Publications from our lab
2025
Khan Md AW, BJM Bohannan, K M Meyer, AM Klein, K Nusslein, JP Grover, JL Mazza Rodrigues. 2025. Community-level metabolic shifts following land use change in the Amazon rainforest identified by a supervised machine learning approach. Environmental Microbiology Reports https://doi.org/10.1111/1758-2229.70088
He D, Dai Z, H Shen, J Lin, K Zhao, JL Mazza Rodrigues, Y Kuzyakov, J Xu. 2025. Microbial life-history strategies and genomic traits between pristine and cropland soils. mSystems https://doi.org/10.1128/msystems.00178-25
Potisap C, P Lawongsa, S Wongratanacheewin, J Duangsri, JB Gontijo, JL Mazza Rodrigues, RW Sermswan. 2025. The soil microorganism Bacillus amyloliquefaciens N3-8 is a biocontrol agent for the pathogen Burkholderia pseudomallei in rice plantation. mSpectrum (accepted)
Venturini A, J Gontijo, L Berrios, JL Mazza Rodrigues, K Peay, SM Tsai. 2025. Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon. mSpectrum https://doi.org/10.1128/spectrum.01561-24
2024
Nguyen TT, A Altman, L Huang, JL Mazza Rodrigues, HE Dahlke, NA Kamennaya, E Levintal. 2024. A portable, open source, low-cost incubation chamber for real-time characterization of soil respiration and microbial activity. Soil Science Society of America Journal https://doi.org/10.1002/saj2.20800
Guo Z, J Liu, L He, JL Mazza Rodrigues, Ning Chen, Y Zuo, N Wang, X Zhu, Y Sun, L Zhang, Y Song, D Zhang, F Yuan, C Song, X Xu. 2024. Dominant edaphic controls of particulate organic carbon in global soils. Global Change Biology https://doi.org/10.1111/gcb.17619
Gontijo JB, FS Paula, W Bieluczyk, AG Franca, D Navroski, J Meandro, AM Venturini, FO Asselta, LW Mendes, MZ Moreira, K Nusslein, BJM Bohannan, PLE Boldelier, JL Mazza Rodrigues, SM Tsai. 2024. Amazon methane-cycling microbial communities from floodplain and upland forests respond differently to a climate change scenario. Environmental Microbiome https://doi.org/10.1186/s40793-024-00596-z
Huang L, AS Rosado, A Wright, RS Correa, L Silva, JL Mazza Rodrigues. 2024. Microbiome recovery in a chronosequence of impoverished Cerrado soils with biosolids applications. Science of the Total Environmental
https://doi.org/10.1016/j.scitotenv.2024.172958
Graham EB, AP Camargo, R Wu, RY Neches, M Nolan, D Paez-Espino, A Copeland, NC Kyrpides, JK Jansson, JE McDermott, KS Hofmockel, Soil Virosphere Consortium (JL Mazza Rodrigues). 2024. A global atlas of soil viruses reveals unexplored diversity and potential biogeochemical impacts. Nature Microbiology
https://doi.org/10.1038/s41564-024-01686-x
Anthony W, S Allison, C Broderick, L Rodriguez, A Clum, H Cross, E Eloe-Fadrosh, S Evans, D Fairbanks, R Gallery, J Gontijo, J Jones, J McDermott, J Pett-Ridge, S Racord, JL Mazza Rodrigues, W Rodriguez-Reillo, K Shek, C Takacs-Vesbach, J Blanchard. 2024. From soil to sequence: Filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology. Environmental Microbiome https://doi.org/10.1186/s40793-024-00599-w
He L, JL Mazza Rodrigues, M Mayes, C-T Lai, D Lipson, X Xu. 2023. Modeling microbial carbon fluxes and stocks in global soils from 1901-2016. Biogeosciences https://doi.org/10.5194/bg-21-2313-2024
Wang Y, L He, J Liu, KA Arndt, JL Mazza Rodrigues, D Zona, DA Lipson, WC Oechel, DM Ricciuto, SD Wullschleger, X Xu. 2024. Intensified positive artic - methane feedback under IPCC climate scenarios in the 21st century. Ecosystems Health and Sustainability https://doi. org/10.34133/ehs.0185
Silva, DF, EJBN Cardoso, L Huang, C Erikson, AMM Silva, VLVP Araujo, DEO Silva, VMM Melo, ASA Ferreira, APA Pereira, JL Mazza Rodrigues. 2024. Functional genes related to N and P cycling in degraded and restored areas from Brazilian drylands. Applied Soil Ecology https://doi.org/10.1016/j.apsoil.2024.105316
Silva DF, JL Mazza Rodrigues, C Erikson, AMM Silva, L Huang, VLVP Araujo, FP Matteoli, LW Mendes, ASF Araujo, APA Pereira, VMM Melo, EJBN Cardoso. 2024. Grazing exclusion-induced changes in soil fungal communities in a highly desertified Brazilian dryland. Microbiological Research https://doi.org/10.1016/j.micres.2024.127763
Xu S, C Gu, JL Mazza Rodrigues, C Li, B Bohannan, K Nusslein, A Margenot. 2023. Soil phosphorus cycling across a 100-year deforestation chronosequence in the Amazon rainforest. Global Change Biology
https://doi.org/10.1111/gcb.17077
2023
Huang L, E Levintal, CB Erikson, A Coyolt, WR Horwath, HE Dahlke, JLM Rodrigues. 2023. Molecular and dual-isotopic profiling of the microbial controls on nitrogen leaching in agricultural soils under managed aquifer recharge. Environment Science & Technology https://doi.org/10.1021/acs.est.3c01356
Sayre JM, D Wang, JY Lin, R Danielson, KM Scow, JLM Rodrigues. 2023. Repeated manure inputs to a forage production soil increase microbial biomass and diversity and select for lower abundance genera. Agriculture, Ecosystems & Environment https://doi.org/10.1016/j.agee.2023.108567
JLM Rodrigues and M Melotto. 2023. Naturally engineered plant microbiomes in resource-limited ecosystems. Trends in Microbiology https://doi.org/10.1016/j.tim.2023.02.006
He L, JLM Rodrigues, M Mayes, C-T Lai, DA Lipson, X Xu. 2023. Historical dynamics of terrestrial carbon during 1901-2016 as simulated by the CLM-Microbe model. Biogeosciences https://doi.org/10.5194/bg-2023-15
Obregon D, LF de Sousa, LW Mendes, MT de Moraes, M Tosi, AM Venturini, KM Meyer, PB de Camargo, BJM Bohannan, JLM Rodrigues, KE Dunfield, SM Tsai. 2023. Shifts in functional traits and interaction patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin. Molecular Ecology
https://doi.org/10.1111/mec.16912
Pinheiro Y, F da Mota, R Peixoto, JD van Elsas, JLM Rodrigues, A Rosado. 2023. A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environment. Communications Biology. https://doi.org/10.1038/s42003-023-04617-4
Levintal E , L Huang, CP Garcia, A Coyotl, MW Fidelibus, WH Horwath, JLM Rodrigues, H Dahlke. 2023. Nitrogen fate during agricultural managed aquifer recharge: linking plant response, hydrologic and geiochemical processes. Science of the Total Environment https://doi.org/10.1016/j.scitotenv.2022.161206
2022
Danielson RE, JLM Rodrigues. 2022. Impacts of land use change on soil microbial communities in the Amazon. Advances in Agronomy. https://doi.org/10.1016/bs.agron.2022.04.001
Liu H, Y Luo, X Song, P Leng, J Li, JLM Rodrigues, Z Hong, Y Kuzyakob, Z Dai, J Xu. 2022. Generalists and specialists decomposing labile and aromatic biochar compounds and sequestering carbon in soil. Geoderma https://doi.org/10.1016/j.geoderma.2022.116176
Alves KJ, VS Pylro, CR Nakayama, VG Vital, RG Taketani, DG Santos, JLM Rodrigues, SM Tsai, FD Andreote. 2022. Methanogenic communities and methane emissions from enriched Amazonia soil under land-use change. Microbiological Research
https://doi.org/10.1016/j.micres.2022.127178
Wang D, JY Lin, JM Sayre, R Schmidt, SJ Fonte, JLM Rodrigues, K Scow. 2022. Compost amendment and cover cropping maintains soil structure and associated C storage by increasing available C and microbial biomass in agricultural soil – a six year field study. Geoderma https://doi.org/10.1016/j.geoderma.2022.116117
Venturini AM, JB Gontijo, A Franca, J Moura, K Nusslein, B Bohannan, JLM Rodrigues, SM Tsai. 2022. Metagenomes from Eastern Brazilian Amazonian floodplains in wet and dry seasons. Microbiology Research Announcements https://doi.org/10.1128/mra.00432-22
Goss-Souza D, SM Tsai, JLM Rodrigues, O Klauberg-Filho, P Sousa, D Baretta, LW Mendes. 2022. Biogeographic responses and niche occupancy of microbial communities following long-term land-use change. Antonie van Leeuvenhoek https://doi.org/10.1007/s10482-022-01761-5
