Report for the EUR-Ocenas Foresight workshop ”Ocean Science meets -omics”
held in Naples, Italy, November 7-November 10, 2010
”Ocean Science meets -omics” was designed to provide a forum to bridge the gaps
between recent developments in Molecular Biology (genomics and proteomics) and
Marine Ecology. The observed macroscopic patterns observed at sea at higher level
of organization (e.g. a community) analyzed by ecologists are only seldom related
to the processes at lower level of organization (e.g. the organisms), normally dealt
with by organismal biologists and almost never described on the basis of the
underlying molecular processes studied by molecular biologists.
This poorly integrated view is aggravated in marine environments because most of
the existing paradigms on mechanisms and forcing, both at molecular and
ecological level, are based on processes occurring in terrestrial environments and
they may result inappropriate or completely different in the marine system. In
addition, molecular processes are linked to responses that are very difficult to
observe because of the intrinsic inaccessibility of the marine environments and, in
particular, because of the minute sizes of most of the organisms of a crucial
component such as plankton.
The exponential growth of tools able to characterize molecular processes in several
classed of molecules, i.e., the -omics, has stimulated several contributions on how
-omics may be applied in marine science. Very seldom an inverse approach has
been used, e.g., selecting crucial questions in marine science and analyze to what
extent -omics can contribute to find answers not only because they represent a
new methodological approach but also, and more important, because of the
understanding of mechanisms and constraints at molecular level.
The contribution of -omics to marine science has grown rapidly over the last years,
and its continuous progress is inspiring new ways of answering old questions. This
also implies bringing together different scientific logics and dictionaries. For
example, the area of marine science that studies plankton communities has to
promote a fertile confrontation with EvoDevo, the discipline that focuses on how
development is regulated and modified to create macroevolutionary transitions.
EvoDevo experience with -omics, combined with the ecological notions of
meroplanktonic developmental stages, are crucial points of contact to elaborate
upon. In 1973, Leigh Van Valen published his famous aphorism “Evolution is the
control of development by ecology”, an excellent example of how different
disciplines can be connected. Although such an emphatic view of the relationships
between environmental components and developmental programming was ahead of
its time, at least in the precise way that Van Valen thought it did, the general
importance of his argument has now become clear, leading to a redefinition of the
theory of evolution (e.g. EcoEvoDevo or Extended Synthesis). Therefore, times are
now ripe for bringing developmental biologists and marine biologists around the
same table, especially if the location is the 19th century Fresco Room of the
Stazione Zoologica Anton Dohrn in Napoli, under the intrigued eyes of Darwin,
Dohrn, Haeckel and Von Baer.
Finally, the initiative responds to one of the key challenges of the EurOceans
Consortium (EOC): fostering an integrative approach, to better understand the
mechanisms at the organism, population and community level and in response to
climatic and environmental changes. In fact, interweaving those different levels of
organization was considered a crucial step to move forward in developing scenarios
for marine ecosystems under anthropogenic and natural forcing in the XXI Century.
Among the key issues of Marine Ecology to develop on during the workshop we
selected:
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The role of biodiversity in shaping plankton communities:
a. Relationship between genetic (cryptic) and functional diversity in viruses,
prokaryotes, protists and metazoans
b. Marine biodiversity and mechanisms of speciation in the marine environment
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Importance and mechanisms of information flow in marine communities:
signalling, perception, behaviour.
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Life histories in marine protists and metazoans: internal and external
regulation, life strategies and developmental stages of marine organisms.
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How Evo-Devo may contribute to Marine Ecology
with the following people contributing to the discussion:
Thomas D. Als (Aqua – Kopenhagen)
Maria Ina Arnone (SZN - Naples)
Philipp Assmy (AWI - Bremenhaven)
Chris Bowler (ENS - Paris)
Ylenia Carotenuto (SZN - Naples)
Angela Falciatore (UPMC - Paris)
Mariella Ferrante (SZN - Naples)
Daniele Iudicone (SZN - Naples)
Amy Kirkham (UEA - Norwich)
Carol E. Lee (UW - Madison)
Patrizio Mariani (Aqua - Kopenhagen)
Thomas Mock (UEA - Norwich)
Maria Grazia Mazzocchi (SZN - Naples)
Marina Montresor (SZN - Naples)
Paola Olivieri (UCL - London)
Gabriele Procaccini (SZN - Naples)
Maurizio Ribera d'Alcala' (SZN - Naples)
Francisco Rodriguez-Valera (UMH - Alicante)
Monia Russo (SZN - Naples)
Remo Sanges (SZN - Naples)
Victor Smetacek (AWI – Bremenhaven)
Mitchell Sogin (MBL - Woods Hole)
Paolo Sordino (SZN - Naples)
Wim Vyverman (Ghent University)
Markus Weinbauer (OOV – Villefranche)
Adriana Zingone (SZN – Naples)
The discussion went on having, as a template, the schedule below:
Sunday November 7
Welcome, Introduction on the scope of the workshop and its structure,
presentation of participants (Maurizio Ribera d'Alcala')
Overview on key questions in Marine Science: the biotic component (Victor
Smetacek)
Overview on key questions in Marine Science. The abiotic forcing and its potential
impact on biota (Daniele Iudicone)
Monday November 8
Morning session: 'Life histories in marine protists and metazoans: internal and
external regulation, life strategies and developmental stages of marine organisms'
Chairs: Victor Smetacek - Wim Vyverman
Thomas Mock – Disclosing regulative mechanisms in diatoms
Wim Vyverman – Molecular control of diatom life cycles
Adriana Zingone - Seasonal rhythms in marine phytoplankton species
Ylenia Carotenuto – Regulation of copepod life cycles by marine diatoms
Discussion on the talks and spot contributions
Afternoon session: 'The role of biodiversity in shaping plankton communities'
Chairs: Mitch Sogin – Carol E. Lee
Markus Weinbauer – Virus and bacteria interactions in the ocean
Mitch Sogin - Are there limits to marine microbial diversity?
