scholarly journals Metatranscriptomic Analysis of Diminutive Thiomargarita-Like Bacteria (“Candidatus Thiopilula” spp.) from Abyssal Cold Seeps of the Barbados Accretionary Prism

2015 ◽  
Vol 81 (9) ◽  
pp. 3142-3156 ◽  
Author(s):  
Daniel S. Jones ◽  
Beverly E. Flood ◽  
Jake V. Bailey
Keyword(s):  
Elemental Sulfur ◽  
Accretionary Prism ◽  
Sulfur Cycle ◽  
Cold Seep ◽  
Cold Seeps ◽  
Content Type ◽  
Nitrogenous Compounds ◽  
Sulfate Reducing ◽  
Sulfur Oxidizing ◽  
Spherical Cells

ABSTRACTLarge sulfur-oxidizing bacteria in the familyBeggiatoaceaeare important players in the global sulfur cycle. This group contains members of the well-known generaBeggiatoa,Thioploca, andThiomargaritabut also recently identified and relatively unknown candidate taxa, including “CandidatusThiopilula” spp. and “Ca. Thiophysa” spp. We discovered a population of “Ca. Thiopilula” spp. colonizing cold seeps near Barbados at a ∼4.7-km water depth. The Barbados population consists of spherical cells that are morphologically similar toThiomargaritaspp., with elemental sulfur inclusions and a central vacuole, but have much smaller cell diameters (5 to 40 μm). Metatranscriptomic analysis revealed that when exposed to anoxic sulfidic conditions, Barbados “Ca. Thiopilula” organisms expressed genes for the oxidation of elemental sulfur and the reduction of nitrogenous compounds, consistent with their vacuolated morphology and intracellular sulfur storage capability. Metatranscriptomic analysis further revealed that anaerobic methane-oxidizing and sulfate-reducing organisms were active in the sediment, which likely provided reduced sulfur substrates for “Ca. Thiopilula” and other sulfur-oxidizing microorganisms in the community. The novel observations of “Ca. Thiopilula” and associated organisms reported here expand our knowledge of the globally distributed and ecologically successfulBeggiatoaceaegroup and thus offer insight into the composition and ecology of deep cold seep microbial communities.

scholarly journals A deep-sea sulfate reducing bacterium directs the formation of zero-valent sulfur via sulfide oxidation

2021 ◽  
Author(s):  
Rui Liu ◽  
Yeqi Shan ◽  
Shichuan Xi ◽  
Xin Zhang ◽  
Chaomin Sun
Keyword(s):  
Deep Sea ◽  
Sulfide Oxidation ◽  
Sulfur Cycle ◽  
Cold Seep ◽  
Cold Seeps ◽  
Protein Activity ◽  
Quinone Oxidoreductase ◽  
Sulfate Reducing ◽  
Thiosulfate Reductase ◽  
Reducing Bacteria

Zero-valent sulfur (ZVS) is a critical intermediate in the biogeochemical sulfur cycle. Up to date, sulfur oxidizing bacteria have been demonstrated to dominate the formation of ZVS. In contrast, formation of ZVS mediated by sulfate reducing bacteria (SRB) has been rarely reported. Here, we report for the first time that a typical sulfate reducing bacterium Desulfovibrio marinus CS1 directs the formation of ZVS via sulfide oxidation. In combination with proteomic analysis and protein activity assays, thiosulfate reductase (PhsA) and sulfide: quinone oxidoreductase (SQR) were demonstrated to play key roles in driving ZVS formation. In this process, PhsA catalyzed thiosulfate to form sulfide, which was then oxidized by SQR to form ZVS. Consistently, the expressions of PhsA and SQR were significantly up-regulated in strain CS1 when cultured in the deep-sea cold seep, strongly indicating strain CS1 might form ZVS in its real inhabiting niches. Notably, homologs of phsA and sqr widely distributed in the metagenomes of deep-sea SRB. Given the high abundance of SRB in cold seeps, it is reasonable to propose that SRB might greatly contribute to the formation of ZVS in the deep-sea environments. Our findings add a new aspect to the current understanding of the source of ZVS.

scholarly journals Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea

2020 ◽  
Vol 11 ◽  
Author(s):  
Tingting Zhang ◽  
Xi Xiao ◽  
Songze Chen ◽  
Jing Zhao ◽  
Zongheng Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
South China Sea ◽  
Bacterial Communities ◽  
Northern South China Sea ◽  
Sulfate Reducing Bacteria ◽  
Cold Seep ◽  
Cold Seeps ◽  
Sulfate Reducing ◽  
Reducing Bacteria ◽  
Rna And Dna

