Table 1 Research questions and hypotheses that shaped the design of the four environmental microbial community datasets

Acid mine drainage bacteria and archaea

1) Are environmental (Env) samples more diverse than bioreactor (BR) biofilms?

H1: Bioreactor growth conditions usually have a higher pH than the environment, and the geochemistry of the drainage might differ from growth media. Thus, environmental biofilms are expected to be more diverse than bioreactor-grown biofilms.

2) Is biofilm diversity higher at higher stages of biofilm development?

H2: As biofilms begin to establish, early growth-stage biofilms are expected to be less diverse. As they mature, more organisms join the community, increasing diversity.

Hypersaline lake viruses

1) How do viral diversities change across spatiotemporal replicates?

H1: Viral diversity will be greatest in pools with larger volume (2010A and 2007A samples).

H2: Community dissimilarity will cluster by site, then by year.

Subsurface bacteria

1) Does acetate addition affect the diversity and composition of soil microbial communities?

H1: Acetate addition will stimulate growth of a subset of the microbial community capable of using it as an electron donor.

2) Does vanadium addition affect the diversity and composition of soil microbial communities?

H2: Vanadium addition will reduce the diversity and evenness of the communities and favor those who can both use acetate as an electron donor and vanadium as an electron receptor and/or tolerate vanadium at high concentrations.

Substrate-associated soil fungi

1) How do plant community type (forest vs. grassland), substrate type (wood vs. straw), and time (6 months vs. 18 months) affect saprotrophic fungal assemblages?

H1: Wood substrates will be more diverse than straw substrates, because the wood substrate is more complex and requires a larger group of fungi to decompose it compared with a simpler substrate, such as straw.

H2: Plant community type will have a greater effect on diversity than substrate type or time, because it will determine which fungi can colonize a substrate.