scholarly journals Novel Bacterial and Archaeal Lineages from an In Situ Growth Chamber Deployed at a Mid-Atlantic Ridge Hydrothermal Vent

2000 ◽  
Vol 66 (9) ◽  
pp. 3798-3806 ◽  
Author(s):  
Anna-Louise Reysenbach ◽  
Krista Longnecker ◽  
Julie Kirshtein
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrogen Oxidation ◽  
Sulfur Metabolism ◽  
Rrna Genes ◽  
Growth Chamber ◽  
In Situ Growth ◽  
Small Subunit Rrna ◽  
Mid Atlantic Ridge

ABSTRACT The phylogenetic diversity was determined for a microbial community obtained from an in situ growth chamber placed on a deep-sea hydrothermal vent on the Mid-Atlantic Ridge (23�22′ N, 44�57′ W). The chamber was deployed for 5 days, and the temperature within the chamber gradually decreased from 70 to 20�C. Upon retrieval of the chamber, the DNA was extracted and the small-subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific for theArchaea or Bacteria domain and cloned. Unique rDNA sequences were identified by restriction fragment length polymorphisms, and 38 different archaeal and bacterial phylotypes were identified from the 85 clones screened. The majority of the archaeal sequences were affiliated with the Thermococcales (71%) and Archaeoglobales (22%) orders. A sequence belonging to the Thermoplasmales confirms that thermoacidophiles may have escaped enrichment culturing attempts of deep-sea hydrothermal vent samples. Additional sequences that represented deeply rooted lineages in the low-temperature eurarchaeal (marine group II) and crenarchaeal clades were obtained. The majority of the bacterial sequences obtained were restricted to the Aquificales(18%), the ɛ subclass of the Proteobacteria(ɛ-Proteobacteria) (40%), and the genusDesulfurobacterium (25%). Most of the clones (28%) were confined to a monophyletic clade within the ɛ-Proteobacteria with no known close relatives. The prevalence of clones related to thermophilic microbes that use hydrogen as an electron donor and sulfur compounds (S0, SO4, thiosulfate) indicates the importance of hydrogen oxidation and sulfur metabolism at deep-sea hydrothermal vents. The presence of sequences that are related to sequences from hyperthermophiles, moderate thermophiles, and mesophiles suggests that the diversity obtained from this analysis may reflect the microbial succession that occurred in response to the shift in temperature and possible associated changes in the chemistry of the hydrothermal fluid.

scholarly journals “Candidatus Desulfobulbus rimicarensis,” an Uncultivated Deltaproteobacterial Epibiont from the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata

2020 ◽  
Vol 86 (8) ◽  
Author(s):  
Lijing Jiang ◽  
Xuewen Liu ◽  
Chunming Dong ◽  
Zhaobin Huang ◽  
Marie-Anne Cambon-Bonavita ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Sulfur Metabolism ◽  
Extracellular Polysaccharides ◽  
Free Living ◽  
Content Type ◽  
Sulfur Disproportionation ◽  
Rimicaris Exoculata ◽  
Mid Atlantic Ridge

ABSTRACT The deep-sea hydrothermal vent shrimp Rimicaris exoculata largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of R. exoculata from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a Deltaproteobacteria epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus Desulfobulbus, representing a potential novel species for which the name “Candidatus Desulfobulbus rimicarensis” is proposed. Genomic and transcriptomic analyses reveal that this bacterium utilizes the Wood-Ljungdahl pathway for carbon assimilation and harvests energy via sulfur disproportionation, which is significantly different from other shrimp epibionts. Additionally, this epibiont has putative nitrogen fixation activity, but it is extremely active in directly taking up ammonia and urea from the host or vent environments. Moreover, the epibiont could be distinguished from its free-living relatives by various features, such as the lack of chemotaxis and motility traits, a dramatic reduction in biosynthesis genes for capsular and extracellular polysaccharides, enrichment of genes required for carbon fixation and sulfur metabolism, and resistance to environmental toxins. Our study highlights the unique role and symbiotic adaptation of Deltaproteobacteria in deep-sea hydrothermal vent shrimps. IMPORTANCE The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe “Candidatus Desulfobulbus rimicarensis,” an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host.

scholarly journals Development of an Easy-to-Operate Underwater Raman System for Deep-Sea Cold Seep and Hydrothermal Vent In Situ Detection