Cold seep ecosystems are developed from methane-rich fluids in organic rich continental slopes, which are the source of various dense microbial and faunal populations. Extensive studies have been conducted on microbial populations in this unique environment; most of them were based on DNA, which could not resolve the activity of extant organisms. In this study, RNA and DNA analyses were performed to evaluate the active archaeal and bacterial communities and their network correlations, particularly those participating in the methane cycle at three sites of newly developed cold seeps in the northern South China Sea (nSCS). The results showed that both archaeal and bacterial communities were significantly different at the RNA and DNA levels, revealing a higher abundance of methane-metabolizing archaea and sulfate-reducing bacteria in RNA sequencing libraries. Site ROV07-01, which exhibited extensive accumulation of deceased Calyptogena clam shells, was highly developed, and showed diverse and active anaerobic archaeal methanotrophs (ANME)-2a/b and sulfate-reducing bacteria from RNA libraries. Site ROV07-02, located near carbonate crusts with few clam shell debris, appeared to be poorly developed, less anaerobic and less active. Site ROV05-02, colonized by living Calyptogena clams, could likely be intermediary between ROV07-01 and ROV07-02, showing abundant ANME-2dI and sulfate-reducing bacteria in RNA libraries. The high-proportions of ANME-2dI, with respect to ANME-2dII in the site ROV07-01 was the first report from nSCS, which could be associated with recently developed cold seeps. Both ANME-2dI and ANME-2a/b showed close networked relationships with sulfate-reducing bacteria; however, they were not associated with the same microbial operational taxonomic units (OTUs). Based on the geochemical gradients and the megafaunal settlements as well as the niche specificities and syntrophic relationships, ANMEs appeared to change in community structure with the evolution of cold seeps, which may be associated with the heterogeneity of their geochemical processes. This study enriched our understanding of more active sulfate-dependent anaerobic oxidation of methane (AOM) in poorly developed and active cold seep sediments by contrasting DNA- and RNA-derived community structure and activity indicators.

Sulfurovum indicum sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal plume in the Northwestern Indian Ocean

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Shaobin Xie ◽  
Shasha Wang ◽  
Dengfeng Li ◽  
Zongze Shao ◽  
Qiliang Lai ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Deep Sea ◽  
Type Species ◽  
Elemental Sulfur ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Sulfur Oxidizing

A novel mesophilic, hydrogen-, and sulfur-oxidizing bacterium, designated strain ST-419T, was isolated from a deep-sea hydrothermal vent plume on the Carlsberg Ridge of the Northwestern Indian Ocean. The isolate was a Gram-staining-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 4–50 °C (optimum 37 °C), pH 5.0–8.6 (optimum pH 6.0) and 1.0–5.0 % (w/v) NaCl (optimum 3.0 %). ST-419T could grow chemlithoautotrophically with molecular hydrogen, sulfide, elemental sulfur and thiosulfate as energy sources. Molecular oxygen, nitrate and elemental sulfur could be used as electron acceptors. The predominant fatty acids were C16 : 1ω7c, C18 : 1ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 42.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that ST-419T represented a member of genus Sulfurovum and was most closely related to Sulfurovum riftiae 1812ET, with 97.6 % sequence similarity. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between ST-419T and S. riftiae 1812ET were 74.6 and 19.6 %, respectively. The combined genotypic and phenotypic data indicate that ST-419T represents a novel species within the genus Sulfurovum , for which the name Sulfurovum indicum sp. nov. is proposed. The type strain is ST-419T (=MCCC 1A17954T=KCTC 25164T).

scholarly journals Isolation, Characterization, and In Situ Detection of a Novel Chemolithoautotrophic Sulfur-Oxidizing Bacterium in Wastewater Biofilms Growing under Microaerophilic Conditions

2004 ◽  
Vol 70 (5) ◽  
pp. 3122-3129 ◽  
Author(s):  
Tsukasa Ito ◽  
Kenichi Sugita ◽  
Satoshi Okabe
Keyword(s):  
Laser Scanning ◽  
Elemental Sulfur ◽  
Sulfur Cycle ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Rrna Gene ◽  
Effective Measure ◽  
Sulfur Oxidizing ◽  
Microaerophilic Conditions