Souza L, DA Obregon, L Domeignoz-Horta, F Gomes, C Almeida, L Merloti, L Mendes, FD Andreote, B Bohannan, JLM Rodrigues, K Nusslein, SM Tsai. 2022. Maintaining grass coverage increases methane uptake in Amazonian pasture soils. Science of the Total Environment. http://dx.doi.org/10.1016/j.scitotenv.2022.156225
Venturini, AM, NMS Dias, JB Gontijo, CA Yoshiura, FS Paula, FM Nakamura, KM Meyer, AG Franca, CD Borgers, J Barlow, E Beringer, KR Nusslein, JLM Rodrigues, BJM Bohannan, SM Tsai. 2022. Increased soil moisture exarcerbates the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon. Environmental Research. https://doi.org/10.1016/j.envres.2022.113139
Ghotbi M, A Durrer, K Frindte, WR Horwath, JLM Rodrigues, I Danso, C Knief. 2022. Topographic attributes overrride impacts of agronomic practices on prokaryotic community struture. Applied Soil Ecology. https://doi.org/10.1016/j.apsoil.2022.104446
Lazick P, JLM Rodrigues, D Geisseler. 2022. Acid stress and compost differentially affect microbial carbon and nitrogen cycling functions in an agricultural soil. Applied Soil Ecology. https://doi.org/10.1016/j.apsoil.2021.104219
2021
Durrer A, AJ Margenot, LCR Silva, BJM Bohannan, K Nusslein, FD Andreoti, J van Haren, SJ Parikh, JLM Rodrigues. 2021. Beyond total carbon costs: Land use change alters soil carbon cycling in the Amazon. Biogeochemistry https://doi.org.10.1007/s10533-020-00743-x
Yoshiura CA, LPP Braga, AM Venturini, AG da Franca, MCCP de Lyra, SM Tsai, JLM Rodrigues. 2021. Influence of inputs combination on the microbial structure of the maize rhizosphere for greenhouse gas fluxes mitigation. Frontiers in Plant Science. https://www.frontiersin.org/articles/10.3389/fpls.2021.683658/full
Lazick P, JLM Rodrigues, D Geisseler. 2021. Sensitivity and variability of soil health indicators in a Mediterranean crop system. Soil Science Society of America J. https://acsess.onlinelibrary.wiley.com/doi/pdfdirect/10.1002/saj2.20278
Hodson AK, JM Sayre, MCCP Lyra, JLM Rodrigues. 2021. Influence of recycle compost on soil food webs, nutrient cycling and tree growth in a young orchard. Agronomy 11:1754 https://doi.org/10.3390/agronomy11091745
Gontijo JB, AM Venturini, CA Yoshiura, CD Borges, JMS Moura, BJM Bohannan, K Nusslein, JLM Rodrigues, FS Paula, SM Tsai. 2021. Not only a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophic metabolisms. Mol. Ecol. https://doi.org/10.1111/mec.15912
Jesus HE, A Enrich-Prast A, SSM Paiva, RS Peixoto, RS Carreira, C Massone, JLM Rodrigues, CK Lee, C Craig, AS Rosado. 2021. Microbial sucession under thaw-freeze cycle events for hydrocarbon degradation in a nutrient-amended Antartic soil. Microorganisms https://doi.org/10.3390/microorganisms9030609
Zhang L, B Ma, C Tang, H Yu, X Lv, JLM Rodrigues, RA Dahlgren, J Xu. 2021. Habitat heterogeneity induced by pyrogenenic organic matter in wildfire-perturbed soils mediates bacterial community assembly processes. The ISME J. https://www.nature.com/articles/s41396-021-00896-z
He L, D Lipson, JLM Rodrigues, M Mayes, RG Bjork, B Glaser, J Rinklebe, X Xu. 2021. Dynamics of fungal and bacterial biomass carbon in natural ecosystems: site-level applications of the CLM-Microbe model. J. Adv. Model. Earth Systems https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020MS002283
Wang L, H Chen, J Wu, L Huang, PC Brookes, JLM Rodrigues, J Xu, X Liu. 2021. Effects of magnetic biochar-microbe composite on Cd remediation and microbial responses in paddy soil. J Hazardous Materials https://doi.org/10.1016/j.jhazmat.2021.125494
2020
Nayfach S, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, D Paez-Espino, IMG/M Data Consortium (JLM Rodrigues). 2020. A genomic catalogue of Earth's microbiome. Nature Biotechnol. https://www.nature.com/articles/s41587-020-0718-6
Kroeger ME, LK Meredith, KM Meyer, KD Webster, PB de Camargo, LF de Souza, SM Tsai, J van Haren, S Saleska, BJM Bohannan, JLM Rodrigues, E Berenguer, J Barlow, K Nusslein. 2020. Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon. The ISME J. https://www.nature.com/articles/s41396-020-00804-x
Allard S, M Costa, A Bulseco, V Helfer, L Wilkins, C Hassenruck, K Zengler, M Zimmer, N Eraso, JLM Rodrigues, N Duke, V Melo, I Vanworterghem, H Junka, H Makonde, D Jimeniz, T Tavarez, M Fusi, D Daffonchio, C Duarte, R Peixoto, A Rosado, J Gilbert, J Bowman. 2020. Introducing the Mangrove Microbiome Initiative: Setting research priorities for mangrove preservation and rehabiliation. mSystems https://msystems.asm.org/content/5/5/e00658-20
Meyer KM, AH Morris, K Webster, AM Klein, ME Kroeger, LK Meredith, A Braendholt, F Nakamura, A Veturini, LF de Souza, KL Shek, R Danielson, J van Haren, PB de Camargo, SM Tsai, F Dini-Andreote, JMS de Moura, J Barlow, E Berenguer, K Nusslein, S Saleska, JLM Rodrigues, BJM Bohannan. 2020. Belowground changes to community structure alter methane-cycling dynamics in Amazonia. Environ. International. https://doi.org/10.1016/j.envint.2020.106131
He L, JLM Rodrigues, NA Soudzilovskaia, M Barcelo, PA Olson, C Song, L Tedersoo, F Yuan, D Lipson, X Xu. 2020. Global biogeography of fungal and bacterial biomass carbon in topsoil. Soil Biol. and Biochem. https://doi.org/10.1016/j.soilbio.2020.108024
Lin JY and JLM Rodrigues. 2020. Genus Geminisphera. In: Oren A. Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc. New Jersey, USA. DOI: 10.1002/9781118960608.gbm01542
Mirza BS, DJ McGlinn, BJM Bohannan, K Nusslein, JM Tiedje, JLM Rodrigues. 2020. Diazotrophs show sign of restoration in Amazon rainforest soils with ecosystem rehabilitation. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.00195-20.
Schmidt JE, JLM Rodrigues , VL Brisson, A. Kent, ACM Gaudin. 2020. Impacts of directed evolution and soil management legacy on maize microbiome. Soil Biol. and Biochem. https://doi.org/10.1016/j.soilbio.2020.107794
Hoda R, M Sattler, MD Sahadat Hussein, JLM Rodrigues. 2020. Boosting landfill gas production from lignin-containing waste via termite hindgut microorganism. Waste Management https://www.sciencedirect.com/science/article/pii/S0956053X20300659
Kotak M, J Lin, J Isanapong, JLM Rodrigues. 2020. Draft genome sequences of two Opitutaceae bacteria strains TAV3 and TAV4 isolated from a wood feeding termite and bioinformatics characterization of their lignocellulolytic enzymes. Microbiol. Res. Announ. https://mra.asm.org/content/9/2/e01192-19
Parsons LS, JM Sayre, C Ender, JLM Rodrigues, A Barberan. 2020. Plant-soil microbial feedbacks in restored and unrestored coastal dune ecosystems in California. Restoration Ecol. https://onlinelibrary.wiley.com/doi/10.1111/rec.13101
2019
Goss-Souza D, LW Mendes, JLM Rodrigues, SM Tsai. 2019. Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept constant. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiz009
Sjöling S, van Elsas JD, Andreote FD, JLM Rodrigues. 2019. Soil metagenomics: deciphering the soil microbial gene pool. Book Chapter In: van Elsas, Trevors, Rosado, and Nanniplerl. Modern Soil Microbiology, 3rd Edition, CRC Press.
Goss-Souza D, LW Mendes, JLM Rodrigues, SM Tsai. 2019. Ecological processes shaping bulk and rhizosphere microbiome assembly in a long-term Amazon forest-to-agriculture coversion. Microb. Ecol. https://doi.org/10.1007/s00248-019-01401-y
Ren H, Q Zhou, J He, Y Hou, JLM Rodrigues, AB Cobb, GWT Wilson, Y Zhang. 2019. Determining landscape-level drivers of variability for over 50 elements. Sci. Total. Environ. 657:279-286.
