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Emerging
Issues in Fish
Larvae Research
Emerging Issues in Fish Larvae Research
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Gilthead seabream larva (42 days after hatching). Photo: Bernd Ueberschär
Manuel Yúfera
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Editor
123
Editor
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Manuel Yúfera
Instituto de Ciencias Marinas de Andalucía,
(ICMAN-CSIC), Campus Universitario
Río San Pedro s/n
Puerto Real, Cádiz
Spain
Fish larvae are amazing organisms. They are among the smallest free-living forms
of vertebrates and exhibit fascinating growth potential. In fish aquaculture, all of the
phases of the life cycle from the fertilized egg to the adults are essential, and if one
of them fails, the whole production cycle fails. The larval phase, however, has
traditionally been considered the most sensitive period both in the wild and for
cultured fish. The vulnerability at this stage has been a powerful driving force for
fundamental and applied research. In this research line, the horizon is to know what
is necessary to allow the fish larvae to grow and develop properly and to become
healthy. The development of basic larviculture procedures based on feeding with
rotifers and Artemia in the 1970s and 1980s allowed a constant supply of fry to
support the increasing fish farming production during the last decades. Research on
fish larvae biology has continued since then and has been aimed at increasing our
basic knowledge and improving rearing methodologies. However, there are still
large knowledge gaps and the rearing process is far from optimal. For years, sci-
entific research has focused on relevant limiting factors seriously affecting survival
and growth, in a sequential manner. New species have been introduced by applying
similar protocols, and only some aspects related to feeding and nutrition have
received scientific attention. This simplistic empirical approach is insufficient for
understanding mechanisms for development and interrelations with the surrounding
rearing water. During the last decade, new analytical tools have opened up new
avenues for research in both physiology and the influence of environmental con-
ditions. In the past few years, books and specialized journals have published
reviews on the different disciplines related to fish larvae biology and aquaculture,
providing wide descriptions of main topics like development, pathologies, nutrition,
feeding, and physiology. These publications have increased our knowledge from a
textbook perspective. It may thus be considered that there is overall, good
knowledge on larval fish biology and on the current reality of larval rearing. Most
of this information, however, is based on a small number of species, and knowledge
in larval biology is advancing fast. Nowadays, there are new research ideas that
have implications not only for fish larvae but also for other vertebrates, and there
are new approaches to old problems, using omics methodologies, for example.
v
vi Preface
The research effort on larvae is now moving beyond the strict interest for growing
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fish; it is also focusing on using them as model organisms for fundamental research.
Moreover, the numerous species being studied within the context of aquaculture
will help to uncover both the variability and the similarities within this diverse
group of vertebrates.
Instead of providing broad overviews covering general topics in larval fish
biology, this book presents examples of novel research in fish larvae with very
specific objectives. It refers to current advances derived from recent projects and a
doctoral thesis targeted at filling specific gaps in our knowledge. By representing
alternative points of view, the different chapters show how rearing and environ-
mental conditions affect physiology and developmental processes from a molecular
basis, and how these factors influence the final characteristics of late larvae and
juveniles. Overall, this book will point to recent findings on the importance of
environmental cycles, some specific nutrients, and the microbial environment on
developmental processes. There are more emerging topics of interest, but with these
few examples we hope to illustrate the dynamism of current research within
this field. These are exciting times for biologists and the discipline of biology—
especially when the target of the research is fish larvae.
vii
viii Contents
Abstract All animals need a mutualistic interaction with their microbiota for
proper development and functioning. Also for the fish-microbiota interaction con-
siderable research has been done, and especially for reared fish larvae this inter-
action is crucial for their viability. However, during the 1980s and 1990s a number
of findings revealed at that time current methods were not suitable for studying the
total microbial community and that data on composition of microbiota was biased.
