Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea.

BACKGROUND: Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly delineated. By exploiting the persistent stratification of the South China Sea (SCS), we performed a 2-year, large spatial scale (10, 100, 1000, and 3000 m) survey, which included a pilot study in 2006 and comprehensive sampling in 2007, to investigate the biological zonation of bacteria and archaea using 16S rRNA tag and shotgun metagenome sequencing. RESULTS: Alphaproteobacteria dominated the bacterial community in the surface SCS, where the abundance of Betaproteobacteria was seemingly associated with climatic activity. Gammaproteobacteria thrived in the deep SCS, where a noticeable amount of Cyanobacteria were also detected. Marine Groups II and III Euryarchaeota were predominant in the archaeal communities in the surface and deep SCS, respectively. Bacterial diversity was higher than archaeal diversity at all sampling depths in the SCS, and peaked at mid-depths, agreeing with the diversity pattern found in global water columns. Metagenomic analysis not only showed differential %GC values and genome sizes between the surface and deep SCS, but also demonstrated depth-dependent metabolic potentials, such as cobalamin biosynthesis at 10 m, osmoregulation at 100 m, signal transduction at 1000 m, and plasmid and phage replication at 3000 m. When compared with other oceans, urease at 10 m and both exonuclease and permease at 3000 m were more abundant in the SCS. Finally, enriched genes associated with nutrient assimilation in the sea surface and transposase in the deep-sea metagenomes exemplified the functional zonation in global oceans. CONCLUSIONS: Prokaryotic communities in the SCS stratified with depth, with maximal bacterial diversity at mid-depth, in accordance with global water columns. The SCS had functional zonation among depths and endemically enriched metabolic potentials at the study site, in contrast to other oceans.

An Ultra-clean Multilayer Apparatus for Collecting Size Fractionated Marine Plankton and Suspended Particles.

The distributions of many trace elements in the ocean are strongly associated with the growth, death, and re-mineralization of marine plankton and those of suspended/sinking particles. Here, we present an all plastic (Polypropylene and Polycarbonate), multi-layer filtration system for collection of suspended particulate matter (SPM) at sea. This ultra-clean sampling device has been designed and developed specifically for trace element studies. Meticulous selection of all non-metallic materials and utilization of an in-line flow-through procedure minimizes any possible metal contamination during sampling. This system has been successfully tested and tweaked for determining trace metals (e.g., Fe, Al, Mn, Cd, Cu, Ni) on particles of varying size in coastal and open ocean waters. Results from the South China Sea at the South East Asia Time-Series (SEATS) station indicate that diurnal variations and spatial distribution of plankton in the euphotic zone can be easily resolved and recognized. Chemical analysis of size-fractionated particles in surface waters of the Taiwan Strait suggests that the larger particles (>153 µm) were mostly biologically derived, while the smaller particles (10 - 63 µm) were mostly composed of inorganic matter. Apart from Cd, the concentrations of metals (Fe, Al, Mn, Cu, Ni) decreased with increasing size.

Carbon and nitrogen isotopic compositions of particulate organic matter and biogeochemical processes in the eutrophic Danshuei Estuary in northern Taiwan.

