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Archaea are ubiquitous in the modern ocean where they are involved in the carbon and nitrogen biogeochemical cycles. However, the majority of Archaea remain uncultured. Archaeal specific membrane intact polar lipids (IPLs) are biomarkers of the presence and abundance of living cells. They comprise archaeol and glycerol dibiphytanyl glycerol tetraethers (GDGTs) attached to various polar headgroups. However, little is known of the IPLs of uncultured marine Archaea, complicating their use as biomarkers. Here, we analyzed suspended particulate matter (SPM) obtained in high depth resolution from a coastal and open ocean site in the eastern tropical South Pacific (ETSP) oxygen deficient zone (ODZ) with the aim of determining possible biological sources of archaeal IPL by comparing their composition by Ultra High Pressure Liquid Chromatography coupled to high resolution mass spectrometry with the archaeal diversity by 16S rRNA gene amplicon sequencing and their abundance by quantitative PCR. Thaumarchaeotal Marine Group I (MGI) closely related to Ca. Nitrosopelagicus and Nitrosopumilus dominated the oxic surface and upper ODZ water together with Marine Euryarchaeota Group II (MGII). High relative abundance of hexose phosphohexose- (HPH) crenarchaeol, the specific biomarker for living Thaumarchaeota, and HPH-GDGT-0, dihexose- (DH) GDGT-3 and -4 were detected in these water masses. Within the ODZ, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaea) of the Woesearchaeota DHVE-6 group and Marine Euryarchaeota Group III (MGIII) were present together with a higher proportion of archaeol-based IPLs, which were likely made by MGIII, since DPANN archaea are supposedly unable to synthesize their own IPLs and possibly have a symbiotic or parasitic partnership with MGIII. Finally, in deep suboxic/oxic waters a different MGI population occurred with HPH-GDGT-1, -2 and DH-GDGT-0 and -crenarchaeol, indicating that here MGI synthesize membrane

Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra‐high‐pressure liquid chromatography coupled to high‐resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80–110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy‐GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME‐1b clades dominated. Correlation analyses suggest that the IPLs GDGT‐0, GDGT‐1, and GDGT‐2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME‐1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho‐dihexose and hexose‐glucuronic acid head groups.

Archaea are ubiquitous in the modern ocean where they are involved in the carbon and nitrogen biogeochemical cycles. However, the majority of Archaea remain uncultured. Archaeal specific membrane intact polar lipids (IPLs) are biomarkers of the presence and abundance of living cells. They comprise archaeol and glycerol dibiphytanyl glycerol tetraethers (GDGTs) attached to various polar headgroups. However, little is known of the IPLs of uncultured marine Archaea, complicating their use as biomarkers. Here, we analyzed suspended particulate matter (SPM) obtained in high depth resolution from a coastal and open ocean site in the eastern tropical South Pacific (ETSP) oxygen deficient zone (ODZ) with the aim of determining possible biological sources of archaeal IPL by comparing their composition by Ultra High Pressure Liquid Chromatography coupled to high resolution mass spectrometry with the archaeal diversity by 16S rRNA gene amplicon sequencing and their abundance by quantitative PCR. Thaumarchaeotal Marine Group I (MGI) closely related to Ca. Nitrosopelagicus and Nitrosopumilus dominated the oxic surface and upper ODZ water together with Marine Euryarchaeota Group II (MGII). High relative abundance of hexose phosphohexose- (HPH) crenarchaeol, the specific biomarker for living Thaumarchaeota, and HPH-GDGT-0, dihexose- (DH) GDGT-3 and -4 were detected in these water masses. Within the ODZ, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaea) of the Woesearchaeota DHVE-6 group and Marine Euryarchaeota Group III (MGIII) were present together with a higher proportion of archaeol-based IPLs, which were likely made by MGIII, since DPANN archaea are supposedly unable to synthesize their own IPLs and possibly have a symbiotic or parasitic partnership with MGIII. Finally, in deep suboxic/oxic waters a different MGI population occurred with HPH-GDGT-1, -2 and DH-GDGT-0 and -crenarchaeol, indicating that here MGI synthesize membrane

Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra‐high‐pressure liquid chromatography coupled to high‐resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80–110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy‐GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME‐1b clades dominated. Correlation analyses suggest that the IPLs GDGT‐0, GDGT‐1, and GDGT‐2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME‐1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho‐dihexose and hexose‐glucuronic acid head groups.

