Citrus Huanglongbing correlated with incidence of Diaphorina citri carrying Candidatus Liberibacter asiaticus and citrus phyllosphere microbiome.

In China, citrus Huanglongbing (HLB) disease is caused by the Candidatus Liberibacter asiaticus bacterium, which is carried by the Asian citrus psyllid Diaphorina citri Kuwayama. It was hypothesized that the epidemic of the HLB may related with the rate of bacterium presence in the insect vector and bacterium content in plant tissues, as well as the phyllosphere microbe communities changes. This study systematically analyzed the presence or absence of Ca. L. asiaticus in citrus tree leaves and in the insect vector D. citri over a 6-year period using real-time PCR. In addition, changes in the number of bacteria carried by D. citri over 12 months were quantified, as well as the relationship between the proportion of D. citri carrying Ca. L. asiaticus and the proportion of plants infected with Ca. L. asiaticus were analyzed. Results showed that the proportion of D. citri carrying bacteria was stable and relatively low from January to September. The bacteria in citrus leaves relatively low in spring and summer, then peaked in December. The proportion of D. citri carrying bacteria gradually declined from 2014 to 2019. The proportion of D. citri carrying Ca. L. asiaticus showed a significant positive correlation with the proportion of diseased citrus. The phyllosphere bacterial and fungal communities on the healthy citrus leaf were significantly different with the disease leaf in April and December. Pathogenic invasions change the citrus phyllosphere microbial community structure. It could be summarized that citrus Huanglongbing correlated with incidence of Diaphorina citri carrying Candidatus Liberibacter asiaticus and citrus phyllosphere microbiome.

Dynamic changes of rhizosphere soil bacterial community and nutrients in cadmium polluted soils with soybean-corn intercropping.

BACKGROUND: Soybean-corn intercropping is widely practised by farmers in Southwest China. Although rhizosphere microorganisms are important in nutrient cycling processes, the differences in rhizosphere microbial communities between intercropped soybean and corn and their monoculture are poorly known. Additionally, the effects of cadmium (Cd) pollution on these differences have not been examined. Therefore, a field experiment was conducted in Cd-polluted soil to determine the effects of monocultures and soybean-corn intercropping systems on Cd concentrations in plants, on rhizosphere bacterial communities, soil nutrients and Cd availability. Plants and soils were examined five times in the growing season, and Illumina sequencing of 16S rRNA genes was used to analyze the rhizosphere bacterial communities. RESULTS: Intercropping did not alter Cd concentrations in corn and soybean, but changed soil available Cd (ACd) concentrations and caused different effects in the rhizosphere soils of the two crop species. However, there was little difference in bacterial community diversity for the same crop species under the two planting modes. Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria and Firmicutes were the dominant phyla in the soybean and corn rhizospheres. In ecological networks of bacterial communities, intercropping soybean (IS) had more module hubs and connectors, whereas intercropped corn (IC) had fewer module hubs and connectors than those of corresponding monoculture crops. Soil organic matter (SOM) was the key factor affecting soybean rhizosphere bacterial communities, whereas available nutrients (N, P, K) were the key factors affecting those in corn rhizosphere. During the cropping season, the concentration of soil available phosphorus (AP) in the intercropped soybean-corn was significantly higher than that in corresponding monocultures. In addition, the soil available potassium (AK) concentration was higher in intercropped soybean than that in monocropped soybean. CONCLUSIONS: Intercropped soybean-corn lead to an increase in the AP concentration during the growing season, and although crop absorption of Cd was not affected in the Cd-contaminated soil, soil ACd concentration was affected. Intercropped soybean-corn also affected the soil physicochemical properties and rhizosphere bacterial community structure. Thus, intercropped soybean-corn was a key factor in determining changes in microbial community composition and networks. These results provide a basic ecological framework for soil microbial function in Cd-contaminated soil.

[Response of Photosynthetic Bacterial Community to Cadmium Contamination in Paddy Soil].

