25.86 · Keiser UniversityAbstractThe authors study the diagram pertaining to lithium and titanium ferrites substituted for zinc, with bismuth and manganese additives. Well ″densified″ polycrystalline materials were obtained with magnetic saturation values lying between 2000 and 3300 Gs, having relatively high Curie points and very low magnetic and dielectric losses. These materials can be used for microwave applications, especially in the X-band and above, or when large medium powers and low insertion losses are needed.Do you want to read the rest of this article?
CitationsCitations1ReferencesReferences0ABSTRACT: This chapter describes a microwave ferrite. The physical phenomenon exploited is the gyromagnetic resonance that appears when the material is subjected to both a static magnetic field and to a microwave field. This effect is inherently non-reciprocal, which accounts for the tensorial nature of the magnetic permeability. This non-reciprocity is widely used in various devices. The saturation magnetization is a fundamental quantity, not only as a factor of efficiency, but also because of the existence of a natural resonance in the internal fields. Consequently, magnetization is the first quantity to be considered in the choice of material for a given application. As in any resonance effect, the linewidth is of prime importance. It is fundamentally related to the damping effects of spin movements, which seem possible to approach by considering either the linewidth off-resonance or the non-linear effects related to the spin waves. Conversely, the linewidth of the main mode observed at resonance, on the polycrystals, is broadened by the magnetocrystalline anisotropy effects or by spurious effects related to faults and porosity. Ferrites now used at microwave frequencies have spinel, G, or hexagonal structures.Article · Dec 1980 ArticleOctober 1974 · IEEE Transactions on Magnetics · Impact Factor: 1.39The influences of simultaneous tetrahedral (aluminium) and octahedral substitutions (tin or indium) upon the magnetic and microwave properties of various YGdFe polycrystalline garnets have been studied. We have obtained interesting new materials with saturation magnetizations between 200 and 900 G which exhibit higher temperature stabilities of the magnetization than those of classical... ArticleOctober 1973A measurement method is presented of permeability tensor elements in a TM IIO-cavity, where anapproximation for Bessel functions is used to set up practical formulas, and where the equipment is designed to separate definitely the two counterrotating modes. The accuracy due to that measurement method allows a good determination of the gyromagnetic effective linewidth. ArticleAugust 1977 · Applied PhysicsPolycrystalline samples of vanadium substituted yttrium-gadolinium iron garnets slightly doped with divalent cobalt were investigated.
In this paper we report experimental results on the initial permeability at 10 kHz, coercive force, effective gyromagnetic
factor and resonance linewidth at X-band. We show that the magnetic properties observed in this system depend for the most
part, on the... ArticleFebruary 1971 · Le Journal de Physique ColloquesL'étude de l'effet de petites substitutions de cobalt dans des grenats polycristallins ferrimagnétiques fait appara?tre deux types de comportements lorsque l'on fait cro?tre le taux de Co. Type A : La perméabilité u présente un maximum, le champ coercitif Hc et la largeur de raie de gyrorésonance ?H un minimum, ce qui s'explique bien par l'action de Co2+ octaédrique sur l'anisotropie. Type B :... Data provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.This publication is from a journal that may support self archiving.Last Updated: 04 Jul 17CitationsSee all >69 ReferencesSee all >4 Figures
18.86 · University of Maryland, College Park30.29 · Stanford University39.87 · Portland State UniversityAbstractABSTRACTA culture-independent molecular phylogenetic survey was carried out for a bacterial and archaeal community of a mineralized crust coating a sulphide spire, which was collected from the Edmond vent field (23° S, 69° E, 3300 m depth) on the Central Indian Ridge. Small-subunit rRNA genes (16S rDNA) were amplified from environmental DNA by PCR utilizing Bacteria-specific, and Archaea-specific 16S rDNA primers. PCR products were cloned and 26 bacterial and nine archaeal unique sequence types (phylotypes) were identified from 150 clones analysed by restriction fragment length polymorphism, representing eight and four distinct lineages, respectively. The majority (&90%) of the bacterial phylotypes group with the ?-Proteobacteria and confirms the global prevalence of ?-Proteobacteria in deep-sea hydrothermal environments. Among the ?-Proteobacteria, &40% of the phylotypes were closely related to the recently isolated deep-sea vent thermophilic chemolithoautotrophic sulphur-reducer, Nautilia lithotrophica. A single bacterial sequence was nearly identical (99% similarity) to the thermophilic hydrogen-oxidizing Hydrogenobacter thermolithotrophum, and is the first report of Hydrogenobacter at deep-sea hydrothermal vents. A majority (97%) of the archaeal phylotypes grouped with the ‘Deep-sea Hydrothermal Vent Euryarchaeotal Group’, a phylogenetic lineage of uncultured Archaea that have only been reported from other deep-sea hydrothermal vents on the Mid-Atlantic Ridge, East Pacific Rise, Juan de Fuca Ridge, Isu–Ogasawara Arc, Okinawa Trough and the Manus Basin. A single sequence was closely related to the hyperthermophilic sulphur-reducing Thermococcales frequently found in diverse deep-sea vent environments. Scanning electron micrographs of the mineralized crust reveal abundant filamentous, rod and coccoidal forms encased in sulphur and sulphide mineral precipitate, suggesting that the thermophilic chemolithoautorophs and sulphide-producing heterotrophs may influence the architecture and sulphur cycling of the sulphide spire.Discover the world's research13+ million members100+ million publications700k+ research projects
