- Open Access
Vertical niche differentiation of comammox Nitrospira in water-level fluctuation zone of the Three Gorges Reservoir, China
Environmental Sciences Europe volume 34, Article number: 118 (2022)
Comammox (CMX) Nitrospira bacteria (NB) can accomplish ammonia oxidation independently, and their niche differentiation holds promise for their ecological and survival functions. In this work, the vertical niche differentiation of CMX NB was investigated in the soils of 6 water-level fluctuation (WLF) zones (both natural and artificial) in the Three Gorges Reservoir (TGR) region. The results demonstrated that the level of clade A amoA was obviously reduced with increasing soil depth in the natural WLF zones and one of the artificial WLF zones. However, in the other two artificial WLF zones, the abundance of this gene was not dramatically reduced with depth. The level of clade B amoA did not markedly decrease with increasing soil depth in most WLF zones and remained stable in the three WLF zones. Total nitrogen (TN) had the most significant effect on the abundance of CMX NB. Clade A.1, clade A.2.1, clade A.2.2, clade A.3, and clade B of CMX NB co-occurred simultaneously in all WLF zones. The number of operational taxonomic units (OTUs) of clade A in the two types of WLF zones first increased and then decreased with increasing depth, whereas the number of OTUs of clade B continuously increased with depth in the artificial WLF zone. Total carbon (TC) and pH, as environmental factors, affected the community structure of CMX NB. This study confirmed the vertical differentiation of the abundance and diversity of CMX NB in the WLF zones of the TGR region, and the artificial restoration of the WLF zones affected the niche differentiation of CMX NB to a certain degree.
Nitrification is a critical link in the nitrogen biogeochemical cycle, and the nitrogen flux in nitrification in terrestrial ecosystems is 330 Tg . Nitrification is a biological process that converts ammonia to nitrate through microorganism catalysis and plays a vital role in global ecosystems. Nitrification mainly consists of two processes, namely, ammonia oxidation and nitrite oxidation . Specifically, ammonia is first oxidized into nitrite by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) , and then nitrite is oxidized into nitrate by nitrite-oxidizing bacteria (NOB) . Daims et al.  and Van Kessel et al. , respectively, discovered a new microorganism for the direct oxidization of ammonia to nitrate, which is called comammox (CMX) Nitrospira bacteria (NB). These bacteria are widely present in artificial engineering systems, including sewage treatment systems  and nitrification reactors , and they are also found in natural ecosystems such as salt marshes , agricultural soils , riparian soils , lake sediments , and forest soils .
All known CMX NB belongs to Nitrospira sublineage II, which can be further divided into clade A and clade B . In 2018, Xia et al. firstly proposed dividing clade A of CMX into clade A.1 and clade A.2 . In 2021, clade A.2 was divided into clade A.2.1 and clade A.2.2 . A new clade, A.3, was discovered in 2019 . There are certain differences in the physiological properties of clade A and clade B . The genes coding for formate dehydrogenase are present in CMX clade B but not in clade A [17, 18], which makes the distribution of the two clades in the oxic–anoxic transition zones different. These differences result in spatial and temporal differentiation [9, 19] to adapt to different environmental conditions.
Soil physicochemical properties change with increasing soil depth, which often leads to the corresponding changes in some soil microbial community structures. Previous studies showed that total nitrogen, inorganic nitrogen, organic matter, TC, and dissolved oxygen generally decreased with increasing soil depth, while pH did not change significantly [20,21,22]. Various ammonia-oxidizing microorganisms have different adaptabilities to ammonia and oxygen, which contribute to bacterial differentiation with increasing soil depth, and this differentiation enables ammonia-oxidizing microorganisms to occupy a wider range of ecological niches. Previous research demonstrated that the average abundance of all AOA, AOB, and CMX was dramatically reduced with increasing soil depth in forests, grasslands, and farmlands . However, in the typical purple paddy soil in Beibei district, Chongqing, China, the abundance of AOA and AOB was dramatically reduced along the soil depth direction, and the abundance of CMX clade A was raised significantly with increasing soil profile depth, but the abundance of clade B exhibited no obvious change trend with increasing soil depth. The abundance of the AOA gene was shown to decrease with depth, while that of the AOB gene decreased in semi-arid soils in southern Australia . In the sediments of a high-altitude freshwater wetland in Yunnan Province, China, AOA diversity decreased with increasing sediment depth, whereas AOB diversity was not significantly correlated with sediment depth . The CMX diversity in bottom sediments (5–10 cm) was higher than that on the surface (0–1 cm) and in middle sediments (1–5 cm) from the tidal flats of the Yangtze Estuary in China . These phenomena indicate that ammonia-oxidizing microorganisms have the ability to vertically differentiate in different habitats to adapt to diverse natural environments.
The Three Gorges Dam is the largest water conservancy project with the largest comprehensive benefit in the world . After the completion of the Three Gorges Dam, the water level in the reservoir region is 175 m in winter and 145 m in summer with a periodic flooding-exposure water-level fluctuation (WLF) area of 348 km2 on both sides of the reservoir region. After the Three Gorges began impounding water in 2003, the original vegetation in the WLF zones could not survive. Some zones where new vegetation can be restored naturally are often referred to as natural WLF zones . Other zones where vegetation can only be restored by artificial planting are artificial WLF zones. Numerous studies showed that periodic flooding exposure can change the material transformation process in the soil in the WLF zone and increase the content of organic matter in the soil .The oxygen content in the soil, especially in the topsoil, changes dramatically during the flooding-exposure period, thus affecting the growth of CMX NB, making them more prone to vertical differentiation.
