Carsten J. Schubert

Carsten J. Schubert
Eawag: Das Wasserforschungs-Institut des ETH-Bereichs | Eawag · Department of Surface Waters Research and Management

PhD

About

291
Publications
42,690
Reads
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11,516
Citations
Citations since 2017
66 Research Items
5294 Citations
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201720182019202020212022202302004006008001,000
201720182019202020212022202302004006008001,000
Additional affiliations
August 2001 - present
Eawag: Das Wasserforschungs-Institut des ETH-Bereichs
Position
  • Head of Department
September 1997 - July 2001
Max Planck Institute for Marine Microbiology
Position
  • Groupleader

Publications

Publications (291)
Article
Full-text available
Even though lake sediments are globally important organic carbon (OC) sinks, the controls on long-term OC storage in these sediments are unclear. Using a multi-proxy approach, we investigate changes in diatom, green algae, and vascular plant biomolecules in sedimentary records from the past centuries across five temperate lakes with different troph...
Article
Full-text available
Eutrophication is expected to increase methane production in freshwater sediments worldwide over the coming decades. Methane-oxidizing bacteria (MOB) consume a significant fraction of this sedimentary methane, but the factors that control their distributions and activities are not understood. By combining genetic approaches ( pmo A, 16S rRNA gene,...
Article
Full-text available
The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investi...
Article
Full-text available
Although lake sediments are globally important organic carbon sinks and therefore important habitats for deep microbial life, the deep lacustrine biosphere has thus far been little studied compared to its marine counterpart. To investigate the impact of the underexplored deep lacustrine biosphere on the sediment geochemical environment and vice ver...
Article
Full-text available
Symbiotic N2-fixing microorganisms have a crucial role in the assimilation of nitrogen by eukaryotes in nitrogen-limited environments1–3. Particularly among land plants, N2-fixing symbionts occur in a variety of distantly related plant lineages and often involve an intimate association between host and symbiont2,4. Descriptions of such intimate sym...
Article
Full-text available
Long-chain polyunsaturated fatty acids are biologically important lipids that are unevenly distributed between and throughout environments. This heterogeneity can affect the evolution of metabolic processes, as populations adapt to the resource landscape that they encounter. Here, we compare fatty acid phenotypes of stickleback over two time scales...
Preprint
Full-text available
Lake Tanganyika’s pelagic fish sustain the second largest inland fishery in Africa and are under pressure from heavy fishing and global warming related increases in stratification. Only little is known about whether basin-scale hydrodynamics – including a more stratified north and an upwelling-driven south – lead to regional fish populations with v...
Preprint
Full-text available
Although lake sediments are globally important organic carbon sinks and therefore important habitats for deep microbial life, the deep lacustrine biosphere has thus far been little studied compared to its marine counterpart. To investigate the impact of the underexplored deep lacustrine biosphere on the sediment geochemical environment and vice ver...
Article
Full-text available
Biological N 2 fixation was key to the expansion of life on early Earth. The N 2 -fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N 2 fixation in Lake Cadagno, an analogue system...
Preprint
Full-text available
The nitrogen (N) cycle is of global importance as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbial transformation processes, few studies have inve...
Article
Full-text available
Macroinvertebrates are widespread in lake sediments and alter sedimentary properties through their activity (bioturbation). Understanding the interactions between bioturbation and sediment properties is important given that lakes are important sinks and sources of carbon and nutrients. We studied the biogeochemical impact of macrofauna on surface s...
Article
Full-text available
We here estimate past temperature and hydroclimate variations in eastern Anatolia for marine isotope stages 4 to 1 (MIS4 to MIS1) respectively using branched glycerol dialkyl glycerol tetraethers (brGDGTs) and the hydrogen isotopic composition of n-C29 leaf-wax n-alkanes (δ²Hwax) stored in the sedimentary record of Lake Van (Turkey). Our millennial...
