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1.  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
2.  Community solar salt production in Goa, India 
Aquatic Biosystems  2012;8:30.
Traditional salt farming in Goa, India has been practised for the past 1,500 years by a few communities. Goa’s riverine estuaries, easy access to sea water and favourable climatic conditions makes salt production attractive during summer. Salt produced through this natural evaporation process also played an important role in the economy of Goa even during the Portuguese rule as salt was the chief export commodity. In the past there were 36 villages involved in salt production, which is now reduced to 9. Low income, lack of skilled labour, competition from industrially produced salt, losses incurred on the yearly damage of embankments are the major reasons responsible for the reduction in the number of salt pans.
Salt pans (Mithagar or Mithache agor) form a part of the reclaimed waterlogged khazan lands, which are also utilised for aquaculture, pisciculture and agriculture. Salt pans in Goa experience three phases namely, the ceased phase during monsoon period of June to October, preparatory phase from December to January, and salt harvesting phase, from February to June. After the monsoons, the salt pans are prepared manually for salt production. During high tide, an influx of sea water occurs, which enters the reservoir pans through sluice gates. The sea water after 1–2 days on attaining a salinity of approximately 5ºBé, is released into the evaporator pans and kept till it attains a salinity of 23 - 25ºBé. The brine is then released to crystallizer pans, where the salt crystallises out 25 - 27ºBé and is then harvested.
Salt pans form a unique ecosystem where succession of different organisms with varying environmental conditions occurs. Organisms ranging from bacteria, archaea to fungi, algae, etc., are known to colonise salt pans and may influence the quality of salt produced.
The aim of this review is to describe salt farming in Goa’s history, importance of salt production as a community activity, traditional method of salt production and the biota associated with salt pans.
doi:10.1186/2046-9063-8-30
PMCID: PMC3543363  PMID: 23198813
Salt pan; Goa; Estuary; Community; Khazan; Tidal influx; India; Salt production
3.  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
4.  The seasonal distribution, diel vertical distribution and feeding behavior of Paraeuchaeta concinna in the shallow subtropical coastal waters of eastern Hong Kong 
Aquatic Biosystems  2012;8:28.
Background
Predatory copepods of the family Euchaetidae are widely distributed in polar, temperate, subtropical and tropical oceans. Paraeuchaeta concinna is the most abundant Euchaetidae in the subtropical coastal seas of Hong Kong and southern China. However, compared to Euchaetidae species in temperate and polar regions, relatively little information is available on the ecology of P. concinna and other Euchaetidae species in the subtropical oceans. This paper provides information on the seasonal abundance of P. concinna in the coastal seas of eastern Hong Kong. The diel vertical distribution of P. concinna, feeding behavior, and predation impact on mesozooplankton in eastern Hong Kong were also investigated.
Results
P. concinna is most abundant in winter and spring. Their abundance decreases shoreward, and densities are generally higher in the open waters of eastern Hong Kong than in the inner parts of Mirs Bay and Tolo Harbour. P. concinna exhibits both diel vertical migration and diel feeding rhythms in Mirs Bay. P. concinna females show strong preference for the copepods of the genera Acrocalanus, Paracalanus, and Parvocalanus, and remove ~4% of their standing stocks daily.
Conclusions
The low abundance of P. concinna during most of the year suggests it is not indigenous to coastal seas of eastern Hong Kong. P. concinna performs diel vertical migration, most likely as a strategy to avoid visual predation. Gut content analysis showed that Acrocalanus, Paracalanus, and Parvocalanus are highly preferred prey of P. concinna. A daily predation impact of ~4% of the standing stocks of Acrocalanus, Paracalanus, and Parvocalanus suggests that P. concinna may play an important role in regulating the populations of these small copepods in Mirs Bay, especially during winter and spring.
doi:10.1186/2046-9063-8-28
PMCID: PMC3543307  PMID: 23127140
Paraeuchaeta concinna; Seasonal distribution; Diel vertical migration; Feeding
5.  Phenotypic and genetic characterization of Dunaliella (Chlorophyta) from Indian salinas and their diversity 
Aquatic Biosystems  2012;8:27.
Background
The genus Dunaliella (Class – Chlorophyceae) is widely studied for its tolerance to extreme habitat conditions, physiological aspects and many biotechnological applications, such as a source of carotenoids and many other bioactive compounds. Biochemical and molecular characterization is very much essential to fully explore the properties and possibilities of the new isolates of Dunaliella. In India, hyper saline lakes and salt pans were reported to bloom with Dunaliella spp. However, except for the economically important D. salina, other species are rarely characterized taxonomically from India. Present study was conducted to describe Dunaliella strains from Indian salinas using a combined morphological, physiological and molecular approach with an aim to have a better understanding on the taxonomy and diversity of this genus from India.
Results
Comparative phenotypic and genetic studies revealed high level of diversity within the Indian Dunaliella isolates. Species level identification using morphological characteristics clearly delineated two strains of D. salina with considerable β-carotene content (>20 pg/cell). The variation in 18S rRNA gene size, amplified with MA1-MA2 primers, ranged between ~1800 and ~2650 base pairs, and together with the phylogeny based on ITS gene sequence provided a pattern, forming five different groups within Indian Dunaliella isolates. Superficial congruency was observed between ITS and rbcL gene phylogenetic trees with consistent formation of major clades separating Indian isolates into two distinct clusters, one with D. salina and allied strains, and another one with D. viridis and allied strains. Further in both the trees, few isolates showed high level of genetic divergence than reported previously for Dunaliella spp. This indicates the scope of more numbers of clearly defined/unidentified species/sub-species within Indian Dunaliella isolates.
