Earth's Biogeochemical Cycles Research Articles

Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset

BackgroundThe world's oceans are home to a diverse array of microbial life whose metabolic activity helps to drive the earth's biogeochemical cycles. Metagenomic analysis has revolutionized our access to these communities, providing a system-scale perspective of microbial community interactions. However, while metagenome sequencing can provide useful estimates of the relative change in abundance of specific genes and taxa between environments or over time, this does not investigate the relative changes in the production or consumption of different metabolites.ResultsWe propose a methodology, Predicted Relative Metabolic Turnover (PRMT) that defines and enables exploration of metabolite-space inferred from the metagenome. Our analysis of metagenomic data from a time-series study in the Western English Channel demonstrated considerable correlations between predicted relative metabolic turnover and seasonal changes in abundance of measured environmental parameters as well as with observed seasonal changes in bacterial population structure.ConclusionsThe PRMT method was successfully applied to metagenomic data to explore the Western English Channel microbial metabalome to generate specific, biologically testable hypotheses. Generated hypotheses linked organic phosphate utilization to Gammaproteobactaria, Plantcomycetes, and Betaproteobacteria, chitin degradation to Actinomycetes, and potential small molecule biosynthesis pathways for Lentisphaerae, Chlamydiae, and Crenarchaeota. The PRMT method can be applied as a general tool for the analysis of additional metagenomic or transcriptomic datasets.

Moisture effects on carbon and nitrogen emission from burning of wildland biomass

Abstract. Carbon (C) and nitrogen (N) released from biomass burning have multiple effects on the Earth's biogeochemical cycle, climate change, and ecosystem. These effects depend on the relative abundances of C and N species emitted, which vary with fuel type and combustion conditions. This study systematically investigates the emission characteristics of biomass burning under different fuel moisture contents, through controlled burning experiments with biomass and soil samples collected from a typical alpine forest in North America. Fuel moisture in general lowers combustion efficiency, shortens flaming phase, and introduces prolonged smoldering before ignition. It increases emission factors of incompletely oxidized C and N species, such as carbon monoxide (CO) and ammonia (NH3). Substantial particulate carbon and nitrogen (up to 4 times C in CO and 75% of N in NH3) were also generated from high-moisture fuels, maily associated with the pre-flame smoldering. This smoldering process emits particles that are larger and contain lower elemental carbon fractions than soot agglomerates commonly observed in flaming smoke. Hydrogen (H)/C ratio and optical properties of particulate matter from the high-moisture fuels show their resemblance to plant cellulous and brown carbon, respectively. These findings have implications for modeling biomass burning emissions and impacts.

Implications of an Anthropic Model of Evolution for Emergence of Complex Life and Intelligence

Structurally complex life and intelligence evolved late on Earth; models for the evolution of global temperature suggest that, due to the increasing solar luminosity, the future life span of the (eukaryote) biosphere will be "only" about another billion years, a short time compared to the approximately 4 Ga since life began. A simple stochastic model (Carter, 1983) suggests that this timing might be governed by the necessity to pass a small number, n, of very difficult evolutionary steps, with n < 10 and a best guess of n = 4, in order for intelligent observers like ourselves to evolve. Here I extend the model analysis to derive probability distributions for each step. Past steps should tend to be evenly spaced through Earth's history, and this is consistent with identification of the steps with some of the major transitions in the evolution of life on Earth. A complementary approach, identifying the critical steps with major reorganizations in Earth's biogeochemical cycles, suggests that the Archean-Proterozoic and Proterozoic-Phanerozoic transitions might be identified with critical steps. The success of the model lends support to a "Rare Earth" hypothesis (Ward and Brownlee, 2000): structurally complex life is separated from prokaryotes by several very unlikely steps and, hence, will be much less common than prokaryotes. Intelligence is one further unlikely step, so it is much less common still.

Long‐term impacts of anthropogenic perturbations on dynamics and speciation of organic carbon in tropical forest and subtropical grassland ecosystems

