Life and the evolution of Earth's atmosphere

CRISPR/Cas: from adaptive immune system in prokaryotes to therapeutic weapon against immune-related diseases

CRISPR/Cas evolved as an adaptive immune system in bacteria and archaea to inactivate foreign viral and plasmid DNA. However, the capacities of various CRISPR/Cas systems for precise genome editing based on sequence homology also allow their use as tools for genomic and epigenomic modification in eukaryotes. Indeed, these genetic characteristics have proven useful for disease modeling and testing the specific functions of target genes under pathological conditions. Moreover, recent studies provide compelling evidence that CRISPR/Cas systems could be useful therapeutic tools against human diseases, including cancer, monogenic disorders, and autoimmune disorders.HighlightsCRISPR/Cas evolved as an adaptive immune system in bacteria and archaea.CRISPR/Cas systems are nowadays used as tools for genomic modification.CRISPR/Cas systems could be useful therapeutic tools against human disease, including autoimmune conditions.

Limited oxygen production in the Mesoarchean ocean

The Archean Eon was a time of predominantly anoxic Earth surface conditions, where anaerobic processes controlled bioessential element cycles. In contrast to "oxygen oases" well documented for the Neoarchean [2.8 to 2.5 billion years ago (Ga)], the magnitude, spatial extent, and underlying causes of possible Mesoarchean (3.2 to 2.8 Ga) surface-ocean oxygenation remain controversial. Here, we report δ¹⁵N and δ¹³C values coupled with local seawater redox data for Mesoarchean shales of the Mozaan Group (Pongola Supergroup, South Africa) that were deposited during an episode of enhanced Mn (oxyhydr)oxide precipitation between ∼2.95 and 2.85 Ga. Iron and Mn redox systematics are consistent with an oxygen oasis in the Mesoarchean anoxic ocean, but δ¹⁵N data indicate a Mo-based diazotrophic biosphere with no compelling evidence for a significant aerobic nitrogen cycle. We propose that in contrast to the Neoarchean, dissolved O₂ levels were either too low or too limited in extent to develop a large and stable nitrate reservoir in the Mesoarchean ocean. Since biological N₂ fixation was evidently active in this environment, the growth and proliferation of O₂-producing organisms were likely suppressed by nutrients other than nitrogen (e.g., phosphorus), which would have limited the expansion of oxygenated conditions during the Mesoarchean.

Mexican Microalgae Biodiversity and State-Of-The-Art Extraction Strategies to Meet Sustainable Circular Economy Challenges: High-Value Compounds and Their Applied Perspectives

In recent years, the demand for naturally derived products has hiked with enormous pressure to propose or develop state-of-the-art strategies to meet sustainable circular economy challenges. Microalgae possess the flexibility to produce a variety of high-value products of industrial interests. From pigments such as phycobilins or lutein to phycotoxins and several polyunsaturated fatty acids (PUFAs), microalgae have the potential to become the primary producers for the pharmaceutical, food, and agronomical industries. Also, microalgae require minimal resources to grow due to their autotrophic nature or by consuming waste matter, while allowing for the extraction of several valuable side products such as hydrogen gas and biodiesel in a single process, following a biorefinery agenda. From a Mexican microalgae biodiversity perspective, more than 70 different local species have been characterized and isolated, whereas, only a minimal amount has been explored to produce commercially valuable products, thus ignoring their potential as a locally available resource. In this paper, we discuss the microalgae diversity present in Mexico with their current applications and potential, while expanding on their future applications in bioengineering along with other industrial sectors. In conclusion, the use of available microalgae to produce biochemically revenuable products currently represents an untapped potential that could lead to the solution of several problems through green technologies. As such, if the social, industrial and research communities collaborate to strive towards a greener economy by preserving the existing biodiversity and optimizing the use of the currently available resources, the enrichment of our society and the solution to several environmental problems could be attained.

Early Evolution of the Mitogen-Activated Protein Kinase Family in the Plant Kingdom

Mitogen-activated protein kinase (MAPK) pathways are central cellular signalling mechanisms in all eukaryotes. They are key regulators of the cell cycle and stress responses, yet evolution of MAPK families took markedly different paths in the animal and plant kingdoms. Instead of the characteristic divergence of MAPK types in animals, in plants an expanded network of ERK-like MAPKs has emerged. To gain insight into the early evolution of the plant MAPK family we identified and analysed MAPKs in 13 representative species across green algae, a large and diverse early-diverging lineage within the plant kingdom. Our results reveal that the plant MAPK gene family emerged from three types of progenitor kinases, which are ubiquitously present in algae, implying their formation in an early ancestor. Low number of MAPKs is characteristic across algae, the few losses or duplications are associated with genome complexity rather than habitat ecology, despite the importance of MAPKs in environmental signalling in flowering plants. ERK-type MAPKs are associated with cell cycle regulation in opisthokont models, yet in plants their stress-signalling function is more prevalent. Unicellular microalgae offer an excellent experimental system to study the cell cycle, and MAPK gene expression profiles show CDKB-like peaks around S/M phase in synchronised Chlamydomonas reinhardtii cultures, suggesting their participation in cell cycle regulation, in line with the notion that the ancestral eukaryotic MAPK was a cell cycle regulator ERK-like kinase. Our work also highlights the scarcity of signalling knowledge in microalgae, in spite of their enormous ecological impact and emerging economic importance.