Article
Full-text available
Small boreal lakes are known to contribute significantly to global CH4 emissions. Lake Lovojärvi is a eutrophic lake in southern Finland with bottom water CH4 concentrations up to 2 mM. However, the surface water concentration, and thus the diffusive emission potential, was low (
Article
Long-chain alkenones, a class of highly specific and widely used lipid biomarkers found in ocean and lake sediments, have been so far found as straight-chain alkyl ketones with 2 to 4 double bonds. Jaraula et al. (2010) reported assignments of a series of tri- to penta-unsaturated alkenones as straight-chain C38 methyl (C38Me) and C39 ethyl (C39Et)...
Article
Full-text available
The sulfur cycle is an important, although understudied facet of today's modern oxygen minimum zones (OMZs). Sulfur cycling is most active in highly productive coastal OMZs where sulfide‐rich sediments interact with the overlying water column, forming a tightly coupled benthic‐pelagic sulfur cycle. In such productive coastal systems, highly eutroph...
Article
Full-text available
Geogenic arsenic (As) contamination of groundwater is a health threat to millions of people worldwide, particularly in alluvial regions of South and Southeast Asia. Mitigation measures are often hindered by high heterogeneities in As concentrations, the cause(s) of which are elusive. Here we used a comprehensive suite of stable isotope analyses and...
Article
Full-text available
Freshwater lakes are essential hotspots for the removal of excessive anthropogenic nitrogen (N) loads transported from the land to coastal oceans. The biogeochemical processes responsible for N removal, the corresponding transformation rates and overall removal efficiencies differ between lakes, however, it is unclear what the main controlling fact...
Article
Lakes cover a global area that is about 35 times smaller than the oceans, but carbon burial in lakes and oceans are on the same order of magnitude. Hence, understanding the processes for such high organic carbon burial in lacustrine systems is essential. We applied proxies typically used for marine environments including amino acid (AA) content and...
Article
Climate warming is causing rapid spatial expansion of ocean warm pools from equatorial latitudes towards the subtropics. Sedentary coral reef inhabitants in affected areas will thus be trapped in high temperature regimes, which may become the “new normal”. In this study, we used clownfish Amphiprion ocellaris as model organism to study reef fish me...
Article
Full-text available
Mitochondria are specialized eukaryotic organelles that have a dedicated function in oxygen respiration and energy production. They evolved about 2 billion years ago from a free-living bacterial ancestor (probably an alphaproteobacterium), in a process known as endosymbiosis1,2. Many unicellular eukaryotes have since adapted to life in anoxic habit...
Article
Climate warming is causing rapid spatial expansion of ocean warm pools from equatorial latitudes towards the subtropics. Sedentary coral reef inhabitants in affected areas will thus be trapped in high temperature regimes, which may become the “new normal”. In this study, we used clownfish Amphiprion ocellaris as model organism to study reef fish me...
Article
Full-text available
In marine and freshwater oxygen-deficient zones, the remineralization of sinking organic matter from the photic zone is central to driving nitrogen loss. Deep blooms of photosynthetic bacteria, which form the suboxic/anoxic chlorophyll maximum (ACM), widespread in aquatic ecosystems, may also contribute to the local input of organic matter. Yet, th...
Preprint
Full-text available
Small boreal lakes are known to contribute significantly to global methane emissions. Lake Lovojärvi is a eutrophic lake in Southern Finland with bottom water methane concentrations up to 2 mM. However, the surface water concentration, and thus the diffusive emission potential, was low (
Article
Full-text available
Coastal lakes (CL) act as limnetic–β-oligohaline systems located on non-tidal coastlines in fresh and salt water mixing zone. Owing to considerable terrestrial nutrient input and a high autochthonous productivity CLs release greenhouse gases (GHG) to the ambient atmosphere, however, neither emission from the system was assessed nor controls on the...
Article
We investigate the uppermost 60 cm of sediment in active pockmarks of a deep-water methane seep site from Vestnesa Ridge offshore NW Svalbard. Using video guided core sampling with a remotely operated vehicle we collected push cores directly from bacterial mats within two active pockmarks, Lunde and Lomvi. Pore water analyses show very shallow sulp...
Article
• Glacial retreat, accompanied by shifts in riparian vegetation and glacier meltwater inputs, alters the energy supply and trophic structure of alpine stream food webs. Our goal in this study was to enhance understanding of dietary niches of macroinvertebrates inhabiting different alpine streams with contrasting glacial and non‐glacial (groundwater...
