Life | September 2018 - Browse Articles

10 pages, 3513 KiB

Open AccessArticle

Biodiversity and Abundance of Cultured Microfungi from the Permanently Ice-Covered Lake Fryxell, Antarctica

by Laurie Connell, Benjamin Segee, Regina Redman, Russell J. Rodriguez and Hubert Staudigel

Life 2018, 8(3), 37; https://doi.org/10.3390/life8030037 - 06 Sep 2018

Cited by 15 | Viewed by 3911

In this work, we explore the biodiversity of culturable microfungi from the water column of a permanently ice-covered lake in Taylor Valley, Antarctica from austral field seasons in 2003, 2008 and 2010, as well as from glacial stream input (2010). The results revealed [...] Read more.

In this work, we explore the biodiversity of culturable microfungi from the water column of a permanently ice-covered lake in Taylor Valley, Antarctica from austral field seasons in 2003, 2008 and 2010, as well as from glacial stream input (2010). The results revealed that there was a sharp decline in total culturable fungal abundance between 9 and 11 m lake depth with a concurrent shift in diversity. A total of 29 species were identified from all three water sources with near even distribution between Ascomycota and Basidomycota (15 and 14 respectively). The most abundant taxa isolated from Lake Fryxell in 2008 were Glaciozyma watsonii (59%) followed by Penicillium spp. (10%), both of which were restricted to 9 m and above. Although seven species were found below the chemocline of 11 m in 2008, their abundance comprised only 10% of the total culturable fungi. The taxa of isolates collected from glacial source input streams had little overlap with those found in Lake Fryxell. The results highlight the spatial discontinuities of fungal populations that can occur within connected oligotrophic aquatic habitats. Full article

(This article belongs to the Special Issue Fungi from Extreme Environments)

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29 pages, 4230 KiB

Open AccessReview

Monosaccharides and Their Derivatives in Carbonaceous Meteorites: A Scenario for Their Synthesis and Onset of Enantiomeric Excesses

by George Cooper, Andro C. Rios and Michel Nuevo

Life 2018, 8(3), 36; https://doi.org/10.3390/life8030036 - 27 Aug 2018

Cited by 14 | Viewed by 7027

Abstract

Carbonaceous meteorites provide the best glimpse into the solar system’s earliest physical and chemical processes. These ancient objects, ~4.56 billion years old, contain evidence of phenomena ranging from solar system formation to the synthesis of organic compounds by aqueous and (likely) low-temperature photolytic [...] Read more.

Carbonaceous meteorites provide the best glimpse into the solar system’s earliest physical and chemical processes. These ancient objects, ~4.56 billion years old, contain evidence of phenomena ranging from solar system formation to the synthesis of organic compounds by aqueous and (likely) low-temperature photolytic reactions. Collectively, chemical reactions resulted in an insoluble kerogen-like carbon phase and a complex mixture of discrete soluble compounds including amino acids, nucleobases, and monosaccharide (or “sugar”) derivatives. This review presents the documented search for sugars and their derivatives in carbonaceous meteorites. We examine early papers, published in the early 1960s, and note the analytical methods used for meteorite analysis as well as conclusions on the results. We then present the recent finding of sugar derivatives including sugar alcohols and several sugar acids: The latter compounds were found to possess unusual “d” enantiomeric (mirror-image) excesses. After discussions on the possible roles of interstellar grain chemistry and meteorite parent body aqueous activity in the synthesis of sugar derivatives, we present a scenario that suggests that most of Earth’s extraterrestrial sugar alcohols (e.g., glycerol) were synthesized by interstellar irradiation and/or cold grain chemistry and that the early solar disk was the location of the initial enantiomeric excesses in meteoritic sugar derivatives. Full article

(This article belongs to the Special Issue Meteorites and the Origin of Life)

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29 pages, 2167 KiB

Open AccessReview

Green Rust: The Simple Organizing ‘Seed’ of All Life?

by Michael J. Russell

Life 2018, 8(3), 35; https://doi.org/10.3390/life8030035 - 27 Aug 2018

Cited by 64 | Viewed by 12820

Abstract

Korenaga and coworkers presented evidence to suggest that the Earth’s mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes [...] Read more.

