How island size and isolation affect bee and wasp ensembles on small tropical islands: a case study from Kepulauan Seribu,Indonesia

Aim To study the effects of isolation and size of small tropical islands on species assemblages of bees (superfamily Apoidea) and wasps (superfamily Vespoidea). Location Twenty islands in the Kepulauan Seribu Archipelago off the coast of west Java, Indonesia. The size of surveyed islands ranges between 0.75 and 41.32 ha; their distance from the coast of Java varies between 3 and 62 km. Methods Field work was conducted from February to May 2005. Bees and wasps were caught with a sweep net during sampling units of 15 min, continuing until four consecutive samples revealed no new species. Total species richness was quantified by the estimators Chao 2, first‐order jackknife and Michaelis–Menten. The software binmatnest was used to test for nestedness of species assemblages. Similarities of species composition between islands were quantified by Sørensen’s similarity index. Results Eighty‐two species were recorded on the 20 surveyed islands. Species richness declined with increasing isolation of islands from the source area, Java. Although the size of the largest island exceeded that of the smallest island by a factor of almost 60, island size only very weakly affected species richness of bees; no effect of island size was found for wasps. Mean body size of species decreased with increasing island isolation. Nestedness of island faunas was only weakly developed. Species composition of both superfamilies was affected by island isolation, but not by island size. Main conclusions While the species–isolation relationship on the very small islands of Kepulauan Seribu followed the prediction of MacArthur and Wilson’s equilibrium theory, the absence of a species–area relationship indicated a weak ‘small‐island effect’, at least in wasps. The combination of an only weakly developed pattern of nested species subsets, the shift in species compositions and the decline of mean body size with increasing island isolation from the source area indicates that biotic interactions and different species traits contribute to the shaping of communities of bees and wasps within the archipelago. The potential of biotic interactions for generating distribution patterns of species within the archipelago is also emphasized by the observed restriction of some species with apparently high dispersal abilities to outer islands.     

Habitat selective factors influencing the distribution of larger benthic foraminiferal assemblages over the Kepulauan Seribu

Symbiont-bearing foraminifera are used to study the effects of habitat deterioration on benthic communities in coral reefs dominated by macroalgae. It is shown that, despite their preference for nutrient deprived conditions, some symbiont-bearing foraminifera occur on reefs heavily affected by nutrient stress and macro-algal dominance, thus highlighting the need for a better understanding of the autecology of species and assemblages in these conditions. Both diversity and habitat fractionation increases as terrestrial and nutrient influence decline. The assemblage structure in the most nearshore reefs are dominated by generalist species, while, additionally, more specialistic species occur at the more offshore reefs. Apart from larger scale gradients in ambient seawater quality, local scale variation in physical environmental conditions, such as habitat structure, are important for the assemblage structure as well.     

Distance-Decay and Taxa-Area Relationships for Bacteria,Archaea and Methanogenic Archaea in a Tropical Lake Sediment

The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.     

Coral diversity across a disturbance gradient in the Pulau Seribu reef complex off Jakarta, Indonesia

Very few coral reefs are located close enough to metropolitan cities to study the influence of large urban populations on reef communities. Here, we compare the impact of a large-scale disturbance gradient with local-scale disturbance on coral richness, cover, and composition in the Jakarta Bay and Pulau Seribu reef complex off Jakarta, Indonesia. We found no effect of local land-use type of coral reef islands on richness, composition or cover, nor did taxon richness differ among zones at the large-scale. There was, however, a pronounced difference in composition and coral cover among zones. Cover was very low and composition differed markedly in the near-shore zone 1 (Jakarta Bay) where human-induced disturbance is most intense. Cover was highest in the outlying reefs of zone 3. The highly perturbed zone 1 reefs were, furthermore, distinguished by the virtual absence of otherwise abundant coral taxa such as Acropora hyacinthus and Porites rus and the prevalence of taxa such as Oulastrea crispata and Favia maxima. Almost 60% of the spatial variation in composition was related to variation in shelf depth and island size. The importance of shelf depth was related to the prevalence of a strong environmental gradient in reef depth, pollution, and mechanical reef disturbance and salinity from Jakarta Bay to the outlying reefs. Although there was a significant univariate relationship between spatial variation in composition and distance, this did not enter into the multivariate model, except when presence–absence data was used, indicating that environmental processes are the primary structuring forces in determining local coral assemblage composition across the Pulau Seribu complex.     

