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1.  Interactions of marine mammals and birds with offshore membrane enclosures for growing algae (OMEGA) 
Aquatic Biosystems  2014;10:3.
Background
OMEGA is an integrated aquatic system to produce biofuels, treat and recycle wastewater, capture CO2, and expand aquaculture production. This system includes floating photobioreactors (PBRs) that will cover hundreds of hectares in marine bays. To assess the interactions of marine mammals and birds with PBRs, 9 × 1.3 m flat panel and 9.5 × 0.2 m tubular PBRs were deployed in a harbor and monitored day and night from October 10, 2011 to Janurary 22, 2012 using infrared video. To observe interactions with pinnipeds, two trained sea lions (Zalophus californianus) and one trained harbor seal (Phoca vitulina richardii) were observed and directed to interact with PBRs in tanks. To determine the forces required to puncture PBR plastic and the effects of weathering, Instron measurements were made with a sea otter (Enhydra lutris) tooth and bird beaks.
Results
A total of 1,445 interactions of marine mammals and birds with PBRs were observed in the 2,424 hours of video recorded. The 95 marine mammal interactions, 94 by sea otters and one by a sea lion had average durations of three minutes (max 44 min) and represented about 1% of total recording time. The 1,350 bird interactions, primarily coots (Fulica americana) and gulls (Larus occidentalis and L. californicus) had average durations of six minutes (max. 170) and represented 5% of recording time. Interactive behaviors were characterized as passive (feeding, walking, resting, grooming, and social activity) or proactive (biting, pecking, investigating, and unspecified manipulating). Mammal interactions were predominantly proactive, whereas birds were passive. All interactions occurred primarily during the day. Ninety-six percent of otter interactions occurred in winter, whereas 73% of bird interactions in fall, correlating to their abundance in the harbor. Trained pinnipeds followed most commands to bite, drag, and haul-out onto PBRs, made no overt undirected interactions with the PBRs, but showed avoidance behavior to PBR tethers. Instron measurements indicated that sea-otter teeth and gull beaks can penetrate weathered plastic more easily than new plastic.
Conclusions
Otter and bird interactions with experimental PBRs were benign. Large-scale OMEGA systems are predicted to have both positive and negative environmental consequences.
doi:10.1186/2046-9063-10-3
PMCID: PMC4049508  PMID: 24955238
Biofuels; Wastewater treatment; Photobioreactors; Renewable energy; Marine mammals; Birds; Sea otter; Gulls; Monterey Bay
2.  Molecular (PCR-DGGE) versus morphological approach: analysis of taxonomic composition of potentially toxic cyanobacteria in freshwater lakes 
Aquatic Biosystems  2014;10:2.
Background
The microscopic Utermöhl method is commonly used for the recognition of the presence and taxonomic composition of potentially toxic cyanobacteria and is especially useful for monitoring reservoirs used as drinking water, recreation and fishery resources. However, this method is time-consuming and does not allow potentially toxic and nontoxic cyanobacterial strains to be distinguished. We have developed a method based on denaturing gradient gel electrophoresis (DGGE) of the marker gene ITS and the mcy-gene cluster, and DNA sequencing. We have attempted to calibrate the DGGE-method with a microscopic procedure, using water samples taken in 2011 from four lakes of the Great Mazurian Lakes system.
Results
Results showed that the classic microscopic method was much more precise and allowed the classification of the majority of cyanobacterial taxa to the species or genus. Using the molecular approach, most of the sequences could only be assigned to a genus or family. The results of DGGE and microscopic analyses overlapped in the detection of the filamentous cyanobacteria. For coccoid cyanobacteria, we only found two taxa using the molecular method, which represented 17% of the total taxa identified using microscopic observations. The DGGE method allowed the identification of two genera of cyanobacteria (Planktothrix and Microcystis) in the studied samples, which have the potential ability to produce toxins from the microcystins group.
Conclusions
The results confirmed that the molecular approach is useful for the rapid detection and taxonomic distinction of potentially toxic cyanobacteria in lake-water samples, also in very diverse cyanobacterial communities. Such rapid detection is unattainable by other methods. However, with still limited nucleotide sequences deposited in the public databases, this method is currently not sufficient to evaluate the entire taxonomic composition of cyanobacteria in lakes.
doi:10.1186/2046-9063-10-2
PMCID: PMC3925352  PMID: 24517495
Cyanobacteria; DGGE; ITS; mcy genes; Microcystins; Microscopic analysis
3.  Aquatic Biosystems reviewer acknowledgement 2013 
Aquatic Biosystems  2014;10:1.
Contributing reviewers
The Aquatic Biosystems editorial team would like to thank the following colleagues who contributed to peer review for the journal in 2013.
doi:10.1186/2046-9063-10-1
PMCID: PMC3896783  PMID: 24433368
4.  High throughput screening of CO2-tolerating microalgae using GasPak bags 
Aquatic Biosystems  2013;9:23.
Background
Microalgae are diverse in terms of their speciation and function. More than 35,000 algal strains have been described, and thousands of algal cultures are maintained in different culture collection centers. The ability of CO2 uptake by microalgae varies dramatically among algal species. It becomes challenging to select suitable algal candidates that can proliferate under high CO2 concentration from a large collection of algal cultures.
Results
Here, we described a high throughput screening method to rapidly identify high CO2 affinity microalgae. The system integrates a CO2 mixer, GasPak bags and microplates. Microalgae on the microplates will be cultivated in GasPak bags charged with different CO2 concentrations. Using this method, we identified 17 algal strains whose growth rates were not influenced when the concentration of CO2 was increased from 2 to 20% (v/v). Most CO2 tolerant strains identified in this study were closely related to the species Scenedesmus and Chlorococcum. One of Scenedesmus strains (E7A) has been successfully tested in in the scale up photo bioreactors (500 L) bubbled with flue gas which contains 10-12% CO2.
