Temporal and spatial distribution of ammonia-oxidizing organisms of two types of wetlands in Northeast China

Metagenomic insights into carbon and nitrogen cycling in the water-land transition zone of inland alkaline wetlands

Inland alkaline wetlands play a crucial role in maintaining ecological functions. However, these wetlands are becoming more vulnerable to the effects of water level fluctuations caused by global climate change, especially concerning carbon (C) and nitrogen (N) cycling. Here, metagenomics sequencing was used to investigate microorganism diversity, C and N cycling gene abundance at three water level types (D (dry), MF (middle flooded), HF (high flooded)) along an inland alkaline wetland. Our findings reveal that water level was the most important factor in regulating the microbial communities. Distinct shifts in community composition were found along the water level increases, without fundamentally altering their composition. With the increase of water level, the relative abundance of pmoA decreased from 2.5 × 10-5 to 5.1 × 10-6. The C cycling processes shift from predominantly CO2-generated processes under low water levels to CO2 and CH4 co-generated processes under high water levels. The relative abundance of nosZ reached 4.9 × 10-5 in HF, while in D and MF, it is recorded at 4.5 × 10-5 and 3.4 × 10-5, respectively. Water levels accelerate N cycling and generating N2O intermediates. Furthermore, our study highlights the dynamic competition and cooperation between C and N cycling processes. This research provides a comprehensive biological understanding of the influence of varying water levels on soil C and N cycling processes in wetland.

Effects of salinity on methane emissions and methanogenic archaeal communities in different habitat of saline-alkali wetlands

The increase in temperature caused by global climate change has promoted the salinization of wetlands. Inland saline-alkaline wetlands have an environment of over-humidity and shallow water and are hot spots for CH4 emissions. However, there are few reports on the effect of salinity on CH4 emissions in inland saline-alkaline wetlands. This study conducted simulation experiments of increased salinity to investigate the impact of salinity, habitat, and their interactions on CH4 emissions, as well as to examine the response of methanogenic archaea to salinity. Overall, salinity inhibited CH4 emissions. But there were different responses in the three habitat soils. Salinity decreased the relative abundance of methanogenic archaea and changed the community structure. In addition, salinity changed soil pH and dissolved organic carbon (DOC) and ammonium (NH4+) concentrations, which were significantly correlated with methanogenic archaea. Our study showed that salinity changed the soil physicochemical properties and characteristics of the methanogenic archaeal community, affecting CH4 emissions.

Water level of inland saline wetlands with implications for CO2 and CH4 fluxes during the autumn freeze-thaw period in Northeast China

Zhalong wetland is the largest inland saline wetland in Asia and susceptible to imbalance and frequent flooding during the freeze-thaw period. Changes in water level and temperature can alter the rate of greenhouse gas release from wetlands and have the potential to alter Earth's carbon budget. However, there are few reports on how water level, temperature, and their interactions affect greenhouse gas flux in inland saline wetland during the freeze-thaw period. This study revealed the characteristics of CO₂ and CH₄ fluxes in Zhalong saline wetlands at different water levels during the autumn freeze-thaw period and clarifies the response of CO₂ and CH₄ fluxes to water levels. The significance analysis of cumulative CO₂ fluxes at different water levels showed that water levels did not have a significant effect on cumulative CO₂ release fluxes from wetlands. Water levels, temperature, soil moisture content, soil nitrate, and ammonium nitrogen content and organic carbon content could explain 24.5-98.9% of CO₂ and CH₄ flux variation. There were significant differences in the average and cumulative CH₄ fluxes at different water levels. The higher the water levels, the higher the CH₄ fluxes. In short, water level had a significant effect on wetland methane fluxes, but not on carbon dioxide fluxes.