Nitrogen (N) cycling influences primary production in the ocean and, hence, the global climate. It is performed by a variety of microorganisms, including eukaryotes, bacteria and archaea in oxic, suboxic, and anoxic waters. Our knowledge of the reactions involved in marine N cycling and its associated microorganisms has greatly increased in the last decade due to the development of multiple culture-independent methods. Among them are gene and lipid biomarkers, which hold taxonomic potential and can be successfully applied in modern day and paleoenvironmental studies. However, many aspects of N cycling and their long-term implications for the marine environment and the global climate still require more study, especially in suboxic and anoxic waters, including the oxygen-deficient zones (ODZs), which are expanding in the modern oceans. Oxygen-depleted waters are not an exclu-sive feature of the modern ocean as oceanic anoxic events (OAE) have been occurring in the geological past and severely affected N cycling. This thesis investigates aspects of the marine N cycle in the modern ocean by applying molecular biomarkers. Particular focus was put on the modern oxygen-de-pleted water systems and on how these systems can be helpful to understand the past OAEs and how in turn past anoxic events can be predictive of the future of the ocean. The work described in this thesis provides new insights into N cycling in oxygen-depleted basins and ODZs. Additionally, it expands the current knowledge on the archaeal diversity in such settings. Finally, it has improved the understanding of past variations in N2 fixation. Future investigations using biomarkers may help to further increase our understanding of present and past N cycling in the ocean.

Nitrogen (N) cycling influences primary production in the ocean and, hence, the global climate. It is performed by a variety of microorganisms, including eukaryotes, bacteria and archaea in oxic, suboxic, and anoxic waters. Our knowledge of the reactions involved in marine N cycling and its associated microorganisms has greatly increased in the last decade due to the development of multiple culture-independent methods. Among them are gene and lipid biomarkers, which hold taxonomic potential and can be successfully applied in modern day and paleoenvironmental studies. However, many aspects of N cycling and their long-term implications for the marine environment and the global climate still require more study, especially in suboxic and anoxic waters, including the oxygen-deficient zones (ODZs), which are expanding in the modern oceans. Oxygen-depleted waters are not an exclu-sive feature of the modern ocean as oceanic anoxic events (OAE) have been occurring in the geological past and severely affected N cycling. This thesis investigates aspects of the marine N cycle in the modern ocean by applying molecular biomarkers. Particular focus was put on the modern oxygen-de-pleted water systems and on how these systems can be helpful to understand the past OAEs and how in turn past anoxic events can be predictive of the future of the ocean. The work described in this thesis provides new insights into N cycling in oxygen-depleted basins and ODZs. Additionally, it expands the current knowledge on the archaeal diversity in such settings. Finally, it has improved the understanding of past variations in N2 fixation. Future investigations using biomarkers may help to further increase our understanding of present and past N cycling in the ocean.

Nitrogen (N) cycling influences primary production in the ocean and, hence, the global climate. It is performed by a variety of microorganisms, including eukaryotes, bacteria and archaea in oxic, suboxic, and anoxic waters. Our knowledge of the reactions involved in marine N cycling and its associated microorganisms has greatly increased in the last decade due to the development of multiple culture-independent methods. Among them are gene and lipid biomarkers, which hold taxonomic potential and can be successfully applied in modern day and paleoenvironmental studies. However, many aspects of N cycling and their long-term implications for the marine environment and the global climate still require more study, especially in suboxic and anoxic waters, including the oxygen-deficient zones (ODZs), which are expanding in the modern oceans. Oxygen-depleted waters are not an exclu-sive feature of the modern ocean as oceanic anoxic events (OAE) have been occurring in the geological past and severely affected N cycling. This thesis investigates aspects of the marine N cycle in the modern ocean by applying molecular biomarkers. Particular focus was put on the modern oxygen-de-pleted water systems and on how these systems can be helpful to understand the past OAEs and how in turn past anoxic events can be predictive of the future of the ocean. The work described in this thesis provides new insights into N cycling in oxygen-depleted basins and ODZs. Additionally, it expands the current knowledge on the archaeal diversity in such settings. Finally, it has improved the understanding of past variations in N2 fixation. Future investigations using biomarkers may help to further increase our understanding of present and past N cycling in the ocean.