Conclusion
Our high throughput CO2 testing system provides a rapid and reliable way for identifying microalgal candidate strains that can grow under high CO2 condition from a large pool of culture collection species. This high throughput system can also be modified for selecting algal strains that can tolerate other gases, such as NOx, SOx, or flue gas.
doi:10.1186/2046-9063-9-23
PMCID: PMC3914841  PMID: 24341988
CO2 sequestration; Microalgae; High through-put selection
5.  Detritus-based assemblage responses under salinity stress conditions in a disused aquatic artificial ecosystem 
Aquatic Biosystems  2013;9:22.
Background
Despite the plethora of approaches, the sensitivity of the methods to measure the relationship between the abundance and biomass curves in stressed detritus-based ecosystems still remain to be refined. In this work, we report the comparison between biomass and abundance in a set of detritus-based macrozoobenthic assemblages located in six sampling pools with different salinity in an artificial aquatic ecosystem (disused Tarquinia Saltworks), using two diversity/dominance approaches (Abundance/Biomass Comparisons, or ABC, and Whittaker plots). We also evaluated the contribution of abundances and biomasses diversity (Simpson index) and nestedness, which measures the order by which macroinvertebrates colonized the detrital resource.
Results
The outputs obtained by both ABC curves and Whittaker plots highlight two different thresholds in assemblage structure: between about 44 and 50 practical salinity unit (psu) and between 50 and 87 psu, respectively. The first threshold was due to a turnover in taxon composition between assemblages, the second threshold (evidenced by Whittaker plots) was due to a change in taxon richness (lower in pools with higher salinity: i.e. > 50 psu). Moreover, a normal-shaped pattern in diversity (Simpson index) emerged, suggestive of an intermediate disturbance effect. The nested pattern did not show significant differences when considering the density and biomass of the sampled taxa, providing similar threshold of salinity in the relative contribution of macrozoobenthos on nestedness.
Conclusions
The use of detailed (ABC and Whittaker plots) and macroscopic (Simpson index and nestedness) approaches is proposed to identify thresholds in the structuring and functioning of detritus-based community of disused aquatic ecosystems: in particular, the inclusion of the parameter of biomass (scarcely utilized in community-based research) appears crucial. The responses of macrozoobenthic assemblages to the salinity stress conditions, in term of abundance and biomass, using a detritus food source (Phragmites australis leaves), may also highlight, by comparing macroscopic and detailed approaches, structuring and functioning patterns to consider for the management of disused artificial ecosystems.
doi:10.1186/2046-9063-9-22
PMCID: PMC4028869  PMID: 24308820
Leaf-detritus; Macrozoobenthos; Abundance/Biomass Comparisons; Whittaker plots; Simpson index; Nestedness; Patchy environment
6.  Microbial community composition of Tirez lagoon (Spain), a highly sulfated athalassohaline environment 
Aquatic Biosystems  2013;9:19.
Background
The aim was to study the seasonal microbial diversity variations of an athalassohaline environment with a high concentration of sulfates in Tirez lagoon (La Mancha, Spain). Despite the interest in these types of environments there is scarce information about their microbial ecology, especially on their anoxic sediments.
Results
We report the seasonal microbial diversity of the water column and the sediments of a highly sulfated lagoon using both molecular and conventional microbiological methods. Algae and Cyanobacteria were the main photosynthetic primary producers detected in the ecosystem in the rainy season. Also dinoflagelates and filamentous fungi were identified in the brines. The highest phylotype abundance in water and sediments corresponded to members of the bacterial phylum Proteobacteria, mainly of the Gamma- and Alphaproteobacteria classes. Firmicutes and Actinobacteria were isolated and identified in Tirez brines and sediment samples. Halophilic sulfate reducing Deltaproteobacteria were also detected (Desulfohalobium).
Conclusions
Important differences have been found in the microbial diversity present in the Tirez water column and the sediments between the wet and dry seasons. Also the Tirez lagoon showed a high richness of the bacterial Alpha- and Deltaproteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and for the archaeal Euryarchaeota.
doi:10.1186/2046-9063-9-19
PMCID: PMC3852488  PMID: 24083554
7.  The structure of winter phytoplankton in Lake Nero, Russia, a hypertrophic lake dominated by Planktothrix-like Cyanobacteria 
Aquatic Biosystems  2013;9:18.
Background
The permanent dominance of Planktothrix-like сyanobacteria has been often reported for shallow eutrophic\hypertrophic lakes in central Europe in summer\autumn. However studies on phytoplankton growth under ice cover in nutrient-rich lakes are very scarce. Lake Nero provides a good example of the contrasting seasonal extremes in environmental conditions. Moreover, the ecosystem underwent a catastrophic transition from eutrophic to hypertrophic 2003–05, with dominance of filamentous cyanobacteria in summer\autumn. Towards the end of the period of ice cover, there is an almost complete lack of light and oxygen but abundance in nutrients, especially ammonium nitrogen, soluble reactive phosphorus and total phosphorus in lake Nero. The aim of the present study was to describe species composition and abundance of the phytoplankton, in relation to the abiotic properties of the habitat to the end of winters 1999–2010. We were interested if Planktothrix-like сyanobacteria kept their dominant role under the ice conditions or only survived, and how did the under-ice phytoplankton community differ from year to year.
Results
Samples collected contained 172 algal taxa of sub-generic rank. Abundance of phytoplankton varied widely from very low to the bloom level. Cyanobacteria (Limnothrix, Pseudanabaena, Planktothrix) were present in all winter samples but did not always dominate. Favourable conditions included low winter temperature, thicker ice, almost complete lack of oxygen and high ammonium concentration. Flagellates belonging to Euglenophyta and Cryptophyta dominated in warmer winters, when phosphorus concentrations increased.
