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278 results on '"Hamilton, Trinity L."'

61. The role of biology in planetary evolution: cyanobacterial primary production in low‐oxygen Proterozoic oceans

Author

Hamilton, Trinity L., Bryant, Donald A., and Macalady, Jennifer L.

Subjects
Atmosphere, Earth, Planet, Fossils, Oceans and Seas, Minireviews, Geology, Environment, Cyanobacteria, Biological Evolution, Biota, Oxygen, Sulfur Isotopes, Minireview, Photosynthesis, Evolution, Planetary, Oxidation-Reduction, Ecosystem
Abstract

Summary Understanding the role of biology in planetary evolution remains an outstanding challenge to geobiologists. Progress towards unravelling this puzzle for Earth is hindered by the scarcity of well‐preserved rocks from the Archean (4.0 to 2.5 Gyr ago) and Proterozoic (2.5 to 0.5 Gyr ago) Eons. In addition, the microscopic life that dominated Earth's biota for most of its history left a poor fossil record, consisting primarily of lithified microbial mats, rare microbial body fossils and membrane‐derived hydrocarbon molecules that are still challenging to interpret. However, it is clear from the sulfur isotope record and other geochemical proxies that the production of oxygen or oxidizing power radically changed Earth's surface and atmosphere during the Proterozoic Eon, pushing it away from the more reducing conditions prevalent during the Archean. In addition to ancient rocks, our reconstruction of Earth's redox evolution is informed by our knowledge of biogeochemical cycles catalysed by extant biota. The emergence of oxygenic photosynthesis in ancient cyanobacteria represents one of the most impressive microbial innovations in Earth's history, and oxygenic photosynthesis is the largest source of O 2 in the atmosphere today. Thus the study of microbial metabolisms and evolution provides an important link between extant biota and the clues from the geologic record. Here, we consider the physiology of cyanobacteria (the only microorganisms capable of oxygenic photosynthesis), their co‐occurrence with anoxygenic phototrophs in a variety of environments and their persistence in low‐oxygen environments, including in water columns as well as mats, throughout much of Earth's history. We examine insights gained from both the rock record and cyanobacteria presently living in early Earth analogue ecosystems and synthesize current knowledge of these ancient microbial mediators in planetary redox evolution. Our analysis supports the hypothesis that anoxygenic photosynthesis, including the activity of metabolically versatile cyanobacteria, played an important role in delaying the oxygenation of Earth's surface ocean during the Proterozoic Eon.

Published
2015

67. Draft genome sequence of the piezotolerant and crude oil-degrading bacterium rhodococcus qingshengii strain TUHH-12

Author

Lincoln, Sara A., Hamilton, Trinity L., Valladares Juárez, Ana Gabriela, Schedler, Martina, Macalady, Jennifer L., Müller, Rudolf, Freeman, Katherine H., Lincoln, Sara A., Hamilton, Trinity L., Valladares Juárez, Ana Gabriela, Schedler, Martina, Macalady, Jennifer L., Müller, Rudolf, and Freeman, Katherine H.

Abstract

We report here the draft genome sequence of Rhodococcus qingshengii strain TUHH-12. The ability of this piezotolerant bacterium to grow on crude oil and tetracosane as sole carbon sources at 150 × 10(5) Pa makes it useful in studies of hydrocarbon degradation under simulated deep-sea conditions.

Published
2018

71. Crystal structure of the L protein of Rhodobacter sphaeroides light-independent protochlorophyllide reductase with MgADP bound: a homologue

Author

Sarma, Ranjana, Barney, Brett M., Hamilton, Trinity L., Jones, Alma, Seefeldt, Lance C., and Peters, John W.

Subjects
Bacterial proteins -- Structure, Bacterial proteins -- Physiological aspects, Bacterial proteins -- Properties, Bacterial proteins -- Research, Ferritin -- Physiological aspects, Ferritin -- Research, Oxidoreductases -- Physiological aspects, Oxidoreductases -- Research, Biological sciences, Chemistry
Abstract

The purification, X-ray structure determination, and nucleotide interaction of the L protein (BchL) of the dark-operative protochlorophyllide reductase (DPOR) from Rhodobacter sphaeroides is described. The results from the comparison of structure of BchL with its close homologue, the nitrogenase Fe protein, provide insight into the discrimination between respective functions of proteins in microbial systems.

Published
2008

74. The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5

Author

Therien, Jesse B., primary, Artz, Jacob H., additional, Poudel, Saroj, additional, Hamilton, Trinity L., additional, Liu, Zhenfeng, additional, Noone, Seth M., additional, Adams, Michael W. W., additional, King, Paul W., additional, Bryant, Donald A., additional, Boyd, Eric S., additional, and Peters, John W., additional

Published
2017
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79. Draft genome sequence of the piezotolerant and crude oil-degrading bacterium rhodococcus qingshengii strain TUHH-12

Author

Lincoln, Sara A., Hamilton, Trinity L., Valladares Juárez, Ana Gabriela, Schedler, Martina, Macalady, Jennifer L., Müller, Rudolf, and Freeman, Katherine H.

Subjects
600: Technik, 540: Chemie
Abstract

We report here the draft genome sequence of Rhodococcus qingshengii strain TUHH-12. The ability of this piezotolerant bacterium to grow on crude oil and tetracosane as sole carbon sources at 150 × 10(5) Pa makes it useful in studies of hydrocarbon degradation under simulated deep-sea conditions.

