scholarly journals Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities

2012 ◽  
Vol 79 (4) ◽  
pp. 1183-1190 ◽  
Author(s):  
Barbara J. MacGregor ◽  
Jennifer F. Biddle ◽  
Jason R. Siebert ◽  
Eric Staunton ◽  
Eric L. Hegg ◽  
...  
Keyword(s):  
Nitrite Reductase ◽  
Pure Culture ◽  
Gulf Of California ◽  
Microbial Mats ◽  
Physiological Role ◽  
Nitrite Reduction ◽  
Cold Seeps ◽  
Single Filament ◽  
Guaymas Basin ◽  
Content Type

ABSTRACTOrange, white, and yellow vacuolatedBeggiatoaceaefilaments are visually dominant members of microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments typically concentrated toward the mat centers. No marine vacuolateBeggiatoaceaeare yet in pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing bacteria. The nearly complete genome sequence of a single orangeBeggiatoa(“CandidatusMaribeggiatoa”) filament from a microbial mat sample collected in 2008 at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid chromatography (HPLC) nano-electrospray tandem mass spectrometry (μLC–MS-MS) of a pigmented band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related to a large group of octaheme cytochromes whose few characterized representatives are hydroxylamine or hydrazine oxidases. The protein was partially purified and shown byin vitroassays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities. From what is known ofBeggiatoaceaephysiology, nitrite reduction is the most likelyin vivorole of the octaheme protein, but future experiments are required to confirm this tentative conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise identification of an abundant mat protein, and its potential activities could be assayed, proof of its physiological role remains elusive in the absence of a pure culture that can be genetically manipulated.

scholarly journals Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps

2015 ◽  
Vol 81 (10) ◽  
pp. 3451-3459 ◽  
Author(s):  
Adrien Vigneron ◽  
Stéphane L'Haridon ◽  
Anne Godfroy ◽  
Erwan G. Roussel ◽  
Barry A. Cragg ◽  
...  
Keyword(s):  
Methane Production ◽  
Gulf Of California ◽  
Microbial Mats ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Cold Seep ◽  
Cold Seeps ◽  
Content Type ◽  
Biogenic Methane ◽  
Gradient Gel Electrophoresis ◽  
Anaerobic Methanotrophs

ABSTRACTIn the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenicArchaeawere detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophicMethanococcoidesburtoniirelatives and several new autotrophicMethanogeniumlineages, confirming the cooccurrence ofMethanosarcinalesandMethanomicrobialesmethanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.

scholarly journals Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

2013 ◽  
Vol 79 (13) ◽  
pp. 3974-3985 ◽  
Author(s):  
Barbara J. MacGregor ◽  
Jennifer F. Biddle ◽  
Andreas Teske
Keyword(s):  
Gulf Of California ◽  
Bacterial Species ◽  
Draft Genome ◽  
Genetic Exchange ◽  
23S Rrna ◽  
Rrna Gene ◽  
Homing Endonucleases ◽  
Guaymas Basin ◽  
Content Type ◽  
Group I

ABSTRACTThe draft genome sequence of a single orangeBeggiatoa(“CandidatusMaribeggiatoa”) filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to thefdxNexcision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceaematches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in otherBeggiatoaceaegenomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.

scholarly journals Comparative study of vent and seep macrofaunal communities in the Guaymas Basin

2015 ◽  
Vol 12 (18) ◽  
pp. 5455-5479 ◽  
Author(s):  
M. Portail ◽  
K. Olu ◽  
E. Escobar-Briones ◽  
J. C. Caprais ◽  
L. Menot ◽  
...  
Keyword(s):  
Deep Sea ◽  
Gulf Of California ◽  
Microbial Mats ◽  
Abiotic Factors ◽  
Ecological Processes ◽  
Guaymas Basin ◽  
The Family ◽  
Family Level ◽  
Higher Temperature ◽  
Macrofaunal Community

