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1.  The effects of physicochemical variables and tadpole assemblages on microalgal communities in freshwater temporary ponds through an experimental approach 
Aquatic Biosystems  2015;11:1.
In freshwater systems, microalgae are the major biomass of microorganisms. They occur in ecosystems that are largely structured by the climatic regime, the physical and chemical environments with which they interact, and the biological interactions that occur within them. Amphibian larvae are most present in standing water habitats where they are important primary and secondary consumers and even predators. Studies conducted in America and Europe have shown that tadpoles play an important role in the regulation of the algal community structure and water quality in ecosystems. This article aimed to study the effects of the physicochemical variables and tadpole assemblages of four species on microalgae in artificial freshwater ponds using an experimental approach in the Pendjari area, a flora and fauna reserve located in the extreme north-west of Benin.
The species of phytoplankton and periphyton recorded in ponds were among the taxonomical groups of chlorophytes, cyanophytes, euglenophytes, diatoms and dinoflagellates. Chlorophytes were the dominant group in the algal communities. Physicochemical variables affected the biomass of the different communities of algae in temporary freshwater ponds. Transparency and pond size were the most determinative variables of the structure of microalgae communities in ponds. Tadpoles of Kassina fusca, Ptychadena. bibroni, and Phrynomantis microps were important for the regulation of the water quality and algal community structure by grazing and filter-feeding.
A decrease in the tadpole population in the artificial temporary ponds due to predation by carnivorous tadpoles of Hoplobatrachus occipitalis caused a disturbance of the algal community structure. This means that the decline of the amphibian population will critically lead to the impoverishment of ecosystems, thereby negatively influencing aquatic and terrestrial ecosystems.
PMCID: PMC4332427  PMID: 25694810
Microalgae; Phytoplankton; Periphyton; Physicochemical variables; Tadpoles assemblages; Experimental approach
2.  A histopathological and biometric comparison between catfish (Pisces, Ariidae) from a harbor and a protected area, Brazil 
Aquatic Biosystems  2014;10:12.
Histopathological lesions and biometric variations in catfish species are statistically associated with chemical contaminant exposure. A histopathological and biometric database for the catfish Sciades herzbergii and Bagre bagre from São Luís Island (Port Area) and Caranguejos Island (Reference Area) is presented. Branchial and hepatic lesions were classified into three reaction patterns: 1) circulatory or inflammatory disturbances; 2) regressive changes; 3) progressive changes. This paper summarizes research efforts aimed at characterizing the biomonitoring potential of catfish from two islands in Brazil, which exhibit great habitat diversity and different levels of human intervention.
The weights and lengths of the catfish caught at the Port Area were smaller than those from the Reference Area. No histopathological lesions were observed in S. herzbergii examined at the reference site (Caranguejos Island). In contrast, 90% of S. herzbergii from sites located in the Port Area (São Luís Island) had one or more types of branchial and hepatic lesions. One or more of the five lesions were observed on 16 B. bagre from São Luís Island and Caranguejos Island.
The utility of histopathological lesions and biometric data as sensitive indicators of the health of wild catfish populations has been demonstrated. Sciades herzbergii proved to be a better species for biomonitoring because it was more sensitive to the impacted site (Port Area) compared with the region relatively free of contaminants (Reference Area).
PMCID: PMC4273438  PMID: 25535566
Biomonitoring; Biomarkers; Sciades herzbergii; Bagre bagre
3.  Benthic infaunal community structuring in an acidified tropical estuarine system 
Aquatic Biosystems  2014;10:11.
Recent studies suggest that increasing ocean acidification (OA) should have strong direct and indirect influences on marine invertebrates. While most theory and application for OA is based on relatively physically-stable oceanic ecological systems, less is known about the effects of acidification on nearshore and estuarine systems. Here, we investigated the structuring of a benthic infaunal community in a tropical estuarine system, along a steep salinity and pH gradient, arising largely from acid-sulphate groundwater inflows (Sungai Brunei Estuary, Borneo, July 2011- June 2012).
