Evaluating host to host transplants as a method to study plant bacterial assembly

The ability to predict plant microbiome assembly will enable new bacterial-based technologies for agriculture. A major step towards this is quantifying the roles of ecological processes on community assembly. This is challenging, in part because individuals within a populations of host plants may be colonised by different assemblages of bacteria, simply because of variation in soil communities proximal to said plants. This creates uncertainty because it is difficult to estimate if the absence of a given species was a) because it was not present to colonise the plant or b) it went locally extinct from competition, predation or similar. To address this, the authors develop a mesocosm system to study bacterial communities of individual plants by replicated transplantation to a recipient host plant population, ensuring new hosts receive a homogenous species pool for colonisation. We sought to understand which factors affected the transplant and, what the main drivers of variation in the model communities were. A nested factorial design was used to investigate the transplantation of cultured or total, root or leaf associated bacterial communities from donor host species to surrogate host species. Specific metrics were developed to quantify colonisation efficiency of communities. The results show the root communities were more effectively transplanted than leaf communities, and a higher proportion of cultured communities were recovered than total communities. For root communities the strongest drivers of beta diversity was the donor host species, and for leaves it was the surrogate host species. Overall the results reveal that root, but not leaf communities are suited to this system reflecting their differing ecological drivers.

Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans

Xylella fastidiosa (Xf) is a plant pathogen causing significant losses in agriculture worldwide. Originating from America, this bacterium caused recent epidemics in southern Europe and is thus considered an emerging pathogen. As the European regulations do not authorize antibiotic treatment in plants, alternative treatments are urgently needed to control the spread of the pathogen and eventually to cure infected crops. One such alternative is the use of phage therapy, developed more than 100 years ago to cure human dysentery and nowadays adapted to agriculture. The first step towards phage therapy is the isolation of the appropriate bacteriophages. With this goal, we searched for phages able to infect Xf strains that are endemic in the Mediterranean area. However, as Xf is truly a fastidious organism, we chose the phylogenetically closest and relatively fast-growing organism X. albineans as a surrogate host for the isolation step. Our results showed the isolation from various sources and preliminary characterization of several phages active on different Xf strains, namely, from the fastidiosa (Xff), multiplex (Xfm), and pauca (Xfp) subspecies, as well as on X. albilineans. We sequenced their genomes, described their genomic features, and provided a phylogeny analysis that allowed us to propose new taxonomic elements. Among the 14 genomes sequenced, we could identify two new phage species, belonging to two new genera of the Caudoviricetes order, namely, Usmevirus (Podoviridae family) and Subavirus (Siphoviridae family). Interestingly, no specific phages could be isolated from infected plant samples, whereas one was isolated from vector insects captured in a contaminated area, and several from surface and sewage waters from the Marseille area.

The retromer is co-opted to deliver lipid enzymes for the biogenesis of lipid-enriched tombusviral replication organelles

Biogenesis of viral replication organelles (VROs) is critical for replication of positive-strand RNA viruses. In this work, we demonstrate that tomato bushy stunt virus (TBSV) and the closely related carnation Italian ringspot virus (CIRV) hijack the retromer to facilitate building VROs in the surrogate host yeast and in plants. Depletion of retromer proteins, which are needed for biogenesis of endosomal tubular transport carriers, strongly inhibits the peroxisome-associated TBSV and the mitochondria-associated CIRV replication in yeast and in planta. In vitro reconstitution revealed the need for the retromer for the full activity of the viral replicase. The viral p33 replication protein interacts with the retromer complex, including Vps26, Vps29, and Vps35. We demonstrate that TBSV p33-driven retargeting of the retromer into VROs results in delivery of critical retromer cargoes, such as 1) Psd2 phosphatidylserine decarboxylase, 2) Vps34 phosphatidylinositol 3-kinase (PI3K), and 3) phosphatidylinositol 4-kinase (PI4Kα-like). The recruitment of these cellular enzymes by the co-opted retromer is critical for de novo production and enrichment of phosphatidylethanolamine phospholipid, phosphatidylinositol-3-phosphate [PI(3)P], and phosphatidylinositol-4-phosphate [PI(4)P] phosphoinositides within the VROs. Co-opting cellular enzymes required for lipid biosynthesis and lipid modifications suggest that tombusviruses could create an optimized lipid/membrane microenvironment for efficient VRO assembly and protection of the viral RNAs during virus replication. We propose that compartmentalization of these lipid enzymes within VROs helps tombusviruses replicate in an efficient milieu. In summary, tombusviruses target a major crossroad in the secretory and recycling pathways via coopting the retromer complex and the tubular endosomal network to build VROs in infected cells.

Behavioral Responses of Tabanidae and Stomoxys calcitrans to Unbaited and Baited Nzi and Horse Pal Traps in Southern Sweden

The distribution and species diversity of tabanids and stable flies, Stomoxys calcitrans Linnaeus, 1758, in the research area, Hästhult (wood pasture) in Sweden, as well as the behavioral responses of biting flies to visual and olfactory cues were highlighted by this study. Beyond the control of tabanids and stable flies through the Nzi and Horse Pal traps that act as a surrogate host, this study sought to demonstrate the attractiveness of biting flies to these traps by comparing the results of the two periods in which the traps were unbaited and baited. The odor attractants, such as urine (a mixture of more than phenol) and acetone used to increase trap yields, made the difference to the Horse Pal and Nzi traps for S. calcitrans (L) because the number of flies caught was significantly higher. Through this study, Nzi trap with bait and Horse Pal trap with and without bait were tested for the first time as regards the tabanids and S. calcitrans (L) in Scandinavia. Surprisingly, the number of tabanids caught in the Nzi trap was equal in both situations with or without bait. The result underlined the idea that the Nzi trap manages to catch a large number of tabanids even in the absence of attractants. It turns out that the Horse Pal trap was just as effective with and without bait in capturing tabanids. Furthermore, the number of tabanids caught in both traps depended on the type of weather, and the number of stable flies depended on the weather and also the type of trap. The results of this study showed that both the visual and olfactory aspects of the Nzi and Horse Pal traps are always essential, being used successfully in the control of biting flies and optimized for various research purposes.

