Ammonia-oxidizing Microorganisms Research Articles

Effects of a Vegetable Eel Co-Culture System on the Soil Ammonia-Oxidizing Microbial Community

(1) Background: A vegetable eel co-culture system is an economically efficient way of agricultural cultivation, which can have an impact on the soil microbial environment and play a pivotal role in the soil nutrient cycle, but there is little research on its impact on soil ammonia-oxidizing microorganisms. (2) Methods: NovaSeq platform sequencing was employed to investigate the richness, structure, and diversity of soil ammonia-oxidizing microbial communities, exploring the effects of a vegetable eel co-culture system on soil nitrogen cycling. Four different planting treatments were set up: unfertilized without vegetable eel (CCK), fertilized without vegetable eel (CRT), unfertilized with vegetable eel (ICK), and fertilized with vegetable eel (IRT). (3) Results: A vegetable eel co-culture system significantly increased soil pH and decreased bulk density under fertilization conditions. The soil nitrification potential rate was enhanced by a vegetable eel co-culture system to an average of 26.3%. A vegetable eel co-culture system significantly altered the community structure of all ammonia-oxidizing microorganisms, with a significant increase in the richness and diversity of ammonia-oxidizing bacteria (AOB) and comammox clade-A, while fertilization significantly increased the diversity of all ammonia-oxidizing microbial communities. Structural equation modeling (SEM) analysis showed that the main environmental factors affecting the structure of the ammonia-oxidizing microbial community were nitrate and total nitrogen. The number of amoA genes in AOB and comammox clade-B was significantly positively correlated with the soil potential N nitrification rate (PNR), which played a leading role in the nitrification of alkaline vegetable soil. The network analysis revealed that a vegetable eel co-culture system improved the modularity of AOB and comammox clade-B by 13.14% and 5.66%. (4) Conclusions: This study showed that the vegetable eel co-culture system stimulated the evolution of ammonia-oxidizing microbial communities by changing the physicochemical properties, which in turn promoted the soil nitrification reaction.

Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.

Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.

Growth of soil ammonia-oxidizing archaea on air-exposed solid surface.

Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOMs), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), Nitrososphaera viennensis EN76 and "Nitrosotenuis chungbukensis" MY2, and a soil ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of N. viennensis EN76 and "N. chungbukensis" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of N. europaea ATCC 19718 was comparable on floating filters and liquid media. N. viennensis EN76 and N. europaea ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of N. viennensis EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, ammonia oxidation (including ammonia monooxygenase subunit C (amoC3) and multicopper oxidases), and defense against H2O2-induced oxidative stress. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the "Ca. Nitrosocosmicus" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.

Shore-to-water spatial variations of complete ammonia oxidizers in a lake in Wuhan, China

Complete ammonia oxidizers (comammox bacteria) can convert ammonia into nitric acid through single-step nitrification. This study explored the spatial variations of comammox bacteria in the lakeshore area of the Houguan Lake in Wuhan, China. The abundance of the two comammox bacteria clades and two traditional ammonia-oxidizing microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), generally showed a gradually decreasing trend from the shore to the water. Moreover, a similar decreasing trend was observed for the respective and total nitrification rate of three types of ammonia-oxidizing microorganisms. The average nitrification rate of AOA, AOB and comammox bacteria was 0.568, 0.718, and 0.935 mg N kg−1 d−1, respectively. Besides, comammox bacteria exhibited a high biological diversity, with clade A and clade B and three subclades of clade A all present. Among different clades, clade B played a dominant role in the ammonia oxidation process. Both the abundance and nitrification rate of comammox bacteria were significantly positively correlated with total carbon and total nitrogen, indicating that these two nutrient substances are important factors influencing this microorganism. Our results demonstrate that the spatial variations of environmental elements in the lakeshore area lead to gradual decreases of comammox bacteria from the shore to the water.