The Danshuei Estuary is distinctive for the relatively short residence time (1-2 d) of its estuarine water and the very high concentration of ammonia, which is the dominant species of dissolved inorganic nitrogen in the estuary, except near the river mouth. These characteristics make the dynamics of nitrogen cycling distinctively different from previously studied estuaries and result in unusual isotopic compositions of particulate nitrogen (PN). The delta(15)N(PN) values ranging from -16.4 per thousand to 3.8 per thousand lie in the lower end of nitrogen isotopic compositions (-16.4 to +18.7 per thousand) of suspended particulate matter observed in estuaries, while the delta(13)C values of particulate organic carbon (POC) and the C/N (organic carbon to nitrogen) ratios showed rather normal ranges from -25.5 per thousand to -19.0 per thousand and from 6.0 to 11.3, respectively. There were three major types of particulate organic matter (POM) in the estuary: natural terrigenous materials consisting mainly of soils and bedrock-derived sediments, anthropogenic wastes and autochthonous materials from the aquatic system. During the typhoon induced flood period in August 2000, the flux-weighted mean of delta(13)C(POC) values was -24.4 per thousand, that of delta(15)N(PN) values was +2.3 per thousand and that of C/N ratio was 9.3. During non-typhoon periods, the concentration-weighted mean was -23.6 per thousand for delta(13)C(POC), -2.6 per thousand for delta(15)N(PN) and 8.0 for C/N ratio. From the distribution of delta(15)N(PN) values of highly polluted estuarine waters, we identified the waste-dominated samples and calculated their mean properties: delta(13)C(POC) value of -23.6+/-0.7 per thousand, delta(15)N(PN) value of -3.0+/-0.1 per thousand and C/N ratio of 8.0+/-1.4. Using a three end-member mixing model based on delta(15)N(PN) values and C/N ratios, we calculated contributions of the three major allochthonous sources of POC, namely, wastes, soils and bedrock-derived sediments, to the estuary. Their contributions were, respectively, 83%, 12% and 5% under non-typhoon conditions, and 9%, 63% and 28% under typhoon conditions. The autochthonous POM had the most varied isotopic compositions, encompassing the full ranges of delta(13)C(POC) (-25.5 to -19.1 per thousand), delta(15)N(PN) (-16.4-3.8 per thousand) and C/N ratio (6.0-11.3). The heavy end of the carbon isotopic composition reflected the typical marine condition and the lower end the estuarine condition, which probably had elevated concentrations of dissolved inorganic carbon with low delta(13)C values due to input from decomposition of organic matter. The lack of isotopically heavy PN, as found in larger estuaries, was attributed to isotopically light starting materials, namely, anthropogenic wastes, the slow phytoplankton growth within the estuary and the rather short residence time; the latter two factors made (15)N enrichment during ammonia consumption very limited. The most isotopically light PN likely originated from phytoplankton incorporating (15)N-depleted nitrate near the river mouth, where ammonia inhibition of nitrate uptake probably stopped.

Modelling diagnosis of heavy metal (copper) transport in an estuary.

A vertical (laterally-averaged) two-dimensional heavy metal transport model was developed to simulate the fluxes of copper in the Danshuei River estuarine system. The toxic model was incorporated into the hydrodynamic, the salt transport and the sediment transport modules. The model has been validated with observed time series data of water surface elevation, current, salinity, and suspended sediment concentrations in 2001 and 2002. An exponential relationship was established to relate variation in partition coefficient of copper to salinity and suspended sediment concentrations in the Danshuei River estuary. Comparisons of the total, dissolved, and particulate copper concentrations calculated by the numerical model and field data along the Danshuei River-Tahan Stream show good agreement. It is noteworthy that the model requires a point source of total copper with the strength of 250 kg/day to account for the observed persistently high total copper concentration near Hsin-Hai Bridge in the Tahan Stream, about 24 km upriver from the river mouth. The huge garbage dump site near the Hsin-Hai Bridge is likely the source of heavy metal pollution. The validated model was then applied to investigate the tidally averaged salinity distributions, residual circulation, suspended sediment, and total copper concentrations under low flow condition. The residual circulation is characterized by the upriver movement of denser saline water in the lower layer and the downriver movement of fresher water in the upper layer. The circulation pattern is driven by the longitudinal gradient of salinity distribution. The residual circulation occurs in the deep channel of Kuan-Du Bridge and Taipei Bridge. Under low flow condition, the limits of salt intrusion are located at Hsin-Hai Bridge. The tidally-averaged sediment concentration distribution exhibits a local maximum concentration around the null point in the Danshuei River-Tahan Stream. A local maximum of total copper concentration, which is nearly as high as that near the point source, occurs around the null point, which is potentially a hot spot of heavy metal accumulation.

Clean Sampling and Analysis of River and Estuarine Waters for Trace Metal Studies.

Most of the trace metal concentrations in ambient waters obtained a few decades ago have been considered unreliable owing to the lack of contamination control. Developments of some techniques aiming to reduce trace metal contamination in the last couple of decades have resulted in concentrations reported now being orders of magnitude lower than those in the past. These low concentrations often necessitate preconcentration of water samples prior to instrumental analysis of samples. Since contamination can appear in all phases of trace metal analyses, including sample collection (and during preparation of sampling containers), storage and handling, pretreatments, and instrumental analysis, specific care needs to be taken in order to reduce contamination levels at all steps. The effort to develop and utilize "clean techniques" in trace metal studies allows scientists to investigate trace metal distributions and chemical and biological behavior in greater details. This advancement also provides the required accuracy and precision of trace metal data allowing for environmental conditions to be related to trace metal concentrations in aquatic environments. This protocol that is presented here details needed materials for sample preparation, sample collection, sample pretreatment including preconcentration, and instrumental analysis. By reducing contamination throughout all phases mentioned above for trace metal analysis, much lower detection limits and thus accuracy can be achieved. The effectiveness of "clean techniques" is further demonstrated using low field blanks and good recoveries for standard reference material. The data quality that can be obtained thus enables the assessment of trace metal distributions and their relationships to environmental parameters.

