It Is Just a Matter of Time: Balancing Homologous Recombination and Non-homologous End Joining at the rDNA Locus During Meiosis

Ribosomal RNA genes (rDNAs) are located in large domains of hundreds of rDNA units organized in a head-to-tail manner. The proper and stable inheritance of rDNA clusters is of paramount importance for survival. Yet, these highly repetitive elements pose a potential risk to the genome since they can undergo non-allelic exchanges. Here, we review the current knowledge of the organization of the rDNA clusters in Arabidopsis thaliana and their stability during meiosis. Recent findings suggest that during meiosis, all rDNA loci are embedded within the nucleolus favoring non-homologous end joining (NHEJ) as a repair mechanism, while DNA repair via homologous recombination (HR) appears to be a rare event. We propose a model where (1) frequent meiotic NHEJ events generate abundant single nucleotide polymorphisms and insertions/deletions within the rDNA, resulting in a heterogeneous population of rDNA units and (2) rare HR events dynamically change rDNA unit numbers, only to be observed in large populations over many generations. Based on the latest efforts to delineate the entire rDNA sequence in A. thaliana, we discuss evidence supporting this model. The results compiled so far draw a surprising picture of rDNA sequence heterogeneity between individual units. Furthermore, rDNA cluster sizes have been recognized as relatively stable when observing less than 10 generations, yet emerged as major determinant of genome size variation between different A. thaliana ecotypes. The sequencing efforts also revealed that transcripts from the diverse rDNA units yield heterogenous ribosome populations with potential functional implications. These findings strongly motivate further research to understand the mechanisms that maintain the metastable state of rDNA loci.

First report of Stenotrophomonas maltophilia causing root soft rot of Sanqi (Panax notoginseng) in China

Sanqi (Panax notoginseng (Burk.) F. H. Chen) is a traditional Chinese medicinal plant with a long planting cycle of 2-3 years that makes it vulnerable to root diseases caused by several pathogens, including Fusarium solani, Alternaria panax, Phytophthoracactorum, and Pseudomonas sp. In April 2019, root soft rot samples of Sanqi were collected from a plantation site in Songming, southwest of China. Typical symptoms included root softening and necrosis, yellow leaf, and stem wilting. Ten diseased roots samples were collected and sterilized with 0.1% HgCl2 for 1 min, 75% ethanol for 2min, and then rinsed thrice with sterile water. Sterilized roots were cut into small pieces of 5 × 5 mm and cultured on the nutrient agar (NA) medium for 48 h at 28°C. From the root cultures, a total of thirteen bacterial strains were obtained. Three strains, SM 2-5, SM 2-13, and SM 2-14 were selected for further study. These three strains were gram-negative, short rod-shaped (1～2×0.5～1μm), non-spore-forming and had polar tufted flagella as observed under a transmission electron microscope (TEM). Also, the strains were positive for oxidase, beta-galactosidase, arginine dihydrolase, and lysine decarboxylase while negative for amylase and urease tested by biochemical methods (Wang 2017). To further determine the pathogenic species, genomic DNA of these three strains was extracted using a Genomic DNA Kit (Tsing Ke, Beijing, China), to PCR amplify 16S rDNA using universal primers 27F/1492R (Wang et al. 2017). Also, S. maltophilia 23S rDNA specific primers SM1/SM4 (Whitby et al. 2000) were used for PCR amplification to confirm the species. 16S rDNA sequence analysis showed that SM 2-5 (GenBank Accession No. MW555227), SM 2-13 (GenBank Accession No. MW555228), and SM 2-14 (GenBank Accession No. MW555229) shared the highest identity (>99.9%) with the S. maltophilia strains (GenBank Accession No. MT323142, MH669295, MN826555). Furthermore, 23S rDNA sequence analysis of SM 2-5 (GenBank Accession No. MZ707732), SM 2-13 (GenBank Accession No. MZ645941) and SM 2-14 (GenBank Accession No. MZ707733) revealed their high identity (>99.8%) with the S. maltophilia species. 16S and 23S rDNA phylogenetic analysis (Mega6.06) using the neighbor-joining (NJ) method with 1,000 bootstrap replicates revealed the three strains clustering with the other S. maltophilia strains. Therefore, based on morphology, metabolic profile, and sequence analysis, the three strains were identified as Stenotrophomonas maltophilia. To test pathogenicity, the strains were grown in the nutrient broth (NB) medium for 48h at 28°C until bacterial suspension reached to OD600≈1.0 (2.0×109CFU/mL). Then, healthy roots of one-year-old Sanqi plants, pre-washed with sterilized water and -poked with a sterilized needle, were soaked in bacterial suspension (2.0×109CFU/mL) of the three strains separately for inoculation 10min. Sterilized water treatment was used as a control. Subsequently, bacteria-inoculated plants were planted in sterile soil pots and cultured in a greenhouse at 28°C with shading rate of 70%. Each treatment group included 3 plants with 3 replicates. Ten days post inoculation, symptoms similar to the ones in natural conditions were observed in the bacteria-inoculated plants. Based on the disease index (Li et al. 2020), we found that among the three strains, SM 2-13 displayed the highest virulence, while no symptoms were observed in the control plants. The same bacterial strains were re-isolated from these inoculated roots and identified by the methods described above. Previous studies showed that some Stenotrophomonas species cause plant diseases such as rice white stripe (Singh et al. 2001), strawberry leaf black spot (Wang et al. 2017), Cyclobalanopsis patelliformis leaf spot (Bian et al. 2020), and Jatropha curcas L. seed borne and stem necrosis (Wang et al. 2018). To our knowledge, this is the first report confirming Stenotrophomonas maltophilia causing root soft rot of Panax notoginseng in China.

