1 / 2018
CEMarin
Corporation Center of
Excellence in Marine
Sciences
Contents Physical and numerical modeling of wave energy
Modeling wave energy 1
dissipation over submerged reefs
The Ocean2100 project 2 Within the framework of the re-
search project “Study of wave
Dissecting life in symbiosis 4
energy dissipation in natural
Alumni network 4 structures and their response
to extreme events”, supported
Alumnus report 5 by COLCIENCIAS (internal code:
Conference report 5 111866044690), the research
group OCEANICOS from Univer-
Book announcement 6 sidad Nacional de Colombia at
About the CEMarin 6 Medellín (UNAL) is currently con-
ducting a multidisciplinary study
in order to better understand the
role of coral reef ecosystems in
wave damping associated with
reef geomorphology and reef
roughness. The group uses a
Computational Fluid Dynamics
model, validated with field data
from a fringing reef at Tesoro
Island (Colombian Caribbean),
to simulate physical processes
along a reef profile. Additionally,
laboratory experiments in a wave
flume are carried out at UNAL by
simulating the rough surface of
Cross-shore reef profile of Tesoro Island
used for numerical simulations in the
OpenFoam model and numerical mesh
details of the shape projection of the
coral species Acropora palmata around
the reef crest.
NEWS
a coral reef with wood cylinders
to quantify possible impacts of
reef restoration/degradation on
the reef’s hydrodynamics. Also,
efforts have been made towards
diagnosing, understanding, and
modeling small-scale hydrody-
namic forces in branching coral
colonies (e.g., Acropora palmata)
in order to better understand
frictional coefficients. This study
might contribute to a better eco-
logical understanding of coral
reef roughness. Moreover, it may
help solving questions about the
effectiveness of coral reef ecosys-
tems in dissipating wave energy
and their general importance for
ecosystem services.
Contact
Juan David Osorio Cano
osoriox@gmail.com
Universidad Nacional de
Colombia, Medellín, Colombia
 2 CEMarin news 1 / 2018

The Ocean2100 long-term global change project

Coral reefs belong to the most
diverse ecosystems on Earth.
However, reef-building corals are
extremely sensitive to environ-
mental change. Around 50% of
the world’s reefs are threatened
by anthropogenic activities and
about 20% of the reefs have been
destroyed already. Major threats
include unsustainable fishing
practices and overfishing, habitat
destruction, environmental pollu-
tion, eutrophication, alterations
of food webs, unsustainable
tourism, sedimentation, global
warming, and ocean acidifica-
tion. There is abundant empirical
evidence for the adverse effects
of these stressors on scleractinian Main experimental setup of the Ocean2100 project. A total of 1944 coral fragments
is maintained in the microcosm system (photo: P. Schubert).
coral species. However, as most
of these effects are multifactorial,
a precise assessment of the indi- al change, remains challenging. coral reefs to address these prob-
vidual contribution of stressors, Although numerous field obser- lems, studies in natural systems
particularly those related to glob- vations are being carried out in are typically confounded by the
presence of variables others than
those of interest. The relationship
can thus be characterized, at
best, as correlative, and a direct
inference of cause and effect re-
mains challenging. Some workers
therefore argue that microcosm
experiments could be a suitable
methodology for addressing
global problems, such as re-
sponses of coral reefs to climate
change. Microcosms enable the
manipulation of a single or few
variables, and to compare the
effects on organisms over time
against control conditions. How-
ever, most microcosm systems
are being set-up for short-term
experiments. This may bias the
Six coral species belonging to the genera Acropora, Pocillopora, and Porites are
studied in the Ocean2100 project. For each genus, a species with complex and
results of the studies as the short-
simple growth form was chosen (setup: J. Reichert). term changes introduced may not