Conclusion
Present work illustrates Indian Dunaliella strains phenotypically and genetically, and confirms the presence of not less than five different species (or sub-species) in Indian saline waters, including D. salina and D. viridis. The study emphasizes the need for a combined morphological, physiological and molecular approach in the taxonomic studies of Dunaliella.
doi:10.1186/2046-9063-8-27
PMCID: PMC3598838  PMID: 23114277
Dunaliella; Diversity; India; 18S rDNA; ITS; rbcL gene
6.  Physicochemical and biological factors controlling water column metabolism in Sundarbans estuary, India 
Aquatic Biosystems  2012;8:26.
Background
Sundarbans is the single largest deltaic mangrove forest in the world, formed at estuarine phase of the Ganges - Brahmaputra river system. Primary productivity of marine and coastal phytoplankton contributes to 15% of global oceanic production. But unfortunately estuarine dynamics of tropical and subtropical estuaries have not yet received proper attention in spite of the fact that they experience considerable anthropogenic interventions and a baseline data is required for any future comparison. This study is an endeavor to this end to estimate the primary productivity (gross and net), community respiration and nitrification rates in different rivers and tidal creeks around Jharkhali island, a part of Sundarbans estuary surrounded by the mangrove forest during a period of three years starting from November’08 to October’11.
Results
Various physical and chemical parameters of water column like pH, temperature, conductivity, dissolved oxygen, turbidity, suspended particulate matter, secchi disc index, tidal fluctuation and tidal current velocity, standing crop and nutrients were measured along with water column productivity. Relationship of net water column productivity with algal biomass (standing crop), nutrient loading and turbidity were determined experimentally. Correlations of bacterial abundance with community respiration and nitrification rates were also explored. Annual integrated phytoplankton production rate of this tidal estuary was estimated to be 151.07 gC m-2 y-1. Gross primary productivity showed marked inter annual variation being lowest in monsoon and highest in postmonsoon period.
Conclusion
Average primary production was a function of nutrient loading and light penetration in the water column. High aquatic turbidity, conductivity and suspended particulate matter were the limiting factors to attenuate light penetration with negative influence on primary production. Community respiration and nitrification rates of the estuary were influenced by the bacterial abundance. The estuary was phosphorus limited in postmonsoon whereas nitrogen-limited in premonsoon and monsoon period. High algal biomass and primary productivity indicated the estuary to be in eutrophic state in most of the time throughout the year. Our study also indicated a seasonal shifting between autotrophic and heterotrophic conditions in Sundarban estuarine ecosystem and it is a tropical, well mixed (high tidal influx) and marine dominated (no fresh water connection) system.
doi:10.1186/2046-9063-8-26
PMCID: PMC3543332  PMID: 23083531
Net ecosystem metabolism; Gross primary productivity; Community respiration; Nitrification; Nutrient load; Sundarban estuary
7.  A revision of Artemia biodiversity in Macaronesia 
Aquatic Biosystems  2012;8:25.
In a biogeographical context, the term Macaronesia broadly embraces the North Atlantic archipelagos of the Azores, Madeira, Selvagens, the Canary Islands, and Cape Verde. The peculiar arid climatic conditions in some of these places have led to the development of marine salt exploitations, which can be counted among the hypersaline habitats of the brine shrimp Artemia (Branchiopoda, Anostraca). Parthenogenetic populations of this anostracan were described in the Canary Islands during the last decades of the 20th century, while the American Artemia franciscana species was recently found in the Cape Verde archipelago. Following an invasive pattern, this exotic species has recently reached the Canary Islands, too. This paper reports information dealing with biotope loss (solar saltworks) in this biogeographical region, together with possible consequences concerning the arrival of invasive species, two factors that frequently promote dramatic biodiversity losses. The discussion of this threat focuses mainly on the Canary Islands archipelago where native species of Artemia still exist.
doi:10.1186/2046-9063-8-25
PMCID: PMC3543279  PMID: 23075404
Artemia; Biodiversity; Macaronesia; Saltworks; Loss of habitats; Invasion
8.  Hematodinium sp. and its bacteria-like endosymbiont in European brown shrimp (Crangon crangon) 
Aquatic Biosystems  2012;8:24.
Background
Parasitic dinoflagellates of the genus Hematodinium are significant pathogens affecting the global decapod crustacean fishery. Despite this, considerable knowledge gaps exist regarding the life history of the pathogen in vivo, and the role of free living life stages in transmission to naïve hosts.
Results
In this study, we describe a novel disease in European brown shrimp (Crangon crangon) caused by infection with a parasitic dinoflagellate of the genus Hematodinium. This is the second example host within the Infraorder Caridea (shrimp) and significantly, the first description within the superfamily Crangonoidea. Based upon analysis of the rRNA gene (SSU) and spacers (ITS1), the parasite in C. crangon is the same as that previously described infecting Nephrops norvegicus and Cancer pagurus from European seas, and to the parasite infecting several other commercially important crab species in the Northern Hemisphere. The parasite is however distinct from the type species, H. perezi, found infecting type hosts (Carcinus maenas and Liocarcinus depurator) from nearby sites within Europe. Despite these similarities, the current study has also described for the first time, a bacteria-like endosymbiont within dinospore stages of the parasite infecting shrimp. The endosymbionts were either contained individually within electron lucent vacuoles within the parasite cell cytoplasm, or remained in direct contact with the parasite cytoplasm or in some cases, the nucleoplasm. In all of these cases, no apparent detrimental effects of colonization were observed within the parasite cell.
