Earth's Biogeochemistry Research Articles

To be or not to be a cytochrome: electrical characterizations are inconsistent with Geobacter cytochrome 'nanowires'.

Geobacter sulfurreducens profoundly shapes Earth's biogeochemistry by discharging respiratory electrons to minerals and other microbes through filaments of a two-decades-long debated identity. Cryogenic electron microscopy has revealed filaments of redox-active cytochromes, but the same filaments have exhibited hallmarks of organic metal-like conductivity under cytochrome denaturing/inhibiting conditions. Prior structure-based calculations and kinetic analyses on multi-heme proteins are synthesized herein to propose that a minimum of ~7 cytochrome 'nanowires' can carry the respiratory flux of a Geobacter cell, which is known to express somewhat more (≥20) filaments to increase the likelihood of productive contacts. By contrast, prior electrical and spectroscopic structural characterizations are argued to be physiologically irrelevant or physically implausible for the known cytochrome filaments because of experimental artifacts and sample impurities. This perspective clarifies our mechanistic understanding of physiological metal-microbe interactions and advances synthetic biology efforts to optimize those interactions for bioremediation and energy or chemical production.

Temperature versus hydrologic controls of chemical weathering fluxes from United States forests

Chemical weathering is a dominant control on modern inland water chemistry and global element budgets over geologic time scales. Due to its central role in the earth's biogeochemistry it remains an intense area of interest. Understanding the controls on chemical weathering is difficult because it has many drivers with overlapping temporal and spatial signals. Of particular interest is the relationship between chemical weathering fluxes and global temperatures due to a negative feedback loop where warmer temperatures leads to more chemical weathering and its associated atmospheric CO2 consumption (Berner et al., 1983). Recently it has been proposed that this negative feedback loop is indirect where the acceleration of the hydrologic cycle by increased global temperatures leads to higher chemical weathering and atmospheric CO2 consumption (Maher and Chamberlain, 2014). Here, fluxes of all major cations and anions are calculated for 150 forested watersheds smaller than 500km2 in order to explore controls on chemical weathering from United States forests. Relationships between watershed hydrology, ion ratios and pH are reported that explain a large amount of across site variation in bicarbonate fluxes. Furthermore, across all watersheds ~32% of the cation flux is not balanced by bicarbonate but by sulfate. Paired alkalinity, temperature and discharge data are used to determine a temperature sensitivity of chemical weathering across 51 forested watersheds with a minimum of 70 measurements. The temperature sensitivity of bicarbonate fluxes is absent at low flow conditions because long residence times leads to chemical equilibrium and transport limitation. As discharge increases and residence time decreases, the temperature sensitivity of chemical weathering is released from transport limitation. The temperature sensitivity then increases with discharge until it levels off at high discharges as the system becomes reaction limited. Records of daily discharge, watershed discharge to flux relationships, and the temperature sensitivity are then used to estimate how chemical fluxes would change with a 20% increase in discharge, and 10° increase in temperature global change scenario. Not surprisingly it is found that increased discharge leads to higher weathering fluxes. Interestingly, wetter years have a higher temperature sensitivity due to a release of the temperature sensitivity from transport limitation. This coupled with a strong direct temperature effect leads to an approximately equal response from temperature and increased discharge using this scenario of global change. Thus periods of time and regions that are subject to both warm and wet conditions may have a particularly strong control on weathering fluxes.

Photosynthetic Versatility in the Genome of Geitlerinema sp. PCC 9228 (Formerly Oscillatoria limnetica 'Solar Lake'), a Model Anoxygenic Photosynthetic Cyanobacterium.

Anoxygenic cyanobacteria that use sulfide as the electron donor for photosynthesis are a potentially influential but poorly constrained force on Earth’s biogeochemistry. Their versatile metabolism may have boosted primary production and nitrogen cycling in euxinic coastal margins in the Proterozoic. In addition, they represent a biological mechanism for limiting the accumulation of atmospheric oxygen, especially before the Great Oxidation Event and in the low-oxygen conditions of the Proterozoic. In this study, we describe the draft genome sequence of Geitlerinema sp. PCC 9228, formerly Oscillatoria limnetica ‘Solar Lake’, a mat-forming diazotrophic cyanobacterium that can switch between oxygenic photosynthesis and sulfide-based anoxygenic photosynthesis (AP). Geitlerinema possesses three variants of psbA, which encodes protein D1, a core component of the photosystem II reaction center. Phylogenetic analyses indicate that one variant is closely affiliated with cyanobacterial psbA genes that code for a D1 protein used for oxygen-sensitive processes. Another version is phylogenetically similar to cyanobacterial psbA genes that encode D1 proteins used under microaerobic conditions, and the third variant may be cued to high light and/or elevated oxygen concentrations. Geitlerinema has the canonical gene for sulfide quinone reductase (SQR) used in cyanobacterial AP and a putative transcriptional regulatory gene in the same operon. Another operon with a second, distinct sqr and regulatory gene is present, and is phylogenetically related to sqr genes used for high sulfide concentrations. The genome has a comprehensive nif gene suite for nitrogen fixation, supporting previous observations of nitrogenase activity. Geitlerinema possesses a bidirectional hydrogenase rather than the uptake hydrogenase typically used by cyanobacteria in diazotrophy. Overall, the genome sequence of Geitlerinema sp. PCC 9228 highlights potential cyanobacterial strategies to cope with fluctuating redox gradients and nitrogen availability that occur in benthic mats over a diel cycle. Such dynamic geochemical conditions likely also challenged Proterozoic cyanobacteria, modulating oxygen production. The genetic repertoire that underpins flexible oxygenic/anoxygenic photosynthesis in cyanobacteria provides a foundation to explore the regulation, evolutionary context, and biogeochemical implications of these co-occurring metabolisms in Earth history.