Geobiology (2003),
1 , 119–127(C) 2003 Blackwell Publishing Ltd 119 Blackwell Publishing Ltd. ORIGINAL ARTICLE Microbial diversity from Central Indian Ridge hydrothermal sulphide deposits Microbial diversity of a sulphide spire located in the Edmond deep-sea hydrothermal vent field on the Central Indian Ridge JOOST HOEK, AMY BANTA, FORREST HUBLER AND ANNA-LOUISE REYSENBACH Department of Biology, Portland State University, PO Box 751, Portland, OR , USA
ABSTRACT A culture-independent molecular phylogenetic survey was carried out for a bacterial and archaeal communityof a mineralized crust coating a sulphide spire, which was collected from the Edmond vent field (23 °
E,3300 m depth) on the Central Indian Ridge. Small-subunit rRNA genes (16S rDNA) were amplified fromenvironmental DNA by PCR utilizing Bacteria-specific, and Archaea-specific 16S rDNA primers. PCR productswere cloned and 26 bacterial and nine archaeal unique sequence types (phylotypes) were identified from 150clones analysed by restriction fragment length polymorphism, representing eight and four distinct lineages,respectively. The majority (&90%) of the bacterial phylotypes group with the
ε -Proteobacteria and confirms theglobal prevalence of
ε -Proteobacteria in deep-sea hydrothermal environments. Among the
ε -Proteobacteria,&40% of the phylotypes were closely related to the recently isolated deep-sea vent thermophilic chemolitho-autotrophic sulphur-reducer,
Nautilia lithotrophica . A single bacterial sequence was nearly identical (99%similarity) to the thermophilic hydrogen-oxidizing
Hydrogenobacter thermolithotrophum , and is the first reportof
Hydrogenobacter
at deep-sea hydrothermal vents. A majority (97%) of the archaeal phylotypes grouped withthe ‘Deep-sea Hydrothermal Vent Euryarchaeotal Group’, a phylogenetic lineage of uncultured Archaea thathave only been reported from other deep-sea hydrothermal vents on the Mid-Atlantic Ridge, East Pacific Rise,Juan de Fuca Ridge, Isu–Ogasawara Arc, Okinawa Trough and the Manus Basin. A single sequence was closelyrelated to the hyperthermophilic sulphur-reducing
Thermococcales
frequently found in diverse deep-sea ventenvironments. Scanning electron micrographs of the mineralized crust reveal abundant filamentous, rod andcoccoidal forms encased in sulphur and sulphide mineral precipitate, suggesting that the thermophilic chemo-lithoautorophs and sulphide-producing heterotrophs may influence the architecture and sulphur cycling of thesulphide spire.Received 13 March 2003; accepted 01 September 2003Corresponding author: Dr Anna-Louise Reysenbach. Tel.: +1 503 725 3864; fax: +1 503 725 8570; e-mail:reysenbacha@pdx.edu INTRODUCTION Seafloor hydrothermal systems venting high-temperature( & 380
° C) metal-rich fluids support some of the most prolificand diverse ecosystems on Earth at seemingly inhospitableconditions. Vent ecosystems are unique in that the primaryproducers are chemolithoautotrophic micro-organisms thatutilize a wide range of available redox couples for energy atthe interface between oxidized seawater and reducedhydrothermal vent fluids (Reysenbach
et al ., 2000a; Luther et al ., 2001). It is hypothesized that chemolithoautotrophs insubsurface regions and surface expressions of hydrothermalsystems have the potential to influence and perhaps controlfluid chemistry and element cycling by the catalysis of aqueousand geochemical reactions (Taylor & Wirsen, 1997; Taylor et al ., 1999).Recently, a molecular phylogenetic approach using 16SrRNA gene sequences has successfully been applied to examinethe bacterial and archaeal diversity of different deep-sea hydro-thermal environments (Haddad
et al ., 1995; Moyer
et al .,1995; Polz & Cavanaugh, 1995; Cary
et al ., 1997; Takai& Horikoshi, 1999; Reysenbach
et al ., 2000b; Campbell &Cary, 2001; Corre
et al ., 2001; Longnecker & Reysenbach,2001; Takai
et al ., 2001; Alain
et al ., 2002a; Huber
et al .,2002; Lopez-Garcia
et al ., 2002; Teske
et al ., 2002). Mostof this research has focused on the actively venting sulphidestructures, and suggests that the diversity of thermophilesmay be coupled to the geochemical and temperature gradients
et al. (C) 2003 Blackwell Publishing Ltd,
Geobiology ,
1 , 119–127 across chimney walls (Tivey & McDuff, 1990; Tivey
et al .,1995; McCollom & Shock, 1997; Luther
et al ., 2001).In this study we report on the characterization of the micro-bial diversity of a sulphide spire from the recently discoveredEdmond vent field on the Central Indian Ridge (Van Dover et al ., 2001). This is the first characterization of microbialdiversity from Central Indian Ridge hydrothermal environ-ments and like that of macrobiological hydrothermal ventdiversity, prior to this study, the Indian Ocean representeda gap in our understanding of the patterns of microbial diver-sity at deep-sea vents. Furthermore, hydrothermal venting atthe Edmond field has been active over long periods of timeand is characterized by a wide range of venting styles (VanDover
