High-throughput sequencing reveals the spatial distribution variability of microbial community in coastal waters in Shenzhen

Zhang, Rui; Liu, Yu; