ORCID Profile
0000-0002-0417-920X
Current Organisation
Curtin University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Geochemistry | Organic Geochemistry | Palaeoecology | Isotope Geochemistry | Palaeontology (incl. Palynology) | Quaternary Environments | Physical Geography and Environmental Geoscience | Exploration Geochemistry | Speciation and Extinction
ANZSRC Socio-Economic Objective (SEO)
Ecosystem Adaptation to Climate Change | Flora, Fauna and Biodiversity of environments not elsewhere classified | Expanding Knowledge in the Earth Sciences | Oil and Gas Exploration | Expanding Knowledge in the Environmental Sciences |
Related Links
Publications
Multifunctional protein nanocarriers for targeted nuclear gene delivery in nondividing cells
Publisher: Wiley
Date: 24-04-2009
DOI: 10.1096/FJ.09-131425
Abstract: Compartmentalization within eukaryotic cells hinders the efficient delivery of therapeutic agents to the cell nucleus. Here we describe novel multifunctional DNA carriers (MDCs) that self-assemble with DNA to form structured nanoparticles that possess virus-like functions for cellular trafficking. MDCs contain, in fusion, the DNA-compacting sperm chromatin component protamine, alpha-melanocyte-stimulating hormone for cell-targeted internalization, the endosome-translocation domain of diphtheria toxin, and an optimized nuclear localization sequence to confer recognition by the nuclear import machinery. The structure of the MDC-DNA particles was examined using atomic force microscopy, and the functionality of each domain assessed using in vitro techniques, including a reconstituted nuclear transport assay in semi-intact cells relying on the use of quantitative confocal laser scanning microscopy. The nanoparticles were internalized in cell-specific fashion and subsequently exited the endosome into the cytoplasm. Notably, the nanoparticles interact with cellular nuclear transport proteins as shown in direct binding assays and are actively trafficked into the cell nucleus of non iding cells, resulting in 3- to 4-fold higher reporter gene expression in growth-arrested human embryonic kidney cells, as well as lower cytotoxicity, than lipid and polyethyleneimine vectors. The importance of each functional domain was examined by comparing MDCs with different domain compositions as controls, as well as using antibodies to block particular pathways. MDCs that utilize cellular signaling pathways have enormous potential to safely and efficiently deliver therapeutic transgenes into the nucleus of non iding cells.
SULFUR AND METHANE CYCLING DURING THE HOLOCENE IN ACE LAKE (ANTARCTICA) REVEALED BY LIPID AND DNA STRATIGRAPHY
Publisher: Kluwer Academic Publishers
Date: 2006
Ongoing Modification of Mediterranean Pleistocene Sapropels Mediated by Prokaryotes
Publisher: American Association for the Advancement of Science (AAAS)
Date: 28-06-2002
Abstract: Late Pleistocene organic-rich sediments (sapropels) from the eastern Mediterranean Sea harbor unknown, metabolically active chemoorganotrophic prokaryotes. As compared to the carbon-lean intermediate layers, sapropels exhibit elevated cell numbers, increased activities of hydrolytic exoenzymes, and increased anaerobic glucose degradation rates, suggesting that microbial carbon substrates originate from sapropel layers up to 217,000 years old. 16 S ribosomal RNA gene analyses revealed that as-yet-uncultured green nonsulfur bacteria constitute up to 70% of the total microbial biomass. Crenarchaeota constitute a smaller fraction (on average, 16%). A slow but significant turnover of glucose could be detected. Apparently, sapropels are still altered by the metabolic activity of green nonsulfur bacteria and crenarchaeota.
DNA and lipid molecular stratigraphic records of haptophyte succession in the Black Sea during the Holocene
Publisher: Elsevier BV
Date: 07-2009
Seqenv: linking sequences to environments through text mining
Publisher: PeerJ
Date: 20-12-2016
DOI: 10.7717/PEERJ.2690
Abstract: Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of in idual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv , to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments in idual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete s les. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv , go to: apple/seqenv .
The Habitat of the Nascent Chicxulub Crater
Publisher: American Geophysical Union (AGU)
Date: 24-11-2020
DOI: 10.1029/2020AV000208
Temperature-dependent variation in the distribution of tetraether membrane lipids of marine Crenarchaeota: Implications for TEX86 paleothermometry
Publisher: American Geophysical Union (AGU)
Date: 12-2004
DOI: 10.1029/2004PA001041
Ancient DNA derived from alkenone-biosynthesizing haptophytes and other algae in Holocene sediments from the Black Sea
Publisher: American Geophysical Union (AGU)
Date: 18-02-2006
DOI: 10.1029/2005PA001188
Drilling-induced and logging-related features illustrated from IODP–ICDP Expedition 364 downhole logs and borehole imaging tools
Publisher: Copernicus GmbH
Date: 22-10-2018
DOI: 10.5194/SD-24-1-2018
Abstract: Abstract. Expedition 364 was a joint IODP and ICDP mission-specific platform (MSP) expedition to explore the Chicxulub impact crater buried below the surface of the Yucatán continental shelf seafloor. In April and May 2016, this expedition drilled a single borehole at Site M0077 into the crater's peak ring. Excellent quality cores were recovered from ∼505 to ∼1335 m below seafloor (m b.s.f.), and high-resolution open hole logs were acquired between the surface and total drill depth. Downhole logs are used to image the borehole wall, measure the physical properties of rocks that surround the borehole, and assess borehole quality during drilling and coring operations. When making geological interpretations of downhole logs, it is essential to be able to distinguish between features that are geological and those that are operation-related. During Expedition 364 some drilling-induced and logging-related features were observed and include the following: effects caused by the presence of casing and metal debris in the hole, logging-tool eccentering, drilling-induced corkscrew shape of the hole, possible re-magnetization of low-coercivity grains within sedimentary rocks, markings on the borehole wall, and drilling-induced changes in the borehole diameter and trajectory.