Preliminary data indicate that sediment pore-water salinity (range: 8.07 - 29.6 psu) declined towards the mainland in correspondence with the above-sediment estuarine water salinity (range: 3.58 – 31.2 psu), whereas the pore-water pH (range: 6.47- 7.72) was generally lower and less variable than the estuarine water pH (range: 5.78- 8.3), along the estuary. Of the thirty six species (taxa) recorded, the polychaetes Neanthes sp., Onuphis conchylega, Nereididae sp. and the amphipod Corophiidae sp., were numerically dominant. Calcified microcrustaceans (e.g., Cyclopoida sp. and Corophiidae sp.) were abundant at all stations and there was no clear distinction in distribution pattern along the estuarine between calcified and non-calcified groups. Species richness increased seawards, though abundance (density) showed no distinct directional trend. Diversity indices were generally positively correlated (Spearman’s rank correlation) with salinity and pH (p <0.05) and negatively with clay and organic matter, except for evenness values (p >0.05). Three faunistic assemblages were distinguished: (1) nereid-cyclopoid-sabellid, (2) corophiid-capitellid and (3) onuphid- nereid-capitellid. These respectively associated with lower salinity/pH and a muddy bottom, low salinity/pH and a sandy bottom, and high salinity/pH and a sandy bottom. However, CCA suggested that species distribution and community structuring is more strongly influenced by sediment particle characteristics than by the chemical properties of the water (pH and salinity).
Infaunal estuarine communities, which are typically adapted to survive relatively acidic conditions, may be less exposed, less sensitive, and less vulnerable than epibenthic or pelagic communities to further acidification of above-sediment waters. These data question the extent to which all marine infaunal communities, including oceanic communities, are likely to be affected by future global CO2-driven acidification.
PMCID: PMC4229668  PMID: 25396048
Community structure; Infauna; Soft-bottom; Tropical estuary; Salinity; Acidification
4.  Molecular analysis of bacterial diversity in mudflats along the salinity gradient of an acidified tropical Bornean estuary (South East Asia) 
Aquatic Biosystems  2014;10:10.
The Brunei River and Bay estuarine system (BES) in the northwest of Borneo is acidic and highly turbid. The system supports extensive intertidal mudflats and presents a potentially steep salinity and pH gradient along its length (45 km). Temporal variation in physical parameters is observed diurnally due to seawater flux during tidal forcing, and stochastically due to elevated freshwater inflow after rains, resulting in a salinity range between 0 and 34 psu. High velocity freshwater run-off from acid sulphate formations during monsoon seasons results in highly variable and acidic conditions (pH 4) at the upper reaches of the BES, whereas the pH is relatively stable (pH 8) at the seaward extremes, due to mixing with seawater from the South China Sea. At their surfaces, the BES mudflats present microbial ecosystems driven by oxygenic phototrophs. To study the effect of various physical parameters on the bacterial diversity of the BES mudflats, surface samples were collected from six sites stretching over 40 km for molecular and phylogentic analysis.
The bacterial diversity at these sites was compared by community fingerprinting analysis using 16S rRNA gene based denaturing gradient gel electrophoresis and by 16S rRNA gene sequencing and phylogenetic analyses. Results revealed functionally conserved, diatom-driven microbial mudflat communities composed of mainly novel, uncultured species. Species composition was evaluated as 50-70% unique for each site along the BES. Clustering of the sequences commonly occurred and revealed that proteobacterial diversity was related to the salinity gradient. When considering all phyla, the diversity varied consistently with physical parameters (including anthropogenic) that are expected to influence microbial composition.
The BES mudflats were found to comprise the typical functional groups of microorganisms associated with photosynthetic carbon flux, sulfur cycling (Gamma- and Deltaproteobacteria), and decomposition (Bacteroidetes). From a structural perspective, however, the mudflats constituted discretely distributed communities along the physical gradient of the BES, composed of largely novel species of Bacteria. This study provides first insights into patterns of bacterial community structure in tropical South East Asian coastal ecosystems that are potentially threatened by increasing variability in pH and salinity, in line with predicted future environmental change.
