Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique

Abstract

Citrus is a valuable crop in Pakistan. It is rich in vitamin C, other nutrients and antioxidants. Huanglongbing (HLB) caused by a bacterium “Candidatus liberibacter asiaticus” (CLas), africanus and americanus has an influence on citrus production around the world. Beside HLB there exist several other bacterial species in citrus groves in Pakistan. The structure and diversity of bacterial species in various ecosystems can be quickly examined using NGS. This approach is considerably quicker and more precise than outdated methods. Healthy or citrus greening infected leaf samples of Grapefruit (Citrus paradisi), C. aurantifolia, and C. reticulata Blanco were used for diversity analysis. In this study high throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves, by using PCR amplicons of 16S rDNA sequences (V5–V7 regions) with Illumina Hi seq. As a result, a total number of 68,722 sequences were produced from the test samples. According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria. C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves. To determine alpha diversity (AD), additional data was analyzed using statistical indices such as Shannon, Chao1, and Simpson. According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively. The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology, which can help us learn more about the interactions between plants and microbes. This research is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology.

Assessment of genetic diversity of latent bacteria in coconut leaves associated with lethal yellowing disease symptoms in Kenya

“…Studying the microbial diversity of diseased plants is a quick way to understand the structure and functioning of bacterial communities, and it could contribute to the isolation and detection of new bacteria (Mushtaq et al., 2022). This study used culture‐independent approaches to investigate the diversity and composition of bacterial communities in coconut leaves showing symptoms of lethal yellowing disease and in healthy leaves, allowing for the identification of their abundance levels.…”

Molecular characterization of divergent isolates of Citrus bent leaf viroid (CBLVd) from citrus cultivars of Punjab, Pakistan

“…Pakistan cultivates citrus on 206,569 hectares, producing 2.36 million tonnes. The Punjab Province, with its favorable environmental conditions, soil compatibility, and adequate water availability, has the highest citrus production in the country compared to other provinces ( Memon and Kasbit, 2017 ; Mushtaq et al, 2022 ). Despite being grown in optimal conditions, the yield of citrus fruit falls short of its potential due to the presence of various pests and diseases, particularly viroids ( Ali et al, 2022 ; Bakhtawar et al, 2022 ).…”

Retraction: Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique

“…The PLOS ONE Editors retract this article [ 1 ] because it was identified as one of a series of submissions for which we have concerns about authorship, competing interests, and peer review. We regret that the issues were not addressed prior to the article’s publication.…”