Sedimentary Paleogenomics: A Novel Window into Palaeoecology, Palaeoenvironment, and Palaeoclimate
Publisher: Test accounts
Date: 2011
Combined DNA and lipid analyses of sediments reveal changes in Holocene haptophyte and diatom populations in an Antarctic lake
Publisher: Elsevier BV
Date: 06-2004
Extent and persistence of photic zone euxinia in Middle–Late Devonian seas – Insights from the Canning Basin and implications for petroleum source rock formation
Publisher: Elsevier BV
Date: 05-2018
Rock fluidization during peak-ring formation of large impact structures
Publisher: Springer Science and Business Media LLC
Date: 10-2018
DOI: 10.1038/S41586-018-0607-Z
Abstract: Large meteorite impact structures on the terrestrial bodies of the Solar System contain pronounced topographic rings, which emerged from uplifted target (crustal) rocks within minutes of impact. To flow rapidly over large distances, these target rocks must have weakened drastically, but they subsequently regained sufficient strength to build and sustain topographic rings. The mechanisms of rock deformation that accomplish such extreme change in mechanical behaviour during cratering are largely unknown and have been debated for decades. Recent drilling of the approximately 200-km-diameter Chicxulub impact structure in Mexico has produced a record of brittle and viscous deformation within its peak-ring rocks. Here we show how catastrophic rock weakening upon impact is followed by an increase in rock strength that culminated in the formation of the peak ring during cratering. The observations point to quasi-continuous rock flow and hence acoustic fluidization as the dominant physical process controlling initial cratering, followed by increasingly localized faulting.
A 43 kyr record of protist communities and their response to oxygen minimum zone variability in the Northeastern Arabian Sea
Publisher: Elsevier BV
Date: 08-2018
Microbial life in the nascent Chicxulub crater
Publisher: Geological Society of America
Date: 17-01-2020
DOI: 10.1130/G46799.1
Abstract: The Chicxulub crater was formed by an asteroid impact at ca. 66 Ma. The impact is considered to have contributed to the end-Cretaceous mass extinction and reduced productivity in the world’s oceans due to a transient cessation of photosynthesis. Here, biomarker profiles extracted from crater core material reveal exceptional insights into the post-impact upheaval and rapid recovery of microbial life. In the immediate hours to days after the impact, ocean resurge flooded the crater and a subsequent tsunami delivered debris from the surrounding carbonate r . Deposited material, including biomarkers diagnostic for land plants, cyanobacteria, and photosynthetic sulfur bacteria, appears to have been mobilized by wave energy from coastal microbial mats. As that energy subsided, days to months later, blooms of unicellular cyanobacteria were fueled by terrigenous nutrients. Approximately 200 k.y. later, the nutrient supply waned and the basin returned to oligotrophic conditions, as evident from N2-fixing cyanobacteria biomarkers. At 1 m.y. after impact, the abundance of photosynthetic sulfur bacteria supported the development of water-column photic zone euxinia within the crater.
Diversity of archaea and detection of crenarchaeotal amoA genes in the rivers Rhine and Têt
Publisher: Inter-Research Science Center
Date: 28-04-2009
DOI: 10.3354/AME01294
Rapid sulfurisation of highly branched isoprenoid (HBI) alkenes in sulfidic Holocene sediments from Ellis Fjord, Antarctica
Publisher: Elsevier BV
Date: 2007
The formation of peak rings in large impact craters
Publisher: American Association for the Advancement of Science (AAAS)
Date: 18-11-2016
Abstract: The Chicxulub impact crater, known for its link to the demise of the dinosaurs, also provides an opportunity to study rocks from a large impact structure. Large impact craters have “peak rings” that define a complex crater morphology. Morgan et al. looked at rocks from a drilling expedition through the peak rings of the Chicxulub impact crater (see the Perspective by Barton). The drill cores have features consistent with a model that postulates that a single over-heightened central peak collapsed into the multiple-peak-ring structure. The validity of this model has implications for far-ranging subjects, from how giant impacts alter the climate on Earth to the morphology of crater-dominated planetary surfaces. Science , this issue p. 878 see also p. 836
Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea.
Publisher: Wiley
Date: 06-03-2019
DOI: 10.1111/GBI.12338
Abstract: Subsurface microbial communities are generally thought to be structured through in situ environmental conditions such as the availability of electron acceptors and donors and porosity, but recent studies suggest that the vertical distribution of a subset of subseafloor microbial taxa, which were present at the time of deposition, were selected by the paleodepositional environment. However, additional highly resolved temporal records of subsurface microbiomes and paired paleoenvironmental reconstructions are needed to justify this claim. Here, we performed a highly resolved shotgun metagenomics survey to study the taxonomic and functional ersity of the subsurface microbiome in Holocene sediments underlying the permanently stratified and anoxic Black Sea. Obligate aerobic bacteria made the largest contribution to the observed shifts in microbial communities associated with known Holocene climate stages and transitions. This suggests that the aerobic fraction of the subseafloor microbiome was seeded from the water column and did not undergo post-depositional selection. In contrast, obligate and facultative anaerobic bacteria showed the most significant response to the establishment of modern-day environmental conditions 5.2 ka ago that led to a major shift in planktonic communities and in the type of sequestered organic matter available for microbial degradation. No significant shift in the subseafloor microbiome was observed as a result of environmental changes that occurred shortly after the marine reconnection, 9 ka ago. This supports the general view that the marine reconnection was a gradual process. We conclude that a high-resolution analysis of downcore changes in the subseafloor microbiome can provide detailed insights into paleoenvironmental conditions and biogeochemical processes that occurred at the time of deposition.
Metagenomics of pigmented and cholesterol gallstones: the putative role of bacteria
Publisher: Springer Science and Business Media LLC
Date: 25-07-2018
DOI: 10.1038/S41598-018-29571-8
Abstract: There is growing evidence for bacteria playing a role in the pathogenesis and formation of pigmented gallstones from humans. These studies mainly involved cultivation of gallstone-associated bacteria and 16S rRNA profiling, providing an indirect link between processes involved in gallstone formation by the bacteria in-situ . Here, we provide functional metagenomic evidence of a range of genes involved in bile stress response, biofilm formation, and anaerobic energy metabolism by Gram-negative Klebsiella in pigmented gallstones from a 76-year-old male patient. Klebsiella was also present in one cholesterol-type stone in a 30-year-old female patient who had additional cholesterol gallstones characterised by Gram-positive bacteria. Pigmented stones further revealed a predominance of genes involved in carbohydrate metabolism, whilst cholesterol stones indicated a profile dominanted by protein metabolism possibly reflecting known chemical differences between Gram-negative and Gram-positive biofilm matrices. Archaeal genes were not detected. Complementary carbon and hydrogen isotopic analyses of cholesterol within the patients’ stones revealed homogeneity, suggesting a common diet or cholesterol biosynthesis pathway that has little influence on microbial composition. This pilot study provides a framework to study microbial processes that play a potential role in gallstone formation across markedly different types of stones and patient backgrounds.
