Module 4 notes

MOOC Innovative methods to assess the distribution of marine ecosystems
MODULE 4
Direct approaches to characterise the distribution of
ecosystems.
4.1 Introduction to Module 4.
In the previous modules, we have paid attention to some of the most important
characteristics of the different types of coastal ecosystems.
First, we analyzed some traditional ecological concepts, related to variability, structure,
processes, diversity or zonation in these systems. This allowed us to introduce a more
innovative characteristic, the ecosystem services, an aspect that is related to a more
integrative vision, that of social-ecological coastal systems.
Therefore, in modules 1 to 3, we answered the first question: "What kind of information
do we need to characterize a coastal system?"
Now it is time to move on to the next question, "How can we obtain information from
coastal systems?"
In this module, we will focus on the different approaches applied to directly characterize
coastal ecosystems.
This includes both traditional methods of field observation and sampling as well as
emerging procedures, based on a) different remote sensing technologies (e.g. satellites,
drones, ROVs, AUVs, etc.), b) the creation of living labs or c) the involvement of citizens
in monitoring specific features (e.g. invasive species, plastics).
In this sense, the globalization of some data sources, mainly associated with the
environmental conditions in which these ecosystems develop, requires specific mention
of international initiatives to standardize systems for collecting and processing
information on these ecosystems.
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4.2 Traditional sampling techniques
In this activity we will introduce you to marine and estuarine traditional sampling
techniques applied to benthic habitats.
In several aspects, including statistics or the environmental survey, sampling is the
process by which researchers select a representative subset of individuals or part of the
total population that could be studied to estimate characteristics of the whole population.
The advantage of sampling is that the use of a smaller number of elements makes the
research more manageable, time efficient, less costly, and more accurate.
Concerning the collection of biological data, and depending on the objective of the study,
there are two basic sampling types:
- destructive sampling, where all the biological material is removed from the sampling
area and transported to the laboratory for further analysis.
- non-destructive sampling, where data are collected without removing biological material
from their original place.
For each biological element and habitat, there is a more appropriate sampling
methodology to use.
Macroinvertebrates may present a very mobile form of living or constitute communities
closely associated to the bottom. These benthic macroinvertebrates, living in association
to the bottom, can be found in soft bottoms or over hard substratum, at intertidal or
subtidal areas.
Intertidal soft bottom communities are usually sampled with a corer (e.g., intertidal areas)
operated manually by a single person, and following a random sampling methodology.
The sampling device may present a square or a circular section shape. The device is
introduced in the sediment (around 20-30 cm) to isolate the sampling area and all the
inner content is removed into a container or a mesh bag for washing. The sampling area
must be known for further estimation of organisms’ density. Subtidal sampling uses more
often grabs as sampling device. Depending on the weight they must be mechanically
operated by a winch.
After collecting, the sample must be carefully inspected to ensure the grab worked in
proper conditions and the minimum volume of sediment was collected.
Macroinvertebrate communities inhabiting rocky shores are usually attached to the
substratum. To collect data from those habitats, usually the organisms are removed for
analysis in the laboratory or the information is registered in situ.
To do the first, a defined area must be marked in the rocky surface and the inner area
scrapped to collect all the biological material attached to the surface. For the second
option, a photograph can be taken and analyzed in the lab or identified in situ the
organisms that are present. With this method, the risk of missing data is higher.
Marine vegetation is composed of macroalgae and angiosperms. Macroalgae are usually
attached to hard substratum and rooted vegetation are found on soft sediments.
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To sample soft sediments, the most common methodologies were already described for
macrobenthic sampling. Samples can be collected by a corer or by using a quadrat that
allows the researcher to identify and photograph the plants for further processing in the
lab. Random and belt sampling methods are usually used here.
For sampling macroalgae thriving at rocky shores, one can mark a quadrat and scrap
the rock surface or photograph it for later identification in the laboratory (as indicated to
macroinvertebrate sampling). For one or the other, it’s important to know the area of the
sample. To complement the information, the researcher may identify organisms present
at the surface of the rock and add it to the presences list. This is typically a stratified
sampling methodology.
Simultaneously, physical and chemical parameters are also registered to allow the
characterization of environmental conditions influencing the organisms. Appropriate
tables and labels should be developed for this purpose.
Environmental parameters may be measured directly from the water column, using
sensors installed in portable multi-sensor probes.
The water turbidity is often registered with the use of a Secchi disk. The disk is dropped
in the water, at the shadow side of the boat and registered the depth to which the disk
gets imperceptible and the depth where it starts to be visible. The average depth is used
as the reference to water clarity.
To determine the concentration of nutrients and other substances, water samples may
be collected with sampling bottles, operated individually or installed in a carousel. The
sampling device is attached to the end of a rope or cable, graduated for measuring the
depth, and equipped with a closing system that allows to collect the sample at a
controlled position in the water column.
Although traditional sampling techniques allow to collect efficiently biological data,
nowadays there are alternative methodologies for sampling biological elements. These
methodologies, aiming a better use of technological resources (e.g., remote sensing),
are less costly, less time consuming, with more autonomy from human intervention, and
following automatic routine protocols that speed up the time needed to turn data
available. These will be further developed in the next activities.
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4.3 Quantifying species distribution of a natural resource.
In this video we are going to show you how to assess species distribution through
traditional sampling techniques in field campaigns.
This is the case of the cartography and evaluation of the macroalgae Gelidium corneum
in the coast of Cantabria (North of Spain) carried out in 1990 and 1991.
The objective of this work was to know the standing stock of the natural resource
Gelidium corneum, a macroalgae commercially exploited. To achieve this purpose the
biomass of the species was mapped, answering the questions: where is it? and how
much is there?
The cartographic technique applied is the one based on transects developed by Mann
