A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology

Microbial biosensors sense and report exposures to stimuli, thereby facilitating our understanding of environmental processes. Successful design and deployment of biosensors hinge on the persistence of the microbial host of the genetic circuit, termed the chassis. However, model chassis organisms may persist poorly in environmental conditions. In contrast, non-model organisms persist better in environmental conditions but are limited by other challenges, such as genetic intractability and part unavailability. Here we identify ecological, metabolic, and genetic constraints for chassis development and propose a conceptual framework for the systematic selection of environmental biosensor chassis. We identify key challenges with using current model chassis and delineate major points of conflict in choosing the most suitable organisms as chassis for environmental biosensing. This framework provides a way forward in the selection of biosensor chassis for environmental synthetic biology

Aromaticity and degree of aromatic condensation of char

The aromatic carbon structure is a defining property of chars and is often expressed with the help of two concepts: (i) aromaticity and (ii) degree of aromatic condensation. The varying extent of these two features is assumed to largely determine the relatively high persistence of charred material in the environment and is thus of interest for e.g. biochar characterization or carbon cycle studies. Consequently, a variety of methods has been used to assess the aromatic structure of chars, which has led to interesting insights but has complicated the comparison of data acquired with different methods. We therefore used a suite of seven methods (elemental analysis, MIR spectroscopy, NEXAFS spectroscopy, 13C NMR spectroscopy, BPCA analysis, lipid analysis and helium pycnometry) and compared 13 measurements from them using a diverse sample set of 38 laboratory chars. Our results demonstrate that most of the measurements could be categorized either into those which assess aromaticity or those which assess the degree of aromatic condensation. A variety of measurements, including relatively inexpensive and simple ones, reproducibly captured the two aromatic features in question, and data from different methods could therefore be compared. Moreover, general patterns between the two aromatic features and the pyrolysis conditions were revealed, supporting reconstruction of the highest heat treatment temperature (HTT) of char

Aromaticity and degree of aromatic condensation of char

The aromatic carbon structure is a defining property of chars and is often expressed with the help of two concepts: (i) aromaticity and (ii) degree of aromatic condensation. The varying extent of these two features is assumed to largely determine the relatively high persistence of charred material in the environment and is thus of interest for, e.g., biochar characterization or carbon cycle studies. Consequently, a variety of methods has been used to assess the aromatic structure of chars, which has led to interesting insights but has complicated the comparison of data acquired with different methods. We therefore used a suite of seven methods (elemental analysis, MIR spectroscopy, NEXAFS spectroscopy, ¹³C NMR spectroscopy, BPCA analysis, lipid analysis and helium pycnometry) and compared 13 measurements from them using a diverse sample set of 38 laboratory chars. Our results demonstrate that most of the measurements could be categorized either into those which assess aromaticity or those which assess the degree of aromatic condensation. A variety of measurements, including relatively inexpensive and simple ones, reproducibly captured the two aromatic features in question, and data from different methods could therefore be compared. Moreover, general patterns between the two aromatic features and the pyrolysis conditions were revealed, supporting reconstruction of the highest heat treatment temperature (HTT) of char.Keywords: Aromaticity, Stability, Aromatic condensation, Pyrolysis, Char, Biochar, Pyrogenic organic matter, Heat treatment temperatur

Young organic matter as a source of carbon dioxide outgassing from Amazonian rivers

Rivers are generally supersaturated with respect to carbon dioxide, resulting in large gas evasion fluxes that can be a significant component of regional net carbon budgets. Amazonian rivers were recently shown to outgas more than ten times the amount of carbon exported to the ocean in the form of total organic carbon or dissolved inorganic carbon. High carbon dioxide concentrations in rivers originate largely from in situ respiration of organic carbon, but little agreement exists about the sources or turnover times of this carbon. Here we present results of an extensive survey of the carbon isotope composition ({sup 13}C and {sup 14}C) of dissolved inorganic carbon and three size-fractions of organic carbon across the Amazonian river system. We find that respiration of contemporary organic matter (less than 5 years old) originating on land and near rivers is the dominant source of excess carbon dioxide that drives outgassing in mid-size to large rivers, although we find that bulk organic carbon fractions transported by these rivers range from tens to thousands of years in age. We therefore suggest that a small, rapidly cycling pool of organic carbon is responsible for the large carbon fluxes from land to water to atmosphere in the humid tropics

Controls on black carbon storage in soils

[1] Fire-derived black carbon (BC: charcoal and soot) has been thought to be a passive player in soils, contributing to the refractory soil organic carbon (SOC) pool, but playing no role in pedogenesis and regional short-term carbon cycling. This model, however, is at odds with recent results on the role of charcoal in soil fertility and its detection in the dissolved organic carbon (DOC) pool. For example, if BC simply accumulated passively in soils, its pattern of accumulation should match a simple model correlating fire frequency to BC storage. Instead, soil type, climate, biota, and land use practices all appear to play roles in controlling whether BC accumulates or is lost from soils. We summarize current knowledge of BC-soil interactions and construct a new paradigm describing the controls on BC storage in soils. We reconcile the refractory-labile BC paradox by proposing a model where BC storage is controlled by (1) fire frequency, (2) ecosystem presence or absence of aromatic precursor carbon and appropriate combustion conditions, (3) biological or physical mixing to remove BC from the soil surface, where it is vulnerable to combustion in future fires, (4) the presence or absence of soil mineral fractions able to sorb BC into the long-term stable carbon pool, and (5) the presence of microbial communities capable of degrading aromatic carbon. We also recognize that soil BC/SOC ratios are strongly influenced by land-use practices and add (6) human activities as a final control

Carbon isotope geochemistry of the Santa Clara River

The Santa Clara River is a prototypical small mountainous river, with a headwater height greater than 1000 m and a basin area smaller than 10,000 m 2. Although individual small mountainous rivers export trivial amounts of sediment and carbon to the ocean, as a group these rivers may export a major fraction (as much as 50%) of the total global river sediment flux [Milliman and Syvitski, 1992], making their geochemistry relevant the study of the ocean's carbon cycle. In addition, many small rivers export sediment in a few high flux events, causing massive, sporadic discharge of carbon onto coastal shelves, discharge conditions very different from those of large rivers. This class of rivers is an end-member of the river-ocean carbon exchange system,. opposite the Earth's largest river, the Amazon. The carbon mass and isotopic properties of the Santa Clara River are significantly different from previously studied large rivers. During the 1997–1998 winter, all Santa Clara carbon pools were old, with flux-weighted average Δl4C values of−428±76‰ for particulate organic carbon, −73±31‰ for dissolved organic carbon, and−644±58‰ for black carbon. The age of exported carbon is primarily due to the deep erosion of old soils and not to inclusion of fossil fuel carbon. Additionally, the δ13C signatures of exported carbon pools were high relative to terrestrial carbon, bearing a signature quite similar to marine carbon (average particulate organic carbon (POC) δ13C = −22.2±0.8‰). The Santa Clara's estuary is small and drains onto the narrow eastern Pacific coastal margin, exporting this old soil organic matter directly into the ocean. If the Santa Clara export patterns are representative of this class of rivers, they may be a significant source of refractory terrestrial carbon to the ocean