Spatial distribution of archaeal and bacterial ammonia oxidizers in the littoral buffer zone of a nitrogen-rich lake

Methane emissions and the microbial community in flooded paddies affected by the application of Fe-stabilized natural organic matter

Redox chemistry involving the quinone/phenol cycling of natural organic matter (NOM) is known to modulate microbial respiration. Complexation with metals or minerals can also affect NOM solubilization and stability. Inspired by these natural phenomena, a new soil amendment approach was suggested to effectively decrease methane emissions in flooded rice paddies. Structurally stable forms of NOM such as lignin and humic acids (HAs) were shown to decrease methane gas emissions in a vial experiment using different soil types and rice straw as a methanogenic substrate, and this inhibitory behavior was likely enhanced by ferric ion-NOM complexation. A mechanistic study using HAs revealed that complexation facilitated the slow release of the humic components. Interestingly, borohydride-based reduction, which transformed quinone moieties into phenols, caused the HAs to lose their inhibitory capacity, suggesting that the electron-accepting ability of HAs is vital for their inhibitory effect. In rice field tests, the humic-metal complexes were shown to successfully mitigate methane generation, while carbon dioxide emissions were relatively unchanged. Microbial community analysis of the rice fields by season revealed a decrease in specific cellulose-metabolizing and methanogenic genera associated with methane emissions. In contrast, the relative abundance of Thaumarchaeota and Actinomycetota, which are associated with NOM and recalcitrant organics, was higher in the presence of Fe-stabilized HAs. These microbial dynamics suggest that the slow release of humic components is effective in modulating the anoxic soil microbiome, possibly due to their electron-accepting ability. Given the simplicity, cost-effectiveness, and soil-friendly nature of complexation processes, Fe-stabilized NOM represents a promising approach for the mitigation of methane emissions from flooded rice paddies.

Anaerobic oxidation of methane in terrestrial wetlands: The rate, identity and metabolism

The recent discovery of anaerobic oxidation of methane (AOM) in freshwater ecosystems has caused a great interest in "cryptic methane cycle" in terrestrial ecosystems. Anaerobic methanotrophs appears widespread in wetland ecosystems, yet, the scope and mechanism of AOM in natural wetlands remain poorly understood. In this paper, we review the recent progress regarding the potential of AOM, the diversity and distribution, and the metabolism of anaerobic methanotrophs in wetland ecosystems. The potential of AOM determined through laboratory incubation or in situ isotopic labeling ranges from 1.4 to 704.0 nmol CH4·g-1 dry soil·d-1. It appears that the availability of electron acceptors is critical in driving different AOM in wetland soils. The environmental temperature and salinity exert a significant influence on AOM activity. Reversal methanogenesis and extracellular electron transfer are likely involved in the AOM process. In addition to anaerobic methanotrophic archaea, the direct involvement of methanogens in AOM is also probable. This review presented an overview of the rate, identity, and metabolisms to unravel the biogeochemical puzzle of AOM in wetland soils.

Distribution characteristics of nitrogen and the related microbial community in the surface sediments of the Songhua River

