Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

Kroeger, Marie E.; Meredith, Laura K.; Meyer, Kyle M.; Webster, Kevin D.; de Camargo, Plinio Barbosa; de Souza, Leandro Fonseca; Tsai, Siu Mui; van Haren, Joost; Saleska, Scott; Bohannan, Brendan J. M.; Mazza Rodrigues, Jorge L.; Berenguer, Erika; Barlow, Jos; Nüsslein, Klaus

doi:10.1038/s41396-020-00804-x

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

Journal Article · Tue Oct 20 00:00:00 EDT 2020 · The ISME Journal

DOI:https://doi.org/10.1038/s41396-020-00804-x· OSTI ID:1735899

^[1]; ^[2]; ^[3]; Webster, Kevin D. ^[4]; de Camargo, Plinio Barbosa ^[5]; ^[5]; ^[5]; van Haren, Joost ^[2]; Saleska, Scott ^[2]; Bohannan, Brendan J. M. ^[6]; ^[7]; Berenguer, Erika ^[8]; Barlow, Jos ^[9]; ^[10]

Univ. of Massachusetts, Amherst, MA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Univ. of Arizona, Tucson, AZ (United States)
Univ. of Oregon, Eugene, OR (United States); Univ. of California, Berkeley, CA (United States)
Planetary Science Inst., Tucson, AZ (United States)
Univ. of Sao Paulo (Brazil)
Univ. of Oregon, Eugene, OR (United States)
Univ. of California, Davis, CA (United States)
Lancaster Univ., Bailrigg (United Kingdom); Univ. of Oxford (United Kingdom)
Lancaster Univ., Bailrigg (United Kingdom)
Univ. of Massachusetts, Amherst, MA (United States)

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

View Accepted Manuscript (DOE)

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC); USDOE National Nuclear Security Administration (NNSA); National Science Foundation (NSF); USDA; North American Electric Reliability Corporation (NERC)

Grant/Contract Number:: 89233218CNA000001

OSTI ID:: 1735899

Report Number(s):: LA-UR--20-22388

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 3 Vol. 15; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (93)

