http://www.aquaticbiosystems.org The latest research articles published by Aquatic Biosystems 2012-02-02T00:00:00Z 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(R) 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 EcoPlateTM 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 x 10^2 - 5.2 x 10^3 colony forming units per ml (cfu ml-1) whereas the density in soil samples ranged from 4.0 x 10^5 - 2.5 x 10^6 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(R) 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 rDNA 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 PDF 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 the 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 PDF 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 PDF We used an ITS2 primary and secondary structure and Compensatory Base Changes (CBCs) analyses on new French and Spanish Dunallela salina strains to investigate their phylogenetic position and taxonomic status within the genus Dunaliella. Our analyses show a great diversity within D. salina (with only some clades not statistically supported) and reveal considerable genetic diversity and structure within Dunaliella, although the CBC analysis did not bolster the existence of different biological groups within this taxon. The ITS2 sequences of the new Spanish and French D. salina strains were very similar except for two of them: ITC5105 "Janubio" from Spain and ITC5119 from France. Although the Spanish one had a unique ITS2 sequence profile and the phylogenetic tree indicates that this strain can represent a new species, this hypothesis was not confirmed by CBCs, and clarification of its taxonomic status requires further investigation with new data. Overall, the use of CBCs to define species boundaries within Dunaliella was not conclusive in some cases, and the ITS2 region does not contain a geographical signal overall. http://www.aquaticbiosystems.org/content/8/1/2 Patricia Assuncao Ruth Jaen-Molina Juli Caujape-Castells Adelina de la Jara Laura Carmona Karen Freijanes Hector Mendoza Aquatic Biosystems 2012, null:2 2012-01-30T00:00:00Z doi:10.1186/2046-9063-8-2 /content/figures/2046-9063-8-2-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 2 2012-01-30T00:00:00Z PDF 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 PDF Solar salinas are man-made systems exploited for the extraction of salt, by solar and wind evaporation of seawater. Salt production achieved by traditional methods is associated with landscapes and environmental and patrimonial values generated throughout history. Since the mid-twentieth century, this activity has been facing a marked decline in Portugal, with most salinas either abandoned or subjected to destruction, making it necessary to find a strategy to reverse this trend.It is, however, possible to generate revenue from salinas at several levels, not merely in terms of good quality salt production, but also by obtaining other products that can be commercialized, or by exploring their potential for tourism, and as research facilities, among others. Furthermore, with an adequate management, biodiversity can be restored to abandoned salinas, which constitute important feeding and breeding grounds for resident and migratory aquatic birds, many of which are protected by European Community Directives.The aims of this manuscript are to present a brief overview on the current state of sea salt exploitation in Portugal and to stress the importance of recovering these salinas for the conservation of this particular environment, for the regional economy, the scientific community and the general public. The Aveiro salina complex is presented in detail, to exemplify salina structure and functioning, as well as current problems and potential solutions for artisanal salinas. http://www.salinesystems.org/content/7/1/3 Carolina Rodrigues Ana Bio Francisco Amat Natividade Vieira Aquatic Biosystems 2011, null:3 2011-11-04T00:00:00Z doi:10.1186/1746-1448-7-3 /content/figures/1746-1448-7-3-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 3 2011-11-04T00:00:00Z XML Alkaline earth elements and alkali metals (Mg, Ca, Na and K) play an important role in the geochemical evolution of saline lakes as the final brine type is defined by the abundance of these elements. The role of major ions in brine evolution has been studied in great detail, but little has been done to investigate the behaviour of minor alkali elements in these systems despite their similar chemical affinities to the major cations. We have examined three major anionic brine types, chloride, sulphate, and bicarbonate-carbonate, in fifteen lakes in North America and Antarctica to determine the geochemical behaviour of lithium, rubidium, strontium, and barium. Lithium and rubidium are largely conservative in all water types, and their concentrations are the result of long-term solute input and concentration through evaporation and/or sublimation. Strontium and barium behaviours vary with anionic brine type. Strontium can be removed in sulphate and carbonate-rich lakes by the precipitation of carbonate minerals. Barium may be removed in chloride and sulphate brines by either the precipitation of barite and perhaps biological uptake. http://www.salinesystems.org/content/7/1/2 Rebecca Witherow W. Berry Lyons Aquatic Biosystems 2011, null:2 2011-10-12T00:00:00Z doi:10.1186/1746-1448-7-2 /content/figures/1746-1448-7-2-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 2 2011-10-12T00:00:00Z XML Halophile proteins can tolerate high salt concentrations. Understanding halophilicity features is the first step toward engineering halostable crops. To this end, we examined protein features contributing to the halo-toleration of halophilic organisms. We compared more than 850 features for halophilic and non-halophilic proteins with various screening, clustering, decision tree, and generalized rule induction models to search for patterns that code for halo-toleration. Up