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41 results for “CCE LTER”
Thresholds and Regime Shifts at Four LTER Sites (CCE, JRN, PAL, SBC) 1951-2009
The existence and causes of abrupt transitions, thresholds, or regime shifts between ecosystem states is of great concern because the likelihood of such transitions is predicted to increase. The science for measuring and responding to state changes, however, is not well developed. This limitation stems from a lack of data-supported case studies of abrupt transitions in all but a few well-studied ecosystems. We used 30-60 years of data on biological responses and putative drivers from ocean, coastal, polar, and dryland ecosystems to illustrate general approaches to analysis of abrupt transitions. The analyses indicate one case in which the state or response variable (krill abundance) tracked abrupt changes in the driver (Pacific Decadal Oscillation) in a linear fashion. Response variables in other cases (sea cucumber abundance, penguin abundance, and perennial grass production) exhibited hysteretic relationships to drivers (wave intensity, sea ice duration, and monsoonal rainfall amounts, respectively) through a variety of response mechanisms. The analyses illustrate that 1) a suite of common concepts and approaches can be used across disparate systems, 2) there are generally insufficient data for the use of leading indicators, particularly considering the abruptness of transition relative to the lifespan of long-lived organisms, 3) information on spatiotemporal context is useful for comparing transitions in similar systems, and 4) ancillary information from associated experiments and observations is critical for interpreting response-driver relationships.
Chlorophyll and phaeopigments measured from discrete bottle samples from CCE LTER process cruises in the California Current System, determined by extraction and bench fluorometry, 2006 - 2024 (ongoing).
Discrete bottle samples taken from various depths in the CCE region are filtered (known volumes) onto GF/F filters onboard the CCE Process cruises (since 2006, ongoing). 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).
Dissolved inorganic nutrients from CCE LTER process cruises, including 5 macro nutrients from water column bottle sample, 2006 - 2024 (ongoing).
Dissolved inorganic nutrients (phytoplankton macro nutrients) are measured from water column bottle samples from the CCE region (since 2006, ongoing) and include nitrate, nitrite, silicate, phosphate and ammonium. They are analyzed in seawater using a colorimetric assay in which light absorbance is measured versus known standards, and final concentrations are calculated (in µmol/L).
CCE LTER process cruise, in the California Current region, event log records including date, time, position and activity for use in post-cruise data integration based on co-sampling indexes. From 2006 to 2019 CCE LTER used a locally developed event logging system. During P2107, CCE LTER started to utilize the R2R Event Logger on UNOL ships, 2006 - 2024 (ongoing).
The event logger program developed and maintained by the California Cooperative Oceanic Fisheries Investigations, SIO, program is used aboard CCE LTER process cruises to create indexes with temporal, spatial and activity information for post-cruise data integration. The event log is configured aboard the ship for the recording of sampling events by both ship crew personnel on the bridge, and research personnel in the lab. The event log is processed post-cruise to correct for various errors.
CCE LTER P1908 Upwelling Filament Ocean Acidification Phytoplankton Iron Incubation Experiments
<p>Metatranscriptome assembly, read counts, and annotations from four sets of trace metal clean ocean acidification experimeints in the California Current Ecosystem. Experiments were conducted during August 2019 as part of the CCE LTER program. Samples were collected at the initial time point (T0), and three pCO<sub>2</sub> treatments (400, 800, and 1200 ppm) with two time points for each experiment. </p> <p>Poly-A selected mRNA was sequenced on an Illumina NovaSeq 6000 and then assembled with Trinity for each separate experiment. Proteins from the assembly were then predicted with Genemark S-T. Taxonomic annotation was performed with DIAMOND BLASTP searches against PhyloDB v1.076 and based on the Lineage Proability Index from the top hits. Functional annotation was similarly performed using KEGG with KEGG Orthology annotation based on KofamKOALA results. Read quantification was conducted with Bowtie2. </p> <p>Predicted proteins from each assembly is provided in fasta format. The read counts and annotations for each experiment are in tab-delimited files. </p>
Parameters from discrete bottle samples on a hydrographic CTD (Conductivity Temperature Depth) cast during CCE LTER process cruises in the CCE region, 2006 - 2019 (ongoing).