PMCID: PMC4229359  PMID: 25392733
Marine Environmental Research; Borneo; Brunei; Mudflats; Acid sulfide; 16S rRNA; Bacterial diversity; Microbial mats
5.  In silico analysis of high affinity potassium transporter (HKT) isoforms in different plants 
Aquatic Biosystems  2014;10:9.
High affinity potassium transporters (HKTs) are located in the plasma membrane of the vessels and have significant influence on salt tolerance in some plants. They exclude Na+ from the parenchyma cells to reduce Na+ concentration. Despite many studies, the underlying regulatory mechanisms and the exact functions of HKTs within different genomic backgrounds are relatively unknown. In this study, various bioinformatics techniques, including promoter analysis, identification of HKT-surrounding genes, and construction of gene networks, were applied to investigate the HKT regulatory mechanism.
Promoter analysis showed that rice HKTs carry ABA response elements. Additionally, jasmonic acid response elements were detected on promoter region of TmHKT1;5. In silico synteny highlighted several unknown and new loci near rice, Arabidopsis thaliana and Physcomitrella patent HKTs, which may play a significant role in salt stress tolerance in concert with HKTs. Gene network prediction unravelled that crosstalk between jasmonate and ethylene reduces AtHKT1;1 expression. Furthermore, antiporter and transferase proteins were found in AtHKT1;1 gene network. Interestingly, regulatory elements on the promoter region of HKT in wild genotype (TmHKT1;5) were more frequent and variable than the ones in cultivated wheat (TaHKT1;5) which provides the possibility of rapid response and better understanding of environmental conditions for wild genotype.
Detecting ABA and jasmonic acid response elements on promoter regions of HKTs provide valuable clues on underlying regulatory mechanisms of HKTs. In silico synteny and pathway discovery indicated several candidates which act in concert with HKTs in stress condition. We highlighted different arrangement of regulatory elements on promoter region of wild wheat (TmHKT1;5) compared to bread wheat (TaHKT1;5) in this study.
PMCID: PMC4181754  PMID: 25279141
HKT; Gene network; Promoter; Regulatory elements; In silico synteny; Pathway discovery
6.  Assessing environmental impacts of offshore wind farms: lessons learned and recommendations for the future 
Aquatic Biosystems  2014;10:8.
Offshore wind power provides a valuable source of renewable energy that can help reduce carbon emissions. Technological advances are allowing higher capacity turbines to be installed and in deeper water, but there is still much that is unknown about the effects on the environment. Here we describe the lessons learned based on the recent literature and our experience with assessing impacts of offshore wind developments on marine mammals and seabirds, and make recommendations for future monitoring and assessment as interest in offshore wind energy grows around the world. The four key lessons learned that we discuss are: 1) Identifying the area over which biological effects may occur to inform baseline data collection and determining the connectivity between key populations and proposed wind energy sites, 2) The need to put impacts into a population level context to determine whether they are biologically significant, 3) Measuring responses to wind farm construction and operation to determine disturbance effects and avoidance responses, and 4) Learn from other industries to inform risk assessments and the effectiveness of mitigation measures. As the number and size of offshore wind developments increases, there will be a growing need to consider the population level consequences and cumulative impacts of these activities on marine species. Strategically targeted data collection and modeling aimed at answering questions for the consenting process will also allow regulators to make decisions based on the best available information, and achieve a balance between climate change targets and environmental legislation.
PMCID: PMC4172316  PMID: 25250175
Marine mammals; Seabirds; Wind turbine; Underwater noise; Collision risk; Human impacts; Cumulative impact assessment; Population consequences
7.  Molecular phylogenetic analysis of bacterial community and characterization of Cr(VI) reducers from the sediments of Tantloi hot spring, India 
Aquatic Biosystems  2014;10:7.
A geothermal ecosystem located at Tantloi, India has been found to be an interesting habitat for microbes of diverse nature. However, the microbial diversity of this habitat is poorly explored. In this study, a detailed phylogenetic study has been carried out to understand the bacterial diversity of this habitat and to identify prospective metal reducers using culture independent approach. The bacterial diversity of the sediments, which contain undetectable levels of Cr(VI), was analysed with respect to chromium reduction and the strains highly resistant to and efficiently reducing chromium under aerobic conditions were isolated and characterized.
