Metagenomic insights into the RDX-degrading potential of the ovine rumen microbiome

Seed bacterial microbiota in post-submergence tolerant and sensitive barley genotypes

Flooding is a predominant abiotic stress for cultivated plants, including barley. This cereal crop shows a large adaptability to different environmental conditions, suggesting the presence of key traits to tolerate adverse conditions. During germination, genetic variations account for dissimilarities in flooding tolerance. However, differences in the seed microbiota may also contribute to tolerance/sensitivity during seedling establishment. This work investigated differences in microbiome among the grains of barley accessions. Two barley phenotypes were compared, each either tolerant or sensitive to a short submergence period followed by a recovery. The study used a metataxonomic analysis based on 16S ribosomal RNA gene sequencing and subsequent functional prediction. Our results support the hypothesis that bacterial microbiota inhabiting the barley seeds are different between sensitive and tolerant barley accessions, which harbour specific bacterial phyla and families. Finally, bacteria detected in tolerant barley accessions show a peculiar functional enrichment that suggests a possible connection with successful germination and seedling establishment.

Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence

Flooding events caused by severe rains and poor soil drainage can interfere with plant germination and seedling establishment. Rice is one of the cereal crops that has unique germination strategies under flooding. One of these strategies is based on the fast coleoptile elongation in order to reach the water surface and re-establish the contact with the air. Microorganisms can contribute to plant health via plant growth promoters and provide protection from abiotic stresses. To characterise the community composition of the microbiome in rice germination under submergence, a 16S rRNA gene profiling metagenomic analysis was performed of temperate japonica rice varieties Arborio and Lamone seedlings, which showed contrasting responses in terms of coleoptile length when submerged. This analysis showed a distinct microbiota composition of Arborio seeds under submergence, which are characterised by the development of a long coleoptile. To examine the potential function of microbial communities under submergence, culturable bacteria were isolated, identified and tested for plant growth-promoting activities. A subgroup of isolated bacteria showed the capacity to hydrolyse starch and produce indole-related compounds under hypoxia. Selected bacteria were inoculated in seeds to evaluate their effect on rice under submergence, showing a response that is dependent on the rice genotype. Our findings suggest that endophytic bacteria possess plant growth-promoting activities that can substantially contribute to rice seedling establishment under submergence.

Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities

Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.

Diversity and abundance of the functional genes and bacteria associated with RDX degradation at a contaminated site pre- and post-biostimulation

Bioremediation is becoming an increasingly popular approach for the remediation of sites contaminated with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Multiple lines of evidence are often needed to assess the success of such approaches, with molecular studies frequently providing important information on the abundance of key biodegrading species. Towards this goal, the current study utilized shotgun sequencing to determine the abundance and diversity of functional genes (xenA, xenB, xplA, diaA, pnrB, nfsI) and species previously associated with RDX biodegradation in groundwater before and after biostimulation at an RDX-contaminated Navy Site. For this, DNA was extracted from four and seven groundwater wells pre- and post-biostimulation, respectively. From a set of 65 previously identified RDX degraders, 31 were found within the groundwater samples, with the most abundant species being Variovorax sp. JS1663, Pseudomonas fluorescens, Pseudomonas putida, and Stenotrophomonas maltophilia. Further, 9 RDX-degrading species significantly (p<0.05) increased in abundance following biostimulation. Both the sequencing data and qPCR indicated that xenA and xenB exhibited the highest relative abundance among the six genes. Several genes (diaA, nsfI, xenA, and pnrB) exhibited higher relative abundance values in some wells following biostimulation. The study provides a comprehensive approach for assessing biomarkers during RDX bioremediation and provides evidence that biostimulation generated a positive impact on a set of key species and genes. KEY POINTS: • A co-occurrence network indicated diverse RDX degraders. • >30 RDX-degrading species were detected. • Nine RDX-degrading species increased following biostimulation. • Sequencing and high-throughput qPCR indicated that xenA and xenB were most abundant.

A Sporolactobacillus-, Clostridium-, and Paenibacillus- Dominant Microbial Consortium Improved Anaerobic RDX Detoxification by Starch Addition

In the present study, an anaerobic microbial consortium for the degradation of hexahydro-1,3,5- trinitro-1,3,5-triazine (RDX) was selectively enriched with the co-addition of RDX and starch under nitrogen-deficient conditions. Microbial growth and anaerobic RDX biodegradation were effectively enhanced by the co-addition of RDX and starch, which resulted in increased RDX biotransformation to nitroso derivatives at a greater specific degradation rate than those for previously reported anaerobic RDX-degrading bacteria (isolates). The accumulation of the most toxic RDX degradation intermediate (MNX [hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine]) was significantly reduced by starch addition, suggesting improved RDX detoxification by the co-addition of RDX and starch. The subsequent MiSeq sequencing that targeted the bacterial 16S rRNA gene revealed that the Sporolactobacillus, Clostridium, and Paenibacillus populations were involved in the enhanced anaerobic RDX degradation. These results suggest that these three bacterial populations are important for anaerobic RDX degradation and detoxification. The findings from this work imply that the Sporolactobacillus, Clostridium, and Paenibacillus dominant microbial consortium may be valuable for the development of bioremediation resources for RDX-contaminated environments.

