scholarly journals Benthic Archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone

2017 ◽  
Author(s):  
Marc A. Besseling ◽  
Ellen C. Hopmans ◽  
Jaap S. Sinninghe Damsté ◽  
Laura Villanueva
Keyword(s):  
16S Rrna ◽  
Relative Abundance ◽  
Surface Sediments ◽  
Membrane Lipids ◽  
Oxygen Minimum Zone ◽  
Rrna Gene ◽  
Polar Head Group ◽  
Group I ◽  
Minimum Zone ◽  
Oxygen Minimum

Abstract. Benthic Archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Recent genomic surveys suggest they are largely involved in anaerobic processing of organic matter but the distribution and abundance of these archaeal groups is still largely unknown. Archaeal membrane lipids composed of isoprenoid diethers or tetraethers (glycerol dibiphytanyl glycerol tetraether, GDGT) are often used as archaeal biomarkers. Here, we compare the archaeal diversity and intact polar lipid (IPL) composition in both surface (0–0.5 cm) and subsurface (10–12 cm) sediments recovered within, just below, and well below the oxygen minimum zone (OMZ) of the Arabian Sea. Archaeal 16S rRNA gene amplicon sequencing revealed a predominance of Thaumarchaeota (Marine Group I, MG-I) in oxygenated sediments. Quantification of archaeal 16S rRNA and ammonia monoxygenase (amoA) of Thaumarchaeota genes and their transcripts indicated the presence of an active in situ benthic population, which coincided with a high relative abundance of hexose phosphohexose crenarchaeol, a specific biomarker for living Thaumarchaeota. On the other hand, anoxic surface sediments within the OMZ and all subsurface sediments were dominated by archaea belonging to the Miscellaneous Crenarchaeota Group (MCG), the Thermoplasmatales and archaea of the DPANN superphylum. Members of the MCG were diverse with a dominance of subgroup MCG-12 in anoxic surface sediments. This coincided with a high relative abundance of IPL GDGT-0 with an unknown polar head group. Subsurface anoxic sediments were characterized by higher relative abundance of GDGT-0, 2 and 3 with dihexose IPL-types, as well as GDGT-0 with a cyclopentanetetraol molecule and a hexose, as well as the presence of specific MCG subgroups, suggesting that these groups could be the biological sources of these archaeal lipids.

scholarly journals Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone

2018 ◽  
Vol 15 (13) ◽  
pp. 4047-4064 ◽  
Author(s):  
Marc A. Besseling ◽  
Ellen C. Hopmans ◽  
R. Christine Boschman ◽  
Jaap S. Sinninghe Damsté ◽  
Laura Villanueva
Keyword(s):  
16S Rrna ◽  
Relative Abundance ◽  
Surface Sediments ◽  
Membrane Lipids ◽  
Oxygen Minimum Zone ◽  
Rrna Gene ◽  
Polar Head Group ◽  
Group I ◽  
Minimum Zone ◽  
Oxygen Minimum

Abstract. Benthic archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Recent genomic surveys suggest they are largely involved in anaerobic processing of organic matter, but the distribution and abundance of these archaeal groups are still largely unknown. Archaeal membrane lipids composed of isoprenoid diethers or tetraethers (glycerol dibiphytanyl glycerol tetraether, GDGT) are often used as archaeal biomarkers. Here, we compare the archaeal diversity and intact polar lipid (IPL) composition in both surface (0–0.5 cm) and subsurface (10–12 cm) sediments recovered within, just below, and well below the oxygen minimum zone (OMZ) of the Arabian Sea. Archaeal 16S rRNA gene amplicon sequencing revealed a predominance of Thaumarchaeota (Marine Group I, MG-I) in oxygenated sediments. Quantification of archaeal 16S rRNA and ammonia monoxygenase (amoA) of Thaumarchaeota genes and their transcripts indicated the presence of an active in situ benthic population, which coincided with a high relative abundance of hexose phosphohexose crenarchaeol, a specific biomarker for living Thaumarchaeota. On the other hand, anoxic surface sediments within the OMZ and all subsurface sediments were dominated by archaea belonging to the Miscellaneous Crenarchaeota Group (MCG), the Thermoplasmatales and archaea of the DPANN (superphylum grouping Micrarchaeota, Diapherotrites, Aenigmarchaeota, Nanohaloarchaeota, Parvarchaeota, Nanoarchaeota, Pacearchaeota and Woesearchaeota). Members of the MCG were diverse, with a dominance of subgroup MCG-12 in anoxic surface sediments. This coincided with a high relative abundance of IPL GDGT-0 with an unknown polar head group. Subsurface anoxic sediments were characterized by higher relative abundance of GDGT-0, -2 and -3 with dihexose IPL types, GDGT-0 with a cyclopentanetetraol molecule and hexose, as well as the presence of specific MCG subgroups, suggesting that these groups could be the biological sources of these archaeal lipids.

