Bacterial community analysis of marine recirculating aquaculture system bioreactors for complete nitrogen removal established from a commercial inoculum

Diversity, community structure, and abundance of nirS-type denitrifying bacteria on suspended particulate matter in coastal high-altitude aquaculture pond water

Denitrifying bacteria harboring the nitrate reductase S (nirS) gene convert active nitrogen into molecular nitrogen, and alleviate eutrophication in aquaculture water. Suspended particulate matter (SPM) is an important component of aquaculture water and a carrier for denitrification. SPM with different particle sizes were collected from a coastal high-altitude aquaculture pond in Maoming City, China. Diversity, community structure, abundance of nirS-type denitrifying bacteria on SPM and environmental influencing factors were studied using high-throughput sequencing, fluorescence quantitative PCR, and statistical analysis. Pseudomonas, Halomonas, and Wenzhouxiangella were the dominant genera of nirS-type denitrifying bacteria on SPM from the ponds. Network analysis revealed Pseudomonas and Halomonas as the key genera involved in the interaction of nirS-type denitrifying bacteria on SPM in the ponds. qPCR indicated a trend toward greater nirS gene abundance in progressively larger SPM. Dissolved oxygen, pH, temperature, and SPM particle size were the main environmental factors influencing changes in the nirS-type denitrifying bacterial community on SPM in coastal high-altitude aquaculture pond water. These findings increase our understanding of the microbiology of nitrogen cycle processes in aquaculture ecosystem, and will help optimize aquatic tailwater treatment strategies.

Characterization of simultaneous ammonium and nitrate removal and microbial communities in airlift reactor using 3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) as carbon source and biofilm carrier

As a novel trend, solid carbon sources are applied to act as electron donors and biofilm carrier in biological denitrification process. In this study, simultaneous nitrate and ammonium removal process in an airlift sequencing batch reactor using 3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) as carbon source and biofilm carrier under intermittent aeration conditions was established to treat effluent of synthetic marine recirculating aquaculture system. The results showed that maximum nitrate and ammonia nitrogen removal rates of 0.45 and 0.09 kg m-3 d-1 were achieved. No significant nitrite accumulation was found during 200-day operation, while effluent dissolved organic carbon accumulation and particle size reduction significantly increased. Microbial community analysis and batch tests illuminate that the generated sludge and attached biofilm played important roles in nitrogen removal. This study demonstrates the potential mechanism for the nitrogen removal process mediated by 3-hydroxybutyrate-co-3-hydroxyvalerate and provide a new idea for the alternative solutions of solid carbon sources.

The Assembly Process of Free-Living and Particle-Attached Bacterial Communities in Shrimp-Rearing Waters: The Overwhelming Influence of Nutrient Factors Relative to Microalgal Inoculation

The ecological functions of bacterial communities vary between particle-attached (PA) lifestyles and free-living (FL) lifestyles, and separately exploring their community assembly helps to elucidate the microecological mechanisms of shrimp rearing. Microalgal inoculation and nutrient enrichment during shrimp rearing are two important driving factors that affect rearing-water bacterial communities, but their relative contributions to the bacterial community assembly have not been evaluated. Here, we inoculated two microalgae, Nannochloropsis oculata and Thalassiosira weissflogii, into shrimp-rearing waters to investigate the distinct effects of various environmental factors on PA and FL bacterial communities. Our study showed that the composition and representative bacteria of different microalgal treatments were significantly different between the PA and FL bacterial communities. Regression analyses and Mantel tests revealed that nutrients were vital factors that constrained the diversity, structure, and co-occurrence patterns of both the PA and FL bacterial communities. Partial least squares path modeling (PLS-PM) analysis indicated that microalgae could directly or indirectly affect the PA bacterial community through nutrient interactions. Moreover, a significant interaction was detected between PA and FL bacterial communities. Our study reveals the unequal effects of microalgae and nutrients on bacterial community assembly and helps explore microbial community assembly in shrimp-rearing ecosystems.