to 251 protein attributes selected by various attribute weighting algorithms as important features contribute to halo-stability; from them 14 attributes selected by 90% of models and the count of hydrogen gained the highest value (1.0) in 70% of attribute weighting models, showing the importance of this attribute in feature selection modeling. The other attributes mostly were the frequencies of di-peptides. No changes were found in the numbers of groups when K-Means and TwoStep clustering modeling were performed on datasets with or without feature selection filtering. Although the depths of induced trees were not high, the accuracies of trees were higher than 94% and the frequency of hydrophobic residues pointed as the most important feature to build trees. The performance evaluation of decision tree models had the same values and the best correctness percentage recorded with the Exhaustive CHAID and CHAID models. We did not find any significant difference in the percent of correctness, performance evaluation, and mean correctness of various decision tree models with or without feature selection. For the first time, we analyzed the performance of different screening, clustering, and decision tree algorithms for discriminating halophilic and non-halophilic proteins and the results showed that amino acid composition can be used to discriminate between halo-tolerant and halo-sensitive proteins. http://www.salinesystems.org/content/7/1/1 Esmaeil Ebrahimie Mansour Ebrahimi Narjes Rahpayma Sarvestani Mahdi Ebrahimi Aquatic Biosystems 2011, null:1 2011-05-18T00:00:00Z doi:10.1186/1746-1448-7-1 /content/figures/1746-1448-7-1-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 1 2011-05-18T00:00:00Z XML Background: Complete genome sequencing together with post-genomic studies provide the opportunity for a comprehensive 'systems biology' understanding of model organisms. For maximum effectiveness, an integrated database containing genomic, transcriptomic, and proteomic data is necessary.DescriptionTo improve data access and facilitate functional genomic studies on haloarchaea in our laboratory, a dedicated database and website, named HaloWeb, was developed. It incorporates all finished and publicly released haloarchaeal genomes, including gene, protein and RNA sequences and annotation data, as well as other features such as insertion element sequences. The HaloWeb database was designed for easy data access and mining, and includes tools for tasks such as genome map generation, sequence extraction, and sequence editing. Popular resources at other sites, e.g., NCBI PubMed and BLAST, COG and KOG protein clusters, KEGG pathways, and GTOP structures were dynamically linked. The HaloWeb site is located at http://halo4.umbi.umd.edu, and at a mirror site, http://halo5.umbi.umd.edu, with all public genomic data and NCBI, KEGG, and GTOP links available for use by the academic community. The database is curated and updated on a regular basis. Conclusions: The HaloWeb site includes all completely sequenced haloarchaeal genomes from public databases. It is currently being used as a tool for comparative genomics, including analysis of gene and genome structure, organization, and function. The database and website are up-to-date resources for researchers worldwide. http://www.salinesystems.org/content/6/1/12 Satyajit DasSarma Melinda Capes Priya DasSarma Shiladitya DasSarma Aquatic Biosystems 2010, null:12 2010-12-30T00:00:00Z doi:10.1186/1746-1448-6-12 /content/figures/1746-1448-6-12-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 12 2010-12-30T00:00:00Z XML Background: Fairy shrimps (Anostraca), tadpole shrimps (Notostraca), clam shrimps (Spinicaudata), algae (primarily filamentous blue-green algae [cyanobacteria]), and suspended organic particulates are dominant food web components of the seasonally inundated pans and playas of the western Mojave Desert in California. We examined the extent to which these branchiopods controlled algal abundance and species composition in clay pans between Rosamond and Rogers Dry Lakes. We surveyed branchiopods during the wet season to estimate abundances and then conducted a laboratory microcosm experiment, in which dried sediment containing cysts and the overlying algal crust were inundated and cultured. Microcosm trials were run with and without shrimps; each type of trial was run for two lengths of time: 30 and 60 days. We estimated the effect of shrimps on algae by measuring chlorophyll content and the relative abundance of algal species. Results: We found two species of fairy shrimps (Branchinecta mackini and B. gigas), one tadpole shrimp (Lepidurus lemmoni), and a clam shrimp (Cyzicus setosa) in our wet-season field survey. We collected Branchinecta lindahli in a pilot study, but not subsequently. The dominant taxa were C. setosa and B. mackini, but abundances and species composition varied greatly among playas. The same species found in field surveys also occurred in the microcosm experiment. There were no significant differences as a function of experimental treatments for either chlorophyll content or algal species composition (Microcoleus vaginatus dominated all treatments). Conclusions: The results suggest that there was no direct effect of shrimps on algae. Although the pans harbored an apparently high abundance of branchiopods, these animals had little role in regulating primary producers in this environment. http://www.salinesystems.org/content/6/1/11 William Brostoff Jeffrey Holmquist Jutta Schmidt-Gengenback Paul Zimba Aquatic Biosystems 2010, null:11 2010-12-08T00:00:00Z doi:10.1186/1746-1448-6-11 Food webs in the Mojave Desert Few studies have previously examined food webs in the seasonally inundated ponds in the Mojave Desert of California. Brostoff et al. have studied the relationships between shrimp and algae in these novel environments. /content/figures/1746-1448-6-11-toc.gif Aquatic Biosystems 2046-9063 ${item.volume} 11 2010-12-08T00:00:00Z XML