2018
Khan Md AW, BJM Bohannan, K Nusslein, JM Tiedje, SG Tringe, E Parlade, A Barberan, and JLM Rodrigues. 2018. Network analysis reveals substantial alteration of microbial co-occurrence patterns due to deforestation in the Amazon rainforest. FEMS Microbiol. Ecol. https://academic.oup.com/femsec/article/95/2/fiy230/5211045
Bresciani L, LN Lemos, N Wale, J Lin, A Strauss, M Duffy, JLM Rodrigues. 2018. Draft genome sequence of the Candidatus Spirobacillus cienkowskii, a pathogen of freshwater Daphnia species, reconstructed from hemolymph metagenomic reads. Microbial. Res. Announc. 7: e01175-18
Dai Z, A Enders, JLM Rodrigues, KL Hanley, PC Brookes, J Xu. 2018. Soil fungal taxonomic and functional composition as affected biochar composition. Soil Biol. Biochem. 126:159-167
Potisap C, AW Khan, A Boomee , JLM Rodrigues, S Wongratanacheewin, RW Sermswan. 2018. Burkholderia pseudomallei-absent soil bacterial community results in secondary metabolites that kill this pathothen. AMB Express. 8:136 (Featured article)
Kroeger M, T Delmont, AM Eren, J Guo, KM Meyer, K Khan, JLM Rodrigues, BJM Bohannan, SG Tringe, CD Borges, JM Tiedje, SM Tsai, K Nusslein. 2018. New biological insights into how deforestation affects soil microbial communities using metagenomics and metagenome-assembled genomes. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.01635
Larson CA, B Mirza, JLM Rodrigues, SI Passy. 2018. Iron limitation effects on nitrogen-fixing organisms with implications for cyanobacterial harmful algal blooms. FEMS Microbiol. Ecol. https:doi.org/10.1093/femsec/fiy046
Ren H, W Gui, Y Bai, C Stein, JLM Rodrigues, GWT Wilson, AB Cobb, Y Zhang, G Yang. 2018. Long-term effects of grazing and topography on extra-radical hyphae of arbuscular mycorrhizal fungi in semi-arid grasslands. Mycorrhiza https://doi.org.10.1007/s00572-017-0812-x
2017
Goss-Souza D, LW Mendes, CD Borges, D Baretta D, SM, JLM Rodrigues. 2017. Soil microbial community dynamics under long-term land use change: from patterns to ecological processes. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fix109 (Editor's Choice)
Soares Jr FL, J Marcon, MCP Silva, N Khakhum, LT Cerdeira, JR Ottoni, DF Domingos, RG Taketani, VM de Oliveira, AO de S Lima, JL Azevedo, JLM Rodrigues, FD Andreote. 2017. A novel multifunctional B-N-acetylhexosaminidase of an oil-spilled mangrove. Bioengineering 4, 62. DOI: 10.3390/bioengineering4030062
Ma B, Z Dai, H Wang, M Dsouza, X Liu, Y He, J Wu, JLM Rodrigues, J Gilbert, P Brookes, J Xu. 2017. Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at continental scale in Eastern China. mSystems DOI: 10.1128/mSystems.00174-16
Meyer KM, AM Klein, JLM Rodrigues, K Nusslein, S Tringe, BS Mirza, JM Tiedje, BJM Bohannan. 2017. Conversion of the Amazon rainforest soil to agriculture alters community traits of methane-cycling organisms. Mol. Ecol. 26:1547-1556
2016
Kang S, JLM Rodrigues, J Ng, T Genry. 2016. Hill number is a reliable diversity measure with high-thorughput sequence data. Scient. Rep. 6:38263
Hambright WS, J Deng, JM Tiedje, I Brettar, JLM Rodrigues. 2016. Shewanella baltica ecotypes have a wide transcriptional variation under the same growth conditions. mSphere 1:e00158-16
Khakum N, U Yordpratum, A Boonmee, U Tattawasart, JLM Rodrigues, RW Sermswan. 2016. Cloning, expression, and characterization of a peptidoglycan hydrolase from the Burkholderia pseudomallei phage ST79. AMB Express 6:77-87
Pylro VS, SM Tsai, JLM Rodrigues, FD Andreote, LFW Roesch et al. 2016. A step forward to empower global microbiome research through local leaderships. Trends Microbiol. 24:767-771
Hamaoui G, JLM Rodrigues, BJM Bohannan, JM Tiedje, K Nusslein. 2016. Land-use changes drives abundance and community structure alterations of thaumarchaeal ammonia oxidizers in tropical rainforest soils in Rondonia, Brazil. Appl. Soil Ecol. 107:48-56
Mueller RC, JLM Rodrigues, K Nusslein, BJM Bohannan. 2016. Land use change in the Amazon rainforest favors generalist fungi. Funct. Ecol. doi: 10.1111/1363-2435.12651
Khakum N, U Yordpratum, A Boonmee, U Tattawasart, JLM Rodrigues, RW Sermswan. 2016. Identification of the Burkholderia pseudomallei bacteriophage ST76 lysis cassette. J. Appl. Microbiol. 121:364-372
2015
Navarette AA, AM Venturini, KM Meyer, AM Womack, JM Tiedje, BJM Bohannan, K Nusslein, SM Tsai, JLM Rodrigues. 2015. Differential response of Acidobacteria subgroups to forest-to-pasture conversion and their biogeographical patterns in the western Brazilian Amazon. Front. Microbiol. 6:1443
Ranjan K FS Paula, RC Mueller, E da C Jesus, K Cenciani, BJM Bohannan, K Nusslein, JLM Rodrigues. 2015. Forest-to-Pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils. Front. Microbiol. 6:779
Ngamsang R, Potisap C, Boonmee A, Lawongsa P, Chaianunporn T, Wongratanacheewin S, JLM Rodrigues, Sermswan RW. 2015. The contribution of soil physicochemical properties to the presence and genetic diversity of Burkholderia pseudomallei. Southeast Asian J. Trop. Med. Publ. Health. 46:38-50
Kotak M, Isanapong J, L Goodwin, D Bruce, A Chen, CS Han, M Huntemann, N Ivanova, ML Land, M Nolan, A Pati, T Woyke, JLM Rodrigues. 2015. Comple genome sequence of the Opitutaceae bacterium strain TAV5, a potential methylotroph of the wood-feeding termite Reticulitermes flavipes. J. Genome Announ. 3:e00060-15.
2014
Paula FS, JLM Rodrigues, J Zhou, L Wu, RC Mueller, BS Mirza, BJM Bohannan, K Nusslein, Y Deng, JM Tiedje, VH Pellizari. 2014. Land use change alters functional gene diversity, composition, and abundance in Amazon forest soil microbial communties. Mol. Ecol. 23:2988-2999.
Mueller RC , FS Paula, BS Mirza, JLM Rodrigues, K Nusslein, BJM Bohannan. 2014. Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest. The ISME J. 8:1548-1550.
2013-1993
Mirza B, C Potisap, K Nusslein, BJM Bohannan, JLM Rodrigues. 2014. Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest. Appl. Environ. Microbiol. 80:281-288. (Journal Cover, highlighted in LiveScience)
Deng J, I Brettar, C Luo, J Auchtung, KT Konstantinidis, JLM Rodrigues, M Hofle, JM Tiedje. 2013. Stability, genotypic, and phenotypic diversity of the Shewanella baltica population in the redox transition zone of the Baltic Sea. Environ. Microbiol. 16:1854-1866.
Rodrigues JLM and J Isanapong. 2013. The family Opitutaceae. The Prokaryotes. 4th Edition. Springer, Singapore.
Isanapong J, WS Hambrigh, AG Willis, A Boonmee, SJ Callister, KE Burnum, L Pasa-Tolic, CD Nicora, JT Wertz, TM Schmidt, JLM Rodrigues. 2013. Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium. The ISME J. 7:1803-1813
Woo JS, S Asuming-Brempong, Q Wang, DM Tourlousse, CR Penton, Y Deng, JLM Rodrigues, S GK Adiku, JW Jones, J Zhou, JR Cole, JM Tiedje. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biol Biochem. 65:33-38.
Rodrigues JLM, VH Pellizari, R Mueller, K Baek, EC Jesus, F Paula, B Mirza, GS Hamaoui Jr, SM Tsai, B Feigl, JM Tiedje, BJM Bohannan, K Nüsslein. 2013. Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc. Acad. Nat. Sci. U.S.A. 110:988-993. (Editor's Choice in Science, Highlights in Nature Microbiology Reviews, National Public Radio, Discovery News)
Duerkop BA, CV Clements, D Rollins, JLM Rodrigues, LV Hooper. 2012. A composite bacteriophage alters colonization by an intestinal comensal bacterium. Proc. Acad. Nat. Sci. U.S.A. 109:17621-17626.