In this study, the natural and artificial WLF zones of the Three Gorges Reservoir (TGR) region were chosen to assess the diversity of ammonia-oxidizing microorganisms and the abundance of AOA, AOB, and CMX NB in the soil. The aim of this research was to (a) reveal the vertical differentiation of CMX NB with soil depth in the WLF zones; (b) analyse the main environmental variables driving such differentiation; and (c) explore the adaptation strategies of different clades of CMX NB to depth changes.
Materials and methods
Study sites and sample collection
In this study, Fuling, Wanzhou, and Zigui were selected as sampling areas representing the upper, middle, and lower reaches of the TGR region, with both natural and artificial WLF zones included. A total of 6 sampling zones were as follows: Fuling natural WLF zone (FL-N), Fuling artificial WLF zone (FL-A), Wanzhou natural WLF zone (WZ-N), Wanzhou artificial WLF zone (WZ-A), Zigui natural WLF zone (ZG-N), and Zigui artificial WLF zone (ZG-A) (Additional file 1: Fig. S1). The vegetation in the natural WLF zone mainly includes naturally grown bermudagrass (Cynodon dactylon (L.) Pers.), Polygonum (Polygonum L.), and Arthraxon hispidus (Arthraxon hispidus (Trin.) Makino). The vegetation in the artificial WLF zone mainly consists of bermudagrass (Cynodon dactylon (L.) Pers.), artificially planted willow (Salix babylonica L.), and Zhongshan fir (Taxodium “Zhongshansha”). The sampling time was August 2021. Soil profile samples were collected at four altitudes of 150, 160, 170, and 175 m, and the sampling depths at each altitude sampling site were 0–5, 5–10, 10–20, 20–30, and 30–40 cm. The collected specimens were kept in an ice box and transported back to the laboratory as soon as possible. Some of the soil specimens were stored at 4 ℃ in the laboratory for the subsequent determination of physicochemical properties. Other samples were frozen at – 80 ℃ for DNA isolation and molecular biology tests.
Then, 25 mL of KCL solution (1 mol L−1) was added to 5 g of soil at a KCL solution/soil ratio of 5:1, and the pH value was measured with a digital acidity metre (METTLER TOLEDO, Switzerland) after leaching for 30 min. The air-dried, ground, and sieved soil specimens were isolated with 1 mol L−1 KCl. The ammonia (NH4+–N), nitrate (NO3−–N), and nitrite (NO2−–N) concentrations in the extract were detected. After the freeze-dried samples passed through a 200-mesh sieve, the total nitrogen (TN) and total carbon (TC) in the soil were determined using an elemental analyser (Elementar Vario ELIII analyser, Germany). After drying to constant weight at 105 ℃, the moisture content (MC) was measured.
DNA extraction and quantitative real-time PCR
The total bacterial genomic DNA of soil specimens was isolated with a Fast DNA Spin Kit for Soil (MPbio, USA). The purity and yield of the DNA extracts were detected using a NanoPhotometer-N60 spectrophotometer (IMPLEN, Germany).
AOA amoA, AOB amoA, CMX clade A amoA, and CMX clade B amoA genes were determined by qRT-PCR assay using QuantStudioTM 6 Flex quantitative PCR instrument (Thermo-Fisher-Scientific, Singapore). The primer pairs used for PCR were Arch-amoAF/Arch-amoAR , amoA-1Fmod/GenAOBR , CA377f/C576r , and CB377f/C576r . PCR was performed on a 10 μL reaction system containing T5 Fast qPCR Mix (5.0 μL), 10 μM of each primer (0.4 μL), ROX Reference Dye II (0.2 μL), template DNA (1.0 μL), and ddH2O (3.0 μL). The primers and amplification conditions are presented in Additional file 1: Table S1.
Amplicon sequencing and phylogenetic analysis
The high-throughput sequencing primer of CMX NB was comamoAF/R . The Illumina NovaSeq PE250 (Shanghai Personal Biotechnology) sequencing platform was used for sequencing. Vsearch (v2.13.4_linux_x86_64) was used to process raw data . The specific processing procedures were as follows. First, the primer fragment of the sequence was excised using cutadapt (v2.3), and the sequence of the unmatched primer was discarded. Then, sequence splicing, quality control, and deduplication were conducted using Vsearch. Next, high-quality sequences with 97% nucleic acid similarity were clustered into operational taxonomic units (OTUs) with chimaeras removed, and the singleton OTUs and their corresponding sequences (in the OTU table) were removed. Last, based on the seed protein sequences of the CMX amoA gene, insertion and deletion errors in the OTU sequences were corrected using RDP FrameBot (v1.2) . The obtained gene sequences were submitted to the NCBI (https://www.ncbi.nlm.nih.gov/) database with the accession number ON677371-ON677405.