Conclusion
A full picture of algal succession in the lake may be obtained only if systematic winter observations are taken into account. Nearly anoxic conditions, severe light deficiency and high concentration of biogenic elements present a highly selective environment for phytoplankton. Hypertrophic water bodies of moderate zone covered by ice in winter and dominated by Planktothrix - like сyanobacteria in summer/autumn may follow several scenarios in the end of winter. It may be intense proliferation сyanobacteria normally dominating in summer, or the switch to the other species like the euglenoids and cryptomonads flagellates, or almost total depletion of phytoplankton.
doi:10.1186/2046-9063-9-18
PMCID: PMC3849563  PMID: 24079446
8.  Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments 
Aquatic Biosystems  2013;9:17.
Background
The Cariaco Basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. Marine water samples were collected in May, 2005 and 2006, at the sampling stations A (10°30′ N, 64°40′ W), B (10°40′ N, 64°45′ W) and D (10°43’N, 64°32’W) from different depths, including surface, redox interface, and anoxic zones. In order to enrich for sulfate reducing bacteria (SRB), water samples were inoculated into anaerobic media amended with lactate or acetate as carbon source. To analyze the composition of enrichment cultures, we performed DNA extraction, PCR-DGGE, and sequencing of selected bands.
Results
DGGE results indicate that many bacterial genera were present that are associated with the sulfur cycle, including Desulfovibrio spp., as well as heterotrophs belonging to Vibrio, Enterobacter, Shewanella, Fusobacterium, Marinifilum, Mariniliabilia, and Spirochaeta. These bacterial populations are related to sulfur coupling and carbon cycles in an environment of variable redox conditions and oxygen availability.
Conclusions
In our studies, we found an association of SRB-like Desulfovibrio with Vibrio species and other genera that have a previously defined relevant role in sulfur transformation and coupling of carbon and sulfur cycles in an environment where there are variable redox conditions and oxygen availability. This study provides new information about microbial species that were culturable on media for SRB at anaerobic conditions at several locations and water depths in the Cariaco Basin.
doi:10.1186/2046-9063-9-17
PMCID: PMC3765856  PMID: 23981583
SRB; Cariaco Basin; Desulfovibrio; Vibrio; DGGE; Culture
9.  Diversity of picoeukaryotes at an oligotrophic site off the Northeastern Red Sea Coast 
Aquatic Biosystems  2013;9:16.
Background
Picoeukaryotes are protists ≤ 3 μm composed of a wide diversity of taxonomic groups. They are an important constituent of the ocean’s microbiota and perform essential ecological roles in marine nutrient and carbon cycles. Despite their importance, the true extent of their diversity has only recently been uncovered by molecular surveys that resulted in the discovery of a substantial number of previously unknown groups. No study on picoeukaryote diversity has been conducted so far in the main Red Sea basin-a unique marine environment characterized by oligotrophic conditions, high levels of irradiance, high salinity and increased water temperature.
Results
We sampled surface waters off the coast of the northeastern Red Sea and analyzed the picoeukaryotic diversity using Sanger-based clone libraries of the 18S rRNA gene in order to produce high quality, nearly full-length sequences. The community captured by our approach was dominated by three main phyla, the alveolates, stramenopiles and chlorophytes; members of Radiolaria, Cercozoa and Haptophyta were also found, albeit in low abundances. Photosynthetic organisms were especially diverse and abundant in the sample, confirming the importance of picophytoplankton for primary production in the basin as well as indicating the existence of numerous ecological micro-niches for this trophic level in the upper euphotic zone. Heterotrophic organisms were mostly composed of the presumably parasitic Marine Alveolates (MALV) and the presumably bacterivorous Marine Stramenopiles (MAST) groups. A small number of sequences that did not cluster closely with known clades were also found, especially in the MALV-II group, some of which could potentially belong to novel clades.
Conclusions
This study provides the first snapshot of the picoeukaryotic diversity present in surface waters of the Red Sea, hence setting the stage for large-scale surveying and characterization of the eukaryotic diversity in the entire basin. Our results indicate that the picoeukaryotic community in the northern Red Sea, despite its unique physiochemical conditions (i.e. increased temperatures, increased salinity, and high UV irradiance) does not differ vastly from its counterparts in other oligotrophic marine habitats.
doi:10.1186/2046-9063-9-16
PMCID: PMC3766091  PMID: 23962380
Picoeukaryotes; Red sea; Protists; SSU rRNA; Microbial diversity
10.  The distribution and diversity of benthic macroinvertebrate fauna in Pondicherry mangroves, India 
Aquatic Biosystems  2013;9:15.
Background
Species distribution, abundance and diversity of mangrove benthic macroinvertebrate fauna and the relationships to environmental conditions are important parts of understanding the structure and function of mangrove ecosystems. In this study seasonal variation in the distribution of macrobenthos and related environmental parameters were explored at four mangrove stations along the Pondicherry coast of India, from September 2008 to July 2010. Multivariate statistical analyses, including cluster analysis, principal component analysis and non-multidimensional scales plot were employed to help define trophic status, water quality and benthic characteristic at the four monitoring stations.
Results
Among the 528 samples collected over 168 ha of mangrove forest 76 species of benthic macroinvertebrate fauna were identified. Macrofauna were mainly composed of deposit feeders, dominated numerically by molluscs and crustaceans. Statistical analyses yielded the following descriptors of benthic macroinvertebrate fauna species distribution: densities between 140–1113 ind. m-2, dominance 0.17-0.50, diversity 1.80-2.83 bits ind-1, richness 0.47-0.74 and evenness 0.45-0.72, equitability 0.38-0.77, berger parker 0.31-0.77 and fisher alpha 2.46-5.70. Increases of species diversity and abundance were recorded during the post monsoon season at station 1 and the lowest diversity was recorded at station 2 during the monsoon season. The pollution indicator organisms Cassidula nucleus, Melampus ceylonicus, Sphaerassiminea minuta were found only at the two most polluted regions, i.e. stations 3 and 4. Benthic macroinvertebrate fauna abundances were inversely related to salinity at the four stations, Based on Bray-Curtis similarity through hierarchical clustering implemented in PAST, it was possible to define three distinct benthic assemblages at the stations.