et al ., 2001), which provides varied microhabitats forthermophilic microbial activity. These features can be used todetermine if variables such as the mineralogy of vent deposits,age of venting and vent fluid temperature affect the microbialcommunity structure. Our results support emerging viewsthat the
ε -Proteobacteria represent the dominant clonesamong the Bacteria and that the Deep-sea Hydrothermal VentEuryarchaeotic Group (DHVEG) is endemic and widespreadamong deep-sea hydrothermal vents. METHODS Sample collection and storage In April 2001, an interdisciplinary investigation team exploredthe hydrothermal systems along the southern edge of the CentralIndian Ridge. We revisited the Kairei vent field (25 ° 19.23 ′
S,70 ° 02.42 ′
E, about 2400 m depth), which was first discoveredby Japanese scientists in August 2000 (Gamo
et al ., 2001), anddiscovered a new vent field, the Edmond vent field (23 ° 52.68 ′
S,69 ° 35.80 ′
E, about 3300 m depth) about 160
km NNW of Kairei(Fig. 1). Active sulphides were collected by the ROV- Jason . Onesample in particular was chosen for detailed analysis. This small(0.5 m) sulphide spire designated ‘Fuzzy Toothpick’ (sample301-11) was collected from the Edmond vent field at a depthof 3290 m. A white mineral deposit completely covered one sideof the small spire (Fig. 2). Samples were processed shipboardand stored at
° C. The sulphide spire was subsectioned, withintact pieces stored in ethanol (70% v/v) at
° C. A layer ( ~ 2 mmthick) of the deposit was removed from selected subsectionsand used for enrichment culturing and DNA extraction. DNA extraction, amplification, cloning and restriction fragment length polymorphism (RFLP) analysis DNA was extracted shipboard from a 1.0-mL aliquot of sampleusing a standard soil extraction kit following the manufacturer’sprotocol (Mo Bio Laboratories Inc., Solana Beach, CA, USA).Extracted DNA was stored in 50
u L of 10 m M
Tris buffer andstored at
° C.16S rRNA genes were amplified by PCR from environmentalDNA and PCR products were cloned and analysed accordingto the methods of Longnecker (2001). DNA was extractedfrom additional subsamples and from other sulphides andsediments collected at Edmond vent field. The 16S rDNA ofthese samples was amplified using denaturing gradient gelelectrophoresis (DGGE) primers (Longnecker, 2001) to con-firm results obtained from the clone libraries and to determineif similar diversity was observed with other samples collectedduring this research cruise. Sequencing and phylogenetic analyses Bacterial and archaeal clones showing unique RFLP patternswere sequenced using the ABI PRISM Big Dye TerminatorFig. 1 Map of the Indian Ocean showing thelocation of the Kairei and Edmond vent fields onthe Central Indian Ridge. Map created using theNOAA satellite images (www.NOAA.gov).
Microbial diversity from Central Indian Ridge hydrothermal sulphide deposits
121 (C) 2003 Blackwell Publishing Ltd,
Geobiology ,
1 , 119–127 Cycle Sequencing Kit and an ABI 310 Genetic Analyseraccording to the manufacturer’s protocol (Applied Bio-systems Inc., Foster City, CA, USA). The complete sequenceof both strands was obtained using a suite of 16S rDNA-specific primers to generate an overlapping set of sequencesthat were assembled into one contiguous sequence usingAutoAssembler (Applied Biosystems Inc.). The followingprimers were used for sequencing: M13F (5 ′ -GTAAAA-CGACGGCCAG-3 ′ ), M13R (5 ′ -CAGGAAACAGCTATGAC)(clones), 357F (5 ′ -CTCCTACGGGAGGCAGCAG-3 ′ ),704F (5 ′ -GTAGCGGTGAAATGCGTAGA-3 ′ ), 1114F(5 ′ -GCAACGAGCGCAACCC-3 ′ ), 1100R (5 ′ -AGGGTT-GCGCTCGTTG-3 ′ ), 519R (5 ′ -ATTACCGCGGCTGCTGG-3 ′ ), 907R (5 ′ -CCGTCAATTCCTTTRAGTTT-3 ′ ) (bacterial),333F (TCCAGGCCCTACGGG), 340RA (5 ′ -CCCCGTA-GGGCCYGG-3 ′ , with Y
C or T), 744RA (5 ′ -CCSGGGTA-TCTAATCC-3 ′ ), 765F (5 ′ -TAGATACCCSSGTAGTCC-3 ′ ,with S
C or G), 1098RAN (5 ′ -GGGTCTCGCTCGTTSCC-3 ′ ), 1100FAN (5 ′ -GGCAACGAGCGMGACCC, with M
Aor C) (archaeal). Secondary structures were used to confirmthe fidelity of the assembled sequences and additional checksfor chimeras were done as described by Longnecker
et al .(2001). Closely related sequences were identified by sequencesimilarity using BLAST. Sequences were manually alignedaccording to secondary structure to related 16S rRNAgene sequences that were obtained from GenBank, usingARB (Ludwig & Strunk, 1996). Approximately 1350 of 1500homologous nucleotides were used to determine phylo-genetic relationships using maximum likelihood analysisand fastDNAml (Olsen
et al ., 1994). The maximumlikelihood bootstrap analyses consisted of 100 pseudorep-licates. Maximum likelihood trees were constructed usingfastDNAml. RESULTS AND DISCUSSION The Edmond vent field is located on the Central Indian Ridgeat the northern end of segment S3 on the eastern rift valleywall
~ 6 km from the adjacent rift axis. It covers an area of about100 m by 90 m and is constructed on a small protrusion thatextends south from the eastern rift wall and forms the north-east corner of a
~ 60-m-deep basin. High- and low-temperatureFig. 2 Video frame capture images (A,B) showing ‘FuzzyToothpick’ prior to sampling in the Edmond vent field of theCentral Indian Ridge (anemones for scale); B is a close up viewof the white outer crust coating one side of the sulphide spire.A scanning electron micrograph (C) of the crust showsabundant mineralized (elemental sulphur) filamentous forms.Arrow indicates hollow tube-like structure of filaments. Scalebar = 2 um.
