Macroscopes to Microscopes: Scales

of Interest for Earth Systems

Raphe Kudela & Jesse Bausell

Ocean Sciences Department

Kudela Lab Field Projects

IronEx II
SOFex

Bering Sea
Gulf of Alaska

NSF Coastal Ocean Processes

GEOHAB
Ocean Observing

50% -- amount of atmospheric oxygen that

comes from phytoplankton.
5% -- fraction of the world coastal oceans
that produces 50% of the planetary
Net Primary Productivity.

65 -- multiplication factor for oceanic carbon

compared to the rest of the biosphere.
50% -- the world's population living within 60
km of the shoreline.
75% -- estimated population living within 60
km of the shoreline by the year 2020.

Biospherical
Instruments

50% -- amount of atmospheric oxygen that

comes from phytoplankton.
5% -- fraction of the world coastal oceans
that produces 50% of the planetary
Net Primary Productivity.

65 -- multiplication factor for oceanic carbon

compared to the rest of the biosphere.
50% -- the world's population living within 60
km of the shoreline.
75% -- estimated population living within 60
km of the shoreline by the year 2020.

Our understanding of the worlds systems depends on observations of ocean color (waterleaving radiance); we infer ocean health, species composition, water quality, carbon cycling,
and trends in these variables by accurately measuring subtle changes in reflectance.

Biospherical
Instruments

50% -- amount of atmospheric oxygen that

comes from phytoplankton.
5% -- fraction of the world coastal oceans
that produces 50% of the planetary
Net Primary Productivity.

65 -- multiplication factor for oceanic carbon

compared to the rest of the biosphere.
50% -- the world's population living within 60
km of the shoreline.
75% -- estimated population living within 60
km of the shoreline by the year 2020.

Our understanding of the worlds systems depends on observations of ocean color (waterleaving radiance); we infer ocean health, species composition, water quality, carbon cycling,
and trends in these variables by accurately measuring subtle changes in reflectance.

And yet.
Legacy & current sensors, optimized for the open ocean, provide inadequate spatial/spectral resolution
90% (or more) of the satellite signal comes from the atmosphere, but existing sensors perform poorly at the
land-sea interface
We cannot currently answer fundamental questions such as:
- Is biomass increasing or decreasing in the coastal ocean?
- Are the organisms potentially harmful or toxic?
- Is the coastal ocean a sink or source for carbon dioxide?
- How are low and high latitude systems (coral reefs, the ice edge) responding to the
unprecedented changes in ocean temperature, pH, and water quality?

Biospherical
Instruments

50% -- amount of atmospheric oxygen that

comes from phytoplankton.
5% -- fraction of the world coastal oceans
that produces 50% of the planetary
Net Primary Productivity.

65 -- multiplication factor for oceanic carbon

compared to the rest of the biosphere.
50% -- the world's population living within 60
km of the shoreline.
75% -- estimated population living within 60
km of the shoreline by the year 2020.

Our understanding of the worlds systems depends on observations of ocean color (waterleaving radiance); we infer ocean health, species composition, water quality, carbon cycling,
and trends in these variables by accurately measuring subtle changes in reflectance.

And yet.
Legacy & current sensors, optimized for the open ocean, provide inadequate spatial/spectral resolution
90% (or more) of the satellite signal comes from the atmosphere, but existing sensors perform poorly at the
land-sea interface
We cannot currently answer fundamental questions such as:
- Is biomass increasing or decreasing in the coastal ocean?
- Are the organisms potentially harmful or toxic?
- Is the coastal ocean a sink or source for carbon dioxide?
- How are low and high latitude systems (coral reefs, the ice edge) responding to the
unprecedented changes in ocean temperature, pH, and water quality?

Biospherical
Instruments

NASA Earth Systems SciencesThe Oceans

Ocean Biology and Biogeochemistry

Focuses on describing, understanding, and predicting the biological and biogeochemical regimes
of the upper ocean, as determined by observation of aquatic optical properties using remote
sensing data

Biological Diversity
What drives the diversity of life on Earth? How is this Biological diversity changing and why? How
are global ecosystems changing? What are the consequences of climate change and increased
human activities for coastal regions?

Ecological Forecasting
Ecological Forecasting employs observations and models to predict the impacts of environmental
change on ecosystems.