Stochastic factors drive dynamics of ammonia-oxidizing archaeal and bacterial communities in aquaculture pond sediment

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in nitrification, which is essential in the global nitrogen cycle. However, their dynamics and the underlying community processes in agricultural ecosystems under disturbance remain largely unknown. In this study we examined the spatiotemporal dynamics of AOA and AOB communities and analyzed their community processes in the sediment of aquaculture ponds across three different areas in China. We found some significant temporal changes in AOA and AOB community diversity and abundances, but no temporal changes in community composition, despite the significant variations in sediment properties between different sampling times. Nevertheless, significant differences were found for AOA and AOB communities between different areas. Distinct area-specific taxa were detected, and they were found to be important in determining the response of AOA and AOB communities to environmental factors. In addition, geographic distance was found to be significantly correlated with AOA and AOB community composition, which demonstrates that dispersal limitation could significantly contribute to the variations in AOA and AOB communities, and stochastic processes were found to be important in structuring AOA/AOB communities in aquaculture ponds. Taken together, our study indicates that the dynamics of AOA and AOB are based on their community characteristics in aquaculture pond sediment. Our results, for the first time, provide evidence for the dynamics of AOA and AOB communities being driven by stochastic factors in a disturbed environment, and might also be of use in the management of the aquaculture environment.

Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems

Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.

Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method

Until recently, the de facto method for short-read-based amplicon reconstruction was a sequence similarity threshold approach (operational taxonomic units [OTUs]). This has changed with the amplicon sequence variant (ASV) method where distributions are fitted to abundance profiles of individual genes using a noise-error model. While OTU-based approaches are still useful for 16S rRNA/18S rRNA genes, where thresholds of 97% to 99% are used, their use for functional genes is still debatable as there is no consensus on clustering thresholds. Here, we compare OTU- and ASV-based reconstruction approaches and taxonomy assignment methods, the naive Bayesian classifier (NBC) and Bayesian lowest common ancestor (BLCA) algorithm, using a functional gene data set from the microbial nitrogen-cycling community in the Brouage mudflat (France). A range of OTU similarity thresholds and ASVs were used to compare amoA (ammonia-oxidizing archaea [AOA] and ammonia-oxidizing bacteria [AOB]), nxrB, nirS, nirK, and nrfA communities between differing sedimentary structures. Significant effects of the sedimentary structure on weighted UniFrac (WUniFrac) distances were observed for AOA amoA when using ASVs, an OTU at a threshold of 97% sequence identity (OTU-97%), and OTU-85%; AOB amoA when using OTU-85%; and nirS when using ASV, OTU-90%, and OTU-85%. For AOB amoA, significant effects of the sedimentary structures on UniFrac distances were observed when using OTU-97% but not ASVs, and the inverse was found for nrfA. Interestingly, conclusions drawn for nirK and nxrB were consistent between amplicon reconstruction methods. We also show that when the sequences in the reference database are related to the environment in question, the BLCA algorithm leads to more phylogenetically relevant classifications. However, when the reference database contains sequences more dissimilar to the ones retrieved, the NBC obtains more information. IMPORTANCE Several analysis pipelines are available to microbial ecologists to process amplicon sequencing data, yet to date, there is no consensus as to the most appropriate method, and it becomes more difficult for genes that encode a specific function (functional genes). Standardized approaches need to be adopted to increase the reliability and reproducibility of environmental amplicon-sequencing-based data sets. In this paper, we argue that the recently developed ASV approach offers a better opportunity to achieve such standardization than OTUs for functional genes. We also propose a comprehensive framework for quality filtering of the sequencing reads based on protein sequence verification.

Nitrification mainly driven by ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in an anammox-inoculated wastewater treatment system

