Health management of marine fish larvae in a microbial world

Abstract

We review the literature on microbial management in larval rearing and give recommendations for future research. Based on a range of different approaches, we show that, as for many farmed animals, detrimental host/microbe interactions are a main reason for low viability of young stages of farmed fish, crustacea and shellfish. The composition of the microbiota of larval stages is determined by both selection and stochastic processes, which makes it possible to steer the colonization of larval fish by controlling the abundance and the inventory of species of the microbes present in aquaculture facilities. The microbiota evolves rapidly during larval development, leading to need for a continuous management. It is important to emphasize that it is not which species, but which functions that the microbiota provide that is important for the viability of the larvae. These functions are difficult to quantify, and we have limited knowledge. We discuss a range of microbial management methods that have been proposed and evaluate current knowledge and use in the industry. We group these methods as 1) targeted and non-targeted decimation, 2) targeted enhancement, and 3) stimulation of the immune system. Many different methods within these three groups are discussed. There has been considerable progress with some methods, but few are well studied. Only a few methods are implemented in the industry. To develop a research program that aims to establish the scientific knowledge-based needed for development of microbial management methods we call for a concerted action with participants from the industry, the research community, and national and international funding agencies. The research should be based on a consensus understanding of the current problems and be more diverse than now, as complex problems need complex solutions.

1 Introduction

Multiple farmed animal species experience high mortality during early life, including chickens, pigs, and farmed fish (Mellor and Stafford, 2004; Ellis et al., 2012). Detrimental host/microbe interactions are often the driver of this mortality, and multiple lines of evidence support this conclusion (see section 2). Prophylactic use of antibiotics in animal production to improve growth and survival is one of the earliest scientific indicators that host-microbe interactions are key (Gustafson and Bowen, 1997). Our experience is from the rearing of fish, and we will use that as a case for the general problem with microbe induced mortality and poor performance in early life stages of reared animals.

Poor and variable viability during the period before metamorphosis is well described for a large number of species of fish, shellfish and crustaceans that we have tried to domesticate. The mortality during larval stages is way higher than during later stages. There are few exceptions to this observation. In aquaculture, it was long assumed that poor viability was mainly due to malnutrition and poor egg quality. However, an increasing number of observations and experiments point to detrimental host/microbe interactions as a main cause. We will give the arguments for this statement in section 2.

If microbes cause problems during young stages of farmed animals there is a need to develop both a strategy and methods for microbial management (terminology used are defined in Table 1). “Methods” is stated in plural, as the problem is too complex to be fixed by one countermeasure. Both the industry and the research community have had too much attention on disease treatment compared to disease prevention - for example, by the overuse of antibiotics. Moreover, research and industrial rearing protocols related to microbial management have mainly focused on decimation of microbes and followed a trial-and-error approach. This strategy is known to give slow and system dependent development. It would be much more productive to use a scientific knowledge-based approach. The fields of microbial ecology and microbial physiology are a good source for such a knowledge-based approach (Robinson et al., 2010).

This paper aims to document that detrimental host/microbe interactions are a main reason for the low and variable viability in aquaculture during early development of reared species. Moreover, we clarify the possibilities and constraints of microbial management based on fundamental concepts and current knowledge regarding the processes that control microbial colonization of farmed fish. Finally, we discuss the possibilities for microbial management and the status of various microbial management methods - including identifying promising management approaches and research gaps. Several review papers have summarized the knowledge on fish microbiota (e.g. Borges et al., 2021; Luan et al., 2023; Diwan et al., 2023; Tayyab et al., 2025). The goal of our paper is to go one step further by a transition from describing and understanding larvae/microbe interaction to the steering of host/larvae interactions in a way that promotes mutualistic larvae/microbe interactions that secure biological, environmental and economic sustainability. Moreover, we hope to stimulate the diversification of microbial management related research and to motivate early career scientist to go into this field of research.

2 Methods

We have done a focused review to address the current status of microbial management. The outline of the paper is presented above. The current scientific and industrial status of microbial management methods is reviewed based on a revision of the classification outlined by Vadstein et al. (1993a). We have previously listed 21 published studies that used different microbial management methods (Vadstein et al., 2018a). We add some new important studies in the current paper, but to avoid “over citation” we focus citations on pioneer studies and recent review papers.

The interest and status of various microbial management methods in science and in the industry, was respectively, evaluated based on search in the high-quality scientific database Web of Science and in Hatchery International, the primary professional magazine for the hatchery industry. We used “Advanced Search” in Web of Science, and “Title” search – which means that the search keywords must be found in the title of publications. For search in the online magazine Hatchery International we used the general search field of the online magazine. By limiting our search to only one professional journal we may have a geographical bias in our results. However, we have not found other journals with focus on the hatchery industry and the magazine has a fairly broad coverage in terms of articles and readers (see https://issuu.com/annexbusinessmedia/docs/hi_-_january_-_february_2025/13). The search expressions with Boolean operators, are given in the main text of the manuscript before the results of the search is presented. Searches were performed the first half of November 2025. Most of the available data are from studies of fish larvae, but data from studies of invertebrates are included. Our focus is on marine larvae, but we use freshwater literature when appropriate. We consider our conclusions relevant for larvae from marine and freshwater fish, shellfish and crustaceans.

3 Results

3.1 Status for the hypothesis of detrimental larvae/microbe interactions as a main cause for low viability of larvae

The problems in larval rearing are reflected in a large range of biological variables (see Vadstein et al., 2018a). The appetite of larvae may be poor and the onset of feeding delayed, diarrhea may be present, growth may be suboptimal or stop at a sensitive developmental stage, animals can be sensitive to stress, and mortality can be high and rapid. Another very important observation is the poor reproducibility between replicated rearing tanks, even when one egg batch is used. These performance variables can be poor due to many causes and is often attributed to egg quality and nutrition. However, the large variability between replicates using one egg batch is not consistent with egg quality or nutrition as the main cause of the problem. Neither is abrupt mortality – often with a loss of 40 to 80% of the individuals in a single day.