Skeletal form and growth in Acropora aspera (Dana) from the Pulau Seribu,Indonesia

Linear extension and calcium carbonate accretion were measured in the branching coral Acropora aspera (Dana) from shallow-water sites around Pulau Pari, Pulau Seribu, Indonesia, during both wet and dry monsoon periods. Skeletal density and corallite form were also monitored in specimens collected from sites, variously affected by wave energy resulting from the monsoonal influence. Although the reversing monsoon appeared to exert the greatest effect on skeleton growth (by influencing temperature and possibly number of “sun-hours”) wave energy was also shown to affect skeletal extension, skeletal accretion, and skeletal density. The scale of differences between growth rate measurements was greatest for weight of skeleton accreted between monsoon period (8-fold), followed by between site differences (maximum 3-fold during west monsoon) and finally between station differences (maximum 3-fold during west monsoon at an outer reef flat and reef edge station). Skeletal extension did not appear to be as sensitive to the reversing monsoon influence as skeletal accretion.     

A Novel Technique for the Reattachment of Large Coral Reef Sponges

Sponges are dominant components of coral reef ecosystems, often exceeding reef-building corals in abundance. Large sponges, often more than 1 m in diameter, may be hundreds to thousands of years old. When damaged or dislodged, large sponges usually die because they are unable to reattach to the reef substratum. Because suitable methods for reattaching dislodged sponges are lacking, they are typically excluded from coral reef restoration efforts. Here we present a novel technique for the reattachment of large sponges that was tested using the Caribbean Giant barrel sponge, Xestospongia muta . Transplants of X. muta were conducted at 15- and 30-m depth off Key Largo, Florida. Despite the active hurricane season of 2005, 90% of deep and 35% of shallow transplants survived, with nearly 80% reattaching to the substratum and growing after 2.3–3 years. This technique may be generally adapted for securing large sponges in coral reef restoration efforts.     

Archaea Appear to Dominate the Microbiome of Inflatella pellicula Deep Sea Sponges

Microbes associated with marine sponges play significant roles in host physiology. Remarkable levels of microbial diversity have been observed in sponges worldwide through both culture-dependent and culture-independent studies. Most studies have focused on the structure of the bacterial communities in sponges and have involved sponges sampled from shallow waters. Here, we used pyrosequencing of 16S rRNA genes to compare the bacterial and archaeal communities associated with two individuals of the marine sponge Inflatella pellicula from the deep-sea, sampled from a depth of 2,900 m, a depth which far exceeds any previous sequence-based report of sponge-associated microbial communities. Sponge-microbial communities were also compared to the microbial community in the surrounding seawater. Sponge-associated microbial communities were dominated by archaeal sequencing reads with a single archaeal OTU, comprising ∼60% and ∼72% of sequences, being observed from Inflatella pellicula. Archaeal sequencing reads were less abundant in seawater (∼11% of sequences). Sponge-associated microbial communities were less diverse and less even than any other sponge-microbial community investigated to date with just 210 and 273 OTUs (97% sequence identity) identified in sponges, with 4 and 6 dominant OTUs comprising ∼88% and ∼89% of sequences, respectively. Members of the candidate phyla, SAR406, NC10 and ZB3 are reported here from sponges for the first time, increasing the number of bacterial phyla or candidate divisions associated with sponges to 43. A minor cohort from both sponge samples (∼0.2% and ∼0.3% of sequences) were not classified to phylum level. A single OTU, common to both sponge individuals, dominates these unclassified reads and shares sequence homology with a sponge associated clone which itself has no known close relative and may represent a novel taxon.     

Coral Reef Community Composition in the Context of Disturbance History on the Great Barrier Reef,Australia

Much research on coral reefs has documented differential declines in coral and associated organisms. In order to contextualise this general degradation, research on community composition is necessary in the context of varied disturbance histories and the biological processes and physical features thought to retard or promote recovery. We conducted a spatial assessment of coral reef communities across five reefs of the central Great Barrier Reef, Australia, with known disturbance histories, and assessed patterns of coral cover and community composition related to a range of other variables thought to be important for reef dynamics. Two of the reefs had not been extensively disturbed for at least 15 years prior to the surveys. Three of the reefs had been severely impacted by crown-of-thorns starfish outbreaks and coral bleaching approximately a decade before the surveys, from which only one of them was showing signs of recovery based on independent surveys. We incorporated wave exposure (sheltered and exposed) and reef zone (slope, crest and flat) into our design, providing a comprehensive assessment of the spatial patterns in community composition on these reefs. Categorising corals into life history groupings, we document major coral community differences in the unrecovered reefs, compared to the composition and covers found on the undisturbed reefs. The recovered reef, despite having similar coral cover, had a different community composition from the undisturbed reefs, which may indicate slow successional processes, or a different natural community dominance pattern due to hydrology and other oceanographic factors. The variables that best correlated with patterns in the coral community among sites included the density of juvenile corals, herbivore fish biomass, fish species richness and the cover of macroalgae. Given increasing impacts to the Great Barrier Reef, efforts to mitigate local stressors will be imperative to encouraging coral communities to persist into the future.     