Francisco Rodriguez-Valera – The shape of prokaryotic biodiversity
Gabriele Procaccini - Genetic structure of phytoplankton populations
Carol E. Lee – Rapid evolution in copepod populations and shifts in the copepod
microbiome in the face of habitat change
Discussion on the talks and spot contributions
Tuesday November 9
Morning session: 'Importance and mechanisms of information flow in marine
communities. Signalling, perception, behaviour'
Chairs: Chris Bowler – Angela Falciatore
Chris Bowler - What can -omics do for revealing diatom biological traits
Angela Falciatore - Photoreceptors to see the marine environment predict/respond
to environmental changes
Patrizio Mariani - Behavioural mediated interactions in plankton communities
Discussion on the talks and spot contributions
Afternoon session on theme 4 'How Evo-Devo may contribute to Marine Ecology'
Chairs: Paola Oliveri – Paolo Sordino
Solicited talks
Paolo Sordino - Do evodevo models dream of sea?
Paola Oliveri – The evolution of Gene Regulatory Networks in planktonic larvae
Ina Arnone – Vision in the sea: insight from sea urchin photoreception
Maria Grazia Mazzocchi - Copepods as model organisms for fundamental biological
understanding
Discussion on the talks and spot contributions
Wednesday November 10
Synthesis session Chairs: Marina Montresor, Maurizio Ribera d'Alcalà
For each session there was an ample discussion.
Below we report a brief abstract of the talks (whose slides can be downloaded
form this site) and summarize some of the key issues raised by the talks and during
the discussion.
The introductory talk by Victor Smetacek was structured along the famous
statement by Dobzansky: “Nothing makes sense in biology except in the light of
evolution”. In other words, understanding the evolutionary trends driving structure
and functioning from organism to ecosystem levels is the key question in biology.
The first example was the evolution of Eukaryotes by endosymbiosis: the
incorporation of prokaryote cells inside other ones. Whereas the former are termed
“endosymbionts” the external cells are called “host cells” but should logically be
termed “exosymbionts”. The shapes of protists are determined by the properties of
the exosymbionts, but because attention has focussed largely on the
endosymbionts, the relationship between form and function in protistan plankton
does not make sense. However, shape is conserved, so it must have a function in
natural selection.
Selection is either by bottom-up or top-down factors. The former imply
competition for resources which result in optimal solutions illustrated in terrestrial
vegetation e,g, by trees which have evolved independently in many plant lineages.
The latter drive defence systems which co-evolve with attack systems known as the
arms race. Unfortunately our understanding of the relationship between bottom-up
and top-down factors in terrestrial ecosystems is seriously flawed by decimation of
megafauna by human hunters that started during the last ice age. It has been
established from regions with intact megafauna in Africa that they determine the
vegetation type, e.g. savannah or acacia forests. Since megafauna decimation is
now continuing in the oceans the structure and productivity of marine ecosystems
is likely to change significantly. The reported decline in ocean productivity over
the past century could be due to this factor. Similarly the ongoing decline in krill
stocks could be due to decimation of their major predators: the baleen whales.
Protistan taxonomy is traditionally based on morphology. Haeckel could not
imagine functions for the prolific shapes of protists hence assumed they were a
product of “organic crystallography” hence “art forms” and otherwise meaningless.