Sensors ◽  
2021 ◽  
Vol 21 (15) ◽  
pp. 5090
Author(s):  
Qingsheng Liu ◽  
Jinjia Guo ◽  
Wangquan Ye ◽  
Kai Cheng ◽  
Fujun Qi ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Methane Hydrate ◽  
Sulfur Cycle ◽  
Cold Seep ◽  
Remotely Operated Vehicle ◽  
Bacterial Mats ◽  
Optical Module ◽  
In Situ Detection

As a powerful in situ detection technique, Raman spectroscopy is becoming a popular underwater investigation method, especially in deep-sea research. In this paper, an easy-to-operate underwater Raman system with a compact design and competitive sensitivity is introduced. All the components, including the optical module and the electronic module, were packaged in an L362 × Φ172 mm titanium capsule with a weight of 20 kg in the air (about 12 kg in water). By optimising the laser coupling mode and focusing lens parameters, a competitive sensitivity was achieved with the detection limit of SO42− being 0.7 mmol/L. The first sea trial was carried out with the aid of a 3000 m grade remotely operated vehicle (ROV) “FCV3000” in October 2018. Over 20,000 spectra were captured from the targets interested, including methane hydrate, clamshell in the area of cold seep, and bacterial mats around a hydrothermal vent, with a maximum depth of 1038 m. A Raman peak at 2592 cm−1 was found in the methane hydrate spectra, which revealed the presence of hydrogen sulfide in the seeping gas. In addition, we also found sulfur in the bacterial mats, confirming the involvement of micro-organisms in the sulfur cycle in the hydrothermal field. It is expected that the system can be developed as a universal deep-sea survey and detection equipment in the near future.

Microbial diversity in deep-sea sediments from the Menez Gwen hydrothermal vent system of the Mid-Atlantic Ridge

2015 ◽  
Vol 24 ◽  
pp. 343-355 ◽  
Author(s):  
Teresa Cerqueira ◽  
Diogo Pinho ◽  
Conceição Egas ◽  
Hugo Froufe ◽  
Bjørn Altermark ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Deep Sea Sediments ◽  
Mid Atlantic Ridge ◽  
Menez Gwen

scholarly journals Specificity of Associations between Bacteria and the Coral Pocillopora meandrina during Early Development

2012 ◽  
Vol 78 (20) ◽  
pp. 7467-7475 ◽  
Author(s):  
Amy Apprill ◽  
Heather Q. Marlow ◽  
Mark Q. Martindale ◽  
Michael S. Rappé
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Roseobacter Clade ◽  
Small Subunit Rrna ◽  
Content Type ◽  
Sterile Seawater ◽  
Show Evidence ◽  
Coral Health

ABSTRACTRelationships between corals and specific bacterial associates are thought to play an important role in coral health. In this study, the specificity of bacteria associating with the coralPocillopora meandrinawas investigated by exposing coral embryos to various strains of cultured marine bacteria, sterile seawater, or raw seawater and examining the identity, density, and location of incorporated cells. The isolates utilized in this experiment included members of the Roseobacter and SAR11 clades of theAlphaproteobacteria, aPseudoalteromonasspecies of theGammaproteobacteria, and aSynechococcusspecies of theCyanobacteriaphylum. Based on terminal restriction fragment length polymorphism analysis of small-subunit rRNA genes, similarities in bacterial communities associated with 170-h-old planulae were observed regardless of treatment, suggesting that bacteria may have been externally associated from the outset of the experiment. Microscopic examination ofP. meandrinaplanulae by fluorescencein situhybridization with bacterial and Roseobacter clade-specific oligonucleotide probes revealed differences in the densities and locations of planulae-associated cells. Planulae exposed to either raw seawater or strains ofPseudoalteromonasand Roseobacter harbored the highest densities of internally associated cells, of which 20 to 100% belonged to the Roseobacter clade. Planulae exposed to sterile seawater or strains of the SAR11 clade andSynechococcusdid not show evidence of prominent bacterial associations. Additional analysis of the raw-seawater-exposed planulae via electron microscopy confirmed the presence of internally associated prokaryotic cells, as well as virus-like particles. These results suggest that the availability of specific microorganisms may be an important factor in the establishment of coral-bacterial relationships.