Seasonal Variation of Metals in Seawater, Sediment, and Manila Clam Ruditapes philippinarum from China

Concentrations of trace metals (Cu, Pb, Zn, Cd, Cr, Hg, and As) were determined for the first time in seawater, sediment, and Manila clam from Deer Island, Liaoning Province, China. The seawater, sediment, and clam samples were collected seasonally at three clam farming sites around Deer Island during 2010–2011. The average concentrations of Cu, Pb, Zn, Cd, Cr, Hg, and As in the seawater samples were 4.16, 0.72, 5.88, 0.45, 2.51, 0.03, and 1.02 μg/l, respectively. The seasonal variations of trace metals in seawater showed a significant difference in the concentrations of Cu, Pb, Zn, Hg, and As among seasons. The average concentrations of Cu, Pb, Zn, Cd, Cr, Hg, and As in the sediment samples were 6.43, 13.80, 53.08, 1.10, 36.40, 0.05, and 4.78 mg/kg dry weight, respectively. Trace metal concentrations in sediment seasonally varied significantly except for Cd and Hg. The average concentrations of Cu, Pb, Zn, Cd, Cr, Hg, and As in the clam samples were 11.28, 0.61, 92.50, 0.58, 3.98, 0.03, and 1.98 mg/kg dry weight, respectively. Concentrations of Cu, Zn, Cd, Cr, and As in Manila clam showed marked seasonal fluctuations with significant difference. Cu and Zn were the metals with the highest mean biosediment accumulation factor values in Manila clam. Besides, significant correlations for the concentrations of Cu and Zn relative to their concentrations in sediment were also found. Such differences in regression analyzes may be explained by differential bioaccumulation of essential and xenobiotic metals. Concentrations of trace metals in Manila clam did not exceed the maximum established regulatory concentrations for human consumption. Moreover, the calculations revealed that the estimated daily intake values for the examined clam samples were below the internationally accepted dietary guidelines and the calculated hazard quotient values were well less than 1, thus strongly indicating that health risk associated with the intake studied metals through the consumption of Manila clam from Deer Island was absent.     

Sediment Composition,Mud-water Interchanges and the Role of Macrophytes in Dal Lake,Kashmir

The particulate phase of lake sediments showed a marked reduction in the concentration of N, P, K and C during late spring and summer. Larger amounts of these elements were found towards the autumn, and these higher levels were maintained through winter until early spring. The reduction in the concentration of these mineral nutrients was greatest during the growing season of the macrophytes.     

Heterotrophic Activity Throughout a Vertical Profile of Seawater and Sediment in Halifax Harbor, Canada

The relative heterotrophic activity of marine microorganisms was determined at two sites by the heterotrophic uptake technique throughout the water column, the sediment-water interface, and the surface layer of sediment. In the water column, uptake was greatest at the surface and steadily decreased with depth. The percentage of the substrate that was respired also decreased with depth from 69 to 56%. The activity of the sediment-water interface was several orders of magnitude greater than that of the overlying water and twice that of the sediment immediately below. Hand-collected water samples carefully taken as close as 1 cm from the sediment-water interface had the same characteristically low activity as the bottom few meters of water. Microautoradiography with ³H-labeled glucose, glutamic acid, or thymidine revealed a general decrease in the percentage of active cells with depth from 35 to <1%. The number of active cells in the interface and sediment averaged <10% of the total population. The data indicate that the sediment-water interface is the most active region in this system due to an increased number of active cells rather than an increased percentage of active cells or increased per-cell activity.     