Anaerobic ammonium oxidation (anammox) process has been acknowledged as an environmentally friendly and time-saving technique capable of achieving efficient nitrogen removal. However, the community of nitrification process in anammox-inoculated wastewater treatment plants (WWTPs) has not been elucidated. In this study, ammonia oxidation (AO) and nitrite oxidation (NO) rates were analyzed with the incubation of activated sludge from Xinfeng WWTPs (Taiwan, China), and the community composition of nitrification communities were investigated by high-throughput sequencing. Results showed that both AO and NO had strong activity in the activated sludge. The average rates of AO and NO in sample A were 6.51 µmol L⁻¹ h⁻¹ and 6.52 µmol L⁻¹ h⁻¹, respectively, while the rates in sample B were 14.48 µmol L⁻¹ h⁻¹ and 14.59 µmol L⁻¹ h⁻¹, respectively. The abundance of the nitrite-oxidizing bacteria (NOB) Nitrospira was 0.89–4.95 × 10¹¹ copies/g in both samples A and B, the abundance of ammonia-oxidizing bacteria (AOB) was 1.01–9.74 × 10⁹ copies/g. In contrast, the abundance of ammonia-oxidizing archaea (AOA) was much lower than AOB, only with 1.28–1.53 × 10⁵ copies/g in samples A and B. The AOA community was dominated by Nitrosotenuis, Nitrosocosmicus, and Nitrososphaera, while the AOB community mainly consisted of Nitrosomonas and Nitrosococcus. The dominant species of Nitrospira were Candidatus Nitrospira defluvii, Candidatus Nitrospira Ecomare2 and Nitrospira inopinata. In summary, the strong nitrification activity was mainly catalyzed by AOB and Nitrospira, maintaining high efficiency in nitrogen removal in the anammox-inoculated WWTPs by providing the substrates required for denitrification and anammox processes.

Effects of biochar on nitrification and denitrification-mediated N2O emissions and the associated microbial community in an agricultural soil

Nitrous oxide (N₂O) is a strong greenhouse gas, and it is of great significance for N₂O reduction to study the effects of biochar on its production pathway. In this research, the contributions and mechanisms of biochar on autotrophic nitrification (ANF), heterotrophic nitrification (HNF), and denitrification (DF) to N₂O emissions were studied by using ¹⁵N stable isotopes and high-throughput sequencing after laboratory incubation. The results showed that biochar addition at 2% (B2) significantly reduced the N₂O emissions from the ANF by an average of 20.6%, while adding 5% biochar (B5) had no significant effect on the ANF. Both B2 and B5 significantly reduced the N₂O emissions from the HNF by 15.7% and 13.2%, respectively, and reduced the N₂O emissions from the DF by 40.9% and 11.7%, respectively. B2 enhanced the relative contribution rate of the ANF to N₂O emissions by 6.3%, while B5 had little effect on it. Biochar addition significantly changed the copy numbers of the AOA and AOB, as well as the nirK, nirS, and nosZ genes, but it had no significant effect on the community composition of the AOA and had minimal effect on the AOB community. B2 significantly increased the abundance of the genus Rhodococcus of nirK type denitrifiers and had a significant effect on the relative abundance of Cupriavidus and Pseudomonas of the nosZ type denitrifiers. These results revealed that the inhibitory effects of biochar on N₂O emissions from nitrification might be attributed to the direct immobilization and adsorption of inorganic N by biochar and to its promotion of the genus Rhodococcus of nirK-type denitrifiers and the genera Cupriavidus and Pseudomonas of the nosZ-type denitrifiers. The soil exchangeable NH₄⁺-N and NO₃^--N concentrations were the primary factors affecting the N₂O emission rates. These results help to elucidate the effects and mechanisms of biochar on N₂O production pathways in agricultural soil.

Resilience of methane cycle and microbial functional genes to drought and flood in an alkaline wetland: A metagenomic analysis

Alkaline wetlands distributed in arid or semi-arid areas are hotspots of methane (CH₄) emissions. Periods of drought and flood, although regular, are stressful events encountered by methanogenic anaerobes in alkaline wetlands. To investigate the response of the CH₄ cycle of alkaline wetlands to such stresses, we take Zhalong wetland as an example, then determined the CH₄ flux and soil microbiomes in the wetland during wet, dry, and flooded periods. The in-situ CH₄ flux in the wet period was 9.55-17.29 mg‧m^-2‧h^-1, but sharply degraded to 3.37-6.61 mg‧m^-2‧h^-1 in the dry period. It resumed to 4.51-20.80 mg‧m^-2‧h^-1 when the wetland was flooded again, which indicated that methanogenesis is quite resilient to drought. Syntrophic acetogenesis, and subsequently aceticlastic methanogenesis, were the dominant methanogenic pathways and resisted drought. Members belonging to Syntrophobacterales were the dominant syntrophic acetogens. They enter a viable but non-culturable (VBNC) state to resist drought. The dominant Methanosarcinales have the ability to repair reactive oxygen species damage during dry periods. The community of CH₄ sink was governed by anaerobic methanotrophs, which entered a VBNC state or used repair systems to survive dry periods. This study revealed the responses of the CH₄ cycle and microbial functional genes to drought and flood in alkaline wetlands.

Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages

AIMS

Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages.

METHODS AND RESULTS

We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and β-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase.

CONCLUSIONS

AOA and AOB play the different ecological roles in SCP sediments at different culture stages.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.

Long-term harvesting of reeds affects greenhouse gas emissions and microbial functional genes in alkaline wetlands

Reed (Phragmites australis) is dominant vegetation in alkaline wetlands that is harvested annually due to its economic value. To reveal the effects of harvesting reeds on the emission of greenhouse gases (GHG), the annual soil physicochemical characteristics and flux of GHGs in a reed wetland without harvesting (NHRW) and with harvesting (HRW) were measured. The results showed that after the harvesting of reeds, the total organic carbon (TOC) and total nitrogen (TN) significantly decreased, and soil temperature significantly increased. The annual cumulative N₂O emissions decreased from 0.73 ± 0.20 kg ha^-1 to -0.57 ± 0.49 kg ha^-1 with the harvesting of reeds. The annual cumulative CH₄ emissions also decreased from 561.88 ± 18.61 kg ha^-1 to 183.13 ± 18.77 kg ha^-1 with the harvesting of reeds. However, harvesting of reeds had only a limited influence on the annual cumulative CO₂ emissions. A Pearson correlation analysis revealed that the CO₂ and N₂O emissions were more sensitive to temperature than the CH₄ emissions. Both structural equation modeling (SEM) analysis and slurry incubation confirmed that higher temperatures offset the reduction of CO₂ emissions after reed harvesting. Metagenomics showed that the abundance of functional genes involved in both GHG sink and source decreased with reed harvesting. This study presents a comprehensive view of reed harvesting on GHG emissions in alkaline wetlands, yielding new insight into the microbial response and offering a novel perspective on the potential impacts of wetland management.

Specific quorum sensing molecules of ammonia oxidizers and their role during ammonium metabolism in Zhalong wetland, China

The primary challenge of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) surviving in wetlands are the rapid and unpredictable environmental changes. To adapt to a fluctuant environment, ammonia oxidizers have to communicate with each other via acyl-homoserine lactones (AHLs). In this study, AOA and AOB in the soil samples taken from Zhalong wetland were incubated. Dynamics of AHLs during the incubation of ammonia oxidizers were measured. Then, the specific AHLs of AOA and AOB were identified, respectively. The results showed that AOA secreted N-butyryl-dl-homoserine lactone (C₄-HSL) and N-octanoyl-l-homoserine lactone (C₈-HSL) to cope with nitrite accumulation, while they secreted N-(3-oxododecanoyl)-dl-homoserine lactone (OXOC₁₂-HSL) to regulate their ammonium metabolism activity. AOB secreted N-hexanoyl-dl-homoserine lactone (C₆-HSL), N-dodecanoyl-l-homoserine lactone (C₁₂-HSL), N-tetradecanoyl-dl-homoserine lactone (C₁₄-HSL) and N-(3-oxododecanoyl)-tetradecanoyl-dl-homoserine lactone (OXOC₁₄-HSL) only to enhance the metabolism activity. The dominant AOA belonged to the Nitrososphaera lineage, while the dominant AOB grouped into the Nitrosomonas lineage. The AHLs receptor homologs were identified in both AOA and AOB, which confirmed that AOA and AOB had the QS system. The present work was the first study that elucidated the QS system of AOA and AOB in multidimensional, and confirmed the role of QS system in ammonia oxidizers' metabolism.