Selected Publications

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RE Garner, SA Kraemer, VE Onana, M Fradette, MP Varin, Y Huot, DA Walsh (2023) A genome catalogue of lake bacterial diversity and its drivers at continental scale. Nature Microbiology, 1-15

MÈ Monchamp, ZE Taranu, RE Garner, T Rehill, O Morissette, LL Iversen, V Fugere, JE Littlefair, N Barbosa da Costa, JE Desforges, JR Sánchez Schacht, AM Derry, SJ Cooke, RDH Barrett, DA Walsh, J Ragoussis, M Albert, ME Cristescu, I Gregory-Eaves (2023). Prioritizing taxa for genetic reference database development to advance inland water conservation. Biological Conservation 280, 109963

S Simpson, V Bettauer, A Ramachandran, S Kraemer, S Mahon, M Medina, Y Vallès, V Dumeaux, H Vallès, D Walsh, MT Hallett (2023). A metagenomic-based study of two sites from the Barbadian reef system. Coral Reefs 42 (2), 359-366

A Oliva, VE Onana, RE Garner, SA Kraemer, M Fradette, DA Walsh, Y Huot (2023). Geospatial analysis reveals a hotspot of fecal bacteria in Canadian prairie lakes linked to agricultural non-point sources. Water Research 231, 119596

T Grevesse, C Guéguen, VE Onana, DA Walsh (2023). Degradation pathways for organic matter of terrestrial origin are widespread and expressed in Arctic Ocean microbiomes. Microbiome 10 (1), 237

MÈ Monchamp, DA Walsh, RE Garner, SA Kraemer, BE Beisner, ME Cristescu, I Gregory‐Eaves (2023). Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis? Environmental DNA 4 (6), 1250-1264

Garner R.E., Kraemer S.A., Onana V.E., Huot Y., Gregory-Eaves I., Walsh D.A. (2022). Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale. mSystems. 7:316

Gauthier J., Walsh D.A., Selbie D.T., Domaizon I., Gregory-Eaves I. (2022). Sedimentary DNA of a human-impacted lake in Western Canada (Cultus Lake) reveals changes in microeukaryotic diversity over the past~ 200 years. Environmental DNA.

Oliva A., Garner R.E., Walsh D., Huot Y. (2022). The occurrence of potentially pathogenic fungi and protists in Canadian lakes predicted using geomatics, in situ and satellite-derived variables: Towards a tele-epidemiological approach. Water Research. 209:117935

MacKeigan P.W., Garner R.E., Monchamp, Walsh D.A., Onana V.E., Kraemer S.A., Pick F.R., Beisner B.E., Agbeti M.D., Barbosa da Costa N., Shapiro B.J., Gregory-Eaves I. (2022). Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes. Harmful Algae. 113:102187

O’Malley M. and Walsh D.A. (2021) Rethinking microbial infallibility in the metagenomics era. FEMS Microbial Ecology 97: fiab092

Kieft K., Zhou Z., Anderson R.E., Buchan A., Campbell B.J., Hallam S.J., Hess M, Sullivan M.B., Walsh D.A., Roux S., Anantharaman K. (2021) Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature Communications 12:3503

Ramachandran A. McLatchie, S. and Walsh D.A. (2021) A novel freshwater to marine evolutionary transition revealed within Methylophilaceae bacteria from the Arctic Ocean. mBio 12: e01306-21

Gauthier J., Walsh D.A., Selbie D.T., Bourgeois A., Griffiths K., Domaizon I., Gregory-Eaves I.
(2021) Evaluating the congruence between DNA-based and morphological taxonomic approaches in water and sediment trap samples: Analyses of a 36-month time series from a temperate monomictic lake. Limnology and Oceanography

Leclerc M., Harrison M.C., Storck V., Planas D., Amyot M., and Walsh D.A. (2021) Microbial diversity and mercury methylation activity in periphytic biofilms at a run-of-river hydroelectric dam and constructed wetlands. mSphere 6: e00021-21

Garner RE, Gregory-Eaves I, Walsh DA. (2020) Sediment Metagenomes as Time Capsules of Lake Microbiomes. MSphere 5:00512-20

Kraemer SA, da Costa NB. Shapiro BJ, Fradette M, Huot Y, Walsh DA. (2020). A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities. The ISME Journal, 1-13

Cui TT, Dawson TJ, McLatchie S. Dunn K, Bielawski J, Walsh DA. (2020) Modelling Free-Living and Particle-Associated Bacterial Assemblages across the Deep and Hypoxic Lower St. Lawrence Estuary. mSphere 5:3