Mirza B and JLM Rodrigues. 2012. Development of a direct isolation procedure for free-living diazotrophs under controlled hypoxic condition. Appl. Environ. Microbiol. 78:5542-5549.
Isanapong J, L Goodwin, D Bruce, A Chen, C Detter, J Han, CS Han, B Held, M Huntemann, N Ivanova, ML Land, K Mavromatis, M Nolan, A Pati, L Pennacchio, S Pitluck, E Szeto, R Tapia, T Woyke, and JLM Rodrigues. 2012. High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes. J. Bacteriol. 194:2744-2745.
Wertz JT, E Kim, JB Breznak, TM Schmidt, JLM Rodrigues. 2012. Genomic and physiological characterization of a symbiotic Verrucomicrobia isolate, Diplosphaera colotermitum gen. nov., sp. nov. reveals microaerophily and nitrogen fixation genes. Appl. Environ. Microbiol. 78:1544-1555.
Rodrigues JLM, MH Serres, JM Tiedje. 2011. Large scale physiological and genomic analyses reveal ecological preference for Shewanella species and expand gene targets at genus level. Appl. Environ. Microbiol. 77:5352-5360. (Journal Cover)
Cruz-García C, AE Murray, JLM Rodrigues, JA Gralnick, LA McCue, MF Romine, FE Löffler, JM Tiedje. 2011. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1. BMC Microbiology. 11:64. doi:10.1186/1471-2180-11-64
Hinsa-Leasure S, L Bhavaraju, JLM Rodrigues, C Bakermans, JM Tiedje. 2010. Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample. FEMS Microbial. Ecol. 74:103-113.
Jesus EC, E Susilawati, S Smith, Q Wang, B Chai, R Farris, JLM Rodrigues, K Telen, JM Tiedje. 2010. Bacterial communities in the rhizosphere of biofuel crops. Biofuel Res. 3:20-27.
Kielak A, JLM Rodrigues, EE Kuramae, PSG Chain, JA van Veen, GA Kowalchuk. 2009. Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiol. Ecol. 71:23-33.
Konstantinidis* KT, MH Serres*, M Romine*, JLM Rodrigues*, L-A McCue, MS Lipton, A Obraztsova, CS Giometti, KH Nealson, JF Fredrikson, JM Tiedje. 2009. Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proc. Acad. Nat. Sci. U.S.A. 106:15909-15914. *First 4 authors with equal contribution. (Highlights in Nature and NBC News)
Sul WJ, J Park, JF Quensen III, JLM Rodrigues, L Seliger, TV Tsoi, GJ Zylstra, JM Tiedje. 2009. Novel biphenyl dioxygenase subunits retrieved from River Raisin sediment using stable isotope probing-derived metagenomic libraries. Appl. Environ. Microbiol. 75:5501-5506.
Silva-Stenico ME, FTH Pacheco, ER Pereira-Filho, JLM Rodrigues, AN Souza, A Etchegaray, JE Gomes, SM Tsai. 2009. Nutritional deficiency in citrus with symptoms of citrus variegated chlorosis disease. Braz. J. Biol. 69:631-637.
Fredrickson JK, MF Romine, AS Believ, JM Auchtung, ME Driscoll, TS Gardner, KH Nealson, AL Osterman, G Pinchuk, JL Reed, DA Rodionov, JLM Rodrigues, DA Saffarini, MH Serres, AM Spormann, IB Zhulin, and JM Tiedje. 2008. Towards environmental systems biology of Shewanella. Nature Microbiol. Reviews. 6:592-603.
Rodrigues JLM, MA Duffy, AJ Tesser, D Ebert, L Mouton, and TM Schmidt. 2008. Phylogenetic characterization and prevalence of “Spirobacillus cienkowskii”, a red-pigmented, spiral-shaped bacterial pathogen of freshwater Daphnia species. Appl. Environ. Microbiol. 74:1575-1582. (Journal Cover)
Leigh MB, VH Pellizari, O Uhlik, R Sutka, JLM Rodrigues, NE Ostrom, J Zhou, JM Tiedje. 2007. Biphenl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). The ISME Journal 1:134-148.
Rodrigues JLM, CA Kachel, MR Aiello, JF Quensen III, OV Maltseva, TV Tsoi, JM Tiedje. 2006. Degradation of Aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp. RHA1(fcb). Appl. Environ. Microbiol. 72:2476-2482.
Saito D, RT Leonardo, JLM Rodrigues, SM Tsai, JF Hofling, RB Gonçalves. 2006. Identification of endodontic infections by sequence analysis of the 16S rDNA clone libraries. J. Medical Microbiol. 55:101-107.
Denef VJ, JA Klappenbach, MA Patrauchan, C Florizone, JLM Rodrigues, TV Tsoi, W Vestraete, LD Eltis, JM Tiedje. 2006. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl. Environ. Microbiol. 72:585-595.
Fedatto LM, ME Silva-Stenico, FTH Pacheco, JLM Rodrigues, SM Tsai. 2006. Detection and characterization of a protease secreted by the plant pathogen Xylella fastidiosa. Microbiol. Res. 161:263-272
Rodrigues JLM, ME Silva-Stenico, AN de Souza, JRS Lopes, SM Tsai. 2005. In situ probing of Xylella fastidiosa in honeydew of a xylem sap-feeding insect using 16S rRNA-targeted fluorescent oligonucleotides. Environ. Microbiol. 8:747-754.
Fiore MF, BA Neilan, JN Copp, JLM Rodrigues, SM Tsai, H Lee, JT Trevors. 2005. Characterization of nitrogen-fixing cyanobacteria in the Brazilian Amazon floodplain. Water Res. 39:5017-5026.
Silva-Stenico ME, FTH Pacheco, E Carilho, JLM Rodrigues, SM Tsai. 2005. Growth and siderophore production of Xylella fastidiosa under iron-limited conditions. Microbiol. Res. 160:429-436.
Tiedje JM, TV Tsoi, KD Pennel, LD Hansen, A Wani, JLM Rodrigues, Y Hrywna, DP Howell. 2005. Enhancing PCB Bioremediation. p.147-214. In Bioremediation of Recalcitrant Compounds. CRC, Boca Raton, FL.
Rodrigues JLM, ME Silva-Stenico, JE Gomes, JRS Lopes, SM Tsai. 2003. Diversity and detection assessment of Xylella fastidiosa through 16S rRNA and gyrB sequences in field-collected plant and insect samples. Appl. Environ. Microbiol. 69:4249-4255
Denef VJ, J Park, JLM Rodrigues, TV Tsoi, SA Hashshan, JM Tiedje. 2003. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ. Microbiol. 5:933-943.
Rodrigues JLM, MR Aiello, JW Urbance, TV Tsoi, JM Tiedje. 2002. Use of both 16S rRNA and engineered functional genes with real time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil. J. Microbiol. Methods 51:181-189.
Rodrigues JLM, O Maltseva, TV Tsoi, R Helton, JF Quensen III, M Fukuda, JM Tiedje. 2001. Development of a Rhodococcus recombinant strain for degradation of products from anaerobic dechlorination of Aroclor 1242. Environ. Sci. & Techn. 35:663-668.
Rodrigues JLM, M Melotto, JTA Oliveira, JAG da Silveira. 1998. Efficiency of soybean nodules in relation to nodulin activities and hydrogenase expression. Brazilian J. Plant Physiol. 10:173-178.
Rodrigues JLM, M Melotto, JAG da Silveira. 1998. Nodulin activies, hydrogenase expression and nitrogen fixation in cowpea inoculated with Hup+ and Hup- symbionts. Brazilian J. Plant Physiol. 10:85-90.
Silveira JAG, JL Contado, JLM Rodrigues, JTA Oliveira. 1998. Phosphoenolpyruvate carboxylase and glutamine synthetase activities in relation to nitrogen fixation in cowpea nodules. Brazilian J. Plant Physiol. 10:19-23.
Rodrigues JLM and Pellizari, VH 1997. Biodegradation of PCBs. In Melo, I.S. de & Azevedo, J.L. de. Microbiologia Ambiental. EMBRAPA. Jaguariuna, SP. 438p.
Rodrigues JLM. 1993. PEP carboxylase and glutamine synthatase nodulins: their relationship with symbiotic N2 fixation efficiency in cowpea and soybean inoculated with Bradyrhizobium japonicum. M.Sc. Thesis. University of São Paulo.
Machado EC, JAG da Silveira, VA Vitorello, JLM Rodrigues. 1992. Photosynthesis, reserves remobilization and grain growth of two maize hybrids submitted to water stress during the grain filling stage. Bragantia. 51:151-159.