The top 35 OTUs with the largest number of OTUs were selected to analyse the representative sequences of each OTU using the BLAST tool (http://www.ncbi.nlm.nih.gov/BLAST), and the closest similar sequences were selected from GenBank. Based on the selected sequences, phylogenetic trees were constructed using MEGA 7.0, and their reliability was assessed through 1000 bootstrap replicates.
One-way ANOVA was conducted using SPSS 25.0, and multiple comparisons were performed by the Duncan method to examine the differences in soil physicochemical indices and gene abundance. Redundancy analysis (RDA) was performed using CANOCO v5.0 to assess the association between gene abundance and environmental variables. Phylogenetic trees were constructed using MEGA7.0, and heatmaps of OTU numbers were plotted using “pheatmap” in R. The Mantel test was used to evaluate the correlation between CMX NB and environmental parameters. Spearman correlation analysis and plotting were performed using the packages “Hmisc” and “Corrplot” in R (version 3.6.1) to assess the correlation between diversity, abundance, and physicochemical factor parameters.
Soil properties of the WLF zone in the TGR region
In the natural WLF zone of the TGR region, the difference in NO3− content among various soil depths was significant (P < 0.05), and the content of the surface layer (0–10 cm) was significantly higher than that of the bottom layer (30–40 cm), at 17.85–4.79 mg/kg (Table 1). No significant differences were found for other indicators (P > 0.05). In the artificial WLF zone, the difference in NO3− content among different soil depths was significant (P < 0.05), and the NO3− content at 0–5 cm was remarkably higher than that at 30–40 cm, which was 18.59–8.38 mg/kg. The differences in other indicators were not significant (P > 0.05). The pH of the natural WLF zone was significantly lower than that in the artificial WLF zone (P < 0.05).
Abundance of CMX NB, AOA, and AOB in the WLF zone of the TGR region
In the natural WLF zone, the level of clade A amoA markedly decreased with soil depth (Fig. 1), and its abundance in the 0–5 cm soil surface layer was 1–3 orders of magnitude higher than that at 30–40 cm. In the artificial WLF zone, the level of clade A amoA significantly decreased in Zigui with increasing soil depth, but in Fuling and Wanzhou, the abundance of this gene exhibited no obvious downwards trend. The level of clade B amoA in the other five fluctuation zones except the Fuling natural WLF zone did not decrease significantly with increasing soil depth, and the abundance remained stable in the 3 WLF zones. In addition, in the two artificial WLF zones of Fuling and Zigui, the abundance value was highest at 10–20 cm.
Overall, the level of AOA amoA decreased with increasing soil depth in the natural WLF zones. In the artificial WLF zone, the level of AOA amoA was dramatically reduced with soil depth at the three sites. In all the WLF zones except the Wanzhou natural WLF zone, the AOB abundance showed a downwards trend with increasing soil depth (Fig. 1).
In the natural WLF zone, the average abundance of the amoA gene of CMX clade A, CMX clade B, AOA, and AOB was 1.51 × 108 copies/g dry sediment, 3.82 × 108 copies/g dry sediment, 1.46 × 109 copies/g dry sediment, and 5.00 × 107 copies/g dry sediment, respectively. In the artificial WLF zone, the average abundance of these four genes was 1.05 × 108 copies/g dry sediment, 4.00 × 108 copies/g dry sediment, 9.61 × 109 copies/g dry sediment, and 1.45 × 108 copies/g dry sediment, respectively. There was a significant difference in the levels of the AOA gene between the natural WLF zone and the artificial WLF zone (P < 0.05), while the amoA gene abundance of the other three ammonia-oxidizing microorganisms exhibited no difference (P > 0.05).
The average abundance of the AOA amoA gene was 1.11 × 109 copies/g dry sediment, which was higher than that in CMX clade B (3.91 × 108 copies/g dry sediment) and CMX clade A (1.14 × 108 copies/g dry sediment). The average level of the AOB amoA gene was relatively low (1.10 × 108 copies/g dry sediment).
Co-existence characteristics of ammonia-oxidizing microorganisms and their correlation with environmental factors
Redundancy analysis (RDA) was performed to reveal the correlations between environmental factors and the amoA gene abundances of 4 types of ammonia-oxidizing microorganisms (CMX clade A, CMX clade B, AOA, and AOB) in the WLF zones of the TGR region using CANOCO v5.0. The first two axes of RDA accounted for 48.44% of the cumulative variance explanation rate (Fig. 2). Clade A was positively correlated with AOA or AOB. The abundance of the amoA gene of comammox clade A was negatively correlated with pH, NO2−, and the C/N ratio and positively correlated with TN, TC, NH4+, NO3−, and MC. The abundance of the amoA gene of CMX clade B was negatively correlated with pH, NO2−, C/N, NH4+, NO3−, and MC but was positively correlated with TN.
In the artificial WLF zone, the amoA gene level of CMX clade A was positively correlated with that of CMX clade B (P < 0.01) (Fig. 3b). However, in the natural WLF zone, there was no correlation in the levels of the amoA gene between the two microorganisms (Fig. 3a). The level of the amoA gene in CMX clade A was positively correlated with that of AOB in both natural and artificial WLF zones (P < 0.05) (Fig. 3). In the natural WLF zone, the amoA gene abundance of CMX clade A was negatively correlated with soil depth (P < 0.01). In the artificial WLF zone, the abundance of the AOB amoA gene was also negatively correlated with soil depth (P < 0.05).