Nitrogen in surface sediments is becoming an ecological risk to the river environment and it is essential to clarify the relationship between the different forms of nitrogen and related microorganisms. A survey was conducted to analyze the distribution characteristics of the nitrogen and related microbial community in the sediments of the Songhua River during normal season and dry season. In the surface sediments of the Songhua River, no total nitrogen (TN) pollution risk was observed according to the U.S. EPA assessment criteria (1000 mg kg-1) for sediment contamination, but TN in several sampling sites (554.9-759.7 mg kg-1) exceeded the alert values (550 mg kg-1) should be concerned according to the guidelines issued by the Ministry of Environment and Energy of Ontario, Canada. The average TN, NH4 +-N, NO3 --N and total organic nitrogen (TON) in the surface sediments of the Songhua River during normal season were higher than those in the dry period. TON was the main form of nitrogen in the sediment of Songhua River, NO2 --N content was lowest and no obvious difference was observed between normal and dry seasons. The highest average NH4 +-N of both seasons occurred in the Nenjiang River, and the highest average NO3 --N of both seasons were found in the main stream of the Songhua River. The community abundance of AOB genes (1.1 × 107 to 2.5 × 108 copies per g soil in normal season, 7.2 × 105 to 3.3 × 108 copies per g soil in dry season) was higher than that (1.2 × 106 to 9.7 × 107 copies per g soil in normal season, 6.6 × 104 to 3.2 × 107 copies per g soil in dry season) of AOA genes in both normal and dry seasons. The denitrifying nirS genes were predominant in both seasons, and their abundance (1.8 × 106 to 8.0 × 108 copies per g soil) in dry season was higher than that (9.7 × 105 to 4.6 × 108 copies per g soil) in normal season. Moreover, the moisture concentration, pH, dissolved oxygen and different formation of nitrogen were key factors affecting the variation of nitrogen-transformation microorganisms during normal and dry seasons. This research could help to explain the relationship between nitrogen transformation and the related microbial community in the surface sediment, which could provide a scientific basis for water ecological restoration and water environment improvement of Songhua River.

Nitrate reduction in the reed rhizosphere of a riparian zone: From functional genes to activity and contribution

The increased nitrogen (N) fertilizer usage caused substantial nitrate (NO₃^-) leaching into groundwater and eutrophication in downstream aquatic systems. Riparian zones positioned as the link interfaces of terrestrial and aquatic environments are effective in NO₃^- removal. However, the microbial mechanisms regulating NO₃^- reduction in riparian zones are still unclear. In this study, four microbial NO₃^- reduction processes were explored in fine-scale riparian soil horizons by isotopic tracing technique, qPCR of functional gene, high-throughput amplicon sequencing, and phylogenetic molecular ecological network analysis. Interestingly, anaerobic ammonium oxidation (anammox) contributed to NO₃^- removal of up to 48.2% only in waterward sediments but not in landward soil. Denitrification was still the most significant contributor to NO₃^- reduction (32.0-91.8%) and N-losses (51.7-100%). Additionally, dissimilatory nitrate reduction to ammonium (DNRA) played a key role in NO₃^- reduction (4.4-67.5%) and was even comparable to denitrification. Community structure analysis of denitrifying, anammox, and DNRA bacterial communities targeting the related functional gene showed that spatial heterogeneity played a greater role than both temporal and soil type (rhizosphere and non-rhizosphere soil) variability in microbial community structuring. Denitrification and DNRA communities were diverse, and their activities did not depend on gene abundance but were significantly related to organic matter, suggesting that gene abundance alone was insufficient in assessing their activity in riparian zones. Based on networks, DNRA plays a keystone role among the microbial NO₃^- reducers. As the last line of defense in the interception of terrestrial NO₃^-, these findings contribute to our understanding of NO₃^- removal mechanisms in riparian zones, and could potentially be exploited to reduce the diffusion of NO₃^- pollution.

Linking abundance and community of microbial N2O-producers and N2O-reducers with enzymatic N2O production potential in a riparian zone

As aquatic-terrestrial ecotones, riparian zones are hotspots not only for denitrification but also for nitrous oxide (N₂O) emission. Due to the potential role of nosZ II in N₂O mitigation, emerging studies in terrestrial ecosystems have taken this newly reported N₂O-reducer into account. However, our knowledge about the interactions between denitrification activities and both N₂O-producers and reducers (especially for nosZ II) in aquatic ecosystems remains limited. In this study, we investigated spatiotemporal distributions of in situ N₂O flux, potential N₂O production rate, and potential denitrification rate, as well as of the related genes in a riparian zone of Baiyangdian Lake. Real-time quantitative PCR (qPCR) and high-throughput sequencing targeted functional genes were used to analyze the denitrifier communities. Results showed that great differences in microbial activities and abundances were observed between sites and seasons. Waterward sediments (constantly flooded area) had the lowest N₂O production potential in both seasons. Not only the environmental factors (moisture content, NH₄⁺ content and TOM) but also the community structure of N₂O-producers and N₂O-reducers (nirK/nirS and nosZ II/nosZ I ratios) could affect the potential N₂O production rate. The abundance of the four functional genes in the winter was higher than in the summer, and the values all peaked at the occasionally flooded area in the winter. The dissimilarity in community composition was mainly driven by moisture content. Altogether, we propose that the N₂O production potential was largely regulated by the community structure of N₂O-producers and N₂O-reducers in riparian zones. Increasing the constantly flooded area and reducing the occasionally flooded area of lake ecosystems may help reduce the level of denitrifier-produced N₂O.

