While various bioremediation techniques have been widely used at oil spill sites, the in situ efficiency of such techniques on recovering the benthic communities in intertidal areas has not been quantified. Here, the performance of several bioremediation tools such as emulsifiers, multi-enzyme liquid (MEL), microbes, and rice-straw was evaluated by a 90-days semi-field experiment, particularly targeting recovery of benthic community. Temporal efficiency in the removal of sedimentary total petroleum hydrocarbons (TPH), reduction of residual toxicity, and recovery of bacterial diversity, microalgal growth, and benthic production was comprehensively determined. Concentrations of TPH and amphipod mortality for all treatments rapidly decreased within the first 10 days. In addition, the density of bacteria and microphytobenthos generally increased over time for all treatments, indicating recovery in the benthic community health. However, the recovery of some nitrifying bacteria, such as the class Nitrospinia (which are sensitive to oil components) remained incomplete (13–56%) during 90 days. Combination of microbe treatments showed rapid and effective for recovering the benthic community, but after 90 days, all treatments showed high recovery efficiency. Of consideration, the “no action” treatment showed a similar level of recovery to those of microbe and MEL treatments, indicating that the natural recovery process could prevail in certain situations.

The challenge of sludge digester liquor treatment is its high ammonium nitrogen (NH₄⁺-N) concentration. Early reports found that complete ammonia oxidation (comammox) was not present and anaerobic ammonia oxidation (anammox) was difficult to achieve in most sludge digester liquor treatments. In this study, NH₄⁺-N removal by cooperation between partial-nitrification, comammox, and anammox processes was achieved in a sequencing batch reactor (SBR) for sludge digester liquor treatment. The results showed that 2100–2200 mg/L of NH₄⁺-N was removed in the SBR with 98.82% removal efficiency. In addition, 55.11% of NH₄⁺-N was converted to nitrite nitrogen (NO₂⁻-N) by partial-nitrification, 25.43% of NH₄⁺-N was converted to nitrate nitrogen (NO₃⁻-N) by comammox, and 18.28% of NH₄⁺-N was removed by anammox. During the operation, in the SBR, the relative abundance of the dominant ammonia-oxidizing bacteria (Chitinophagaceae) was 18.89%, that of the dominant anammox bacteria (Candidatus Kuenenia) was 0.10%, and that of the dominant comammox bacteria (Nitrospira) was 0.20%. Therefore, the high nitrogen removal efficiency in this system was considered the result of the combination of the three processes. These results showed that comammox and anammox could play very important roles in nitrogen transformation and energy-saving in nitrogen removal systems.

The application of low ozone dosage to minimize the problems caused by filamentous foaming was evaluated in two bioreactors of an urban wastewater treatment plant. Filamentous and nitrifying bacteria, as well as protist and metazoa, were monitored throughout a one-year period by FISH and conventional microscopy to examine the effects of ozone application on these specific groups of microorganisms. Multivariate data analysis was used to determine if the ozone dosage was a key factor determining the low carbon and nitrogen removal efficiencies observed throughout the study period, as well as to evaluate its impact on the biological communities monitored. The results of this study suggested that ozonation did not significantly affect the COD removal efficiency, although it had a moderate effect on ammonia removal efficiency. Filamentous bacteria were the community most influenced by ozone (24.9% of the variance explained by ozone loading rate), whilst protist and metazoa were less affected (11.9% of the variance explained). Conversely, ozone loading rate was not a factor in determining the nitrifying bacterial community abundance and composition, although this environmental variable was correlated with ammonia removal efficiency. The results of this study suggest that different filamentous morphotypes were selectively affected by ozone.