16S rRNA gene sequence analysis of Tantloi hot spring microbial community revealed a significant bacterial diversity represented by at least ten taxonomic divisions of Bacteria with clear predominance of Thermus. Similar sequence analysis of rRNA gene library clones derived from bacterial consortia enriched from sediments in presence of Cr(VI) revealed the abundance of the family Bacillaceae. Under aerobic conditions at 65°C, the consortia reduced 1 mM of Cr(VI) completely within 24 h and 5 mM in 6 days. A complete reduction of 1 mM Cr(VI) has been shown by five of our isolates within 36 h. 16S rRNA gene sequences of all the isolates showed high degree of similarity (97-99%) to Bacillaceae with ten of them being affiliated to Anoxybacillus. Crude extract as well as the soluble fraction from isolates TSB-1 and TSB-9 readily reduced Cr(VI); TSB-1 showed higher chromium reductase activity.
Most of the Tantloi Spring Bacterial (TSB) sequences analyzed in different taxonomic divisions could be related to representatives with known metabolic traits which indicated presence of organisms involved in redox processes of a variety of elements including iron, sulphur and chromium. Approximately 80% of the sequences obtained in this study represented novel phylotypes indicating the possibility of discovery of bacteria with biotechnologically important new biomolecules. Again, highly chromium-resistant and remarkably active Cr(VI)-reducing Anoxybacillus strains isolated in this study could serve as potential candidates for designing chromium bioremediation strategies at high temperatures and also at high chromium concentrations.
PMCID: PMC4168125  PMID: 25243065
Phylogenetic analysis; Bacterial community; Hot spring; Chromium reduction; Bioremediation
8.  The Manx shearwater (Puffinus puffinus) as a candidate sentinel of Atlantic Ocean health 
Aquatic Biosystems  2014;10:6.
Seabirds have been historically used to monitor environmental contamination. The aim of the present study was to test the suitability of a species belonging to the Procellariiformes group, the Manx shearwater, Puffinus puffinus, as a sentinel of environmental health, by determining contaminant levels (trace metals and organochlorine compounds) from carcass tissues and by isolating Vibrio spp. and Aeromonas spp. from live specimens. To this end, 35 Puffinus puffinus carcasses wrecked on the north-central coast of the state of Rio de Janeiro, Brazil, and two carcasses recovered in Aracruz, on the coast of the state of Espírito Santo, Brazil, were sampled, and fragments of muscle and hepatic tissues were collected for contaminant analyses. Swabs from eleven birds found alive at the north-central coast of Rio de Janeiro were collected for isolation of the aforementioned bacteria.
The average concentration in dry weight (dw) of the trace metals were: mercury 7.19 mg kg-1(liver) and 1.23 mg kg-1 (muscle); selenium 34.66 mg kg-1 (liver) and 7.98 mg kg-1 (muscle); cadmium 22.33 mg kg-1 (liver) and 1.11 mg kg-1 (muscle); and lead, 0.1 mg kg--1 (liver) and 0.16 mg kg-1 (muscle). Organochlorine compounds were detected in all specimens, and hexachlorbiphenyls, heptachlorbiphenyls and DDTs presented the highest levels. Regarding microbiological contamination, bacteria from the Vibrio genus were isolated from 91% of the analyzed specimens. Vibrio harveyi was the predominant species. Bacteria from the Aeromonas genus were isolated from 18% of the specimens. Aeromonas sobria was the only identified species.
The results indicate that Puffinus puffinus seems to be a competent ocean health sentinel. Therefore, the monitoring of contaminant levels and the isolation of public health interest bacteria should proceed in order to consolidate this species importance as a sentinel.
