scholarly journals Novel, Attached, Sulfur-Oxidizing Bacteria at Shallow Hydrothermal Vents Possess Vacuoles Not Involved in Respiratory Nitrate Accumulation

2004 ◽  
Vol 70 (12) ◽  
pp. 7487-7496 ◽  
Author(s):  
Karen M. Kalanetra ◽  
Sherry L. Huston ◽  
Douglas C. Nelson
Keyword(s):  
Hydrothermal Vents ◽  
Repeated Measurements ◽  
Rrna Gene ◽  
Nitrate Accumulation ◽  
Sulfur Bacteria ◽  
Physiological Properties ◽  
Large Central Vacuole ◽  
White Point ◽  
Sulfur Oxidizing ◽  
Shallow Hydrothermal Vents

ABSTRACT Novel, vacuolate sulfur bacteria occur at shallow hydrothermal vents near White Point, Calif. There, these filaments are attached densely to diverse biotic and abiotic substrates and extend one to several centimeters into the surrounding environment, where they are alternately exposed to sulfidic and oxygenated seawater. Characterizations of native filaments collected from this location indicate that these filaments possess novel morphological and physiological properties compared to all other vacuolate bacteria characterized to date. Attached filaments, ranging in diameter from 4 to 100 μm or more, were composed of cylindrical cells, each containing a thin annulus of sulfur globule-filled cytoplasm surrounding a large central vacuole. A near-complete 16S rRNA gene sequence was obtained and confirmed by fluorescent in situ hybridization to be associated only with filaments having a diameter of 10 μm or more. Phylogenetic analysis indicates that these wider, attached filaments form within the gamma proteobacteria a monophyletic group that includes all previously described vacuolate sulfur bacteria (the genera Beggiatoa, Thioploca, and Thiomargarita) and no nonvacuolate genera. However, unlike for all previously described vacuolate bacteria, repeated measurements of cell lysates from samples collected over 2 years indicate that the attached White Point filaments do not store internal nitrate. It is possible that these vacuoles are involved in transient storage of oxygen or contribute to the relative buoyancy of these filaments.

Some Physiological Properties of Three Novel Fe(II)- and Sulfur-Oxidizing Strains Affiliated to Alicyclobacillus

2009 ◽  
Vol 71-73 ◽  
pp. 247-250
Author(s):  
C.Y. Jiang ◽  
Xu Guo ◽  
X.Y. You ◽  
Yan Yang Liu ◽  
S.J. Liu
Keyword(s):  
16S Rrna ◽  
Mine Drainage ◽  
Carbon Sources ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Phylogenetic Studies ◽  
Physiological Properties ◽  
Sulfur Oxidizing

This study focused on the soils of sofataric region and acid mine drainage from a copper mine. Based on cultivation, 8 and 6 strains that grow on Fe(II) and sulfur compounds, respectively, were obtained from samples from these two environments. Analysis of 16S rRNA genes of the 14 strains indicated that they were affiliated to Acidithiobacillus, Alicyclobacillus, Sulfobacillus and Leptospirillum. Physiological and phylogenetic studies indicated that three strains (TC-34, TC-71 and ZJ-6) might represent three novel members of Alicyclobacillus. These strains showed 94.8-97.1% 16S rRNA gene identity to other species of Alicyclobacillus. Otherwise, strain TC-34, TC-71 and ZJ-6 showed a range of phenotypic characteristics that differentiated them from previously recognized Alicyclobacillus species, including the growth temperature, assimilation of carbon sources and production of acids from a range of compounds. Chemoautotrophic growth using Fe2+, elemental sulfur and tetrathionate as sole energy source was observed. Especially strain TC-71 was obligately dependent on Fe(II) for growth and quickly oxidized Fe2+. It is concluded that the Fe(II)-oxidizers are metabolically diverse and represent novel Alicyclobacillus species. These are proposed to take part in biogeochemical cycling of iron and sulfur in the solfataric region and could be relevant for biomining.

Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from a deep-sea hydrothermal field, and an emended description of the genus Thiohalomonas

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 235-241 ◽  
Author(s):  
Koji Mori ◽  
Ken-ichiro Suzuki ◽  
Kaoru Yamaguchi ◽  
Tetsuro Urabe ◽  
Satoshi Hanada
Keyword(s):  
Hydrothermal Vents ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Emended Description ◽  
Novel Genus And Species ◽  
Sulfur Oxidizing

A novel, obligately chemolithoautotrophic, sulfur-oxidizing bacterial strain, designated strain gps52T, was isolated from a rock sample collected near the hydrothermal vents of the Suiyo Seamount in the Pacific Ocean. The cells possessed a Gram-stain-negative-type cell wall and contained menaquinone-8(H4) and menaquinone-9(H4) as respiratory quinones, and C16 : 1ω7c, C16 : 0 and C18 : 1ω7c as major cellular fatty acids. Neither storage compounds nor extensive internal membranes were observed in the cells. Strain gps52T grew using carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as electron acceptor. Optimal growth was observed at 32 °C, pH 6.5 and with 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain gps52T belongs to the family Ectothiorhodospiraceae and is different from any other known bacteria, with sequence similarities of less than 93 %. Based on phenotypic and phylogenetic findings, the isolate is considered to represent a novel genus and species in the family Ectothiorhodospiraceae , and the name Thiogranum longum gen. nov., sp. nov. is proposed. The type strain is gps52T ( = NBRC 101260T = DSM 19610T). An emended description of the genus Thiohalomonas is also proposed.

Phaeospirillum oryzae sp. nov., a spheroplast-forming, phototrophic alphaproteobacterium from a paddy soil

2011 ◽  
Vol 61 (7) ◽  
pp. 1656-1661 ◽  
Author(s):  
K. V. N. S. Lakshmi ◽  
Ch. Sasikala ◽  
S. Takaichi ◽  
Ch. V. Ramana
Keyword(s):  
Sequence Similarity ◽  
Molecular Genetic ◽  
Rrna Gene ◽  
Sulfur Bacteria ◽  
Physiological Properties ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Taxonomic Approach ◽  
Molecular Genetic Evidence ◽  
Type Strains

Two strains (JA317T and JA559) of spiral shaped, spheroplast-forming, anaerobic, Gram-negative, motile purple non-sulfur bacteria were isolated from rhizosphere soils of paddy and were characterized by a polyphasic taxonomic approach. Bacteriochlorophyll a and carotenoids, rhodopin, lycopene and rhodopin glucoside, were present as photosynthetic pigments. Intracellular photosynthetic membranes were of stacked type. The major fatty acids were C18 : 1ω7c, C16 : 0 and C16 : 1ω6c/C16 : 1ω7c in both strains. The genomic DNA G+C content was 63.3±0.8 mol%. The two strains were closely related (mean DNA–DNA hybridization >85 %). Phylogenetic analysis showed that the strains clustered with the species of the genus Phaeospirillum, which belongs to the family Rhodospirillaceae within the class Alphaproteobacteria. Based on 16S rRNA gene sequence analysis, strains JA317T and JA559 showed highest sequence similarity with the type strains of Phaeospirillum chandramohanii (98.2 %), Phaeospirillum molischianum (97.4 %) and Phaeospirillum fulvum (97.1 %) of the family Rhodospirillaceae. Strain JA317T can be clearly distinguished from P. chandramohanii with respect to spheroplast formation and several other morphological and physiological properties. DNA–DNA relatedness of strain JA317T with its closest relatives of the genus Phaeospirillum was less than 55 %. It is evident from the phenotypic, chemotaxonomic and molecular genetic evidence that strain JA317T represents a novel species of the genus Phaeospirillum, for which the name Phaeospirillum oryzae sp. nov., is proposed. The type strain of the species is JA317T ( = NBRC 104938T  = KCTC 5704T).

scholarly journals Phylogenetic Diversity of Archaea in Shallow Hydrothermal Vents of Eolian Islands, Italy