Removal of organic and inorganic contaminants from the air, soil, and water by algae

Rapid increases in human populations and development has led to a significant exploitation of natural resources around the world. On the other hand, humans have come to terms with the consequences of their past mistakes and started to address current and future resource utilization challenges. Today's primary challenge is figuring out and implementing eco-friendly, inexpensive, and innovative solutions for conservation issues such as environmental pollution, carbon neutrality, and manufacturing effluent/wastewater treatment, along with xenobiotic contamination of the natural ecosystem. One of the most promising approaches to reduce the environmental contamination load is the utilization of algae for bioremediation. Owing to their significant biosorption capacity to deactivate hazardous chemicals, macro-/microalgae are among the primary microorganisms that can be utilized for phytoremediation as a safe method for curtailing environmental pollution. In recent years, the use of algae to overcome environmental problems has advanced technologically, such as through synthetic biology and high-throughput phenomics, which is increasing the likelihood of attaining sustainability. As the research progresses, there is a promise for a greener future and the preservation of healthy ecosystems by using algae. They might act as a valuable tool in creating new products.

Comparision of nitrogen removal characteristic and microbial community in freshwater and marine recirculating aquaculture systems

Recirculating aquaculture system (RAS) has a good prospect in aquaculture, but its nitrogen removal characteristics and microbial community changes in freshwater and marine water remain unclear. In this study, six RAS were designed and divided into freshwater group and marine water group with salinity of 0‰ and 32‰, respectively, and operated for 54 days to test changes in nitrogen (NH₄⁺-N, NO₂^--N, NO₃^--N), extracellular polymeric substances and microbial communities. The results showed that ammonia nitrogen was rapidly reduced and almost converted to nitrate nitrogen in the freshwater RAS but to nitrite nitrogen in marine RAS. Compared with freshwater RAS, marine RAS had lower tightly bound extracellular polymeric substances and worse stability and settleability condition. 16S rRNA amplicon sequencing reflected significantly lower bacterial diversity and richness in marine RAS. Microbial community structure at phylum level showed lower relative abundance of Proteobacteria, Actinobacteria, Firmicutes, Nitrospirae, but higher abundance of Bacteroidetes under a salinity of 32‰. High salinity decreased the abundance of funtional genera (Nitrosospira, Nitrospira, Pseudomonas, Rhodococcus, Comamonas, Acidovorax, f_Comamonadaceae), which may account for nitrite accumulation and low nitrogen removal capacity in marine RAS. These findings could provide theoretical and practical basis for improving the start-up speed of high-salinity nitrification biofilm.

Candidatus Scalindua, a Biological Solution to Treat Saline Recirculating Aquaculture System Wastewater

Recirculating aquaculture systems (RAS) are promising candidates for the sustainable development of the aquaculture industry. A current limitation of RAS is the production and potential accumulation of nitrogenous wastes, ammonium (NH4+), nitrite (NO2−) and nitrate (NO3−), which could affect fish health and welfare. In a previous experiment, we have demonstrated that the marine anammox bacteria Candidatus Scalindua was a promising candidate to treat the wastewater (WW) of marine, cold-water RAS. However, the activity of the bacteria was negatively impacted after a direct exposure to RAS WW. In the current study, we have further investigated the potential of Ca. Scalindua to treat marine RAS WW in a three-phase experiment. In the first phase (control, 83 days), Ca. Scalindua was fed a synthetic feed, enriched in NH4+, NO2− and trace element (TE) mix. Removal rates of 98.9% and 99.6% for NH4+ and NO2−, respectively, were achieved. In the second phase (116 days), we gradually increased the exposure of Ca. Scalindua to nitrogen-enriched RAS WW over a period of about 80 days. In the last phase (79 days), we investigated the needs of TE supplementation for the Ca. Scalindua after they were fully acclimated to 100% RAS WW. Our results show that the gradual exposure of Ca. Scalindua resulted in a successful acclimation to 100% RAS WW, with maintained high removal rates of both NH4+ and NO2− throughout the experiment. Despite a slight decrease in relative abundance (from 21.4% to 16.7%), Ca. Scalindua remained the dominant species in the granules throughout the whole experiment. We conclude that Ca. Scalindua can be successfully used to treat marine RAS WW, without the addition of TE, once given enough time to acclimate to its new substrate. Future studies need to determine the specific needs for optimal RAS WW treatment by Ca. Scalindua at pilot scale.