Article
Full-text available
Previous studies have shown that microbially produced methane can be a dominant carbon source of lacustrine sedimentary macrofauna in eutrophic lakes, most likely through grazing on methane-oxidizing bacteria. Here we investigate the contributions of different carbon sources to macrofaunal biomass across five lakes in central Switzerland that range...
Article
Full-text available
Lake sediments are globally important carbon sinks. Although the fate of organic carbon (OC) in lake sediments depends significantly on microorganisms, only few studies have investigated controls on lake sedimentary microbial communities. Here we investigate the impact of anthropogenic eutrophication, which affects redox chemistry and organic matte...
Article
Full-text available
Amino acids (AA) and, more recently, amino sugars (AS) in marine or lacustrine sediments have been increasingly used as paleoproxies. In order to assess AA and AS compositional changes during simulated microbial degradation, as well as to understand the importance of amino-compound re-synthesis by microbes during early diagenesis, decomposition exp...
Article
Paleoclimatic changes during MIS7 and MIS6 remain poorly described in the Near East. We quantified source-specific biomarkers in Lake Van sediments during the interglacial/glacial cycle MIS7/MIS6. Long-chain n-alkanes produced by land-derived vegetation, as well as long-chain alkenones and sterols (namely brassicasterol and dinosterol) produced by...
Poster
Full-text available
Climate warming is causing the rapid expansion of tropical warm pools in the oceans at rates exceeding 2 million square kilometers per decade. This phenomenon is leading to increasingly larger ocean areas delimited by high temperature isotherms, especially in the range between 29˚C and 30˚C. From an ecological perspective, this means that marine an...
Article
Well prepared It is well known that species radiate into new niches by adapting to novel environments. But why do some species radiate in this way, while other, related, species do not. Ishikawa et al. looked across sticklebacks to determine why some, originally marine, lineages were able to colonize postglacial freshwater environments (see the Per...
Article
Full-text available
Ice-covered periods might significantly contribute to lake emissions at ice-melt, yet a comprehensive understanding of under-ice carbon dioxide (CO2) dynamics is still lacking. This study investigated the processes driving spatiotemporal patterns of under-ice CO2 in large Lake Onego. In March 2015 and 2016, under-ice CO2, dissolved inorganic carbon...
Article
Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, w...
Preprint
Full-text available
Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, w...
Article
Full-text available
Significance Reliable prediction of future climate conditions requires a thorough understanding of climate variability throughout Earth’s history. Microbial molecular fossils, such as bacterial membrane-spanning tetraether lipids [branched glycerol dialkyl glycerol tetraethers (brGDGTs)], have proven to be particularly useful for the assessment of...
Article
Compound specific hydrogen isotope ratios (2H/1H) of lipid biomarkers preserved in sediments are used as paleohydro- logic proxies. However, several variables, including contributions from different source organisms and their growth rates, can influence 2H/1H fractionation between lipids and source water. Significant uncertainties remain about how...
Article
Proxy-indicators in lake sediments provide the only approach by which the dynamics of in-lake methane cycling can be examined on multi-decadal to centennial time scales. This information is necessary to constrain how lacustrine methane production, oxidation and emissions are expected to respond to global change drivers. Several of the available pro...
Article
Full-text available
Fate and reactivity of dissolved organic matter (DOM) is directly linked to its chemical composition. Therefore, molecular characterisation, for example using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), is used for a better understanding of those factors. To study organic compounds in the water column, an efficient extr...
Article
Full-text available
Methanotrophic bacteria represent an important biological filter regulating methane emissions into the atmosphere. Planktonic methanotrophic communities in freshwater lakes are typically dominated by aerobic gamma‐proteobacteria, with a contribution from alpha‐proteobacterial methanotrophs and the NC10 bacteria. The NC10 clade encompasses methanotr...
Chapter
Lakes and reservoirs have been only in the early twenty-first century identified to be main methane emitters to the atmosphere (Bastviken et al., Glob Biogeochem Cycles 18:1–12, 2004; St. Louis et al., Bioscience 50:766–775, 2000). With an estimated yearly amount of 12–29.6 Tg CH4 for reservoirs (Deemer et al., Bioscience 66:949–964, 2016) and up t...