Korenaga and coworkers presented evidence to suggest that the Earth’s mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence Fe^II/Fe^III oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them—the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells. Full article

(This article belongs to the Special Issue Geochemistry and the Origin of Life)

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10 pages, 2647 KiB

Open AccessArticle

The Ser/Thr Kinase PknH Is Essential for Maintaining Heterocyst Pattern in the Cyanobacterium Anabaena sp. Strain PCC 7120

by Shun-ichi Fukushima and Shigeki Ehira

Life 2018, 8(3), 34; https://doi.org/10.3390/life8030034 - 24 Aug 2018

Cited by 6 | Viewed by 5407

Abstract

In the filamentous cyanobacterium Anabaena sp. strain, PCC 7120, heterocysts (which are nitrogen-fixing cells) are formed in the absence of combined nitrogen in the medium. Heterocysts are separated from one another by 10 to 15 vegetative cells along the filaments, which consist of [...] Read more.

In the filamentous cyanobacterium Anabaena sp. strain, PCC 7120, heterocysts (which are nitrogen-fixing cells) are formed in the absence of combined nitrogen in the medium. Heterocysts are separated from one another by 10 to 15 vegetative cells along the filaments, which consist of a few hundred of cells. hetR is necessary for heterocyst differentiation; and patS and hetN, expressed in heterocysts, play important roles in heterocyst pattern formation by laterally inhibiting the expression of hetR in adjacent cells. The results of this study indicated that pknH, which encodes a Ser/Thr kinase, was also involved in heterocyst pattern formation. In the pknH mutant, the heterocyst pattern was normal within 24 h after nitrogen deprivation, but multiple contiguous heterocysts were formed from 24 to 48 h. A time-lapse analysis of reporter strains harboring a fusion between gfp and the hetR promoter indicated that pknH was required to suppress hetR expression in cells adjacent to the preexisting heterocysts. These results indicated that pknH was necessary for the lateral inhibition of heterocyst differentiation to maintain the heterocyst pattern. Full article

(This article belongs to the Special Issue Developmental Biology in Cyanobacteria)

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16 pages, 1321 KiB

Open AccessArticle

Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World

by Wim Hordijk, Jonathan Naylor, Natalio Krasnogor and Harold Fellermann

Life 2018, 8(3), 33; https://doi.org/10.3390/life8030033 - 18 Aug 2018

Cited by 16 | Viewed by 4717

Abstract

Autocatalytic sets are self-sustaining and collectively catalytic chemical reaction networks which are believed to have played an important role in the origin of life. Simulation studies have shown that autocatalytic sets are, in principle, evolvable if multiple autocatalytic subsets can exist in different [...] Read more.

Autocatalytic sets are self-sustaining and collectively catalytic chemical reaction networks which are believed to have played an important role in the origin of life. Simulation studies have shown that autocatalytic sets are, in principle, evolvable if multiple autocatalytic subsets can exist in different combinations within compartments, i.e., so-called protocells. However, these previous studies have so far not explicitly modeled the emergence and dynamics of autocatalytic sets in populations of compartments in a spatial environment. Here, we use a recently developed software tool to simulate exactly this scenario, as an important first step towards more realistic simulations and experiments on autocatalytic sets in protocells. Full article

(This article belongs to the Special Issue Systems Protobiology: Origin of Life by Mutually Catalytic Networks)

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22 pages, 88343 KiB

Open AccessArticle

Jarosite and Alunite in Ancient Terrestrial Sedimentary Rocks: Reinterpreting Martian Depositional and Diagenetic Environmental Conditions

by Sally L. Potter-McIntyre and Thomas M. McCollom

Life 2018, 8(3), 32; https://doi.org/10.3390/life8030032 - 03 Aug 2018

Cited by 8 | Viewed by 5370

Abstract

Members of the alunite group are precipitated at low pH (<1 to ~4) in oxidizing environments, are unstable in circumneutral conditions, and are widespread on Mars. At Mollies Nipple in Kane County, Utah, USA, jarosite and alunite are abundant as diagenetic cements in [...] Read more.

Members of the alunite group are precipitated at low pH (<1 to ~4) in oxidizing environments, are unstable in circumneutral conditions, and are widespread on Mars. At Mollies Nipple in Kane County, Utah, USA, jarosite and alunite are abundant as diagenetic cements in Jurassic sandstones. This research characterizes the jarosite and alunite cements with the goal of determining their origin, and tests the hypothesis that jarosite and alunite may be more stable than the current understanding indicates is possible. Previous studies have placed the jarosite- and alunite-bearing caprock at Mollies Nipple in the Navajo Sandstone, but the presence of water-lain deposits, volcanic ash, volcanic clasts, and peloids show that it is one of the overlying Middle Jurassic units that records sea level transgressions and regressions. A paragenetic timing, established from petrographic methods, shows that much of the cement was precipitated early in a marginal marine to coastal dune depositional environment with a fluctuating groundwater table that drove ferrolysis and evolved the groundwater to a low pH. Microbial interaction was likely a large contributor to the evolution of this acidity. Jarosite and alunite are clearly more stable in natural environments than is predicted by laboratory experiments, and therefore, the Martian environments that have been interpreted as largely acidic and/or dry over geologic time may have been more habitable than previously thought. Full article