From Aquaculture to Aquaculture: Production of the Fish Feed Additive Astaxanthin by Corynebacterium glutamicum Using Aquaculture Sidestream

Circular economy holds great potential to minimize the use of finite resources, and reduce waste formation by the creation of closed-loop systems. This also pertains to the utilization of sidestreams in large-scale biotechnological processes. A flexible feedstock concept has been established for the industrially relevant Corynebacterium glutamicum, which naturally synthesizes the yellow C50 carotenoid decaprenoxanthin. In this study, we aimed to use a preprocessed aquaculture sidestream for production of carotenoids, including the fish feed ingredient astaxanthin by C. glutamicum. The addition of a preprocessed aquaculture sidestream to the culture medium did not inhibit growth, obviated the need for addition of several components of the mineral salt's medium, and notably enhanced production of astaxanthin by an engineered C. glutamicum producer strain. Improved astaxanthin production was scaled to 2 L bioreactor fermentations. This strategy to improve astaxanthin production was shown to be transferable to production of several native and non-native carotenoids. Thus, this study provides a proof-of-principle for improving carotenoid production by C. glutamicum upon supplementation of a preprocessed aquaculture sidestream. Moreover, in the case of astaxanthin production it may be a potential component of a circular economy in aquaculture.

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

BACKGROUND

Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems.

RESULTS

We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria.

CONCLUSION

The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.

Enriched microbial communities for ammonium and nitrite removal from recirculating aquaculture systems

The aim of this study was the enrichment of high-performance microbial communities in biofilters for removal of ammonium and nitrite from aquaculture water. Ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) were enriched from different environmental water samples. The microbial communities with higher ammonium and nitrite removal activity were selected and adapted to different temperatures [9 °C, 15 °C, room temperature (25 °C), and 30 °C]. The expression of genes involved in nitrification including ammonia monooxygenase (AMO) and nitrite oxidoreductase (NXR) were measured in temperature-adapted AOB and NOB microbiomes. The microbial species present in the selected microbiomes were identified via 16s rRNA sequencing. The microbial communities containing Nitrosomonas oligotropha and Nitrobacter winogradskyi showed the highest ammonium and nitrite removal activity at all temperatures used for adaptation. Furthermore, the microbial communities do not contain any pathogenic bacteria. They also exhibited the highest expression of AMO and NXR genes. Using the enriched microbial communities, we achieved a 288% and 181% improvement in ammonium and nitrite removal over the commonly used communities in biofilters at 9 °C, respectively. These results suggest that the selected microbiomes allowed for a significant improvement of water quality in a recirculating aquaculture system (RAS).

Enhanced mainstream nitrogen removal from synthetic wastewater using gel-immobilized anammox in fluidized bed bioreactors: Process performance and disintegration mechanisms

Anammox retention, which is crucial for successful nitrogen removal because of slow growth, is still a major challenge. Fixed film processes or gel-immobilization techniques can minimize biomass washout. However, the detachment mechanisms from gel-immobilized beads are still unclear. Despite the widely known advantages of fluidized bed reactor (FBR) with respect to biomass retention, the technology has not been investigated for anammox processes, and thus, the current study evaluated the feasibility of using immobilized anammox gel beads as a carrier media in anammox fluidized bed reactor (AFBR), with a particular focus on understanding detachment mechanisms. The study optimized the packing ratio in AFBR and compared holed and non-holed beads. The optimum packing ratio (on a volumetric basis) was 30% (v/v) with a nitrogen removal rate (NRR) of 0.40 kg N/m³-d at a volumetric nitrogen loading rate (NLR) of 0.51 kg N/m³-d. Biomass detachment rates increased linearly with specific anammox activity (SAA). The fluidized bed reactor employing holed (more porous) anammox gel beads (HFBR) exhibited 20% lower biomass detachment rates than the non-holed fluidized bed reactor (NHFBR). Moreover, the HFBR achieved a maximum NRR of 0.81 kg N/m³-d at NLR of 1.01 kg N/m³-d after 35 days without operational problems, whereas the NHFBR with non-holed anammox gel beads failed after 30 days. The hindrance to diffusion of the generated nitrogen gas was the main mechanism of beads breakup and biomass washout, and thus, the sustainability of the beads hinges on increased external porosity. Therefore, developing microporous gel beads is critical for achieving a high rate stable anammox process that overcomes the limitations of the current technologies.

