J. S. Sinninghe-Damste

NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University · Department of Marine Microbiology and Biogeochemistry

The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome...

The California Current system (CCS) hosts one of the largest oxygen minimum zones (OMZs) in the world: the eastern North Pacific (ENP) OMZ, which is dissociated into subtropical and tropical regions (i.e. the ESTNP and ETNP). In the modern ENP OMZ, bioavailable nitrogen (N) is lost via denitrification and anaerobic ammonium oxidation (anammox). Eve...

The composition of membrane lipids varies in a number of ways as adjustment to growth conditions. Variations in head group composition and carbon skeleton and degree of unsaturation of glycerol-bound acyl or alkyl groups results in a high structural complexity of the lipidome of bacterial cells. We studied the lipidome of the mesophilic, sulfate-re...

Beta-mannans are insoluble plant polysaccharides with beta-1,4-linked mannose as the backbone. We used three forms of this polysaccharide, namely, pure mannan, glucomannan, and galactomannan, to enrich haloarchaea, which have the ability to utilize mannans for growth. Four mannan-utilizing strains obtained in pure cultures were closely related to e...

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmenta...

Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply for the f...

A marked sedimentological change in subsurface sediments from the entire Baltic Proper, the Baltic Sea, has been previously noted. Our detailed work on a variety of multi-cores from basin-wide transects indicates that this sedimentological change was caused by a large shift in environmental conditions during the 1950s. Until the 1950s, the water co...

Recently developed temperature proxies based on hydroxylated isoprenoid Glycerol Dialkyl Glycerol Tetraethers (OH-isoGDGTs), such as %OH, RI − OH, RI − OH′ and OH C , have shown potential for reconstructing past temperature changes. However, progress has been limited by the lack of a global core-top calibration with ample geographical coverage. Her...

The California current system (CCS) hosts one of the largest oxygen minimum zones (OMZs) in the world: the Eastern North Pacific (ENP) OMZ, which is dissociated into a subtropical and tropical region (i.e., the ESTNP and ETNP). In the modern ENP OMZ, bioavailable nitrogen (N) is lost via denitrification and anaerobic ammonium oxidation (anammox). E...

The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome...

The authors regret that there is a mistake in the strain collection number: instead of UQ 51487 it should be UQM 51487 in the protologue Table 3 of their paper.

High-resolution paleoclimate records from tropical continental settings are greatly needed to advance understanding of global climate dynamics. The International Continental Scientific Drilling Program (ICDP) project DeepCHALLA recovered a 214.8-meter long sediment sequence from Lake Chala, a deep and permanently stratified (meromictic) crater lake...

Background: Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (>1,000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophys...

Heterocytous cyanobacteria are important players in the carbon and nitrogen cycle. They can fix dinitrogen by using heterocytes, specialized cells containing the oxygen-sensitive nitrogenase enzyme surrounded by a thick polysaccharide and glycolipid layer which prevents oxygen diffusion and nitrogenase inactivation. Heterocyte glycolipids can be us...

Two strains of neutrophilic haloaloarchaea were selectively enriched from hypersaline lakes in southwestern Siberia using β-1,3-glucans as a substrate. The strains were nearly identical in their phenotypes and according to phylogenomic analysis, represent a distant novel species group in the genus Halapricum of the family Haloarculaceae. The main p...

Our knowledge about the physiology of deep sea (>1,000 m) microorganisms involved in organic matter (OM) degradation is still scare due to the lack of available isolates, especially from sulfidic environments. In this study, we successfully cultivated and characterized the physiology of a wide range of novel piezotolerant anaerobic bacteria affilia...

Marine Isotope Stage (MIS) 4 (ca. 71–57 ka; within the Middle Weichselian Substage) is considered a significant Pleistocene glaciation, but it remains poorly constrained in comparison to that of the Late Weichselian Last Glacial Maximum (LGM; ca. 29–19 ka, during MIS 2), or even the Late Saalian MIS 6 (ca. 190–130 ka). Most MIS 4 glacial landforms...

