Communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria in shrimp ponds

The difference between drainage channels and sewers in rural areas: from sewage quality to bacterial characteristics

Channels and sewers are commonly used to collect sewage during extensively rural areas. The sewage and bacterial characteristics of rural sewage collection systems can influence their operation and maintenance performance which further affect appropriate system decision. In this study, eight rural sewage collection systems (four each of channels and sewers) were applied to evaluate the sewage quality, bacterial characteristics, and their differences of two kinds of collection systems. The results indicate that significantly distinction existed between the rural sewage collection systems of channels and sewers. Sewage in channels had higher suspended solid (SS) concentration but lower sulfide concentration than that in sewers. The SS, sulfate, and chemical oxygen demand (COD) removal capacity in channels was nearly 3.5, 4.0, and 0.6 times than those in sewers. At least 14 genera and 18 species of bacteria showed significantly distinction between channels and sewers even their main phylum, genus, and species of bacteria communities was Proteobacteria (∼70.3%), Acinetobacter (∼22.3%), and Pseudomonas fragi (∼13.8%), respectively. The structural characteristics and bacterial function caused the difference between channels and sewers. Overall, this study revealed the intrinsic and essential differences of channels and sewers, providing basic and meaningful data for rural sewage collection systems decision.

Ammonia-Oxidizing Bacterial Communities in Tilapia Pond Systems and the Influencing Factors

This study investigated ammonia-oxidizing bacterial communities in water and surface sediments of three tilapia ponds and their relationship with differences in the ponds, monthly variations in the water, and the physico-chemical parameters. Samples were collected from ponds with different stocking densities, after which DNA was extracted, 16S rRNA genes were amplified, the Illumina high-throughput sequencing was performed, and then the Silva and FunGene databases were used to investigate the ammonia-oxidizing bacterial communities. In total, 308,488 valid reads (144,931 in water and 163,517 in sediment) and 240 operational taxonomic units (207 in water and 225 in sediment) were obtained. Further analysis showed that the five genera of Nitrosospira, Nitrosococcus, Nitrosomonas, Proteobacteria_unclassified, and Nitrosomonadaceae_unclassified were distributed not only in the water, but also in surface sediments of all three ponds. Further, not only the abundance of these five genera, but also their diversities were affected by monthly variations in the water and by sediment differences among the ponds. Moreover, the total nitrogen (TN), nitrate, total phosphorus (TP), and sulphate were the main factors influencing the ammonia-oxidizing bacterial communities in the water, whereas TP was the main influencing factor in the sediments. Moreover, the parameter changes, especially those caused by differences in the ponds, were closely related to the cultivation management (stocking density and feed coefficients).

A Review of Ammonia-Oxidizing Archaea and Anaerobic Ammonia-Oxidizing Bacteria in the Aquaculture Pond Environment in China

The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.

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.

Implementation of a constructed wetland for the sustainable treatment of inland shrimp farming water

In the Mekong delta, inland-based shrimp breeding requires significant inflow of high-quality freshwater. In turn, discharge of substantial loads of poor-quality effluents negatively impacts adjacent water bodies and favors disease outbreaks. This project describes the implementation of a laboratory-based continuous closed recirculation aquaculture system composed of a constructed wetland (CW) with horizontal subsurface flow as a water treatment filter for mesohaline conditions, functioning under high loading rate (HLR = 1.54 m/d with HRT = 1.31 h). This CW was equipped of successive compartment dedicated to the successive elimination of the contaminants of interests. CW performance was measured over a complete growth cycle of the White-leg shrimps (Litopenaeus vannamei). Results showed that the designed system was pertinent, improving water quality of the shrimp culture substantially. Complete removal of nitrite was attained, with a concomitant reduction of respectively 78% and 76% of nitrate and COD. Bacteria enumeration tests showed that Vibrio sp. cells were fully removed, and that a 3 Log reduction was reached in total aerobic bacteria.

