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report_refs.bib
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%% This BibTeX bibliography file was created using BibDesk.
%% https://bibdesk.sourceforge.io/
%% Created for Claborne, Daniel at 2019-08-29 10:31:12 -0700
%% Saved with string encoding Unicode (UTF-8)
@article{Hughey_2001,
Author = {Hughey, Christine A. and Hendrickson, Christopher L. and Rodgers, Ryan P. and Marshall, Alan G. and Qian, Kuangnan},
Date-Added = {2019-08-29 10:30:01 -0700},
Date-Modified = {2019-08-29 10:30:01 -0700},
Doi = {10.1021/ac010560w},
Issn = {1520-6882},
Journal = {Analytical Chemistry},
Month = {Oct},
Number = {19},
Pages = {4676--4681},
Publisher = {American Chemical Society (ACS)},
Title = {Kendrick Mass Defect Spectrum: A Compact Visual Analysis for Ultrahigh-Resolution Broadband Mass Spectra},
Url = {http://dx.doi.org/10.1021/ac010560w},
Volume = {73},
Year = {2001},
Bdsk-Url-1 = {http://dx.doi.org/10.1021/ac010560w}}
@article{LAROWE20112030,
Abstract = {The oxidative degradation of organic matter is a key process in the biogeochemical functioning of the earth system. Quantitative models of organic matter degradation are therefore essential for understanding the chemical state and evolution of the Earth's near-surface environment, and to forecast the biogeochemical consequences of ongoing regional and global change. The complex nature of biologically produced organic matter represents a major obstacle to the development of such models, however. Here, we compare the energetics of the oxidative degradation of a large number of naturally occurring organic compounds. By relating the Gibbs energies of half reactions describing the complete mineralization of the compounds to their average nominal carbon oxidation state, it becomes possible to estimate the energetic potential of the compounds based on major element (C, H, N, O, P, S) ratios. The new energetic description of organic matter can be combined with bioenergetic theory to rationalize observed patterns in the decomposition of natural organic matter. For example, the persistence of cell membrane derived compounds and complex organics in anoxic settings is consistent with their limited catabolic potential under these environmental conditions. The proposed approach opens the way to include the thermodynamic properties of organic compounds in kinetic models of organic matter degradation.},
Author = {Douglas E. LaRowe and Philippe Van Cappellen},
Date-Added = {2019-08-29 10:29:41 -0700},
Date-Modified = {2019-08-29 10:29:41 -0700},
Doi = {https://doi.org/10.1016/j.gca.2011.01.020},
Issn = {0016-7037},
Journal = {Geochimica et Cosmochimica Acta},
Number = {8},
Pages = {2030 - 2042},
Title = {Degradation of natural organic matter: A thermodynamic analysis},
Url = {http://www.sciencedirect.com/science/article/pii/S0016703711000378},
Volume = {75},
Year = {2011},
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0016703711000378},
Bdsk-Url-2 = {https://doi.org/10.1016/j.gca.2011.01.020}}
@article{Rivas_Ubach_2018,
Author = {Rivas-Ubach, Albert and Liu, Yina and Bianchi, Thomas S. and Toli{\'c}, Nikola and Jansson, Christer and Pa{\v s}a-Toli{\'c}, Ljiljana},
Date-Added = {2019-08-29 10:29:19 -0700},
Date-Modified = {2019-08-29 10:29:19 -0700},
Doi = {10.1021/acs.analchem.8b00529},
Issn = {1520-6882},
Journal = {Analytical Chemistry},
Month = {Apr},
Number = {10},
Pages = {6152--6160},
Publisher = {American Chemical Society (ACS)},
Title = {Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms},
Url = {http://dx.doi.org/10.1021/acs.analchem.8b00529},
Volume = {90},
Year = {2018},
Bdsk-Url-1 = {http://dx.doi.org/10.1021/acs.analchem.8b00529}}
@article{BAILEY2017133,