in 1972. This methodology meets the premises needed for the evaluation of natural
resources: objectivity, simplicity, reproducibility and comparability.
The application of the Mann method to the cartography of Gelidium fields is based on
the location of perpendicular transects to the coast. Along these transects samples are
taken at different depths, harvesting the algae present on known surfaces areas.
So, firstly transects were established each km, taking into account that it is a regional
study. Some of this transects could be directly removed, since there were located in soft
bottoms where Gelidium cannot grow.
The total biomass corresponding to a coastal sector (Bt) was estimated based on the
different parameters of this formula. Bm is the average biomass per square meter, C is
the cover percentage, Am is the average band width and L is the length of the sector.
Let’s see in detail each of these parameters.
To estimate the biomass two samples of 50 x 50 cm were taken by scuba diving at 4, 8,
12 and 16 m, this last depth is approximately the maximum reaches by Gelidium.
Then, wet and dry weight were obtained in the laboratory.
To estimate the cover percentage a correction factor included in the Mann method was
applied. This way, the biomass was corrected according to the coverage of each depth
stratum as explained in this formula.
To determine the length of the transect, direct or indirect methods can be used, as for
example by establishing singular points that correspond to the start and end point and
estimate its length in a nautical chart.
Finally, the sector length was measured as the distance between transects, as a
quantification of the stretches of coast that the species occupied.
Now we are going to analyse one of the twenty sectors in which the coast has been
divided. Each of the sectors has similar characteristics, as slope or orientation. This is
the map with Gelidium biomass distribution in one of the sectors. There are 9 transects,
one of which is null because there is not Gelidium in the area. In the other transects
several samples have been taken to estimate the biomass of Gelidium fields.
This handmade mapping is still very useful. Although now we visualize it in a geographic
information system, this cartography allows to evaluate the commercial interest of the
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species fields and to provide basic information that facilitates the management of the
resource.
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4.4 Fundamentals and applications of remote sensing.
Welcome to this introduction to remote sensing. In this lesson I will explain how data
collected by sensors that are on-board of satellites, airplanes and drones are used, and
why such data are so important for scientists working on coastal vegetation. Remote
Sensing is the science of obtaining qualitative and quantitative information about an
object without being in direct physical contact with the object. An optical sensor, like the
one in the camera of your cell phone, is a perfect example of a remote sensor.
There are two groups of remote sensors: passive and active sensors. Your camera has
a passive sensor, as do many satellites orbiting the Earth. During the day passive
sensors take advantage of the electromagnetic energy emitted by the Sun that reaches
the targets, which is then reflected and captured by the sensors. However your camera
may become an active instrument at night, like when you need to activate the flash to
illuminate the target and take the photo.
Now, if we consider an instrument on-board a satellite, we can easily picture the journey
that the electromagnetic energy does before being captured by the remote sensor: it is
emitted by a source (the Sun or the instrument itself), it reaches the top of the
atmosphere and then travels through the atmosphere, reaching the Earth surface; it
interacts with the different targets on the Earth surface and then is reflected, travelling
back to the top of the atmosphere and can be captured by the satellite remote sensor.
The sensor has one or more detector elements that convert the light incoming from a
finite portion of the Earth surface into an electric signal and then it is quantized as an
integer value, called the Digital Number. The finite portion of the Earth surface sampled
by the detector element is defined as a pixel, derived from the term picture element. As
the satellite moves while the sensor scans the Earth surface, the digital image is
constituted by a large number of pixels that form a grid. This type of data is also known
as raster data.
Therefore, the data that the satellite transmits to a ground station are grids of digital
numbers that carry information about the Earth surface. However, we must focus on
each step of the journey of the light energy in order to interpret these numbers correctly.
Let’s start with the light emitted by the Sun. Due to its extremely high temperature, the
Sun emits electromagnetic radiation that span a very wide spectrum of wavelengths. The
electromagnetic wave consist of two fluctuating fields, one electric and the other
magnetic. The two vectors are orthogonal to one another, and both are perpendicular to
the direction of travel. The wavelength is the mean distance between consecutive
maximums or minimums of the wave.
The Sun emits very short electromagnetic waves, for example Ultra Violet waves, or
UVs, with wavelengths from 10 to 400 nm, as well as very long waves, for example
Microwaves from about 1 mm to 1 m. In between we have the visible portion of the
electromagnetic spectrum that ranges from 400 to 700 nm as well as the infrared portion,
from around 700 nm to 1 mm.
Different portions of the spectrum can be used to study different surfaces and processes,
for example the visible and infrared portions are the most used by scientist to study
vegetation.
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But let’s go back to the journey of sunlight. Once the electromagnetic energy emitted by
the Sun reaches the top of the Earth atmosphere and starts its path through the
atmosphere, atmospheric gases and water vapour interact with it, blocking or diminishing
the radiation differently for different wavelengths. Luckily, for example, ozone in the
stratosphere protects us from UV radiation, absorbing it before it reaches the Earth
surface.
Only the light belonging to some portions of the spectrum reaches the Earth Surface. We
call the portions of the spectrum that are not severely influenced by atmospheric
absorption, and which transmit to the Earth surface Atmospheric windows. These
portions are very important for remote sensing, because if we want to study the Earth
Surface we must create sensors that sample within the atmospheric windows.
And finally we are at the Earth Surface! The characteristics of the incident energy and
what happens to it when it interacts with the Earth’s surface is of critical importance in
remote sensing. In general, when the incident energy reaches an object, it is partially
reflected, partially absorbed and partially transmitted. However all these processes
depend on the nature of the incoming energy and the physical-chemical characteristics
of the target.
Let’s take a leaf, for example. The incident radiation interacts with its cells, chlorophylls
for example strongly absorb radiation in the red and blue wavelengths to perform
photosynthesis, but reflects green wavelengths and this is why vegetation is perceived
to be green. Other pigments in the leaf absorb radiation at different wavelengths. Part of