PMCID: PMC4154383  PMID: 25191536
Puffinus puffinus; Brazil; Sentinel; Metal; Organochlorines; Vibrio; Aeromonas
9.  Analysis of β-N-methylamino-L-alanine (BMAA) in spirulina-containing supplements by liquid chromatography-tandem mass spectrometry 
Aquatic Biosystems  2014;10:5.
Over the last decade the amino acid beta-N-methylamino-L-alanine (BMAA) has come under intense scrutiny. International laboratory and epidemiological research continues to support the hypothesis that environmental exposure to BMAA (e.g., through dietary practices, water supply) can promote the risk of various neurodegenerative diseases. A wide variety of cyanobacteria spp. have previously been reported to produce BMAA, with production levels dependent upon species, strain and environmental conditions. Since spirulina (Arthrospira spp.) is a member of the cyanobacteria phylum frequently consumed via dietary supplements, the presence of BMAA in such products may have public health implications. In the current work, we have analyzed ten spirulina-containing samples for the presence of BMAA; six pure spirulina samples from two separate raw materials suppliers, and four commercially-available multi-ingredient products containing 1.45 g of spirulina per 8.5 g serving. Because of controversy surrounding the measurement of BMAA, we have used two complementary liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods: one based on reversed phase LC (RPLC) with derivatization and the other based on hydrophilic interaction LC (HILIC). Potential matrix effects were corrected for by internal standardization using a stable isotope labeled BMAA standard. BMAA was not detected at low limits of detection (80 ng/g dry weight) in any of these product samples. Although these results are reassuring, BMAA analyses should be conducted on a wider sample selection and, perhaps, as part of ongoing spirulina production quality control testing and specifications.
PMCID: PMC4130116  PMID: 25120905
Spirulina; Dietary supplements; BMAA; β-N-methylamino-L-alanine; Food chain
10.  Efficient conversion of solar energy to biomass and electricity 
Aquatic Biosystems  2014;10:4.
The Earth receives around 1000 W.m−2 of power from the Sun and only a fraction of this light energy is able to be converted to biomass (chemical energy) via the process of photosynthesis. Out of all photosynthetic organisms, microalgae, due to their fast growth rates and their ability to grow on non-arable land using saline water, have been identified as potential source of raw material for chemical energy production. Electrical energy can also be produced from this same solar resource via the use of photovoltaic modules. In this work we propose a novel method of combining both of these energy production processes to make full utilisation of the solar spectrum and increase the productivity of light-limited microalgae systems. These two methods of energy production would appear to compete for use of the same energy resource (sunlight) to produce either chemical or electrical energy. However, some groups of microalgae (i.e. Chlorophyta) only require the blue and red portions of the spectrum whereas photovoltaic devices can absorb strongly over the full range of visible light. This suggests that a combination of the two energy production systems would allow for a full utilization of the solar spectrum allowing both the production of chemical and electrical energy from the one facility making efficient use of available land and solar energy. In this work we propose to introduce a filter above the algae culture to modify the spectrum of light received by the algae and redirect parts of the spectrum to generate electricity. The electrical energy generated by this approach can then be directed to running ancillary systems or producing extra illumination for the growth of microalgae. We have modelled an approach whereby the productivity of light-limited microalgae systems can be improved by at least 4% through using an LED array to increase the total amount of illumination on the microalgae culture.
PMCID: PMC4062565  PMID: 24976951
Solar energy; Biofuel; Photovoltaics; Microalgae; Renewable
11.  Interactions of marine mammals and birds with offshore membrane enclosures for growing algae (OMEGA) 
Aquatic Biosystems  2014;10:3.
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.
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.
Otter and bird interactions with experimental PBRs were benign. Large-scale OMEGA systems are predicted to have both positive and negative environmental consequences.
PMCID: PMC4049508  PMID: 24955238
Biofuels; Wastewater treatment; Photobioreactors; Renewable energy; Marine mammals; Birds; Sea otter; Gulls; Monterey Bay
12.  Molecular (PCR-DGGE) versus morphological approach: analysis of taxonomic composition of potentially toxic cyanobacteria in freshwater lakes 
Aquatic Biosystems  2014;10:2.
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 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.
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.