Microbial Electrochemical Technologies for Sustainable Nitrogen Removal in Marine and Coastal Environments

For many years, the world's coastal marine ecosystems have received industrial waste with high nitrogen concentrations, generating the eutrophication of these ecosystems. Different physicochemical-biological technologies have been developed to remove the nitrogen present in wastewater. However, conventional technologies have high operating costs and excessive production of brines or sludge which compromise the sustainability of the treatment. Microbial electrochemical technologies (METs) have begun to gain attention due to their cost-efficiency in removing nitrogen and organic matter using the metabolic capacity of microorganisms. This article combines a critical review of the environmental problems associated with the discharge of the excess nitrogen and the biological processes involved in its biogeochemical cycle; with a comparative analysis of conventional treatment technologies and METs especially designed for nitrogen removal. Finally, current METs limitations and perspectives as a sustainable nitrogen treatment alternative and efficient microbial enrichment techniques are included.

Ni-Fe oxide-PEDOT modified anode coupled with BAF treating ammonia and nitrite in recirculating seawater of aquaculture system

Efficient ammonia and nitrite removal in low nutrient recirculating seawater of recirculating aquaculture system (RAS) is critical for healthy cultivation. However, it is hard for conventional biological aerated filters (BAFs) to meet this demand under short hydraulic retention time (HRT). The electrooxidation-BAFs (E-BAFs) were constructed for efficient seawater treatment in a RAS of Sebastes schlegelii, with high activity anodic catalyst Ni-Fe oxide-PEDOT. Satisfactory ammonia removal (88.2% in E-BAFs, 33.7% higher than the control, stage 3) and nitrite removal (69.9 % in E-BAFs, 45.3% in the control) were achieved at HRT of 50 min. The proportion of nitrifying bacteria (Nitrospira, Nitrosomonas and Nitrosopumilus) and nitrification/denitrification genes (amoCAB, nxrAB, narGHI, et. al) were higher in E-BAFs than the control, suggesting better potential in functional bacteria enrichment. Aerobic colony number in RAS with E-BAFs was lower and specific growth rate (SGR) of Sebastes schlegelii (3.79%) was significantly higher, indicating a better culture effect.

Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration

BACKGROUND

Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. Commercial RAS must be allowed to equilibrate following installation, before fish can be introduced. There is little information available regarding the bacterial community structure in commercial zebrafish housing systems, or the time-point at which the system or biofilter reaches a microbiological equilibrium in RAS in general.

METHODS

A zebrafish housing system was monitored at multiple different system sites including tank water in six different tanks, pre- and post-particulate filter water, the fluidized bed biofilter substrate, post-carbon filter water, and water leaving the ultra-violet (UV) disinfection unit and entering the tanks. All of these samples were collected in quadruplicate, from prior to population of the system with zebrafish through 18 weeks post-population, and analyzed using both 16S rRNA amplicon sequencing and culture using multiple agars and annotation of isolates via matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. Sequencing data were analyzed using traditional methods, network analyses of longitudinal data, and integration of culture and sequence data.

RESULTS

The water microbiome, dominated by Cutibacterium and Staphylococcus spp., reached a relatively stable richness and composition by approximately three to four weeks post-population, but continued to evolve in composition throughout the study duration. The microbiomes of the fluidized bed biofilter and water leaving the UV disinfection unit were distinct from water at all other sites. Core taxa detected using molecular methods comprised 36 amplicon sequence variants, 15 of which represented Proteobacteria including multiple members of the families Burkholderiaceae and Sphingomonadaceae. Culture-based screening yielded 36 distinct isolates, and showed moderate agreement with sequencing data.

CONCLUSIONS

The microbiome of commercial RAS used for research zebrafish reaches a relatively stable state by four weeks post-population and would be expected to be suitable for experimental use following that time-point.

