University of California - Davis :: Department of Land, Air, and Water Resources

Publications


2017

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.

Ma B, Z Dai, H Wang, M Dsouza, X Liu, Y He, J Wu,  JLM Rodrigues, J Gilbert, P Brookes, and 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.  DOI: 10.1111/mec.14011


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 AndreoteLFW 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 BohannanJM 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, and 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, and VH Pellizari. 2014. Land use change alters functional gene diversity, composition, and abundance in Amazon forest soil microbial communties. Mol. Ecol. 23:2988-2999.

ISME  Mueller RC , FS Paula, BS Mirza, JLM Rodrigues, K Nusslein, and BJM Bohannan. 2014. Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest. The ISME J. 8:1548-1550.

Mirza B, C Potisap, K Nusslein, BJM Bohannan, and JLM Rodrigues. 2013. 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, and 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.

2013

Rodrigues JLM and J Isanapong. 2013. The family Opitutaceae. The Prokaryotes. 4th Edition. Springer, Singapore.

ISME  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.

PNAS  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)

2012

PNAS  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.


Previous Years

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.

PNAS  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.

NRlogo 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, and 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.

  Plant and Environmental Sciences Building, room 3308, University of California - Davis, CA, 95616