Key role of NH4+-N in the removal of oxacillin during managed aquifer recharge: Reconsidering the recharge limitation

Frequent occurrence of trace antibiotics in reclaimed water is concerning, which inevitably causes aquifer contamination in the case of managed aquifer recharge (MAR). Global governments have formulated strict reclaimed water standards to ensure the safety of water reuse. Recent studies have found that improved antibiotics removal is intimately associated with high ammonia-oxidizing activity. However, the role of NH4+-N in the removal of residual antibiotics of reclaimed water during MAR remains unknown. NH4+-N removal and the effects of ammonia oxidation on antibiotics biodegradation in the aquifer are the most significant facts for solving the above collision. In this work, the effects of NH4+-N (0, 1 and 5 mg/L) in a model refractory antibiotic (oxacillin (OXA), 100 μg/L) attenuation were deciphered by employing three individual simulated MAR columns, which so called N0, N1 and N5. The results showed that 5 mg/L NH4+-N in influent upregulated the abundance of amo genes by 28.9 %-68.0 % in N5. And the enriched functional genes encoding key degradation enzymes enhanced the OXA removal by 18.7 % and alleviated the oxidative stress caused by antibiotics. Subsequently, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) and human bacterial pathogens (HBPs) abundance were all significantly decreased. Moreover, the intimate association between ammonia-oxidizing microorganisms (AOM) and candidate OXA degraders based on microbial network analysis further supported the significance of AOM on OXA biodegradation. This study provides comprehensive evidence that appropriate amounts of NH4+-N are beneficial in antibiotics and antibiotic resistance risk reduction, providing compelling insights for refine NH4+-N recharge limitation.

Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea.

This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 102 to 2.17 × 106 copies per gram of sediment and from 6.6 × 101 to 7.65 × 104 copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50°C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

Impacts of Biochar and Gypsum on Ammonia-Oxidizing Microorganisms in Coastal Saline Soil

Nitrification is the core step of the soil nitrogen cycle and directly affects the nitrogen use efficiency in agricultural systems. Biochar and gypsum are two important soil amendments widely used in coastal saline farmland. However, little is known about their effects on nitrification and ammonia-oxidizing microorganisms. A one-year pot experiment with three treatments including biochar application (BC), gypsum application (SG), and no amendment (CK) was conducted, and the responses of the nitrification rate, amoA gene copies, and the diversity and community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to biochar and gypsum were evaluated. The results indicated that biochar and gypsum application both resulted in alterations to the soil properties. They both had inhibiting effects on nitrification and AOB amoA gene copies, whereas they had no significant effect on AOA amoA gene copies. Biochar had no significant effect on the diversity indexes of AOA, but it significantly reduced the Shannon index of AOB. Meanwhile, gypsum had no significant influence on the diversity indexes of both AOA and AOB. Biochar and gypsum did not significantly affect the community structure of AOA but did induce changes in that of AOB. In detail, biochar significantly enhanced the relative abundance of the dominant cluster Nitrosospira, whereas gypsum led to a notable increase in the relative abundance of unclassified_o_Nitrosomonadales. The Shannon index of AOB had a significant negative correlation with soil TOC, TN, and NH4+ content, and soil pH was the first primary environmental factor that affected the AOB community structure. In conclusion, biochar and gypsum inhibited nitrification by suppressing the activities of AOB and changed the diversities and community structure of AOB by altering related soil properties.

Straw Returning Alleviates the Inhibition of Soil Nitrification Medicated by Ammonia-Oxidizing Archaea under Low Nitrogen Fertilization

Straw returning may stimulate soil microbial activity, thereby influencing microbial-mediated soil nitrification, which can lead to nitrate leaching and nitrogen (N) loss. However, its effects under long-term nitrogen fertilization remain unclear. At an experimental station with 34 years of fertilizer application (0, 135, and 270 kg ha−1 N), we investigated how nitrogen fertilization and straw returning affected the soil potential nitrification rate (PNR) and ammonia-oxidizing microorganisms (AOM). Our results suggest that N fertilization concurrently inhibits soil PNR, but this inhibition can be alleviated by straw returning, particularly with low nitrogen fertilization (p < 0.05). Long-term N fertilization significantly decreased the abundance of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete ammonia-oxidizing bacteria cladeB (CAOB-cladeB). Straw returning increased AOA abundance and diversity, especially with low or no fertilization (p < 0.05). Furthermore, the partial least squares path model demonstrated that AOA abundance affected soil PNR by altering the AOA community. According to random forest analysis, soil pH and AOA beta diversity were the primary factors affecting soil PNR (explaining 10.76% and 10.03% of the variation, respectively). Overall, our findings highlight the importance of straw returning and AOA in soil nitrification under long-term nitrogen fertilization, emphasizing the need to consider these interactions for sustainable agriculture.

