Surface ammonium loading rate shifts ammonia-oxidizing communities in surface water-fed rapid sand filters

Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health

To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.

Comammox Nitrospira was the dominant ammonia oxidizer in an acidic biofilm reactor at pH 5.5 and pH 5

Nitrification is a vital process in the biological removal of inorganic nitrogen compounds. In order to ensure the stability and effectiveness of this process, buffer solutions should be added to the system to maintain neutral to slightly alkaline conditions. With a focus on the newly discovered comammox Nitrospira, this research investigates the transition of the nitrifying community within a biofilm reactor under different acidic levels (initiated at pH 6 and gradually decreased to pH 5). During the 305-day continuous operation experiment, it was observed that responsible ammonia oxidizers transitioned from ammonia-oxidizing bacteria (AOB) during the initial stages (setup stage and early stage of pH 6) to comammox Nitrospira under pH 5.5 and pH 5. Further analysis using next-generation sequencing targeting both the 16S rRNA region and amoA region revealed a shift in the dominant cluster of both Nitrospirae and comammox Nitrospira under varying pH conditions. Our study identified a distinct cluster of comammox Nitrospira that is phylogenetically closed to sequences found in acidic environments, but exhibits dissimilarity from known comammox Nitrospira isolates and the majority of environmental sequences. This cluster was found to be prevalent in the acidic biofilm reactor studied and thrived particularly well at pH 5. These findings underscore the potential significance of this distinct, uncultivated group of comammox Nitrospira in performing ammonia oxidation under acidic conditions. KEY POINTS: • Ammonia was effectively removed under pH 5.5 and 5 in the biofilm reactor • The dominant ammonia oxidizer was comammox Nitrospira when pH was 5.5 and 5 • A potential acidophilic cluster of comammox Nitrospira was identified in this acidic biofilm reactor.

Comparative analyses of gut microbiota reveal ammonia detoxification and nitrogen assimilation in Cyprinus carpio var. specularis

The complex niche of fish gut is often characterized by the associated microorganisms that have implications in fish gut-health nexus. Although efforts to distinguish the microbial communities have highlighted their disparate structure along the gut length, remarkably little information is available about their distinct structural and functional profiles in different gut compartments in different fish species. Here, we performed comparative taxonomic and predictive functional analyses of the foregut and hindgut microbiota in an omnivorous freshwater fish species, Cyprinus carpio var. specularis, commonly known as mirror carp. Our analyses showed that the hindgut microbiota could be distinguished from foregut based on the abundance of ammonia-oxidizing, denitrifying, and nitrogen-fixing commensals of families such as Rhodospirillaceae, Oxalobacteraceae, Nitrosomonadaceae, and Nitrospiraceae. Functionally, unique metabolic pathways such as degradation of lignin, 2-nitrobenzoate, vanillin, vanillate, and toluene predicted within hindgut also hinted at the ability of hindgut microbiota for assimilation of nitrogen and detoxification of ammonia. The study highlights a major role of hindgut microbiota in assimilating nitrogen, which remains to be one of the limiting nutrients within the gut of mirror carp.

Age and environment are the main drivers shaping the wild common sole (Solea solea) microbiota

Microbiota plays an essential role in fish growth and health and may be influenced by the changing environmental conditions. Here, we explored the microbiota of wild common sole, one of the most important fishery resources in the Mediterranean Sea, collected from different areas in the North Adriatic Sea. Our results show that the sole microbiota differs from that of the surrounding environment and among the different body sites (gill, skin and gut). Gut microbiota composition showed to be strongly related to fish age, rather than maturity, sex or sampling site. Age-related shifts in gut microbial communities were identified, with increased abundances of Bacteroidia and Desulfobacteria, unveiling potential microbial proxies for age estimation crucial for fisheries management. Our results expand the limited knowledge of the wild common sole microbiota, also in the light of the potential usefulness of the fish microbiota as a tool for future stock identification and connectivity studies.

Microbial ecology of drinking water from source to tap

As drinking water travels from its source, through various treatment processes, hundreds to thousands of kilometres of distribution network pipes, to the taps in private homes and public buildings, it is exposed to numerous environmental changes, as well as other microbes living in both water and on surfaces. This review aims to identify the key locations and factors that are associated with changes in the drinking water microbiome throughout conventional urban drinking water systems from the source to the tap water. Over the past 15 years, improvements in cultivation-independent methods have enabled studies that allow us to answer such questions. As a result, we are beginning to move towards predicting the impacts of disturbances and interventions resulting ultimately in management of drinking water systems and microbial communities rather than mere observation. Many challenges still exist to achieve effective management, particularly within the premise plumbing environment, which exhibits diverse and inconsistent conditions that may lead to alterations in the microbiota, potentially presenting public health risks. Finally, we recommend the establishment of global collaborative projects on the drinking water microbiome that will enhance our current knowledge and lead to tools for operators and researchers alike to improve global access to high-quality drinking water.

