Particle-attached and free-living bacterial communities in a contrasting marine environment: Victoria Harbor, Hong Kong

Diversity of particle-attached and free-living marine bacteria in Victoria Harbor, Hong Kong, and its adjacent coastal and estuarial environments was investigated using DNA fingerprinting and clone library analysis. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes showed that bacterial communities in three stations of Victoria Harbor were similar, but differed from those in adjacent coastal and estuarine stations. Particle-attached and free-living bacterial community composition differed in the Victoria Harbor area. DNA sequencing of 28 bands from DGGE gel showed Alphaproteobacteria was the most abundant group, followed by the Bacteroidetes, and other Proteobacteria. Bacterial species richness (number of DGGE bands) differed among stations and populations (particle-attached and free-living; bottom and surface). BIOENV analysis indicated that the concentrations of suspended solids were the major contributing parameter for the spatial variation of total bacterial community structure. Samples from representative stations were selected for clone library (548 clones) construction and their phylogenetic distributions were similar to those of sequences from DGGE. Approximately 80% of clones were affiliated to Proteobacteria, Bacteroidetes and Cyanobacteria. The possible influences of dynamic pollution and hydrological conditions in the Victoria Harbor area on the particle-attached and free-living bacterial community structures were discussed.

Particle-attached and free-living bacterial communities in a contrasting marine environment: Victoria Harbor, Hong Kong

Diversity of particle-attached and free-living marine bacteria in Victoria Harbor, Hong Kong, and its adjacent coastal and estuarial environments was investigated using DNA fingerprinting and clone library analysis. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes showed that bacterial communities in three stations of Victoria Harbor were similar, but differed from those in adjacent coastal and estuarine stations. Particle-attached and free-living bacterial community composition differed in the Victoria Harbor area. DNA sequencing of 28 bands from DGGE gel showed Alphaproteobacteria was the most abundant group, followed by the Bacteroidetes, and other Proteobacteria. Bacterial species richness (number of DGGE bands) differed among stations and populations (particle-attached and free-living; bottom and surface). BIOENV analysis indicated that the concentrations of suspended solids were the major contributing parameter for the spatial variation of total bacterial community structure. Samples from representative stations were selected for clone library (548 clones) construction and their phylogenetic distributions were similar to those of sequences from DGGE. Approximately 80% of clones were affiliated to Proteobacteria, Bacteroidetes and Cyanobacteria. The possible influences of dynamic pollution and hydrological conditions in the Victoria Harbor area on the particle-attached and free-living bacterial community structures were discussed.

Characteristics of the microzooplankton community in Jiaozhou Bay, Qingdao, China

The species composition and abundance of microzooplankton at 10 marine and five coastal stations (Hongdao, Daguhe, Haibohe, Huangdao and Hangxiao) in the Jiaozhou Bay (Qingdao, China) were studied in 2001. The microzooplankton community was found to be dominated by Tintinnopsis beroidea, Tintinnopsis urnula, Tintinnopsis brevicollis and Cvdonellopsis sp. The average abundance of microzooplankton was highly variable among stations. Specifically, the abundance of microzooplankton was higher at inshore stations and lower in the center of the bay (St. 5), bay mouth (St. 9) and outside the bay (St. 10). The highest average annual densities (346 ind./L) was observed at St. 3, while the lowest (55 ind./L) was at St. 10. Two abundance peaks were recorded in May (324 ind./L) and February (300 ind./L). The distribution of microzooplankton in three sampling layers at the 10 stations was relatively homogenous and the abundance decreased slightly as the water depth increased. At coastal stations, the highest average annual density was recorded at Hongdao Station (677 ind./L), followed by Daguhe Station (616 ind./L), Haibohe Station (400 ind./L), Huangdao Station (275 ind./L) and Hangxiao Station (73 ind./L). Furthermore, a 24-h sampling analysis conducted at Hangxiao Station revealed that the microzooplankton assemblages were characterized by a bimodal diel vertical migration pattern, with the highest densities occurring at dusk (154 ind./L), followed by dawn (146 ind./L), noon (93 ind./L) and midnight (77 ind./L). The density of microzooplankton in the Jiaozhou Bay was in the middle range of the densities of temperate coastal waters worldwide.

