Effects of applying inorganic fertilizer and organic manure for 35 years on the structure and diversity of ammonia‐oxidizing archaea communities in a Chinese Mollisols field

Abstract

In this study, we investigated the physicochemical properties of soil, and the diversity and structure of the soil ammonia-oxidizing archaea (AOA) community, when subjected to fertilizer treatments for over 35 years. We collected soil samples from a black soil fertilization trial in northeast China. Four treatments were tested: no fertilization (CK); manure (M); nitrogen (N), phosphorus (P), and potassium (K) chemical fertilizer (NPK); and N, P, and K plus M (MNPK). We employed 454 high-throughput pyrosequencing to measure the response of the soil AOA community to the longterm fertilization. The fertilization treatments had different impacts on the shifts in the soil properties and AOA community. The utilization of manure alleviated soil acidification and enhanced the soybean yield. The soil AOA abundance was increased greatly by inorganic and organic fertilizers. In addition, the community Chao1 and ACE were highest in the MNPK treatment. In terms of the AOA community composition, Thaumarchaeota and Crenarchaeota were the main AOA phyla in all samples.Compared with CK and M, the abundances of Thaumarchaeota were remarkably lower in the MNPK and NPK treatments. There were distinct shifts in the compositions of the AOA operational taxonomic units (OTUs) under different fertilization management practices. OTU51 was the dominant OTU in all treatments, except for NPK. OTU79 and OTU11 were relatively abundant OTUs in NPK. Only Nitrososphaera AOA were tracked from the black soil. Redundancy analysis indicated that the soil pH and soil available P were the two main factors that affected the AOA community structure. The abundances of AOA were positively correlated with the total N and available P concentrations, and negatively correlated with the soil pH.

Responses of Soil Abiotic Properties and Microbial Community Structure to 25-Year Cucumber Monoculture in Commercial Greenhouses

“…Notably, soil acidification was not as severe as salinization in the present study, so that significantly low pH values were only observed in CMY7. The findings are inconsistent with the results of previous findings, where both long-term monoculture and over-fertilization increased soil acidification [12,31,33]. For example, in a previous study in Shouguang, Shandong province, vegetable soil pH and soil EC were significantly negatively correlated under greenhouse production [12].…”

“…However, we did not observe such a correlation in Wafangdian, Liaoning province. The generally minor shifts in pH could be attributed to long-term manure and compost application, since organic manure could effectively buffer soil acidification [11,29,33].…”

Probe capture enrichment sequencing ofamoAgenes discloses diverse ammonia-oxidizing archaeal and bacterial populations

“…Diluted metagenomic mock samples were prepared, in which the total concentrations of the six amoA genes were adjusted to 10 6 , 10 5 , and 10 4 copies/ng of DNA using commercially available plasmid DNA, referred to as Mock-copy1e6, Mock-copy1e5, and Mock-copy1e4, respectively. The adjusted concentrations were compatible with those in a wide range of environments such as soil (Bahram et al, 2022;Bannert et al, 2011;Ding et al, 2020;Han et al, 2013;Marusenko et al, 2013), wastewater (Spasov et al, 2020;Wang et al, 2021;Zhang et al, 2015), estuaries (Hollibaugh et al, 2011), and seawater (Christman et al, 2011). OTUs were de novo predicted using pooled reads from three capture and three non-capture samples.…”

“…However, the target genes typically exist at low concentrations in heterogeneous DNA samples. The concentration of amoA was estimated to be up to 10 8 copies per ng of DNA in soil (Bahram et al, 2022; Bannert et al, 2011; Ding et al, 2020; Han et al, 2013; Marusenko et al, 2013), wastewater (Spasov et al, 2020; Wang et al, 2021; Zhang et al, 2015), estuaries (Hollibaugh et al, 2011), and seawater (Christman et al, 2011) using quantitative real-time PCR (qPCR), and less than 0.001% and 0.05% of the metagenomic and metatranscriptomic reads, respectively, were assigned to the amoA gene from soil samples (Bahram et al, 2022; Clark et al, 2021; Paungfoo-Lonhienne et al, 2017). This low concentration limits the community-wide analysis of genes of interest to a realizable sequencing depth.…”

Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system

“…Previous studies have reported contrasting results about the relative abundance and structural composition of AOA communities. Some studies demonstrated that different N fertilizer management approaches significantly impact the AOB communities over AOA ( Sun et al, 2019 ; Ding et al, 2020 ), whereas a few studies revealed that the structural composition and the relative abundance of AOA communities were significantly sensitive to different fertilizer management strategies ( Mukhtar et al, 2019 ). Amazingly, the structural composition of AOA has been noticed to depict an intensive correlation between AOA composition and soil properties and environmental conditions, which necessarily reported that a single soil or environmental parameter does not decide the structural composition of AOA in the soil ( Jiang et al, 2014 ; Zhang et al, 2019a ).…”