Using metacommunity ecology to understand environmental metabolomes

Danczak, Robert E.; Chu, Rosalie K.; Fansler, Sarah J.; Goldman, Amy E.; Graham, Emily B.; Tfaily, Malak M.; Toyoda, Jason; Stegen, James C.

doi:10.1038/s41467-020-19989-y

Title: Using metacommunity ecology to understand environmental metabolomes

Journal Article · Fri Dec 11 00:00:00 EST 2020 · Nature Communications

DOI:https://doi.org/10.1038/s41467-020-19989-y· OSTI ID:1735391

Danczak, Robert E.;

;

; Goldman, Amy E.;

; Tfaily, Malak M.;

;

Abstract Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1735391

Alternate ID(s):: OSTI ID: 1737553

Report Number(s):: PNNL-SA-152827; 6369; PII: 19989

Journal Information:: Nature Communications, Journal Name: Nature Communications Vol. 11 Journal Issue: 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (99)

Biological Determinants of Species Diversity Shmida, Avi; Wilson, Mark V. Journal of Biogeography, Vol. 12, Issue 1 https://doi.org/10.2307/2845026	journal	January 1985
Methane and nitrous oxide porewater concentrations and surface fluxes of a regulated river Villa, Jorge A.; Smith, Garrett J.; Ju, Yang Science of The Total Environment, Vol. 715 https://doi.org/10.1016/j.scitotenv.2020.136920	journal	May 2020
Estimating and mapping ecological processes influencing microbial community assembly Stegen, James C.; Lin, Xueju; Fredrickson, Jim K. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00370	journal	May 2015
Chemical and microbial diversity covary in fresh water to influence ecosystem functioning Tanentzap, Andrew J.; Fitch, Amelia; Orland, Chloe Proceedings of the National Academy of Sciences, Vol. 116, Issue 49 https://doi.org/10.1073/pnas.1904896116	journal	November 2019
Abiotic and Biotic Controls on Soil Organo–Mineral Interactions: Developing Model Structures to Analyze Why Soil Organic Matter Persists Dwivedi, Dipankar; Tang, Jinyun; Bouskill, Nicholas Reviews in Mineralogy and Geochemistry, Vol. 85, Issue 1 https://doi.org/10.2138/rmg.2019.85.11	journal	September 2019
Columbia River Surface Water and Pore Water Unaligned FTICR-MS Data Associated with “Using Community Assembly Metrics from Metacommunity Ecology to Understand Environmental Metabolomes” Danczak, Robert E.; Chu, Rosalie K.; Fansler, Sarah J. Environmental System Science Data Infrastructure for a Virtual Ecosystem; River Corridor and Watershed Biogeochemistry SFA https://doi.org/10.15485/1675028	dataset	January 2020
The merging of community ecology and phylogenetic biology Cavender-Bares, Jeannine; Kozak, Kenneth H.; Fine, Paul V. A. Ecology Letters, Vol. 12, Issue 7 https://doi.org/10.1111/j.1461-0248.2009.01314.x	journal	July 2009
Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions Feng, Youzhi; Chen, Ruirui; Stegen, James C. Molecular Ecology, Vol. 27, Issue 24 https://doi.org/10.1111/mec.14914	journal	November 2018
Expanding the role of reactive transport models in critical zone processes Li, Li; Maher, Kate; Navarre-Sitchler, Alexis Earth-Science Reviews, Vol. 165 https://doi.org/10.1016/j.earscirev.2016.09.001	journal	February 2017
ggplot2 Wickham, Hadley Use R! https://doi.org/10.1007/978-3-319-24277-4	book	January 2016
Does the Chemodiversity of Bacterial Exometabolomes Sustain the Chemodiversity of Marine Dissolved Organic Matter? Noriega-Ortega, Beatriz E.; Wienhausen, Gerrit; Mentges, Andrea Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00215	journal	February 2019
Thermodynamically controlled preservation of organic carbon in floodplains Boye, Kristin; Noël, Vincent; Tfaily, Malak M. Nature Geoscience, Vol. 10, Issue 6 https://doi.org/10.1038/ngeo2940	journal	May 2017
Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes Wang, Jianjun; Shen, Ji; Wu, Yucheng The ISME Journal, Vol. 7, Issue 7 https://doi.org/10.1038/ismej.2013.30	journal	February 2013