the radiation is also absorbed by the water contained in the leaf. After all these
interactions, part of the radiation is transmitted through the leaf to other leaves
underneath or to the ground. The radiation that is not absorbed nor transmitted is
reflected upward, carrying information about the leaf. It goes through the atmosphere
one more time before reaching the satellite sensor.
In summary, remote sensing sensors capture the radiation reflected by targets, store it
as grids of digital numbers so that we can use them to determine the characteristics of
such targets. However, remember that the electromagnetic energy journeys through the
atmosphere twice, so we must account for the double interference. Mathematical models
that simulate the interference of the atmosphere on the electromagnetic signal are used
to correct the raw data collected by remote sensors. Moreover, since the radiation
reflected by the surfaces depends on the incident radiation, the reflected radiation must
be divided by the incident radiation, retrieving a quantity named Spectral Reflectance
which is therefore a percentage of the incident radiation.
So, spectral reflectance curves are a sort of signature of the target. Here we see that
each material has a particular spectral reflectance curve that differs from the curves of
other materials. The spectral reflectance curve of green vegetation has two minima, or
dips, that correspond to the blue and red wavelengths at which chlorophyll absorb the
incident radiation. The peak in the green wavelengths tells us that vegetation reflects
green light. The large peak in the near-infrared wavelengths tells us that vegetation
reflects almost 50% of the radiation in that portion of the electromagnetic spectrum. All
this information are of key importance in vegetation studies using remote sensing.
Let’s consider for example a sensor that has four bands, one in the blue, one in the
green, one in the red and finally one in the near-infrared portions of the spectrum. We
immediately notice the large difference between the near-infrared band, where
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vegetation reflects radiation, and the red band, where vegetation absorbs. The
normalized difference between near-infrared and red bands has been widely used by
scientists working on vegetation and has been called Normalized Difference Vegetation
Index, NDVI. This index is very famous because it has been found to be a good indicator
of the photosynthetic activity of green vegetation and can be coupled to biophysical
parameters such as vegetation aboveground biomass, vigor, phenology, etc.
It is important to underline that vegetation indexes as the NDVI need to be linked with
field data to examine correlations in order to retrieve reliable results.
To conclude, I just want to mention that in this lesson we have only seen some basic
principles of optical remote sensing. There are several other remote sensing instruments
that make use of other types of data, for example active sensors that emit pulses in the
microwave portion of the electromagnetic spectrum. Moreover, in coastal systems,
sensors may be on-board Autonomous Underwater Vehicles (AUVs) or Remotely
Operated Vehicles (ROVs) and can be used to explore the sea bottom.
In the next lesson, I will show you an example of how remote sensing is used to
categorize saltmarsh vegetation.
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4.5 Quantifying estuaries vegetation
In this lesson, we will show you how scientists quantify vegetation in an intertidal
saltmarsh system using remote sensing. This lesson will build on an earlier lesson about
saltmarshes, and deepen your understanding on saltmarsh plant zonation.
Coastal salt marshes are wetlands that develop in the upper intertidal zone and their
origin and survival critically depend on the delicate equilibrium between erosion and
deposition processes and sea-level rise. The presence of vegetation that grows on salt
marshes is a key factor for their survival, because vegetation roots stabilise the soil, the
aboveground parts trap inorganic sediments when high tides flood the marsh and plants
themselves provide aboveground and belowground organic matter. Over time, this
contributes to soil accretion.
Plants that grow on saltmarshes are called halophytes, which are salt-tolerant plants that
can complete their entire life cycle in saline environments. The spatial distribution of
halophytes in salt marshes is not random, but organised in characteristic patches. We
may have monospecific patches, for example in the case of Spartina maritima, or we can
have patches characterised by two or more species, for example for the association
dominated by Limonium narbonense and Sarcocornia fruticosa.
Salinity is one of the important controlling factors of plant zonation, especially at the scale
of the entire estuary, where we distinguish between salt and brackish water marshes.
The first type develops near the estuary mouth, where the salinity is high, while the
second type develops in the inner estuary, where the salinity is typically low due to fresh
water inputs from the river. Other controlling factors are oxygen availability for roots, soil
chemistry, nutrient availability and interspecific competition.
In order to study the spatial distribution of different species across a salt marsh, we may
apply different methods. Since marshes usually cover large areas in an estuary, and
often present difficult terrain for field surveying, remote sensing has been widely applied
to study marsh vegetation distribution. This method is particularly useful for determining
“Cover” and “Biomass”.
So far, we have learned that “Cover” is the percentage of the ground surface covered by
each vegetation species, and in the field, we can use quadrats of known area to estimate
plant cover more easily. We have also learned that remote sensing provides “raster” data
collected over surfaces, hence providing a grid of square or rectangular pixels. If we are
able to calibrate field observations of vegetation cover with image pixels, it allows us to
estimate the proportion of pixels covered by each species. With this we can produce a
map of the vegetation cover across large marsh areas. This technique is generally called
“spectral unmixing”.
As for the detection of plant biomass, remote sensing can be used to provide indices that
correlate with the aboveground biomass, for example the so-called Normalised
Difference Vegetation Index or NDVI that we have seen in the remote sensing lesson.
NDVI is an indicator of photosynthetic activity of green vegetation and a number of
studies show that NDVI generally increases as the aboveground biomass increases.
Once calibrated to the particular vegetation type, the NDVI retrieved from remote sensing
can give us a relatively good prediction of the amount and spatial distribution of
aboveground plant biomass.
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It is extremely important to underline that all remote sensing methods must be calibrated
using field observations in order to assess trustable quantitative relations. Moreover, in
order to provide a reliable estimation of the error, the mapping results must be
quantitatively compared to independent ground-truthing measurements.
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4.6 Global databases of marine biological and physical information
In the previous videos we have seen how to acquire biological data from field sampling
and from remote sensing, but there is an easiest way to obtain the data when we are
working in a large area: the global and free access databases.
