Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome

Microbial communities associated with plant leaf surfaces (i.e. the phyllosphere) are increasingly recognized for their role in plant health. While accumulating evidence suggests a role for host filtering of its microbiota, far less is known about how community composition is shaped by dispersal, including from neighboring plants. We experimentally manipulated the local plant neighborhood within which tomato, pepper, or bean plants were grown in a three-month field trial. Focal plants were grown in the presence of con- or hetero-specific neighbors (or no neighbors) in a fully factorial combination. At 30-day intervals, focal plants were harvested and replaced with a new age- and species-matched cohort while allowing neighborhood plants to continue growing. 16S community profiling revealed that the strength of host filtering effects (i.e. interspecific differences in composition) decreased over time. In contrast, the strength of neighborhood effects increased over time, suggesting dispersal from neighboring plants becomes more important as neighboring plant biomass increases. We next implemented a cross-inoculation study in the greenhouse using inoculum generated from the field plants to directly test host filtering of microbiomes while controlling for directionality and source of dispersal. This experiment further demonstrated that focal host species, the host from which the microbiome came, and in one case the donor hosts' neighbors, contribute to variation in phyllosphere bacterial composition. Overall, our results suggest that local dispersal is a key factor in phyllosphere assembly, and that demographic factors such as nearby neighbor identity and biomass or age are important determinants of phyllosphere microbiome diversity.

Ameliorating Effects of Different Extracts of Culinary Mushroom Species on the Production Performance of Healthy and Eimeria Infected Commercial Broiler Birds

In this research, three edible mushroom species including Pleurotus (P.) ostreatus, P. sajor-caju and Lentinus (L.) edodes were processed for hot water, methanolic and polysaccharide extracts. These extracts were administered to commercial broiler birds. Production performance was determined as weight gains and feed conversion ratios (FCR) in healthy birds on weekly basis. Further, groups were subjected to oral Eimeria infection and weight gains were monitored from days 4 to 12 post inoculation. Study revealed significantly higher (P < 0.05) weight gains in experimental groups given different mushroom extracts during 4th, 5th and 6th weeks of experiment in comparison to control. Feed conversion ratios observed in the control groups were significantly higher (P < 0.05) as compared to experimental groups especially methanolic extracts of all three mushroom species during 5th and 6th weeks of the experiment. After Eimeria inoculation, weight gains of the experimental groups given different mushroom extracts were significantly higher (P < 0.05) on 10th, 11th and 12th day. Results concluded that aqueous, methanolic and polysaccharide extracts of P. ostreatus, P. sajor-caju and L. edodes had potential to improve the production in healthy birds and may also enhance the weights in commercial broiler birds suffering from Eimeria infection. © 2021 Friends Science Publishers

Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in ‘Honeycrisp’

Breeding apple cultivars with resistance offers a potential solution to fire blight, a damaging bacterial disease caused by Erwinia amylovora. Most resistance alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm with poor fruit quality, which reduces breeding utility. This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S. apple breeding programs. Twenty-seven important breeding parents (IBPs) were represented by 314 offspring from 32 full-sib families, with ‘Honeycrisp’ being the most highly represented IBP. Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data, QTLs were consistently mapped on chromosomes (Chrs.) 6, 7, and 15. These QTLs together explained ~28% of phenotypic variation. The Chr. 6 and Chr. 15 QTLs colocalized with previously reported QTLs, while the Chr. 7 QTL is possibly novel. ‘Honeycrisp’ inherited a rare reduced-susceptibility allele at the Chr. 6 QTL from its grandparent ‘Frostbite’. The highly resistant IBP ‘Enterprise’ had at least one putative reduced-susceptibility allele at all three QTLs. In general, lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs. This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm. Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.