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth’s climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane oxidizing archaea. Five of these MAGs represent under-sampled (e.g., Verstraetearchaeota, Methanonatronarchaeia, ANME-1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation significantly expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea (‘Ca. Methanoliparia’). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.

Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine

Human activities on the Earth's surface change the landscape of natural ecosystems. Mining practices are one of the most severe human activities, drastically altering the chemical, physical and biological properties of the soil environment. Bacterial communities in soil play an important role in the maintenance of ecological relationships. This work shows bacterial diversity, metabolic repertoire and physiological behavior in five ecosystems samples with different levels of impact. These ecosystems belong to a historical area in Iron Quadrangle, Minas Gerais, Brazil, which suffered mining activities until its total depletion without recovery since today. The results revealed Proteobacteria as the most predominant phylum followed by Acidobacteria, Verrucomicrobia, Planctomycetes, and Bacteroidetes. Soils that have not undergone anthropological actions exhibit an increase ability to degrade carbon sources. The richest soil with the high diversity was found in ecosystems that have suffered anthropogenic action. Our study shows profile of diversity inferring metabolic profile, which may elucidate the mechanisms underlying changes in community structure in situ mining sites in Brazil. Our data comes from contributing to know the bacterial diversity, relationship between these bacteria and can explore strategies for natural bioremediation in mining areas or adjacent areas under regeneration process in iron mining areas.

Spatial Structure of Glycogen Molecules in Cells

Glycogen is a strongly branched polymer of α-D-glucose, with glucose residues in the linear chains linked by 1→4-bonds (~93% of the total number of bonds) and with branching after every 4-8 residues formed by 1→6-glycosidic bonds (~7% of the total number of bonds). It is thought currently that a fully formed glycogen molecule (β-particle) with the self-glycosylating protein glycogenin in the center has a spherical shape with diameter of ~42 nm and contains ~ 55,000 glucose residues. The glycogen molecule also includes numerous proteins involved in its synthesis and degradation, as well as proteins performing a carcass function. However, the type and force of bonds connecting these proteins to the polysaccharide moiety of glycogen are significantly different. This review presents the available data on the spatial structure of the glycogen molecule and its changes under various physiological and pathological conditions.

Translating Divergent Environmental Stresses into a Common Proteome Response through the Histidine Kinase 33 (Hik33) in a Model Cyanobacterium

The histidine kinase Hik33 plays important roles in mediating cyanobacterial response to divergent types of abiotic stresses including cold, salt, high light (HL), and osmotic stresses. However, how these functions are regulated by Hik33 remains to be addressed. Using a hik33-deficient strain (Δhik33) of Synechocystis sp. PCC 6803 (Synechocystis) and quantitative proteomics, we found that Hik33 depletion induces differential protein expression highly like that induced by divergent types of stresses. This typically includes downregulation of proteins in photosynthesis and carbon assimilation that are necessary for cell propagation, and upregulation of heat shock proteins, chaperons, and proteases that are important for cell survival. This observation indicates that depletion of Hik33 alone mimics divergent types of abiotic stresses, and that Hik33 could be important for preventing abnormal stress response in the normal condition. Moreover, we found most proteins of plasmid origin were significantly upregulated in Δhik33, though their biological significance remains to be addressed. Together, the systematically characterized Hik33-regulated cyanobacterial proteome, which is largely involved in stress responses, builds the molecular basis for Hik33 as a general regulator of stress responses.

Photoprotection: extending lessons learned from studying natural sunscreens to the design of artificial sunscreen constituents

Evolution has ensured that plants and animals have developed effective protection mechanisms against the potentially harmful effects of incident ultraviolet radiation (UVR). Tanning is one such mechanism in humans, but tanning only occurs post-exposure to UVR. Hence, there is ever growing use of commercial sunscreens to pre-empt overexposure to UVR. Key requirements for any chemical filter molecule used in such a photoprotective capacity include a large absorption cross-section in the UV-A and UV-B spectral regions and the availability of one or more mechanisms whereby the absorbed photon energy can be dissipated without loss of the molecular integrity of the chemical filter. Here we summarise recent experimental (mostly ultrafast pump-probe spectroscopy studies) and computational progress towards unravelling various excited state decay mechanisms that afford the necessary photostability in chemical filters found in nature and those used in commercial sunscreens. We also outline ways in which a better understanding of the photophysics and photochemistry of sunscreen molecules selected by nature could aid the design of new and improved commercial sunscreen formulations.

A Genetic Toolbox for Modulating the Expression of Heterologous Genes in the Cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria, genetic models for photosynthesis research for decades, have recently become attractive hosts for producing renewable fuels and chemicals, owing to their genetic tractability, relatively fast growth, and their ability to utilize sunlight, fix carbon dioxide, and in some cases, fix nitrogen. Despite significant advances, there is still an urgent demand for synthetic biology tools in order to effectively manipulate genetic circuits in cyanobacteria. In this study, we have compared a total of 17 natural and chimeric promoters, focusing on expression of the ethylene-forming enzyme (EFE) in the cyanobacterium Synechocystis sp. PCC 6803. We report the finding that the E. coli σ⁷⁰ promoter Ptrc is superior compared to the previously reported strong promoters, such as PcpcB and PpsbA, for the expression of EFE. In addition, we found that the EFE expression level was very sensitive to the 5'-untranslated region upstream of the open reading frame. A library of ribosome binding sites (RBSs) was rationally designed and was built and systematically characterized. We demonstrate a strategy complementary to the RBS prediction software to facilitate the rational design of an RBS library to optimize the gene expression in cyanobacteria. Our results show that the EFE expression level is dramatically enhanced through these synthetic biology tools and is no longer the rate-limiting step for cyanobacterial ethylene production. These systematically characterized promoters and the RBS design strategy can serve as useful tools to tune gene expression levels and to identify and mitigate metabolic bottlenecks in cyanobacteria.