Importancia ecológico-económica del aprovechamiento de los bosques

Satisfacer las necesidades de la población de una manera racional, perdurable y ecológicamente sensata es el principal reto de las sociedades modernas. En muchas de ellas, los recursos forestales han desempeñado un papel preponderante en el desarrollo de la civilización y la contribución de la industria forestal al producto interno bruto es significativa. Este no es el caso de México. La hipótesis central de este trabajo es que el uso de la madera no es nocivo para el medio ambiente. La madera es uno de los materiales para construcción más benignos. Es un recurso natural renovable económicamente atractivo para usos estructurales y arquitectónicos. Los materiales no renovables emplean considerablemente más energía por unidad de producción que la madera. La madera como material de construcción tiene grandes ventajas. Como aislante, la madera es más eficiente energéticamente. Su eficiencia estructural en términos de la energía necesaria para producirla es mayor. Los bosques en crecimiento activo son enormes almacenadores de carbono. Ningún otro material provee este servicio ecológico que reduce el efecto invernadero. Otro punto destacado es el papel del bosque como elemento biosférico que regula la hidrología y la biogeoquímica terrestre. El secreto para obtener todos estos beneficios está en cultivar el bosque; utilizarlo para la producción de bienes de consumo, con un gasto energético reducido y hacerlo que crezca para que produzca más oxígeno, capture más bióxido de carbono y conserve el suelo al mismo tiempo.

Extensive hydrogen supersaturations in the western South Atlantic Ocean suggest substantial underestimation of nitrogen fixation

AbstractThe nitrogen cycle is fundamental to Earth's biogeochemistry. Yet major uncertainties of quantification remain, particularly regarding the global oceanic nitrogen fixation rate. Hydrogen is produced during nitrogen fixation and will become supersaturated in surface waters if there is net release from diazotrophs. Ocean surveys of hydrogen supersaturation thus have the potential to illustrate the spatial and temporal distribution of nitrogen fixation and to guide the far more onerous but quantitative methods for measuring it. Here we present the first transect of high resolution measurements of hydrogen supersaturations in surface waters along a meridional 10,000 km cruise track through the Atlantic. We compare measured saturations with published measurements of nitrogen fixation rates and also with model‐derived values. If the primary source of excess hydrogen is nitrogen fixation and has a hydrogen release ratio similar to Trichodesmium, our hydrogen measurements would point to similar rates of fixation in the North and South Atlantic, roughly consistent with modeled fixation rates but not with measured rates, which are lower in the south. Possible explanations would include any substantial nitrogen fixation by newly discovered diazotrophs, particularly any having a hydrogen release ratio similar to or exceeding that of Trichodesmium; undersampling of nitrogen fixation south of the equator related to excessive focus on Trichodesmium; and methodological shortcomings of nitrogen fixation techniques that cause a bias toward colonial diazotrophs relative to unicellular forms. Alternatively, our data are affected by an unknown hydrogen source that is greater in the southern half of the cruise track than the northern.

The molecular biogeochemistry of manganese(II) oxidation

Micro-organisms capable of oxidizing the redox-active transition metal manganese play an important role in the biogeochemical cycle of manganese. In the present mini-review, we focus specifically on Mn(II)-oxidizing bacteria. The mechanisms by which bacteria oxidize Mn(II) include a two-electron oxidation reaction catalysed by a novel multicopper oxidase that produces Mn(IV) oxides as the primary product. Bacteria also produce organic ligands, such as siderophores, that bind to and stabilize Mn(III). The realization that this stabilized Mn(III) is present in many environments and can affect the redox cycles of other elements such as sulfur has made it clear that manganese and the bacteria that oxidize it profoundly affect the Earth's biogeochemistry.

Seawater sulfur isotope fluctuations in the Cretaceous.

