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Life
Volume 3
Issue 2
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Life, Volume 3, Issue 2 (June 2013) – 5 articles , Pages 295-362

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575 KiB  
Article
Heterotrophic Protists in Hypersaline Microbial Mats and Deep Hypersaline Basin Water Columns
by Virginia P. Edgcomb and Joan M. Bernhard
Life 2013, 3(2), 346-362; https://doi.org/10.3390/life3020346 - 22 May 2013
Cited by 21 | Viewed by 10751
Abstract
Although hypersaline environments pose challenges to life because of the low water content (water activity), many such habitats appear to support eukaryotic microbes. This contribution presents brief reviews of our current knowledge on eukaryotes of water-column haloclines and brines from Deep Hypersaline Anoxic [...] Read more.
Although hypersaline environments pose challenges to life because of the low water content (water activity), many such habitats appear to support eukaryotic microbes. This contribution presents brief reviews of our current knowledge on eukaryotes of water-column haloclines and brines from Deep Hypersaline Anoxic Basins (DHABs) of the Eastern Mediterranean, as well as shallow-water hypersaline microbial mats in solar salterns of Guerrero Negro, Mexico and benthic microbialite communities from Hamelin Pool, Shark Bay, Western Australia. New data on eukaryotic diversity from Shark Bay microbialites indicates eukaryotes are more diverse than previously reported. Although this comparison shows that eukaryotic communities in hypersaline habitats with varying physicochemical characteristics are unique, several groups are commonly found, including diverse alveolates, strameonopiles, and fungi, as well as radiolaria. Many eukaryote sequences (SSU) in both regions also have no close homologues in public databases, suggesting that these environments host unique microbial eukaryote assemblages with the potential to enhance our understanding of the capacity of eukaryotes to adapt to hypersaline conditions. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
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Figure 1
<p>Hamelin Pool, Shark Bay, W. Australia microbialites. (<b>A</b>) smooth mat; (<b>B</b>) colloform mat.</p> Full article ">Figure 2
<p>Stacked histogram of eukaryotic operational taxonomic units (out) composition of (97% sequence similarity, weighted data presentation) in Hamelin Pool, Australia microbialite and water samples based on eukaryote sequences (SSU) rRNA signatures (cDNA template). Y-axis corresponds to fraction of OTUs affiliating with each grouping out of 100%. S = smooth mat, C = colloform, P = Pustular.</p> Full article ">Figure 3
<p>LSCM images of microbialites in FLEC sections from Hamelin Pool. (<b>A</b>) Sediment-water interface showing masses of cyanobacteria comprising pustular mat; (<b>B</b>) Foraminifer (*) inhabiting smooth mat; (<b>C</b>) Foraminifera (*) inhabiting colloform mat. Arrows = indeterminate protists; * = foraminifer; + = ooid with concentric layering. Scales = 200 µm.</p> Full article ">Figure 4
<p>Discovery Basin, Eastern Mediterranean Sea (3,582 m depth). Image taken with ROV <span class="html-italic">Jason</span>, showing the Deep Hypersaline Anoxic Basins (DHAB) “beach” (white zone where the halocline intersects the seafloor) at the edge of the brine pool (right). Note floating garbage in the brine pool.</p> Full article ">Figure 5
<p>Scanning electron micrographs of microbial eukaryotes from the water-column haloclines of Urania and Discovery Basins in the Eastern Mediterraean Sea. (<b>A</b>) A scuticociliate morphotype consistently associated with epibiotic bacteria (<b>B</b>) that has been found to be the most abundant eukaryotic morphotype in the Urania halocline [<a href="#B45-life-03-00346" class="html-bibr">45</a>]; (<b>B</b>) A flagellate in Urania halocline. (<b>C</b>) A larger ciliate associated with long (10–20 µm), thin, filamentous bacteria, which was the most abundant eukaryotic morphotype in the Discovery halocline [<a href="#B45-life-03-00346" class="html-bibr">45</a>]. Scale bars = 2 µm. Photos by William Orsi.</p> Full article ">
720 KiB  
Article
Prebiotic Chemistry: Geochemical Context and Reaction Screening
by Henderson James Cleaves II
Life 2013, 3(2), 331-345; https://doi.org/10.3390/life3020331 - 29 Apr 2013
Cited by 43 | Viewed by 12687
Abstract
The origin of life on Earth is widely believed to have required the reactions of organic compounds and their self- and/or environmental organization. What those compounds were remains open to debate, as do the environment in and process or processes by which they [...] Read more.