High throughput quantification of the functional genes associated with RDX biodegradation using the SmartChip real-time PCR system

The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a contaminant at many military sites. RDX bioremediation as a clean-up approach has been gaining popularity because of cost benefits compared to other methods. RDX biodegradation has primarily been linked to six functional genes (diaA, nfsI, pnrB, xenA, xenB, xplA). However, current methods for gene quantification have the risk of false negative results because of low theoretical primer coverage. To address this, the current study designed new primer sets using the EcoFunPrimer tool based on sequences collected by the Functional Gene Pipeline and Repository and these were verified based on residues and motifs. The primers were also designed to be compatible with the SmartChip Real-Time PCR system, a massively parallel singleplex PCR platform (high throughput qPCR), that enables quantitative gene analysis using 5,184 simultaneous reactions on a single chip with low volumes of reagents. This allows multiple genes and/or multiple primer sets for a single gene to be used with multiple samples. Following primer design, the six genes were quantified in RDX-contaminated groundwater (before and after biostimulation), RDX-contaminated sediment, and uncontaminated samples. The final 49 newly designed primer sets improved upon the theoretical coverage of published primer sets, and this corresponded to more detections in the environmental samples. All genes, except diaA, were detected in the environmental samples, with xenA and xenB being the most predominant. In the sediment samples, nfsI was the only gene detected. The new approach provides a more comprehensive tool for understanding RDX biodegradation potential at contaminated sites.

Effects of acute exposures of 2,4,6-trinitrotoluene and inorganic lead on the fecal microbiome of the green anole (Anolis carolinensis)

Microbiome studies focused on ecologically relevant vertebrate models like reptiles have been limited. Because of their relatively small home range, fast maturation, and high fecundity, lizards are an excellent reptilian terrestrial indicator species. For this study we used the green anole, Anolis carolinensis, to assess the impact of military relevant contaminants on fecal microbiome composition. Fourteen day sub-acute exposures were conducted via oral gavage with 2,4,6-Trinitrotoluene (TNT) and inorganic lead at doses of 60 mg/kg and 20 mg/kg of body weight, respectively. Body weights and food consumption were monitored and fecal samples were collected for high-throughput 16S rRNA gene amplicon sequencing and analytical chemistry at days 0 and 15. At the end of the study, liver and gut were harvested for body burden data. Chemical analysis confirmed accumulation of TNT, TNT transformation products, and lead in liver tissue and fecal samples. Bacterial community analysis of fecal material revealed significant differences between day 0 and day 15 of TNT exposed anoles with an operational taxonomic unit (OTU) within the genus Erwinia representing 32% of the microbial community in TNT exposed anoles. Predictable changes in gut microbiome composition could offer an easily assayed, noninvasive biomarker for specific chemical exposure providing enhanced scientific support to risk assessments on military installations.

Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants

Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption. To date, hundreds to thousands of microbial phylotypes have been identified in the rumen using culture-independent molecular-based approaches, and genomic information of rumen microorganisms is rapidly accumulating through the single genome sequencing. However, functional characteristics of the rumen microbiome have not been well described because there are numerous uncultivable microorganisms in the rumen. The advent of metagenomics and metatranscriptomics along with advanced bioinformatics methods can help us better understand mechanisms of the rumen fermentation, which is vital for improving nutrient utilization and animal productivity. Therefore, in this review, we summarize a general workflow to conduct rumen metagenomics and metatranscriptomics and discuss how the data can be interpreted to be useful information. Moreover, we review recent literatures studying associations between the rumen microbiome and host phenotypes (e.g., feed efficiency and methane emissions) using these approaches, aiming to provide a useful guide to include studying the rumen microbiome as one of the research objectives using these 2 approaches.

Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome

BACKGROUND

Grazing mammals rely on their ruminal microbial symbionts to convert plant structural biomass into metabolites they can assimilate. To explore how this complex metabolic system adapts to the host animal's diet, we inferred a microbiome-level metabolic network from shotgun metagenomic data.