Hydrographic CTD (Conductivity Temperature Depth) measurements from discrete water samples are taken on individual CTD rosette casts, deployed on CCE Process cruises (since 2006, ongoing) 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.
Size fractionation for total Chl a within the surface layer and calculated size distribution of total Chl a from discrete bottle samples collected during CCE LTER process cruises in the CCE region, 2006 - 2024 (ongoing).
Water for size fractionation of chlorophyll a is sampled from ~10m depth (surface layer) in the CCE study area. The size distribution of total chlorophyll a is determined by filtering water though filters of differing pore sizes. These are then extracted in acetone and analyzed fluorometrically with Turner Designs 10-AU Fluorometer on CCE Process cruises (since 2006, ongoing). Chlorophyll a and taxon-specific pigments (chlorophylls and carotenoids) are qualitatively and quantitatively characterized in the lab onshore by several size fractions (< 1µm to > 20µm) utilizing High Performance Liquid Chromatography (HPLC) analysis. The samples analyzed within the CCE region are used to develop a metric for phytoplankton community structure that can be used to monitor its state and changes thereof over time.
Water column primary production per day integrated over the euphotic zone from CCE LTER process cruises in the California Current System, 2006 - 2021 (ongoing).
Derived dataset of vertically integrated primary production (uptake rate of carbon) of particulate organic carbon (POC) using 14C uptake measurements from in situ incubations, filtering methods and measured in mg/m²/day.
Measurements, from CCE LTER process cruises in the California Current region, of dissolved inorganic concentrations of nutrient iron and of iron limitation at selected stations and depths, 2006 - 2021 (ongoing).
Measurements are made of dissolved iron, total iron and the potential for phytoplankton iron limitation on CCE LTER Process cruises (since 2006, ongoing) in coastal transition zones of the southern California Current System. This is a weak upwelling regime that is relatively low in nutrients and chlorophyll. Changes in phytoplankton (Chla response to Fe+) and nutrient parameters upon iron addition are also investigated.
Total dissolved organic carbon and nitrogen measurements at selected depths in the water column from CCE LTER process cruises in the California Current System, 2006 - 2021 (ongoing).
Water column bottle samples at multiple depths are taken during CCE Process cruises (since 2006, ongoing) at various CTD stations, and measurements of total organic carbon (TOC) and total nitrogen (TN) are performed onshore in the lab. TOC includes both dissolved and particulate organic carbon (DOC and POC, respectively). TN includes particulate and dissolved organic nitrogen as well as dissolved inorganic nitrogen species. In open ocean waters, POC is subtracted from TOC, and likely provides an accurate estimate of DOC because particles are typically small and homogeneously distributed in the sample. In coastal waters, and at stations where relatively high chlorophyll concentrations are present, the TOC measurement is not easily converted to DOC by subtracting POC values. Experience has shown that particles in these regions are large and inhomogeneously distributed. Therefore, samples collected in the CCE are reported as TOC and TN, expressed as micromoles of carbon (nitrogen) per liter of sea water.
Sediment trap fecal pellets enumerations collected aboard CCE LTER process cruises in the California Current system, 2007, 2008 and 2016.
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). ‘Sample’ refers to which of two samples the fecal pellet was contained within. ‘PelletID’ is the identifier for each fecal pellet in a sample. ‘Conversion Factor’ accounts for the proportion of a sample that was sorted for fecal pellets, as well as the deployment duration and cross-sectional area of the sediment trap. To determine the mass flux of fecal pellets of a certain type: 1) Sum the pellet mass for all fecal pellets of that type in a given sample and 2) multiply by the Conversion factor for that sample. ‘Shape’ is an identifier for the shape of a fecal pellet: 1) ovoid, 2) cylindrical, 3) spherical, 4) tabular, 5) amorphous, 6) ellipsoidal, 7) degraded fecal mater
Vertical profiles of in-situ biogenic silica (bSi) from discrete rosette bottle samples from CCE-LTER starting with cruise P1706.
Samples are taken at discrete depths from rosette bottles in the California Current Ecosystem and measured for biogenic silica (bSi) concentration to create bSi depth profiles. Diatom community and physiology affect biogenic silica concentration. These data are being used to investigate the effects of Fe limitation on carbon and silica cycling in the CCE.