During the last 30 years a substantial number of studies have investigated the role of microbes in the viability of early life stages of reared aquatic species. What is particularly interesting and compelling about these studies is that many different experimental approaches were used (Table 2). These approaches include removal and addition of microbes, quantitative and qualitative changes to the microbes of the rearing environment, the use of selection to steer composition of the microbiota, microbe-free systems, and unmanipulated comparative studies. The overall conclusion across these very different studies is robust: microbes, and in particular microbial community composition, strongly influence the viability of larvae, including appetite, growth, development, survival, stress tolerance and gene expression. In many studies the effect size is substantial. For example, in many studies that use selection to steer composition of the microbiota (specifically using K-selection to avoid detrimental r-strategist microbes) the effect size for various performance variables was typically a factor two increase in performance (Vadstein et al., 2018b).

Observations done on industrial scale confirm the above conclusion, although the problem at industrial scale is not well documented in the scientific or professional literature. There seems to be a large degree of reluctance by companies to discuss and/or reveal the problem of low and irreproducible viability of larvae, as customers and investors might fear that this will influence their robustness. Yet, in its “Strategic research and innovation agenda” the European Aquaculture Technology and Innovation Platform (https://eatip.eu/) has stated that an in-depth knowledge of host microbial interactions is an important priority for the advancement in sustainable aquaculture.

The scientific studies cited above and those related to Table 2, and information based on discussions with people in the industry over 30 years, makes it fair to state that detrimental host/microbe interactions is a main reason for the poor performance observed in young stages of aquaculture species. We hypothesize that the main problem is not obligate pathogens, but dysbiosis. With dysbiosis we mean an imbalance in the microbiota at the community level, which results in a lack of microbial community functionality, and with detrimental outcome. Biological ecologists would call this imbalance an “alternative stable state”, by which they mean that the situation will persist unless there is an intervention that can return the microbial community to its previous (healthy) state.

We do not intend to minimize the fact that pathogens can present substantial problems in farmed animals. However, pathogens are not commonly the cause of early life mortality in fish, because in many cases pathogens cannot be detected.

It is important to note that the problem of early life mortality is not universal among farmed fish species. Some species are more mature and robust just after hatching, such as Atlantic salmon (Salmo salar) and wolf-fish (Anarhichas spp). Fish species that recently have been domesticated can be particularly vulnerable to early life mortality due to the lack of biological knowledge to guide their husbandry. With more experience and the development of robust rearing protocols, a reduction in mortality is normally obtained. E.g. in the industrial production of seabream in Greece the survival is now close to 50% at metamorphosis (pers. comm. Pavlos Makridis). However, normally we talk about a change in survival from 0-3% to a survival of only 15-30%. We would state that as long as survival is below 80-90% the rearing protocol is suboptimal. An important finding from humans is that suboptimal conditions early in life can result in a range of health problems at later stages (Langley-Evans, 2015; Morniroli et al., 2023; Zheng et al., 2025), and this likely applies to all (reared) vertebrates. Interestingly, Fallet et al. (2022) showed that exposure of oyster (Crassostrea gigas) to a natural versus an UV treated water gave a markedly increased survival when challenged with a pathogen later in life as well as in the subsequent generation, thus extending the conclusion to also include at least one invertebrate. Moreover, as poor performance until the juvenile stage is a general problem with farmed fish and shellfish, we should aim for knowledge based generalizable solutions. This is much more effective than letting the individual farmers find system and species dependent solutions based on trial and error.

The conclusion that detrimental host/microbe interactions are a main reason for the poor performance observed for young stages of aquaculture species, leads to some questions that need to be addressed if we aim to solve this problem:

• How large is the variation in the microbiome between individual larvae?

• How is the microbial environment of the rearing system influencing the colonization process of reared fish larvae?

• Do factors that influence microbial community assembly change with development?

• Are microbial communities of larvae easily invaded by new species of microbes from the environment?

• Is it possible to steer the microbiota of larvae?

• What is the relationship between structure and function of the larval microbiome?

We will elaborate on the first five questions in the next section, and the final question in section 3.3.

3.2 What determines the composition of microbiota in larvae?

Understanding what determines the composition and why larval microbiomes vary is crucial if we are to design approaches to manipulate them, as these realities sets the boundary conditions for our possibilities for microbial management. Several studies indicate large variation in microbiota composition between individuals (e.g. Burns et al., 2016; Forberg et al., 2016; Trinh et al., 2017; Bakke et al., 2015; Vestrum et al., 2020; Deng et al., 2021, and references within). An early study of Atlantic cod (Gadus morhua) showed that variation between individuals from the same rearing tank was comparable to the variation between rearing systems using different technologies and located distantly (Fjellheim et al., 2012).

The sources of this variation are not obvious. The microbiota of the feed does not seem to have a strong structuring effect on the microbiota of young stages (Bakke et al., 2019 and references within), but this may be different for adult stages. However, different composition of the microbiota in the water affects the composition of the microbiota of e.g. Atlantic cod (Vadstein et al., 2018b; Vestrum et al., 2020), Atlantic salmon (Mathisen et al., 2025) and Nile tilapia (Oreochromis niloticus; Deng et al., 2021). Interestingly, in the two experiments with Atlantic cod and Nile tilapia, it was observed for both species that when groups that had received water with different microbiota were transferred to the same water, i.e. same microbiota, this resulted in a convergence to the same composition of the microbiota of the fish (Vadstein et al., 2018b; Deng et al., 2021). The microbiota of fish is, however, not a mirror image of the microbiota in the water, as microbiome similarity (measured using the Bray-Curtis metric, a metric commonly used by microbial ecologists) between water and fish bacterial community composition was 55-95, 35–45 and 3-25% in three studies (Bakke et al., 2015 and 2019, Vestrum et al., 2020). This indicates that not all microbes found in water can establish in the fish and that the relative abundance of different microbial species differs between fish and their surrounding environment. It is not known to what extent this is due to fish/microbe or microbe/microbe interactions. An important finding is that groups of larvae exposed to three water types with different microbiota for 30 days resulted in a factor 2 effect on the survival at day 60 after hatching, with average survival ranging from 11 to 21% (Vadstein et al., 2018b, and references within).

