The abundance and community structure of active ammonia-oxidizing archaea and ammonia-oxidizing bacteria shape their activities and contributions in coastal wetlands

The significant contribution of comammox bacteria to nitrification in a constructed wetland revealed by DNA-based stable isotope probing

The discovery of Comammox bacteria (CMX) has changed our traditional concept towards nitrification, yet its role in constructed wetlands (CWs) remains unclear. This study investigated the contributions of CMX and two canonical ammonia-oxidizing microorganisms, ammonia-oxidizing bacteria (AOB) and archaea to nitrification in four regions (sediment, shoreside, adjacent soil, and water) of a typical CW using DNA-based stable isotope probing. The results revealed that CMX not only widely occurred in sediment and shoreside zones with high abundance (5.08 × 104 and 6.57 × 104 copies g-1 soil, respectively), but also actively participated in ammonia oxidation, achieving ammonia oxidation rates of 1.43 and 2.00 times that of AOB in sediment and shoreside, respectively. Phylogenetic analysis indicated that N. nitrosa was the dominant and active CMX species. These findings uncovered the crucial role of CMX in nitrification of sediment and shoreside, providing a new insight into nitrogen cycle of constructed wetlands.

Response of bacterial and micro-eukaryotic communities to spatio-temporal fluctuations of wastewater in full scale constructed wetlands

How microbial communities respond to wastewater fluctuations is poorly understood. Full-scale surface flow constructed wetlands (SFCWs) were constructed for investigating microbial communities. Results showed that influent wastewater changed sediment bacterial community composition seasonally, indicating that a single bacterial taxonomic group had low resistance (especially, Actinobacteriota and Gammaproteobacteria). However, copy numbers of 16S rRNA, ammonia oxidizing archaea, ammonia oxidizing bacteria, nirS and nirK in the first stage SFCWs were 2.49 × 1010, 3.48 × 109, 5.76 × 106, 8.77 × 108 and 9.06 × 108 g-1 dry sediment, respectively, which remained stable between seasons. Moreover, decreases in the nitrogen concentration in wastewater, changed microbial system state from heterotrophic to autotrophic. Micro-eukaryotic communities were more sensitive to wastewater fluctuations than bacterial communities. Overall, results revealed that microbial communities responded to spatio-temporal fluctuations in wastewater through state changes and species asynchrony. This highlighted complex processes of wastewater treatment by microbial components in SFCWs.

Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate

Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.

Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China

Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg-1 N ha-1) was 23.35 % higher than that at the intermediate rate (100-150 kg-1 N ha-1) and 20.77 % higher than that at the low rate (< 100 kg-1 N ha-1). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4+ content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.

Driving force of tidal pulses on denitrifiers-dominated nitrogen oxide emissions from intertidal wetland sediments

Intertidal wetland sediments are an important source of atmospheric nitrogen oxides (NOx), but their contribution to the global NOx budget remains unclear. In this work, we conducted year-round and diurnal observations in the intertidal wetland of Jiaozhou Bay to explore their regional source-sink patterns and influence factors on NOx emissions (initially in the form of nitric oxide) and used a dynamic soil reactor to further extend the mechanisms underlying the tidal pulse of nitric oxide (NO) observed in our investigations. The annual fluxes of NOx in the vegetated wetland were significantly higher than those in the wetland without vegetation. Their annual variations could be attributed to changes in temperature and the amount of organic carbon in the sediment, which was derived from vegetated plants and promoted the carbon-nitrogen cycle. Anaerobic denitrifiers had advantages in the intertidal wetland sediment and accounted for the major NO production (63.8 %) but were still limited by nitrite and nitrate concentrations in the sediment. Moreover, the tidal pulse was likely a primary driver of NOx emissions from intertidal wetlands over short periods, which was not considered in previous investigations. The annual NO exchange flux considering the tide pulse contribution (8.93 ± 1.72 × 10-2 kg N ha-1 yr-1) was significantly higher than that of the non-pulse period (4.14 ± 1.13 × 10-2 kg N ha-1 yr-1) in our modeling result for the fluxes over the last decade. Therefore, the current measurement of NOx fluxes underestimated the actual gas emission without considering the tidal pulse.

Effects of different aeration strategies and ammonia-nitrogen loads on nitrification performance and microbial community succession of mangrove constructed wetlands for saline wastewater treatment

In highly salinized environments, nitrification is the process that limits the rate of nitrogen transformation and removal. Therefore, this study concentrated on the impacts of different aeration strategies and NH4+-N loads on the nitrification performance of mangrove constructed wetlands (CWs), as well as investigating the succession mechanism of ammonia-oxidizing microorganisms (AOMs). The results showed that both the CW with continuous aeration (CA-CW) and intermittent aeration (IA-CW) achieved a nitrification efficiency of more than 98% under an NH4+-N loading of 1.25-4.7 g/(m2·d). However, the total nitrogen removal rates of IA-CW under low and high ammonia-nitrogen loads (LAL, 20.09 ± 4.4% and HAL, 8.77 ± 1.35%, respectively) were higher than those of CA-CW (16.11 ± 4.7% and 3.32 ± 2.3%, respectively), especially under HAL (p < 0.05). Pearson correlation analysis showed that under different operating conditions, the differential secretion of Kandelia candel rhizosphere organic matter had a certain regulatory effect on nitrification and denitrification groups such as Candidatus Nitrocosmicus, Nitrancea, Truepera, Pontibacter, Halomonas, and Sulfurovum in the wetland root layer. The quantitative polymerase chain reaction revealed that the NH4+-N load rate was the primary factor driving the succession of the AOMs, with different aeration strategies exacerbating this process. Overall, this study revealed that the dominant AOMs in mangrove CWs could be significantly altered by regulating the aeration modes and pollution loads to adjust the rhizosphere organic matter in situ, thereby resulting in more efficient nitrification.

Shifts of soil archaeal nitrification and methanogenesis with elevation in water level fluctuation zone of the three Gorges Reservoir, China

The water level fluctuation zone is a unique ecological zone exposed to long-term drying and flooding and plays a critical role in the transport and transformation of carbon and nitrogen materials in reservoir-river systems. Archaea are a vital component of soil ecosystems in the water level fluctuation zones, however, the distribution and function of archaeal communities in responde to long-term wet and dry alternations are still unclear. The community structure of archaea in the drawdown areas at various elevations of the Three Gorges Reservoir was investigated by selecting surface soils (0-5 cm) of different inundation durations at three sites from upstream to downstream according to the flooding pattern. The results revealed that prolonged flooding and drying increased the community diversity of soil archaea, with ammonia-oxidizing archaea being the dominant species in non-flooded regions, while methanogenic archaea were abundant in soils that had been flooded for an extended period of time. Long-term alternation of wetting and drying increases methanogenesis but decreases nitrification. It was determined that soil pH, NO3--N, TOC and TN are significant environmental factors affecting the composition of soil archaeal communities (P = 0.02). Long-term flooding and drying changed the community composition of soil archaea by altering environmental factors, which in turn influenced nitrification and methanogenesis in soils at different elevations. These findings contribute to our understanding of soil carbon and nitrogen transport transformation processes in the water level fluctuation zone as well as the effects of long-term wet and dry alternation on soil carbon and nitrogen cycles. The results of this study can provide a basis for ecological management, environmental management, and long-term operation of reservoirs in water level fluctuation zones.

Effects of landscape modification on coastal sediment nitrogen availability, microbial functional gene abundances and N2O production potential across the tropical-subtropical gradient

Wetland sediment is an important nitrogen pool and a source of the greenhouse gas nitrous oxide (N₂O). Modification of coastal wetland landscape due to plant invasion and aquaculture activities may drastically change this N pool and the related dynamics of N₂O. This study measured the sediment properties, N₂O production and relevant functional gene abundances in 21 coastal wetlands across five provinces along the tropical-subtropical gradient in China, which all had experienced the same sequence of habitat transformation from native mudflats (MFs) to invasive Spartina alterniflora marshes (SAs) and subsequently to aquaculture ponds (APs). Our results showed that change from MFs to SAs increased the availability of NH₄⁺-N and NO₃^--N and the abundance of functional genes related to N₂O production (amoA, nirK, nosZ Ⅰ, and nosZ Ⅱ), whereas conversion of SAs to APs resulted in the opposite changes. Invasion of MFs by S. alterniflora increased N₂O production potential by 127.9%, whereas converting SAs to APs decreased it by 30.4%. Based on structural equation modelling, nitrogen substrate availability and abundance of ammonia oxidizers were the key factors driving the change in sediment N₂O production potential in these wetlands. This study revealed the main effect patterns of habitat modification on sediment biogeochemistry and N₂O production across a broad geographical and climate gradient. These findings will help large-scale mapping and assessing landscape change effects on sediment properties and greenhouse gas emissions along the coast.

Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands

Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N₂O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N₂O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N₂O through lab-scale subsurface CWs. The N₂O emission flux of CW at 8 °C was 1.23 mg m^-2·h^-1, significantly lower than that at 25 °C (1.92 mg m^-2·h^-1). The contribution of ammonia oxidation to N₂O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N₂O production from AOA increased from 1.91 ng N·g^-1 at 25 °C to 4.11 ng N·g^-1 soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N₂O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N₂O at low temperature.

