M. Claire Horner-Devine, Jessica M. Silver, Mathew A. Leibold, Brendan J. M. Bohannan, Robert K. Colwell, Jed A. Fuhrman, Jessica L. Green, Cheryl R. Kuske, Jennifer B. H. Martiny, Gerard Muyzer, Lise Øvreås, Anna-Louise Reysenbach, and Val H. Smith. 2007. A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88:1345–1353.

Appendix A. Breakdown of microbial data sets by taxon, habitat, method, and gene.

LITERATURE CITED

Beaver, J. R. and T. L. Crisman (1989). Analysis of the Community Structure of Planktonic Ciliated Protozoa Relative to Trophic State in Florida Lakes. Hydrobiologia 174(3): 177-184.

Benlloch, S., A. Lopez-Lopez, et al. (2002). Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern. Environmental Microbiology 4(6): 349-360.

Besemer, K., M. M. Moeseneder, et al. (2005). Complexity of bacterial communities in a river-floodplain system (Danube, Austria). Applied and Environmental Microbiology 71(2): 609-620.

Bjelland, T. and S. Ekman (2005). Fungal diversity in rock beneath a crustose lichen as revealed by molecular markers. Microbial Ecology 49(4): 598-603.

Blum, L. K., M. S. Roberts, et al. (2004). Distribution of microbial communities associated with the dominant high marsh plants and sediments of the United States east coast. Microbial Ecology 48(3): 375-388.

Brodie, E., S. Edwards, et al. (2002). Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem. Microbial Ecology 44(3): 260-270.

Brodie, E., S. Edwards, et al. (2003). Soil fungal community structure in a temperate upland grassland soil. Fems Microbiology Ecology 45(2): 105-114.

Carlson, C. (unpublished data).

Carney, K. M., P. A. Matson, et al. (2004). Diversity and composition of tropical soil nitrifiers across a plant diversity gradient and among land-use types. Ecology Letters 7(8): 684-694.

Casamayor, E., R. Massana, et al. (2002). Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern. Environmental Microbiology 4(6): 338-348.

Chandran, M. R., K. Chandran, et al. (1998). Limnological profile of ponds in tropical India. Verh. Int. Ver. Theor. Angew. Limnol 26: 1529-1535.

Crump, B. (unpublished data).

Edlund, A., T. Soule, et al. (2006). Microbial community structure in polluted Baltic Sea sediments. Environmental Microbiology 8(2): 223-232.

Eiler, A. and S. Bertilsson (2004). Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes. Environmental Microbiology 6(12): 1228-1243.

Engel, A. S., M. L. Porter, et al. (2004). Bacterial diversity and ecosystem function of filamentous microbial mats from aphotic (cave) sulfidic springs dominated by chemolithoautotrophic Epsilonproteobacteria. Fems Microbiology Ecology 51(1): 31-53.

Estrada, M., P. Henriksen, et al. (2004). Diversity of planktonic photo auto trophic microorganisms along a salinity gradient as depicted by Microscopy, Flow cytometry, pigment analysis and DNA-based methods. Fems Microbiology Ecology 49(2): 281-293.

Evans, J. H. (1997). Spatial and seasonal distribution of phytoplankton in an African Rift Valley lake (L. Albert, Uganda, Zaire). Hydrobiologia 354: 1-16.

Fierer, N. (unpublished data).

Filion, M., R. C. Hamelin, et al. (2004). Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery. Applied and Environmental Microbiology 70(6): 3541-3551.

Francis, C. A., J. C. Cornwell, et al. (In prep). Linking nitrite reductase (nirS) gene diversity to environmental gradients and biogeochemical function in Chesapeake Bay sediments.

Francis, C. A., G. D. O-Mullan, et al. (2003). Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments. Geobiology 1: 129-140.

Franklin, R. and A. Mills (2003). Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiology Ecology 44(3): 335-346.

Frias-Lopez, J., G. T. Bonheyo, et al. (2003). Cyanobacteria associated with coral black band disease in Caribbean and Indo-Pacific Reefs. Applied and Environmental Microbiology 69(4): 2409-2413.

Frias-Lopez, J., J. S. Klaus, et al. (2004). Bacterial community associated with black band disease in corals. Applied and Environmental Microbiology 70(10): 5955-5962.

Frias-Lopez, J., A. L. Zerkle, et al. (2002). Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. Applied and Environmental Microbiology 68(5): 2214-2228.

Friedrich, U., K. Prior, et al. (2002). High bacterial diversity of a waste gas-degrading community in an industrial biofilter as shown by a 16S rDNA clone library. Environmental Microbiology 4(11): 721-734.

Friedrich, U., H. Van Langenhove, et al. (2003). Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA-targeting oligonucleotide probes. Environmental Microbiology 5(3): 183-201.

Green, J. L., A. J. Holmes, et al. (2004). Spatial scaling of microbial eukaryote diversity. Nature 432(7018): 747-750.

Hackl, E., S. Zechmeister-Boltenstern, et al. (2004). Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Applied and Environmental Microbiology 70(9): 5057-5065.

Hamelin, J. (unpublished data).

Hawkes, C. V. and V. R. Flechtner (2002). Biological soil crusts in a xeric Florida shrubland: composition, abundance, and spatial heterogeneity of crusts with different disturbance histories. Microbial Ecology 43(1): 1-12.

Hewson, I. (unpublished data).

Hewson, I., D. G. Capone, et al. (2006). Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the West Tropical Atlantic. Aquatic Microbial Ecology 43(1): 11-22.