Thiocyanate (SCN⁻)-based autotrophic denitrification (AD) has recently been demonstrated as a promising technology that could be integrated with anaerobic ammonium oxidation (Anammox) to achieve simultaneous removal of nitrogen and SCN⁻. However, there is still a lack of a complete SCN⁻-based AD model, and the potential microbial competition/synergy between AD bacteria and Anammox bacteria under different operating conditions remains unknown, which significantly hinders the possible application of coupling SCN⁻-based AD with Anammox. To this end, a complete SCN⁻-based AD model was firstly developed and reliably calibrated/validated using experimental datasets. The obtained SCN⁻-based AD model was then integrated with the well-established Anammox model and satisfactorily verified with experimental data from a system coupling AD with Anammox. The integrated model was lastly applied to investigate the impacts of influent NH₄⁺-N/NO₂⁻-N ratio and SCN⁻ concentration on the steady-state microbial composition as well as the removal of nitrogen and SCN⁻. The results showed that the NH₄⁺-N/NO₂⁻-N ratio in the presence of a certain SCN⁻ level should be controlled at a proper value so that the maximum synergy between AD bacteria and Anammox bacteria could be achieved while their competition for NO₂⁻ would be minimized. For the simultaneous maximum removal (>95%) of nitrogen and SCN⁻, there existed a negative relationship between the influent SCN⁻ concentration and the optimal NH₄⁺-N/NO₂⁻-N ratio needed.

The Yangtze River, which is the largest in Euro-Asian, receives tremendous anthropogenic nitrogen input and is typically characterized by severe eutrophication and hypoxia. Two major processes, denitrification and anaerobic ammonium oxidation (anammox), play vital roles for removing nitrogen global in nitrogen cycling. In the current study, sediment samples were collected from both latitudinal and longitudinal transects along the coastal Yangtze River and the East China Sea (ECS). We investigated community composition and distributions of nosZ gene-encoded denitrifiers by high throughput sequencing, and also quantified the relative abundances of both denitrifying and anammox bacteria by q-PCR analysis. Denitrifying communities showed distinct spatial distribution patterns that were impacted by physical (water current and river runoffs) and chemical (nutrient availability and organic content) processes. Both denitrifying and anammox bacteria contributed to the nitrogen removal in Yangtze Estuary and the adjacent ECS, and these two processes shifted from coastal to open ocean with reverse trends: the abundance of nosZ gene decreased from coastal to open ocean while anammox exhibited an increasing trend based on quantifications of hzsB and 16S rRNA genes. Further correspondence correlation analysis revealed that salinity and nutrients were the main factors in structuring composition and distribution of denitrifying and anammox bacteria. This study improved our understanding of dynamic processes in nitrogen removal from estuarine to open ocean. We hypothesize that denitrification is the major nitrogen removal pathway in estuaries, but in open oceans, low nutrient and organic matter concentrations restrict denitrification, thus increasing the importance of anammox as a nitrogen removal process.

Denitrification is considered as the dominant nitrogen (N) removing pathway, however, anaerobic oxidation of ammonium (anammox) also plays a significant part in N loss in agricultural ecosystems. Large N inputs into agricultural soils may stimulate the growth of anammox bacteria, resulting in high activity and diversity of anammox bacteria and subsequent more N loss. In some specific niches, like oxic-anoxic interface, three processes, nitrification, anammox and denitrification couple with each other, and significant anammox reaction could be observed. Soil parameters like pH, dissolved oxygen, salinity, oxidation-reduction potential (ORP), and substrate concentrations impact the anammox process. Here we summarize the current knowledge on anammox activity and contribution to N loss, abundance and diversity of anammox bacteria, factors affecting anammox, and the relationship between anammox and other N loss pathways in agricultural soils. We propose that more investigations are required for (1) the role of anammox to N loss with different agricultural management strategies; (2) microscale research on the coupling of nitrification-anammox-denitrification, that might be a very complex process but ideal model for further studies responsible for N cycling in terrestrial ecosystems; and (3) new methods to estimate differential contributions of anammox, codenitrification and denitrification in total N loss in agricultural ecosystems. New research will provide much needed information to quantify the contribution of anammox in N loss from soils at landscape, ecosystem and global scales.

