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41 results for “CCE LTER”
Cell counts (per liter) by size groups of diatoms, autotrophic and heterotrophic plankton, via epifluorescent microscopy (EPI) from CCE LTER process cruises in the California Current region, 2006 - 2016.
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for abundance of diatoms, autotrophic (dinoflagellate and other eukaryotes) and heterotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the process cruises (since 2006, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore.
Size group (pico, nano, micro) and group total carbon estimates from cell counts via epifluorescent microscopy (EPI) of heterotrophic and autotrophic plankton from CCE LTER process cruises in the California Current region, 2006 - 2016
Microbial community assemblages of the California Current Ecosystem (CCE) are assessed for biomass of heterotrophic (dinoflagellate and other eukaryotes) and autotrophic (dinoflagellate and other eukaryotes) plankton using high-throughput digital epifluorescence microscopy (EPI). Samples to estimate the nano- and microplankton (0.2-2.0-µm and 2.0-20-µm size, respectively) are collected at various depths, preserved, stained, and filtered onto a membrane filter and mounted on a glass microscope slide aboard the process cruises (since 2006, ongoing). Slides are then frozen at -80°C for subsequent imaging and analysis in the laboratory onshore. Carbon biomass is computed from cell biovolumes.
Chlorophyll and phaeopigments measured from discrete bottle samples from CCE LTER P0904 student cruise in the California Current System, determined by extraction and bench fluorometry, April 2009.
Discrete bottle samples taken from various depths in the California Current System aboard CCE LTER P0904 student cruise. Samples were frozen aboard the ship and taken back to the lab for extraction and analysis. Samples are filtered (known volumes) onto GF/F filters. The filters are placed into culture tubes containing 90% acetone, and the fluorescence of the samples is read on a fluorometer after 24 to 48 hours. The samples are then acidified to degrade the chlorophyll to phaeopigments (non-photosynthetic pigments) and a second reading is taken. The readings prior to and after acidification are used to calculate concentrations of both chlorophyll a and phaeopigments (i.e. phaeophytin).
Parameters from discrete bottle samples on a hydrographic CTD (Conductivity Temperature Depth) cast during CCE LTER P0904 student cruise, April 2009.
Hydrographic CTD (Conductivity Temperature Depth) measurements from discrete water samples are taken on individual CTD rosette casts, deployed on CCE P0904 student cruise in the Southern California region. Seawater is collected in up to 24 Niskin bottles at specific depths (up to 1000m), determined by the chlorophyll maximum and mixed layer depth as the instrument is lowered through the water column. The samples are filtered and analyzed at sea and used to assess the CTD sensor data quality. Measurements include depth, temperature, salinity, density (sigma theta), oxygen, O2 saturation, PAR (radiation, surface radiation and irradiance), fluorescence and transmission. Salinity checks are performed with a salinometer back at the lab.
Conductivity Temperature Depth (CTD) sensor profile data binned by depth from stations within the CCE region from CCE LTER P0904 student cruise, April 2009.
Data from deployed Seabird 911 CTD mounted on a 24-bottle rosette during P0904 student cruise in the CCE region. The CTD-rosette is lowered into the ocean (to depths up to 1000m) at selected hydrographic stations and multiple times across fronts, using the ship's conductive-wire winch. Data from many sensors are transmitted up the conductive wire and displayed real-time on a data aquistion computer. Discrete seawater samples are collected in 10L bottles at specific depths determined by the chlorophyll maximum and mixed layer depth. These samples are analyzed at sea and used to assess the CTD sensor data quality, plus measure additional properties. Processed CTD profile data are binned by depth and include: depth, temperature, salinity, density (sigma theta), oxygen, O2 saturation, PAR (radiation, surface radiation, and % irradiance), fluorescence, transmission, and nitrate. These data are then compared to the seawater sample data, and corrected if necessary.
Fecal pellet flux summary from samples collected during CCE LTER process cruises in the California Current system, 2007 – present.