Biodiversity of CMX NB
A total of 35,740 high-quality CMX NB amoA gene sequences were detected from the WLF zone of the TGR region and were clustered into 14,813 OTUs with 97% nucleic acid similarity. The selected top 35 OTUs sequences with a relative abundance of OTUs greater than 0.5% and similar sequences from the NCBI database were applied to build a phylogenetic tree via the neighbour-joining method (Fig. 4). The 35 selected OTUs accounted for 65.71% of the CMX amoA gene sequences. The phylogenetic tree contained two clades, of which clade A contained 17 OTUs and clade B contained 18 OTUs. Clade A was further divided into clade A.1 (1 OTU), clade A.2.1 (13 OTUs), clade A.2.2 (2 OTUs), and clade A.3 (1 OTU).
The distribution of 35 OTUs is shown in Fig. 5. In both the natural WLF zone and artificial WLF zone, at the five soil profile depths, clade B was the most dominant species, followed by clade A.2.1.
As the soil depth increased, the number of OTUs in clade A in the two types of WLF zones increased first and then decreased, with the largest OTU number in the 20–30 cm soil layer (Fig. 6). The OTUs number of clade B had no obvious distribution regularity in the natural WLF zone but showed an increasing trend with depth in the artificial WLF zone. In the natural WLF zone, the number of OTUs of clade A.1 increased along the soil depth from 0 to 30 cm. In both types of WLF zones, the OTU number of clade A.2.1 exhibited a decreasing trend along the vertical direction. In the artificial WLF zone, the OTU number of clade A.2.2 increased along the soil depth from 0 to 30 cm, while in the natural WLF zone, it exhibited no obvious change. Clade A.3 had a tendency to gradually increase in OTU number with depth in the artificial WLF zone. The OTU number of clade B was significantly larger at 30–40 cm.
The connections of CMX at different depths were explored by co-occurrence network plots (Fig. 7). Among all samples, clade B possessed the highest number of nodes (49.05%–53.61%), followed by clade A.2 (34.71–40.82%). However, the average degree of clade A.2 was greater than that of clade B. The membership relationships at different depths graphs mainly showed positive interaction connections (0–5 cm: 57.27%; 5–10 cm: 64.46%; 10–20 cm: 62.73%; 20–30 cm: 58.71%; 30–40 cm: 72.26%). In the two types of zone samples, artificial WLF zones possessed more positive interaction connections than natural WLF zones (artificial: 65.02%; natural: 59.53%) (Additional file 1: Fig. S2).
Correlation between community structure of CMX NB and physicochemical factors
In the natural WLF zone, the number of OTUs of clade A.1 was remarkably correlated with NO3− and the C/N ratio (P < 0.05) (Fig. 8a), but in the artificial WLF zone, the number of OTUs of clade A.1 was markedly correlated with NO2− and MC (P < 0.05) (Fig. 8b). In the natural and artificial WLF zones, the number of OTUs of clade A.2 was correlated with both pH and TC (P < 0.05) (Fig. 8), but in the artificial WLF zone, the number of OTUs of clade A.3 was correlated with pH, TN, and TC (P < 0.05). In the natural and artificial WLF zones, the number of OTUs of clade B was correlated with pH, TC, and C/N (P < 0.05) (Fig. 8). In the artificial WLF zone, the Chao1 index and Shannon index, which characterize community abundance and diversity, respectively, were positively correlated with TC (P < 0.01).
Effect of vertical depth of soil on abundance of CMX NB
Our results demonstrated that the level of the CMX clade A amoA gene decreased with increasing soil depth in the WLF zone of the TGR region, and this gene abundance in the surface soil was remarkably higher than that in the deep soil. However, the abundance of the CMX clade B amoA gene did not decrease significantly. This indicated that the two CMX clades were differentiated with depth and that these two clades exhibited different adaptability to depth, with clade B having the higher adaptability.
The abundance of the amoA gene of CMX (3.58 × 108–4.00 × 1013 copies/g dry sediment) in this study was higher than that in plain wetland ecosystems and Yangtze River estuary regions [9, 14]. Soil in the WLF zone is flooded at high water levels, which gives it some similarity to wetland soil. However, different from other wetland soils, due to the influence of periodic inundation, the nutrient composition in the Three Gorges WLF zone showed a general downwards trend during the inundation period [36, 37]. Some studies showed that CMX are more adaptable to low-nutrient environments [2, 38]. The soil oxygen content will increase with the decrease in soil moisture during the outcropping period, which is also conducive to the growth of CMX. These two factors may be the main reason for the higher abundance of CMX in the Three Gorges WLF zone than in the wetland.