The exogenic sulfur cycle is tightly coupled with the carbon and oxygen cycles, and therefore a central component of Earth's biogeochemistry. Here we present a high-resolution record of the sulfur isotopic composition of seawater sulfate for the Cretaceous. The general enrichment of isotopically light sulfur that prevailed during the Cretaceous may have been due to increased volcanic and hydrothermal activity. Two excursions toward isotopically lighter sulfur represent periods of lower rates of pyrite burial, implying a shift in the location of organic carbon burial to terrestrial or open-ocean settings. The concurrent changes in seawater sulfur and inorganic carbon isotopic compositions imply short-term variability in atmospheric oxygen partial pressure.

Focus Issue on Environmental Microbiology: The Microbial Signaling Frontier

The smallest organisms may have played the largest role in influencing the Earth's biogeochemistry, and a special section in this week's issue of Science called Environmental Microbiology ( ) indicates that microorganisms have affected terrestrial, aquatic, and atmospheric environments through their sheer abundance, diversity, and metabolic potential. Understanding how various microbial communities assemble, function, and survive requires elucidating how their physical, chemical, and biological components interconnect. How does a particular consortium of bacteria form or catabolize particular metals and minerals in the ocean or in the deep layers of the Earth's mantle? How do certain microorganisms thrive in aerobic, anaerobic, or extreme conditions of temperature, pH, or salinity? The dynamic relations of species with one another and with their environment help define a particular microbial ecosystem. Such relations are regulated in part by biochemical processes that control how microorganisms respond to, and affect, their local environment as well as each other. We are at the frontier of understanding how particular networks of genes, proteins, and signaling pathways define microbial communities and consequently, the microbiology that underlies earth history. The general ubiquity and diversity of microbial eukaryotes and prokaryotes, described in Viewpoints by Finlay ( ) and by Torsvik et al . ( ) , indicates that microorganisms can make a living just about anywhere, and as a result, microbial communities are heterogenous and complex. Clues to the microbial strategies employed for survival and growth in a given environment have been gleaned from studying isolated species or mixed populations under defined conditions. For example, bacteria may detect changes in osmolarity and temperature through physical changes in their membranes and associated alterations in membrane-associated signaling proteins such as receptors and ion channels [see Perspective by Los and Murata ( ) in the STKE Archive]. Reviews by Reysenbach and Shock ( ) and by Fenchel ( ) point out that because motility is the primary mechanism by which microorganisms seek out optimal environments, nearly all microorganisms are motile during some part of their life cycle. Gliding, amoeboid-like motion, or flagella-driven movement can propel a microorganism in the right direction. A Perspective by Dahlquist ( ) describes our current understanding of how a bacterium can respond to temporal changes in the intensity or concentration of a stimulus by modulating its flagellar rotary engine. Alterations in bacterial orientation and movement (chemotaxis) involve transducing a perceived environmental change to the flagella motor. A phosphorelay signaling system is in place that couples transmembrane chemoreceptors with a sensor kinase and a response regulator, a cascade that ultimately affects the rotational bias of the flagella. Signal amplification can occur at multiple points of this pathway and receptor methylation further marks a of a bacterium's exposure to a stimulus, ensuring appropriate responses to the same stimulus later on. Santos and Shiozaki ( ) describe a similar phosphorelay system in yeast, indicating that growth responses and morphological transitions in such lower eukaryotes utilize a conserved signaling mechanism (see Review in the STKE Archive). Stock et al . ( ) points out that although each bacterium in a population should move toward optimal conditions for survival and growth, microbial dispersal requires a diversity of responses that permits exploration in other directions. A molecular understanding of how bacteria efficiently interpret multiple stimuli and choose the best direction to move in is not yet clear. In contrast to a free-swimming state, three-dimensional biofilms represent stable, surface-adherent communities of bacteria that are largely cooperative and communicate through chemical signals. They are not only geologically important, but their link to persistent bacterial infections and antibiotic resistance have made them a force to be reckoned with in medicine. A Review by Schembri et al . ( ) describes the signaling mechanisms that Gram-negative bacteria use to control adhesion during biofilm development. Managing adhesion in response to environmental conditions requires the expression of adhesin molecules and cell surface extensions called fimbrae in coordination with a process called autoaggregation. A cell-to-cell signaling mechanism called quorum sensing is also in place to monitor biofilm population density. If the community structure is such that expansion into nutrient-rich areas is needed, bacterial signaling molecules called N -acylhomoserine lactones are synthesized that stimulate biosurfactant production and induce cellular flagellation to move the biofilm. As Newman and Banfield ( ) point out in their Review, our present knowledge of microbial life in geological systems and the evolution of Earth history has involved integration of geochemical and biological data. Genomic sequence information, DNA microtechnology, and development of good model systems should bring further insight into the relationships between gene expression, inter- and intracellular signaling, and survival strategies that underlie the diversity and complexity of microbial life. Featured in This Focus Issue on Environmental Microbiology Related Resources at STKE