ABSTRACT We successfully isolated a novel aerobic chemolithotrophic sulfur-oxidizing bacterium, designated strain SO07, from wastewater biofilms growing under microaerophilic conditions. For isolation, the use of elemental sulfur (S0), which is the most abundant sulfur pool in the wastewater biofilms, as the electron donor was an effective measure to establish an enrichment culture of strain SO07 and further isolation. 16S rRNA gene sequence analysis revealed that newly isolated strain SO07 was affiliated with members of the genus Halothiobacillus, but it was only distantly related to previously isolated species (89% identity). Strain SO07 oxidized elemental sulfur, thiosulfate, and sulfide to sulfate under oxic conditions. Strain SO07 could not grow on nitrate. Organic carbons, including acetate, propionate, and formate, could not serve as carbon and energy sources. Unlike other aerobic sulfur-oxidizing bacteria, this bacterium was sensitive to NaCl; growth in medium containing more than 150 mM was negligible. In situ hybridization combined with confocal laser scanning microscopy revealed that a number of rod-shaped cells hybridized with a probe specific for strain SO07 were mainly present in the oxic biofilm strata (ca. 0 to 100 μm) and that they often coexisted with sulfate-reducing bacteria in this zone. These results demonstrated that strain SO07 was one of the important sulfur-oxidizing populations involved in the sulfur cycle occurring in the wastewater biofilm and was primarily responsible for the oxidation of H2S and S0 to SO4 2− under oxic conditions.

scholarly journals Complete Genome Sequence of Desulfovibrio desulfuricans IC1, a Sulfonate-Respiring Anaerobe

2019 ◽  
Vol 8 (31) ◽  
Author(s):  
Leslie A. Day ◽  
Kara B. De León ◽  
Megan L. Kempher ◽  
Jizhong Zhou ◽  
Judy D. Wall
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Desulfovibrio Desulfuricans ◽  
Sulfur Cycle ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Content Type ◽  
Sulfate Reducing ◽  
Protein Coding Genes

We report the complete genome sequence of the anaerobic, sulfonate-respiring, sulfate-reducing bacterium Desulfovibrio desulfuricans IC1. The genome was assembled into a single 3.25-Mb circular chromosome with 2,680 protein-coding genes identified. Sequencing of sulfonate-metabolizing anaerobes is key for understanding sulfonate degradation and its role in the sulfur cycle.

scholarly journals Succession of Internal Sulfur Cycles and Sulfur-Oxidizing Bacterial Communities in Microaerophilic Wastewater Biofilms

2005 ◽  
Vol 71 (5) ◽  
pp. 2520-2529 ◽  
Author(s):  
Satoshi Okabe ◽  
Tsukasa Ito ◽  
Kenichi Sugita ◽  
Hisashi Satoh
Keyword(s):  
In Situ Hybridization ◽  
Sulfur Cycle ◽  
Rrna Gene ◽  
Second Phase ◽  
Sulfate Reducing ◽  
Sulfur Oxidizing ◽  
Reducing Activity ◽  
Two Phases ◽  
Microelectrode Measurements

ABSTRACT The succession of sulfur-oxidizing bacterial (SOB) community structure and the complex internal sulfur cycle occurring in wastewater biofilms growing under microaerophilic conditions was analyzed by using a polyphasic approach that employed 16S rRNA gene-cloning analysis combined with fluorescence in situ hybridization, microelectrode measurements, and standard batch and reactor experiments. A complete sulfur cycle was established via S0 accumulation within 80 days in the biofilms in replicate. This development was generally split into two phases, (i) a sulfur-accumulating phase and (ii) a sulfate-producing phase. In the first phase (until about 40 days), since the sulfide production rate (sulfate-reducing activity) exceeded the maximum sulfide-oxidizing capacity of SOB in the biofilms, H2S was only partially oxidized to S0 by mainly Thiomicrospira denitirificans with NO3 − as an electron acceptor, leading to significant accumulation of S0 in the biofilms. In the second phase, the SOB populations developed further and diversified with time. In particular, S0 accumulation promoted the growth of a novel strain, strain SO07, which predominantly carried out the oxidation of S0 to SO4 2− under oxic conditions, and Thiothrix sp. strain CT3. In situ hybridization analysis revealed that the dense populations of Thiothrix (ca. 109 cells cm−3) and strain SO07 (ca. 108 cells cm−3) were found at the sulfur-rich surface (100 μm), while the population of Thiomicrospira denitirificans was distributed throughout the biofilms with a density of ca. 107 to 108 cells cm−3. Microelectrode measurements revealed that active sulfide-oxidizing zones overlapped the spatial distributions of different phylogenetic SOB groups in the biofilms. As a consequence, the sulfide-oxidizing capacities of the biofilms became high enough to completely oxidize all H2S produced by SRB to SO4 2− in the second phase, indicating establishment of the complete sulfur cycle in the biofilms.