Effects of increased pCO(2) and temperature on the North Atlantic spring bloom. I. The phytoplankton community and biogeochemical response

The North Atlantic spring bloom is one of the largest annual biological events in the ocean, and is characterized by dominance transitions from siliceous (diatoms) to calcareous (coccolithophores) algal groups. To study the effects of future global change on these phytoplankton and the biogeochemical cycles they mediate, a shipboard continuous culture experiment (Ecostat) was conducted in June 2005 during this transition period. Four treatments were examined: (1) 12 degrees C and 390 ppm CO2 (ambient control), (2) 12 degrees C and 690 ppm CO2 (high pCO(2)) (3) 16 degrees C and 390 ppm CO2 (high temperature), and (4) 16 degrees C and 690 ppm CO2 ('greenhouse'). Nutrient availability in all treatments was designed to reproduce the low silicate conditions typical of this late stage of the bloom. Both elevated pCO(2) and temperature resulted in changes in phytoplankton community structure. Increased temperature promoted whole community photosynthesis and particulate organic carbon (POC) production rates per unit chlorophyll a. Despite much higher coccolithophore abundance in the greenhouse treatment, particulate inorganic carbon production (calcification) was significantly decreased by the combination of increased pCO(2) and temperature. Our experiments suggest that future trends during the bloom could include greatly reduced export of calcium carbonate relative to POC, thus providing a potential negative feedback to atmospheric CO2 concentration. Other trends with potential climate feedback effects include decreased community biogenic silica to POC ratios at higher temperature. These shipboard experiments suggest the need to examine whether future pCO2 and temperature increases on longer decadal timescales will similarly alter the biological and biogeochemical dynamics of the North Atlantic spring bloom.

Onshore-offshore variations of copepod community in northern South China Sea

Copepod communities in onshore and offshore waters show a gradient from primarily near shore to primarily oceanic species. Understanding the transition between these communities is fundamental to determining the range of coastal influence. Copepod communities in the northern South China Sea (nSCS) were studied based on samples collected by vertically towing a net in 10 February-6 March (winter) and 26 August-6 September (summer) of 2004. Calanoida species richness, total copepod abundance, Shannon-Weaver diversity index, and onshore-offshore occurrence of dominant species showed obvious change from onshore to offshore waters. Although the offshore stations had lower abundance than the shelf stations, they had more species and larger diversity index. Abundance of some species (groups) with dominance index > 5% (Calanus sinicus, Euchaeta spp., Temora spp., Paracalanus parvus, and Subeucalanus subtenuis) declined from onshore to offshore waters. Warm water species (Pleuromamma abdominalis, P. gracilis, and P. robusta) occurred in offshore waters in both cruises. Station (q-type) cluster analysis in winter and summer separated copepod community into onshore and offshore communities at similar to 40% level of similarity. The two communities were divided at the position of similar to 100-m isobath. In summer, C. sinicus occurred in the upwelling area east of Hainan Island, indicating the presence of an oversummering stock of this species.

Influence of filtering and biodeposition by the cultured scallop Chlamys farreri on benthic-pelagic coupling in a eutrophic bay in China

In coastal ecosystems, suspension-cultured bivalve filter feeders may exert a strong impact on phytoplankton and other suspended particulate matter and induce strong pelagic-benthic coupling via intense filtering and biodeposition. We designed an in situ method to determine spatial variations in the filtering-biodeposition process by intensively suspension-cultured scallops Chlamys farreri in summer in a eutrophic bay (Sishili Bay, China), using cylindrical biodeposition traps directly suspended from longlines under ambient environmental conditions. Results showed that bivalve filtering-biodeposition could substantially enhance the deposition of total suspended material and the flux of C, N and P to the benthos, indicating that the suspended filter feeders could strongly enhance pelagic-benthic coupling and exert basin-scale impacts in the Sishili Bay ecosystem. The biodeposition rates of 1-yr-old scallops varied markedly among culture sites (33.8 to 133.0 mg dry material ind.(-1) d(-1)), and were positively correlated with seston concentrations. Mean C, N and P biodeposition rates were 4.00, 0.51, 0.11 mg ind.-1 d-1, respectively. The biodeposition rates of 2-yr-old scallops were almost double these values. Sedimentation rates at scallop culture sites averaged 2.46 times that at the reference site. Theoretically, the total water column of the bay could be filtered by the cultured scallops in 12 d, with daily seston removal amounting to 64%. This study indicated that filtering-biodeposition by suspension-cultured scallops could exert long-lasting top-down control on phytoplankton biomass and other suspended material in the Sishili Bay ecosystem. In coastal waters subject to anthropogenic N and P inputs, suspended bivalve aquaculture could be advantageous, not only economically, but also ecologically, by functioning as a biofilter and potentially mitigating eutrophication pressures. Compared with distribution-restricted wild bivalves, suspension-cultured bivalves in deeper coastal bays may be more efficient in processing seston on a basin scale.

