Hydrazine Synthase, a Unique Phylomarker with Which To Study the Presence and Biodiversity of Anammox Bacteria

Harhangi, Harry R.; Roy, Mathilde Le; Alen, Theo van; Hu, Baolan; Groen, J.P.; Kartal, Boran; Tringe, Susannah G.; Quan, Zhe‐Xue; Jetten, Mike S. M.; Camp, Huub J. M. Op den

doi:10.1128/aem.07113-11

Cited by 232 publications

(154 citation statements)

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“…The abundance of the anammox bacteria in the examined soil samples was estimated on the basis of the quantification of the anammox bacterial hzsA genes using the qPCR method described by Harhangi et al (37). The qPCR results further confirmed the occurrence of anammox bacteria in the collected samples.…”

Section: Resultsmentioning

confidence: 54%

“…Each PCR mixture (25 l) was composed of 12.5 l 2ϫ SsoFast EvaGreen supermix (Bio-Rad, CA), 0.5 l forward and reverse primers, and 1 l template DNA. The PCR thermal cycle program was performed as previously described (37). The standard curve was constructed from a series of 10-fold dilutions of a known copy number of the plasmid DNA, ranging from 1.28 ϫ 10 Ϫ8 to 1.28 ϫ 10 Ϫ2 ng of DNA per well.…”

Section: Methodsmentioning

confidence: 99%

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Broad Distribution of Diverse Anaerobic Ammonium-Oxidizing Bacteria in Chinese Agricultural Soils

Shen

Liu

Lou

et al. 2013

Appl Environ Microbiol

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bAnaerobic ammonium-oxidizing (anammox) bacteria have been detected in many marine and freshwater ecosystems. However, little is known about the distribution, diversity, and abundance of anammox bacteria in terrestrial ecosystems. In this study, anammox bacteria were found to be present in various agricultural soils collected from 32 different locations in China. Phylogenetic analysis of the 16S rRNA genes showed "Candidatus Brocadia," "Candidatus Kuenenia," "Candidatus Anammoxoglobus," and "Candidatus Jettenia" in the collected soils, with "Candidatus Brocadia" being the dominant genus. Quantitative PCR showed that the abundance of anammox bacteria ranged from 6.38 ؋ 10 4 ؎ 0.42 ؋ 10 4 to 3.69 ؋ 10 6 ؎ 0.25 ؋ 10 6 copies per gram of dry weight. Different levels of diversity, composition, and abundance of the anammox bacterial communities were observed, and redundancy analysis indicated that the soil organic content and the distribution of anammox communities were correlated in the soils examined. Furthermore, Pearson correlation analysis showed that the diversity of the anammox bacteria was positively correlated with the soil ammonium content and the organic content, while the anammox bacterial abundance was positively correlated with the soil ammonium content. These results demonstrate the broad distribution of diverse anammox bacteria and its correlation with the soil environmental conditions within an extensive range of Chinese agricultural soils.

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Section: Resultsmentioning

confidence: 54%

Section: Methodsmentioning

confidence: 99%

Broad Distribution of Diverse Anaerobic Ammonium-Oxidizing Bacteria in Chinese Agricultural Soils

Shen

Liu

Lou

et al. 2013

Appl Environ Microbiol

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“…Hydrazine synthase (hzs) is a very important enzyme in anammox metabolism and is responsible for the synthesis of hydrazine from nitric oxide and ammonium (39,40). In this study, the primer set hzsA_1597f-hzsA_1857r, targeting subunit ␣ of the hzs genes of anammox bacteria, was used to determine the abundance of anammox bacteria, as pre-viously described (41). The abundance of n-damo bacteria was estimated by quantifying their 16S rRNA genes using the primer set qP1f-qP1r, as previously described (30).…”

Section: Methodsmentioning

confidence: 99%

Evidence for the Cooccurrence of Nitrite-Dependent Anaerobic Ammonium and Methane Oxidation Processes in a Flooded Paddy Field

