A Novel Group of Rhizobium tumorigenes-Like Agrobacteria Associated with Crown Gall Disease of Rhododendron and Blueberry

Isolation and characterization of bacteriophages for controlling Rhizobium radiobacter - causing stem and crown gall of highbush blueberry

Introduction

Stem and crown gall disease caused by the plant pathogen Rhizobium radiobacter has a significant impact on highbush blueberry (Vaccinium corymbosum) production. Current methods for controlling the bacterium are limited. Lytic phages, which can specifically target host bacteria, have been widely gained interest in agriculture.

Methods

In this study, 76 bacteriophages were recovered from sewage influent and screened for their inhibitory effect against Rhizobium spp. The phages were genetically characterized through whole-genome sequencing, and their lytic cycle was confirmed.

Results

Five potential candidate phages (isolates IC12, IG49, AN01, LG08, and LG11) with the ability to lyse a broad range of hosts were chosen and assessed for their morphology, environmental stability, latent period, and burst size. The morphology of these selected phages revealed a long contractile tail under transmission electron microscopy. Single-step growth curves displayed that these phages had a latent period of 80-110 min and a burst size ranging from 8 to 33 phages per infected cell. None of these phages contained any antimicrobial resistance or virulence genes in their genomes. Subsequently, a combination of two-, three- and four-phage cocktails were formulated and tested for their efficacy in a broth system. A three-phage cocktail composed of the isolates IC12, IG49 and LG08 showed promising results in controlling a large number of R. radiobacter strains in vitro. In a soil/peat-based model, the three-phage cocktail was tested against R. radiobacter PL17, resulting in a significant reduction (p < 0.05) of 2.9 and 1.3 log10 CFU/g after 24 and 48 h of incubation, respectively.

Discussion

These findings suggest that the three-phage cocktail (IC12, IG49 and LG08) has the potential to serve as a proactive antimicrobial solution for controlling R. radiobacter on blueberry.

Diversity and Evolutionary History of Ti Plasmids of "tumorigenes" Clade of Rhizobium spp. and Their Differentiation from Other Ti and Ri Plasmids

Agrobacteria are important plant pathogens responsible for crown/cane gall and hairy root diseases. Crown/cane gall disease is associated with strains carrying tumor-inducing (Ti) plasmids, while hairy root disease is caused by strains harboring root-inducing (Ri) plasmids. In this study, we analyzed the sequences of Ti plasmids of the novel "tumorigenes" clade of the family Rhizobiaceae ("tumorigenes" Ti plasmids), which includes two species, Rhizobium tumorigenes and Rhizobium rhododendri. The sequences of reference Ti/Ri plasmids were also included, which was followed by a comparative analysis of their backbone and accessory regions. The "tumorigenes" Ti plasmids have novel opine signatures compared with other Ti/Ri plasmids characterized so far. The first group exemplified by pTi1078 is associated with production of agrocinopine, nopaline, and ridéopine in plant tumors, while the second group comprising pTi6.2 is responsible for synthesis of leucinopine. Bioinformatic and chemical analyses, including opine utilization assays, indicated that leucinopine associated with pTi6.2 most likely has D,L stereochemistry, unlike the L,L-leucinopine produced in tumors induced by reference strains Chry5 and Bo542. Most of the "tumorigenes" Ti plasmids have conjugative transfer system genes that are unusual for Ti plasmids, composed of avhD4/avhB and traA/mobC/parA regions. Next, our results suggested that "tumorigenes" Ti plasmids have a common origin, but they diverged through large-scale recombination events, through recombination with single or multiple distinct Ti/Ri plasmids. Lastly, we showed that Ti/Ri plasmids could be differentiated based on pairwise Mash or average amino-acid identity distance clustering, and we supply a script to facilitate application of the former approach by other researchers.