Stimulating ammonia oxidizing bacteria (AOB) activity drives the ammonium oxidation rate in a constructed wetland (CW)

An integrated approach to document high ammonium oxidation rate in Guanjinggang constructed wetland (GJG-CW) was performed and the results showed that the substantial ammonium oxidation rate could be obtained by enhancing Ammonia Oxidizing Bacteria (AOB) activity rather than Ammonia Oxidizing Archaea (AOA) activity. In the plant-bed/ditch system, ditch center and plant-bed fringe were two active zones for NH₄⁺-N removal with ammonium oxidation rate peaking at 2.98±0.04 and 2.15±0.02mgNkg^-1d^-1, respectively. The enhanced AOB activity were achieved by increasing water level fluctuations, extending hydraulic retention time (HRT) and stimulating substrate availability, which subsequently enhanced NH₄⁺-N removal by 34.06% in GJG-CW. However, the high AOB activity was not correlated with high AOB abundance, but was instead mostly determined by specific AOB taxa, particularly Nitrosomonas, which dominated in the active AOB. The increased cell-specific AOA activity and high AOA diversity were also achieved using those engineering measures. Although the AOA activity decreased overall with extended HRT and increased NH₄⁺-N contents in GJG-CW, AOA still played a major role on ammonium oxidation in plant-bed soil. The study illustrated that artificially enhancing AOB activity and certain species in anthropogenically polluted water ecosystems would be an effective strategy to improve NH₄⁺-N removal.

Assessment of potential bioavailability of heavy metals in the sediments of land-freshwater interfaces by diffusive gradients in thin films

It is important to understand the potential bioavailability of heavy metals in the sediments of land-freshwater interfaces (between terrestrial and aquatic ecosystems). Therefore, we evaluated the pollution of Cr, Ni, Cu, Zn, As, and Cd in land-freshwater interface sediments/soils according to total concentrations, and used sequential extraction method to measure different fractions of Cd. Then, the diffusive gradients in thin films (DGT) technique was employed to study the potential bioavailability of metals. Results showed that the concentrations of exchangeable and weak acid soluble fraction and oxidizable fraction were higher in ecotone area, and the values of reducible fraction and residual fraction were higher in deep water area. There existed significant positive correlations between [Cd]-DGT (concentration of Cd measured by DGT) and EXC-Cd (exchangeable and weak acid soluble fraction of Cd) (r² = 0.65), but the significant negative correlation was found between [Cd]-DGT and RES-Cd (Residual fraction of Cd) (r² = 0.52). DGT technique is a feasible method to measure potential bioavailability of heavy metals for risk assessment in the sediments/soils of land-freshwater interfaces.

Increased Denitrification Rates Associated with Shifts in Prokaryotic Community Composition Caused by Varying Hydrologic Connectivity