Abstract. Understanding the ecological processes and connectivity of chemosynthetic deep-sea ecosystems requires comparative studies. In the Guaymas Basin (Gulf of California, Mexico), the presence of seeps and vents in the absence of a biogeographic barrier, and comparable sedimentary settings and depths offers a unique opportunity to assess the role of ecosystem-specific environmental conditions on macrofaunal communities. Six seep and four vent assemblages were studied, three of which were characterised by common major foundation taxa: vesicomyid bivalves, siboglinid tubeworms and microbial mats. Macrofaunal community structure at the family level showed that density, diversity and composition patterns were primarily shaped by seep- and vent-common abiotic factors including methane and hydrogen sulfide concentrations, whereas vent environmental specificities (higher temperature, higher metal concentrations and lower pH) were not significant. The type of substratum and the heterogeneity provided by foundation species were identified as additional structuring factors and their roles were found to vary according to fluid regimes. At the family level, seep and vent similarity reached at least 58 %. All vent families were found at seeps and each seep-specific family displayed low relative abundances (< 5 %). Moreover, 85 % of the identified species among dominant families were shared between seep and vent ecosystems. This study provides further support to the hypothesis of continuity among deep-sea seep and vent ecosystems.

scholarly journals Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California)

2013 ◽  
Vol 7 (8) ◽  
pp. 1595-1608 ◽  
Author(s):  
Adrien Vigneron ◽  
Perrine Cruaud ◽  
Patricia Pignet ◽  
Jean-Claude Caprais ◽  
Marie-Anne Cambon-Bonavita ◽  
...  
Keyword(s):  
Gulf Of California ◽  
Cold Seeps ◽  
Guaymas Basin ◽  
Methane Oxidizer

scholarly journals Comparative study of vent and seep macrofaunal communities in the Guaymas Basin

2015 ◽  
Vol 12 (11) ◽  
pp. 8497-8571 ◽  
Author(s):  
M. Portail ◽  
K. Olu ◽  
E. Escobar-Briones ◽  
J. C. Caprais ◽  
L. Menot ◽  
...  
Keyword(s):  
Deep Sea ◽  
Gulf Of California ◽  
Microbial Mats ◽  
Abiotic Factors ◽  
Common Species ◽  
Ecological Processes ◽  
Community Patterns ◽  
Guaymas Basin ◽  
Higher Temperature ◽  
Macrofaunal Community

Abstract. Understanding the ecological processes and connectivity of chemosynthetic deep-sea ecosystems requires comparative studies. In the Guaymas Basin (Gulf of California, Mexico), the presence of seeps and vents in the absence of biogeographic barrier, comparable sedimentary settings and depths offers a unique opportunity to assess the role of ecosystem specific environmental conditions on macrofaunal communities. Six seep and four vent assemblages were studied, three of which were characterised by common major foundation taxa: vesicomyid bivalves, siboglinid tubeworms and microbial mats. Macrofaunal community structure at the family level showed that density, diversity and composition patterns were primarily shaped by seep and vent common abiotic factors including methane and hydrogen sulphide concentrations. The type of substratum and the heterogeneity provided by foundation species were identified as additional structuring factors and their roles were found to vary according to fluid regimes. Surprisingly, the presence of vent environmental specificities, with higher temperature, higher metal concentrations and lower pH was not significant in explaining community patterns. Moreover, Guaymas seep and vent shared an important number of common species suggesting frequent connections between the two ecosystems. Finally, this study provides further support for the hypothesis of continuity among deep-sea seep and vent ecosystems.

scholarly journals Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

2015 ◽  
Vol 197 (21) ◽  
pp. 3400-3408 ◽  
Author(s):  
Lara Rajeev ◽  
Amy Chen ◽  
Alexey E. Kazakov ◽  
Eric G. Luning ◽  
Grant M. Zane ◽  
...  
Keyword(s):  
Nitrite Reductase ◽  
Nitrite Reduction ◽  
System Response ◽  
Desulfovibrio Vulgaris ◽  
Two Component System ◽  
Component System ◽  
Content Type ◽  
Sulfate Reducing ◽  
Low Concentrations ◽  
Two Component

ABSTRACTSulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields.Desulfovibrio vulgarisHildenborough, a model SRB, carries a cytochromec-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of thenrfHAoperon in response to nitrite stress. We also show thatnrfRis needed for fitness at low cell densities in the presence of nitrite because inactivation ofnrfRaffects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of thenrfHAoperon using purified NrfR in gel shift assays. We discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizingDesulfovibriospp.IMPORTANCEThe NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of thenrfAgene has been studied in only a few nitrate-utilizing bacteria. Here, we show that inD. vulgaris, a bacterium that does not respire nitrate, the expression ofnrfHAis induced by NrfR upon nitrite stress. This is the first report of regulation ofnrfAby a sigma54-dependent two-component system. Our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB.