(This article belongs to the Special Issue Water–Rock Interactions and Life)

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12 pages, 519 KiB

Open AccessArticle

Global Molecular Diversity of the Halotolerant Fungus Hortaea werneckii

by Alessia Marchetta, Bert Gerrits van den Ende, Abdullah M. S. Al-Hatmi, Ferry Hagen, Polona Zalar, Montarop Sudhadham, Nina Gunde-Cimerman, Clara Urzì, Sybren De Hoog and Filomena De Leo

Life 2018, 8(3), 31; https://doi.org/10.3390/life8030031 - 23 Jul 2018

Cited by 25 | Viewed by 4973

Abstract

A global set of clinical and environmental strains of the halotolerant black yeast-like fungus Hortaea werneckii are analyzed by multilocus sequencing and AFLP, and physiological parameters are determined. Partial translation elongation factor 1-α proves to be suitable for typing because of the presence/absence [...] Read more.

A global set of clinical and environmental strains of the halotolerant black yeast-like fungus Hortaea werneckii are analyzed by multilocus sequencing and AFLP, and physiological parameters are determined. Partial translation elongation factor 1-α proves to be suitable for typing because of the presence/absence of introns and also the presence of several SNPs. Local clonal expansion could be established by a combination of molecular methods, while the population from the Mediterranean Sea water also responds differently to combined temperature and salt stress. The species comprises molecular populations, which in part also differ physiologically allowing further diversification, but clinical strains did not deviate significantly from their environmental counterparts. Full article

(This article belongs to the Special Issue Fungi from Extreme Environments)

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14 pages, 2803 KiB

Open AccessArticle

Roof-Inhabiting Cousins of Rock-Inhabiting Fungi: Novel Melanized Microcolonial Fungal Species from Photocatalytically Reactive Subaerial Surfaces

by Constantino Ruibal, Laura Selbmann, Serap Avci, Pedro M. Martin-Sanchez and Anna A. Gorbushina

Life 2018, 8(3), 30; https://doi.org/10.3390/life8030030 - 15 Jul 2018

Cited by 21 | Viewed by 4267

Abstract

Subaerial biofilms (SAB) are an important factor in weathering, biofouling, and biodeterioration of bare rocks, building materials, and solar panel surfaces. The realm of SAB is continually widened by modern materials, and the settlers on these exposed solid surfaces always include melanized, stress-tolerant [...] Read more.

Subaerial biofilms (SAB) are an important factor in weathering, biofouling, and biodeterioration of bare rocks, building materials, and solar panel surfaces. The realm of SAB is continually widened by modern materials, and the settlers on these exposed solid surfaces always include melanized, stress-tolerant microcolonial ascomycetes. After their first discovery on desert rock surfaces, these melanized chaetothyrialean and dothidealean ascomycetes have been found on Mediterranean monuments after biocidal treatments, Antarctic rocks and solar panels. New man-made modifications of surfaces (e.g., treatment with biocides or photocatalytically active layers) accommodate the exceptional stress-tolerance of microcolonial fungi and thus further select for this well-protected ecological group. Melanized fungal strains were isolated from a microbial community that developed on highly photocatalytic roof tiles after a long-term environmental exposure in a maritime-influenced region in northwestern Germany. Four of the isolated strains are described here as a novel species, Constantinomyces oldenburgensis, based on multilocus ITS, LSU, RPB2 gene phylogeny. Their closest relative is a still-unnamed rock-inhabiting strain TRN431, here described as C. patonensis. Both species cluster in Capnodiales, among typical melanized microcolonial rock fungi from different stress habitats, including Antarctica. These novel strains flourish in hostile conditions of highly oxidizing material surfaces, and shall be used in reference procedures in material testing. Full article

(This article belongs to the Special Issue Fungi from Extreme Environments)

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18 pages, 2562 KiB

Open AccessArticle

Metagenomic Analysis of Microbial Community Compositions and Cold-Responsive Stress Genes in Selected Antarctic Lacustrine and Soil Ecosystems

by Hyunmin Koo, Joseph A. Hakim, Casey D. Morrow, Michael R. Crowley, Dale T. Andersen and Asim K. Bej

Life 2018, 8(3), 29; https://doi.org/10.3390/life8030029 - 11 Jul 2018

Cited by 30 | Viewed by 6563

Abstract

This study describes microbial community compositions, and various cold-responsive stress genes, encompassing cold-induced proteins (CIPs) and cold-associated general stress-responsive proteins (CASPs) in selected Antarctic lake water, sediment, and soil metagenomes. Overall, Proteobacteria and Bacteroidetes were the major taxa in all metagenomes. Prochlorococcus and [...] Read more.