Simultaneous enumeration of diatom, protozoa and meiobenthos from marine sediments using Ludox-QPS method

The Ludox-QPS method is a newly developed technique, which combines the Ludox HS 40 density centrifugation and quantitative protargol stain, to enumerate marine ciliates with good taxonomic resolution. We tested the method for simultaneous enumeration of diatoms, protozoa and meiobenthos and compared its extraction efficiency for meiobenthos with that of the routine Ludox-TM centrifugation and a modified protocol using Ludox HS 40. We conducted the evaluation with a sample size of 8.3 ml each from sandy, muddy-sand and muddy sediments collected from the intertidal area of the Yellow Sea in summer 2006 and spring 2007. The Ludox-QPS method not only produced high extraction efficiencies of 97 +/- 1.3% for diatoms and 97.6 +/- 0.8% for ciliates, indicating a reliable enumeration for eukaryotic microbenthos, but also produced excellent extraction efficiencies of on average 97.3% for total meiobenthos, 97.9% for nematodes and 97.8% for copepods from sands, muddy sands and mud. By contrast, the routine Ludox-TM centrifugation obtained only about 74% of total meiobenthos abundance with one extraction cycle, and the modified Ludox HS 40 centrifugation yielded on average 93% of total meiobenthos: 89.4 +/- 2.0% from sands, 93 +/- 4.1% from muddy sands and 97.1 +/- 3.0% from mud. Apart from the sediment type, sample volume was another important factor affecting the extraction efficiency for meiobenthos. The extraction rate was increased to about 96.4% when using the same modified Ludox centrifugation for a 4 ml sediment sample. Besides the excellent extraction efficiency, the Ludox-QPS method obtained higher abundances of meiobenthos, in particular nematodes, than the routine Ludox centrifugation, which frequently resulted in an uncertain loss of small meiobenthos during the sieving process. Statistical analyses demonstrated that there were no significant differences between the meiobenthos communities revealed by the Ludox-QPS method and the modified Ludox HS 40 centrifugation, showing the high efficiency of the Ludox-QPS method for simultaneous enumeration of diatom, protozoa and meiobenthos. Moreover, the comparatively high taxonomic resolution of the method, especially for diatoms and ciliates, makes it feasible to investigate microbial ecology at community level.

Community structure of macrobenthos in coastal water off Rushan, southern Shandong Peninsula, and the relationships with environmental factors

To understand the present actuality of the marine ecosystem in the southern coastal water region of the Shandong Peninsula and the impact of the global change and the human activities to the marine ecosystem of the region, the macrobenthic community structure was researched based on data from 26 sampling stations carried out on four seasonal cruises from December 2006 to November 2007. The data was analyzed using PRIMER 6.0 and SPSS 15.0 software packages. The results showed that 236 macrobenthic species in total were collected from the research region by the field works. Most of the species belong to Polychaeta (76 species), Mollusca (75) and Crustacea (60). Of which, 33 species were common species by the four cruises. The dominant species were different among the four seasons, however, the polychaete species Nephtys oligobranchia and Sternaspis scutata were always dominant in the four seasons. The abundances and biomasses of the macrobenthos from the research region were variable in tire four seasons. The results of CLUSTER and MDS analysis showed that the similarities of macrobenthic structures among the stations were low, most of the similarities were at about 40% of similarity values, only that of two stations were up to 60%. In accordance with the similarity values of the macrobenthic structures, the 26 stations were clustered as six groups at arbitrary similarity level of 30%. The ABC curve indicated that the marcofauna communities in the research region had riot been disturbed distinctly. The results of BIOENV and BVSTEP (Spearman) analysis implied that the concentrations of organic matter in bottom water and heavy metal copper in sediment, water depth and temperature of bottom were the most significant environmental factors to affect the macrobentic community.