AbstractAnthropogenic perturbations have profoundly modified the Earth's biogeochemical cycles, the most prominent of these changes being manifested by global carbon (C) cycling. We investigated long‐term effects of human‐induced land‐use and land‐cover changes from native tropical forest (Kenya) and subtropical grassland (South Africa) ecosystems to agriculture on the dynamics and structural composition of soil organic C (SOC) using elemental analysis and integrated 13C nuclear magnetic resonance (NMR), near‐edge X‐ray absorption fine structure (NEXAFS) and synchrotron‐based Fourier transform infrared‐attenuated total reflectance (Sr‐FTIR‐ATR) spectroscopy. Anthropogenic interventions led to the depletion of 76%, 86% and 67% of the total SOC; and 77%, 85% and 66% of the N concentrations from the surface soils of Nandi, Kakamega and the South African sites, respectively, over a period of up to 100 years. Significant proportions of the total SOC (46–73%) and N (37–73%) losses occurred during the first 4 years of conversion indicating that these forest‐ and grassland‐derived soils contain large amounts of labile soil organic matter (SOM), potentially vulnerable to degradation upon human‐induced land‐use and land‐cover changes. Anthropogenic perturbations altered not only the C sink capacity of these soils, but also the functional group composition and dynamics of SOC with time, rendering structural composition of the resultant organic matter in the agricultural soils to be considerably different from the SOM under natural forest and grassland ecosystems. These molecular level compositional changes were manifested: (i) by the continued degradation of O‐alkyl and acetal‐C structures found in carbohydrate and holocellulose biomolecules, some labile aliphatic‐C functionalities, (ii) by side‐chain oxidation of phenylpropane units of lignin and (iii) by the continued aromatization and aliphatization of the humic fractions possibly through selective accumulation of recalcitrant H and C substituted aryl‐C and aliphatic‐C components such as (poly)‐methylene units, respectively. These changes appeared as early as the fourth year after transition, and their intensity increased with duration of cultivation until a new quasi‐equilibrium of SOC was approached at about 20 years after conversion. However, subtle but persistent changes in molecular structures of the resultant SOM continued long after (up to 100 years) a steady state for SOC was approached. These molecular level changes in the inherent structural composition of SOC may exert considerable influence on biogeochemical cycling of C and bioavailability of essential nutrients present in association with SOM, and may significantly affect the sustainability of agriculture as well as potentials of the soils to sequester C in these tropical and subtropical highland agroecosystems.

The carbon cycle and associated redox processes through time.

Earth's biogeochemical cycle of carbon delivers both limestones and organic materials to the crust. In numerous, biologically catalysed redox reactions, hydrogen, sulphur, iron, and oxygen serve prominently as electron donors and acceptors. The progress of these reactions can be reconstructed from records of variations in the abundance of 13C in sedimentary carbonate minerals and organic materials. Because the crust is always receiving new CO2 from the mantle and a portion of it is being reduced by photoautotrophs, the carbon cycle has continuously released oxidizing power. Most of it is represented by Fe3+ that has accumulated in the crust or been returned to the mantle via subduction. Less than 3% of the estimated, integrated production of oxidizing power since 3.8 Gyr ago is represented by O2 in the atmosphere and dissolved in seawater. The balance is represented by sulphate. The accumulation of oxidizing power can be estimated from budgets summarizing inputs of mantle carbon and rates of organic-carbon burial, but levels of O2 are only weakly and indirectly coupled to those phenomena and thus to carbon-isotopic records. Elevated abundances of 13C in carbonate minerals ca 2.3 Gyr old, in particular, are here interpreted as indicating the importance of methanogenic bacteria in sediments rather than increased burial of organic carbon.

The Search for a Molecular-Level Understanding of the Processes that Underpin the Earth's Biogeochemical Cycles

Evidence of connections between microbial activity and the Earth’s biogeochemical cycles is all around us, and motivates our interest in the mechanisms of microbial transformations, their rates, and the distribution of microbial activities across environment types and over Earth history. In general, the approach to investigating a geomicrobiological process begins with biological and geochemical characterization of the environment of interest. Geochemical characteristics constrain available metabolisms (e.g., McCollom and Shock 1997) and patterns can reveal processes not recognized initially to be microbially mediated. The membership of microbial communities can be assayed through cultivation and cultivation-independent methods. However, this task is not without its challenges. There is little consensus about the ways in which organisms should be grouped into relevant ecological units such as species (Gevers et al. 2005). Even using standard classification techniques, the extent of microbial diversity appears vast, and recent analyses suggest that current estimates may tremendously under predict the amount of genetic diversity in the biosphere. In addition, a single organism type may contain far more genes than expected based on genomic sequencing of an isolate of that species because species populations can exhibit internal heterogeneity. Thus, it seems that comprehensive characterization of the microbial membership of an environment over space and time is a problem of almost incomprehensible magnitude. Furthermore, microbial census taking is only the first step. Beyond documenting the assemblage of organisms present, we need to know how they are distributed, what are they doing, how they are doing it, and the ways that their activities impact the physical and chemical characteristics of their surroundings. In the near future, the only systems in which it will be plausible to tackle the level of characterization required for relatively comprehensive analyses are the simplest ones. For example, in samples of relatively low geochemical and biological complexity, it …

Considerations in miniaturizing simplified agro-ecosystems for advanced life support

Miniaturizing the Earth's biogeochemical cycles to support human life during future space missions is the goal of the NASA research and engineering program in advanced life support. Mission requirements to reduce mass, volume, and power have focused efforts on (1) a maximally simplified agro-ecosystem of humans, food crops, and microbes; and, (2) a design for optimized productivity of food crops with high light levels over long days, with hydroponics, with elevated carbon dioxide and other controlled environmental factors, as well as with genetic selection for desirable crop properties. Mathematical modeling contributes to the goals by establishing trade-offs, by analyzing the growth and development of experimental crops, and by pointing to the possibilities of directed phasic control using modified field crop models to increase the harvest index.