This study describes microbial community compositions, and various cold-responsive stress genes, encompassing cold-induced proteins (CIPs) and cold-associated general stress-responsive proteins (CASPs) in selected Antarctic lake water, sediment, and soil metagenomes. Overall, Proteobacteria and Bacteroidetes were the major taxa in all metagenomes. Prochlorococcus and Thiomicrospira were highly abundant in waters, while Myxococcus, Anaeromyxobacter, Haliangium, and Gloeobacter were dominant in the soil and lake sediment metagenomes. Among CIPs, genes necessary for DNA replication, translation initiation, and transcription termination were highly abundant in all metagenomes. However, genes for fatty acid desaturase (FAD) and trehalose synthase (TS) were common in the soil and lake sediment metagenomes. Interestingly, the Lake Untersee water and sediment metagenome samples contained histone-like nucleoid structuring protein (H-NS) and all genes for CIPs. As for the CASPs, high abundances of a wide range of genes for cryo- and osmo-protectants (glutamate, glycine, choline, and betaine) were identified in all metagenomes. However, genes for exopolysaccharide biosynthesis were dominant in Lake Untersee water, sediment, and other soil metagenomes. The results from this study indicate that although diverse microbial communities are present in various metagenomes, they share common cold-responsive stress genes necessary for their survival and sustenance in the extreme Antarctic conditions. Full article

(This article belongs to the Section Microbiology)

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16 pages, 903 KiB

Open AccessReview

The Nitrogen Heterocycle Content of Meteorites and Their Significance for the Origin of Life

by Zita Martins

Life 2018, 8(3), 28; https://doi.org/10.3390/life8030028 - 11 Jul 2018

Cited by 42 | Viewed by 5679

Abstract

Carbonaceous chondrites are very primitive meteorites that are rich in carbon. They contain many soluble organic compounds, including nitrogen heterocycles. These play a crucial role in present-day living organisms as they are components of the genetic material and of the co-factors of enzymes. [...] Read more.

Carbonaceous chondrites are very primitive meteorites that are rich in carbon. They contain many soluble organic compounds, including nitrogen heterocycles. These play a crucial role in present-day living organisms as they are components of the genetic material and of the co-factors of enzymes. This review outlines the nitrogen heterocycle content of carbonaceous meteorites. The potential mechanisms of formation of these molecules are also described. Measurements of the compound-specific carbon and hydrogen isotopic compositions are mentioned as a way of establishing the origin of the nitrogen heterocycles detected in meteorites. Full article

(This article belongs to the Special Issue Meteorites and the Origin of Life)

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15 pages, 2681 KiB

Open AccessArticle

Bioremediation of Landfill Leachate with Fungi: Autochthonous vs. Allochthonous Strains

by Federica Spina, Valeria Tigini, Alice Romagnolo and Giovanna Cristina Varese

Life 2018, 8(3), 27; https://doi.org/10.3390/life8030027 - 04 Jul 2018

Cited by 31 | Viewed by 5323

Abstract

Autochthonous fungi from contaminated wastewater are potential successful agents bioremediation thanks to their adaptation to pollutant toxicity and to competition with other microorganisms present in wastewater treatment plant. Biological treatment by means of selected fungal strains could be a potential tool to integrate [...] Read more.

