Abundance Of Ammonia-oxidizing Microorganisms Research Articles

Dynamic response of soil microbial communities and network to hymexazol exposure

Fungicides are an essential component of current agricultural practices, but their extensive use has raised concerns about their effects on non-target soil microorganisms, which carry out essential ecosystem functions. However, despite the complexity of microbial communities, many studies investigating their response to fungicides focus only on bacteria or fungi at one point in time. In this study, we used amplicon sequencing to assess the effect of the fungicide hymexazol on the diversity, composition, and co-occurrence network of soil bacteria, fungi, and protists at 7, 21, and 60 days after application. We found that hymexazol had very little effect on microbial alpha-diversity, but that microbial community composition and OTU differential abundance were altered over the duration of the experiment, even after hymexazol concentrations were undetectable. The co-occurrence patterns within and between microbial kingdoms were affected by hymexazol dose, suggesting that indirect effects may play a role in the microbial community response. Nitrogen cycling was also affected, with a transient hymexazol-associated increase in the abundance of ammonia-oxidizing microorganisms and soil nitrate concentration. These findings highlight that the effects of fungicides on soil microorganisms are dynamic and extensive, spanning several taxonomic kingdoms.

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.

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.

Syringic acid from rice roots inhibits soil nitrification and N2O emission under red and paddy soils but not a calcareous soil.

Syringic acid (SA) is a novel biological nitrification inhibitor (BNIs) discovered in rice root exudates with significant inhibition of Nitrosomonas strains. However, the inhibitory effect of SA on nitrification and nitrous oxide (N2O) emissions in different soils and the environmental factors controlling the degree of inhibition have not been studied. Using 14-day microcosm incubation, we investigated the effects of different concentrations of SA on nitrification activity, abundance of ammonia-oxidizing microorganisms, and N2O emissions in three typical agricultural soils. The nitrification inhibitory efficacy of SA was strongest in acidic red soil, followed by weakly acidic paddy soil, with no significant effect in an alkaline calcareous soil. Potential nitrification activity (PNA) were also greatly reduced by SA additions in paddy and red soil. Pearson correlation analysis showed that the inhibitory efficacy of SA might be negatively correlated with soil pH and positively correlated with clay percentage. SA treatments significantly reduced N2O emissions by 69.1-79.3% from paddy soil and by 40.8%-46.4% from red soil, respectively, but no effect was recorded in the calcareous soil. SA addition possessed dual inhibition of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) abundance in paddy and red soil. Structural equation modelling revealed that soil ammonium (NH4 +) and dissolved organic carbon content (DOC) were the key variables explaining AOA and AOB abundance and subsequent N2O emissions. Our results support the potential for the use of the BNI SA in mitigating N2O emissions and enhancing N utilization in red and paddy soils.

Effects of Ionized Water Addition on Soil Nitrification Activity and Nitrifier Community Structure

Water ionization is an efficient physical water treatment technology, and crop water and nutrient use efficiencies can be improved using ionized water for irrigation. In order to explore the effect of ionized water on soil nitrification and nitrifying microorganisms, we conducted a laboratory soil incubation experiment with the addition of ionized water and ordinary water under different soil water contents (equal to 30%, 60%, 100% and 175% of the field capacity, θFC). During the soil incubation, we analyzed soil inorganic nitrogen transformation, ammonia oxidation gene abundances and nitrifying microbial community structure. The results showed that, no matter adding ordinary water or ionized water, the soil nitrification rate and the abundance of ammonia oxidizing bacteria in the 100%θFC treatment were significantly higher than those in other water conditions, while the abundance of ammonia oxidizing archaea was not affected by the soil water content. With the same soil water content, the nitrification rate of ionized water treatment was stronger than that of the ordinary water treatment. Although the absolute abundance of ammonia-oxidizing microorganisms in ionized water treatment was significantly lower than that of ordinary water (p < 0.05), the relative abundance of some dominant nitrifying microbial genera in the ionized water treatment was significantly higher (p < 0.05). The dominant genera may play a key role in the nitrification process. The results show that ionized water irrigation can significantly promote the nitrification of silt loam soil, especially under 100%θFC conditions, and may regulate soil nitrification by affecting some dominant nitrifying microorganisms. This study provides a theoretical basis for understanding the biological regulation mechanism of ionized water irrigation on soil nutrient transformation and for application of ionized water to field irrigation.

Different nutrient levels, rather than seasonal changes, significantly affected the spatiotemporal dynamic changes of ammonia-oxidizing microorganisms in Lake Taihu.

Ammonia-oxidizing microorganisms (AOM) play crucial roles in the degradation of ammonia nitrogen in freshwater lakes. Hence, it is necessary to reveal the spatiotemporal dynamic changes of AOM in freshwater lakes. Here, we conducted a study on the spatial and temporal dynamic changes of AOM in different lake regions under gradient nutrient levels in Lake Taihu, and found that the abundance of AOM had significant spatial changes, while the seasonal changes had relatively little effect on the abundance of AOM. We also found that ammonia-oxidizing archaea (AOA) were adapted to freshwater habitats with low nutrient levels, while ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing bacteria (AAOB) had higher abundance in high nutrient level lake regions. Moreover, the amoA gene abundance of AOB was much higher than that of AOA, indicating that AOB was the dominant aerobic ammonia oxidizer in the water of Lake Taihu. In addition, temperature, pH and dissolved oxygen all had a positive effect on AOM, especially AOB; while C- and N-related physicochemical factors had a significant positive effect on AAOB, but exhibited a significant negative correlation with AOA. The community structure of AOM also had obvious spatial changes and Group I.1a, Nitrosomonas and Candidatus Brocadia fulgida were the dominant cluster of AOA, AOB and AAOB, respectively.

Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean.

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean.

Multiple factors affect diversity and abundance of ammonia-oxidizing microorganisms in iron mine soil.

Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. In this study, four soil samples collected from a desert zone in an iron-exploration area and others from farmland and planted forest soil in an iron mine surrounding area. We analyzed the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in iron-mining area near the Miyun reservoir using ammonia monooxygenase. A subunit gene (amoA) as molecular biomarker. Quantitative polymerase chain reaction was applied to explore the relationships between the abundance of AOA and AOB and soil physicochemical parameters. The results showed that AOA were more abundant than AOB and may play a more dominant role in the ammonia-oxidizing process in the whole region. PCR-denaturing gradient gel electrophoresis was used to analyze the structural changes of AOA and AOB. The results showed that AOB were much more diverse than AOA. Nitrosospira cluster three constitute the majority of AOB, and AOA were dominated by group 1.1b in the soil. Redundancy analysis was performed to explore the physicochemical parameters potentially important to AOA and AOB. Soil characteristics (i.e. water, ammonia, organic carbon, total nitrogen, available phosphorus, and soil type) were proposed to potentially contribute to the distributions of AOB, whereas Cd was also closely correlated to the distributions of AOB. The community of AOA correlated with ammonium and water contents. These results highlight the importance of multiple drivers in microbial niche formation as well as their affect on ammonia oxidizer composition, both which have significant consequences for ecosystem nitrogen functioning.