College of Agriculture and Bioresources

Research Area(s)

  • Soil biology
  • Protist diversity and systematics
  • Soil micro-invertebrates
  • Nutrient cycling
  • Food webs
  • Community structure
  • Microbial ecology


Soil Science

Research Interests

(Numbers in text refer to the selected publications below)

Eukaryote Systematics and Classification

In 2005 we provided a major overhaul of the global classification of eukaryotes from a synthesis of the phylogenetic information available at the time, which has become the accepted standard classification [22]. Several classification innovations were necessary to accomplish this, and much vigorous discussion at conferences and by correspondence (1998-2005). A discussion paper followed [19], and two further revisions. The last revision in 2019 also included functional assignments across all protists, and a modern taxonomy in Chinese script for Asian languages [5].

In 2020 the Phylocode came into effect alongside the publication of the book of Phylonyms describing the eukaryote taxonomy according to phylogenetic nomenclature [2]. This concluded the long saga to develop a new modern code of nomenclature for biological species.

Eukaryote Global Soil Biodiversity

In a well-cited paper we estimated the number of species on Earth [11]. We published two synthesis papers on primers to study protists from environmental DNA sequences [5, 8]. We also provided functional groups assignments to protists denoting whether they applied to the family of genus level classification [5]. We have assembled DNA sequences from the Americas and Eastern Asia representing two parallel N-S transects. The American biomes represented are boreal forest (Alberta), grasslands (Saskatchewan), tropical forests (Costa Rica, Panama, Ecuador); the Asian transects represent N-S transect in Mongolia from boreal to southern Gobi desert, Japan N-S forests, NE China boreal to arid grassland transect, Thailand two tropical forests. Analysis and manuscripts are in progress.

Development and Biotechnology

Scaling-up pulse innovations for food and nutrition security in southern Ethiopia. Grant: $4 million, CIFSRF-IDRC-DFATD Government of Canada. Since 1997 this project continued to grow in scope and impact through a continuous turnover of researchers. The project provides a second annual crop of modern locally developed legume varieties, to improve household income and nutrition. In 2017 we were transferring our project to the regional government authorities and local entrepreneurs to expand our farm outreach and education; and our nutrition outreach and education to mothers and woman-led households.

Designing crops for Global Food Security. Grant: $35.5 million, Government of Canada. This is a large interdisciplinary project that aims to rejuvenate and modernise research in crop development [ ]. It is held and managed through the Global Institute for Food Security [ ], which was founded to perform research that will help deliver transformative innovation to agriculture in both the developed and the developing world.

Sustainable Agriculture (No-tillage, Pasture and Grassland, Organic Agriculture)

  1. No-tillage plots were compared to tillage plots under cotton cultivation, with/out Bt cultivars, and assayed for soil biodiversity at the University of Georgia long term agricultural research experimental plots, and several commercial farms in Southern Georgia [21].
  2. Grant: $1 million, NSERC Strategic Grant, Government of Canada. A whole system study was conducted at an agricultural research field station of dairy cow pasture under extensive to intensive management, to represent less, similar, and more management than typical commercial operations. Protists, microarthropods, nematodes, earthworms, beetles and other insects, and plants were identified after 3-5 years; grass yield and grazed biomass, along with cow diet and nutrition were monitored; whole system life cycle analysis of energy use was calculated [14, 15].
  3. Mathematical model of pathogen dispersal between plots in organic agriculture, against a background of conventional agriculture, indicated there was a critical ratio of “total area under organic” to “total area under conventional” that identified a bifurcation from situations “under control” to “epidemic” related to dispersal and mitigation efficiency for pathogens [12].
  4. Mine tailings accumulating over decades provide a chronosequence of natural succession from the oldest piles to the newest. Studies were conducted of succession and remediation efforts along the hills of tailings to assay remediation success and biodiversity recovery [9, 16].
  5. No-tillage chronosequence (up to 45 y), tillage, agriculture succession to secondary grasslands, and natural grasslands were assayed for soil eukaryote biodiversity at various Saskatchewan locations. Nitrogen fixation by the free-living bacteria were assayed. Manuscripts in progress.

Soil Biology and Ecology

Soil Protist Ecology

Protists had been neglected from soil biology and soil ecology studies, even though they represent an abundant and very diverse group of organisms responsible for most of the bacteria biomass turnover. (The main reason was using bacteriological techniques that are unsuitable for protistological work.) Through a series of workshops and symposia, the community was educated about their diversity and functions (2000-2005). We developed and published standard protocols for field sampling and routine techniques in the laboratory [18]. Soil protists were incorporated in detail into the protist classification from phylogenetic publications [5]. Several papers on the ecology of protists have been published, including two recent synthetic and critical reviews [6, 7, 20]. Several functional response curves have been obtained from cultured species that remain to be published.