Schulz F, Roux S, Paez-Espino D. Jungbluth S, Walsh DA, Denef VJ, McMahon KD, Konstantinidis KT, Eloe-Fadrosh EA, Kyrpides NC, Woyke T. (2020) Giant virus diversity and host interactions through global metagenomics. Nature 578:432

Fasching C, Akotoye C, Bižić M, Fonvielle J, Ionescu D, Mathavarajah S, Zoccarato L, Walsh DA, Grossart HP, Xenopoulos MA. (2020) Linking stream microbial community functional genes to dissolved organic matter and inorganic nutrients. Limnology and Oceanography 65:S71

Grossart HP, Massana R, McMahon KD, Walsh DA. (2020) Linking metagenomics to aquatic microbial ecology and biogeochemical cycles. Limnology and Oceanography 65:S2

Kraemer S, Ramachandran A, Colatriano D, Lovejoy C, Walsh DA. (2020) Diversity and biogeography of SAR11 bacteria from the Arctic Ocean. The ISME Journal 14:79

Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh DA, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NK (2019). Diversity, evolution, and classification of virophages uncovered through global metagenomics. Microbiome 7:157

Huot Y, Brown CA, Potvin G, Antoniades D, Baulch HM, Beisner BE, Bélanger S, Brazeau S, Cabana H, Cardille JA, del Giorgio PA, Gregory-Eaves I, Fortin M-J, Lang AS, Laurion I, Maranger R, Prairie YT, Rusak JA, Segura PA, Siron R, Smol JP, Vinebrooke RD ; David A Walsh DA. (2019) The NSERC Canadian Lake Pulse Network: A national assessment of lake health providing science for water management in a changing climate. Science of The Total Environment 695:133668

Hosseinpour B, Saborimanesh N, Yerushalmi L, Walsh DA, Mulligan CN. (2019) Start-up of oxygen-limited autotrophic partial nitrification-anammox process for treatment of nitrite-free wastewater in a single-stage hybrid bioreactor. Environmental Technology, 1-9

Saborimanesh N, Walsh DA, Yerushalmi L, EC Arriagada EC, Mulligan CN. (2019) Pilot-scale application of a single-stage hybrid airlift BioCAST bioreactor for treatment of ammonium from nitrite-limited wastewater by a partial nitrification/anammox process. Environmental Science and Pollution Research 26:25573

Saito M, Bertrand E, Duffy M, Gaylord D, Held N, Hervey J, Hettich R, Jagtap P, Janech M, Kinkade D, Leary D, McIlvin M, Moore E, Morris R, Neely B, Nunn B, Saunders J, Shepherd A, Symmonds N, Walsh D.A. (2019) Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. Journal of Proteome Research. 18:1461

Massé S, Botrel M, Walsh DA, Maranger R. (2019) Annual nitrification dynamics in a seasonally ice-covered lake. PLoS ONE. 14:3

Tran P, Ramachandran A, Khawesik O, Beisner BE, Rautio M, Huot Y, Walsh DA. (2018) Microbial life under ice: metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered lakes. Environmental Microbiology. 20:2568.

Colatriano D, Tran P, Guégeun C, Williams WJ, Lovejoy C, Walsh DA. (2018) Genomic evidence for the degradation of terrestrial organic matter by Arctic Ocean Chloroflexi bacteria. Communications Biology. 1:90

Ramachandran A and Walsh DA. (2015) Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems. FEMS Microbiol Ecology. 

Colatriano D, Ramachandran A, Yergeau E, Maranger R, Gélinas Y, Walsh DA. (2015) Metaproteomics of aquatic microbial communities in a deep and stratified estuary. Proteomics. 3566-79.

Thibodeau G, Walsh DA, Beisner BE. (2015) Rapid eco-evolutionary responses in perturbed phytoplankton communities. Proc Bio Sci.

Colatriano D. and Walsh DA. (2015) An aquatic microbial metaproteomics workflow: from cells to tryptic peptides suitable for tandem spectrometry-based analysis. J Vis Exp. 

Walsh DA. (2014) Consequences of climate change on microbial life in the ocean. Microbiology Today.
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El-Swais H, Dunn KA, Bielawski JP, Li WKW, Walsh DA. (2014) Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton. Environmetal Microbiology.

Georges AA, El-Swais H, Craig SE, Li WKW, Walsh DA. (2014) Metaproteomic analysis of a winter to spring succession in coastal Northwest Atlantic Ocean microbial plankton. ISME J. 8: 1301-13

Walsh DA, Lafontaine J, Grossart HP. (2013) On the eco-evolutionary relationships of fresh and saltwater bacteria and the role of lateral gene transfer in their evolution. In Lateral Gene Transfer in Evolution, U. Gophna (Ed). 55-77.