The transition from hunter-gatherer-fisher groups to agrarian societies is arguably the most significant change in human prehistory. In the European plain there is evidence for fully developed agrarian societies by 7,500 cal. yr BP, yet a well-established agrarian society does not appear in the north until 6,000 cal. yr BP for unknown reasons. Here we show a sudden increase in summer temperature at 6,000 cal. yr BP in northern Europe using a well-dated, high resolution record of sea surface temperature (SST) from the Baltic Sea. This temperature rise resulted in hypoxic conditions across the entire Baltic sea as revealed by multiple sedimentary records and supported by marine ecosystem modeling. Comparison with summed probability distributions of radiocarbon dates from archaeological sites indicate that this temperature rise coincided with both the introduction of farming, and a dramatic population increase. The evidence supports the hypothesis that the boundary of farming rapidly extended north at 6,000 cal. yr BP because terrestrial conditions in a previously marginal region improved.

Heterocyst glycolipids (HGs) are lipids exclusivelyproduced by heterocystous dinitrogen-fixingcyanobacteria. The Baltic Sea is an ideal environment tostudy the distribution of HGs and test their potential asbiomarkers because of its recurring summer phytoplanktonblooms, dominated by a few heterocystous cyanobacterialspecies of the genera Nodularia and Aphanizomenon.A multi-core and a gravity core from the Gotland Basinwere analyzed to determine the abundance and distributionof a suite of selected HGs at a high resolution to investigatethe changes in past cyanobacterial communities during theHolocene. The HG distribution of the sediments depositedduring the Modern Warm Period (MoWP) was comparedwith those of cultivated heterocystous cyanobacteria, includingthose isolated from Baltic Sea waters, revealinghigh similarity. However, the abundance of HGs droppedsubstantially with depth, and this may be caused by eithera decrease in the occurrence of the cyanobacterial bloomsor diagenesis, resulting in partial destruction of the HGs.The record also shows that the HG distribution has remainedstable since the Baltic turned into a brackish semi-enclosedbasin ?7200 cal. yr BP. This suggests that the heterocystouscyanobacterial species composition remained relativelystable as well. During the earlier freshwater phase of theBaltic (i.e., the Ancylus Lake and Yoldia Sea phases),the distribution of the HGs varied much more than in thesubsequent brackish phase, and the absolute abundance ofHGs was much lower than during the brackish phase. Thissuggests that the cyanobacterial community adjusted to thedifferent environmental conditions in the basin. Our resultsconfirm the potential of HGs as a specific biomarker ofheterocystous cyanobacteria in paleo-environmental studies.

The transition from hunter-gatherer-fisher groups to agrarian societies is arguably the most significantchange in human prehistory. In the European plain there is evidence for fully developed agrariansocieties by 7,500 cal. yr BP, yet a well-established agrarian society does not appear in the north until6,000 cal. yr BP for unknown reasons. Here we show a sudden increase in summer temperature at6,000 cal. yr BP in northern Europe using a well-dated, high resolution record of sea surface temperature(SST) from the Baltic Sea. This temperature rise resulted in hypoxic conditions across the entire Balticsea as revealed by multiple sedimentary records and supported by marine ecosystem modeling.Comparison with summed probability distributions of radiocarbon dates from archaeological sitesindicate that this temperature rise coincided with both the introduction of farming, and a dramaticpopulation increase. The evidence supports the hypothesis that the boundary of farming rapidlyextended north at 6,000 cal. yr BP because terrestrial conditions in a previously marginal regionimproved.