Soft sediment ecology of Lough Hyne Marine Reserve - spatial and temporal patterns

Distribution of soft sediment benthic fauna and the environmental factors affecting them were studied, to investigate changes across spatial and temporal scales. Investigations took place at Lough Hyne Marine Reserve using a range of methods. Data on the sedimentation rates of organic and inorganic matter were collected at monthly intervals for one year at a number of sites around the Lough, by use of vertical midwater-column sediment traps. Sedimentation of these two fractions were not coupled; inorganic matter sedimentation depended on hydrodynamic and weather factors, while the organic matter sedimentation was more complex, being dependent on biological and chemical processes in the water column. The effects of regular hypoxic episodes on benthic fauna due to a natural seasonal thermocline were studied in the deep Western Trough, using camera-equipped remotely-operated vehicle to follow transects, on a three-monthly basis over one year. In late summer, the area below the thermocline of the Western Trough was devoid of visible fauna. Decapod crustaceans were the first taxon to make use of ameliorating oxygen conditions in autumn, by darting below the thermocline depth, most likely to scavenge. This was indicated by tracks that they left on the surface of the Trough floor. Some species, most noticeably Fries’ goby Lesueurigobius friesii, migrated below the thermocline depth when conditions were normoxic and established semi-permanent burrows. Their population encompassed all size classes, indicating that this habitat was not limited to juveniles of this territorial species. Recolonisation by macrofauna and burrowing megafauna was studied during normoxic conditions, from November 2009 to May 2010. Macrofauna displayed a typical post-disturbance pattern of recolonisation with one species, the polychaete Scalibregma inflatum, occurring at high abundance levels in March 2010. In May, this population had become significantly reduced and a more diverse community was established. The abundance of burrowing infauna comprising decapods crabs and Fries’ gobies, was estimated by identifying and counting their distinctive burrow structures. While above the summer thermocline depth, burrow abundance increased in a linear fashion, below the thermocline depth a slight reduction of burrow abundance occurred in May, when oxygen conditions deteriorated again. The majority of the burrows occurring in May were made by Fries’ gobies, which are thought to encounter low oxygen concentrations in their burrows. Reduction in burrow abundance of burrowing shrimps Calocaris macandreae and Callianassa subterranea (based on descriptions of burrow structures from the literature), from March to May, might be related to their reduced activity in hypoxia, leading to loss of structural burrow maintenance. Spatial and temporal changes to macrofaunal assemblage structures were studied seasonally for one year across 5 sites in the Lough and subject to multivariate statistical analysis. Assemblage structures were significantly correlated with organic matter levels in the sediment, the amounts of organic matter settling out of the water column one month before macrofaunal sampling took place as well as current speed and temperature. This study was the first to investigate patterns and processes in the Lough soft sediment ecology across all 3 basins on a temporal and spatial scale. An investigation into the oceanographic aspects of the development, behaviour and break-down of the summer thermocline of Lough Hyne was performed in collaboration with researchers from other Irish institutions.

Exploiting the diverse microbial ecology of marine sponges

Marine sponges (phylum Porifera) are the oldest extant metazoan animals on earth and host large populations of symbiotic microbes: Bacteria, Archaea and unicellular Eukaryota. Those microbes play ecological functions which are essential to the health of the host including carbon, nitrogen and sulfur cycling as well as host defence through the production of bioactive secondary metabolites which protect against infection and predation. The diversity of sponge-associated microbes is remarkable with thousands of OTUs reported from individual sponge species. Amongst those populations are sponge-specific microbes which may be specific to sponges or specific to sponge species. While marine natural product discovery concerns many animal phyla, Porifera account for the largest proportion of novel compounds. Evidence suggests that many of these compounds are the products of symbiotic microbes. Descriptions of sponge-associated microbial community structures have been advanced by the development of next-generation sequencing technologies while the discovery and exploitation of sponge derived bioactive compounds has increased due to developments in sequence-based and function-based metagenomics. Here, we use pyrosequencing to describe the bacterial communities associated with two shallow, temperate water sponges (Raspailia ramosa and Stelligera stuposa) from Irish coastal waters and to describe the bacterial and archaeal communities of a single sponge species (Inflatella pellicula) from two different depths in deep waters in the Atlantic Ocean, including at a depth of 2900m, a depth far greater than that of any previous sequence-based sponge-microbe investigation. We identified diverse microbial communities in all sponges and the presence of sponge-specific taxa recruiting to previously described and novel spongespecific clusters. We also identified archaeal communities which dominated sponge-microbe communities. We demonstrate that sponge-associated microbial communities differ from seawater communities indicating host selection processes. We used sequence-based metagenomic techniques to identify genes of potential industrial and pharmacological interest in the metagenomes of various sponge species and functionbased metagenomic screening in an attempt to identify lipolytic and antibacterial activities from metagenomic clones from the metagenome of the marine sponge Stelletta normani. In addition we have cultured diverse bacterial species from sponge tissues, many of which display antimicrobial activities against clinically relevant bacterial and yeast test strains. Other isolates represent novel species in the genus Maribacter and require emendments to the description of that genus.