et al. (C) 2003 Blackwell Publishing Ltd,
Geobiology ,
1 , 119–127 venting is roughly centred at 23 ° 52.68 ′
S, 69 ° 35.80 ′
W withina narrow depth range between
~ 3290 and 3320 m. The Edmondvent field is dominated by old disaggregated sulphide structuresand massive sulphide talus, indicating that hydrothermal activityhas been focused at this site over long periods of time (VanDover
et al ., 2001). High-temperature venting occurs as clustersof large (up to 20 m in height and 2 m in diameter) multiple-orifice black smoker chimneys, similar to the black smokercomplex at the TAG hydrothermal field (Fouquet
et al .,1993). Within and between the clusters, smaller (up to 5 m inheight), branched candelabra-like structures vent black smokerfluids at lower flow rates. ‘Beehive’ structures, similar to thosedescribed from the Snake Pit hydrothermal field on the Mid-Atlantic Ridge (Fouquet
et al ., 1993), are common at Edmond.They are grey, very porous, bulbous structures, with clearfluid diffusing from the surfaces. Occasionally, black fluidsdiffuse from the upper portions of the beehives. Widespreadareas of diffuse flow characterize the Edmond vent field.Fe-oxyhydroxide sediments are abundant, reaching severalcentimetres in thickness in depressions, and coating manyof the sulphide structures and much of the talus (Van Dover et al ., 2001). White and black crusts were frequently observedon sulphide structures.The sulphide studied in depth in this report was located inan area of diffuse hydrothermal fluid flow where maximumtemperatures of 70
° C were recorded in close proximity to thespire. A white crust ( ~ 2 mm thick) completely covered oneside of the sulphide spire (Fig. 2). Preliminary X-ray diffrac-tion (XRD) analyses of the mineralized crust indicate that it isdominated by elemental sulphur mixed with halite, sphaleriteand minor amounts of barite (S. Humphris and M. K. Tivey,personal communication). A closer examination of the whitedeposit using DAPI-stained smears and scanning electronmicroscopy (SEM) revealed that the deposit is a biofilm-likecrust containing filamentous (Fig. 2C), rod and coccoidal formsencased in mineral precipitate. Phylogenetic analyses of 16SrRNA genes amplified from environmental DNA extractedfrom the crust indicate the presence of both bacterial and archaealDNA. RFLP analysis of 150 clones from separate bacterial andarchaeal clone libraries revealed unique bacterial ( n
26) andarchaeal ( n
9) 16S rDNA phylotypes. These were found torepresent eight distinct bacterial and four distinct archaeallineages (Table 1). Although the number of each unique sequencetype is not indicative of its abundance in the environment anddoes not necessarily represent an exhaustive assessment of thediversity, collectors curves using all clones suggested that wehad sampled a representation of environmental microbial var-iability in the mineral crust covering the sulphide. Fluorescent in situ
hybridization (FISH) using bacterial-specific probesindicated that bacteria represented about 60% of the microbialdiversity on the sulphide spire (data not shown). The preva-lence of bacterial diversity on the surfaces of actively ventingsulphide structures is supported by other studies using differentmolecular phylogenetic techniques (FISH, T-RFLP, quantitativePCR, RNA–RNA hybridization) (Reysenbach
et al ., 2000b;Longnecker & Reysenbach, 2001; Takai
et al., 2001).Bacterial diversityThe bacterial phylotypes were primarily affiliated (&90%) withthe Epsilon subclass of the Proteobacteria (ε-Proteobacteria)(Fig. 3). Furthermore, DGGE of 16S rDNA amplified fromthis and other outer surfaces of chimneys collected at theEdmond vent field confirmed the prevalence of ε-Proteobacteria(data not shown). A single clone (one out of 108) was 99%similar to the thermophilic hydrogen-oxidizing microaerophile,Hydrogenobacter thermolithotrophum. To our knowledge, thisis the first time Hydrogenobacter has been identified from adeep-sea hydrothermal environment, although its close relative,a strain of the hydrogen-oxidizing Persephonella marinus, wasgrown in enrichment cultures from this sample (Reysenbachet al., 2002). Among the ε-Proteobacteria, the majority of thesequences (&40%) belonged to two phylotypes (representedby FT17B01 and FT17B03). Sequences from these phylotypesbranched with Nautilia lithotrophica, a recent isolate from adeep-sea hydrothermal vent along the East Pacific Rise (13° N)(Miroshnichenko et al., 2002). This novel organism is a strictlyanaerobic, moderately thermophilic, facultative chemolitho-autotroph that couples the oxidation of H2 to the reductionof S°. The majority of the remaining clones (56%) branchedwith uncultured ε-Proteobacteria identified from biofilms ofactively venting hydrothermal vents (Moyer et al., 1995;Reysenbach et al., 2000a), from deep-sea hydrothermaland non-hydrothermal sediments (Li et al., 1999a,b,c; Teskeet al., 2002), and with sulphide-oxidizing epibionts of thehydrothermal vent annelid Alvinella pompejana (Polz &Cavanaugh, 1995; Campbell et al., 2001), and of the ventshrimp Rimicaris exoculata (Cary et al., 1997). Additionally,a single clone (FT17B100) branched with the sulphur-reducingSulfurospirilum. This limited diversity is unlike the novel CentralIndian Ridge vent scaly snail’s microflora, which was muchTable 1 Summary of the bacterial and archaeal phylotypes identified from theEdmond vent field along the Central Indian RidgeType sequencePercentage of clones (n)Phylogenetic affiliation Accession no.Bacterial clonesFT17B01 46 (44) ε-Proteobacteria AY251057FT17B05 34 (32) ε-Proteobacteria AY251058FT17B08 19 (18) ε-Proteobacteria AY251059FT17B100 1 (1) ε-Proteobacteria AY251060FT17B14 1 (1) Aquificales AY251061Archaeal clonesFT17A03 30 (13) DHVEG AY251064FT17A09 33 (15) DHVEG AY251065FT17A19 30 (13) DHVEGFT17A18 7 (3) Thermococcales AY251066
Microbial diversity from Central Indian Ridge hydrothermal sulphide deposits
