Bacterial diversity analysis of coastal superficial seawaters near aquaculture facilities, using MALDI-TOF approach and Ribopeaks database

Freitas, Jorge; Perestrelo, Rosa; Vaz‐Pires, Paulo

doi:10.1016/j.aquaculture.2022.738263

Cited by 4 publications

(3 citation statements)

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“…VITEK database limitations have been documented in earlier research. 43 In addition, The VITEK system primarily relies on phenotypic characteristics and biochemical tests for bacterial identification, while 16S rRNA gene sequencing is a genotypic method. Differences in genotype and phenotype can lead to discordant results.…”

Section: Discussionmentioning

confidence: 99%

Bacterial Diversity in Al-Asfar Lake, Al Ahsa Oasis, Saudi Arabia

Al Mousa,

Aldayel,

Genena

et al. 2024

J. Pure Appl. Microbiol.

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This study aimed to investigate bacterial diversity in Al-Asfar Lake, Al Ahsa Oasis, Saudi Arabia, based on a polyphasic approach. Water samples were collected and divided into two parts. For the culture-dependent approach, different media such as Tryptic Soy Agar (TSA), and Blood Agar (BA) were used. The obtained 29 isolates were diverse with respect to phenotypic characteristics revealed by VITEK. 18 isolates were selected for 16S rRNA sequencing based on the initial screening by VITEK. Since some types of bacteria do not grow on media, the DNA in the second part was isolated directly and subjected to metagenomic analysis. VITEK disclosed a total of 19 species belonging to 3 phyla: Pseudomonadota, Actinomycetota, and Bacillota, while the 16S rRNA sequencing revealed 12 species that could be amplified and sequenced. Metagenomic analysis exhibited variation in the relative abundance of 13 phyla, 18 classes, 20 families, 16 genera, and 24 species. Four dominant phyla are represented, including Firmicutes, Cyanobacteria, Bacteroidota, and Proteobacteria, respectively. Furthermore, functional gene screening revealed 33 functional categories including the metabolism of cofactors, vitamins, and xenobiotic biodegradation. This study affords insights into the bacterial diversity and fundamental biogeochemical processes in the lake and paves the way for the potential exploitation of microbial wealth in biotechnological applications.

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Section: Discussionmentioning

confidence: 99%

Bacterial Diversity in Al-Asfar Lake, Al Ahsa Oasis, Saudi Arabia

Al Mousa,

Aldayel,

Genena

et al. 2024

J. Pure Appl. Microbiol.

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“…It enables differential identification of filamentous fungi, yeasts, bacteria, mycobacteria, and protozoan parasites from a variety of environments using the distinct protein and peptide profiles of microbial cells. (Ashfaq et al, 2022; Freitas et al, 2022; Santos et al, 2016; Tarfeen et al, 2022). In a previous study, while 92% of the 13 isolates of five Fusarium spp.…”

Section: Discussionmentioning

confidence: 99%

Morphological and molecular characterization of Fusarium incarnatum as a causal disease agent of pepper (Capsicum annuum) fruit rot

Soylu,

Atay,

Kara

et al. 2023

Journal of Phytopathology

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Chilli pepper (Capsicum annuum L.) is one of the most important commercially cultivated and consumed vegetables in Turkey. During a disease survey, typical symptoms of fruit rot were observed on mature chilli pepper fruits in several surveyed fields and on dried pepper fruits obtained from local retailers/bazaars in Hatay Province, Turkey. Disease incidence varied from 15 to 45% of the plants in the inspected fields. Following standard isolation procedures, 40 fungal isolates were isolated, purified and single‐spore cultures were obtained from surface‐disinfected, rotted dried pepper tissue. Of these isolates, six fungal isolates with dense, cottony white aerial mycelia that became beige with age, were isolated on a potato sucrose agar. All isolates were found to be pathogenic on artificially inoculated chilli pepper fruit. Based on morphological characteristics, the isolates were initially identified as Fusarium incarnatum (Desm.) Sacc. 1886. Morphological identification of F. incarnatum isolates was further confirmed by MALDI‐TOF and molecular analyses using the sequences of the internal transcribed spacer (ITS), partial translation elongation factor‐1α (TEF‐1α) and second largest subunit of RNA polymerase II (RPB2) loci. Phylogenetic analysis based on ITS, TEF‐1α, RPB2 and concatenation of TEF‐1α, RPB2 loci sequences performed with several isolates of Fusarium spp. confirmed that representative fungal isolates (MKUZF1 and MKUZF4) belong to F. incarnatum. To our knowledge, this is the first report of F. incarnatum causing fruit rot in chilli peppers grown in Turkey.

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“…Compared to traditional PCR and other immunoassay-based approaches, Yan et al recent work verified the resilience of this technology to identify new Corona virus efficiently (Yan et al 2021 ). Apart, from this it has also proven a reliable procedure for identifying microorganisms from many ecosystems (Ashfaq et al 2022 ; Santos et al 2016 ; Freitas et al 2022 ). The high throughput profiling using this approach of the diverse microbial biomolecules can unravel their key function in ecosystems (Weigt et al 2018 ).…”

Section: Introductionmentioning

confidence: 99%