Show these notes with Cruise Track included

Progress Report JGOFS Process Cruise 6: Bio-optics Cruise

One of the objectives of this cruise, besides understanding carbon fluxes
in the Arabian Sea, is to sample unique phytoplankton assemblages
associated with hydrographic features, describe the algal optical
signatures, and how these would affect pigment retrievals using
remotely-sensed ocean color.    Our cruise has required more flexibility in
the station track than usual, because we are selecting  courses based on
satellite and underway data.  We are following most of the standard JGOFS
cruise track,  but have time built into the schedule to study three other
features during the cruise.  Seas have been calm and winds very light, as
expected for this inter-monsoon period.
        Before describing our observations, I will first mention the
scientists and equipment on board .  We are towing the UOR (Undulating
Optical Recorder), ably manned by Matt  Pinkerton and Colin Barret, from
Jim Aiken's group at the Plymouth Marine Laboratory.  This instrument
oscillates in the top 100m as the ship steams at 11kts.  It measures
temperature, salinity, fluorescence, downwelling irradiance, and upwelling
radiance at 7 wavelengths.  The UOR provides the equivalent of a 100m CTD
and optics cast every 4 km giving us tremendous hydrographic, optical and
biological resolution in the upper water column.
        The vertical distribution of inherent and apparent properties are
being characterized with a bio-optical profiling system (Chuck Trees,
CHORS).  Discrete samples are also being collected for total particulate
and phytoplankton pigment absorption analyses.   The team of John Marra and
Chris Kinkade (Lamont)  and Zachary Johnson (Duke Univ.) have been
measuring primary production at all stations.  The team has also been
conducting PvsE experiments each day while on station.  John has his
non-linear regression program working, and with input on the phytoplankton
pigment absorption, has been able to estimate phi-max (the maximum quantum
yield, molC/mol Photons) in quasi-real-time, that is, within a couple of
days of the experiment.  Bob Bidigare (Univ. Hawaii) is doing the pigment
work, including shipboard extractions for fluorometric analysis and
collection of HPLC  samples for analysis ashore.  Jim McCarthy and John
Nevins (Harvard Univ.) have been conducting nitrogen cycling studies.  Rob
Olson and Alexi Shalapyonok (Woods Hole) have been analyzing algal
populations with an EPICS flow cytometer and watching the diel  variability
of the algal optical properties.  Metal concentrations are being estimated
by Sue Vink (Chris Measures group, Univ. Hawaii) using the towed "wee
fish".  This uses a peristaltic pump to collect water and deliver it to the
hydro-lab.  It also provides minimumally perturbed samples for collecting
underway samples and performing incubations every 2 hours.  Esa Peltola and
Tim Kemerer (Millero Lab, RSMAS) have been measuring pCO2 and alkalinities
along track and at all shallow and deep hydrocasts.  The TAMU group (Guy
Rosinbaum and Pat Pease) have been sampling aerosols and surface waters for
dust concentrations.   Dennis Hansell and Rachel Parsons (Bermuda
Biological) have been measuring DOC and DON.  Particulate carbons and
nitrogens, suspended calcite samples, and cell count samples are being
prepared by Jessica Nelson (Univ. New England).   J. Fritz and D. Drapeau,
(U.Miami & Bigelow Lab) have been running the surface underway system,
measuring calcification, and performing real-time microscopy to document
the algal species composition at each station.  The hydroteam
(Krogslund,Lopez, Guffy, Wells and Williams) have been processing
nutrients, salinities and oxygens around the clock, as fast as we can
acquire them. Andy Maffei (WHOI) has been improving the ship's internet
access, and actually providing the first on-line links of the Thompson to
the world wide web via Inmar-sat.  Ed Webb and Erik Quiroz are assisting
with CTD operations.  Marine techs (Reelander and Martin) continually amaze
all hands with their ability to solve the multitude of problems that come
up over the course of each day (fixing everything from xerox machines to
        Our cruise track took us by Gulf of Oman Arabesque stations, across
the R'as Al Hadd front, to the first station of the JGOFS line.  From here,
we diverted to study this impressive feature further.  Using real-time
satellite imagery from Bob Arnone's HRPT receiver, we navigated a saw-tooth
pattern across the front (3  crossings) and then performed 3 stations
perpendicular to it.  Surface velocities along the front were about a knot,
and it moved considerably from day to day, requiring expert navigation from
the bridge to find it, and stay within it.   The development of a warm-core
eddy, just north of the front, provided a dramatic insight into how dynamic
this area can be.   Our first feature station was in the middle of this
eddy, where surface chlorophyll levels were 0.5 mg/m3 with weak subsurface
chlorophyll maxima of 1.0 mg/m3 at 30m.      Algal populations were
dominated by picoplankton, Synechococcus and Prochlorococcus.  The
nitracline and oxygen minimum were at 35m at the eddy center and  DOC/DON
concentrations were high in this warm water.    Calcification rates have
been lower than expected (about a third of those measured during the
monsoon cruise).  Highest integrated calcification rates were observed at
the nearshore stations (33 mg/m2-d).
        Our first long station was at the R'as Al Hadd front.  Finding this
spot was more difficult than anticipated, because it had moved almost 15
miles south from our previous fixes with the AVHRR.  We were using a
shipboard underway system to map surface chlorophyll, temperature, salinity
and light scatter during the search.  Just when we thought we had somehow
missed it (we were 1 hour overdue to the front), the ship "kissed" the edge