Soil Greenhouse Gas Fluxes, Environmental Controls, and the Partitioning of N ₂ O Sources in UK Natural and Seminatural Land Use Types: GHG Fluxes in Natural Ecosystems Sgouridis, Fotis; Ullah, Sami Journal of Geophysical Research: Biogeosciences, Vol. 122, Issue 10 https://doi.org/10.1002/2017JG003783	journal	October 2017
The effect of traditional slash-and-burn agriculture on soil organic matter, nutrient content, and microbiota in tropical ecosystems of Papua New Guinea Kukla, Jaroslav; Whitfeld, Timothy; Cajthaml, Tomáš Land Degradation & Development, Vol. 30, Issue 2 https://doi.org/10.1002/ldr.3203	journal	November 2018
Physiological Ecology of Methanogens Zinder, Stephen H. Methanogenesis https://doi.org/10.1007/978-1-4615-2391-8_4	book	January 1993
ggplot2 Wickham, Hadley Use R! https://doi.org/10.1007/978-3-319-24277-4	book	January 2016
Syntrophism Among Prokaryotes Schink, Bernhard; Stams, Alfons J. M. The Prokaryotes https://doi.org/10.1007/978-3-642-30123-0_59	book	January 2013
Factors affecting competition between type I and type II methanotrophs in two-organism, continuous-flow reactors Graham, DavidW.; Chaudhary, JayeshA.; Hanson, RichardS. Microbial Ecology, Vol. 25, Issue 1 https://doi.org/10.1007/BF00182126	journal	January 1993
Competition for electron donors among nitrate reducers, ferric iron reducers, sulfate reducers, and methanogens in anoxic paddy soil Achtnich, Christof; Bak, Friedhelm; Conrad, Ralf Biology and Fertility of Soils, Vol. 19, Issue 1 https://doi.org/10.1007/BF00336349	journal	January 1995
Acetate and carbon dioxide assimilation by Desulfovibrio vulgaris (Marburg), growing on hydrogen and sulfate as sole energy source Badziong, Werner; Ditter, Bernhard; Thauer, Rudolf K. Archives of Microbiology, Vol. 123, Issue 3 https://doi.org/10.1007/BF00406665	journal	December 1979
Effect of soil characteristics on sequential reduction and methane production in sixteen rice paddy soils from China, the Philippines, and Italy Yao, H.; Conrad, R.; Wassmann, R. Biogeochemistry, Vol. 47, Issue 3 https://doi.org/10.1007/BF00992910	journal	December 1999
Changes in the origin and quality of soil organic matter after pasture introduction in Rondônia (Brazil) Feigl, Brigitte J.; Melillo, Jerry; Cerri, Carlos C. Plant and Soil, Vol. 175, Issue 1 https://doi.org/10.1007/BF02413007	journal	August 1995
Land-Use Change and Biogeochemical Controls of Methane Fluxes in Soils of Eastern Amazonia Verchot, Louis V.; Davidson, Eric A.; Cattânio, J. Henrique Ecosystems, Vol. 3, Issue 1 https://doi.org/10.1007/s100210000009	journal	January 2000
Soil carbon dioxide and methane fluxes from forests and other land use types in an African tropical montane region Wanyama, I.; Pelster, D. E.; Butterbach-Bahl, K. Biogeochemistry, Vol. 143, Issue 2 https://doi.org/10.1007/s10533-019-00555-8	journal	February 2019
Seasonal variation of soil chemical properties and CO2 and CH4 fluxes in unfertilized and P-fertilized pastures in an Ultisol of the Brazilian Amazon Fernandes, Silvana Aparecida Pavan; Bernoux, Martial; Cerri, Carlos C. Geoderma, Vol. 107, Issue 3-4 https://doi.org/10.1016/S0016-7061(01)00150-1	journal	June 2002
Methanogenesis and Methanotrophy in Soil: A Review Serrano-Silva, N.; Sarria-GuzmÁN, Y.; Dendooven, L. Pedosphere, Vol. 24, Issue 3 https://doi.org/10.1016/S1002-0160(14)60016-3	journal	June 2014
Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass Ferry, James G. Current Opinion in Biotechnology, Vol. 22, Issue 3 https://doi.org/10.1016/j.copbio.2011.04.011	journal	June 2011
Metabolic versatility in methanogens Costa, Kyle C.; Leigh, John A. Current Opinion in Biotechnology, Vol. 29 https://doi.org/10.1016/j.copbio.2014.02.012	journal	October 2014
Targeted metagenomics of active microbial populations with stable-isotope probing Coyotzi, Sara; Pratscher, Jennifer; Murrell, J. Colin Current Opinion in Biotechnology, Vol. 41 https://doi.org/10.1016/j.copbio.2016.02.017	journal	October 2016
Denitrifying anaerobic methane oxidation in intertidal marsh soils: Occurrence and environmental significance Zheng, Yanling; Hou, Lijun; Chen, Feiyang Geoderma, Vol. 357 https://doi.org/10.1016/j.geoderma.2019.113943	journal	January 2020
Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil Eilers, Kathryn G.; Debenport, Spencer; Anderson, Suzanne Soil Biology and Biochemistry, Vol. 50 https://doi.org/10.1016/j.soilbio.2012.03.011	journal	July 2012
Soil metaproteomics – Comparative evaluation of protein extraction protocols Keiblinger, Katharina M.; Wilhartitz, Inés C.; Schneider, Thomas Soil Biology and Biochemistry, Vol. 54 https://doi.org/10.1016/j.soilbio.2012.05.014	journal	November 2012
Methane-Dependent Mineral Reduction by Aerobic Methanotrophs under Hypoxia Zheng, Yue; Wang, Huan; Liu, Yan Environmental Science & Technology Letters, Vol. 7, Issue 8 https://doi.org/10.1021/acs.estlett.0c00436	journal	June 2020
Consequence of forest-to-pasture conversion on CH ₄ fluxes in the Brazilian Amazon Basin Steudler, Paul A.; Melillo, Jerry M.; Feigl, Brigitte J. Journal of Geophysical Research: Atmospheres, Vol. 101, Issue D13 https://doi.org/10.1029/96JD01551	journal	August 1996
Production of nitrous oxide and consumption of methane by forest soils Keller, M.; Goreau, T. J.; Wofsy, S. C. Geophysical Research Letters, Vol. 10, Issue 12 https://doi.org/10.1029/GL010i012p01156	journal	December 1983
Stable-isotope probing as a tool in microbial ecology Radajewski, Stefan; Ineson, Philip; Parekh, Nisha R. Nature, Vol. 403, Issue 6770, p. 646-649 https://doi.org/10.1038/35001054	journal	February 2000
Detection and classification of atmospheric methane oxidizing bacteria in soil Bull, Ian D.; Parekh, Nisha R.; Hall, Grahame H. Nature, Vol. 405, Issue 6783 https://doi.org/10.1038/35012061	journal	May 2000
Reproducibility and quantitation of amplicon sequencing-based detection Zhou, Jizhong; Wu, Liyou; Deng, Ye The ISME Journal, Vol. 5, Issue 8 https://doi.org/10.1038/ismej.2011.11	journal	February 2011
Capturing the genetic makeup of the active microbiome in situ Singer, Esther; Wagner, Michael; Woyke, Tanja The ISME Journal, Vol. 11, Issue 9 https://doi.org/10.1038/ismej.2017.59	journal	June 2017
Shotgun metagenomics, from sampling to analysis Quince, Christopher; Walker, Alan W.; Simpson, Jared T. Nature Biotechnology, Vol. 35, Issue 9 https://doi.org/10.1038/nbt.3935	journal	September 2017
DADA2: High-resolution sample inference from Illumina amplicon data Callahan, Benjamin J.; McMurdie, Paul J.; Rosen, Michael J. Nature Methods, Vol. 13, Issue 7 https://doi.org/10.1038/nmeth.3869	journal	May 2016
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity Carini, Paul; Marsden, Patrick J.; Leff, Jonathan W. Nature Microbiology, Vol. 2, Issue 3 https://doi.org/10.1038/nmicrobiol.2016.242	journal	December 2016
DNA stable-isotope probing Neufeld, Josh D.; Vohra, Jyotsna; Dumont, Marc G. Nature Protocols, Vol. 2, Issue 4 https://doi.org/10.1038/nprot.2007.109	journal	April 2007
Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing Wilhelm, Roland C.; Singh, Rahul; Eltis, Lindsay D. The ISME Journal, Vol. 13, Issue 2 https://doi.org/10.1038/s41396-018-0279-6	journal	September 2018
An evolving view of methane metabolism in the Archaea Evans, Paul N.; Boyd, Joel A.; Leu, Andy O. Nature Reviews Microbiology, Vol. 17, Issue 4 https://doi.org/10.1038/s41579-018-0136-7	journal	January 2019
Aerobic methane oxidation under copper scarcity in a stratified lake Guggenheim, Carole; Brand, Andreas; Bürgmann, Helmut Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-40642-2	journal	March 2019
SEEG initiative estimates of Brazilian greenhouse gas emissions from 1970 to 2015 de Azevedo, Tasso Rezende; Costa Junior, Ciniro; Brandão Junior, Amintas Scientific Data, Vol. 5, Issue 1 https://doi.org/10.1038/sdata.2018.45	journal	May 2018
Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway Welander, P. V.; Metcalf, W. W. Proceedings of the National Academy of Sciences, Vol. 102, Issue 30 https://doi.org/10.1073/pnas.0502623102	journal	July 2005
Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2 Baani, M.; Liesack, W. Proceedings of the National Academy of Sciences, Vol. 105, Issue 29 https://doi.org/10.1073/pnas.0702643105	journal	July 2008
Methane monooxygenase gene expression mediated by methanobactin in the presence of mineral copper sources Knapp, C. W.; Fowle, D. A.; Kulczycki, E. Proceedings of the National Academy of Sciences, Vol. 104, Issue 29 https://doi.org/10.1073/pnas.0702879104	journal	July 2007
Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities Rodrigues, J. L. M.; Pellizari, V. H.; Mueller, R. Proceedings of the National Academy of Sciences, Vol. 110, Issue 3 https://doi.org/10.1073/pnas.1220608110	journal	December 2012
Amazon plant diversity revealed by a taxonomically verified species list Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara Proceedings of the National Academy of Sciences, Vol. 114, Issue 40 https://doi.org/10.1073/pnas.1706756114	journal	September 2017
STAMP: statistical analysis of taxonomic and functional profiles Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip Bioinformatics, Vol. 30, Issue 21 https://doi.org/10.1093/bioinformatics/btu494	journal	July 2014
Forest-to-pasture conversion and recovery based on assessment of microbial communities in Eastern Amazon rainforest Pedrinho, Alexandre; Mendes, Lucas William; Merloti, Luis Fernando FEMS Microbiology Ecology, Vol. 95, Issue 3 https://doi.org/10.1093/femsec/fiy236	journal	December 2018
Denitrovibrio acetiphilus, a novel genus and species of dissimilatory nitrate-reducing bacterium isolated from an oil reservoir model column Myhr, S.; Torsvik, T. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 4 https://doi.org/10.1099/00207713-50-4-1611	journal	July 2000
Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Ivanov, M. V.; Lysenko, A. M.; Petrunyaka, V. V. International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 2 https://doi.org/10.1099/00207713-51-2-433	journal	March 2001
Thioalkalivibrio thiocyanoxidans sp. nov. and Thioalkalivibrio paradoxus sp. nov., novel alkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria capable of growth on thiocyanate, from soda lakes. Lysenko, Anatoly M.; Sorokin, Dimitry Yu; Mityushina, Lubov L. International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 2 https://doi.org/10.1099/00207713-52-2-657	journal	March 2002
Distribution and diversity of V errucomicrobia methanotrophs in geothermal and acidic environments: Diversity of verrucomicrobial methanotrophs Sharp, Christine E.; Smirnova, Angela V.; Graham, Jaime M. Environmental Microbiology, Vol. 16, Issue 6 https://doi.org/10.1111/1462-2920.12454	journal	April 2014
Microbial community structure and soil p H correspond to methane production in A rctic A laska soils Wagner, Robert; Zona, Donatella; Oechel, Walter Environmental Microbiology, Vol. 19, Issue 8 https://doi.org/10.1111/1462-2920.13854	journal	July 2017
Factors governing extracellular DNA degradation dynamics in soil Sirois, Sara Hope; Buckley, Daniel H. Environmental Microbiology Reports, Vol. 11, Issue 2 https://doi.org/10.1111/1758-2229.12725	journal	December 2018
Detecting active methanogenic populations on rice roots using stable isotope probing Lu, Yahai; Lueders, Tillmann; Friedrich, Michael W. Environmental Microbiology, Vol. 7, Issue 3 https://doi.org/10.1111/j.1462-2920.2005.00697.x	journal	March 2005
Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis Dumont, Marc G.; Radajewski, Stefan M.; Miguez, Carlos B. Environmental Microbiology, Vol. 8, Issue 7 https://doi.org/10.1111/j.1462-2920.2006.01018.x	journal	July 2006
Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide Strittmatter, Axel W.; Liesegang, Heiko; Rabus, Ralf Environmental Microbiology, Vol. 11, Issue 5 https://doi.org/10.1111/j.1462-2920.2008.01825.x	journal	May 2009
Ironing out the wrinkles in the rare biosphere through improved OTU clustering: Ironing out the wrinkles in the rare biosphere Huse, Susan M.; Welch, David Mark; Morrison, Hilary G. Environmental Microbiology, Vol. 12, Issue 7 https://doi.org/10.1111/j.1462-2920.2010.02193.x	journal	March 2010
CO2 flux from soil in pastures and forests in southwestern Amazonia Salimon, C. I.; Davidson, E. A.; Victoria, R. L. Global Change Biology, Vol. 10, Issue 5 https://doi.org/10.1111/j.1529-8817.2003.00776.x	journal	May 2004
Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing: Methanotrophs in landfill soil CÃ©bron, AurÃ©lie; Bodrossy, Levente; Chen, Yin FEMS Microbiology Ecology, Vol. 62, Issue 1 https://doi.org/10.1111/j.1574-6941.2007.00368.x	journal	October 2007
