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Josh D. Neufeld

Associate Professor

Josh D. NeufeldBachelor of Science (BSc), Master of Science (MSc) McGill, Doctor of Philosophy (PhD) UBC

Email: jneufeld@uwaterloo.ca

Telephone: (519) 888-4567 ext. 38344

Office: Biology 1 275

Lab: B1 167, ext. 38346

Research Group: Neufeld Research Group

Research interests

Microbial communities are responsible for the biogeochemical cycling of trace gases, fertility of soils and aquatic environments, healthy function of the human body, metabolic production for the food industry, and countless applications in biotechnology. Despite a profound influence of microorganisms on human life and the global climate, very little is known about the distribution and diversity of microorganisms in natural communities, the vast resource of genes associated with the majority of uncultured microbial life, and the identities of most microbial species on earth: those adapted to life at low abundance.

Stable isotope probingThe Neufeld lab is actively involved in research that spans three complementing research areas:

1. Microbial diversity and ecology: My lab seeks to understand the causes of microbial diversity, the importance of diversity for ecosystem function, and the relationship between taxonomic and functional diversity. Environmental sandboxes will include the great lakes, agricultural soils, and the arctic tundra. Recent work has shown that extreme arctic tundra soils harbour some of the most diverse microbial communities on earth: why is that and what will be the impact of global warming on these communities?

2. Carbon and nitrogen cycling in the environment: New organisms and pathways involved in carbon and nitrogen cycling are continually being discovered in soil and aquatic environments. By combining stable isotope probing and metagenomics, my lab seeks to better understand the organisms and pathways involved in carbon and nitrogen transformations in different environments and under changing conditions. The analysis of selected model organisms will complement and confirm exploration and discovery using cultivation-independent techniques.

Metagenomics in Dr. Neufeld's lab3. Revealing the rare biosphere: Most microbial species exist at low abundance, resist cultivation, and have escaped detection by DNA-based analyses. These organisms are likely contributors to community stability and function, and represent an enormous pool of uncharacterised genes and enzymes, useful for medical and industrial applications. We are developing new molecular methods to identify and characterise these low-abundance organisms.

If you are interested in pursuing graduate work in this exciting area of environmental microbiology, please contact me at my email address.

Publications

  • Sonthiphand P, Cejudo E, Schiff S, Neufeld JD. 2013. Wastewater effluent impacts ammonia-oxidizing prokaryotes of the Grand River, Canada. Appl. Environ. Microbiol. In press.

  • Zamanzadeh M, Parker WJ, Verastegui Y, Neufeld JD. 2013. Biokinetic and molecular studies of methanogens in phased anaerobic digestion systems. Bioresour. Technol. In press.

  • Duguma D, Rugman-Jones P, Kaufman MG, Hall M, Neufeld JD, Stouthamer R, Walton WE. 2013. Bacterial communities associated with Culex mosquito larvae and two emergent aquatic plants of bioremediation importance. PLoS ONE. In press.

  • Lynch MDJ, Masella AP, Hall MW, Bartram AK, Neufeld JD. 2013. AXIOME: automated exploration of microbial diversity. GigaScience. In press.

  • Sonthiphand P, Neufeld JD. 2013. Evaluating primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments. PLoS ONE. In press.

  • Zamanzadeh M, Parker WJ, Verastegui Y, Neufeld JD. 2013. Biokinetics and bacterial communities of propionate oxidizing bacteria in phased anaerobic sludge digestion systems. Water Res. In press.

  • Engel K et al. 2013. Meeting Report: 1st International Functional Metagenomics Workshop May 7–8, 2012, St. Jacobs, Ontario, Canada. Stand Genomic Sci. doi:10.4056/sigs.3406845

  • Barret M, Gagnon, N, Kalmokoff M, Topp E, Verastegui Y, Brooks SPJ, Matias F, Neufeld JD, Talbot G. 2012. Identification of Methanoculleus spp. as active methanogens during anoxic incubations of swine manure storage tank samples. Appl. Environ. Microbiol. In press.

  • Sauder LA, Peterse F, Schouten S, Neufeld JD. 2012. Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant. Environ. Microbiol. 14:2589-2600.

  • Lynch MDJ, Bartram AK, Neufeld JD. 2012. Targeted recovery of novel phylogenetic diversity from next-generation sequence data. ISME J. In press.