Conclusions
From a different multivariate statistical analysis of the different environmental parameters regarding species diversity and abundance of benthic macroinvertebrate fauna, it was found that benthic communities are highly affected by all the environmental parameters governing the distribution and diversity variation of the macrofaunal community in Pondicherry mangroves. Salinity, dissolved oxygen levels, organic matter content, sulphide concentration were the most significant parameters.
doi:10.1186/2046-9063-9-15
PMCID: PMC3751066  PMID: 23937801
Density; Diversity; Mangroves; Benthic macroinvertebrate fauna; Seasonal variation
11.  Cyanobacteria in wetlands of the industrialized Sambalpur District of India 
Aquatic Biosystems  2013;9:14.
Background
Cyanobacteria are common components of phytoplankton communities in most freshwater ecosystems. Proliferations of cyanobacteria are often caused by high nutrient loading, and as such can serve as indicators of declining water quality. Massive industrialization in developing countries, like India, has polluted fresh water bodies, including wetlands. Many industries directly discard their effluents to nearby water sources without treatment. In the Sambalpur District of India effluents reach the reservoir of the worlds largest earthen dam i.e Hirakud Dam. This study examines cyanobacteria communities in the wetlands of Sambalpur District, Odisha, India, including areas subjected to industrial pollution.
Result & Discussion
The genera Anabaena, Oscillatoria, Chroococcus, Phormidium were dominant genera of polluted wetlands of Sambalpur districts. A positive correlation was found between total cyanobacterial species and dissolved oxygen levels, but cyanobacterial diversity was inversely related to BOD, COD, TSS, and TDS. High dissolved oxygen content was also associated with regions of lower cyanobacteria biomass.
Conclusion
Cyanobacterial abundance was positively correlated to content of oxidisable organic matter, but negatively correlated to species diversity. Lower dissolved oxygen was correlated to decreased diversity and increased dominance by Anabaena, Oscillatoria, Chroococcus, Phormidium species, observed in regions characterized by deteriorated water quality.
doi:10.1186/2046-9063-9-14
PMCID: PMC3735473  PMID: 23845058
Wetlands; Cyanobacteria; Eutrophication; Industrialization; Pollution
12.  Optimization of bacteriocin production by Lactobacillus sp. MSU3IR against shrimp bacterial pathogens 
Aquatic Biosystems  2013;9:12.
Background
Aquaculture is one amongst the growing and major food producing sectors. Shrimp culture is one of the subsectors of aquaculture that attracts more attention because of the economic interest. However, the shrimp culture systems have been facing severe consequences and economical losses due to disease outbreaks. Risk of disease outbreak can be combated with the application of probiotics. For economically viable production of such probiotic products, the present study provides information on the optimization and partial purification of bacteriocin produced by a goat milk isolate Lactobacillus sp. MSU3IR against the shrimp bacterial pathogens.
Results
Bacteriocin production was estimated as a measure of bactericidal activity (arbitrary Unit/ml) over the test strains. The optimum culture conditions and media components for maximum bacteriocin production by Lactobacillus sp. MSU3IR were: pH: 5.0, temperature: 30°C, carbon source: lactose; nitrogen source: ammonium acetate; NaCl: 3.0% and surfactant: Tween 80. MRS medium was found to extend better bacteriocin production than other tested media. Upon partial purification of bacteriocin, the SDS-PAGE analysis had manifested the presence of two peptide bands with the molecular weight of 39.26 and 6.38 kDa, respectively.
Conclusion
The present results provide baseline trend for the statistical optimization, scale up process and efficient production of bacteriocin by the candidate bacterial strain Lactobacillus sp. MSU3IR which could be used to replace the usage of conventional chemotherapeutics in shrimp culture systems.
doi:10.1186/2046-9063-9-12
PMCID: PMC3679972  PMID: 23725298
Aquaculture; Bacteriocin; Lactobacillus; Probiotics; Shrimp pathogens
13.  Variation in spatial and temporal incidence of the crustacean pathogen Hematodinium perezi in environmental samples from Atlantic Coastal Bays 
Aquatic Biosystems  2013;9:11.
Background
Hematodinium perezi, a parasitic dinoflagellate, infects and kills blue crabs, Callinectes sapidus, along the Atlantic and Gulf coasts of the United States. The parasite proliferates within host hemolymph and tissues, and also produces free-swimming biflagellated dinospores that emerge from infected crabs. Infections in C. sapidus recur annually, and it is not known if biotic or environmental reservoirs contribute to reinfection and outbreaks. To address this data gap, a quantitative PCR assay based on the internal transcribed spacer 2 (ITS2) region of H. perezi rRNA genes was developed to asses the temporal and spatial incidence of the parasite in Delaware and Maryland coastal bays.
Results
A previously-used PCR assay for H. perezi, based on the small subunit rRNA gene sequence, was found to lack adequate species specificity to discriminate non-Hematodinium sp. dinoflagellate species in environmental samples. A new ITS2-targeted assay was developed and validated to detect H. perezi DNA in sediment and water samples using E. coli carrying the H. perezi rDNA genes. Application of the method to environmental samples identified potential hotspots in sediment in Indian River Inlet, DE and Chincoteague Bay, MD and VA. H. perezi DNA was not detected in co-occurring shrimp or snails, even during an outbreak of the parasite in C. sapidus.