These databases provide us biological data, and also environmental data, that we can
use as surrogate of species or habitats distribution. Let’s start with the most commonly
used biological databases. GBIF and OBIS are the reference database for species
distribution.
In GBIF, we can search species, as for example Posidonia oceanica. Here we can see
an overview of its worldwide distribution. If we go to occurrences, we have several filters
available and we can download the selected data.
In OBIS, we can search the same species. If we go to mapper we can also observe the
general distribution and apply specific selections before downloading the data.
OCLE is a specific database with information about macroalgae distribution in the NE
Atlantic coast. In the OCLE web-site we should go to contents, then to biological, to
select the period historical, the species and the parameter (intertidal or subtidal). After
click search we select the year and the season. We can visualize data in a map and we
can also download it.
EMODnet Biology is another database with species distribution information along Europe
coasts. In data download toolbox we can search for any term in the dataset.
Another kind of biological information that we can obtain is the distribution of habitats, as
in Ocean Data Viewer. Here we can search a habitat, as for example mangroves. We go
to view dataset details where we have different information and the option to download
data.
Another information that could be useful are land uses. We highlight three databases
with this information: Land Cover from Copernicus, GlobCover from ESA and LandCover
by National Mapping Organizations.
In the Copernicus Land Cover service, we have the Global Land Cover viewer for maps
and area statistics, where we can visualize single class and fractional covers in several
years, as well as download it.
In the GlobCover portal provided by the ESA we can directly download this map.
Finally, in the Global Land Cover by National Mapping Organizations we can also
download the map directly after selecting the version most appropriate for our objective.
There is also another kind of information related with management purposes that can be
obtained this way, protected areas from the world database. Here we can search for a
specific protected area or to visualize all the protected areas worldwide.
Let’s continue with the environmental data.
In the marine domain one of the most commonly used is Bio-ORACLE. This database
includes historical and projected data for climate change scenarios. Besides, one of the
differences with other databases is that it includes both surface and benthic marine
realms. In Bio-Oracle we can explore the data and visualize it worldwide. We can also
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download data after making the selection according to what we need (temporal period,
depth of layers and different variables).
Another relevant database is MARSPEC. The distinctive feature of MARSPEC is that it
includes paleoclimatic data. So, in the MARSPEC web site we have climatic and
geophysical information available for the actual and paleo period. As with Bio-ORACLE,
we can download the data.
If we are interested in historical data, which covers both terrestrial and marine
environment, we can use MERRAclim. In this case, data is available in the scientific
paper which compiles all the information. So, we have to use the paper to get the
information. At the end of the paper in the data citation section we click the link to
download the data.
If we are working in the coast line, we can also use WorldClim, which provides historical
and projected climate and weather data, but just only in the terrestrial domain. Through
this website, we can download historical and projected data with different resolutions.
Again, EMODnet provides several environmental information in different data portals,
such as Bathymetry, Geology and Physics.
Finally, we can also look for regional databases depending on our objectives and study
area. For example, the European database OCLE provides a wide range of physical and
chemical variables, including hydrodynamic information.
We visited this website before when talking about biological data, but for environmental
data we should go to the “contents” section and click on physical. Then we have to select
the period, the variable and the parameter. For the historical period data is split into five-
yearly datasets. Again, we can visualize it on a map or to download it.
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4.7 How to use a global database
In this video we will continue talking about global databases, but now we are going to
focus on the data downloaded and how to work with them.
We are going to download both biological and physical data.
The species we are going to work with is Saccorhiza polyschides, a large brown algae
common in the Atlantic coast. In addition, we have selected several environmental
variables that determine the distribution of this macroalgae species: maximum, mean
and minimum sea surface temperature, mean salinity and mean photosynthetically
active radiation.
First, we are going to download the species distribution from GBIF. So, we go to the
website www.gbif.org. We can directly go to occurrences and write the scientific name
of our species, in this case Saccorhiza polyschides. We click yes to limit our search to
this taxon. Occurrence status: present. In basis of record we select human observation
to be sure it is not a preserved specimen in a museum. In location we click including
coordinates because we need to use georeferenced information. For example, we want
presences from year 2000 to present. And this will be our selection.
In the map we can observe the data spatial distribution. And we go to download. We
have to login with our email account after we register. We download simple data. It may
take a while to prepare the download data. Here we have the DOI in case we need to
cite the data. We click download.
Once we have downloaded the file we extract. We can open it with excel and use text to
columns to observe data in a proper way.
So, here we have the taxonomic information. Then, this columns show the location
information and also very important to note the latitude and longitude coordinates. Here
the date of observation and in the final columns the creative commons and the data
authors.
Let’s continue with the environmental information. In this case, we are going to download
data from the website Bio-ORACLE.org. We go to download manager. In this case, we
want to work with present data so we select present. We click surface layer. Format file:
ASCII. We select for the variable temperature the parameters max, mean and min. We
add also mean salinity and mean photosynthetically active radiation. The last step is to
write here our email address and the file is sent. So, in the email we receive, there is the
paper we should cite when we use the information and the raster layers requested. Let’s
download for example maximum temperature. We again extract the data and we have
an asci file that looks like this.
The optimal way to open and view the content is with a geographic information system,
as QGIS. In QGIS we add the layer and here we have the maximum temperature
worldwide. We can make a zoom in our study area of interest, the European Atlantic
coast where we find the presences of Saccorhiza polyschides.
Now it is your turn to visit these websites and explore the variables you are interested in!
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4.8 INTERVIEW: Challenges in sharing marine ecosystem information (with