Several recent methodological revolutions have boosted the possibilities for
addressing questions related to fish larvae-microbiota interactions that previously
lacked suitable tools for proper evaluation. These methodological achievements
include the development of experimental rearing systems including gnotobiotic
systems for fish, new visualization tools, and molecular “omics” tools for charac-
terizing the response of the host on a variety of levels and for characterizing both
composition and activity of fish microbiota. We present and review these tools and
give examples on how they have been used to improve our understanding of fish
larvae-microbiota interactions. With respect to understanding, this includes in
particular how the microbiota is established and maintained, what the functionality
of the microbiota is and how it affects fish health, and finally how we can apply this
knowledge for management of a healthy and beneficial microbiota in aquaculture
settings.
Keywords Microbiome Germ-free model systems Imaging
Molecular methods Omics
1.1 Introduction
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Traditionally, experiments with fish are run in cultivation tanks. These are normally
just a downscaling of aquaculture production systems, and therefore realistic sys-
tems from an aquaculture perspective. However, the degree of experimental control
for fish-microbe studies is limited. Below we will describe different experimental
systems, going from high relevance/low control to low relevance/high control.
4 R. I. Vestrum et al.
high control systems can be used to study mechanisms and hypotheses which then
can be verified in systems where the fish live a more normal life, i.e. low control
systems. We will try to highlight pros and cons within the different systems.
Traditional rearing tanks can have variable volumes and can be run in traditional
flow-through systems (FTS) or as recirculating aquaculture systems (RAS), where
the water is reused after removal of waste and toxic substances. Tank volumes
depend on the size of the fish and the population size needed for experimental
reasons. From an ethical point of view and due to legislation the number of animals
used in an experiment should be as low as possible, but especially in applied
research the experimental systems should be relevant for a practical setting. This
might create a conflict between ethics and the practical relevance of new knowl-
edge. The use of FTS versus RAS has clear implications for fish-microbe studies, as
for RAS there will also be a recirculation of microbes. In some situations this can be
an advantage (maintaining the effect of the fish on the microbiota), whereas in other
cases a disadvantage (a high background concentration of microbes). FTS versus
RAS is therefore an important part of the experimental design. Traditional rearing
tanks have limited possibilities to control the microbiota in the rearing water. This
includes import and export of microbes, but particularly microbial growth in the
rearing tanks. For example, in studies with probiotics, it might be difficult to predict
the probiotic microbes’ ability to establish in the system as the competitive situation
with background microbes will vary depending on the species present and system
design. However, we have shown that it is possible to control and stabilize the
microbiota in rearing tanks through a selection regime against some microbes, and
favoring others (r- and K-selection) (Attramadal et al. 2014).
One of the drawbacks of using normal rearing tanks is that you have limited
possibilities for controlling import and export of microbes. Another problem is that
one fish may affect the other individuals in the same tank. This is important as
moribund individuals may infect healthy individuals, and that there is a continuous
sharing of microbes by defecation and re-ingestion (Reitan et al. 1998). A way out
of this problem is to rear single individuals in small units. Size and type of units
may vary from e.g. 40 ml in plastic cups (Forberg et al. 2016) to 2 ml in
24-multiwell plates (Fjellheim et al. 2010; Sandlund and Bergh 2008). Size of the
system may vary dependent on species and the length of the experiment. These
types of systems can be run without water exchange for yolk sac stages and early
1 Investigating Fish Larvae-Microbe Interactions … 5
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Fig. 1.1 Survival of yolk-sac larvae of Atlantic cod (Gadus morhua) incubated together with
different bacteria, including background bacteria (positive control), a pathogen (negative control)
and three probiotics candidates, versus time. Each treatment included 72 individuals. Data from
Fjellheim et al. (2010)
first feeding (Fjellheim et al. 2010; Sandlund and Bergh 2008) or with an irregular
water exchange for longer experiments (Forberg et al. 2016). In systems with water
exchange, there are possibilities for maintaining some degree of control of the
microbes entering the system by e.g. adding a defined or described microbiota. It is,
however, important to keep in mind that the way by which the renewal of the water
takes place may create different types of selection regimes for the microbiota in the
rearing unit (e.g. continuous versus periodic dilution rate).
