Thomas Holler

Max Planck Institute for Marine Microbiology

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Kai‐Uwe Hinrichs

University of Bremen

Gunter Wegener

Max Planck Institute for Marine Microbiology

Katrin Knittel

Max Planck Institute for Marine Microbiology

Antje Boëtius

University of Bremen

Marcus Elvert

University of Bremen

Benjamin Brunner

The University of Texas at El Paso

Yu‐Shih Lin

National Sun Yat-sen University

Marcel M. M. Kuypers

Max Planck Institute for Marine Microbiology

Matthias Y. Kellermann

Carl von Ossietzky Universität Oldenburg

Andreas Teske

University of North Carolina at Chapel Hill

Cooperative Institutions

Max Planck Institute for Marine Microbiology

Max Planck Society

University of Bremen

Aarhus University

Woods Hole Oceanographic Institution

Indiana University Bloomington

United States Geological Survey

Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences

GEOMAR Helmholtz Centre for Ocean Research Kiel

College of Marin

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

Assessing production of the ubiquitous archaeal diglycosyl tetraether lipids in marine subsurface sediment using intramolecular stable isotope probing

Environmental Microbiology (2012)

Yu‐Shih Lin Julius S. Lipp Marcus Elvert Thomas Holler Kai‐Uwe Hinrichs

Summary The membrane lipids diglycosyl‐glycerol dibiphytanyl glycerol tetraethers ( 2G ‐ GDGTs ) in marine subsurface sediments are believed to originate from uncultivated benthic archaea, yet the production of 2G ‐ GDGTs from subseafloor samples has not been demonstrated in vitro . In order to validate sedimentary biosynthesis of 2G ‐ GDGTs , we performed a stable carbon isotope probing experiment on a subseafloor sample with six different 13 C ‐labelled substrates (bicarbonate, methane, acetate, leucine, glucose and S pirulina platensis biomass). After 468 days of anoxic incubation, only glucose and S . platensis resulted in label uptake in lipid moieties of 2G ‐ GDGTs , indicating incorporation of carbon from these organic substrates. The hydrophobic moieties of 2G ‐ GDGTs showed minimal label incorporation, with up to 4‰ 13 C enrichment detected in crenarchaeol‐derived tricyclic biphytane from the S . platensis ‐supplemented slurries. The 2G ‐ GDGT ‐derived glucose or glycerol moieties also showed 13 C incorporation (Δδ 13 C = 18–38‰) in the incubations with glucose or S . platensis , consistent with a lipid salvage mechanism utilized by marine benthic archaea to produce new 2G ‐ GDGTs . The production rates were nevertheless rather slow, even when labile organic matter was supplied. The 2G ‐ GDGT turnover times of 1700–20 500 years were much longer than those estimated for subseafloor microbial communities, implying that sedimentary 2G ‐ GDGTs as biomarkers of benthic archaea are cumulative records of past and present generations.

Stable-isotope probing

10.1111/j.1462-2920.2012.02888.x

Cite

Citations (36)

Thermophilic anaerobic oxidation of methane by marine microbial consortia

The ISME Journal (2011)

Thomas Holler Friedrich Widdel Katrin Knittel Rudolf Amann Matthias Y. Kellermann

10.1038/ismej.2011.77

Cite

Citations (189)

Microbiological investigation of methane‐ and hydrocarbon‐discharging mud volcanoes in the Carpathian Mountains, Romania

Environmental Microbiology (2005)

Karine Alain Thomas Holler Florin Musat Marcus Elvert Tina Treude

Summary Paclele Mici is a terrestrial mud volcano field located in the Carpathian Mountains (Romania), where thermal alteration of sedimentary organic compounds leads to methane, higher hydrocarbons and other petroleum compounds that are continuously released into the environment. The hydrocarbons represent potential substrates for microorganisms. We studied lipid biomarkers, stable isotope ratios, the effect of substrate (methane, other organic compounds) addition and 16S rRNA genes to gain insights into the hitherto unknown microbial community at this site. Quantitative real‐time polymerase chain reaction analysis demonstrated that bacteria were much more abundant than archaea. Phylogenetic analyses of 16S rDNA clone sequences indicated the presence of bacterial and archaeal lineages generally associated with the methane cycle (methanogens, aerobic and anaerobic methanotrophs), the sulfur cycle (sulfate reducers), and groups linked to the anaerobic degradation of alkanes or aromatic hydrocarbons. The presence of sulfate reducers, methanogens and methanotrophs in this habitat was also confirmed by concurrent surveys of lipid biomarkers and their isotopic signatures. Incubation experiments with several common and complex substrates revealed the potential of the indigenous microbial community for sulfate reduction, methanogenesis and aerobic methanotrophy. Additionally, consistently to the detection of methane‐oxidizing archaea (ANME) and 13 C‐depleted archaeal lipids, a weak but significant activity of anaerobic methane oxidation was measured by radiotracer techniques and in vitro . This survey is the first to report the presence and activity of ANME in a terrestrial environment.

