biosynthesis of nanoparticles has received increasing attention due to the growing need todevelop safe, time-effective and environmentally friendly technologies for nano-materialssynthesis. This paper reports the one pot green synthesis of silver nanoparticles (AgNPs)using the leaf bud extract of a mangrove plant, Rhizophora mucronata and their antimicrobialeffects against aquatic pathogens. Highly stable AgNPs were synthesized by treating themangrove leaf bud extract with aqueous silver nitrate solution at 15 psi pressure and 121degreesCfor 5 minutes. Results: The biosynthesized AgNPs were characterized by UV-visible spectrum, at 426 nm. The XRayDiffraction (XRD) pattern revealed the face-centered cubic geometry of AgNPs. FourierTransform Infra Red (FTIR) spectroscopic analysis was carried out to identify the possiblebiomolecules responsible for biosynthesis of AgNPs from the leaf bud extract. The size andshape of the well-dispersed AgNPs were documented with the help of High ResolutionTransmission Electron Microscopy (HRTEM) with a diameter ranged from 4 to 26 nm.However a maximum number of particles were observed at 4 nm in size. The antibacterialeffects of AgNPs were studied against aquatic pathogens Proteus spp., Pseudomonas fluorescens and Flavobacterium spp., isolated from infected marine ornamental fish,Dascyllus trimaculatus. Conclusion: This study reveals that the biosynthesized AgNPs using the leaf bud extract of a mangroveplant (R. mucronata) were found equally potent to synthetic antibiotics. The size of theinhibition zone increases when the concentration of the AgNPs increased and variesaccording to species. http://www.aquaticbiosystems.org/content/8/1/11 Jaganathan Umashankari Dhinakarasamy Inbakandan Thipramalai Ajithkumar Thangavel Balasubramanian Aquatic Biosystems 2012, null:11 2012-05-18T00:00:00Z doi:10.1186/2046-9063-8-11 Recipe for a silver bullet against pathogens A simple, efficient and eco-friendly synthesis of silver nanoparticles is reported using mangrove leaf extracts which represents a promising approach for controlling aquatic pathogens and an alternative to synthetic antibiotics. /content/figures/2046-9063-8-11-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 11 2012-05-18T00:00:00Z PDF The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such "microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons. http://www.aquaticbiosystems.org/content/8/1/10 Terry McGenity Benjamin Folwell Boyd McKew Gbemisola Sanni Aquatic Biosystems 2012, null:10 2012-05-16T00:00:00Z doi:10.1186/2046-9063-8-10 /content/figures/2046-9063-8-10-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 10 2012-05-16T00:00:00Z PDF Background: Halomonas boliviensis is a halophilic bacterium that is included in the gamma-Proteobacteria sub-group, and is able to assimilate different types of carbohydrates. H. boliviensis is also able to produce poly(3-hydroxybutyrate) (PHB) in high yields using glucose as the carbon precursor. Accumulation of PHB by microorganisms is induced by excess of intracellular NADH.The genome sequences and organization in microorganisms should be the result of evolution and adaptation influenced by mutation, gene duplication, horizontal gen transfer (HGT) and recombination. Furthermore, the nearly neutral theory of evolution sustains that genetic modification of DNA could be neutral or selected, albeit most mutations should be at the border between neutrality and selection, i.e. slightly deleterious base substitutions in DNA are followed by a slightly advantageous substitutions. Results: This article reports the genome sequence of H. boliviensis. The chromosome size of H. boliviensis was 4 119 979 bp, and contained 3 863 genes. A total of 160 genes of H. boliviensis were related to carbohydrate transport and metabolism, and were organized as: 70 genes for metabolism of carbohydrates; 47 genes for ABC transport systems and 43 genes for TRAP-type C4-dicarboxylate transport systems. Protein sequences of H. boliviensis related to carbohydrate transport and metabolism were selected from clusters of orthologous proteins (COGs). Similar proteins derived from the genome sequences of other 41 archaea and 59 bacteria were used as reference. We found that most of the 160 genes in H. boliviensis, c.a. 44%, were obtained from other bacteria by horizontal gene transfer, while 13% of the genes were acquired from haloarchaea and thermophilic archaea, only 34% of the genes evolved among Proteobacteria and the remaining genes encoded proteins that did not cluster with any of the proteins obtained from the reference strains. Furthermore, the diversity of the enzymes derived from these genes led to polymorphism in glycolysis and gluconeogenesis. We found further that an optimum ratio of glucose and sucrose in the culture medium of H. boliviensis favored cell growth and PHB production. Conclusions: Results obtained in this article depict that most genetic modifications and enzyme polymorphism in the genome of H. boliviensis were mainly influenced by HGT rather than nearly neutral mutations. Molecular