Microbially-mediated fossil-bearing carbonate concretions and their significance for palaeoenvironmental reconstructions: A multi-proxy organic and inorganic geochemical appraisal
Publisher: Elsevier BV
Date: 05-2016
Preservation potential of ancient plankton DNA in Pleistocene marine sediments
Publisher: Wiley
Date: 23-08-2011
DOI: 10.1111/J.1472-4669.2011.00290.X
Abstract: Recent studies have shown that ancient plankton DNA can be recovered from Holocene lacustrine and marine sediments, including from species that do not leave diagnostic microscopic fossils in the sediment record. Therefore, the analysis of this so-called fossil plankton DNA is a promising approach for refining paleoecological and paleoenvironmental information. However, further studies are needed to reveal whether DNA of past plankton is preserved beyond the Holocene. Here, we identified past eukaryotic plankton members based on 18S rRNA gene profiling in eastern Mediterranean Holocene and Pleistocene sapropels S1 (~9 ka), S3 (~80 ka), S4 (~105 ka), and S5 (~125 ka). The majority of preserved ~400- to 500-bp-long 18S rDNA fragments of microalgae that were studied in detail (i.e. from haptophyte algae and dinoflagellates) were found in the youngest sapropel S1, whereas their specific lipid biomarkers (long-chain alkenones and dinosterol) were also abundant in sediments deposited between 80 and 124 ka BP. The late-Pleistocene sediments mainly contained eukaryotic DNA of marine fungi and from terrestrial plants, which could have been introduced via the river Nile at the time of deposition and preserved in pollen grains. A parallel analysis of Branched and Isoprenoid Tetraethers (i.e. BIT index) showed that most of the organic matter in the eastern Mediterranean sediment record was of marine (e.g. pelagic) origin. Therefore, the predominance of terrestrial plant DNA over plankton DNA in older sapropels suggests a preferential degradation of marine plankton DNA.
Biomarker and 16S rDNA evidence for anaerobic oxidation of methane and related carbonate precipitation in deep-sea mud volcanoes of the Sorokin Trough, Black Sea
Publisher: Elsevier BV
Date: 05-2005
Neoglacial climate anomalies and the Harappan metamorphosis
Publisher: Copernicus GmbH
Date: 13-11-2018
Abstract: Abstract. Climate exerted constraints on the growth and decline of past human societies but our knowledge of temporal and spatial climatic patterns is often too restricted to address causal connections. At a global scale, the inter-hemispheric thermal balance provides an emergent framework for understanding regional Holocene climate variability. As the thermal balance adjusted to gradual changes in the seasonality of insolation, the Intertropical Convergence Zone migrated southward accompanied by a weakening of the Indian summer monsoon. Superimposed on this trend, anomalies such as the Little Ice Age point to asymmetric changes in the extratropics of either hemisphere. Here we present a reconstruction of the Indian winter monsoon in the Arabian Sea for the last 6000 years based on paleobiological records in sediments from the continental margin of Pakistan at two levels of ecological complexity: sedimentary ancient DNA reflecting water column environmental states and planktonic foraminifers sensitive to winter conditions. We show that strong winter monsoons between ca. 4500 and 3000 years ago occurred during a period characterized by a series of weak interhemispheric temperature contrast intervals, which we identify as the early neoglacial anomalies (ENA). The strong winter monsoons during ENA were accompanied by changes in wind and precipitation patterns that are particularly evident across the eastern Northern Hemisphere and tropics. This coordinated climate reorganization may have helped trigger the metamorphosis of the urban Harappan civilization into a rural society through a push–pull migration from summer flood-deficient river valleys to the Himalayan piedmont plains with augmented winter rains. The decline in the winter monsoon between 3300 and 3000 years ago at the end of ENA could have played a role in the demise of the rural late Harappans during that time as the first Iron Age culture established itself on the Ghaggar-Hakra interfluve. Finally, we speculate that time-transgressive land cover changes due to aridification of the tropics may have led to a generalized instability of the global climate during ENA at the transition from the warmer Holocene thermal maximum to the cooler Neoglacial.
Peering inside the peak ring of the Chicxulub Impact Crater—its nature and formation mechanism
Publisher: Wiley
Date: 03-2019
DOI: 10.1111/GTO.12261
Microbial diversity and methanogenic activity of antrim shale formation waters from recently fractured wells
Publisher: Frontiers Media SA
Date: 2013
Erratum to: Rock fluidization during peak-ring formation of large impact structures (Nature, (2018), 562, 7728, (511-518), 10.1038/s41586-018-0607-z)
Publisher: Springer Science and Business Media LLC
Date: 13-11-2018
DOI: 10.1038/S41586-018-0748-0
Abstract: In this Article, the middle initial of author Kosei E. Yamaguchi (of the IODP-ICDP Expedition 364 Science Party) was missing and his affiliation is to Toho University (not Tohu University). These errors have been corrected online.
217 000-year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment
Publisher: Wiley
Date: 14-09-2007
DOI: 10.1111/J.1462-2920.2006.01134.X
Abstract: Deep-sea sediments of the eastern Mediterranean harbour a series of dark, organic carbon-rich layers, so-called sapropels. Within these layers, the carotenoid isorenieratene was detected. Since it is specific for the obligately anaerobic phototrophic green sulfur bacteria, the presence of isorenieratene may suggest that extended water column anoxia occurred in the ancient Mediterranean Sea during periods of sapropel formation. Only three carotenoids (isorenieratene, beta-isorenieratene and chlorobactene) are typical for green sulfur bacteria and thus do not permit to differentiate between the approximately 80 known phylotypes. In order to reconstruct the paleoecological conditions in more detail, we searched for fossil 16S rRNA gene sequences of green sulfur bacteria employing ancient DNA methodology. 540 bp-long fossil sequences could indeed be lified from up to 217 000-year-old sapropels. In addition, such sequences were also recovered from carbon-lean intermediate sediment layers deposited during times of an entirely oxic water column. Unexpectedly, however, all the recovered 16S rRNA gene sequences grouped with freshwater or brackish, rather than truly marine, types of green sulfur bacteria. It is therefore feasible that the molecular remains of green sulfur bacteria originated from populations which thrived in adjacent freshwater or estuarine coastal environments rather than from an indigenous pelagic population.