Khan Md AW, BJM Bohannan, K M Meyer, AM Klein, K Nusslein, JP Grover, JL Mazza Rodrigues. 2025. Community-level metabolic shifts following land use change in the Amazon rainforest identified by a supervised machine learning approach. Environmental Microbiology Reports https://doi.org/10.1111/1758-2229.70088
He D, Dai Z, H Shen, J Lin, K Zhao, JL Mazza Rodrigues, Y Kuzyakov, J Xu. 2025. Microbial life-history strategies and genomic traits between pristine and cropland soils. mSystems https://doi.org/10.1128/msystems.00178-25
Potisap C, P Lawongsa, S Wongratanacheewin, J Duangsri, JB Gontijo, JL Mazza Rodrigues, RW Sermswan. 2025. The soil microorganism Bacillus amyloliquefaciens N3-8 is a biocontrol agent for the pathogen Burkholderia pseudomallei in rice plantation. mSpectrum (accepted)
Venturini A, J Gontijo, L Berrios, JL Mazza Rodrigues, K Peay, SM Tsai. 2025. Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon. mSpectrum https://doi.org/10.1128/spectrum.01561-24
2024
Nguyen TT, A Altman, L Huang, JL Mazza Rodrigues, HE Dahlke, NA Kamennaya, E Levintal. 2024. A portable, open source, low-cost incubation chamber for real-time characterization of soil respiration and microbial activity. Soil Science Society of America Journal https://doi.org/10.1002/saj2.20800
Guo Z, J Liu, L He, JL Mazza Rodrigues, Ning Chen, Y Zuo, N Wang, X Zhu, Y Sun, L Zhang, Y Song, D Zhang, F Yuan, C Song, X Xu. 2024. Dominant edaphic controls of particulate organic carbon in global soils. Global Change Biology https://doi.org/10.1111/gcb.17619
Gontijo JB, FS Paula, W Bieluczyk, AG Franca, D Navroski, J Meandro, AM Venturini, FO Asselta, LW Mendes, MZ Moreira, K Nusslein, BJM Bohannan, PLE Boldelier, JL Mazza Rodrigues, SM Tsai. 2024. Amazon methane-cycling microbial communities from floodplain and upland forests respond differently to a climate change scenario. Environmental Microbiome https://doi.org/10.1186/s40793-024-00596-z
Huang L, AS Rosado, A Wright, RS Correa, L Silva, JL Mazza Rodrigues. 2024. Microbiome recovery in a chronosequence of impoverished Cerrado soils with biosolids applications. Science of the Total Environmental
https://doi.org/10.1016/j.scitotenv.2024.172958
Graham EB, AP Camargo, R Wu, RY Neches, M Nolan, D Paez-Espino, A Copeland, NC Kyrpides, JK Jansson, JE McDermott, KS Hofmockel, Soil Virosphere Consortium (JL Mazza Rodrigues). 2024. A global atlas of soil viruses reveals unexplored diversity and potential biogeochemical impacts. Nature Microbiology
https://doi.org/10.1038/s41564-024-01686-x
Anthony W, S Allison, C Broderick, L Rodriguez, A Clum, H Cross, E Eloe-Fadrosh, S Evans, D Fairbanks, R Gallery, J Gontijo, J Jones, J McDermott, J Pett-Ridge, S Racord, JL Mazza Rodrigues, W Rodriguez-Reillo, K Shek, C Takacs-Vesbach, J Blanchard. 2024. From soil to sequence: Filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology. Environmental Microbiome https://doi.org/10.1186/s40793-024-00599-w
He L, JL Mazza Rodrigues, M Mayes, C-T Lai, D Lipson, X Xu. 2023. Modeling microbial carbon fluxes and stocks in global soils from 1901-2016. Biogeosciences https://doi.org/10.5194/bg-21-2313-2024
Wang Y, L He, J Liu, KA Arndt, JL Mazza Rodrigues, D Zona, DA Lipson, WC Oechel, DM Ricciuto, SD Wullschleger, X Xu. 2024. Intensified positive artic - methane feedback under IPCC climate scenarios in the 21st century. Ecosystems Health and Sustainability https://doi. org/10.34133/ehs.0185
Silva, DF, EJBN Cardoso, L Huang, C Erikson, AMM Silva, VLVP Araujo, DEO Silva, VMM Melo, ASA Ferreira, APA Pereira, JL Mazza Rodrigues. 2024. Functional genes related to N and P cycling in degraded and restored areas from Brazilian drylands. Applied Soil Ecology https://doi.org/10.1016/j.apsoil.2024.105316
Silva DF, JL Mazza Rodrigues, C Erikson, AMM Silva, L Huang, VLVP Araujo, FP Matteoli, LW Mendes, ASF Araujo, APA Pereira, VMM Melo, EJBN Cardoso. 2024. Grazing exclusion-induced changes in soil fungal communities in a highly desertified Brazilian dryland. Microbiological Research https://doi.org/10.1016/j.micres.2024.127763
Xu S, C Gu, JL Mazza Rodrigues, C Li, B Bohannan, K Nusslein, A Margenot. 2023. Soil phosphorus cycling across a 100-year deforestation chronosequence in the Amazon rainforest. Global Change Biology
https://doi.org/10.1111/gcb.17077
2023
Huang L, E Levintal, CB Erikson, A Coyolt, WR Horwath, HE Dahlke, JLM Rodrigues. 2023. Molecular and dual-isotopic profiling of the microbial controls on nitrogen leaching in agricultural soils under managed aquifer recharge. Environment Science & Technology https://doi.org/10.1021/acs.est.3c01356
Sayre JM, D Wang, JY Lin, R Danielson, KM Scow, JLM Rodrigues. 2023. Repeated manure inputs to a forage production soil increase microbial biomass and diversity and select for lower abundance genera. Agriculture, Ecosystems & Environment https://doi.org/10.1016/j.agee.2023.108567
JLM Rodrigues and M Melotto. 2023. Naturally engineered plant microbiomes in resource-limited ecosystems. Trends in Microbiology https://doi.org/10.1016/j.tim.2023.02.006
He L, JLM Rodrigues, M Mayes, C-T Lai, DA Lipson, X Xu. 2023. Historical dynamics of terrestrial carbon during 1901-2016 as simulated by the CLM-Microbe model. Biogeosciences https://doi.org/10.5194/bg-2023-15
Obregon D, LF de Sousa, LW Mendes, MT de Moraes, M Tosi, AM Venturini, KM Meyer, PB de Camargo, BJM Bohannan, JLM Rodrigues, KE Dunfield, SM Tsai. 2023. Shifts in functional traits and interaction patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin. Molecular Ecology
https://doi.org/10.1111/mec.16912
Pinheiro Y, F da Mota, R Peixoto, JD van Elsas, JLM Rodrigues, A Rosado. 2023. A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environment. Communications Biology. https://doi.org/10.1038/s42003-023-04617-4
Levintal E , L Huang, CP Garcia, A Coyotl, MW Fidelibus, WH Horwath, JLM Rodrigues, H Dahlke. 2023. Nitrogen fate during agricultural managed aquifer recharge: linking plant response, hydrologic and geiochemical processes. Science of the Total Environment https://doi.org/10.1016/j.scitotenv.2022.161206
2022
Danielson RE, JLM Rodrigues. 2022. Impacts of land use change on soil microbial communities in the Amazon. Advances in Agronomy. https://doi.org/10.1016/bs.agron.2022.04.001
Liu H, Y Luo, X Song, P Leng, J Li, JLM Rodrigues, Z Hong, Y Kuzyakob, Z Dai, J Xu. 2022. Generalists and specialists decomposing labile and aromatic biochar compounds and sequestering carbon in soil. Geoderma https://doi.org/10.1016/j.geoderma.2022.116176
Alves KJ, VS Pylro, CR Nakayama, VG Vital, RG Taketani, DG Santos, JLM Rodrigues, SM Tsai, FD Andreote. 2022. Methanogenic communities and methane emissions from enriched Amazonia soil under land-use change. Microbiological Research
https://doi.org/10.1016/j.micres.2022.127178
Wang D, JY Lin, JM Sayre, R Schmidt, SJ Fonte, JLM Rodrigues, K Scow. 2022. Compost amendment and cover cropping maintains soil structure and associated C storage by increasing available C and microbial biomass in agricultural soil – a six year field study. Geoderma https://doi.org/10.1016/j.geoderma.2022.116117
Venturini AM, JB Gontijo, A Franca, J Moura, K Nusslein, B Bohannan, JLM Rodrigues, SM Tsai. 2022. Metagenomes from Eastern Brazilian Amazonian floodplains in wet and dry seasons. Microbiology Research Announcements https://doi.org/10.1128/mra.00432-22
Goss-Souza D, SM Tsai, JLM Rodrigues, O Klauberg-Filho, P Sousa, D Baretta, LW Mendes. 2022. Biogeographic responses and niche occupancy of microbial communities following long-term land-use change. Antonie van Leeuvenhoek https://doi.org/10.1007/s10482-022-01761-5