continues on next page

 CEMarin news 1 / 2018
Stress analysis in zooxanthellae using
PAM chlorophyll fluorometry (photo:
C. Martins).
be realistic. Moreover an assess-
ment of evolutionary adaptations
of corals remains difficult.
To overcome these problems,
a group of Colombian and
German scientists started in
2015 to set up the ‘Ocean2100’
global change experiment at
Justus Liebig University, Giessen
(Germany) as a scientific
lighthouse project of the
Corporation CEMarin (Bogota,
Colombia).
The project is designed to assess
the response of six species of
scleractinian corals (Acropora
humilis, A. millepora, Pocillopora
verrucosa, P. damicornis, Porites
lutea, and P. cylindrica) to
global change. The two main
parameters of concern are
elevated water temperatures
and ocean acidification.
Therefore, water temperatures
are being increased and
pH values decreased in the
treatment groups over a
period of 10 years to finally
match the conditions predicted
under the IPCC high emission
scenario (RCP 8.5) for the year
2100. Additional parameters
simulated are changes in salinity,
sedimentation, microplastic
pollution, and eutrophication/
changes in food webs.
The project includes i) whole-
genome and transcriptome
studies of the coral species using
next-generation sequencing,
ii) analyses of differential
morphological changes in
coral colonies (control vs.
treatment groups) using 3D
scanning and fractal dimension
analyses, iii) analyses of shifts
in microbial communities using
metagenomic and quorum
sensing approaches, iv)
differential stress analyses in
zooxanthellae using chlorophyll
3
fluorometry, and v) assessment
of reactive oxygen species
using electron spin resonance
spectroscopy.
The long-term objectives of
the Ocean2100 experiment are
to identify the individual and
cumulative impact of stressors
on coral health together with
the underlying processes,
to establish a multivariate
coral stress model, and to
subsequently monetize the
impacts as a basis for coral reef
conservation and restoration.
The Ocean2100 facilities at
Giessen University are open to
all CEMarin researchers and can
be used free of charge.
For more details see the
YouTube presentation at:
https://www.youtube.com/
watch?v=utjzNwlkJZs
Contact
Thomas Wilke
tom.wilke@allzool.bio.uni-
giessen.de
JLU Giessen, Germany
Comparison of photographs and 3D
models of six coral species (modified
from Reichert et al., 2016, Limnol.
Oceanogr. Methods 14).
 4 CEMarin news 1 / 2018
Dissecting life in symbiosis: Holobiont profiling in the stony coral Porites rus
Many cnidarians, including cor-
als, engage in complex symbiotic
associations, comprising the eu-
karyotic host, photosynthetic al-
gae, and highly diverse microbial
communities – together referred
to as holobiont. This taxonomic
complexity makes sequencing
and assembling coral host ge-
nomes extremely challenging.
Therefore, previous cnidarian
genomic projects were based
on symbiont-free tissue samples
(e.g., in situ complexity reduc-
tion). However, this approach
may not be applicable to the
majority of cnidarian species for
ecological reasons.
Announcement: CEMarin alumni network
Login page of the CEMarin alumni
network at www.cemarin.org.
We therefore evaluated the
performance of an alternative
method based on binning (in
silico reduction of taxonomic
complexity) for reconstructing the
genome of the stony coral Porites
rus from a hologenomic sample,
and compared it to traditional
approaches.
Our results demonstrate that
binning performs well for holog-
enomic data, producing sufficient
reads for assembling the draft
genome of P. rus. An assembly
evaluation based on operational
criteria showed comparable re-
sults to symbiont-free approaches
in terms of completeness and
Scientific networking is an im-
portant aspect of career build-
ing. Therefore, the CEMarin has
started to develop an interna-
tional alumni network. It allows
researchers to stay in touch with
friends and colleagues abroad
and to benefit from news and
announcements. It consists of
three parts: i) a communication
platform, ii) a news platform,
and iii) a career service platform.
usefulness, despite a high degree
of fragmentation in our assembly.
In addition, we found that binning
provides sufficient data for ex-
ploratory k-mer estimation of ge-
nomic features, such as genome
size and heterozygosity.
Considering the recent decline
of coral reefs on the one hand
and previous limitations to coral
genome sequencing on the other
hand, binning may facilitate rapid
and reliable genome assembly.
This study also provides an impor-
tant milestone in taking binning
from the metagenomic to the ho-
logenomic and from the prokary-
otic to the eukaryotic level.
Contact
Juan Sebastian Celis
juan.s.celis-melo@uni-giessen.de
JLU Giessen, Germany
Overview of host DNA sampling ap-
proaches in cnidarian genomic projects
(drawing: S. Celis).
Until summer 2018, the alumni
network will be available at the
CEMarin webpage. CEMarin
alumni will be informed in detail
and receive their specific login
data.
Contact
Carina Marek
CEMarin alumni coordinator
carina.marek@bio.uni-giessen.de
JLU Giessen, Germany
CEMarin news 1 / 2018
Alumnus report: Pedro Pablo Vallejo
My name is Pedro Pablo Vallejo
and I am a chemist at the Uni-
versity of Antioquia, Medellín.
I joined the Colombian Interin-
stitutional Doctorate Program
in Marine Sciences (DICM) in
2012. As part of my doctorate,
I participated in the CEMarin
course program in Santa Marta.
For my PhD thesis, I studied
spatial and temporal variations
of metal concentrations in ma-
rine sediments from the Gulf of
Urabá, Colombian Caribbean,
and their control by natural and
anthropic factors. Awaiting my
Conference report: Mangrove Symposium Bremen
The Annual Mangrove Sympo-
sium entitled “Transforming
tides into mangroves: Knowl-
edge-based conservation and
sustainable use of mangroves”
of the IUCN-SCC Mangrove
Specialist Group was held from
12−17 September 2017 at the
Leibniz Center for Tropical Ma-
rine Research (ZMT) in Bremen,
Germany.
Martha Lucia Palacios Peñaran-
da presented first results of her
PhD thesis in marine sciences
– Ecosystem carbon stocks of
mangrove forest in the Colom-
bian Pacific.
Among the many ecosystem ser-
vices provided by mangrove eco-
systems, their role in carbon (C)
sequestration and storage is high
compared to other tropical for-
est systems. However, detailed
information on amount and
variation of mangroves C storage
are still lacking. To address this
5
thesis defence, at present, I
am working as a researcher and
teacher in the Management
and Environmental Modelling
Group (GAIA) at University of
Antioquia.
Currently I am exploring postdoc
opportunities at universities and
research institutions in the field
of marine sciences.
Contact
Pedro Pablo Vallejo
piterjuls@gmail.com
University of Antioquia,
Medellín, Colombia
gap and examine the range of C climate change mitigation strate-
stocks in mangroves, we quanti- gies in Pacific mangrove systems
fied C stocks of Pacific Colombian of South America.
mangroves comparing two estu- This study is performed in col-
arine bays with different anthro- laboration with Jaime R. Can-
pogenic environmental impacts. tera K. and Enrique J. Peña S.
We also examined differences in from Universidad del Valle, Co-
ecosystem C stocks due to size of lombia.
trees and structure of mangrove
forest vegetation. Ecosystem C
stocks ranged from 23022.45 x
106 Mg C ha-1 and 13.59 x 106
Mg C ha-1 in both coastal estu-
aries. Below ground biomass
represented the single largest
pool of total C in these ecosys-
tems. We found significant dif-
ferences in ecosystem C stocks
based on location (Malaga Bay
and Buenaventura Bay) or man-
grove type (riverine and basin).
Combined with other ecosystem Contact
services, the understanding of Martha L. Palacios P.
mangrove ecosystem values of mlpalacios@uao.edu.co
C stocks will be important in the Universidad del Valle,
formulation of conservation and Cali, Colombia
 6 CEMarin news 1 / 2018