Response of sediment bacterial communities to the drainage of wastewater from aquaculture ponds in different seasons

Bacterial communities play an important role in diffuse sediment pollution in aquaculture farms. Previous studies have revealed the short-term influence of wastewater drainage on the bacterial communities but the seasonal response of the sediment bacterial communities to wastewater drainage from aquaculture farms remains unclear. This study used the 16S rRNA approach to explore the profiles of bacterial communities over four seasons in a typical crab aquaculture farm that included a pond and an outlet ditch. Nineteen sediment samples and an equal number of water samples were collected and analysed during spring, summer, autumn, and winter during 2018-19. Our results showed that Proteobacteria, Chloroflexi, and Bacteroides were the predominant phyla in aquaculture pond sediment with the relative abundance of 28.95%, 17.32%, and 15.31%, respectively. The relative abundance of Proteobacteria and Bacteroides was higher in autumn and winter, and the relative abundance of Chloroflexi was highest in spring. The Shannon diversity index value ranged from 6.17 to 9.30 and showed significant positive correlation (P < 0.01) with the concentrations of TN, NH₄⁺-N, and TP in the water. The variation in the bacterial community and relative abundance in outlet ditch sediment were consistent with those in the pond sediment. Our results show that determinisation of the bacterial community composition in the outlet ditch sediment provides a novel tool to monitor watersheds sensitive to the influence of aquacultures.

Patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge in Lhasa River

The increased anthropogenic activities in the Tibetan Plateau may threaten the river environmental safety. However, limited information is available on the Lhasa River in the Tibetan Plateau, which is known as the remaining pure land on Earth. Here, we firstly investigated the distribution patterns of bacterial and archaeal communities in sediments in response to dam construction and sewage discharge along the reaches of the Lhasa River. The total organic carbon, total Nitrogen (N), nitrate and ammonium contents and the relative abundance of bacteria and archaea significantly increased in reservoir sites in comparison with sites below dam, and they also gradually increased from upstream to downstream in sewage discharge sites. By contrast, the diversity of sediment bacteria and archaea in reservoir sites were significantly less than that in sites below dam and sewage discharge sites at Operational Taxonomic Units (OTUs) level. The dominant species were water-bloom cyanobacteria in the reservoir area of Zhikong Dam and Proteobacteria in the sewage discharge sites, which were significantly correlated with the nutrient concentration. The abundance of nitrogen functional genes significantly also increased in reservoir sites and the downstream of sewage discharge areas. These results suggested that dam construction and sewage discharge caused the increase of sediment bacterial communities and nutrient levels and potentially induced eutrophication in the Lhasa River.

Evaluation of the effects of different stocking densities on the sediment microbial community of juvenile hybrid grouper (♀Epinephelus fuscoguttatus × ♂ Epinephelus lanceolatus) in recirculating aquaculture systems

Aquatic microorganisms are an important part of aquatic ecosystems because they are involved in nutrient cycling and water quality, eventually influencing fish productivity. However, at present, reports on the effect of stocking density on microorganisms in sediment samples in recirculating aquaculture systems (RAS) are relatively rare. In this study, the changes in the microbial community in an RAS were investigated under different stocking densities of juvenile hybrid grouper (♀Epinephelus fuscoguttatus × ♂Epinephelus lanceolatus). Total DNA was extracted from the sediment samples, the 16S rDNA gene was amplified, and the bacterial community was analysed by Illumina high-throughput sequencing. We identified 741 OTUs from a total of 409,031 reads. Based on the analysis of bacterial composition, richness, diversity, bacterial 16S and rDNA gene abundance; sediment sample comparisons; and the existence of specific bacterial taxa within four densities, we concluded that the dominant phyla in all samples were similar and included: Proteobacteria, Bacteroidetes, Nitrospirae, Planctomycetes, Verrucomicrobia, and Chloroflexi. However, their relative distributions differed at different fish densities. Linear discriminant analysis further indicated that the stocking treatment influenced the sediment bacterial community. This study indicates that under RAS aquaculture, mode density is a factor regulating the microbial community, which provides insights into microbe management in RAS culture.

