A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining

Abstract

Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.

Contrasting soil fungal communities at different habitats in a revegetated copper mine wasteland

“…Moreover, the development of metagenomics has suggested the possibility that we may get a better understanding of changes in microbial metabolic potential following revegetation of mine wastelands through analyzing metagenomes from related experiments. To date, however, there are only two metagenomic studies on the topic (Gastauer et al, 2019;Sun and Badgley, 2019). By comparing 15 soil metagenomes from a post-mining forest rehabilitation chronosequence spanning 6-31 years plus an unmined reference forest, Sun and Badgley (2019) showed significant differences between these metagenomes in the relative abundances of genes involved in carbon (C) cycling but not in those of genes responsible for nitrogen (N) cycling.…”

“…By comparing 15 soil metagenomes from a post-mining forest rehabilitation chronosequence spanning 6-31 years plus an unmined reference forest, Sun and Badgley (2019) showed significant differences between these metagenomes in the relative abundances of genes involved in carbon (C) cycling but not in those of genes responsible for nitrogen (N) cycling. In contrast, the paper of Gastauer et al (2019) only provided a complete data set of 34 soil metagenomes from a post-mining rehabilitation chron-osequence spanning 0-6 years plus three reference sites, but did not make any detailed analysis of or discussion on the data set. Nonetheless, neither of the two studies presented data on fungi.…”

“…This phenomenon can be attributed largely to the fact that at this stage fungal sequences are generally found to account for only a small proportion of all the sequences in metagenomic libraries of various samples, which limits our ability to uncover the functional potentials of soil fungal communities via metagenomics (Cuadros-Orellana et al, 2013;Sun and Badgley, 2019). In this context, we took advantage of the Illumina HiSeq 2500 (a widely used nextgeneration sequencing platform; Goodwin et al, 2016) to sequence fungal ITS2 region to get some clues for a better understanding of the responses of soil fungal communities to revegetation. To that end, 4000 m 2 of vegetation was reestablished on an extremely acidic (pH 2.5) Cu mine tailings pond with the use of eight plant species (including four grasses, two legumes, one non-grass herb and one nonlegume forb) and 120 soil fungal communities at three types of habitats in the revegetated mine wasteland were characterized.…”

Integrating Environmental Variables by Multivariate Ordination enables the Reliable Estimation of Mineland Rehabilitation Status

“…To test our method, we analyzed a rehabilitating chronosequence after open-cast iron ore mining situated between 19º10'-19º13' S and 57º33'-57º37' W in the Urucum Massif, Corumbá and Ladário municipalities, Mato Grosso do Sul, midwestern Brazil (Gastauer et al, 2019). The We sampled three bare soil, i.e., nonrevegetated, seven rehabilitating (two-, three-and six-yearold stands), and three reference sites ( Fig.…”

DNA Barcoding and Genomics in the Megadiverse Amazon Altitude Fields

“…We are also establishing eDNA methods, as well as metagenomics and metaproteomics data for environmental monitoring of ferruginous fields phytophysiognomies, areas under rehabilitation processes, and caves 8 . Together these data constitute the most profound molecular representation of any environment in Brazil.…”