The soil oxygen content in the WLF zone, especially in the topsoil, changed drastically during the flooding-exposure period, thus inevitably affecting the growth of CMX NB. Previous studies showed that clade A had higher metabolic diversity than clade B , and clade A not only used ammonia as a metabolic substrate but also utilized urea, cyanate, and hydrogen as substrates for nitrification [6, 18, 40]. However, the evolution rate of ammonia oxidation-related proteins was faster in clade B genomes than in clade A genomes . It may be this advantage that enables clade B to respond more quickly to environmental conditions with frequently changing water levels, which might explain why clade B maintained relatively stable abundances in 3 WLF zones, even reaching the highest abundance at a depth of 10–20 cm in both natural and artificial WLF zones.
Soil vertical depth affects the community structure of CMX NB
With increasing depth, soil environmental conditions change, thus affecting microbial community structure . Previous studies also reported depth-dependent changed in the community structure of typical ammonia-oxidizing microorganisms in lake or wetland sediments . AOA diversity was reduced with increasing sediment depth, while AOB diversity was not significantly related to sediment depth . In subtropical estuarine wetlands, the relative abundance of CMX clade A.2.2 was reduced with depth, while clade A.3 exhibited the opposite trend . In Chongming eastern tidal flat sediment samples, the abundance of CMX clade A.1 in shallow surface sediments (1–5 cm) was higher than that in deep layer sediments (5–10 cm) in summer and winter, while that of clade A.2 exhibited the opposite trend .
Our results showed that the number of OTUs in clade A first increased and then decreased with increasing depth. Clade A.2.1 showed a decreasing trend along the vertical depth, the number of OTUs in clade A.2.2 increased along the soil depth direction from 0 to 30 cm in the artificial WLF zone, and clade A.3 in the artificial WLF zone exhibited an increasing trend with depth. However, the number of OTUs of clade B in the artificial WLF zone showed an increasing trend with depth, and clade B was dominant in the 30–40 cm soil layer. These results showed that in the Three Gorges WLF zone, clade A.2.1 preferred an environment with relatively high oxygen content and richer nutrients, while clade A.2.2, clade A.3, and clade B were more suitable for the hypoxic and oligotrophic environments in the WLF zone.
The results also showed that clade B was predominant in the CMX community in the WLF zone of the TGR region, followed by clade A.2.1. Clade B was the dominant CMX species in low-ammonia soils , which might mainly be because clade B adopted an Amt-type ammonia transporter, whereas clade A possessed an Rh-type ammonia transporter similar to betaproteobacterial AOB. In environments with a large ammonia concentration fluctuation , clade B employing the Amt-type transporter is more competitive . This might be an important reason why clade B was predominant in the WLF zone in this study.
Physicochemical factors affecting the community structure of CMX NB
TN is a pivotal factor affecting the level of the CMX amoA gene . In this work, TN was positively correlated with the level of the CMX clade A gene. The microcosm experiment showed that under the condition of insufficient external ammonia supply, CMX NB also had continuous amoA gene transcription , indicating that CMX NB had a competitive advantage over other ammonia-oxidizing microorganisms under low ammonia conditions. This might be because the slow organic nitrogen mineralization process provided sufficient ammonia for the growth of CMX NB with a high ammonia affinity [45, 46].
In the natural WLF zone of this study, the community structures of clade A.2 and clade B were significantly affected by pH and TC. In the artificial WLF zone, the community structures of clades A.1, A.2, A.3, and B were significantly affected by pH and TC. This suggested that pH and TC were important environmental drivers of niche differentiation for CMX, AOB, and AOA in soil habitats.
CMX NB had a greater competitive advantage over other ammonia-oxidizing microorganisms in acidic soils than in neutral and alkaline soils. This might be because CMX NB had a high affinity for ammonia nitrogen. Acidic soils are oligotrophic environments with very low concentrations of free ammonia, and pH strongly affects substrate availability for CMX NB through ammonia dissociation equilibrium [47, 48]. Another reason might be that the CMX NB genome (such as Nitrospira inopinata) consists of a Kdp potassium uptake system encoding KdpABC and kdpDE gene clusters. This system is similar to the pH balance system in AOA, and it is crucial for low pH adaptation. This system is involved in the uptake of potassium and generation of a reverse membrane potential to maintain equilibrium under low pH conditions .
In the artificial WLF zone of the TGR, a significant positive correlation was found between the soil TC content and the Chao1 index or the Shannon index of CMX NB. The abundance of the amoA gene in both clade A and clade B was significantly positively correlated with soil TC content. These findings indicated that TC could promote the growth of CMX NB in the WLF zone of the TGR region. TC might affect ammonia oxidation by modulating the concentrations of organic carbon. A relatively high organic carbon concentration was reported to enhance ammonia oxidation . Sun et al. also found that organic carbon content affected the community structure of CMX NB . In addition, high total carbon content was beneficial to improving the soil C/N ratio. CMX NB in Chinese agricultural soils was found to prefer soils with a high C/N ratio . However, the abundance of CMX NB in US forest soils was negatively correlated with the soil C/N ratio . These different results showed that the growth of CMX NB was not only related to the content of TC and TN but also to their existing forms in the soil.