Conclusions
The presence of bacteria-like endosymbionts within dinospore life stages presumes that the relationship between the dinoflagellate and the bacteria is extended beyond the period of liberation of spores from the infected host shrimp. In this context, a potential role of endosymbiosis in the survival of free-living stages of the parasite is possible. The finding offers a further intriguing insight into the life history of this enigmatic pathogen of marine crustacean hosts and highlights a potential for mixotrophy in the parasitic dinoflagellates contained within the genus Hematodinium.
doi:10.1186/2046-9063-8-24
PMCID: PMC3487949  PMID: 22958655
ITS1; Phylogenetics; Dinoflagellate; Bacteria; Crustacean; Disease; Fishery
9.  Phylogenetic diversity of actinomycetes cultured from coastal multipond solar saltern in Tuticorin, India 
Aquatic Biosystems  2012;8:23.
Background
Hypersaline solar salterns are extreme environments in many tropical and subtropical regions throughout the world. In India, there are several coastal solar salterns along with the coastal line of the Bay of Bengal and Arabian Sea and inland solar salterns around Sambhar saltlake, from which sodium chloride is obtained for human consumption and industrial needs. Studies on characterization of such coastal and inland solar salterns are scarce and both the bacterial and archaeal diversity of these extreme saline environment remains poorly understood. Moreover, there are no reports on exclusive diversity of actinomycetes inhabiting Indian solar salterns.
Results
Soil sediments were collected from both concentrator and crystallizer ponds of solar salterns and subjected to detailed physico-chemical analysis. Actinomycetes were selectively isolated by employing selective processing methods and agar media. A total of 12 representatives were selected from the 69 actinomycete isolates obtained from the saltern soil samples, using Amplified Ribosomal DNA Restriction Analysis. Sequencing and analysis of 16S rDNA from chosen representative isolates displayed the presence of members affiliated to actinobacterial genera: Streptomyces, Micromonospora, Nocardia, Nocardiopsis, Saccharopolyspora and Nonomuraea. The genus Streptomyces was found to be the dominant among the isolates. Furthermore, rare actinomycete genus Nonomuraea was isolated for the first time from Indian solar salterns.
Conclusions
To the best of our knowledge, this study constitutes the first characterization of actinomycete diversity centred on solar salterns located in the eastern coastal region of India. Furthermore, this is the very first report of isolation of Nonomuraea species from solar salterns and also from India. As actinomycetes encompass recurrently foremost sources of biotechnologically important member of the microbial communities, the actinomycetes retrieved from the Indian saltern soil samples laid the platform to search for novel biotechnologically significant bioactive substances.
doi:10.1186/2046-9063-8-23
PMCID: PMC3496644  PMID: 22950748
Solar saltern; Actinomycete; ARDRA; Phylogeny; 16S rDNA; Nonomuraea
10.  An annotated list of fish parasites (Isopoda, Copepoda, Monogenea, Digenea, Cestoda, Nematoda) collected from Snappers and Bream (Lutjanidae, Nemipteridae, Caesionidae) in New Caledonia confirms high parasite biodiversity on coral reef fish 
Aquatic Biosystems  2012;8:22.
Background
Coral reefs are areas of maximum biodiversity, but the parasites of coral reef fishes, and especially their species richness, are not well known. Over an 8-year period, parasites were collected from 24 species of Lutjanidae, Nemipteridae and Caesionidae off New Caledonia, South Pacific.
Results
Host-parasite and parasite-host lists are provided, with a total of 207 host-parasite combinations and 58 parasite species identified at the species level, with 27 new host records. Results are presented for isopods, copepods, monogeneans, digeneans, cestodes and nematodes. When results are restricted to well-sampled reef fish species (sample size > 30), the number of host-parasite combinations is 20–25 per fish species, and the number of parasites identified at the species level is 9–13 per fish species. Lutjanids include reef-associated fish and deeper sea fish from the outer slopes of the coral reef: fish from both milieus were compared. Surprisingly, parasite biodiversity was higher in deeper sea fish than in reef fish (host-parasite combinations: 12.50 vs 10.13, number of species per fish 3.75 vs 3.00); however, we identified four biases which diminish the validity of this comparison. Finally, these results and previously published results allow us to propose a generalization of parasite biodiversity for four major families of reef-associated fishes (Lutjanidae, Nemipteridae, Serranidae and Lethrinidae): well-sampled fish have a mean of 20 host-parasite combinations per fish species, and the number of parasites identified at the species level is 10 per fish species.
Conclusions
Since all precautions have been taken to minimize taxon numbers, it is safe to affirm than the number of fish parasites is at least ten times the number of fish species in coral reefs, for species of similar size or larger than the species in the four families studied; this is a major improvement to our estimate of biodiversity in coral reefs. Our results suggest that extinction of a coral reef fish species would eventually result in the coextinction of at least ten species of parasites.
doi:10.1186/2046-9063-8-22
PMCID: PMC3507714  PMID: 22947621
Biodiversity; Coral reefs; Parasites; Coextinction; Lutjanidae; New Caledonia; South Pacific
11.  Cloning of aquaporin-1 of the blue crab, Callinectes sapidus: its expression during the larval development in hyposalinity 
Aquatic Biosystems  2012;8:21.