The collection and enumeration of sinking fecal pellets on CCE LTER Process cruises has been led by Mike Stukel since 2007. Sinking particles are collected in VERTEX-style particle interceptor traps (PIT) with an 8:1 aspect ratio, 70-mm diameter, and a baffle on top comprised of 13 smaller beveled tubes with a similar 8:1 aspect ratio. Tubes are deployed with a formalin-brine for a duration of 2-5 days. After recovery, samples are gently split on a Folsom splitter and typically 3/8 to 1/2 of two separate tubes are utilized for fecal pellet enumeration. After the cruise, samples for fecal pellet enumeration are placed in a settling chamber to allow fecal pellets to settle out. Overlying water is then strained through a 60-um filter to collect any pellets that may have remained in the water. Pellets were then placed on a gridded Petri dish and analyzed using a Zeiss Discovery stereomicroscope. Pellets were separated from other particles and photographed with a dedicated camera. Image processing was then conducted using either Image J or Image Pro to extract area and maximum feret length for each fecal pellet. Pellets were classified by shape and shape-appropriate equations were used to determine the volume of each fecal pellet. Volume was converted to mass using the equations in Stukel et al. (2013). Fecal pellet mass flux is the sum of the mass of all fecal pellets for a sample multiplied by a conversion factor that takes into account the proportion of the gridded petri dish that was enumerated, the fraction of the PIT tube that was used for fecal pellet enumeration, the cross-sectional area of the PIT tube, and the deployment duration. Standard error of the mean is determined from the two samples enumerated for each sediment trap deployment. For more details please see Stukel et al. (2013) or Morrow et al. (submitted). Knauer, G. A., J. H. Martin and K. W. Bruland (1979). "Fluxes of particulate carbon, nitrogen, and phosphorus in the upper water column of the Northe
Picophytoplankton and bacteria abundances analyzed with flow cytometry (FCM) from CCE LTER process cruises the California Current region, 2006 - 2017.
Picophytoplankton populations and non-pigmented prokaryotes are sampled within the California Current Ecosystem (CCE) for abundances at various depths. Seawater is collected from Niskin bottles and cells are fixed in the field aboard the process cruises (since 2006, ongoing) with paraformaldehyde, and stained with a DNA-specific dye back in the laboratory. The cells are enumerated by an Altra flow cytometer (with a syringe pump for volumetric sample delivery) simultaniously with argon ion lasers, to distinguish three major populations of photoautotrophs (Prochlorococcus, Synechococcus, and pico-eukaryotes) and the assemblage of heterotrophic prokaryotes collectively referred to as H-Bact.
Conductivity Temperature Depth (CTD) sensor profile data binned by depth from stations within the CCE region from CCE LTER process cruises, 2006 - 2017 (ongoing).
Since 2006 (ongoing), the CCE LTER program has deployed a Seabird 911 CTD mounted on a 24-bottle rosette during Process cruises in the CCE region. The CTD-rosette is lowered into the ocean (to depths up to 1000m) at selected hydrographic stations and multiple times across fronts, using the ship's conductive-wire winch. Data from many sensors are transmitted up the conductive wire and displayed real-time on a data aquistion computer. Discrete seawater samples are collected in 10L bottles at specific depths determined by the chlorophyll maximum and mixed layer depth. These samples are analyzed at sea and used to assess the CTD sensor data quality, plus measure additional properties. Processed CTD profile data are binned by depth and include: depth, temperature, salinity, density (sigma theta), oxygen, O2 saturation, PAR (radiation, surface radiation, and % irradiance), fluorescence, transmission, and nitrate. These data are then compared to the seawater sample data, and corrected if necessary.
High Performance Liquid Chromatography (HPLC) pigment analysis from rosette bottle samples at various depths from CCE LTER process cruises in the California Current System, 2006 to 2017.
High Performance Liquid Chromatography (HPLC) samples are collected from rosette bottles (from three to eight different depths in the photic zone) at stations located within the CCE region on Process cruises (since 2006, ongoing). The HPLC method is used to measure concentrations of chlorophylls and carotenoids in samples of particulate matter, which includes filtering and freezing the filter while at sea. The taxon-specific phyto-pigments are extracted back onshore. Concentrations of chlorophyll a are used as a proxy for phytoplankton biomass and concentrations of other taxon-specific pigments are used to determine contributions of phytoplankton taxa to total phytoplankton biomass.
Picophytoplankton and bacteria total carbon estimates from cell counts analyzed with flow cytometry (FCM) from CCE LTER process cruises in the California Current region, 2006 - 2017.