Published
2015
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91. Cyanobacterial photosynthesis under sulfidic conditions: insights from the isolate Leptolyngbyasp. strain hensonii

Author

Hamilton, Trinity L, Klatt, Judith M, de Beer, Dirk, and Macalady, Jennifer L

Abstract

We report the isolation of a pinnacle-forming cyanobacterium isolated from a microbial mat covering the sediment surface at Little Salt Spring—a flooded sinkhole in Florida with a perennially microoxic and sulfidic water column. The draft genome of the isolate encodes all of the enzymatic machinery necessary for both oxygenic and anoxygenic photosynthesis, as well as genes for methylating hopanoids at the C-2 position. The physiological response of the isolate to H2S is complex: (i) no induction time is necessary for anoxygenic photosynthesis; (ii) rates of anoxygenic photosynthesis are regulated by both H2S and irradiance; (iii) O2production is inhibited by H2S concentrations as low as 1 μMand the recovery rate of oxygenic photosynthesis is dependent on irradiance; (iv) under the optimal light conditions for oxygenic photosynthesis, rates of anoxygenic photosynthesis are nearly double those of oxygenic photosynthesis. We hypothesize that the specific adaptation mechanisms of the isolate to H2S emerged from a close spatial interaction with sulfate-reducing bacteria. The new isolate, Leptolyngbyasp. strain hensonii, is not closely related to other well-characterized Cyanobacteria that can perform anoxygenic photosynthesis, which further highlights the need to characterize the diversity and biogeography of metabolically versatile Cyanobacteria. The isolate will be an ideal model organism for exploring the adaptation of Cyanobacteria to sulfidic conditions.

Published
2018
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92. Geobiological feedbacks and the evolution of thermoacidophiles

Author

Colman, Daniel R, Poudel, Saroj, Hamilton, Trinity L, Havig, Jeff R, Selensky, Matthew J, Shock, Everett L, and Boyd, Eric S

Abstract

Oxygen-dependent microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O2. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O2, and that these events likely occurred in the recent evolutionary past. Comparative genomic analyses indicated that archaeal thermoacidophiles from independent lineages are enriched in similar protein-coding genes, consistent with convergent evolution aided by horizontal gene transfer. Because the generation of acidic environments and their successful habitation characteristically require O2, these results suggest that thermoacidophilic Archaea and the acidity of their habitats co-evolved after the evolution of oxygenic photosynthesis. Moreover, it is likely that dissolved O2concentrations in thermal waters likely did not reach levels capable of sustaining aerobic thermoacidophiles and their acidifying activity until ~0.8 Ga, when present day atmospheric levels were reached, a time period that is supported by our estimation of divergence times for archaeal thermoacidophilic clades.

Published
2018
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95. Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance.

Author

Preisner, Eva C., Fichot, Erin B., Norman, Robert S., Hamilton, Trinity L., and Lee, Charles K.

Subjects
MICROBIAL mats, BIOSPHERE, ECOLOGICAL disturbances
Abstract

The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the protein synthesis potential (PSP) of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. This ecosystem experienced a large shift in salinity (230 to 65 g kg-1) during 2011-2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and PSP of abundant and rare taxa, suggesting overall compositional and functional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low PSP across conditions, the overall community PSP increased post-disturbance, with significant shifts occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and PSP. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models. [ABSTRACT FROM AUTHOR]

Published
2016
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96. Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area.

Author

Neng Fei Wang, Tao Zhang, Xiao Yang, Shuang Wang, Yong Yu, Long Long Dong, Yu Dong Guo, Yong Xing Ma, Jia Ye Zang, Ventosa, Antonio, and Hamilton, Trinity L.

Subjects
SOIL microbiology, BACTERIAL communities, BACTERIAL genetics, LAKE sediment microbiology, LAKES
Abstract

This study assessed the diversity and composition of bacterial communities within soils and lake sediments from an Arctic lake area (London Island, Svalbard). A total of 2,987 operational taxonomic units were identified by high-throughput sequencing, targeting bacterial 16S rRNA gene. The samples from four sites (three samples in each site) were significantly different in geochemical properties and bacterial community composition. Proteobacteria and Acidobacteria were abundant phyla in the nine soil samples, whereas Proteobacteria and Bacteroidetes were abundant phyla in the three sediment samples. Furthermore, Actinobacteria, Chlorobi, Chloroflexi, Elusimicrobia, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria significantly varied in their abundance among the four sampling sites. Additionally, members of the dominant genera, such as Clostridium, Luteolibacter, Methylibium, Rhodococcus, and Rhodoplanes, were significantly different in their abundance among the four sampling sites. Besides, distance-based redundancy analysis revealed that pH (p < 0.001), water content (p < 0.01), ammonium nitrogen (NH-4, p < 0.01), silicate silicon (SiO42- -Si, p < 0.01), nitrite nitrogen (NO2- -N, p < 0.05), organic carbon (p < 0.05), and organic nitrogen (p < 0.05) were the most significant factors that correlated with the bacterial community composition. The results suggest soils and sediments from a lake area in the Arctic harbor a high diversity of bacterial communities, which are influenced by many geochemical factors of Arctic environments. [ABSTRACT FROM AUTHOR]

Published
2016
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97. The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions.

Author

Bukin, Sergei V., Pavlova, Olga N., Manakov, Andrei Y., Kostyreva, Elena A., Chernitsyna, Svetlana M., Mamaeva, Elena V., Pogodaeva, Tatyana V., Zemskaya, Tamara I., Grunden, Amy Michele, and Hamilton, Trinity L.

Subjects
MICROBIAL contamination, BIOSPHERE, METHANE
Abstract

The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from lowtemperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids. [ABSTRACT FROM AUTHOR]

Published
2016
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