adaptation and evolution experienced by H. boliviensis were also a response to environmental conditions such as the type and amount of carbohydrates in its ecological niche. Consequently, the genome evolution of H. boliviensis showed to be strongly influenced by the type of microorganisms, genetic interaction among microbial species and its environment. Such trend should also be experienced by other prokaryotes. A system for PHB production by H. boliviensis that takes into account the evolutionary adaptation of this bacterium to the assimilation of combinations of carbohydrates suggests the feasibility of a bioprocess economically viable and environmentally friendly. http://www.aquaticbiosystems.org/content/8/1/9 Daniel Guzman Andrea Balderrama-Subieta Carla Cardona-Ortuno Monica Guevara-Martinez Nataly Callisaya-Quispe Jorge Quillaguaman Aquatic Biosystems 2012, null:9 2012-04-17T00:00:00Z doi:10.1186/2046-9063-8-9 Bioplastic genes in halophilic bacteria The ability of halophilic bacterium Halomonas boliviensis, a bioplastic producer, to grow on different carbon sources can be explained by the large number of genes related to carbohydrate uptake and metabolism, many acquired from other bacteria by HGT. /content/figures/2046-9063-8-9-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 9 2012-04-17T00:00:00Z PDF Coastal solar saltworks of Brazil are exploited for sea salt, which becomes progressively concentrated by evaporation. This study aimed to review the current and new potential uses of these systems, in order to provide more dynamic for this activity. The first evaporation ponds are also used for artisanal fisheries, ensuring the livelihood of many families. All the brine rich in secondary salts (bittern) can be widely used by the chemical industry, while the Brazil shows an incipient production of "flower of salt", a salt with distinct characteristics with higher market value than sodium chloride. On the other hand, the saltponds have a high potential for management and obtaining of large populations of Artemia spp., purifying the brine through the action as biological filter. This microcrustacean occurs naturally in intermediate salinity ponds, being commonly used in aquaculture. Species of microalgae and halobacteria found in the saltworks are employed for extraction of beta-carotene and glycerol, used in an extensive list of products with high commercial value. These ecosystems represent refuge zones for many species of migratory birds, becoming imperative to promote the conservation of these hypersaline wetlands. http://www.aquaticbiosystems.org/content/8/1/8 Renato De Medeiros Rocha Diogenes Costa Milton Lucena-Filho Rodolfo Bezerra David Medeirosa Antonio Azevedo-Silva Cristian Araujo Lauro Xavier-Filho Aquatic Biosystems 2012, null:8 2012-04-10T00:00:00Z doi:10.1186/2046-9063-8-8 /content/figures/2046-9063-8-8-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 8 2012-04-10T00:00:00Z XML Background: The well-lit surface waters of oligotrophic gyres significantly contribute to global primary production. Marine cyanobacteria of the genus Prochlorococcus are a major fraction of photosynthetic organisms within these areas. Labile phosphate is considered a limiting nutrient in some oligotrophic regions such as the Caribbean Sea, and as such it is crucial to understand the physiological response of primary producers such as Prochlorococcus to fluctuations in the availability of this critical nutrient. Results: Prochlorococcus strains representing both high light (HL) (MIT9312) and low light (LL) (NATL2A and SS120) ecotypes were grown identically in phosphate depleted media (10 μM Pi). The three strains displayed marked differences in cellular protein expression, as determined by high throughput large scale quantitative proteomic analysis. The only strain to demonstrate a significantly different growth rate under reduced phosphate conditions was MIT9312. Additionally, there was a significant increase in phosphate-related proteins such as PhoE (> 15 fold increase) and a depression of the Rubisco protein RbcL abundance in this strain, whereas there appeared to be no significant change within the LL strain SS120. Conclusions: This differential response between ecotypes highlights the relative importance of phosphate availability to each strain and from these results we draw the conclusion that the expression of phosphate acquisition mechanisms are activated at strain specific phosphate concentrations. http://www.aquaticbiosystems.org/content/8/1/7 Matthew Fuszard Phillip Wright Catherine Biggs Aquatic Biosystems 2012, null:7 2012-03-19T00:00:00Z doi:10.1186/2046-9063-8-7 /content/figures/2046-9063-8-7-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 7 2012-03-19T00:00:00Z XML Variations in climate, watershed characteristics and lake-internal processes often result in a large variability of food-web complexity in lake ecosystems. Some of the largest ranges in these environmental parameters can be found in lakes across the northern Great Plains as they are characterized by extreme gradients in respect