Effects of estuarine sediment hypoxia on nitrogen fluxes and ammonia oxidizer gene transcription

Abell, Guy C. J.; Banks, Joanne; Ross, D. J.; Keane, John; Robert, Stanley; Revill, Andrew T.; Volkman, John K.

doi:10.1111/j.1574-6941.2010.00988.x

Cited by 51 publications

(30 citation statements)

References 47 publications

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“…Our results thus suggest that (i) glycolipids are mainly derived from the water column, (ii) HPHcrenarchaeol is relatively rapidly degraded and (iii) benthic AOA are actively producing IPL-crenarchaeol in the (sub-)surface of the sediment underneath the OMZ, probably occupying a low oxygen niche (cf. Chen et al, 2008;Abell et al, 2011;. Interestingly, while the HPH-crenarchaeol shows subsurface maxima indicating in situ production, the ratio of IPL-derived vs. CL-crenarchaeol does not increase as perhaps would be expected (Fig.…”

Section: Sedimentary Production and Preservation Of Gdgtsmentioning

confidence: 65%

Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum zone. Part II: Selective preservation and degradation in sediments and consequences for the TEX86

Lengger

Hopmans

Reichart

et al. 2012

Geochimica et Cosmochimica Acta

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The TEX 86 is a proxy based on a ratio of pelagic archaeal glycerol dibiphytanyl glycerol tetraether lipids (GDGTs), and used for estimating past sea water temperatures. Concerns exist that in situ production of GDGTs lipids by sedimentary Archaea may affect its validity. In this study, we investigated the influence of benthic GDGT production on the TEX 86 by analyzing the concentrations and distributions of GDGTs present as intact polar lipids (IPLs) and as core lipids (CLs) in three sediment cores deposited under contrasting redox conditions across a depth range from 900 to 3000 m below sea level in and below the Arabian Sea oxygen minimum zone (OMZ). Direct analysis of IPLs with crenarchaeol as CL via HPLC/ESI-MS 2 revealed that surface sediments in the OMZ were relatively depleted in the phospholipid hexose, phosphohexose (HPH)-crenarchaeol compared to suspended particulate matter from the water column, suggesting preferential and rapid degradation of this IPL. In sediment cores recovered from deeper, more oxic environments, concentrations of HPH-crenarchaeol peaked at the surface, probably due to in situ production by ammonia-oxidizing Archaea, followed by a rapid decrease with increasing depth. No surface maximum was observed in the sediment core from within the OMZ. In contrast, the glycolipids, monohexose-crenarchaeol and dihexose-crenarchaeol, did not change in concentration with depth in the sediment, indicating that they were relatively well preserved and likely mostly derived from fossil pelagic GDGTs. These results suggest that phospholipids are more sensitive to degradation, while glycolipids might be preserved over longer time scales, in line with previous incubation and modeling studies. Furthermore, in situ produced IPL-GDGTs did not accumulate as IPLs, and did not influence the CL-TEX 86 . This suggests that in-situ produced GDGT lipids were more susceptible to degradation than fossil CL and IPL and did not accumulate as CL. In agreement, no significant changes of TEX 86 with sediment depth in the core lipids were observed. However, consistent differences between IPL-derived TEX 86 and CL-TEX 86 were found. These could be explained by a different composition of CL-GDGT of the glyco-and phospholipids, in combination with dissimilar degradation rates of phospholipids vs. glycolipids. We also observed consistent differences in both IPL-derived and CL-TEX 86 between the different cores, equivalent to 3°C when converted to temperature, despite the proximity of the core locations. These differences may potentially be due to a larger addition of GDGTs produced in deeper, colder waters to the (sub)surface-derived GDGTs for the deeper core sites.

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Section: Sedimentary Production and Preservation Of Gdgtsmentioning

confidence: 65%

Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum zone. Part II: Selective preservation and degradation in sediments and consequences for the TEX86

Lengger

Hopmans

Reichart

et al. 2012

Geochimica et Cosmochimica Acta

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“…Previous studies have demonstrated that sediment, the primary site of estuarine nitrification, may contain both AOA and AOB, with some estuarine regions dominated by AOB (Mosier & Francis 2008, Santoro et al 2008) and others by AOA (Beman & Francis 2006, Abell et al 2010. The reason for the presence of one group of seemingly functionally equivalent groups over another in the environment is unclear, although it has been suggested that pH (Nicol et al 2008), nitrite (Sahan & Muyzer 2008), sulphide and phosphate (Erguder et al 2009) and salinity (Mosier & Francis 2008) may be important, whilst large variations in salinity, oxygen and hydrological factors may shape the structure of these communities (Stehr et al 1995, Cébron et al 2003, Francis et al 2003, Dang et al 2008, Abell et al 2010, Abell et al 2011.…”

Section: Introductionmentioning

confidence: 99%

Nitrifying and denitrifying microbial communities and their relationship to nutrient fluxes and sediment geochemistry in the Derwent Estuary, Tasmania

Abell¹,

Ross²,

Keane³

et al. 2013

Aquat. Microb. Ecol.