The study of variation in microbiome structure is a rapidly changing field and has greatly benefited from the introduction of approaches and methods from the science of biological ecology (Prosser et al., 2007; Robinson et al., 2010; Costello et al., 2012; Nemergut et al., 2013; McDonald et al., 2020). Ecologists divide the potential causes of variation in multispecies communities (such as the microbiomes of fish) into four categories: selection among species, ecological drift, dispersal, and speciation (Vellend, 2010). We don’t consider speciation in this article, as it is not very relevant for the time scale of larval development. The three remaining processes can be grouped as deterministic (selection) and stochastic (drift and dispersal).

This conceptual framework has been applied to fish microbiomes. For example, studies on young zebrafish (Danio rerio) show that 70 to 85% of the variability in the composition of microbiomes between individuals can be explained by neutral processes (drift and dispersal), but with age this percentage was reduced to 40% (Burns et al., 2016). The dispersal rate between individuals as part of neutral processes was significant, as 12 to 17% of the microbiota came from that source pool during early stages. It is interesting and important that at the individual level a correlation has been found between composition of the microbiota and the growth rate of larvae for both Mangrove Killifish (Kryptolebias marmoratus) and Atlantic cod (Forberg et al., 2016; Trinh et al., 2017).

James C. Stegen and coworkers have developed an approach which distinguish selection and dispersal from other stochastic processes (Stegen et al., 2013). However, the important underlying assumptions of this approach have not been properly tested. This approach has been used to quantify the importance of stochastic processes and selection during larval development in fish, and it indicates similar importance of stochastic processes and selection during all larval stages (Li et al., 2017; Vestrum et al., 2020; Keating et al., 2022; Gundersen et al., 2023). Thus, neutral processes and selection are of similar importance for larval stages. This may seem contradictory to the conclusion by Burns et al. (2016), but reflects the fact that Burns et al. assumed that the bacterial source pool of microbes was other fish and did not include the environmental microbiota as part of the bacterial source pool.

The microbiota of larvae goes through a succession throughout the development to the juvenile stage. Based on the Bray-Curtis similarity metric, the composition of the microbiota changes significantly over time periods of 3 to 7 days in Atlantic cod (Trinh et al., 2017; Vadstein et al., 2018b), with similarities typically as low as 30% (range 14-58) between time points.

How well does the microbiota of the animal resist a pulse (i.e. a single introduction) of new species? This question is relevant for the use of probiotics. Despite extensive research on probiotics in larval rearing, this is not systematically studied. However, Skjermo et al. studied this with four probiotic candidates for Atlantic cod (see Bakke et al., 2019). Most probiotic candidates were not clever colonizers, and there was more resistance against invasion in established than in pioneer communities. In general, the response of bacterial communities to disturbances/invasions has low predictability, which likely is attributed to the neglect of stochastic processes in predictions (Zhou and Ning, 2017).

In conclusion, our understanding of how the microbiota of larval stages of fish is established initially and develops during the larval stage has improved considerably during the last 10 years. We know that inter-individual variation is large, and that this affects the viability of the larvae. Importantly, the composition of the microbiota of larvae changes significantly at the time scale of days, and microbial management is therefore a continuous process. It seems that stochastic processes and selection affect the assembly of the larval microbiota to a similar extent. It is therefore possible to manipulate the microbiota of the larvae by steering the composition of the microbiota in their source “species pool”, i.e. in feed and rearing water. Importantly, for species of microbes that are actively selected for their presence may be sufficient, but for species where stochastic processes are important the absolute and relative abundance in the source pool is important. Experimental data suggest that for larval stages the water microbes are a more important source pool than feed microbes. This points to the crucial importance of the composition of the microbes in the environment surrounding larvae, the “species pool”, for the colonization and viability of the larvae. However, there is still a need for more knowledge regarding the assembly of the microbiota of larvae before this knowledge can serve as a solid base for microbial management.

3.3 Composition versus activity of microbiota

As indicated above much of what we know about host/microbe interactions is based on the quantification of the relative abundance of microbes associated with larvae and in their environment. The absolute abundance, which is a more important variable, is almost never determined and has its own technical difficulties (Denzer et al., 2020). What matters for the functionality of the microbiota is, however, their activity, i.e. the production of active molecules by the microbiota. Little is known about the activity of the larval microbiota in vivo.

To get around this problem, ever more sophisticated tools for characterizing microbial communities are available, such as full length 16S RNA sequencing and high throughput metagenome sequencing. However, one must keep in mind that these technologies describe which genomes that are present in a sample, and this results in two problems. First, part of the DNA that is extracted from any sample is cell free DNA and not from intact microbial cells (Grabuschnig et al., 2020). Cell free DNA of microbial origin could be from many sources, such as microbial cells lysed through digestion, the action of the Type 6 secretion system (Singh and Kumari, 2023) or bacteriophage activity (Kirsch et al., 2021). Although it is possible to separate intracellular and extracellular microbial DNA (Bairoliya et al., 2022), it has rarely been applied in larval studies. Secondly, it is currently fashionable to predict microbial community activity from relative abundance data using software packages such as FAPROTAX or PICRUSt2. Although this generates useful information, such software predictions are imprecise for species that do not have fully sequenced genomes. Even more important, at any temporal-spatial event only a fraction of the genome is expressed. There are also indications that the current knowledge of environmental microbial genomes is too limited to predict microbial community activity with precision (Sun et al., 2020).