Chicxulub and the Exploration of Large Peak-Ring Impact Craters through Scientific Drilling
Publisher: Geological Society of America
Date: 07-09-2017
DOI: 10.1130/GSATG352A.1
Unique Prokaryotic Consortia in Geochemically Distinct Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools
Publisher: Public Library of Science (PLoS)
Date: 20-08-2012
Specific and selective peptide-membrane interactions revealed using quartz crystal microbalance
Publisher: Elsevier BV
Date: 12-2007
Vertical distribution of metabolically active eukaryotes in the water column and sediments of the Black Sea
Publisher: Oxford University Press (OUP)
Date: 12-2009
DOI: 10.1111/J.1574-6941.2009.00756.X
Abstract: Recent DNA-based phylogenetic studies have reported high eukaryotal ersities in a wide range of settings including s les obtained from anoxic environments. However, parallel RNA-based surveys are required in order to verify whether the species detected are in fact metabolically active in such extreme environments. The Black Sea is the World's largest anoxic basin but remains unders led with respect to molecular eukaryotic ersity studies. Here, we report the distribution of active eukaryotes (18S rRNA-based survey) along a vertical nutrient and redox gradient in the water column and surface sediments of the Black Sea. A wide variety of eukaryotes were active in suboxic deep waters. Notably, certain species were active but escaped detection during a parallel 18S rDNA survey. The 18S rDNA survey from surface sediments yielded taxa of pelagic origin but none of these were identified from the water column at the time of s ling. Our data also indicate that gene transcripts do not always provide unequivocal proof that active microorganisms are indigenous to a specific position in an environmental gradient, because certain zoo- and phytoplankton species were still viable with detectable 18S rRNA in up to 300-year-old sulfidic sediments that underlie approximately 830 m of sulfidic waters.
Extraordinary rocks from the peak ring of the Chicxulub impact crater: P-wave velocity, density, and porosity measurements from IODP/ICDP Expedition 364
Publisher: Elsevier BV
Date: 08-2018
Correction for Wuchter et al., Archaeal nitrification in the ocean
Publisher: Proceedings of the National Academy of Sciences
Date: 27-03-2007
Sources for sedimentary bacteriohopanepolyols as revealed by 16S rDNA stratigraphy
Publisher: Wiley
Date: 08-04-2008
DOI: 10.1111/J.1462-2920.2008.01601.X
Abstract: Bacteriohopanoids are widespread lipid biomarkers in the sedimentary record. Many aerobic and anaerobic bacteria are potential sources of these lipids which sometimes complicates the use of these biomarkers as proxies for ecological and environmental changes. Therefore, we applied preserved 16S ribosomal RNA genes to identify likely Holocene biological sources of bacteriohopanepolyols (BHPs) in the sulfidic sediments of the permanently stratified postglacial Ace Lake, Antarctica. A suite of intact BHPs were identified, which revealed a variety of structural forms whose composition differed through the sediment core reflecting changes in bacterial populations induced by large changes in lake salinity. Stable isotopic compositions of the hopanols formed from periodic acid-cleaved BHPs, showed that some were substantially depleted in (13)C, indicative of their methanotrophic origin. Using sensitive molecular tools, we found that Type I and II methanotrophic bacteria (respectively Methylomonas and Methylocystis) were unique to the oldest lacustrine sediments (> 9400 years BP), but quantification of fossil DNA revealed that the Type I methanotrophs, including methanotrophs related to methanotrophic gill symbionts of deep-sea cold-seep mussels, were the main precursors of the 35-amino BHPs (i.e. aminopentol, -tetrol and -triols). After isolation of the lake approximately 3000 years ago, one Type I methanotroph of the 'methanotrophic gill symbionts cluster' remained the most obvious source of aminotetrol and -triol. We, furthermore, identified a Synechococcus phylotype related to pelagic freshwater strains in the oldest lacustrine sediments as a putative source of 2-methylbacteriohopanetetrol (2-Me BHT). This combined application of advanced geochemical and paleogenomical tools further refined our knowledge about Holocene biogeochemical processes in Ace Lake.
7000 years of Emiliania huxleyi viruses in the Black Sea
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-07-2011
Abstract: Sequencing ancient DNA from a marine sediment traces population shifts of phytoplankton and their viruses over 7000 years.
Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: A basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids
Publisher: Wiley
Date: 22-01-2007
DOI: 10.1111/J.1462-2920.2006.01227.X
Abstract: Within the upper 400 m at western, central and eastern stations in the world's largest stratified basin, the Black Sea, we studied the qualitative and quantitative distribution of putative nitrifying Archaea based on their genetic markers (16S rDNA, amoA encoding for the alpha-subunit of archaeal ammonia monooxygenase), and crenarchaeol, the specific glycerol diphytanyl glycerol tetraether of pelagic Crenarchaeota within the Group I.1a. Marine Crenarchaeota were the most abundant Archaea (up to 98% of the total archaeal 16S rDNA copies) in the suboxic layers with oxygen levels as low as 1 microM including layers where previously anammox bacteria were described. Different marine crenarchaeotal phylotypes (both 16S rDNA and amoA) were found at the upper part of the suboxic zone as compared with the base of the suboxic zone and the upper 15-30 m of the anoxic waters with prevailing sulfide concentrations of up to 30 microM. Crenarchaeol concentrations were higher in the sulfidic chemocline as compared with the suboxic zone. These results indicate an abundance of putative nitrifying Archaea at very low oxygen levels within the Black Sea and might form an important source of nitrite for the anammox reaction.
Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments
Publisher: Springer Science and Business Media LLC
Date: 26-07-1999
Abstract: Specific lification of 16S rRNA gene fragments in combination with denaturing gradient gel electrophoresis (DGGE) was used to generate fingerprints of Chromatiaceae, green sulfur bacteria, Desulfovibrionaceae, and beta-Proteobacteria. Sequencing of the gene fragments confirmed that each primer pair was highly specific for the respective phylogenetic group. Applying the new primer sets, the bacterial ersity in the chemoclines of a eutrophic freshwater lake, a saline meromictic lake, and a laminated marine sediment was investigated. Compared to a conventional bacterial primer pair, a higher number of discrete DGGE bands was generated using our specific primer pairs. With one exception, all 15 bands tested yielded reliable 16S rRNA gene sequences. The highest ersity was found within the chemocline microbial community of the eutrophic freshwater lake. Sequence comparison revealed that the six sequences of Chromatiaceae and green sulfur bacteria detected in this habitat all represent distinct and previously unknown phylotypes. The lowest ersity of phylotypes was detected in the chemocline of the meromictic saline lake, which yielded only one sequence each of the Chromatiaceae, beta-2-Proteobacteria, and Desulfovibrionaceae, and no sequences of green sulfur bacteria. The newly developed primer sets are useful for the detection of previously unknown phylotypes, for the comparison of the microbial ersity between different natural habitats, and especially for the rapid monitoring of enrichments of unknown bacterial species.