123(C) 2003 Blackwell Publishing Ltd, Geobiology, 1, 119–127more diverse and included members of the epsilon, delta andgamma proteobacteria (S. Goffredi, personal communication).The growing database from microbial diversity assessmentsusing culture-independent molecular phylogenetic techniquesincreasingly recognizes the importance of ε-Proteobacteria indeep-sea hydrothermal environments (Haddad et al., 1995;Moyer et al., 1995; Polz & Cavanaugh, 1995a; Cary et al.,1997; Reysenbach et al., 2000b; Campbell & Cary, 2001;Corre et al., 2001; Longnecker & Reysenbach, 2001; Alainet al., 2002a; Lopez-Garcia et al., 2002; Teske et al., 2002).In addition to their presence at deep-sea hydrothermal vents,ε-Proteobacteria have been identified in terrestrial hotsprings,oil fields, activated sludge and marine snow (Snaidr et al., 1997;Hugenholtz et al., 1998; Rath et al., 1998; Gevertz et al.,2000; Watanabe et al., 2000). All ε-Proteobacteria isolatedto date are involved in the sulphur cycle by either reduc-ing elemental sulphur to sulphide or oxidizing sulphide tosulphur, with some bacteria capable of carrying out bothreactions (Macy et al., 1986; Schumacher et al., 1992). Inaddition to this sulphur metabolism, many ε-Proteobacteriaare able to utilize a variety of electron acceptors includingoxygen (under microaerophilic conditions), nitrate, severalsulphur species, arsenate, selenate, manganese, and Fe(III)(Oremland et al., 1994; Laverman et al., 1995; Finster et al.,1997; Stolz et al., 1999; Alain et al., 2002b; Takai et al., inpress). These thermophilic (facultative) chemolithoautotrophicFig. 3 The bacterial 16S rRNA phylogenetic tree was constructed using maximum likelihood analysis. Methanocaldococcus jannaschii was used as the outgroup.The numbers at the nodes are the bootstrap values. Bootstrap values (in per cent) are based on 100 replicates each and are shown for branches with more than60% bootstrap support. GenBank accession numbers follow the clone or organism name. New clones are shown in bold type and are marked with an asterisk. Thescale bar represents the expected number of changes per nucleotide position.
J. HOEK et al.(C) 2003 Blackwell Publishing Ltd, Geobiology, 1, 119–127sulphur-reducing organisms may have the potential to influ-ence and perhaps control fluid/rock chemistry and sulphurcycling in deep-sea hydrothermal environments. They mayalso play an important role in the development of mineralizedmicrobial mats, which frequently coat actively venting sul-phide structures, and of marcasite crusts, which encase thetubes of Paralvinella sp. (Juniper et al., 1992).Archaeal diversityA total of nine unique archaeal 16S rDNA phylotypes wereidentified by RFLP analysis (and were independently confirmedusing DGGE analysis of 16S rRNA genes amplified fromsubsamples taken of the mineralized crust). These representfour distinct archaeal lineages (Table 1), of which &90%branched with a group of uncultured Archaea that appear tobe endemic to vents (Reysenbach & Shock, 2002). This group,known as the ‘Deep-sea Hydrothermal Vent EuryarchaeotalGroup’ (DHVEG), has been identified from deep-sea hydro-thermal vents and sediments on the Mid-Atlantic Ridge(Reysenbach et al., 2000b), Juan de Fuca Ridge (Longnecker,2001), Okinawa Trough, Izu–Ogasawara arc (Takai &Horikoshi, 1999), Manus basin (Takai et al., 2001) and theEast Pacific Rise (Takai & Horikoshi, 1999; Reysenbach et al.,2000b; Longnecker, 2001; Takai et al., 2001). In addition toidentifying phylotypes that are related to the DHVEG, a singleclone was most closely related to the hyperthermophilic sulphur-reducing heterotrophic Thermococcales frequently isolated fromdiverse deep-sea vent environments. None of these Archaeawas detected in chemolithoautrophic enrichment cultures ofthis sulphide (under nitrate-reducing, hydrogen-oxidizing,sulphate-reducing, sulphur-reducing and methanogenic con-ditions) (Reysenbach et al., 2002). Furthermore, DGGE ofadditional sulphide and sediment samples from the Edmondvent field revealed sequences related to methanogens such asMethanocaldococcus and Methanothermus (data not shown),in addition to the DHVEG sequences described above.The identification of DHVEG 16S rRNA genes from deep-sea hydrothermal vents on the Central Indian Ridge expandsthe known distribution of this phylogenetic lineage. Althoughcurrently nothing is known about the physiology of thisgroup of uncultivated organisms, Takai et al. (2001) suggestthermophily for the DHVEG lineage as this group is repre-sented by short branch lengths in phylogenetic trees and hasa high G + C content of the 16S rRNA gene. Furthermore,sequences belonging to hyperthermophilic Thermococcalesare often obtained from the same samples. The distant phylo-genetic association of the DHVEG with the thermophilic,acidophilic Picrophilus and Thermoplasmales (Fig. 4) suggeststhat thermoacidophiles may occupy certain niches in deep-sea hydrothermal vents. As yet, no extreme thermoacido-philes have been isolated from deep-sea hydrothermal ventsdespite the low pH (&4.5) of end-member hydrothermalfluid (Von Damm, 1995).The Thermococcales are some of the most commonly isolatedorganisms from deep-sea hydrothermal vent environments,although they are not always detected using a phylogeneticapproach (Takai & Horikoshi, 1999; Reysenbach et al., 2001).Our results, which support similar results obtained fromnumerous deep-sea hydrothermal vent environments (Rey-senbach et al., 2000b; Longnecker, 2001; Takai et al., 2001),suggest that the Thermococcales may represent only a smallpercentage of the total diversity of many vent communitieswhen compared to organisms such as the ε-Proteobacteriaand members of the DHVEG lineage. However, the occur-rence of Thermococcales in deep-sea vent environments may beindicative of more established communities. For example, suc-cessional changes in the archaeal diversity of growth chambersdeployed on vents showed increasing dominance of Thermo-coccales over time (Reysenbach et al., 2000b, 2002), and Ther-mococcales isolated from low-temperature fluid of diffuse flowareas at deep-sea vents are thought to derive from stable sub-seafloor environments (Summit & Baross, 2001); however,Cowen