PMCID: PMC3925352  PMID: 24517495
Cyanobacteria; DGGE; ITS; mcy genes; Microcystins; Microscopic analysis
13.  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.
PMCID: PMC3896783  PMID: 24433368
14.  High throughput screening of CO2-tolerating microalgae using GasPak bags 
Aquatic Biosystems  2013;9:23.
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.
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.
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.
PMCID: PMC3914841  PMID: 24341988
CO2 sequestration; Microalgae; High through-put selection
15.  Detritus-based assemblage responses under salinity stress conditions in a disused aquatic artificial ecosystem 
Aquatic Biosystems  2013;9:22.
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.
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.
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.
PMCID: PMC4028869  PMID: 24308820
Leaf-detritus; Macrozoobenthos; Abundance/Biomass Comparisons; Whittaker plots; Simpson index; Nestedness; Patchy environment
16.  Use of vital wheat gluten in aquaculture feeds 
Aquatic Biosystems  2013;9:21.
In aquaculture, when alternative protein sources of Fish Meal (FM) in diets are investigated, Plant Proteins (PP) can be used. Among them, Vital Wheat Gluten (VWG) is a proteinaceous material obtained from wheat after starch extraction. “It is mainly composed of two types of proteins, gliadins and glutenins, which confer specific visco-elasticity that’s to say ability to form a network providing suitable binding. This will lead to specific technological properties that are notably relevant to extruded feeds”. Besides these properties, VWG is a high-protein ingredient with an interesting amino-acid profile. Whereas it is rather low in lysine, it contains more sulfur amino acids than other PP sources and it is high in glutamine, which is known to improve gut health and modulate immunity. VWG is a protein source with one of the highest nitrogen digestibility due to a lack of protease inhibitor activity and to the lenient process used to make the product. By this way, addition of VWG in diet does not adversely affect growth performance in many fish species, even at a high level, and may secure high PP level diets that can induce health damages.
PMCID: PMC3833847  PMID: 24237766
Vital wheat gluten; Fish; Protein; Digestibility; Performance; Health
17.  Infaunal macrobenthic community dynamics in a manipulated hyperhaline ecosystem: a long-term study 
Aquatic Biosystems  2013;9:20.
Understanding the responses of ecological communities to human-induced perturbations is crucial for establishing conservation goals. Ecological communities are dynamic entities undergoing fluctuations due to their intrinsic characteristics as well as anthropogenic pressures varying over time. In this respect, long-term studies, based on large spatial and temporal datasets, may provide useful information in understanding patterns and processes influencing the communities’ structure. Theoretical evidence suggests that a role of biodiversity is acting as a compensatory buffer against environmental variability by decreasing the temporal variance in ecosystem functioning and by raising the level of community response to perturbations through the selection of better performing species. Therefore, the spatial and temporal changes in the specialization of the community components may be used as an effective tool to monitor the effects of natural and anthropogenic alterations of the environment in dynamic systems. We examined the temporal dynamics of macroinvertebrate community structure in the hyperhaline habitat of Tarquinia Saltworks (central Italy). We aimed at: (i) investigating the relationships between the level of community specialization and the alterations of the environment across fourteen years; (ii) comparing the ability of aggregate community parameters such as the average abundance vs. species specialization in describing patterns of community composition.
We arranged the data in three sub-sets according to three periods, each characterized by different environmental conditions. The mean abundance of sampled macroinvertebrates showed a significant change (p < 0.01) only in the community inhabiting the saltwork basin closely connected to the sea, characterized by the highest environmental variation (i.e. the coefficient of variation, CV, of the aggregate environmental variability over the study period, CVrange = 0.010 - 0.2). Here we found marine species like Modiolus adriaticus (Lamarck, 1819), Neanthes irrorata (Malmgren, 1867), and Amphiglena mediterranea (Leydig, 1851), which inhabited the saltworks during the halt period but disappeared during the subsequent eutrophication phase. Conversely, species specialization showed a significant decrease for each sampled community in the presence of habitat degradation and a recovery after ecological restoration. The widest fluctuations of specialization were recorded for the community inhabiting the saltwork basin with the highest long-term environmental variability.
