Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site

Abstract

Background: Ferrovum spp. are abundant in acid mine drainage sites globally where they play an important role in biogeochemical cycling. All known taxa in this genus are Fe(II) oxidizers. Thus, co-occurring members of the genus could be competitors within the same environment. However, we found multiple, co-occurring Ferrovum spp. in Cabin Branch, an acid mine drainage site in the Daniel Boone National Forest, KY.

Results: Here we describe the distribution of Ferrovum spp. within the Cabin Branch communities and metagenome assembled genomes (MAGs) of two new Ferrovum spp. In contrast to previous studies, we recovered multiple 16S rRNA gene sequence variants suggesting the commonly used 97% cutoff may not be appropriate to differentiate Ferrovum spp. We also retrieved two nearly-complete Ferrovum spp. genomes from metagenomic data. The genomes of these taxa differ in several key ways relating to nutrient cycling, motility, and chemotaxis.

Conclusions: Previously reported Ferrovum genomes are also diverse with respect to these categories suggesting that the genus Ferrovum contains substantial metabolic diversity. This diversity likely explains how the members of this genus successfully co-occur in Cabin Branch and why Ferrovum spp. are abundant across geochemical gradients.

Keywords: Acidophlic; Biofilm; Carbon fixation; Co-occurrence; Denoised sequence variants; Ferrovum; Iron oxidation; Metagenome; Microcosm; Nitrogen.

Fig. 1

Sketch of the Cabin Branch sampling site with associated images and geochemistry. Emergence = point at which flow emerges from the groundwater source. Limestone lined channel (LLC) = fabricated channel lined with limestone gravels as part of remediation. Retention Pond (Rose Pool) = fabricated retention pond as part of remediation. Labeled stars denote sampling locations, with aqueous geochemistry shown for sites where metagenomic analyses were performed

Fig. 2

16S rRNA gene tree of Ferrovum spp. Group nomenclature from [18]. DSVs found in the emergence are indicated by circles, triangles indicate those found in the limestone lined channel, and squares those found in the Rose Pool

Fig. 3

Relative abundance of Ferrovum DSVs in each of the sampled communities as determined by 16S rRNA sequencing. Each Ferrovum DSV is represented by a unique color. Grey bars indicate estimated abundance of Ferrovum from the metagenomic datasets

Fig. 4

Concatenated gene tree containing all Ferrovum bins retrieved from the metagenomic datasets. Colored rectangles indicate the bins that belong to a given MAG. Bootstrap values (based on 100 bootstrap samplings) are shown for each node where bootstrap support is > 50%

Fig. 5

Maximum likelihood phylogeny phylogeny of Cyc-2 like gene found in published Ferrovum genomes and the MAGs retrieved in this study. Accession numbers are provided in parentheses. Numbers represent bootstrap support values based on 100 bootstrap samplings

Fig. 6

Potential cycling of C, S, P, and N in Ferrovum MAGs from Cabin Branch as predicted by the gene content of the MAGs. Proteins are color coded based on their presence or absence in each genome. Modeled after [18]

Fig. 7

Images and carbon uptake rates for Cabin Branch emergence (E), limestone lined channel (LLC), and Rose Pool retention pond sites. L = light treatment, D = dark treatment (wrapped in aluminum foil), W = white filaments/mat, G = green filaments/mat