Heavy metal pollution in rice fields leads to huge losses in rice yield every year and is thus of increasing concern. Therefore, it is important to understand the changes in the microecology and physicochemical properties of paddy soil under different levels of cadmium pollution. The purpose of this study was to investigate the response of the photosynthetic bacterial community in paddy soil to different cadmium pollution levels using 16S sequencing technology. The results showed that pH, total cadmium, and available cadmium content decreased gradually with the increase in cadmium pollution. The soil α diversity was slightly different in the high cadmium (Cd), medium Cd, and low Cd groups; however, the enriched photosynthetic populations and photosynthetic bacterial communities were significantly different among these groups. The effective connections between photosynthetic bacterial species in the high Cd group were significantly greater than those in the medium and low Cd groups, the connections were closer, and the density was higher. Alkaline nitrogen, pH, available (P/K), total (N/P), organic matter, total cadmium, and available cadmium were important factors affecting the photosynthetic bacterial community and were significantly correlated with the photosynthetic bacterial community, explaining 59.90% of the variation in the photosynthetic bacterial community. Effective Cd content was significantly positively correlated with Methylorubrum populi, Methylorubrum extorquens, Methylobacterium sp. Leaf125, and Rhodopseudomonas sp. AAP120 (R>0.05, P<0.05). This study will provide a theoretical basis for the microbial remediation of cadmium contamination in paddy fields. This study is important for understanding the effects of cadmium pollution on specific functional microbial populations in paddy soils.

Scale-Dependent Effects of Growth Stage and Elevational Gradient on Rice Phyllosphere Bacterial and Fungal Microbial Patterns in the Terrace Field.

The variation of phyllosphere bacterial and fungal communities along elevation gradients may provide a potential link with temperature, which corresponds to an elevation over short geographic distances. At the same time, the plant growth stage is also an important factor affecting phyllosphere microorganisms. Understanding microbiological diversity over changes in elevation and among plant growth stages is important for developing crop growth ecological theories. Thus, we investigated variations in the composition of the rice phyllosphere bacterial and fungal communities at five sites along an elevation gradient from 580 to 980 m above sea level (asl) in the Ziquejie Mountain at the seedling, heading, and mature stages, using high-throughput Illumina sequencing methods. The results revealed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, and Bacteroidetes, and the dominant fungal phyla were Ascomycota and Basidiomycota, which varied significantly at different elevation sites and growth stages. Elevation had a greater effect on the α diversity of phyllosphere bacteria than on that phyllosphere fungi. Meanwhile, the growth stage had a great effect on the α diversity of both phyllosphere bacteria and fungi. Our results also showed that the composition of bacterial and fungal communities varied significantly along elevation within the different growth stages, in terms of both changes in the relative abundance of species, and that the variations in bacterial and fungal composition were well correlated with variations in the average elevation. A total of 18 bacterial and 24 fungal genera were significantly correlated with elevational gradient, displaying large differences at the various growth stages. Soluble protein (SP) shared a strong positive correlation with bacterial and fungal communities (p < 0.05) and had a strong significant negative correlation with Serratia, Passalora, unclassified_Trichosphaeriales, and antioxidant enzymes (R > 0.5, p < 0.05), and significant positive correlation with the fungal genera Xylaria, Gibberella, and Penicillium (R > 0.5, p < 0.05). Therefore, it suggests that elevation and growth stage might alter both the diversity and abundance of phyllosphere bacterial and fungal populations.

Differences in Tetracycline Antibiotic Resistance Genes and Microbial Community Structure During Aerobic Composting and Anaerobic Digestion.

Antibiotics are widely added to swine forage and are the main reason for the environmental accumulation of antibiotic resistance genes (ARGs) in swine manure-dwelling microorganisms. Aerobic composting (AC) and anaerobic digestion (AD) are efficient methods for converting swine manure to bio-fertilizer while degrading residual antibiotics. However, the influence of these methods on ARG accumulation and the difference in their efficiency have rarely been investigated. In this study, we explored the variations in four tetracycline antibiotics (TCs) and their associated ARGs and in microbial communities after AC and AD treatment. After full-scale manure AC and AD, the four TCs were removed effectively. AD had a higher TC removal efficiency than AC and a slower rate of TC-associated ARG accumulation. In addition, the community structure was more stable in the AC and AD manures than in untreated manure, and the relationship among microbial species also evolved into competition from mutualism after both AC and AD treatment. It was also speculated that the genera Acholeplasma and Arthrobacter were the possible hosts of tetO, tetW, and tetQ; the shift in the prokaryotic community composition and the alleviation of selective pressure by TC degradation led to decreased relative abundance of ARGs in AD- and AC-treated manure.

