Abstract Pan.toe'a. Gr. masc. adj. pantoios , of all sorts and sources; N.L. fem. n. Pantoea , [bacteria] from diverse [geographical and ecological] sources. Pseudomonadota / Gammaproteobacteria / Enterobacterales / Enterobacteriaceae / Pantoea The genus Pantoea comprises a versatile assemblage of Gram‐negative and facultatively anaerobic bacteria. These bacteria occur in association with plant and animal hosts, as beneficial or pathogenic members of the communities or as free‐living in various environments. Cells of the members of this genus are non‐spore‐forming and nonencapsulated rods, ranging between 0.5 and 1.3 by 1.0 and 3.8 μm. The formation of symplasmata occurs in some members of the genus. Most are motile by means of peritrichous flagella, with some members producing a yellow pigment. The genus currently consists of 23 validly and effectively published species, ranging widely in isolation source and apparent pathogenic ability. The genomes of these organisms range markedly in size, with the median genome size being 4.85 Mb. The genomic pool of these organisms is diverse, contributing to their ecological versatility. Conserved genes within the genus are mainly involved in core housekeeping functions. This genus forms part of the family Enterobacteriaceae , with a close evolutionary relationship to Erwinia , Izhakiella , Mixta , Phaseolibacter , Rosenbergiella , and Tatumella . The G + C content of their DNA, as determined from genome sequences, ranges between 51.80 and 59.60%. Various members of this genus are considered pathogens or opportunistic pathogens, while some isolates display biotechnological and agricultural potential. DNA G + C content based on genome (mol%) : 51.90–59.60. Type species : Pantoea agglomerans (Beijerinck 1988) Gavini et al. 1989 VP .
With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.
Abstract The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
Abstract The phylum Chloroflexota is ubiquitous; however, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the class Dehalococcoidia within the phylum Chloroflexota . A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility; a peptidoglycan-containing cell envelope; and heterotrophic activity on aromatics and plant-associated compounds. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia , ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. This evolutionary past explains the widespread genomic potential to degrade terrestrial organic matter among marine Dehalococcoidia and raises new questions about the timing and selective forces driving their successful niche expansion into the global oceans.
Metabolite identification for MassIVE dataset MSV000090480 in positive mode (https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=895e11f85bac44f2828880c77ff4ef8f)
Table S2. Extended summary of protein families (Pfams) counts associated with the genes of interest found in publically available UViGs from thermal environments in the IMG/VR v4 database.
Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection of biosignatures for extraterrestrial life; however, traditional light microscopy is poorly suited for this purpose, as it requires sample preparation, involves fragile moving parts, and has a limited volume of view. In this study, we deployed a field-portable digital holographic microscope (DHM) to explore microbial motility in Badwater Spring, a saline spring in Death Valley National Park, and complemented DHM imaging with 16S rRNA gene amplicon sequencing and shotgun metagenomics. The DHM identified diverse morphologies and distinguished run-reverse-flick and run-reverse types of flagellar motility. PICRUSt2- and literature-based predictions based on 16S rRNA gene amplicons were used to predict motility genotypes/phenotypes for 36.0–60.1% of identified taxa, with the predicted motile taxa being dominated by members of Burkholderiaceae and Spirochaetota. A shotgun metagenome confirmed the abundance of genes encoding flagellar motility, and a Ralstonia metagenome-assembled genome encoded a full flagellar gene cluster. This study demonstrates the potential of DHM for planetary life detection, presents the first microbial census of Badwater Spring and brine pool, and confirms the abundance of mobile microbial taxa in an extreme environment.
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