Bacterial Diversity Associated with Cinachyra cavernosa and Haliclona pigmentifera,Cohabiting Sponges in the Coral Reef Ecosystem of Gulf of Mannar,Southeast Coast of India

Sponges are abundant, diverse and functionally important organisms of coral reef ecosystems. Sponge-associated microorganisms have been receiving greater attention because of their significant contribution to sponge biomass, biogeochemical cycles and biotechnological potentials. However, our understanding of the sponge microbiome is limited to a few species of sponges from restricted geographical locations. Here, we report for the first time the bacterial diversity of two cohabiting sponges, viz. Cinachyra cavernosa and Haliclona pigmentifera, as well as that in the ambient water from the coral reef ecosystems of the Gulf of Mannar, located along the southeast coast of India. Two hundred and fifty two clones in the 16S rRNA gene library of these sponges were grouped into eight distinct phyla, of which four belonged to the core group that are associated only with sponges. Phylogenetic analysis of the core bacteria showed close affinity to other sponge-associated bacteria from different geographical locations. γ-Proteobacteria, Chloroflexi, Planctomycetes and Deferribacter were the core groups in C. cavernosa while β and δ-Proteobacteria performed this role in H. pigmentifera. We observed greater OTU diversity for C. cavernosa (H^ǀ 2.07) compared to H. pigmentifera (H^ǀ 1.97). UniFrac analysis confirmed the difference in bacterial diversity of the two sponge species and also between the sponges and the reef water (p<0.001). The results of our study restate the existence of a host driven force in shaping the sponge microbiome.     

Diversity of Methane-Cycling Archaea in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers

The zonation of anaerobic methane-cycling Archaea in hydrothermal sediment of Guaymas Basin was studied by general primer pairs (mcrI, ME1/ME2, mcrIRD) targeting the alpha subunit of methyl coenzyme M reductase gene (mcrA) and by new group-specific mcrA and 16S rRNA gene primer pairs. The mcrIRD primer pair outperformed the other general mcrA primer pairs in detection sensitivity and phylogenetic coverage. Methanotrophic ANME-1 Archaea were the only group detected with group-specific primers only. The detection of 14 mcrA lineages surpasses the diversity previously found in this location. Most phylotypes have high sequence similarities to hydrogenotrophs, methylotrophs, and anaerobic methanotrophs previously detected at Guaymas Basin or at hydrothermal vents, cold seeps, and oil reservoirs worldwide. Additionally, five mcrA phylotypes belonging to newly defined lineages are detected. Two of these belong to deeply branching new orders, while the others are new species or genera of Methanopyraceae and Methermicoccaceae. Downcore diversity decreases from all groups detected in the upper 6 cm (∼2 to 40°C, sulfate measurable to 4 cm) to only two groups below 6 cm (>40°C). Despite the presence of hyperthermophilic genera (Methanopyrus, Methanocaldococcus) in cooler surface strata, no genes were detected below 10 cm (≥60°C). While mcrA-based and 16S rRNA gene-based community compositions are generally congruent, the deeply branching mcrA cannot be assigned to specific 16S rRNA gene lineages. Our study indicates that even among well-studied metabolic groups and in previously characterized model environments, major evolutionary branches are overlooked. Detecting these groups by improved molecular biological methods is a crucial first step toward understanding their roles in nature.     

Persistence and Change in Community Composition of Reef Corals through Present,Past, and Future Climates

The reduction in coral cover on many contemporary tropical reefs suggests a different set of coral community assemblages will dominate future reefs. To evaluate the capacity of reef corals to persist over various time scales, we examined coral community dynamics in contemporary, fossil, and simulated future coral reef ecosystems. Based on studies between 1987 and 2012 at two locations in the Caribbean, and between 1981 and 2013 at five locations in the Indo-Pacific, we show that many coral genera declined in abundance, some showed no change in abundance, and a few coral genera increased in abundance. Whether the abundance of a genus declined, increased, or was conserved, was independent of coral family. An analysis of fossil-reef communities in the Caribbean revealed changes in numerical dominance and relative abundances of coral genera, and demonstrated that neither dominance nor taxon was associated with persistence. As coral family was a poor predictor of performance on contemporary reefs, a trait-based, dynamic, multi-patch model was developed to explore the phenotypic basis of ecological performance in a warmer future. Sensitivity analyses revealed that upon exposure to thermal stress, thermal tolerance, growth rate, and longevity were the most important predictors of coral persistence. Together, our results underscore the high variation in the rates and direction of change in coral abundances on contemporary and fossil reefs. Given this variation, it remains possible that coral reefs will be populated by a subset of the present coral fauna in a future that is warmer than the recent past.     