Diversity of the Pacific Ocean coral reef microbiome

Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.

Community composition and abundance of complete ammonia oxidation (comammox) bacteria in the Lancang River cascade reservoir

The construction of the reservoir has changed the nitrogen migration and transformation processes in the river, and a large amount of sediment deposition in the reservoir may also lead to the spatial differentiation of complete ammonia oxidation (comammox) bacteria. The study investigated the abundance and diversity of comammox bacteria in the sediments of three cascade reservoirs, namely, Xiaowan, Manwan, and Nuozhadu on the Lancang River in China. In these reservoirs, the average amoA gene abundance of clade A and clade B of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) was 4.16 ± 0.85 × 10⁵, 1.15 ± 0.33 × 10⁵, 7.39 ± 2.31 × 10⁴, and 3.28 ± 0.99 × 10⁵ copies g^-1, respectively. The abundance of clade A was higher than that of other ammonia oxidizing microorganisms. The spatial variation of comammox bacteria abundance differed among different reservoirs, but the spatial variation trends of the two clades of comammox bacteria in the same reservoir were similar. At each sampling point, clade A1, clade A2, and clade B coexisted, and clade A2 was usually the dominant species. The connection between comammox bacteria in the pre-dam sediments was looser than that in non-pre-dam sediments, and comammox bacteria in pre-dam sediments exhibited a simpler network structure. The main factor affecting comammox bacteria abundance was NH₄⁺-N, while altitude, temperature, and conductivity of overlying water were the main factors affecting comammox bacteria diversity. Environmental changes caused by differences in the spatial distribution of these cascade reservoirs may be the main driver of the changes of community composition and abundance of comammox bacteria. This study confirms that the construction of cascade reservoirs results in niche spatial differentiation of comammox bacteria.

Nitrogen-metabolising microorganism analysis in rapid sand filters from drinking water treatment plant

Sand filters (SFs) are common treatment processes for nitrogen pollutant removal in drinking water treatment plants (DWTPs). However, the mechanisms on the nitrogen-cycling role of SFs are still unclear. In this study, 16S rRNA gene amplicon sequencing was used to characterise the diversity and composition of the bacterial community in SFs from DWTPs. Additionally, metagenomics approach was used to determine the functional microorganisms involved in nitrogen cycle in SFs. Our results showed that Pseudomonadota, Acidobacteria, Nitrospirae and Chloroflexi dominated in SFs. Subsequently, 85 high-quality metagenome-assembled genomes (MAGs) were retrieved from metagenome datasets of selected SFs involving nitrification, assimilatory nitrogen reduction, denitrification and anaerobic ammonia oxidation (anammox) processes. Read mapping to reference genomes of Nitrospira and the phylogenetic tree of the ammonia monooxygenase subunit A gene, amoA, suggested that Nitrospira is abundantly found in SFs. Furthermore, according to their genetic content, a nitrogen metabolic model in SFs was proposed using representative MAGs and pure culture isolate. Quantitative real-time polymerase chain reaction (qPCR) showed that ammonia-oxidising bacteria (AOB) and archaea (AOA), and complete ammonia oxidisers (comammox) were ubiquitous in the SFs, with the abundance of comammox being higher than that of AOA and AOB. Moreover, we identified a bacterial strain with a high NO₃-N removal rate as Pseudomonas sp. DW-5, which could be applied in the bioremediation of micro-polluted drinking water sources. Our study provides insights into functional nitrogen-metabolising microbes in SFs of DWTPs.

Treatability Studies on the Optimization of Ozone and Carbon Dosages for the Effective Removal of Contaminants from Secondary Treated Effluent

This study investigates the novel and advanced integrated pilot-scale treatment system of removal of contaminants in the secondary effluent from municipal wastewater. The main intent of this work is to assess the combination of pressure sand filter (PSF), ultrafiltration (UF), ozone (O3), and granular activated carbon (GAC) to treat wastewater and evaluate its suitability for water reuse. The experiments were carried out in a following condition: $\text{PSF}+\text{UF}+\text{O}3+\text{GAC}$ , $\text{PSF}+\text{O}3+\text{GAC}$ , and $\text{PSF}+\text{UF}+\text{GAC}$ . Configuration 1 was found to be more effective when compared to the other two and almost there occurred complete removal of contaminants. Whereas configuration 2 had the lowest removal efficiency of all, and configuration 3 had quite positive results. The influence of process parameters such as ozone dosage, flow rate, and filtration time was optimized. The optimized filtration time was 20 min with the filtration feed flow rate of 300 LPH. The best configuration of this treatment process produced a removal efficiency of about 80 to 90% with the ozone dosage of 8.33 mg/L with a flow rate of 4 l/min, whereas there occurred complete removal by the subsequent action of GAC. Moreover, the biodegradability of wastewaters as measured by the BOD5/COD ratio increased from 0.45 to 0.53. The proposed integrated pilot-scale process was effective in removing contaminants to the required level of discharge in the environment or reuse and it will pave the way to provide significant benefits to wastewater treatment.

