Bing-Bing Li, Sarah S. Roley, David S. Duncan, Jiarong Guo, John F. Quensen, Han-Qing Yu, and James M. Tiedje. 2021. Long-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analyses. Soil Biology & Biochemistry. 160, 108349. doi:

Zhang, B., C. R. Penton, Z. Yu, C. Xue, Q. Chen, Z. Chen, C. Yan, Q. Zhang, M. Zhao, J. F. Quensen and J. M. Tiedje. 2021. A new primer set for Clade I nosZ that recovers genes from a broader range of taxa. Biology and Fertility of Soils. 57:523–531: doi: 10.1007/s00374-021-01544-6.

Guo, J.,  J. F. Quensen, Y. Sun, Q. Wang, C. T. Brown, J. R. Cole and J. M. Tiedje . 2019. Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes. Frontiers in Genetics 10 (957). doi:10.3389/fgene.2019.00957.

Gomes, E. A., U. G. P. Lana, J.F. Quensen, S.M. de Sousa, Z.M. Oliveira, J. Guo, L. J. M. Guimarães, and J.M. Tiedje. 2018.  Root-associated microbiome of maize genotypes with contrasting phosphorus use efficiency. Phytobiomes.

Stedtfeld, Robert, Tiffany Stedtfeld, Kelly Fader, Maggie Williams, Prianca Bhaduri, John Quensen, Timothy Zacharewski, James Tiedje, Syed Hashsham. 2017.  TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome. FEMS Microbiology Ecology 93(5): doi: 10.1093/femsec/fix058.

Zheng, Bangzhou, C. Ryan Penton, Chao Xue, John F. Quensen, Sarah S. Roley, Jiarong Guo, Aaron Garoutte, Tianling Zheng, and James. M. Tiedje. 2017. Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems. Soil Biology & Biochemistry 112:140-152.

Jesus, E., C. Liang, J. F. Quensen, E. Susilawati, R. D. Jackson, T. C. Balser, and J. M. Tiedje. 2016. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States. Global Change Biology Bioenergy 8:481-494.

Liang, C., E. d. C. Jesus, D. S. Duncan, J. F. Quensen, R. D. Jackson, T. C. Balser, and J. M. Tiedje. 2016. Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA. Soil Biology & Biochemistry 94:173-180.

Zhu, Y.-G., J.-Q. Su, Z. Cao, K. Xue, J. Quensen, G.-X. Guo, Y.-F. Yang, J. Zhou, H.-Y. Chu, and J. M. Tiedje. 2016. A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation. Science Bulletin 61:1052-1060.

Su, J.-Q., L.-J. Ding, K. Xue, H.-Y. Yao, J. Quensen, S.-J. Bai, W.-X. Wei, J.-J. Wu, J. I. Zhou, J. M. Tiedje, and Y.-G. Zhu. 2015. Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil. Molecular Ecology 24:136-150.

Zaborin, A., D. Smith, K. Garfield, J. Quensen, B. Shaksheer, M. Kade, M. Tirrell, J. Tiedje, J. A. Gilbert, O. Zaborina, and J. C. Alverdy. 2014. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness, mBio, vol. 5, Issue:5, Article Number: e01361-14.

Yang, J. Quensen, J. Mathieu, Q. Wang, J. Wang, M. Li, J. M. Tiedje, P. J. J. Alvarez. 2013. Pyrosequencing reveals higher impact of silver nanoparticles than Ag(+) on the microbial community structure of activated sludge. Water Research 10/2013.

Jin, W. Bothfeld, S. Austin, T. K. Sato, A. La Reau, H. Li, M. Foston, C. Gunawan, R. D. Leduc, J. F. Quensen, A. Higbee, R. Ranatunga, C. W. Donald, G. Bone, A. J. Ragauskas, J. M. Tiedje, D. R. Noguera, B. E. Dale, Y. Zhang, V. Balan. 2013. Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate. Bioresource technology 08/2013; 147C:212-220.

Wang, J. F. Quensen, J. A. Fish, T. K. Lee, Y. Sun, J. M. Tiedje, J. R. Cole. 2013. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. mBio 01/2013; 4(5).

Penton, C. R., T. A. Johnson, J. F. Quensen, S. Iwai, J. R. Cole, J. M. Tiedje. 2013. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. Frontiers in microbiology. 01/2013; 4:279.

He, R., M. J. Wooller, J. W. Pohlman, C. Catranis, J. Quensen, J. M. Tiedje, and M. B. Leigh. 2012. Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing. Environmental Microbiology 14:1403-1419.

He, R., M. J. Wooller, J. W. Pohlman, J. Quensen, J. M. Tiedje, and M. B. Leigh. 2012. Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments. ISME Journal 6:1937-1948.

He, R., M. J. Wooller, J. W. Pohlman, J. Quensen, J. M. Tiedje, and M. B. Leigh. 2012. Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes. Applied and Environmental Microbiology 78:4715-4723.

Rosenzweig, N., J. M. Tiedje, J. F. Quensen, Q. X. Meng, and J. J. J. Hao. 2012. Microbial communities associated with potato common scab-suppressive soil determined by pyrosequencing analyses. Plant Disease 96:718-725.