"Candidatus Nitrosotenuis aquarius," an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter

Ammonia is a metabolic waste product excreted by aquatic organisms that causes toxicity when it accumulates. Aquaria and aquaculture systems therefore use biological filters that promote the growth of nitrifiers to convert ammonia to nitrate. Ammonia-oxidizing bacteria (AOB) have been isolated from aquarium biofilters and are available as commercial supplements, but recent evidence suggests that ammonia-oxidizing archaea (AOA) are abundant in aquarium biofilters. In this study, we report the cultivation and closed genome sequence of the novel AOA representative "Candidatus Nitrosotenuis aquarius," which was enriched from a freshwater aquarium biofilter. "Ca Nitrosotenuis aquarius" oxidizes ammonia stoichiometrically to nitrite with a concomitant increase in thaumarchaeotal cells and a generation time of 34.9 h. "Ca Nitrosotenuis aquarius" has an optimal growth temperature of 33°C, tolerates up to 3 mM NH₄Cl, and grows optimally at 0.05% salinity. Transmission electron microscopy revealed that "Ca Nitrosotenuis aquarius" cells are rod shaped, with a diameter of ∼0.4 μm and length ranging from 0.6 to 3.6 μm. In addition, these cells possess surface layers (S-layers) and multiple proteinaceous appendages. Phylogenetically, "Ca Nitrosotenuis aquarius" belongs to the group I.1a Thaumarchaeota, clustering with environmental sequences from freshwater aquarium biofilters, aquaculture systems, and wastewater treatment plants. The complete 1.70-Mbp genome contains genes involved in ammonia oxidation, bicarbonate assimilation, flagellum synthesis, chemotaxis, S-layer production, defense, and protein glycosylation. Incubations with differential inhibitors indicate that "Ca Nitrosotenuis aquarius"-like AOA contribute to ammonia oxidation within the aquarium biofilter from which it originated.IMPORTANCE Nitrification is a critical process for preventing ammonia toxicity in engineered biofilter environments. This work describes the cultivation and complete genome sequence of a novel AOA representative enriched from a freshwater aquarium biofilter. In addition, despite the common belief in the aquarium industry that AOB mediate ammonia oxidation, the present study suggests an in situ role for "Ca Nitrosotenuis aquarius"-like AOA in freshwater aquarium biofilters.

Advances in algal-prokaryotic wastewater treatment: A review of nitrogen transformations, reactor configurations and molecular tools

The synergistic activity of algae and prokaryotic microorganisms can be used to improve the efficiency of biological wastewater treatment, particularly with regards to nitrogen removal. For example, algae can provide oxygen through photosynthesis needed for aerobic degradation of organic carbon and nitrification and harvested algal-prokaryotic biomass can be used to produce high value chemicals or biogas. Algal-prokaryotic consortia have been used to treat wastewater in different types of reactors, including waste stabilization ponds, high rate algal ponds and closed photobioreactors. This review addresses the current literature and identifies research gaps related to the following topics: 1) the complex interactions between algae and prokaryotes in wastewater treatment; 2) advances in bioreactor technologies that can achieve high nitrogen removal efficiencies in small reactor volumes, such as algal-prokaryotic biofilm reactors and enhanced algal-prokaryotic treatment systems (EAPS); 3) molecular tools that have expanded our understanding of the activities of algal and prokaryotic communities in wastewater treatment processes.

Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun

Rhizospheric microbes play important roles in plant growth and heavy metals (HMs) transformation, possessing great potential for the successful phytoremediation of environmental pollutants. In the present study, the rhizosphere of Elsholtzia haichowensis Sun was comprehensively studied to uncover the influence of environmental factors (EFs) on the whole microbial communities including bacteria, fungi and archaea, via quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. By analyzing molecular ecological network and multivariate regression trees (MRT), we evaluated the distinct impacts of 37 EFs on soil microbial community. Of them, soil pH, HMs, soil texture and nitrogen were identified as the most influencing factors, and their roles varied across different domains. Soil pH was the main environmental variable on archaeal and bacterial community but not fungi, explaining 25.7%, 46.5% and 40.7% variation of bacterial taxonomic composition, archaeal taxonomic composition and a-diversity, respectively. HMs showed important roles in driving the whole microbial community and explained the major variation in different domains. Nitrogen (NH₄-N, NO₃-N, NO₂-N and TN) explained 47.3% variation of microbial population composition and 15.9% of archaeal taxonomic composition, demonstrating its influence in structuring the rhizospheric microbiome, particularly archaeal and bacterial community. Soil texture accounted for 10.2% variation of population composition, 28.9% of fungal taxonomic composition, 19.2% of fungal a-diversity and 7.8% of archaeal a-diversity. Rhizosphere only showed strong impacts on fungi and bacteria, accounting for 14.7% and 4.9% variation of fungal taxonomic composition and bacterial a-diversity. Spatial distance had stronger influence on bacteria and archaea than fungi, but not as significant as other EFs. For the first time, our study provides a complete insight into key influential EFs on rhizospheric microbes and how their roles vary across microbial domains, giving a hand for understanding the construction of microbial communities in rhizosphere.

Archaeal community compositions in tilapia pond systems and their influencing factors

Archaea, like the bacterial communities are gradually being realized as key players in the biogeochemical progress of water ecosystems. In this study, tilapia aquaculture ponds were used for an in-depth understanding of archaeal community compositions in water and surface sediment. Some of the main functions, as well as the communities' response patterns, to time variations, pond differences and some physio-chemical parameters were investigated. The results revealed the dominant phylum in both the water and surface sediment, as Euryarchaeota, while, the most abundant classes were: Halobacteria and Methanomicrobia respectively. Significant differences in the archaeal community compositions in the water and surface sediment, were observed in the early stages of cultivation, which became minimal at the later stage of the GIFT tilapia cultivation. Additionally to the differences in the most abundant classes, more OTUs were observed in water samples than in surface sediment samples. The methane generation could be attributed to the large proportion of methanogens found in both pond water and in the surface sediment. Furthermore, the archaeal community compositions in water and the surface sediment were shaped mainly by temporal variations and pond differences respectively. In the pond water, the archaeal community compositions were highly co-related to the concentration changes of ammonia, sulfate and total nitrogen; while in the surface sediment, the correlation to the content changes was significant in total phosphorus. The archaeal community compositions in surface sediment should be considered as an indicator for future environmental capacity studies in aquaculture.

Differences in nitrite-oxidizing communities and kinetics in a brackish environment after enrichment at low and high nitrite concentrations

Nitrite accumulation in shrimp ponds can pose serious adverse effects to shrimp production and the environment. This study aims to develop an effective process for the enrichment of ready-to-use nitrite-oxidizing bacteria (NOB) inocula that would be appropriate for nitrite removal in brackish shrimp ponds. To achieve this objective, the effects of nitrite concentrations on NOB communities and nitrite oxidation kinetics in a brackish environment were investigated. Moving-bed biofilm sequencing batch reactors and continuous moving-bed biofilm reactors were used for the enrichment of NOB at various nitrite concentrations, using sediment from brackish shrimp ponds as seed inoculum. The results from NOB population analysis with quantitative polymerase chain reaction (qPCR) show that only Nitrospira were detected in the sediment from the shrimp ponds. After the enrichment, both Nitrospira and Nitrobacter coexisted in the reactors controlling effluent nitrite at 0.1 and 0.5 mg-NO2(-)-N/L. On the other hand, in the reactors controlling effluent nitrite at 3, 20, and 100 mg-NO2(-)-N/L, Nitrobacter outcompeted Nitrospira in many orders of magnitude. The half saturation coefficients (Ks) for nitrite oxidation of the enrichments at low nitrite concentrations (0.1 and 0.5 mg-NO2(-)-N/L) were in the range of 0.71-0.98 mg-NO2(-)-N/L. In contrast, the K(s) values of NOB enriched at high nitrite concentrations (3, 20, and 100 mg-NO2(-)-N/L) were much higher (8.36-12.20 mg-NO2(-)-N/L). The results suggest that the selection of nitrite concentrations for the enrichment of NOB inocula can significantly influence NOB populations and kinetics, which could affect the effectiveness of their applications in brackish shrimp ponds.