The Morphology, Taxonomy, and Phylogenetic Analyses of Five Freshwater Colonial Peritrich Ciliates (Alveolata, Ciliophora), Including the Descriptions of Two New Species

The morphology and phylogeny of two new sessilid species, Zoothamnium weishanicum n. sp. and Epicarchesium sinense n. sp., two insufficiently known species, Zoothamnium arbusculaEhrenberg, 1831 and Zoothamnium hentscheliKahl, 1935, and a well-known species, Carchesium polypinum (Linnaeus, 1767) Ehrenberg, 1838, collected from freshwater habitats of China, were investigated. Zoothamnium weishanicum n. sp. is characterized by its inverted bell-shaped zooids, double-layered peristomial lip, alternately branched stalk, and two different-length rows in infundibular polykinety 3 (P3). Epicarchesium sinense n. sp. is recognized by its asymmetric-pyriform zooids, single-layered peristomial lip, conspicuous cortical blisters on the pellicle, dichotomously branched stalk, and P3 containing one short inner row and two long outer rows. Based on previous and newly obtained data of the three known species, improved diagnoses and redescriptions are provided including, for the first time, data on the infraciliature of Z. arbuscula and Z. hentscheli. In addition, we analyzed the phylogeny of each species based on SSU rDNA sequence data.

Entyloma eranthidis sp. nov. on Eranthis longistipitata from Uzbekistan

A new smut fungus, Entyloma eranthidis on Eranthis longistipitata from Uzbekistan, revealed by molecular, morphological, and ecological evidence, is described and illustrated. It differs from all other species of Entyloma by host specialization on Eranthis and by having longer (≤35(–38) μm) spores and thicker (≤10(–12) μm) spore walls. ITS rDNA sequence analysis indicates that the new species does not cluster with other species of Entyloma on Ranunculaceae.

Gerronema nemorale: first report of the genus and species from Pakistan

Basidiomata of a Gerronema species, collected in Murree, Punjab, Pakistan, have been confirmed as G. nemorale by morphological and ITS1-5.8S-ITS2 rDNA sequence analyses. This is the first report of the genus Gerronema from Pakistan, and the first record of G. nemorale for the South Asian region.

A new species of Podosphaera sect. Sphaerotheca subsect. Sphaerotheca from India—first report of powdery mildew causing wilting and ultimately death of leaves of Filipendula vestita

Podosphaera filipendulensis, a new teleomorph of powdery mildew was discovered on living leaves of Filipendula vestita (Rosaceae). It is the first species of powdery mildew that causes wilting and ultimately death of apical infected leaves of F. vestita. It is described, illustrated and compared with other Podosphaera species reported on Rosaceae and a key to all species reported on Rosaceae is provided. The phylogeny of this species has been inferred from internal transcribed spacer (ITS) rDNA sequence data. Phylogenetically, P. filipendulensis is close to P. ferruginea var. ferruginea and P. macularis but differs in having larger chasmothecia, smaller peridium cells, shorter, narrower and aseptate appendages, 8-spored asci and smaller ascospores.

Extracellular Pyomelanin Pigment Production, Purification and Characterization with Streptomyces griseus MPPS2

Melanins are natural pigments widely distributed in nature from bacteria to humans. These complex, negatively charged, amorphous, high molecular mass natural biopolymers have many different bioactive properties such as antimicrobial, antiviral, antioxidant, liver protective effects etc. In this study, some chemical and physical properties of the extracellular pyomelanin pigment purified from Streptomyces griseus MPPS2 was investigated via XRD (X-Ray diffraction), FT-IR (Fourier transform infra-red) and 1H NMR (Nuclear magnetic resonance). Additionally, the melanin pigment-producing Streptomyces griseus MPPS2 strain was identified at species level by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) and 16S rDNA sequence analysis. 16S rDNA sequence analysis result was deposited in NCBI under accession number MT825616.

Taxonomy and molecular phylogeny of four karyorelictid species belonging to the genera Apotrachelocerca and Tracheloraphis (Protozoa: Ciliophora), with descriptions of two new species

The taxonomy and phylogeny of four trachelocercid ciliates, Apotrachelocerca orientalis sp. nov., Tracheloraphis apoligostriata sp. nov., T. oligostriata and T. prenanti, isolated from marine habitats in Qingdao, China, were studied. The new species, A. orientalis sp. nov., can be distinguished from its most closely related congener, A. arenicola, by the absence of cortical granules and its conspicuously different SSU rDNA sequence. Tracheloraphis apoligostriata sp. nov. differs from the similar T. oligostriata by its body shape, distribution pattern of the cortical granules and SSU rDNA sequence. Based on available data, we suggest that T. prenanti can be defined by its colourless, globular cortical granules, which indicates that this species should be removed from the T. phoenicopterus-complex. Phylogenetic analyses based on SSU rDNA sequence data indicates that: A. orientalis sp. nov. groups with A. arenicola with full support, together sister to all other trachelocercid species; and T. cf. phoenicopterus, T. prenanti, T. oligostriata and T. apoligostriata sp. nov. form a clearly outlined clade.