Picophytoplankton populations and non-pigmented prokaryotes are sampled within the California Current Ecosystem (CCE) for abundances from various depths. Seawater is collected from Niskin bottles and cells are fixed in the field aboard the survey cruises (since 2004, ongoing) with paraformaldehyde, and stained with a DNA-specific dye back in the laboratory. The cells are enumerated by an Altra flow cytometer (with a syringe pump for volumetric sample delivery) simultaniously with argon ion lasers, to distinguish three major populations of photoautotrophs (Prochlorococcus, Synechococcus, and pico-eukaryotes) and the assemblage of heterotrophic prokaryotes collectively referred to as H-Bact. FCM abundance estimates for each are converted to carbon biomass equivalents using mixed-layer estimates.
Nitrate uptake estimates phytoplankton incorporation of dissolved NO3- at selected depths from CCE LTER process cruises in the California Current System, 2011 – 2016 (ongoing).
Nitrate uptake samples (1.1-L) of seawater are taken each day shortly before noon on the CTD rosette up-cast during the CCE Process cruises (since 2011, ongoing). Approximate nitrate concentrations are determined at sea and the samples are spiked with 15NO3- at a concentration equivalent to ~10% ambient nitrate. Samples (one sample per depth) are incubated for 24 hours in polycarbonate bottles held at natural light and temperature conditions on the in situ array. After recovery samples are filtered onto pre-combusted GF/F filters, which are analyzed for particulate nitrogen and δ15N by mass spectrometry in the Scripps Analytical Facility. Accurate nitrate concentrations are determined after the cruise from frozen and filtered samples analyzed by autoanalyzer (see separate Dissolved Inorganic Nutrients dataset by Ralf Goericke). Nitrate uptake is calculated using the equations in Dugdale & Wilkerson (1986). In surface waters where nitrate concentrations are often quite low, we spike with a minimum of 10 nmol L-1 15NO3-. Since this can lead to a bias (high) in calculated nitrate uptake, when post-cruise nitrate analyses showed that our spike concentration was greater than 10% of ambient nitrate, we multiplied by the uptake calculated from the equations of Dugdale & Wilkerson (1986) by (ambient NO3-)/(ambient NO3- + added 15NO3-). Primary production was simultaneously estimated from 14C uptake in triplicate 250-mL bottles (plus a dark bottle) incubated similarly on the in situ array (see separate Primary Production – Particulate dataset by Ralf Goericke). We calculated f-ratios by assuming that phytoplankton uptake occurred at Redfield carbon:nitrogen ratios of 106:16 (mol:mol). To eliminate the impact of phytoplankton that may be engaged in luxury nitrate uptake in the deep euphotic zone, we also report conservative nitrate uptake, which is the minimum of nitrate uptake or primary production divided by the Redfield C:N ratio. This value thus sets a maximum for nitrate
Sediment trap Rhizaria flux from sediment trap samples collected aboard CCE LTER process cruises in the California Current system, 2011 - present.
The collection and enumeration of sinking rhizarian cells on CCE LTER Process cruises has been led by Mike Stukel since 2007. Sinking particles are collected in VERTEX-style particle interceptor traps (PIT) with an 8:1 aspect ratio, 70-mm diameter, and a baffle on top comprised of 13 smaller beveled tubes with a similar 8:1 aspect ratio. Typically 8-12 tubes were deployed with a formalin-brine for a duration of 2-5 days. After recovery, samples were immediately gravity filtered through a 47-mm, 200-μm mesh nitex filter and analyzed under a stereomicroscope. The two dominant taxa of giant rhizaria (Aulosphaeridae and Castanellidae) were then enumerated in each sample. We note, however, that at least two distinct morphotypes of Aulosphaeridae were seen in the sample (but analyzed together because they had similar size and shape) and several smaller rhizarian taxa were also noticed, but not quantified because they are likely not quantitatively captured by our 200-μm filter. Mean and standard deviation of samples from different tubes are reported for each depth. For more details please see Stukel et al. (2013) or Biard et al. (submitted). Biard, T., J. W. Krause, M. R. Stukel and M. D. Ohman (submitted). "The significance of giant Phaeodarians (Rhizaria) to biogenic silica export in the California Current Ecosystem." Global Biogeochem. Cycles. Knauer, G. A., J. H. Martin and K. W. Bruland (1979). "Fluxes of particulate carbon, nitrogen, and phosphorus in the upper water column of the Northeast Pacific." Deep-Sea Research 26(1): 97-108. Stukel, M. R., M. D. Ohman, C. R. Benitez-Nelson and M. R. Landry (2013). "Contributions of mesozooplankton to vertical carbon export in a coastal upwelling system." Marine Ecology Progress Series 491: 47-65
Carbon:234Thorium ratios of sinking particles collected by sediment trap and large particles collected by in situ pump on CCE-LTER Process Cruises. 2006 - 2017 (ongoing).