to lake morphometry and water chemistry, with individual parameters often varying over several orders of magnitude. To evaluate the effects of environmental conditions on trophic complexity in prairie lake food-webs, we analyzed carbon and nitrogen stable isotopes of fishes, zooplankton and littoral macroinvertebrates in 20 lakes across southern Saskatchewan. Our two-year study identified very diverse patterns of trophic complexity, with was predominantly associated with among-lake differences. Small but significant temporal effects were also detected, which were predominantly associated with changes in productivity. The most influential parameters related to changes in trophic complexity among lakes were salinity, complexity of fish assemblage, and indicators of productivity (e.g. nutrients, Chl a). Generally, trophic diversity, number of trophic levels, and trophic redundancy were highest in productive freshwater lakes with diverse fish communities. Surprisingly, mesosaline lakes that were characterized by very low or no predation pressure from fishes were not colonized by invertebrate predators as it is often the case in boreal systems; instead, trophic complexity was further reduced. Together, prairie lake food-webs appear to be highly sensitive to changes in salinity and the loss of piscivorous fishes, making freshwater and mesosaline lakes most vulnerable to the impacts of climate variability. This is particularly important as global circulation models predict future climate warming to have disproportionate negative impacts on hydrologic conditions in this area. http://www.aquaticbiosystems.org/content/8/1/6 Ryan Cooper Bjorn Wissel Aquatic Biosystems 2012, null:6 2012-03-16T00:00:00Z doi:10.1186/2046-9063-8-6 /content/figures/2046-9063-8-6-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 6 2012-03-16T00:00:00Z XML Background: La Sal del Rey ("the King's Salt") is one of several naturally-occurring salt lakes in Hidalgo County, Texas and is part of the Lower Rio Grande Valley National Wildlife Refuge. The research objective was to isolate and characterize halophilic microorganisms from La Sal del Rey. Water samples were collected from the lake and a small creek that feeds into the lake. Soil samples were collected from land adjacent to the water sample locations. Sample salinity was determined using a refractometer. Samples were diluted and cultured on a synthetic saline medium to grow halophilic bacteria. The density of halophiles was estimated by viable plate counts. A collection of isolates was selected, gram-stained, tested for catalase, and characterized using API 20E® test strips. Isolates were putatively identified by sequencing the 16S rDNA. Carbon source utilization by the microbial community from each sample site was examined using EcoPlate™ assays and the carbon utilization total activity of the community was determined. Results: Results showed that salinity ranged from 4 parts per thousand (ppt) at the lake water source to 420 ppt in water samples taken just along the lake shore. The density of halophilic bacteria in water samples ranged from 1.2 × 102 - 5.2 × 103 colony forming units per ml (cfu ml-1) whereas the density in soil samples ranged from 4.0 × 105 - 2.5 × 106 colony forming units per gram (cfu g-1). In general, as salinity increased the density of the bacterial community decreased. Microbial communities from water and soil samples were able to utilize 12 - 31 carbon substrates. The greatest number of substrates utilized was by water-borne communities compared to soil-based communities, especially at lower salinities. The majority of bacteria isolated were gram-negative, catalase-positive, rods. Biochemical profiles constructed from API 20E® test strips showed that bacterial isolates from low-salinity water samples (4 ppt) showed the greatest phenotypic diversity with regards to the types and number of positive tests from the strip. Isolates taken from water samples at the highest salinity (420 ppt) tended to be less diverse and have only a limited number of positive tests. Sequencing of 16S DNA displayed the presence of members of bacterial genera Bacillus, Halomonas, Pseudomonas, Exiguobacterium and others. The genus Bacillus was most commonly identified. None of the isolates were members of the Archaea probably due to dilution of salts in the samples. Conclusions: The La Sal del Rey ecosystem supports a robust and diverse bacterial community despite the high salinity of the lake and soil. However, salinity does appear to a limiting factor with regards to the density and diversity of the bacterial communities that inhabit the lake and surrounding area. http://www.aquaticbiosystems.org/content/8/1/5 Kristen Phillips Frederic Zaidan Omar Elizondo Kristine Lowe Aquatic Biosystems 2012, null:5 2012-02-02T00:00:00Z doi:10.1186/2046-9063-8-5 /content/figures/2046-9063-8-5-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 5 2012-02-02T00:00:00Z XML Enzymes from extremophilic microorganisms usually catalyze chemical reactions in non-standard conditions. Such conditions promote