Hensen coined the term plankton in 1887 and proposed that phytoplankton
provided food for the marine organisms thereby launching the “agricultural
paradigm” which became the justification for the study of plankton, previously
alluded to as “philosophical dirt”. This paradigm was extended in recent decades
to the study of elemental cycles in the ocean (biogeochemistry) which has gained
particular relevance in light of climate regulation by the carbon cycle. Since
diatoms play a key role in the carbon cycle, understanding the factors that result in
carbon sequestration by the biological pump is now an important question that can
and is being addressed by molecular biological techniques. It was argued that
plankton evolution is ruled by protection and not competition. The many shapes of
plankton reflect defence responses to specific attack systems ranging from
pathogens, parasitoids to predators. Proof has come from measuring the strength
of diatom frustules which have been shown to be surprisingly resistant to external
pressure and probably selected by the crushing abilities of the mandibles of major
herbivores in the ocean: copepods and euphausiids.
Feeding on protistan cells is now known to be highly selective: from parasitoids,
protozoa to copepods. Prey recognition is by chemical cues but also by
proprioception enabled by cilia and sensory hairs (mechanoreceptors) of the
protozoa and metazoa respectively. Since in vegetatively multiplying unicellular
organisms the individual is a cloud of cells emanating from the zygote, would-be
herbivores have ample opportunity to sample single cells from the clone, like
leaves from a tree, and shape the course of evolution. The consequences of natural
selection of defences (arms race) for elemental cycles are far-reaching because
cycles of biogenic elements depends on their ratios (C:N:P:SI:Fe, etc) in the bodies
(cells), armour (exoskeletons) and waste products of the dominant organisms. This
will influence air/sea exchange of gases: CO2, DMS, but also N2O, CH4 depending
on the depth of remineralisation (ballast) which determines the redox state in the
water column. Further, the arms race will slow growth rates because energy and
materials are diverted away from reproduction to defence, as in the economies of
human societies. As a result, the sediment surface of the oceans is determined by
the nature of the war fought in the overlying water.
A corollary of the current paradigm that marine ecosystems are driven by bottomup factors is that phytoplankton species are geared to proximate conditions
(resource availability: light and nutrient supply) because phytoplankton are
assumed to be selected by maximising growth rates. Ultimate factors such as
complex behaviour of single cells and evolution of life cycles are overlooked. These
aspects are governed by regulatory mechanisms that turn cycles of growth and
death on and off. Cell death in protists is only now beginning to receive the
attention it deserves following the discovery of apoptotic mechanisms in various
groups of phytoplankton. Indeed, it is this field which can profit significantly from
the application of the various branches of molecular biology (omics). As an
example, it is well-known that only a few cells of the many isolates selected for
culture from the wild survive. It is possible that the cells successfully cultured have
different regulatory mechanisms or even lack them (i.e. they are the equivalent of
cancer cells in metaphytes and metazoa) compared to those that cannot be
cultured. Possibly they belong to different individuals of the same species. Further,
it is also well-known that cultured cells of many species tend to lose their original
shape suggesting that shape is indeed influenced by proximate conditions in the
wild environment that might be related to cues emanating from other species, in
particular pathogens, parasitoids and predators. It is hoped that the application of
omics will provide ecologists with insights on the repertoire of potential responses
in planktonic organisms.
Terrestrial ecology has got it wrong: insects are not the main herbivores as widely
believed, because a crucial role was played by megafauna.
We have reduced the ocean megafauna in the terrestrial environment and also in
marine environment, where copepods may be considered the key structuring agent
even more than insects on land.
Natural selection works by death and not by encouragement. The ones that make it
are the ones that successfully avoided being killed. Traits are based on this.
Daniele Iudicone addressed the issue of plankton diversity and speciation in
relation with physical forcing. He noted that variability in forcing in marine
environment is peculiar and, quite different from forcing in terrestrial
environment. In addition, Marine Ecology has a much less robust theoretical
framework than terrestrial ecology. Both aspects determine a gap in our
understanding of causal links between physical forcing and plankton dynamics.
Present analyses show that both selectionist and neutral theories seem supported
by plankton ecology and natural history, with the latter view being more popular
among physicists.
The analysis of physical processes which affect species distribution and richness
may be conducted at different scales. At large scale, dispersal and immigration are
crucial processes for determining community structure and diversity. But physical
dispersal can be counteracted by reduced temperature tolerance. For example
tropical species in the terrestrial environment cannot survive the high latitudes,
thus there is a limit on how they can compensate by dislocation changes in
temperature.
Temperature influences metabolic rates, then tropical–temperate systems pose
different constraints than polar systems, which may also affect size, to which
metabolic rates are also linked. While temperature stays as a robust descriptor of
a geographical region, other characteristics conventionally taken as typical, should
be analyzed more in depth. For example, tropics are not so stable as they were
usually thought to be. The structure of the mixed layer shows high variability,
which affects niche partitioning and species distribution.