scholarly journals Ammonia-Oxidizing β-Proteobacteria from the Oxygen Minimum Zone off Northern Chile

2007 ◽  
Vol 73 (11) ◽  
pp. 3547-3555 ◽  
Author(s):  
Verónica Molina ◽  
Osvaldo Ulloa ◽  
Laura Farías ◽  
Homero Urrutia ◽  
Salvador Ramírez ◽  
...  
Keyword(s):  
16S Rrna ◽  
Waste Treatment ◽  
Treatment Plant ◽  
Oxygen Minimum Zone ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Northern Chile ◽  
Clone Libraries ◽  
Minimum Zone ◽  
Oxygen Minimum

ABSTRACT The composition of ammonia-oxidizing bacteria from the β-Proteobacteria subclass (βAOB) was studied in the surface and upper-oxycline oxic waters (2- to 50-m depth, ∼200 to 44 μM O2) and within the oxygen minimum zone (OMZ) suboxic waters (50- to 400-m depth, ≤10 μM O2) of the eastern South Pacific off northern Chile. This study was carried out through cloning and sequencing of genes coding for 16S rRNA and the ammonia monooxygenase enzyme active subunit (amoA). Sequences affiliated with Nitrosospira-like cluster 1 dominated the 16S rRNA gene clone libraries constructed from both oxic and suboxic waters. Cluster 1 consists exclusively of yet-uncultivated βAOB from marine environments. However, a single clone, out of 224 obtained from the OMZ, was found to belong to Nitrosospira lineage cluster 0. To our knowledge, cluster 0 sequences have been derived from βAOB isolated only from sand, soil, and freshwater environments. Sequences in clone libraries of the amoA gene from the surface and upper oxycline could be grouped in a marine subcluster, also containing no cultured representatives. In contrast, all 74 amoA sequences originating from the OMZ were either closely affiliated with cultured Nitrosospira spp. from clusters 0 and 2 or with other yet-uncultured βAOB from soil and an aerated-anoxic Orbal process waste treatment plant. Our results reveal the presence of Nitrosospira-like βAOB in both oxic and suboxic waters associated with the OMZ but with a clear community shift at the functional level (amoA) along the strong oxygen gradient.

scholarly journals Short-term fate of phytodetritus in sediments across the Arabian Sea Oxygen Minimum Zone

2008 ◽  
Vol 5 (1) ◽  
pp. 43-53 ◽  
Author(s):  
J. H. Andersson ◽  
C. Woulds ◽  
M. Schwartz ◽  
G. L. Cowie ◽  
L. A. Levin ◽  
...  
Keyword(s):  
Arabian Sea ◽  
Inorganic Carbon ◽  
Surface Sediments ◽  
Dissolved Inorganic Carbon ◽  
Oxygen Minimum Zone ◽  
Short Term ◽  
Minimum Zone ◽  
Algal Material ◽  
Oxygen Minimum

Abstract. The short-term fate of phytodetritus was investigated across the Pakistan margin of the Arabian Sea at water depths ranging from 140 to 1850 m, encompassing the oxygen minimum zone (~100–1100 m). Phytodetritus sedimentation events were simulated by adding ~44 mmol 13C-labelled algal material per m2 to surface sediments in retrieved cores. Cores were incubated in the dark, at in situ temperature and oxygen concentrations. Overlying waters were sampled periodically, and cores were recovered and sampled (for organisms and sediments) after durations of two and five days. The labelled carbon was subsequently traced into bacterial lipids, foraminiferan and macrofaunal biomass, and dissolved organic and inorganic pools. The majority of the label (20 to 100%) was in most cases left unprocessed in the sediment at the surface. The largest pool of processed carbon was found to be respiration (0 to 25% of added carbon), recovered as dissolved inorganic carbon. Both temperature and oxygen were found to influence the rate of respiration. Macrofaunal influence was most pronounced at the lower part of the oxygen minimum zone where it contributed 11% to the processing of phytodetritus.

scholarly journals Sedimentary phosphorus and iron cycling in and below the oxygen minimum zone of the northern Arabian Sea