et al. (2003) found no evidence of Thermococcalesfrom fluid sampled directly from a 300-m-deep overpres-surized borehole on the flanks of the Juan de Fuca Ridge.Furthermore, we have screened for an enzyme of thedissimilatory sulphate reduction pathway, dissimilatory sulphitereductase (EC 1.8.99.3, dsr, Wagner et al., 1998; Klein et al.,2001; Dhillon et al., 2003) to determine the role sulphatereducers might have in active sulphide environments. Althoughwe did not detect any putative sulphate reducers in either ofthe bacterial and archaeal 16S rDNA assessments, we did detectdsr genes. These were most closely related to the archaeonArchaeoglobus fulgidus dissimilatory sulphite reductase (datanot shown). Although very speculative, it is possible that addi-tional analysis or metagenomic analysis of this sample mayreveal that these dsr genes are affiliated with the DHVEGgroup. Interestingly, similar assessment from another deep-sea vent site, the Guaymas Basin, where Archaeoglobus wasdetected in 16S rDNA clone libaries, detected no Archaeoglo-bales dsr genes (Dhillon et al., 2003). This points to the carethat needs to be taken when interpreting data from microbialassessments using only one gene. Combining both functionaland molecular phylogenetic diversity assessments will lead toadditional insights into the diversity and metabolic function ofmicrobial communities.Nevertheless, the development of molecular phylogene-tic techniques for assessing microbial diversity has greatlyexpanded our view of the microbial diversity associatedwith actively venting sulphide deposits. From diversity studiesof sulphides collected from geographically distant hydro-thermal sites, some patterns are emerging. For instance, ε-Proteobacteria dominate most structures and are restricted tothe outer portions of the sulphides. It is likely these are sulphuroxidizers and reducers. However, owing to their phylogeneticdiversity, it is likely that this group of organisms is metabolicallydiverse and induces different mineralogical and geochemical
Microbial diversity from Central Indian Ridge hydrothermal sulphide deposits
125(C) 2003 Blackwell Publishing Ltd, Geobiology, 1, 119–127transformations on the sulphides. Furthermore, the consistentdetection of the archaeal DHVEG sequences suggests thatthis group most likely plays a significant role in the sulphidecommunity structure. With our current microbial census, it isnow possible to begin designing experiments to address theeffect that the metabolism of these dominant phylotypes mighthave on the mineralogy of sulphides. Additionally, screeningfor functional genes will provide further insights in to themetabolic potential of these environments.ACKNOWLEDGEMENTSWe thank the Captain and crews of the R/V Knorr and ROVJason for their invaluable assistance at sea. Shore-based andshipboard technical and engineering staff of the WHOI DeepSubmergence Group played a key role in the acquisition ofdata. We thank members of the ALR laboratory for theircritical reviews of this manuscript. The research cruise wassupported by an NSF grant (OCE9712358) to Cindy LeeFig. 4 The archaeal 16S rRNA phylogenetic tree was constructed using maximum likelihood analysis. Aquifex pyrophilus was used as outgroup. The numbers at thenodes are the bootstrap values. Bootstrap values (in per cent) are based on 100 replicates each and are shown for branches with more than 70% bootstrap support.GenBank accession numbers follow the clone or organism name. New clones are shown in bold type and are marked with an asterisk. The scale bar represents theexpected number of changes per nucleotide position.
J. HOEK et al.(C) 2003 Blackwell Publishing Ltd, Geobiology, 1, 119–127Van Dover and data analysis was supported by an NSFgrant (OCE-0083134) and a NASA-Exobiology grant toA.-L.R.REFERENCESAlain K, Olagnon M, Desbruyeres D, Page A, Barbier G, Juniper SK, Querellou J, Cambon-Bonavita MA (2002a) Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis. FEMS Microbiology and Ecology 42, 463–476.Alain K, Querellou J, Lesongeur F, Pignet P, Crassous P, Raguenes G, Cueff V, Cambon-Bonavita MA (2002b) Caminibacter hydrogeniphilus gen. nov., sp nov., a novel thermophilic, hydrogen-oxidizing bacterium isolated from an East Pacific Rise hydrothermal vent. International Journal of Systematic and Evolutionary Microbiology 52, .Campbell BJ, Cary SC (2001) Characterization of a novel spirochete associated with the hydrothermal vent polychaete annelid, Alvinella pompejana. 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CitationsCitations53ReferencesReferences69Their cooler exteriors, richest in microbial biomass, are often covered with conspicuous white, orange or dark-coloured biofilms (e.g. Hoek et al., 2003; Takai et al., 2008; Olins et al., 2013). ABSTRACT: Sulfide 'chimneys' characteristic of seafloor hydrothermal venting are diverse microbial habitats. (13) C/(12) C ratios of microbial lipids have rarely been used to assess carbon assimilation pathways on these structures, despite complementing gene- and culture-based approaches. Here, we integrate analyses of the diversity of intact polar lipids (IPL) and their side-chain δ(13) C values (δ(13) Clipid ) with 16S rRNA gene-based phylogeny to examine microbial carbon flow on active and inactive sulfide structures from the Manus Basin. Surficial crusts of active structures, dominated by Epsilonproteobacteria, yield bacterial δ(13) Clipid values higher than biomass δ(13) C (total organic carbon), implicating autotrophy via the reverse tricarboxylic acid cycle. Our data also suggest δ(13) Clipid values vary on individual active structures without accompanying microbial diversity changes. Temperature and/or dissolved substrate effects - likely due to variable advective-diffusive fluxes to chimney exteriors - may be responsible for differing (13) C fractionation during assimilation. In an inactive structure, δ(13) Clipid values lower than biomass δ(13) C and a distinctive IPL and 16S rRNA