Currently, wastewater treatment plant (WWTP) upgrades have been implemented in various countries to improve the water quality of the receiving ecosystems and protect aquatic species from potential deleterious effects. The impact of WWTP upgrades on biological communities and functions in receiving waters is a fundamental issue that remains largely unaddressed, especially for microbial communities. Here, we selected two wastewater-dominant rivers in Beijing (China) as study sites, i.e., one river receiving water from an upgraded WWTP to explore the impacts of upgrade on aquatic ecosystems and another river receiving water from a previously upgraded WWTP as a reference. After a five-year investigation, we found that WWTP upgrade significantly decreased total organic nitrogen (N) in the receiving river. As a biological response, N-metabolism-related bacterioplankton are accordingly altered in composition and tend to intensively interact according to the network analysis. Metagenomic analysis based on the N-cycling genes and metagenomic-assembled genomes revealed that WWTP upgrade decreased the abundance of nitrifying bacteria but increased that of denitrifying and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in the receiving river, according to their marker gene abundances. After calculation of the ratios between DNRA and denitrifying bacteria and quantification of genes/bacteria related to ammonium cycling, we deduced the changes in N-metabolism-related bacteria are likely an attempt to provide enough bioavailable N for plankton growth as conservation of ammonium was enhanced in receiving river after WWTP upgrade.

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.

Bacteria involved with ecosystem N cycling in the rhizosphere of submerged macrophytes are abundant and diverse. Any declines of submerged macrophytes can have a great influence on the abundance and diversity of denitrifying bacteria and anammox bacteria. Natural decline, tardy decline, and sudden decline methods were applied to cultivated Potamogeton crispus. The abundance of anammox bacteria and nirS denitrifying bacteria in rhizosphere sediment were detected using real-time fluorescent quantitative PCR of 16S rRNA, and phylogenetic trees were constructed to analyze the diversities of these two microbes. The results indicated that the concentration of NH₄⁺ in pore water gradually increased with increasing distances from the roots, whereas, the concentration of NO₃⁻ showed a reverse trend. The abundance of anammox bacteria and nirS denitrifying bacteria in sediment of declined P. crispus populations decreased significantly over time. The abundance of these two microbes in the sudden decline group were significantly higher (P > 0.05) than the other decline treatment groups. Furthermore, the abundances of these two microbes were positively correlated, with RDA analyses finding the mole ratio of NH₄⁺/NO₃⁻ being the most important positive factor affecting microbe abundance. Phylogenetic analysis indicated that the anammox bacteria Brocadia fuigida and Scalindua wagneri, and nirS denitrifying bacteria Herbaspirillum and Pseudomonas, were the dominant species in declined P. crispus sediment. We suggest the sudden decline of submerged macrophytes would increase the abundance of anammox bacteria and denitrifying bacteria in a relatively short time.

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.

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.

This study focused on the combined effect of environmental conditions (temperature) and contamination (polycyclic aromatic hydrocarbons, PAHs) on the activity of soil microorganisms (nitrifying bacteria). Phenanthrene (Phe) at five contamination levels (0, 1, 10, 100 and 1000 mg kg−1 dry mass of soil) was employed as a model PAH compound in laboratory experiments that were conducted at three temperatures (i.e., 20 °C (recommended by ISO 15685 method), 15 and 30 °C). Three soils with different properties were used in these studies, and the activity of the nitrifying bacteria was assessed based on nitrification potential (NP) determinations. For the statistical evaluation of the results, the ANCOVA (analysis of covariance) method for three independent variables (i.e., temperature, phenanthrene concentration, soil matrix (as a qualitative variable)) and their interactions was employed. The results indicated on the significant interaction of all studied factors. Temperature influenced the toxicity of Phe towards NP, and this effect was related to the Phe concentration as well as was varied for the different soils. A low content of soil organic matter (controlling bioavailability of phenanthrene to soil microorganisms) enhanced the combined effect of temperature and Phe toxicity, and a high biological activity of the soil (high NP values) increased the effect of high temperature on the Phe stimulatory influence. The results indicate that the temperature should not be neglected in tests evaluating PAH ecotoxicity, especially for reliable ecological risk assessment.

A 3-month-long experiment was conducted to ascertain the effects of different concentrations of myclobutanil (0.4 mg kg⁻¹ soil [T1]; 1.2 mg kg⁻¹ soil [T3]; and 4 mg kg⁻¹ soil [T10]) on soil microbial biomass, respiration, and soil nitrogen transformations using two typical agricultural soils (Henan fluvo-aquic soil and Shanxi cinnamon soil). Soil was sampled after 7, 15, 30, 60, and 90 days of incubation to determine myclobutanil concentration and microbial parameters: soil basal respiration (RB), microbial biomass carbon (MBC) and nitrogen (MBN), NO−3–N and NH+4–N concentrations, and gene abundance of total bacteria, N2-fixing bacteria, fungi, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB). The half-lives of the different doses of myclobutanil varied from 20.3 to 69.3 d in the Henan soil and from 99 to 138.6 d in the Shanxi soil. In the Henan soil, the three treatments caused different degrees of short-term inhibition of RB and MBC, NH+4–N, and gene abundance of total bacteria, fungi, N2-fixing bacteria, AOA, and AOB, with the exception of a brief increase in NO−3–N content during the T10 treatment. The MBN (immobilized nitrogen) was not affected. In the Shanxi soil, MBC, the populations of total bacteria, fungi, and N2-fixing bacteria, and NH+4–N concentration were not significantly affected by myclobutanil. The RB and MBN were decreased transitorily in the T10 treatment. The NO−3–N concentrations and the abundance of both AOA and AOB were erratically stimulated by myclobutanil. Regardless of whether stimulation or suppression occurred, the effects of myclobutanil on the two soil types were short term. In summary, myclobutanil had no long-term negative effects on the soil microbial biomass, respiration, and soil nitrogen transformations in the two types of soil, even at 10-fold the recommended dosage.

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.