Souza L, DA Obregon, L Domeignoz-Horta, F Gomes, C Almeida, L Merloti, L Mendes, FD Andreote, B Bohannan, JLM Rodrigues, K Nusslein, SM Tsai. 2022. Maintaining grass coverage increases methane uptake in Amazonian pasture soils. Science of the Total Environment. http://dx.doi.org/10.1016/j.scitotenv.2022.156225
Venturini, AM, NMS Dias, JB Gontijo, CA Yoshiura, FS Paula, FM Nakamura, KM Meyer, AG Franca, CD Borgers, J Barlow, E Beringer, KR Nusslein, JLM Rodrigues, BJM Bohannan, SM Tsai. 2022. Increased soil moisture exarcerbates the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon. Environmental Research. https://doi.org/10.1016/j.envres.2022.113139
Ghotbi M, A Durrer, K Frindte, WR Horwath, JLM Rodrigues, I Danso, C Knief. 2022. Topographic attributes overrride impacts of agronomic practices on prokaryotic community struture. Applied Soil Ecology. https://doi.org/10.1016/j.apsoil.2022.104446
Lazick P, JLM Rodrigues, D Geisseler. 2022. Acid stress and compost differentially affect microbial carbon and nitrogen cycling functions in an agricultural soil. Applied Soil Ecology. https://doi.org/10.1016/j.apsoil.2021.104219
2021
Durrer A, AJ Margenot, LCR Silva, BJM Bohannan, K Nusslein, FD Andreoti, J van Haren, SJ Parikh, JLM Rodrigues. 2021. Beyond total carbon costs: Land use change alters soil carbon cycling in the Amazon. Biogeochemistry https://doi.org.10.1007/s10533-020-00743-x
Yoshiura CA, LPP Braga, AM Venturini, AG da Franca, MCCP de Lyra, SM Tsai, JLM Rodrigues. 2021. Influence of inputs combination on the microbial structure of the maize rhizosphere for greenhouse gas fluxes mitigation. Frontiers in Plant Science. https://www.frontiersin.org/articles/10.3389/fpls.2021.683658/full
Lazick P, JLM Rodrigues, D Geisseler. 2021. Sensitivity and variability of soil health indicators in a Mediterranean crop system. Soil Science Society of America J. https://acsess.onlinelibrary.wiley.com/doi/pdfdirect/10.1002/saj2.20278
Hodson AK, JM Sayre, MCCP Lyra, JLM Rodrigues. 2021. Influence of recycle compost on soil food webs, nutrient cycling and tree growth in a young orchard. Agronomy 11:1754 https://doi.org/10.3390/agronomy11091745
Gontijo JB, AM Venturini, CA Yoshiura, CD Borges, JMS Moura, BJM Bohannan, K Nusslein, JLM Rodrigues, FS Paula, SM Tsai. 2021. Not only a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophic metabolisms. Mol. Ecol. https://doi.org/10.1111/mec.15912
Jesus HE, A Enrich-Prast A, SSM Paiva, RS Peixoto, RS Carreira, C Massone, JLM Rodrigues, CK Lee, C Craig, AS Rosado. 2021. Microbial sucession under thaw-freeze cycle events for hydrocarbon degradation in a nutrient-amended Antartic soil. Microorganisms https://doi.org/10.3390/microorganisms9030609
Zhang L, B Ma, C Tang, H Yu, X Lv, JLM Rodrigues, RA Dahlgren, J Xu. 2021. Habitat heterogeneity induced by pyrogenenic organic matter in wildfire-perturbed soils mediates bacterial community assembly processes. The ISME J. https://www.nature.com/articles/s41396-021-00896-z
He L, D Lipson, JLM Rodrigues, M Mayes, RG Bjork, B Glaser, J Rinklebe, X Xu. 2021. Dynamics of fungal and bacterial biomass carbon in natural ecosystems: site-level applications of the CLM-Microbe model. J. Adv. Model. Earth Systems https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020MS002283
Wang L, H Chen, J Wu, L Huang, PC Brookes, JLM Rodrigues, J Xu, X Liu. 2021. Effects of magnetic biochar-microbe composite on Cd remediation and microbial responses in paddy soil. J Hazardous Materials https://doi.org/10.1016/j.jhazmat.2021.125494
2020
Nayfach S, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, D Paez-Espino, IMG/M Data Consortium (JLM Rodrigues). 2020. A genomic catalogue of Earth's microbiome. Nature Biotechnol. https://www.nature.com/articles/s41587-020-0718-6
Kroeger ME, LK Meredith, KM Meyer, KD Webster, PB de Camargo, LF de Souza, SM Tsai, J van Haren, S Saleska, BJM Bohannan, JLM Rodrigues, E Berenguer, J Barlow, K Nusslein. 2020. Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon. The ISME J. https://www.nature.com/articles/s41396-020-00804-x
Allard S, M Costa, A Bulseco, V Helfer, L Wilkins, C Hassenruck, K Zengler, M Zimmer, N Eraso, JLM Rodrigues, N Duke, V Melo, I Vanworterghem, H Junka, H Makonde, D Jimeniz, T Tavarez, M Fusi, D Daffonchio, C Duarte, R Peixoto, A Rosado, J Gilbert, J Bowman. 2020. Introducing the Mangrove Microbiome Initiative: Setting research priorities for mangrove preservation and rehabiliation. mSystems https://msystems.asm.org/content/5/5/e00658-20
Meyer KM, AH Morris, K Webster, AM Klein, ME Kroeger, LK Meredith, A Braendholt, F Nakamura, A Veturini, LF de Souza, KL Shek, R Danielson, J van Haren, PB de Camargo, SM Tsai, F Dini-Andreote, JMS de Moura, J Barlow, E Berenguer, K Nusslein, S Saleska, JLM Rodrigues, BJM Bohannan. 2020. Belowground changes to community structure alter methane-cycling dynamics in Amazonia. Environ. International. https://doi.org/10.1016/j.envint.2020.106131
He L, JLM Rodrigues, NA Soudzilovskaia, M Barcelo, PA Olson, C Song, L Tedersoo, F Yuan, D Lipson, X Xu. 2020. Global biogeography of fungal and bacterial biomass carbon in topsoil. Soil Biol. and Biochem. https://doi.org/10.1016/j.soilbio.2020.108024
Lin JY and JLM Rodrigues. 2020. Genus Geminisphera. In: Oren A. Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Inc. New Jersey, USA. DOI: 10.1002/9781118960608.gbm01542
Mirza BS, DJ McGlinn, BJM Bohannan, K Nusslein, JM Tiedje, JLM Rodrigues. 2020. Diazotrophs show sign of restoration in Amazon rainforest soils with ecosystem rehabilitation. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.00195-20.
Schmidt JE, JLM Rodrigues , VL Brisson, A. Kent, ACM Gaudin. 2020. Impacts of directed evolution and soil management legacy on maize microbiome. Soil Biol. and Biochem. https://doi.org/10.1016/j.soilbio.2020.107794
Hoda R, M Sattler, MD Sahadat Hussein, JLM Rodrigues. 2020. Boosting landfill gas production from lignin-containing waste via termite hindgut microorganism. Waste Management https://www.sciencedirect.com/science/article/pii/S0956053X20300659
Kotak M, J Lin, J Isanapong, JLM Rodrigues. 2020. Draft genome sequences of two Opitutaceae bacteria strains TAV3 and TAV4 isolated from a wood feeding termite and bioinformatics characterization of their lignocellulolytic enzymes. Microbiol. Res. Announ. https://mra.asm.org/content/9/2/e01192-19
Parsons LS, JM Sayre, C Ender, JLM Rodrigues, A Barberan. 2020. Plant-soil microbial feedbacks in restored and unrestored coastal dune ecosystems in California. Restoration Ecol. https://onlinelibrary.wiley.com/doi/10.1111/rec.13101
2019
Goss-Souza D, LW Mendes, JLM Rodrigues, SM Tsai. 2019. Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept constant. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiz009
Sjöling S, van Elsas JD, Andreote FD, JLM Rodrigues. 2019. Soil metagenomics: deciphering the soil microbial gene pool. Book Chapter In: van Elsas, Trevors, Rosado, and Nanniplerl. Modern Soil Microbiology, 3rd Edition, CRC Press.
Goss-Souza D, LW Mendes, JLM Rodrigues, SM Tsai. 2019. Ecological processes shaping bulk and rhizosphere microbiome assembly in a long-term Amazon forest-to-agriculture coversion. Microb. Ecol. https://doi.org/10.1007/s00248-019-01401-y
Ren H, Q Zhou, J He, Y Hou, JLM Rodrigues, AB Cobb, GWT Wilson, Y Zhang. 2019. Determining landscape-level drivers of variability for over 50 elements. Sci. Total. Environ. 657:279-286.