An example of the use of 24-multiwell plates with single individuals in 2 ml of
water is shown in Fig. 1.1. In this experiment, unfed yolk-sac larvae were exposed
to either probiotic candidates, a pathogen (negative control) or only background
bacteria (positive control). As shown in the figure, you get reliable results with a
limited number of individuals (in this case 72 individuals per treatment), and the
reproducibility is very good (unpublished results). This simple system easily
revealed that one probiotic candidate actually was pathogenic (ID 4-29). In systems
with rearing of single individuals, it is possible to reduce the number of individuals
used for the experiment to a minimum, and confidence intervals for the survival can
be calculated from surviving individuals and the total number of individuals based
on binomial statistics (Box et al. 1978). Moreover, chi-square and exact tests can be
used for statistical analysis.
The pros of these systems should be evident based on the information above.
The down side is mainly the simplicity of the system and for some species the
difficulty of rearing the fish for sufficiently long periods. The simplicity includes
lack of interactions between individuals of fish, which is an advantage for some
6 R. I. Vestrum et al.
for doing experiments in different types of systems, and selecting the systems based
on the aim of the study.
If traditional rearing tanks is on one end of the experimental system scale, germ-free
and gnotobiotic systems are on the other end. A germ-free system has no microbes
at all, and in a gnotobiotic system the biota in the system is known (= gnotos) and
predefined. This can only be achieved by first generating germ-free test animals or
fish, which are then deliberately colonized by one or several bacterial strains known
to the researcher. Gnotobiotic systems were first developed for mammals such as
rats, but also for fish several gnotobiotic systems have been published (Table 1.1).
In general, the procedure of creating germ-free fish involves a first step with surface
disinfection of the eggs and subsequent hatching in an environment without
microbes. The subsequent rearing under germ-free or gnotobiotic conditions may be
in the presence or absence of antibiotics. When rearing the fish with antibiotics, you
can only use antibiotic resistant bacteria and there is also a possibility of negative
effects on larvae due to long term exposure to antibiotics (Moullan et al. 2015). As
documented in Table 1.1, many different techniques have been used to surface
disinfect the eggs, and gnotobiotic systems have been attempted for several fish
species.
The main advantage of using these systems is the high degree of control of the
microbial environment. This is appealing for many types of experiments with a
reductionistic approach—a strategy with a long history of success in natural sci-
ence. The main disadvantage of germ-free and gnotobiotic systems is the com-
plexity in performing these experiments. A reproducible method for achieving
germ-free larvae is needed, and avoiding contamination during the experiment is
also crucial (i.e. maintain them germ-free or gnotobiotic). In the cases were the fish
is fed live prey, the prey also needs to be germ-free. When using Artemia as live
feed it is possible to hatch them from disinfected cysts, and this makes the process
more straightforward. However, when using e.g. rotifers a germ-free culture has to
be established, they have to be reared germ-free, and therefore must be fed
germ-free feed (microalgae or yeast). Moreover, this production line has to be kept
throughout the germ-free or gnotobiotic fish experiment. One problem not given
much attention in the literature, is the maintenance of the gnotobiotic condition.
When only one microbe is added it is a presence/absence problem, but when several
species are added in a given ratio it is not straight forward to maintain this ratio.
This has to do with the selection regimes in the rearing unit and due to renewal of
water (see also Sect. 1.2).
Results generated from one fish species may not be easily transferrable to
another, as germ-free zebrafish (Danio rerio) seem to be less developed than
conventional fish (Rawls et al. 2004), while germ-free sea bass larvae have more
Other documents randomly have
different content
The town is utterly gone. There are those who Hippo
argue that this or that was not done as history
relates, because of this or that no vestige remains; and if tradition
tells them that Rome built here or there, they deny it, because they
cannot find walls, however much they dig (within the funds their
patrons allow them). These men are common in the universities of
Europe. They are paid to be common. They should see Hippo.