Recent advances have shown how the increased temporal and spatial variability of species’ abundance within the communities may be a signal of habitat disturbance, even in the absence of an apparent decline. Such approach could also be used as a sensitive monitoring tool, able to detect whether or not communities are subjected to increasing biotic homogenization. Also, the increased functional similarity triggered by habitat degradation may impact on species at higher trophic levels, such as the waterbirds wintering in the area or using it as a stopover during migration.
PMCID: PMC4175097  PMID: 24192133
Hyperhaline habitat; Wetlands; Central Tyrrhenian Sea; Biomonitoring; Macroinvertebrates community; Long-term study; Species specialization index; Biodiversity homogenization
18.  Microbial community composition of Tirez lagoon (Spain), a highly sulfated athalassohaline environment 
Aquatic Biosystems  2013;9:19.
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.
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).
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.
PMCID: PMC3852488  PMID: 24083554
19.  The structure of winter phytoplankton in Lake Nero, Russia, a hypertrophic lake dominated by Planktothrix-like Cyanobacteria 
Aquatic Biosystems  2013;9:18.
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.
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.
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.
PMCID: PMC3849563  PMID: 24079446
20.  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.
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.
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.
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.
PMCID: PMC3765856  PMID: 23981583
SRB; Cariaco Basin; Desulfovibrio; Vibrio; DGGE; Culture
21.  Diversity of picoeukaryotes at an oligotrophic site off the Northeastern Red Sea Coast 
Aquatic Biosystems  2013;9:16.
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.
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.
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.
PMCID: PMC3766091  PMID: 23962380
Picoeukaryotes; Red sea; Protists; SSU rRNA; Microbial diversity
22.  The distribution and diversity of benthic macroinvertebrate fauna in Pondicherry mangroves, India 
Aquatic Biosystems  2013;9:15.
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.
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.
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.
PMCID: PMC3751066  PMID: 23937801
Density; Diversity; Mangroves; Benthic macroinvertebrate fauna; Seasonal variation
23.  Cyanobacteria in wetlands of the industrialized Sambalpur District of India 
Aquatic Biosystems  2013;9:14.
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.
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.
PMCID: PMC3735473  PMID: 23845058
Wetlands; Cyanobacteria; Eutrophication; Industrialization; Pollution
24.  A commentary on the XIIIth International Rotifer Symposium (Shillong, 2012) 
Aquatic Biosystems  2013;9:13.
Rotifers have attracted the attention of biologists for well over 200 years. Interest in these exquisite animals rests in their diverse morphology, short generation time resulting in high growth rates, ability to withstand desiccation, and wide distribution, coupled with evidence of cryptic speciation. Moreover, three modes of reproduction are present in the phylum: obligatory sexuality, cyclical parthenogenesis, and obligatory ameiotic parthenogenesis. Thus, this phylum offers a rich field of study. Recognizing the need to share advances in knowledge, a triennial meeting, the International Rotifer Symposium (IRS), was begun in 1976. The most recent symposium (13th IRS) was held at Shillong (India) from 18–24, November 2012. In this commentary we considered the development of rotifer research as viewed through the lens of more than 35 years of IRS. Initially papers presented at the IRS focused on ecology, morphology, and pure taxonomic problems, with little applied work being reported. However, after more than three decades, the emphasis has swung to a balance of both basic (e.g., aging, ecology, genetics, and taxonomy) and applied (aquaculture and ecotoxicology) research.
PMCID: PMC3707760  PMID: 23816315
Aging; Aquaculture; Cryptic speciation; Ecology; Ecotoxicology; Genetics; Taxonomy
25.  Optimization of bacteriocin production by Lactobacillus sp. MSU3IR against shrimp bacterial pathogens 
Aquatic Biosystems  2013;9:12.
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.
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.
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.
PMCID: PMC3679972  PMID: 23725298
Aquaculture; Bacteriocin; Lactobacillus; Probiotics; Shrimp pathogens

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