Showing posts with label Paper. Show all posts
Showing posts with label Paper. Show all posts

Monday, August 23, 2010

More Publications

The ISME Journal advance online publication 15 July 2010; doi: 10.1038/ismej.2010.106

Big sulfur bacteria

Bo Barker Jørgensen1
1Department of Biological Sciences, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
Correspondence: BB Jørgensen, E-mail: bo.barker@biology.au.dk

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The ISME Journal , (5 August 2010) doi:10.1038/ismej.2010.121

Identity of epibiotic bacteria on symbiontid euglenozoans in O2-depleted marine sediments: evidence for symbiont and host co-evolution

V P Edgcomb, S A Breglia, N Yubuki, D Beaudoin, D J Patterson, B S Leander and J M Bernhard

Abstract
A distinct subgroup of euglenozoans, referred to as the ‘Symbiontida,’ has been described from oxygen-depleted and sulfidic marine environments. By definition, all members of this group carry epibionts that are intimately associated with underlying mitochondrion-derived organelles beneath the surface of the hosts. We have used molecular phylogenetic and ultrastructural evidence to identify the rod-shaped epibionts of the two members of this group, Calkinsia aureus and B.bacati, hand-picked from the sediments of two separate oxygen-depleted, sulfidic environments. We identify their epibionts as closely related sulfur or sulfide-oxidizing members of the epsilon proteobacteria. The epsilon proteobacteria generally have a significant role in deep-sea habitats as primary colonizers, primary producers and/or in symbiotic associations. The epibionts likely fulfill a role in detoxifying the immediate surrounding environment for these two different hosts. The nearly identical rod-shaped epibionts on these two symbiontid hosts provides evidence for a co-evolutionary history between these two sets of partners. This hypothesis is supported by congruent tree topologies inferred from 18S and 16S rDNA from the hosts and bacterial epibionts, respectively. The eukaryotic hosts likely serve as a motile substrate that delivers the epibionts to the ideal locations with respect to the oxic/anoxic interface, whereby their growth rates can be maximized, perhaps also allowing the host to cultivate a food source. Because symbiontid isolates and additional small subunit rDNA gene sequences from this clade have now been recovered from many locations worldwide, the Symbiontida are likely more widespread and diverse than presently known.

Recent Publications On Meiofauna

The ISME Journal , (13 May 2010)

doi:10.1038/ismej.2010.63
 
Meiofauna reduces bacterial mineralization of naphthalene in marine sediment

Johan Näslund, Francisco JA Nascimento and Jonas S Gunnarsson


Abstract
The role of sediment-living meiofauna, benthic invertebrates smaller than 1000 μm such as nematodes and ostracods, on the mineralization of naphthalene, a common polycyclic aromatic hydrocarbon (PAH) in marine sediments, was studied in microcosms using radiorespirometry. A method to extract live meiofauna was developed and used in order to experimentally manipulate meiofauna abundance and group diversity. Higher abundances of meiofauna were found to significantly decrease naphthalene mineralization. Furthermore, a change in the bacterial community composition (studied using terminal restriction fragment length polymorphism) was also observed in presence of higher meiofauna abundance, as well as a lower number of cultivable naphthalene-degrading bacteria. The reduced mineralization of naphthalene and the altered bacterial community composition in the presence of increased meiofauna abundance is likely the result of top-down control by meiofauna. This study shows that higher abundances of meiofauna can significantly decrease the microbial mineralization of PAHs such as naphthalene and also significantly modify the bacterial community composition in natural marine sediments.

Tuesday, June 15, 2010

Recent Publications On Meiofauna

 


Dongsung Kim1 and Yoshihisa ShirayamaContact Information
(1)  Marine Living Resources Research Division, Korea Ocean Research & Development Institute, Ansan P.O. Box 29, Seoul, 425-600, Korea
(2)  Seto Marine Biological Laboratory, Graduate School of Science, Kyoto University, Shirahama-cho, Wakayama 649-2211, Japan

Received: 10 September 2009  Revised: 24 November 2009  Accepted: 24 November 2009  Published online: 25 March 2010
Abstract  
Ingestion rates of free-living marine nematodes were measured using colloidal iron as a tracer. Detritus labeled with colloidal iron was fed to the dominant nematode species and cultured. The iron ingested by the animals was quantified using a scanning electron microscope equipped with differential X-ray energy analyzer (EDX). Average ingestion rates (µgC ind.−1day−1) measured were 0.28 for Symplocostoma sp., 0.29 for Polygastrophora sp., 0.73 for Mesacanthion sp. and 0.15 for Metachromadora sp. These values were higher than the values determined using radioactive organic materials as tracers, though the present method is considered to provide conservative values. This result thus strongly suggests that the ingestion rates of nematodes measured so far were underestimated, and the use of colloidal iron has advantages over the use of radioactive organic matter as a tracer.
Keywords  Ingestion rates - nematodes - colloidal iron - EDX - subtidal
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Maria BalsamoContact Information, L. Guidi1, M. Ferraguti2, L. Pierboni1 and R. M. Kristensen3
(1)  Dipartimento di Scienze dell’Uomo, dell’Ambiente e della Natura, Università di Urbino, Urbino, Italy
(2)  Dipartimento di Biologia, Università di Milano, Via Celoria 26, 20133 Milan, Italy
(3)  Zoological Museum, Natural History Museum, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen OE, Denmark