Evidence of comammox bacteria playing a dominant role in Lake Taihu sediments based on metagenomic analysis

The nitrification process plays an important role in the nitrogen cycle, in which the ammonia-oxidation process mediated by microorganisms is the rate-limiting step. Environmental factors can affect the distribution and activity of ammonia-oxidizing microorganisms (AOM), including ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizer (comammox Nitrospira). At present, most studies have used amoA as a marker gene for the ammonia oxidation process to analyze the differences among AOM community composition and abundance in the environment. In this study, metagenomic sequencing was used to study the differences in community composition and functional gene distribution of nitrifying microorganisms in the sediments of Lake Taihu with different eutrophication levels. It was found that comammox Nitrospira and typical nitrite oxidizer NOB Nitrospira, which belong to Nitrospirota, had higher relative abundance at most sites compared to AOB and AOA. Furthermore, the network analysis of genes related to nitrogen cycle showed that the main survival mode of nitrogen metabolizing microorganisms was mutualism. Besides, the microbial genomes in the sediments of Lake Taihu were reconstructed by metagenomic binning, which showed that among the 167 bins obtained, 2 bins (bin 9 and bin 32) were annotated as comammox Nitrospira, and had high abundance in the macrophytes-dominated lakes (such as South Lake Taihu and West Coast). In addition, bin 9, which belongs to comammox Nitrospira, annotates amoA genes associated with ammonia oxidation, and other genes associated with urea decomposition and transport, suggesting functional diversity. Overall, these findings suggest that AOM have different distribution characteristics, among which comammox Nitrospira has high diversity and may be potentially dominant in macrophytes-dominated lakes.

High-rate pig manure substitution enhances comammox Nitrospira abundance and diversity in the Cinnamomum camphora coppice planting soils

Comammox Nitrospira represents a groundbreaking discovery in nitrogen cycle research, showcasing its remarking ability for complete ammonia oxidation, which challenges prior conceptions of nitrification. In this study, we examined the response of comammox Nitrospira gene abundance, diversity, and community structure to different rates of pig manure substitution (0 %, 25 %, 50 %, 75 %, and 100 %) in subtropical agroforestry soils. The abundance of ammonia-oxidizing microorganisms was assessed by qPCR, whereas the diversity and structure of comammox Nitrospira were determined by high-throughput sequencing. Our findings revealed that pig manure substitution led to an increase in soil pH, available phosphorus (AP), comammox Nitrospira abundance, and diversity within soils under Cinnamomum camphora coppice planting. Soil pH and AP were the primary factors influencing the diversity and community structure of comammox Nitrospira. Moreover, pig manure substitution significantly influenced the composition of comammox Nitrospira, notably by increasing the relative abundance of clade A.2.1 while reducing that of clade A.2.2. However, pig manure substitution did not exert a significant impact on net nitrification rates, suggesting bacterial relative abundances were more sensitive to manure substitution compared to the underlying biogeochemical processes. Overall, our results offer new insights into the response of comammox Nitrospira to different rates of pig manure substitution in Cinnamomum camphora coppice planting soils, highlighting the pivotal role of soil AP and pH as the key determinants shaping comammox Nitrospira diversity and community structure.

The superiority of hydrophilic polyurethane in comammox-dominant ammonia oxidation during low-strength wastewater treatment

Carriers have been extensively employed to enhance nitrification performance during low-strength wastewater treatment by retaining slow-growing ammonia oxidizing microorganisms (AOMs). Still, there is a dearth of systematic understanding of biofilm properties and microbial community structure formed on different carriers. In this study, hydrophilic polyurethane foam (PUF) carriers were prepared and compared with five widely used commercial carriers, namely Kaldness 3, Biochip, activated carbon, volcanic rock, and zeolite. The results indicated that the biofilms formed on carriers enhanced microbial ammonia oxidation activity. Additionally, the biofilm developed on the PUF demonstrated the most superior performance among all selected carriers, not only exhibiting the highest abundant and the most active AOMs, with amoA gene abundance of 1.41 × 1013 copies/m3 and specific ammonia oxidation rate of 9.84 g NH4+-N/(m3 × h), but also possessing a compact structure, with 3.41 kg VSS/m3 and 46.83 mg extracellular polymeric substances/g VSS. The high-throughput sequencing analysis revealed that the comammox (CMX) Nitrospira dominated on biofilm due to the intrinsically low apparent half-saturation constant for substrate. A unique ecological community structure was established on PUF, characterized by low species diversity and high homogeneity in alignment with community characteristics of CMX. The biofilms on PUF contributed to the proliferation of CMX Nitrospira dominated by Nitrospira nitrosa, achieving the highest proportion among colonial three AOMs at 86.58 %. The appropriate average pore size, superior hydrophilicity, and large specific surface area of PUF carriers provided a robust foundation for the exceptional ammonia oxidation performance of the formed biofilms.