Sul, W. J., J. Park, J. F. Quensen, J. L. M. Rodrigues, L. Seliger, T. V. Tsoi, G. J. Zylstra, and J. M. Tiedje. 2009. DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Applied and Environmental Microbiology 75:5501-5506.

Tsuneta, T., R. Loch-Caruso, J. F. Quensen, S. A. Boyd, M. Hanna, and C. Grindatti. 2008. Stimulatory effects of a microbially dechlorinated polychlorinated biphenyl (PCB) mixture on rat uterine contraction in vitro. Environmental Research 107:185-193.

Parnell, J. J., J. Park, V. Denef, T. Tsoi, S. Hashsham, J. Quensen, and J. A. Tiedje. 2006. Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress. Applied and Environmental Microbiology 72:6607-6614.

Rodrigues, J. L. M., C. A. Kachel, M. R. Aiello, J. F. Quensen, O. V. Maltseva, T. V. Tsoi, and J. M. Tiedje. 2006. Degradation of Aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp strain RHA1(fcb). Applied and Environmental Microbiology 72:2476-2482.

Magar, V. S., R. C. Brenner, G. W. Johnson, and J. F. Quensen. 2005. Long-term recovery of PCB-contaminated sediments at the Lake Hartwell superfund site: PCB dechlorination. 2. Rates and extent. Environmental Science & Technology 39:3548-3554.

Magar, V. S., G. W. Johnson, R. C. Brenner, J. F. Quensen, E. A. Foote, G. Durell, J. A. Ickes, and C. Peven-McCarthy. 2005. Long-term recovery of PCB-contaminated sediments at the Lake Hartwell superfund site: PCB dechlorination. 1. End-member characterization. Environmental Science & Technology 39:3538-3547.

Goris, J., P. De Vos, J. Caballero-Mellado, J. Park, E. Falsen, J. F. Quensen, J. M. Tiedje, and P. Vandamme. 2004. Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400(T) and relatives as Burkholderia xenovorans sp nov. International Journal of Systematic and Evolutionary Microbiology 54:1677-1681.

Smithwick, L. A., J. F. Quensen, A. Smith, D. T. Kurtz, L. London, and P. J. Morris. 2004. The inhibition of LPS-induced splenocyte proliferation by ortho-substituted and microbially dechlorinated polychlorinated biphenyls is associated with a decreased expression of cyclin D2. Toxicology 204:61-74.

Smithwick, L. A., A. Smith, J. F. Quensen, A. Stack, L. London, and P. J. Morris. 2003. Inhibition of LPS-induced splenocyte proliferation by orthosubstituted polychlorinated biphenyl congeners. Toxicology 188:319-333.

Bae, J., M. A. Mousa, J. F. Quensen, S. A. Boyd, and R. Loch-Caruso. 2001. Stimulation of contraction of pregnant rat uterus in vitro by non-dechlorinated and microbially dechlorinated mixtures of polychlorinated biphenyls. Environmental Health Perspectives 109:275-282.

Michel, F. C., J. Quensen, and C. A. Reddy. 2001. Bioremediation of a PCB-contaminated soil via composting. Compost Science & Utilization 9:274-284.

Quensen, J. F., J. M. Tiedje, M. K. Jain, and S. A. Mueller. 2001. Factors controlling the rate of DDE dechlorination to DDMU in Palos Verdes margin under anaerobic conditions. Environmental Science & Technology 35:286-291.

Rodrigues, J. L. M., O. V. Maltseva, T. V. Tsoi, R. R. Helton, J. F. Quensen, M. Fukuda, and J. M. Tiedje. 2001. Development of a Rhodococcus recombinant strain for degradation of products from anaerobic dechlorination of PCBs. Environmental Science & Technology 35:663-668.

Ganey, P. E., J. F. Quensen, M. A. Mousa, S. A. Boyd, M. A. Wagner, and L. J. Fischer. 2000. Biological activity associated with noncoplanar polychlorinated biphenyls after microbial dechlorination of Aroclor 1242((R)) and Aroclor 1254((R)). Environmental Toxicology and Chemistry 19:1311-1316.

Hrywna, Y., T. V. Tsoi, O. V. Maltseva, J. F. Quensen, and J. M. Tiedje. 1999. Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls. Applied and Environmental Microbiology 65:2163-2169.

Maltseva, O. V., T. V. Tsoi, J. F. Quensen, M. Fukuda, and J. M. Tiedje. 1999. Degradation of anaerobic reductive dechlorination products of Aroclor 1242 by four aerobic bacteria. Biodegradation 10:363-371.

Ye, D. Y., J. F. Quensen, J. M. Tiedje, and S. A. Boyd. 1999. 2-bromoethanesulfonate, sulfate, molybdate, and ethanesulfonate inhibit anaerobic dechlorination of polychlorobiphenyls by pasteurized microorganisms. Applied and Environmental Microbiology 65:327-329.

Zwiernik, M. J., J. F. Quensen, and S. A. Boyd. 1999. Residual petroleum in sediments reduces the bioavailability and rate of reductive dechlorination of Aroclor 1242. Environmental Science & Technology 33:3574-3578.