Non-negligible roles of archaea in coastal carbon biogeochemical cycling

Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO₂ fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.

Novel database and cut-off value for bacterial amoA gene revealed a spatial variability pattern of the ammonia-oxidizing bacteria community from river to sea

Ammonia-oxidizing bacteria (AOB) catalyze the first step of nitrification, oxidizing ammonia to nitrite, and are characterized by amoA gene encoding ammonia monooxygenase. To analyze the AOB community effectively, an integral taxonomy database containing 14,058 amoA sequences and the optimal cut-off value at 95 % for OTU clustering were determined. This method was evaluated to be efficient by the analysis of environmental samples from the river, estuary, and sea. Using this method, a significant spatial variance of the AOB community was found. The diversity of AOB was highest in the estuary and lowest in the ocean. Nitrosomonas were the predominant AOB in the sediments of the freshwater river and estuary. Nearly all the AOB-amoA sequences belonged to uncultured bacterium in the sediments of deep sea. In general, an integral AOB taxonomic database and a suitable cut-off value were constructed for the comprehensive exploration of the diversity of AOB from river to sea.

Distribution of ammonia oxidizers and their role in N2 O emissions in the reservoir riparian zone

As a transitional boundary between terrestrial and aquatic ecosystems, the riparian zone is considered a hotspot for N₂ O production because of the active nitrogen processes. Ammoxidation is an important microbial pathway for N₂ O production, but the distribution of ammonia oxidizers under different land-use types in the reservoir riparian zone and what role they played in N₂ O emissions are still not clear. We investigated spatiotemporal distributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their role in N₂ O emissions in different land-use types along the riparian zone of Miyun Reservoir: grassland, sparse woods, and woodland. We found significant differences in both AOA abundance and AOB diversity indices among land-use types. AOA and AOB communities were significantly separated by different land-use types. The main drivers to determine the distribution of ammonia-oxidizing microbial community were soil water content, NH₄ ⁺ , NO₃ ^- , and total organic carbon (TOC). In situ N₂ O flux was highest in woodland with a mean value of 12.28 μg/m² ·h, and it was substantially decreased by 121% and 123% in sparse woods and grassland. TOC content was decreased by 20% and 40% in sparse woods and grassland compared with woodland, and it was significantly positively correlated with in situ N₂ O flux. Meanwhile, AOB diversity indices were significantly correlated with in situ N₂ O flux. These results showed that the heterogeneity of physicochemical properties among different land-use types affected the community of AOA and AOB in riparian zones. AOB not AOA, and community diversity rather than abundance, played a role in N₂ O emissions.

Metagenomics reveals bacterioplankton community adaptation to long-term thermal pollution through the strategy of functional regulation in a subtropical bay

Thermal effluents from coastal nuclear power plants have led to undesirable pollution and subsequent ecological impacts on local marine ecosystems. However, despite the ecological importance, we know little about the impacts on functionality of bacterioplankton subjected in systems with long-term thermal pollution. We used metagenomic sequencing to study of the effect of thermal pollution on bacterioplankton community metagenomics in summer in a subtropical bay located on the northern coast of the South China Sea. Thermal pollution (>15 y), which resulted in an increase in the summer seawater temperature around 8°C and caused seawater temperature up to approximate 39°C, significantly decreased bacterioplankton metabolic potentials in photosynthesis, organic carbon synthesis, and energy production. The bacterioplankton community metagenomics underwent a significant change in its structure from Synechococcus-dominant autotrophy to Alteromonas, Vibrio, and Pseudoalteromonas-dominated heterotrophy, and significantly up-regulated genes involved in organic compound degradation and dissimilatory nitrate reduction for the matter and energy acquisition under thermal pollution. Moreover, the bacterioplankton community metagenomics showed an up-regulation with heating of genes involved in DNA repair systems, heat shock responsive chaperones and proteins, and proteins involved in other biological processes, such as biofilm formation and the biosynthesis of unsaturated fatty acids and glycan, to adapt to the thermal environment. Collectively, it indicates a functional regulation of bacterioplankton adaptation to high-temperature stress, which might advance the understanding of the molecular mechanisms of community adaptation to global extreme warming in aquatic ecosystems.