The different responses of AOA and AOB communities to irrigation systems in the semi-arid region of Northeast China.

Ammonia oxidation is the rate-limiting step in nitrification and the key step in the nitrogen (N) cycle. Most soil nutrients and biological indicators are extremely sensitive to irrigation systems, from the perspective of improving soil fertility and soil ecological environment, the evaluation of different irrigation systems and suitability of selection, promote crop production and soil quality, study the influence of the soil microenvironment contribute to accurate evaluation of irrigation farmland soil health. Based on the amoA gene, the abundance and community diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their responses to soil physicochemical factors and enzyme activities were studied in semi-arid areas of Northeast China. The study consisted of three irrigation systems: flood irrigation (FP), shallow buried drip irrigation (DI), and mulched drip irrigation (MF). The results showed that DI and MF significantly increased the contents of alkaline hydrolyzed nitrogen (AN), nitrate nitrogen (NO3--N), soil moisture, and the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). Compared with FP, DI significantly increased the abundance of soil AOA and AOB, while MF significantly increased the abundance of soil AOB. Irrigation systems significantly affected the community composition of ammonia-oxidizing microorganisms (AOM). Also, AN and soil moisture had the greatest influence on the community composition of AOA and AOB, respectively. The AOB community had better stability and stress resistance. Moreover, the symbiotic network of AOB in the three irrigation systems was more complex than that of AOA. Compared with FP, the AOA community under treatment DI had higher complexity and stability, maintaining the versatility and sustainability of the ecosystem, while the AOB community under treatment MF had higher transfer efficiency in terms of matter and energy. In conclusion, DI and MF were more conducive to the propagation of soil AOM in the semi-arid area of Northeast China, which can provide a scientific basis for rational irrigation and N regulation from the perspective of microbiology.

Nitrification inhibitors impose distinct effects on comammox bacteria and canonical ammonia oxidizers under high N fertilization regimes

The response of complete ammonia-oxidizing (comammox) bacteria to variable nitrogen (N) inputs and nitrification inhibitors (NIs) remains poorly understood. We conducted two experiments, in a soil where both clade A and B comammox Nitrospira were present, to identify the type (ammonium sulphate vs. urea) and the level of N-fertilization (0–500 mg-N-kg‐1d.w. soil) that are conducive to the growth of comammox, compared to canonical ammonia-oxidizing microorganisms (AOM), and subsequently to assess their response to three commercial (DCD, nitrapyrin, DMPP) and a new potent (ethoxyquin) NI under these favourable N fertilization regimes. The highest concentration of ammonium sulphate stimulated comammox compared to canonical AOM which showed a dose-dependent increase by both N sources. DMPP primarily, and DCD, imposed a more persistent inhibition on nitrification than nitrapyrin and ethoxyquin, a result which did not concur with the soil persistence of NIs (DMPP was the least persistent among the commercial NIs) but was mostly driven by their selective inhibitory activity on ammonia-oxidizing bacteria (AOB) that prevailed in the studied soil. The inhibition of AOB by DMPP and DCD was complemented by the proliferation of comammox and ammonia-oxidizing archaea (AOA). NIs induced significant changes on AOB and comammox communities. Comammox Nitrospira clade B were enriched by DCD and DMPP but depleted by nitrapyrin and ethoxyquin. We showed that (i) releasing comammox Nitrospira and AOA from AOB competition allows them to proliferate efficiently, even under high inorganic ammonium conditions; (ii) comammox clade B are more responsive than clade A to high inorganic N input and NIs.