aggregation, precipitation, and denaturation, reducing the activity of most non-extremophilic enzymes, frequently due to the absence of sufficient hydration. Some extremophilic enzymes maintain a tight hydration shell and remain active in solution even when liquid water is limiting, e.g. in the presence of high ionic concentrations, or at cold temperature when water is close to the freezing point. Extremophilic enzymes are able to compete for hydration via alterations especially to their surface through greater surface charges and increased molecular motion. These properties have enabled some extremophilic enzymes to function in the presence of non-aqueous organic solvents, with potential for design of useful catalysts. In this review, we summarize the current state of knowledge of extremophilic enzymes functioning in high salinity and cold temperatures, focusing on their strategy for function at low water activity. We discuss how the understanding of extremophilic enzyme function is leading to the design of a new generation of enzyme catalysts and their applications to biotechnology. http://www.aquaticbiosystems.org/content/8/1/4 Ram Karan Melinda Capes Shiladitya DasSarma Aquatic Biosystems 2012, null:4 2012-02-02T00:00:00Z doi:10.1186/2046-9063-8-4 /content/figures/2046-9063-8-4-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 4 2012-02-02T00:00:00Z XML Background: Killer whales (Orcinus orca) are the most widely distributed cetacean, occurring in all oceans worldwide, and within ocean regions different ecotypes are defined based on prey preferences. Prey items are largely unknown in the eastern Canadian Arctic and therefore we conducted a survey of Inuit Traditional Ecological Knowledge (TEK) to provide information on the feeding ecology of killer whales. We compiled Inuit observations on killer whales and their prey items via 105 semi-directed interviews conducted in 11 eastern Nunavut communities (Kivalliq and Qikiqtaaluk regions) from 2007-2010. Results: Results detail local knowledge of killer whale prey items, hunting behaviour, prey responses, distribution of predation events, and prey capture techniques. Inuit TEK and published literature agree that killer whales at times eat only certain parts of prey, particularly of large whales, that attacks on large whales entail relatively small groups of killer whales, and that they hunt cooperatively. Inuit observations suggest that there is little prey specialization beyond marine mammals and there are no definitive observations of fish in the diet. Inuit hunters and elders also documented the use of sea ice and shallow water as prey refugia. Conclusions: By combining TEK and scientific approaches we provide a more holistic view of killer whale predation in the eastern Canadian Arctic relevant to management and policy. Continuing the long-term relationship between scientists and hunters will provide for successful knowledge integration and has resulted in considerable improvement in understanding of killer whale ecology relevant to management of prey species. Combining scientists and Inuit knowledge will assist in northerners adapting to the restructuring of the Arctic marine ecosystem associated with warming and loss of sea ice. http://www.aquaticbiosystems.org/content/8/1/3 Steven Ferguson Jeff Higdon Kristin Westdal Aquatic Biosystems 2012, null:3 2012-01-30T00:00:00Z doi:10.1186/2046-9063-8-3 Killer whale predation behaviour Traditional ecological knowledge and scientific observations combine to provide an accurate picture of killer whale feeding ecology and prey preference in the Canadian Arctic, highlighting preferred hunting strategies and prey avoidance behaviour. /content/figures/2046-9063-8-3-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 3 2012-01-30T00:00:00Z XML Aquatic biological systems are a critical part of the structure and function of earth's biosphere. While attention of the scientific community is often focused on the reaction of biological systems to changes in the environment, these systems also have profound effects, or actions, on the environment. Throughout the evolutionary history of earth, the rise and/or fall of different aquatic biosystems has impacted the character of the biosphere. At no time have environmental changes been more important to all life on earth than in the modern era, which underscores the need for the new journal, Aquatic Biosystems. We welcome submission of original research manuscripts, reviews, and commentaries to the journal. http://www.aquaticbiosystems.org/content/8/1/1 Edward Phlips Shiladitya DasSarma Aquatic Biosystems 2012, null:1 2012-01-30T00:00:00Z doi:10.1186/2046-9063-8-1 Re-launch to Aquatic Biosystems In their introductory Editorial, co Editors-in-Chief Shiladitya DasSarma and Edward Phlips discuss the need for the new journal title and how its expanded scope and Editorial Board will facilitate the dissemination of topical research across the journals interdisciplinary spectrum. /content/figures/2046-9063-8-1-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 1 2012-01-30T00:00:00Z XML