While modern developments in agriculture have allowed for increases in crop yields and rapid human population growth, they have also drastically altered biogeochemical cycles, including the biotransformation of nitrogen. Denitrification is a critical process performed by bacteria and fungi that removes nitrate in surface waters, thereby serving as a potential natural remediation strategy. We previously reported that constant inundation resulted in a coupling of denitrification gene abundances with denitrification rates in sediments, but these relationships were not maintained in periodically-inundated or non-inundated environments. In this study, we utilized Illumina next-generation sequencing to further evaluate how the microbial community responds to these hydrologic regimes and how this community is related to denitrification rates at three sites along a creek in an agricultural watershed over 2 years. The hydrologic connectivity of the sampling location had a significantly greater influence on the denitrification rate (P = 0.010), denitrification gene abundances (P < 0.001), and the prokaryotic community (P < 0.001), than did other spatiotemporal factors (e.g., creek sample site or sample month) within the same year. However, annual variability among denitrification rates was also observed (P < 0.001). Furthermore, the denitrification rate was significantly positively correlated with water nitrate concentration (Spearman's ρ = 0.56, P < 0.0001), denitrification gene abundances (ρ = 0.23-0.47, P ≤ 0.006), and the abundances of members of the families Burkholderiaceae, Anaerolinaceae, Microbacteriaceae, Acidimicrobineae incertae sedis, Cytophagaceae, and Hyphomicrobiaceae (ρ = 0.17-0.25, P ≤ 0.041). Prokaryotic community composition accounted for the least amount of variation in denitrification rates (22%), while the collective influence of spatiotemporal factors and gene abundances accounted for 37%, with 40% of the variation related to interactions among all parameters. Results of this study suggest that the hydrologic connectivity at each location had a greater effect on the prokaryotic community than did spatiotemporal differences, where inundation is associated with shifts favoring increased denitrification potential. We further establish that while complex interactions among the prokaryotic community influence denitrification, the link between hydrologic connectivity, microbial community composition, and genetic potential for biogeochemical cycling is a promising avenue to explore hydrologic remediation strategies such as periodic flooding.

Occurrence and abundance of ammonia-oxidizing archaea and bacteria from the surface to below the water table, in deep soil, and their contributions to nitrification

Using molecular biology methods (qualitative and quantitative PCR), we determined the occurrence and abundance of ammonia‐oxidizing archaea (AOA) and ammonia‐oxidizing bacteria (AOB) from a dry inland soil in Basel, Switzerland, and from the riparian zone of Baiyangdian Lake, China. We also determined the contributions of these microorganisms to ammonia oxidization at different depths based on the nitrification rate. The number of archaeal amoA genes (the key functional gene in AOA) was larger than the number of bacterial amoA genes in each sample, suggesting a dominant role for the AOA amoA gene in environments with a low ammonium concentration. In Baiyangdian Lake, the number of archaeal amoA genes was highest at 6 m and lowest at 12 m from the land–water interface in the soil (at depths from 40 to 60 cm), close to the groundwater, which suggests that AOA become more competitive in environments with a low dissolved oxygen content and are promoted by low pH. The nitrification rate was significantly negatively correlated with depth in the Baiyangdian Lake soil and significantly positively correlated with the number of AOB amoA genes at this site, 6 m from the water.

Ubiquitous anaerobic ammonium oxidation in inland waters of China: an overlooked nitrous oxide mitigation process

Denitrification has long been regarded as the only pathway for terrestrial nitrogen (N) loss to the atmosphere. Here we demonstrate that large-scale anaerobic ammonium oxidation (anammox), an overlooked N loss process alternative to denitrification which bypasses nitrous oxide (N₂O), is ubiquitous in inland waters of China and contributes significantly to N loss. Anammox rates in aquatic systems show different levels (1.0–975.9 μmol N m⁻² h⁻¹, n = 256) with hotspots occurring at oxic-anoxic interfaces and harboring distinct biogeochemical and biogeographical features. Extrapolation of these results to the China-national level shows that anammox could contribute about 2.0 Tg N yr⁻¹, which equals averagely 11.4% of the total N loss from China’s inland waters. Our results indicate that a significant amount of the nitrogen lost from inland waters bypasses denitrification, which is important for constructing more accurate climate models and may significantly reduce potential N₂O emission risk at a large scale.

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China

Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira.