Genomics of the "tumorigenes" clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov

Tumorigenic members of the family Rhizobiaceae, known as agrobacteria, are responsible for crown and cane gall diseases of various crops worldwide. Tumorigenic agrobacteria are commonly found in the genera Agrobacterium, Allorhizobium, and Rhizobium. In this study, we analyzed a distinct "tumorigenes" clade of the genus Rhizobium, which includes the tumorigenic species Rhizobium tumorigenes, as well as strains causing crown gall disease on rhododendron. Here, high-quality, closed genomes of representatives of the "tumorigenes" clade were generated, followed by comparative genomic and phylogenomic analyses. Additionally, the phenotypic characteristics of representatives of the "tumorigenes" clade were analyzed. Our results showed that the tumorigenic strains isolated from rhododendron represent a novel species of the genus Rhizobium for which the name Rhizobium rhododendri sp. nov. is proposed. This species also includes additional strains originating from blueberry and Himalayan blackberry in the United States, whose genome sequences were retrieved from GenBank. Both R. tumorigenes and R. rhododendri contain multipartite genomes, including a chromosome, putative chromids, and megaplasmids. Synteny and phylogenetic analyses indicated that a large putative chromid of R. rhododendri resulted from the cointegration of an ancestral megaplasmid and two putative chromids, following its divergence from R. tumorigenes. Moreover, gene clusters specific for both species of the "tumorigenes" clade were identified, and their biological functions and roles in the ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.

First Report of Diaporthe phoenicicola causing leaf spot on blueberry (Vaccinium virgatum) in China

Blueberry (Vaccinium virgatum), a member of the Ericaceae family, is an increasingly important crop in China because of its abundant nutritional benefits and economic value (Kuzmanović et al. 2019). In October 2021, leaf spots were detected on 'Rabbiteye' blueberry at the Agricultural Science and Technology Park of Jiangxi Agricultural University in Nanchang, China (28°45'51"N, 115°50'52"E), which caused severe defoliation of the crop and fruit yield losses of 25% (Figure 1A). Disease surveys were conducted at that time; the results showed that disease incidence was 75.5%, observed in 151 of the 200 accessions sampled, and this disease had not been found at other cultivation fields in Nanchang. Lesions with taupe to dark brown margins were irregularly shaped and associated with leaf margins. Spots coalesced to form larger lesions, with black pycnidia present in more mature lesions. To identify the causal agent, 10 small pieces (5 mm2) of leaf tissue excised from the lesion margins were surface sterilized in 75% ethanol solution for 30 s and 0.1% mercuric chloride solution for 2 min, rinsed three times with sterile distilled water, then placed on potato dextrose agar (PDA) at 25°C for 5 to 7 days in darkness. Five fungal isolates showing similar morphological characteristics were obtained as pure cultures by single-spore isolation. All fungal colonies on PDA were floccose, dense, and white (Figure 1B.C). Black pycnidia developed on PDA at 25°C under a 12/12 h light/dark cycle for 30 days. Alpha conidia were 6.17 to 8.53 × 1.64 to 3.20 µm (average 6.94 × 2.52 µm, n = 100), aseptate, hyaline, fusiform to ellipsoidal, often biguttulate. Beta conidia were 15.26 to 25.41 × 0.92 to 1.40 µm (average 20.14 × 1.27 µm, n = 30), aseptate, hyaline, linear to hamate (Figure 1D). Based on morphological characteristics, the fungal isolates were suspected to be Diaporthe spp. (Gomes et al. 2013). To further confirm the identity of this putative pathogen, two representative isolates (LGM1 and LGM2) were selected for molecular identification. The internal transcribed spacer region (ITS), translation elongation factor 1α (EF1-α), histone H3 (HIS), calmodulin (CAL), and β-tubulin (TUB2) genes were amplified from gDNA and sequenced using primers ITS1/ITS4 (Peever et al. 2004), EF1-728F/EF1-986R and CAL228F/CAL737R (Carbone et al. 1999), CYLH3F/H3-1b (Crous et al. 2004), Bt2a/Bt2b (Glass and Donaldson 1995), respectively. GenBank accession numbers of isolate LGM1 and LGM2 were OM778771 to 72 for the ITS region, OM868228 to 29 for EF1-α, OM837771 to 72 for TUB2, ON206971 to 72 for CAL, ON206973 to 74 for HIS. BLAST results showed that the ITS, EF1-α, TUB2, HIS, and CAL sequences showed 99% (538/545 bp), 100% (322/322 bp), 99% (480/484 bp), 99% (459/460 bp), 99% (430/433 bp) identity, respectively, with those of Diaporthe phoenicicola (GenBank accession no. MW504735, MW514099, MW514142, MW514067, MT409304). Two maximum likelihood phylogenetic trees were built based on the sequences of ITS, EF1-α, HIS, CAL, and TUB2 by using MEGA 5. The two isolates LGM1 and LGM2 clustered with D. phoenicicola (Figure 2 and 3). The fungus was identified as D. phoenicicola by combining morphological and molecular characteristics. To evaluate the pathogenicity, three healthy young potted V. virgatum plants were spray inoculated with a conidial suspension of 106 conidia/ml. Another set of three plants that were sprayed with sterilized distilled water served as the controls. The experiment was repeated three times, and all plants were maintained in a climate box (12 h light/dark) at 25°C with 80% relative humidity. Five days after inoculation, no symptoms were observed on control plants (Figure 1F), and all inoculated plants showed symptoms (brown flecks) similar to those observed in the field (Figure 1E). The fungus was reisolated from the infected tissues and confirmed as D. phoenicicola by morphological and molecular identification, and could not be isolated from the controls, fulfilling Koch's postulates. To our knowledge, this is the first report of D. phoenicicola causing leaf spot on blueberry in China. The discovery of this new disease and the identification of the pathogen will provide useful information for developing specific control measures and potential sources for resistance to this disease caused by D. phoenicicola.

Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria

Members of the agrobacteria-rhizobia complex (ARC) have multiple and diverse plasmids. The extent to which these plasmids are shared and the consequences of their interactions are not well understood. We extracted over 4000 plasmid sequences from 1251 genome sequences and constructed a network to reveal interactions that have shaped the evolutionary histories of oncogenic virulence plasmids. One newly discovered type of oncogenic plasmid is a mosaic with three incomplete, but complementary and partially redundant virulence loci. Some types of oncogenic plasmids recombined with accessory plasmids or acquired large regions not known to be associated with pathogenicity. We also identified two classes of partial virulence plasmids. One class is potentially capable of transforming plants, but not inciting disease symptoms. Another class is inferred to be incomplete and non-functional but can be found as coresidents of the same strain and together are predicted to confer pathogenicity. The modularity and capacity for some plasmids to be transmitted broadly allow them to diversify, convergently evolve adaptive plasmids and shape the evolution of genomes across much of the ARC. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.

T-DNA regions from 350 Agrobacterium genomes: maps and phylogeny

Analysis of 350 Agrobacterium wgs sequences reveals complex evolutionary history of T-DNA regions Virulent Agrobacterium strains transfer one or more plasmid DNA fragments to plant cells during a well-characterized transformation process. The transferred DNA sequences (T-DNA regions) are delimited by 25 nucleotide long conserved border sequences. Until recently, relatively few T-DNA regions were known. However, due to increased whole genome sequencing efforts, about 400 Agrobacterium sequences have now become available, 350 of which contain T-DNA regions. Detailed analysis identified 92 different T-DNA regions and several new T-DNA genes. T-DNA regions can be divided into three groups. I. Typical Agrobacterium rhizogenes T-DNA regions with rol genes. II. A large group of T-DNA regions with iaa and ipt genes, which can be further subdivided into seven subgroups. III. A small group of unusual T-DNA regions. The evolutionary relation between the T-DNA regions could not be completely elucidated, because of the lack of evolutionary intermediates. Several clusters of highly related structures suggest that evolution of T-DNA regions proceeds by slow, progressive evolution of gene sequences, accompanied by rapid changes in overall structure, due to recombination between T-DNA regions of different origins, and insertion of bacterial insertion sequences (IS). Divergence values for T-DNA genes suggest that they were recruited at different times in evolution. An attempt was made to link T-DNA region evolution to plasmid evolution. The present study provides a solid basis for further studies on T-DNA region diversity and evolution.

Microbiome Modulation-Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants

Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying in vitro interactions are well studied. In contrast, in situ effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated via the plant.