Anaerobic ammonium oxidation (anammox) is recognized as an important bioprocess for nitrogen removal, yet little is known about the associated microbial communities in urban river networks which are intensively disturbed by human activity. In the present study, we investigated the community composition and abundance of anammox bacteria in the urban river network of Shanghai, and explored their potential correlations with nitrogen removal activities and the environmental parameters. High biodiversity of anammox bacteria was detected in the sediment of urban river networks, including Candidatus Brocadia, Scalindua, Jettenia, and Kuenenia. Anammox bacterial abundance ranged from 3.7 × 10⁶ to 3.9 × 10⁷ copies g⁻¹ dry sediment based on 16S rRNA gene, which was strongly correlated to the metabolic activity of anammox bacteria (P < 0.01). A strong linkage between anammox bacteria and denitrifiers was detected (P < 0.05), implying a potential metabolic interdependence between these two nitrogen-removing microbes was existed in urban river networks. Sediment ammonium (NH₄⁺) made a significant contribution to the anammox bacterial community-environment relationship, while anammox bacterial abundance related significantly with sediment total organic carbon (TOC) and silt contents (P < 0.05). However, no statistically significant correlation was observed between cell-specific anammox rate and the measured environmental factors (P > 0.05). In general, the community composition and abundance of anammox bacteria in different hierarchies of the river network was homogeneous, without significant spatial variations (P > 0.05). These results provided an opportunity to further understand the microbial mechanism of nitrogen removal bioprocesses in urban river networks.

Intensive farming practices are typically used for aquaculture. To prevent disease outbreaks, antibiotics are often used to reduce pathogenic bacteria in aquaculture animals. However, the effects of antibiotics on water quality and microbial communities in euryhaline fish culture ponds are largely unknown. The aim of this study was to investigate the interactions between sulfamethoxazole (SMX), water quality and microbial communities in milkfish (Chanos chanos) culture ponds. The results of small-scale milkfish pond experiments indicated that the addition of SMX decreased the abundance of ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB) and photosynthetic bacteria. Consequently, the levels of ammonia and total phosphorus in the fish pond water increased, causing algal and cyanobacterial blooms to occur. In contrast, the addition of the SMX-degrading bacterial strains A12 and L effectively degraded SMX and reduced the levels of ammonia and total phosphorus in fish pond water. Furthermore, the abundances of AOB, NOB and photosynthetic bacteria were restored, and algal and cyanobacterial blooms were inhibited. This study demonstrate the influences of SMX on water quality and microbial community composition in milkfish culture ponds. Moreover, the use of the bacterial strains A12 and L as dual function (bioaugmentation and water quality maintenance) beneficial bacteria was shown to provide an effective approach for the bioremediation of SMX-contaminated euryhaline milkfish culture ponds.

Ammonia oxidation is the rate-limiting step in nitrification process and dominated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). In the present study, a highly enriched culture of AOA was obtained from urban polluted water in Shahe River, Shenzhen, China. The optimum growth conditions were identified by orthogonal analysis as 37 °C, with pH 7.0 and initial ammonia concentration of 1.0 mM. Under these conditions, the highest abundance of AOA was obtained as 4.6 × 10⁷ copies/ng DNA. Growth of AOA in polluted river water showed significant reduction in ammonia concentration in AOA-enriched cultures without antibiotics after 10 days of incubation, while synchronous increase in nitrate concentration was up to 12.7 mg/L. However, AOA-enriched by antibiotic showed insignificant changes in ammonia or nitrite concentration. This study showed that AOB play an important role in ammonia oxidation of polluted river water, and AOA alone showed insignificant changes in ammonia or nitrite concentrations. Therefore, the ammonia oxidation performance of natural water could not be improved by adding high concentration AOA bacterial liquid.

Ionic liquids (ILs) are extensively used in several chemistry fields. And research about the effects of ILs on soil microbes is needed. In this study, brown soil was exposed to 1-butyl-3-methylimidazolium bromide ([C₄mim]Br), 1-hexyl-3-methylimidazolium bromide ([C₆mim]Br) and 1-decyl-3-methylimidazolium bromide ([C₁₀mim]Br). The toxicities of the three ILs are evaluated by measuring the soil culturable microbial number, enzyme activity, microbial diversity and, abundance of the ammonia monooxygenase (amoA) genes of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Results showed that all tested ILs caused a decrease in culturable microbial abundance. Tested ILs exposure inhibit urease activity and promote acid phosphatase and β-glucosidase activities. Tested ILs reduced soil microbial diversity and the abundances of AOB-amoA and AOA-amoA genes significantly. After a comparison of the integrated biomarker response (IBR) index, the toxicities of tested ILs to soil microorganisms were as follows: [C₁₀mim]Br > [C₆mim]Br > [C₄mim]Br. Among all collected biomarkers, the abundance of the AOA-amoA gene was the most sensitive one and was easily affected after ILs exposure.