High abundance and diversity of nitrite-dependent anaerobic methane-oxidizing bacteria in a paddy field profile

The discovery of nitrite-dependent anaerobic methane oxidation (n-damo) mediated by 'Candidatus Methylomirabilis oxyfera' with nitrite and methane as substrates has connected biogeochemical carbon and nitrogen cycles in a new way. The paddy fields often carry substantial methane and nitrate, thus may be a favorable habitat for n-damo bacteria. In this paper, the vertical-temporal molecular fingerprints of M. oxyfera-like bacteria, including abundance and community composition, were investigated in a paddy soil core in Jiangyin, near the Yangtze River. Through qPCR investigation, high abundance of M. oxyfera-like bacteria up to 1.0 × 10(8) copies (g d.w.s.)(-1) in summer and 8.5 × 10(7) copies (g d.w.s.)(-1) in winter was observed in the ecotone of soil and groundwater in the paddy soil core, which was the highest in natural environments to our knowledge. In the ecotone, the ratio of M. oxyfera-like bacteria to total bacteria reached peak values of 2.80% in summer and 4.41% in winter. Phylogenetic analysis showed n-damo bacteria in the paddy soil were closely related to M. oxyfera and had high diversity in the soil/groundwater ecotone. All of the results indicated the soil/groundwater ecotone of the Jiangyin paddy field was a favorable environment for the growth of n-damo bacteria.

Nitrification in lake sediment with addition of drinking water treatment residuals

Drinking water treatment residuals (WTRs), non-hazardous by-products generated during potable water production, can effectively reduce the lake internal phosphorus (P) loading and improve water quality in lakes. It stands to reason that special attention regarding the beneficial reuse of WTRs should be given not only to the effectiveness of P pollution control, but also to the effects on the migration and transformation of other nutrients (e.g., nitrogen (N)). In this work, based on laboratory enrichment tests, the effects of WTRs addition on nitrification in lake sediment were investigated using batch tests, fluorescence in situ hybridization, quantitative polymerase chain reaction and phylogenetic analysis techniques. The results indicated that WTRs addition had minor effects on the morphologies of AOB and NOB; however, the addition slightly enhanced the sediment nitrification potential from 12.8 to 13.2 μg-N g(-1)-dry sample h(-1) and also increased the ammonia oxidation bacteria (AOB) and nitrite oxidizing bacteria (NOB) abundances, particularly the AOB abundances (P < 0.05), which increased from 1.11 × 10(8) to 1.31 × 10(8) copies g(-1)-dry sample. Moreover, WTRs addition was beneficial to the enrichment of Nitrosomonas and Nitrosospira multiformis and promoted the emergence of a new Nitrospira cluster, causing the increase in AOB and NOB diversities. Further analysis showed that the variations of nitrification in lake sediment after WTRs addition were primarily due to the decrease of bioavailable P, the introduction of new nitrifiers and the increase of favorable carriers for microorganism attachment in sediments. Overall, these results suggested that WTRs reuse for the control of lake internal P loading would also lead to conditions that are beneficial to nitrification.

amoA-encoding archaea and thaumarchaeol in the lakes on the northeastern Qinghai-Tibetan Plateau, China

All known ammonia-oxidizing archaea (AOA) belong to the phylum Thaumarchaeota within the domain Archaea. AOA possess the diagnostic amoA gene (encoding the alpha subunit of ammonia monooxygenase) and produce lipid biomarker thaumarchaeol. Although the abundance and diversity of amoA gene-encoding archaea (AEA) in freshwater lakes have been well-studied, little is known about AEA ecology in saline/hypersaline lakes. In this study, the distribution of the archaeal amoA gene and thaumarchaeol were investigated in nine Qinghai–Tibetan lakes with a salinity range from freshwater to salt-saturation (salinity: 325 g L^-1). The results showed that the archaeal amoA gene was present in hypersaline lakes with salinity up to 160 g L^-1. The archaeal amoA gene diversity in Tibetan lakes was different from those in other lakes worldwide, suggesting Tibetan lakes (high elevation, strong ultraviolet, and dry climate) may host a unique AEA population of different evolutionary origin from those in other lakes. Thaumarchaeol was present in all of the studied hypersaline lakes, even in those where no AEA amoA gene was observed. Future research is needed to determine the ecological function of AEA and possible sources of thaumarchaeol in the Qinghai–Tibetan hypersaline lakes.