  • Masella AP, Bartram AK, Brown DG, Truszkowski JM, Neufeld JD. 2012. PANDAseq: Paired-eND Assembler for Illumina sequences. BMC Bioinformatics. 13:31.
  • Jansson J, Neufeld JD, Moran MA, Gilbert JA. 2012. Omics for understanding microbial functional dynamics. Environ. Microbiol. Rep. 14:1-3.
  • Stearns JC, Lynch MDJ, Senadheera DB, Tenenbaum HC, Goldberg MB, Cvitkovitch DG, Croitoru K, Moreno-Hagelsieb G, Neufeld JD. 2011. Bacterial biogeography of the human digestive tract. Sci. Rep. 1:170.
  • Kristiansen A, Lindholst S, Feilberg A, Nielsen PH, Neufeld JD, Nielsen JL. 2011. Butyric acid and dimethyl disulfide assimilating microorganisms in a biofilter treating air emissions from a livestock facility. Appl. Environ. Microbiol. 77:8595-8604.
  • Engel K, Pinnell L, Cheng J, Charles TC, Neufeld JD. 2011. Nonlinear electrophoresis for purification of soil DNA for metagenomics. J. Microbiol. Meth. 88:35-40.
  • Neufeld JD, Engel K, Cheng J, Moreno-Hagelsieb G, Rose DR, Charles TC. 2011. Open resource metagenomics: a model for sharing metagenomic libraries. Stand Genomic Sci. 5:203-210.
  • Avrahami S, Jia Z, Neufeld JD, Murrell JC, Conrad R, Küsel K. 2011. Active autotrophic ammonia oxidizing prokaryotes from simulated stream biofilms respond to temperature manipulation under two ammonium loads. Appl. Environ. Microbiol. 77:7329-7338.
  • Moore T, Xing Y, Lazenby B, Lynch MDJ, Schiff S, Robertson W, Timlin R, Lanza S, Ryan MC, Aravena R, Fortin D, Clark I, Neufeld JD. 2011. Prevalence of anaerobic ammonium-oxidizing bacteria in contaminated groundwater. Environ. Sci. Technol. 45:7217-7225.
  • Sauder L, Engel K, Stearns JC, Masella AP, Pawlizyn R, Neufeld JD. 2011. Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters. PLoS ONE. 6:e23281.
  • Robertson WD, Moore T, Spoelstra J, Li L, Elgood R, Clark ID, Schiff SL, Aravena R, Neufeld JD. 2011. Natural attenuation of septic system nitrogen by anammox. Ground Wat. 50:541-553.
  • Chu H, Neufeld JD, Walker VK, Grogan P. 2011. The influence of vegetation type on the dominant soil bacteria, archaea and fungi in a low Arctic tundra landscape. Soil. Sci. Soc. Am. J. 75:1756-1765.
  • Yilmaz P et al. 2011. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol. 29:415-420.
  • Bartram A, Lynch MDJ, Stearns JC, Moreno-Hagelsieb G, Neufeld JD. 2011. Generation of multi-million 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl. Environ. Microbiol. 77:3846-3852.
  • Dunford E, Neufeld JD. 2010. DNA Stable-Isotope Probing (DNA-SIP). J Vis. Exp. e2027.
  • Pinnell LJ, Charles TC, Neufeld JD. 2010. Stable-isotope probing and metagenomics. Stable Isotopes in Microbial Molecular Ecology. Whiteley A, Murrell JC (Eds.) ASM Press.
  • Chen Y, Dumont MG, Neufeld JD, McNamara NP, Murrell JC. 2010. Towards “focused metagenomics”:a case study combining DNA stable-isotope probing, multiple displacement amplification and metagenomics. Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. de Bruijn FJ (Ed.) Wiley/Blackwell.
  • Chen Y, Neufeld JD, Dumont MG, Friedrich M, Murrell JC. 2010. Enrichment strategies for focusing metagenomic libraries on active community members. Molecular Methods in Metagenomics. Streit WR, Daniels W (Eds.)
  • Leigh MB, Taylor L, Neufeld JD. 2010. Clone libraries of ribosomal RNA gene sequences for characterization of bacterial and fungal communities. Hydrocarbon Microbiology. Timmis K (Ed.) Springer Berlin Heidelberg. pp. 3969-3993.
  • Gilbert JA, Zhang K, Neufeld JD. 2010. Multiple displacement amplification. Hydrocarbon Microbiology. Timmis K (Ed.) Springer Berlin Heidelberg. pp. 4255-4263.
  • Green SJ, Leigh MB, Neufeld JD. 2010. Denaturing gradient gel electrophoresis (DGGE) for microbial community analysis. Hydrocarbon Microbiology. Timmis K (Ed.) Springer Berlin Heidelberg. pp. 4137-4158.
  • Bartram AK, Poon C, Neufeld JD. 2009. Nucleic acid contamination of glycogen used in nucleic acid precipitation and assessment of linear polyacrylamide as an alternative co-precipitant. Biotechniques. 47:1019–1022.
  • Moussard H, Stralis-Pavese N, Neufeld JD, Murrell JC. 2009. Identification of active methylotrophic bacteria inhabiting surface sediment of a marine estuary. Environ. Microbiol. Rep. 1:424-433.
  • Chen Y, Dumont MG, Neufeld JD, Bodrossy L, Stralis-Pavese N, McNamara N, Ostle N, Briones MJI, Murrell JC. 2008. Revealing the uncultivated majority:  combining DNA stable-isotope probing, mulitple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands. Environ. Microbiol. 10:2609-2622.
  • Neufeld JD, Moussard H, Murrell JC, Schäfer H. 2008. Substrate-specific clades of active marine methylotrophs associated with a phytoplankton bloom in a temperate coastal environment. Appl. Environ. Microbiol. 74:7321-7328.