Joana Beja from VLIZ).
Interviewer:
What is EMODnet? How is it related with other databases?
Joana Beja:
EMODnet is a European funded project that, through a network of organisations,
promotes ocean observations, make data available according to international standards,
e.g. as interoperable layers and data products. The main philosophy behind EMODnet
is “collect once, use many times”. EMODnet covers seven themes, Bathymetry, Biology,
Chemistry, Geology, Human Activities, Physics and Seabed Habitats.
EMODnet Biology currently has 22 partner organisations’ spread across Europe and
covering all European seas. As we use the EurOBIS infrastructure for our data
management, our data are also shared and available with OBIS (Ocean Biodiversity
Information System) and the European marine data is also shared with GBIF (Global
Biodiversity Information System). This data exchange allow for a wider dissemination
within the international community.
Interviewer:
How is the data infrastructure of EMODnet Biology organized to assure that information
from different sources can be exchange?
Joana Beja:
Within our thematic lot we use the Darwin Core standard for the data. A few years ago,
we collaborated on the development of an extension to this standard, which allows for
the mapping of measurements or facts associated with the biological samples. By the
use of controlled vocabularies to describe the marine regions, species, measurements
or facts we improve its value and the interoperability with other types of data, e.g
chemical or physical oceanography data.
Interviewer:
Why are databases so important? And, more specifically, what are the benefits of sharing
marine biodiversity data?
Joana Beja:
Without data, science does not advance and policy makers will not be able to make
informed decisions on the matters they legislate about. Databases are an essential
component of data management especially when they are accessible and openly
available to users. The act as long term repositories and allow for the future curation of
data.
As we deal with biological data, we understand that some data are sensitive, e.g
commercial significant or endangered. We have systems in place to deal with these
constraints and still make the data available and reusable.
By making marine biodiversity data available to all, we support scientists in their
research, by, e.g providing information on past/current species distributions and
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occurrences, we support policy makers by e.g. contributing to global, national or regional