RESULTS

Using comparative genomics, we then linked this microbial network to that of the host animal using a set of interface metabolites likely to be transferred to the host. When the host sheep were fed a grain-based diet, the induced microbial metabolic network showed several critical differences from those seen on the evolved forage-based diet. Grain-based (e.g., concentrate) diets tend to be dominated by a smaller set of reactions that employ metabolites that are nearer in network space to the host's metabolism. In addition, these reactions are more central in the network and employ substrates with shorter carbon backbones. Despite this apparent lower complexity, the concentrate-associated metabolic networks are actually more dissimilar from each other than are those of forage-fed animals. Because both groups of animals were initially fed on a forage diet, we propose that the diet switch drove the appearance of a number of different microbial networks, including a degenerate network characterized by an inefficient use of dietary nutrients. We used network simulations to show that such disparate networks are not an unexpected result of a diet shift.

CONCLUSION

We argue that network approaches, particularly those that link the microbial network with that of the host, illuminate aspects of the structure of the microbiome not seen from a strictly taxonomic perspective. In particular, different diets induce predictable and significant differences in the enzymes used by the microbiome. Nonetheless, there are clearly a number of microbiomes of differing structure that show similar functional properties. Changes such as a diet shift uncover more of this type of diversity.

Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater

Hexahydro‐1,3,5‐trinitro‐1,3,5‐triazine (RDX) is a high explosive released to the environment as a result of weapons manufacturing and testing worldwide. At Los Alamos National Laboratory, the Technical Area (TA) 16 260 Outfall discharged high‐explosives‐bearing water from a high‐explosives‐machining facility to Cañon de Valle during 1951 through 1996. These discharges served as a primary source of high‐explosives and inorganic‐element contamination in the area. Data indicate that springs, surface water, alluvial groundwater, and perched‐intermediate groundwater contain explosive compounds, including RDX (hexahydro‐1,3,5‐trinitro‐1,3,5‐triazine); HMX (octahydro‐1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocine); and TNT (2,4,6‐trinitrotoluene). RDX has been detected in the regional aquifer in several wells, and a corrective measures evaluation is planned to identify remedial alternatives to protect the regional aquifer. Perched‐intermediate groundwater at Technical Area 16 is present at depths from 650 ft to 1200 ft bgs. In this study, we examined the microbial diversity in a monitoring well completed in perched‐intermediate groundwater contaminated by RDX, and examined the response of the microbial population to biostimulation under varying geochemical conditions. Results show that the groundwater microbiome was dominated by Actinobacteria and Proteobacteria. A total of 1,605 operational taxonomic units (OTUs) in 96 bacterial genera were identified. Rhodococcus was the most abundant genus (30.6%) and a total of 46 OTUs were annotated as Rhodococcus. One OTU comprising 25.2% of total sequences was closely related to a RDX ‐degrading strain R. erythropolis HS4. A less abundant OTU from the Pseudomonas family closely related to RDX‐degrading strain P. putida II‐B was also present. Biostimulation significantly enriched Proteobacteria but decreased/eliminated the population of Actinobacteria. Consistent with RDX degradation, the OTU closely related to the RDX‐degrading P. putida strain II‐B was specifically enriched in the RDX‐degrading samples. Analysis of the accumulation of RDX‐degradation products reveals that during active RDX degradation, there is a transient increase in the concentration of the degradation products MNX, DNX, TNX, and NDAB. The accumulation of these degradation products suggests that RDX is degraded via sequential reduction of the nitro functional groups followed by abiotic ring‐cleavage. The results suggest that strict anaerobic conditions are needed to stimulate RDX degradation under the TA‐16 site‐specific conditions.

Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations

The ruminal microbial community is remarkably diverse, containing 100s of different bacterial and archaeal species, plus many species of fungi and protozoa. Molecular studies have identified a “core microbiome” dominated by phyla Firmicutes and Bacteroidetes, but also containing many other taxa. The rumen provides an ideal laboratory for studies on microbial ecology and the demonstration of ecological principles. In particular, the microbial community demonstrates both redundancy (overlap of function among multiple species) and resilience (resistance to, and capacity to recover from, perturbation). These twin properties provide remarkable stability that maintains digestive function for the host across a range of feeding and management conditions, but they also provide a challenge to engineering the rumen for improved function (e.g., improved fiber utilization or decreased methane production). Direct ruminal dosing or feeding of probiotic strains often fails to establish the added strains, due to intensive competition and amensalism from the indigenous residents that are well-adapted to the historical conditions within each rumen. Known exceptions include introduced strains that can fill otherwise unoccupied niches, as in the case of specialist bacteria that degrade phytotoxins such as mimosine or fluoroacetate. An additional complicating factor in manipulating the ruminal fermentation is the individuality or host specificity of the microbiota, in which individual animals contain a particular community whose species composition is capable of reconstituting itself, even following a near-total exchange of ruminal contents from another herd mate maintained on the same diet. Elucidation of the interactions between the microbial community and the individual host that establish and maintain this specificity may provide insights into why individual hosts vary in production metrics (e.g., feed efficiency or milk fat synthesis), and how to improve herd performance.