Bacterial community compositions and nitrogen metabolism function in a cattle farm wastewater treatment plant revealed by Illumina high-throughput sequencing

Bacteria play an important role in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). Exploring the microbial community structure and diversity is essential to improving the performance of wastewater treatment processes. This study employed Illumina MiSeq high-throughput sequencing to investigate the microbial community composition and diversity in a cattle farm wastewater treatment plant (Cf-WWTP). The results showed that the dominant phyla in the whole process were Proteobacteria, Bacteroidetes, and Firmicutes. The principal coordinate analysis (PCoA) indicated that the different stages had a significant impact on the microbial community structure; Bacteroidetes was the dominant phylum in the anearobic stage and Proteobacteria was the dominant phylum in the anoxic-oxic stage. Redundancy analysis (RDA) revealed that total phosphorus (TP) was the most significant factor that regulated the microbial community composition, followed by chemical oxygen demand (COD), total nitrogen (TN), and pH. Proteobacteria, Patescibacteria, and Chloroflexi were simultaneously negatively correlated with TN, COD, and TP. Nitrogen metabolic pathway and transformation mechanism was elucidated by a complete denitrification function predicted with phylogenetic investigation of communities with reconstruction of unobserved states (PICRUSt), as well as detection of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). These results provide new insights into our understanding of microbial community and metabolic functions of Cf-WWTP.

Dynamics of Microbial Community During Nitrification Biofilter Acclimation with Low and High Ammonia

The acclimation of a nitrifying biofilter is a crucial and time-consuming task for setting up a recirculating aquaculture system (RAS). Gaining a better understanding of the dynamics of the microbial community during the acclimation period in the system could be useful for the development of mature nitrifying biofilters. In this study, high-throughput DNA sequencing was applied to monitor the microbial communities on a biofilter during the acclimation period (7 weeks) in high (100 mg N/L) and low (5 mg N/L) total ammonia nitrogen (TAN) treatments. Both treatments were successful for developing a mature nitrifying biofilter, dominated by Proteobacteria, Bacteroidetes, and Nitrospirae. Complete nitrification was found after 7 days of biofilter acclimation as indicated by decreasing TAN concentration, increasing nitrate concentration, and high abundances of the nitrifying bacteria, Nitrosomonadaceae and Nitrospiraceae. The beta diversity analysis of microbial communities showed different clustering of the samples between high and low TAN treatment groups. A greater abundance of nitrifying bacteria was found in the high TAN treatments (27-51%) than in the low TAN treatment (15-29%). The bacterial diversity in biofilters acclimated at high TAN concentration (Shannon's index 5.40-6.15) were lower than those found at low TAN treatment levels (Shannon's index 6.40-7.01). The higher diversity in biofilters acclimated at low TAN concentrations, consisting of Planctomycetes and Archaea, might benefit the nutrient recycling in the system. Although nitrification activity was observed from the first week of the acclimation period, the acclimation period should be taken as at least 6 weeks for full development of nitrifying biofilm. Moreover, the reduction of potentially pathogenic Vibrio on biofilters was found at that period.

Anammox enrichment: impact of sludge retention time on nitrogen removal

Enrichment of anammox bacteria has long been considered to be time-consuming because of the slow growth rate. This study evaluated the impact of sludge retention time (SRT) on the enrichment of anammox bacteria with a focus on nitrogen removal and specific anammox activity (SAA) in sequencing batch reactors (SBR). A total of eight different SRTs in the range of 30-1280 days at nitrogen loading rates (NLR) range from 12.1 to 122.1 mg/L-d were used to evaluate the anammox activity. SAA was negligible during the first 105 days due to denitrification and continued to increase thereafter to peak at 0.22 g N/g VSS-d on day 530 as the solids and hydraulic retention times (SRT and HRT) decreased from 120 to 80 days and 10 to 2 days, respectively. The stability of SAA (0.21 ± 0.02 g N/g VSS-d) from day 503 to day 670 indicates that anammox bacteria should be enriched at SRTs ranging from 30 to 80 days and NLR of 122.1 mg N/L-d. Moreover, the SBR achieved a maximum nitrogen removal efficiency of 86.6% at an SRT of 30 days and an NLR of 122 mg/L-d. Microbial analysis indicated that the two most abundant microorganisms accounting for 48% of the bacterial population are Anammoxoglobus followed by the heterotrophic denitrifier Rhizobiales. The maximum specific growth rate (was estimated as 0.062 d-1, consistent with typical of 0.057 d-1. The average first-order decay rate was estimated as 0.008 d-1, and the half-saturation constants (ks) averaged 16.2 mg NH4-N/L.