2018
Khan Md AW, BJM Bohannan, K Nusslein, JM Tiedje, SG Tringe, E Parlade, A Barberan, and JLM Rodrigues. 2018. Network analysis reveals substantial alteration of microbial co-occurrence patterns due to deforestation in the Amazon rainforest. FEMS Microbiol. Ecol. https://academic.oup.com/femsec/article/95/2/fiy230/5211045
Bresciani L, LN Lemos, N Wale, J Lin, A Strauss, M Duffy, JLM Rodrigues. 2018. Draft genome sequence of the Candidatus Spirobacillus cienkowskii, a pathogen of freshwater Daphnia species, reconstructed from hemolymph metagenomic reads. Microbial. Res. Announc. 7: e01175-18
Dai Z, A Enders, JLM Rodrigues, KL Hanley, PC Brookes, J Xu. 2018. Soil fungal taxonomic and functional composition as affected biochar composition. Soil Biol. Biochem. 126:159-167
Potisap C, AW Khan, A Boomee , JLM Rodrigues, S Wongratanacheewin, RW Sermswan. 2018. Burkholderia pseudomallei-absent soil bacterial community results in secondary metabolites that kill this pathothen. AMB Express. 8:136 (Featured article)
Kroeger M, T Delmont, AM Eren, J Guo, KM Meyer, K Khan, JLM Rodrigues, BJM Bohannan, SG Tringe, CD Borges, JM Tiedje, SM Tsai, K Nusslein. 2018. New biological insights into how deforestation affects soil microbial communities using metagenomics and metagenome-assembled genomes. Front. Microbiol. https://doi.org/10.3389/fmicb.2018.01635
Larson CA, B Mirza, JLM Rodrigues, SI Passy. 2018. Iron limitation effects on nitrogen-fixing organisms with implications for cyanobacterial harmful algal blooms. FEMS Microbiol. Ecol. https:doi.org/10.1093/femsec/fiy046
Ren H, W Gui, Y Bai, C Stein, JLM Rodrigues, GWT Wilson, AB Cobb, Y Zhang, G Yang. 2018. Long-term effects of grazing and topography on extra-radical hyphae of arbuscular mycorrhizal fungi in semi-arid grasslands. Mycorrhiza https://doi.org.10.1007/s00572-017-0812-x
2017
Goss-Souza D, LW Mendes, CD Borges, D Baretta D, SM, JLM Rodrigues. 2017. Soil microbial community dynamics under long-term land use change: from patterns to ecological processes. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fix109 (Editor's Choice)
Soares Jr FL, J Marcon, MCP Silva, N Khakhum, LT Cerdeira, JR Ottoni, DF Domingos, RG Taketani, VM de Oliveira, AO de S Lima, JL Azevedo, JLM Rodrigues, FD Andreote. 2017. A novel multifunctional B-N-acetylhexosaminidase of an oil-spilled mangrove. Bioengineering 4, 62. DOI: 10.3390/bioengineering4030062
Ma B, Z Dai, H Wang, M Dsouza, X Liu, Y He, J Wu, JLM Rodrigues, J Gilbert, P Brookes, J Xu. 2017. Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at continental scale in Eastern China. mSystems DOI: 10.1128/mSystems.00174-16
Meyer KM, AM Klein, JLM Rodrigues, K Nusslein, S Tringe, BS Mirza, JM Tiedje, BJM Bohannan. 2017. Conversion of the Amazon rainforest soil to agriculture alters community traits of methane-cycling organisms. Mol. Ecol. 26:1547-1556
2016
Kang S, JLM Rodrigues, J Ng, T Genry. 2016. Hill number is a reliable diversity measure with high-thorughput sequence data. Scient. Rep. 6:38263
Hambright WS, J Deng, JM Tiedje, I Brettar, JLM Rodrigues. 2016. Shewanella baltica ecotypes have a wide transcriptional variation under the same growth conditions. mSphere 1:e00158-16
Khakum N, U Yordpratum, A Boonmee, U Tattawasart, JLM Rodrigues, RW Sermswan. 2016. Cloning, expression, and characterization of a peptidoglycan hydrolase from the Burkholderia pseudomallei phage ST79. AMB Express 6:77-87
Pylro VS, SM Tsai, JLM Rodrigues, FD Andreote, LFW Roesch et al. 2016. A step forward to empower global microbiome research through local leaderships. Trends Microbiol. 24:767-771
Hamaoui G, JLM Rodrigues, BJM Bohannan, JM Tiedje, K Nusslein. 2016. Land-use changes drives abundance and community structure alterations of thaumarchaeal ammonia oxidizers in tropical rainforest soils in Rondonia, Brazil. Appl. Soil Ecol. 107:48-56
Mueller RC, JLM Rodrigues, K Nusslein, BJM Bohannan. 2016. Land use change in the Amazon rainforest favors generalist fungi. Funct. Ecol. doi: 10.1111/1363-2435.12651
Khakum N, U Yordpratum, A Boonmee, U Tattawasart, JLM Rodrigues, RW Sermswan. 2016. Identification of the Burkholderia pseudomallei bacteriophage ST76 lysis cassette. J. Appl. Microbiol. 121:364-372
2015
Navarette AA, AM Venturini, KM Meyer, AM Womack, JM Tiedje, BJM Bohannan, K Nusslein, SM Tsai, JLM Rodrigues. 2015. Differential response of Acidobacteria subgroups to forest-to-pasture conversion and their biogeographical patterns in the western Brazilian Amazon. Front. Microbiol. 6:1443
Ranjan K FS Paula, RC Mueller, E da C Jesus, K Cenciani, BJM Bohannan, K Nusslein, JLM Rodrigues. 2015. Forest-to-Pasture conversion increases the diversity of the phylum Verrucomicrobia in Amazon rainforest soils. Front. Microbiol. 6:779
Ngamsang R, Potisap C, Boonmee A, Lawongsa P, Chaianunporn T, Wongratanacheewin S, JLM Rodrigues, Sermswan RW. 2015. The contribution of soil physicochemical properties to the presence and genetic diversity of Burkholderia pseudomallei. Southeast Asian J. Trop. Med. Publ. Health. 46:38-50
Kotak M, Isanapong J, L Goodwin, D Bruce, A Chen, CS Han, M Huntemann, N Ivanova, ML Land, M Nolan, A Pati, T Woyke, JLM Rodrigues. 2015. Comple genome sequence of the Opitutaceae bacterium strain TAV5, a potential methylotroph of the wood-feeding termite Reticulitermes flavipes. J. Genome Announ. 3:e00060-15.
2014
Paula FS, JLM Rodrigues, J Zhou, L Wu, RC Mueller, BS Mirza, BJM Bohannan, K Nusslein, Y Deng, JM Tiedje, VH Pellizari. 2014. Land use change alters functional gene diversity, composition, and abundance in Amazon forest soil microbial communties. Mol. Ecol. 23:2988-2999.
Mueller RC , FS Paula, BS Mirza, JLM Rodrigues, K Nusslein, BJM Bohannan. 2014. Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest. The ISME J. 8:1548-1550.
2013-1993
Mirza B, C Potisap, K Nusslein, BJM Bohannan, JLM Rodrigues. 2014. Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest. Appl. Environ. Microbiol. 80:281-288. (Journal Cover, highlighted in LiveScience)
Deng J, I Brettar, C Luo, J Auchtung, KT Konstantinidis, JLM Rodrigues, M Hofle, JM Tiedje. 2013. Stability, genotypic, and phenotypic diversity of the Shewanella baltica population in the redox transition zone of the Baltic Sea. Environ. Microbiol. 16:1854-1866.
Rodrigues JLM and J Isanapong. 2013. The family Opitutaceae. The Prokaryotes. 4th Edition. Springer, Singapore.
Isanapong J, WS Hambrigh, AG Willis, A Boonmee, SJ Callister, KE Burnum, L Pasa-Tolic, CD Nicora, JT Wertz, TM Schmidt, JLM Rodrigues. 2013. Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium. The ISME J. 7:1803-1813
Woo JS, S Asuming-Brempong, Q Wang, DM Tourlousse, CR Penton, Y Deng, JLM Rodrigues, S GK Adiku, JW Jones, J Zhou, JR Cole, JM Tiedje. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biol Biochem. 65:33-38.
Rodrigues JLM, VH Pellizari, R Mueller, K Baek, EC Jesus, F Paula, B Mirza, GS Hamaoui Jr, SM Tsai, B Feigl, JM Tiedje, BJM Bohannan, K Nüsslein. 2013. Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc. Acad. Nat. Sci. U.S.A. 110:988-993. (Editor's Choice in Science, Highlights in Nature Microbiology Reviews, National Public Radio, Discovery News)
Duerkop BA, CV Clements, D Rollins, JLM Rodrigues, LV Hooper. 2012. A composite bacteriophage alters colonization by an intestinal comensal bacterium. Proc. Acad. Nat. Sci. U.S.A. 109:17621-17626.
