Sulfate-reducing microorganisms in wetlands - fameless actors in carbon cycling and climate change

Abstract

Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink. Their response to global warming and environmental pollution is one of the largest unknowns in the upcoming decades to centuries. In this review, we highlight the role of sulfate-reducing microorganisms (SRM) in the intertwined element cycles of wetlands. Although regarded primarily as methanogenic environments, biogeochemical studies have revealed a previously hidden sulfur cycle in wetlands that can sustain rapid renewal of the small standing pools of sulfate. Thus, dissimilatory sulfate reduction, which frequently occurs at rates comparable to marine surface sediments, can contribute up to 36-50% to anaerobic carbon mineralization in these ecosystems. Since sulfate reduction is thermodynamically favored relative to fermentative processes and methanogenesis, it effectively decreases gross methane production thereby mitigating the flux of methane to the atmosphere. However, very little is known about wetland SRM. Molecular analyses using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] as marker genes demonstrated that members of novel phylogenetic lineages, which are unrelated to recognized SRM, dominate dsrAB richness and, if tested, are also abundant among the dsrAB-containing wetland microbiota. These discoveries point toward the existence of so far unknown SRM that are an important part of the autochthonous wetland microbiota. In addition to these numerically dominant microorganisms, a recent stable isotope probing study of SRM in a German peatland indicated that rare biosphere members might be highly active in situ and have a considerable stake in wetland sulfate reduction. The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change.

Keywords: dissimilatory (bi)sulfite reductase; dsrAB; peatland; rare biosphere; rice paddy; sulfate-reducing microorganisms; sulfur cycle; sulfur pollution.

Figure 1

Compilation of sulfate reduction rates from large peat soil mesocosms [60 cm in diameter and 60 cm in depth; left column (A,C,E); Knorr and Blodau, 2009] and from field samples [right column (B,D,F); Knorr et al., 2009] of the German peatland Schlöppnerbrunnen II. Both, data from mesocosm and field samples demonstrate decreasing maximum sulfate reduction rates with increasing exposure to water logging, which represents anoxic conditions (A,B). Maximum sulfate reduction rates depended on prevailing sulfate concentrations (C,D) and a similar wide span in sulfate reduction rates was observed above and below the water table with the water table representing the transition zone between oxic to anoxic conditions (E,F). Time spans in the legend represent the incubation time (days) of soils below the water table (WT). Negative and positive values on the abscissa (x-axis) in subfigure (E) and (F) represent relative positions above and below the water table, respectively.

Figure 2

Schematic overview of the proposed sulfur cycle in freshwater wetlands. Abbreviations: DOM-Q, quinone moieties of dissolved organic matter, $\text{R}-\text{O}-{\text{SO}}_3^{-},$ organic sulfate esters, TRIS, total reactive inorganic sulfur, CBS, carbon bonded sulfur.

Figure 3

DsrAB consensus tree showing the affiliation of dsrAB sequences from freshwater wetlands (sequences and lineages marked in green). Environmental DsrAB sequences not affiliated with sequences from cultured microorganisms were grouped into an “uncultured dsrAB lineage” on the approximate family level if at least two sequences with ≥64% amino acid identity formed a monophyletic cluster and contained no sequence that was ≥64% identical to a sequence outside this lineage. The conservative 64% limit was inferred from DsrAB of cultured representatives belonging to 10 known families with a minimum intra-family amino acid sequence identity of 64–89%. Bootstrap support for identified clusters is shown by split circles (right: maximum likelihood, 1000 re-samplings; left: maximum parsimony, 100 re-samplings) at the respective branches with black indicating ≥90% support, gray indicating ≥70% support, and white/absence of circles indicating <70% support. Family level DsrAB lineages were summarized to superclusters if their monophyletic origin was supported by bootstrap values of ≥70%. The color code of environmental DsrAB sequences or of dots behind uncultured family level DsrAB lineages indicates the habitat where the respective sequences were retrieved from (this data is not provided for recognized families). For phylogenetic inference of deduced DsrAB amino acid sequences, insertions and deletions were removed from the data set by using an alignment mask (indel filter), which resulted in 502 amino acid positions for comparative analyses. Distance matrix (Neighbor Joining with PAM as amino acid replacement model), maximum likelihood (RAxML with PAM as amino acid replacement model), and maximum-parsimony algorithms were used as provided in the ARB software package (Ludwig et al., 2004) to determine the phylogenetic relatedness of the analyzed DsrAB sequences. Reverse DsrAB of sulfur-oxidizing bacteria were used as outgroup (Loy et al., 2009). A strict consensus tree was constructed from the individual trees obtained with the different algorithms using the Phylip (Felsenstein, 1989) and ARB (Ludwig et al., 2004) software packages. Branch lengths of the consensus tree were inferred by the Fitch algorithm using a Jukes–Cantor derived distance matrix (Phylip), the scale bar represents 10% estimated sequence divergence. Affiliation of short DsrA or DsrB sequences (<542 amino acids) retrieved from freshwater wetlands was inferred using the consensus tree and the quick-add-parsimony tool within ARB. Uncultured family level DsrAB lineages that comprise such short DsrA and DsrB sequences but no near full-length DsrAB sequences from freshwater wetlands are colored green but are not marked with a green dot.

Figure 4

Relative abundances (as inferred from quantitative dsrA- or 16S rRNA gene-targeted PCR analyses) of recognized and putative SRM in the model peatland Schlöppnerbrunnen II. This figure is based on data from Loy et al. (2004); Schmalenberger et al. (2007); Pester et al. (2010); Steger et al. (2011). The abundance of the large number of other dsrAB OTUs (including dsrAB related to Desulfomonile and Desulfobacca spp.), which were also detected at Schlöppnerbrunnen II, and their contribution to sulfate reduction is currently unknown (Loy et al., ; Schmalenberger et al., ; Pester et al., ; Steger et al., 2011).