Stochastic Community Assembly: Does It Matter in Microbial Ecology? Zhou, Jizhong; Ning, Daliang Microbiology and Molecular Biology Reviews, Vol. 81, Issue 4 https://doi.org/10.1128/MMBR.00002-17	journal	October 2017
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
pez : phylogenetics for the environmental sciences Pearse, William D.; Cadotte, Marc W.; Cavender-Bares, Jeannine Bioinformatics, Vol. 31, Issue 17 https://doi.org/10.1093/bioinformatics/btv277	journal	May 2015
Functional beta-diversity patterns reveal deterministic community assembly processes in eastern North American trees: Functional beta diversity and tree community assembly Siefert, Andrew; Ravenscroft, Catherine; Weiser, Michael D. Global Ecology and Biogeography, Vol. 22, Issue 6 https://doi.org/10.1111/geb.12030	journal	December 2012
Functional Molecular Diversity of Marine Dissolved Organic Matter Is Reduced during Degradation Mentges, Andrea; Feenders, Christoph; Seibt, Maren Frontiers in Marine Science, Vol. 4 https://doi.org/10.3389/fmars.2017.00194	journal	June 2017
UniFrac: an effective distance metric for microbial community comparison Lozupone, Catherine; Lladser, Manuel E.; Knights, Dan The ISME Journal, Vol. 5, Issue 2 https://doi.org/10.1038/ismej.2010.133	journal	September 2010
Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities Wu, Wenxue; Lu, Hsiao-Pei; Sastri, Akash The ISME Journal, Vol. 12, Issue 2 https://doi.org/10.1038/ismej.2017.183	journal	November 2017
Conceptual Synthesis in Community Ecology Vellend, Mark The Quarterly Review of Biology, Vol. 85, Issue 2 https://doi.org/10.1086/652373	journal	June 2010
Patterns and Processes of Microbial Community Assembly Nemergut, D. R.; Schmidt, S. K.; Fukami, T. Microbiology and Molecular Biology Reviews, Vol. 77, Issue 3 https://doi.org/10.1128/MMBR.00051-12	journal	September 2013
Phylogenetic and structural response of heterotrophic bacteria to dissolved organic matter of different chemical composition in a continuous culture study: Bacterial diversity and dissolved organic matter Landa, M.; Cottrell, M. T.; Kirchman, D. L. Environmental Microbiology, Vol. 16, Issue 6 https://doi.org/10.1111/1462-2920.12242	journal	September 2013
Disentangling the importance of ecological niches from stochastic processes across scales Chase, Jonathan M.; Myers, Jonathan A. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 366, Issue 1576 https://doi.org/10.1098/rstb.2011.0063	journal	August 2011
Characterization of poplar metabotypes via mass difference enrichment analysis: Mass difference network analysis in poplar Moritz, Franco; Kaling, Moritz; Schnitzler, Jörg-Peter Plant, Cell & Environment, Vol. 40, Issue 7 https://doi.org/10.1111/pce.12878	journal	April 2017
From Plant Traits to Plant Communities: A Statistical Mechanistic Approach to Biodiversity Shipley, B.; Vile, D.; Garnier, E. Science, Vol. 314, Issue 5800 https://doi.org/10.1126/science.1131344	journal	November 2006
Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data Breitling, Rainer; Ritchie, Shawn; Goodenowe, Dayan Metabolomics, Vol. 2, Issue 3 https://doi.org/10.1007/s11306-006-0029-z	journal	July 2006
Advanced Solvent Based Methods for Molecular Characterization of Soil Organic Matter by High-Resolution Mass Spectrometry Tfaily, Malak M.; Chu, Rosalie K.; Tolić, Nikola Analytical Chemistry, Vol. 87, Issue 10 https://doi.org/10.1021/acs.analchem.5b00116	journal	April 2015
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R Paradis, Emmanuel; Schliep, Klaus Bioinformatics, Vol. 35, Issue 3 https://doi.org/10.1093/bioinformatics/bty633	journal	July 2018