Physical processes are also crucial in speciation if they create physical barriers. Are
there barriers created by physical processes in the present ocean? Patterns in
plankton distributions at the global scale would suggest the presence of very few
barriers, one being the Antarctic Circumpolar Current, but several passages exist
that allow for colonization and dispersal.
Focusing on the vertical dimension the most characteristic feature in the global
ocean is the Deep Chlorophyll Maximum. This cannot be explained only by the
physical forcing and variability as shown by models on BATS or HOT time series.
There has been a suggestion, with some support by modeling, that high diversity
may be maintained by environmental variability, leading to a chaotic unpredictable
pattern. The DCM has been use as a test case for analyzing those patterns, but
results may depend on the numerical approach used.
Climatic perturbations (NAO etc) at large scale, which are not periodic and display
chaotic patterns, apparently affect fish abundance patterns. Though, the evidence
is statistical, and so far non mechanistic reconstruction has been produced.
Also at microscale physics may have a different, and less relevant impact, that
thought before. For example, turbulence has no net effect on the sinking of single
cells. It may have influence on the the dispersion patterns of tracers at microscale
(chemical signals – nutrients, pheromones) which overlap to the size spectra of
phytoplankton, under turbulent regime.
The picture emerging from the overview is that a more in depth analysis is needed,
first to better characterize the physical variability over all the scales, second to
better characterize the plankton response to that variability. The former may
profit of the significant improvement in the oceanographic observational capacities
and technologies, while the latter is having a dramatic impulse by omics.
Selected issues raised and/or stimulated by the introductory talks:
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What are the selective forces shaping the evolution of planktonic processes?
What is the shape for? The shape is there to be perceived. How do the
planktonic organisms perceive shapes? Mechanical perception in copepods,
but also in unicellulars (Protoperidinium explores the prey before feeding,
which suggests a sort of memory). Shape of unicellular organisms is also
taken as indicator of diversity: the forcing factor might be defence from
predation. The same shape is shared by autotrophic and heterotrophic
species.
We have been always constrained by what our organs, even potentaited by
instruments, could detect. Also the shape of very small organisms can be
more complex that we can perceive, e.g., bacteria and viruses (deep water
bacteria and giant viruses). Novel views can derive from the improvement of
observational tools: we expect new information on the functioning of the
organisms and, in this respect -omics is a new observation tool as long as
opens the view to molecular processes.
There has been an historical bias on photosynthesis (endosymbiont) and not
on the hosting organism (exosymbiont)
The time of evolution of this complexity (the boring proterozoic) it might be
related to the long time required to the development of the complex
metabolism of bacteria. They were subsequently used when endosymbiosis
started.
What is the target of selection? Not the individual cell, but the clone of cells
that share the same genetic fingerprint.
‘Optimal solutions’ in the plants (e.g. trees, etc): how can we define similar
‘optimal solutions’. Functional groups in the plankton? Examples from
zooplankton: copepods adapted to escape; cladocerans (Daphnids) adapted
to reproduce, i.e., spreading progeny in the lakes, the investment is in the
number. They can hide in turbid waters and do not have to invest so much in
escape.
The role of megafauna in conditioning the environment: example from
terrestrial systems and the oceans, with the extermination of whales and
overfishing (feedback on the quantity and quality of plankton)
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Are there some constrains in the cellular organization of unicellulars?
Perception and propioception (perceiving the others and themselves – is
there memory in unicellulars? Different responses when in preconditioned
environments)
Which role has been played by the energetic constraints: in fact an
important point in the evolution of unicellulars is represented by the
evolution of mitochondria in terms of the increase of utilization of energy
(focus on chloroplast)
Is genome size related to the complexity of the organisms (yes for bacteria –
we ignore what happens for unicellular eukaryotes – NO for multicellulars)
Monday morning session: 'Life histories in marine protists and metazoans: internal
and external regulation, life strategies and developmental stages of marine
organisms'
Thomas Mock – Disclosing regulative mechanisms in diatoms
A conserved nuclear protein regulates cell division in marine centric diatoms.
Marine diatoms exhibit a ‘bloom and bust’ life cycle, which means they quickly
dominate phytoplankton communities when conditions become favorable. This
opportunistic growth is the reason why they contribute to about 25% of global
carbon fixation. A fast changing environment has been regarded as the most
important driver for diatoms’ lifestyle and there are decades of research that
confirm the importance of light, dissolved inorganic carbon, nutrients and
temperature for their growth. However, the mechanism that enables translation of
favorable environmental conditions into a bloom is unknown. Here we show that
the conserved DNA associated protein is a major regulator responsible for cell
division and thus bloom formation in marine centric diatoms. Over-expression of
this novel gene in Thalassiosira pseudonana caused a distinct phenotype,
characterized by fast recovery and growth after a period of nitrogen starvation,
which led to out competition of a wild-type culture. Comparative whole-genome
expression profiling of the transgenic strain and wild type under simulated bloom
conditions revealed that the novel protein regulates various transcription factors
and methyltransferases among many unknown diatom specific genes. Many of these
proteins regulated by this novel DNA associated protein could be identified in
natural diatom blooms confirming their significance for bloom formation. Our
results demonstrate how the formation of a diatom bloom is enabled by a master
regulator of transcription to translate favorable environmental conditions into fast
growth. These data are not only fundamental for our understanding on how these
organisms fix 10 billion tons of CO2 per year but they might also have implications
on how we can grow microalgae more efficiently to decrease our CO2 footprint.
