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

Variations of microbiota in three types of typical military contaminated sites: Diversities, structures, influence factors, and co-occurrence patterns

Contamination with energetic compounds (ECs) is common in military sites and poses a great risk to the environment and human health. However, its effects on the soil bacterial communities remain unclear. This study assessed the variations of bacterial communities, co-occurrence patterns, and their influence factors in three types of typical military-contaminated sites (artillery range, military-industrial site, and ammunition destruction site). The results showed that the most polluted sites were ammunition destruction sites, followed by military-industrial sites, whereas pollution in the artillery ranges was minimal. The average concentrations of ECs including 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in the study sites ranged 120-1.67 × 10⁵, 20-7.20 × 10⁴, and 180-2.38 × 10⁵ μg/kg, respectively. Bacterial diversity and community structure in military-industrial and ammunition destruction sites were significantly changed, but not in artillery ranges. TNT, pH, and soil moisture are the critical factors affecting bacterial communities in contaminated military sites. Co-occurrence network analysis indicated that the pressure of ECs affected bacterial interactions and microbiota function. Our findings provide new insights into the variations in bacterial communities in EC-contaminated military sites and references for the bioremediation of ECs.

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

Environmental contamination by hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX), and Octahydro-1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetrazocine (HMX), the two most widely used compounds for military operations, is a long-standing problem at the manufacturing and decommissioning plants. Since explosives contamination has previously been shown to favour the growth of specific bacterial communities, the present study attempts to identify the specialist bacterial communities and their potential functional and metabolic roles by using amplicon targeted and whole-metagenome sequencing approaches (WMS) in samples collected from two distinct explosives manufacturing sites. We hypothesize that the community structure and functional attributes of bacterial population are substantially altered by the concentration of explosives and physicochemical conditions. The results highlight the predominance of Planctomycetes in contrast to previous reports from similar habitats. The detailed phylogenetic analysis revealed the presence of OTU's related to bacterial members known for their explosives degradation. Further, the functional and metabolic analyses highlighted the abundance of putative genes and unidentified taxa possibly associated with xenobiotic biodegradation. Our findings suggest that microbial species capable of utilizing explosives as a carbon, energy, or electron source are favoured by certain selective pressures based on the prevailing physicochemical and geographical conditions.

Exploring the Distinct Distribution of Archaeal Communities in Sites Contaminated with Explosives

Most of the research on bioremediation and estimation of microbial diversity in waste contaminated sites is focused on the domain Bacteria, whereas details on the relevance of Archaea are still lacking. The present study examined the archaeal diversity and predicted metabolic pathways in two discrete sites (SITE1 and SITE2) contaminated with explosives (RDX and HMX) by amplicon-targeted sequencing of 16S rRNA genes. In total, 14 soil samples were processed, and 35,758 OTUs were observed, among which 981 OTUs were classified as Archaea, representing ~2.7% of the total microbial diversity in our samples. The majority of OTUs belonged to phyla Euryarchaeota (~49%), Crenarchaeota (~24%), and Thaumarchaeota (~23%), while the remaining (~4%) OTUs were affiliated to Candidatus Parvarchaeota, Candidatus Aenigmarchaeota, and Candidatus Diapherotrites. The comparative studies between explosives contaminated and agricultural soil samples (with no history of explosives contamination) displayed significant differences between the compositions of the archaeal communities. Further, the metabolic pathways pertaining to xenobiotic degradation were presumably more abundant in the contaminated sites. Our data provide a first comprehensive report of archaeal communities in explosives contaminated sites and their putative degradation role in such ecosystems which have been as yet unexplored.

Microbial diversity in a military impacted lagoon (Vieques, Puerto Rico) and description of "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. comprising a new bacterial family

The Anones Lagoon, located in the Island Municipality of Vieques, Puerto Rico (PR), received extensive bombing by the US Navy during military exercises for decades until 2003 when military activities ceased. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR's capital city). Consistent with low anthropogenic inputs, Guaniquilla exhibited the highest degree of diversity with a lower frequency of genes related to xenobiotics metabolism between the three lagoons. Notably, a clear shift was observed in Anones, with Euryarchaeota becoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique metagenome-assembled genomes (MAGs) were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants, and we propose to name one of them as "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. within the Gammaproteobacteria class. Collectively, these results provide new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and provide a reference point for assessing other similarly impacted sites and associated bioremediation efforts.

Microbial community structure and metabolome profiling characteristics of soil contaminated by TNT, RDX, and HMX

This experiment was conducted to evaluate the ecotoxicity of typical explosives and their mechanisms in the soil microenvironment. Here, TNT (trinitrotoluene), RDX (cyclotrimethylene trinitramine), and HMX (cyclotetramethylene tetranitramine) were used to simulate the soil pollution of single explosives and their combination. The changes in soil enzyme activity and microbial community structure and function were analyzed in soil, and the effects of explosives exposure on the soil metabolic spectrum were revealed by non-targeted metabonomics. TNT, RDX, and HMX exposure significantly inhibited soil microbial respiration and urease and dehydrogenase activities. Explosives treatment reduced the diversity and richness of the soil microbial community structure, and the microorganisms able to degrade explosives began to occupy the soil niche, with the Sphingomonadaceae, Actinobacteria, and Gammaproteobacteria showing significantly increased relative abundances. Non-targeted metabonomics analysis showed that the main soil differential metabolites under explosives stress were lipids and lipid-like molecules, organic acids and derivatives, with the phosphotransferase system (PTS) pathway the most enriched pathway. The metabolic pathways for carbohydrates, lipids, and amino acids in soil were specifically inhibited. Therefore, residues of TNT, RDX, and HMX in the soil could inhibit soil metabolic processes and change the structure of the soil microbial community.

Biodegradation and physiological response mechanism of Bacillus aryabhattai to cyclotetramethylenete-tranitramine (HMX) contamination

This study aims to reveal the biodegradation and interaction mechanism of cyclotetramethylenete-tranitramine (HMX) by a newly isolated bacteria. In this study, a bacterial strain (Bacillus aryabhattai) with high efficiency for HMX degradation was used as the test organism to analyze the changes in growth status, cell function, and mineral metabolism following exposure to different stress concentrations (0 and 5 mg L^-1) of HMX. Non-targeted metabonomics was used to reveal the metabolic response of this strain to HMX stress. The results showed that when the HMX concentration was 5 mg L^-1, the removal rate of HMX within 24 h of inoculation with Bacillus aryabhatta was as high as 90.5%, the OD₆₀₀ turbidity was 1.024, and the BOD₅ was 225 mg L^-1. Scanning electron microscope (SEM) images showed that the morphology of bacteria was not obvious Variety, Fourier transform infrared spectroscopy (FTIR) showed that the cell surface -OH functional groups drifted, and ICP-MS showed that the cell mineral element metabolism was disturbed. Non-targeted metabonomics showed that HMX induced the differential expression of 254 metabolites (133 upregulated and 221 downregulated). The main differentially expressed metabolites during HMX stress were lipids and lipid-like molecules, and the most significantly affected metabolic pathway was purine metabolism. At the same time, the primary metabolic network of bacteria was disordered. These results confirmed that Bacillus aryabhattai has a high tolerance to HMX and can efficiently degrade HMX. The degradation mechanism involves the extracellular decomposition of HMX and transformation of the degradation products into intracellular purines, amino sugars, and nucleoside sugars that then participate in cell metabolism.

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

Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.