Microbial diversity of a sulfide black smoker in main endeavour hydrothermal vent field, Juan de Fuca Ridge

Zhou, Huaiyang; Li, Jiangtao; Peng, Xiaotong; Meng, Jun; Wang, Fengping; Ai, Yuncan

doi:10.1007/s12275-008-0311-z

Cited by 43 publications

(56 citation statements)

References 62 publications

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“…Collectively, our culture-dependent and independent analyses suggest that Methanocaldococcus abundances are generally very low at the Endeavour Segment and Axial Volcano, with the exception of the Marker 113 and 9-m sites. This is in agreement with previous culture-dependent and independent surveys at Endeavour (29,40). Many low-temperature vent sites (or so-called "diffuse vents") are located just meters away from focused high-temperature fluid flow, possibly confining hyperthermophiles to a thin and shallow subsurface biotic reaction zone, where they would yield little net growth and biogenic fluid chemistry alteration.…”

supporting

confidence: 90%

Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents

Eecke

Butterfield

Huber

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Microbial productivity at hydrothermal vents is among the highest found anywhere in the deep ocean, but constraints on microbial growth and metabolism at vents are lacking. We used a combination of cultivation, molecular, and geochemical tools to verify pure culture H 2 threshold measurements for hyperthermophilic methanogenesis in low-temperature hydrothermal fluids from Axial Volcano and Endeavour Segment in the northeastern Pacific Ocean. Two Methanocaldococcus strains from Axial and Methanocaldococcus jannaschii showed similar Monod growth kinetics when grown in a bioreactor at varying H 2 concentrations. Their H 2 half-saturation value was 66 μM, and growth ceased below 17-23 μM H 2 , 10-fold lower than previously predicted. By comparison, measured H 2 and CH 4 concentrations in fluids suggest that there was generally sufficient H 2 for Methanocaldococcus growth at Axial but not at Endeavour. Fluids from one vent at Axial (Marker 113) had anomalously high CH 4 concentrations and contained various thermal classes of methanogens based on cultivation and mcrA/mrtA analyses. At Endeavour, methanogens were largely undetectable in fluid samples based on cultivation and molecular screens, although abundances of hyperthermophilic heterotrophs were relatively high. Where present, Methanocaldococcus genes were the predominant mcrA/mrtA sequences recovered and comprised ∼0.2-6% of the total archaeal community. Field and coculture data suggest that H 2 limitation may be partly ameliorated by H 2 syntrophy with hyperthermophilic heterotrophs. These data support our estimated H 2 threshold for hyperthermophilic methanogenesis at vents and highlight the need for coupled laboratory and field measurements to constrain microbial distribution and biogeochemical impacts in the deep sea. I t is estimated that perhaps a third [56-90 petagrams (Pg)] of the Earth's total bacterial and archaeal carbon (106-333 Pg) exists within marine subsurface sediments (1-3). These global estimates do not include microbial carbon in igneous ocean crust, wherein an additional 200 Pg of carbon has been proposed to exist primarily within its porous extrusive layer (layer 2A), where hydrothermal fluids circulate through basalt as old as 65 Ma (4). Therefore, microbes in marine sediments and ocean crust have the potential to have a significant impact on biogeochemical fluxes and carbon cycles in the deep ocean. Methanogenesis and sulfate reduction are often the predominant anaerobic microbial processes in many deep subsurface marine sediments, especially near continental margins (5, 6), and methanogens and sulfate reducers are also frequently found in deep subsurface terrestrial basalts (7-9). However, models of the rates and constraints of various aerobic and anaerobic biogeochemical processes in deep subsurface environments, especially within hard rock, are nascent because of these environments being difficult to access. This has generated interest in quantitatively modeling habitability and biogeochemical processes within the deep subsurface using...

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supporting

confidence: 90%

Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents

Eecke

Butterfield

Huber

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…(Takai and Nakamura, 2010;Flores et al, 2011). In sulfide material from the black smoker edifice Dudley in the MEF, Epsilonproteobacteria comprise more than half of the bacteria clones (Zhou et al, 2009). Functional genes from a Mothra sulfide sample show that microbial communities are mainly fueled by sulfur oxidation coupled to CO 2 fixation via the Calvin cycle (Xie et al, 2011). This observation is in keeping with the predominant CO 2 fixation role of Epsilonproteobacteria.…”

Section: Seismicity From 2003 To 2004mentioning

confidence: 67%

Endeavour Segment of the Juan de Fuca Ridge: One of the Most Remarkable Places on Earth

Kelley¹,

Carbotte²,

Caress³

et al. 2012

oceanog

106

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“…The present findings offer a complementary and simpler perspective on the difference in the prevalence of CRISPR-Cas between hyperthermophiles and mesophiles: extremely large populations in which CRISPR-Cas becomes useless according to the model results are known only for mesophiles, whereas hyperthermophiles typically exist as smaller populations (71)(72)(73)(74) in which CRISPR-Cas immunity is predicted to be efficient. More specifically, in deep-sea marine hydrothermal sediments, the cell densities of hyperthermophilic prokaryotes (primarily, Archaea) appear to vary approximately from 10 5 to 10 8 cells per g (72,(75)(76)(77)(78)(79). In contrast, substantially higher prokaryotic cell densities, on the order of 10 9 cells per g and even greater have been reported for shallow water, mesophilic sediments (80)(81)(82)(83)(84)(85)(86).…”

Section: Discussionmentioning

confidence: 96%

Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context

et al. 2013

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A stochastic, agent-based mathematical model of the coevolution of the archaeal and bacterial adaptive immunity system, CRISPR-Cas, and lytic viruses shows that CRISPR-Cas immunity can stabilize the virus-host coexistence rather than leading to the extinction of the virus. In the model, CRISPR-Cas immunity does not specifically promote viral diversity, presumably because the selection pressure on each single proto-spacer is too weak. However, the overall virus diversity in the presence of CRISPR-Cas grows due to the increase of the host and, accordingly, the virus population size. Above a threshold value of total viral diversity, which is proportional to the viral mutation rate and population size, the CRISPR-Cas system becomes ineffective and is lost due to the associated fitness cost. Our previous modeling study has suggested that the ubiquity of CRISPR-Cas in hyperthermophiles, which contrasts its comparative low prevalence in mesophiles, is due to lower rates of mutation fixation in thermal habitats. The present findings offer a complementary, simpler perspective on this contrast through the larger population sizes of mesophiles compared to hyperthermophiles, because of which CRISPR-Cas can become ineffective in mesophiles. The efficacy of CRISPR-Cas sharply increases with the number of proto-spacers per viral genome, potentially explaining the low information content of the proto-spacer-associated motif (PAM) that is required for spacer acquisition by CRISPR-Cas because a higher specificity would restrict the number of spacers available to CRISPR-Cas, thus hampering immunity. The very existence of the PAM might reflect the tradeoff between the requirement of diverse spacers for efficient immunity and avoidance of autoimmunity.

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Microbial diversity of a sulfide black smoker in main endeavour hydrothermal vent field, Juan de Fuca Ridge

Cited by 43 publications

References 62 publications

Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents

Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents

Endeavour Segment of the Juan de Fuca Ridge: One of the Most Remarkable Places on Earth

Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context

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