Background
Ontogenetic variation in salinity adaptation has been noted for the blue crab, Callinectes sapidus, which uses the export strategy for larval development: females migrate from the estuaries to the coast to spawn, larvae develop in the ocean, and postlarvae (megalopae) colonize estuarine areas. We hypothesized that C. sapidus larvae may be stenohaline and have limited osmoregulatory capacity which compromises their ability to survive in lower salinity waters. We tested this hypothesis using hatchery-raised larvae that were traceable to specific life stages. In addition, we aimed to understand the possible involvement of AQP-1 in salinity adaptation during larval development and during exposure to hyposalinity.
Results
A full-length cDNA sequence of aquaporin (GenBank JQ970426) was isolated from the hypodermis of the blue crab, C. sapidus, using PCR with degenerate primers and 5′ and 3′ RACE. The open reading frame of CasAQP-1 consists of 238 amino acids containing six helical structures and two NPA motifs for the water pore. The expression pattern of CasAQP-1 was ubiquitous in cDNAs from all tissues examined, although higher in the hepatopancreas, thoracic ganglia, abdominal muscle, and hypodermis and lower in the antennal gland, heart, hemocytes, ovary, eyestalk, brain, hindgut, Y-organs, and gill. Callinectes larvae differed in their capacity to molt in hyposalinity, as those at earlier stages from Zoea (Z) 1 to Z4 had lower molting rates than those from Z5 onwards, as compared to controls kept in 30 ppt water. No difference was found in the survival of larvae held at 15 and 30 ppt. CasAQP-1 expression differed with ontogeny during larval development, with significantly higher expression at Z1-2, compared to other larval stages. The exposure to 15 ppt affected larval-stage dependent CasAQP-1 expression which was significantly higher in Z2- 6 stages than the other larval stages.
Conclusions
We report the ontogenetic variation in CasAQP-1 expression during the larval development of C. sapidus and the induction of its expression at early larval stages in the exposure of hyposalinity. However, it remains to be determined if the increase in CasAQP-1 expression at later larval stages may have a role in adaptation to hyposalinity.
doi:10.1186/2046-9063-8-21
PMCID: PMC3489796  PMID: 22943628
Aquaporin; Blue crab larvae; Ontogenetic variation; Osmoregulation; Salinity tolerance
12.  Influence of light, temperature and salinity on dissolved organic carbon exudation rates in Zostera marina L. 
Aquatic Biosystems  2012;8:19.
Background
Marine angiosperms, seagrasses, are sentinel species of marine ecosystem health and function. Seagrass carbon budgets provide insight on the minimum requirements needed to maintain this valuable resource. Carbon budgets are a balance between C fixation, growth, storage and loss rates, most of which are well characterized. However, relatively few measurements of dissolved organic carbon (DOC) leaf exudation or rhizodeposition rates exist for most seagrass species. Here I evaluate how eelgrass (Zostera marina L.) DOC exudation is affected by a single factor manipulation (light, temperature or salinity). Eelgrass plants were hydroponically exposed to treatments in experimental chambers (separate leaf and rhizome/root compartments) with artificial seawater medium. Regression analysis of changes in the DOC concentration through time was used to calculate DOC exudation rates.
Results
Exudation rates were similar across all treatments in all experiments. For all experiments, pooled leaf DOC exudation ranged between 0.032 and 0.069 mg C gdw-1 h-1, while rhizodeposition ranged between 0.024 and 0.045 mg C gdw-1 h-1. These rates are consistent with previously published values and provide first-order estimates for mechanistic models.
Conclusions
Zostera marina carbon losses from either leaf exudation or rhizodeposition account for a small proportion of gross primary production (1.2-4.6%) and appear to be insensitive to short-term (e.g., hours to days) environmental variations in chamber experiments. Based on these preliminary experiments, I suggest that Z. marina DOC exudation may be a passive process and not an active transport process.
doi:10.1186/2046-9063-8-19
PMCID: PMC3479412  PMID: 22938529
Carbon balance; Seagrass; Exudation; Rhizodeposition; Gradients
13.  Abundance, species composition of microzooplankton from the coastal waters of Port Blair, South Andaman Island 
Aquatic Biosystems  2012;8:20.
Background
Microzooplankton consisting of protists and metazoa <200 μm. It displays unique feeding mechanisms and behaviours that allow them to graze cells up to five times their own volume. They can grow at rates which equal or exceed prey growth and can serve as a viable food source for metazoans. Moreover, they are individually inconspicuous, their recognition as significant consumers of oceanic primary production. The microzooplankton can be the dominant consumers of phytoplankton production in both oligo- and eutrophic regions of the ocean and are capable of consuming >100% of primary production.
Results
The microzooplankton of the South Andaman Sea were investigated during September 2011 to January 2012. A total of 44 species belong to 19 genera were recorded in this study. Tintinnids made larger contribution to the total abundance (34%) followed in order by dinoflagellates (24%), ciliates (20%) and copepod nauplii (18%). Foraminifera were numerically less (4%). Tintinnids were represented by 20 species belong to 13 genera, Heterotrophic dinoflagellates were represented by 17 species belong to 3 genera and Ciliates comprised 5 species belong to 3 genera. Eutintinus tineus, Tintinnopsis cylindrical, T. incertum, Protoperidinium divergens, Lomaniella oviformes, Strombidium minimum were the most prevalent microzooplankton. Standing stock of tintinnids ranged from 30–80 cells.L-1 and showed a reverse distribution with the distribution of chlorophyll a relatively higher species diversity and equitability was found in polluted harbour areas.
