Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management. The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition. The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.

On the Qinghai–Tibet Plateau, nitrogen (N) cycling, such as nitrification and denitrification, in the alpine meadow soils have been considerably affected by grazing, with possible consequences for nitrous oxide (N2O) emissions. However, there is a lack of understanding about how the potential nitrification activity (PNA) and the potential denitrification activity (PDA) might be affected by the grazing intensity. We collected the soil samples in alpine meadow in the east of the Qinghai–Tibet Plateau that was grazed at different intensities from 2015 in peak growing season 2021. We determined the soil physical and chemical properties, the functional gene abundances of nitrifiers and denitrifiers, and the soil PNA and PDA to explore the relationships between a range of abiotic and biotic factors and the PNA and PDA. We found that the PNA and the nitrifiers were significantly affected by the grazing intensity but that the PDA and the denitrifiers were not. The ammonia-oxidizing archaea (AOA) abundance was highest but the ammonia-oxidizing bacteria (AOB)abundance was lower than the control significantly at the highest grazing intensity. The AOA abundance and the soil NH4+-N explained most of the variation in the PNA. The pH was the main predictor of the PDA and controlled the nirS abundance but not the nirK and nosZ abundances. Overall, the PNA was more responsive to the grazing intensity than the PDA. These findings can improve estimations of the nitrification and denitrification process and N2O emissions in alpine meadow.

No studies have examined the effect of experimental warming on the microbial biomass and community composition of soil in agricultural ecosystem on the Qinghai-Tibet Plateau. Thus it is unclear whether the influences of experimental warming on microbial communities in soil are related to warming magnitude in croplands on this Plateau. This study performed warming experiment (control, low- and high-level) in a highland barley system of the Lhasa River in May 2014 to examine the correlation between the response of microbial communities in soil to warming and warming magnitude. Topsoil samples (0–10 and 10–20 cm) were collected on September 14, 2014. Experimental warming at both low and high levels significantly increased soil temperature by 1.02 °C and 1.59 °C, respectively at the depth of 15 cm. Phospho lipid fatty acid (PLFA) method was used to determine the microbial community in soil. The low-level experimental warming did not significantly affect the soil's total PLFA, fungi, bacteria, arbuscular mycorrhizal fungi (AMF), actinomycetes, gram-positive bacteria (G+), gram-negative bacteria (G–), protozoa, the ratio of fungi to bacteria (F/B ratio), and ratio of G+ to G– (G+/G– ratio) at the 0–10 and 10–20 cm depth. The low-level experimental warming also did not significantly alter the composition of microbial community in soil at the 0–10 and 10–20 cm depth. The high-level experimental warming significantly increased total PLFA by 74.4%, fungi by 78.0%, bacteria by 74.0%, AMF by 66.9%, actinomycetes by 81.4%, G+ by 67.0% and G– by 74.4% at the 0–10 cm depth rather than at 10–20 cm depth. The high-level experimental warming significantly altered microbial community composition in soil at the 0–10 cm depth rather than at 10-20 cm depth. Our findings suggest that the response of microbial communities in soil to warming varied with warming magnitudes in the highland barley system of the Lhasa River.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity.

To explore the differences in structure and diversity of nirK-type denitrifying microbial community in marsh soils at different invasion stages of Spartina alterniflora, the mudflat (MF, before invasion) and the S. alterniflora marsh after seaward invasion for 1-2 years (SAN) and 6-7 years (SA) in Shanyutan of the Minjiang River estuary were investigated by high-through put sequencing method. Results showed that the seaward invasion of S. alterniflora reduced the richness and diversity of nirK-type denitrifying microbial community in marsh soils. The nirK-type denitrifying microbial community in soils at different invasion stages included Proteobacteria and Actinobacteria, with Proteobacteria as the dominant one. The seaward invasion of S. alterniflora greatly altered the composition of nirK-type denitrifying microbial community in marsh soils. The highest relative abundance of genus in soils from different invasion stages were Bradyrhizobium, Mesorhizobium and Alcaligenes, respectively. The seaward invasion of S. alterniflora increased the spatial heterogeneity of nirK-type denitrifying microbial community composition in marsh soils. In SAN plot, the enhancement of spatial heterogeneity was primarily due to higher environmental disturbances in plots and the increased spatial heterogeneity of environmental variables caused by the seaward invasion of S. alterniflora. The seaward invasion of S. alterniflora altered the physico-chemical properties (e.g., grain composition, pH and moisture) and N nutrient conditions (total N, NH4+-N and NO3--N) in marsh soils, which greatly altered the structure and diversity of nirK-type denitrifying microbial community. Our findings reveal the microbial mechanism of denitrification process in marsh soils during the seaward invasion of S. alterniflora.