Gut Fluorescence measurements of mesozooplankton grazing on autotrophic prey. Samples collected in the CCE-LTER region on Process Cruises from 2006 to the present. Summaries for each Lagrangian Cycle.
Mesozooplankton are collected with plankton nets (typically a 71-cm diameter, 202-um mesh Bongo net) and samples flash frozen at sea in liquid N2 for subsequent shore-based measurements of ingested phytoplankton chlorophyll-a. Measurements of mesozooplankton gut fluorescence are done by fluorometric analysis on a Turner Designs fluorometer of gut pigments extracted in 90% acetone. Analyses are done on mesozooplankton size-fractionated into 5 different categories on Nitex mesh (> 0.2 mm, 0.5 mm, 1.0 mm, 2.0 mm, 5.0 mm). The pigment content (as Chl-a and phaeopigments) is then expressed as mass of pigment ingested per m3 of water filtered, or divided by the dry weight biomass of the mesozooplankton in the same sample in order to obtain mass-specific ingestion per m3 of water. Application of published values of the temperature-dependent gut passage time are used to estimate the mesozooplankton grazing rate, as pigments ingested per m3 per unit time, or the corresponding mass-specific rate of ingestion. Samples for gut fluorescence assays have been collected on CCE-LTER Process Cruises since 2006 and these collections are ongoing.
Dry weight biomass measurements of net-collected mesozooplankton. Samples collected in the CCE-LTER region on Process Cruises from 2006 to the present. Summaries for each Lagrangian Cycle.
Mesozooplankton are collected with plankton nets (typically a 71-cm diameter, 202-um mesh Bongo net) and samples flash frozen at sea in liquid N2 for subsequent shore-based measurements of dry weight biomass. Measurements are made by weighing pre-tared Nitex mesh on an analytical balance, for mesozooplankton size-fractionated into 5 different categories (> 0.2 mm, 0.5 mm, 1.0 mm, 2.0 mm, 5.0 mm). Biomass is expressed as dry mass of zooplankton per m3 of water filtered, or when multiplied by the maximum depth of the tow, as integrated dry mass of zooplankton per m2 of sea surface. Samples for dry weight biomass have been collected on CCE-LTER Process Cruises since 2006 and these collections are ongoing.
Primary production estimates from 14C uptake (in situ), determined by the incorporation of inorganic carbon into particulate organic carbon (POC) due to photosynthesis at selected light levels from CCE LTER process cruises in the California Current System, 2006 - 2021 (ongoing).
Primary productivity samples of seawater are taken each day shortly before noon on the CTD rosette up-cast during the CCE Process crusies (since 2006, ongoing). Light penetration below the surface is estimated from the Secchi disk depth. Niskin bottles from depths with ambient light intensities corresponding to light levels simulated by on-deck incubators are identified and sampled. Primary production is estimated from 14C uptake using this simulated in situ technique (followed by filtering) by which the assimilation of dissolved inorganic carbon by phytoplankton yields a measure (in µg/L/day) of the rate of photosynthetic primary production (particulate organic carbon, POC) at selected light levels in the euphotic zone within the CCE study area.
Assembled file of one minute averages for high resolution surface meteorological (Met) and sea water intake (SWI) data from continuous underway measurements from CCE LTER process cruises in the CCE region, 2006 - 2019.
As the research vessel is underway for the duration of a CCE Process Cruise (since 2006, ongoing), 30 parameters are continuously measured regarding the oceanographic surface and atmospheric and navigational environment of the vessel, along the ship's trackline in the CCE region.
Measurements, from CCE LTER process cruises in the California Current region, of total dissolvable inorganic concentrations of the nutrient iron, 2017 - (ongoing).
Seawater profiles or discrete samples for total dissolvable iron (TDFe) analysis are collected with the trace metal rosette or GO-FLO bottles, respectively, in stations located within the CCE LTER region in the California Current System. The total dissolvable iron concentration is obtained by collecting unfiltered seawater samples in 250 mL LDPE bottles and storing them at pH 1.8 for 6 months or more. The acidified seawater sample is then filtered using acid cleaned 0.4 um PES membrane Titan 3 syringe filters and determined by flow injection chemiluminescent (FI-CL) analysis at Scripps Insitution of Oceanography since 2017 (ongoing).