biodiversity assessments through which policies can be set, we support industry by, e.g
providing the data on which assessment tools and/or services can be built upon and
assist with better management of said industry. We also provide support to citizens as
they can themselves query our holdings and find biodiversity information relevant for the
area of their residence.
By creating data products, we also demonstrate the potential contribution that the data
we manage can have and the observations that can be extracted from the biodiversity
distribution.
Interviewer:
What are the main difficulties and challenges you have to deal with in your daily working
with biological data?
Joana Beja:
The main difficulties are adhering to the standard we use and continuously improving it
so that the data can become ‘FAIRer’. The data we work with originates from a variety
of activities, from research studies, to monitoring programs, but also citizen science
observations. It is not always certain that all information will be available and that the
data that are submitted to us are of quality and well described. There is a lot of human
power behind making data FAIR, some procedures can be automated, but having a
human eye is essential to ensure that data make sense and that the vocabularies
mapped to each parameter or species are correct and make sense.
Interviewer:
What is the future of EMODnet Biology?
Joana Beja:
Hopefully a bright and diverse future! We are currently on phase IV of the project and
many changes are inline. There is work ongoing to centralise EMODnet Biology, this
means that our portal will cease to exist and all our data, products, tools, information will
be available via the EMODnet Central Portal. Aside from the continuous data ingestion
and exploring new collaborations with various data providers, we are also working on
developing new data products and explore opportunities to collaborate with the other
EMODnet themes, so the products can be more over-arching. We are involved with OBIS
to define a standard on how to deal marine genomics data; this is an area that is
becoming increasingly important and appropriate data management is essential. We
want to strengthen our participation and interaction with the Regional Sea Commissions
and see how we can better address their needs with what we have to offer.
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4.9 Real time monitoring of marine ecosystems
Real-time ocean monitoring is revolutionising the study of the sea and the marine
ecosystems. Marine observatories, such as the Balearic Islands Coastal Observing and
Forecasting System (SOCIB), provide comprehensive descriptions of the physical forcing,
circulation, primary productivity and water column properties that subsidize and structure
habitats in the coastal ocean. SOCIB (video), placed on the Western Mediterranean, is a
multi-platform multidisciplinary and integrated ocean observing & forecasting system
aligned with the scientific, environmental and social priorities of the 2030 Agenda and
the Decade of Ocean Sciences for Sustainable Development (2021-2030).
Animal-borne instruments are a new addition to SOCIB since 2017, tracked sea turtles
complement the observing system with unique and cost-effective data providing
information on essential biodiversity variables and contributing to knowledge based
marine conservation.
Here are the subtitles of the video “Oceanographer turtles” (Source:SOCIB,
https://www.socib.es/):
Observing platforms for conservation and dynamic ocean management. The Caretta
caretta turtle makes a long migratory journey from the Atlantic Ocean to the
Mediterranean through the Gulf Stream. The waters of the Balearic Islands are an
important feeding ground for the oceanic-phase juveniles of this species. In the
Mediterranean Sea, the main threats to turtles are accidental capture in fishing gear,
collision with boats and entanglement in drifting plastics.
In order to develop conservation programmes, it is necessary to study the environmental
factors that determine their movements and habitat use. The "Oceanographer turtles"
project combines real-time monitoring of turtles with operational oceanography. Placed
on the turtles shells, the satellite sensors send information on their position and diving
depth. Their sensors also measure sea temperature to study the state of the oceans,
turning turtles into oceanographers of opportunity that are integrated into the SOCIB's
multi-platform system. Underwater drones, drifting buoys that follow currents and
numerical models provide researchers with real-time information on environmental
conditions. The integration of all the data received makes it possible to provide forecasts
of turtle habitat and assess the risk of interaction with human activities. This new
knowledge will allow the development of future management and conservation tools.
16
4.10 Monitoring community change with Autonomous Reef Monitoring