Anthropogenic climate change is predicted to severely impact the global hydrological cycle¹, particularly in tropical regions where agriculture-based economies depend on monsoon rainfall². In the Horn of Africa, more frequent drought conditions in recent decades3,4 contrast with climate models projecting precipitation to increase with rising temper...

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmenta...

The eastern Mediterranean Sea (EMS) sedimentary record is periodically interspersed with organic-rich ‘sapropel’ layers. Sapropels are characteristic of basin-wide anoxic events, triggered by precession-forced insolation maxima. Relatively subdued insolation maxima, however, are not always expressed as distinct sapropel events. The EMS sedimentary...

Rivers play a key role in the global carbon cycle by transporting terrestrial organic matter (TerrOM) from land to the ocean. Upon burial in marine sediments, this TerrOM may be a significant long-term carbon sink, depending on its composition and properties. However, much remains unknown about the dispersal of different types of TerrOM in the mari...

The composition of the core lipids and intact polar lipids (IPLs) of five Rubrobacter species was examined. Methylated (ω-4) fatty acids (FAs) characterized the core lipids of Rubrobacter radiotolerans, R. xylanophilus and R. bracarensis. In contrast, R. calidifluminis and R. naiadicus lacked ω-4 methyl FAs but instead contained abundant (i.e., 34-...

The deep-sea is characterized by extreme conditions, such as high hydrostatic pressure (HHP) and near-freezing temperature. Piezophiles, microorganisms adapted to high pressure, have developed key strategies to maintain the integrity of their lipid membrane at these conditions. The abundance of specific membrane lipids, such as those containing uns...

Bacterial membranes are composed of fatty acids (FAs) ester-linked to glycerol-3-phosphate, while archaea have membranes made of isoprenoid chains ether-linked to glycerol-1-phosphate. Many archaeal species organize their membrane as a monolayer of membrane-spanning lipids (MSLs). Exceptions to this “lipid divide” are the production by some bacteri...

Sulfurimonas species are among the most abundant sulfur-oxidizing bacteria in the marine environment. They are capable of using different electron acceptors, this metabolic flexibility is favorable for their niche adaptation in redoxclines. When oxygen is depleted, most Sulfurimonas spp. (e.g., Sulfurimonas gotlandica) use nitrate (NO3−) as an elec...

Hydroxylated glycerol dibiphytanyl glycerol tetraethers (OH-GDGTs) produced by both marine and freshwater thaumarchaea are increasingly used for the reconstruction of past sea surface temperature (SST). They occur throughout the modern Baltic Sea, but it is unknown if OH-GDGTs can be used for assessing past SST in this area, where salinity has chan...

Rivers play a key role in the global carbon cycle by transporting terrestrial organic matter (TerrOM) from land to the ocean. Upon burial in marine sediments, this TerrOM may be a significant long-term carbon sink, depending on its composition and properties. However, much remains unknown about the dispersal of different types of TerrOM in the mari...

Planctomycetes of the family Pirellulaceae are commonly addressed as budding aquatic bacteria with a complex lifestyle. Although this family is well represented by cultured and taxonomically characterized isolates, nearly all of them were obtained from brackish or marine habitats. The examples of described freshwater Pirellulaceae planctomycetes ar...

A pure culture of alkaliphilic haloarchaeon strain AArc-ST capable of anaerobic growth by carbohydrate-dependent sulfur respiration was obtained from hypersaline lakes in southwestern Siberia. According to phylogenetic analysis, AArc-ST formed a new genus level branch most related to the genus Natronoarchaeum in the order Halobacteriales. The strai...

Several pure cultures of alkaliphilic haloaloarchaea were enriched and isolated from hypersaline soda lakes in southwestern Siberia using amylopectin and fructans as substrates. Phylogenomic analysis placed the isolates into two distinct groups within the class Halobacteria. Four isolates forming group 1 were closely related to a recently described...