It is now believed that techniques that use information from RNA or proteins (e.g. meta-transcriptomics and meta-proteomics approaches) and even at the metabolic level will allow us to understand the functional dynamics of microbial communities better, including those in fish larvae. Combined meta-transcriptomics and meta-proteomics approaches (at the community level or community member level) might indeed be needed as there are many biochemical steps along the way between transcription on the one hand and protein concentration or enzyme activity on the other hand (Buccitelli and Selbach, 2020). This is especially relevant for host microbial interference (Galazzo et al., 2020; Zhang et al., 2025). Meta-transcriptomics and meta-proteomics are, however, still difficult to perform on larvae due to the small size of fish larvae. This is also the case for metabolic studies. In these type of study, individual larval fish are pooled to obtain enough sample to extract metabolites (Mang et al., 2024). This contradicts the recent findings that on one hand variability in the microbial community composition among individuals can be large and on the other hand that a high number of biological replicates is needed for proper interpretation. E.g. Panteli et al. (2020) suggested 9 pooled samples is required to describe the standing microbial diversity in the larval population at a level needed to map host microbial interactions at the larval fish community.

Borges et al. (2021) have summarized and critically reviewed the available data on the importance of microbial activity for larval growth and development. The larval host microbiome is involved in epithelial cell differentiation and maturation, in nutrition and modulation of immunity. With respect to opportunistic pathogens, the following lacking knowledge is very important: regulation of the expression of virulence factor in vivo (some of them regulated by quorum sensing), evasion of the immune response by for example phenotype switching, and modulation/silencing of the immunological response of larvae to an ongoing infection.

A way around the analytical difficulties and complexity is to hypothesize: If young stages are protected from detrimental microbes, they can select the functions they need if the source pool contains microbes with those functionalities. Work by John Rawls and colleagues on the microbiota of mice and zebrafish support such a hypothesis. They inoculated mice with the microbiota of zebrafish (Danio rerio) and vice versa, and showed that the host tried to model their normal microbiota with the inoculated foreign microbes (Rawls et al., 2006). Moreover, although the molecular mechanisms may not be known, there is a great deal known about “colonization resistance” as a phenomenon, and this could be manipulated even if the mechanisms are not yet identified (Woelfel et al., 2024).

In addition to the direct studies of the activity of the microbiota and its implications for the larvae, one can take the step from structure to function also by understanding the microbial ecology of the host-associated microbiota (Robinson et al., 2010). Ecological theory has already been used to a better understanding of the function of the human microbiota and has already led to the use of restoration treatment of patients with serious C. difficile infections.

In conclusion, there is still a big need for more knowledge regarding the mode of action of the normal microbiota, probiotics, opportunistic pathogens and pathogens in vivo. Currently knowledge of their presence/relative abundance is the easiest information to generate, but in the future it will be important to unveil how these factors steer interaction with the host, how they can influence the microbial community composition and activity, including the microbial interaction network.

3.4 Microbial management strategies: status of our current toolbox

Today the dominant strategy to solve microbial problems in the aquaculture industry is treatment, i.e. to treat problems rather than to prevent problems. The same is the situation for domestic animals. The same is the situation for a large range of aquaculture species and for various developmental stages. As a consequence, there is an overuse of antibiotics in the aquaculture industry in many places (e.g. Romero, 2012; Schar et al., 2020). This is not sustainable, will contribute to the global antibiotic resistance crisis, and gives this food production industry a bad image. As aquaculture systems are open, although to a variable degree, they can cause antibiotic resistance both within the systems and in the local environment. Relatively little is known about the development and spread of antibiotic resistance in aquaculture facilities (Hassen, 2026), but there is no doubt that the problem is significant. The unregulated us of antibiotics in many countries, is of major concern. A success story on a 99.9% reduction in use of antibiotics in the Norwegian salmon farming is presented below. The exception from the treatment approach is the application of standard hygienic routines and the development of vaccines, which are forms of prevention.

Microbial management to improve larval viability is a strategy with an explicit focus on prevention, i.e. controlling the microbiota in an environment to secure stable functionality of the microbial communities in a way that reduces the risk of detrimental fish/microbe interactions. The functionality of a production system is normally defined anthropocentrically, i.e. economically. However, improving microbial functionality for domestic animals increase animal welfare and reduce the use of antimicrobial chemicals, and this have economic implications (Figure 1). This is because animal welfare and production efficiency go hand in hand when it is based on biological criteria. Microbial management can be done with both the whip and the carrot philosophy. However, because microbes are smarter than us, the whip philosophy only works on a short timescale. The carrot philosophy requires knowledge of microbial ecology and a focus on the microbiome of the rearing system.

Figure 1

In this paper we focus on the short timescale of larval development, but much of what we discuss is relevant for longer timescales. A special case with a long timescale is animal breeding. Both for farmed animals and reared fish there are breeding programs with evolutionary consequences for the reared species. Traditionally breeding has focused on traits affecting growth, but recently traits affecting disease resistance and animal welfare have been included. The next that should be considered is selection for a well-functioning microbiota with high stability and resilience, and with resistance to invasion by detrimental microbes. A description of this idea is given in David et al. (2019).

The strong effect of microbial management, i.e. proactive prevention, is well documented for humans and for cultivation of Atlantic salmon. Compared to 1900, deaths due to infectious diseases in the human populations of Europe and North America are now dramatically reduced. Infectious diseases caused approximately half of all deaths in the USA in 1900 but was reduced to less than 10% only a hundred years later (Armstrong et al., 1999). It is a general misconception that this achievement was caused by the introduction of antibiotics (i.e. treatment). Interestingly, the reduction in deaths due to infection was by more than 80% in the USA many years before antibiotics were introduced in 1945 (Armstrong et al., 1999). This important achievement was caused primarily by improved sanitary conditions and the development of vaccines (i.e. prevention).

Similarly, in the production of Atlantic salmon in Norway there was huge problems with furunculosis and Coldwater vibriosis during the period 1987-1992. This resulted in a dramatic increase in the use of antibiotics (Figure 1). The use of antibiotics in the production of salmon, i.e. treatment, peaked at almost 900 grams per ton of salmon produced in 1987, and the total use of antibiotics by the Norwegian salmon aquaculture industry was 49 tons that year. During a 5-year period the use of antibiotics was reduced by a factor 220, to only 4 grams of antibiotics per tons of salmon produced. In 2023 the use was 0.34 g per tons produced, which is a 99.96% reduction in the use of antibiotics in the Norwegian salmon production when compared to the peak year. This success was due to prevention, which most people think was caused by the development of new vaccines. But not only. The development of new types of feed and better hygienic routines also contributed to this success. The two examples above should serve as strong motivation for moving from a treatment to a prevention strategy also in larval rearing, by using microbial management.