Structure (ARMS)
Monitoring of marine ecosystems is essential for the preservation of biodiversity through

space and time. The purpose of the monitoring is to track the past, observe the present
and forecast the future.
This allows for adaptive management and conservation plans that better protect marine
resources and ecosystems and consequently human well-being.
In this lesson, I will show you how benthic marine biodiversity is being monitored in terms
of community structure using an innovative and standardized method at Palinuro, a
location on the Southern coast of the Tyrrhenian Sea, Mediterranean.
There are several methods to monitor marine benthic biodiversity. Traditional methods
include manual sample collection with a scraper, quadrat sampling by divers and
analysis of photo images. Some of these methods are covered in more detail in the
“Traditional sampling techniques” lesson.
With the advent of new technologies, scientists can also collect samples and images
using remotely operated and autonomous vehicles.
Whichever method you use to perform monitoring there, is one main rule that you have
to take into account: and that is Standardization. Standardization is pivotal for comparing
data across regions (e.g. different research institutes) and across time.
You have to standardize the rules for choosing which sites are to be monitored and at
which scales, which depends on the variability of the physical environment and oceanic
connectivity.
You have to standardize the sampling methods and finally you have to standardize the
methods to assess species compositions. We will see later that for this last point,
integration of different methods of analysis is a must.
Currently, ARMS, which stand for Autonomous Reef Monitoring Structures are one of
the best standardized ways to monitor changes in the structure of benthic communities
through time and space.
ARMS are standardized 3D collectors of marine life. They are stacks of 9 grey PVC
plates 22.5 cm X 22.5 cm separated by spacers that create an alternating series of open
and closed layouts. This mini-hotel is than fixed to a base plate of 35 cm X 45 cm that
can be fixed on the sea bottom.
ARMS mimic the complex structure of the sea floor. They provide hard surfaces as well
as nooks and crannies that sea creatures like to live on and among. They are usually
deployed on the sea floor for a certain period of time, after which they are retrieved and
brought back to the lab to check for organisms that can be found living inside. The
deployment of ARMS in the field usually ranges from 3 to 12 months depending on the
aims of the study.
VIDEO: This video clip shows marine biologists working with ARMS in the field. Here we
were in Palinuro, in the south of Italy at a depth of about 20 meters. In addition to the
17
ARMS structure, you can see we installed a series of plastic pan scrubbers as well.
These provide a different sort of habitat for marine organisms and have been given the
fancy name of artificial substrate units or ASUs.
We fixed the ARMS on the sea floor using an underwater drill. You can see the ARMS
are completely covered by sessile organisms and in particular with algae after one year
of deployment. After this period at sea, we recovered the ARMS and substituted them
with a new fresh set of ARMS. These will remain in the field for another year so that we
can monitor the benthic community over time. Before bringing the ARMS to the surface,
we place them in a plastic box and secure them with bungee cord. This ensures that we
do not lose the mobile fauna that live inside the mini-hotel.
Once we get back to the laboratory, we put the ARMS into a bin. We disassemble each
structure. And put each plate into a tray with filtered sea water We photography each
side of the plate. And then scrape each plate. We put all scrapings in a blender and
blend. Finally, we preserve the sampled material in ethanol for further analysis.
First, we divide all the mobile fauna within the structure into different size classes. To do
this, we put the sample through three different sieves (100, 500 and 2000 micron). Once
all the plates are processed, we use different methods of analysis to detect community
composition. We measure the % cover of the sessile fauna on the plates using photo
analysis. We identify mobile organisms based on their morphology using stereoscopes.
Finally, we use genetic tools such as barcoding and metabarcoding to evaluate species
diversity across communities
But what are DNA barcoding and metabarcoding?
Well, DNA barcodes are similar to product barcodes you find on supermarket shelves.
DNA barcodes are short sections of an organism’s gene that are unique for each species.
By comparing the DNA barcode gene sequence of an unknown sample to available
global databases, we can quickly and reliably identify the species.
Metabarcoding is barcoding but at larger scale of analysis. We extract all the DNA from
a bulk sample for example the scraped organisms form an ARMS plate. From this DNA
we sequence a specific region, and by comparing these sequences to global databases,
we can assign all the amplified sequences to specific species in the community based
on similarity.
In summary, ARMS provide a tool that is simple and standardized to monitor community
change. With ARMS we can track community changes across different spatial scales
from local to global and across different time periods. This integrative approach using
the different methods to evaluate community composition and species presence is
fundamental to better protect biodiversity.
18
4.11 From data to decision support through digital solutions
The marine environment is very dynamic, as we can see from the pictures of “isla de
Mouro”, located at the Santander Bay, in the North of Spain. Understanding all the
Environmental phenomena that take place at the coastal zone is a big challenge.
Multidisciplinary teams, composed by oceanographers, biologists, engineers, among
others, work together to analyse and represent the real world making use of digital
technologies.
Basically, the real world is conceptualized and translated into digital data that can be
managed and analysed by specific software. The use of information technologies allows
us to represent past, present and future conditions of any place in the Globe. This ability
is like having a travel time machine.
Decision support systems transform digital data into information that will provide new
knowledge for decision support. Let’s see the first step, how is the data obtained.
Scientists make use of three main ways to observe and measure the marine phenomena:
(1) collecting in situ observations, (2) using remote sensing technologies and (3)
implementing numerical models.
In situ observations are collected by scientists and stored and managed in digital
repositories. In addition, sensors such as buoys or meteorological stations are
continuously observing specific variables and centralizing the measurements in data
management systems.
Remote sensing techniques, using drones and satellites, are becoming fundamental
tools to observe the Planet. The sensors used monitor large surfaces, being able to
provide data with very high resolutions. Currently, the amount of open Earth Observation
data is huge; see the Sentinel family from the Copernicus programme. It is remarkable
the very high resolutions (spatial and temporal) from the commercial programmes.
On the other hand, numerical models make use of mathematical equations to try to make
an approximation to the real phenomena under study. To do this, they require
observations (from in situ or remote sensing techniques) and computer power to perform
their operations.
In conclusion, we can have large volumes of data derived from different techniques,
which must be translated into information for decision support. In this process (Data to
information) is very important to know the end users capacities and adapt the information
for their needs, providing the knowledge required for decision support.
Technically, two data models are mainly used to provide a digital representation of the
real world: vector data model and raster data model. In the vector data model, the entities
are represented with points, lines and polygons, while the raster model represents the
information in data meshes that cover an entire surface (for example, satellite data).
It is important to emphasize that digital solutions must be designed under a user-oriented
approach, taking into account the different types of users (general public, scientists,
technicians or managers).
19
Next, I am going to show you examples of different solutions for different users. We will
start with the spectral library, which has been designed for remote sensing experts. The
system stores and manages spectral signatures reflected by natural species such as
Zostera noltei.
Scientists analyse the spectral signature of satellite images to monitor the marine
environment. In this case, the results obtained are shared with the general public and
managers, providing a simple visualization of the evolution of the spatial distribution of
Zostera noltei in Santander Bay in recent years.
Meteo-oceanographic data and presences of marine species in Europe can be
downloaded and easily visualized through the OCLE System. The System facilitates the
scientific community's assessment of the climate change effects on littoral and oceanic
ecosystems.
The Red Natura 2000 GeoViewer was designed for public users and managers, it
provides and easy access to the spatial information related with the Natura 2000 in
Cantabria region, including habitats, species, pressures, and other information.
The MARES GeoViewer shows to the general public and managers the risk assessment
of the Cantabrian estuaries in the face of rising sea levels due to climate change.
In conclusion, all the examples previously showed try to provide new knowledge to end
users. User engagement and co-design of the digital solutions with end users through
an iterative process is highly recommended to achieve successful decision support
solutions.
20
4.12 INTERVIEW: A new approach: citizen science and marine