An unusual 17α,21β(H)-bacteriohopanetetrol in Holocene sediments from Ace Lake (Antarctica)
Publisher: Elsevier BV
Date: 08-2008
Characterization of Microbial Communities Found in the Human Vagina by Analysis of Terminal Restriction Fragment Length Polymorphisms of 16S rRNA Genes
Publisher: American Society for Microbiology
Date: 12-2005
DOI: 10.1128/AEM.71.12.8729-8737.2005
Abstract: To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the human vagina were used to construct model communities that were subsequently used to develop efficient means for the isolation of genomic DNA and an optimal strategy for T-RFLP analyses. The various genera in the model community could best be resolved by digesting licons made using bacterial primers 8f and 926r with HaeIII fewer strains could be resolved using other primer-enzyme combinations, and no combination successfully distinguished certain species of the same genus. To demonstrate the utility of the approach, s les from five women that had been collected over a 2-month period were analyzed. Differences and similarities among the vaginal microbial communities of the women were readily apparent. The T-RFLP data suggest that the communities of three women were dominated by a single phylotype, most likely species of Lactobacillus . In contrast, the communities of two other women included numerically abundant populations that differed from Lactobacillus strains whose 16S rRNA genes had been previously determined. The T-RFLP profiles of s les from all the women were largely invariant over time, indicating that the kinds and abundances of the numerically dominant populations were relatively stable throughout two menstrual cycles. These findings show that T-RFLP of 16S rRNA genes can be used to compare vaginal microbial communities and gain information about the numerically dominant populations that are present.
Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology
Publisher: Wiley
Date: 20-05-2019
Abstract: Coccolithoviruses (EhVs) are large, double-stranded DNA-containing viruses that infect the single-celled, marine coccolithophore Emiliania huxleyi. Given the cosmopolitan nature and global importance of E. huxleyi as a bloom-forming, calcifying, photoautotroph, E. huxleyi-EhV interactions play a key role in oceanic carbon biogeochemistry. Virally-encoded glycosphingolipids (vGSLs) are virulence factors that are produced by the activity of virus-encoded serine palmitoyltransferase (SPT). Here, we characterize the dynamics, ersity and catalytic production of vGSLs in an array of EhV strains in relation to their SPT sequence composition and explore the hypothesis that they are a determinant of infectivity and host demise. vGSL production and ersity was positively correlated with increased virulence, virus replication rate and lytic infection dynamics in laboratory experiments, but they do not explain the success of less-virulent EhVs in natural EhV communities. The majority of EhV-derived SPT licon sequences associated with infected cells in the North Atlantic derived from slower infecting, less virulent EhVs. Our lab-, field- and mathematical model-based data and simulations support ecological scenarios whereby slow-infecting, less-virulent EhVs successfully compete in North Atlantic populations of E. huxleyi, through either the preferential removal of fast-infecting, virulent EhVs during active infection or by having access to a broader host range.
Ocean Drilling Perspectives on Meteorite Impacts
Publisher: The Oceanography Society
Date: 03-2019
Exploring preserved fossil dinoflagellate and haptophyte DNA signatures to infer ecological and environmental changes during deposition of sapropel S1 in the eastern Mediterranean
Publisher: American Geophysical Union (AGU)
Date: 16-04-2011
DOI: 10.1029/2010PA001948
Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables
Publisher: Oxford University Press (OUP)
Date: 12-2007
DOI: 10.1111/J.1574-6941.2007.00397.X
Abstract: The spatial and temporal distribution of pelagic Archaea was studied in the southern North Sea by rRNA hybridization, sequencing and quantification of 16S rRNA gene and membrane lipid analyses and related to physical, chemical and biological parameters to determine the factors influencing archaeal biogeography. A clear temporal variability was observed, with marine Crenarchaeota (Group I.1a) being relatively more abundant in winter and Euryarchaeota dominating the archaeal assemblage in spring and summer. Spatial differences in the lateral distribution of Crenarchaeota were also evident. In fact, their abundance was positively correlated with the copy number of the gene encoding the alpha subunit of crenarchaeotal ammonia monooxygenase (amoA) and with concentrations of ammonia, nitrate, nitrite and phosphorus. This suggests that most Crenarchaeota in the North Sea are nitrifiers and that their distribution is determined by nutrient concentrations. However, Crenarchaeota were not abundant when larger phytoplankton (>3 microm) dominated the algal population. It is hypothesized that together with nutrient concentration, phytoplankton biomass and community structure can predict crenarchaeotal abundance in the southern North Sea. Euryarchaeotal abundance was positively correlated with chlorophyll a concentrations, but not with phytoplankton community structure. Whether this is related to the potential of Euryarchaeota to perform aerobic anoxygenic phototrophy remains to be shown, but the conspicuous seasonal distribution pattern of Crenarchaeota and Euryarchaeota suggests that they occupy a different ecological niche.
Ancient DNA from marine sediments
Publisher: Elsevier BV
Date: 09-2019
Alkenone distribution in Lake Van sediment over the last 270 ka: influence of temperature and haptophyte species composition
Publisher: Elsevier BV
Date: 11-2014
Microbial Communities in the Chemocline of a Hypersaline Deep-Sea Basin (Urania Basin, Mediterranean Sea)
Publisher: American Society for Microbiology
Date: 12-2001
DOI: 10.1128/AEM.67.12.5392-5402.2001
Abstract: The Urania basin is a hypersaline sulfidic brine lake at the bottom of the eastern Mediterranean Sea. Since this basin is located at a depth of ∼3,500 m below the sea surface, it receives only a small amount of phytoplankton organic carbon. In the present study, the bacterial assemblages at the interface between the hypersaline brine and the overlaying seawater were investigated. The sulfide concentration increased from 0 to 10 mM within a vertical interval of 5 m across the interface. Within this chemocline, the total bacterial cell counts and the exoenzyme activities were elevated. Employing 11 cultivation methods, we isolated a total of 70 bacterial strains. The 16S ribosomal DNA sequences of 32 of the strains were identical to environmental sequences detected in the chemocline by culture-independent molecular methods. These strains were identified as flavobacteria, Alteromonas macleodii , and Halomonas aquamarina . All 70 strains could grow chemoorganoheterotrophically under oxic conditions. Sixty-six strains grew on peptone, casein hydrolysate, and yeast extract, whereas only 15 strains did not utilize polymeric carbohydrates. Twenty-one of the isolates could grow both chemoorganotrophically and chemolithotrophically. While the most probable numbers in most cases ranged between 0.006 and 4.3% of the total cell counts, an unsually high value of 54% was determined above the chemocline with media containing amino acids as the carbon and energy source. Our results indicate that culturable bacteria thriving at the oxic-anoxic interface of the Urania basin differ considerably from the chemolithoautotrophic bacteria typical of other chemocline habitats.