Review on strategies of close-to-natural wetland restoration and a brief case plan for a typical wetland in northern China

Wetlands play an important role in sustaining ecosystems on the earth, which regulate water resources, adjust local climate and produce food for human beings, etc. However, wetlands are facing huge challenges due to human activities and other natural evolution, such as area shrinkage, function weakening and biodiversity decrease, and so on, therefore, some wetlands need to be urgently restored. In this study, the main technology components of close-to-natural restoration of wetlands were summarized. The ecological water requirement and water resource allocation can be optimized for the water balance between social, economy and ecology, which is a key prerequisite for maintaining wetland ecosystem. The pollution of wetland sediments and soils can be assessed by various indicators to provide the scientific basis for natural restoration of wetland base, and suitable strategies should be taken according to the actual conditions of wetland bases. The hydrological connectivity in wetlands and with related water system can be numerically simulated to make the optimal plan for improvement of hydrological connectivity. The ecological restoration of wetlands with the synergetic function of plants, animals and microorganisms was summarized, to improve the quality of wetland water environment and maintain the ecosystem stability. Based on the wetland close-to-natural restoration strategies, a brief ecological restoration plan for a typical wetland, Zaozhadian Wetland, near Xiong'an New Area in the north China was proposed from water resource guarantee, base pollution management, hydrological connectivity improvement and biological restoration. The close-to-natural restoration shows more effective, sustainable and long-lasting and thus a practical prospect.

Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China's coastal wetlands

Planktonic bacteria and archaea play a key role in maintaining ecological functions in aquatic ecosystems; however, their biogeographic patterns and underlying mechanisms have not been well known in coastal wetlands including multiple types and at a large space scale. Therefore, planktonic bacteria and archaea and related environmental factors were investigated in twenty-one wetlands along China's coast to understand the above concerns. The results indicated that planktonic bacteria had different biogeographic pattern from planktonic archaea, and both patterns were not dependent on the wetland's types. Deterministic selection shapes the former's community structure, whereas stochastic processes regulate the latter's, being consistent with the fact that planktonic archaea have a larger niche breadth than planktonic bacteria. Planktonic bacteria and archaea co-occur, and their co-occurrence rather than salinity is more important in shaping their community structure although salinity is found to be a main environmental deterministic factor in the coastal wetland waters. This study highlights the role of planktonic bacteria-archaea co-occurrence on their biogeographic patterns, and thus provides a new insight into studying underlying mechanisms of microbial biogeography in coastal wetlands.

Bioaugmented constructed wetlands for efficient saline wastewater treatment with multiple denitrification pathways

Six laboratory-scale constructed wetlands (CWs) were used to quantify the nitrogen removal (NR) capacity in the treatment of saline wastewater at high (6:1) and low (2:1) carbon-nitrogen ratios (C/N), with and without bioaugmentation of aerobic-denitrifying bacterium. Sustained high-efficiency nitrification was observed throughout the operation. However, under different C/N ratios, although the bioaugmentation of aerobic-denitrifying bacterium promoted the removal of NO₃^--N and TN, there were still great differences in denitrification. Molecular biology experiments revealed ammonia-oxidizing archaea, together with the Nitrosomonas and Nitrospira, led to highly efficient nitrification. Furthermore, aerobic-denitrifying bacterium and sulfur-driven denitrifiers were the core denitrification groups in CWs. By performing these combined experiments, it was possible to determine the optimal CW design and the most relevant NR processes for the treatment of salty wastewater. The results suggest that the bioaugmentation of salt-tolerant functional bacteria with multiple NR pathways are crucial for the removal of salty wastewater pollutants.

Determining the effect of sertraline on nitrogen transformation through the microbial food web in sediments based on 15N-DNA-stable isotope probing

Antidepressants may influence the food web and alter the nitrogen cycle through top-down forces. However, the effect of antidepressants on the key nitrogen-using species in the benthic microbial food web remains unclear, particularly the resulting changes in the nitrogen transformation process within the microecosystems. Therefore, in this study, we employed DNA stable-isotope probing to detect nitrogen-converting organisms at various trophic levels and quantify the nitrogen transformation process for the first time. The input of sertraline greatly increased nitrogen-transforming microorganisms and promoted more species to participate in the nitrogen transformation process. 100 μg/L sertraline was observed to stimulate the predation of bacteria via protozoa and metazoan, increasing the total nitrogen flow flux through the microbial food web to 31.50%, 1.32 times that of the natural condition. The results confirm that at sertraline concentrations close to the lowest observable effect concentration in the meiobenthos (100 μg/L), key components in the microbial food web were largely interfered and exerted a long-term interference on the nutrient cycle in the river sediment ecosystem. These findings confirm that sertraline has negative effects on river ecosystems from the perspective of microbial food webs and open a new line of inquiry into assessing ecological risks of antidepressants.

Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques

In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO₃)₂ injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO₃)₂ injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO₃)₂ injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO₃)₂ runs. Taken together, Ca(NO₃)₂ was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.