scholarly journals An experimental study on short-term changes in the anaerobic oxidation of methane in response to varying methane and sulfate fluxes

2009 ◽  
Vol 6 (5) ◽  
pp. 867-876 ◽  
Author(s):  
G. Wegener ◽  
A. Boetius
Keyword(s):  
Cold Seep ◽  
Anaerobic Oxidation Of Methane ◽  
Cold Seeps ◽  
Anaerobic Oxidation ◽  
Short Term ◽  
Sulfate Reducing ◽  
Oxidation Of Methane ◽  
Column System ◽  
Methane Fluxes ◽  
Anaerobic Methanotrophs

Abstract. A major role in regulation of global methane fluxes has been attributed to the process of anaerobic oxidation of methane (AOM), which is performed by consortia of methanotrophic archaea and sulfate reducing bacteria. An important question remains how these energy limited, slow growing microorganisms with generation times of 3–7 months respond to rapid natural variations in methane fluxes at cold seeps. We used an experimental flow-through column system filled with cold seep sediments naturally enriched in methanotrophic communities, to test their responses to short-term variations in methane and sulfate fluxes. At stable methane and sulfate concentrations of ~2 mM and 28 mM, respectively, we measured constant rates of AOM and sulfate reduction (SR) for up to 160 days of incubation. When percolated with methane-free medium, the anaerobic methanotrophs ceased to produce sulfide. After a starvation phase of 40 days, the addition of methane restored former AOM and SR rates immediately. At methane concentrations between 0–2.3 mM we measured a linear correlation between methane availability, AOM and SR. At constant fluid flow velocities of 30 m yr−1, ca. 50% of the methane was consumed by the anaerobic methanotrophic (ANME) population at all concentrations tested. Reducing the sulfate concentration from 28 to 1 mM, a decrease in AOM and SR by 50% was observed, and 45% of the methane was consumed. Hence, the marine anaerobic methanotrophs (ANME) are capable of oxidizing substantial amounts of methane over a wide and variable range of fluxes of the reaction educts.

scholarly journals Microbial Sulfur Cycle in Two Hydrothermal Chimneys on the Southwest Indian Ridge

mBio ◽  
2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Huiluo Cao ◽  
Yong Wang ◽  
On On Lee ◽  
Xiang Zeng ◽  
Zongze Shao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Sulfur Oxidation ◽  
Sulfur Cycle ◽  
Southwest Indian Ridge ◽  
Sulfate Reducing ◽  
Sulfur Oxidizing ◽  
Indian Ridge ◽  
Midocean Ridge ◽  
Reducing Bacteria ◽  
Hydrothermal Fields

ABSTRACT Sulfur is an important element in sustaining microbial communities present in hydrothermal vents. Sulfur oxidation has been extensively studied due to its importance in chemosynthetic pathways in hydrothermal fields; however, less is known about sulfate reduction. Here, the metagenomes of hydrothermal chimneys located on the ultraslow-spreading Southwest Indian Ridge (SWIR) were pyrosequenced to elucidate the associated microbial sulfur cycle. A taxonomic summary of known genes revealed a few dominant bacteria that participated in the microbial sulfur cycle, particularly sulfate-reducing Deltaproteobacteria. The metagenomes studied contained highly abundant genes related to sulfur oxidation and reduction. Several carbon metabolic pathways, in particular the Calvin-Benson-Bassham pathway and the reductive tricarboxylic acid cycles for CO2 fixation, were identified in sulfur-oxidizing autotrophic bacteria. In contrast, highly abundant genes related to the oxidation of short-chain alkanes were grouped with sulfate-reducing bacteria, suggesting an important role for short-chain alkanes in the sulfur cycle. Furthermore, sulfur-oxidizing bacteria were associated with enrichment for genes involved in the denitrification pathway, while sulfate-reducing bacteria displayed enrichment for genes responsible for hydrogen utilization. In conclusion, this study provides insights regarding major microbial metabolic activities that are driven by the sulfur cycle in low-temperature hydrothermal chimneys present on an ultraslow midocean ridge. IMPORTANCE There have been limited studies on chimney sulfides located at ultraslow-spreading ridges. The analysis of metagenomes of hydrothermal chimneys on the ultraslow-spreading Southwest Indian Ridge suggests the presence of a microbial sulfur cycle. The sulfur cycle should be centralized within a microbial community that displays enrichment for sulfur metabolism-related genes. The present study elucidated a significant role of the microbial sulfur cycle in sustaining an entire microbial community in low-temperature hydrothermal chimneys on an ultraslow spreading midocean ridge, which has characteristics distinct from those of other types of hydrothermal fields.

