Merging Fungal and Bacterial Community Profiles via an Internal Control

Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing

Microbiome studies using high-throughput sequencing are increasingly incorporating absolute quantitative approaches to overcome the inherent limitations of relative abundances. In this study, we have designed and experimentally validated a set of 12 unique synthetic rRNA operons, which we refer to as rDNA-mimics, to serve as spike-in standards for quantitative profiling of fungal/eukaryotic and bacterial microbiomes. The rDNA-mimics consist of conserved sequence regions from natural rRNA genes to act as binding sites for common universal PCR primers, and bioinformatically designed variable regions that allow their robust identification in any microbiome sample. All constructs cover multiple rRNA operon regions commonly targeted in fungal/eukaryotic microbiome studies (SSU-V9, ITS1, ITS2, and LSU-D1D2) and two of them also include an artificial segment of the bacterial 16S rRNA gene (SSU-V4) for cross-domain application. We validated the quantitative performance of the rDNA-mimics using defined mock communities and representative environmental samples. In particular, we show that rDNA-mimics added to extracted DNA or directly to the samples prior to DNA extraction precisely reflects the total amount of fungal and/or bacterial rRNA genes in the samples. We demonstrate that this allows accurate estimation of differences in microbial loads between samples, thereby confirming that the rDNA-mimics are suitable for absolute quantitative analyses of differential microbial abundances.

Nutrient and Microbiome-Mediated Plant-Soil Feedback in Domesticated and Wild Andropogoneae: Implications for Agroecosystems

Plants influence the abiotic and biotic environment of the rhizosphere, affecting plant performance through plant-soil feedback (PSF). We compared the strength of nutrient and microbe-mediated PSF and its implications for plant performance in domesticated and wild grasses with a fully crossed greenhouse PSF experiment using four inbred maize genotypes (Zea mays ssp. mays b58, B73-wt, B73-rth3, and HP301), teosinte (Z. mays ssp. parviglumis), and two wild prairie grasses (Andropogon gerardii and Tripsacum dactyloides) to condition soils for three feedback species (maize B73-wt, teosinte, Andropogon gerardii). We found evidence of negative PSF based on growth, phenotypic traits, and foliar nutrient concentrations for maize B73-wt, which grew slower in maize-conditioned soil than prairie grass-conditioned soil. In contrast, teosinte and A. gerardii showed few consistent feedback responses. Both rhizobiome and nutrient-mediated mechanisms were implicated in PSF. Based on 16S rRNA gene amplicon sequencing, the rhizosphere bacterial community composition differed significantly after conditioning by prairie grass and maize plants, and the final soil nutrients were significantly influenced by conditioning, more so than by the feedback plants. These results suggest PSF-mediated soil domestication in agricultural settings can develop quickly and reduce crop productivity mediated by PSF involving changes to both the soil rhizobiomes and nutrient availability.

Uncovering the metabolic pathway of novel Burkholderia sp. for efficient triclosan degradation and implication: Insight from exogenous bioaugmentation and toxicity pressure

Triclosan (TCS), a synthetic and broad-spectrum antimicrobial agent, is frequently detected in various environmental matrices. A novel TCS degrading bacterial strain, Burkholderia sp. L303, was isolated from local activated sludge. The strain could metabolically degrade TCS up to 8 mg/L, and optimal conditions for TCS degradation were at temperature of 35 °C, pH 7, and an increased inoculum size. During TCS degradation, several intermediates were identified, with the initial degradation occurring mainly through hydroxylation of aromatic ring, followed by dechlorination. Further intermediates such as 2-chlorohydroquinone, 4-chlorocatechol, and 4-chlorophenol were produced via ether bond fission and C-C bond cleavage, which could be further transformed into unchlorinated compounds, ultimately resulting in the complete stoichiometric free chloride release. Bioaugmentation of strain L303 in non-sterile river water demonstrated better degradation than in sterile water. Further exploration of the microbial communities provided insights into the composition and succession of the microbial communities under the TCS stress as well as during the TCS biodegradation process in real water samples, the key microorganisms involved in TCS biodegradation or showing resistance to the TCS toxicity, and the changes in microbial diversity related to exogenous bioaugmentation, TCS input, and TCS elimination. These findings shed light on the metabolic degradation pathway of TCS and highlight the significance of microbial communities in the bioremediation of TCS-contaminated environments.

Solutions in microbiome engineering: prioritizing barriers to organism establishment

Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.