The origin of life on Earth is widely believed to have required the reactions of organic compounds and their self- and/or environmental organization. What those compounds were remains open to debate, as do the environment in and process or processes by which they became organized. Prebiotic chemistry is the systematic organized study of these phenomena. It is difficult to study poorly defined phenomena, and research has focused on producing compounds and structures familiar to contemporary biochemistry, which may or may not have been crucial for the origin of life. Given our ignorance, it may be instructive to explore the extreme regions of known and future investigations of prebiotic chemistry, where reactions fail, that will relate them to or exclude them from plausible environments where they could occur. Come critical parameters which most deserve investigation are discussed. Full article
(This article belongs to the Special Issue Prebiotic Chemistry: Chemical Evolution of Organics on the Primitive Earth)
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Graphical abstract

Graphical abstract
Full article ">Figure 1
<p>Some possible environments for the origin of life which are still extant on modern Earth. (<b>A</b>) Deserts or drying lake beds; (<b>B</b>) Deep sea hydrothermal environments; (<b>C</b>) Glacial or other icy environments; (<b>D</b>) Subaerial hot springs; (<b>E</b>) Drying lagoons or beaches.</p> Full article ">Figure 2
<p>Major events in the history of life on Earth, and the difficulty of pegging events in the evolutionary history of extant organism’s geological timeline and the origin of life. Dating of the origin of the eukarya is taken from [<a href="#B44-life-03-00331" class="html-bibr">44</a>,<a href="#B56-life-03-00331" class="html-bibr">56</a>]. Red lines indicate thermophilic or hyperthermophilic lineages and their extrapolation back to LUCA as proposed by [<a href="#B57-life-03-00331" class="html-bibr">57</a>]. The idea that LUCA was possibly a surviving branch of a previously more diverse ecosystem is represented by the deeper tree shown in lilac. Dating of the origin of life remains unconstrained, and the tree could be stretched or compressed, locally or globally, in time. Lineages to the right of the dashed line should be understood to extend to the present. Figure adapted from [<a href="#B58-life-03-00331" class="html-bibr">58</a>].</p> Full article ">Figure 3
<p>Interconnectedness of environmental conditions with potential early Earth organic chemistry with respect to possible sites for the origin of life. Illustration modified with the permission from [<a href="#B64-life-03-00331" class="html-bibr">64</a>].</p> Full article ">Figure 4
<p>Direct Analysis in Real Time of Flight (DART-ToF) mass spectrum of the reaction products from the reaction of 1 M HCHO with 1 M NH<sub>4</sub>CN. Although this is formally the Strecker synthesis of glycine, clearly a much more complex reaction mixture is generated, in which glycine (m/z MH+ ~76.1) is a relatively minor component.</p> Full article ">Figure 5
<p>Example of a reaction matrix for screening prebiotic reactions.</p> Full article ">
184 KiB  
Article
Is Struvite a Prebiotic Mineral?
by Maheen Gull and Matthew A. Pasek
Life 2013, 3(2), 321-330; https://doi.org/10.3390/life3020321 - 29 Apr 2013
Cited by 24 | Viewed by 9981
Abstract
The prebiotic relevance of mineral struvite, MgNH4PO4·6H2O, was studied experimentally as a phosphorylating reagent and, theoretically, to understand the geochemical requirements for its formation. The effectiveness of phosphorylation by the phosphate mineral, monetite, CaHPO4, was also [...] Read more.
The prebiotic relevance of mineral struvite, MgNH4PO4·6H2O, was studied experimentally as a phosphorylating reagent and, theoretically, to understand the geochemical requirements for its formation. The effectiveness of phosphorylation by the phosphate mineral, monetite, CaHPO4, was also studied to compare to the efficiency of struvite. The experiments focused on the phosphorylation reactions of the minerals with organic compounds, such as nucleosides, glycerol and choline chloride, and heat at 75 °C for about 7–8 days and showed up to 28% phosphorylation of glycerol. In contrast, the compositional requirements for the precipitation of struvite are high ammonium and phosphate concentrations, as well as a little Ca2+ dissolved in the water. Combined, these requirements suggest that it is not likely that struvite was present in excess on the early Earth to carry out phosphorylation reactions. The present study focuses on the thermodynamic aspects of struvite formation, complementing the results given by Orgel and Handschuh (1973), which were based on the kinetic effects. Full article
(This article belongs to the Special Issue Prebiotic Chemistry: Chemical Evolution of Organics on the Primitive Earth)
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Graphical abstract

Graphical abstract
Full article ">Figure 1
<p><sup>31</sup>P-NMR spectra demonstrating phosphorylation of (<b>a</b>) glycerol and (<b>b</b>) choline by struvite. The unlabeled peak (~1.2 ppm) is dissolved orthophosphate.</p> Full article ">Figure 2
<p>Mg/Ca ratio and ammonia or P<sub>H2</sub> concentration requirements for struvite precipitation over a pH of 7.6–7.9, at 25 °C, with a phosphate concentration of 10<sup>–5</sup> M.</p> Full article ">Figure 3
<p>Phosphate and ammonia concentration requirements for struvite precipitation over a pH of 7.6–7.9, at 25 °C, with an Mg/Ca ratio of 10,000. The dotted line represents ammonium concentrations greater than the current quantity of nitrogen in the Earth’s atmosphere, and the dash-dot line occurs where struvite precipitation competes with Mg<sub>3</sub>(PO<sub>4</sub>)<sub>2</sub> precipitation or farringtonite.</p> Full article ">
147 KiB  
Review
Hot Spring Metagenomics
by Olalla López-López, María Esperanza Cerdán and María Isabel González-Siso
Life 2013, 3(2), 308-320; https://doi.org/10.3390/life3020308 - 25 Apr 2013
Cited by 73 | Viewed by 11289
Abstract
Hot springs have been investigated since the XIX century, but isolation and examination of their thermophilic microbial inhabitants did not start until the 1950s. Many thermophilic microorganisms and their viruses have since been discovered, although the real complexity of thermal communities was envisaged [...] Read more.