Autochthonous fungi from contaminated wastewater are potential successful agents bioremediation thanks to their adaptation to pollutant toxicity and to competition with other microorganisms present in wastewater treatment plant. Biological treatment by means of selected fungal strains could be a potential tool to integrate the leachate depuration process, thanks to their fungal extracellular enzymes with non-selective catalytical activity. In the present work, the treatability of two real samples (a crude landfill leachate and the effluent coming from a traditional wastewater treatment plant) was investigated in decolorization experiments with fungal biomasses. Five autochthonous fungi, Penicillium brevicompactum MUT 793, Pseudallescheria boydii MUT 721, P. boydii MUT 1269, Phanerochaete sanguinea MUT 1284, and Flammulina velutipes MUT 1275, were selected in a previous miniaturized decolorization screening. Their effectiveness in terms of decolorization, enzymatic activity (laccases and peroxidases), biomass growth and ecotoxicity removal was compared with that of five allochthonous fungal strains, Pleurotus ostreatus MUT 2976, Porostereum spadiceum MUT 1585, Trametespubescens MUT 2400, Bjerkanderaadusta MUT 3060 and B. adusta MUT 2295, selected for their well known capability to degrade recalcitrant pollutants. Moreover, the effect of biomass immobilization on polyurethane foam (PUF) cube was assessed. The best decolorization (60%) was achieved by P. spadiceum MUT 1585, P. boydii MUT 721 and MUT 1269. In the first case, the DP was achieved gradually, suggesting a biodegradation process with the involvement of peroxidases. On the contrary, the two autochthonous fungi seem to bioremediate the effluent mainly by biosorption, with the abatement of the toxicity (up to 100%). The biomass immobilization enhanced enzymatic activity, but not the DP. Moreover, it limited the biomass growth for the fast growing fungi, MUT 721 and MUT 1269. In conclusion, robust and versatile strains coming from well-characterized collections of microorganisms can obtain excellent results comparing and even exceeding the bioremediation yields of strains already adapted to pollutants. Full article

(This article belongs to the Special Issue Fungi from Extreme Environments)

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18 pages, 2695 KiB

Open AccessArticle

The ABC Transporter Components HgdB and HgdC are Important for Glycolipid Layer Composition and Function of Heterocysts in Anabaena sp. PCC 7120

by Dmitry Shvarev, Carolina N. Nishi, Lars Wörmer and Iris Maldener

Life 2018, 8(3), 26; https://doi.org/10.3390/life8030026 - 02 Jul 2018

Cited by 14 | Viewed by 5714

Abstract

Anabaena sp. PCC 7120 is a filamentous cyanobacterium able to fix atmospheric nitrogen in semi-regularly spaced heterocysts. For correct heterocyst function, a special cell envelope consisting of a glycolipid layer and a polysaccharide layer is essential. We investigated the role of the genes [...] Read more.

Anabaena sp. PCC 7120 is a filamentous cyanobacterium able to fix atmospheric nitrogen in semi-regularly spaced heterocysts. For correct heterocyst function, a special cell envelope consisting of a glycolipid layer and a polysaccharide layer is essential. We investigated the role of the genes hgdB and hgdC, encoding domains of a putative ABC transporter, in heterocyst maturation. We investigated the subcellular localization of the fusion protein HgdC-GFP and followed the differential expression of the hgdB and hgdC genes during heterocyst maturation. Using a single recombination approach, we created a mutant in hgdB gene and studied its phenotype by microscopy and analytical chromatography. Although heterocysts are formed in the mutant, the structure of the glycolipid layer is aberrant and also contains an atypical ratio of the two major glycolipids. As shown by a pull-down assay, HgdB interacts with the outer membrane protein TolC, which indicates a function as a type 1 secretion system. We show that the hgdB-hgdC genes are essential for the creation of micro-oxic conditions by influencing the correct composition of the glycolipid layer for heterocyst function. Our observations confirm the significance of the hgdB-hgdC gene cluster and shed light on a novel mode of regulation of heterocyst envelope formation. Full article

(This article belongs to the Special Issue Developmental Biology in Cyanobacteria)

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17 pages, 894 KiB

Open AccessArticle

Bioinformatic Workflows for Generating Complete Plastid Genome Sequences—An Example from Cabomba (Cabombaceae) in the Context of the Phylogenomic Analysis of the Water-Lily Clade

by Michael Gruenstaeudl, Nico Gerschler and Thomas Borsch

Life 2018, 8(3), 25; https://doi.org/10.3390/life8030025 - 21 Jun 2018

Cited by 9 | Viewed by 5503

Abstract

The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck [...] Read more.

The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and results of sequencing, assembling, annotating and quality-checking of three complete plastid genomes of the aquatic plant genus Cabomba as well as subsequent gene alignment and phylogenetic tree inference. We accompany our findings by a detailed description of the bioinformatic workflow employed. Importantly, we share a total of eleven software scripts for each of these bioinformatic processes, enabling other researchers to evaluate and replicate our analyses step by step. The results of our analyses illustrate that the plastid genomes of Cabomba are highly conserved in both structure and gene content. Full article

(This article belongs to the Special Issue Open Science Phyloinformatics: Resources, Methods, and Analyses)

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