Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments

Li, Meng; Cao, Huiluo; Hong, Yiguo; Gu, Ji‐Dong

doi:10.1007/s00253-010-2929-0

Cited by 138 publications

(88 citation statements)

References 54 publications

(82 reference statements)

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“…3A) showed that anammox bacteria and AOA were dominant across the sample sites with low ammonia concentrations (Ͻ0.07 mg TAN liter Ϫ1 ), and the proportion of both AOA and anammox bacterial genes decreased across the sampling sites within the WWTP plume proportional to AOB. These results from temperate river sediments are consistent with recent research demonstrating a positive correlation between anammox bacteria and AOA in mangrove sediments, with abundances affected by ammonia input (46). Two available AOA pure cultures showed a low half-saturation constant (K m ) for ammonia uptake, which supports the predominance of AOA in oligotrophic environments (47,48).…”

Section: Resultssupporting

confidence: 80%

Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada

Sonthiphand

Cejudo

Schiff

et al. 2013

Appl Environ Microbiol

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The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH 3 and NH 4 ؉ ) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO 3 ؊ or N 2 ), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities.T he Grand River is the largest watershed in Southwestern Ontario, draining into Lake Erie, and is impacted by ammonia (NH 3 and NH 4 ϩ ) sources that directly affect water quality. The oxidation of anthropogenic ammonia to less toxic forms (e.g., NO 3 Ϫ or N 2 ) by ammonia-oxidizing prokaryotes (AOP) helps prevent ammonia from exceeding toxicity thresholds for aquatic organisms and limits for downstream drinking water intake. AOP include aerobic ammonia-oxidizing bacteria (AOB) and archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria.Nitrification is composed of two biological processes: ammonia and nitrite oxidation. Ammonia oxidation is considered the rate-limiting step in nitrification (1) and was believed for many decades to be mediated solely by a group of chemolithoautotrophic AOB (2). In 2005, AOA were also discovered (3). Although studies have confirmed the presence and abundance of AOA in both natural (e.g., references 4-6) and engineered (e.g., references 7-9) environments, relative contributions to ammonia oxidation in these environments are difficult to assess. Although AOA, rather than AOB, were active in soil microcosms and acid soils due to low ammonia availability and their kinetic constant (K m ) for ammonia (10), AOB showed e...

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Section: Resultssupporting

confidence: 80%

Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada

Sonthiphand

Cejudo

Schiff

et al. 2013

Appl Environ Microbiol

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“…Mangroves provide a unique ecological environment for diverse microbial communities (Kathiresan and Bingham 2001), including Archaea, the third domain of life that are often found in a wide range of environments (Chaban et al 2006). To date, studies focused on Archaea in mangrove ecosystems have dealt mainly with archaeal communities (Yan et al 2006;Rooney-Varga et al 2007;Pires 2010;Mendes et al 2012;Pires et al 2012;Tian et al 2012;Bhattacharyya et al 2015), methanogenic archaea (Mohanraju and Natarajan 1992;Lyimo et al 2000;Lyimo et al 2009;Taketani et al 2010), and ammoniaoxidizing archaea (Li et al 2011;Li and Gu 2013;Wang et al 2013;Wang and Gu 2014), but it still remains unclear whether there are differences in the composition, structure, and diversity of the archaeal communities in the sediments of different mangrove species.…”

Section: Introductionmentioning

confidence: 99%

Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China

Guan

Chen

et al. 2016

J Soils Sediments

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Purpose Knowledge of archaeal communities is essential for understanding of the mechanism of carbon and nitrogen cycle in the mangrove sediment ecosystem. Presently, little is known about archaeal communities in the Dongzhaigang mangrove sediments. This study aimed to characterize the archaeal communities in sediments of different mangrove stands and to find out the correlations between archaeal communities and the environmental factors of sediments.Materials and methods Sediment samples were collected from the Dongzhaigang mangrove forest for analysis of soil properties and archaeal communities, by national standard methods and Illumina Miseq archaeal 16S ribosomal RNA (rRNA) gene sequencing, respectively. Results and discussion The archaeal community in the Dongzhaigang mangrove forest was constituted by some phyla from BTACK^and BDPANN^supergroups, and dominated by Euryarchaeota. Among sediments of the four mangroves in Dongzhaigang, principal coordinates analysis (PCoA) scatter plot showed a trend of difference in the archaeal community structure in the Bruguiera gymnoihiza and Kandelia candel stands from that in the Laguncularia racemosa and Sonneratia apetala stands. The abundance of the order Methanosarcinales was the highest in the sediments of K. candel mangroves, whereas the order of Methanobacteriales dominated in B. gymnoihiza sediments. The highest richness and diversity values of Archaea occurred in K. candel sediments, while the lowest in B. gymnoihiza. Pearson correlation showed the significant relationships between sediment properties and some dominant genera, with a positive and significant correlation between sediment properties and genus Methanobacterium, coinciding with the maximum values of sediment properties and abundance of Methanobacterium in the sediment of B. gymnoihiza. Such results indicated that the difference of archaeal community structure among mangrove sediments may be caused by the different sediment characteristics. Methanogenic communities in the Dongzhaigang mangrove forest sediments were, at the order level, constituted by Methanobacteriales, Methanomicrobiales, Methanosarcinales, and Methanomassiliicoccales. Conclusions The investigation indicated that the Dongzhaigang mangrove sediment ecosystems support (2016( ) 16:1995( -2004( DOI 10.1007( /s11368-016-1427 diverse archaeal communities and methanogenic communities, and that there was a general trend of difference in the archaeal community structure in the B. gymnoihiza and K. candel mangrove sediments from that in the L. racemosa and S. apetala sediments. Such difference may be caused by the difference in sediment characteristics.

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“…However, this view was challenged by the discovery of genes encoding proteins with homology to ammonia monooxygenases (amoA) in genome fragments of archaea which are affiliated with the phylum Thaumarchaeota (11,12,13). Since ammonia-oxidizing archaea (AOA) were discovered, they have been detected in various environments, including soils and sediments (12,14,15,16,17), estuaries (11,18,19,20), subterranean environments (21), oxic and suboxic marine layers (22,23,24), sponges (25), corals (26), and wastewater sludge (27). So far, most studies have shown that a large proportion of the Thaumarchaeota are autotrophic and capable of performing the oxidation of ammonia to nitrite (15,22), although several studies reported that some of these archaea may also be able to assimilate organic compounds, like amino acids (13,28).…”

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confidence: 99%

Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

Zheng

Newell

Liu

et al. 2014

Appl Environ Microbiol

141

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d Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase ␣ subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB amoA genes was greater than that of AOA amoA genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal amoA gene abundance and not with bacterial amoA gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments.

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Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments

Cited by 138 publications

References 54 publications

Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada

Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada

Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China

Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

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