Effects of Salinity and Immobilization Period on the Nitrification and Denitrification Co-processes during Biofilter Acclimation in a Marine Recirculating Aquaculture System

Abstract

Biological filtration plays an important role in a sustainable recirculating aquaculture system. To provide the appropriate conditions for biofilter acclimation, the effects of the salinity and acclimation period on nitrogen removal and microbial diversity were evaluated. Nitrification rate (NR) of the shrimp tank biofilter increased during the first 4 weeks and decreased thereafter. The highest NR was found in the 5 PSU salinity tank at week 2, whereas in the other salinities (15 and 25 PSU) the highest NR was observed at week 4. Meanwhile, the denitrification rate (DNR) increased significantly on week 8 and the highest DNRs were obtained after switching from an aerobic to an anoxic condition with methanol supplement. Under this anoxic condition the biofilter acclimated in seawater had the highest DNR. Changes in the microbial community during immobilization were monitored using Illumina MiSeq DNA sequencing. Proteobacteria and Bacteriodetes were the most abundant phyla found in this study. For nitrifiers, Nitrosomonadaceae were found from the first week of acclimation, while only one operational taxonomic unit (OTU) of Nitrospiraceae was observed. Under the anoxic condition at the end of the shrimp culture, two OTUs of Nitrospiraceae were found in both the 15 and 25 PSU tanks.

Prokaryotic diversity in marine and freshwater recirculating aquaculture systems

“…In the case of marine/brackish RAS biofilters, studies have demonstrated the common occurrence of prevalent aerobic or facultatively anaerobic chemoorganotrophic genera such as Arenibacter , 67,88 Colwellia , 58,72 Gaetbulibacter , 54,72 Pseudomonas , 67,72,89 Pseudoalteromonas , 8,54,58,90 Vibrio , 21,54,57,58,67,89,91 Photobacterium 54 and Planctomyces 45,72 . Furthermore, there have been reports on the prevalence of the methylotrophic genus Methylotenera , 2,88 and the heterotrophic sulphur oxidizing genus Sulfitobacter 67 . Regarding the nitrifying community, the main ammonium oxidizers are Nitrosomonas , 2,5,19,44,45,62,68,72,86,89,92 Nitrosospira 31,86,89 and Nitrosopumilus , 19,44 while the prominent nitrite oxidizing genera are Nitrospira 45,62,67,72,86,88,89,93 which also includes comammox species, and to a lesser extend ‘ Candidatus Nitrotoga’, 5,31,86 Nitrospina 62,72,76 and Nitrobacter 5,44 …”

“…Furthermore, there have been reports on the prevalence of the methylotrophic genus Methylotenera , 2,88 and the heterotrophic sulphur oxidizing genus Sulfitobacter 67 . Regarding the nitrifying community, the main ammonium oxidizers are Nitrosomonas , 2,5,19,44,45,62,68,72,86,89,92 Nitrosospira 31,86,89 and Nitrosopumilus , 19,44 while the prominent nitrite oxidizing genera are Nitrospira 45,62,67,72,86,88,89,93 which also includes comammox species, and to a lesser extend ‘ Candidatus Nitrotoga’, 5,31,86 Nitrospina 62,72,76 and Nitrobacter 5,44 …”

“…While heterotrophic nitrification is a slower process compared with autotrophic nitrification, it is possible that it could overall surpass the latter when considering the widespread distribution of heterotrophs in RAS compartments, and their possible higher abundance or growth rates compared with autotrophic nitrifiers 99 . Comparison of nitrification rates in similar biofilters operating at different salinity levels (5, 15 and 25 PSU) in RAS rearing whiteleg shrimp has revealed higher nitrification rates at lower salinities 88 . Meanwhile, it has been reported that nitrifying biofilms form faster on biofilters operating in brackish water compared with seawater, and that these brackish water biofilter communities can achieve complete nitrification at a similar pace as freshwater biofilters, albeit with lower community diversity and different composition 5 .…”

“…9,31,86 Nitrospira is the only commonly identified genus capable of nitrite oxidation or comammox, 7,10,12,31,45,52,53,[84][85][86][87] while 'Candidatus Nitrotoga' is another nitrite oxidizer identified in freshwater RAS. 5,31,86 In the case of marine/brackish RAS biofilters, studies have demonstrated the common occurrence of prevalent aerobic or facultatively anaerobic chemoorganotrophic genera such as Arenibacter, 67,88 Colwellia, 58,72 Gaetbulibacter, 54,72 Pseudomonas, 67,72,89 Pseudoalteromonas, 8,54,58,90 Vibrio, 21,54,57,58,67,89,91 Photobacterium 54 and Planctomyces. 45,72 Furthermore, there have been reports on the prevalence of the methylotrophic genus Methylotenera, 2,88 and the heterotrophic sulphur oxidizing genus Sulfitobacter.…”

“…45,72 Furthermore, there have been reports on the prevalence of the methylotrophic genus Methylotenera, 2,88 and the heterotrophic sulphur oxidizing genus Sulfitobacter. 67 Regarding the nitrifying community, the main ammonium oxidizers are Nitrosomonas, 2,5,19,44,45,62,68,72,86,89,92 Nitrosospira 31,86,89 and Nitrosopumilus, 19,44 while the prominent nitrite oxidizing genera are Nitrospira 45,62,67,72,86,88,89,93 which also includes comammox species, and to a lesser extend 'Candidatus Nitrotoga', 5,31,86 Nitrospina 62,72,76 and Nitrobacter. 5,44 Furthermore, a comparison 21 between bacterial community composition of a commercial biofilter inoculant to the communities that were established on marine RAS nitrification and denitrification biofilters that had utilized the inoculant and then were exposed to ambient sea water, reported that about half of the total OTUs which were identified in the samples were also present in the inoculum.…”