of the feature, we  even had begun our turn back one minute before; all
hands, particularly this chief scientist, were elated to watch the
temperature and salinity finally plummet, as cool northern Arabian Sea
water slid along warmer, saltier Gulf of Oman water.  While the UOR picked
up some very high fluorescence values in two patches at the frontal edge,
typical chlorophyll a concentrations were closer to 0.6 mg/m3.  We chose
the part of the front with lower fluorescence values, indicative of the
cooler Arabian Sea side of the front, with reduced stability.  We then
watched the populations over the next day and a half.   The nitracline and
oxygen minimum were at 40m at this station and algal populations were
characterized by large numbers of diatoms (Rhizosolenia and Nitzschia),
along with armored and naked dinoflagellates,  cryptomonads,
coccolithophores, and a very healthy population of Synechococcus.   DOC/DON
concentrations were lower in this frontal area than to the north or south,
presumably as deeper water, with low concentrations of refractory DOC
surfaced.   The pCO2 at this station was 389 ppm.  Aluminum and iron
concentrations in the near-shore stations have been 15nM and 10nM,
        Our next station was  along the convergence between the
northeasterly-flowing Arabian Sea water and a southwesterly-flowing
filament from the Pakistani continental shelf (as interpreted from AVHRR
and the ship's acoustic Doppler).  This provided nice contrast to the
previous station; algal populations were characterized by smaller cells
(pennate diatoms, naked dinoflagellates, cryptomonads, and cyanobacteria)
and surface nitrate was about 0.5uM.  The oxygen minimum deepened to about
100 meters.   For these first 8 stations, primary productivity has  ranged
from 942-2500 mg C/m2/d.  Pbmax values have been as high as 17 mgC/mgChl-h
at the 15% light depth.  At one station, phi-max's  averaged  0.02 over
depth, but at a station noted for a cryptophyte bloom, phi-max's jumped to
0.03-0.06, changing as a function of depth.
        We re-joined the JGOFS grid at 21o 11' x 63o33' .  As in process 4,
these stations showed increasing oligotrophy and the vertical gradient into
the oxygen minimum became steeper as we steamed eastward.   The pCO2
remained at 388ppm and the mixed layer chlorophyll concentrations of about
0.2 mg/m3 have been the norm with subsurface chlorophyll maxima at about
50-60m (0.6-0.9mg/m3).  Phaeopigment concentrations were elevated in the
lower euphotic zone.  HPLC analysis will be necessary to determine if this
feature was caused by phaeopigments or high levels of Chlorophyll b.  We
are currently at the southern-most station of the JGOFS grid.  The 1% light
depth for 490nm wavelengths is at 87m  (based on vertical profiles and UOR
measurements).   Algal populations are characterized by scant few pennate
diatoms, a few naked dinoflagellates and a weak subsurface prochlorophyte
peak.   While there are plenty of detached coccoliths and plated
coccolithophores in the water, calcification rates are lower than the
near-shore stations.   The pCO2 has increased to 398 ppm and metal
concentrations at the eastern and southern stations have dropped
considerably (10nM and 1-2nM for Al and Fe, respectively).
        The biological and optical variability has not been as low as
expected, as evidenced from the high resolution underway data.  During one
UOR recovery in the eastern part of the JGOFS study area, we stopped in the
middle of what appeared to be a cyclonic eddy, the border of which
consisted of a  6 mile wide band of water upwelled from about 50m.  This
"band" was populated by several species of large  diatoms.  Due to clouds,
we have not had good AVHRR coverage of this southerly part of the study
area; we can only guess the origin of such a dramatic "oasis" in an
otherwise featureless  part of the cruise track.
        A double pigment peak was observed at our last two stations, the
upper peak populated by a rich diatom flora and the lower (~120m) well into
the oxygen minimum,  was overwhelmingly dominated by Prochlorococcus as
observed in the flow cytometer and microscope.  Prochlorophytes in the
oxygen minimum also were observed in Process cruise 4.   Floral diversity
has  been easily observed in the phytoplankton pigment absorption spectra
where 3 peaks (474, 490, and 550 nm) were present in many samples from the
surface 30m.  The 490 and 550 nm peaks are typical of cyanobacteria and
cryptomonads and their associated phycobilin pigment complexes.  The peak
at 474 nm, until HPLC analysis has been completed, is speculated to be
elevated concentrations of zeaxanthin.  The presence of such peaks is not
typical for most oceanic areas and therefore would have a great effect on
the retrieval of ocean color from satellite.  This is especially true for
the 550 nm peak which was used as the "hinge point" for past CZCS data
processing.  We look forward to sampling other unique assemblages during
this expedition.
        As we steam up the southern line, we are watching two areas in the
satellite imagery for our remaining two feature investigations: the area
south of Masirah has had persistent filaments extending well off shore, and
the area between Ras ash Sharbatat and Ras Marbat has shown a persistent
large eddy.  Both would likely  be sites of intense biological activity and
provide us with the bio-optical variability that we are looking for.
        As always, Captain Gomes and the crew of the Thompson have been
superb for station keeping, equipment handling, and all aspects of ship
operations.  No progress report would  be complete without mention of the
great food being prepared by the galley staff.  Our biggest problem seems
to be watching our weight.  Hard work from all hands, combined with calm
seas, has made for a most scientifically-profitable expedition.

William Balch, Bigelow Laboratory for Ocean Sciences
 Chief Scientist for Process Cruise #6