Heterocyst glycolipids (HGs) are lipids exclusivelyproduced by heterocystous dinitrogen-fixingcyanobacteria. The Baltic Sea is an ideal environment tostudy the distribution of HGs and test their potential asbiomarkers because of its recurring summer phytoplanktonblooms, dominated by a few heterocystous cyanobacterialspecies of the genera Nodularia and Aphanizomenon.A multi-core and a gravity core from the Gotland Basinwere analyzed to determine the abundance and distributionof a suite of selected HGs at a high resolution to investigatethe changes in past cyanobacterial communities during theHolocene. The HG distribution of the sediments depositedduring the Modern Warm Period (MoWP) was comparedwith those of cultivated heterocystous cyanobacteria, includingthose isolated from Baltic Sea waters, revealinghigh similarity. However, the abundance of HGs droppedsubstantially with depth, and this may be caused by eithera decrease in the occurrence of the cyanobacterial bloomsor diagenesis, resulting in partial destruction of the HGs.The record also shows that the HG distribution has remainedstable since the Baltic turned into a brackish semi-enclosedbasin ?7200 cal. yr BP. This suggests that the heterocystouscyanobacterial species composition remained relativelystable as well. During the earlier freshwater phase of theBaltic (i.e., the Ancylus Lake and Yoldia Sea phases),the distribution of the HGs varied much more than in thesubsequent brackish phase, and the absolute abundance ofHGs was much lower than during the brackish phase. Thissuggests that the cyanobacterial community adjusted to thedifferent environmental conditions in the basin. Our resultsconfirm the potential of HGs as a specific biomarker ofheterocystous cyanobacteria in paleo-environmental studies.

The transition from hunter-gatherer-fisher groups to agrarian societies is arguably the most significantchange in human prehistory. In the European plain there is evidence for fully developed agrariansocieties by 7,500 cal. yr BP, yet a well-established agrarian society does not appear in the north until6,000 cal. yr BP for unknown reasons. Here we show a sudden increase in summer temperature at6,000 cal. yr BP in northern Europe using a well-dated, high resolution record of sea surface temperature(SST) from the Baltic Sea. This temperature rise resulted in hypoxic conditions across the entire Balticsea as revealed by multiple sedimentary records and supported by marine ecosystem modeling.Comparison with summed probability distributions of radiocarbon dates from archaeological sitesindicate that this temperature rise coincided with both the introduction of farming, and a dramaticpopulation increase. The evidence supports the hypothesis that the boundary of farming rapidlyextended north at 6,000 cal. yr BP because terrestrial conditions in a previously marginal regionimproved.

In the last decade our understanding of the marine nitrogen cycle has improved considerably thanks to the discovery of two novel groups of microorganisms: ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria. Both groups are important in oxygen-deficient zones (ODZs), where they substantially affect the marine N budget. These two groups of microbes are also well known for producing specific membrane lipids, which can be used as biomarkers to trace their presence in the environment. We investigated the occurrence and distribution of AOA and anammox bacteria in the water column of the eastern tropical North Pacific (ETNP) ODZ, one of the most prominent ODZs worldwide. Suspended particulate matter (SPM) was collected at different depths of the water column in high resolution, at both a coastal and an open-ocean setting. The SPM was analyzed for AOA- and anammox bacteria-specific intact polar lipids (IPLs), i.e., hexose-phosphohexose (HPH)-crenarchaeol and phosphatidylcholine (PC)-monoether ladderane. Comparison with oxygen profiles reveals that both the microbial groups are able to thrive at low (< 1 µM) concentrations of oxygen. Our results indicate a clear niche segregation of AOA and anammox bacteria in the coastal waters of the ETNP but a partial overlap of the two niches of these microbial species in the open-water setting. The latter distribution suggests the potential for an interaction between the two microbial groups at the open-ocean site, although the nature of this hypothetical interaction (i.e., either competition or cooperation) remains unclear.

In the last decade our understanding of the marine nitrogen cycle has improved considerably thanks to the discovery of two novel groups of microorganisms: ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria. Both groups are important in oxygen-deficient zones (ODZs), where they substantially affect the marine N budget. These two groups of microbes are also well known for producing specific membrane lipids, which can be used as biomarkers to trace their presence in the environment. We investigated the occurrence and distribution of AOA and anammox bacteria in the water column of the eastern tropical North Pacific (ETNP) ODZ, one of the most prominent ODZs worldwide. Suspended particulate matter (SPM) was collected at different depths of the water column in high resolution, at both a coastal and an open-ocean setting. The SPM was analyzed for AOA- and anammox bacteria-specific intact polar lipids (IPLs), i.e., hexose-phosphohexose (HPH)-crenarchaeol and phosphatidylcholine (PC)-monoether ladderane. Comparison with oxygen profiles reveals that both the microbial groups are able to thrive at low (< 1 µM) concentrations of oxygen. Our results indicate a clear niche segregation of AOA and anammox bacteria in the coastal waters of the ETNP but a partial overlap of the two niches of these microbial species in the open-water setting. The latter distribution suggests the potential for an interaction between the two microbial groups at the open-ocean site, although the nature of this hypothetical interaction (i.e., either competition or cooperation) remains unclear.