Conclusions
H. perezi is present in water and sediment samples in Maryland and Delaware coastal bays from April through November with a wide spatial and temporal variability in incidence. Sampling sites with high levels of H. perezi DNA in both bays share characteristics of silty, organic sediments and low tidal currents. The environmental detection of H. perezi in spring, ahead of peak prevalence in crabs, points to gaps in our understanding of the parasite’s life history prior to infection in crabs as well as the mode of environmental transmission. To better understand the H. perezi life cycle will require further monitoring of the parasite in habitats as well as hosts. Improved understanding of potential environmental transmission to crabs will facilitate the development of disease forecasting.
doi:10.1186/2046-9063-9-11
PMCID: PMC3651331  PMID: 23641869
Blue crab; Hematodinium; Parasite; Disease reservoir; Fishery
14.  Impact of TBT on the vitellogenesis and sex hormones in freshwater prawn Macrobrachium rosenbergii (De Man, 1879) 
Aquatic Biosystems  2013;9:10.
Background
Tributyltin (TBT) is a ubiquitous persistent xenobiotic that can be found in freshwater, estuarine and marine ecosystem. TBT is a strong endocrine disrupting compound (EDC) that can cause toxic threat to aquatic organisms. Imposex, sexual deformities and endocrine dysfunctions are the causes of TBT to most of the aquatic organisms. Effect of TBT on the vitellogenesis and sex hormonal changes in Macrobrachium rosenbergii has never been reported. Hence, the present investigation was undertaken to find out the impact of TBT on histological changes in the different reproductive tissues, sex hormonal alterations and level of biomarkers like vitellogenin and vitellin in M. rosenbergii.
Results
The present investigation documents the possible impact of tributyltin (TBT) on the vitellogenesis in freshwater female prawn M. rosenbergii. TBT at 10 ng/l, 100 ng/l and 1000 ng/l concentrations were exposed individually to prawns for a period of three months. At higher concentration of 1000 ng/l, the ovarian development was arrested and ovary remained at spent stage. At lower concentration of TBT (10 ng/l), the development proceeded up to early vitellogenic stage. At intermediate concentration of 100 ng/l TBT, the ovary remained at pre vitellogenic stage and thereafter no development was noticed. Histological results indicated the normal ovarian development with vitellogenic oocytes, filled with yolk globules in control prawn. On the other hand, the TBT treated groups showed reduction in yolk globules, fusion of developing oocytes and abundance of immature oocytes. Immunofluorescence staining denoted the remarkable reduction in vitellin content in ovary of TBT treated prawn. Hence, TBT had conspicuously inhibited the vitellogenesis by causing hormonal imbalance in M. rosenbergii.
Conclusion
TBT had notably inhibited the vitellogenesis due to hormonal imbalance. This endocrine dysfunction ultimately impaired the oogenesis in the freshwater female prawn M. rosenbergii.
doi:10.1186/2046-9063-9-10
PMCID: PMC3653679  PMID: 23634699
Macrobrachium rosenbergii; Tributyltin; Ovarian development; Vitellogenesis; Sex hormones
15.  Factors controlling bacteria and protists in selected Mazurian eutrophic lakes (North-Eastern Poland) during spring 
Aquatic Biosystems  2013;9:9.
Background
The bottom-up (food resources) and top-down (grazing pressure) controls, with other environmental parameters (water temperature, pH) are the main factors regulating the abundance and structure of microbial communities in aquatic ecosystems. It is still not definitively decided which of the two control mechanisms is more important. The significance of bottom-up versus top-down controls may alter with lake productivity and season. In oligo- and/or mesotrophic environments, the bottom-up control is mostly important in regulating bacterial abundances, while in eutrophic systems, the top-down control may be more significant.
Results
The abundance of bacteria, heterotrophic (HNF) and autotrophic (ANF) nanoflagellates and ciliates, as well as bacterial production (BP) and metabolically active cells of bacteria (CTC, NuCC, EST) were studied in eutrophic lakes (Mazurian Lake District, Poland) during spring. The studied lakes were characterized by high nanoflagellate (mean 17.36 ± 8.57 × 103 cells ml-1) and ciliate abundances (mean 59.9 ± 22.4 ind. ml-1) that were higher in the euphotic zone than in the bottom waters, with relatively low bacterial densities (4.76 ± 2.08 × 106 cells ml-1) that were lower in the euphotic zone compared to the profundal zone. Oligotrichida (Rimostrombidium spp.), Prostomatida (Urotricha spp.) and Scuticociliatida (Histiobalantium bodamicum) dominated in the euphotic zone, whereas oligotrichs Tintinnidium sp. and prostomatids Urotricha spp. were most numerous in the bottom waters. Among the staining methods used to examine bacterial cellular metabolic activity, the lowest percentage of active cells was recorded with the CTC (1.5–15.4%) and EST (2.7–14.2%) assay in contrast to the NuCC (28.8–97.3%) method.
Conclusions
In the euphotic zone, the bottom-up factors (TP and DOC concentrations) played a more important role than top-down control (grazing by protists) in regulating bacterial numbers and activity. None of the single analyzed factors controlled bacterial abundance in the bottom waters. The results of this study suggest that both control mechanisms, bottom-up and top-down, simultaneously regulated bacterial community and their activity in the profundal zone of the studied lakes during spring. In both lake water layers, food availability (algae, nanoflagellates) was probably the major factor determining ciliate abundance and their composition. In the bottom waters, both groups of protists appeared to be also influenced by oxygen, temperature, and total phosphorus.
doi:10.1186/2046-9063-9-9
PMCID: PMC3626790  PMID: 23566491
Bacteria; Metabolic activity; Protists; Eutrophic lakes
16.  Kinetics of arsenite removal by halobacteria from a highland Andean Chilean Salar 
Aquatic Biosystems  2013;9:8.
Background
The purpose of this study was to identify arsenite-oxidizing halobacteria in samples obtained from Salar de Punta Negra, II Region of Chile. Seven bacterial isolates, numbered as isolates I to VII, grown in a culture medium with 100 ppm as NaAsO2 (As (III)) were tested. Bacterial growth kinetics and the percent of arsenite removal (PAR) were performed simultaneously with the detection of an arsenite oxidase enzyme through Dot Blot analysis.