Soil food webs and community structure

A series of laboratory microcosms were used to study grazing interactions, competition, and food webs in the Fungi-fungivory pathway; some included 15N and 13C stable isotope tracer studies [4, 10]. Natural abundance studies of soils with the same isotopes were used to discern between food webs in forest or grassland. A synthesis paper to modernize the presentation and understanding of soil food web complexity was written with an international consortium of colleagues (in submission/review).

A variety of opportunistic papers were published related to diverse topics in soil biology and ecology. These include topics on silicon-rhizobacteria-salinity [1], organic matter dynamics and aggregate size distribution, collembola diet, biochar and phosphorous, FTIR remote sensing measurements of leaf nitrogen, microfossils in amber [13], spider cold-hardiness, and a new but common temperate forest soil flatworm.

Municipal Solid Waste Compost, compost tea foliar sprays

MSW composts and foliar sprays were prepared for strawberry and raspberry cultivation, and the results published in a series of papers from a PhD thesis (J. Hargreaves). This led to a well cited synthesis in a review of MSW compost utility in agriculture [17].

Ciliate Cell Cycles, and Eukaryote Cell Size Regulation

In continuation of the focus of Prof. J.D. Berger’s research, we progressed in understanding cell cycle control points and cell size regulation in Paramecium. We initiated studies on the molecular biology of cell cycle regulation in Paramecium, with both wild type and mutant lines. We described detailed timing of cell growth and division morphological markers in Paramecium and Sterkiella (Oxytricha) for placing molecular events and control points in the cell cycle [23, 24]. A synthesis of cell size regulation in protists was written in a PhD thesis (Adl, 1998).

Selected Publications

Significant Books and Chapters

Adl, M.S. and Blaine Mathison. 2019. Taxonomy and classification of human eukaryotic parasites. In: Manual of Clinical Microbiology, 12th edn. American Society of Microbiologists. Chapter 135, 2379-2388.

Adl, M.S. and Simpson, A.G. 2007. Microbial Eukaryotes. Chapter 23. In: Microbial Life 2nd edn, Perry J.J., Staley J.T. and Lory S. Sinauer Associates, Sunderland Mass., pp. 686-736. 

The Ecology of Soil Decomposition (Adl, 2003), CABI

Selected Publications

(Number of times cited (Google Scholar) in square brackets, as of July 2020)