In 1993 Vadstein et al. divided methods for microbial management into three groups and suggested different methods for each of them. We have revised this division and added more methods and examples to the three groups, as we find it useful to group the different tools that can be used in aquaculture to manage microbes (Table 3). Below we summarize the scientific status for these three groups and their different methods and try to describe their status and use in the aquaculture industry.

3.4.1 Targeted and non-targeted reduction of microbes

This group of microbial management methods includes the targeted and non-targeted killing of microbes, and the removal of organic matter that can sustain microbial growth. The methods listed in Table 3 vary considerably in terms of how well they are developed for practical use in aquaculture. Disinfection of water and direct removal/reduction of organic matter are well developed and implemented in all modern aquaculture facilities. However, there is room for improvement when it comes to system design and avoidance of organic matter accumulation (e.g. in pipe bends and corners) as this may result in production of toxic hydrogen sulphide. The disinfection of eggs is also a well-developed method for a considerable number of species and conditions (De Swaef et al., 2016), but there is room for improvement. For more advanced methods of organic matter removal, such as the use of biofilters and ultrafiltration, there are only a limited number of studies and all have been done at laboratory (not industrial) scale (e.g. Viadero and Noblet, 2002; Fossmark et al., 2020). We are not aware of any studies on the use of generalist predators with limited selective ability, aimed to increase general mortality in the microbial community in aquaculture systems. There is, however, data on predation rates on bacteria by the commonly used live feed in marine aquaculture – the moderate generalist predators rotifers (Brachionus spp) and Artemia (Vadstein et al., 1993b; Makridis and Vadstein, 1999), and these data suggest that predation can significantly increase the loss rate of bacteria.

Current aquaculture practice has a focus on non-selective reduction of microbes, and in particular removal of organic matter and disinfection of intake water to aquaculture facilities and inside recirculating aquaculture systems (RAS). Removal of organic matter is a good strategy to reduce the probability of bacterial blooms (Fossmark et al., 2020). When we searched Hatchery International, the word “disinfection” returned 48 hits for articles and “organic matter” 30 articles. This indicates a clear interest for these topics in the industry. A Title search in Web of Science using “disinfection AND (aquaculture OR fish OR shrimp)” returned 79 hits, including 5 review papers, and “(organic matter) AND (aquaculture OR fish OR shrimp)” returned 174 hits. Thus, there is considerable interest in these topics, both in the industry and the research community. However, most studies have a practical “engineering” approach with the aim to reduce the quantity of microbes.

One important aim of disinfection is to set up a hygienic barrier from the environment. However, the industry seems to have as a paradigm that the only good bacterium is a dead bacterium, and that good microbial water quality has as low a concentration of bacteria as possible. Therefore, disinfection is used on water entering the rearing tanks. However, the bacterial (re-)growth in rearing tanks can be considerable, especially with disinfection, and in many cases most of the bacteria in the rearing tank are ‘born’ inside the tank (Vadstein et al., 2018a). In systems for the rearing of European lobster larvae (Homarus gammarus), disinfection of the water entering the rearing tank created selection for opportunistic bacteria and resulted in a 20% reduction in the survival of lobster larvae compared to the control treatment (Attramadal et al., 2021). Similar results have later been found for mud crab (Scylla paramamosain), with a 40% reduction in survival caused by UV (Zhu et al., 2026).

In addition to non-targeted approaches for the reduction of microbes in aquaculture systems, targeted approaches have also been proposed. Predatory bacteria (bacteria that feed on other bacteria) are one such approach (Najnine et al., 2020). In particular, BALOs (Bdellovibrio And Like Organisms) have been proposed for this use. However, most research on BALOs in aquaculture has used the type-strain Bdellovibrio bacteriovorus. This species is originally isolated from soil and may not be well adapted to the environment of aquaculture facilities. Recently, new BALO species were isolated from research aquaculture facilities, one housing three-spine stickleback (Gasterosteus aculeatus) and another housing zebrafish (Maher et al., 2026). Such isolates could be useful tools for the targeted reduction of bacteria in aquaculture facilities. The range of bacterial types that these predators can control, i.e. their selectivity, is not well understood. Until recently BALOs have been considered as generalist predators of gram-negative bacteria. This is challenged by recent research (see Ezzedinea et al., 2022). For example, some BALOs can consume gram positive bacteria and even the eukaryotic alga Nannochloropsis salina. Moreover, we now know that the prey selectivity of BALOs range from generalists with a wide variety of prey to specialists who are restricted to a specific type of prey. For example, Maher et al. (2026) describe a BALO with a very narrow prey range. This flexibility in selection of prey makes BALOs a flexible microbial management tool – it could be possible to use them to control specific pathogens, to control wider phylogenetic groups, or to impose a more general mortality on the bacterial community. At NTNU we have observed likely BALOs in aquaculture facilities by 16S amplicon sequencing (Ingrid Bakke pers. com.), but little is known about their function. Searching Web of Science using the expression “(BALO OR Bdellovibrio) AND (aquaculture OR fish OR shrimp)” for Titles returned 9 hits and dated back to 2009. Typically, there is one paper published per year. Search in Hatchery International using “BALO OR Bdellovibrio” returned no hit. The above illustrate that BALOs is a poorly studied approach, but definitely with a potential.

