Microorganisms represent by far the most abundant life form in all aquaculture systems. Understanding the role of the aquaculture microbiome in disease demands analytical methods that enable the measurement of all microbes, and that can provide a temporally resolved view of the microbiome. Unfortunately, our knowledge on the aquaculture microbiome has largely been derived from cultivation-based methods which detect only a small fraction of the microbiome (e.g. < 0.1 - 1 %). High-resolution monitoring campaigns that unveil the structure, interactions and dynamics of the microbes in these systems are scarce, yet, they are the key to furthering our understanding of the role of the microbiome in disease outbreaks.
Here, we developed and tested a novel microbial fingerprinting technique based on flow cytometry that takes into account all bacterial cells and is both rapid (i.e. < 30 min) and reproducible (i.e. CV < 5%). We tested this method in an experimental set-up of replicate rearing tanks of shrimp (L. vannamei) throughout the nauplii (N5) and postlarvae (PL10) development phases. At a sampling frequency of two times per day, we observed strong tank- and development-phase dependent dynamics in microbial load and fingerprint. The microbial load increased by almost 1.5 log10 fold changes during the Z1 - Z3 development stages and reached a maximum of approximately 5e7 cells mL-1 at the M1-M3 development phases. Several tanks also showed sudden reductions in microbial load during the transition from mysis to the postlarvae stages. These changes in microbial load were accompanied by significant changes in microbial fingerprint during developmental transitions highlighting that both the physiological and taxonomic properties of the microbial community were under constant change during the shrimp development. Our findings grant additional insights into how the microbiome responds to animal development and aquaculture practices.