Mirza B and JLM Rodrigues. 2012. Development of a direct isolation procedure for free-living diazotrophs under controlled hypoxic condition. Appl. Environ. Microbiol. 78:5542-5549.
Isanapong J, L Goodwin, D Bruce, A Chen, C Detter, J Han, CS Han, B Held, M Huntemann, N Ivanova, ML Land, K Mavromatis, M Nolan, A Pati, L Pennacchio, S Pitluck, E Szeto, R Tapia, T Woyke, and JLM Rodrigues. 2012. High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes. J. Bacteriol. 194:2744-2745.
Wertz JT, E Kim, JB Breznak, TM Schmidt, JLM Rodrigues. 2012. Genomic and physiological characterization of a symbiotic Verrucomicrobia isolate, Diplosphaera colotermitum gen. nov., sp. nov. reveals microaerophily and nitrogen fixation genes. Appl. Environ. Microbiol. 78:1544-1555.
Rodrigues JLM, MH Serres, JM Tiedje. 2011. Large scale physiological and genomic analyses reveal ecological preference for Shewanella species and expand gene targets at genus level. Appl. Environ. Microbiol. 77:5352-5360. (Journal Cover)
Cruz-García C, AE Murray, JLM Rodrigues, JA Gralnick, LA McCue, MF Romine, FE Löffler, JM Tiedje. 2011. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1. BMC Microbiology. 11:64. doi:10.1186/1471-2180-11-64
Hinsa-Leasure S, L Bhavaraju, JLM Rodrigues, C Bakermans, JM Tiedje. 2010. Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample. FEMS Microbial. Ecol. 74:103-113.
Jesus EC, E Susilawati, S Smith, Q Wang, B Chai, R Farris, JLM Rodrigues, K Telen, JM Tiedje. 2010. Bacterial communities in the rhizosphere of biofuel crops. Biofuel Res. 3:20-27.
Kielak A, JLM Rodrigues, EE Kuramae, PSG Chain, JA van Veen, GA Kowalchuk. 2009. Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiol. Ecol. 71:23-33.
Konstantinidis* KT, MH Serres*, M Romine*, JLM Rodrigues*, L-A McCue, MS Lipton, A Obraztsova, CS Giometti, KH Nealson, JF Fredrikson, JM Tiedje. 2009. Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proc. Acad. Nat. Sci. U.S.A. 106:15909-15914. *First 4 authors with equal contribution. (Highlights in Nature and NBC News)
Sul WJ, J Park, JF Quensen III, JLM Rodrigues, L Seliger, TV Tsoi, GJ Zylstra, JM Tiedje. 2009. Novel biphenyl dioxygenase subunits retrieved from River Raisin sediment using stable isotope probing-derived metagenomic libraries. Appl. Environ. Microbiol. 75:5501-5506.
Silva-Stenico ME, FTH Pacheco, ER Pereira-Filho, JLM Rodrigues, AN Souza, A Etchegaray, JE Gomes, SM Tsai. 2009. Nutritional deficiency in citrus with symptoms of citrus variegated chlorosis disease. Braz. J. Biol. 69:631-637.
Fredrickson JK, MF Romine, AS Believ, JM Auchtung, ME Driscoll, TS Gardner, KH Nealson, AL Osterman, G Pinchuk, JL Reed, DA Rodionov, JLM Rodrigues, DA Saffarini, MH Serres, AM Spormann, IB Zhulin, and JM Tiedje. 2008. Towards environmental systems biology of Shewanella. Nature Microbiol. Reviews. 6:592-603.
Rodrigues JLM, MA Duffy, AJ Tesser, D Ebert, L Mouton, and TM Schmidt. 2008. Phylogenetic characterization and prevalence of “Spirobacillus cienkowskii”, a red-pigmented, spiral-shaped bacterial pathogen of freshwater Daphnia species. Appl. Environ. Microbiol. 74:1575-1582. (Journal Cover)
Leigh MB, VH Pellizari, O Uhlik, R Sutka, JLM Rodrigues, NE Ostrom, J Zhou, JM Tiedje. 2007. Biphenl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). The ISME Journal 1:134-148.
Rodrigues JLM, CA Kachel, MR Aiello, JF Quensen III, OV Maltseva, TV Tsoi, JM Tiedje. 2006. Degradation of Aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp. RHA1(fcb). Appl. Environ. Microbiol. 72:2476-2482.
Saito D, RT Leonardo, JLM Rodrigues, SM Tsai, JF Hofling, RB Gonçalves. 2006. Identification of endodontic infections by sequence analysis of the 16S rDNA clone libraries. J. Medical Microbiol. 55:101-107.
Denef VJ, JA Klappenbach, MA Patrauchan, C Florizone, JLM Rodrigues, TV Tsoi, W Vestraete, LD Eltis, JM Tiedje. 2006. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl. Environ. Microbiol. 72:585-595.
Fedatto LM, ME Silva-Stenico, FTH Pacheco, JLM Rodrigues, SM Tsai. 2006. Detection and characterization of a protease secreted by the plant pathogen Xylella fastidiosa. Microbiol. Res. 161:263-272
Rodrigues JLM, ME Silva-Stenico, AN de Souza, JRS Lopes, SM Tsai. 2005. In situ probing of Xylella fastidiosa in honeydew of a xylem sap-feeding insect using 16S rRNA-targeted fluorescent oligonucleotides. Environ. Microbiol. 8:747-754.
Fiore MF, BA Neilan, JN Copp, JLM Rodrigues, SM Tsai, H Lee, JT Trevors. 2005. Characterization of nitrogen-fixing cyanobacteria in the Brazilian Amazon floodplain. Water Res. 39:5017-5026.
Silva-Stenico ME, FTH Pacheco, E Carilho, JLM Rodrigues, SM Tsai. 2005. Growth and siderophore production of Xylella fastidiosa under iron-limited conditions. Microbiol. Res. 160:429-436.
Tiedje JM, TV Tsoi, KD Pennel, LD Hansen, A Wani, JLM Rodrigues, Y Hrywna, DP Howell. 2005. Enhancing PCB Bioremediation. p.147-214. In Bioremediation of Recalcitrant Compounds. CRC, Boca Raton, FL.
Rodrigues JLM, ME Silva-Stenico, JE Gomes, JRS Lopes, SM Tsai. 2003. Diversity and detection assessment of Xylella fastidiosa through 16S rRNA and gyrB sequences in field-collected plant and insect samples. Appl. Environ. Microbiol. 69:4249-4255
Denef VJ, J Park, JLM Rodrigues, TV Tsoi, SA Hashshan, JM Tiedje. 2003. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ. Microbiol. 5:933-943.
Rodrigues JLM, MR Aiello, JW Urbance, TV Tsoi, JM Tiedje. 2002. Use of both 16S rRNA and engineered functional genes with real time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil. J. Microbiol. Methods 51:181-189.
Rodrigues JLM, O Maltseva, TV Tsoi, R Helton, JF Quensen III, M Fukuda, JM Tiedje. 2001. Development of a Rhodococcus recombinant strain for degradation of products from anaerobic dechlorination of Aroclor 1242. Environ. Sci. & Techn. 35:663-668.
Rodrigues JLM, M Melotto, JTA Oliveira, JAG da Silveira. 1998. Efficiency of soybean nodules in relation to nodulin activities and hydrogenase expression. Brazilian J. Plant Physiol. 10:173-178.
Rodrigues JLM, M Melotto, JAG da Silveira. 1998. Nodulin activies, hydrogenase expression and nitrogen fixation in cowpea inoculated with Hup+ and Hup- symbionts. Brazilian J. Plant Physiol. 10:85-90.
Silveira JAG, JL Contado, JLM Rodrigues, JTA Oliveira. 1998. Phosphoenolpyruvate carboxylase and glutamine synthetase activities in relation to nitrogen fixation in cowpea nodules. Brazilian J. Plant Physiol. 10:19-23.
Rodrigues JLM and Pellizari, VH 1997. Biodegradation of PCBs. In Melo, I.S. de & Azevedo, J.L. de. Microbiologia Ambiental. EMBRAPA. Jaguariuna, SP. 438p.
Rodrigues JLM. 1993. PEP carboxylase and glutamine synthatase nodulins: their relationship with symbiotic N2 fixation efficiency in cowpea and soybean inoculated with Bradyrhizobium japonicum. M.Sc. Thesis. University of São Paulo.
Machado EC, JAG da Silveira, VA Vitorello, JLM Rodrigues. 1992. Photosynthesis, reserves remobilization and grain growth of two maize hybrids submitted to water stress during the grain filling stage. Bragantia. 51:151-159.
