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1. Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4, Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata

   https://doi.org/10.1128/genomeA.00410-18  

   Wanees, Abanoub E.; Zaslow, Shari J.; Potter, Savannah J.; Hsieh, Brandon P.; Boss, Brianna L.; Izquierdo, Javier A. (May 2018, Genome Announcements)

   ABSTRACT Sphingobium sp. strain AEW4 is a novel isolate from rhizosphere soil attached to the root of the American beachgrass Ammophila breviligulata . The genomic sequence consisted of 4,678,518 bp and 4,428 protein-coding sequences. Here we report the draft genome sequence of this strain and some initial insights on its plant growth-promoting capabilities. 

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2. Complete Genome Sequence of Serratia quinivorans Strain 124R, a Facultative Anaerobe Isolated on Organosolv Lignin as a Sole Carbon Source

   https://doi.org/10.1128/MRA.00409-19  

   Chaput, Gina; Ford, Jacob; DeDiego, Lani; Narayanan, Achala; Tam, Wing Yin; Whalen, Meghan; Huntemann, Marcel; Clum, Alicia; Spunde, Alex; Pillay, Manoj; et al (May 2019, Microbiology Resource Announcements)

   ABSTRACT The complete genome sequence of the gammaproteobacterial isolate Serratia quinivorans 124R consists of 5 Mb over 2 scaffolds and a G+C content of 52.85%. Genes relating to aromatic metabolism reflect its isolation on organosolv lignin as a sole carbon source under anoxic conditions as well as the potential for lignin biorefinery applications. 

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3. Reference Whole Genome Sequence Analyses and Characterization of a Novel Carnobacterium maltaromaticum Distinct Sequence Type Isolated from a North American Gray Wolf (Canis lupus) Gastrointestinal Tract

   https://doi.org/10.3390/vetsci12050410  

   Klews, C Cristoph; Bryant, Jessika L; McCabe, Jennifer; Atchley, Ariel N; Cousins, Thomas W; Barnard-Davidson, Maya; Ackermann, Mark R; Netherland, Michael; Hasan, Nur A; Jordan, Peter A; et al (May 2025, Veterinary Sciences)

   We hypothesize that bacteria isolated from free-ranging animals could potentially be useful for practical applications. To meet this objective a Gram-positive bacterium was isolated from the gastrointestinal (GI) tract of a Gray Wolf (Canis lupus) using Brucella broth with hemin and vitamin K (BBHK). By small ribosomal RNA (16S) gene sequencing the bacterium was initially identified as a novel Carnobacterium maltaromaticum strain. The bacterium could be propagated both anaerobically and aerobically and was both catalase/oxidase negative and negative by the starch hydrolysis as well as negative using lipase assays. The reference whole genome sequence (WGS) was obtained using both Illumina and Nanopore sequencing. The genome assembly was 3,512,202 bp in length, encoding core bacterial genes with a GC% content of 34.48. No lysogenic bacteriophage genes were detected, although the genome harbors genes for the expression of bacteriocin and other secondary metabolites with potential antimicrobial properties. Multilocus sequence typing (MLST), WGS phylogenetics, average nucleotide identity (ANI), and single nucleotide polymorphism (SNP) analyses of the isolate’s genome indicate this bacterium is a newly identified Carnobacterium maltaromaticum sequence type (ST). Members of the Carnobacteria have anti-listeria activities, highlighting their potential functional properties. Consequently, the isolate could be a potential probiotic for canids and this is the first report on an axenic C. maltaromaticum culture from the genus Canis. 

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4. Genome Sequence of Fusarium Isolate MYA-4552 from the Midgut of Anoplophora glabripennis , an Invasive, Wood-Boring Beetle

   https://doi.org/10.1128/genomeA.00544-16  

   Herr, Joshua R.; Scully, Erin D.; Geib, Scott M.; Hoover, Kelli; Carlson, John E.; Geiser, David M. (July 2016, Genome Announcements)

   The Fusarium solani species complex (FSSC) is a clade of environmentally ubiquitous fungi that includes plant, animal, and insect associates. Here, we report the draft genome sequence of the undescribed species FSSC 6 (isolate MYA-4552), housed in the gut of the wood-boring cerambycid beetle Anoplophora glabripennis . 

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5. Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium

   https://doi.org/10.1128/spectrum.02346-21  

   Chaput, Gina; Ford, Jacob; DeDiego, Lani; Narayanan, Achala; Tam, Wing Yin; Whalen, Meghan; Huntemann, Marcel; Clum, Alicia; Spunde, Alex; Pillay, Manoj; et al (June 2022, Microbiology Spectrum)

   Rotaru, Amelia-Elena (Ed.)

   ABSTRACT Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae . Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni . We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications. 

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