The most targeted approach for the reduction of microbes is the use of bacteriophages, viruses that kill bacteria. Bacteriophages are found in all aquatic environments, including aquaculture systems, and are normally highly selective (i.e. capable of killing only particular bacterial strains or species) (Suttle, 2007; Domingo-Calap and Delgado-Martinez, 2018). Bacteriophages have been successfully used to reduce the abundance of specific microbes in terrestrial agriculture (Villalpando-Aguilar et al., 2022), and in humans (Pires et al., 2020). The use of bacteriophages was a hot topic in human medicine before antibiotics were developed (Salmond and Fineran, 2015). Recently they have gained new interest due to the dramatic increase in antibiotic resistance. The use of bacteriophages has only recently been tested in aquaculture, but is attracting increasing interest (Liu et al., 2022). Some aquaculture studies have shown promising results, i.e. increased survival in shrimp (Karunasagar et al., 2007), Atlantic salmon (Higuera et al., 2013), Artemia (Kalatzis et al., 2016), and a range of other fish species (reviewed by Oliveira et al., 2012). Failure in bacteriophage treatment can have several reasons, but an overlooked effect is how phage treatment indirectly can affect the overall composition of the bacterial community through production of organic growth substrate during lysis of the target organism (Gundersen et al., 2023). Searching Web of Science using the expression “(phage* OR bacteriophage*) AND (aquaculture OR fish OR shrimp)” for Titles returned 157 hits (22 review papers) and with the oldest highly relevant paper published in 2000. Despite the growing interest in using bacteriophages in aquaculture in the scientific community, we found only 4 articles on this topic published in Hatchery International. The only limitation of bacteriophage treatment is that it can only be used against identified problem bacteria for which bacteriophages have been isolated. Moreover, the target microbe can develop defense against a given bacteriophage, but isolation of new and effective phage strains is normally not difficult, and it is possible to use a mixture of bacteriophages. Two bacteriophage products for treating yersiniosis and winter wounds, were launched by ACD Pharma in Norway in 2018. The company Proteon Pharmaceutical has the product BAFADOR on the market, aiming at controlling Aeromonas and Pseudomonas, also for hatchery application. As the products are used to treat the water there is limited restrictions of their use - unlike for animal/human medicine. In conclusion, it appears as phage treatment is slowly making its way to industrial application.

3.4.2 Targeted enhancement of microbes

The second group of microbial management methods includes different ways of selection for desirable bacteria, addition of bacteria directly to the water, or by incorporating desirable bacteria into feed. The methods listed in Table 3 vary considerably in terms of how well they are developed for practical use in aquaculture. The most common but not established method related to selective enhancement is the use of probiotics (beneficial bacteria added to food or water) (see Balcázar et al., 2006; Hoseinifar et al., 2024, and references within). A search in Web of Science returned a list with a total of 794 articles and 107 review articles when using the expression “probiotic* AND (aquaculture OR fish OR shrimp OR larvae)”. The number of review papers related to probiotics alone is higher than the total number of publications related to all other selective enhancement methods (107). Since 2008 more than 15 papers have been published per year (rang16-84). Balcázar et al. (2006) conclude that the use of probiotics “in large part a result of historical and empirical use and not based on scientific criteria”, is consistent with our evaluations.

Only one probiont is approved for aquaculture by the European Union (P. acidilactici CNCM I-4622). It must, however, be noted that approval is not required if a probiont is added directly to the water. Two aspects are striking in the published research. First, selection for probiotics is mainly based on one strategy – search for antagonists toward known pathogens, typically Vibrio species. This is despite the fact that in most cases true pathogens are not detected and that the importance of such antagonistic effects are not documented in vivo. Second, most studies of probiotics include the addition of only one probiont, and this can result in a perturbation of the microbial community and result in a destabilization. This negative side effect is not properly studied.

The effect of probiotics on the viability of larvae varies considerably within and between studies. For example, increase in survival can be from zero, to moderate (3-20%) to high (40-80%). Importantly the variability between replicated rearing tanks and experiments varies almost to the same extent for a given probiont (Hoseinifar et al., 2024). The last is important as it illustrate that at this stage probiotics in aquaculture is not a reliable and reproducible microbial management method. It is also notable that several studies do not report data documenting that the probiont successfully colonized fish or the rearing system. A thorough study with exposure to four probiotic candidates at seven larval stages of Atlantic cod, revealed poor ability to colonize larvae (see Bakke et al., 2019). During the period spanning 2 to 45 days after hatching only one of the four probiotic candidates was able to colonize the larvae in relative densities above 5%. On the day of hatching and 45 days after hatching the colonization success was a bit higher. Normally the probionts were nearly excluded from the larvae 4 days after the administration.

To advance the efficient application of probiotics in larviculture, efforts could focus on attempts to reconcile the many scientific reports on the positive effect of probiotic supplementation with the apparent colonisation resistance noticed in other studies.

There has been some interest in the use of probiotics in the industry, but the knowledge base is not sufficient to guide the industry in their implementation. Hatchery International has 35 articles matching a search on “probiot*”. Thus, also industry-wise probiotics is totally dominating in the interest in microbial management methods. The work involved in growing sufficient amounts of probionts is considerable, and not an area of expertise that fish farmers have. Therefore, the use of probiotics is likely stopped by farmers if the effect is not clearly biologically significant at an early stage of testing.

There are several methods for the selection of desirable bacteria, including microbial maturation, RAS (recirculating aquaculture systems), and prebiotics (organic compounds that can support the growth of specific populations of bacteria). Maturation and RAS are both based on selecting against opportunistic r-strategic bacteria when used properly (Vadstein et al., 2018b). Studies on experimental scales reveal high effect sizes of typically 50 to 100% improvement on variables such as appetite, growth rate, mortality and stress tolerance of fish larvae (reviewed by Vadstein et al., 2018b).

Prebiotics have been tested in aquaculture to a limited extent (Amenyogbe et al., 2020). 81 articles with “prebiotic* AND (aquaculture OR fish OR shrimp)” in the title have been published (Web of Science). Surprisingly, 31 articles are listed as review papers. This indicate that the prospects of using prebiotics in aquaculture represents more than a third of the papers, and that relatively few experiments have been conducted. For agricultural herbivorous animals mostly oligosaccharides have been studied, and it is mostly these compounds that have been tested in aquaculture. It can be questioned how relevant oligosaccharides are for carnivorous aquatic animals, as they have little carbohydrates in their diet and have thus not coevolved with the bacteria selected for by adding oligosaccharides.