Confined methane-water interfacial layers and thickness measurements using in situ Raman spectroscopy

Gas-liquid interfaces broadly impact our planet, yet confined interfaces behave differently than unconfined ones. We report the role of tangential fluid motion in confined methane-water interfaces. The interfaces are created using microfluidics and investigated by in situ 1D, 2D and 3D Raman spectroscopy. The apparent CH₄ and H₂O concentrations are reported for Reynolds numbers (Re), ranging from 0.17 to 8.55. Remarkably, the interfaces are comprised of distinct layers of thicknesses varying from 23 to 57 μm. We found that rarefaction, mixture, thin film, and shockwave layers together form the interfaces. The results indicate that the mixture layer thickness (δ) increases with Re (δ ∝ Re), and traditional transport theory for unconfined interfaces does not explain the confined interfaces. A comparison of our results with thin film theory of air-water interfaces (from mass transfer experiments in capillary microfluidics) supports that the hydrophobicity of CH₄ could decrease the strength of water-water interactions, resulting in larger interfacial thicknesses. Our findings help explain molecular transport in confined gas-liquid interfaces, which are common in a broad range of societal applications.

Dynamics of lipids and metabolites during the cell cycle of Chlamydomonas reinhardtii

Metabolites and lipids are the final products of enzymatic processes, distinguishing the different cellular functions and activities of single cells or whole tissues. Understanding these cellular functions within a well-established model system requires a systemic collection of molecular and physiological information. In the current report, the green alga Chlamydomonas reinhardtii was selected to establish a comprehensive workflow for the detailed multi-omics analysis of a synchronously growing cell culture system. After implementation and benchmarking of the synchronous cell culture, a two-phase extraction method was adopted for the analysis of proteins, lipids, metabolites and starch from a single sample aliquot of as little as 10-15 million Chlamydomonas cells. In a proof of concept study, primary metabolites and lipids were sampled throughout the diurnal cell cycle. The results of these time-resolved measurements showed that single compounds were not only coordinated with each other in different pathways, but that these complex metabolic signatures have the potential to be used as biomarkers of various cellular processes. Taken together, the developed workflow, including the synchronized growth of the photoautotrophic cell culture, in combination with comprehensive extraction methods and detailed metabolic phenotyping has the potential for use in in-depth analysis of complex cellular processes, providing essential information for the understanding of complex biological systems.

Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event

Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis. Results show that Fe2+ can indeed substitute for Mg2+ in catalytic function of these enzymes. Additionally, we use calculations to unravel differences in energetics, structures and reactivities of relevant Mg2+ and Fe2+ complexes. Computation explains why Fe2+ can be a more potent cofactor than Mg2+ in a variety of folding and catalytic functions. We propose that the rise of O2 on Earth drove a Fe2+ to Mg2+ substitution in proteins and nucleic acids, a hypothesis consistent with a general model in which some modern biochemical systems retain latent abilities to revert to primordial Fe2+-based states when exposed to pre-GOE conditions.

Redfield Ratios in Inland Waters: Higher Biological Control of C:N:P Ratios in Tropical Semi-arid High Water Residence Time Lakes

The canonical Redfield C:N:P ratio for algal biomass is often not achieved in inland waters due to higher C and N content and more variability when compared to the oceans. This has been attributed to much lower residence times and higher contributions of the watershed to the total organic matter pool of continental ecosystems. In this study we examined the effect of water residence times in low latitude lakes (in a gradient from humid to a semi-arid region) on seston elemental ratios in different size fractions. We used lake water specific conductivity as a proxy for residence time in a region of Eastern Brazil where there is a strong precipitation gradient. The C:P ratios decreased in the seston and bacterial size-fractions and increased in the dissolved fraction with increasing water retention time, suggesting uptake of N and P from the dissolved pool. Bacterial abundance, production and respiration increased in response to increased residence time and intracellular nutrient availability in agreement with the growth rate hypothesis. Our results reinforce the role of microorganisms in shaping the chemical environment in aquatic systems particularly at long water residence times and highlights the importance of this factor in influencing ecological stoichiometry in all aquatic ecosystems.

