A complete genome sequence of pathovar YM7902.

pathovar YM7902 was originally isolated as a pathogen of cucumber in Japan. Here, we report a nearly complete genome sequence for this strain, assembled using a hybrid approach combining Illumina paired-end reads and longer reads sequenced using technology from Oxford Nanopore.

sp. nov., a yellow-pigmented gammaproteobacterium found as an endohyphal symbiont of endophytic Ascomycota.

We isolated and described a yellow-pigmented strain of bacteria (strain 9143), originally characterized as an endohyphal inhabitant of an endophytic fungus in the Ascomycota. Although the full-length sequence of its 16S rRNA gene displays 99 % similarity to , genomic hybridization demonstrated <30 % genomic similarity between 9143 and its closest named relatives, further supported by average nucleotide identity results. This and related endohyphal strains form a well-supported clade separate from and other validly named species including the most closely related .

Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background.

Synonymous mutations are changes to DNA sequence, which occur within translated genes but which do not affect the protein sequence. Although often referred to as silent mutations, evidence suggests that synonymous mutations can affect gene expression, mRNA stability, and even translation efficiency. A collection of both experimental and bioinformatic data has shown that synonymous mutations can impact cell phenotype, yet less is known about the molecular mechanisms and potential of beneficial or adaptive effects of such changes within evolved populations.

Pantailocins: phage-derived bacteriocins from and subsp. .

Phage-derived bacteriocins (tailocins) are ribosomally synthesized structures produced by bacteria in order to provide advantages against competing strains under natural conditions. Tailocins are highly specific in their target range and have proven to be effective for the prevention and/or treatment of bacterial diseases under clinical and agricultural settings. We describe the discovery and characterization of a new tailocin locus encoded within genomes of and subsp.

Draft genome sequences for ATCC 35400 and subspecies ICMP 10132.

Here, we describe draft genome sequences for two bacterial isolates from the genus . ATCC 35400 was originally isolated from honeydew melon and was obtained from the American Type Culture Collection. subspecies ICMP 10132 was originally isolated from sugarcane and classified as , but average nucleotide identity and discriminatory PCR support species reclassification.

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes.

A beneficial synonymous substitution in EF-Tu is contingent on genetic background.

Synonymous mutations are changes to DNA sequence that occur within translated genes but which do not affect the protein sequence. Although often referred to as silent mutations, evidence suggests that synonymous mutations can affect gene expression, mRNA stability, and even translation efficiency. A collection of both experimental and bioinformatic data has shown that synonymous mutations can impact cell phenotype, yet less is known about the molecular mechanisms and potential of beneficial or adaptive effects of such changes within evolved populations.

Interspecies killing activity of tailocins.

Tailocins are ribosomally synthesized bacteriocins, encoded by bacterial genomes, but originally derived from bacteriophage tails. As with both bacteriocins and phage, tailocins are largely thought to be species-specific with killing activity often assumed to be directed against closely related strains. Previous investigations into interactions between tailocin host range and sensitivity across phylogenetically diverse isolates of the phytopathogen have demonstrated that many strains possess intraspecific tailocin activity and that this activity is highly precise and specific against subsets of strains.

Prevalence of an Insect-Associated Genomic Region in Environmentally Acquired Symbionts.

Microbial symbionts are critical for the development and survival of many eukaryotes. Recent research suggests that the genes enabling these relationships can be localized in horizontally transferred regions of microbial genomes termed "symbiotic islands." Recently, a putative symbiotic island was found that may facilitate symbioses between true bugs and numerous species, based on analysis of five symbionts.

Transcriptional Profiles of a Foliar Fungal Endophyte (, Ascomycota) and Its Bacterial Symbiont (, ) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction.

Symbiosis with bacteria is widespread among eukaryotes, including fungi. Bacteria that live within fungal mycelia (endohyphal bacteria) occur in many plant-associated fungi, including diverse Mucoromycota and Dikarya. sp.

Genome Context Influences Evolutionary Flexibility of Nearly Identical Type III Effectors in Two Phytopathogenic Pseudomonads.

Integrative Conjugative Elements (ICEs) are replicons that can insert and excise from chromosomal locations in a site-specific manner, can conjugate across strains, and which often carry a variety of genes useful for bacterial growth and survival under specific conditions. Although ICEs have been identified and vetted within certain clades of the agricultural pathogen , the impact of ICE carriage and transfer across the entire species complex remains underexplored. Here we identify and vet an ICE (PmaICE-DQ) from pv.

