Geomicrobiology of deep‐sea deposits: estimating community diversity from low‐temperature seafloor rocks and minerals

Rogers, Daniel R.; Santelli, Cara M.; Edwards, Katrina J.

doi:10.1046/j.1472-4669.2003.00009.x

Cited by 45 publications

(53 citation statements)

References 31 publications

(45 reference statements)

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“…Marinobacter aquaeolei VT8 was obtained from the American Type Culture Collection (strain number 700491) and cultivated according to ATCC recommendations. DNA was isolated based on methods adapted from Rogers et al (58).…”

Section: Methodsmentioning

confidence: 99%

Genomic Potential of Marinobacter aquaeolei, a Biogeochemical “Opportunitroph”

Singer

Webb

Nelson

et al. 2011

Appl Environ Microbiol

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112

109

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The genus of Marinobacter is one of the most ubiquitous in the global oceans and assumed to significantly impact various biogeochemical cycles. The genome structure and content of Marinobacter aquaeolei VT8 was analyzed and compared with those from other organisms with diverse adaptive strategies. Here, we report the many "opportunitrophic" genetic characteristics and strategies that M. aquaeolei has adopted to promote survival under various environmental conditions. Genome analysis revealed its metabolic potential to utilize oxygen and nitrate as terminal electron acceptors, iron as an electron donor, and urea, phosphonate, and various hydrocarbons as alternative N, P, and C sources, respectively. Miscellaneous sensory and defense mechanisms, apparently acquired via horizontal gene transfer, are involved in the perception of environmental fluctuations and antibiotic, phage, toxin, and heavy metal resistance, enabling survival under adverse conditions, such as oil-polluted water. Multiple putative integrases, transposases, and plasmids appear to have introduced additional metabolic potential, such as phosphonate degradation. The genomic potential of M. aquaeolei and its similarity to other opportunitrophs are consistent with its cosmopolitan occurrence in diverse environments and highly variable lifestyles.

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Section: Methodsmentioning

confidence: 99%

Genomic Potential of Marinobacter aquaeolei, a Biogeochemical “Opportunitroph”

Singer

Webb

Nelson

et al. 2011

Appl Environ Microbiol

Self Cite

112

109

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“…The cell densities on the reacted chimney sulfides were on the order of 10 5 cells mm Ϫ2 . Further studies with sulfides from an active high-temperature chimney revealed that the microbial communities were dominated by bacteria and that diversity levels decreased with increasing oxidation of the chimney material (470). In addition to Zetaproteobacteria, which have been documented on fresher sulfide material, species related to the Gammaproteobacteria grouping of Marinobacter and Halomonas are commonly found in 16S rRNA gene surveys of sulfide materials with a range of oxidation states (134,470).…”

Section: Vol 75 2011 Microbial Ecology Of the Dark Ocean 389mentioning

confidence: 99%

“…Further studies with sulfides from an active high-temperature chimney revealed that the microbial communities were dominated by bacteria and that diversity levels decreased with increasing oxidation of the chimney material (470). In addition to Zetaproteobacteria, which have been documented on fresher sulfide material, species related to the Gammaproteobacteria grouping of Marinobacter and Halomonas are commonly found in 16S rRNA gene surveys of sulfide materials with a range of oxidation states (134,470). More recent analysis of vent chimneys surrounding chloride-enriched or -depleted vents at the Brothers Volcano on the Kermadec Arc revealed that archaeal communities do not appear to vary with chloride influence, being dominated by marine benthic group E, while the bacterial communities do appear to vary with chloride enrichment (534).…”

Section: Vol 75 2011 Microbial Ecology Of the Dark Ocean 389mentioning

confidence: 99%

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

Orcutt

Sylvan

Knab

et al. 2011

Microbiol Mol Biol Rev

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590

499

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SUMMARY The majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.

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“…Studies of the role of microbial communities on the weathering of hydrothermal vent deposits at Endeavour show that community diversity decreases with decreasing reactivity of the sulfide component and increasing presence of alteration products (Rogers et al, 2003).…”

Section: Seismicity From 2003 To 2004mentioning

confidence: 99%