Results
An arsenite oxidase enzyme was detected in all isolates, expressed constitutively after 10 generations grown in the absence of As (III). Bacterial growth kinetics and corresponding PAR values showed significant fluctuations over time. PARs close to 100% were shown by isolates V, VI, and VII, at different times of the bacterial growth phase; while isolate II showed PAR values around 40%, remaining constant over time.
Conclusion
Halobacteria from Salar de Punta Negra showed promising properties as arsenite removers under control conditions, incubation time being a critical parameter.
doi:10.1186/2046-9063-9-8
PMCID: PMC3616940  PMID: 23547876
Arsenic; Removal; Halobacteria; Arsenite-Oxidase
17.  Molecular identification of microorganisms associated with the brine shrimp Artemia franciscana 
Aquatic Biosystems  2013;9:7.
Background
Prior research on the microorganisms associated with the brine shrimp, Artemia franciscana, has mainly been limited to culture-based identification techniques or feeding studies for aquaculture. Our objective was to identify bacteria and archaea associated with Artemia adults and encysted embryos to understand the role of microbes in the Artemia life cycle and, therefore, their importance in a hypersaline food chain.
Results
We used small subunit (SSU) 16S ribosomal RNA gene sequencing to identify bacteria and archaea associated with adults and encysted Artemia embryos from one of their natural environments – Great Salt Lake (GSL), Utah, USA. We found that bacterial sequences most closely related to the genera Halomonas and Vibrio were commonly extracted from GSL adult Artemia, while bacterial sequences most similar to the genera Halomonas, Psychroflexus and Alkalilimnicola dominate in GSL water. Encysted embryos (cysts) yielded bacterial sequences from the genera Idiomarina and Salinivibrio, which were absent from adults and water. Common archaeal sequences in adults were most closely related to the genera Haloterrigena and Haloarcula, while all of the archaeal sequences from GSL water were most similar to the genus Halogeometricum. Cyst derived archaeal sequences were most closely related to the genera Halorubrum and Haloarcula.
Conclusions
In addition to identifying microbial rRNA sequences that are specific to different stages of the Artemia life cycle, we observed striking differences in the sequences associated with the adult Artemia population in samples collected from GSL at different times and locations. While our study was limited in scope and the sample was small, our findings provide a foundation for future research into how the bacteria and archaea associated with Artemia influence the Artemia life cycle, and GSL food web.
doi:10.1186/2046-9063-9-7
PMCID: PMC3599907  PMID: 23497541
18.  Effects of flow restoration on mussel growth in a Wild and Scenic North American River 
Aquatic Biosystems  2013;9:6.
Background
Freshwater mussels remain among the most imperiled species in North America due primarily to habitat loss or degradation. Understanding how mussels respond to habitat changes can improve conservation efforts. Mussels deposit rings in their shell in which age and growth information can be read, and thus used to evaluate how mussels respond to changes in habitat. However, discrepancies between methodological approaches to obtain life history information from growth rings has led to considerable uncertainty regarding the life history characteristics of many mussel species. In this study we compared two processing methods, internal and external ring examination, to obtain age and growth information of two populations of mussels in the St. Croix River, MN, and evaluated how mussel growth responded to changes in the operation of a hydroelectric dam.
Results
External ring counts consistently underestimated internal ring counts by 4 years. Despite this difference, internal and external growth patterns were consistent. In 2000, the hydroelectric dam switched from operating on a peaking schedule to run-of-the-river/partial peaking. Growth patterns between an upstream and downstream site of the dam were similar both before and after the change in operation. At the downstream site, however, older mussels had higher growth rates after the change in operation than the same sized mussels collected before the change.
Conclusions
Because growth patterns between internal and external processing methods were consistent, we suggest that external processing is an effective method to obtain growth information despite providing inaccurate age information. External processing is advantageous over internal processing due to its non-destructive nature. Applying this information to analyze the influence of the operation change in the hydroelectric dam, we suggest that changing to run-of-the-river/partial peaking operation has benefited the growth of older mussels below the dam.
doi:10.1186/2046-9063-9-6
PMCID: PMC3605298  PMID: 23452382
Unionidae; Annuli; Growth processing methods; Hydroelectric dam; Flow regulation
19.  The quantitative proteomic response of Synechocystis sp. PCC6803 to phosphate acclimation 
Aquatic Biosystems  2013;9:5.
Background
Inorganic phosphate (Pi) is a critical nutrient for all life and is periodically limiting in marine and freshwater provinces, yet little is understood how organisms acclimate to fluctuations in Pi within their environment. To investigate whole cell adaptation, we grew Synechocystis sp. PCC6803, a model freshwater cyanobacterium, in 3%, and 0.3% inorganic phosphate (Pi) media. The cells were allowed to acclimate over 60 days, and cells were harvested for quantitative high throughput mass spectrometry-based proteomics using the iTRAQ™ labelling technology.
Results
In total, 120 proteins were identified, and 52 proteins were considered differentially abundant compared to the control. Alkaline phosphatase (APase) activities correlated significantly (p < 0.05) with observed relative PhoA abundances. PstS1 and PstS2 were both observed, yet PstS1 was not differentially more abundant than the control. Phycobilisome protein abundances appeared to be coordinated, and are significantly less abundant in 0.3% Pi than 3% Pi cultures. Also, the central metabolic cell function appears to have shifted towards the production of (NADPH) reducing energy and nucleotide sugars.