Conclusions
The change of environmental variability affects the species composition and abundance of microzooplankton varied spatially and temporarily. The observations clearly demonstrated that the harbor area differed considerably from other area in terms of species present and phytoplankton biomass. Further, the phytoplankton abundance is showed to be strongly influenced by tintinnid with respect to the relationship of prey–predator. Consequently, further investigation on microzooplankton grazing would shed light on food web dynamics.
doi:10.1186/2046-9063-8-20
PMCID: PMC3543198  PMID: 22938564
Microzooplankton; Tintinnids; Plankton distribution; South Andaman Sea
14.  Stream invertebrate communities of Mongolia: current structure and expected changes due to climate change 
Aquatic Biosystems  2012;8:18.
Background
Mongolia’s riverine landscape is divided into three watersheds, differing in extent of permafrost, amount of precipitation and in hydrological connectivity between sub-drainages. In order to assess the vulnerability of macroinvertebrate communities to ongoing climate change, we consider the taxonomic and functional structures of stream communities in two major watersheds: The Central Asian Internal Watershed (CAIW) and the Arctic Ocean Watershed (AOW), together covering 86.1% of Mongolia’s surface area. We assess the consequences of the hydrological connectivity between sub-drainages on the nestedness and distinctness of the stream communities. And accordingly, we discuss the expected biotic changes to occur in each watershed as a consequence of climate change.
Results
Gamma and beta diversities were higher in the CAIW than the AOW. High community nestedness was also found in the CAIW along with a higher heterogeneity of macroinvertebrate assemblage structure. Assemblages characteristic of cold headwater streams in the CAIW, were typical of the drainages of the Altai Mountain range. Macroinvertebrate guilds of the CAIW streams exhibited traits reflecting a high stability and low resilience capacity for eutrophication. In contrast, the community of the AOW had lower nestedness and a combination of traits reflecting higher stability and a better resilience capacity to disturbances.
Conclusion
Higher distinctness of stream communities is due to lower connectivity between the drainages. This was the case of the stream macroinvertebrate communities of the two major Mongolian watersheds, where connectivity of streams between sub-drainages is an important element structuring their communities. Considering differences in the communities’ guild structure, hydrological connectivity and different magnitudes of upcoming impacts of climate change between the two watersheds, respective stream communities will be affected differently. The hitherto different communities will witness an increasing differentiation and divergent adaptations for the upcoming changes. Accordingly, in an increasing awareness to protect Mongolia’s nature, our results encourage adapting conservation planning and management strategies specifically by watershed.
doi:10.1186/2046-9063-8-18
PMCID: PMC3493306  PMID: 22920537
Macroinvertebrates; Nestedness; Hydrological connectivity; Conservation; Central Asia; Aquatic insects
15.  Disruption of Yarrowia lipolytica biofilms by rhamnolipid biosurfactant 
Aquatic Biosystems  2012;8:17.
Background
Yarrowia lipolytica is an ascomycetous dimorphic fungus that exhibits biofilm mode of growth. Earlier work has shown that biosurfactants such as rhamnolipids are efficient dispersants of bacterial biofilms. However, their effectiveness against fungal biofilms (particularly Y. lipolytica) has not been investigated. The aim of this study was to determine the effect of rhamnolipid on a biofilm forming strain of Y. lipolytica. Two chemical surfactants, cetyl-trimethyl ammonium bromide (CTAB) and sodium dodecyl sulphate (SDS) were used as controls for comparison.
Results
The methylene blue dye exclusion assay indicated an increase in fungal cell permeability after rhamnolipid treatment. Microtiter plate assay showed that the surfactant coating decreased Y. lipolytica biofilm formation by 50%. Rhamnolipid treatment disrupted pre-formed biofilms in a more effective manner than the other two surfactants. Confocal laser scanning microscopic studies showed that biofilm formation onto glass surfaces was decreased by 67% after sub-minimum inhibitory concentration (sub-MIC) treatment with rhamnolipids. The disruption of biofilms after rhamnolipid treatment was significant (P<0.05) when compared to SDS and CTAB.
Conclusion
The results indicate a potential application of the biological surfactant to disrupt Y. lipolytica biofilms.
doi:10.1186/2046-9063-8-17
PMCID: PMC3445841  PMID: 22839701
Biofilm; Biosurfactant; CTAB; Rhamnolipid; SDS; Yarrowia lipolytica
16.  Temporal distribution of genetically homogenous ‘free-living’ Hematodinium sp. in a Delmarva coastal ecosystem 
Aquatic Biosystems  2012;8:16.
Background
Significant damage to crustacean fisheries worldwide has been associated with Hematodinium sp. It has been postulated that Hematodinium sp. requires passage through the water column and/or intermediate hosts to complete its life cycle. Thus, an understanding of the prevalence and seasonality of Hematodinium sp. within environmentally-derived samples should yield insight into potential modes of disease transmission, and how these relate to infection cycles in hosts.
Results
We conducted a two year survey, from 2010–2011, in which 48 of 546 (8.8%) of environmental samples from the Maryland and Virginia coastal bays were positive for Hematodinium sp. between April and November, as based upon endpoint PCR analysis specific to blue crab isolates. Detection in both water and sediment was roughly equivalent, and there were no obvious seasonal patterns. However, there was a high detection in April water samples, which was unanticipated owing to the fact that crabs infected with Hematodinium sp. have not been observed in this early month of the seasonal disease cycle. Focusing on three sites of high prevalence (Sinnickson, VA; Tom’s Cove, VA; and Newport Bay, MD) Hematodinium sp. population diversity was analyzed using standard cloning methods. Of 131 clones, 109 (83.2%) were identical, 19 displayed a single nucleotide substitution, and 4 contain two nucleotide substitutions.
