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, cooccurring 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.

Metagenome assembled genomes of novel taxa from an acid mine drainage environment

“…Groundwater at Cabin Branch emerges at pH 2.90 and flows down a limestone-lined channel with a pH of 2.92 (installed as a passive remediation strategy) and enters a pool ("Rose Pool) which has a pH of 2.97. Dissolved oxygen increases down the drainage site (77.5 µmol/L at the emergence, 401 µmol/L in Rose Pool) and Fe(II) concentration ranges from 403 µmol/L at the emergence, 882.0 µmol/L in the limestone-lined channel, and 11.16 µmol/L in Rose Pool (33) We recovered 256 bins from metagenomes: 38 from the emergence, 32 from the limestone-lined channel, 66 from the Rose Pool, and 120 from the coassembly. Of these, 56 were >70% complete with <3% contamination.…”

“…The MAGs ranged in relative abundance from ~4.3% to ~0.17% (Figures 1 and 2). The Ferrovum MAGs (MAG 23 and and MAG24) were described in (33)and MAG 7 is closely related to a previously described genome (59,60). Below, we examine functions that are most relevant to AMD ecosystems including aerobic respiration, carbon fixation, nitrogen cycling and biogeochemical cycling of sulfur and iron in each MAG by phylogenetic group.…”

“…Methods for sample collection, DNA extraction and sequencing, and metagenome assembly and binning were described previously (33) and we include brief descriptions below.…”

“…Nine are from the gammaproteobacterial order Burkholderiales. Two of these were described previously and were not analyzed here (33).…”

“…Even in well-studied AMD groups like the Gammaproteobacteria, multiple closely related taxa may occur in AMD sites but may play different roles from their close relatives. For example, multiple Ferrovum taxa differ in their ability to fix nitrogen (30)(31)(32)(33). This intragenus metabolic diversity complicates our ability to understand biogeochemical cycling in AMD environments.…”