Hot springs have been investigated since the XIX century, but isolation and examination of their thermophilic microbial inhabitants did not start until the 1950s. Many thermophilic microorganisms and their viruses have since been discovered, although the real complexity of thermal communities was envisaged when research based on PCR amplification of the 16S rRNA genes arose. Thereafter, the possibility of cloning and sequencing the total environmental DNA, defined as metagenome, and the study of the genes rescued in the metagenomic libraries and assemblies made it possible to gain a more comprehensive understanding of microbial communities—their diversity, structure, the interactions existing between their components, and the factors shaping the nature of these communities. In the last decade, hot springs have been a source of thermophilic enzymes of industrial interest, encouraging further study of the poorly understood diversity of microbial life in these habitats. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
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Graphical abstract

Graphical abstract
Full article ">
699 KiB  
Review
Magnetotactic Bacteria from Extreme Environments
by Dennis A. Bazylinski and Christopher T. Lefèvre
Life 2013, 3(2), 295-307; https://doi.org/10.3390/life3020295 - 26 Mar 2013
Cited by 41 | Viewed by 10508
Abstract
Magnetotactic bacteria (MTB) represent a diverse collection of motile prokaryotes that biomineralize intracellular, membrane-bounded, tens-of-nanometer-sized crystals of a magnetic mineral called magnetosomes. Magnetosome minerals consist of either magnetite (Fe3O4) or greigite (Fe3S4) and cause cells [...] Read more.
Magnetotactic bacteria (MTB) represent a diverse collection of motile prokaryotes that biomineralize intracellular, membrane-bounded, tens-of-nanometer-sized crystals of a magnetic mineral called magnetosomes. Magnetosome minerals consist of either magnetite (Fe3O4) or greigite (Fe3S4) and cause cells to align along the Earth’s geomagnetic field lines as they swim, a trait called magnetotaxis. MTB are known to mainly inhabit the oxic–anoxic interface (OAI) in water columns or sediments of aquatic habitats and it is currently thought that magnetosomes function as a means of making chemotaxis more efficient in locating and maintaining an optimal position for growth and survival at the OAI. Known cultured and uncultured MTB are phylogenetically associated with the Alpha-, Gamma- and Deltaproteobacteria classes of the phylum Proteobacteria, the Nitrospirae phylum and the candidate division OP3, part of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum. MTB are generally thought to be ubiquitous in aquatic environments as they are cosmopolitan in distribution and have been found in every continent although for years MTB were thought to be restricted to habitats with pH values near neutral and at ambient temperature. Recently, however, moderate thermophilic and alkaliphilic MTB have been described including: an uncultured, moderately thermophilic magnetotactic bacterium present in hot springs in northern Nevada with a probable upper growth limit of about 63 °C; and several strains of obligately alkaliphilic MTB isolated in pure culture from different aquatic habitats in California, including the hypersaline, extremely alkaline Mono Lake, with an optimal growth pH of >9.0. Full article
(This article belongs to the Section Microbiology)
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<p>Picture showing the sampling of sediment and water (A) at the Great Boiling Springs (GBS) geothermal field in Gerlach, Nevada, in September 2009. (B) Sampling at Mono Lake, a hypersaline, hyperalkaline endorheic lake situated in California, in February 2010. Tufas, large carbonaceous concretions coming out of the lake can be seen in the background.</p> Full article ">Figure 2
<p>Transmission electron microscope (TEM) images of cells and magnetosomes of the thermophilic magnetotactic bacterium strain HSMV-1 (<span class="html-italic">Candidatus</span> Thermomagnetovibrio paiutensis. (A) TEM image of a cell of HSMV-1 showing a single polar flagellum (black arrow) and a single chain of bullet-shaped magnetosomes (white arrow). (B) High magnification TEM image of a magnetosome chain of strain HSMV-1.</p> Full article ">Figure 3
<p>Scanning-transmission electron microscope (STEM) and TEM images of alkaliphilic magnetotactic bacteria. STEM images of cells from (A) the hypersaline Mono Lake, California and (B) a brackish pool at Death Valley Junction (Micrographs courtesy of Tanya Prozorov Ames Laboratory, U.S. Department of Energy, Ames, USA). (C) TEM image of a bullet-shaped magnetosome chain of strain ZZ-1 (Reprinted, with permission, from [<a href="#B20-life-03-00295" class="html-bibr">20</a>]).</p> Full article ">
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