Conclusions
Our data suggests a continuous presence of Hematodinium sp. in both water and sediment of a combined Maryland and Virginia coastal bay ecosystem. The detection of Hematodinium sp. in the water column in April is an earlier manifestation of the parasite than predicted, pointing to an as yet unknown stage in its development prior to infection. That the population is relatively homogenous ranging from April to November, at three distinct sites, supports a hypothesis that one species of Hematodinium is responsible for infections within the ecosystem.
doi:10.1186/2046-9063-8-16
PMCID: PMC3413547  PMID: 22828185
Hematodinium; Life cycle; Environment; Population
17.  Culturable halophilic archaea at the initial and crystallization stages of salt production in a natural solar saltern of Goa, India 
Aquatic Biosystems  2012;8:15.
Background
Goa is a coastal state in India and salt making is being practiced for many years. This investigation aimed in determining the culturable haloarchaeal diversity during two different phases of salt production in a natural solar saltern of Ribandar, Goa. Water and sediment samples were collected from the saltern during pre-salt harvesting phase and salt harvesting phase. Salinity and pH of the sampling site was determined. Isolates were obtained by plating of the samples on complex and synthetic haloarchaeal media. Morphology of the isolates was determined using Gram staining and electron microscopy. Response of cells to distilled water was studied spectrophotometrically at 600nm. Molecular identification of the isolates was performed by sequencing the 16S rRNA.
Results
Salinity of salt pans varied from 3-4% (non-salt production phase) to 30% (salt production phase) and pH varied from 7.0-8.0. Seven haloarchaeal strains were isolated from water and sediment samples during non-salt production phase and seventeen haloarchaeal strains were isolated during the salt production phase. All the strains stained uniformly Gram negative. The orange-red acetone extract of the pigments showed similar spectrophotometric profile with absorption maxima at 393, 474, 501 and 535 nm. All isolates obtained from the salt dilute phase were grouped within the genus Halococcus. This was validated using both total lipid profiling and 16S rRNA data sequencing. The isolates obtained from pre-salt harvesting phase were resistant to lysis. 16S rRNA data showed that organisms belonging to Halorubrum, Haloarcula, Haloferax and Halococcus genera were obtained during the salt concentrated phase. The isolates obtained from salt harvesting phase showed varied lysis on suspension in distilled water and /or 3.5% NaCl.
Conclusion
Salterns in Goa are transiently operated during post monsoon season from January to May. During the pre-salt harvesting phase, all the isolates obtained belonged to Halococcus sp. During the salt harvesting phase, isolates belonging to Halorubrum, Haloarcula, Haloferax and Halococcus genera were obtained. This study clearly indicates that Halococcus sp. dominates during the low salinity conditions.
doi:10.1186/2046-9063-8-15
PMCID: PMC3444409  PMID: 22747590
Archaea; Haloarchaea; Hypersaline; Solar saltern
18.  The roles of abiotic factors, dispersal, and species interactions in structuring stream assemblages of black flies (Diptera: Simuliidae) 
Aquatic Biosystems  2012;8:14.
Background
The patterns and drivers of species assemblages represent the core of community ecology. We focus on the assemblages of a single family of ubiquitous lotic insects, the Simuliidae (black flies), of which the larvae play a critical role in resource turnover in steams. We use Mantel tests and null models to tease out the potential influence of abiotic stream conditions, species interactions, and dispersal on the assemblage patterns of larval black flies over two spatial scales (within and across ecoregions) and two seasons (spring and summer).
Results
When stream sites were considered across ecoregions in the spring, stream conditions and dispersal were correlated significantly with species similarity; however, within ecoregions in the spring, dispersal was important only in the Piedmont and Sandhills and abiotic factors only in the Mountains. In contrast, results of the summer analyses within and across ecoregions were congruent; assemblage similarity was significantly correlated with stream conditions both across and within ecoregions. Null models suggested that patterns of species segregation in the spring were consistent with a community structured by competition, whereas patterns in the summer were consistent with species assemblages influenced by abiotic factors.
Conclusions
Species composition of black flies at streams sites is correlated with dispersal factors and stream conditions, but results vary over spatial and temporal scales. Communities of black flies can be viewed within a metacommunity context; local assemblages are consistent with species sorting and mass effects. Given that black flies have a terrestrial stage, with females deciding where to place the eggs, a full understanding of the processes that determine local aquatic assemblages will require integration of the dynamics of the aquatic immature stages and the terrestrial adults.
doi:10.1186/2046-9063-8-14
PMCID: PMC3541213  PMID: 22742597
Black flies; Community structure; Competition; Co-occurrence; Dispersal; Mantel tests; Null models; Simuliidae; Streams
19.  Do Marmorkrebs, Procambarus fallax f. virginalis, threaten freshwater Japanese ecosystems? 
Aquatic Biosystems  2012;8:13.
Background
One marbled crayfish, Marmorkrebs, Procambarus fallax f. virginalis (Hagen, 1870), was discovered in a natural ecosystem in Japan in 2006. Because Marmorkrebs are parthenogenetic, they could establish a population from only a single individual, and thus pose a risk for becoming established in Japan, as they have in other countries. There are two major reasons to be concerned about the possibility of Marmorkrebs establishing viable populations in Japan. First, Japan’s only endemic crayfish, Cambaroides japonicus (De Haan, 1841), lives throughout Hokkaido and is endangered. Introduced Marmorkrebs are potential competitors that could further threaten C. japonicus. Second, Marmorkrebs live in rice paddies in Madagascar and consume rice. Marmorkrebs populations could reduce rice yields in Japan.