Wim Vyverman – Molecular control of diatom life cycles
Phytoplankton life cycles can be very complex. Different groups vary in the
duration and growth potential of haploid and diploid phases. Theoretical modeling
suggests that haplo-diplonty may be selected in low fertilization environments
while diplonty may be favoured in more variable environments. Overall, diploid
organisms should be more fit when evolutionary change is limited by mutation,
whereas haploid organisms should be more fit when evolutionary change is limited
by selection. However, empirical studies testing these hypotheses in phytoplankton
are still largely lacking. In addition, several groups of protists show large variation
in mating system, affecting the genomic composition of the offspring and in some
cases contributing to the rapid evolution of reproductive isolation. While there is
increasing direct and indirect new evidence for the prevailance of sexual
reproduction in phytoplankton, genomic and transcriptomic studies are starting to
provide the first insights into the molecular controls of phytoplankton life cycle
transitions. At each point in time, a phytoplankton cell has the possibility of
commitment to cell division, formation of resting stages, sexual reproduction or
programmed cell death. Although clonal phytoplankton populations can be seen as
an individual entity, diatoms and other phytoplankton groups demonstrate that
size-controlled differentiation into sub-populations with very different physiologies
and fates occur. To what extent external or internal regulatory controls are
responsible for this differentiation largely remains an unanswered question. New
model species have been developed to address these questions and complement
existing models for which genome information is available. Recent studies on the
heterothallic pennate diatom Seminavis robusta are starting to elucidate the
nature of cell-size controlled differentiation of vegetative cells into sexually
capable cells. Both mating-types produce a diffusible cytostatic pheromone that
globally arrests complementary mating type cells in the G1-phase. This has the
potential of increasing mating success of a population as it extends the time
available for encounters between compatible mating types. Bio-assay experiments
using pheromone-coated beads demonstrate increased motility and chemotaxis of
pre-conditioned cells to the beads. Gene expression analysis showed significant
changes in gene expression patterns associated with the transition of the sexual
size threshold as well as during mating. While ongoing transcriptome sequencing
will provide a more extensive view of these changes, evidence the involvement of
hedgehog signaling support the idea of cellular differentiation which is governed by
cell size reduction.
Adriana Zingone - Seasonal rhythms in marine phytoplankton species
The most conspicuous event in phytoplankton seasonal cycle is the spring bloom,
which is tightly coupled with nutrient and light availability and is hence rather
predictable
. Expanding the same argument one would think that also temporal patterns of
species occurrence (Species
phenologies) should be driven by environmental conditions (light, temperature,
nutrients, turbulence, etc.)
. By contrast data show that there is a mismatch by the high interannual variability
in environmental parameters and the rather regular occurrence of several species.
Many of them display a wide tolerance to temperature variations and, more
important, display a significant mismatch between the theoretical (as derived from
lab experiments) and the realized growth niche
. For several diatoms, which show a striking synchrony and regularity in the
occurrence over many sites, neither recurrent abiotic forcing nor timed spore
germination may explain the timing of the individual blooms. Likewise for the end
of the bloom which is seldom coupled with nutrient depletion
, selective grazing or viral attack.
A close analysis of population structure of species which 'bloom' more than once
per year suggests that each episode might be due to a different (cryptic) species.
This in turn hints at the possibility of frequent events of sympatric speciation in
phytoplankton. Internal circumannual clocks have been invoked to explain the cyst
germination in Dinoflagellates or spore germination in diatoms, but the entrainers
are still elusive. Even species which do not seem to form spores, follow an annual
or pluriannual cycle for sexual reproduction, despite an annual bloom.
Sharp increase in the abundance of single species, i.e., individual blooms, are key
events in the natural history of the species because they favor sexual reproduction,
allow to make evolutionary experiments and acts as an interface between the
species and the natural selection.
Ylenia Carotenuto – Regulation of copepod life cycles by marine diatoms.
Seasonal cycles of copepod population in temperate regions are usually uncoupled
to seasonal cycles of phytoplankton bloom, mainly formed by diatoms. The reason
for such a mismatch has been traditionally related to the very complex life cycles
of copepods, which are characterized by several naupliar and copepodite larval
stages. However, the last 15 years of studies has shown that diatoms produce a
plethora of fatty acids-derived molecules, named oxylipins, which impaired several
reproductive traits of copepods (hatching success, larval survival and sex ratio).