Received: 4 February 2009  Revised: 30 April 2009  Accepted: 11 May 2009  Published online: 30 June 2009
Communicated by H.-D. Franke.
Abstract  The genus Diuronotus (Gastrotricha Chaetonotida) includes two species, D. aspetos and D. rupperti; its morphological affinity with the genus Musellifer has been pointed out. Here, new morphological data from light and electron microscopy and the description of the spermatozoon of D. aspetos are reported, with the aim of clarifying the phylogenetic position of the genus. The mouth cavity has a wreath of stout, protrusible processes. The two secondary furcal tubes are inserted ventrally and are covered with elongate scales. All the caudal tubes contain a duo-gland adhesive system. Three kinds of ciliated sensory receptors are described for the first time in Diuronotus. The filiform spermatozoon consists of an acrosome, a nuclear-mitochondrial complex, and a flagellum. The acrosome including two long and different cones, the single, giant mitochondrion surrounding the nuclear base, and the axoneme arising from a deep nuclear ‘fossa’ appear as autapomorphic characters. The keeled, solid cuticular body scales and the spermatozoon with a supernumerary membrane are features shared with Musellifer delamarei. The structure of the accessory fibres is a strong spermatological similarity between the families Muselliferidae and Xenotrichulidae. Thus morphological and spermatological characters support the inclusion of D. aspetos and M. delamarei into the family Muselliferidae recently described. The comparative spermatology also suggests that Xenotrichulidae may be the sister group of Muselliferidae.

Keywords   Diuronotus aspetos  - Gastrotricha - Chaetonotida - Ultrastructure - Spermatozoon 

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Ilse BartschContact Information
(1)  Forschungsinstitut Senckenberg, DZMB, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
Received: 9 April 2009  Revised: 14 October 2009  Accepted: 2 November 2009  Published online: 24 November 2009
Abstract  
Isobactrus is a worldwide-spread genus. Most species live in the upper and middle area of a more or less regularly emerged zone. The species diversity is distinctly higher in the northern than in the southern hemisphere. At present, the genus consists of 29 species. An analysis of the geographical distribution of 36 external morphological characters revealed a uniformity in the combination of states of northern Pacific species, but a heterogeneity in the characters of northern Atlantic species. Several character states demonstrate a distinct north/south or north/tropics/south distribution. A parsimony analysis revealed basal northern Atlantic clades, a northern Pacific clade that also includes Northern Atlantic species and an Indo-Pacific clade with a tropical area cluster. The present data suggest that the genus Isobactrus evolved in the Palaearctic Ocean and might represent a basal lineage within the family Halacaridae.

Keywords  Halacaroidea - Characters - Distribution - Phylogeny - Palaearctic Ocean 

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Tuesday, May 18, 2010

Paper: Molecular ecology

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

ABSTRACT

Biodiversity assessment is the key to understanding the relationship between biodiversity and ecosystem functioning, but there is a well-acknowledged biodiversity identification gap related to eukaryotic meiofaunal organisms. Meiofaunal identification is confounded by the small size of taxa, morphological convergence and intraspecific variation. However, the most important restricting factor in meiofaunal ecological research is the mismatch between diversity and the number of taxonomists that are able to simultaneously identify and catalogue meiofaunal diversity. Accordingly, a molecular operational taxonomic unit (MOTU)-based approach has been advocated for en mass meiofaunal biodiversity assessment, but it has been restricted by the lack of throughput afforded by chain termination sequencing. Contemporary pyrosequencing offers a solution to this problem in the form of environmental metagenetic analyses, but this represents a novel field of biodiversity assessment. Here, we provide an overview of meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction to PCR, sequencing and the bioinformatic interrogation of multiple, independent samples using 454 Roche sequencing platforms. We report two examples of environmental metagenetic nuclear small subunit 18S (nSSU) analyses of marine and tropical rainforest habitats and provide critical appraisals of the level of putative recombinant DNA molecules (chimeras) in metagenetic data sets. Following stringent quality control measures, environmental metagenetic analyses achieve MOTU formation across the eukaryote domain of life at a fraction of the time and cost of traditional approaches. The effectiveness of Roche 454 sequencing brings substantial advantages to studies aiming to elucidate the molecular genetic richness of not only meiofaunal, but also all complex eukaryotic communities.


Molecular Ecology

Volume 19 Issue s1, Pages 4 - 20
Special Issue: Next Generation Molecular Ecology
Published Online: 10 Feb 2010
© 2010 Blackwell Publishing Ltd

Further information HERE