Abstract = {Spatial isolation of soil organic carbon (SOC) in different sized pores may be a mechanism by which otherwise labile carbon (C) could be protected in soils. When soil water content increases, the hydrologic connectivity of soil pores also increases, allowing greater transport of SOC and other resources from protected locations, to microbially colonized locations more favorable to decomposition. The heterogeneous distribution of specialized decomposers, C, and other resources throughout the soil indicates that the metabolism or persistence of soil C compounds is highly dependent on short-distance transport processes. The objective of this research was to characterize the complexity of C in pore waters held at weak and strong water tensions (effectively soil solution held behind coarse- and fine-pore throats, respectively) and evaluate the microbial decomposability of these pore waters. We saturated intact soil cores and extracted pore waters with increasing suction pressures to sequentially sample pore waters from increasingly fine pore domains. Ultrahigh resolution mass spectrometry of the SOC was used to profile the major biochemical classes (i.e., lipids, proteins, lignin, carbohydrates, and condensed aromatics) of compounds present in the pore waters; some of these samples were then used as substrates for growth of Cellvibrio japonicus (DSMZ 16018), Streptomyces cellulosae (ATCC{\textregistered} 25439{\texttrademark}), and Trichoderma reseei (QM6a) in 7 day incubations. The soluble C in finer pores was more complex than the soluble C in coarser pores, and the incubations revealed that the more complex C in these fine pores is not recalcitrant. The decomposition of this complex C led to greater losses of C through respiration than the simpler C from coarser pore waters. Our research suggests that soils that experience repeated cycles of drying and wetting may be accompanied by repeated cycles of increased CO2 fluxes that are driven by i) the transport of C from protected pools into active, ii) the chemical quality of the potentially soluble C, and iii) the type of microorganisms most likely to metabolize this C.},
Author = {V.L. Bailey and A.P. Smith and M. Tfaily and S.J. Fansler and B. Bond-Lamberty},
Date-Added = {2019-08-29 10:28:28 -0700},
Date-Modified = {2019-08-29 10:28:28 -0700},
Doi = {https://doi.org/10.1016/j.soilbio.2016.11.025},
Issn = {0038-0717},
Journal = {Soil Biology and Biochemistry},
Keywords = {Pore water, Carbon protection, Soil organic carbon, Soil structure, Decomposability},
Pages = {133 - 143},
Title = {Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains},
Url = {http://www.sciencedirect.com/science/article/pii/S0038071716306447},
Volume = {107},
Year = {2017},
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0038071716306447},
Bdsk-Url-2 = {https://doi.org/10.1016/j.soilbio.2016.11.025}}
@article{Kim_2003,
Author = {Kim, Sunghwan and Kramer, Robert W. and Hatcher, Patrick G.},
Date-Added = {2019-08-29 10:27:23 -0700},
Date-Modified = {2019-08-29 10:27:23 -0700},
Doi = {10.1021/ac034415p},
Issn = {1520-6882},
Journal = {Analytical Chemistry},
Month = {Oct},
Number = {20},
Pages = {5336--5344},
Publisher = {American Chemical Society (ACS)},
Title = {Graphical Method for Analysis of Ultrahigh-Resolution Broadband Mass Spectra of Natural Organic Matter, the Van Krevelen Diagram},
Url = {http://dx.doi.org/10.1021/ac034415p},
Volume = {75},
Year = {2003},
Bdsk-Url-1 = {http://dx.doi.org/10.1021/ac034415p}}
@article{Koch_2016_erratum,
Author = {Koch, B. P. and Dittmar, T.},
Date-Added = {2019-08-29 10:26:43 -0700},
Date-Modified = {2019-08-29 10:30:56 -0700},
Doi = {10.1002/rcm.7433},
Eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/rcm.7433},
Journal = {Rapid Communications in Mass Spectrometry},
Number = {1},
Pages = {250-250},
Title = {From mass to structure: an aromaticity index for high-resolution mass data of natural organic matter},
Url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/rcm.7433},
Volume = {30},
Year = {2016},
Bdsk-Url-1 = {https://onlinelibrary.wiley.com/doi/abs/10.1002/rcm.7433},
Bdsk-Url-2 = {https://doi.org/10.1002/rcm.7433}}
@article{Koch_2006,
Author = {Koch, B. P. and Dittmar, T.},
Date-Added = {2019-08-29 10:25:03 -0700},
Date-Modified = {2019-08-29 10:25:03 -0700},
Doi = {10.1002/rcm.2386},
Issn = {0951-4198},
Journal = {Rapid Communications in Mass Spectrometry},
Month = {Feb},
Number = {5},
Pages = {926--932},
Publisher = {Wiley},
Title = {From mass to structure: an aromaticity index for high-resolution mass data of natural organic matter},
Url = {http://dx.doi.org/10.1002/rcm.2386},
Volume = {20},
Year = {2006},
Bdsk-Url-1 = {http://dx.doi.org/10.1002/rcm.2386}}