Our hypothesis is that oxylipins reduce recruitment of copepod population during
diatom bloom, thus explaining the observed ecological mismatch between diatom
bloom and maximum copepod abundances in situ. The mechanism of actions of
these oxylipins on copepods is still unclear, although a common observed effect is
the induction of apoptosis in several copepod stages and tissues (deformed naupliar
appendages, cleaving embryos, female gonads, etc). We are, therefore,
approaching the problem by using an –omic approach. In particular, we would like
to perform a Suppressive Subtractive Hybridization on copepods feeding on a
diatom-producing oxylipins, in order to investigate with genes are differentially
expressed in copepods after diatom feeding. We hope this approach will help
clarify the mechanism of action on diatom oxylipins on copepod reproduction.
Selected issues raised and/or stimulated by the talks:
How the problem ov mates encounter is solevd for species which do not have
motile gamets?
- How general is the regularity in time patterns of occurrence, and to what
extent the concept of 'opportunistic' species has to be abandoned?
- Are different size classes of apparently the same species different
genotypes?
- Is size reduction in diatoms the dominant trigger for starting the sexual
phase, or may be directly or indirectly triggered by grazing pressure?
- What is the role of internal and external triggers in species
seasonality and what are the external cues that may act as synchronizers for the
different phases of the bloom?
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Do unicellular algae measure the annual time in a similar way than higher
plants?
What kind of relationship/communication exist among phytoplankton species
and between them and their
potential/effective predators?
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How can we cope the mechanisms described by Thomas Mock with the waek
coupling with environmental factors showed by Adriana Zingone?
Monday afternoon session: The Role of biodiversity in shaping plankton
communities
Markus Weinbauer discussed viral lifestyles, the role of viruses in the microbial
food webs, viral diversity, the control of host through viral infection and the
impact of viruses on biogeochemical cycling. Viruses are the most abundant
biological forms in the oceans. They outnumber microbial populations by at least
an order of magnitude and exhibit enormous genetic complexity; the majority of
viral genes show no close matches to sequences in molecular databases. There is a
correlation between depth and lifestyle. For example, in the meso- and
bathypelagic (<200M) lysogenic lifestyles for viruses dominate where they are more
likely to serve as agents for horizontal gene transfer between microbial genomes
than cause death through lysis. With increasing depth, e.g. in the Mediterranean
sea, lytic lifestyle also decreases in frequency. Viral induced mortality is only 16%
in coastal and 64% in mesopelagic but increases to 89% in bathypelagic sediments.
Lytic life cycles play a major role in controlling bacterial populations but the viral
induced lysis of cells release of constituents plays a major role in carbon and
nutrient cycling.
Mitchell Sogin discussed the impact of next generation sequencing on studies of
microbial diversity. Instead of simply retrieving rRNA amplicons from the most
abundant microbial taxa, the deeper sequencing effort afforded by next generation
sequencing detects low-abundance taxa and reveals that microbial diversity in the
oceans is orders of magnitude greater than previously appreciated. This increased
level of diversity is not an artifact of sequencing error and when analyzed using a
novel preclusting technology, the number of OTUs provides a conservative estimate
of microbial diversity. These low abundance taxa often represent organisms not
represented in molecular databases and collectively are referred to the rare
biosphere. The estimated number of different bacteria in the oceans is greater
than 500,000 with most being members of the proteobacteria. However this is a
conservative estimate and does not take into account that many microbes with
distinctly different genomes sometimes have very similar or identical ribosomal
RNAs. Nor does it account for the fact that the sampling of 1200 different sites
represents less than one part in 1018 parts of the oceans. Sogin described several
explanations for the rare biosphere including their being representative of dispersal
from sites where they are endemic. He also described examples where rare
biosphere members became abundant in response to environmental shifts.
Francisco Rodriguez-Valera presented a description of the microbial pan genome
which posits that for recognized microbial species, different strains have different
collection of genes superimposed upon a core genome. The accessory genes might
exchange between the strains through horizontal gene transfer principally
mediated through bacterial phages. The common view of microbial evolution is
that periodic selection results in clonal replacement. But if this is true, it becomes
necessary to explain how diversity is maintained where a large number of genes are
not shared by different strains. To resolve this question, Francisco Rodriquez
Valera describes a model that maintains constant-diversity through phage
predation. He showed that periodic selection and phage predation can work
together to allow for section of favored strains yet permit the overall maintenance
of genetic diversity in a given pan-genome. The boundaries of an individual pan-
genome are difficult to define with currently available data but as more genomes
and metagenomes are studied, a clearly delineation of the pan genome will
emerge.