Results
We created five models in MaxEnt of the potential distribution of Marmorkrebs in Japan. All models showed eastern Honshu, Shikoku and Kyushu contain suitable habitats for Marmorkrebs. Hokkaido, the main habitat for C. japonicus, contained much less suitable habitat in most models, but is where the only Marmorkrebs in Japan to date was found.
Conclusions
Marmorkrebs appear to be capable of establishing populations in Japan if introduced. They appear to pose minimal threat to C. japonicus, but may negatively affect rice production.
doi:10.1186/2046-9063-8-13
PMCID: PMC3460755  PMID: 22738196
20.  Distribution, genetic analysis and conservation priorities for rare Texas freshwater molluscs in the genera Fusconaia and Pleurobema (Bivalvia: Unionidae) 
Aquatic Biosystems  2012;8:12.
Background
Freshwater bivalves in the order Unionoida are considered to be one of the most endangered groups of animals in North America. In Texas, where over 60% of unionids are rare or very rare, 15 species have been recently added to the state’s list of threatened species, and 11 are under consideration for federal listing. Due to insufficient survey efforts in the past decades, however, primary data on current distribution and habitat requirement for most of these rare species are lacking, thus challenging their protection and management. Taxonomic identification of endemic species based on shell morphology is challenging and complicates conservation efforts. In this paper we present historic and current distributional data for three rare Texas species, Fusconaia askewi, F. lananensis, and Pleurobema riddellii, collected during our 2003–2011 state-wide surveys and suggest appropriate conservation measures. In addition, we tested the genetic affinities of Fusconaia and similar species collected from eastern Texas and western Louisiana using cox1 and nad1 sequences.
Results
We found that F. askewi still inhabits four river basins in eastern and northeastern Texas and can be locally abundant, while P. riddellii was found only in one river basin. Pleurobema riddellii was well-separated from F. askewi and grouped with the P. sintoxia clade. The sequences for F. lananensis were very similar to those for F. askewi, with a maximum difference of just over 1% for nad1 and only 0.7% for cox1, similar to the variation between F. askewi alleles. Except for one low difference (1.55%) with the partial cox1 sequence for F. burkei, all other Fusconaia populations, including those from the Calcasieu drainage, differed by over 2.3% for both genes.
Conclusions
Our study suggested that F. lananensis is not a valid species, and it is likely that only one Fusconaia species (F. askewi or its probable senior synonym F. chunii) is currently present in East Texas, thus simplifying conservation efforts. Distribution range of both these regional endemics (F. askewi and P. riddellii) has been reduced in the last 80 years.
doi:10.1186/2046-9063-8-12
PMCID: PMC3422191  PMID: 22731520
Freshwater molluscs; Fusconaia askewi; Fusconaia lananensis; Pleurobema riddellii; Molecular identification; Taxonomy; Distribution; Habitat requirements; Conservation priorities
21.  Mangrove plant, Rhizophora mucronata (Lamk, 1804) mediated one pot green synthesis of silver nanoparticles and its antibacterial activity against aquatic pathogens 
Aquatic Biosystems  2012;8:11.
Background
Biosynthesis of nanoparticles has received increasing attention due to the growing need to develop safe, time-effective and environmentally friendly technologies for nano-materials synthesis. This paper reports the one pot green synthesis of silver nanoparticles (AgNPs) using the leaf bud extract of a mangrove plant, Rhizophora mucronata and their antimicrobial effects against aquatic pathogens. Highly stable AgNPs were synthesized by treating the mangrove leaf bud extract with aqueous silver nitrate solution at 15 psi pressure and 121°C for 5 minutes.
Results
The biosynthesized AgNPs were characterized by UV-visible spectrum, at 426 nm. The X-Ray Diffraction (XRD) pattern revealed the face-centered cubic geometry of AgNPs. Fourier Transform Infra Red (FTIR) spectroscopic analysis was carried out to identify the possible biomolecules responsible for biosynthesis of AgNPs from the leaf bud extract. The size and shape of the well-dispersed AgNPs were documented with the help of High Resolution Transmission Electron Microscopy (HRTEM) with a diameter ranged from 4 to 26 nm. However a maximum number of particles were observed at 4 nm in size. The antibacterial effects of AgNPs were studied against aquatic pathogens Proteus spp., Pseudomonas fluorescens and Flavobacterium spp., isolated from infected marine ornamental fish, Dascyllus trimaculatus.
Conclusion
This study reveals that the biosynthesized AgNPs using the leaf bud extract of a mangrove plant (R. mucronata) were found equally potent to synthetic antibiotics. The size of the inhibition zone increases when the concentration of the AgNPs increased and varies according to species.
doi:10.1186/2046-9063-8-11
PMCID: PMC3411493  PMID: 22608057
Silver nanoparticles; Rhizophora mucronata; One pot green synthesis; Antimicrobial; Aquatic pathogens
22.  Marine crude-oil biodegradation: a central role for interspecies interactions 
Aquatic Biosystems  2012;8:10.
The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such “microbial modules” interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons.
doi:10.1186/2046-9063-8-10
PMCID: PMC3465203  PMID: 22591596
Hydrocarbon; Crude oil; Salt marsh; Marine microbiology; Biodegradation; Bioremediation; Microbial interactions; Biogeochemistry; Alcanivorax
23.  Evolutionary patterns of carbohydrate transport and metabolism in Halomonas boliviensis as derived from its genome sequence: influences on polyester production 
Aquatic Biosystems  2012;8:9.