Probing the hydrothermal system of the Chicxulub impact crater
Publisher: American Association for the Advancement of Science (AAAS)
Date: 29-05-2020
Abstract: The Chicxulub impact event generated a long-duration hydrothermal system suitable for microbial life.
Identification of organic matter sources in sulfidic late Holocene Antarctic fjord sediments from fossil rDNA sequence analysis
Publisher: American Geophysical Union (AGU)
Date: 09-05-2007
DOI: 10.1029/2006PA001309
Fossil DNA in Cretaceous Black Shales: Myth or Reality?
Publisher: Mary Ann Liebert Inc
Date: 04-2006
Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records
Publisher: Elsevier BV
Date: 11-2011
Early Anthropogenic Transformation of the Danube-Black Sea System
Publisher: Springer Science and Business Media LLC
Date: 30-08-2012
DOI: 10.1038/SREP00582
Identification of photosynthetic plankton communities using sedimentary ancient DNA and their response to late-holocene climate change on the Tibetan Plateau
Publisher: Springer Science and Business Media LLC
Date: 17-10-2014
DOI: 10.1038/SREP06648
Nitric oxide production and antioxidant function during viral infection of the coccolithophore Emiliania huxleyi
Publisher: Springer Science and Business Media LLC
Date: 03-01-2019
Aerobic and anaerobic methanotrophs in the Black Sea water column
Publisher: Wiley
Date: 04-07-2006
DOI: 10.1111/J.1462-2920.2006.01079.X
Abstract: Inputs of CH(4) from sediments, including methane seeps on the continental margin and methane-rich mud volcanoes on the abyssal plain, make the Black Sea the world's largest surface water reservoir of dissolved methane and drive a high rate of aerobic and anaerobic oxidation of methane in the water column. Here we present the first combined organic geochemical and molecular ecology data on a water column profile of the western Black Sea. We show that aerobic methanotrophs type I are responsible for methane oxidation in the oxic water column and ANME-1- and ANME-2-related organisms for anaerobic methane oxidation. The occurrence of methanotrophs type I cells in the anoxic zone suggests that inactive cells settle to deeper waters. Molecular and biomarker results suggest that a clear distinction between the occurrence of ANME-1- and ANME-2-related lineages exists, i.e. ANME-1-related organisms are responsible for anaerobic methane oxidation below 600 m water depth, whereas ANME-2-related organisms are responsible for this process in the anoxic water column above approximately 600 m water depth.
The first day of the Cenozoic
Publisher: Proceedings of the National Academy of Sciences
Date: 09-09-2019
Abstract: Highly expanded Cretaceous–Paleogene (K-Pg) boundary section from the Chicxulub peak ring, recovered by International Ocean Discovery Program (IODP)–International Continental Scientific Drilling Program (ICDP) Expedition 364, provides an unprecedented window into the immediate aftermath of the impact. Site M0077 includes ∼130 m of impact melt rock and suevite deposited the first day of the Cenozoic covered by m of micrite-rich carbonate deposited over subsequent weeks to years. We present an interpreted series of events based on analyses of these drill cores. Within minutes of the impact, centrally uplifted basement rock collapsed outward to form a peak ring capped in melt rock. Within tens of minutes, the peak ring was covered in ∼40 m of brecciated impact melt rock and coarse-grained suevite, including clasts possibly generated by melt–water interactions during ocean resurge. Within an hour, resurge crested the peak ring, depositing a 10-m-thick layer of suevite with increased particle roundness and sorting. Within hours, the full resurge deposit formed through settling and seiches, resulting in an 80-m-thick fining-upward, sorted suevite in the flooded crater. Within a day, the reflected rim-wave tsunami reached the crater, depositing a cross-bedded sand-to-fine gravel layer enriched in polycyclic aromatic hydrocarbons overlain by charcoal fragments. Generation of a deep crater open to the ocean allowed rapid flooding and sediment accumulation rates among the highest known in the geologic record. The high-resolution section provides insight into the impact environmental effects, including charcoal as evidence for impact-induced wildfires and a paucity of sulfur-rich evaporites from the target supporting rapid global cooling and darkness as extinction mechanisms.
Palaeobiology of red and white blood cell-like structures, collagen and cholesterol in an ichthyosaur bone
Publisher: Springer Science and Business Media LLC
Date: 23-10-2017
DOI: 10.1038/S41598-017-13873-4
Abstract: Carbonate concretions are known to contain well-preserved fossils and soft tissues. Recently, biomolecules ( e . g . cholesterol) and molecular fossils (biomarkers) were also discovered in a 380 million-year-old concretion, revealing their importance in exceptional preservation of biosignatures. Here, we used a range of microanalytical techniques, biomarkers and compound specific isotope analyses to report the presence of red and white blood cell-like structures as well as platelet-like structures, collagen and cholesterol in an ichthyosaur bone encapsulated in a carbonate concretion from the Early Jurassic (~182.7 Ma). The red blood cell-like structures are four to five times smaller than those identified in modern organisms. Transmission electron microscopy (TEM) analysis revealed that the red blood cell-like structures are organic in composition. We propose that the small size of the blood cell-like structures results from an evolutionary adaptation to the prolonged low oxygen atmospheric levels prevailing during the 70 Ma when ichthyosaurs thrived. The δ 13 C of the ichthyosaur bone cholesterol indicates that it largely derives from a higher level in the food chain and is consistent with a fish and cephalopod diet. The combined findings above demonstrate that carbonate concretions create isolated environments that promote exceptional preservation of fragile tissues and biomolecules.