Current aquaculture practice has limited focus on enhancement through selection of microbes. This is despite the fact that the species composition of microbes seems to have a bigger impact on the viability of larval stages than the total concentration of microbes. The seabass and seabream hatcheries in France noted that the occurrence of disease and microbial problems declined significantly when rearing technology was changed from traditional flow-through systems to RAS (Jean Paul Blancheton, pers. comm.). Other people in and connected to the industry have made the same observation and include increased robustness of the fish as a key difference (Joana Sapo and Peter Sorgeloos, pers. comm.). However, no real attempts have been made to clarify the reason for these improvements – e.g. lower probability of introducing detrimental bacteria to the system because the amount of intake of water is dramatically reduced, that bacteria in the biofilters consume most of the organic matter produced under conditions that selected against detrimental bacteria (K-selection), etc. Moreover, the beneficial effects of a RAS system might be lying in the fact that the variable “ratio of organic input in the system versus the microbial biomass in the system” is being stabilized in space and time. Even though the mechanisms are not clear, the observations are a strong indicator of the importance of the rearing technology for handling microbial problems. It is interesting to notice that despite the well documented positive effects of mature water and RAS in larval rearing at laboratory scale, there has been no attempts to validate under which conditions K-selection works to improve larval survival at an industrial scale. The use of prebiotics has attracted little interest in the industry, indicated by the fact that only 5 articles were found in Hatchery International when searching for titles containing “prebiot*”.

3.4.3 Stimulation of the immune system

The third group of microbial management methods is improvement of the resistance against microbes by stimulation of the immune system (Table 3). Vaccination is the most common method of immunostimulation in aquaculture. This is supported by a search in Web of Science using “vaccine AND (aquaculture OR fish OR shrimp)” which returned 346 hits, including 52 review articles. Moreover, Hatchery International returned 69 hits when using the term “vaccine*”. It is important to remember that traditional vaccination is not relevant for invertebrates, as they only have innate immunity. Vaccination has two inherent requirements – that the specific immune system is fully developed and that a specific problem bacterium has been identified. In general the first requirement is not met for larval stages, as the acquired immune system is either missing or not fully mature before metamorphosis (Vadstein et al., 2013). Moreover, for many species that we try to cultivate we are in most cases not able to identify specific pathogens. In such situations vaccination is not a possible microbial management method. However, in cases where specific problem bacteria have been identified it is possible to vaccinate the female broodstock, and this will result in transfer of a limited amount of specific immunoglobulins to the eggs. It has been shown that this approach results in parental transfer of immunoglobulins, but also several innate immune factors can be transferred maternally (reviewed by Vadstein, 1997; Zhang et al., 2013). The pioneering study by Sin et al. (1994) illustrates the potential. They found that immunization of mothers increased the protection against a pathogenic protozoa with a relative protection during challenge of 78 to 98%, depending on conditions. Even though few studies have investigated this proposed microbial management tool in aquaculture, there are an increasing number of studies on transgenerational immune priming (Roth et al., 2018; Ma and Cain, 2025). These studies show an increased expression of immune variables in larval fish upon challenge to the same pathogen to which the parent had been exposed. A more general protective effect in larval fish can be expected by the transfer of maternal complement compounds, cytokine and antimicrobial proteins (Ma and Cain, 2025). Another novel method is trained immunity, the phenomenon that an exposure to glucan or pathogen associated molecular patterns might result in long term memory in innate immunity cells, with an increase in immunological response to a homologous or heterologous compounds (You et al., 2024). Such stimulation by e.g. probiotics, needs to be studied in greater detail using novel tools and proper sampling protocols (see Panteli et al., 2020).

Stimulation of the general immune system is what has attracted most attention in cultivation of larvae. In total 56 papers and 8 review papers are published on the topic (Web of Science, Title search “(immunostimulation OR immunomodulation OR (train* AND immuni*)) AND (aquaculture OR fish OR shrimp)”). The first studies were published in the mid 80ies, and a considerable number of immunostimulants have been tested on a variety of species and under different experimental conditions (Vadstein, 1997; Rojo-Cebreros et al., 2018). For invertebrates immune priming can be done by exposing the innate immune system to sub-lethal concentrations of pathogens or non-pathogenic microbes. This “primes” their immune cells and give faster defense during future exposure to real pathogens (Wang et al., 2025). Positive responses are documented in a large range of response variables, including activation of the immune system, increased tolerance to stress, protection against pathogens during challenge, and reduced mortality. Recently it has been shown that administration of the immunostimulant β-glucan also can have a large positive impact on the composition of the bacterial community in the rearing system, through a reduction in opportunistic species (Bandara et al., 2026). This is until now an unknown side effect.

Current aquaculture practice has little focus on methods for improvement of the general resistance of aquaculture species to detrimental microbes, except for vaccination and various attempts to improve fish health (e.g. hygiene and nutrition). Whereas a search on “vaccine” in Hatchery International returned 69 hits, “immunostimu* OR immunomodu*” returned only 9 hits.

There are several ways that nutrition can stimulate the immunity and general health of animals. Such compounds can stimulate the immunity directly (e.g. vitamin C) or indirectly through improvement of epithelium health (e.g. poly-hydroxybutyrate) (Dawood et al., 2018). For larval stages the requirements of various nutritional factors are poorly characterized, maybe except for fatty acids. Therefore the relationship between nutrients and immune status is not a research field for larvae. We do not dare to make statements on the effect of nutrients on host/microbe interaction mediated through the immune system, but this can be an interesting area for research.

3.4.4 Overall status of microbial management methods

The overview provided above reveals that research has contributed to the development and industrialization of microbial management approaches in the aquaculture industry. However, the step from experimental studies to pilot scale studies has been and still is a bottleneck. The reasons for this can be many and is a challenge both for the research community and for the industry. Communication between the problem owners (the industry) and the problem solvers (the research community) is likely the Achilles heel. Moreover, the development of the industry from a dominance of many small companies that were doomed to “collaborate or vanish” to large companies with their own R&D department and a “we know something that the others don’t” attitude can be counter-productive at the industrial level. For further development a first step is to have a joint understanding of the current situation, including problems experienced in the industry and countermeasures tested at laboratory scale. Moreover, the industry should try to identify areas that are pre-competitive, meaning that the new knowledge is not related to patents, but may serve as the basic stepping stone for development of new solutions. Such an exercise will provide a shared understanding of possible directions for how to solve problems and will identify fundamental knowledge gaps.