Conclusions
This acclimation response bears strong similarity to the previously reported response to nitrogen deprivation within Synechocystis sp. PCC 6803. However, it also demonstrates some characteristics of desiccation stress, such as the regulation of fatty acids and increased abundance of rehydrin in the 3% Pi culture.
doi:10.1186/2046-9063-9-5
PMCID: PMC3600050  PMID: 23442353
Cyanobacteria; iTRAQ; Phosphate acclimation; Phycobilisome; Pentose phosphate pathway; Ribose sugars; Synechocystis
20.  Indo-Pacific bottlenose dolphin (Tursiops aduncus) habitat preference in a heterogeneous, urban, coastal environment 
Aquatic Biosystems  2013;9:3.
Background
Limited information is available regarding the habitat preference of the Indo-Pacific bottlenose dolphin (Tursiops aduncus) in South Australian estuarine environments. The need to overcome this paucity of information is crucial for management and conservation initiatives. This preliminary study investigates the space-time patterns of habitat preference by the Indo-Pacific bottlenose dolphin in the Port Adelaide River-Barker Inlet estuary, a South Australian, urbanised, coastal environment. More specifically, the study aim was to identify a potential preference between bare sand substrate and seagrass beds, the two habitat types present in this environment, through the resighting frequency of recognisable individual dolphins.
Results
Photo-identification surveys covering the 118 km2 sanctuary area were conducted over 2 survey periods May to August 2006 and from March 2009 to February 2010. Sighting frequency of recognisable individual Indo-Pacific bottlenose dolphins established a significant preference for the bare sand habitat. More specifically, 72 and 18% of the individuals sighted at least on two occasions were observed in the bare sand and seagrass habitats respectively. This trend was consistently observed at both seasonal and annual scales, suggesting a consistency in the distinct use of these two habitats.
Conclusions
It is anticipated that these results will benefit the further development of management and conservation strategies.
doi:10.1186/2046-9063-9-3
PMCID: PMC3574012  PMID: 23369354
Bottlenose dolphin; Conservation; estuaries; Photo-identification; Management; Habitat type
21.  Bacterial diversity of the rock-water interface in an East Antarctic freshwater ecosystem, Lake Tawani(P)† 
Aquatic Biosystems  2013;9:4.
Schirmacher Oasis is one of the few ice-free plateaus in East Antarctica that maintains a unique distribution of over 120 microbial-rich, dynamic freshwater lakes, most of which are unexplored. In this study, we describe the bacterial diversity of the rock-water interface in Lake Tawani(P) using culture-independent Bacterial Tag Encoded FLX Amplicon Pyrosequencing (bTEFAP), clone library construction, and culture-based analysis targeting the eubacterial 16S rRNA gene. Lake Tawani(P)was formed in a fossil valley by the accumulation of snow and glacial melt through surface channels into a low-catchment depression. Overall this lake exhibited thirteen bacterial phyla and one-hundred and twelve genera. The Qiime bioinformatics analysis on the bTEFAP alone exhibited higher coverage of the bacterial composition in Lake Tawani(P) than the clone library construction or culture-based methodology. Particularly due to the higher sensitivity of the bTEFAP approach, we detected and differentiated members of the phyla: Chloroflexi, Gemmatimonadetes, Planctomycetes, Nitrospira, and Candidate Division TM7 that other methods were unable to reveal. Nevertheless we found that the use of multiple approaches identified a more complete bacterial community than by using any single approach. Investigating the bacterial diversity of the Schirmacher Oasis lakes, especially those connected through surface channels and encompassed by valleys, will help unravel the dynamic nature of these unique seasonal, freshwater lakes, which potentially harbors highly adapted bacterial taxa with defined ecological functions.
doi:10.1186/2046-9063-9-4
PMCID: PMC3740781  PMID: 23369372
Culture-independent; Culture-dependent; Antarctic freshwater lake; 16S rRNA; bTEFAP; Pyrosequencing; Metagenomics
22.  Wastewater use in algae production for generation of renewable resources: a review and preliminary results 
Aquatic Biosystems  2013;9:2.
Microalgae feedstock production can be integrated with wastewater and industrial sources of carbon dioxide. This study reviews the literature on algae grown on wastewater and includes a preliminary analysis of algal production based on anaerobic digestion sludge centrate from the Howard F. Curren Advanced Wastewater Treatment Plant (HFC AWTP) in Tampa, Florida and secondary effluent from the City of Lakeland wastewater treatment facilities in Lakeland, Florida. It was demonstrated that a mixed culture of wild algae species could successfully be grown on wastewater nutrients and potentially scaled to commercial production. Algae have demonstrated the ability to naturally colonize low-nutrient effluent water in a wetland treatment system utilized by the City of Lakeland. The results from these experiments show that the algae grown in high strength wastewater from the HFC AWTP are light-limited when cultivated indoor since more than 50% of the outdoor illumination is attenuated in the greenhouse.
An analysis was performed to determine the mass of algae that can be supported by the wastewater nutrients (mainly nitrogen and phosphorous) available from the two Florida cities. The study was guided by the growth and productivity data obtained for algal growth in the photobioreactors in operation at the University of South Florida. In the analysis, nutrients and light are assumed to be limited, while CO2 is abundantly available. There is some limitation on land, especially since the HFC AWTP is located at the Port of Tampa. The temperature range in Tampa is assumed to be suitable for algal growth year round. Assuming that the numerous technical challenges to achieving commercial-scale algal production can be met, the results presented suggest that an excess of 71 metric tons per hectare per year of algal biomass can be produced. Two energy production options were considered; liquid biofuels from feedstock with high lipid content, and biogas generation from anaerobic digestion of algae biomass. The total potential oil volume was determined to be approximately 337,500 gallons per year, which may result in the annual production of 270,000 gallons of biodiesel when 80% conversion efficiency is assumed. This production level would be able to sustain approximately 450 cars per year on average. Potential biogas production was estimated to be above 415,000 kg/yr, the equivalent of powering close to 500 homes for a year.
doi:10.1186/2046-9063-9-2
PMCID: PMC3561657  PMID: 23289706
23.  Gene encoding prolactin in cinnamon clownfish Amphiprion melanopus and its expression upon acclimation to low salinities 
Aquatic Biosystems  2013;9:1.