2012 ◽  
Vol 9 (7) ◽  
pp. 2603-2624 ◽  
Author(s):  
P. Kraal ◽  
C. P. Slomp ◽  
D. C. Reed ◽  
G.-J. Reichart ◽  
S. W. Poulton
Keyword(s):  
Arabian Sea ◽  
Bottom Water ◽  
Surface Sediments ◽  
Lower Boundary ◽  
Oxygen Minimum Zone ◽  
Apatite Formation ◽  
Northern Arabian Sea ◽  
Minimum Zone ◽  
Oxygen Minimum ◽  
Burial Efficiency

Abstract. In this study, we investigate phosphorus (P) and iron (Fe) cycling in sediments along a depth transect from within to well below the oxygen minimum zone (OMZ) in the northern Arabian Sea (Murray Ridge). Pore-water and solid-phase analyses show that authigenic formation of calcium phosphate minerals (Ca-P) is largely restricted to where the OMZ intersects the seafloor topography, likely due to higher depositional fluxes of reactive P. Nonetheless, increased ratios of organic carbon to organic P (Corg/Porg) and to total reactive P (Corg/Preactive) in surface sediments indicate that the overall burial efficiency of P relative to Corg decreases under the low bottom water oxygen concentrations (BWO) in the OMZ. The relatively constant Fe/Al ratio in surface sediments along the depth transect suggest that corresponding changes in Fe burial are limited. Sedimentary pyrite contents are low throughout the ~25 cm sediment cores at most stations, as commonly observed in the Arabian Sea OMZ. However, pyrite is an important sink for reactive Fe at one station in the OMZ. A reactive transport model (RTM) was applied to quantitatively investigate P and Fe diagenesis at an intermediate station at the lower boundary of the OMZ (bottom water O2: ~14 μmol L−1). The RTM results contrast with earlier findings in showing that Fe redox cycling can control authigenic apatite formation and P burial in Arabian Sea sediment. In addition, results suggest that a large fraction of the sedimentary Ca-P is not authigenic, but is instead deposited from the water column and buried. Dust is likely a major source of this Ca-P. Inclusion of the unreactive Ca-P pool in the Corg/P ratio leads to an overestimation of the burial efficiency of reactive P relative to Corg along the depth transect. Moreover, the unreactive Ca-P accounts for ~85% of total Ca-P burial. In general, our results reveal large differences in P and Fe chemistry between stations in the OMZ, indicating dynamic sedimentary conditions under these oxygen-depleted waters.

scholarly journals Distribution of Membrane Lipids of Planktonic Crenarchaeota in the Arabian Sea

2002 ◽  
Vol 68 (6) ◽  
pp. 2997-3002 ◽  
Author(s):  
Jaap S. Sinninghe Damsté ◽  
W. Irene C. Rijpstra ◽  
Ellen C. Hopmans ◽  
Fredrick G. Prahl ◽  
Stuart G. Wakeham ◽  
...  
Keyword(s):  
Surface Waters ◽  
Arabian Sea ◽  
Membrane Lipids ◽  
Oxygen Minimum Zone ◽  
Central Pacific ◽  
Central Pacific Ocean ◽  
Biological Studies ◽  
Intact Core ◽  
Minimum Zone ◽  
Oxygen Minimum

ABSTRACT Intact core tetraether membrane lipids of marine planktonic Crenarchaeota were quantified in water column-suspended particulate matter obtained from four depth intervals (∼70, 500, 1,000 and 1,500 m) at seven stations in the northwestern Arabian Sea to investigate the distribution of the organisms at various depths. Maximum concentrations generally occurred at 500 m, near the top of the oxygen minimum zone, and the concentrations at this depth were, in most cases, slightly higher than those in surface waters. In contrast, lipids derived from eukaryotes (cholesterol) and from eukaryotes and bacteria (fatty acids) were at their highest concentrations in surface waters. This indicates that these crenarchaeotes are not restricted to the photic zone of the ocean, which is consistent with the results of recent molecular biological studies. Since the Arabian Sea has a strong oxygen minimum zone between 100 and 1,000 m, with minimum oxygen levels of <1 μM, the abundance of crenarchaeotal membrane lipids at 500 m suggests that planktonic Crenarchaeota are probably facultative anaerobes. The cell numbers we calculated from the concentrations of membrane lipids are similar to those reported for the Central Pacific Ocean, supporting the recent estimation of M. B. Karner, E. F. DeLong, and D. M. Karl ( Nature 409 : 507-510, 2001 ) that the world's oceans contain ca. 1028 cells of planktonic Crenarchaeota.