Strain-specific incorporation of methanotrophic biomass into eukaryotic grazers in a rice field soil revealed by PLFA-SIP: Soil eukaryotes grazing on methanotrophs Murase, Jun; Hordijk, Kees; Tayasu, Ichiro FEMS Microbiology Ecology, Vol. 75, Issue 2 https://doi.org/10.1111/j.1574-6941.2010.01007.x	journal	December 2010
Growth of methanotrophs in methane and oxygen counter gradients Amaral, John A.; Knowles, Roger FEMS Microbiology Letters, Vol. 126, Issue 3 https://doi.org/10.1111/j.1574-6968.1995.tb07421.x	journal	March 1995
Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related Holmes, Andrew J.; Costello, Andria; Lidstrom, Mary E. FEMS Microbiology Letters, Vol. 132, Issue 3 https://doi.org/10.1111/j.1574-6968.1995.tb07834.x	journal	October 1995
Methanotrophs and copper Semrau, Jeremy D.; DiSpirito, Alan A.; Yoon, Sukhwan FEMS Microbiology Reviews, Vol. 34, Issue 4 https://doi.org/10.1111/j.1574-6976.2010.00212.x	journal	July 2010
Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities Paula, Fabiana S.; Rodrigues, Jorge L. M.; Zhou, Jizhong Molecular Ecology, Vol. 23, Issue 12 https://doi.org/10.1111/mec.12786	journal	June 2014
Soil microbiome responses to the short-term effects of Amazonian deforestation Navarrete, Acacio A.; Tsai, Siu M.; Mendes, Lucas W. Molecular Ecology, Vol. 24, Issue 10 https://doi.org/10.1111/mec.13172	journal	April 2015
Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms Meyer, Kyle M.; Klein, Ann M.; Rodrigues, Jorge L. M. Molecular Ecology, Vol. 26, Issue 6 https://doi.org/10.1111/mec.14011	journal	February 2017
Climate Change, Deforestation, and the Fate of the Amazon Malhi, Y.; Roberts, J. T.; Betts, R. A. Science, Vol. 319, Issue 5860 https://doi.org/10.1126/science.1146961	journal	January 2008
Classifying drivers of global forest loss Curtis, Philip G.; Slay, Christy M.; Harris, Nancy L. Science, Vol. 361, Issue 6407 https://doi.org/10.1126/science.aau3445	journal	September 2018
Phylogenetic Comparison of the Methanogenic Communities from an Acidic, Oligotrophic Fen and an Anaerobic Digester Treating Municipal Wastewater Sludge Steinberg, L. M.; Regan, J. M. Applied and Environmental Microbiology, Vol. 74, Issue 21 https://doi.org/10.1128/AEM.00553-08	journal	September 2008
Metatranscriptomic Analysis of Arctic Peat Soil Microbiota Tveit, Alexander T.; Urich, Tim; Svenning, Mette M. Applied and Environmental Microbiology, Vol. 80, Issue 18 https://doi.org/10.1128/AEM.01030-14	journal	July 2014
Expanding the Verrucomicrobial Methanotrophic World: Description of Three Novel Species of Methylacidimicrobium gen. nov. van Teeseling, Muriel C. F.; Pol, Arjan; Harhangi, Harry R. Applied and Environmental Microbiology, Vol. 80, Issue 21 https://doi.org/10.1128/AEM.01838-14	journal	August 2014
Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog Esson, Kaitlin C.; Lin, Xueju; Kumaresan, Deepak Applied and Environmental Microbiology, Vol. 82, Issue 8 https://doi.org/10.1128/AEM.03640-15	journal	February 2016
Molecular Characterization of Functional and Phylogenetic Genes from Natural Populations of Methanotrophs in Lake Sediments Costello, Andria M.; Lidstrom, Mary E. Applied and Environmental Microbiology, Vol. 65, Issue 11 https://doi.org/10.1128/AEM.65.11.5066-5074.1999	journal	November 1999
High-Affinity Methane Oxidation by a Soil Enrichment Culture Containing a Type II Methanotroph Dunfield, Peter F.; Liesack, Werner; Henckel, Thilo Applied and Environmental Microbiology, Vol. 65, Issue 3 https://doi.org/10.1128/AEM.65.3.1009-1014.1999	journal	March 1999
Metabolism of Benzoate, Cyclohex-1-ene Carboxylate, and Cyclohexane Carboxylate by "Syntrophus aciditrophicus" Strain SB in Syntrophic Association with H2-Using Microorganisms Elshahed, M. S.; Bhupathiraju, V. K.; Wofford, N. Q. Applied and Environmental Microbiology, Vol. 67, Issue 4 https://doi.org/10.1128/AEM.67.4.1728-1738.2001	journal	April 2001
Energy Conservation and Hydrogenase Function in Methanogenic Archaea, in Particular the Genus Methanosarcina Mand, Thomas D.; Metcalf, William W. Microbiology and Molecular Biology Reviews, Vol. 83, Issue 4 https://doi.org/10.1128/MMBR.00020-19	journal	September 2019
How, When, and Where Relic DNA Affects Microbial Diversity Lennon, J. T.; Muscarella, M. E.; Placella, S. A. mBio, Vol. 9, Issue 3 https://doi.org/10.1128/mBio.00637-18	journal	June 2018