Degradation of polyethylene plastic in soil and effects on microbial community composition

Ammonia oxidation, the first and rate-limiting step of nitrification, can be strongly influenced by agricultural practices, but little is known about the effects of fertilization and irrigation combination on ammonia oxidizers in agricultural soils. This study was designed to reveal how fertilizer type and irrigation frequency affect the ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities in a northern Chinese wheat-maize rotation soil. Soil samples were collected from a long-term field experiment under different fertilization and irrigation regimes located in Wuqiao Experimental Station of China Agricultural University in June 2016. The abundance, diversity, and composition of AOA and AOB in the soils were investigated by using real-time PCR and Illumina Miseq sequencing approaches. The abundance of AOA was higher in the irrigated treatments, but lower in the treatments without irrigation, than that of AOB. The AOA abundance was positively correlated with soil moisture, pH, and NO3 −-N, while the AOB abundance was positively correlated with TN and NO3 −-N. Soil potential nitrification activity (PNA) was significantly positively correlated with the AOB abundance. Both fertilizer type and irrigation frequency significantly affected Shannon, ACE, and Chao1 indices of the AOB community, while only irrigation frequency had a significant impact on Shannon index of the AOA community. PCoA analysis results indicated that irrigation frequency greatly affected the AOA community structure, while fertilizer type played a more important role in affecting the AOB community structure. Mantel test and correlation heatmap analysis results indicated that soil moisture, pH, and NH4 +-N were significantly correlated to the AOA community structure, and TN and SOC were significantly correlated to the AOB community structure. This study demonstrated that irrigation frequency greatly influenced the AOA community, while fertilizer type had a stronger effect on the AOB community. It was AOB but not AOA played a more important role in soil nitrification. Moreover, soil moisture, pH, and TN were the main determinants in driving the AOA community and TN and SOC were the main factors in influencing the AOB community.

Effects of solarization on microbial communities in soil were investigated with an incubation experiment and in a greenhouse experiment with isolated bed culture of tomato (Solanum lycopersicum L.) by molecular techniques. Microbial biomass carbon in soil was decreased by about half in the incubation experiment treated with 45°C for 14 days and the greenhouse experiment with solarization for 45 days. Bacterial and fungal communities in soil were affected by the heat and solarization treatments in both the experiments and greatly different from the communities in the unheated soil or the soil before solarization. Copy number of amoA gene of ammonia-oxidizing bacteria in soil was decreased to one-tenth or less by the treatments in both the experiments. This study revealed that the solarization made a great impact on the abundance and composition of microbial communities in soil.

Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.

Many studies have shown the simulated effects of nitrogen (N) deposition on soil microbial community composition by adding N directly to the forest floor but have ignored the N retention process by the canopy. This study was conducted to compare the responses of soil microbial biomass and community composition between soil application of N (SAN) and foliage application of N (FAN). A pot experiment was designed with (1) two N application methods (SAN and FAN), (2) three N application levels (5.6, 15.6 and 20.6 g N m−2 year−1), and (3) two tree species (Schima superba Gardn. et Champ. and Pinus massoniana Lamb.) following a nested factorial design. Soil microbial biomass and community composition were determined using phospholipid fatty acids (PLFAs) techniques after 1 and 1.5 years of treatments. Nitrogen addition increased (P < 0.05) soil NH4+-N content and soil NO3−-N content and decreased (P < 0.05) soil pH and soil microbial (bacterial, fungal, and actinomycete) biomass for both N application methods. Compared with the SAN treatment, the FAN treatment had higher (P < 0.05) pH and lower (P < 0.05) contents of soil NH4+-N and soil NO3−-N. Soil microbial biomass and community composition were significantly different between the different N addition levels under the SAN treatment, but they showed no significant difference (P < 0.05) between the different N addition levels under the FAN treatment. The soil microbial biomass in the S. superba soil was higher (P < 0.05) than that in the P. massoniana soil for the FAN treatment, with the opposite trend observed under the SAN treatment. Moreover, redundancy analysis showed that soil microorganisms were significantly correlated with soil pH, soil water content, NH4+-N, and NO3−-N. The results showed that N addition affected soil properties, microbial biomass, and the composition of microbial communities; however, the FAN treatment had less influence on soil properties and soil microorganisms than did the SAN treatment over short time scales, and the extent of this effect was different between coniferous and broadleaf trees.

Biowaste compost amendment modifies soil biogeochemical cycles and microbial community according to aggregate classes

Nitrification plays a central role in global nitrogen cycle, which is affected by interaction between soil microfauna and microorganisms. The impact of synchronized changes in nematodes and ammonia oxidizers within aggregate fractions on nitrification was investigated in an acid soil under 10-year manure application. Nematodes, ammonia oxidizers and potential nitrification activity (PNA) were examined in three soil aggregate fractions under four fertilization regimes. Pyrosequencing data revealed that the dominant bacterial amoA operational taxonomic units (OTUs) were related to Nitrosospira species, while archaeal OTUs were affiliated with Nitrososphaera and Nitrosotalea species. PNA was more strongly correlated with ammonia-oxidizing bacteria (AOB) abundance than ammonia-oxidizing archaea (AOA) abundance, although AOA were dominant in the acid soil. Plant parasites had a negative effect on AOB abundance; however, bacterivores stimulated AOB abundance and contributed more to PNA than plant parasites. Aggregate fractions exerted significant impacts on AOA abundance and AOB community composition. Total carbon content strongly affected the abundance and composition of AOA community, while soil pH primarily affected that of AOB community. Soil variables explained 62.7% and 58.1% variations, and nematode variables explained 11.7% and 19.5% variations in the AOA and AOB community composition respectively.