Article
Full-text available
Although lakes play a major role in the storage of organic carbon, processes involved are not yet very well characterized, especially for oligotrophic lakes. Whether a lake functions as a net source or sink for carbon depends on relative rates of primary production, inputs of terrestrial organic matter and respiration. The microbial community will...
Article
Sedimentary plant wax ²H/¹H ratios are important tools for understanding hydroclimate and environmental changes, but large spatial and temporal uncertainties exist about transport mechanisms from ecosystem to sediments. To assess atmospheric pathways, we collected aerosol samples for two years at four locations within a ∼60 km radius in northern Sw...
Article
The diagenesis of amino compounds in Lake Baikal was studied in sediment trap material (18 different water depths between 50–1350 m) and underlying sediment (0–40 cm). Total hydrolysable amino acids (THAA), the amino acid (AA) composition including D- and L-enantiomers and amino sugars were analyzed. The study provides information on early diagenes...
Article
Full-text available
The hydrogen isotopic composition (δ²H) of lipid biomarkers has diverse applications in the fields of paleoclimatology, biogeochemistry, and microbial community dynamics. Large changes in hydrogen isotope fractionation have been observed among microbes with differing core metabolisms, while environmental factors including temperature and nutrient a...
Article
We investigated methane-derived authigenic carbonate (MDAC) crusts and nodules from a cold seep site on the northern Norwegian continental shelf in ca. 220m water depth to determine the timing and mode of their formation. Gas bubbling observed during remotely operated vehicle (ROV)-assisted sampling of MDAC crusts revealed ongoing seep activity. Au...
Article
Full-text available
We monitored CH4 emissions during the ice-free period of an Alpine hydropower reservoir in the Swiss Alps, Lake Klöntal, to investigate mechanisms responsible for CH4 variability and to estimate overall emissions to the atmosphere. A floating eddy-covariance platform yielded total CH4 and CO2 emission rates at high temporal resolution, while hydroa...
Article
Full-text available
Swimming organisms can enhance mixing in their natural environments by creating eddies in their wake and by dragging water along. However, these mixing mechanisms are inefficient for microorganisms, because swimming-induced variations in velocity, temperature and dissolved substances are evened out before they can be advected. In bioconvection, how...
Article
Full-text available
Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous b...
Article
Full-text available
In closed-basin lakes, sediment porewater salinity can potentially be used as a conservative tracer to reconstruct past fluctuations in lake level. However, until now, porewater salinity profiles did not allow quantitative estimates of past lake-level changes because, in contrast to the oceans, significant salinity changes (e.g., local concentratio...
Article
The Joux Valley (Swiss Jura Mountains) has a rather unusual history of human occupation, characterized by tardive but extensive settlement since the Late Middle Ages, followed by an intensive period of industrial development. To estimate the links between human activities and environmental consequences, sediment cores were retrieved in Lake Joux an...
Article
Full-text available
The hydrogen isotope composition (δ²H) of biomarkers produced by algae is strongly influenced by the δ²H values of the water in which they grew. δ²H values of algal biomarkers preserved in lake sediments are thus a useful tool for reconstructing past changes in lake water δ2H values, which can be used to infer hydroclimate variability. However, stu...
Article
Lipid biomarkers were analyzed in Lake Van sediments covering the last 600 ka, with a focus on the period between 110 and 10 ka, when a broad maximum in pore water salinity as a relict from the past suggests dry conditions. The occurrence and distribution of biomarkers indicative for terrestrial plants (long-chain n-alkane C29), haptophyte algae (m...
Article
Full-text available
Bottom-water oxygen supply is a key factor governing the biogeochemistry and community composition of marine sediments. Whether it also determines carbon burial rates remains controversial. We investigated the effect of varying oxygen concentrations (170 to 0 μM O2) on microbial remineralization of organic matter in seafloor sediments and on commun...
Article
Full-text available
The microbial segment of food webs plays a crucial role in lacustrine food-web functioning and carbon transfer, thereby influencing carbon storage and CO2 emission and uptake in freshwater environments. Variability in microbial carbon processing (autotrophic and heterotrophic production and respiration based on glucose) with depth was investigated...