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1. Predation-resistant Pseudomonas bacteria engage in symbiont-like behavior with the social amoeba Dictyostelium discoideum

   https://doi.org/10.1038/s41396-023-01535-5  

   Steele, Margaret I.; Peiser, Jessica M.; Shreenidhi, P. M.; Strassmann, Joan E.; Queller, David C. (October 2023, The ISME Journal)

   Abstract The soil amoeba Dictyostelium discoideum acts as both a predator and potential host for diverse bacteria. We tested fifteen Pseudomonas strains that were isolated from transiently infected wild D. discoideum for ability to escape predation and infect D. discoideum fruiting bodies. Three predation-resistant strains frequently caused extracellular infections of fruiting bodies but were not found within spores. Furthermore, infection by one of these species induces secondary infections and suppresses predation of otherwise edible bacteria. Another strain can persist inside of amoebae after being phagocytosed but is rarely taken up. We sequenced isolate genomes and discovered that predation-resistant isolates are not monophyletic. Many Pseudomonas isolates encode secretion systems and toxins known to improve resistance to phagocytosis in other species, as well as diverse secondary metabolite biosynthetic gene clusters that may contribute to predation resistance. However, the distribution of these genes alone cannot explain why some strains are edible and others are not. Each lineage may employ a unique mechanism for resistance. 

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2. Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp.

   https://doi.org/10.3389/ffunb.2023.1285531  

   Cailleau, Guillaume; Hanson, Buck T.; Cravero, Melissa; Zhioua, Sami; Hilpish, Patrick; Ruiz, Celia; Robinson, Aaron J.; Kelliher, Julia M.; Morales, Demosthenes; Gallegos-Graves, La Verne; et al (December 2023, Frontiers in Fungal Biology)

   Members of the fungal genusMorchellaare widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained fromMorchellaisolates grownin vitro. These investigations included diverse representatives from both Elata and EsculentaMorchellaclades. Unique bacterial community compositions were observed across the various structures examined, both within and across individualMorchellaisolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genusPseudomonasandRalstoniaconstituted the core bacterial associates ofMorchellamycelia and sclerotia, while other genera (e.g.,Pedobacterspp.,Deviosaspp., andBradyrhizobiumspp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance ofPseudomonasas a key member of the bacteriome was supported by the isolation of severalPseudomonasstrains from mycelia duringin vitrocultivation. Four of the six mycelial-derivedPseudomonasisolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and variousMorchellaisolates. Genome sequences obtained from thesePseudomonasisolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence thatPseudomonasspp. are frequently associated withMorchellaand these associations may greatly impact fungal physiology. 

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3. Comparative Genomics Analysis of the Aromatic and Xenobiotic Degradation Capacities and Heavy Metal Resistance in Seven Environmentally Derived Bacterial Isolates

   https://doi.org/10.1007/s11270-023-06495-2  

   Kneubehl, Alexander R.; Iyer, Rupa (July 2023, Water, Air, & Soil Pollution)

   This work is a comparative genomics investigation of the aromatic and xenobiotic compound degradation capabilities and heavy metal resistance of environmental bacterial isolates previously identified by our lab, Achromobacter xylosoxidans ADAF13, Exiguobacterium sp. KKBO11, Ochrobactrum anthropi FRAF13, Pseudomonas putida CBF10-2, Pseudomonas stutzeri ODKF13, Rhizobium radiobacter GHKF11, and Stenotrophomonas maltophilia CBF10-1. This work sought to assess the potential of these isolates as bioremediation tools. We found a variety of aromatic degradation pathways though none directly acts on industrial compounds such as polycyclic aromatic compounds, benzene, phthalate, or xylene. Achromobacter xylosoxidans ADAF13, P. putida CBF10-2, and P. stutzeri ODKF13 showed the most complete pathways for aromatic compound degradation and halobenzoate degradation. All isolates contained heavy metal resistance genes for arsenic, cadmium, copper, chromium, lead, mercury, and zinc. Arsenic resistance genes were the most common among isolates and were organized into structurally diverse ars operons. Collectively, our data indicated that A. xylosoxidans ADAF13, P. putida CBF10-2, and P. stutzeri ODKF13 are strong candidates for further enhancement and development as bioremediation tools. 

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4. Complete Genome Sequences of Eight Streptococcus equi subsp. zooepidemicus Strains Isolated from Mares in Estrus with Endometritis

   https://doi.org/10.1128/MRA.01321-20  

   Borlee, Grace I.; Lakin, Steven M.; Kapuscinski, Marylee L.; Abdo, Zaid; Stenglein, Mark D.; McCue, Patrick M.; Borlee, Bradley R. (July 2021, Microbiology Resource Announcements)

   Dunning Hotopp, Julie C. (Ed.)

   ABSTRACT Eight isolates of Streptococcus equi subsp. zooepidemicus were isolated from mares with clinical cases of endometritis. S. equi subsp. zooepidemicus strains were chosen for sequencing based on differing levels of biofilm production in vitro . Using Illumina short-read sequencing in conjunction with MinION sequencing, we report the genomes of eight isolates. 

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5. High-quality genomes of Paenibacillus spp. RC334 and RC343, isolated from a long-term forest soil warming experiment

   https://doi.org/10.1128/MRA.00371-23  

   Kitzmiller, Claire E.; Tran, Wyatt C.; Sullivan, Brendan; Cortez, Florencia; Choudoir, Mallory; Simoes, Rachel; Dayarathne, Nipuni; DeAngelis, Kristen M. (August 2023, Microbiology Resource Announcements)

   Baltrus, David A. (Ed.)

   ABSTRACT Paenibacillus spp. RC334 and RC343 were isolated from heated soil in a long-term soil warming experiment. Both genomes were 5.98 Mb and assembled as a single contig. We describe the assembly and annotation of the two high-quality draft genomes for these isolates here. 

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