Marine aquaculture regulates dissimilatory nitrate reduction processes in a typical semi-enclosed bay of southeastern China

Marine aquaculture in semi-enclosed bays can significantly influence nutrient cycling in coastal ecosystems. However, the impact of marine aquaculture on the dynamics of dissimilatory nitrate reduction processes (DNRPs) and the fate of reactive nitrogen remain poorly understood. In this study, the rates of DNRPs and the abundances of related functional genes were investigated in aquaculture and non-aquaculture areas. The results showed that marine aquaculture significantly increased the denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) rates and decreased the rate of anaerobic ammonium oxidation (ANA), as compared with non-aquaculture sites. DNF was the dominant pathway contributing to the total nitrate reduction, and its contribution to the total nitrate reduction significantly increased from 66.72% at non-aquaculture sites to 78.50% at aquaculture sites. Marine aquaculture can significantly affect the physicochemical characteristics of sediment and the abundances of related functional genes, leading to variations in the nitrate reduction rates. Although nitrate removal rates increased in the marine aquaculture area, ammonification rates and the nitrogen retention index in the aquaculture areas were 2.19 and 1.24 times, respectively, higher than those at non-aquaculture sites. Net reactive nitrogen retention exceeded nitrogen removal in the aquaculture area, and the retained reactive nitrogen could diffuse with the tidal current to the entire bay, thereby aggravating N pollution in the entire study area. These results show that marine aquaculture is the dominant source of nitrogen pollution in semi-enclosed bays. This study can provide insights into nitrogen pollution control in semi-enclosed bays with well-developed marine aquaculture.

The complex microbiome in aquaponics: significance of the bacterial ecosystem

Purpose

Aquaponics is a technology that has minimal impact on the environment and which is often promoted as a solution for sustainable food production. Developing aquaponics sustainably requires a thorough understanding of the biological components of the system. Recent reports on the bacterial populations of aquaponics systems using new DNA sequencing technologies are revealing a complex and diverse microbial ecosystem. The purpose of this review is to present information on microbial composition and various factors affecting bacterial activity in aquaponics systems. Approaches for establishing a bacterial ecosystem during the setup of an aquaponics system, and microbiological safety of aquaponics products are also highlighted.

Methods

This review was developed by evaluating and synthesising current literature of peer-reviewed publications related to aquaponics and microbial communities. Based on the results from credible academic journals, publications were categorised into five groups: methods used to characterise microbiomes, biofiltration microorganisms, bacterial diversity, biofilter establishment, and safety of aquaponics products.

Results

The microbial ecosystem is essential for biological filtration of water through the mineralisation of nutrients required for plant growth in an integrated system. The aquaponics microbiome is complex, and bacterial composition varies between the different compartments of these systems. Establishing these bacterial ecosystems is essential for optimal functioning of aquaponics. At the phylum level, Proteobacteria and Bacteroidetes are dominant in aquaponics systems. Despite bacteria being fundamental to aquaponics, there are currently no reports of human pathogens in aquaponics products.

Conclusion

Knowledge of the composition of bacterial populations in aquaponics systems will enhance understanding of relationships and functions within the microbiome. This in turn will allow for the establishment of sustainable and healthy aquaponics systems for food production.

Effects of different habitats on the bacterial community composition in the water and sediments of Lake Taihu, China

Bacterial communities are sensitive to environmental fluctuations, and a better understanding of the relationships between bacterial community distribution and complex environmental conditions is important for the remediation of lake ecosystems. In this study, bacterial communities from 7 water and 7 sediment samples in 3 different regions (east, the hydrophyte-dominated region; north, the transitional region; west, the highly polluted region) of Lake Taihu were investigated via high-throughput sequencing. The physicochemical characterization showed that there were obvious differences in the trophic statuses of the three lake regions, which were mainly due to the differences in pollutant concentration and hydrophyte coverage. The Shannon and Simpson values indicated that the diversity of bacterial communities in water was the highest in the eastern region, followed by the northern and western regions, while there was no significant difference in the bacterial community characteristics in sediments among lake regions. We found that the western lake region had the highest Cyanobacteria concentration (34.71%), suggesting that Cyanobacteria may have competitive advantages over the other bacterioplankton in water columns without plants. The abundances of Chlorobi detected in the water samples in the east (2.69%) and north (6.66%) were higher than those in the west because the high turbidity in the western lake region was unsuitable for the growth of Chlorobi. Nitrospirae (average 6.36%) and Chloroflexi (average 11.62%) were more common in the sediments than in the water of Lake Taihu, suggesting that the nutrient level of Lake Taihu sediment was higher than that of water bodies. Welch's t test revealed that there were significant differences in species abundance (such as Microcystis, Synechococcus, Flavobacterium, and hgcI_clade) among the different regions, except that the east was relatively similar to the north. Canonical correspondence analysis demonstrated that TN, TP, and DO showed significant effects on the relative abundance of the dominant bacterial genera in water, while TOC, TP, and TN were positively correlated with TOC, TP and TN. This study provides useful information for understanding the variation in the diversity of bacterial communities in different habitats of Lake Taihu.