gene diversity suggest a shift to a more diverse community and an alternate carbon assimilation pathway after venting ceases. We discuss here the potential of IPL and δ(13) Clipid analyses to elucidate carbon flow in hydrothermal structures when combined with other molecular tools. Full-text · Article · Jun 2014 +1 more author...Soon after completing the expedition, comparative analyses of DNA sequences revealed that the animal taxa inhabiting these vents had their closest affinities with cognate species from the western Pacific back arc basins, except for the dominant shrimp species, which was closely related to Atlantic Rimicaris (Van Dover et al., 2001). A new snail with pyrite-covered scales on its foot (Waré n et al., 2003) revealed novel forms of bacterial symbiosis ARTICLE IN PRESS (Goffredi et al., 2004b), and molecular analysis of a sulfide spire revealed many new microbes (Hoek et al., 2003). Opportunities to communicate research findings have also improved through efforts of organizations that are dedicated to disseminating biodiversity data. ABSTRACT: Many new species of animals have been discovered during the past 40 years of deep-ocean exploration, particularly in chemosynthetic habitats such as hydrothermal vents and cold-water hydrocarbon seeps. Estimating species diversity in these environments is difficult, however, because insufficient sampling often fails to capture the range of organismic variability in time and space. Molecular systematic studies have revealed a number of taxonomic problems that derive from insufficient sampling and a shallow knowledge base regarding many deep-sea taxa. For example, numerous morphologically cryptic species exist among the vesicomyid clams and lepetodrilid limpets that dominate vents and seeps worldwide, suggesting that species richness may be significantly underestimated in these taxa. In contrast, discrete morphotypes of siboglinid tubeworms that are products of developmental plasticity were assigned synonymous species names. Also, distinct juvenile and adult forms of vent shrimp were assigned synonymous genus and species names. Though molecular studies have resolved many of these problems, they are not a panacea because they also suffer from insufficient sampling of taxa and genes, and from contamination of DNA sequences. Working carefully together, molecular and traditional systematists should eventually generate more accurate species lists that allow unbiased estimates of species richness in deep-sea environments. Full-text · Article · Sep 2009 ophilic and mesophilic methanogens , 74 and revealed the presence of sulfate reducing bacteria and archaea and of methanotrophic 75 bacteria ( Nakagawa et al . 2004 , Nercessian et al . 2005a ) . Furthermore , 16S rRNA - based 76 studies of vent microbial communities indicated that Epsilonproteobacteria were 77 associated with sulfide structures ( Hoek et al . 2003 , Longnecker et al . 2001 ) , and showed 78 that between 66 and 98% of the microorganisms associated with various types of 79 colonization substrates that were deployed in the vicinity of chimney orifices belonged to 80 this class of the Proteobacteria ( Alain et al . 2004 , Lopez - Garcia et al . 2003 ) . 81 Recent work on the isolatioABSTRACT: The bacterial and archaeal communities of three deep-sea hydrothermal vent systems located on the Mid-Atlantic Ridge (MAR; Rainbow, Logatchev and Broken Spur) were investigated using an integrated culture-dependent and independent approach. Comparative molecular phylogenetic analyses, using the 16S rRNA gene and the deduced amino acid sequences of the alpha and beta subunits of the ATP citrate lyase encoding genes were carried out on natural microbial communities, on an enrichment culture obtained from the Broken Spur chimney, and on novel chemolithoautotrophic bacteria and reference strains originally isolated from several different deep-sea vents. Our data showed that the three MAR hydrothermal vent chimneys investigated in this study host very different microbial assemblages. The microbial community of the Rainbow chimney was dominated by thermophilic, autotrophic, hydrogen-oxidizing, sulfur- and nitrate-reducing Epsilonproteobacteria related to the genus Caminibacter. The detection of sequences related to sulfur-reducing bacteria and archaea (Archaeoglobus) indicated that thermophilic sulfate reduction might also be occurring at this site. The Logatchev bacterial community included several sequences related to mesophilic sulfur-oxidizing bacteria, while the archaeal component of this chimney was dominated by sequences related to the ANME-2 lineage, suggesting that anaerobic oxidation of methane may be occurring at this site. Comparative analyses of the ATP citrate lyase encoding genes from natural microbial communities suggested that Epsilonproteobacteria were the dominant primary producers using the reverse TCA cycle (rTCA) at Rainbow, while Aquificales of the genera Desulfurobacterium and Persephonella were prevalent in the Broken Spur chimney.Article · Sep 2008 +1 more author...All other clones detected at B-LC shared low sequence similarity with Candidatus ''A. boonei ,'' and grouped with clones detected at other hydrothermal vent environments [Hoek et al., 2003; Dhillon et al., 2005; Nakagawa et al., 2005 Takai et al., 2001]. A separate clone library was also constructed using korarchaeotal-specific primers Kb228F and Ua1406R [Brunk and Eis, 1998]. ABSTRACT: The bacterial and archaeal diversity of a hydrothermal vent microbial community at Brothers volcano situated in the Kermadec arc, ~400 km off the north coast of New Zealand, was examined using culture-independent molecular analysis. An unusual microbial community was detected with only 1% and 40% of the bacterial phylotypes exhibiting &92% small subunit (SSU) rRNA gene sequence similarity with cultivated and noncultivated microbes, respectively. Of the 29 bacterial representative phylotypes, over one third of the SSU rRNA gene sequences retrieved belonged to uncultivated candidate