Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

Temperature, salinity, fluorescence, and sigma-t density measured by CTD are reported for 5 stations in Fisher's Island Sound.

Note: Stations 1, 3, and 5 were at a drogue. For stations 2 and 4, the ship moved about 1 kilometer away from the drogue. When station 2 was sampled, the drogue had moved east of it and sampling occurred up-current from the drogue. Tide was ebb --> slack --> flood.

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Header Information from Sea-Bird SBE19 Data File:
Software Version 1.59
Temperature SN = 504; Conductivity SN = 504

SEACAT PROFILER V2.1e SN 504 05/30/12 13:51:21.934
pressure sensor: serial no = 184805, range = 100 psia, tc = -585
clk = 32767.742 iop = 142 vmain = 11.9 vlith = 5.3
ncasts = 5 samples = 1684 free = 19973 lwait = 0 msec
sample rate = 1 scan every 0.5 seconds
minimum raw conductivity frequency for pump turn on = 0 hertz; pump delay = 30 seconds
battery cutoff = 7.2 volts; number of voltages sampled = 4

cast 0: 05/30 09:50:19 samples 0 to 388 nquan = 7 nvalues = 389
cast 1: 05/30 10:53:36 samples 389 to 774 nquan = 7 nvalues = 386
cast 2: 05/30 11:23:25 samples 775 to 1113 nquan = 7 nvalues = 339
cast 3: 05/30 11:46:51 samples 1114 to 1358 nquan = 7 nvalues = 245
cast 4: 05/30 12:12:29 samples 1359 to 1683 nquan = 7 nvalues = 325

units = specified
name 0 = sigma-t00: Density [sigma-t, Kg/m^3 ]
name 1 = depSM: Depth [salt water, m], lat = 41.00
name 2 = wetStar: Fluorescence, WET Labs WETstar [mg/m^3]
name 3 = sal00: Salinity, Practical [PSU]
name 4 = t090C: Temperature [ITS-90, deg C]
name 5 = timeS: Time, Elapsed [seconds]
name 6 = flag: 0.000e+00

interval = seconds: 0.5; bad_flag = -9.990e-29

sensor 1 = Frequency 0, Temperature; Temp. Sensor ID: 55; SerialNumber: 504;
CalibrationDate: 28-Jan-11

sensor = 2 Frequency 1, Conductivity; Cond. Sensor ID: 3; SerialNumber: 504;
CalibrationDate: 28-Jan-11

sensor = 3 A/D voltage 0, Oxygen Current, Beckman/YSI; Oxygen Sensor ID: 36; SerialNumber: 230238;
CalibrationDate: 21-Mar-2011

sensor = 4 A/D voltage 1, Oxygen Temperature, Beckman/YSI; Oxygen Sensor ID: 39; SerialNumber: 230238;
CalibrationDate: 21-Mar-2011

sensor = 5 A/D voltage 2, Fluorometer, WET Labs WETstar; FluoroWetlabWetstar Sensor ID: 21; SerialNumber: WS3S-166;
CalibrationDate: 23-Feb-2011; ScaleFactor: 15.400

sensor = 6 A/D voltage 3, Free

sensor = 7 Pressure voltage, Pressure, Strain Gauge; Pressure Sensor ID: 49; SerialNumber: 504;
CalibrationDate: 04-Feb-11

datcnv_skipover = 0
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Only downcast data is included; surface equilibration has been edited out.

The WetStar Fluorometer calibrated by Seabird (Feb 2011) was NOT validated with contemporaneous filtered samples, so values reported should be considered relative. CTD data was processed with SeaBird software.

The Ocean's biomass and diversity are predominantly microbial, yet this aspect of diversity remains underexplored. Efforts in recent years have begun to document microbial diversity in marine systems, and to elucidate the processes that structure assemblages across space and time. This project focuses on two important sister clades of microbial eukaryotes, the oligotrich and choreotrich ciliates. These organisms comprise a major component of planktonic food webs as they graze on phytoplankton, and are in turn eaten by zooplankton and larval fish.

Earlier molecular work on ciliate diversity relied on light microscopy, construction of clone libraries and Sanger sequencing. This revealed a high degree of cryptic diversity (similar species that are genetically distinct), which is surprising, given the long-held idea that all microbes are globally distributed and that few species exist, at least as compared to animals and plants. This past work also showed that ciliate assemblages contain a few highly abundant forms and many rare ones, consistent with the concept of a "rare biosphere". However, these methods are limited by high costs of both labor and materials, so that efforts to sample any local assemblage comprehensively usually resulted in undersaturation (repeated sampling continued to uncover new species). Next generation approaches are needed to truly assess the depths of biodiversity in planktonic ciliates.

This project brings together investigators with strengths in ecology, taxonomy and oceanography (PI McManus) and in molecular evolution, systematics and bioinformatics (PI Katz). Pyrosequencing will be used to sample the oligotrich and choreotrich ciliates ’to exhaustion’ in coastal environments. Denaturing gradient gel electrophoresis (DGGE), a technique that generates a fingerprint of the diversity in a sample, will be used to pre-select samples for pyrosequencing based on where strong gradients are observed in the composition of assemblages in relation to environmental factors (density fronts, thermolclines, etc.). Using these approaches, combined with the informatics pipeline already in place, this project will address three specific objectives:

Objective 1. Determine the spatial scale of variability in ciliate diversity by measuring how ciliate assemblages change over meter, kilometer, 100 km, and basin scales.

Objective 2. Assess the contributions of different size classes of ciliates to overall assemblage diversity.

Objective 3. Experimentally evaluate factors that control the temporal shift of individual species from rarity to commonness in a natural assemblage, and vice versa.

Note: See the related collaborative project, "Patterns of diversity in planktonic ciliates: spatio-temporal scales and community assembly in the coastal ocean", funded by awards OCE-1435515 and OCE-1436003.