Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

Abstract

Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide (CO2) and methane (CH4) production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between natural, mined, and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and CH4 or CO2 production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought about by these land uses.

Keywords: archaea; bacteria; carbon dioxide; decomposition; methane; methanogen.

Figure 1

Bacterial 16S rRNA gene-based phylogenetic tree (neighbor-joining method) of representative sequences retrieved from sites at Rivière du Loup and Shippagan in bold and similar sequences from GenBank. Distances were computed using the maximum composite likelihood method in the MEGA v5 package. Vertical bars and labels refer to phyla. In reference to Figure 2, sequences with open circles, black squares, and black upward pointing triangles represent classes in the phylum Proteobacteria, black circles represent the phylum Adicobacteria, black diamonds represent the phylum Actinobacteria, open and black upward pointing triangles represent classes in the phylum Firmicutes, and open squares represent the phylum Verrucomicrobia. Scale bar units are the number of base substitutions per site.

Figure 2

Bacterial (A and B) and archaeal (C) community compositions (averaged across replicates) based on in silico mapping of terminal restriction sites of cloned sequences across natural (Nat), actively mined (Min), mined and abandoned (Abd), and mined and restored (Rst) sites at Rivère du Loup and Shippagan. Unlabeled portions of each community (i.e., where bars did not add up to 100%) were a result of not being able to assign T-RFs to specific clone library sequences isolated from the anoxic samples.

Figure 3

Archaeal 16S rRNA gene-based phylogenetic tree (neighbor-joining method) of sequences retrieved from sites at Rivière du Loup and Shippagan in bold and similar sequences from GenBank. Distances were computed using the maximum composite likelihood method in the MEGA v5 package. In reference to Figure 2, black circles represent clones related to unknown Crenarchaeota or the single sequence EC Arch 32, open circles and black diamonds represent unknown Euryarchaeota, upward pointing black triangles represent the class Methanobacteria, and downward pointing black triangles represent Rice Cluster II. Scale bar units are the number of base substitutions per site.

Figure 4

Hierarchical cluster analysis (calculated with Ward's method; Euclidean distances) of bacterial and archaeal communities in peat from natural, actively mined, once mined and then abandoned, and once mined and then restored sites that had new peat accumulation at Rivière du Loup (RDL) and Shippagan (SHP). Operational taxonomic units were defined as unique T-RFs from T-RFLP analysis of 16S rDNA amplified from peat incubated under oxic or anoxic conditions.

Figure 5

CCA bi-plot of bacterial and archaeal communities in peat sampled from natural, actively mined, once mined and then abandoned, and once mined and restored mined sites that had new peat accumulation at Rivière du Loup and Shippagan. Operational taxonomic units were defined as unique T-RFs from T-RFLP analysis of 16S rDNA amplified from peat incubated under oxic or anoxic conditions. Significant peat properties and CO₂ production correlating most strongly with the first 2 axes, defined by OTU presence and abundances, are indicated with arrows. See Table 4 for additional related canonical correspondence analysis results.