scholarly journals Protist communities in a marine oxygen minimum zone off Costa Rica by 454 pyrosequencing

2015 ◽  
Vol 12 (16) ◽  
pp. 13483-13509 ◽  
Author(s):  
H. Jing ◽  
E. Rocke ◽  
L. Kong ◽  
X. Xia ◽  
H. Liu ◽  
...  
Keyword(s):  
Costa Rica ◽  
Water Column ◽  
454 Pyrosequencing ◽  
18S Rrna Gene ◽  
Oxygen Minimum Zone ◽  
Community Diversity ◽  
Rrna Gene ◽  
Minimum Zone ◽  
Clear Shift ◽  
Oxygen Minimum

Abstract. Marine planktonic protists, including microalgae and protistan grazers, are an important contributor to global primary production and carbon and mineral cycles, however, little is known about their population shifts along the oxic-anoxic gradient in the water column. We used 454 pyrosequencing of the 18S rRNA gene and gene transcripts to study the community composition of whole and active protists throughout a water column in the Costa Rica Dome, where a stable oxygen minimum zone (OMZ) exists at a depth of 400~700 m. A clear shift of protist composition from photosynthetic Dinoflagellates in the surface to potential parasitic Dinoflagellates and Ciliates in the deeper water was revealed along the vertical profile at both rRNA and rDNA levels. Those protist groups recovered only at the rDNA level represent either lysed aggregates sinking from the upper waters or potential hosts for parasitic groups. UPGMA clustering demonstrated that total and active protists in the anoxic core of OMZ (550 m) were distinct from those in other water depths. The reduced community diversity and presence of a parasitic/symbiotic trophic lifestyle in the OMZ, especially the anoxic core, suggests that OMZs can exert a selective pressure on protist communities. Such changes in community structure and a shift in trophic lifestyle could result in a modulation of the microbial loop and associated biogeochemical cycling.

scholarly journals Sedimentary phosphorus and iron cycling in and below the oxygen minimum zone of the northern Arabian Sea

2012 ◽  
Vol 9 (3) ◽  
pp. 3829-3880 ◽  
Author(s):  
P. Kraal ◽  
C. P. Slomp ◽  
D. C. Reed ◽  
G.-J. Reichart ◽  
S. W. Poulton
Keyword(s):  
Arabian Sea ◽  
Bottom Water ◽  
Surface Sediments ◽  
Lower Boundary ◽  
Oxygen Minimum Zone ◽  
Apatite Formation ◽  
Northern Arabian Sea ◽  
Minimum Zone ◽  
Oxygen Minimum ◽  
Burial Efficiency

Abstract. In this study, we investigate phosphorus (P) and iron (Fe) cycling in sediments along a depth transect from within to well below the oxygen minimum zone (OMZ) in the northern Arabian Sea (Murray Ridge). Pore-water and solid-phase analyses show that authigenic formation of calcium phosphate minerals (Ca-P) is largely restricted to where the OMZ intersects the seafloor topography, likely due to higher depositional fluxes of reactive P. Nonetheless, increased ratios of organic carbon to organic P (Corg/Porg) and to total reactive P (Corg/Preactive) in surface sediments indicate that the overall burial efficiency of P relative to Corg decreases under the low bottom water oxygen concentrations (BWO) in the OMZ. The relatively constant Fe/Al ratio in surface sediments along the depth transect suggest that corresponding changes in Fe burial are limited. Sedimentary pyrite contents are low throughout the ~25-cm sediment cores at most stations, as commonly observed in the Arabian Sea OMZ. However, pyrite is an important sink for reactive Fe at one station in the OMZ. A reactive transport model (RTM) was applied to quantitatively investigate P and Fe diagenesis at an intermediate station at the lower boundary of the OMZ (bottom water O2: ~14 μ mol l−1). The RTM results contrast with earlier findings in showing that Fe redox cycling can control authigenic apatite formation and P burial in Arabian Sea sediment. In addition, results suggest that a large fraction of the sedimentary Ca-P is not authigenic, but is instead deposited from the water column and buried. Dust is likely a major source of this Ca-P. Inclusion of the unreactive Ca-P pool in the Corg/P ratio leads to an overestimation of the burial efficiency of reactive P relative to Corg along the depth transect. Moreover, the unreactive Ca-P accounts for ~85% of total Ca-P burial. In general, our results reveal large differences in P and Fe chemistry between stations in the OMZ, indicating dynamic sedimentary conditions under these oxygen-depleted waters.

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