Hewson, I. and J. A. Fuhrman (2004). Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Applied and Environmental Microbiology 70(6): 3425-3433.

Hewson, I. and J. A. Fuhrman (2006). Improved strategy for comparing microbial assemblage fingerprints. Microbial Ecology 51(2): 147-153.

Hewson, I. and J. A. Fuhrman (2006). Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities. Marine Ecology Progress Series 306: 79-86.

Hewson, I., J. A. Steele, et al. (2006). Temporal and spatial scales of oligotrophic surface water bacterioplankton assemblage variation. Marine Ecology Progress Series 311:67-77.

Hewson, I., J. A. Steele, et al. (2006). Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition. Limnology and Oceanography 51(3): 1274-1283.

Horz, H. P., V. Rich, et al. (2005). Methane-oxidizing bacteria in a California upland grassland soil: Diversity and response to simulated global change. Applied and Environmental Microbiology 71(5): 2642-2652.

Kuske, C. R., Housman, et al. (unpublished data).

Kuske, C. R., L. O. Ticknor, et al. (2002). Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Applied and Environmental Microbiology 68(4): 1854-1863.

Kuske, C. R., Yeager, et al (unpublished data).

Lage, M. (unpublished data).

Lau, W. W. Y., P. A. Jumars, et al. (2002). Genetic diversity of attached bacteria in the hindgut of the deposit-feeding shrimp Neotrypaea (formerly Callianassa) californiensis (Decapoda : Thalassinidae). Microbial Ecology 43(4): 455-466.

Lavrentyev, P. J., M. J. McCarthy, et al. (2004). Estuarine microbial food web patterns in a Lake Erie coastal wetland. Microbial Ecology 48(4): 567-577.

Lawley, B., S. Ripley, et al. (2004). Molecular analysis of geographic patterns of eukaryotic diversity in Antarctic soils. Applied and Environmental Microbiology 70(10): 5963-5972.

Leclerc, M., J. P. Delgenes, et al. (2004). Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing. Environmental Microbiology 6(8): 809-819.

Lipson, D. A. and S. K. Schmidt (2004). Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains. Applied and Environmental Microbiology 70(5): 2867-2879.

Lukesova, A. (2001). Soil algae in brown coal and lignite post-mining areas in central Europe (Czech Republic and Germany). Restoration Ecology 9(4): 341-350.

Massana, R., E. F. DeLong, et al. (2000). A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Applied and Environmental Microbiology 66(5): 1777-1787.

Moran, N. (unpublished data).

Nicol, G. W., D. Tscherko, et al. (2005). Primary succession of soil Crenarchaeota across a receding glacier foreland. Environmental Microbiology 7(3): 337-347.

Noguez, A. M., H. T. Arita, et al. (2005). Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest. Global Ecology and Biogeography 14(3): 241-248.

Oliver, I., A. Holmes, et al. (2004). Land systems as surrogates for biodiversity in conservation planning. Ecological Applications 14(2): 485-503.

Roose-Amsaleg, C., Y. Brygoo, et al. (2004). Ascomycete diversity in soil-feeding termite nests and soils from a tropical rainforest. Environmental Microbiology 6(5): 462-469.

Sabbe, K., D. A. Hodgson, et al. (2004). Salinity, depth and the structure and composition of microbial mats in continental Antarctic lakes. Freshwater Biology 49(3): 296-319.

Salles, J. F., J. A. van Veen, et al. (2004). Multivariate analyses of Burkholderia species in soil: Effect of crop and land use history. Applied and Environmental Microbiology 70(7): 4012-4020.

Smith, A. H. and R. I. Mackie (2004). Effect of condensed tannins on bacterial diversity and metabolic activity in the rat gastrointestinal tract. Applied and Environmental Microbiology 70(2): 1104-1115.

Suzuki, M. T., C. M. Preston, et al. (2004). Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microbial Ecology 48(4): 473-488.

van Waasbergen, L. G., D. L. Balkwill, et al. (2000). Genetic diversity among Arthrobacter species collected across a heterogeneous series of terrestrial deep-subsurface sediments as determined on the basis of 16S rRNA and recA gene sequences. Applied and Environmental Microbiology 66(8): 3454-3463.

Webster, G., T. M. Embley, et al. (2002). Grassland management regimens reduce small-scale heterogeneity and species diversity of beta-proteobacterial ammonia oxidizer populations. Applied and Environmental Microbiology 68(1): 20-30.

Weidner, S., W. Arnold, et al. (1996). Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Applied and Environmental Microbiology 62(3): 766-771.

Weidner, S., W. Arnold, et al. (2000). Phylogenetic analysis of bacterial communities associated with leaves of the seagrass Halophila stipulacea by a culture-independent small-subunit rRNA gene approach. Microbial Ecology 39(1): 22-31.

Winter, C., A. Smit, et al. (2004). Impact of virioplankton on archaeal and bacterial community richness as assessed in seawater batch cultures. Applied and Environmental Microbiology 70(2): 804-813.

Yeager, C. M., J. L. Kornosky, et al. (2004). Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado plateau and Chihuahuan desert. Applied and Environmental Microbiology 70(2): 973-983.

Yeager, C. M., D. E. Northup, et al. (2005). Changes in nitrogen-fixing and ammonia-oxidizing bacterial communities in soil of a mixed conifer forest after wildfire. Applied and Environmental Microbiology 71(5): 2713-2722.