A comparative study of microbial communities in four soil slurries capable of RDX degradation using illumina sequencing

Abstract

The nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has contaminated many military sites. Recently, attempts to remediate these sites have focused on biostimulation to promote RDX biodegradation. Although many RDX degrading isolates have been obtained in the laboratory, little is known about the potential of microorganisms to degrade this chemical while existing in a soil community. The current study examined and compared the RDX degrading communities in four soil slurries to elucidate the potential of natural systems to degrade this chemical. These soils were selected as they had no previous exposure to RDX, therefore their microbial communities offered an excellent baseline to determine changes following RDX degradation. High throughput sequencing was used to determine which phylotypes experienced an increase in relative abundance following RDX degradation. For this, total genomic DNA was sequenced from (1) the initial soil, (2) soil slurry microcosms following RDX degradation and (3) control soil slurry microcosms without RDX addition. The sequencing data provided valuable information on which phylotypes increased in abundance following RDX degradation compared to control microcosms. The most notable trend was the increase in abundance of Brevundimonas and/or unclassified Bacillaceae 1 in the four soils studied. Although isolates of the family Bacillaceae 1 have previously been linked to RDX degradation, isolates of the genus Brevundimonas have not been previously associated with RDX degradation. Overall, the data suggest these two phylotypes have key roles in RDX degradation in soil communities.

Uncovering the structure and function of specialist bacterial lineages in environments routinely exposed to explosives

“…S7b). Contrary to very few studies reporting degraders in class a-proteobacteria (Van Aken et al 2004;Ronen et al 2008;Jayamani and Cupples 2015b) our study suggests their considerable abundance (Fig. S7a) which might be due to their ability to degrade a wide variety of substrates.…”

“…Although various culture‐independent studies have revealed bacterial community structures at various explosives‐contaminated sites (Cupples 2013; Jayamani and Cupples 2015b; Eberly et al . 2016; Wang et al .…”

“…Although various culture-independent studies have revealed bacterial community structures at various explosives-contaminated sites (Cupples 2013;Jayamani and Cupples 2015b;Eberly et al 2016;Wang et al 2016;Fuller et al 2020), the present work gives a broader view of prokaryotic community composition. The soil samples (16 nos.)…”

“…In addition, the 16S rRNA gene sequences of known explosives degrading strains were manually downloaded from the NCBI nucleotide database and further used to assess the phylogenetic placement of observed OTU's using genome net server (https://www.genome.jp/ ) (accessed on 23 May 2022) with default settings. The SRA data files under project PRJNA263419 and accession numbers SAMN03100356 to SAMN03100363 (Jayamani and Cupples 2015b) were also used for comparison with data from the present study.…”

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

“…Recent studies have characterized microbial communities from contaminated environments using next-generation sequencing (17,18), and the applicability of the Illumina technology for affordable high-throughput amplicon deep sequencing has been reported (19)(20)(21), allowing the identification of key players at contaminated sites (22). Molecular techniques also allow the study of microbial diversity and key catabolic genes in situ.…”