Silver concentrations in Colorado, USA, watersheds using improved methodology.

River water samples were collected at five sites in the state of Colorado, USA, to assess the impact of municipal and industrial discharges on Ag concentrations and speciation in surface waters. Samples were collected and analyzed for total (unfiltered collections), filtered (0.1 and 0.4 microm), particulate (> or = 0.45 microm), and colloidal Ag (3 kDa-0.1 m) using ultraclean protocols. A series of laboratory experiments were conducted to assess bias from sample storage, digestion, and preconcentration protocols. In general, upstream unfiltered and particulate Ag concentrations fell within a fairly narrow range, 3.1 to 21 ng/L and 0.2 to 1.7 microg/g, respectively. Downstream unfiltered and particulate Ag concentrations showed a more broad range, 2.8 to 1,110 ng/L and 0.5 to 104 microg/g, respectively, and reflected attenuated impacts of Ag-laden discharge effluents. However, Ag concentrations in the 0.1-microm filter-passing fraction 0.8 to 1.2 km downstream from major treatment plant effluents were all below the chronic silver criteria. On average, more than 60% of the 0.1-microm filter-passing Ag was associated with colloidal macromolecular organic matter. Silver concentrations in colloids (microg/g) were, on average, the same as those in suspended particulate matter. The percentage abundance of colloidal Ag was similar to that of dissolved organic carbon, suggesting that strong Ag binding ligands exist in both the colloidal and the particle size fractions, as these macromolecular ligands likely play a major role in Ag speciation.

Geochemical behavior of 210Pb and 210Po in the nearshore waters off western Taiwan.

Dissolved and particulate (210)Pb and (210)Po were determined at 15 stations along the coastline off western Taiwan in April 2007. The (210)Pb activities in dissolved and particulate phases fell within a relatively small range of 2.4-5.2 dpm 100 L(-1) and 1.0-3.2 dpm 100 L(-1), respectively. The dissolved and particulate (210)Po activities also fell within a small range of 0.8-3.4 dpm 100 L(-1) and 1.1-2.9 dpm 100 L(-1), respectively. The correlation of the distribution coefficients (K(d)) of (210)Pb and (210)Po with particle concentration in turbid waters are not as evident as in the open ocean. The mass balance calculation shows that the residence times of (210)Pb and (210)Po with respect to particle removal from the nearshore waters ranges from 3 to 15 days and from 14 to 125 days, respectively. The flux of particulate organic carbon was estimated by (210)Po proxy and ranged from 4.8 to 33.7 mmol-C m(-2) d(-1).

Distributions and removal fluxes of trace metals in the water column of the Hung-Tsai Trough off southwestern Taiwan.

Vertical profiles of dissolved and particulate Mn, Fe, Ni, Cu, Zn, Cd, Pb, and (234)Th were determined in the Hung-Tsai Trough off southwestern Taiwan during 19-23 November, 2004. Except in the case of Cd, the distribution coefficient (K(d)) of the trace elements showed a negative correlation with the suspended particle concentration. Based on the average K(d) values, the general sequence of particle affinities for the eight trace elements is, from highest to lowest, Fe>Mn≈Pb>Zn≈Th>Cd≈Cu≈Ni. The trace metal data was coupled with the particle removal flux estimated from (234)Th/(238)U disequilibrium to investigate metal removal by particle sinking from the euphotic layer. The residence time of trace elements with respect to particle removal from the euphotic layer was estimated. A negative correlation between the residence time and the distribution coefficient for the trace metals was found.

Removal fluxes of Mn and Fe from the nearshore waters along the west coast of Taiwan.

Dissolved and particulate Mn and Fe in the nearshore waters were determined at 27 stations along the west coast of Taiwan during 19-23 November 2004. The latitudinal distributions of Mn and Fe were very similar; however, the concentration in the dissolved phase was lower, whereas that in the particulate phase was higher in the northern regime. The higher percentage of Fe than Mn that was associated with particles resulted in a two-order of magnitude higher particle-water partition coefficient for Fe, K(d)(Fe), than that for Mn, K(d)(Mn). The removal fluxes of Mn and Fe could be estimated by multiplying the particulate (234)Th removal flux with the Mn/(234)Th and Fe/(234)Th ratios in suspended particles, which ranged from 0.1 to 3.8 mmol m(-2) d(-1) for Mn, and from 3.4 to 194.5 mmol m(-2) d(-1) for Fe. Residence times ranged from 1 to 20 days for Mn and Fe were estimated in the nearshore.