Analysis of a novel RNA virus in a wild northern white-breasted hedgehog (Erinaceus roumanicus)

Tombusviruses are generally considered plant viruses. A novel tombus-/carmotetravirus-like RNA virus was identified in a faecal sample and blood and muscle tissues from a wild northern white-breasted hedgehog (Erinaceus roumanicus). The complete genome of the virus, called H14-hedgehog/2015/HUN (GenBank accession number MN044446), is 4,118 nucleotides in length with a readthrough stop codon of type/group 1 in ORF1 and lacks a poly(A) tract at the 3′ end. The predicted ORF1-RT (RdRp) and the capsid proteins had low (31-33%) amino acid sequence identity to unclassified tombus-/noda-like viruses (Hubei tombus-like virus 12 and Beihai noda-like virus 10), respectively, discovered recently in invertebrate animals. An in vivo experimental plant inoculation study showed that an in vitro-transcribed H14-hedgehog/2015/HUN viral RNA did not replicate in Nicotiana benthamiana, Chenopodium quinoa, or Chenopodium murale, the most susceptible hosts for plant-origin tombusviruses.

Evolution of host resistance and damage-limiting mechanisms to an emerging bacterial pathogen

Understanding how hosts minimise the cost of emerging infections has fundamental implications for epidemiological dynamics and the evolution of pathogen virulence. Despite this, few experimental studies conducted in natural populations have explicitly tested whether hosts evolve resistance, which prevents infections or reduces pathogen load through immune activation, or tolerance, which limits somatic damages without decreasing pathogen load. In addition, none have done so controlling for the virulence of the pathogen isolate used, despite critical effects on host responses to infection. Here, we conducted an experimental inoculation study to test whether eastern North American house finches (Haemorrhous mexicanus) have evolved resistance or tolerance to their emerging bacterial pathogen, Mycoplasma gallisepticum, using 55 distinct isolates of varying virulence. First, we show that peak pathogen loads, which occurred around 8 days post-inoculation, did not differ between experimentally inoculated finches from disease-exposed (eastern) versus unexposed (western) population. However, pathogen loads subsequently decreased faster and to a greater extent in finches from exposed populations, indicating that they were able to clear the infection through adaptive immune processes. Second, we found no between-population difference in the regression of clinical symptom severity on pathogen load; if tolerance had evolved then the slope of this regression is predicted to be shallower (less negative) in the exposed population. However, finches from exposed populations displayed lower symptom severity for a given pathogen load, suggesting that damage-limitation mechanisms have accompanied the evolution of immune clearance. These observations show that resistance and damage-limitation mechanisms - including, but not limited to the standard conceptualisation of tolerance - should not be seen as mutually exclusive. Nevertheless, we propose that host resistance is especially likely to evolve in response to pathogens such as M. gallisepticum that require virulence for successful infection and transmission.

Efficacy of Antimicrobial Compounds on Surface Decontamination of Seven Shiga Toxin–Producing Escherichia coli and Salmonella Inoculated onto Fresh Beef†

Several antimicrobial compounds have been used in commercial meat processing plants for decontamination of pathogens on beef carcasses, but there are many commercially available, novel antimicrobial compounds that may be more effective and suitable for use in beef processing pathogen-reduction programs. Sixty-four prerigor beef flanks (cutaneous trunci) were used in a study to determine whether hypobromous acid, neutral acidified sodium chlorite, and two citric acid–based antimicrobial compounds effectively reduce seven Shiga toxin–producing Escherichia coli (STEC) serogroups and Salmonella on the surface of fresh beef. Two cocktail mixtures were inoculated onto prerigor beef flank surfaces. Cocktail mixture 1 was composed of STEC serogroups O26, O103, O111, O145, and O157; and cocktail mixture 2 was composed of STEC serogroups O45, O121, and O157 and Salmonella. The inoculated fresh beef flanks were subjected to spray treatments with four antimicrobial compounds. Following antimicrobial treatments, both control and treated fresh beef samples were either enumerated immediately or were stored for 48 h at 4°C before enumeration. All four antimicrobial compounds caused 0.7- to 2.0-log reductions of STEC, Salmonella, aerobic plate counts, and Enterobacteriaceae. Results also indicated that the four antimicrobial compounds were as effective at reducing the six non-O157 STEC strains as they were at reducing E. coli O157:H7 on the surfaces of fresh beef. The recovery of all seven STEC strains and Salmonella in a low-inoculation study indicated that none of the four antimicrobial compounds eliminated all of the tested pathogens.

