Presence of an unusual 17α,21β(H)-bacteriohopanetetrol in Holocene sediments from Ace Lake (Antarctica)

Author Posting. © Elsevier B.V., 2008. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Organic Geochemistry 39 (2008): 1029-1032, doi:10.1016/j.orggeochem.2008.01.008.Whilst investigating the intact biohopanoid (bacteriohopanepolyol, BHP) distribution in Holocene sediments from Ace Lake (Antarctica), we have identified the presence of ab- bacteriohopanetetrol in sediments aged up to 9400 years BP. To our knowledge, this is the first time that an intact polyfunctionalised BHP with the “geological” 17α,21β(H) configuration has been identified in a sediment. Previously, this structure has only been observed in species of the nitrogen fixing bacterium Frankia. Its presence here in the sedimentary environment has implications for the interpretation of hopanoid ββ/αβ ratios in the geological record.This work was supported by grants from the Australian Antarctic Science Advisory Committee (1166 to J.V.) and the Netherlands Organization for Scientific Research (NWO; 851.20.006 to J.S.S.D. and NWO-VENI grant 016.051.014 to M.J.L.C.) We gratefully acknowledge the NERC for funding (HMT) and The Science Research Infrastructure Fund (SRIF) from HEFCE for funding the purchase of the Thermo Electron Finnigan LCQ ion trap mass spectrometer

Seqenv : linking sequences to environments through text mining

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 individual, 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 individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. 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 How to cite this article Sinclair et al. (2016), Seqenv: linking sequences to environments through text mining. PeerJ 4:e2690; DOI 10.7717/peerj.2690 and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography

Vertical distribution of metabolically active eukaryotes in the water column and sediments of the Black Sea

Recent DNA-based phylogenetic studies have reported high eukaryotal diversities in a wide range of settings including samples 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 undersampled with respect to molecular eukaryotic diversity 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 sampling. 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 ~830 m of sulfidic waters. © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved

Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential

International audienceDes connaissances approfondies sur la variation spatiale et temporelle de la diversité et de la fonction microbiennes sont nécessaires pour une meilleure compréhension des réponses écologiques et évolutives au changement global. En particulier, l'étude de l'ancien ADN microbien conservé dans les archives sédimentaires des lacs et des océans peut nous aider à évaluer les réponses des microbes aquatiques dans le passé et à faire des prédictions sur les changements futurs de la biodiversité dans ces écosystèmes. Les progrès récents des méthodes de génétique moléculaire appliquées à l'analyse de l'ADN historiquement déposé dans les sédiments ont non seulement permis l'identification taxonomique des communautés microbiennes aquatiques passées, mais également permis de retracer leur évolution et leur adaptation aux perturbations épisodiques et aux changements environnementaux progressifs. Néanmoins, certains défis demeurent pour que les scientifiques tirent pleinement parti du domaine en développement rapide de la paléogénétique, notamment la capacité limitée à détecter des taxons rares et à reconstruire des génomes complets pour des études évolutives. Ici, nous fournissons un bref examen de certaines des avancées récentes dans le domaine de la paléomicrobiologie environnementale et discutons des défis restants liés à l'application de méthodes de génétique moléculaire pour étudier la diversité microbienne, l'écologie et l'évolution dans les archives de sédiments. Nous prévoyons que, dans un avenir proche, la paléomicrobiologie environnementale apportera un nouvel éclairage sur les processus d'évolution du génome microbien et les réponses de l'écosystème microbien aux changements environnementaux du Quaternaire à un niveau de détail sans précédent. Ces informations peuvent, par exemple, contribuer aux reconstructions géologiques des cycles biogéochimiques et prédire les réponses des écosystèmes aux perturbations environnementales, y compris dans le contexte des changements globaux induits par l'homme

Alkenone distribution in Lake Van sediment over the last 270 ka: influence of temperature and haptophyte species composition

Fossil long-chain alkenones have been used for several decades to reconstruct past ocean surface water temperatures and gained recent interest as a paleotemperature proxy for continental lake settings. However, factors besides temperature can affect alkenone distributions in haptophyte algae, and alkenone compositions can differ between haptophyte species. Alkenone-biosynthesizing haptophyte algae are genetically much more diverse in lakes than in the marine realm, and species-level variations in alkenone compositions could have implications for alkenone paleothermometry. Here, we performed a paired analysis of alkenone distributions and haptophyte species compositions using ancient DNA in up to 270 ka-old sediments of Lake Van in Turkey to reveal a possible species-effect on fossil alkenone distributions and paleotemperature estimates. The same predominant haptophyte in Lake Van today prevailed also since the last ~100 ka. However, a calibration of alkenone paleotemperature especially in the oldest analyzed intervals is complicated due to a more complex haptophyte species composition predominated by a haptophyte (LVHap_6), which is phylogenetically different from sequences recovered from currently existing lakes including Lake Van and from haptophyte species existing in culture. Thepredominance of LVHap_6 coincided with the presence of alkenone MeC38:3 and relatively highMeC37:3/4 (2.4) and MeC38:4/5 ratios (3.0). Uk37 index values in the sediment core over the last 270 ka reflect relative changes in past temperature and are additionally linked to haptophyte species composition. A sustained period of high salinity, as indicated by pore-water salinity measurements, could potentially have triggered the succession of haptophytes as sources of alkenones in Lake Van

Decoupling Physical from Biological Processes to Assess the Impact of Viruses on a Mesoscale Algal Bloom

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 diverse environmental stresses on the fate of phytoplankton blooms and derived carbon in the ocean

Impact‐Induced Porosity and Microfracturing at the Chicxulub Impact Structure

International audienc

Peering inside the peak ring of the Chicxulub Impact Crater-its nature and formation mechanism

The IODP-ICDP Expedition 364 drilled into the Chicxulub crater, peering inside its well-preserved peak ring. The borehole penetrated a sequence of post-impact carbonates and a unit of suevites and clast-poor impact melt rock at the top of the peak ring. Beneath this sequence, basement rocks cut by pre-impact and impact dykes, with breccias and melt, were encountered at shallow depths. The basement rocks are fractured, shocked and uplifted, consistent with dynamic collapse, uplift and long-distance transport of weakened material during collapse of the transient cavity and final crater formation