Higher Ramie mosaic virus transmission efficiency by females than by males of Bemisia tabaci MED.

Begomoviruses can modify their transmission vector, Bemisia tabaci, to benefit their spread, although this may not always be the case. Here, the new begomovirus Ramie mosaic virus (RaMoV) and its vector B. tabaci MED, which is dominant in China and many regions of the world, were used as a model to examine direct and indirect interaction and virus transmission by B. tabaci MED of different sexes. No significant direct or indirect effects of RaMoV were observed in B. tabaci MED females, although RaMoV could shorten the life span of B. tabaci MED females by up to 4 days. A test of RaMoV transmission by different sexes of B. tabaci MED showed that there was higher virus transmission efficiency by females than males. Overall, RaMoV is transmitted by B. tabaci MED in a sex-dependent manner, and further research is needed to uncover the mechanism of the difference in RaMoV transmission by different sexes of B. tabaci.

The effects of Rhodopseudomonas palustris PSB06 and CGA009 with different agricultural applications on rice growth and rhizosphere bacterial communities.

In recent years, the photosynthetic bacteria have been used widely in agriculture, but the effects of different agricultural applications on crop rhizosphere microorganism and crops are lack. In this study, we provide new insights into the structure and composition of the rice root-associated microbiomes as well as the effect on crop of the Rhodopseudomonas palustris(R. palustris) PSB06 and CGA009 at the rice seedling stage with seed immersion and root irrigation. Compare with CK group, the length of stem, the peroxidase (POD), and superoxide dismutase (SOD) activities in PSB06 treatment group was significantly higher, while the length of stem in CGA009 treatment group was significantly higher. The POD and SOD activities in CGA009 treatment groups only were higher slightly than the CK group. In the study, the dominant phyla were Proteobacteria (51.95-61.66%), Bacteroidetes (5.40-9.39%), Acidobacteria (4.50-10.52%), Actinobacteria (5.06-8.14%), Planctomycetes (2.90-4.48%), Chloroflexi (2.23-5.06%) and Firmicutes (2.38-7.30%), accounted for 87% bacterial sequences. The principal coordinate analysis (pCoA) and mantel results showed the two application actions of R. palustris CGA009 and PSB06 had significant effects on rice rhizosphere bacterial communities (p < 0.05). The PSB06 can significantly promote the rice growth and enhance stress resistance of rice at the seedling stage, while the R. palustris CGA009 has no significant effect on rice. Dissimilarity test and canonical correspondence analysis (CCA) results showed that the TN and pH were the key factors affecting rice rhizosphere bacterial community in the seedling stage. This study will provide some guidance advices for the study of the microecological regulation of photosynthetic bacteria on crops.

Variations in phyllosphere microbial community along with the development of angular leaf-spot of cucumber.

The phyllosphere is colonized by a wide variety of microorganisms including epiphytes, plant-pathogenic fungus, bacteria, as well as human or animal pathogens. However, little is known about how microbial community composition changes with the development of angular leaf-spot of cucumber. Here, 18 mixed samples were collected based on the lesion coverage rate (LCR) of angular leaf-spot of cucumber from three disease severity groups (DM1: symptomatic-mild, DM2: symptomatic-moderate, DM3: symptomatic-severe). In our study, the microbial community structure and diversity were examined by Illumina MiSeq sequencing. A significant differences was observed in α diversity and community structure among three disease severity groups. The phyllosphere microbiota was observed to be dominated by bacterial populations from Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal species from Ascomycota and Basidiomycota. In addition, some plant-specific microbe such as Sphingomonas, Methylobacterium, Pseudomonas, and Alternaria showed significant changes in their relative abundance of population. The LCR was correlated negatively with Sphingomonas, Methylobacterium, Quadrisphaera, and Lactobacillus, whereas correlated positively with Pseudomonas and Kineococcus (p < 0.05). The LCR was negatively correlated with Alternaria and Arthrinium of the fungal communities (p < 0.05). Molecular ecological networks of the microbial communities were constructed to show the interactions among the OTUs. Our current results indicated that the competitive relationships among species were broken with the development of angular leaf-spot of cucumber. The microbial community composition changed over the development of angular leaf-spot of cucumber. The result of molecular ecological networks indicated that the overall bacterial community tends toward mutualism from the competition. The development of angular leaf-spot of cucumber affected the ecosystem functioning by disrupting the stability of the microbial community network. This work will help us to understand the host plant-specific microbial community structures and shows how these communities change throughout the development of angular leaf-spot of cucumber.