Ultrastructural characteristics of spermatogenesis in three species of deep-sea hydrothermal vent mytilids

1997 ◽  
Vol 75 (2) ◽  
pp. 308-316 ◽  
Author(s):  
Marcel Le Pennec ◽  
Peter G. Beninger
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
The North ◽  
Male Gametes ◽  
Bathymodiolus Thermophilus ◽  
Nutritional Biology ◽  
Protandric Hermaphroditism ◽  
Mid Atlantic Ridge ◽  
Ultrastructural Characteristics ◽  
Species Specific

To enhance our understanding of the reproductive biology of deep-sea hydrothermal vent mytilids, the histology of the male gonad and the ultrastructure of its gametes were studied in Bathymodiolus thermophilus, B. puteoserpentis, and B. elongatus. Specimens of B. thermophilus were collected at the 13°N site on the East Pacific ridge, while B. puteoserpentis were sampled from the Snake Pit site of the mid-Atlantic ridge and B. elongatus were obtained from the North Fiji Basin. Gonad histology conformed to the typical bivalve profile; the differences in the proportions of acinal and interacinal tissue, as well as differences in acinal fullness in B. puteoserpentis, indicate that gametogenesis is discontinuous in these deep-sea mytilids. Evidence of protandric hermaphroditism was observed in B. elongatus, which exhibited acini containing both maturing and residual male gametes and immature oocytes. The ultrastructural characteristics of the male gametes conform to those described for littoral bivalve species, and the spermatozoon is of the primitive type. No species-specific differences in spermatozoon ultrastructure were discerned. No evidence of bacterial inclusions was found in either the gametes or the associated gonad cells in any of the species examined. The male gametes are thus probably not vectors for the endosymbiotic bacteria that characterize the nutritional biology of the adults in this genus.

scholarly journals Microbial Composition of Near-Boiling Silica-Depositing Thermal Springs throughout Yellowstone National Park

2002 ◽  
Vol 68 (10) ◽  
pp. 5123-5135 ◽  
Author(s):  
Carrine E. Blank ◽  
Sherry L. Cady ◽  
Norman R. Pace
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hydrogen Oxidation ◽  
Large Subunit ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Microbial Composition

ABSTRACT The extent of hyperthermophilic microbial diversity associated with siliceous sinter (geyserite) was characterized in seven near-boiling silica-depositing springs throughout Yellowstone National Park using environmental PCR amplification of small-subunit rRNA genes (SSU rDNA), large-subunit rDNA, and the internal transcribed spacer (ITS). We found that Thermocrinis ruber, a member of the order Aquificales, is ubiquitous, an indication that primary production in these springs is driven by hydrogen oxidation. Several other lineages with no known close relatives were identified that branch among the hyperthermophilic bacteria. Although they all branch deep in the bacterial tree, the precise phylogenetic placement of many of these lineages is unresolved at this time. While some springs contained a fair amount of phylogenetic diversity, others did not. Within the same spring, communities in the subaqueous environment were not appreciably different than those in the splash zone at the edge of the pool, although a greater number of phylotypes was found along the pool's edge. Also, microbial community composition appeared to have little correlation with the type of sinter morphology. The number of cell morphotypes identified by fluorescence in situ hybridization and scanning electron microscopy was greater than the number of phylotypes in SSU clone libraries. Despite little variation in Thermocrinis ruber SSU sequences, abundant variation was found in the hypervariable ITS region. The distribution of ITS sequence types appeared to be correlated with distinct morphotypes of Thermocrinis ruber in different pools. Therefore, species- or subspecies-level divergences are present but not detectable in highly conserved SSU sequences.

In Situ Measurements of Chemical Distributions in a Deep-Sea Hydrothermal Vent Field

Science ◽  
1986 ◽  
Vol 231 (4742) ◽  
pp. 1139-1141 ◽  
Author(s):  
K. S. JOHNSON ◽  
C. L. BEEHLER ◽  
C. M. SAKAMOTO-ARNOLD ◽  
J. J. CHILDRESS
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
In Situ Measurements ◽  
Hydrothermal Vent Field

Periodic deep‐sea hydrothermal vent activities observed by hydrophones at Mariana, Okinawa, and Mid‐Atlantic Ridge

1996 ◽  
Vol 100 (4) ◽  
pp. 2639-2639
Author(s):  
Kasahara Junzo ◽  
Sato Toshinori ◽  
Nishizawa Azusa ◽  
Fujioka Kantaro
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Mid Atlantic Ridge

scholarly journals Abundant and Diverse Fungal Microbiota in the Murine Intestine

2006 ◽  
Vol 72 (1) ◽  
pp. 793-801 ◽  
Author(s):  
Alexandra J Scupham ◽  
Laura L. Presley ◽  
Bo Wei ◽  
Elizabeth Bent ◽  
Natasha Griffith ◽  
...  
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Culture Independent ◽  
Specific Pathogen ◽  
Health And Disease ◽  
Oligonucleotide Fingerprinting ◽  
Rrna Sequences

ABSTRACT Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4′,6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.

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