Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

Abstract

High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a ‘divide and conquer' strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the ‘divide and conquer' strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

“…Advanced high-throughput molecular approaches such as 16S rRNA gene sequencing, metagenomic and metatranscriptomic profiling, and functional genes microarray provide a route to phylogenetic and functional insight of the microbial community without the requirement for laboratory cultivation [28,29]. The recent efforts significantly increased our knowledge of the microbial diversity and community function in AMD ecosystems [29,47].…”

“…The nitrogen cycle is also critical for the microbial community because the resource of nitrogen is usually limited in AMD environments [1]. However, based on a transcriptional analysis, Hua et al found that the nifH gene encoding enzymes involved in nitrogen fixation was highly expressed in rare taxa, suggesting that rare species likely perform essential ecological functions in AMD biogeochemistry [28].…”

“…However, based on a transcriptional analysis, Hua et al found that the nifH gene encoding enzymes involved in nitrogen fixation was highly expressed in rare taxa, suggesting that rare species likely perform essential ecological functions in AMD biogeochemistry [28]. In generating AMD, the dissolving of sulfide minerals by associated microbes decreases the solution pH and releases a high amount of metals.…”

“…More than 100 known genera have been detected in extreme AMD-generating conditions in South China, revealing a considerable microbial diversity in these environments ( Figure 1). Except for several dominant species directly related to iron/sulfur-oxidizing, a large number of rare taxa constitute a "rare biosphere" in the community and may perform a crucial function in AMD ecosystems [28,43]. Although a large number of the observed operational taxonomic units (OTUs) cannot be classified into a specific genus, advanced high-throughput sequencing approaches offer more comprehensive information about the microbial community than traditional cultivation methods [44,45].…”

Sulfur Isotope Fractionation as an Indicator of Biogeochemical Processes in an AMD Passive Bioremediation System

“…However, the predominant Fe oxidizer shifted to one related to a Ferrovum, a genus that has also been detected in a wide range of AMD sites [39][40][41][42][43]. This community analysis also suggested limited biological S cycling in the pretreated AMD drainage as only 2% of the analyzed sequences were related to a potential S oxidizing Thiomonas species and no sequences related to S or SO 4 2− reducers were detected ( Figure 3).…”