How Locally Designed Access and Use Controls Can Prevent the Tragedy of the Commons in a Mexican Small-Scale Fishing Community

The Seri people, a self-governed community of small-scale fishermen in the Gulf of California, Mexico, have ownership rights to fishing grounds where they harvest highly valuable commercial species of bivalves. Outsiders are eager to gain access, and the community has devised a set of rules to allow them in. Because Seri government officials keep all the economic benefits generated from granting this access for themselves, community members create alternative entry mechanisms to divert those benefits to themselves. Under Hardin’s model of the tragedy of the commons, this situation would eventually lead to the overexploitation of the fishery. The Seri people, however, are able to simultaneously maintain access and use controls for the continuing sustainability of their fishing grounds. Using insights from common- pool resources theory, I discuss how Seri community characteristics help mediate the conflict between collective action dilemmas and access and use controls.

Lack of cross-scale linkages reduces robustness of community-based fisheries management.

Community-based management and the establishment of marine reserves have been advocated worldwide as means to overcome overexploitation of fisheries. Yet, researchers and managers are divided regarding the effectiveness of these measures. The "tragedy of the commons" model is often accepted as a universal paradigm, which assumes that unless managed by the State or privatized, common-pool resources are inevitably overexploited due to conflicts between the self-interest of individuals and the goals of a group as a whole. Under this paradigm, the emergence and maintenance of effective community-based efforts that include cooperative risky decisions as the establishment of marine reserves could not occur. In this paper, we question these assumptions and show that outcomes of commons dilemmas can be complex and scale-dependent. We studied the evolution and effectiveness of a community-based management effort to establish, monitor, and enforce a marine reserve network in the Gulf of California, Mexico. Our findings build on social and ecological research before (1997-2001), during (2002) and after (2003-2004) the establishment of marine reserves, which included participant observation in >100 fishing trips and meetings, interviews, as well as fishery dependent and independent monitoring. We found that locally crafted and enforced harvesting rules led to a rapid increase in resource abundance. Nevertheless, news about this increase spread quickly at a regional scale, resulting in poaching from outsiders and a subsequent rapid cascading effect on fishing resources and locally-designed rule compliance. We show that cooperation for management of common-pool fisheries, in which marine reserves form a core component of the system, can emerge, evolve rapidly, and be effective at a local scale even in recently organized fisheries. Stakeholder participation in monitoring, where there is a rapid feedback of the systems response, can play a key role in reinforcing cooperation. However, without cross-scale linkages with higher levels of governance, increase of local fishery stocks may attract outsiders who, if not restricted, will overharvest and threaten local governance. Fishers and fishing communities require incentives to maintain their management efforts. Rewarding local effective management with formal cross-scale governance recognition and support can generate these incentives.

Intraspecific variation in a predator affects community structure and cascading trophic interactions.

Intraspecific phenotypic variation in ecologically important traits is widespread and important for evolutionary processes, but its effects on community and ecosystem processes are poorly understood. We use life history differences among populations of alewives, Alosa pseudoharengus, to test the effects of intraspecific phenotypic variation in a predator on pelagic zooplankton community structure and the strength of cascading trophic interactions. We focus on the effects of differences in (1) the duration of residence in fresh water (either seasonal or year-round) and (2) differences in foraging morphology, both of which may strongly influence interactions between alewives and their prey. We measured zooplankton community structure, algal biomass, and spring total phosphorus in lakes that contained landlocked, anadromous, or no alewives. Both the duration of residence and the intraspecific variation in foraging morphology strongly influenced zooplankton community structure. Lakes with landlocked alewives had small-bodied zooplankton year-round, and lakes with no alewives had large-bodied zooplankton year-round. In contrast, zooplankton communities in lakes with anadromous alewives cycled between large-bodied zooplankton in the winter and spring and small-bodied zooplankton in the summer. In summer, differences in feeding morphology of alewives caused zooplankton biomass to be lower and body size to be smaller in lakes with anadromous alewives than in lakes with landlocked alewives. Furthermore, intraspecific variation altered the strength of the trophic cascade caused by alewives. Our results demonstrate that intraspecific phenotypic variation of predators can regulate community structure and ecosystem processes by modifying the form and strength of complex trophic interactions.