Here was a great town of the Empire. It detained the host of
Vandals, slaves and nomads for a year. It was the seat of the most
famous bishopric of its day, and within its walls, while the siege still
endured, St. Augustine died. It counted more than Palermo or
Genoa: almost as much as Narbonne. It has completely
disappeared. There are not a few bricks scattered, nor a line of
Roman tiles built into a wall. There is nothing. A farmer in his
ploughing once disturbed a few fragments of mosaic, but that is all:
they can make a better show at Bignor in the Sussex weald, where
an unlucky company officer shivered out his time of service with
perhaps a hundred men.
In the heart of the Tell, behind the mountains Calama
which hide the sea, yet right in the storms of the
sea, in its clouds and weather, stands a little town which was called
Calama in the Roman time and is now, since the Arabs, called
Guelma.
It is the centre of that belt of hills. A broad valley, one of the
hundreds which build up the complicated pattern of the
Mediterranean slope, lies before the platform upon which the fortress
rose. A muddy river nourishes it, and all the plain is covered with the
new farms and vineyards—beyond them the summits and the
shoulders that make a tumbled landscape everywhere along the
northern shores of Africa guard the place whichever way one turns.
From the end of every street one sees a mountain.
If a man had but one day in which to judge the nature of the
province, he could not do better than come to this town upon some
winter evening when it was already dark, and wake next morning to
see the hurrying sky and large grey hills lifting up into that sky all
around and catching the riot of its clouds. It is high and cold: there is
a spread of pasture in its fields and a sense of Europe in the air. No
device in the architecture indicates an excessive heat in summer and
even the trees are those of Italy or of Provence. Its site is a survival
from the good time when the Empire packed this soil with the cities
of which so great a number have disappeared: it is also a promise of
what the near future may produce, a new harvest of settled and
wealthy walls, for it is in the refounding of such municipalities that the
tradition of Europe will work upon Africa and not in barren adventure
southward towards a sky which is unendurable to our race and under
which we can never build and can hardly govern.
Guelma is typical in every way. It was Berber before the Romans
came, but nothing remains of its founders or of whatever punic
influence its first centuries may have felt. Of Rome so much endures
that the heavy walls and the arches are, as it were, the framework of
the place.
In the citadel a great fragment larger than The Permanence of
anything else in the town runs right across the Rome
soldiers’ quarters, pierced with the solid arches that once supported
the palace of Calama. Only the woodwork has disappeared. The
stones which supported the flooring still stand out unbroken, and the
whole wall, though it is not very high—hardly higher than the big
barracks around it—remains in the mind, as though it had a right to
occupy one’s memory of the Kasbah by a sort of majesty which
nothing that has been built since its time has inherited. Here, as
throughout the Empire, the impression of Rome is as indefinable as
it is profound, but one can connect some part of it at least with the
magnitude of the stones and the ponderous simplicity of their
courses, with the strength that the half-circle and the straight line
convey, and with the double evidence of extreme antiquity and
extreme endurance; for there is something awful in the sight of so
many centuries visibly stamped upon the stone, and able to evoke
every effect of age but not to compel decay.
This nameless character which is the mark of the Empire, and
carries, as it were, a hint of resurrection in it, is as strong in what has
fallen as in what stands. A few bricks built at random into a mud wall
bear the sign of Rome and proclaim her title: a little bronze
unearthed at random in the rubbish heaps of the Rummel is a
Roman Victory: a few flag-stones lying broken upon a deserted path
in the woodlands is a Roman Road: nor do any of these fragments
suggest the passing of an irrecoverable good, but rather its
continued victory. To see so many witnesses small and great is not
to remember a past or a lost excellence, but to become part of it and
to be conscious of Rome all about one to-day. It is a surety also for
the future to see such things.
