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Processes in Microbial Ecology - Notes

PME2012-FinalFrontcover.jpgby David L. Kirchman

Oxford University Press

First Edition, March 2012

Order it from: OUP USA, OUP UK, or Amazon

368 pages; 200 illustrations; 9.7 x 7.4


Footnotes and more references

The table below gives a few comments on selected topics and provides references not cited in the book. Readers are encouraged to contact me (kirchman@udel.edu) if other studies should be cited or other points should be made here.

This page is continuously updated, so come back (frequently) for more.


Page Number




Fisher et al. (2012) is a brief review of emerging diseases caused by fungi.



Dennis et al. (2013) used an interesting combination of methods to demonstrate chemotaxis by select bacterial taxa in a freshwater lake.



Multi-species biofilms, the norm for films in natural environments, are reviewed by Elias and Banin (2012).



Elber et al. (2012) reported that "cryptogamic covers", those algae on rocks and soils, contribute 7% of global primary production.



Lomas et al. (1999) examined the effect of temperature on diatoms. See also Boyd et al. (2013).



Bernard et al. (2012) discuss the impact of earthworms on bacteria and organic matter degradation.



For Table 6.4, the primary factor limiting diazotrophs is probably energy, at least for heterotrophic diazotrophs. Also, nitrogen has a negative impact on N2 fixation.



Some bacterial taxa, such as Gammaproteobacteria, may be limited by P in the Eastern Mediterranean Sea, but SAR11 is not, according to Sebastian and Gasol (2013).



Cordero et al. (2012) present a fascinating example of social communication among vibrios isolated from a coastal ocean.



See also Hansen et al. (1997) who examined the effect of prey size on predation.



See Fig. 1.1D for another example of a ciliate.



The efficiency of phytoplankton and bacteria-based food webs was examined by Berglund et al. (2007).



Many harmful algae are mixotrophs, as discussed in Burkholder et al. (2008).



Payet and Suttle (2013) discuss the impact of trophic status on lysogeny in the Arctic Ocean.



One old study about pseudolosogeny is Ripp and Miller (1998).



A great book about viruses jumping from animals to humans is Spillover by Quammen (2012). 



The story of glycosphingolipids, viruses and algal death continues with Vardi et al. (2012).



For another study of global patterns in bacterial community structure, see Barberan and Casamayor (2010).



For a more up-to-date comparison of 16S rRNA and protein-coding genes, see Roux et al. (2011).



Merbt et al. (2012) discuss the impact of light on ammonia monooxygenase in bacteria and archaea.



Organic carbon oxidation by arbuscular mycorrhizal fungi may be affected by climate change, according to Cheng et al. (2012).


Barberan, A., and E. O. Casamayor. 2010. Global phylogenetic community structure and beta-diversity patterns in surface bacterioplankton metacommunities. Aquat. Microb. Ecol. 59: 1-10.

Berglund, J., U. Muren, U. Bamstedt, and A. Andersson. 2007. Efficiency of a phytoplankton-based and a bacteria-based food web in a pelagic marine system. Limnol. Oceanogr. 52: 121-131.

Bernard, L., L. Chapuis-Lardy, T. Razafimbelo, M. Razafindrakoto, A.-L. Pablo, E. Legname, J. Poulain, T. Bruls, M. O'donohue et al. 2012. Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil. ISME J. 6: 213-222.

Burkholder, J. M., P. M. Glibert, and H. M. Skelton. 2008. Mixotrophy, a major mode of nutrition for harmful algal species in eutrophic waters. Harmful Algae 8: 77-93.

Boyd, P. W., T. A. Rynearson, E. A. Armstrong, F. Fu, K. Hayashi, Z. Hu, D. A. Hutchins, R. M. Kudela, E. Litchman, M. R. Mulholland, U. Passow, R. F. Strzepek, K. A. Whittaker, E. Yu, and M. K. Thomas. 2013. Marine Phytoplankton Temperature versus Growth Responses from Polar to Tropical Waters – Outcome of a Scientific Community-Wide Study. PLoS ONE 8: e63091.

Cheng, L., F. L. Booker, C. Tu, K. O. Burkey, L. Zhou, H. D. Shew, T. W. Rufty, and S. Hu. 2012. Arbuscular Mycorrhizal Fungi Increase Organic Carbon Decomposition Under Elevated CO2. Science 337: 1084-1087.

Cordero, O. X., H. Wildschutte, B. Kirkup, S. Proehl, L. Ngo, F. Hussain, F. Le Roux, T. Mincer, and M. F. Polz. 2012. Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance. Science 337: 1228-1231.

Dennis, P. G., J. Seymour, K. Kumbun, and G. W. Tyson. 2013. Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients. ISME J. 7: 1661-1664.

Elbert, W., B. Weber, S. Burrows, J. Steinkamp, B. Budel, M. O. Andreae, and U. Poschl. 2012. Contribution of cryptogamic covers to the global cycles of carbon and nitrogen. Nature Geosci. 5: 459-462.

Elias, S., and E. Banin. 2012. Multi-species biofilms: living with friendly neighbors. FEMS Microbiol. Rev. 36: 990-1004.

Fisher, M. C., D. A. Henk, C. J. Briggs, J. S. Brownstein, L. C. Madoff, S. L. Mccraw, and S. J. Gurr. 2012. Emerging fungal threats to animal, plant and ecosystem health. Nature 484: 186-194.

Hansen, P. J., P. K. Bjornsen, and B. W. Hansen. 1997. Zooplankton grazing and growth: Scaling within the 2-2,000-micron body size range. Limnol. Oceanogr. 42: 687-704.

Lomas, M. W., and P. M. Glibert. 1999. Temperature regulation of nitrate uptake: A novel hypothesis about nitrate uptake and reduction in cool-water diatoms. Limnol. Oceanogr. 44: 556-572.

Merbt, S. N., D. A. Stahl, E. O. Casamayor, E. Martí, G. W. Nicol, and J. I. Prosser. 2012. Differential photoinhibition of bacterial and archaeal ammonia oxidation. FEMS Microb. Let. 327: 41-46.

Payet, J. P., and C. A. Suttle. 2013. To kill or not to kill: The balance between lytic and lysogenic viral infection is driven by trophic status. Limnol. Oceanogr. 58: 465-474.

Quammen, D. 2012. Spillover: animal infections and the next human pandemic, 1st ed. W.W. Norton & Co. 587 p. pp.

Ripp, S., and R. V. Miller. 1998. Dynamics of the pseudolysogenic response in slowly growing cells of Pseudomonas aeruginosa. Microbiology 144: 2225-2232.

Roux, S., F. Enault, G. Le Bronner, and D. Debroas. 2011. Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems. FEMS Microbiol. Ecol. 78: 617-628.

Sebastian, M., and J. M. Gasol. 2013. Heterogeneity in the nutrient limitation of different bacterioplankton groups in the Eastern Mediterranean Sea. ISME J. 7: 1665-1668.

Vardi, A., L. Haramaty, B. a. S. Van Mooy, H. F. Fredricks, S. A. Kimmance, A. Larsen, and K. D. Bidle. 2012. Host–virus dynamics and subcellular controls of cell fate in a natural coccolithophore population. Proc. Natl. Acad. Sci. USA 109: 19327-19332.

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