Our results showed that CMX NB widely existed in the WLF zones of the TGR region of the Yangtze River in China, and these WLF zones were relatively rich in the CMX community and that clade A.1, clade A.2.1, clade A.2.2, clade A.3, and clade B coexisted. The amoA gene abundances of AOA, AOB, and CMX clade A showed a significant decreasing trend with soil depth. However, the abundance of clade B did not decrease significantly, indicating that clade B was more adaptable to depth changes. The number of OTUs of clade A.1, A2.2, A3, and B in the soil all showed an increasing trend with soil depth, while clade A2.1 exhibited a decreasing trend with vertical depth. This study confirmed the niche differentiation phenomenon of CMX NB in the WLF zones of the TGR region.
Availability of data and materials
The CMX NB sequences have been uploaded to NCBI GenBank, with accession numbers of ON677371 to ON677405.
Kuypers MMM, Marchant HK, Kartal B (2018) The microbial nitrogen-cycling network. Nat Rev Microbiol 16(5):263–276. https://doi.org/10.1038/nrmicro.2018.9
Costa E, Perez J, Kreft JU (2006) Why is metabolic labour divided in nitrification? Trends Microbiol 14(5):213–219. https://doi.org/10.1016/j.tim.2006.03.006
Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437(7058):543–546. https://doi.org/10.1038/nature03911
Teske A, Alm E, Regan JM, Toze S, Rittmann BE, Stahl DA (1994) Evolutionary relationships among ammonia-oxidizing and nitrite-oxidizing bacteria. J Bacteriol 176(21):6623–6630. https://doi.org/10.1128/jb.176.21.6623-6630.1994
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M (2015) Complete nitrification by Nitrospira bacteria. Nature 528(7583):504. https://doi.org/10.1038/nature16461
Van Kessel MAHJ, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJM, Kartal B, Jetten MSM, Lucker S (2015) Complete nitrification by a single microorganism. Nature 528(7583):555. https://doi.org/10.1038/nature16459
Xia F, Wang JG, Zhu T, Zou B, Rhee SK, Quan ZX (2018) Ubiquity and diversity of complete ammonia oxidizers (comammox). Appl Environ 84(24):e01390-e1418. https://doi.org/10.1128/aem.01390-18
Zhao YX, Hu JJ, Yang WL, Wang JQ, Jia ZJ, Zheng P, Hu BL (2021) The long-term effects of using nitrite and urea on the enrichment of comammox bacteria. Sci Total Environ 755(2):142580. https://doi.org/10.1016/j.scitotenv.2020.142580
Wang DQ, Zhou CH, Nie M, Gu JD, Quan ZX (2021) Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants. Sci Total Environ 768:144993. https://doi.org/10.1016/j.scitotenv.2021.144993
Wang ZH, Cao YQ, Zhu-Barker X, Nicol GW, Wright AL, Jia ZJ, Jiang XJ (2019) Comammox Nitrospira clade B contributes to nitrification in soil. Soil Biol Biochem 135:392–395. https://doi.org/10.1016/j.soilbio.2019.06.004
Wang SY, Wang XM, Jiang YY, Han C, Jetten MSM, Schwark L, Zhu GB (2021) Abundance and functional importance of complete ammonia oxidizers and other nitrifiers in a riparian ecosystem. Environ Sci Technol 55(8):4573–4584. https://doi.org/10.1021/acs.est.0c00915
Shi Y, Jiang YY, Wang SY, Wang XM, Zhu GB (2020) Biogeographic distribution of comammox bacteria in diverse terrestrial habitats. Sci Total Environ 717:137257. https://doi.org/10.1016/j.scitotenv.2020.137257
Li CY, Hu HW, Chen QL, Chen DL, He JZ (2020) Niche differentiation of clade A comammox Nitrospira and canonical ammonia oxidizers in selected forest soils. Soil Biol Biochem 149:107925. https://doi.org/10.1016/j.soilbio.2020.107925
Sun DY, Zhao MY, Tang XF, Liu M, Hou LJ, Zhao Q, Li J, Gu JD, Han P (2021) Niche adaptation strategies of different clades of comammox Nitrospira in the Yangtze Estuary. Int Biodeterior 164:105286. https://doi.org/10.1016/j.ibiod.2021.105286
Li CY, Hu HW, Chen QL, Chen DL, He JZ (2019) Comammox Nitrospira play an active role in nitrification of agricultural soils amended with nitrogen fertilizers. Soil Biol Biochem 138:107609. https://doi.org/10.1016/j.soilbio.2019.107609
Hu HW, He JZ (2017) Comammox-a newly discovered nitrification process in the terrestrial nitrogen cycle. J Soils Sediments 17(12):2709–2717. https://doi.org/10.1007/s11368-017-1851-9
Koch H, Lucker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, Nielsen PH, Wagner M, Daims H (2015) Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. PNAS 112(36):11371–11376. https://doi.org/10.1073/pnas.1506533112
Palomo A, Pedersen AG, Fowler SJ, Dechesne A, Sicheritz-Ponten T, Smets BF (2018) Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira. ISME J 12(7):1779–1793. https://doi.org/10.1038/s41396-018-0083-3