There is a field where this perpetuity and this The Peasant’s Wall
escape from Time refresh the traveller with
peculiar power. It is a field of grass in the uplands across which the
wind blows with vigour towards distant hills. Here a peasant of the
place (no one knows when, but long ago) fenced in his land with
Roman stones. The decay of Islam had left him aimless, like all his
peers. He could not build or design. He could not cut stone or mould
brick. When he was compelled to enclose his pasture, the only
material he could use was the work of the old masters who had
trained his fathers but whom he had utterly forgotten or remembered
only in the vague name of “Roum.” It was long before the reconquest
that he laboriously raised that wall. Some shadow of Turkish power
still ruled him from Constantine. No one yet had crossed the sea
from Europe to make good mortar or to saw in the quarries again. It
is with a lively appreciation that one notes how all he did is perishing
or has perished. The poor binding he put in has crumbled. The slabs
slope here and there. But the edges of those stones, which are
twenty times older than his effort, remain. They will fall again and lie
where he found them; but they and the power that cut them are alike
imperishable.
It has been said that the men of antiquity had The Landscape of
no regard for landscape, and that those principal Antiquity
poems upon which all letters repose betray an indifference to
horizons and to distant views. The objection is ill-found, for even the
poems let show through their admirable restraint the same passion
which we feel for hills, and especially for the hills of home: they
speak also of land-falls and of returning exiles, and an Homeric man
desired, as he journeyed, to see far off the smoke rising from his
own fields and after that to die. But much stronger than anything
their careful verse can give us of this appetite for locality is the
emplacement of their buildings.
Mr. March-Phillips has very well described the The Theatre of
spirit which built a certain temple into the Calama
scenery of a Sicilian valley. Here (he says), in a place now deserted,
the white pillars ornament a jutting tongue of land, and are so placed
that all the lines of the gorge lead up to them, and that the shrine
becomes the centre of a picture, and, as it were, of a composition. Of
this antique consciousness of terrestrial beauty all southern Europe
is full, and here in Guelma, upon an edge of the high town, the site of
the theatre gives evidence of the same zeal.
The side of a hill was chosen, just where the platform of the city
breaks down sharply upon the plain below. There, so that the people
and the slaves upon the steps could have a worthy background for
their plays, the half-circle of the auditorium was cut out like a quarry
from the ground. Beyond the actors, and giving a solemnity to the
half-religious concourse of the spectators, the mountains of the Tell
stood always up behind the scene, and the height, not only of those
summits but of the steps above the plain, enhanced the words that
were presented. We have to-day in Europe no such aids to the
senses. We have no such alliance of the air and the clouds with our
drama, nor even with our patriotism—such as the modern world has
made it. The last centuries of the Empire had all these things in
common: great verse inherited from an older time, good statuary,
plentiful fountains, one religion, and the open sky. Therefore its
memory has outlasted all intervening time, and it itself the Empire,
(though this truth is as yet but half-received,) has re-arisen.
There is one great note in the story of our race The Greatness of
which the least learned man can at once The First Four
appreciate, if he travels with keen eyes looking Centuries
everywhere for antiquity, but which the most learned in their books
perpetually ignore, and ignore more and more densely as research
develops. That note is the magnitude of the first four centuries.
Everybody knows that the ancient world ran down into the
completed Roman Empire as into a reservoir, and everybody knows
that the modern world has flowed outwards from that reservoir by
various channels. Everybody knows that this formation of a United
Europe was hardly completed in the first century, that it was at last
conscious of disintegration in the fifth. The first four centuries are
therefore present as dates in everybody’s mind, yet the significance
of the dates is forgotten.
Historians have fallen into a barren contemplation of the Roman
decline, and their readers with difficulty escape that attitude. Save in
some few novels, no writer has attempted to stand in the shoes of
the time and to see it as must have seen it the barber of Marcus
Aurelius or the stud-groom of Sidonius’ Palace. We know what was
coming, the men of the time knew it no more than we can know the
future. We take at its own self-estimate that violent self-criticism
which accompanies vitality, and we are content to see in these 400
years a process of mere decay.
The picture thus impressed upon us is certainly false. There is
hardly a town whose physical history we can trace, that did not
expand, especially towards the close of that time. There was hardly
an industry or a class (notably the officials) that had not by an
accumulation of experience grown to create upon a larger and a
larger scale its peculiar contribution to the State; and far the larger
part of the stuff of our own lives was created, or was preserved, by
that period of unity.