Cyanobacterial nitrogenases: phylogenetic diversity, regulation and functional predictions

Cyanobacteria is a remarkable group of prokaryotic photosynthetic microorganisms, with several genera capable of fixing atmospheric nitrogen (N2) and presenting a wide range of morphologies. Although the nitrogenase complex is not present in all cyanobacterial taxa, it is spread across several cyanobacterial strains. The nitrogenase complex has also a high theoretical potential for biofuel production, since H2 is a by-product produced during N2 fixation. In this review we discuss the significance of a relatively wide variety of cell morphologies and metabolic strategies that allow spatial and temporal separation of N2 fixation from photosynthesis in cyanobacteria. Phylogenetic reconstructions based on 16S rRNA and nifD gene sequences shed light on the evolutionary history of the two genes. Our results demonstrated that (i) sequences of genes involved in nitrogen fixation (nifD) from several morphologically distinct strains of cyanobacteria are grouped in similarity with their morphology classification and phylogeny, and (ii) nifD genes from heterocytous strains share a common ancestor. By using this data we also discuss the evolutionary importance of processes such as horizontal gene transfer and genetic duplication for nitrogenase evolution and diversification. Finally, we discuss the importance of H2 synthesis in cyanobacteria, as well as strategies and challenges to improve cyanobacterial H2 production.

Trophic Mode-Dependent Proteomic Analysis Reveals Functional Significance of Light-Independent Chlorophyll Synthesis in Synechocystis sp. PCC 6803

The photosynthetic model organism Synechocystis sp. PCC 6803 can grow in different trophic modes, depending on the availability of light and exogenous organic carbon source. However, how the protein profile changes to facilitate the cells differentially propagate in different modes has not been comprehensively investigated. Using isobaric labeling-based quantitative proteomics, we simultaneously identified and quantified 45% Synechocystis proteome across four different trophic modes, i.e., autotrophic, heterotrophic, photoheterotrophic, and mixotrophic modes. Among the 155 proteins that are differentially expressed across four trophic modes, proteins involved in nitrogen assimilation and light-independent chlorophyll synthesis are dramatically upregulated in the mixotrophic mode, concomitant with a dramatic increase of P_II phosphorylation that senses carbon and nitrogen assimilation status. Moreover, functional study using a mutant defective in light-independent chlorophyll synthesis revealed that this pathway is important for chlorophyll accumulation under a cycled light/dark illumination regime, a condition mimicking day/night cycles in certain natural habitats. Collectively, these results provide the most comprehensive information on trophic mode-dependent protein expression in cyanobacterium, and reveal the functional significance of light-independent chlorophyll synthesis in trophic growth.

Plasticity of Candida albicans Biofilms

Candida albicans, the most pervasive fungal pathogen that colonizes humans, forms biofilms that are architecturally complex. They consist of a basal yeast cell polylayer and an upper region of hyphae encapsulated in extracellular matrix. However, biofilms formed in vitro vary as a result of the different conditions employed in models, the methods used to assess biofilm formation, strain differences, and, in a most dramatic fashion, the configuration of the mating type locus (MTL). Therefore, integrating data from different studies can lead to problems of interpretation if such variability is not taken into account. Here we review the conditions and factors that cause biofilm variation, with the goal of engendering awareness that more attention must be paid to the strains employed, the methods used to assess biofilm development, every aspect of the model employed, and the configuration of the MTL locus. We end by posing a set of questions that may be asked in comparing the results of different studies and developing protocols for new ones. This review should engender the notion that not all biofilms are created equal.

2D and 3D Mechanobiology in Human and Nonhuman Systems

Mechanobiology involves the investigation of mechanical forces and their effect on the development, physiology, and pathology of biological systems. The human body has garnered much attention from many groups in the field, as mechanical forces have been shown to influence almost all aspects of human life ranging from breathing to cancer metastasis. Beyond being influential in human systems, mechanical forces have also been shown to impact nonhuman systems such as algae and zebrafish. Studies of nonhuman and human systems at the cellular level have primarily been done in two-dimensional (2D) environments, but most of these systems reside in three-dimensional (3D) environments. Furthermore, outcomes obtained from 3D studies are often quite different than those from 2D studies. We present here an overview of a select group of human and nonhuman systems in 2D and 3D environments. We also highlight mechanobiological approaches and their respective implications for human and nonhuman physiology.

One step beyond a ribosome: The ancient anaerobic core

Life arose in a world without oxygen and the first organisms were anaerobes. Here we investigate the gene repertoire of the prokaryote common ancestor, estimating which genes it contained and to which lineages of modern prokaryotes it was most similar in terms of gene content. Using a phylogenetic approach we found that among trees for all 8779 protein families shared between 134 archaea and 1847 bacterial genomes, only 1045 have sequences from at least two bacterial and two archaeal groups and retain the ancestral archaeal–bacterial split. Among those, the genes shared by anaerobes were identified as candidate genes for the prokaryote common ancestor, which lived in anaerobic environments. We find that these anaerobic prokaryote common ancestor genes are today most frequently distributed among methanogens and clostridia, strict anaerobes that live from low free energy changes near the thermodynamic limit of life. The anaerobic families encompass genes for bifunctional acetyl-CoA-synthase/CO-dehydrogenase, heterodisulfide reductase subunits C and A, ferredoxins, and several subunits of the Mrp-antiporter/hydrogenase family, in addition to numerous S-adenosyl methionine (SAM) dependent methyltransferases. The data indicate a major role for methyl groups in the metabolism of the prokaryote common ancestor. The data furthermore indicate that the prokaryote ancestor possessed a rotor stator ATP synthase, but lacked cytochromes and quinones as well as identifiable redox-dependent ion pumping complexes. The prokaryote ancestor did possess, however, an Mrp-type H⁺/Na⁺ antiporter complex, capable of transducing geochemical pH gradients into biologically more stable Na⁺-gradients. The findings implicate a hydrothermal, autotrophic, and methyl-dependent origin of life. This article is part of a Special Issue entitled ‘EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2–6, 2016’, edited by Prof. Paolo Bernardi.