GENESIS OF THE AUTHIGENIC DEPOSITS ASSOCIATED WITH COLD SEEPS SITES IN GUAYMAS BASIN (GULF OF CALIFORNIA-MEXICO)

2020 ◽  
Author(s):  
Felipe Gil bernal ◽  
◽  
Emmanuel Escorcia-Ocampo ◽  
Montserrat Moreno Torres ◽  
Carles Canet ◽  
...  
Keyword(s):  
Gulf Of California ◽  
Cold Seeps ◽  
Guaymas Basin

scholarly journals Characteristics and Evolution of sill-driven off-axis hydrothermalism in Guaymas Basin – the Ringvent site

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Andreas Teske ◽  
Luke J. McKay ◽  
Ana Christina Ravelo ◽  
Ivano Aiello ◽  
Carlos Mortera ◽  
...  
Keyword(s):  
Gulf Of California ◽  
Sedimentary Cover ◽  
Intermediate Stage ◽  
Hydrothermal Activity ◽  
Hydrothermal Systems ◽  
Spreading Center ◽  
Cold Seeps ◽  
Guaymas Basin ◽  
Thermal Anomalies ◽  
New Type

Abstract The Guaymas Basin spreading center, at 2000 m depth in the Gulf of California, is overlain by a thick sedimentary cover. Across the basin, localized temperature anomalies, with active methane venting and seep fauna exist in response to magma emplacement into sediments. These sites evolve over thousands of years as magma freezes into doleritic sills and the system cools. Although several cool sites resembling cold seeps have been characterized, the hydrothermally active stage of an off-axis site was lacking good examples. Here, we present a multidisciplinary characterization of Ringvent, an ~1 km wide circular mound where hydrothermal activity persists ~28 km northwest of the spreading center. Ringvent provides a new type of intermediate-stage hydrothermal system where off-axis hydrothermal activity has attenuated since its formation, but remains evident in thermal anomalies, hydrothermal biota coexisting with seep fauna, and porewater biogeochemical signatures indicative of hydrothermal circulation. Due to their broad potential distribution, small size and limited life span, such sites are hard to find and characterize, but they provide critical missing links to understand the complex evolution of hydrothermal systems.

scholarly journals Archaeal Populations in Hypersaline Sediments Underlying Orange Microbial Mats in the Napoli Mud Volcano

2011 ◽  
Vol 77 (9) ◽  
pp. 3120-3131 ◽  
Author(s):  
Cassandre Sara Lazar ◽  
Stéphane L'Haridon ◽  
Patricia Pignet ◽  
Laurent Toffin
Keyword(s):  
Microbial Mats ◽  
Archaeal Community ◽  
Community Diversity ◽  
Mud Volcano ◽  
Anaerobic Oxidation Of Methane ◽  
Cold Seeps ◽  
Content Type ◽  
Methane Cycling ◽  
Oxidation Of Methane ◽  
Sediment Layers

ABSTRACTMicrobial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the “active” archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophicArchaea(ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophicMethanococcoidesin shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano.

scholarly journals Microbial Communities Under Distinct Thermal and Geochemical Regimes in Axial and Off-Axis Sediments of Guaymas Basin

2021 ◽  
Vol 12 ◽  
Author(s):  
Andreas Teske ◽  
Gunter Wegener ◽  
Jeffrey P. Chanton ◽  
Dylan White ◽  
Barbara MacGregor ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Gulf Of California ◽  
Hydrothermal Vents ◽  
Active Sites ◽  
Cold Seep ◽  
Sediment Surface ◽  
Energy Sources ◽  
Cold Seeps ◽  
Guaymas Basin ◽  
Microbiological Characteristics

Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial valley, and cold seep sites at Octopus Mound, a carbonate mound with abundant methanotrophic cold seep fauna at the Central Seep location on the northern off-axis flanking regions, show consistent geochemical and microbial differences between hot, temperate, cold seep, and background sites. The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. Thermal, biogeochemical, and microbiological characteristics of the sampling locations indicate that sediment thermal regime and seep-derived or hydrothermal energy sources structure the microbial communities at the sediment surface.

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