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 156 ◽  
Author(s):  
Concetta Gugliandolo ◽  
Teresa L. Maugeri
Keyword(s):  
Hydrothermal Vents ◽  
Inorganic Compounds ◽  
Archaeal Community ◽  
Hydrothermal Systems ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Vulcano Island ◽  
High Concentrations ◽  
Shallow Hydrothermal Vents ◽  
The 16S Rrna Gene

Shallow hydrothermal systems (SHS) around the Eolian Islands (Italy), related to both active and extinct volcanism, are characterized by high temperatures, high concentrations of CO2 and H2S, and low pH, prohibitive for the majority of eukaryotes which are less tolerant to the extreme conditions than prokaryotes. Archaea and bacteria are the key elements for the functioning of these ecosystems, as they are involved in the transformation of inorganic compounds released from the vent emissions and are at the basis of the hydrothermal system food web. New extremophilic archaea (thermophilic, hyperthermophilic, acidophilic, alkalophilic, etc.) have been isolated from vents of Vulcano Island, exhibiting interesting features potentially valuable in biotechnology. Metagenomic analyses, which mainly involved molecular studies of the 16S rRNA gene, provided different insights into microbial composition associated with Eolian SHS. Archaeal community composition at Eolian vent sites results greatly affected by the geochemistry of the studied vents, principally by hypersaline conditions and declining temperatures. Archaeal community in sediments was mostly composed by hyperthermophilic members of Crenarchaeota (class Thermoprotei) and Euryarchaeota (Thermococci and Methanococci) at the highest temperature condition. Mesophilic Euryarchaeota (Halobacteria, Methanomicrobia, and Methanobacteria) increased with decreasing temperatures. Eolian SHS harbor a high diversity of largely unknown archaea, and the studied vents may be an important source of new isolates potentially useful for biotechnological purposes.

scholarly journals Sulfur bacteria promote dissolution of authigenic carbonates at marine methane seeps

2021 ◽  
Author(s):  
Dalton J. Leprich ◽  
Beverly E. Flood ◽  
Peter R. Schroedl ◽  
Elizabeth Ricci ◽  
Jeffery J. Marlow ◽  
...  
Keyword(s):  
Carbonate Rocks ◽  
Sulfur Oxidation ◽  
Methane Seeps ◽  
Etch Pits ◽  
Active Dissolution ◽  
Authigenic Carbonates ◽  
Sulfur Bacteria ◽  
Sulfur Oxidizing ◽  
Sulfur Oxidizing Bacteria

AbstractCarbonate rocks at marine methane seeps are commonly colonized by sulfur-oxidizing bacteria that co-occur with etch pits that suggest active dissolution. We show that sulfur-oxidizing bacteria are abundant on the surface of an exemplar seep carbonate collected from Del Mar East Methane Seep Field, USA. We then used bioreactors containing aragonite mineral coupons that simulate certain seep conditions to investigate plausible in situ rates of carbonate dissolution associated with sulfur-oxidizing bacteria. Bioreactors inoculated with a sulfur-oxidizing bacterial strain, Celeribacter baekdonensis LH4, growing on aragonite coupons induced dissolution rates in sulfidic, heterotrophic, and abiotic conditions of 1773.97 (±324.35), 152.81 (±123.27), and 272.99 (±249.96) μmol CaCO3 • cm−2 • yr−1, respectively. Steep gradients in pH were also measured within carbonate-attached biofilms using pH-sensitive fluorophores. Together, these results show that the production of acidic microenvironments in biofilms of sulfur-oxidizing bacteria are capable of dissolving carbonate rocks, even under well-buffered marine conditions. Our results support the hypothesis that authigenic carbonate rock dissolution driven by lithotrophic sulfur-oxidation constitutes a previously unknown carbon flux from the rock reservoir to the ocean and atmosphere.

scholarly journals Coupling of Bacterial Endosymbiont and Host Mitochondrial Genomes in the Hydrothermal Vent Clam Calyptogena magnifica