Jiang Y, Pan J, Wang X, Wang Y, Liu S, Zhou J, Zhu G, Liu C, Wang W (2020) Research on abundance, community structure and influencing factors of complete ammonia oxidizing (comammox) bacteria in Chaohu Lake. Acta Sci Circum 40(4):1260–1268
Wan Q, Wang S, Zhao W, Ma L, Jia Z, Jiang X (2019) Vertical abundance variations of incomplete ammonia oxidizers and comammox in purple paddy soil in Chongqing. Acta Microbiol Sin 59(2):291–302
Zeleke J, Lu SL, Wang JG, Huang JX, Li B, Ogram AV, Quan ZX (2013) Methyl coenzyme M reductase A (mcrA) gene-based investigation of methanogens in the mudflat sediments of Yangtze River Estuary, China. Microb Ecol 66(2):257–267. https://doi.org/10.1007/s00248-012-0155-2
Wang F, Liang XL, Ma SH, Liu LZ, Wang JK (2021) Ammonia-oxidizing archaea are dominant over comammox in soil nitrification under long-term nitrogen fertilization. J Soils Sediments 21(4):1800–1814. https://doi.org/10.1007/s11368-021-02897-z
Hu JJ, Zhao YX, Yao XW, Wang JQ, Zheng P, Xi CAW, Hu BL (2021) Dominance of comammox Nitrospira in soil nitrification. Sci Total Environ 780:146558. https://doi.org/10.1016/j.scitotenv.2021.146558
Banning NC, Maccarone LD, Fisk LM, Murphy DV (2015) Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil. Sci Rep 5(1):11146. https://doi.org/10.1038/srep11146
Liu Y, Zhang JX, Zhang XL, Xie SG (2014) Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland. Appl Microbiol Biotechnol 98(12):5697–5707. https://doi.org/10.1007/s00253-014-5651-5
Jiang Q, Xia F, Zhu T, Wang D, Quan Z (2019) Distribution of comammox and canonical ammonia-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary at different depths over four seasons. J Appl Microbiol 127(2):533–543. https://doi.org/10.1111/jam.14337
He Q, Peng SJ, Zhai J, Xiao HW (2011) Development and application of a water pollution emergency response system for the Three Gorges Reservoir in the Yangtze River, China. J Environ Sci (China) 23(4):595–600. https://doi.org/10.1016/s1001-0742(10)60424-x
Bai BW, Wang HY, Li XY, Feng YL, Zhi L (2005) A comparative study of the plant community of the future water-level-fluctuating zone and the natural water-level-fluctuatingzone in the three gorges reservoir. J Southwest Agric Univ 27(5):684
Guo J, Jiang X, Zhou X, Meng Y, Jia Z (2016) Impact of periodical flooding-drying on nitrification and ammonia oxidizers in hydro-fluctuation belt of the Three Gorges Reservoir. Acta Microbiol Sin 56(6):983–999. https://doi.org/10.13343/j.cnki.wsxb.20150402
Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. PNAS 102(41):14683–14688. https://doi.org/10.1073/pnas.0506625102
Meinhardt KA, Bertagnolli A, Pannu MW, Strand SE, Brown SL, Stahl DA (2015) Evaluation of revised polymerase chain reaction primers for more inclusive quantification of ammonia-oxidizing archaea and bacteria. Environ Microbiol Rep 7(2):354–363. https://doi.org/10.1111/1758-2229.12259
Jiang R, Wang JG, Zhu T, Zou B, Wang DQ, Rhee SK, An D, Ji ZY, Quan ZX (2020) Use of newly designed primers for quantification of complete ammonia-oxidizing (Comammox) bacterial clades and strict nitrite oxidizers in the genus Nitrospira. Appl Environ Microbiol 86(20):e01775-e1820. https://doi.org/10.1128/aem.01775-20
Li CY, Hu HW, Chen QL, Yan ZZ, Nguyen BAT, Chen DL, He JZ (2021) Niche specialization of comammox Nitrospira clade A in terrestrial ecosystems. Soil Biol Biochem 156:108231. https://doi.org/10.1016/j.soilbio.2021.108231
Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016) Vsearch: a versatile open source tool for metagenomics. PeerJ. https://doi.org/10.7717/peerj.2584
Wang Q, Quensen JF, Fish JA, Lee TK, Sun YN, Tiedje JM, Cole JR (2013) Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using framebot, a New Informatics Tool. MBio 4(5):e00592-e613. https://doi.org/10.1128/mBio.00592-13
Jiang P, Shi DM, Hu XQ, Huang XZ, Li YX, Guo TL (2015) Soil stability characteristics of mulberry lands at hydro-fluctuation belt in the Three Gorges Reservoir area, China. Environ Monit Assess 187(10):634. https://doi.org/10.1007/s10661-015-4834-6
Cheng RM, Wang XR, Xiao WF, Guo QS, Feng XH (2009) Study on the soil physical properties and metal content in the early submerged water-level-fluctuating zone of Three Gorges reservoir. J Soil Water Conserv 23(5):156–161
Koch H, van Kessel M, Lucker S (2019) Complete nitrification: insights into the ecophysiology of comammox Nitrospira. Appl Microbiol Biotechnol 103(1):177–189. https://doi.org/10.1007/s00253-018-9486-3