Coccolithovirus facilitation of carbon export in the North Atlantic
Publisher: Springer Science and Business Media LLC
Date: 12-03-2018
DOI: 10.1038/S41564-018-0128-4
Abstract: Marine phytoplankton account for approximately half of global primary productivity
Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential.
Publisher: Wiley
Date: 07-02-2022
Abstract: In-depth knowledge about spatial and temporal variation in microbial ersity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future bio ersity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo-genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial ersity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for ex le, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human-induced global changes.
Rapid recovery of life at ground zero of the end-Cretaceous mass extinction
Publisher: Springer Science and Business Media LLC
Date: 30-05-2018
The transcriptional response of microbial communities in thawing Alaskan permafrost soils
Publisher: Frontiers Media SA
Date: 16-03-2015
Late-Holocene succession of dinoflagellates in an Antarctic fjord using a multi-proxy approach: Paleoenvironmental genomics, lipid biomarkers and palynomorphs
Publisher: Wiley
Date: 06-2009
DOI: 10.1111/J.1472-4669.2009.00202.X
Abstract: Recent work has shown that paleoenvironmental genomics, i.e. the application of genomic tools to analyze preserved DNA in sedimentary records, is a promising approach to reconstruct the ersity of past planktonic communities. This provides information about past ecological and environmental changes. A major advantage of this approach is that in idual species, including those that did not leave other characteristic markers, can be identified. In this study, we determined which dinoflagellate marker (i.e. 18S rDNA, dinosterol or dinocysts) provided the most detailed information about the late-Holocene succession of dinoflagellates in an Antarctic Fjord (Ellis Fjord, Vestfold Hills). The preserved rDNA revealed two intervals in the 2750-year-old sediment record. The dinoflagellate ersity was the highest until approximately 1850 cal yr bp and included phylotypes related to known dinosterol producers. A lower concentration of dinosterol in sediments <1850 cal yr bp coincided with a community shift towards a predominance of the autotrophic sea-ice dinoflagellate Polarella glacialis, which is not a source of dinosterol. Remarkably, cultures of P. glacialis are known to produce other diagnostic sterols, but these were not recovered here. In addition, conspicuous resting cysts of P. glacialis were not preserved in the analyzed sediments. Overall, dinocysts were rare and the paleoenvironmental genomics approach revealed the highest ersity of dinoflagellates in Ellis Fjord, and was the only approach that recorded a shift in dinoflagellate composition at approximately 1850 cal yr bp indicative of a colder climate with more extensive ice cover - this timing coincides with a period of changing climate reported for this region.
Holocene virus/host molecular dynamics in the Black Sea
Publisher: Elsevier BV
Date: 11-2012
New shock microstructures in titanite (CaTiSiO5) from the peak ring of the Chicxulub impact structure, Mexico
Publisher: Springer Science and Business Media LLC
Date: 05-2019
First high-resolution marinopalynological stratigraphy of Late Quaternary sediments from the central part of the Bulgarian Black Sea area
Publisher: Elsevier BV
Date: 04-2013
Decoupling Physical from Biological Processes to Assess the Impact of Viruses on a Mesoscale Algal Bloom
Publisher: Elsevier BV
Date: 09-2014
DOI: 10.1016/J.CUB.2014.07.046
Abstract: Phytoplankton blooms are ephemeral events of exceptionally high primary productivity that regulate the flux of carbon across marine food webs [1-3]. Quantification of bloom turnover [4] is limited by a fundamental difficulty to decouple between physical and biological processes as observed by ocean color satellite data. This limitation hinders the quantification of bloom demise and its regulation by biological processes [5, 6], which has important consequences on the efficiency of the biological pump of carbon to the deep ocean [7-9]. Here, we address this challenge and quantify algal blooms' turnover using a combination of satellite and in situ data, which allows identification of a relatively stable oceanic patch that is subject to little mixing with its surroundings. Using a newly developed multisatellite Lagrangian diagnostic, we decouple the contributions of physical and biological processes, allowing quantification of a complete life cycle of a mesoscale (∼10-100 km) bloom of coccolithophores in the North Atlantic, from exponential growth to its rapid demise. We estimate the amount of organic carbon produced during the bloom to be in the order of 24,000 tons, of which two-thirds were turned over within 1 week. Complimentary in situ measurements of the same patch area revealed high levels of specific viruses infecting coccolithophore cells, therefore pointing at the importance of viral infection as a possible mortality agent. Application of the newly developed satellite-based approaches opens the way for large-scale quantification of the impact of erse environmental stresses on the fate of phytoplankton blooms and derived carbon in the ocean.
Contributions to the European Pollen Database. 22. Vegetation development in the central part of the Bulgarian Black Sea coast during the last 13 000 years
Publisher: Informa UK Limited
Date: 09-05-2014
Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene
Publisher: Proceedings of the National Academy of Sciences
Date: 06-05-2013
Abstract: The complex interplay of climate shifts over Eurasia and global sea level changes modulates freshwater and saltwater inputs to the Black Sea. The dynamics of the hydrologic changes from the Late Glacial into the Holocene remain a matter of debate, and information on how these changes affected the ecology of the Black Sea is sparse. Here we used Roche 454 next-generation pyrosequencing of sedimentary 18S rRNA genes to reconstruct the plankton community structure in the Black Sea over the last ca. 11,400 y. We found that 150 of 2,710 species showed a statistically significant response to four environmental stages. Freshwater chlorophytes were the best indicator species for lacustrine conditions ( .0 ka B.P.), although the copresence of previously unidentified marine taxa indicated that the Black Sea might have been influenced to some extent by the Marmara Sea since at least 9.6 ka calendar (cal) B.P. Dinoflagellates, cercozoa, eustigmatophytes, and haptophytes responded most dramatically to the gradual increase in salinity after the latest marine reconnection and during the warm and moist mid-Holocene climatic optimum. According to paired analysis of deuterium/hydrogen (D/H) isotope ratios in fossil alkenones, salinity increased rapidly with the onset of the dry Subboreal after ∼5.2 ka B.P., leading to an increase in marine fungi and the first occurrence of marine copepods. A gradual succession of dinoflagellates, diatoms, and chrysophytes occurred during the refreshening after ∼2.5 ka cal B.P. with the onset of the cool and wet Subatlantic climate and recent anthropogenic perturbations.
Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses
Publisher: Frontiers Media SA
Date: 16-11-2020
Archaeal nitrification in the ocean
Publisher: Proceedings of the National Academy of Sciences
Date: 15-08-2006
Abstract: Marine Crenarchaeota are the most abundant single group of prokaryotes in the ocean, but their physiology and role in marine biogeochemical cycles are unknown. Recently, a member of this clade was isolated from a sea aquarium and shown to be capable of nitrification, tentatively suggesting that Crenarchaeota may play a role in the oceanic nitrogen cycle. We enriched a crenarchaeote from North Sea water and showed that its abundance, and not that of bacteria, correlates with ammonium oxidation to nitrite. A time series study in the North Sea revealed that the abundance of the gene encoding for the archaeal ammonia monooxygenase alfa subunit ( amoA ) is correlated with a decline in ammonium concentrations and with the abundance of Crenarchaeota. Remarkably, the archaeal amoA abundance was 1–2 orders of magnitude higher than those of bacterial nitrifiers, which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. Analysis of Atlantic waters of the upper 1,000 m, where most of the ammonium regeneration and oxidation takes place, showed that crenarchaeotal amoA copy numbers are also 1–3 orders of magnitude higher than those of bacterial amoA . Our data thus suggest a major role for Archaea in oceanic nitrification.
Light regulation of coccolithophore host–virus interactions
Publisher: Wiley
Date: 08-10-2019
DOI: 10.1111/NPH.15459
Abstract: Viruses that infect photoautotrophs have a fundamental relationship with light, given the need for host resources. We investigated the role of light on Coccolithovirus (EhV) infection of the globally distributed coccolithophore, Emiliania huxleyi. Light was required for EhV adsorption, and viral production was highest when host cultures were maintained in continuous light or at irradiance levels of 150-300 μmol m
Erratum: 217 000-Year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment (Environmental Microbiology (2007) 9, (238-249))
Publisher: Wiley
Date: 08-01-2007
Functional exoenzymes as indicators of metabolically active bacteria in 124,000-year-old sapropel layers of the eastern Mediterranean Sea
Publisher: American Society for Microbiology
Date: 06-2000
DOI: 10.1128/AEM.66.6.2589-2598.2000
Abstract: Hydrolytic exoenzymes as indicators of metabolically active bacteria were investigated in four consecutive sapropel layers collected from bathyal sediments of the eastern Mediterranean Sea. For comparison, the organic carbon-poor layers between the sapropels, sediment from the anoxic Urania basin, and sediments of intertidal mud flats of the German Wadden Sea were also analyzed. The sapropel layers contained up to 1.5 · 10 8 bacterial cells cm −3 , whereas cell numbers in the intermediate layers were lower by a factor of 10. In sapropels, the determination of exoenzyme activity with fluorescently labeled substrate analogues was impaired by the strong adsorption of up to 97% of the enzymatically liberated fluorophores (4-methylumbelliferone [MUF] and 7-amino-4-methylcoumarin [MCA]) to the sediment particles. Because all established methods for the extraction of adsorbed fluorophores proved to be inadequate for sapropel sediments, we introduce a correction method which is based on the measurement of equilibrium adsorption isotherms for both compounds. Using this new approach, high activities of aminopeptidase and alkaline phosphatase were detected even in a 124,000-year-old sapropel layer, whereas the activity of β-glucosidase was low in all layers. So far, it had been assumed that the organic matter which constitutes the sapropels is highly refractory. The high potential activities of bacterial exoenzymes indicate that bacteria in Mediterranean sapropels are metabolically active and utilize part of the subfossil kerogen. Since a high adsorption capacity was determined not only for the low-molecular-weight compounds MUF and MCA but also for DNA, the extraordinarily strong adsorption of structurally different substrates to the sapropel matrix appears to be the major reason for the long-term preservation of biodegradable carbon in this environment.
Bioavailability of soil organic matter and microbial community dynamics upon permafrost thaw
Publisher: Wiley
Date: 09-05-2011
DOI: 10.1111/J.1462-2920.2011.02489.X
Abstract: Amplified Arctic warming could thaw 25% of the permafrost area by 2100, exposing vast amounts of currently fixed organic carbon to microbially mediated decomposition and release of greenhouse gasses through soil organic matter (SOM) respiration. We performed time-series incubation experiments with Holocene permafrost soils at 4°C for up to 11 days to determine changes in exoenzyme activities (EEAs) (i.e. phosphatase, β-glucosidase, aminopeptidase) as a measure for the bioavailability of SOM in response to permafrost thaw. We also profiled SSU rRNA transcripts to follow the qualitative and quantitative changes in viable prokaryotes and eukaryotes during incubation. EEA, amount of rRNA transcripts and microbial community structures differed substantially between the various soil intervals in response to thaw: after 11 days of incubation, the active layer became slightly depleted in C and P and harboured bacterial phyla indicative of more oligotrophic conditions (Acidobacteria). A fast response in phosphatase and β-glucosidase upon thaw, and a predominance of active copiotrophic Bacteroidetes, showed that the upper permafrost plate serves as storage of easily degradable carbon derived from the overlying thawed active layer during summer. EEA profiles and microbial community dynamics furthermore suggest that the deeper and older permafrost intervals mainly contain recalcitrant SOM, and that extracellular soil-bound exoenzymes play a role in the initial cleavage of biopolymers, which could kick-start microbial growth upon thaw. Basidiomycetous fungi and Candidate Sub ision OP5 bacteria were the first to respond in freshly thawed deeper permafrost intervals, and might play an important role in the decomposition of recalcitrant SOM to release more labile substrates to support the major bacterial phyla (β-Proteobacteria, Actinobacteria, Firmicutes), which predominated thereafter.
Evolution of the methane cycle in Ace Lake (Antarctica) during the Holocene: Response of methanogens and methanotrophs to environmental change
Publisher: Elsevier BV
Date: 10-2004
Related Organisations
Woods Hole Oceanographic Institution
Location: United States of America
Related Funding Activities
Discovery Projects - Grant ID: DP220100051
Start Date: 12-2022
End Date: 12-2025
Amount: $484,598.00
Funder: Australian Research Council
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Start Date: 01-2016
End Date: 04-2021
Amount: $455,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP160102587
Start Date: 01-2016
End Date: 12-2019
Amount: $412,570.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP180100982
Start Date: 07-2018
End Date: 07-2021
Amount: $348,145.00
Funder: Australian Research Council
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