observatories (with Macarena Marambio from ICM)
Interviewer:
Hi everyone! In this lesson we are going to introduce you to a novel approach to direct
characterize marine ecosystems and spaces distribution which is getting great attention
from the scientific community but also from environmental from environmental
management agencies.
This approach is known as citizen science, to introduce you to this topic we have been
very lucky to count with the collaboration of Macarena Marambio, a researcher at the
Instituto de Ciencias del Mar of the spanish research council, specialised in gelatinus
zooplankton.
She has been part of the marine citizen science platform Observadores del Mar since
the beginning. Being nowadays part of the scientific area coordination and responsible
of the jellyfish allen project of the platform.
Hi Macarena, it is such a pleasure to be here interviewing you today, thank you very
much for your time. We have some questions for you today related to the general concept
of citizen science and also to the Observadores del Mar platform, which is for us a great
example of how citizens can get involved in conservation.
So let's start with the general questions. What is citizen science?
Macarena Marambio:
Hi, thank you to you for the invitation, it's a pleasure to be here.
Well, according to the European Citizen Science Association, the concept of citizen
science includes different ways of involving society in scientific activities and processes.
The most characteristic aspect is that citizens actively participate in research projects in
different kind of projects by contributing to generate new knowledge. This participation
can be actively at different steps of the projects. Citizen science also can be applied to
a wide variety of fields such us for example ecology, medicine, archaeology,
computacional science or even history, among others. Nowadays, it’s really useful for a
lot of fields and with the latest developments of technological information and different
systems, we are assisting to an actual boom of citizen science and it has been used in
a lot of projects around the world.
Interviewer:
What are the main goals of citizen science?
Macarena Marambio:
Well, the main goals of citizen science depend on your objective, but from my point of
view, it has a three main objectives.
First, we can say that it is to increase scientific knowledge through the participation of
society. that means significantly in some way enlarge our capacity to observe and gather
21
data. In some way, citizens are our eyes in the field, so they can lead us to obtain data
in a large time and space.
Second, it will be maybe to raise social awareness about environmental problems
because citizen science projects are great vehicles for the dissemination of many
different environmental issues so it’s important for the society to get involved and in some
way take their own responsabilities on different threats that nature is facing right now, for
example the impact on climate change and the spread of invasive species.
Third, all of them are important, but the third one will be to promote dialogue between
society and the scientific community because this is usually, uh, there was a big lap
between these two parts and now it's important that if society is involved, it's easier to
get some solutions and strategies for applying for the management and conservation.
Interviewer:
Regarding to the study of marine ecosystems under distribution in which aspects citizen
science can play a key role. Could you give us some examples?
Macarena Marambio:
Yes, well, citizen science nowadays it’s really important because we are still lack a basic
of information that is key to assure the efficient management and conservation of marine
ecosystems, for instance, we still do not know the precise distribution of some marine
species, for example, even there are some that haven’t been discovered, so in that case,
in the case for example of some corals, even jellyfish or macroalgae, it is a necessary,
it’s a key role, citizen science is also importantant because it can provide information on
the arrival of exotic species. So it means that citizen science can work as an early alarm
or prevention for some things and also the changes in the phenology of the species, for
example, in reproduction periods because for most of the scientific projects it's some
way impossible to be everywhere at everytime, so having like a large observation
network that it’s conformed by citizen scientists, we can have the eyes and the
information are in the field, for example, the whole year in some areas. So we can get all
the information that we need for getting that data.
Interviewer:
What are the main advantages that citizen science offer relative to traditional science in
the study of marine ecosystems and their distribution?
Macarena Marambio:
Well, mainly that scientific research teams have limited human and technological
resource that this things constrained the exploration and the monitoring of marine
ecosystems at the spatial and time scales required for developing the optimal
management and conservation plans so in, in this way the advantage of applying citizen
science is that it allows broadening our observation capacity and so the data we get it’s
enlarging the time scales and the space.
Inés (Interviewer):
What are the main challenges of applying citizen science to the study of marine
ecosystems under distribution?
Macarena Marambio:
22
Well, I think that maybe, the main challenges we can classify them into:
One is to face the generation, the growth and to maintain the community of citizens and
entities that actively participate in the projects along the time, so the engagement of
these participants is really important and in some way the existence of multiple projects
is a source of confusion among participants. So, in order to avoid this, the strategy may
be to look for synergies and collaborations among different initiatives of citizen science
but this is not always easy beacause not all the projects have the same line of research
or objectives.
But then, another challenge really important is to assure the quality of the data obtained
and for this it’s really necessary to develop clear standardized protocols, in order to
capacitate the participants so that the data collected is okay and it’s in the right way, in
order to be analyzed and then it comes the validation of the data because it’s important
that there are some scientific teams behind these citizen science platforms, in order to
assure that those that has been collected and they are validated, so it can be used, for
example, for scientific publications.
Interviewer:
What is “Observadores del Mar” and what kind of projects are included?
Macarena Marambio:
Well, it's a marine citizen science platform, it's a platform where different projects are
included and the objective is mainly to support the conservation of the marine
environment. It develops simple and direct scientific protocols to allow citizens to answer
questions related to different challenges in marine conservation. Currently, it includes 15
projects that cover mainly five different scientific topics: biodiversity, endangered
species, alien or invasive species, marine debris and climate change. So the idea of
Observadores del Mar is to really help society to get involved in the problem and in the
solution. It's a way to feel part of the whole process.
Interviewer:
What are the most common stakeholders involved in the projects of Observadores del
Mar and what are their main motivations?
Macarena Marambio:
The main stakeholders involved in Observadores del Mar are the general public and the
different entities that develop their activity in the sea in the marine environment and also
the educational community. The main motivational factors are the social awareness
about the impact of human activities on the marine environment and the willingness to
collaborate with the scientific community in order to find solutions and to contribute to
the conservation of the marine environment.
Interviewer:
Based on the experience of Observadores del Mar what are the most critical factors to
assure the successful of citizen science projects?
Macarena Marambio:
23
Well, here we go to maybe the same answers that we got from the main challenges. It's
in some way the engagement because to keep a continuous communication between
citizens and the scientific community and the dialogue between them both it’s really
important but the usefulness of the data so this comes with the development of
standardized protocols and in order to assure the collection of the data and then the
validation of the data it’s also very important because what participants don't want or
don't like is to feel like they are gathering the data and making the effort, they want to
contribute but then this data goes anywhere. So that’s why it’s really important that in
some way to show the usefulness of this data, for example, in publications or in
management policies or in different products that can be obtained with the collection of
this data.
Interviewer:
Is there an example of a project from Observadores del Mar where the data have been
used in a scientific product such a paper or a book or for the management of an
ecosystem?
Macarena Marambio:
Yes, in fact, the data gathered by some projects through the citizen observations have
already been used in scientific papers and in some publications and they have
contributed to the knowledge of the different threats that the marine environment faces.
For example, in the case of invasive species because citizen science may contribute to
the early detection of some species and there are a lot of papers that they publish the
first record of this species in this area and these are mostly done by citizen scientists
because they are the eyes the whole time in the field.
Interviewer:
And based on the experience of Observadores del Mar how do you think citizen science
affects the relationship between science and the general public?
Macarena Marambio:
Well I think for sure that citizen science has a positive impact, it's a great way to get
involved in marine conservation and feeling part of the solution to the problem. Then, the
solution, for example, to the loss of biodiversity or climate change is really very important
to society and also to feel the responsibility, I am responsible for this but I can also help
in gathering data for solutions. The participation in any step of a scientific project is a
clear way to broaden also the knowledge and the interest about the marine environment
so the knowledge and the interest are the key to increase society's willingness to
contribute to the protection and conservation of marine ecosystems.
Interviewer:
Thank you very much Macarena for such a great interview and for introducing us to
marine citizen science, a great tool to expand scientific knowledge about marine
ecosystems to promote dialogue between citizens and scientists to raise social
awareness about threats to the marine environment. All these components are key to
make progress in marine conservation.
Macarena Marambio:
24
Thanks to you
25
26

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MOOC Innovative methods to assess the distribution of marine ecosystems

4.1 Introduction to Module 4.

4.2 Traditional sampling techniques

4.3 Quantifying species distribution of a natural resource.

4.4 Fundamentals and applications of remote sensing.

4.5 Quantifying estuaries vegetation

4.6 Global databases of marine biological and physical information

4.7 How to use a global database

4.8 INTERVIEW: Challenges in sharing marine ecosystem information (with

occurrences, we support policy makers by e.g. contributing to global, national or regional

4.9 Real time monitoring of marine ecosystems

4.10 Monitoring community change with Autonomous Reef Monitoring

Monitoring of marine ecosystems is essential for the preservation of biodiversity through

4.11 From data to decision support through digital solutions

4.12 INTERVIEW: A new approach: citizen science and marine

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