Efficient nitrogen removal from onsite wastewater by a novel continuous flow biofilter

Soil-based passive biofiltration system is an economically feasible technology for nitrogen removal from onsite wastewater. However, the conventional design requires a large system footprint with limited treatment capacity. In this study, a novel continuous flow biofilter (CFB) with adjustable recirculation and continuous flow pattern was developed for onsite wastewater treatment with a small footprint. Efficient total nitrogen removal (80.1-97.5%) was observed at various hydraulic loadings (0.03-0.12 m³ m^-2 d^-1), nitrogen loadings (1.1-8.6 g N m^-2 d^-1) and recycle ratios (2-3) when treating septic tank effluent (STE), with low effluent TN (0.7-13.6 mg N L^-1). Nitrous oxide was observed in the denitrification effluent indicating incomplete denitrification at elevated dissolved oxygen levels (3.3-5.8 mg L^-1). Nitrogen removal rate (2.9-7.0 g N m^-2 d^-1) and ammonium removal rate (2.4-7.2 g N m^-2 d^-1) were positively correlated with nitrogen loadings increase (1.1-8.6 g N m^-2 d^-1) but were not significantly impacted by the hydraulic loading rate change (0.08-0.12 m³ m^-2 d^-1). The total biomass abundance and nitrifying microorganisms decreased significantly as the nitrification columns depth increased, while homogeneous microbial distribution was observed in the denitrification columns. The abundance of ammonium oxidizing archaea (AOA) increased significantly at increased hydraulic and nitrogen loading rate, while the ammonium oxidizing bacteria (AOB) abundance remained steady. The abundance of functional genes involved in denitrification process (nirS, nirK and nosZ) responded differently when hydraulic and nitrogen loading rate changes. Collectively, this study suggested the CFB could efficiently remove nitrogen from onsite wastewater with fluctuating influent compositions and various hydraulic loadings.

Dominance of comammox Nitrospira in soil nitrification

The first and limiting step of nitrification is catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recently, complete ammonia oxidizers (comammox Nitrospira) have been discovered to perform complete nitrification in one cell, yet their role in soil nitrification is still unclear. This study investigated the abundance and contribution of aerobic ammonia oxidizers in typical soil habitats, and assessed the role of comammox Nitrospira in ammonia-oxidizing communities. The results showed that comammox Nitrospira were dominant in 70% of the samples and their abundance displayed a significant positive correlation with nitrification potential. The median amoA gene transcription level of comammox Nitrospira exceeded that of AOA and AOB in in-situ soils. The abundance of comammox Nitrospira was negatively correlated with soil pH, dominating in 84% of soil samples with pH < 6.17. The results challenge the role of AOA and AOB in soils, highlighting the importance of comammox Nitrospira in soil nitrification, especially in acid soils. This work supports better understanding and regulation of the soil nitrogen cycle.

Optical-Switch-Enabled Microfluidics for Sensitive Multichannel Colorimetric Analysis

The implementation of colorimetric analysis within microfluidic environments engenders significant benefits with respect to reduced sample and reagent consumption, system miniaturization, and real-time measurement of flowing samples. That said, conventional approaches to colorimetric analysis within microfluidic channels are hampered by short optical pathlengths and single-channel configurations, which lead to poor detection sensitivities and low analytical throughputs. Although the use of multiplexed light source/photodetector modules allows for multichannel analysis, such configurations significantly increase both instrument complexity and cost. To address these issues, we present a four-channel colorimetric measurement scheme within an optical-switch-enabled microfluidic chip (OSEMC) fabricated by two-photon stereolithography. The integration of optical switches enables sequential signal readout from each detection channel, and thus, only a single light source and a photodetector are required for operation. Optical switches can be controlled in a bespoke manner by changing the medium in the switch channel between a "light-transmitting" fluid and a "light-blocking" fluid using pneumatic microvalves. Such optical switches are characterized by fast response times (approximately 200 ms), tunable switching frequencies (between 0.1 and 1.0 Hz studied), and excellent stability. Operational performance demonstrates both good sensitivity and reproducibility through the colorimetric analysis of nitrite and ammonium samples using four detection channels. Furthermore, the use of OSEMC for parallel and real-time analysis of flowing samples is investigated via characterization of the adsorption kinetics of tartrazine on activated charcoal and the catalytic reaction kinetics of horseradish peroxidase (HRP).