Gabriele Procaccini discussed population genetic structure in phytoplankton
populations, focusing on several species of diatoms. Overall, the talk emphasized
the high degree to which phytoplankton populations could display high levels of
genetic diversity over space and time. Previous studies had found population
genetic structure on large geographic scales (e.g. between continents), despite
high dispersal potential and perceived lack of geographical barriers in the sea. In
this study, population genetic analyses, using ITS and microsatellite sequences,
revealed that distinct populations of Pseudo-nitzschia multistriata lived in
sympatry in the Gulf of Naples and that distinct genotypes predominated in
different years. Results revealed the co-occurrence of two genetically-distinct but
closely related populations (FST = 0,091) in the Gulf of Naples, but only in one year
and not the next. Laboratory experiments indicated that crosses between
genetically divergent strains were interfertile. Such crosses enhanced genotypic
diversity of hybrid populations relative to the parental populations. Genetic
structure varies in diatom populations over time, possibly due to admixture,
migration, sexual reproduction, and selection on existing mutations.
Carol Lee discussed approaches for studying adaptation in response to
environmental change, using invasive populations as model systems.
Recent observations are showing that many invaders are crossing boundaries
between distinct habitat types, such as the numerous brackishwater invaders into
the North American Great Lakes. Within the past century, the copepod Eurytemora
affinis has invaded freshwater habitats multiple times independently from saline
sources. Common garden experiments and experimental evolution approaches
revealed evolutionary shifts in physiological tolerance, ionic regulation, and gene
expression associated with freshwater invasions. Results showed striking parallel
evolutionary shifts in ion regulatory functions across independent invasions and in
laboratory selection experiments, indicating the evolutionary lability in these
traits. In addition, there were parallel shifts in copepod microbial community
composition during independent invasions from salt to freshwater habitats.
However, a core microbiome remained constant across all populations in all
locations, and is likely to be moving with the copepod during habitat shifts. The
observations in this study provide a case study of how physiological diversity might
arise in nature. In addition, it reveals the first glimpse into the immense diversity
within the copepod microbiome, an uncharacterized component of the ecosystem.
The copepod microbiome might have critically important functional consequences
for the invading host as well as on ecosystem processes.
Selected issues raised and/or stimulated by the talks:
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Importance and frequency of lateral gene transfer in prokaryotes and
unicellular eukaryotes and different mechanisms for it
Relevance of mutations vs. endosymbiosis in the eukaryotes evolutionary
Link between genetic and functional diversity in the rare flora
Population dynamics in unicellular eukaryotes: evidence for different
patterns in different genotypes of the same species
Mechanisms regulating the pangenome
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The contribution of rare biosphere to the genetic poll and to the functionin
of tmarine ecosystem
Tuesday morning session: Signaling, perception and behavioral responses
Chris Bowler introduced the session mentioning that a rather well known example
of signaling within plankton was first described almost 20 years ago, and concerns
the production by diatoms of toxic aldehydes that can reduce hatching success in
copepods feeding on diatom-rich diets (Ianora et al., 2004). Although the topic
remains controversial, there is little doubt that signaling is an important
phenomenon regulating life histories in the plankton, and perhaps also influences
trophic food webs and the biogeochemical cycling of nutrients.
Unlike for the copepods, molecular and genomic resources for diatoms are
reasonably well advanced (Bowler et al., 2009). Their responses to external signals
such as nutrients and light can therefore be addressed with some precision and in
the context of fully sequenced genome sequences. In one set of experiments it has
been shown how the evolutionary history of diatoms, being derived from a
combination of at least three distinct ancestral organisms and having acquired a
wide range of genes from bacteria, has been used to advantage to allow novel
metabolic conversions that can potentially allow diatoms to respond more
efficiently to episodic incoming of nutrients such as iron and nitrate (Allen et al.,
2008).
While the chimeric origins of diatoms may have provided an unusual assortment of
genes for macroevolutionary processes to generate a highly successful biological
machine following tens of millions of years of selection, the means by which
diversity is actually generated in diatoms is an important topic to address. It has
been shown that diatoms possess an unusual complement of transposable elements
and that the activities of at least some of them are responsive to stress (Maumus et
al., 2009), so it is possible that they enhance genome diversification in diatoms. An
additional aspect that should be addressed is the contribution of epigenetic
phenomena to organismal adaptation to the environment over microevolutionary
time scales. Such an option could provide a reversible means for an organism to try
new combinations which could eventually be fixed genetically by point mutations in
the DNA sequence. It would be of interest to explore the existence of such
environmentally-driven adaptability in the plankton.
