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Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil.

ABSTRACT: Nitrification is the two-step aerobic oxidation of ammonia to nitrate via nitrite in the nitrogen-cycle on earth. However, very limited information is available on how fertilizer regimes affect the distribution of nitrite oxidizers, which are involved in the second step of nitrification, across aggregate size classes in soil. In this study, the community compositions of nitrite oxidizers (Nitrobacter and Nitrospira) were characterized from a red soil amended with four types of fertilizer regimes over a 26-year fertilization experiment, including control without fertilizer (CK), swine manure (M), chemical fertilization (NPK), and chemical/organic combined fertilization (MNPK). Our results showed that the addition of M and NPK significantly decreased Nitrobacter Shannon and Chao1 index, while M and MNPK remarkably increased Nitrospira Shannon and Chao1 index, and NPK considerably decreased Nitrospira Shannon and Chao1 index, with the greatest diversity achieved in soils amended with MNPK. However, the soil aggregate fractions had no impact on that alpha-diversity of Nitrobacter and Nitrospira under the fertilizer treatment. Soil carbon, nitrogen and phosphorus in the soil had a significant correlation with Nitrospira Shannon and Chao1 diversity index, while total potassium only had a significant correlation with Nitrospira Shannon diversity index. However, all of them had no significant correlation with Nitrobacter Shannon and Chao1 diversity index. The resistance indices for alpha-diversity indexes (Shannon and Chao1) of Nitrobacter were higher than those of Nitrospira in response to the fertilization regimes. Manure fertilizer is important in enhancing the Nitrospira Shannon and Chao1 index resistance. Principal co-ordinate analysis revealed that Nitrobacter- and Nitrospira-like NOB communities under four fertilizer regimes were differentiated from each other, but soil aggregate fractions had less effect on the nitrite oxidizers community. Redundancy analysis and Mantel test indicated that soil nitrogen, carbon, phosphorus, and available potassium content were important environmental attributes that control the Nitrobacter- and Nitrospira-like NOB community structure across different fertilization treatments under aggregate levels in the red soil. In general, nitrite-oxidizing bacteria community composition and alpha-diversity are depending on fertilizer regimes, but independent of the soil aggregate.

SUBMITTER: Han S

PROVIDER: S-EPMC5951965 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:In agricultural soils fertilized with a high amount of ammonium nitrogen, the pH decreases because of the oxidation of ammonia by nitrifiers. Molecular-based analyses have revealed that members of the genus Nitrospira dominate over other nitrifiers in some acidic soils. However, terrestrial Nitrospira are rarely cultivated and little is known about their ecophysiology. In addition, recent studies discovered a single microbe with the potential to oxidize both ammonia and nitrite (complete ammonia oxidizer; comammox) within Nitrospira, which had been previously recognized as a nitrite oxidizer. Despite their broad distribution, there are no enrichment samples of comammox from terrestrial or acidic environments. Here, we report the selective enrichment of both comammox and nitrite-oxidizing Nitrospira from the acidic soil of a heavily fertilized tea field. Long-term enrichment was performed with two individual continuous-feeding bioreactors capable of controlling ammonia or nitrite concentration and pH. We found that excessive ammonium supply was a key factor to enhance the growth of comammox Nitrospira under acidic conditions. Additionally, a low concentration of nitrite was fed to prevent the accumulation of free nitrous acid and inhibition of cell growth under low pH, resulting in the selective enrichment of nitrite-oxidizing Nitrospira. Based on 16S rRNA gene analysis, Nitrospira accounting for only 1.2% in an initial soil increased to approximately 80% of the total microorganisms in both ammonia- and nitrite-fed bioreactors. Furthermore, amoA amplicon sequencing revealed that two phylotypes belonging to comammox clade A were enriched in an ammonia-fed bioreactor. One group was closely related to previously cultivated strains, and the other was classified into a different cluster consisting of only uncultivated representatives. These two groups coexisted in the bioreactor controlled at pH 6.0, but the latter became dominant after the pH decreased to 5.5. Additionally, a physiological experiment revealed that the enrichment sample oxidizes ammonia at pH <4, which is in accordance with the strongly acidic tea field soil; this value is lower than the active pH range of isolated acid-adapted nitrifiers. In conclusion, we successfully enriched multiple phylotypes of comammox and nitrite-oxidizing Nitrospira and revealed that the pH and concentrations of protonated N-compounds were potential niche determinants.

Project description:Green manure application is a common practice to improve soil fertility in China. However, the impact of different green manure-fertilizer combinations on the soil microbial communities in the low-fertility immature red soil in southern China remains unclear. In this study, we conducted a pot experiment using two common green manure crops, ryegrass (Lolium perenne L.) and Chinese milk vetch (Astragalus sinicus L.), along with a fallow treatment. We also considered three combined fertilizer management strategies, including mineral, humic acid, and organic manure fertilizers. We evaluated the soil microbial biomass, activity, communities, functional prediction and their correlation with soil properties during green manure growth and incorporation periods, to assess the potential alterations caused by different green manure and fertilizer combinations. Our findings indicate that green manure application, particularly in combination with organic fertilizers, increased the alpha diversity of the soil bacterial community, while the opposite trend was observed in the fungal community. The application of green manure altered the soil microbial communities during both growth and incorporation periods, especially the taxa that participate in carbon, nitrogen and sulfur cycles. Notably, ryegrass significantly increased the relative abundance of bacterial phylum Firmicutes and fungal phylum Ascomycota, whereas Chinese milk vetch significantly stimulated the bacterial phylum Acidobacteria and fungal phylum Glomeromycota. Compared with fallow treatments, green manure application significantly increased the soil pH by 4.1%-12.4%, and microbial biomass carbon by 29.8%-72.9%, regardless of the types of combined fertilizer. Additionally, the application of green manure resulted in a 35.6%-142.6% increase in urease activity and a 65.9%-172.9% increase in β-glucosidase activity compared to fallow treatments, while led to a 22.5%-55.6% decrease in catalase activity. Further analysis revealed that the changes in both bacterial and fungal communities positively correlated with soil pH, soil organic matter, total nitrogen and alkali hydrolyzed nitrogen contents. Moreover, the relationship between the soil microbial community and soil enzyme activities was regulated by the specific green manure species. In conclusion, our results provide insight into the effects of different green manure-fertilizer combinations on soil microorganisms and their underlying mechanisms in improving soil fertility in the low-fertility immature red soil.

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Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil.

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