Background
Prolactin (PRL) is a key hormone for osmoregulation in fish. Levels of PRL in the pituitary gland and plasma ion composition of clownfish seem to change to regulate their hydromineral balance during adaptation to waters of different salinities. In order to understand osmoregulatory mechanism and its association with growth performance and PRL in fish, the gene encoding PRL and its expression level in cinnamon clownfish Amphiprion melanopus upon acclimation to low salinity was analyzed.
Results
The PRL gene of A. melanopus encoded a protein of 212 amino acid residues comprised of a putative signal peptide of 24 amino acids and a mature protein of 188 amino acids. Analysis of growth performance under different salinities of 34, 25, 15, and 10 ppt indicated that cinnamon clownfish could survive under salinities as low as 10 ppt. A higher rate of growth was observed at the lower salinities as compared to that of 34 ppt. Upon shifting the salinity of the surrounding water from 34 ppt to 15 ppt, the level of the PRL transcripts gradually increased to reach the peak level until 24 h of acclimation at 15 ppt, but decreased back as adaptation continued to 144 h. In contrast, levels of plasma Na+, Cl-, and osmolality decreased at the initial stage (4–8 h) of acclimation at 15 pt but increased back as adaptation continued till 144 h.
Conclusion
Cinnamon clownfish could survive under salinities as low as 10 ppt. Upon shifting the salinity of the surrounding water from 34 ppt to 15 ppt, the level of the PRL transcripts gradually increased during the initial stage of acclimation but decreased back to the normal level as adaptation continued. An opposite pattern of changes - decrease at the beginning followed by an increase - in the levels of plasma Na+, Cl-, and osmolality was found upon acclimation to low salinity. The results suggest an involvement of PRL in the processes of osmoregulation and homeostasis in A. melanopus.
doi:10.1186/2046-9063-9-1
PMCID: PMC3562158  PMID: 23276106
Osmoregulation; Prolactin; Osmoregulation; Clownfish; Amphiprion melanopus
24.  Influence of zinc on the calcium carbonate biomineralization of Halomonas halophila 
Aquatic Biosystems  2012;8:31.
Background
The salt tolerance of halophilic bacteria make them promising candidates for technical applications, like isolation of salt tolerant enzymes or remediation of contaminated saline soils and waters. Furthermore, some halophilic bacteria synthesize inorganic solids resulting in organic–inorganic hybrids. This process is known as biomineralization, which is induced and/or controlled by the organism. The adaption of the soft and eco-friendly reaction conditions of this formation process to technical syntheses of inorganic nano materials is desirable. In addition, environmental contaminations can be entrapped in biomineralization products which facilitate the subsequent removal from waste waters. The moderately halophilic bacteria Halomonas halophila mineralize calcium carbonate in the calcite polymorph. The biomineralization process was investigated in the presence of zinc ions as a toxic model contaminant. In particular, the time course of the mineralization process and the influence of zinc on the mineralized inorganic materials have been focused in this study.
Results
H. halophila can adapt to zinc contaminated medium, maintaining the ability for biomineralization of calcium carbonate. Adapted cultures show only a low influence of zinc on the growth rate. In the time course of cultivation, zinc ions accumulated on the bacterial surface while the medium depleted in the zinc contamination. Intracellular zinc concentrations were below the detection limit, suggesting that zinc was mainly bound extracellular. Zinc ions influence the biomineralization process. In the presence of zinc, the polymorphs monohydrocalcite and vaterite were mineralized, instead of calcite which is synthesized in zinc-free medium.
Conclusions
We have demonstrated that the bacterial mineralization process can be influenced by zinc ions resulting in the modification of the synthesized calcium carbonate polymorph. In addition, the shape of the mineralized inorganic material is chancing through the presence of zinc ions. Furthermore, the moderately halophilic bacterium H. halophila can be applied for the decontamination of zinc from aqueous solutions.
doi:10.1186/2046-9063-8-31
PMCID: PMC3520789  PMID: 23198844
25.  Interactive effects of chemical and biological controls on food-web composition in saline prairie lakes 
Aquatic Biosystems  2012;8:29.
Salinity is restricting habitatability for many biota in prairie lakes due to limited physiological abilities to cope with increasing osmotic stress. Yet, it remains unclear how salinity effects vary among major taxonomic groups and what role other environmental parameters play in shaping food-web composition. To answer these questions, we sampled fish, zooplankton and littoral macroinvertebrates in 20 prairie lakes (Saskatchewan, Canada) characterized by large gradients in water chemistry and lake morphometry. We showed that salinity thresholds differed among major taxonomic groups, as most fishes were absent above salinities of 2 g L-1, while littoral macroinvertebrates were ubiquitous. Zooplankton occurred over the whole salinity range, but changed taxonomic composition as salinity increased. Subsequently, the complexity of fish community (diversity) was associated with large changes in invertebrate communities. The directional changes in invertebrate communities to smaller taxa indicated that complex fish assemblages resulted in higher predation pressure. Most likely, as the complexity of fish community decreased, controls of invertebrate assemblages shifted from predation to competition and ultimately to productivity in hypersaline lakes. Surprisingly, invertebrate predators did not thrive in the absence of fishes in these systems. Furthermore, the here identified salinity threshold for fishes was too low to be a result of osmotic stress. Hence, winterkill was likely an important factor eliminating fishes in low salinity lakes that had high productivity and shallow water depth. Ultimately, while salinity was crucial, intricate combinations of chemical and biological mechanisms also played a major role in controlling the assemblages of major taxonomic groups in prairie lakes.
doi:10.1186/2046-9063-8-29
PMCID: PMC3547742  PMID: 23186395
Lake food-web; Diversity; Fish; Invertebrates; Salinity; Winter kill

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