That our European rivers are embanked and canalised, that we
alone have roads, that we alone build well and permanently, that we
alone in our art can almost attain reality, that we alone can judge all
that we do by ideas, and that therefore we alone are not afraid of
change and can develop from within—in a word, that we alone are
Christians we derive from that time.
Our theory of political justice was partly formulated, partly handed
on, by those generations; our whole scheme of law, our conceptions
of human dignity and of right. Even in the details our structure of
society descends from that source: we govern, or attempt to govern,
by representation because the monastic institutions of the end of the
Empire were under a necessity of adopting that device: we associate
the horse with arms and with nobility because the last of the Romans
did so.
If a man will stand back in the time of the Antonines and will look
around him and forward toward our own day, the consequence of the
first four centuries will at once appear. He will see the unceasing
expansion of the paved imperial ways. He will conceive those great
Councils of the Church which would meet indifferently in centres
1500 miles apart, in the extremity of Spain or on the Bosphorus: a
sort of moving city whose vast travel was not even noticed nor called
a feat. He will be appalled by the vigour of the western mind between
Augustus and Julian when he finds that it could comprehend and
influence and treat as one vast State what is even now, after so
many centuries of painful reconstruction, a mosaic of separate
provinces. He will calculate with what rapidity and uniformity the
orders of those emperors who seem to us the lessening despots of a
failing state were given upon the banks of the Euphrates, to be
obeyed upon the Clyde. He will then appreciate why the Rome which
Europe remembers, and upon which it is still founded, was not the
Rome of literature with its tiny forum and its narrow village streets,
but something gigantic like that vision which Du Bellay had of a
figure with one foot upon the sunrise and its hands overspreading
ocean.
Indeed this great poet expresses the thing more vividly by the
sound of three lines of his than even the most vivid history could do.
This was the might and the permanence from which we sprang.
To establish the character of the Empire and its creative mission is
the less easy from the prejudice that has so long existed against the
action of religion, and especially of that religion which the Empire
embraced as its cataclysm approached. The acceptation of the
creed is associated in every mind with the eclipse of knowledge and
with a contempt for the delights which every mind now seeks. It is
often thought the cause, always the companion, of decay, and so far
has this sentiment proceeded that in reading books upon Augustine
or upon Athanasius one might forget by what a sea and under what
a sunlight the vast revolution was effected.
It is true that when every European element had mixed to form
one pattern, things local and well done disappeared. The vague
overwhelming and perhaps insoluble problems which concern not a
city but the whole world, the discovery of human doom and of the
nature and destiny of the soul, these occupied such minds as would
in an earlier time have bent themselves to simpler and more feasible
tasks than the search after finality. It is true that plastic art, and to a
less extent letters, failed: for these fringes of life whose perfection
depends upon detail demand for their occasional flowering small and
happy States full of fixed dogmas and of certain usages. But though
it lost the visible powers antiquity had known, the Empire at its end,
when it turned to the contemplation of eternity, broadened much
more than our moderns—who are enemies of its religious theory—
will admit. The business which Rome undertook in her decline was
so noble and upon so great a scale that when it had succeeded,
then, in spite of other invasions, the continuity of Europe was saved.
We absorbed the few barbarians of the fifth century, we had even the
vitality to hold out in the terror and darkness of the ninth, and in the
twelfth we re-arose. It was the character of the Western Empire
during the first four centuries, and notably its character towards their
close, which prevented the sleep of the Dark Ages from being a
death. These first four centuries cast the mould which still constrains
us; they formed our final creed, they fixed the routes of commerce
and the sites of cities, and perpetually in the smallest trifles of
topography you come across them still: the boundary of Normandy,
as we know it to-day, was fixed by Diocletian. If there can be said of
Europe what cannot be said of any other part of the world, that its
civilisation never grew sterile and never disappeared, then we owe
the power of saying such a thing to that long evening of the
Mediterranean.