Dissolved and particulate organic carbon in the Sea of Okhotsk

Data on distribution of dissolved and particulate organic matter obtained during Cruises 21 and 24 of R/V Akademik A. Nesmeyanov in June-August 1992 and 1993 are presented. In general a remarkable heterogeneity in distributions of both dissolved and particulate organic carbon is revealed. Concentrations of dissolved organic carbon vary from 98 to 700 µmol/l and those of particulate organic carbon vary from 3 to 50 µmol/l. Maximum concentrations are commonly observed in the shelf region while minimum concentrations - in the central basin. Run-off of the Amur River raises dissolved matter concentration in the Sakhalin Bay, while oil exploitation at the Sakhalin shelf maximizes particulate organic carbon concentration and minimizes dissolved one. Concentrations of dissolved and particulate organic carbon in the surface microlayer were estimated for the first time and are shown to be 1.5-2.0 times higher than in surface waters.

Hydrographic measurements from C.S.S. Hudson Cruise 82-002, Canadian Technical Report of Hydrography and Ocean Sciences No. 118, 112 pp (digital version)

This archive consists of the hydrographic data collected on Cruise 82-002 of C.S.S. Hudson, April 11 to May 2, 1982. 78 stations were occupied on a line running near 48°N from the mouth of the English Channel to the Grand Banks of Newfoundland. Pressure, temperature and salinity were measured by a Guildline digital CTP system. Salinity, dissolved oxygen, silicate, nitrate and phosphate were measured from water samples collected on the CTP upcasts. CTP and discrete bottle data and associated derived parameters are tabulated at standard levels. This is the digital version of the printed report (of 1989, see further details), published in 2006 with the information system Pangaea.

(Table 1) Productivity characteristics of phytoplankton and some concomitant factors in the Kara Sea in September 1993

Primary production in water column (P_p) varied from 107 to 312 mg C/m**2/day in Yenisey Bay: from 25 to 63 mg C/m**2/day in Obskaya Guba: and from 20 to 359 mg C/m**2/day in the open sea, that is: in the western Kara Sea and Ob-Yenisey shoals. The average concentration of chlorophyll a in the photosynthesis layer (C_ph) ranged from 0.2 to 1.8 mg/m**3 in these two regions, lower than in the estuaries of Ob (1.6-21.7 mg/m**3) and Yenisey (2.0-5.2 mg/m**3) Rivers. An inverse relation between surface salinity (S) and chlorophyll concentration (C_s) and chlorophyll concentration in the photosynthesis layer was found for all of the regions. The highest values of C_s and C_ph (0.8-22 mg/m**3) were measured at S<10 ppt, and the lowest values (0.2-0.8 mg/m**3) at S>22 ppt. A similar correlation of S with values of Pp occurred only in the Yenisey Bay and offshore regions. Obtained results agree well with the "outwelling" hypothesis. It states that large part of organic matter produced in estuaries is not used in estuarine trophic chains but is transported into adjacent sea areas and increases their productivity. Low values of Pp in the study regions may be attributed to such unfavorable factors as deficiency in nutrients, low temperature and turbidity, and lack of solar radiation.

Ingestion and clearance rates of Copepods

Feeding activity, selective grazing and the potential grazing impact of two dominant grazers of the Polar Frontal Zone, Calanus simillimus and Rhincalanus gigas, and of copepods < 2 mm were investigated with incubation experiments in the course of an iron fertilized diatom bloom in November 2000. All grazers were already actively feeding in the low chlorophyll waters prior to the onset of the bloom. C. simillimus maintained constant clearance rates and fed predominantly on diatoms. R. gigas and the small copepods strongly increased clearance and ingestion of diatoms in response to their enhanced availability. All grazers preyed on microzooplankton, most steadily on ciliates, confirming the view that pure herbivory appears to be the exception rather than the rule in copepod feeding. The grazers exhibited differences in feeding behavior based on selectivity indices. C. simillimus and R. gigas showed prey switching from dinoflagellates to diatoms in response to the phytoplankton bloom. All grazers most efficiently grazed on large diatoms leading to differences in daily losses for large and small species, e.g. Corethron sp. or Thalassionema nitzschioides. Species-specific diatom mortality rates due to grazing suggest that the high feeding activity of C. simillimus prior to and during the bloom played a role in shaping diatom population dynamics

