Ammonia oxidizers in river sediments of the Qinghai-Tibet Plateau and their adaptations to high-elevation conditions

Zhang, Sibo; Qin, Wei; Xia, Xinghui; Xia, Lingzi; Li, Siling; Zhang, Liwei; Bai, Yubei; Wang, Gongqin

doi:10.1016/j.watres.2020.115589

Cited by 47 publications

(28 citation statements)

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“…Cenarchaeum symbiosum was the first genome sequenced from AOA, yielding new perspective on the evolution, metabolic potential, and environmental distribution of this ubiquitous archaeal lineage [ 8 ]. Their habitat range encompasses the oceanic water column from its surface to hadal depths [ 3 , 9 ], polar oceans [ 10 ], symbiotic systems [ 11 ], and terrestrial systems of extremes of pH, temperature, and elevation [ 12 – 15 ]. They are now recognized to exert the primary control on nitrification in oligotrophic environments [ 16 – 18 ].…”

Section: Introductionmentioning

confidence: 99%

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

et al. 2020

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Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.

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Section: Introductionmentioning

confidence: 99%

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

et al. 2020

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“…Ammonia oxidizers including AOA, AOB, and comammox are ubiquitous in various environments ( Chao et al, 2016 ;Daims et al, 2015 ;Liu et al, 2020 ;Pjevac et al, 2017 ;Prosser and Nicol, 2012 ;Zhang et al, 2020 ;Zhao et al, 2020 ). In the nitrifying environments of WWTPs, AOB represent the majority of ammoniaoxidizing microorganisms (AOM) ( Mussmann et al, 2011 ); AOA and comammox have also regularly been detected by cultivation or molecular tools ( Chao et al, 2016 ;Daims et al, 2015 ;Pjevac et al, 2017 ;Sauder et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Biotransformation of lincomycin and fluoroquinolone antibiotics by the ammonia oxidizers AOA, AOB and comammox: A comparison of removal, pathways, and mechanisms

et al. 2021

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In this study, we evaluated the biotransformation mechanisms of lincomycin (LIN) and three fluoroquinolone antibiotics (FQs), ciprofloxacin (CFX), norfloxacin (NFX), and ofloxacin (OFX), which regularly enter aquatic environments through human activities, by different ammonia-oxidizing microorganisms (AOM). The organisms included a pure culture of the complete ammonia oxidizer (comammox) Nitrospira inopinata , an ammonia oxidizing archaeon (AOA) Nitrososphaera gargensis , and an ammonia-oxidizing bacterium (AOB) Nitrosomonas nitrosa Nm90. The removal of these antibiotics by the pure microbial cultures and the protein-normalized biotransformation rate constants indicated that LIN was significantly co-metabolically biotransformed by AOA and comammox, but not by AOB. CFX and NFX were significantly co-metabolized by AOA and AOB, but not by comammox. None of the tested cultures transformed OFX effectively. Generally, AOA showed the best biotransformation capability for LIN and FQs, followed by comammox and AOB. The transformation products and their related biotransformation mechanisms were also elucidated. i) The AOA performed hydroxylation, S-oxidation, and demethylation of LIN, as well as nitrosation and cleavage of the piperazine moiety of CFX and NFX; ii) the AOB utilized nitrosation to biotransform CFX and NFX; and iii) the comammox carried out hydroxylation, demethylation, and demethylthioation of LIN. Hydroxylamine, an intermediate of ammonia oxidation, chemically reacted with LIN and the selected FQs, with removals exceeding 90%. Collectively, these findings provide important fundamental insights into the roles of different ammonia oxidizers and their intermediates on LIN and FQ biotransformation in nitrifying environments including wastewater treatment systems.

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“…Both groups of taxa perform a similar function of ammonia monooxygenase enzymatic pathway; therefore, the amoA gene is commonly used as a functional marker for ecological assessment of these taxa [ 2 , 4 ]. However, many previous studies suggested that their relative abundances vary from fractional to several orders of magnitude, depending upon a variety of environmental factors—such as pH, salinity, organic carbon, temperature, ammonium and moisture content [ 5 , 6 , 7 , 8 , 9 , 10 ]. For instance, AOA dominates nitrification in low ammonium, low pH, and high temperature environments, while AOB dominates nitrification in high ammonium and low temperature environments [ 5 , 11 , 12 , 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

“…We do not know whether high-elevation wetlands have microbial aspects that are similar to other wetlands or if their microbial community structure and function are unique. Two previous studies have investigated ammonia-oxidizer communities in the overlying water and sediments of five rivers in the Qinghai–Tibetan Plateau, and found that the high-elevation conditions (low temperature, low ammonium concentration, and intensive solar radiation) shaped distinctive community compositions and distribution patterns for ammonia oxidizers in the five rivers, as compared with low-elevation rivers [ 10 , 16 ]. These observations highlight the necessity of better understanding how a wider range environmental condition can regulate ammonia-oxidizer communities.…”

Section: Introductionmentioning

confidence: 99%

Environmental Factors, More Than Spatial Distance, Explain Community Structure of Soil Ammonia-Oxidizers in Wetlands on the Qinghai–Tibetan Plateau

et al. 2020

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In wetland ecosystems, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), which are, therefore, important for studying nitrogen cycling. However, the ammonia-oxidizer communities in the typical high-elevation wetlands are poorly understood. Here, we examined ammonia-oxidizer communities in soils from three wetland types and 31 wetland sites across the Qinghai–Tibetan Plateau. The amoA gene of AOA and AOB was widespread across all wetland types. Nitrososphaera clade (Group I.1b) overwhelmingly dominated in AOA community (90.36%), while Nitrosospira was the principal AOB type (64.96%). The average abundances of AOA and AOB were 2.63 × 104 copies g−1 and 9.73 × 103 copies g−1. The abundance of AOA amoA gene was higher in riverine and lacustrine wetlands, while AOB amoA gene dominated in palustrine wetlands. The environmental conditions, but not spatial distance, have a dominant role in shaping the pattern of ammonia-oxidizer communities. The AOA community composition was influenced by mean annual temperature (MAT) and mean annual precipitation (MAP), while MAT, conductivity and plant richness, pH, and TN influenced the AOB community composition. The net nitrification rate had a significant correlation to AOB, but not AOA abundance. Our results suggest a dominant role for climate factors (MAT and MAP) in shaping community composition across a wide variety of wetland sites and conditions.

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Ammonia oxidizers in river sediments of the Qinghai-Tibet Plateau and their adaptations to high-elevation conditions

Cited by 47 publications

References 46 publications

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

Biotransformation of lincomycin and fluoroquinolone antibiotics by the ammonia oxidizers AOA, AOB and comammox: A comparison of removal, pathways, and mechanisms

Environmental Factors, More Than Spatial Distance, Explain Community Structure of Soil Ammonia-Oxidizers in Wetlands on the Qinghai–Tibetan Plateau

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