Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron

Abstract

Tropical forest soils decompose litter rapidly with frequent episodes of anoxia, making it likely that bacteria using alternate terminal electron acceptors (TEAs) such as iron play a large role in supporting decomposition under these conditions. The prevalence of many types of metabolism in litter deconstruction makes these soils useful templates for improving biofuel production. To investigate how iron availability affects decomposition, we cultivated feedstock-adapted consortia (FACs) derived from iron-rich tropical forest soils accustomed to experiencing frequent episodes of anaerobic conditions and frequently fluctuating redox. One consortium was propagated under fermenting conditions, with switchgrass as the sole carbon source in minimal media (SG only FACs), and the other consortium was treated the same way but received poorly crystalline iron as an additional terminal electron acceptor (SG + Fe FACs). We sequenced the metagenomes of both consortia to a depth of about 150 Mb each, resulting in a coverage of 26× for the more diverse SG + Fe FACs, and 81× for the relatively less diverse SG only FACs. Both consortia were able to quickly grow on switchgrass, and the iron-amended consortium exhibited significantly higher microbial diversity than the unamended consortium. We found evidence of higher stress in the unamended FACs and increased sugar transport and utilization in the iron-amended FACs. This work provides metagenomic evidence that supplementation of alternative TEAs may improve feedstock deconstruction in biofuel production.

Keywords: Anaerobic decomposition; Panicum virgatum; archaea; bacteria; feedstock-adapted consortia; metagenomics; switchgrass; tropical forest soil.

Figure 1

Phyla that are at least 2-fold differentially represented in one metagenome compared to the other, and had greater than one representative detected. Phyla with gene counts over-represented in the iron-amended consortium (SG + Fe) are colored brown, while phyla with gene counts over-represented in the unamended consortium (SG only) are colored light green.

Figure 2

Network analysis of feedstock adapted consortia grown on switchgrass only (SG only), SG plus iron oxides (FeOx), SG plus nitrate (NO₃^-), or SG plus sulfate (SO₃^-). Each point represents one taxon, and the size of the point corresponds to the number of connections (edges) associated with the taxon. Edges (grey lines) indicate a minimum correlation of Pearson r = 0.9 as well as statistical significance (P<0.01). On the left, taxa are colored by taxonomy according to their assigned phylum; on the right, taxa are colored based on whether they are generalists (present in all four treatments) or specialists (present in one treatment only and absent in the rest).

Figure 3

Illustration of pfams that were differentially represented in SG only compared to SG + Fe. On the left, pfams are listed for the consortium grown in switchgrass only with no iron (SG only), and on the right, pfams are listed for the consortium grown in switchgrass with iron (SG + Fe). This illustration is based on data from Table 7.