Shen

Liu

Huang

et al. 2014

Appl Environ Microbiol

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113

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Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two of the most recent discoveries in the microbial nitrogen cycle. In the present study, we provide direct evidence for the cooccurrence of the anammox and n-damo processes in a flooded paddy field in southeastern China. Stable isotope experiments showed that the potential anammox rates ranged from 5.6 to 22.7 nmol N 2 g ؊1 (dry weight) day ؊1 and the potential n-damo rates varied from 0.2 to 2.1 nmol CO 2 g ؊1 (dry weight) day ؊1 in different layers of soil cores. Quantitative PCR showed that the abundance of anammox bacteria ranged from 1.0 ؋ 10 5 to 2.0 ؋ 10 6 copies g ؊1 (dry weight) in different layers of soil cores and the abundance of n-damo bacteria varied from 3.8 ؋ 10 5 to 6.1 ؋ 10 6 copies g ؊1 (dry weight). Phylogenetic analyses of the recovered 16S rRNA gene sequences showed that anammox bacteria affiliated with "Candidatus Brocadia" and "Candidatus Kuenenia" and n-damo bacteria related to "Candidatus Methylomirabilis oxyfera" were present in the soil cores. It is estimated that a total loss of 50.7 g N m ؊2 per year could be linked to the anammox process, which is at intermediate levels for the nitrogen flux ranges of aerobic ammonium oxidation and denitrification reported in wetland soils. In addition, it is estimated that a total of 0.14 g CH 4 m ؊2 per year could be oxidized via the n-damo process, while this rate is at the lower end of the aerobic methane oxidation rates reported in wetland soils.

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“…To date, phylogenetic analysis based on 16S rRNA genes suggested that anammox bacteria are affiliated within the phylum Planctomycetes, including five genera of Candidatus Anammoxoglobus, Candidatus Brocadia, Candidatus Jettenia, Candidatus Kuenenia and Candidatus Scalindua (Schmid et al, 2005). Recently, functional hzs genes were identified as a specific molecular marker for quantifying and characterizing anammox bacteria (Harhangi et al, 2012), and the hzsA and hzsB genes have been found in a few wetlands, agricultural and marine ecosystems (Humbert et al, 2012;Shen et al, 2013;Lipsewers et al, 2014). Furthermore, anammox bacteria are considered to be habitat-specific with certain groups observed to be dominant in distinct environments (Humbert et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Activity, abundance and community structure of anammox bacteria along depth profiles in three different paddy soils

Bai

et al. 2015

Soil Biology and Biochemistry

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a b s t r a c tAnaerobic ammonium oxidation (anammox) is a globally important nitrogen-cycling process mediated by specialized microbes, and has been demonstrated to be ubiquitous in anoxic natural settings and bioreactors. However, our knowledge of its prevalence in different paddy soil types and along the depth profiles remains largely undocumented. Here, mesocosm incubations were constructed to investigate the activity and community compositions of anammox bacteria across different depth layers of three different paddy soils. 15N tracer experiments showed that anammox rates were prevalent in almost all depth layers of an inceptisol (Binhai, BH) and an oxisol (Leizhou, LZ), but was absent in an ultisol (Taoyuan, TY). The functional gene hzsB of anammox bacteria was only detected in BH and LZ soil profiles with detected anammox activity. Anammox accounted for 0.4%e12.2% of the total N 2 production, and anammox rates were 0.02e0.77 nmol N g À1 dry soil h À1 and significantly correlated with soil pH and electric conductivity. Anammox activity and abundance of hzsB genes were significantly lower in the surface soil layers (0e5 cm) than in the sub-surface soil layers (20e60 cm). Candidatus Brocadia, Candidatus Kuenenia and Candidatus Jettenia were detected by cloning and sequencing, with Candidatus Brocadia being dominant in all the three soils and Candidatus Jettenia being more frequently detected in the LZ soil. The operational taxonomic unit number and diversity indices of anammox bacterial 16S rRNA gene increased with soil depth. Our results demonstrate that anammox is more common and active in alkaline soils than in acidic soils, in deep paddy soil layers than in surface soil layers, and that anammox activities are likely to be regulated by soil chemical properties such as pH, salinity and redox potential.

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Hydrazine Synthase, a Unique Phylomarker with Which To Study the Presence and Biodiversity of Anammox Bacteria

Cited by 232 publications

References 50 publications

Broad Distribution of Diverse Anaerobic Ammonium-Oxidizing Bacteria in Chinese Agricultural Soils

Broad Distribution of Diverse Anaerobic Ammonium-Oxidizing Bacteria in Chinese Agricultural Soils

Evidence for the Cooccurrence of Nitrite-Dependent Anaerobic Ammonium and Methane Oxidation Processes in a Flooded Paddy Field

Activity, abundance and community structure of anammox bacteria along depth profiles in three different paddy soils

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