Zhu GB, Wang XM, Wang SY, Yu LB, Armanbek G, Yu J, Jiang LP, Yuan DD, Guo ZR, Zhang HR, Zheng L, Schwark L, Jetten MSM, Yadav AK, Zhu YG (2022) Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox). Sci Total Environ 829:154590. https://doi.org/10.1016/j.scitotenv.2022.154590
Camejo PY, Domingo JS, McMahon KD, Noguera DR (2017) Genome-enabled insights into the ecophysiology of the comammox bacterium “Candidatus nitrospira nitrosa”. Msystems 2(5):e00059-e117. https://doi.org/10.1128/mSystems.00059-17
Horton DJ, Theis KR, Uzarski DG, Learman DR (2019) Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes. Fems Microbiol Ecol 95(4):fiz003. https://doi.org/10.1093/femsec/fiz033
Inceoglu O, Lliros M, Garcia-Armisen T, Crowe SA, Michiels C, Darchambeau F, Descy JP, Servais P (2015) Distribution of bacteria and archaea in meromictic tropical Lake Kivu (Africa). Aquat Microb Ecol 74(3):215–233. https://doi.org/10.3354/ame01737
Lin YX, Ye GP, Hu HW, Yang P, Wan S, Feng MM, He ZY, He JZ (2022) Plant species-driven distribution of individual clades of comammox Nitrospira in a subtropical estuarine wetland. Microb Ecol. https://doi.org/10.1007/s00248-021-01940-3
Dai H, Jiang Q, Quan Z (2020) Distribution of complete ammonia oxidizers (Comammox) in different seasons and depths in tidal-flat wetland. J Mirobiol 40(5):35–42
Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, Daebeler A, Romano S, Albertsen M, Stein LY, Daims H, Wagner M (2017) Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature 549(7671):269. https://doi.org/10.1038/nature23679
Osterholz WR, Rinot O, Liebman M, Castellano MJ (2017) Can mineralization of soil organic nitrogen meet maize nitrogen demand? Plant Soil 415(1–2):73–84. https://doi.org/10.1007/s11104-016-3137-1
Anthonisen AC, Loehr RC, Prakasam TBS, Srinath EG (1976) Inhibition of nitrification by ammonia and nitrous-acid. J Water Pollut Control Fed 489(5):835–852
Park S, Bae W (2009) Modeling kinetics of ammonium oxidation, nitrite oxidation under simultaneous inhibition by free ammonia and free nitrous acid. Process Biochem 44(6):631–640. https://doi.org/10.1016/j.procbio.2009.02.002
Herbold CW, Lehtovirta-Morley LE, Jung MY, Jehmlich N, Hausmann B, Han P, Loy A, Pester M, Sayavedra-Soto LA, Rhee SK, Prosser JI, Nicol GW, Wagner M, Gubry-Rangin C (2017) Ammonia-oxidising archaea living at low pH: Insights from comparative genomics. Environ Microbiol 19(12):4939–4952. https://doi.org/10.1111/1462-2920.13971
Lehtovirta-Morley LE, Sayavedra-Soto LA, Gallois N, Schouten S, Stein LY, Prosser JI, Nicol GW (2016) Identifying potential mechanisms enabling acidophily in the ammonia-oxidizing archaeon “Candidatus Nitrosotalea devanaterra.” Appl Environ Microbiol 82(9):2608–2619. https://doi.org/10.1128/aem.04031-15
Sun DY, Tang XF, Zhao MY, Zhang ZX, Hou LJ, Liu M, Wang BZ, Klumper U, Han P (2020) Distribution and diversity of comammox Nitrospira in coastal wetlands of China. Front Microbiol 11:589268. https://doi.org/10.3389/fmicb.2021.731921
Xu SY, Wang BZ, Li Y, Jiang DQ, Zhou YT, Ding A, Zong YX, Ling X, Zhang S, Lu H (2020) Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils. Sci Total Environ 706:135684. https://doi.org/10.1016/j.scitoteuv.2019.136684
Osburn ED, Barrett JE (2020) Abundance and functional importance of complete ammonia-oxidizing bacteria (comammox) versus canonical nitrifiers in temperate forest soils. Soil Biol Biochem 145:107801. https://doi.org/10.1016/j.soilbio.2020.107801
This research was funded by the National Natural Science Foundation of China (Nos. 92047203, 92047204, U1802241 and U2040211), the National Key Research and Development Project (No. 2021YFC3201002), the project of China Three Gorges Corporation (No. 201903144), the China Institute of Water Resources and Hydropower Research (No. SKL2020TS07), and the Follow-up Work of the Three Gorges Project (No. 2136902).
Ethics approval and consent to participate
Consent for publication
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Mingming Hu and Jianwei Zhao are co-corresponding authors
Additional file 1.
Table S1. qPCR primers and amplification protocols. Figure S1. Soil sampling sites. Figure S2. Co-occurrence network analysis of all CMX NB clades in natural and artificial water-level fluctuation zones.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Ding, H., Zhou, M., Wang, Y. et al. Vertical niche differentiation of comammox Nitrospira in water-level fluctuation zone of the Three Gorges Reservoir, China. Environ Sci Eur 34, 118 (2022). https://doi.org/10.1186/s12302-022-00700-5
- Three Gorges water-level fluctuation zone
- Comammox Nitrospira
- Ecological niche
- Ammonia-oxidizing archaea
- Ammonia-oxidizing bacteria