The ratio of carbon to 234Thorium on particles can be used to convert water column 234Th measurements to sinking carbon flux estimates and to investigate particle scavenging in the ocean. Carbon:234Th ratios of two types of particles are measured: true sinking particles collected by sediment trap and large (>50-µm) particles collected using a McLane in situ Pump. Sinking particles are collected in VERTEX-style particle interceptor traps (PIT) with an 8:1 aspect ratio, 70-mm diameter, and a baffle on top comprised of 13 smaller beveled tubes with a similar 8:1 aspect ratio. Tubes are deployed with a formalin-brine for a duration of 2-5 days. After recovery, samples were gravity filtered through a 200-µm filter. The 200-µm filtered was then immediately examined under a stereomicroscope and mesozooplankton swimmers were removed from the sample. On P0704, P0810, and P1106 cruises the remaining (non-swimmer) portion of the material on the >200-µm filter was then re-combined with the <200-µm portion of the sample. Samples were then filtered through a pre-combusted quartz (QMA) filter. On P1208, P1604, and P1706 cruises the >200-µm and <200-µm fractions were filtered separately onto QMA filters to determine C:234Th ratios of different size classes of sinking particles. Typically, triplicate whole PIT tubes were filtered for C:234Th ratios. However, on some cycles with very high flux, samples were first split on a Folsom splitter. On some cycles, the mesozooplankton ‘swimmers’ were saved and filtered onto a separate QMA filter to quantify the C:234Th ratio of mesozooplankton. QMA filters were all dried and mounted in RISO sample holders. >50-µm particles were also collected using McLane in situ pumps (typically deployed for a period of ~1 hour at the same depth of the sediment traps). In situ pump samples were rinsed off of the 147-mm nitex mesh filters used with the pump onto a pre-combusted QMA filter, which was similarly dried and mounted in a RISO sample holder. Samples
Selected modeled output variables from ROMS 4DVAR model fits for the P1706 and P1604 CCE-LTER process cruises
Values for Kz and w were extracted from a three-dimensional physical model (9 km horizontal resolution, 42 vertical layers) developed using the Regional Ocean Modeling System (ROMS) four-dimensional variational data assimilation system (4DVAR) (Moore et al., 2011), then depth-interpolated linearly to calculate values at the MLD. Initial and boundary conditions were taken from the California Current System Reanalysis product produced by the University of California, Santa Cruz. Surface forcing was taken from the 9-km resolution Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS) (Doyle, Jiang, Chao, & Farrara, 2009; Hodur, 1997). We assimilated satellite remote sensing products (sea surface height from Ssalto/Duacs and sea surface temperature from AVHRR) and in situ temperature and salinity data vertical profiles collected during CTD measurements on our cruise. Assimilated data were used to update model initial conditions and surface forcing to generate a dynamically-consistent month-long model fit covering the duration of each cruise and producing 8-hr averaged outputs. For detailed descriptions of our ROMS 4DVAR approach, see (Song et al., 2012) and (Miller, Song, & Subramanian, 2015). Kz and w were interpolated to CTD cast locations from the 9-km ROMS 4DVAR solution using bilinear 2D interpolation from the four points comprising the nearest neighbors to the cast coordinates.
Integrated daily photosynthetically active radiation (PAR) measured aboard CCE LTER process cruises in the California current, 2006, 2007 and 2008.
Photosynthetically active radiation designates the spectral range (wave band) of solar radiation from 400 to 700 nanometers that photosynthetic organisms are able to use in the process of photosynthesis. Daily integrated values were produced for days during three CCE LTER process cruises in the California Current region in 2006, 2007 and 2008.
