Lineage‐specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group

Bacterial plasmids can vary from small selfish genetic elements to large autonomous replicons that constitute a significant proportion of total cellular DNA. By conferring novel function to the cell, plasmids may facilitate evolution but their mobility may be opposed by co‐evolutionary relationships with chromosomes or encouraged via the infectious sharing of genes encoding public goods. Here, we explore these hypotheses through large‐scale examination of the association between plasmids and chromosomal DNA in the phenotypically diverse Bacillus cereus group. This complex group is rich in plasmids, many of which encode essential virulence factors (Cry toxins) that are known public goods. We characterized population genomic structure, gene content and plasmid distribution to investigate the role of mobile elements in diversification. We analysed coding sequence within the core and accessory genome of 190 B. cereus group isolates, including 23 novel sequences and genes from 410 reference plasmid genomes. While cry genes were widely distributed, those with invertebrate toxicity were predominantly associated with one sequence cluster (clade 2) and phenotypically defined Bacillus thuringiensis. Cry toxin plasmids in clade 2 showed evidence of recent horizontal transfer and variable gene content, a pattern of plasmid segregation consistent with transfer during infectious cooperation. Nevertheless, comparison between clades suggests that co‐evolutionary interactions may drive association between plasmids and chromosomes and limit wider transfer of key virulence traits. Proliferation of successful plasmid and chromosome combinations is a feature of specialized pathogens with characteristic niches (Bacillus anthracis, B. thuringiensis) and has occurred multiple times in the B. cereus group.     

Isolation of five rice nonendosperm tissue‐expressed promoters and evaluation of their activities in transgenic rice

Using promoters expressed in nonendosperm tissues to activate target genes in specific plant tissues or organs with very limited expression in the endosperm is an attractive approach in crop transgenic engineering. In this article, five putative nonendosperm tissue‐expressed promoters were cloned from the rice genome and designated P_OsNETE1, P_OsNETE2, P_OsNETE3, P_OsNETE4 and P_OsNETE5. By qualitatively and quantitatively examining GUSplus reporter gene expression in transgenic rice plants, P_OsNETE1‐P_OsNETE5 were all found to be active in the roots, leaves, stems, sheaths and panicles but not in the endosperm of plants at different developmental stages. In addition, P_OsNETE2, P_OsNETE4 and P_OsNETE5 were also inactive in rice embryos. Among these promoters, P_OsNETE4 and P_OsNETE5 exhibited higher activities in all of the tested tissues, and their activities in stems, leaves, roots and sheaths were higher than or comparable to those of the rice Actin1 promoter. We also progressively monitored the activities of P_OsNETE1‐P_OsNETE5 in two generations of single‐copy lines and found that these promoters were stably expressed between generations. Transgenic rice was produced using P_OsNETE4 and P_OsNETE5 to drive a modified Bt gene, mCry1Ab. Bt protein expressed in the tested plants ranged from 1769.4 to 4428.8 ng/g fresh leaves, whereas Bt protein was barely detected in the endosperm. Overall, our study identified five novel nonendosperm tissue‐expressed promoters that might be suitable for rice genetic engineering and might reduce potential social concern regarding the safety of GMO crops.     

Ten years of life in compost: temporal and spatial variation of North German Caenorhabditis elegans populations

The nematode Caenorhabditis elegans is a central laboratory model system in almost all biological disciplines, yet its natural life history and population biology are largely unexplored. Such information is essential for in‐depth understanding of the nematode's biology because its natural ecology provides the context, in which its traits and the underlying molecular mechanisms evolved. We characterized natural phenotypic and genetic variation among North German C. elegans isolates. We used the unique opportunity to compare samples collected 10 years apart from the same compost heap and additionally included recent samples for this and a second site, collected across a 1.5‐year period. Our analysis revealed significant population genetic differentiation between locations, across the 10‐year time period, but for only one location a trend across the shorter time frame. Significant variation was similarly found for phenotypic traits of likely importance in nature, such as choice behavior and population growth in the presence of pathogens or naturally associated bacteria. Phenotypic variation was significantly influenced by C. elegans genotype, time of isolation, and sampling site. The here studied C. elegans isolates may provide a valuable, genetically variable resource for future dissection of naturally relevant gene functions.     