My Kind of Biology Wolfe, Ralph S. Annual Review of Microbiology, Vol. 45, Issue 1 https://doi.org/10.1146/annurev.mi.45.100191.000245	journal	October 1991
The Regulation of Methane Oxidation in Soil Mancinelli, R. L. Annual Review of Microbiology, Vol. 49, Issue 1 https://doi.org/10.1146/annurev.mi.49.100195.003053	journal	October 1995
Impact of No-Tillage and Conventional Tillage Systems on Soil Microbial Communities Mathew, Reji P.; Feng, Yucheng; Githinji, Leonard Applied and Environmental Soil Science, Vol. 2012 https://doi.org/10.1155/2012/548620	journal	January 2012
Hydrogenotrophic Methanogenesis and Autotrophic Growth of Methanosarcina thermophila Lackner, Nina; Hintersonnleitner, Anna; Wagner, Andreas Otto Archaea, Vol. 2018 https://doi.org/10.1155/2018/4712608	journal	July 2018
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin Bokulich, Nicholas A.; Kaehler, Benjamin D.; Rideout, Jai Ram Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0470-z	journal	May 2018
PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets Pinto, Ameet J.; Raskin, Lutgarde; Bertilsson, Stefan PLoS ONE, Vol. 7, Issue 8, Article No. e43093 https://doi.org/10.1371/journal.pone.0043093	journal	August 2012
Developing Cost-Effective Field Assessments of Carbon Stocks in Human-Modified Tropical Forests Berenguer, Erika; Gardner, Toby A.; Ferreira, Joice PLOS ONE, Vol. 10, Issue 8 https://doi.org/10.1371/journal.pone.0133139	journal	August 2015
Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform Wen, Chongqing; Wu, Liyou; Qin, Yujia PLOS ONE, Vol. 12, Issue 4 https://doi.org/10.1371/journal.pone.0176716	journal	April 2017
Climatic Benefits From the 2006–2017 Avoided Deforestation in Amazonian Brazil West, Thales A. P.; Börner, Jan; Fearnside, Philip M. Frontiers in Forests and Global Change, Vol. 2 https://doi.org/10.3389/ffgc.2019.00052	journal	September 2019
Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils Lammel, Daniel R.; Feigl, Brigitte J.; Cerri, Carlos C. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01057	journal	October 2015
Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00703	journal	May 2016
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes Kroeger, Marie E.; Delmont, Tom O.; Eren, A. M. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01635	journal	July 2018
Nitrous oxide fluxes and nitrogen cycling along a pasture chronosequence in Central Amazonia, Brazil Wick, B.; Veldkamp, E.; de Mello, W. Z. Biogeosciences, Vol. 2, Issue 2 https://doi.org/10.5194/bg-2-175-2005	journal	January 2005
pmoA amplicon sequence files for Rondonia DNA-SIP methane cycling study Kroeger, Marie figshare https://doi.org/10.6084/m9.figshare.10565552	dataset	January 2019
pmoA raw amplicon sequences Para Kroeger, Marie figshare https://doi.org/10.6084/m9.figshare.10565690	dataset	January 2019
mcrA raw amplicon sequence files Para Kroeger, Marie figshare https://doi.org/10.6084/m9.figshare.10565801.v1	dataset	January 2019
mcrA raw amplicon sequence files from Rondonia Kroeger, Marie figshare https://doi.org/10.6084/m9.figshare.10565870.v1	dataset	January 2019
16S raw amplicon sequences from Para Kroeger, Marie figshare https://doi.org/10.6084/m9.figshare.10565897	dataset	January 2019
16S raw amplicon sequence files from Rondonia Kroeger, Marie figshare https://doi.org/10.6084/m9.figshare.10565957.v1	dataset	January 2019
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes Kroeger, Marie; Delmont, Tom; Eren, A. Murat figshare https://doi.org/10.6084/m9.figshare.5151571.v1	dataset	January 2018
SEEG initiative estimates of Brazilian greenhouse gas emissions from 1970 to 2015 Azevedo, Tasso Rezende; Junior, Ciniro Costa; Junior, Amintas Brandão figshare https://doi.org/10.6084/m9.figshare.c.3860152.v1	collection	January 2018

Similar Records

Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms

Journal Article · Tue Jan 17 23:00:00 EST 2017 · Molecular Ecology · OSTI ID:1379749

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biological science
Microbial ecology
Soil microbiology

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

Citation Formats

References (93)

Similar Records

Related Subjects