Host ecotype generates evolutionary and epidemiological divergence across a pathogen metapopulation

The extent and speed at which pathogens adapt to host resistance varies considerably. This presents a challenge for predicting when—and where—pathogen evolution may occur. While gene flow and spatially heterogeneous environments are recognized to be critical for the evolutionary potential of pathogen populations, we lack an understanding of how the two jointly shape coevolutionary trajectories between hosts and pathogens. The rust pathogen Melampsora lini infects two ecotypes of its host plant Linum marginale that occur in close proximity yet in distinct populations and habitats. In this study, we found that within-population epidemics were different between the two habitats. We then tested for pathogen local adaptation at host population and ecotype level in a reciprocal inoculation study. Even after controlling for the effect of spatial structure on infection outcome, we found strong evidence of pathogen adaptation at the host ecotype level. Moreover, sequence analysis of two pathogen infectivity loci revealed strong genetic differentiation by host ecotype but not by distance. Hence, environmental variation can be a key determinant of pathogen population genetic structure and coevolutionary dynamics and can generate strong asymmetry in infection risks through space.

Transmission Efficiency of ‘Candidatus Liberibacter solanacearum’ and Potato Zebra Chip Disease Progress in Relation to Pathogen Titer, Vector Numbers, and Feeding Sites

With diseases caused by vector-borne plant pathogens, acquisition and inoculation are two primary stages of the transmission, which can determine vector efficiency in spreading the pathogen. The present study was initiated to quantify acquisition and inoculation successes of ‘Candidatus Liberibacter solanacearum’, the etiological agent of zebra chip disease of potato, by its psyllid vector, Bactericera cockerelli (Hemiptera: Triozidae). Acquisition success was evaluated in relation to feeding site on the host plant as well as the acquisition access period. Inoculation success was evaluated in relation to vector number (1 and 4) on the plants. Acquisition success was influenced by the feeding site on the plant. The highest acquisition success occurred when insects had access to the whole plant. The results of the inoculation study indicated that the rate of successfully inoculated plants increased with the vector number. Plants inoculated with multiple psyllids had higher bacterial titer at the point of inoculation. Although disease incubation period was significantly shorter in plants inoculated with multiple psyllids, this effect was heterogeneous across experimental blocks, and was independent of pathogen quantity detected in the leaflets 3 days postinoculation. Disease progress was not affected by bacterial quantity injected or psyllid numbers.

Phylogenetic multilocus sequence analysis identifies seven novel Ensifer genospecies isolated from a less-well-explored biogeographical region in East Africa

The diversity of 71 rhizobial strains belonging to the genus Ensifer , isolated from root nodules of woody legumes growing in southern Ethiopia, was studied using multilocus sequence analysis (MLSA) and phenotypic approaches. Phylogenetic analyses based on core genes revealed that 43 strains were clustered in seven distinct and consistent positions (genospecies I–VII), while another 25 strains were also distinct but were discrepant in their placement on the different gene trees. The remaining three strains occupied the same phylogenetic branches as defined Ensifer species and thus were not distinct. Irrespective of their chromosomal background, the majority of the test strains were highly related with respect to their nifH and nodC gene sequences, suggesting that these symbionts might have acquired these genes recently from a common origin. On the nifH phylogenetic tree, the branch containing the test strains and reference species isolated from woody legumes in Africa was clearly separate from those isolated outside the continent, suggesting that these symbionts have a long history of separate evolution within Ensifer for this gene. A cross-inoculation study showed that our strains were capable of eliciting effective nodulation on the homologous host and on other host species. This suggests a potential to improve nitrogen fixation by selecting for broad-host-range inoculants. Our study confirms the presence of a wide diversity of Ensifer in East Africa and, while contributing to the general knowledge of the biodiversity within the genus, also highlights the need to focus on previously less-well-explored biogeographical regions to unravel as-yet-unidentified rhizobial resources.