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Life arose without oxygen, the universal ancestor (Luca) was an anaerobe.

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We used phylogenetic and physiological criteria to identify genes present in Luca.

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An ancient core of 65 metabolic genes shed light on Luca's anaerobic lifestyle.

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Ancient core genes are most widespread among modern methanogens and clostridia.

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The data implicate a major role for methyl groups in Luca's anaerobic metabolism.

Advances in genomics, transcriptomics and proteomics of toxin-producing cyanobacteria

A common misconception persists that the genomes of toxic and non-toxic cyanobacterial strains are largely conserved with the exception of the presence or absence of the genes responsible for toxin production. Implementation of -omics era technologies has challenged this paradigm, with comparative analyses providing increased insight into the differences between strains of the same species. The implementation of genomic, transcriptomic and proteomic approaches has revealed distinct profiles between toxin-producing and non-toxic strains. Further, metagenomics and metaproteomics highlight the genomic potential and functional state of toxic bloom events over time. In this review, we highlight how these technologies have shaped our understanding of the complex relationship between these molecules, their producers and the environment at large within which they persist.

Manganese Compounds as Water-Oxidizing Catalysts: From the Natural Water-Oxidizing Complex to Nanosized Manganese Oxide Structures

All cyanobacteria, algae, and plants use a similar water-oxidizing catalyst for water oxidation. This catalyst is housed in Photosystem II, a membrane-protein complex that functions as a light-driven water oxidase in oxygenic photosynthesis. Water oxidation is also an important reaction in artificial photosynthesis because it has the potential to provide cheap electrons from water for hydrogen production or for the reduction of carbon dioxide on an industrial scale. The water-oxidizing complex of Photosystem II is a Mn-Ca cluster that oxidizes water with a low overpotential and high turnover frequency number of up to 25-90 molecules of O2 released per second. In this Review, we discuss the atomic structure of the Mn-Ca cluster of the Photosystem II water-oxidizing complex from the viewpoint that the underlying mechanism can be informative when designing artificial water-oxidizing catalysts. This is followed by consideration of functional Mn-based model complexes for water oxidation and the issue of Mn complexes decomposing to Mn oxide. We then provide a detailed assessment of the chemistry of Mn oxides by considering how their bulk and nanoscale properties contribute to their effectiveness as water-oxidizing catalysts.

The Archean Nickel Famine Revisited

Iron formations (IF) preserve a history of Precambrian oceanic elemental abundance that can be exploited to examine nutrient limitations on early biological productivity. However, in order for IF to be employed as paleomarine proxies, lumped-process distribution coefficients for the element of interest must be experimentally determined or assumed. This necessitates consideration of bulk ocean chemistry and which authigenic ferric iron minerals controlled the sorption reactions. It also requires an assessment of metal mobilization reactions that might have occurred in the water column during particle descent and during post-depositional burial. Here, we summarize recent developments pertaining to the interpretation and fidelity of the IF record in reconstructions of oceanic trace element evolution. Using an updated compilation, we reexamine and validate temporal trends previously reported for the nickel content in IF (see Konhauser et al., 2009 ). Finally, we reevaluate the consequences of methanogen Ni starvation in the context of evolving views of the Archean ocean-climate system and how the Ni famine may have ultimately facilitated the rise in atmospheric oxygen.

Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria under Aerobic and Anaerobic Environments

Chlorophyll a (Chl) is a light-absorbing tetrapyrrole pigment that is essential for photosynthesis. The molecule is produced from glutamate via a complex biosynthetic pathway comprised of at least 15 enzymatic steps. The first half of the Chl pathway is shared with heme biosynthesis, and the latter half, called the Mg-branch, is specific to Mg-containing Chl a. Bilin pigments, such as phycocyanobilin, are additionally produced from heme, so these light-harvesting pigments also share many common biosynthetic steps with Chl biosynthesis. Some of these common steps in the biosynthetic pathways of heme, Chl and bilins require molecular oxygen for catalysis, such as oxygen-dependent coproporphyrinogen III oxidase. Cyanobacteria thrive in diverse environments in terms of oxygen levels. To cope with Chl deficiency caused by low-oxygen conditions, cyanobacteria have developed elaborate mechanisms to maintain Chl production, even under microoxic environments. The use of enzymes specialized for low-oxygen conditions, such as oxygen-independent coproporphyrinogen III oxidase, constitutes part of a mechanism adapted to low-oxygen conditions. Another mechanism adaptive to hypoxic conditions is mediated by the transcriptional regulator ChlR that senses low oxygen and subsequently activates the transcription of genes encoding enzymes that work under low-oxygen tension. In diazotrophic cyanobacteria, this multilayered regulation also contributes in Chl biosynthesis by supporting energy production for nitrogen fixation that also requires low-oxygen conditions. We will also discuss the evolutionary implications of cyanobacterial tetrapyrrole biosynthesis and regulation, because low oxygen-type enzymes also appear to be evolutionarily older than oxygen-dependent enzymes.

Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment

Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world's largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments.

Cellular inorganic carbon fluxes in Trichodesmium: a combined approach using measurements and modelling

To predict effects of climate change on phytoplankton, it is crucial to understand how their mechanisms for carbon acquisition respond to environmental conditions. Aiming to shed light on the responses of extra- and intracellular inorganic C (Ci) fluxes, the cyanobacterium Trichodesmium erythraeum IMS101 was grown with different nitrogen sources (N2 vs NO3 (-)) and pCO2 levels (380 vs 1400 µatm). Cellular Ci fluxes were assessed by combining membrane inlet mass spectrometry (MIMS), (13)C fractionation measurements, and modelling. Aside from a significant decrease in Ci affinity at elevated pCO2 and changes in CO2 efflux with different N sources, extracellular Ci fluxes estimated by MIMS were largely unaffected by the treatments. (13)C fractionation during biomass production, however, increased with pCO2, irrespective of the N source. Strong discrepancies were observed in CO2 leakage estimates obtained by MIMS and a (13)C-based approach, which further increased under elevated pCO2. These offsets could be explained by applying a model that comprises extracellular CO2 and HCO3 (-) fluxes as well as internal Ci cycling around the carboxysome via the CO2 uptake facilitator NDH-14. Assuming unidirectional, kinetic fractionation between CO2 and HCO3 (-) in the cytosol or enzymatic fractionation by NDH-14, both significantly improved the comparability of leakage estimates. Our results highlight the importance of internal Ci cycling for (13)C composition as well as cellular energy budgets of Trichodesmium, which ought to be considered in process studies on climate change effects.

Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters

Anaerobic digestion (AD) is a biological process where different trophic groups of microorganisms break down biodegradable organic materials in the absence of oxygen. A wide range of AD technologies is being used to convert livestock manure, municipal and industrial wastewaters, and solid organic wastes into biogas. AD gains importance not only because of its relevance in waste treatment but also because of the recovery of carbon in the form of methane, which is a renewable energy and is used to generate electricity and heat. Despite the advances on the engineering and design of new bioreactors for AD, the microbiology component always poses challenges. Microbiology of AD processes is complicated as the efficiency of the process depends on the interactions of various trophic groups involved. Due to the complex interdependence of microbial activities for the functionality of the anaerobic bioreactors, the genetic expression of mcrA, which encodes a key enzyme in methane formation, is proposed as a parameter to monitor the process performance in real time. This review evaluates the current knowledge on microbial groups, their interactions, and their relationship to the performance of anaerobic biodigesters with a focus on using mcrA gene expression as a tool to monitor the process.

Bacterial influences on animal origins

Animals evolved in seas teeming with bacteria, yet the influences of bacteria on animal origins are poorly understood. Comparisons among modern animals and their closest living relatives, the choanoflagellates, suggest that the first animals used flagellated collar cells to capture bacterial prey. The cell biology of prey capture, such as cell adhesion between predator and prey, involves mechanisms that may have been co-opted to mediate intercellular interactions during the evolution of animal multicellularity. Moreover, a history of bacterivory may have influenced the evolution of animal genomes by driving the evolution of genetic pathways for immunity and facilitating lateral gene transfer. Understanding the interactions between bacteria and the progenitors of animals may help to explain the myriad ways in which bacteria shape the biology of modern animals, including ourselves.

Fluorine-rich planetary environments as possible habitats for life

In polar aprotic organic solvents, fluorine might be an element of choice for life that uses selected fluorinated building blocks as monomers of choice for self-assembling of its catalytic polymers. Organofluorine compounds are extremely rare in the chemistry of life as we know it. Biomolecules, when fluorinated such as peptides or proteins, exhibit a "fluorous effect", i.e., they are fluorophilic (neither hydrophilic nor lipophilic). Such polymers, capable of creating self-sorting assemblies, resist denaturation by organic solvents by exclusion of fluorocarbon side chains from the organic phase. Fluorous cores consist of a compact interior, which is shielded from the surrounding solvent. Thus, we can anticipate that fluorine-containing "teflon"-like or "non-sticking" building blocks might be monomers of choice for the synthesis of organized polymeric structures in fluorine-rich planetary environments. Although no fluorine-rich planetary environment is known, theoretical considerations might help us to define chemistries that might support life in such environments. For example, one scenario is that all molecular oxygen may be used up by oxidation reactions on a planetary surface and fluorine gas could be released from F-rich magma later in the history of a planetary body to result in a fluorine-rich planetary environment.

Abundance of the multiheme c-type cytochrome OmcB increases in outer biofilm layers of electrode-grown Geobacter sulfurreducens

When Geobacter sulfurreducens utilizes an electrode as its electron acceptor, cells embed themselves in a conductive biofilm tens of microns thick. While environmental conditions such as pH or redox potential have been shown to change close to the electrode, less is known about the response of G. sulfurreducens to growth in this biofilm environment. To investigate whether respiratory protein abundance varies with distance from the electrode, antibodies against an outer membrane multiheme cytochrome (OmcB) and cytoplasmic acetate kinase (AckA) were used to determine protein localization in slices spanning ∼25 µm-thick G. sulfurreducens biofilms growing on polished electrodes poised at +0.24 V (vs. Standard Hydrogen Electrode). Slices were immunogold labeled post-fixing, imaged via transmission electron microscopy, and digitally reassembled to create continuous images allowing subcellular location and abundance per cell to be quantified across an entire biofilm. OmcB was predominantly localized on cell membranes, and 3.6-fold more OmcB was detected on cells 10–20 µm distant from the electrode surface compared to inner layers (0–10 µm). In contrast, acetate kinase remained constant throughout the biofilm, and was always associated with the cell interior. This method for detecting proteins in intact conductive biofilms supports a model where the utilization of redox proteins changes with depth.