  1. Etessami, H., and Adl, S. Can interactions between silicon and non–rhizobial bacteria help in improving nodulation and nitrogen fixation in salinity–stressed legumes? A review. Rhizosphere 15, DOI: 10.1016/j.rhisph.2020.100229 [cited 0]
  2. de Queiroz, K., P. D. Cantino, and J. A. Gauthier (eds.). 2020. Phylonyms: A Companion to the PhyloCode. CRC Press, Boca Raton, FL. [NA]
  3. Min Liu, Sina Adl, Xiaoyong Cui; Yuqiang Tian, Xingliang Xu, Yakov Kuzyakov. 2020. In situ methods of plant-microbial interactions for nitrogen in rhizosphere. Rhizosphere 13, 100186. [cited 2]
  4. V. Crotty, S. Adl. 2019. Competition and predation in soil fungivorous microarthropods using stable isotope ratio mass spectrometry. Frontiers in Microbiology (Special issue: The Soil Microbiome and Multi-Trophic Interactions That Regulate Soil Carbon and Nutrient Flux),  [cited 3]
  5. Sina M. Adl, David Bass, Christopher E. Lane, Julius Lukeš, Conrad L. Schoch, Alexey Smirnov, Sabine Agatha, Cedric Berney, Matthew W. Brown, Fabien Burki, Paco Cárdenas, Ivan Čepička, Ludmila Chistyakova, Javier del Campo, Micah Dunthorn, Bente Edvardsen, Yana Eglit, Laure Guillou, Vladimír Hampl, Aaron A. Heiss, Mona Hoppenrath, Timothy Y. James, Anna Karnkowska, Sergey Karpov, Eunsoo Kim, Martin Kolisko, Alexander Kudryavtsev, Daniel J. G. Lahr, Enrique Lara, Line Le Gall, Denis H. Lynn, David G. Mann, Ramon Massana, Edward A. D. Mitchell , Christine Morrow, Jong Soo Park, Jan W. Pawlowski, Martha J. Powell, Daniel J. Richter, Sonja Rueckert, Lora Shadwick, Satoshi Shimano, Alastair G. B. Simpson, Frederick W. Spiegel, Guifré Torruella, Noha Youssef, Vasily Zlatogursky, Qianqian Zhang. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66 (1):4-117. [cited 237]
  6. Stefan Geisen, Edward A. D. Mitchell, Sina Adl, Michael Bonkowski, Micah Dunthorn, Flemming Ekelund, Leonardo D. Fernández, Alexandre Jousset, Valentyna Krashevska, David Singer, Frederick W. Spiegel, Julia Walochnik and Enrique Lara. 2018. Soil protists: a fertile frontier in soil biology research, FEMS Microbiology Reviews 42 (3): 293–323.[cited 61]
  7. Geisen, S., and 46 others. 2017. Soil Protistology rebooted: and 30 questions to start with. Soil Biology and Biochemistry 111: 94-103. [cited 37]
  8. Adl, M.S., Habura, A., Eglit, Y. 2014. Amplification primers of SSU rDNA for soil protists. Soil Biology and Biochemistry 69: 328-342. [cited 46
  9. Frouz, J., Thébault, E., Pižl, V., Adl, S., Cajthaml, T., Baldrián, P., Háněl, L., Starý, J., Tajovský, K., Materna, J., Nováková, A., and de Ruiter, P.C.   Soil food web changes during spontaneous succession at post mining sites: A possible ecosystem engineering effect on food web organization?  PLoS ONE, 8(11): e79694. [cited 19]
  10. Crotty, F.V. Adl, S.M., Blackshaw, R.P., and Murray J.P. 2012. Using stable isotopes to differentiate trophic feeding channels within soil food webs. Journal of Eukaryotic Microbiology 59(6):520-526. [cited 40]
  11. Mora, D.P. Tittensor, S. Adl, A.G.B. Simpson, B. Worm. 2011. How many species are there on Earth and in the Ocean? PLOS-Biology, 9(8): e1001127. [cited 2,110]
  12. Adl, M.S., Iron, D., and Kolokolnikov, T. 2011. Organic agriculture benefits from conventional agriculture. Science of the Total Environment, 409:2192-2197. [cited 22]
  13. Adl, M.S., Girard, V., M. Lak, G. Breton, D. Néraudeau. Reconstructing the soil food web of a 100 million years old forest. Soil Biology and Biochemistry, 43:726-735. [cited 15]
  14. Mills, A.S., Adl, M.S. 2011. Changes in nematode abundances and body length in response to management intensive grazing in a low-input temperate pasture. Soil Biology and Biochemistry 43(1):150-158. [cited 21]
  15. Maharning, A., Mills, A.S., Adl, M.S. 2009. Soil community changes during secondary succession to naturalized grasslands. Applied Soil Ecology 41:137-147. [cited 125]
  16. Adl, M.S. 2008. Setting the tempo in land remediation: short-term and long-term patterns in biodiversity recovery. Invited review for Microbes and Environment 23(1):13-19. [cited 13]
  17. Hargreaves, J.C., Adl, M.S. and Warman, P.R. 2008. A review of the use of composted municipal solid waste in agriculture. Agriculture Environment Ecosystems 123:1-14. [cited 510]
  18. Adl, M.S, Acosta-Mercado, D., Anderson, T.R. and Lynn, D.H. 2007. Protozoa. Chapter 36.In: Soil Sampling and Methods of Analysis, 2nd edn, (Ed. M. Carter Published by the Canadian Soil Science Society), pp. 455-469. [NA]
  19. Adl, M.S., Leander, B.S., Simpson, Archibald, J.M., Anderson, O.R., Barta, J.R., Bass, D., Bowser, S.S., Brugerolle, G., Farmer, M.A., Karpov, S., Kolisko, M., Lane, C.E., Lodge, J., Lynn, D.H., Mann, D.G., Meisterfeld, R., Mendoza, L., Moestrup, Ø., Mozley-Standridge, S.E., Smirnov, A.V., Spiegel, F.W. 2007. Diversity, Nomenclature and Taxonomy of Protists. Systematic Biology 56(4):684-689. [cited 247]
  20. Adl, M.S. and Gupta, V.V.S.R. 2006. Review: Protists in soil ecology and forest nutrient cycling. Canadian Journal of Forest Research, 36: 1805-1817. [cited 77]
  21. Adl, M.S., Coleman, D.C. and Read, R. 2006. Slow recovery of biodiversity after 25 years of no-tillage management. Agriculture, Ecosystem and Environment 114: 323-334. [cited 98]
  22. Adl, M.S., Simpson, A.G.B., Farmer, M.A., Andersen, R.A., Anderson, O.R., Barta, J.R., Bowser, S.S., Brugerolle, G., Fensome, R.A., Fredericq, S., James, T.Y., Karpov, S., Kugrens, P., Krug, J., Lane, C.E., Lewis, L.A., Lodge, J., Lynn, D.H., Mann, D.G., McCourt, R.M., Mendoza, L., Moestrup, Ø., Mozley-Standridge, S.E., Nerad, T.A., Shearer, C.A., Smirnov, A.V., Spiegel, F.W., Taylor, F. J. R. 2005. The new classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology 52(5): 399-451. [cited 1,979]
  23. Zhang H., Adl M.S. and Berger J.D. 1999. Two distinct classes of mitotic cyclin homologues, cyc1 and cyc2, are involved in cell cycle regulation of the ciliate Paramecium tetraurelia. Journal Eukaryotic Microbiology 46: 585-596. [cited 12]
  24. Adl M.S. and Berger J.D. 1996. Commitment to division in ciliate cell cycles. Journal of Eukaryotic Microbiology 43: 77-86. [cited 22]