  • Jensen S, Neufeld JD,Birkeland NK, Hovland M, Murrell JC. 2008. Methane assimilation and trophic interactions with marine Methylomicrobium in deep-water coral reef sediment off the coast of Norway. FEMS Microbiol. Ecol. 66:320-330.
  • Jensen S, Neufeld JD, Hovland M, Murrell JC. 2008. Insight into the microbial community structure of a Norwegian deep-water coral reef environment. Deep Sea Res. 55:1554-1563.
  • Neufeld JD, Li J, Mohn WW. 2008. Scratching the surface of the rare biosphere with ribosomal sequence tag primers. FEMS Microbiol. Lett. 283:146-153.
  • Binga E, Lasken R, Neufeld JD. 2008. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J. 2:233-241.
  • Neufeld JD, Chen Y, Dumont MG, Murrell JC. 2008. Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ. Microbiol. 10:1526-1535.
  • Neufeld JD, Schäfer H, Boden R, Murrell JC. 2007. Stable isotope probing of the marine environment implicates Methylophaga and uncultured Gammaproteobacteria in the consumption of methanol and methylamine. ISME J. 1:480-491.
  • Neufeld JD, Murrell JC. 2007. Witnessing the last supper of uncultivated microbial cells with Raman-FISH. ISME J. 1:269-270.
  • Neufeld JD, Wagner M, Murrell JC. 2007. Who eats what, where and when? Isotope-labelling experiments are coming of age. ISME J. 1:103-110.
  • Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich M, Murrell JC. 2007. DNA stable isotope probing. Nature Protocols. 2:860-866.
  • Booth T, Gilbert J, Neufeld JD, Ball J, Thurston M, Chipman K, Joint I, Field D. 2007. Handlebar:A flexible, web-based inventory manager for handling barcoded samples. Biotechniques. 42:300-302.
  • Neufeld JD, Dumont MG, Vohra J, Murrell JC. 2007. Methodological considerations for the application of stable isotope probing in microbial ecology. Microbiol. Ecol. 53:435-442.
  • Dumont MG, Neufeld JD, Murrell JC. 2006. Isotopes as tools for microbial ecologists. Curr. Opin. Biotech. 17:57-58.
  • Neufeld JD, de Lorenzo V, Mohn WW. 2006. Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. Environ. Microbiol. 8:126-140.
  • Mohn WW, Mertens B, Neufeld JD, de Lorenzo V. 2006. Distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from Spain. Environ. Microbiol. 8:60-68.
  • Neufeld JD, Mohn WW. 2006. Assessment of microbial phylogenetic diversity based on environmental nucleic acids. In Molecular Identification, Systematics, and Population Structure of Prokaryotes. Stackebrandt (Ed.) Heidelberg: Springer-Verlag, pp. 219-260.
  • Neufeld JD, Mohn WW. 2005. Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed with serial analysis of ribosomal sequence tags. Appl. Environ. Microbiol. 71:5710-5718.
  • Neufeld JD, Mohn WW. 2005. Fluorophore-labeled primers improve the sensitivity, versatility, and normalization of denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 71:4893-4896.
  • Neufeld JD, Yu Z, Lam W, Mohn WW. 2004. SARST, Serial Analysis of Ribosomal Sequence Tags. In Molecular Microbial Ecology Manual (MMEM), 2nd edition. Kowalchuk, GA, de Bruijn, FJ, Head, IM, Akkermans, AD, and van Elsas, JD (Eds.) London:Kluwer Academic Publishing, pp. 543-568.
  • Leckie SE, Prescott CE, Grayston SJ, Neufeld JD, Mohn WW. 2004. Characterization of humus microbial communities in two adjacent forest types that differ in nitrogen availability. Microb. Ecol. 48:29-40.
  • Neufeld JD, Yu Z, Lam W, Mohn WW. 2004. Serial analysis of ribosomal sequence tags (SARST):a high-throughput method for profiling complex microbial communities. Environ. Microbiol. 6:131-144.
  • Leckie SE, Prescott CE, Grayston SJ, Neufeld JD, Mohn WW. 2004. Comparison of chloroform fumigation-extraction, phospholipid fatty acid, and DNA methods to determine microbial biomass in forest humus. Soil Biol. Biochem. 36:529-532.
  • Neufeld JD, Driscoll BT, Knowles R, Archibald FS. 2001. Quantifying functional-gene populations:a comparison of gene abundance and corresponding enzymatic activity using denitrification and nitrogen fixation in pulp and paper mill effluent treatment systems. Can. J. Microbiol. 47:925-934.
  • Gauthier F, Neufeld JD, Driscoll BT, Archibald FS. 2000. Coliform bacteria and nitrogen fixation in pulp and paper mill effluent treatment systems. Appl. Environ. Microbiol. 66:5155-5160.
  • Neufeld JD, Knowles R. 1999. Inhibition of nitrifiers and methanotrophs from an agricultural humisol by allylsulfide and its implications for environmental studies. Appl. Environ. Microbiol. 65:2461-2465.
Affiliation: 
University of Waterloo

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