Ammonia-oxidising archaea (AOA) have recently been described as having an important role in soil nitrification. However, published data on factors which influence their distribution and their impact on a soil’s potential nitrification rates (PNR) are sparse, particularly compared with the amount of information available regarding ammonia-oxidising bacteria (AOB). This study had two aims. First, to investigate which environmental factors affect the AOA : AOB ratio in soils from two agricultural regions, and second, to explore whether the abundance of either AOA or AOB correlated with PNR. Samples were collected from 45 sites within the cropping regions of Western Australia and South Australia. Soils were tested for pH, NH4+/NO3–, organic carbon (C), total nitrogen (N), C : N ratio, PNR, and electrical conductivity. Climate data were obtained from the Queensland Climate Change Centre for Excellence SILO website. Abundances of AOA and AOB were measured using real-time PCR quantification of the gene encoding the ammonia monooxygenase enzyme (amoA). Multivariate statistical analysis was applied to assess correlations between PNR, soil properties, and abundance of AOA or AOB. In the majority samples AOA were present, but their abundance, and the AOA : AOB ratio, varied considerably between sites. Multivariate analysis showed that the distribution of AOA and AOB and the AOA : AOB ratio were strongly correlated with climatic and seasonal factors. Sites where samples were collected during dry, hot periods tended to be AOA-dominated, whereas samples collected during cool, wet periods tended to be AOB-dominated or have equal abundances of AOA and AOB. The PNRs were correlated with total N content, organic C content, and soil pH. There was no clear correlation between AOA or AOB and PNR. This study shows that both AOA and AOB are widespread in Western Australian and South Australian soils and their abundance and ratio are affected by climate and season. It also shows that PNR is more strongly influenced by soil fertility factors than by the AOA : AOB ratio.

Long-term mineral fertilizer substitution by organic fertilizer and the effect on the abundance and community structure of ammonia-oxidizing archaea and bacteria in paddy soil of south China

To investigate the effects of kitchen waste on the chemical properties of acidic red soil and the community structure of ammonia–oxidizing archaea (AOA) and ammonia–oxidizing bacteria (AOB), a study was conducted in the flue–cured tobacco farmland ecosystem of the Erlongtan small watershed in central Yunnan. Eight fertilization methods were applied: no fertilization control CK, single application of chemical fertilizer T1 (1 t·hm−2), kitchen waste combined with a chemical fertilizer (T2:12 t·hm−2 + 1 t·hm−2, T3:15 t·hm−2 + 1 t·hm−2, T4:18 t·hm−2 + 1 t·hm−2), and single application of kitchen waste (T5:12 t·hm−2, T6:15 t·hm−2, T7:18 t·hm−2). The numbers twelve, fifteen, and eighteen in brackets represent the amount of food waste applied, and one represents the amount of chemical fertilizer applied. The study evaluated the effects of kitchen waste on soil chemical properties, the community structure and composition of AOA and AOB, and the relationship between soil chemical properties and these microbial communities in acidic red soil. The results showed that: (1) single application of kitchen waste (T5, T6, T7) effectively improved soil nutrient status (SOC increased by 15.79–217.24%; TN increased by 1.53–92.99%; NH4+–N increased by 18.19–520.74%; NO3−–N) increased by 15.54–750.61%), and alleviated acidification. (2) Temporal variations had a more significant effect on the community structure of AOA and AOB than different treatments. The dominant phyla of AOA were Thaumarchaeota, Crenarchaeot. The dominant phylum of AOB was Proteobacteria, and the dominant genera were Nitrosospira and norank_Bacteri. (3) The number of AOA co–occurrence network nodes were equivalent to that of AOB, but AOB had more connection edges, indicating a more complex interaction network. In contrast, AOA exhibited higher modularity, reflecting tighter internal connections and greater stability. The AOA co–occurrence network showed stronger performance during the maturity and fallow stages, while AOB interactions were most active during the topping stage. (4) AOA demonstrated a strong correlation with soil chemical properties during the topping and maturity stages, whereas AOB showed a stronger correlation at the rosette and fallow stages. Among soil chemical factors, pH and SOC were identified as the primary drivers influencing AOA and AOB community abundance and structural differentiation. In conclusion, kitchen waste application enhances the nutrient content of acidic red soil and influences the niche differentiation of AOA and AOB, thereby affecting nitrogen recycling. This approach represents an environmentally friendly and sustainable fertilization method.