Supplementary Text
Data collection and beta diversity of microbial communities from global AMD and associated
environments
We searched papers in Web of Science and reviewed molecular inventory studies that
explored using a 16S rRNA clone library approach microbial communities in natural AMD
and associated environments (such as acidic biofilm, sediment and tailings) distributed
globally. Researches that retrieved sequences from artificial and semi-artificial acidic
environments, such as enrichments, bioreactors, and bioleaching and wetland systems, were
excluded from the metadata. 16S rRNA clone sequences were identified and recovered from
GenBank. Samples with detailed information of OTUs and their relative retrieval in the clone
library, or the overall community composition with relative abundance of each of the lineages
(i.e., phylum, or sub-phylum for the Proteobacteria) were remained for further analyses. Site
locations and environmental parameters including pH, temperature and concentrations of
sulfate and total iron (ferric and ferrous irons) that were mostly recorded across the studies
were summarized. It should be noted that we did not aim to conduct an exhaustive literature
search but rather to reveal broad community patterns in these typical acidic environments
through a meta-analysis of representative studies.
We aligned representative sequences of the OTUs from each sample using NAST (DeSantis
et al., 2006). Well-aligned sequences were imported to the ARB program (Ludwig et al., 2004)
and added using the parsimony insertion tool to a tree with >200 000 sequences available at
the Greengenes website (http://greengenes.lbl.gov). The reconstructed phylogenetic tree was
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uploaded to the Fast UniFrac web interface (Hamady et al., 2010) to implement the weighted
UniFrac analysis. Community composition of each sample was identified by taxonomic
classification (RDP Classifier) of the OTUs and their relative recovery in the original clone
libraries.
References
DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM et al. (2006).
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes.
Nucleic Acids Res 34: W394-W399.
Hamady M, Lozupone C, Knight R. (2010). Fast UniFrac: facilitating high-throughput
phylogenetic analyses of microbial communities including analysis of pyrosequencing and
PhyloChip data. ISME J 4: 17-27.
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar et al. (2004). ARB: a
software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
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