Ocean Carbon and Biogeochemistry

Ecological Forecasting employs observations and models to predict the impacts of environmental
change on ecosystems.

North Atlantic Aerosols and

Marine Ecosystems Study

EXport Processes in the

Ocean from RemoTe Sensing
Goal: Predict the
export and fate of
ocean Net Primary
Production (NPP)
from satellite and
other observations
.
Hypothesis: Carbon
export from the
euphotic zone and its
fate within the twilight
zone can be predicted
from space

Coral Reef Airborne

Laboratory

Airborne Sensors: Linking Legacy

to Next Generation Platforms

From the Ocean to the Coast

WHO TURNED UP THE HEAT?

2014: The Warmest Year In the Modern Record

2015

The Blob(s),
Ridiculously Resilient
Ridges

Normalized
Difference
Vegetation
Index

Where Californias Drinking Water Comes From

Source: Nature Conservancy, http://www.nature.org/media/california/

WHO TURNED OFF THE WATER?

A Tour of California Hotspots

San Joaquin Marsh33,500 g/L
Lake Chabot11,000 g/L;
800,000 g/L scum

Pinto Lake1,000 g/L annually;

2.9 million g/L scum

Earthdata.nasa.gov/labs/worldview

The California Current is Getting Greener

Kahru et al. 2013

Decadal Trends in the California Current:

- Mixed Layer Depth is shoaling
- Surface temperatures are increasing
- Stratification intensity is increasing
- Nutrient concentrations, ratios shifting
Rare

2001

2002

2003

2004

2005

Dinoflagellates

Dominant

2006

2007

2008

2009

2010

2011

2012

2013

2014

2015

First-Order Questions
How are basin-scale oscillations
changing the biology and chemistry of
the oceans?
How does the drought modulate the
coastal ocean (or does it not matter?)
What is going to happen in the future?
Is this the new normal?

Optics Primer
IOP- Inherent optical property
eg. absorption (a), scattering (b), attenuation (c)
AOP- Apparent optical property
eg. irradiance (E), radiance (L)

Ed()
remote sensing reflectance

Rrs = g

bb
a + bb

Lu

Lu()

aw
aCDOM

Ed

c=a+b
btot = bf + bb

aph
ad

bb

atot = aw + aph + ad + aCDOM

bf

Fluor

Rrs, Lwn, & Ed used in satellite models

to predict IOPs
Lwn()

Rrs()

remote sensing reflectance

Rrs = g

bb
a + bb

Lu

Ed

Lwn Lu + Lsky

SeaWiFS Chl a

10.0

1.0

0.1
Adapted from Kahru & Mitchell 2001

0.1

1.0

10.0

In situ Chl a (mg m-3)

The Coastal Ocean

Conundrum
Unlike terrestrial remote sensing, the target is
constantly moving--we need very rapid image
analysis
The ocean is a dark target atmospheric
correction is critical.
Multiple sensors, multiple problems
Scales of interest range from 10s of meters to
100s of kilometers (but the available sensors
rarely match these requirements!)

Ocean Color is a + bb

http://seawifs.gsfc.nasa.gov/SEAWIFS.html

Scattering in the ocean

Coccolithophore
Emiliania huxleyi
http://earthguide.ucsd.edu/earthguide/imagelibrary/emilianiahuxleyi.html

Absorption in the Ocean

Confluence of Rio Negro and Amazon Rivers, Brazil

Image shamelessly swiped from internet from Star

Absorption plus Scattering

Zhao, Temimi, Ghedira, ISPRS J. Photog. Remote Sens., 101: 125-136

All Optical Sensors (Satellites)

Work Similarly
The differences are in:
Sensitivity
Number of bands
Spatial resolution

What we CAN measure:

bbw + bbp
Lu
Rrs ( )
= cons tan t
Ed
aw + a ph + adm + bbw + bbp
What were reasonably good at measuring: Chlorophyll
What we WANT TO measure:
-Water Quality
-Phytoplankton Species (such as Harmful Algal Blooms)
-Biogeochemistry
-Long-term trends

Spatial Resolution

September 12, 2006 Time sequence of 710 nm:

Diurnal migration of the bloom?

