Exploration and discovery in Yellowstone Lake: results from high-resolution sonar imaging, seismic reflection profiling, and submersible studies

Morgan, Lisa A.; Shanks, Wayne C.; Lovalvo, Dave; Johnson, Samuel Y.; Stephenson, William J.; Pierce, Kenneth L.; Harlan, Stephen S.; Finn, Carol A.; Lee, G.; Webring, Michael W.; Schulze, Boris; Duhn, J.; Sweeney, Ronald E.; Balistrieri, Laurie S.

doi:10.1016/s0377-0273(02)00503-6

Cited by 99 publications

(183 citation statements)

References 25 publications

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“…A geothermally active region of the early earth that was generally cold could contain numerous lakes and ponds, similar to Yellowstone lake in the USA, and many other environments on the modern earth, in which hydrothermal vents release plumes of hot water into cold lake water [66]. In such an environment, protocells would exist at low temperatures most of the time, during which template copying could occur, punctuated by short intervals at high temperature, leading to strand separation and an influx of nutrients such as nucleotides.…”

Section: Discussionmentioning

confidence: 99%

“…Strand separation could occur during transient high-temperature excursions, resulting from entrainment in the hot water emanating from a lacustrine hydrothermal vent, followed by rapid thermal quenching as the hot effluent mixes with surrounding cold lake or pond water [66,67]. However, the decreasing temperature will initiate strand reannealing, which competes with template copying.…”

Section: Strand Re-annealingmentioning

confidence: 99%

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The eightfold path to non-enzymatic RNA replication

2012

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The first RNA World models were based on the concept of an RNA replicase -a ribozyme that was a good enough RNA polymerase that it could catalyze its own replication. Although several RNA polymerase ribozymes have been evolved in vitro, the creation of a true replicase remains a great experimental challenge. At first glance the alternative, in which RNA replication is driven purely by chemical and physical processes, seems even more challenging, given that so many unsolved problems appear to stand in the way of repeated cycles of nonenzymatic RNA replication. Nevertheless the idea of non-enzymatic RNA replication is attractive, because it implies that the first heritable functional RNA need not have improved replication, but could have been a metabolic ribozyme or structural RNA that conferred any function that enhanced protocell reproduction or survival. In this review, I discuss recent findings that suggest that chemically driven RNA replication may not be completely impossible.

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Section: Discussionmentioning

confidence: 99%

Section: Strand Re-annealingmentioning

confidence: 99%

The eightfold path to non-enzymatic RNA replication

2012

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“…In a major metagenomic survey of this lake, samples were taken at three general different locations, representing the northern region which is rich in lake floor hydrothermal vent activity (9)(10)(11), the West Thumb region where additional lake floor vents occur but that differ in chemistry relative to the northern lake vents (9,12), and the Southeast Arm region of the lake where as yet there is no known lake floor geothermal activity. These sampling locations represent (i) different hydrothermal vents, (ii) microbial streamers associated with vent openings, (iii) mixing zones, where vent waters mix with lake water, and (iv) photic-zone water column samples, with some taken above sampled vents.…”

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confidence: 99%

Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

Zhou

Sun

Childers

et al. 2015

J Virol

101

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Virophages are a unique group of circular double-stranded DNA viruses that are considered parasites of giant DNA viruses, which in turn are known to infect eukaryotic hosts. In this study, the genomes of three novel Yellowstone Lake virophages (YSLVs)-YSLV5, YSLV6, and YSLV7-were identified from Yellowstone Lake through metagenomic analyses. The relative abundance of these three novel virophages and previously identified Yellowstone Lake virophages YSLV1 to -4 were determined in different locations of the lake, revealing that most of the sampled locations in the lake, including both mesophilic and thermophilic habitats, had multiple virophage genotypes. This likely reflects the diverse habitats or diversity of the eukaryotic hosts and their associated giant viruses that serve as putative hosts for these virophages. YSLV5 has a 29,767-bp genome with 32 predicted open reading frames (ORFs), YSLV6 has a 24,837-bp genome with 29 predicted ORFs, and YSLV7 has a 23,193-bp genome with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a close evolutionary relationship with YSLV1 to -4, whereas YSLV5 and YSLV7 are distantly related to the others, and YSLV7 represents the fourth novel virophage lineage. In addition, the genome of YSLV5 has a G؉C content of 51.1% that is much higher than all other known virophages, indicating a unique host range for YSLV5. These results suggest that virophages are abundant and have diverse genotypes that likely mirror diverse giant viral and eukaryotic hosts within the Yellowstone Lake ecosystem. IMPORTANCEThis study discovered novel virophages present within the Yellowstone Lake ecosystem using a conserved major capsid protein as a phylogenetic anchor for assembly of sequence reads from Yellowstone Lake metagenomic samples. The three novel virophage genomes (YSLV5 to -7) were completed by identifying specific environmental samples containing these respective virophages, and closing gaps by targeted PCR and sequencing. Most of the YSLV genotypes were associated primarily with photiczone and nonhydrothermal samples; however, YSLV5 had a unique distribution with an occurrence in vent samples similar to that in photic-zone samples and with a higher GC content that suggests a distinct host and habitat compared to other YSLVs. In addition, genome content and phylogenetic analyses indicate that YSLV5 and YSLV7 are distinct from known virophages and that additional as-yet-uncharacterized virophages are likely present within the Yellowstone Lake ecosystem.

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“…Hydrothermal venting in deep freshwater lakes has been discovered and studied in detail at only a few locations worldwide, including Lake Baikal, Siberia (Crane et al, 1991); Crater Lake, Oregon, USA (Dymond et al, 1989); Yellowstone Lake, Wyoming, USA (Remsen et al, 1990;Morgan et al, 2003); Lake Tanganyika, East Africa (Tiercelin et al, 1993); and Lake Taupo, North Island, New Zealand (de Ronde et al, 2002). In each of these cases, the tectonic and volcanic setting of the lakes, areas of high heat flow through the sediments, observations of water temperature anomalies, and/or presence of gas bubble plumes were the basis for SCUBA, ROV, or manned submersible explorations to locate individual sites of active venting on the lake beds.…”

Section: Introductionmentioning

confidence: 99%