Angela Falciatore focused her talk on photoreception in diatoms. A blue light
cryptochrome photoreceptor has been described in those organisms that has roles
both in photoperception and in coping with the mutagenic effects of ultraviolet
light (Coesel et al., 2009). Finally, diatoms have been found to possess an unusual
member of the stress-related light harvesting chlorophyll protein family (denoted
LHCX1) that appears to play a key role in managing diatom photosynthetic activity
in a highly variable light environment (Bailleul et al., 2010). These latter examples
highlight the need for a photosynthetic organism to be able to interpret different
kinds of information coming from a common stimulus, in this case light, because
light can either be a signal, a source of energy, or a stress. From recent studies it
has therefore emerged that the diatoms appear to have mastered the art, and can
even anticipate how to respond appropriately! Thus, although physiology has
largely been a failure in planktonic organisms over the last decades, the availability
of complete genome sequences and a set of experimental model organisms that
can be used as hypothesis generators has achieved some success.
Patrizio Mariani argued that their large diversity in todays oceans is the
evolutionary outcome of three of life’s common tasks: to feed, to survive and to
reproduce. While in autotrophic species these tasks are mainly governed by
morphological adaptations and less so by behaviour, behaviour plays a prominent
role for zooplankton in their pursuit of these three main missions (Kiørboe, 2008).
In a dilute environment, feeding, survival and reproductive strategies are strongly
regulated by the probability of encountering food items, predators and mates.
Zooplankton have therefore developed a series of hydrodynamical, chemical and
behavioural responses to optimize their reproductive outcome (fitness), which
might be measured as the net energy income over their life time. Some of these
behaviours (e.g., swimming patterns and activity, prey switching, diel vertical
migration) can be reproduced using simple models that optimize the individuals’
fitness. Changes in zooplankton behaviour have large consequences at population
and community levels in the plankton (Mariani et al., submitted); in simple models
population and community properties emerge as a result of individual interactions.
Similar to life history traits, genes provide mechanistic as well as evolutionary
insights about the ecology. One way forward may therefore be to explore the
genetic basis of key traits in planktonic organisms.
Selected issues raised and/or stimulated by the talks:
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It is important to define functions of unknown genes and there is a need for
high throughput technologies.
Trait-based rather than organism based approach is better suited for
ecosystem models. An example is phytoplankron having light harvesting
investment, or nutrient harvesting investment. It is a process oriented
approach. Different behaviors are the traits which has to be balanced in
copepods. Diel vertical migration as best example to show behavioral
plasticity.
Behavioral capacity of copepod is extraordinary. Similar roles in ecosystem
but different behaviors for feeding, reproducing, escaping. Adaptive
behaviour of individuals has a profound effect on the dynamics of the
population and the organisms they feed on and on the succession. This is
bottom-up rather than top-down.
How much signaling is controlled from bottom up and how much is top down?
Tuesday afternoon session: How Evo-Devo may contribute to Marine Ecology
Paolo Sordino provided an introduction to the main historical and conceptual steps
that have lead to the recognized marriage between developmental genetics,
evolution and ecology at the theoretical and experimental levels. The argument
was supported by case studies in which developmental innovations are clearly
selected at the population level (in a neo-darwinian framework) by ecological
niches. The idea of addressing evolution, development and ecology all at once in
the ascidian Ciona intestinalis, a marine invertebrate with a prominent status as
laboratory pal in bioscience, and a widespread census of coastal populations, offers
a unique opportunity for the analysis of micro- and macroevolutionary variation in
a basal chordate.
Paola Oliveri introduced her studies of Gene Regulatory Networks in the
development and evolution of planktonic larvae of echinoderm. She showed that
the same developmental process, the formation of the larval endoskeleton, acts
through the employment of different transcription factors among echinoderm
classes, suggesting a large plasticity of the molecular identities, but not necessarily
of the underlying network logic or subcircuits.
Ina Arnone “Vision in the sea” was a broad integration of developmental genetics,
ecology and behaviour, where she discussed the evolution of photoreception in
metazoans, then focusing on the pivotal role of opsins in studying how sea urchins
perceive light through an unpredictably diverged organization of the visual system.
Maria Grazia Mazzocchi presented copepods as one of the most important group of
animals in marine environments, especially in terms of their abundance, diversity,
and fundamental roles in the functioning of planktonic systems. Copepods have an
unusually diverse range of body forms and life styles and represent a unique system
for the analysis of developmental and ecological constraints and adaptations.
Selected issues raised and/or stimulated by the talks:
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How the cell specification mechanisms veolved in metazoans are linked to
cell types in unicellular eukaryotes
The importance of spatial organization during the development, which il
likely absent in unicellular organisms
The difference in gene concept in the Ecological and Evodevo communities,
being a well-defined function and regulation that changes at the
macroevolutionary level for Evodevo, and a matrix of varying allelic
frequencies at the microevolutionary level for molecular marine ecologists
Link between the tight developmental program and the phenotypic plasticity