Influence of Coral Reef Rugosity on Fish Communities in Marine Reserves Around Lombok Island,Indonesia

Environmental Biology of Fishes - Coral reef structural form is widely considered a key factor with respect to the availability of shelter and foraging spaces for fishes and invertebrates. However,...     

Improved Isolation of Vibrio vulnificus from Seawater and Sediment with Cellobiose-Colistin Agar

An improved selective medium, cellobiose-colistin (CC) agar, gave a significantly higher (P < 0.05) isolation rate of Vibrio vulnificus from water and sediment samples than did modified cellobiose-polymyxin B-colistin (mCPC) agar. In a total of 446 alkaline peptone water preenrichments amended with polymyxin B, V. vulnificus was isolated from 154 preenrichments (35%) with mCPC agar and from 179 preenrichments (40%) with CC agar. CC agar gave a higher plating efficiency of V. vulnificus cells than did cellobiose-polymyxin B-colistin (CPC) agar, mCPC agar, or thiosulfate-citrate-bile salts-sucrose (TCBS) agar; the only significant difference was observed with TCBS agar, which gave much lower plating efficiencies than the other selective media. Determination of MICs demonstrated that the concentrations of colistin and polymyxin B in CPC agar inhibit growth of a proportion of V. vulnificus strains.     

极端嗜盐古菌遗传转化系统的研究

对极端嗜盐古菌遗传转化系统的研究进展进行了综述,内容包括抗性标记基因的选择,基因克隆和表达载体系统的发展以及受体系统的改造。     

Picoplankton dynamics in Davies Reef lagoon, the Great Barrier Reef, Australia

The diel variations in abundance and frequency of dividing cells(FDC) of coccoid cyanobacteria in a coral reef lagoon were investigatedin June, September and December 1989, and April 1990. Cyanobacteriaand picoplanktonic eukaryotes (<3 µm) were sampledmonthly from January to December 1990. The average abundancesof cyanobacteria and eukaryotes ranged between 1.17–10.0610⁴cells ml^–1 and 0.16–2.4110⁴ cells ml^–1, respectively,with abundances of both being higher in summer (November-April)than in winter (May-October). The ratio of cyanobacteria toeukaryotes fluctuated from 1.93 to 8.67, independent of theseasonal variation in their abundances. The instantaneous growthrate of cyanobacteria, which was estimated from the daytimeabundance increment, ranged between 0.430 and 3.144 day^–1The estimated daily specific growth rate of cyanobacteria bythe FDC method ranged between 0.231 and 0.966 day^–1. InApril, despite the high specific growth rate and low flushingconditions. cyanobacterial abundance showed a cyclic diel pattern,suggesting a strong grazing impact on their population.     

Assessment of Acropora palmata in the Mesoamerican Reef System

The once-dominant shallow reef-building coral Acropora palmata has suffered drastic geographical declines in the wider Caribbean from a disease epidemic that began in the late 1970s. At present there is a lack of quantitative data to determine whether this species is recovering over large spatial scales. Here, we use quantitative surveys conducted in 107 shallow-water reef sites between 2010 and 2012 to investigate the current distribution and abundance of A. palmata along the Mesoamerican Reef System (MRS). Using historical data we also explored how the distribution and abundance of this species has changed in the northern portion of the MRS between 1985 and 2010–2012. A. palmata was recorded in only a fifth of the surveyed reef sites in 2010–2012. In the majority of these reef sites the presence of A. palmata was patchy and rare. Only one site (Limones reef), in the northernmost portion of the MRS, presented considerably high A. palmata cover (mean: 34.7%, SD: 24.5%). At this site, the size-frequency distribution of A. palmata colonies was skewed towards small colony sizes; 84% of the colonies were healthy, however disease prevalence increased with colony size. A comparison with historical data showed that in the northern portion of the MRS, in 1985, A. palmata occurred in 74% of the 31 surveyed sites and had a mean cover of 7.7% (SD = 9.0), whereas in 2010–2012 this species was recorded in 48% of the sites with a mean cover of 2.9% (SD = 7.5). A. palmata populations along the MRS are failing to recover the distribution and abundance they had prior to the 1980s. Investigating the biological (e.g., population genetics) and environmental conditions (e.g., sources of stress) of the few standing reefs with relatively high A. palmata cover is crucial for the development of informed restoration models for this species.