Conductivity Temperature Depth (CTD) Log of CTD casts from CCE LTER process cruises in the CCE region, 2006 - 2019 (ongoing).
Individual casts of Conductivity, Temperature and Depth (CTD) are logged on CCE Process cruises (since 2006, ongoing) in the Southern California region. The log includes time, location, number of bottles, cast and event numbers and other information about CTD casts.
Phytoplankton growth and microzooplankton grazing rates from CCE LTER Process cruises in the California Current System, 2006 - 2017.
Rates of phytoplankton community growth and microzooplankton grazing on phytoplankton were assessed from chlorophyll a analyses of in situ dilution incubations as described in Landry et al. (2009). For each experiment (Array #), seawater was collected from predawn CTD (~2 a.m. local time) casts at 6-8 depths spanning the upper to lower euphotic zone. For each depth, we prepared a pair of polycarbonate bottles (2.7 L), one with whole seawater (100%), and one with 33% whole seawater (diluted with 0.1-µm filtered seawater) at each depth. Seawater was filtered directly from the Niskin bottles using a peristaltic pump, silicone tubing and an in-line Suporcap filter capsule that had previously been acid washed (10% trace-metal grade HCl followed by Milli-Q and seawater rinses). Dilution treatment bottles received pre-measured volumes of filtered water from the collection depths, and then were gently filled (silicone tubing below the water level) with unscreened water from the Niskin bottles. The filled bottles were tightly capped, placed into net bags and clipped onto attached rings at the depth of collection on a tether line attached to a satellite-tracked surface drifter (WOCE SVP) with a top strobe light, Globalstar telemetry and a 3-m holey-sock drogue centered at 15-m (mixed layer). Incubations were done in situ for 24-h (daily) to get daily averaged rates. In most cases, repeated experiments/deployments were done over the course of 2-5 days, using water collected each morning at the location of the drifter. These back-to-back experiments define experimental “cycles”. The second set of experiments were set up, before recovering the first. Hand recovery of the array, switching of net bags and redeployment was generally completed in 15-20 min. Rate estimates are based on initial and final subsamples (250 ml) taken for fluorometric analyses of Chl a. The samples were immediately filtered onto GF/F filters, and the Chl a extracted with 90% acetone in a dark refrigerator
Daily weather summaries (temperature, precipitation and wind) for station SAN DIEGO LINDBERGH FIELD, CA US (GHCND:USW00023188), obtained from NOAA National Climatic Data Center and re-published through CCE LTER data system for community use as regionally relevant data, 1939 - Oct 2019.
Data provided here are obtained from the Global Historical Climatology Network - Daily (GHCN-Daily) database, provided by NOAA National Centers for Environmental Information (formerly NCDC). Data are periodically downloaded by CCE LTER Information Management and imported into the local data system for use by the local scientific community as regionally relevant data. The data contained in this dataset are from the SAN DIEGO LINDBERGH FIELD, CA US station (GHCND:USW00023188) at 32.7336°, -117.1831° beginning in July 1, 1939. The Global Historical Climatology Network - Daily (GHCN-Daily) dataset integrates daily climate observations from approximately 30 different data sources. Version 3 was released in September 2012 with the addition of data from two additional station networks. Changes to the processing system associated with the version 3 release also allowed for updates to occur 7 days a week rather than only on most weekdays. Version 3 contains station-based measurements from well over 90,000 land-based stations worldwide, about two thirds of which are for precipitation measurement only. Other meteorological elements include, but are not limited to, daily maximum and minimum temperature, temperature at the time of observation, snowfall and snow depth. Over 25,000 stations are regularly updated with observations from within roughly the last month. The dataset is also routinely reconstructed (usually every week) from its roughly 30 data sources to ensure that GHCN-Daily is generally in sync with its growing list of constituent sources. During this process, quality assurance checks are applied to the full dataset. Where possible, GHCN-Daily station data are also updated daily from a variety of data streams. Station values for each daily update also undergo a suite of quality checks.
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