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb-long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.

Bioprecipitation: a feedback cycle linking earth history, ecosystem dynamics and land use through biological ice nucleators in the atmosphere

Landscapes influence precipitation via the water vapor and energy fluxes they generate. Biologically active landscapes also generate aerosols containing microorganisms, some being capable of catalyzing ice formation and crystal growth in clouds at temperatures near 0 °C. The resulting precipitation is beneficial for the growth of plants and microorganisms. Mounting evidence from observations and numerical simulations support the plausibility of a bioprecipitation feedback cycle involving vegetated landscapes and the microorganisms they host. Furthermore, the evolutionary history of ice nucleation-active bacteria such as Pseudomonas syringae supports that they have been part of this process on geological time scales since the emergence of land plants. Elucidation of bioprecipitation feedbacks involving landscapes and their microflora could contribute to appraising the impact that modified landscapes have on regional weather and biodiversity, and to avoiding inadvertent, negative consequences of landscape management.

Electrochemically produced hydrogen peroxide affects Joliot-type oxygen-evolution measurements of photosystem II

The main technique employed to characterize the efficiency of water-splitting in photosynthetic preparations in terms of miss and double hit parameters and for the determination of Si (i=2,3,0) state lifetimes is the measurement of flash-induced oxygen oscillation pattern on bare platinum (Joliot-type) electrodes. We demonstrate here that this technique is not innocent. Polarization of the electrode against an Ag/AgCl electrode leads to a time-dependent formation of hydrogen peroxide by two-electron reduction of dissolved oxygen continuously supplied by the flow buffer. While the miss and double hit parameters are almost unaffected by H₂O₂, a time dependent reduction of S1 to S₋₁ occurs over a time period of 20 min. The S1 reduction can be largely prevented by adding catalase or by removing O₂ from the flow buffer with N₂. Importantly, we demonstrate that even at the shortest possible polarization times (40s in our set up) the S₂ and S₀ decays are significantly accelerated by the side reaction with H₂O₂. The removal of hydrogen peroxide leads to unperturbed S₂ state data that reveal three instead of the traditionally reported two phases of decay. In addition, even under the best conditions (catalase+N₂; 40s polarization) about 4% of S₋₁ state is observed in well dark-adapted samples, likely indicating limitations of the equal fit approach. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy.

Regulation of mercaptopyruvate sulfurtransferase activity via intrasubunit and intersubunit redox-sensing switches

SIGNIFICANCE

Redox regulates 3-mercaptopyruvate sulfurtransferase (MST, EC 2.8.1.2) activity via both intermolecular and intramolecular redox-sensing switches. The intermolecular switch comprises an intermolecular disulfide bond that forms a homodimer. On the other hand, the intramolecular switch is a catalytic site cysteine that forms a low redox potential sulfenate. Both switches are reduced by thioredoxin with the reducing system, including thioredoxin reductase and NADPH, and to a much lesser extent by reduced glutathione. It becomes clear that MST serves as not only an enzyme in cysteine catabolism, but also as an antioxidant protein.

RECENT ADVANCES

New findings have been accumulated that, in the catalytic process of MST, hydrogen peroxide is possibly produced by persulfide of the sulfur-accepted substrate and sulfur oxides are possibly produced in the redox cycle of persulfide formed at the catalytic site cysteine of the reaction intermediate. Further, we recently succeeded to produce MST knockout (KO) mice.

CRITICAL ISSUES

A congenital metabolic disorder, mercaptolactate-cysteine disulfiduria (MCDU) is caused by MST defect with or without mental retardation. The MST KO mouse is just a MCDU model. Recent findings suggest that hydrogen sulfide and/or sulfur oxides are involved in the neurobehavioral changes in MCDU.

FUTURE DIRECTIONS

We investigate the pathogenesis of MCDU by performing a comprehensive analysis of the MST KO mice to clarify the functional diversity of MST and biological importance of hydrogen sulfide and sulfur oxides in the brain.

Metabolic reprogramming by viruses in the sunlit and dark ocean

Background

Marine ecosystem function is largely determined by matter and energy transformations mediated by microbial community interaction networks. Viral infection modulates network properties through mortality, gene transfer and metabolic reprogramming.

Results

Here we explore the nature and extent of viral metabolic reprogramming throughout the Pacific Ocean depth continuum. We describe 35 marine viral gene families with potential to reprogram metabolic flux through central metabolic pathways recovered from Pacific Ocean waters. Four of these families have been previously reported but 31 are novel. These known and new carbon pathway auxiliary metabolic genes were recovered from a total of 22 viral metagenomes in which viral auxiliary metabolic genes were differentiated from low-level cellular DNA inputs based on small subunit ribosomal RNA gene content, taxonomy, fragment recruitment and genomic context information. Auxiliary metabolic gene distribution patterns reveal that marine viruses target overlapping, but relatively distinct pathways in sunlit and dark ocean waters to redirect host carbon flux towards energy production and viral genome replication under low nutrient, niche-differentiated conditions throughout the depth continuum.

