Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales

Host selection tendency of key microbiota in arid desert lichen crusts

Lichen genus Endocarpon in biological soil crust form was chosen as a model to investigate the bacterial communities for the first time across four vertically distinct strata. Key bacterial microbiota in lichen thallus were discovered, which were gradually filtered and mainly derived from the crust soil, with clear host selection tendency. The study provided key information to better understand the homeostasis maintenance mechanism of the lichen symbiont and community assembly of desert lichen crust.

Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents

Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of these regions encode bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that are now maintained in genomes of some bacteria and archaea and are hypothesized to enable exchange of DNA within bacterial populations. In Alphaproteobacteria, genes homologous to the "head-tail" gene cluster that encodes structural components of the Rhodobacter capsulatus GTA (RcGTA) are found in many taxa, even if they are only distantly related to Rhodobacter capsulatus. Yet, in most genomes available in GenBank RcGTA-like genes have annotations of typical viral proteins, and therefore are not easily distinguished from their viral homologs without additional analyses. Here, we report a "support vector machine" classifier that quickly and accurately distinguishes RcGTA-like genes from their viral homologs by capturing the differences in the amino acid composition of the encoded proteins. Our open-source classifier is implemented in Python and can be used to scan homologs of the RcGTA genes in newly sequenced genomes. The classifier can also be trained to identify other types of GTAs, or even to detect other elements of viral ancestry. Using the classifier trained on a manually curated set of homologous viruses and GTAs, we detected RcGTA-like "head-tail" gene clusters in 57.5% of the 1,423 examined alphaproteobacterial genomes. We also demonstrated that more than half of the in silico prophage predictions are instead likely to be GTAs, suggesting that in many alphaproteobacterial genomes the RcGTA-like elements remain unrecognized.

Interactions between elevated CO2 levels and floating aquatic plants on the alteration of bacterial function in carbon assimilation and decomposition in eutrophic waters

Elevated atmospheric CO₂ concentration (eCO₂) may have different effects on the bacterial community with regard to C assimilation and decomposition in eutrophic waters compared to that in fresh waters with intermediate levels of nutrients and oceans. Aquatic plant growth under eCO₂ could further modify microbial activities associated with the C cycle in eutrophic waters. Therefore, there is an urgent need to further study how eCO₂ and its interactions with the growth of aquatic plants affect the composition and function of the bacterial community involved in mediating the C cycle in eutrophic waters. Accordingly, we designed a microcosm experiment to investigate the effects of ambient and high CO₂ concentrations on bacterial community composition and function in eutrophic waters with and without the growth of Eichhornia crassipes (Mart.) Solms. The results from 16S rRNA gene sequencing, function prediction, and q-PCR showed that eCO₂ significantly increased the abundance of bacterial and functional genes involved in CO₂ assimilation (photosynthetic bacteria; cbbL IA & IC, cbbL ID, cbbM, pufM) and C decomposition (Acidimicrobiia, Thermoleophilia, Gaiellales; ChiA), illustrating the functional enrichment with photoautotrophy, hydrocarbon degradation, cellulolysis, and aromatic hydrocarbon degradation. However, eCO₂ decreased the abundance of some chemoautotrophic bacteria, including nitrifying bacteria (Nitrospirae, Nitrosomonadaceae). In contrast, the cultivation of E. crassipes decreased the abundance of photosynthetic bacteria but increased the abundance of bacteria involved in complex C decomposition associated with root exudates and degradation, e.g. Fibrobacteres, Sphingobacteriales, Sphingomonadales, and Rhizobiales. eCO₂ and growth of E. crassipes had opposite effects on algal density in eutrophic waters, creating interactive effects that further decreased the diversity of the bacterial community and abundance of some CO₂-assimilating bacteria with nitrifying characteristics (Nitrosomonadaceae) and some C-degrading bacteria (Fibrobacteres) with denitrifying properties (Flavobacteriaceae, Sphingomonadaceae, and Gemmobacter). Therefore, the interactions between aquatic plants and the bacterial community in eutrophic waters under eCO₂ would be beneficial to the environment and help alleviate the greenhouse effect.

Gene Transfer Agents in Symbiotic Microbes

Prokaryotes commonly undergo genome reduction, particularly in the case of symbiotic bacteria. Genome reductions tend toward the energetically favorable removal of unnecessary, redundant, or nonfunctional genes. However, without mechanisms to compensate for these losses, deleterious mutation and genetic drift might otherwise overwhelm a population. Among the mechanisms employed to counter gene loss and share evolutionary success within a population, gene transfer agents (GTAs) are increasingly becoming recognized as important contributors. Although viral in origin, GTA particles package fragments of their "host" genome for distribution within a population of cells, often in a synchronized manner, rather than selfishly packaging genes necessary for their spread. Microbes as diverse as archaea and alpha-proteobacteria have been known to produce GTA particles, which are capable of transferring selective advantages such as virulence factors and antibiotic resistance. In this review, we discuss the various types of GTAs identified thus far, focusing on a defined set of symbiotic alpha-proteobacteria known to carry them. Drawing attention to the predicted presence of these genes, we discuss their potential within the selective marine and terrestrial environments occupied by mutualistic, parasitic, and endosymbiotic microbes.

Characteristics of two myoviruses induced from the coastal photoheterotrophic bacterium Porphyrobacter sp. YT40

In this study, we characterized two induced myoviruses from one marine photoheterotrophic bacterium Porphyrobacter sp. YT40 belonging to the Sphingomonadales family in Alphaproteobacteria. The genome sequence of prophage A is ∼36.9 kb with an average GC content of 67.1%, and its core or functional genes are homologous to Mu or Mu-like phages. Furthermore, induced viral particles from prophage A show a knob-like neck structure, which is only found in bacteriophage Mu. The genome size of prophage B is ∼36.8 kb with an average GC content of 65.3%. Prophage B contains a conserved gene cluster Q-P-O-N-M-L, which is unique in P2 phages. Induced viral particles from prophage B display an icosahedral head with a diameter of ∼55 nm and a 130 ± 5 nm long contractile tail. To our knowledge, this is the first report that characterizes the induced P2-like phage in marine Alphaproteobacteria. Phylogeny analyses suggest that these two types of prophages are commonly found in sequenced bacteria of the Sphingomonadales family. This study sheds light on the ongoing interaction between marine bacteria and phages, and improves our understanding of bacterial genomic plasticity and evolution.

Phylogenetic insights into the diversity of Chryseobacterium species

The genus Chryseobacterium was formally established in 1994 and contains 112 species with validly published names. Most of these species are yellow or orange coloured, and contain a flexirubin-type pigment. The genomes of 83 of these 112 species have been sequenced in view of their importance in clinical microbiology and potential applications in biotechnology. The National Center for Biotechnology Information taxonomy browser lists 1415 strains as members of the genus Chryseobacterium, of which the genomes of 94 strains have been sequenced. In this study, by comparing the 16S rDNA and the deduced proteome sequences, at least 20 of these strains have been proposed to represent novel species of the genus Chryseobacterium. Furthermore, a yellow-coloured bacterium isolated from dry soil in the USA (and identified as Flavobacterium sp. strain B-14859) has also been reconciled as a novel member of the genus Chryseobacterium based on the analysis of 16S rDNA sequences and the presence of flexirubin. Yet another bacterium (isolated from a water sample collected in the Western Ghats of India and identified as Chryseobacterium sp. strain WG4) was also found to represent a novel species. These proposals need to be validated using polyphasic taxonomic approaches.