Mousa, M. A., P. E. Ganey, J. F. Quensen, B. V. Madhukar, K. Chou, J. P. Giesy, L. J. Fischer, and S. A. Boyd. 1998. Altered biologic activities of commercial polychlorinated biphenyl mixtures after microbial reductive dechlorination. Environmental Health Perspectives 106:1409-1418.

Quensen, J. F., M. A. Mousa, S. A. Boyd, J. T. Sanderson, K. L. Froese, and J. P. Giesy. 1998. Reduction of aryl hydrocarbon receptor-mediated activity of polychlorinated biphenyl mixtures due to anaerobic microbial dechlorination. Environmental Toxicology and Chemistry 17:806-813.

Quensen, J. F., S. A. Mueller, M. K. Jain, and J. M. Tiedje. 1998. Reductive dechlorination of DDE to DDMU in marine sediment microcosms. Science 280:722-724

Zwiernik, M. J., J. F. Quensen, and S. A. Boyd. 1998. FeSO4 amendments stimulate extensive anaerobic PCB dechlorination. Environmental Science & Technology 32:3360-3365.

Angus, W. G. R., M. A. Mousa, V. M. Vargas, J. F. Quensen, S. A. Boyd, and M. L. Contreras. 1997. Inhibition of L-aromatic amino acid decarboxylase by polychlorinated biphenyls. Neurotoxicology 18:857-867.

Quensen, J. F., and D. S. Woodruff. 1997. Associations between shell morphology and land crab predation in the land snail Cerion. Functional Ecology 11:464-471

Mousa, M. A., J. F. Quensen, K. Chou, and S. A. Boyd. 1996. Microbial dechlorination alleviates inhibitory elects of PCBs on mouse gamete fertilization in vitro. Environmental Science & Technology 30:2087-2092.

Pellizari, V. H., S. Bezborodnikov, J. F. Quensen, and J. M. Tiedje. 1996. Evaluation of strains isolated by growth on naphthalene and biphenyl for hybridization of genes to dioxygenase probes and polychlorinated biphenyl-degrading ability. Applied and Environmental Microbiology 62:2053-2058.

Yadav, J. S., J. F. Quensen, J. M. Tiedje, and C. A. Reddy. 1995. Degradation of polychlorinated biphenyl mixtures (Aroclor-1242, Aroclor-1254, Aroclor-1260) by the white-rot fungus Phanerochaete-chrysosporium as evidenced by congener-specific analysis. Applied and Environmental Microbiology 61:2560-2565.

Ye, D. Y., J. F. Quensen, J. M. Tiedje, and S. A. Boyd. 1995. Evidence for para dechlorination of polychlorobiphenyls by methanogenic bacteria. Applied and Environmental Microbiology 61:2166-2171.

Morris, P. J., J. F. Quensen, J. M. Tiedje, and S. A. Boyd. 1993. An assessment of the reductive debromination of polybrominated biphenyls in the Pine River reservoir. Environmental Science & Technology 27:1580-1586.

Griffith, G. D., J. R. Cole, J. F. Quensen, and J. M. Tiedje. 1992. Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile-tiedjei in D2O. Applied and Environmental Microbiology 58:409-411.

Morris, P. J., W. W. Mohn, J. F. Quensen, J. M. Tiedje, and S. A. Boyd. 1992. Establishment of a polychlorinated biphenyl-degrading enrichment culture with predominantly metadechlorination. Applied and Environmental Microbiology 58:3088-3094.

Morris, P. J., J. F. Quensen, J. M. Tiedje, and S. A. Boyd. 1992. Reductive debromination of the commercial polybrominated biphenyl mixture Firemaster BP6 by anaerobic microorganisms from sediments. Applied and Environmental Microbiology 58:3249-3256.

Ye, D. Y., J. F. Quensen, J. M. Tiedje, and S. A. Boyd. 1992. Anaerobic dechlorination of polychlorobiphenyls (Aroclor-1242) by pasteurized and ethanol-treated microorganisms from sediments. Applied and Environmental Microbiology 58:1110-1114.

Quensen, J. F., S. A. Boyd, and J. M. Tiedje. 1990. Dechlorination of 4 commercial polychlorinated biphenyl mixtures (Aroclors) by anaerobic microorganisms from sediments. Applied and Environmental Microbiology 56:2360-2369.

Quensen, J. F., J. M. Tiedje, and S. A. Boyd. 1988. Reductive dechlorination of polychlorinated-biphenyls by anaerobic microorganisms from sediments. Science 242:752-754.

Oh, S. Y., J. Quensen, F. Matsumura, and H. Momose. 1985. Transformation of Bacillus-subtilus with DNA-encoding naphthalene degradation from Bacillus-megaterium. Environmental Toxicology and Chemistry 4:21-27.

Quensen, J. F., and F. Matsumura. 1984. Transfer of degradative capabilities – Bacillus-subtilis to Bacillus-megateriaum by plasmid transfer techniques. ACS Symposium Series 259:327-341.