Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils

Clark, Ian M.; Hughes, David; Fu, Qingling; Abadie, Maïder; Hirsch, P. R.

doi:10.1038/s41598-021-95100-9

Cited by 43 publications

(21 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The AOA are autotrophs and they can fix carbon through a modified version of the 3- hydroxypropionate/4-hydroxybutyrate pathway ( Walker et al, 2010 ; Könneke et al, 2014 ). AOB members of the Nitrosomonadaceae family are obligate autotrophs that can only fix carbon through the Calvin cycle ( Clark et al, 2021 ). This could represent another evolutionary advantage for AOA in tropical floodplain soils, as DOC and total carbon had a significant effect on their variance ( Figure 3A ).…”

Section: Discussionmentioning

confidence: 99%

Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities

et al. 2022

View full text Add to dashboard Cite

Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2–), which can be further oxidized to nitrate (NO3–). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2– and NO3–, with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4+) and NO3–—and NO2–—dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.

show abstract

Section: Discussionmentioning

confidence: 99%

Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities

et al. 2022

View full text Add to dashboard Cite

show abstract

“…First, bacterial profiles can be obtained using metagenomics analysis, in which the entire DNA of the microorganism community is analyzed through random sequencing and not just by sequencing specifically targeted genes [7]. The advantages of the latest generation of sequencing include fast reading times [8], providing unbiased detection of organisms in samples [9], displaying community diversity, and characterizing the composition of microorganisms [19]. The reading results produced by MinION are of high quality, and the resulting taxonomy is accurate at 99.5% [20].…”

Section: It Can Increase Cancer Risk Factors Due To Carcinogenicmentioning

confidence: 99%

“…The most abundant nitrite-forming bacteria in soil metagenomics were Nitrosospira (50-80%), Nitrosomonas (13-41%), and gammaproteobacteria (<10%). These bacteria do not compete directly in the soil but occupy complementary niches [8]. Nitrosomonas are heterotrophic bacteria and produce the enzyme catalase, which plays a role in the process of ammonia oxidation to nitrite.…”

Section: It Can Increase Cancer Risk Factors Due To Carcinogenicmentioning

confidence: 99%

See 1 more Smart Citation

A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird's nest on Sumatera Island, Indonesia

et al. 2022

View full text Add to dashboard Cite

Background and Aim: Since the past decade, metagenomics has been used to evaluate sequenced deoxyribonucleic acid of all microorganisms in several types of research. Nitrite contamination originates from the natural environment in Swiftlet farmhouses (SFHs) and can influence nitrite levels in edible bird's nest (EBN). It is strongly speculated that the conversion process into nitrite is influenced by the bacteria present in SFHs. Nitrite can cause adverse effects on human health. The previous research has focused on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. This study aimed to a metagenomics analysis of bacteria present in the dirt of SFHs and evaluated nitrite levels in EBN on Sumatera Island. Materials and Methods: In total, 18 SFHs on Sumatera Island were selected, and EBN and dirt samples were collected from each SFH, resulting in 18 EBN and 18 dirt SFH samples. Raw uncleaned white EBN and dirt from three areas of SFH were collected. The samples were analyzed for nitrite levels using a spectrophotometer, and the metagenomics sequencing of SFH dirt samples was performed using the MinIon nanopore method. The sequenced data were analyzed using the EPI2ME software. Results: Of the 18 raw uncleaned white EBN samples, 9 (50%) had <30 ppm nitrite levels. The top five bacterial genera in SFH dirt samples in Group A (nitrite levels >30 ppm) were Aeromonas, Escherichia, Acinetobacter, Arcobacter, and Acetoanaerobium. Those in Group B (nitrite levels <30 ppm) were Aeromonas, Pseudomonas, Shewanella, Escherichia, and Acinetobacter. There were 12 genera of nitrifying bacteria in Group A and 8 in Group B. The total cumulative read of nitrifying bacteria in Groups A and B were 87 and 38 reads, respectively. Conclusion: This is the first study to show that characteristic bacteria present in the dirt of SFHs might significantly influence the conversion from nitrogen to nitrite. Approximately 50% of raw uncleaned EBN samples had <30 ppm nitrite levels. Aeromonas was the most dominant bacterial genus found in Groups A and B. The variations in genus and cumulative reads nitrifying bacteria in group A were greater than those in Group B. This study provides information on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. Metagenomics data were obtained from the reading using the software EPI2ME. Further research is needed on the bacterial target species that can convert nitrite in SFHs.

show abstract

“…Recently, metagenomics survey has enabled the easy identification of microorganisms. Known and unknown nitrifying microorganism strain has been identified from different habitats via metagenomics analysis (Clark et al, 2021). The establishment of the presence of nitrifying bacteria and archaea provides a guide on what type is to be isolated and cultured.…”

Section: Identification and Isolation Of Nitrifying Bacteria And Archaeamentioning

confidence: 99%

Sustainable Intensification of Maize in the Industrial Revolution: Potential of Nitrifying Bacteria and Archaea

Ayiti

Babalola

2022

Front. Sustain. Food Syst.

View full text Add to dashboard Cite

Sustainable intensification is a means that proffer a solution to the increasing demand for food without degrading agricultural land. Maize is one of the most important crops in the industrial revolution era, there is a need for its sustainable intensification. This review discusses the role of maize in the industrial revolution, progress toward sustainable production, and the potential of nitrifying bacteria and archaea to achieve sustainable intensification. The era of the industrial revolution (IR) uses biotechnology which has proven to be the most environmentally friendly choice to improve crop yield and nutrients. Scientific research and the global economy have benefited from maize and maize products which are vast. Research on plant growth-promoting microorganisms is on the increase. One of the ways they carry out their function is by assisting in the cycling of geochemical, thus making nutrients available for plant growth. Nitrifying bacteria and archaea are the engineers of the nitrification process that produce nitrogen in forms accessible to plants. They have been identified in the rhizosphere of many crops, including maize, and have been used as biofertilizers. This study's findings could help in the development of microbial inoculum, which could be used to replace synthetic fertilizer and achieve sustainable intensification of maize production during the industrial revolution.

show abstract

Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils

Cited by 43 publications

References 48 publications

Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities

Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities

A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird's nest on Sumatera Island, Indonesia

Sustainable Intensification of Maize in the Industrial Revolution: Potential of Nitrifying Bacteria and Archaea

Contact Info

Product

Resources

About