Photosynthetically active radiation (PAR) at depths from 0 to 100 meters, expressed as percentage of surface PAR, measured aboard CCE LTER process cruises in the California current, 2006, 2007 and 2008.
Photosynthetically active radiation designates the spectral range (wave band) of solar radiation from 400 to 700 nanometers that photosynthetic organisms are able to use in the process of photosynthesis. Daily values at depths from 0 to 100 meters, expressed as percentage of surface PAR were produced for days during three CCE LTER process cruises in the California Current region in 2006, 2007 and 2008.
N-S and E-W components of the current (averaged by cruise cycle) as measured by a shipboard Acoustic Doppler Current Profiler (ADCP) aboard the CCE LTER process cruise in the California Current region, 2007.
Underway measurements by the ADCP are made (about every 15 mins) on cruises to determine how fast water is moving across an entire water column, then averaged by cruise cycle. The ADCP measures the absolute speed of water currents with sound waves (Doppler effect) at multiple depths within the water column, and profile data are available immediately. For these data, the N-S and E-W components of the current were averaged by cycle.
Index of visual monitoring efforts, weather conditions and position updates from CalCOFI cruises in the California Current System, 2008 - 2009. This dataset has been superseded by knb-lter-cce.262.
Field observations are carried out to gain understanding of cetacean ecology and habitat. Visual monitoring for cetaceans has been conducted on quarterly CalCOFI cruises since July 2004 using standard line-transect protocol (Burnham et al. 1980;Buckland et al. 1993; Barlow 1995). Visual observers watch during daylight hours, when weather permits (Beaufort sea states 0 to 5 and visibility greater than 1 nautical mile) and while the ship transits between CalCOFI stations.
Index of visual monitoring, location, species behavior, and identification from CalCOFI cruises in the California Current System, 2008 - 2009. This dataset has been superseded by knb-lter-cce.262.
Visual monitoring efforts for cetaceans has been conducted on quarterly CalCOFI cruises since July 2004. This effort utilizes a standard line-transect protocol (Burnham et al. 1980;Buckland et al. 1993; Barlow 1995). Visual observers watch during daylight hours, when weather permits (Beaufort sea states 0 to 5 and visibility greater than 1 nautical mile) and while the ship transits between CalCOFI stations. A team of two observers search for cetaceans in a 90 degree field of view from the bow to beam of the ship, alternating between 18 and 50 power binoculars and the naked eye.
This data set is six 30-day ocean state estimation products for LTER-CCE cruises. The time periods of data assimilation fits for each LTER-CCE cruise are the following: 2006: 5/8 - 6/6, 2007: 4/1- 4/30, 2008 : 10/1 - 10/30, 2009 : 4/15 - 5/14, 2011 : 6/17 - 7/16, 2012 : 7/27 - 8/25
Used the sea surface height, sea surface temperature data measured from the space, and in situ temperature and salinity data from varied observational platforms including CCE-LTER cruises, we constrained the numerical ocean circulation model, Regional Ocean Modeling System (ROMS), so that the model simulation closely follows the observed ocean states. Data files are in netcdf format containing longitude, latitude, bathymetry, sea surface height, ocean current, temperature, salinity, density anomaly and surface fluxes. ROMS has a terrain following vertical coordinate and resolves shallow coastal regions better by construction. As a result, the depth of vertical level changes depending on the depth of bathymetry. This data set is the product of the investigations presented in Miller, A. J., H. Song and A. C. Subramanian, 2015: The physical oceanographic environment during the CCE-LTER years: Changes in climate and concepts. Deep-Sea Research II, 112, 6-17. Song, H., A. J. Miller, S. McClatchie, E. D. Weber, K. M. Nieto and D. M. Checkley, 2012: Application of a data-assimilation model to variability of Pacific sardine spawning and survivor habitats with ENSO in the California Current System. Journal of Geophysical Research-Oceans, 117, C03009, doi:10.1029/2011JC007302. We gratefully acknowledge continued funding from NSF (California Current Ecosystem LTER: OCE-0417616 and OCE-1026607) and NOAA (IOOS: NA17RJ1231)
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