Sulfate-Reducing Bacteria

Mud volcano

10.1111/j.1462-2920.2005.00922.x

Cite

Citations (140)

Substantial ¹³C/¹²C and D/H fractionation during anaerobic oxidation of methane by marine consortia enriched in vitro

Environmental Microbiology Reports (2009)

Thomas Holler Gunter Wegener Katrin Knittel Antje Boëtius Benjamin Brunner

The anaerobic oxidation of methane (AOM) by methanotrophic archaea and sulfate-reducing bacteria is the major sink of methane formed in marine sediments. The study of AOM as well as of methanogenesis in different habitats is essentially connected with the in situ analysis of stable isotope ((13) C/(12) C, D/H) signatures (δ-values). For their kinetic interpretation, experimental (cultivation-based) isotope fractionation factors (α-values) are richly available in the case of methanogenesis, but are scarce in the case of AOM. Here we used batch enrichment cultures with high AOM activity and without background methanogenesis from detrital remnants to determine (13) C/(12) C and D/H fractionation factors. The enrichment cultures which originated from three marine habitats (Hydrate Ridge, NE Pacific; Amon Mud Volcano, Mediterranean Sea; NW shelf, Black Sea) were dominated by archaeal phylotypes of anaerobic methanotrophs (ANME-2 clade). Isotope fractionation factors calculated from the isotope signatures as a function of the residual proportion of methane were 1.012-1.039 for (13) CH4 /(12) CH4 and 1.109-1.315 for CDH3 /CH4 . The present values from in vitro experiments were significantly higher than values previously estimated from isotope signature distributions in marine sediment porewater, in agreement with the overlap of other processes with AOM in the natural habitat.

10.1111/j.1758-2229.2009.00074.x

Cite

Citations (123)

Carbon and sulfur back flux during anaerobic microbial oxidation of methane and coupled sulfate reduction

Proceedings of the National Academy of Sciences (2011)

Thomas Holler Gunter Wegener Helge Niemann Christian Deusner Timothy G. Ferdelman

Microbial degradation of substrates to terminal products is commonly understood as a unidirectional process. In individual enzymatic reactions, however, reversibility (reverse reaction and product back flux) is common. Hence, it is possible that entire pathways of microbial degradation are associated with back flux from the accumulating product pool through intracellular intermediates into the substrate pool. We investigated carbon and sulfur back flux during the anaerobic oxidation of methane (AOM) with sulfate, one of the least exergonic microbial catabolic processes known. The involved enzymes must operate not far from the thermodynamic equilibrium. Such an energetic situation is likely to favor product back flux. Indeed, cultures of highly enriched archaeal–bacterial consortia, performing net AOM with unlabeled methane and sulfate, converted label from 14 C-bicarbonate and 35 S-sulfide to 14 C-methane and 35 S-sulfate, respectively. Back fluxes reached 5% and 13%, respectively, of the net AOM rate. The existence of catabolic back fluxes in the reverse direction of net reactions has implications for biogeochemical isotope studies. In environments where biochemical processes are close to thermodynamic equilibrium, measured fluxes of labeled substrates to products are not equal to microbial net rates. Detection of a reaction in situ by labeling may not even indicate a net reaction occurring in the direction of label conversion but may reflect the reverse component of a so far unrecognized net reaction. Furthermore, the natural isotopic composition of the substrate and product pool will be determined by both the forward and back flux. This finding may have to be considered in the interpretation of stable isotope records.

Exergonic reaction

Bicarbonate

Microbial Metabolism

10.1073/pnas.1106032108

Cite

Citations (143)

Carbon isotope equilibration during sulphate-limited anaerobic oxidation of methane

Nature Geoscience (2014)

Marcos Y. Yoshinaga Thomas Holler Tobias Goldhammer Gunter Wegener J. Pohlman

Atmospheric methane

Carbon fibers

10.1038/ngeo2069

Cite

Citations (189)

Assessing sub‐seafloor microbial activity by combined stable isotope probing with deuterated water and ¹³C‐bicarbonate

Environmental Microbiology (2012)

Gunter Wegener Marlene Bausch Thomas Holler Nguyễn Mạnh Thắng Xavier Prieto Mollar

Summary Sub‐seafloor sediments are populated by large numbers of microbial cells but not much is known about their metabolic activities, growth rates and carbon assimilation pathways. Here we introduce a new method enabling the sensitive detection of microbial lipid production and the distinction of auto‐ and heterotrophic carbon assimilation. Application of this approach to anoxic sediments from a Swedish fjord allowed to compare the activity of different functional groups, the growth and turnover times of the bacterial and archaeal communities. The assay involves dual stable isotope probing (SIP) with deuterated water (D 2 O) and 13 C DIC ( d issolved i norganic c arbon). Culture experiments confirmed that the D content in newly synthesized lipids is in equilibrium with the D content in labelled water, independent of whether the culture grew hetero‐ or autotrophically. The ratio of 13 C DIC to D 2 O incorporation enables distinction between these two carbon pathways in studies of microbial cultures and in environmental communities. Furthermore, D 2 O‐SIP is sufficiently sensitive to detect the formation of few hundred cells per day in a gram of sediment. In anoxic sediments from a Swedish fjord, we found that > 99% of newly formed lipids were attributed to predominantly heterotrophic bacteria. The production rate of bacterial lipids was highest in the top 5 cm and decreased 60‐fold below this depth while the production rate of archaeal lipids was rather low throughout the top meter of seabed. The contrasting patterns in the rates of archaeal and bacterial lipid formation indicate that the factors controlling the presence of these two lipid groups must differ fundamentally.