Conclusions

Given half of ocean microbes are infected by viruses at any given time, these findings of broad viral metabolic reprogramming suggest the need for renewed consideration of viruses in global ocean carbon models.

Earth's punctuated tectonic evolution: cause and effect

Peaks in the Precambrian preserved crustal record are associated with major volcanic, tectonic and climatic events. These include addition of juvenile continental crust, voluminous high-temperature volcanism, massive mantle depletion, widespread orogeny and mineralization, large apparent polar wander velocity spikes, and subsequent palaeomagnetic intensity increases. These events impinge on the glaciation record, atmospheric and ocean chemistry, and on the rise of oxygen. Here we summarize and assess a number of geodynamic models that have been proposed to explain the observed episodicity in the Precambrian record. We find that episodic behaviour from nonlinear slab-driven models best explains the observed record. Examples of such slab-driven systems include mantle avalanches or episodic subduction. In these cases, rapid descent of slabs into the mantle drives fast plate motions and convergence at the surface. This is accompanied by large-scale upwellings of deep hot mantle, which contribute to voluminous volcanism. Further modelling will determine the relative importance of each mechanism, and reinforce the fundamental contribution of the mantle to the evolution of Earth's surface systems.

Functional proteomic discovery of Slr0110 as a central regulator of carbohydrate metabolism in Synechocystis species PCC6803

The unicellular photosynthetic model-organism cyanobacterium Synechocystis sp. PCC6803 can grow photoautotrophically using CO2 or heterotrophically using glucose as the sole carbon source. Several pathways are involved in carbon metabolism in Synechocystis, and the concerted regulation of these pathways by numerous known and unknown genes is critical for the survival and growth of the organism. Here, we report that a hypothetical protein encoded by the open reading frame slr0110 is necessary for heterotrophic growth of Synechocystis. The slr0110-deletion mutant is defective in glucose uptake, heterotrophic growth, and dark viability without detectable defects in autotrophic growth, whereas the level of photosystem II and the rate of oxygen evolution are increased in the mutant. Quantitative proteomic analysis revealed that several proteins in glycolysis and the oxidative pentose phosphate pathway are down-regulated, whereas proteins in photosystem II and phycobilisome are significantly up-regulated, in the mutant. Among the down-regulated proteins are glucose transporter, glucokinase, glucose-6-phosphate isomerase, and glucose-6-phosphate dehydrogenase and its assembly protein OpcA, suggesting that glycolysis, oxidative pentose phosphate, and glycogen synthesis pathways are significantly inhibited in the mutant, which was further confirmed by enzymatic assays and quantification of glycogen content. These findings establish Slr0110 as a novel central regulator of carbon metabolism in Synechocystis, and shed light on an intricate mechanism whereby photosynthesis and carbon metabolism are well concerted to survive the crisis when one or more pathways of the system are impaired.

Convergent evolution of hyperswarming leads to impaired biofilm formation in pathogenic bacteria

Most bacteria in nature live in surface-associated communities rather than planktonic populations. Nonetheless, how surface-associated environments shape bacterial evolutionary adaptation remains poorly understood. Here, we show that subjecting Pseudomonas aeruginosa to repeated rounds of swarming, a collective form of surface migration, drives remarkable parallel evolution toward a hyperswarmer phenotype. In all independently evolved hyperswarmers, the reproducible hyperswarming phenotype is caused by parallel point mutations in a flagellar synthesis regulator, FleN, which locks the naturally monoflagellated bacteria in a multiflagellated state and confers a growth rate-independent advantage in swarming. Although hyperswarmers outcompete the ancestral strain in swarming competitions, they are strongly outcompeted in biofilm formation, which is an essential trait for P. aeruginosa in environmental and clinical settings. The finding that evolution in swarming colonies reliably produces evolution of poor biofilm formers supports the existence of an evolutionary trade-off between motility and biofilm formation.

The use and misuse of photosynthesis in the quest for novel methods to harness solar energy to make fuel

This short review will illustrate that photosynthesis can provide a real contribution towards our sustain- able, green fuel requirements in the future. However, it is argued that the focus on biofuels is misplaced and that, in the longer term, investment in artificial photosynthesis will prove much more beneficial.

The life history of Pseudomonas syringae: linking agriculture to earth system processes

The description of the ecology of Pseudomonas syringae is moving away from that of a ubiquitous epiphytic plant pathogen to one of a multifaceted bacterium sans frontières in fresh water and other ecosystems linked to the water cycle. Discovery of the aquatic facet of its ecology has led to a vision of its life history that integrates spatial and temporal scales spanning billions of years and traversing catchment basins, continents, and the planet and that confronts the implication of roles that are potentially conflicting for agriculture (as a plant pathogen and as an actor in processes leading to rain and snowfall). This new ecological perspective has also yielded insight into epidemiological phenomena linked to disease emergence. Overall, it sets the stage for the integration of more comprehensive contexts of ecology and evolutionary history into comparative genomic analyses to elucidate how P. syringae subverts the attack and defense responses of the cohabitants of the diverse environments it occupies.