Experimental evolution of the megaplasmid pMPPla107 in enables identification of genes contributing to sensitivity to an inhibitory agent.

Horizontally transferred elements, such as plasmids, can burden host cells with various metabolic and fitness costs and may lead to other potentially detrimental phenotypic effects. Acquisition of the megaplasmid pMPPla107 by various Pseudomonads causes sensitivity to a growth-inhibiting substance that is produced in cultures by Pseudomonads during growth under standard laboratory conditions. After approximately 500 generations of laboratory passage of populations containing pMPPla107, strains from two out of six independent passage lines displayed resistance to this inhibitory agent.

What makes a megaplasmid?

Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders of magnitude larger. Historically, research has tended to focus on smaller plasmids that are usually easier to isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation that very large plasmids-known as megaplasmids-are widespread, diverse, complex, and often encode key traits in the biology of their host microorganisms.

Prophylactic Application of Tailocins Prevents Infection by .

Tailocins are phage-derived bacteriocins that demonstrate great potential as agricultural antimicrobials given their high killing efficiency and their precise strain-specific targeting ability. Our group has categorized and characterized tailocins produced by and tailocin sensitivities of the phytopathogen , and here we extend these experiments to test whether prophylactic tailocin application can prevent infection of by . pv.

Draft Genome Sequences of Multiple Isolates from Arizona.

strains are bacteria that are well known for their distinctive physiology, behaviors, and ecology, as well as for being prodigious producers of diverse antibiotics. Here, we report draft genome sequences for eight strains that were isolated from multiple sky islands in Arizona and sequenced using an Oxford Nanopore Technologies Flongle adapter and MinION system.

Genomic Background Governs Opposing Responses to Nalidixic Acid upon Megaplasmid Acquisition in .

Horizontal gene transfer is a significant driver of evolutionary dynamics across microbial populations. Although the benefits of the acquisition of new genetic material are often quite clear, experiments across systems have demonstrated that gene transfer events can cause significant phenotypic changes and entail fitness costs in a way that is dependent on the genomic and environmental context. Here, we test for the generality of one previously identified cost, sensitization of cells to the antibiotic nalidixic acid after acquisition of an ∼1-Mb megaplasmid, across strains and species.

Leadership.

We asked group leaders how they foster mutually reinforcing research productivity and psychological safety in their teams.

Complete Genome Sequences for sp. Strains 29A and 43A.

sp. strains 29A and 43A were originally isolated from the phyllosphere of individual plants of (Brassicaceae). Here, we report complete genome sequences for these two closely related strains, assembled using a hybrid approach combining Illumina paired-end reads and longer reads sequenced on an Oxford Nanopore MinION flow cell.

Best Practices for Successfully Writing and Publishing a Genome Announcement in .

(MRA) provides peer-reviewed announcements of scientific resources for the microbial research community. We describe the best practices for writing an announcement that ensures that these publications are truly useful resources. Adhering to these best practices can lead to successful publication without the need for extensive revisions.

Can Survive Tailocin Killing via Persistence-Like and Heterogenous Resistance Mechanisms.

Phage tail-like bacteriocins (tailocins) are bacterially produced protein toxins that mediate competitive interactions between cocolonizing bacteria. Both theoretical and experimental research has shown there are intransitive interactions between bacteriocin-producing, bacteriocin-sensitive, and bacteriocin-resistant populations, whereby producers outcompete sensitive cells, sensitive cells outcompete resistant cells, and resistant cells outcompete producers. These so-called rock-paper-scissors dynamics explain how all three populations occupy the same environment, without one driving the others extinct.

Bacterial dispersal and biogeography as underappreciated influences on phytobiomes.

Bacterial strains are not distributed evenly throughout the environment. Here I explore how differential distribution and dispersal patterns of bacteria could affect interactions and coevolutionary dynamics with plants, and highlight ways that variation could be taken advantage of to develop robust and effective microbial consortia to inoculate crops. Questions about biogeographical patterns in viruses, fungi, and other eukaryotes are equally as prevalent and important for agriculture, and are in some cases more thoroughly explored.