Potential of bioinsecticidal Bacillus thuringiensis inoculum to suppress gray mold in tomato based on induced systemic resistance

The potential of the active ingredient of a commercial bioinsecticide, XenTari^® (Bacillus thuringiensis [BT] serovar aizawai strain ABTS‐1857), to suppress gray mold in tomato plants was elucidated. First, a suspension of the active ingredient of XenTari^® and a liquid culture of the bacterial strain as BT inocula were sprayed onto detached leaves or drenched into pots of tomato seedlings, and then, propagules of the gray mold fungus, Botrytis cinerea, were inoculated onto the leaves. The gray mold disease was significantly suppressed when rhizospheres were drenched with either inoculum, but not when inocula were sprayed onto detached leaves of seedlings. Both BT inocula were verified not to directly inhibit the mycelial growth of B. cinerea based on in vitro culture plate assays. Additionally, real‐time RT‐PCR analysis verified that the active ingredient increased the expression levels of defence‐related genes, such as PR‐1(P6) and P4, in the leaves of tomato seedlings. These results suggest that the active ingredient has the potential to suppress gray mold disease in tomato, not through direct antagonistic interactions with B. cinerea, but rather through systemic activation of the plant defence system by increased expression of several defence‐related genes.     

Suppression of Tobacco Mosaic Virus by Bacillus amyloliquefaciens Strain Ba33

Suppression of Tobacco Mosaic Virus (TMV) by B. amyloliquefaciens Ba33 was evaluated on Nicotiana tabacum by spraying before (①), after (②) and simultaneously with (③) TMV inocula. The results suggested that Ba33 treatments reduced local necrotic lesion number and disease index, showing ③ treatment was the best and ① treatment was better than ② treatment in TMV suppression. It also showed Ba33 virus‐contaminated scissors could be disinfected by dipping. Field trials showed that Ba33 had an inhibitory effect of 48.59% in 2009 and 50.54% in 2010, close to the effect of Ningnanmycin, a registered antiviral agent in tobacco. In conclusion, Ba33 might be used as a soil disinfector and an antiviral agent against TMV.     

Contemporary evolution of a Lepidopteran species,Heliothis virescens,in response to modern agricultural practices

Adaptation to human‐induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages, and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve (i) shifts in host plant selection mechanisms to avoid cotton, (ii) changes in detoxification mechanisms required for cotton‐feeding vs. feeding on other hosts or (iii) loss of resistance to previously used management practices including insecticides. Here, we begin to address whether such changes occurred in H. virescens populations between 1997 and 2012, as Bt‐cotton cultivation spread through the agricultural landscape. For our study, we produced an H. virescens genome assembly and used this in concert with a ddRAD‐seq‐enabled genome scan to identify loci with significant allele frequency changes over the 15‐year period. Genetic changes at a previously described H. virescens insecticide target of selection were detectable in our genome scan and increased our confidence in this methodology. Additional loci were also detected as being under selection, and we quantified the selection strength required to elicit observed allele frequency changes at each locus. Potential contributions of genes near loci under selection to adaptive phenotypes in the H. virescens cotton system are discussed.     

Characterization of blackleg and soft rot from potato in northern Thailand

Blackleg and soft rot of potato cause economic loss through reduced yield and quality. The causal agents of bacterial blackleg and soft rot of potato were identified based on biological data and sequence analyses of the 16S rDNA gene. Between 2016 and 2018, diseased potato stems and tubers were collected in Chai Prakan District, Chiang Mai Province, and Chiang Khum District, Pa Yao Province. The symptoms included black stem lesions, soft rot on tubers, wilting, break down of the stem vascular ring and foliar yellowing. Of 13 bacterial isolates, five were identified as Pectobacterium carotovorum subsp. brasiliense, four‐Dickeya dadantii, two‐Pseudomonas putida and two‐Bacillus altitudinis. Pathogenicity tests of P. carotovorum subsp. brasiliense and D. dadantii resulted in lower leaves turning yellow and wilting followed by blackleg symptoms on lower stems and maceration of tuber tissue. Symptoms caused by P. putida were yellowing and wilting of leaves. B. altitudinis caused yellowing of the lower leaves and wilting followed by drying of leaf tissue. This is a first report of these bacterial pathogens causing blackleg and soft rot of potato in Thailand.