0908

0938

1006

1124

1204

1238

Diatoms
Dinoflagellates

Haptophytes
Cryptophytes

Chlorophytes
Cyanophytes

UPCE

Sherry Palacios, NASA Ames Research Center

Spectral Resolution

Spectral Resolution
Dinoflagellates

Diatoms

Challenge: two optically similar species

Aphanizomenon flos-aquae

Microcystis spp.

Detecting Blue-Green Algae

0.04

Several algorithms have

been developed, including
the Cyanobacterial Index
(CI) and various
phycocyanin absorption
methods.

0.035

0.03

0.025
-1

)
0.02

Rrs (sr
0.015

0.01
AMI (Peak Width / Dip Width)
0.005

0
400

450

500

550

600

650

700

Wavelength (nm)

Kudela et al. 2015, Remote Sens. Env.

750

800

We generalized the
spectral shape methods to
take advantage of
hyperspectral data, and
also developed a
Scattering Line Height
(SLH) algorithm which
works with almost any
sensor, including MASTER

Predicting Toxic Blooms

Kudela et al. 2015, Remote Sens. Env.

Phytoplankton Functional Types

San Francisco Bay
contains ~ 600
Phytoplankton
Species
(microscopy)
Ammonium

www.baykeeper.org

Mercury

The Delta drains ~40% of Californias

watershed
The Delta contains 90% of Californias
remaining coastal wetlands
In normal years, about 50% of the
water is diverted from the Delta
SF Bay is among the 6 most endangered
estuaries due to sea level rise

PCBs

Prasinophytes

Chlorophytes

Diatoms

Raphidophytes

Chrysophytes

Dinoflagellates

CLASSES OF INTEREST

Eustigmatophytes

Cryptophytes

Microscopy: 97-99% of phytoplankton

explained
Euglenophytes

CHEMTAX (HPLC): 94-98% of

phytoplankton explained

Cyanobacteria

HPLC captures the dominant groups identified

by microscopy, as well as rare/poorly
enumerated groups
Eustigmatophyte(
1.8%(

Others(
3.0%(

Cyanobacteria(
3.2%(

HPLC/CHEMTAX

Cryptophytes(
9.0%(
Dino.latellates(
14.3%(

Diatoms(
68.8%(

Eustigmatophyte(

1.0%(

Others(
2.3%(

Cyanobacteria(
0.1%(

Microscopy

Cryptophytes(
11.9%(

Dino/latellates(
10.1%(

Diatoms(
74.6%(

PHYDOTax HPLC Microscopy

River
S657

S649
S3

S6
S13
S16

Ocean

S18

DiatomDinoflagellate
Cyanobacteria
Cryptophyte
Chlorophyte

Haptophytes
Cryptophytes

HPLC/CHEMTAX &
PHYDOTAX = Same Food
Quality Index
Food Quality from Space!

Food Quality Index = 0.2 x Cyano + 0.525 x Chloro + 0.7 x Diat + 0.95 x Cryso

Waiting for HyspIRISentinel 2

S2 Image from 17 September 2015

San Lorenzo River

Pinto Lake (Microcystis)
(toxic Cylindrospermopsin bloom)

Quarry Lake
(closed for
microcystins)

Lake Chabot
(dog deaths
from
microcystins)

The Scattering Line

Height (SLH)
algorithm was
modified for S2
bands using AVIRIS
data to test transfer
We can identify
cyano blooms (but
not PFTs) now!

Moving Beyond Pigments

Benoit et al. (2010) demonstrated that TSS is highly correlated to metals

Press (2015) demonstrated that OLI can translate this to high-resolution maps

WCT Fe (g L-1)

WCT Cu (g L-1)

Using OLI as a proxy for HyspIRI, we can already map metal

distributions in SFB for 12 metals

HyspIRIMoving to Ecosystem Health

TODAY, we can map water quality in San Francisco Bay
(OLI)
Distribution of metals
Chlorophyll, TSS, CDOM, DOC

TODAY, we can track cyanobacterial blooms at HyspIRI

spatial resolution (Sen2)
With HyspIRI, we can:
Identify PFTs and calculate Food Quality
Distinguish toxic/non-toxic cyanobacterial blooms
Map kelp forest physiology

We can move beyond simple state variables to water

quality and ecosystem health (finally!)

MODIS AQUA

Landsat8

Sentinel-2

NASA
Ocean
Science

HsypIRI