Contains fulltext : 117171.pdf (publisher's version ) (Open Access)

Hydrothermally active sediments are highly productive, chemosynthetic areas which are characterized by the rapid turnover of particulate organic matter under extreme conditions in which ammonia is liberated. These systems might be suitable habitats for anaerobic ammonium oxidizing (anammox) bacteria but this has not been investigated in detail. Here we report the diversity and abundance of anammox bacteria in sediments that seep cold hydrocarbon-rich fluids and hydrothermal vent areas of the Guaymas Basin in the Cortés Sea using the unique functional anammox marker gene, hydrazine synthase (hzsA). All clones retrieved were closely associated to the “Candidatus Scalindua” genus. Phylogenetic analysis revealed two distinct clusters of hzsA sequences (Ca. Scalindua hzsA cluster I and II). Comparison of individual sequences from both clusters showed that several of these sequences had a similarity as low as 76% on nucleotide level. Based on the analysis of this phylomarker, a very high interspecies diversity within the marine anammox group is apparent. Absolute numbers of anammox bacteria in the sediments samples were determined by amplification of a 257 bp fragment of the hszA gene in a qPCR assay. The results indicate that numbers of anammox bacteria are generally higher in cold hydrocarbon-rich sediments compared to the vent areas and the reference zone. Ladderanes, lipids unique to anammox bacteria were also detected in several of the sediment samples corroborating the hzsA analysis. Due to the high concentrations of reduced sulfur compounds and its potential impact on the cycling of nitrogen we aimed to get an indication about the key players in the oxidation of sulfide in the Guaymas Basin sediments using the alpha subunit of the adenosine-5'-phosphosulfate (APS) reductase (aprA). Amplification of the aprA gene revealed a high number of gammaproteobacterial aprA genes covering the two sulfur-oxidizing bacteria aprA lineages as well as sulfate-reducers

Contains fulltext : 117171.pdf (publisher's version ) (Open Access)

Contains fulltext : 117171.pdf (Publisher’s version ) (Open Access)

Hydrothermally active sediments are highly productive, chemosynthetic areas which are characterized by the rapid turnover of particulate organic matter under extreme conditions in which ammonia is liberated. These systems might be suitable habitats for anaerobic ammonium oxidizing (anammox) bacteria but this has not been investigated in detail. Here we report the diversity and abundance of anammox bacteria in sediments that seep cold hydrocarbon-rich fluids and hydrothermal vent areas of the Guaymas Basin in the Cortés Sea using the unique functional anammox marker gene, hydrazine synthase (hzsA). All clones retrieved were closely associated to the “Candidatus Scalindua” genus. Phylogenetic analysis revealed two distinct clusters of hzsA sequences (Ca. Scalindua hzsA cluster I and II). Comparison of individual sequences from both clusters showed that several of these sequences had a similarity as low as 76% on nucleotide level. Based on the analysis of this phylomarker, a very high interspecies diversity within the marine anammox group is apparent. Absolute numbers of anammox bacteria in the sediments samples were determined by amplification of a 257 bp fragment of the hszA gene in a qPCR assay. The results indicate that numbers of anammox bacteria are generally higher in cold hydrocarbon-rich sediments compared to the vent areas and the reference zone. Ladderanes, lipids unique to anammox bacteria were also detected in several of the sediment samples corroborating the hzsA analysis. Due to the high concentrations of reduced sulfur compounds and its potential impact on the cycling of nitrogen we aimed to get an indication about the key players in the oxidation of sulfide in the Guaymas Basin sediments using the alpha subunit of the adenosine-5'-phosphosulfate (APS) reductase (aprA). Amplification of the aprA gene revealed a high number of gammaproteobacterial aprA genes covering the two sulfur-oxidizing bacteria aprA lineages as well as sulfate-reducers