Single generation allele introgression into pure chicken breeds using Sire Dam Surrogate (SDS) mating

SummaryPoultry is the most abundant livestock species with over 60 billion chickens raised globally per year. While most chicken are produced from highly selected commercial flocks the many indigenous chicken breeds, which have low productivity and have not been highly selected, play an important role in rural economies across the world as they are well adapted to local environmental and scavenging conditions. The ability to rapidly transfer genetic changes between breeds of chicken will permit the transfer of beneficial alleles between poultry breeds as well as allow validation of genetic variants responsible for different phenotypic traits. Here, we generate a novel inducibly sterile surrogate host chicken. Introducing donor genome edited primordial cells into the sterile male and female host embryos produces chicken carrying only exogenous germ cells. Subsequent direct mating of the surrogate hosts, Sire Dam Surrogate (SDS) mating, recreates pure chicken breeds carrying the edited allele in heterozygous or homozygous states. We demonstrate the transfer and validation of two feather trait alleles, Dominant white and Frizzle traits into two pure chicken breeds using the SDS surrogate hosts. This technology will allow the rapid reconstitution of chicken breeds carrying desired genetic changes to investigate climate adaptation and disease resilience traits.

Exploitation of Host Factors and Cellular Pathways by Tombusviruses for the Biogenesis of the Viral Replication Organelles

Plus-stranded RNA viruses recruit cellular vesicles and co-opt cellular proteins involved in cellular metabolism and lipid biosynthesis to build viral replicase complexes (VRCs) within the large viral replication compartments. We use tombusviruses (TBSV), which are small (+)RNA viruses, as model plant viruses to study virus replication, recombination, and virus–host interactions using yeast (Saccharomyces cerevisiae) as a surrogate host. Several systematic genome-wide screens and global proteomic and lipidomic approaches have led to the identification of ~500 host proteins/genes that are implicated in TBSV replication. We characterized the role of two-dozen co-opted host proteins, sterols, and phosphatidylethanolamine in tombusvirus VRC assembly and viral RNA synthesis. We provide evidence on the critical roles of phosphoinositides and co-opted membrane-shaping proteins in VRC formation. We also present data that tombusviruses hijack the glycolytic and fermentation pathways to obtain ATP, which is required for the biogenesis of the replication compartment. Finally, we show evidence that TBSV usurps COPII and endosomal vesicles to form a unique microenvironment involving peroxisomes and endoplasmic reticulum (ER) to support viral replication. These new insights highlight the amazingly complex nature of virus-host interactions.

A Mesophilic Aeromonas salmonicida Strain Isolated from an Unsuspected Host, the Migratory Bird Pied Avocet

Aeromonas salmonicida is a Gram-negative bacterium, known as a fish pathogen since its discovery. Although the species was initially considered psychrophilic, a mesophilic subspecies (pectinolytica) and many other mesophilic strains still not attributed to subspecies have been described in the last two decades. These mesophilic strains were sampled from various sources, including humans, and some of them are known to be pathogenic. In this study, we describe a strain, JF2480, which was isolated from the spleen, and also found the kidney and liver of a dead pied avocet (Recurvirostra avosetta), a type of migratory bird inhabiting aquatic environments. A core genome phylogenomic analysis suggests that JF2480 is taxonomically distant from other known A. salmonicida subspecies. The genome sequence confirms that the strain possesses key virulence genes that are present in the typical A. salmonicida psychrophilic subspecies, with the exception of the genes encoding the type three secretion system (T3SS). Bacterial virulence assays conducted on the surrogate host Dictyostelium discoideum amoeba confirmed that the strain is virulent despite the lack of T3SS. Bacterial growth curves showed that strain JF2480 grow well at 40 °C, the body temperature of the pied avocet, and even faster at 41 °C, compared to other mesophilic strains. Discovery of this strain further demonstrates the extent of the phylogenomic tree of this species. This study also suggests that A. salmonicida can infect a wider array of hosts than previously suspected and that we need to rethink the way we perceive A. salmonicida’s natural environment.

Reviving rare chicken breeds using genetically engineered sterility in surrogate host birds

In macrolecithal species, cryopreservation of the oocyte and zygote is not possible due to the large size and quantity of lipid deposited within the egg. For birds, this signifies that cryopreserving and regenerating a species from frozen cellular material are currently technically unfeasible. Diploid primordial germ cells (PGCs) are a potential means to freeze down the entire genome and reconstitute an avian species from frozen material. Here, we examine the use of genetically engineered (GE) sterile female layer chicken as surrogate hosts for the transplantation of cryopreserved avian PGCs from rare heritage breeds of chicken. We first amplified PGC numbers in culture before cryopreservation and subsequent transplantation into host GE embryos. We found that all hatched offspring from the chimera GE hens were derived from the donor rare heritage breed broiler PGCs, and using cryopreserved semen, we were able to produce pure offspring. Measurement of the mutation rate of PGCs in culture revealed that 2.7 × 10−10 de novo single-nucleotide variants (SNVs) were generated per cell division, which is comparable with other stem cell lineages. We also found that endogenous avian leukosis virus (ALV) retroviral insertions were not mobilized during in vitro propagation. Taken together, these results show that mutation rates are no higher than normal stem cells, essential if we are to conserve avian breeds. Thus, GE sterile avian surrogate hosts provide a viable platform to conserve and regenerate avian species using cryopreserved PGCs.