A salty start: Brackish water start-up as a microbial management strategy for nitrifying bioreactors with variable salinity

Nitrifying biofilms developed in brackish water are reported to be more robust to salinity changes than freshwater biofilms. This makes them a promising strategy for water treatment systems with variable salinity, such as recirculating aquaculture systems for Atlantic salmon. However, little is known about the time required for nitrification start-up in brackish water or the microbial community dynamics. To investigate the development of nitrifying biofilms at intermediate salinity, we compared the startup of moving bed biofilm reactors with virgin carriers in brackish- (12‰ salinity) and freshwater. After 60 days, the brackish water biofilm had half the nitrification capacity of the freshwater biofilm, with a less diverse microbial community, lower proportion of nitrifiers, and a significantly different nitrifying community composition. Nitrosomonas and Nitrosospira-like bacteria were the main ammonia oxidizers in the brackish water biofilms, whereas Nitrosomonas was dominant in freshwater biofilms. Nitrotoga was the dominant nitrite oxidizer in both treatments. Despite the lower nitrification capacity in the brackish water treatment, the low ammonia and nitrite concentration with rapidly increasing nitrate concentration indicated that complete nitrification was established in both reactors within 60 days. The results suggest that biofilms develop nitrification in brackish water in comparable time as in freshwater, and brackish start-up can be a strategy for bioreactors with varying salinity.

Feed Supplementation with a Commercially Available Probiotic Solution Does Not Alter the Composition of the Microbiome in the Biofilters of Recirculating Aquaculture Systems

Recirculating aquaculture relies on the treatment of ammonia compounds from the water by a bacterial flora growing inside biofilters. Another increasingly common practice in aquaculture is the supplementation of feed with live probiotic bacteria to boost the immune system of the farmed animals and hinder the implantation of pathogenic bacteria. In the present study, we investigated the bacterial flora within the biofilters of recirculating farming units in which African catfish (Clarias gariepinus) were being farmed. Our results suggested that these two farming systems could be compatible as feeding of the probiotic feed had no detectable effect on the composition of the microbiome within the biofilters and none of the bacteria from the feed could be detected in the biofilters. These findings suggest that supplementation of the fish feed with probiotic supplements did not interfere with the microbiome residing inside the biofilter and that it is a safe practice in recirculating aquaculture systems.

Effects of Hydraulic Retention Time and Influent Nitrate-N Concentration on Nitrogen Removal and the Microbial Community of an Aerobic Denitrification Reactor Treating Recirculating Marine Aquaculture System Effluent

The effects of hydraulic retention time (HRT) and influent nitrate-N concentration on nitrogen removal and the microbial community composition of an aerobic denitrification reactor treating recirculating marine aquaculture system effluent were evaluated. Results showed that over 98% of nitrogen was removed and ammonia-N and nitrite-N levels were below 1 mg/L when influent nitrate-N was below 150 mg/L and HRT over 5 h. The maximum nitrogen removal efficiency and nitrogen removal rate were observed at HRT of 6 or 7 h when influent nitrate-N was 150 mg/L. High-throughput DNA sequencing analysis revealed that the microbial phyla Proteobacteria and Bacteroidetes were predominant in the reactor, with an average relative total abundance above 70%. The relative abundance of denitrifying bacteria of genera Halomonas and Denitratisoma within the reactor decreased with increasing influent nitrate-N concentrations. Our results show the presence of an aerobically denitrifying microbial consortium with both expected and unexpected members, many of them relatively new to science. Our findings provide insights into the biological workings and inform the design and operation of denitrifying reactors for marine aquaculture systems.

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus)

Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.