Pumpkin powdery mildew disease severity influences the fungal diversity of the phyllosphere.

Phyllosphere microbiota play a crucial role in plant-environment interactions and their microbial community and function are influenced by biotic and abiotic factors. However, there is little research on how pathogens affect the microbial community of phyllosphere fungi. In this study, we collected 16 pumpkin (Cucurbita moschata) leaf samples which exhibited powdery mildew disease, with a severity ranging from L1 (least severe) to L4 (most severe). The fungal community structure and diversity was examined by Illumina MiSeq sequencing of the internal transcribed spacer (ITS) region of ribosomal RNA genes. The results showed that the fungal communities were dominated by members of the Basidiomycota and Ascomycota. The Podosphaera was the most dominant genus on these infected leaves, which was the key pathogen responsible for the pumpkin powdery mildew. The abundance of Ascomycota and Podosphaera increased as disease severity increased from L1 to L4, and was significantly higher at disease severity L4 (P < 0.05). The richness and diversity of the fungal community increased from L1 to L2, and then declined from L2 to L4, likely due to the biotic pressure (i.e., symbiotic and competitive stresses among microbial species) at disease severity L4. Our results could give new perspectives on the changes of the leaf microbiome at different pumpkin powdery mildew disease severity.

[Effects of Rhodopseudomonas palustris PSB06 on Pepper Rhizosphere Microbial Community Structure].

The use of biological pesticide can greatly reduce the soil pollution in the environment. Exploring the effect of biological pesticide on community diversity and distribution of pathogenic bacteria will provide theoretic basis for subsequent researches on biological pesticide micro-ecological control. In order to explore the microbial ecological mechanism of pepper phytophthora blight, this research compared the difference of microbial diversity between rhizosphere soil of infected and healthy plants, and the effects of Rhodopseudomonas palustris PSB06 on microbial diversities of plant rhizosphere soil were investigated using Illumina MiSeq sequencing technology. The results showed that there was less difference in the microbial diversity from the same soil between the seventh day and the fourteenth day. The microbial diversity of rhizosphere soil of healthy plants was higher than that of rhizosphere soil of infected plants. The soil sprayed with Rhodopseudomonas palustris PSB06 exhibited the highest diversity. Moreover, the abundance of Actinomycetes in the rhizosphere soil of healthy plants was higher than that of infected plants, and the highest abundance of Actinomycetes was observed in the soil sprayed with Rhodopseudomonas palustris PSB06. The microbial diversity between rhizosphere soil of infected and healthy plants was significantly different. Spraying Rhodopseudomonas palustris PSB06 could significantly alter the microbial community structure of the soil. It could also increase the diversity of microorganism and the abundance of Actinomycetes in the soil.

Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).

A novel actinobacterial strain, designated SDT, was isolated from rhizosphere soil of Chinese cabbage in Shandong province, China. The cells were aerobic, Gram-staining-positive, oxidase- and catalase-positive, short rods and formed white colonies on trypticase soy agar. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid and alanine, glutamic acid and leucine. Diphosphatidylglycerol was the predominant polar lipid. The predominant cellular fatty acid was C18 : 1ω9c; minor components were anteiso-C15 : 0 and anteiso-C17 : 0. The only isoprenoid quinone was demethylmenaquinone 7 (DMK-7), and the DNA G+C content was 72.7 mol%. Based on the full-length 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain SDT were Patulibacter medicamentivorans DSM 25962T (96.9 %), Patulibacter minatonensis DSM 18081T (96.7 %), Patulibacter americanus DSM 16676T (96.2 %) and Patulibacter ginsengiterrae DSM 25990T (95.9 %). Considering combined phenotypic and genotypic characteristics, it is proposed that strain SDT represents a novel species of the genus Patulibacter, for which the name Patulibacter brassicae sp. nov. is proposed. The type strain is SDT (=CICC 24108T=KCTC 39817T).