Evidence of complete ammonia-oxidizing microbial communities and their contribution to N2O emissions in typical vegetable fields across China

No information is available for the newly found complete ammonia-oxidizing bacteria (COX) under globally intensified agriculture. In addition to the canonical ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), few studies have evaluated the structure and ecological niche of the community of COX. No information is available on their relative contributions to the ammonia oxidation process and related nitrous oxide (N2O) emissions in intensively managed vegetable fields. Therefore, in this study, fourteen soil samples were collected from vegetable fields across mainland China covering four climatic zones with distinct soil pH conditions. Two sets of microcosm incubations were combined to determine the rate of ammonia oxidation and N2O emissions distinguishing AOA, AOB and COX. The results indicated that COX coexisted with canonical ammonia-oxidizing microorganisms and its abundance was 1–4 orders of magnitude higher than those of AOA and AOB. COX abundance was highest in the subtropics and lowest in the tropics, whereas the ratio of COX to total ammonia-oxidizing microorganisms was highest in the tropics. The average contribution of COX to ammonia oxidation rate and N2O emission was 17.0% and 19.5%, respectively, while AOA contributed 47.1% to ammonia oxidation and AOB contributed 43.2% to N2O emissions. Interestingly, the contribution of COX to N2O emissions exceeded that of AOB in tropic acidic and AOA in subtropic alkaline soils. Based on high-throughput sequencing, the dominant genera of AOA, AOB, and COX were Nitrosopumilus, Nitrosospira, and Nitrospira, respectively. Reyranella and Rudaea were detected as a novel genus from COX. Furthermore, the N2O emissions were significantly positively correlated with Ktedonobacter in AOB, and negatively correlated with Nitrosomonas in AOB and Nitrospira in COX. In summary, COX coexisted with AOA and AOB while showed limited direct influence, but competed with AOA and AOB through ecological niche, which altered nitrification and N2O emissions in intensified vegetable fields.

Control of nitrogen and odor emissions during chicken manure composting with a carbon-based microbial inoculant and a biotrickling filter

Although aerobic composting is usually utilized in livestock manure disposal, the emission of odorous gases from compost not only induces harm to the human body and the environment, but also causes loss of nitrogen, sulfur, and other essential elements, resulting in a decline in product quality. The impact of biotrickling filter (BTF) and insertion of carbon-based microbial agent (CBMA) on compost maturation, odor emissions, and microbial population during the chicken manure composting were assessed in the current experiment. Compared with the CK group, CBMA addition accelerated the increase in pile temperature (EG group reached maximum temperature 10 days earlier than CK group), increased compost maturation (GI showed the highest increase of 41.3% on day 14 in EG group), resulted in 36.59% and 14.60% increase in NO3−-N content and the total nitrogen retention preservation rate after composting. The deodorization effect of biotrickling filter was stable, and the removal rates of NH3, H2S, and TVOCs reached more than 90%, 96%, and 56%, respectively. Furthermore, microbial sequencing showed that CBMA effectively changed the microbial community in compost, protected the ammonia-oxidizing microorganisms, and strengthened the nitrification of the compost. In addition, the nitrifying and denitrifying bacteria were more active in the cooling period than they were in the thermophilic period. Moreover, the abundance of denitrification genes containing nirS, nirK, and nosZ in EG group was lower than that in CK group. Thus, a large amount of nitrogen was retained under the combined drive of BTF and CBMA during composting. This study made significant contributions to our understanding of how to compost livestock manure while reducing releases of odors and raising compost quality.

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.

Ammonium enrichment reduces the diversity and changes the composition of ammonia-oxidizing microbial communities in agricultural soil media