2003 ◽  
Vol 69 (4) ◽  
pp. 2058-2064 ◽  
Author(s):  
Luis A. Hurtado ◽  
Mariana Mateos ◽  
Richard A. Lutz ◽  
Robert C. Vrijenhoek
Keyword(s):  
Dna Sequences ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Nuclear Gene ◽  
Sexual Population ◽  
Origin And Evolution ◽  
Bacterial Endosymbionts ◽  
Sulfur Oxidizing ◽  
Tight Association ◽  
Clam Population

ABSTRACT The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Vesicomyidae) depends for its nutrition on sulfur-oxidizing symbiotic bacteria housed in its gill tissues. This symbiont is transmitted vertically between generations via the clam's eggs; however, it remains uncertain whether occasionally symbionts are horizontally transmitted or acquired from the environment. If symbionts are transmitted strictly vertically through the egg cytoplasm, inheritance of symbiont lineages should behave as if coupled to the host's maternally inherited mitochondrial DNA. This coupling would be obscured, however, with low rates of horizontal or environmental transfers, the equivalent of recombination between host lineages. Population genetic analyses of C. magnifica clams and associated symbionts from eastern Pacific hydrothermal vents clearly supported the hypothesis of strictly maternal cotransmission. Host mitochondrial and symbiont DNA sequences were coupled in a clam population that was polymorphic for both genetic markers. These markers were not similarly coupled with sequence variation at a nuclear gene locus, as expected for a randomly mating sexual population. Phylogenetic analysis of the two cytoplasmic genes also revealed no evidence for recombination. The tight association between vesicomyid clams and their vertically transmitted bacterial endosymbionts is phylogenetically very young (<50 million years) and may serve as a model for the origin and evolution of eukaryotic organelles.

scholarly journals Phylogenetically novel uncultured microbial cells dominate Earth microbiomes

2018 ◽  
Author(s):  
Karen G. Lloyd ◽  
Joshua Ladau ◽  
Andrew D. Steen ◽  
Junqi Yin ◽  
Lonnie Crosby
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hydrothermal Vents ◽  
Hot Springs ◽  
Laboratory Culture ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Microbial Cells ◽  
Taxonomic Groups

AbstractTo unequivocally determine a microbe’s physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically-novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been well-studied, their global abundances, or number of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly-available metagenome and metatranscriptome databases, which we show are largely free of the culture-bias present in primer-amplified 16S rRNA gene surveys, to their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundance of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, non-human hosts, snow and bioreactors (22-87% uncultured genera to classes and 0-64% uncultured phyla). The exceptions were human and human-associated environments which were dominated by cultured genera (45-97%). We estimate that uncultured genera and phyla could comprise 7.3 × 1029(81%) and 2.2 × 1029(25%) microbial cells, respectively. Uncultured phyla were over-represented in meta transcript omes relative to metagenomes (46-84% of sequences in a given environment), suggesting that they are viable, and possibly more active than cultured clades. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate non-human environments on Earth, and their undiscovered physiologies may matter for Earth systems.

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).

Limnovirga soli gen. nov., sp. nov., isolated from river sediment

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Kyung June Yim ◽  
Dong-Hyun Jung ◽  
Seok Won Jang ◽  
Sanghwa Park
Keyword(s):  
Phylogenetic Trees ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Genome Analyses