Graphical Method for Analysis of Ultrahigh-Resolution Broadband Mass Spectra of Natural Organic Matter, the Van Krevelen Diagram Kim, Sunghwan; Kramer, Robert W.; Hatcher, Patrick G. Analytical Chemistry, Vol. 75, Issue 20 https://doi.org/10.1021/ac034415p	journal	October 2003
Quantifying community assembly processes and identifying features that impose them Stegen, James C.; Lin, Xueju; Fredrickson, Jim K. The ISME Journal, Vol. 7, Issue 11 https://doi.org/10.1038/ismej.2013.93	journal	June 2013
Development and comparison of formula assignment algorithms for ultrahigh-resolution mass spectra of natural organic matter Fu, Qing-Long; Fujii, Manabu; Riedel, Thomas Analytica Chimica Acta, Vol. 1125 https://doi.org/10.1016/j.aca.2020.05.048	journal	August 2020
From mass to structure: an aromaticity index for high-resolution mass data of natural organic matter Koch, B. P.; Dittmar, T. Rapid Communications in Mass Spectrometry, Vol. 20, Issue 5 https://doi.org/10.1002/rcm.2386	journal	February 2006
A simple and efficient method for the solid-phase extraction of dissolved organic matter (SPE-DOM) from seawater: SPE-DOM from seawater Dittmar, Thorsten; Koch, Boris; Hertkorn, Norbert Limnology and Oceanography: Methods, Vol. 6, Issue 6 https://doi.org/10.4319/lom.2008.6.230	journal	June 2008
ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data Yu, Guangchuang; Smith, David K.; Zhu, Huachen Methods in Ecology and Evolution, Vol. 8, Issue 1 https://doi.org/10.1111/2041-210X.12628	journal	September 2016
Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone Graham, Emily B.; Crump, Alex R.; Kennedy, David W. Science of The Total Environment, Vol. 642 https://doi.org/10.1016/j.scitotenv.2018.05.256	journal	November 2018
Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data Jia, Xiu; Dini-Andreote, Francisco; Falcão Salles, Joana Microorganisms, Vol. 8, Issue 6 https://doi.org/10.3390/microorganisms8060798	journal	May 2020
Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11237	journal	April 2016
How to measure and test phylogenetic signal: How to measure and test phylogenetic signal Münkemüller, Tamara; Lavergne, Sébastien; Bzeznik, Bruno Methods in Ecology and Evolution, Vol. 3, Issue 4 https://doi.org/10.1111/j.2041-210X.2012.00196.x	journal	April 2012
Freshwater microbial community diversity in a rapidly changing High Arctic watershed Cavaco, Maria Antonia; St. Louis, Vincent Lawrence; Engel, Katja FEMS Microbiology Ecology, Vol. 95, Issue 11 https://doi.org/10.1093/femsec/fiz161	journal	October 2019
Disentangling the Drivers of Diversity Along Latitudinal and Elevational Gradients Kraft, N. J. B.; Comita, L. S.; Chase, J. M. Science, Vol. 333, Issue 6050 https://doi.org/10.1126/science.1208584	journal	September 2011
Linking soil biology and chemistry in biological soil crust using isolate exometabolomics Swenson, Tami L.; Karaoz, Ulas; Swenson, Joel M. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-017-02356-9	journal	January 2018
Root exudate metabolomes change under drought and show limited capacity for recovery Gargallo-Garriga, Albert; Preece, Catherine; Sardans, Jordi Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-30150-0	journal	August 2018
Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness Gotelli, Nicholas J.; Colwell, Robert K. Ecology Letters, Vol. 4, Issue 4 https://doi.org/10.1046/j.1461-0248.2001.00230.x	journal	July 2001
Using null models to disentangle variation in community dissimilarity from variation in α-diversity Chase, Jonathan M.; Kraft, Nathan J. B.; Smith, Kevin G. Ecosphere, Vol. 2, Issue 2 https://doi.org/10.1890/ES10-00117.1	journal	February 2011
Automated Analysis of Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectra of Natural Organic Matter Kujawinski, Elizabeth B.; Behn, Mark D. Analytical Chemistry, Vol. 78, Issue 13 https://doi.org/10.1021/ac0600306	journal	July 2006