An evident conclusion emerging from the above overview of microbial management methods is the strong bias toward decimation of microbes by for example disinfection, and on probiotics. For these two topics a holistic approach is often missing. Two examples are that the negative consequences of disinfection due to regrowth of bacteria is normally overlooked (see above), and that the screening for probiotic candidates has a strong bias toward screening for bacteria with antagonism toward known pathogens even though obligate pathogens are often not detected. Little has happened with respect to these problems during the 10 years since De Schryver and Vadstein (2014) concluded that the “current low richness and evenness in research hampers the progress” in microbial management.

4 Conclusions, research strategy and future prospects

The conclusions from our analysis of the current status of host/microbe interactions and microbial management in larval rearing can be summarized in the following five bullet points:

• Detrimental host/microbe interactions are a main reason for the poor performance and lack of reproducibility in larval rearing. Many studies and different approaches support this.

• The composition of the microbiota of larvae is determined by both selection and stochastic processes, and this puts constraints on possibilities for steering of the larval microbiota. Different approaches must be used to consider selection and stochastic driven processes.

• It is not the species composition, but which functions the microbiota provide which is important for the viability of the larvae. These functions are hard to quantify, and we have limited knowledge.

• Microbial management in larval rearing is a prerequisite for sustainable development of aquaculture and to steer away from the high use of antibiotics. Sustainability is related to animal welfare, economy, environmental issues including use of chemicals and antibiotics, and the general image the industry has in the public.

• Many methods for microbial management have been proposed, but few are well studied - especially with respect to mechanisms and functionality. Moreover, there is a strong bias in terms of which tools that are studied, the work so far is too fragmented, and too much is based on trial and error in the industry.

These conclusions should serve as a scientific basis for developing a knowledge-based research strategy for microbial management in larval rearing as a basis for establishing sustainable development in larval rearing. It is important to remember that for most species of fish and shellfish the larval stage is a bottleneck in the production, and consequently we need to develop microbial management methods.

In discussions within the scientific community and with the industry, two of us (OV and PB) have experienced a tendency for proposing “The Solution”, meaning the one thing that can solve the problem. However, complex problems require complex solutions. To solve the detrimental larvae/microbe problem is a question about changing probabilities, and therefore we should not rely on one countermeasure only. Philosophically we should learn from best practice in drinking water supply, where multiple barriers are used to reduce the probability of supplying the public with harmful drinking water. A consequence of this is that several different types of microbial management methods should be included in the future strategy, as several similar methods will not give the same robustness.

What we have experienced during the last 50 years of larval rearing in aquaculture, is that single companies and research units have not enabled us to progress in a way that secures efficient and stable production of metamorphosed fish and shellfish. For some species there has been tremendous progress, but normally the knowledge cannot be transformed 100% to other research facilities and other species. Remember our statement from section two that “as long as survival is below 80-90% the rearing protocol is suboptimal”.

Based on the above we state that nobody can efficiently solve the microbial management problem alone, so this problem calls for a concerted action. For companies it may seem a non-viable strategy to share knowledge among competitors. To this we state that the knowledge most urgently needed is pre-competitive - it is the knowledge needed as a fundament to make solutions. Examples are; what is critical for securing that mutualistic bacteria colonize the larvae and what make them colonize for a prolonged time, which processes in a RAS are critical for securing a healthy microbiota in the rearing tanks, and which probiotic characteristics are most important for maintaining a healthy gut microbiota and avoiding invasion by detrimental bacteria.

A consequence of our reasoning and arguments above is that our suggestion for a concerted action should include participants from the industry, the research community, and national and international funding agencies. The research should be a joint venture between industry and funding agencies, and the quality of the research should be secured through active and coordinated leadership by profiled scientists. Moreover, motivated scientists from relevant basic disciplines should be included in the research. The first step in a concerted action would be to establish a joint understanding of the problem and to identify elements and methods in a future microbial management. The research should be more diverse than now, as complex problems need complex solutions. An example of successful joint research is the breeding program for Atlantic salmon in Norway that has been ongoing for several decades. Through a joint action the improvements in the genetic characteristics that improve growth and disease resistance have been progressing rapidly, and to the benefit of all farmers.

As concluded above, in larval rearing too much of the R&D in the industry and within the research community, has focused on solving practical problems. The consequence is that when solutions are found in the industry there is not necessarily an understanding of why it works, and when the facilities are rebuilt, the problem may reappear. Similarly, a research group can find a probiont that has a clear positive effect on performance of larvae, but without knowing the mechanism behind. So, when the probiont loses its effect due genetic selection, it is back to square one. The alternative is to use a scientific, knowledge-based approach that results in generic and system independent knowledge. This is the only way to build a solid knowledge base for the industry. As mentioned above, such knowledge is pre-competitive, as it serves as the knowledge base for making solutions. The aquaculture feed companies have successfully followed such a strategy.

A viable industry in the 21st century must consider environmental consequences of their activity and must be proactive. In general, larval rearing has limited feed induced environmental consequences as the total use of feed is low. Hence the probability for eutrophication and saprobiation is low in most cases. However, there is a considerable use of chemicals, of which disinfectants and antibiotics have the largest consequences. Good microbial management will dramatically reduce the use of antibiotics (Vadstein et al., 2018b) and we should aim for a ban of prophylactic use of antibiotics. Moreover, animals with a good start in life have shown to be more robust to a large range of illnesses later in life. Microbial management in larval rearing thus contributes to animal welfare throughout the life cycle and reduces the likeliness of disease and spread of pathogens. Finally, we should aim for international regulatory rules that stimulates sustainable development and consider cost-effectiveness in the development of a microbial management strategy. We hope it is evident from our synthesis of knowledge and the proposed strategy for future research given above, that establishing the knowledge needed for the development of a microbial management strategy is an urgent need for the aquaculture industry.

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