Bacterial membranes are composed of fatty acids ester-linked to glycerol-3-phosphate, while archaea possess membranes made of isoprenoid chains ether-linked to glycerol-1-phosphate. Many archaeal species organize their membrane as a monolayer of membrane-spanning lipids (MSLs). Exceptions to this ‘lipid divide’ are the production by some bacterial...

Hydroxylated glycerol dibiphytanyl glycerol tetraethers (OH-GDGTs) produced by both marine and freshwater thaumarchaea are increasingly used for the reconstruction of past sea surface temperature (SST). They occur throughout the modern Baltic Sea, but it is unknown if their OH-GDGTs can be used for assessing past SST in this area, where salinity ha...

In acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acid...

In the Miocene, a large wetland system extended from the Andean foothills into western Amazonia. This system has no modern analogue and the driving mechanisms are not yet fully understood. Dynamic topography and Andean uplift are thought to have controlled deposition, with allocyclic base level changes driven by eustasy and orbital forcing also pla...

Quantitative continental climate reconstructions covering the last glacial cycle from the Iberian Peninsula are scarce. In order to fill this gap, we obtained for the first time a high-resolution mean annual air temperature (MAAT) record based on the distribution of specific bacterial membrane lipids (i.e., branched glycerol dialkyl glycerol tetrae...

[This corrects the article DOI: 10.3389/fmicb.2018.02775.].

Large quantities of carbon are stored in marine dissolved organic matter (DOM), and its recycling has a major effect on the carbon cycle. Microbes are responsible for turnover of DOM. Little is known about how the complex pool of DOM shapes microbial communities and vice versa, especially in anoxic systems. In this study, we characterized the DOM p...

Isoprenoidal glycerol dialkyl glycerol tetraether (isoGDGT) lipids occur ubiquitously in freshwater and marine environments. Since their distribution varies with temperature, sedimentary isoGDGTs have been used as proxies for the reconstruction of past continental climate for almost two decades. Yet, their application in lacustrine sediments is sti...

Membrane-spanning lipids are present in a wide variety of archaea but they are rarely in bacteria. Nevertheless, the (hyper)thermophilic members of the order Thermotogales harbor tetraester, tetraether, and mixed ether/ester membrane-spanning lipids mostly composed of core lipids derived from diabolic acids, C30, C32 and C34 dicarboxylic acids with...

Interpreting lipid biomarkers in the sediment archive requires a good understanding of their application and limitations in modern systems. Recently it was discovered that marine bacteria performing anaerobic ammonium oxidation (anammox), belonging to the genus Ca. Scalindua, uniquely synthesize a stereoisomer of bacteriohopanetetrol (“BHT-x”). The...

The long-chain diol index (LDI) is a relatively new proxy for sea surface temperature (SST) which has been rarely applied in upwelling regions. Here, we evaluated its application by comparison with other SST records obtained by commonly used proxies, that is, the Mg/Ca ratio of the planktonic foraminifera species Globigerinoides ruber and the alken...

Baleen from mysticete whales is a well-preserved proteinaceous material that can be used to identify migrations and feeding habits for species whose migration pathways are unknown. Analysis of δ ¹³ C and δ ¹⁵ N values from bulk baleen have been used to infer migration patterns for individuals. However, this approach has fallen short of identifying...

The westernmost Mediterranean is one of the most sensitive areas to global climate change and high sedimentation rates allow recording high frequency variability. We present a high-resolution paleotemperature reconstruction over the last 35 kyr using, for the first time, four independent organic sea surface temperature (SST) proxies (UK'37, TEXH86,...

Members of the Psychrilyobacter spp. of the phylum Fusobacteria have been recently suggested to be amongst the most significant primary degraders of the detrital organic matter in sulfidic marine habitats, despite representing only a small proportion (<0.1%) of the microbial community. In this study, we have isolated a previously uncultured Psychri...

Isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs) are membrane lipids of Archaea. Organic biomarker proxies associated with these lipids, such as the TEX 86 paleothermometer and Branched and Isoprenoid Tetraether (BIT) index, are often used in paleoenvironmental reconstructions for the marine environment, but their general applicability i...

Interpreting lipid biomarkers in the sediment archive requires a good understanding of their application and 10 limitations in modern systems. Recently it was discovered that marine bacteria performing anaerobic ammonium oxidation (anammox), belonging to the genus Ca. Scalindua, uniquely synthesize a stereoisomer of bacteriohopanetetrol ('BHT-x')....

Nine pure cultures of neutrophilic haloaloarchaea capable of anaerobic growth by carbohydrate-dependent sulfur respiration were isolated from hypersaline lakes in southwestern Siberia and southern Russia. According to phylogenomic analysis the isolates were closely related to each other and formed a new species within the genus Halapricum (family H...

Arctic warming is expected to accelerate northward migration of the boreal zone, altering the boreal wildfire regime, with changes in fire frequency, intensity, size, and fire season length. The closest analogue to these future high latitude climate conditions occurred during the Pliocene Epoch (2.58–5.33 Ma). Palaeoenvironmental reconstructions at...

Lipids, as one of the main building blocks of cells, can provide valuable information on microorganisms in the environment. Traditionally, gas or liquid chromatography coupled to mass spectrometry (MS) has been used to analyze environmental lipids. The resulting spectra were then processed through individual peak identification and comparison with...

Structurally diverse, specialized lipids are crucial components of microbial membranes and other organelles and play essential roles in ecological functioning. The detection of such lipids in the environment can reveal not only the occurrence of specific microbes but also the physicochemical conditions to which they are adapted to. Traditionally, l...

Bacteriohopanepolyols (BHPs) are lipids with great chemotaxonomic potential for microbial populations and biogeochemical processes in the environment. The most commonly used methods for BHP analysis are chemical degradation followed by gas chromatography-mass spectrometry (MS) or derivatization followed by high performance liquid chromatography (HP...

Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors...

Microorganisms attached to particles have been shown to be different from free‐living microbes and to display diverse metabolic activities. However, little is known about the ecotypes associated to particles and their substrate preference in anoxic marine waters. Here, we investigate the microbial community colonizing particles in the anoxic and su...

Crenarchaeol is a glycerol dialkyl glycerol tetraether lipid produced exclusively in Archaea of the phylum Thaumarchaeota. This membrane-spanning lipid is undoubtedly the structurally most sophisticated of all known archaeal lipids and an iconic molecule in organic geochemistry. The 66-membered macrocycle possesses a unique chemical structure featu...

Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compa...

Branched glycerol monoalkyl glycerol tetraethers (brGMGTs) are membrane-spanning lipids which were initially identified in marine settings and have more recently been found in peats and lake sediments. In the latter settings, their abundance relative to that of the branched glycerol dialkyl glycerol tetraethers (brGDGTs) appears to increase under w...

The genus Thioalkalivibrio comprises sulfur-oxidizing bacteria thriving in soda lakes at high pH and salinity. Depending on the geographical location and the season, these lakes can strongly vary in temperature. To obtain a comprehensive understanding of the molecular and physiological adaptations to low temperature, we compared the responses of tw...

The fractional abundance of branched glycerol dialkyl glycerol tetraether (brGDGT) membrane lipids in coastal marine sediments has been posited as a proxy for the reconstruction of terrestrial temperatures on the nearby land, based on the assumption that they are produced in soils and delivered to the marine realm by rivers following erosion. Here,...

Eutrophic lakes are major contributors to global aquatic methane emissions. Methanotrophy, performed by methane oxidizing bacteria, results in the production of biomass, fermentation products and/or CO2 , making methane-derived carbon available to non-methanotrophic organisms. Methanotrophs can co-occur with methylotrophs which are expected to cons...