divisions including OP1, OP3, OP5, OP8, OD1, and OP11. All archaeal phylotypes belonged to the phylum Euryarchaeota in the uncultivated groups deep hydrothermal vent euryarchaeotal (DHVE) I and II or to the phylum Korarchaeota. Like the bacterial clone library, only a small proportion of archaeal SSU rRNA gene sequences (~2% and 20%) displayed &92% sequence identity with any archaeal isolates or noncultivated microbes, respectively. Although the bacterial phylotypes detected were phylogenetically most similar to microbial communities detected in methane, hydrocarbon, and carbon dioxide-based hydrothermal and seep environments, no phylotypes directly associated with anaerobic methane oxidation and mcrA activity could be detected. The geochemical composition of the vent fluids at the Brothers-lower cone sample site is unusual and we suggest that it may play a prominent role in the species selection of this microbial community. Full-text · Article · Aug 2008 +1 more author...Nercessian et al. 2003; Hoek et al. 2003; Reysenbach and Shock 2002; Takai et al. 1999 Takai et al. , 2001). In some cases it has been reported as the most dominant clone type in archaeal clone libraries (Hoek et al. 2003), yet the physiology of these organisms was unclear. Recently, Reysenbach et al. (2006) isolated and cultivated a member of the DHVE2 phylogenetic DHVE2 cluster, Candidatus ''Aciduliprofundum boonei'', and showed it to be an obligate thermoacidophilic sulphur and iron reducing heterotroph capable of growing from pH 3.3 to 5.8 and between 60 and 75°C. ABSTRACT: The lipid composition of Candidatus &Aciduliprofundum boonei&, the only cultivated representative of archaea falling in the DHVE2 phylogenetic cluster, a group of microorganisms ubiquitously occurring at hydrothermal vents, was studied. The predominant core membrane lipids in this thermophilic euryarchaeote were found to be composed of glycerol dibiphytanyl glycerol tetraethers (GDGTs) containing 0-4 cyclopentyl moieties. In addition, GDGTs with an additional covalent bond between the isoprenoid hydrocarbon chains, so-called H-shaped GDGTs, were present. The latter core lipids have been rarely reported previously. Intact polar lipid analysis revealed that they predominantly consist of GDGTs with a phospho-glycerol headgroup. Full-text · Article · Feb 2008 +1 more author...Along these gradients, many microhabitats are formed and a high diversity of micro-organisms can develop. Even though an increasing number of bacterial clone sequences in the databases originate from deep-sea habitats and also from deep-sea hydrothermal fields (Hoek et al., 2003; Ló pez-García et al., 2003; Radjasa et al., 2001; Reysenbach et al., 2000), at present only a small number of deep-sea bacteria have been cultivated. ABSTRACT: A novel Gram-negative, motile, aerobic rod-shaped bacterium was isolated from a Bathymodiolus sp. specimen collected from the Logatchev hydrothermal vent field at the Mid-Atlantic Ridge. The novel strain, M41(T), was catalase- and oxidase-positive and metabolised various carbohydrates and amino acids. It grew well in marine broth with an optimal growth temperature of 31 degrees C to 34 degrees C (range 4-40 degrees C) and salinity requirement of 3% (range 0.3-9%). The pH range for growth was pH 4.6 to 9.5, with an optimum at pH 8.0. The predominant fatty acids were C(16:1)omega7c, C(16:0) and C(18:1)omega7c. The DNA G+C content of strain M41(T) was 52.2 mol%. The 16S rRNA gene sequence was 94 % similar to that of the type strain of Oceanospirillum beijerinckii, the closest cultivated relative. Other related type strains were Oceanospirillum multiglobuliferum (93% gene sequence similarity), Neptunomonas naphthovorans (92%) and Marinobacterium jannaschii (92%). According to phylogenetic analysis and physiological characteristics, it is suggested that strain M41(T) represents a new genus and novel species for which the name Amphritea atlantica gen. nov., sp. nov. is proposed. The type strain is M41(T) (=DSM 18887(T)=LMG 24143(T)). Full-text · Article · Feb 2008 Project[...]ArticleMarch 2012 · FEMS Microbiology Ecology · Impact Factor: 3.57Iron-silica-rich low-temperature hydrothermal precipitates were collected from the CDE hydrothermal field located at the East Lau Spreading Center. Phylogenetic analysis showed that the precipitates were dominated by the members of α-proteobacteria and marine group I archaea. Ultrastructural analysis suggested the bacteriogenic origin of the iron-silica-rich deposits. Distinctive biosignatures... ArticleAugust 2010 · Sedimentary Geology · Impact Factor: 2.67Microbial biomineralization in submarine hydrothermal environments provides an insight into the formation of vent microfossils and the interactions between microbes, elements and minerals throughout the geological record. Here, we investigate microbial biomineralization of a deep-sea vent community in the Edmond vent field and provide ultrastructural evidence for the formation of microfossils... ArticleMay 2011 · Journal of Asian Earth Sciences · Impact Factor: 2.74A combined inorganic and organic geochemical study was carried out on sediments collected from the Kairei hydrothermal field on the Central Indian Ridge (CIR) and the Logatchev hydrothermal field on the Mid Atlantic Ridge (MAR). Analysis of the major and trace elements as well as the minerals shows that the Kairei hydrothermal sediments are formed by the mixing of silica-rich hydrothermal... ArticleMarch 2009 · Biology of Metals · Impact Factor: 2.50This study reports on the accumulation of iron within the tube wall of the deep sea vent macro invertebrate Vestimentiferan Ridgeia piscesae collected from Juan de Fuca ridge. Combining an array of approaches including environmental scanning electron microscope (ESEM), electron probe micro-analysis (EPMA), X-ray microanalysis (EDS) and transmission electron microscope (TEM), we provide... Data provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.This publication is from a journal that may support self archiving.}