Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils

Dai, Yu; Wu, Zhen; Zhou, Qiheng; Zhao, Qun; Li, Ningning; Xie, Shuguang; Liu, Yong

doi:10.1016/j.resmic.2015.07.012

Cited by 11 publications

(3 citation statements)

References 49 publications

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“…The most abundant AOTU1 ( Figures 2A ) showed a negative correlation with TOC ( Figure 6B ), while the dominant OTU of AOB exhibited a positive correlation with TOC ( Supplementary Figure S1 ). This aligned with findings in other environments, such as ponds, estuaries and upland soils ( Dai et al, 2015 , 2018 ; Wei et al, 2021 ; Zhu et al, 2023 ). Most AOA are autotrophs and well adapted to oligotrophic environments due to their highly efficient CO 2 -fixation pathway of hydroxypropionate/hydroxybutyrate (HP/HB) cycle, as indicated by genomic studies ( Kobayashi et al, 2018 ; Zhao and Zhang, 2022 ).…”

Section: Discussionsupporting

confidence: 88%

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Li,

Cheng,

Liu

et al. 2024

Front. Microbiol.

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Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48–100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl− played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

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Section: Discussionsupporting

confidence: 88%

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Li,

Cheng,

Liu

et al. 2024

Front. Microbiol.

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“…10 ). However, the growth for some genera that are indispensable for nutrient cycling 21 – 23 were inhibited by DBP, including Nitrososphaera , Streptomyces , Frankia , Conexibacter , Pseudonocardia , Acidothermus , Nocardiopsis , Lactococcus , Mycobacterium , Pseudomonas and Tetrasphaera . Nitrososphaera , Frankia and Conexibacter .…”

Section: Discussionmentioning

confidence: 99%

Dibutyl phthalate alters the metabolic pathways of microbes in black soils

You

Wang

et al. 2018

Sci Rep

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Dibutyl phthalate (DBP) is well known as a high-priority pollutant. This study explored the impacts of DBP on the metabolic pathways of microbes in black soils in the short term (20 days). The results showed that the microbial communities were changed in black soils with DBP. In nitrogen cycling, the abundances of the genes were elevated by DBP. DBP contamination facilitated 3′-phosphoadenosine-5′-phosphosulfate (PAPS) formation, and the gene flux of sulfate metabolism was increased. The total abundances of ABC transporters and the gene abundances of the monosaccharide-transporting ATPases MalK and MsmK were increased by DBP. The total abundance of two-component system (TCS) genes and the gene abundances of malate dehydrogenase, histidine kinase and citryl-CoA lyase were increased after DBP contamination. The total abundance of phosphotransferase system (PTS) genes and the gene abundances of phosphotransferase, Crr and BglF were raised by DBP. The increased gene abundances of ABC transporters, TCS and PTS could be the reasons for the acceleration of nitrogen, carbon and sulfate metabolism. The degrading-genes of DBP were increased markedly in soil exposed to DBP. In summary, DBP contamination altered the microbial community and enhanced the gene abundances of the carbon, nitrogen and sulfur metabolism in black soils in the short term.

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“…6). All these suggested that AOA community structure could be influenced by P (Dai et al, 2015). Hence, strong P sorption increased more AP in material, further favoring the abundance and activity of nitrifiers and denitrifiers as well as shaping their community composition, which was beneficial for N removal.…”

Section: Simultaneous Improvement Of P and N Removal And Mechanismsmentioning

confidence: 98%

Efficiency promotion and its mechanisms of simultaneous nitrogen and phosphorus removal in stormwater biofilters

Zhou

Cao

et al. 2016

Bioresource Technology

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Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils

Cited by 11 publications

References 49 publications

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Dibutyl phthalate alters the metabolic pathways of microbes in black soils

Efficiency promotion and its mechanisms of simultaneous nitrogen and phosphorus removal in stormwater biofilters

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