Chemodiversity of dissolved organic matter in lakes driven by climate and hydrology Kellerman, Anne M.; Dittmar, Thorsten; Kothawala, Dolly N. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4804	journal	May 2014
Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra Tolić, Nikola; Liu, Yina; Liyu, Andrey Analytical Chemistry, Vol. 89, Issue 23 https://doi.org/10.1021/acs.analchem.7b03318	journal	November 2017
An Ordination of the Upland Forest Communities of Southern Wisconsin Bray, J. Roger; Curtis, J. T. Ecological Monographs, Vol. 27, Issue 4 https://doi.org/10.2307/1942268	journal	February 1957
CREST – Classification Resources for Environmental Sequence Tags Lanzén, Anders; Jørgensen, Steffen L.; Huson, Daniel H. PLoS ONE, Vol. 7, Issue 11 https://doi.org/10.1371/journal.pone.0049334	journal	November 2012
Effects of fluctuating river flow on groundwater/surface water mixing in the hyporheic zone of a regulated, large cobble bed river Arntzen, Evan V.; Geist, David R.; Dresel, P. Evan River Research and Applications, Vol. 22, Issue 8 https://doi.org/10.1002/rra.947	journal	January 2006
Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers Danczak, Robert E.; Johnston, Michael D.; Kenah, Chris mSystems, Vol. 3, Issue 4 https://doi.org/10.1128/mSystems.00066-18	journal	July 2018
The evolutionary ecology of metacommunities Urban, M.; Leibold, M.; Amarasekare, P. Trends in Ecology & Evolution, Vol. 23, Issue 6 https://doi.org/10.1016/j.tree.2008.02.007	journal	June 2008
Temporal turnover in the composition of tropical tree communities: functional determinism and phylogenetic stochasticity Swenson, Nathan G.; Stegen, James C.; Davies, Stuart J. Ecology, Vol. 93, Issue 3 https://doi.org/10.1890/11-1180.1	journal	March 2012
The Problem and Promise of Scale Dependency in Community Phylogenetics Swenson, Nathan G.; Enquist, Brian J.; Pither, Jason Ecology, Vol. 87, Issue 10 https://doi.org/10.1890/0012-9658(2006)87[2418:TPAPOS]2.0.CO;2	journal	October 2006
Stochastic and deterministic assembly processes in subsurface microbial communities Stegen, James C.; Lin, Xueju; Konopka, Allan E. The ISME Journal, Vol. 6, Issue 9 https://doi.org/10.1038/ismej.2012.22	journal	March 2012
ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data Bramer, Lisa M.; White, Amanda M.; Stratton, Kelly G. PLOS Computational Biology, Vol. 16, Issue 3 https://doi.org/10.1371/journal.pcbi.1007654	journal	March 2020
Phylogenetic conservatism of functional traits in microorganisms Martiny, Adam C.; Treseder, Kathleen; Pusch, Gordon The ISME Journal, Vol. 7, Issue 4 https://doi.org/10.1038/ismej.2012.160	journal	December 2012
Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities Sengupta, Aditi; Indivero, Julia; Gunn, Cailene Biogeosciences, Vol. 16, Issue 19 https://doi.org/10.5194/bg-16-3911-2019	journal	January 2019
Phylogenies and Community Ecology Webb, Campbell O.; Ackerly, David D.; McPeek, Mark A. Annual Review of Ecology and Systematics, Vol. 33, Issue 1 https://doi.org/10.1146/annurev.ecolsys.33.010802.150448	journal	November 2002
Interactions between sunlight and microorganisms influence dissolved organic matter degradation along the aquatic continuum: Interactions between sunlight and microorganisms Cory, Rose M.; Kling, George W. Limnology and Oceanography Letters, Vol. 3, Issue 3 https://doi.org/10.1002/lol2.10060	journal	February 2018
Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession Dini-Andreote, Francisco; Stegen, James C.; van Elsas, Jan Dirk Proceedings of the National Academy of Sciences, Vol. 112, Issue 11 https://doi.org/10.1073/pnas.1414261112	journal	March 2015
The metacommunity concept: a framework for multi-scale community ecology: The metacommunity concept Leibold, M. A.; Holyoak, M.; Mouquet, N. Ecology Letters, Vol. 7, Issue 7 https://doi.org/10.1111/j.1461-0248.2004.00608.x	journal	June 2004
Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms Rivas-Ubach, Albert; Liu, Yina; Bianchi, Thomas S. Analytical Chemistry, Vol. 90, Issue 10 https://doi.org/10.1021/acs.analchem.8b00529	journal	April 2018
Conservation evaluation and phylogenetic diversity Faith, Daniel P. Biological Conservation, Vol. 61, Issue 1 https://doi.org/10.1016/0006-3207(92)91201-3	journal	January 1992
Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains Bailey, V. L.; Smith, A. P.; Tfaily, M. Soil Biology and Biochemistry, Vol. 107 https://doi.org/10.1016/j.soilbio.2016.11.025	journal	April 2017
Trait Evolution, Community Assembly, and the Phylogenetic Structure of Ecological Communities Kraft, Nathan J. B.; Cornwell, William K.; Webb, Campbell O. The American Naturalist, Vol. 170, Issue 2 https://doi.org/10.1086/519400	journal	August 2007
Terrestrial and marine perspectives on modeling organic matter degradation pathways Burd, Adrian B.; Frey, Serita; Cabre, Anna Global Change Biology, Vol. 22, Issue 1 https://doi.org/10.1111/gcb.12987	journal	July 2015
ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries Colby, Sean M.; Thomas, Dennis G.; Nuñez, Jamie R. Analytical Chemistry, Vol. 91, Issue 7 https://doi.org/10.1021/acs.analchem.8b04567	journal	February 2019
The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes Martínez, Inés; Stegen, James C.; Maldonado-Gómez, Maria X. Cell Reports, Vol. 11, Issue 4 https://doi.org/10.1016/j.celrep.2015.03.049	journal	April 2015
Soil pH mediates the balance between stochastic and deterministic assembly of bacteria Tripathi, Binu M.; Stegen, James C.; Kim, Mincheol The ISME Journal, Vol. 12, Issue 4 https://doi.org/10.1038/s41396-018-0082-4	journal	March 2018
Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities Fine, Paul V. A.; Kembel, Steven W. Ecography, Vol. 34, Issue 4 https://doi.org/10.1111/j.1600-0587.2010.06548.x	journal	August 2011
Abundant carbon substrates drive extremely high sulfate reduction rates and methane fluxes in Prairie Pothole Wetlands Dalcin Martins, Paula; Hoyt, David W.; Bansal, Sheel Global Change Biology, Vol. 23, Issue 8 https://doi.org/10.1111/gcb.13633	journal	February 2017
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1219	journal	November 2012
The Controls of Iron and Oxygen on Hydroxyl Radical (•OH) Production in Soils Trusiak, Adrianna; Treibergs, Lija; Kling, George Soil Systems, Vol. 3, Issue 1 https://doi.org/10.3390/soilsystems3010001	journal	December 2018
Universal molecular structures in natural dissolved organic matter Zark, Maren; Dittmar, Thorsten Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05665-9	journal	August 2018
VSEARCH: a versatile open source tool for metagenomics Rognes, Torbjørn; Flouri, Tomáš; Nichols, Ben PeerJ, Vol. 4 https://doi.org/10.7717/peerj.2584	journal	January 2016
The contentious nature of soil organic matter Lehmann, Johannes; Kleber, Markus Nature, Vol. 528, Issue 7580 https://doi.org/10.1038/nature16069	journal	November 2015
Effects of Competition, Predation, and Dispersal on Species Richness at Local and Regional Scales Shurin, Jonathan B.; Allen, Emily G. The American Naturalist, Vol. 158, Issue 6 https://doi.org/10.1086/323589	journal	December 2001
Kendrick Mass Defect Spectrum: A Compact Visual Analysis for Ultrahigh-Resolution Broadband Mass Spectra Hughey, Christine A.; Hendrickson, Christopher L.; Rodgers, Ryan P. Analytical Chemistry, Vol. 73, Issue 19 https://doi.org/10.1021/ac010560w	journal	October 2001
Assembly of forest communities across East Asia – insights from phylogenetic community structure and species pool scaling Feng, Gang; Mi, Xiangcheng; Eiserhardt, Wolf L. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep09337	journal	March 2015
Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems Danczak, R. E.; Daly, R. A.; Borton, M. A. mSystems, Vol. 5, Issue 2 https://doi.org/10.1128/mSystems.00098-20	journal	March 2020
Sequential extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry Tfaily, Malak M.; Chu, Rosalie K.; Toyoda, Jason Analytica Chimica Acta, Vol. 972 https://doi.org/10.1016/j.aca.2017.03.031	journal	June 2017
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Elevated [CO2] changes soil organic matter composition and substrate diversity in an arid ecosystem Tfaily, Malak M.; Hess, Nancy J.; Koyama, Akihiro Geoderma, Vol. 330 https://doi.org/10.1016/j.geoderma.2018.05.025	journal	November 2018
Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance Goldfarb, Katherine C.; Karaoz, Ulas; Hanson, China A. Frontiers in Microbiology, Vol. 2 https://doi.org/10.3389/fmicb.2011.00094	journal	January 2011
Evaluation of the Orbitrap Mass Spectrometer for the Molecular Fingerprinting Analysis of Natural Dissolved Organic Matter Hawkes, Jeffrey A.; Dittmar, Thorsten; Patriarca, Claudia Analytical Chemistry, Vol. 88, Issue 15 https://doi.org/10.1021/acs.analchem.6b01624	journal	July 2016
A guide to phylogenetic metrics for conservation, community ecology and macroecology: A guide to phylogenetic metrics for ecology Tucker, Caroline M.; Cadotte, Marc W.; Carvalho, Silvia B. Biological Reviews, Vol. 92, Issue 2 https://doi.org/10.1111/brv.12252	journal	January 2016
Coupling among Microbial Communities, Biogeochemistry and Mineralogy across Biogeochemical Facies Stegen, James C.; Konopka, Allan; McKinley, James P. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep30553	journal	July 2016
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A. The ISME Journal, Vol. 6, Issue 8 https://doi.org/10.1038/ismej.2012.8	journal	March 2012
Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound Organic Carbon Via Biochemical and Thermodynamic Processes: OC Oxidation Processes Across Vegetation Graham, Emily B.; Tfaily, Malak M.; Crump, Alex R. Journal of Geophysical Research: Biogeosciences, Vol. 122, Issue 12 https://doi.org/10.1002/2017JG003967	journal	December 2017
Defining seasonal marine microbial community dynamics Gilbert, Jack A.; Steele, Joshua A.; Caporaso, J. Gregory The ISME Journal, Vol. 6, Issue 2 https://doi.org/10.1038/ismej.2011.107	journal	August 2011
Picante: R tools for integrating phylogenies and ecology Kembel, S. W.; Cowan, P. D.; Helmus, M. R. Bioinformatics, Vol. 26, Issue 11 https://doi.org/10.1093/bioinformatics/btq166	journal	April 2010
Assembly processes of trophic guilds in the root mycobiome of temperate forests Schröter, Kristina; Wemheuer, Bernd; Pena, Rodica Molecular Ecology, Vol. 28, Issue 2 https://doi.org/10.1111/mec.14887	journal	May 2018
Fundamental drivers of dissolved organic matter composition across an Arctic effective precipitation gradient Kellerman, Anne M.; Arellano, Ana; Podgorski, David C. Limnology and Oceanography, Vol. 65, Issue 6 https://doi.org/10.1002/lno.11385	journal	December 2019
Degradation of natural organic matter: A thermodynamic analysis LaRowe, Douglas E.; Van Cappellen, Philippe Geochimica et Cosmochimica Acta, Vol. 75, Issue 8 https://doi.org/10.1016/j.gca.2011.01.020	journal	April 2011
Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology Stegen, James C.; Johnson, Tim; Fredrickson, James K. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-02922-9	journal	February 2018
Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models Wieder, William R.; Hartman, Melannie D.; Sulman, Benjamin N. Global Change Biology, Vol. 24, Issue 4 https://doi.org/10.1111/gcb.13979	journal	November 2017

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