Abstract. Saukoly SA, Meitiniarti VI, Nugroho RA, Krave AS. 2024. Ammonium enrichment reduces the diversity and changes the composition of ammonia-oxidizing microbial communities in agricultural soil media. Biodiversitas 25: 916-923. Nitrification is the process of ammonium oxidation to form nitrites and nitrates. Ammonium availability in the soil is one of the factors influencing the activity, abundance, and diversity of ammonia-oxidizing microorganisms (AOM). This study aimed to determine the effect of enriching a soil media with different ammonium concentrations on the abundance and diversity of AOM as well as the potential for nitrification. Soil as the media was prepared from an agricultural land receiving cow dung sewage. The media was then placed in the microcosms, and was added to a nitrification medium containing ammonium at three levels; 0 (control soil), 200 (low ammonium-enriched soil), and 500 mg L-1 (high ammonium-enriched soil). The microcosms were further incubated for 42 days at room temperature. The nitrification potential determination was based on the formation of nitrite from ammonium oxidation. The abundance of AOM and the potential nitrification were measured every 14-day interval, including day 0 as the initial condition. The AOM composition was analyzed based on the similarity level of the amoA gene sequence to the NCBI BLAST GenBank database. However, this analysis was only conducted for the control and high ammonium-enriched soil. This study indicated that ammonium enrichment increased the nitrification activity and the abundance of AOM, but it decreased the diversity of AOM communities. There were positive correlations between nitrification and nitrate potential, as well as between ammonium content and AOM abundance. Negative correlations appeared between pH and nitrification potential, nitrate concentrations, ammonium concentrations, and MPN. The diversity of ammonium-oxidizing archaea (AOA) in the control soil was higher than in the high ammonium-enriched soil. The enrichment with ammonium also changed the AOA composition. The Candidatus Nitrosocosmicus oleophilus strain of the MY3 chromosome was the most dominant archaea in the control and high ammonium-enriched soil. This implies that the high diversity of AOA in this soil may be beneficial for further use of the soil as a source for inocula in the development of nitrifiers-based biofertilizers.

Cooperation among nitrifying microorganisms promotes the irreversible biotransformation of sulfamonomethoxine

Ammonia-oxidizing microorganisms, including AOA (ammonia-oxidizing archaea), AOB (ammonia-oxidizing bacteria), and Comammox (complete ammonia oxidization) Nitrospira, have been reported to possess the capability for the biotransformation of sulfonamide antibiotics. However, given that nitrifying microorganisms coexist and operate as communities in the nitrification process, it is surprising that there is a scarcity of studies investigating how their interactions would affect the biotransformation of sulfonamide antibiotics. This study aims to investigate the sulfamonomethoxine (SMM) removal efficiency and mechanisms among pure cultures of phylogenetically distinct nitrifiers and their combinations. Our findings revealed that AOA demonstrated the highest SMM removal efficiency and rate among the pure cultures, followed by Comammox Nitrospira, NOB, and AOB. However, the biotransformation of SMM by AOA N. gargensis is reversible, and the removal efficiency significantly decreased from 63.84 % at 167 h to 26.41 % at 807 h. On the contrary, the co-culture of AOA and NOB demonstrated enhanced and irreversible SMM removal efficiency compared to AOA alone. Furthermore, the presence of NOB altered the SMM biotransformation of AOA by metabolizing TP202 differently, possibly resulting from reduced nitrite accumulation. This study offers novel insights into the potential application of nitrifying communities for the removal of sulfonamide antibiotics (SAs) in engineered ecosystems.

Enhanced ammonia removal in tidal flow constructed wetland by incorporating steel slag: Performance, microbial community, and heavy metal release

Utilizing alkaline solid wastes, such as steel slag, as substrates in tidal flow constructed wetlands (TFCWs) can effectively neutralize the acidity generated by nitrification. However, the impacts of steel slag on microbial communities and the potential risk of heavy metal release remain poorly understood. To address these knowledge gaps, this study compared the performance and microbial community structure of TFCWs filled with a mixture of steel slag and zeolite (TFCW-S) to those filled with zeolite alone (TFCW-Z). TFCW-S exhibited a much higher NH4+-N removal efficiency (98.35 %) than TFCW-Z (55.26 %). Additionally, TFCW-S also achieved better TN and TP removal. The steel slag addition helped maintain the TFCW-S effluent pH at around 7.5, while the TFCW-Z effluent pH varied from 3.74 to 6.25. The nitrification and denitrification intensities in TFCW-S substrates were significantly higher than those in TFCW-Z, consistent with the observed removal performance. Moreover, steel slag did not cause excessive heavy metal release, as the effluent concentrations were below the standard limits. Microbial community analysis revealed that ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and complete ammonia-oxidizing bacteria coexisted in both TFCWs, albeit with different compositions. Furthermore, the enrichment of heterotrophic nitrification-aerobic denitrification bacteria in TFCW-S likely contributed to the high NH4+-N removal. In summary, these findings demonstrate that the combined use of steel slag and zeolite in TFCWs creates favorable pH conditions for ammonia-oxidizing microorganisms, leading to efficient ammonia removal in an environmentally friendly manner.

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.