scholarly journals Mimicking the Microbial Oxidation of Elemental Sulfur with a Biphasic Electrochemical Cell

2021 ◽  
Author(s):  
Marco F. Suárez-Herrera ◽  
Jose Solla-Gullon ◽  
Micheal D. Scanlon
Keyword(s):  
Driving Force ◽  
Elemental Sulfur ◽  
Electrochemical Cell ◽  
Sulfur Oxidation ◽  
Sulfur Cycle ◽  
Ambient Conditions ◽  
Microbial Oxidation ◽  
Artificial System ◽  
Sulfur Oxidizing ◽  
Aqueous Anions

<p>The lack of an artificial system that mimics elemental sulfur (S<sub>8</sub>) oxidation by microorganisms inhibits a deep mechanistic understanding of the sulfur cycle in the biosphere and the metabolism of sulfur-oxidizing microorganisms. In this article, we present a biphasic system that mimics biochemical sulfur oxidation under ambient conditions using a liquid|liquid (L|L) electrochemical cell and gold nanoparticles (AuNPs) as an interfacial catalyst. The interface between two solvents of very different polarity is an ideal environment to oxidise S<sub>8</sub>, overcoming the <a>incompatible solubilities </a>of the hydrophobic reactants (O<sub>2</sub> and S<sub>8</sub>) and hydrophilic products (H<sup>+</sup>, SO<sub>3</sub><sup>2–</sup>, SO<sub>4</sub><sup>2–</sup>, <i>etc.</i>). The interfacial AuNPs provide a catalytic surface onto which O<sub>2</sub> and S<sub>8</sub> can adsorb. Control over the driving force for the reaction is provided by polarizing the L|L interface externally and tuning the Fermi level of the interfacial AuNPs by the adsorption of aqueous anions.</p>

Pyrite and the Global Environment

Pyrite ◽  
2015 ◽  
Author(s):  
David Rickard
Keyword(s):  
Iron Sulfide ◽  
Sulfide Oxidation ◽  
Sulfate Reducing Bacteria ◽  
Sulfide Mineral ◽  
Sulfur Cycle ◽  
Sulfate Reducing ◽  
Global Dynamic ◽  
Sulfur Oxidizing ◽  
Life On Earth ◽  
Reducing Bacteria

The two basic processes concerning pyrite in the environment are the formation of pyrite, which usually involves reduction of sulfate to sulfide, and the destruction of pyrite, which usually involves oxidation of sulfide to sulfate. On an ideal planet these two processes might be exactly balanced. But pyrite is buried in sediments sometimes for hundreds of millions of years, and the sulfur in this buried pyrite is removed from the system, so the balance is disturbed. The lack of balance between sulfide oxidation and sulfate reduction powers a global dynamic cycle for sulfur. This would be complex enough if this were the whole story. However, as we have seen, both the reduction and oxidation arms of the global cycle are essentially biological—specifically microbiological—processes. This means that there is an intrinsic link between the sulfur cycle and life on Earth. In this chapter, we examine the central role that pyrite plays, and has played, in determining the surface environment of the planet. In doing so we reveal how pyrite, the humble iron sulfide mineral, is a key component of maintaining and developing life on Earth. In Chapter 4 we concluded that Mother Nature must be particularly fond of pyrite framboids: a thousand billion of these microscopic raspberry-like spheres are formed in sediments every second. If we translate this into sulfur production, some 60 million tons of sulfur is buried as pyrite in sediments each year. But this is only a fraction of the total amount of sulfide produced every year by sulfate-reducing bacteria. In 1982 the Danish geomicrobiologist Bo Barker Jørgensen discovered that as much as 90% of the sulfide produced by sulfate-reducing bacteria was rapidly reoxidized by sulfur-oxidizing microorganisms. Sulfate-reducing microorganisms actually produce about 300 million tons of sulfur each year, but about 240 million tons is reoxidized. The magnitude of the sulfide production by sulfate-reducing bacte­ria can be appreciated by comparison with the sulfur produced by volcanoes. As discussed in Chapter 5, it was previously supposed that all sulfur, and thus pyrite, had a volcanic origin. In fact volcanoes produce just 10 million tons of sulfur each year.

Sign in / Sign up

Export Citation Format

Share Document