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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
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Crotophaga ani. Linn.
Petit Bout-de-Petun, pl. enl. 102. f. 2.
Zenaida Galapagoensis.
2. Columba loricata. Licht. Vög. Verz. s. 67.
Columba gymnophthalmus, Temm., Pig. i. 18.
—— leucoptera, Pr. Max. Reise, 2, p. 242.
—— picazuro, Temm. Pig. p. 111.
Picazuro, Azara, Voy. No. 317.
A specimen was given me, which was shot on the lofty Cordillera of
Coquimbo, only a little below the snow-line. At a similar height, on
the Andes, behind Copiapo, which appear so entirely destitute of
vegetation, that any one would have thought that no living creature
could have found subsistence there, I saw a covey. Five birds rose
together, and uttered noisy cries; they flew like grouse, and were very
wild. I was told that this species never descends to the lower
Cordillera. These two species, in their respective countries, occupy
the place of the ptarmigan of the northern hemisphere.
Tinochorus rumicivorus. Eschsch.
Thinocorus rumicivorus, Eschsch. Zool. Atl. pl. 2.
Tinochorus Eschscholtzii, Less. Cent. Zool. pl. 50.
These birds are very common on the northern shores of the Plata.
They do not rise in coveys, but generally by pairs. They do not
conceal themselves nearly so closely as the English partridge, and
hence great numbers may be seen in riding across the open grassy
plains. Note, a shrill whistle. It appears a very silly bird: a man on
horseback, by riding round and round in a circle, or rather in a spire,
so as to approach closer each time, may knock on the head almost as
many as he pleases. The more common method is to catch them with
a running noose, or little lazo, made of the stem of an ostrich’s
feather, fastened to the end of a long stick.[23] A boy on a quiet old
horse will frequently thus catch thirty or forty in a day. The flesh of
this bird, when cooked, is most delicately white, but rather tasteless.
The egg of this species, I believe, closely resembles that of the two
following.
2. Nothura minor. Wagl.
Nothura minor, Wagl. Syst. Av. p. sp. 4.
Tinamus minor, Spix, Av. Br. pl. 82.
Rhea Darwinii.
2. Rhea Darwinii. Gould.
Plate XLVII.
Gould, in Proceedings of Zoological Soc. 1837, p 35.
The skin round and in front of the eyes is less bare in R. Darwinii;
and small bristly feathers, directed forwards, reach over the nostrils.
The feet and tarsi are nearly of the same size in the two species. In
the R. Darwinii, short plumose feathers extend downwards in a
point on the sides of the tarsus, for about half its length. The upper
two-thirds of the tarsus, in front, is covered with reticulated scales in
place of the broad transverse band-like scales of the R. Americana;
and the scales of the lower third are not so large as in the latter. In
the R. Darwinii the entire length of the back of the tarsus is covered
with reticulated scales, which increase in size from the heel upwards:
in the common Rhea, the scales on the hinder side of the tarsus are
reticulated only on the heel, and about an inch above it; all the upper
part consisting of transverse bands, similar to those in front.
The first notice I received of this species was at the Rio Negro, in
Northern Patagonia, where I repeatedly heard the Gauchos talking of
a very rare bird, called Avestruz Petise. They described it as being
less than the common ostrich (which is there abundant), but with a
very close general resemblance. They said its colour was dark and
mottled, and that its legs were shorter, and feathered lower down
than those of the common ostrich. It is more easily caught by the
bolas than the other species. The few inhabitants who had seen both
kinds, affirmed that they could distinguish them apart, from a long
distance. The eggs, however, of the small species appeared more
generally known, and it was remarked with surprise, that they were
very little less than those of the common Rhea, but of a slightly
different form, and with a tinge of pale blue. Some eggs which I
picked up on the plains of Patagonia, agree pretty well with this
description; and I do not doubt are those of the Petise. This species
occurs most rarely in the neighbourhood of the Rio Negro; but about
a degree and a half further south they are tolerably abundant. One
Gaucho, however, told me he distinctly recollected having seen one,
many years before, near the mouth of the Rio Colorado, which is
north of the Rio Negro. They are said to prefer the plains near the
sea. When at Port Desire in Patagonia (Lat. 48°), Mr. Martens shot
an ostrich; I looked at it, and from most unfortunately forgetting at
the moment, the whole subject of the Petises, thought it was a two-
third grown one of the common sort. The bird was skinned and
cooked before my memory returned. But the head, neck, legs, wings,
many of the larger feathers, and a large part of the skin, had been
preserved. From these a very nearly perfect specimen has been put
together, and is now exhibited in the museum of the Zoological
Society. M. A. D’Orbigny, a distinguished French naturalist, when at
the Rio Negro, made great exertions to procure this bird, but had not
the good fortune to succeed. He mentions it in his Travels (vol. ii. p.
76.) and proposes (in case, I presume, of his obtaining a specimen at
some future time, and thus being able to characterize it,) to call it
Rhea pennata. A notice of this species was given long since (A.D.
1749) by Dobrizhoffer, in his account of the Abipones (vol. i. Eng.
Trans. p. 314). He says, “You must know, moreover, that Emus differ
in size and habits in different tracts of land; for those that inhabit the
plains of Buenos Ayres and Tucuman are larger, and have black,
white, and grey feathers; those near to the Strait of Magellan are
smaller, and more beautiful, for their white feathers are tipped with
black at the extremity, and their black ones in like manner terminate
in white.”
Among the Patagonian Indians in the Strait of Magellan, we found
a half-bred Indian, who had lived some years with this tribe, but had
been born in the northern provinces. I asked him if he had ever
heard of the Avestruz Petise? He answered by saying, “Why there are
none others in these southern countries.” He informed me that the
number of eggs in the nest of the Petise is considerably less than with
the other kind, namely, not more than fifteen on an average; but he
asserted that more than one female deposited them. At Santa Cruz
we saw several of these birds. They were excessively wary: I think
they could see a person approaching, when he was so far off as not to
distinguish the ostrich. In ascending the river few were seen; but in
our quiet and rapid descent, many, in pairs and by fours or fives,
were observed. It was remarked by some of the officers, and I think
with truth, that this bird did not expand its wings, when first starting
at full speed, after the manner of the northern kind. The fact of these
ostriches swimming across the river has been mentioned. In
conclusion, I may repeat that the R. Americana inhabits the eastern
plains of S. America as far as a little south of the Rio Negro, in lat.
41°, and that the R. Darwinii takes its place in Southern Patagonia;
the part about the Rio Negro being neutral territory. Wallis saw
ostriches at Bachelor’s river (lat 53° 54′), in the Strait of Magellan,
which must be the extreme southern possible range of the Petise.
Order—GRALLATORES.