Fjord

Bicarbonate

Assimilation (phonology)

Microbial loop

Stable-isotope probing

Microbial Metabolism

Microbial food web

Bacterial growth

10.1111/j.1462-2920.2012.02739.x

Cite

Citations (75)

Effect of Storage Conditions on Archaeal and Bacterial Communities in Subsurface Marine Sediments

Geomicrobiology Journal (2010)

Yu-Shih Lin Jennifer F. Biddle Julius S. Lipp Beth N. Orcutt Thomas Holler

We have studied the effects of slow infiltration of oxygen on microbial communities in refrigerated legacy samples from ocean drilling expeditions. Storage was in heat-sealed, laminated foil bags with a N2 headspace for geomicrobiological studies. Analysis of microbial lipids suggests that Bacteria were barely detectable in situ but increased remarkably during storage. Detailed molecular examination of a methane-rich sediment horizon showed that refrigeration triggered selective growth of ANME-2 archaea and a drastic change in the bacterial community. Subsequent enrichment targeting methanogens yielded exclusively methylotrophs, which were probably selected for by high sulfate levels caused by oxidation of reduced sulfur species. We provide recommendations for sample storage in future ocean drilling expeditions.

Sulfate-Reducing Bacteria

Bacterial growth

10.1080/01490450903410423

Cite

Citations (21)

Autotrophy as a predominant mode of carbon fixation in anaerobic methane-oxidizing microbial communities

Proceedings of the National Academy of Sciences (2012)

Matthias Y. Kellermann Gunter Wegener Marcus Elvert Marcos Y. Yoshinaga Yu‐Shih Lin

The methane-rich, hydrothermally heated sediments of the Guaymas Basin are inhabited by thermophilic microorganisms, including anaerobic methane-oxidizing archaea (mainly ANME-1) and sulfate-reducing bacteria (e.g., HotSeep-1 cluster). We studied the microbial carbon flow in ANME-1/ HotSeep-1 enrichments in stable-isotope–probing experiments with and without methane. The relative incorporation of 13 C from either dissolved inorganic carbon or methane into lipids revealed that methane-oxidizing archaea assimilated primarily inorganic carbon. This assimilation is strongly accelerated in the presence of methane. Experiments with simultaneous amendments of both 13 C-labeled dissolved inorganic carbon and deuterated water provided further insights into production rates of individual lipids derived from members of the methane-oxidizing community as well as their carbon sources used for lipid biosynthesis. In the presence of methane, all prominent lipids carried a dual isotopic signal indicative of their origin from primarily autotrophic microbes. In the absence of methane, archaeal lipid production ceased and bacterial lipid production dropped by 90%; the lipids produced by the residual fraction of the metabolically active bacterial community predominantly carried a heterotrophic signal. Collectively our results strongly suggest that the studied ANME-1 archaea oxidize methane but assimilate inorganic carbon and should thus be classified as methane-oxidizing chemoorganoautotrophs.

Autotroph

10.1073/pnas.1208795109

Cite

Citations (158)

Use of carbon monoxide and hydrogen by a bacteria–animal symbiosis from seagrass sediments

Environmental Microbiology (2015)

Manuel Kleiner Cecilia Wentrup Thomas Holler Gaute Lavik Jens Harder

The gutless marine worm Olavius algarvensis lives in symbiosis with chemosynthetic bacteria that provide nutrition by fixing carbon dioxide (CO2 ) into biomass using reduced sulfur compounds as energy sources. A recent metaproteomic analysis of the O. algarvensis symbiosis indicated that carbon monoxide (CO) and hydrogen (H2 ) might also be used as energy sources. We provide direct evidence that the O. algarvensis symbiosis consumes CO and H2 . Single cell imaging using nanoscale secondary ion mass spectrometry revealed that one of the symbionts, the γ3-symbiont, uses the energy from CO oxidation to fix CO2 . Pore water analysis revealed considerable in-situ concentrations of CO and H2 in the O. algarvensis environment, Mediterranean seagrass sediments. Pore water H2 concentrations (89-2147 nM) were up to two orders of magnitude higher than in seawater, and up to 36-fold higher than previously known from shallow-water marine sediments. Pore water CO concentrations (17-51 nM) were twice as high as in the overlying seawater (no literature data from other shallow-water sediments are available for comparison). Ex-situ incubation experiments showed that dead seagrass rhizomes produced large amounts of CO. CO production from decaying plant material could thus be a significant energy source for microbial primary production in seagrass sediments.

Carbon fibers

10.1111/1462-2920.12912

Cite

Citations (53)