A cream-coloured, Gram-stain-negative, rod-shaped bacterium, designated strain KSC-6T, was isolated from soil sampled at the Gapcheon River watershed in Daejeon, Republic of Korea. The organism does not require NaCl for growth and grows at pH 6.0–8.0 (optimum, pH 7.0) and 10–37 °C (optimum, 25 °C). Phylogenetic trees based on the 16S rRNA gene sequences reveal that strain KSC-6T belongs to the family Chitinophagaceae within the order Chitinophagales and is most closely related to Panacibacter ginsenosidivorans Gsoil 1550T (95.9% similarity). The genomic DNA G+C content was 38.9 mol%. The major cellular fatty acids (>8 %) of strain KCS-6T were iso-C15:0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone 7 and the predominant polar lipids were phosphatidylethanolamine, five unidentified aminolipids and two unidentified lipids. Based on genome analyses, low digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values with closely related genera, and differential chemotaxonomic and physiological properties, we suggest that strain KCS-6T represents a novel species in a new genus in the family Chitinophagaceae , for which the name Limnovirga soli gen. nov., sp. nov. (type strain KCS-6T=KCCM 43337T=NBRC 114336T) is proposed.

scholarly journals Genomic Insights into Two Novel Fe(II)-Oxidizing Zetaproteobacteria Isolates Reveal Lifestyle Adaption to Coastal Marine Sediments

2020 ◽  
Vol 86 (17) ◽  
Author(s):  
Nia Blackwell ◽  
Casey Bryce ◽  
Daniel Straub ◽  
Andreas Kappler ◽  
Sara Kleindienst
Keyword(s):  
Oxidative Stress ◽  
Marine Sediments ◽  
Hydrothermal Vents ◽  
Sequence Similarity ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Coastal Marine Sediments ◽  
Content Type ◽  
Coastal Marine ◽  
Stress Related Genes

ABSTRACT The discovery of the novel Zetaproteobacteria class greatly expanded our understanding of neutrophilic, microaerophilic microbial Fe(II) oxidation in marine environments. Despite molecular techniques demonstrating their global distribution, relatively few isolates exist, especially from low-Fe(II) environments. Furthermore, the Fe(II) oxidation pathways used by Zetaproteobacteria remain poorly understood. Here, we present the genomes (>99% genome completeness) of two Zetaproteobacteria, which are the only cultivated isolates originating from typical low-Fe [porewater Fe(II), 70 to 100 μM] coastal marine sediments. The two strains share <90% average nucleotide identity (ANI) with each other and <80% ANI with any other Zetaproteobacteria genome. The closest relatives were Mariprofundus aestuarium strain CP-5 and Mariprofundus ferrinatatus strain CP-8 (96 to 98% 16S rRNA gene sequence similarity). Fe(II) oxidation of strains KV and NF is most likely mediated by the putative Fe(II) oxidase Cyc2. Interestingly, the genome of strain KV also encodes a putative multicopper oxidase, PcoAB, which could play a role in Fe(II) oxidation, a pathway found only in two other Zetaproteobacteria genomes (Ghiorsea bivora TAG-1 and SCGC AB-602-C20). The strains show potential adaptations to fluctuating O2 concentrations, indicated by the presence of both cbb3- and aa3-type cytochrome c oxidases, which are adapted to low and high O2 concentrations, respectively. This is further supported by the presence of several oxidative-stress-related genes. In summary, our results reveal the potential Fe(II) oxidation pathways employed by these two novel chemolithoautotrophic Fe(II)-oxidizing species and the lifestyle adaptations which enable the Zetaproteobacteria to survive in coastal environments with low Fe(II) and regular redox fluctuations. IMPORTANCE Until recently, the importance and relevance of Zetaproteobacteria were mainly thought to be restricted to high-Fe(II) environments, such as deep-sea hydrothermal vents. The two novel Mariprofundus isolates presented here originate from typical low-Fe(II) coastal marine sediments. As well as being low in Fe(II), these environments are often subjected to fluctuating O2 concentrations and regular mixing by wave action and bioturbation. The discovery of two novel isolates highlights the importance of these organisms in such environments, as Fe(II) oxidation has been shown to impact nutrients and trace metals. Genome analysis of these two strains further supported their lifestyle adaptation and therefore their potential preference for coastal marine sediments, as genes necessary for surviving dynamic O2 concentrations and oxidative stress were identified. Furthermore, our analyses also expand our understanding of the poorly understood Fe(II) oxidation pathways used by neutrophilic, microaerophilic Fe(II) oxidizers.

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