Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre

Mincer, Tracy J.; Church, Matthew J.; Taylor, Lance T.; Preston, Christina M.; Karl, David M.; DeLong, Edward F.

doi:10.1111/j.1462-2920.2007.01239.x

Cited by 463 publications

(636 citation statements)

References 60 publications

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“…The ratio of AOA to AOB was larger than 1 at about 75% of the sites, and the greatest value of this ratio was primarily observed in the Hengshui and Xingtai reaches. In the natural environment, AOA are generally more abundant than AOB (Wessén et al, 2011;Leininger et al, 2006;Wu et al, 2010), and the abundance of AOA (Mincer et al, 2007) and AOB (Stehr et al, 1995) in the water column is commonly in the range of 10 2 to 10 5 gene copies/mL, which is consistent with the results of the present study.…”

Section: Physicochemical Characteristicssupporting

confidence: 82%

Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals

Chao

Shan

Zhang

et al. 2014

Journal of Environmental Sciences

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a b s t r a c tThe Haihe River is characterized by high ammonia pollution. Therefore, it is necessary to determine how environmental factors, such as heavy metals in the river limit the spatial distribution of ammonia-oxidizing microorganisms. In this study, the relationships between five heavy metals and ammonia-oxidizing microorganisms were studied. The results showed that under high ammonia, low oxygen and high concentrations of suspended particles, ammonia-oxidizing bacteria (AOB) ranged from 10 1.3 to 10 4.8 gene copies/mL and ammonia-oxidizing archaea (AOA) ranged from 10 2.7 to 10 4.9 gene copies/mL. The average metal concentrations in water were 23.57 (Cr), 21.58 (Ni), 65.09 (Cu), 622.03 (Zn) and 10.16 (As) μg/L, with those of Zn, Cu and Cr being higher than the US EPA criteria. Scatter plots of microbial abundance and metals indicated that both AOA and AOB were limited by heavy metals, but in different ways. As had an inhibitory effect on AOB, while Ni and Zn promoted AOA, and the other metals investigated showed no significant correlation with microbial abundance. Overall, our results indicated that the effects of heavy metals on ammonia-oxidizing microorganisms in water are complex, and that the final effect is determined by the physiological role of each element in the microorganisms, as well as environmental conditions such as complexation of organic matter, not simply the total metal concentration.

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Section: Physicochemical Characteristicssupporting

confidence: 82%

Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals

Chao

Shan

Zhang

et al. 2014

Journal of Environmental Sciences

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“…The CN strains are also highly similar on the 16S and amoA level to abundant groups of open ocean archaea from a range of oceanic provinces including the Sargasso Sea, Fernandina Island and the coast of Africa as indicated by BLAST searches of the Global Ocean Survey dataset (Rusch et al, 2007). Previous amoAbased phylogenies of AOA have shown that water column-derived sequences fall into two clusters termed 'A' and 'B' (Francis et al, 2005) thought to represent a depth-dependent partitioning of AOA (Hallam et al, 2006;Mincer et al, 2007;Beman et al, 2008 (Wuchter et al, 2006), and estimates of in situ per-cell activity rates in the California Current (0.2-15 fmol cell À1 day À1 ) (Santoro et al, 2010).…”

Section: Phylogenymentioning

confidence: 94%

“…Mesophilic archaea are ubiquitous and abundant members of diverse marine environments including coastal waters (Mincer et al, 2007;Beman et al, 2010), marine sediments, estuaries (Mosier and Francis, 2008;Bernhard et al, 2010;Urakawa et al, 2010), stratified basins (Coolen et al, 2007;Lam et al, 2007) and open ocean water columns (Beman et al, 2008;Church et al, 2010;Santoro et al, 2010). The recent cultivation of the first mesophilic marine archaeon, Nitrosopumilus maritimus, (Konneke et al, 2005;Martens-Habbena et al, 2009), two thermophilic archaea, Nitrosocaldus yellowstonii and Nitrosophaera gargensis (Hatzenpichler et al, 2008;de la Torre et al, 2008) and a freshwater archaeon, Nitrosoarchaeum limnia (Blainey et al, 2011) established that at least some of these organisms are chemolithoautotrophic ammonia oxidizers.…”

Section: Introductionmentioning

confidence: 99%

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

2011

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Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98-99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawaterbased liquid medium while stoichiometrically converting ammonia (NH 3 ) to nitrite (NO 2 À ). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect ( 15 e NH3 ) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15 e NH3 ranged from 13% to 41%, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15 e NH3 is similar.

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“…A number of recent studies suggest that AOA dominate in marine habitats (Wuchter et al, 2006;Mincer et al, 2007;Beman et al, 2008). In contrast, Mosier and Francis, (2008) found that copies of b-proteobacterial amoA were two orders of magnitude higher than archaeal amoA in high-salinity estuarine sediments.…”

Section: Introductionmentioning

confidence: 90%

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

et al. 2010

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Ammonia oxidation is a central process in the nitrogen cycle. Particularly in marine and estuarine environments, few experiments have been conducted to tease apart the factors influencing their abundance and composition. To investigate the effect of nitrogen and phosphorus availability on ammonia-oxidizing bacteria (AOB), we conducted a nutrient enrichment experiment in a Maine salt marsh and sampled sediment communities in three seasons over 2 years. We assessed community composition using terminal restriction fragment length polymorphism analysis and sequencing of cloned fragments of the ammonia monooxygenase (amoA) gene. Almost all of the amoA sequences fell within the marine and estuarine-specific Nitrosospira-like clade. Applied separately, nitrogen and phosphorus significantly altered AOB composition; however, together the nutrients had an interactive effect, and composition did not change. In contrast, nutrient enrichment did not alter AOB abundance. Furthermore, the response of AOB composition to nutrient enrichment varied over time. We conclude that closely related taxa within the marine/estuarine-specific Nitrosospira-like clade vary in their preference for nutrient concentrations, and this preference may depend on other temporally variable abiotic factors. Finally, AOB composition was highly variable within and across years even in untreated plots. Further studies are needed to test how these different aspects of compositional variability in AOB communities influence nitrogen cycling.

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Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre

Cited by 463 publications

References 60 publications

Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals

Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

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