(Table 1) Nutrient concentrations and carbon isotopes of sea ice segments and brine sampled during Nathaniel B. Palmer cruises NBP98-07 and NBP06-08, Ross Sea

We examined controls on the carbon isotopic composition of sea ice brines and organic matter during cruises to the Ross Sea, Antarctica in November/December 1998 and November/December 2006. Brine samples were analyzed for salinity, nutrients, total dissolved inorganic carbon (sum CO2), and the 13C/12C ratio of Sum CO2 (d13C(sum CO2)). Particulate organic matter from sea ice cores was analyzed for percent particulate organic carbon (POC), percent total particulate nitrogen (TPN), and stable carbon isotopic composition (d13C(POC)). Sum CO2 in sea ice brines ranged from 1368 to 7149 µmol/kg, equivalent to 1483 to 2519 µmol/kg when normalized to 34.5 psu salinity (s sum CO2), the average salinity of Ross Sea surface waters. Sea ice primary producers removed up to 34% of the available sum CO2, an amount much higher than the maximum removal observed in sea ice free water. Carbonate precipitation and CO2 degassing may reduce s sum CO2 by a similar amount (e.g., 30%) in the most hypersaline sea ice environments, although brine volumes are low in very cold ice that supports these brines. Brine d13C(sum CO2) ranged from -2.6 to +8.0 per mil while d13C(POC) ranged from -30.5 to -9.2 per mil. Isotopic enrichment of the sum CO2 pool via net community production accounts for some but not all carbon isotopic enrichment of sea ice POC. Comparisons of s sum CO2, d13C(sum CO2), and d13C(POC) within sea ice suggest that epsilon p (the net photosynthetic fractionation factor) for sea ice algae is ~8 per mil smaller than the epsilon p observed for phytoplankton in open water regions of the Ross Sea. These results have implications for modeling of carbon uptake and transformation in the ice-covered ocean and for reconstruction of past sea ice extent based on stable isotopic composition of organic matter in sediment cores.

Data on the biogeochemical cycle of methane in the ocean

Geological, mineralogical and microbiological aspects of the methane cycle in water and sediments of different areas in the oceans are under consideration in the monograph. Original and published estimations of formation- and oxidation rates of methane with use of radioisotope and isotopic methods are given. The role of aerobic and anaerobic microbial oxidation of methane in production of organic matter and in formation of authigenic carbonates is considered. Particular attention is paid to processes of methane transformation in areas of its intensive input to the water column from deep-sea hydrothermal sources, mud volcanoes, and cold methane seeps.

Optimization of sample preparation for next-generation sequencing with Illumina Genome Analyzer II

The growing interest for sequencing with higher throughput in the last decade has led to the development of new sequencing applications. This thesis concentrates on optimizing DNA library preparation for Illumina Genome Analyzer II sequencer. The library preparation steps that were optimized include fragmentation, PCR purification and quantification. DNA fragmentation was performed with focused sonication in different concentrations and durations. Two column based PCR purification method, gel matrix method and magnetic bead based method were compared. Quantitative PCR and gel electrophoresis in a chip were compared for DNA quantification. The magnetic bead purification was found to be the most efficient and flexible purification method. The fragmentation protocol was changed to produce longer fragments to be compatible with longer sequencing reads. Quantitative PCR correlates better with the cluster number and should thus be considered to be the default quantification method for sequencing. As a result of this study more data have been acquired from sequencing with lower costs and troubleshooting has become easier as qualification steps have been added to the protocol. New sequencing instruments and applications will create a demand for further optimizations in future.