The long-chain diol index (LDI) is a relatively new proxy for sea surface temperature (SST) which has been rarely applied in upwelling regions. Here, we evaluated its application by comparison with other SST records obtained by commonly used proxies, i.e. the Mg/Ca ratio of the planktonic foraminifera species Globigerinoides ruber and the alkenone...

Soil bacteria rank among the most diverse groups of organisms on Earth and actively impact global processes of carbon cycling, especially in the emission of greenhouse gases like methane, CO2 and higher gaseous hydrocarbons. An abundant group of soil bacteria are the mycobacteria, which colonize various terrestrial, marine and anthropogenic environ...

Surface sediments were collected in a transect from the Amazon river delta to open marine sites in the north Atlantic Ocean in order to characterize spatial contrasts in the deposited organic carbon (OC), allowing to uncover the role of the river plume on the sedimentation of OC. Analysis of isoprenoidal and branched glycerol dialkyl glycerol tetra...

Long-chain diols (LCDs) are lipids commonly found in freshwater environments. They are produced in lake waters and in low water-flow regions of rivers but their sources and the controls on their abundance are poorly constrained. To be able to use LCD as environmental proxy (e.g. for reconstructing lake temperature and as a freshwater indicator in m...

Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol-1-phosphate (G1P), while Bacteria/ Eukarya produce membranes consisting of fatty acids ester-bound to glycerol-3-phosphate (G3P). This dichotomy in membrane lipid composition (i.e., the 'lipid divide') is believed to have arisen after the Last Universal Common Ances...

Crenarchaeol is a glycerol dialkyl glycerol tetraether lipid produced exclusively in Archaea of the phylum Thaumarchaeota. This membrane-spanning lipid is undoubtedly the structurally most sophisticated of all known archaeal lipids and an iconic molecule in organic geochemistry. The 66-membered macrocycle possesses a unique chemical structure featu...

Crenarchaeol is a glycerol dialkyl glycerol tetraether lipid produced exclusively in Archaea of the phylum Thaumarchaeota. This membrane-spanning lipid is undoubtedly the structurally most sophisticated of all known archaeal lipids and an iconic molecule in organic geochemistry. The 66-membered macrocycle possesses a unique chemical structure featu...

This study describes the first asymmetric total synthesis of the proposed structure of the archaeal membrane-spanning tetraether lipid crenarchaeol. The synthetic material was compared by NMR and GC-MS analysis with natural crenarchaeol. Detailed NMR analysis ultimately enabled the structure revision of crenarchaeol, identifying one out of 22 stere...

Records of carbon dioxide concentrations (partial pressure expressed as pCO 2) over Earth's history provide trends that are critical to understand our changing world. To better constrain pCO2 estimations, here we test organic pCO2 proxies against the direct measurements of pCO2 recorded in ice cores. Based on the concept of stable carbon isotopic f...

Lake sediments are important archives of continental climate history, and their lipid biomarker content can be exploited to reconstruct paleoenvironmental conditions. Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids widely used in paleoclimate studies to reconstruct past temperature. However, major gaps still e...

Soil bacteria rank among the most diverse groups of organisms on Earth and actively impact global processes of carbon cycling, especially in the emission of greenhouse gases like methane, CO2 and higher gaseous hydrocarbons. An abundant group of soil bacteria are the mycobacteria, which colonize various habitats due to their impermeable cell envelo...

Baleen from mysticete whales is a well-preserved proteinaceous material that can be used to identify migrations and feeding habits for species whose migration pathways are unknown. Analysis of δ13C and δ15N from bulk baleen has been used to infer migration patterns for individuals. However, this approach has fallen short of identifying migrations b...

Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open‐ocean DMW. This review summarizes the current knowledge...

An anaerobic enrichment with CO from sediments of hypersaline soda lakes resulted in a methane-forming binary culture, whereby CO was utilized by a bacterium and not the methanogenic partner. The bacterial isolate ANCO1 forms a deep-branching phylogenetic lineage at the level of a new family within the class "Natranaerobiia". It is an extreme haloa...