Background
Halomonas boliviensis is a halophilic bacterium that is included in the γ-Proteobacteria sub-group, and is able to assimilate different types of carbohydrates. H. boliviensis is also able to produce poly(3-hydroxybutyrate) (PHB) in high yields using glucose as the carbon precursor. Accumulation of PHB by microorganisms is induced by excess of intracellular NADH.
The genome sequences and organization in microorganisms should be the result of evolution and adaptation influenced by mutation, gene duplication, horizontal gen transfer (HGT) and recombination. Furthermore, the nearly neutral theory of evolution sustains that genetic modification of DNA could be neutral or selected, albeit most mutations should be at the border between neutrality and selection, i.e. slightly deleterious base substitutions in DNA are followed by a slightly advantageous substitutions.
Results
This article reports the genome sequence of H. boliviensis. The chromosome size of H. boliviensis was 4 119 979 bp, and contained 3 863 genes. A total of 160 genes of H. boliviensis were related to carbohydrate transport and metabolism, and were organized as: 70 genes for metabolism of carbohydrates; 47 genes for ABC transport systems and 43 genes for TRAP-type C4-dicarboxylate transport systems. Protein sequences of H. boliviensis related to carbohydrate transport and metabolism were selected from clusters of orthologous proteins (COGs). Similar proteins derived from the genome sequences of other 41 archaea and 59 bacteria were used as reference. We found that most of the 160 genes in H. boliviensis, c.a. 44%, were obtained from other bacteria by horizontal gene transfer, while 13% of the genes were acquired from haloarchaea and thermophilic archaea, only 34% of the genes evolved among Proteobacteria and the remaining genes encoded proteins that did not cluster with any of the proteins obtained from the reference strains. Furthermore, the diversity of the enzymes derived from these genes led to polymorphism in glycolysis and gluconeogenesis. We found further that an optimum ratio of glucose and sucrose in the culture medium of H. boliviensis favored cell growth and PHB production.
Conclusions
Results obtained in this article depict that most genetic modifications and enzyme polymorphism in the genome of H. boliviensis were mainly influenced by HGT rather than nearly neutral mutations. Molecular adaptation and evolution experienced by H. boliviensis were also a response to environmental conditions such as the type and amount of carbohydrates in its ecological niche. Consequently, the genome evolution of H. boliviensis showed to be strongly influenced by the type of microorganisms, genetic interaction among microbial species and its environment. Such trend should also be experienced by other prokaryotes. A system for PHB production by H. boliviensis that takes into account the evolutionary adaptation of this bacterium to the assimilation of combinations of carbohydrates suggests the feasibility of a bioprocess economically viable and environmentally friendly.
doi:10.1186/2046-9063-8-9
PMCID: PMC3384467  PMID: 22510370
Halomonas boliviensis; Halophilic bacterium; Halomonas; Halomonadaceae; Biopolyesters; Polyhydroxyalkanoates; Genome evolution; Population genetics
24.  Brazilian solar saltworks - ancient uses and future possibilities 
Aquatic Biosystems  2012;8:8.
Coastal solar saltworks of Brazil are exploited for sea salt, which becomes progressively concentrated by evaporation. This study aimed to review the current and new potential uses of these systems, in order to provide more dynamic for this activity. The first evaporation ponds are also used for artisanal fisheries, ensuring the livelihood of many families. All the brine rich in secondary salts (bittern) can be widely used by the chemical industry, while the Brazil shows an incipient production of "flower of salt", a salt with distinct characteristics with higher market value than sodium chloride. On the other hand, the saltponds have a high potential for management and obtaining of large populations of Artemia spp., purifying the brine through the action as biological filter. This microcrustacean occurs naturally in intermediate salinity ponds, being commonly used in aquaculture. Species of microalgae and halobacteria found in the saltworks are employed for extraction of beta-carotene and glycerol, used in an extensive list of products with high commercial value. These ecosystems represent refuge zones for many species of migratory birds, becoming imperative to promote the conservation of these hypersaline wetlands.
doi:10.1186/2046-9063-8-8
PMCID: PMC3349464  PMID: 22490329
Wetland; Salt production; Management; Brazil; Conservation
25.  Comparative quantitative proteomics of prochlorococcus ecotypes to a decrease in environmental phosphate concentrations 
Aquatic Biosystems  2012;8:7.
Background
The well-lit surface waters of oligotrophic gyres significantly contribute to global primary production. Marine cyanobacteria of the genus Prochlorococcus are a major fraction of photosynthetic organisms within these areas. Labile phosphate is considered a limiting nutrient in some oligotrophic regions such as the Caribbean Sea, and as such it is crucial to understand the physiological response of primary producers such as Prochlorococcus to fluctuations in the availability of this critical nutrient.
Results
Prochlorococcus strains representing both high light (HL) (MIT9312) and low light (LL) (NATL2A and SS120) ecotypes were grown identically in phosphate depleted media (10 μM Pi). The three strains displayed marked differences in cellular protein expression, as determined by high throughput large scale quantitative proteomic analysis. The only strain to demonstrate a significantly different growth rate under reduced phosphate conditions was MIT9312. Additionally, there was a significant increase in phosphate-related proteins such as PhoE (> 15 fold increase) and a depression of the Rubisco protein RbcL abundance in this strain, whereas there appeared to be no significant change within the LL strain SS120.
Conclusions
This differential response between ecotypes highlights the relative importance of phosphate availability to each strain and from these results we draw the conclusion that the expression of phosphate acquisition mechanisms are activated at strain specific phosphate concentrations.
doi:10.1186/2046-9063-8-7
PMCID: PMC3349580  PMID: 22480396
Prochlorococcus; PstS; PhoA; PhoE; Growth; Phosphate

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