Book announcement: Corals in a Changing World

Corals comprise of a wide vari-
ety of colonial marine inverte-
brates belonging to the Phylum
Cnidaria. They are a source of
a number of goods, as well as
economic and ecological ser-
vices, for coastal communities
and for many people around
the world. However, due to a
diverse number of natural and
anthropogenic stressors, corals
have seen a severe decline over
the past few decades. Being
aware of the importance and
relevance of coral reefs, the
aim of this book, Corals in a
Changing World, is to provide
scientific information regarding
the actual status, and in some
cases, resilience state of coral
reef systems. Additionally, this
book presents and discusses
coral disturbances such us
bleaching, low temperatures,
and local and global environ-
mental and ecological aspects
that have caused an increase of
algae and cyanobacteria, which
are detrimental to coral reefs.
It also discusses the use of well
maintained coral microcosms
as a solid basis for perform-
ing controlled environmental
experiments. Finally, there are
chapters presenting innovative
technological tools for coral bio-
diversity characterization and
their importance as a source
of marine compounds to be
converted into drugs.
The book will be published in
spring 2018. The respective link
will be made available at the
web page of InTechOpen for
the readers to download, read,
and share all chapters for free
(www.intechopen.com).
The book is edited by Dr. Car-
menza Duque Beltrán (emeritus
professor) from the National
University of Colombia and Dr.
Edisson Tello Camacho (assis-
tant professor) from La Sabana
University, Colombia.

About the CEMarin (www.cemarin.org)

The main office of the CEMarin located
in the headquarters of the University of
Antioquia in Bogotá.
The CEMarin (Corporation Center
of Excellence in Marine Sciences)
is an international, non-profit
organization. Founded in 2009
by Colombian and German uni-
versities, it aims at answering
fundamental environmental
and socio-economical questions
related to marine ecosystems
in Latin America. It integrates
interdisciplinary marine research
with innovative post-graduate
training, and international net-
working across natural and social
disciplines. Member institutions
of the CEMarin are: Universidad
de Los Andes (Bogotá, Colom-
bia), Universidad Nacional de
Colombia (Bogotá, Colombia),
Universidad de Antioquia (Me-
dellín, Colombia), Universidad de
Bogotá Jorge Tadeo Lozano (Bo-
gotá, Colombia), Universidad del
Valle (Cali, Colombia), and Justus
Liebig University Giessen (Gies-
sen, Germany). The CEMarin is
one of worldwide four Centers
of Excellence supported by the
German Academic Exchange
Service (DAAD).
CEMarin
Carrera 21 No. 35-53
Barrio la Soledad
Bogotá, Colombia
Tel.: (+571) 3002715
E-mail: info@cemarin.org
Skype: corporacioncemarin

The CEMarin news is a biannual newsletter of the corporation CEMarin. For contributions to the
newsletter, please contact Carina Marek (carina.marek@bio.uni-giessen.de). The next issue will be
released in August 2018. Editorial deadline is 30 June 2018.