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1. Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons

   https://doi.org/10.1038/s41396-022-01245-4  

   Qi, Mingsheng ; Berry, Jeffrey C. ; Veley, Kira M. ; O’Connor, Lily ; Finkel, Omri M. ; Salas-González, Isai ; Kuhs, Molly ; Jupe, Julietta ; Holcomb, Emily ; Glavina del Rio, Tijana ; et al ( May 2022 , The ISME Journal)

   Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-threeArabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. TwoArthrobacterstrains caused root growth inhibition (RGI) inArabidopsisand sorghum. In the context of synthetic communities,Variovoraxstrains were able to protect plants fromArthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized byArthrobacterhad reduced growth and leaf water content. Plants colonized by bothArthrobacterandVariovoraxperformed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance ofArthrobacterand plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.

    

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2. Design and implementation of an affordable laboratory‐scale bioreactor for the production of microbial natural products

   https://doi.org/10.1002/eng2.12059  

   Theodore, Christine M. ; Loveridge, Steven T. ; Crews, Mitchell S. ; Lorig‐Roach, Nicholas ; Crews, Phillip ( November 2019 , Engineering Reports)

   Large‐scale bacteria culturing can present many challenges for small academic laboratories. To address these challenges a cost effective, laboratory scale bioreactor was designed and implemented. The constructed bioreactor addresses common problems that small or teaching‐focused laboratories face when attempting scale up cultures. The design utilizes materials commonly found in standard chemistry laboratories that are easily assembled with minor modifications. The system was validated through the replication of natural product production in shake flasks and the bioreactor. Additionally, measurements were done to ensure the designed bioreactor had comparablek_Lavalues to common shake flask conditions. We anticipate that this design will be of use to other small academic natural product groups as well as teaching laboratories as it offers an economical way to undertake large scale culturing of microorganisms.

    

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3. Unusual Boronium Salt Shows Antifungal Activity Comparable to a Commercial Quaternary Ammonium Disinfectant

   https://doi.org/10.1002/slct.202104344  

   Ravine, Terrence J. ; Soltani, Mohammad ; Davis, Jr., James H. ; Salter, Edward A. ; Wierzbicki, Andrzej ( March 2022 , ChemistrySelect)

   Previously, a boronium salt possessing a terminal benzyl group was reported to have greater antibacterial activity than a commercial quaternary ammonium disinfectant solution againstEscherichia coli,Pseudomonas aeruginosa, andStaphylococcus aureus. Results of the current study indicate that the same boronium salt without a benzyl group, exhibited equal or better antifungal activity against actively growingCandida albicansyeast andAspergillus fumigatusmold when compared to the same quat disinfectant. This same compound also displayed antifungal activity against dormantA. fumigatusspores comparable to the quat disinfectant. In contrast, the boronium ion with a benzyl group was 4–16X less effective than either the non‐benzylated form or quat disinfectant for all 3 fungal test conditions. The observation that the boronium salt without a benzyl group exhibited substantial antifungal activity in the current study but did not display any antibacterial activity in the previous study is of particular interest. This finding represents a flip‐flop outcome from the previous bacterial testing. It suggests that the presence of a terminal benzyl group greatly influences the boronium ion's ability to interact with fungal membranes.

    

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4. Chemotaxis in shear flow: Similarity solutions of the steady‐state chemoattractant and bacterial distributions

   https://doi.org/10.1002/aic.16713  

   Shim, Suin ; Stone, Howard A. ; Ford, Roseanne M. ( July 2019 , AIChE Journal)

   When chemotactic bacteria are exposed to a concentration gradient of chemoattractant while flowing along a channel, the bacteria accumulate at the interface between the chemoattractant source and bacterial suspension. Assuming that the interface is no‐slip, we can apply the shear flow approximation near the no‐slip boundary and solve a steady‐state convection‐diffusion model for both chemoattractant and bacterial concentrations. We suggest similarity solutions for the two‐dimensional problem and identify a critical length scaleη_cfor bacteria chemotaxis in a given concentration gradient. The analysis identifies three dimensionless groups representing, respectively, chemotactic sensitivity, the chemotaxis receptor constant, and the bacteria diffusion coefficient, which typically show coupled effects in experimental systems. We study the effect of the dimensionless groups separately and provide understanding of the system involving shear flow and chemotaxis.

    

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5. Remote collection of microorganisms at two depths in a freshwater lake using an unmanned surface vehicle (USV)

   https://doi.org/10.7717/peerj.4290  

   Powers, Craig ; Hanlon, Regina ; Schmale III, David G. ( January 2018 , PeerJ)

   Microorganisms are ubiquitous in freshwater aquatic environments, but little is known about their abundance, diversity, and transport. We designed and deployed a remote-operated water-sampling system onboard an unmanned surface vehicle (USV, a remote-controlled boat) to collect and characterize microbes in a freshwater lake in Virginia, USA. The USV collected water samples simultaneously at 5 and 50 cm below the surface of the water at three separate locations over three days in October, 2016. These samples were plated on a non-selective medium (TSA) and on a medium selective for the genusPseudomonas(KBC) to estimate concentrations of culturable bacteria in the lake. Mean concentrations ranged from 134 to 407 CFU/mL for microbes cultured on TSA, and from 2 to 8 CFU/mL for microbes cultured on KBC. There was a significant difference in the concentration of microbes cultured on KBC across three sampling locations in the lake (P= 0.027), suggesting an uneven distribution ofPseudomonasacross the locations sampled. There was also a significant difference in concentrations of microbes cultured on TSA across the three sampling days (P= 0.038), demonstrating daily fluctuations in concentrations of culturable bacteria. There was no significant difference in concentrations of microbes cultured on TSA (P= 0.707) and KBC (P= 0.641) across the two depths sampled, suggesting microorganisms were well-mixed between 5 and 50 cm below the surface of the water. About 1 percent (7/720) of the colonies recovered across all four sampling missions were ice nucleation active (ice+) at temperatures warmer than −10 °C. Our work extends traditional manned observations of aquatic environments to unmanned systems, and highlights the potential for USVs to understand the distribution and diversity of microbes within and above freshwater aquatic environments.

    

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