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Mineralisation, nitrification and denitrification in sediments are key processes that contribute to the removal of nitrogen from coastal waters. Together these processes are important in preventing the buildup of nitrogen, which can lead to eutrophication in estuarine systems. Spatial and temporal patterns in the composition of nitrifier (bacterial [AOB] and archaeal ammonia oxidizers [AOA]; amoA), denitrifier (nirS) and total bacterial and archaeal (16S rRNA gene) communities in sediment from the Derwent Estuary in southeast Tasmania, Australia, were contrasted with key environmental parameters and benthic nutrient fluxes. Spatial and temporal factors were significant in terms of shaping microbial community composition. Organic matter composition (C:N isotope ratios, %N and %C) was significantly related to the abundance of the different microbial guilds. There was a significant correlation between both the sediment nitrogen content and carbon stable isotope ratio with community composition for total bacteria, AOA and denitrifiers. Sediment chlorophyll a was significantly associated with AOB composition and carbon isotope ratio was related to total archaeal community composition.

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“…NH 4 + concentration can also determine the differential growth of AOB and AOA in soil in that AOA prefers a less NH 4 + (Verhamme et al 2011). An increase in NH 4 + concentration is indicative of a reduced nitrification efficiency (Abell et al 2011). In treatment T3 in the present study, the NH 4 + concentration increased as that of NO 2 − increased after PNP degradation by strain WBC-3.…”

Section: Discussionmentioning

confidence: 42%

“…However, the magnitudes of the relative contributions of AOB and AOA, which have ecologically equivalent functions, to ammonia oxidation are still largely unknown. It has been suggested that many environmental factors including pH (Nicol et al 2008), salinity (Mosier and Francis 2008), NH 4 + (Hofferle et al 2010;Martens-Habbena et al 2009;Verhamme et al 2011), and dissolved oxygen concentration (Abell et al 2011) may play a critical role in their individual dominance and the niche segregation of ammonia oxidizers. These findings have stimulated a reassessment of ammonia-oxidizer community ecology, and consequently, the nitrification process in agricultural ecosystems should be re-evaluated.…”

Section: Introductionmentioning

confidence: 99%

“…To date, most studies on the factors affecting the niche separation of nitrifying bacteria and archaea have focused on specific soil properties such as soil pH value (Nicol et al 2008) and dissolved oxygen (Abell et al 2011), but there is little information available regarding the response and adaption of AOB and AOA to dynamic bioaugmentation processes when the elements involved are converted from one substance to another, particularly when the elements are channeled into the nitrogen cycle. Information regarding the effects of such a dynamic bioaugmentation process on ammonia-oxidizer community composition and activity will be important for understanding their niche specialization.…”

Section: Introductionmentioning

confidence: 99%

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Effects of bioaugmentation in para-nitrophenol-contaminated soil on the abundance and community structure of ammonia-oxidizing bacteria and archaea

Chi

Liu

Zhou

2015

Appl Microbiol Biotechnol

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Pseudomonas sp. strain WBC-3 mineralizes the priority pollutant para-nitrophenol (PNP) and releases nitrite (NO 2 − ), which is probably involved in the nitrification. In this study, the rate of PNP removal in soil bioaugmented with strain WBC-3 was more accelerated with more NO 2 − accumulation than in uninoculated soils. Strain WBC-3 survived well and remained stable throughout the entire period. Realtime polymerase chain reaction (real-time PCR) indicated a higher abundance of ammonia-oxidizing bacteria (AOB) than ammonia-oxidizing archaea (AOA), suggesting that AOB played a greater role in nitrification in the original sampled soil. Real-time PCR and multivariate analysis based on the denaturing gradient gel electrophoresis showed that PNP contamination did not significantly alter the abundance and community structure of ammonia oxidizers except for inhibiting the AOB abundance. Bioaugmentation of PNP-contaminated soil showed a significant effect on AOB populations and community structure as well as AOA populations. In addition, ammonium (NH 4 + ) variation was found to be the primary factor affecting the AOB community structure, as determined by the correlation between the community structures of ammonia oxidizers and environmental factors. It is here proposed that the balance between archaeal and bacterial ammonia oxidation could be influenced significantly by the variation in NH 4 + levels as caused by bioaugmentation of contaminated soil by a pollutant containing nitrogen.

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Effects of estuarine sediment hypoxia on nitrogen fluxes and ammonia oxidizer gene transcription

Cited by 51 publications

References 47 publications

Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum zone. Part II: Selective preservation and degradation in sediments and consequences for the TEX86

Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum zone. Part II: Selective preservation and degradation in sediments and consequences for the TEX86

Nitrifying and denitrifying microbial communities and their relationship to nutrient fluxes and sediment geochemistry in the Derwent Estuary, Tasmania

Effects of bioaugmentation in para-nitrophenol-contaminated soil on the abundance and community structure of ammonia-oxidizing bacteria and archaea

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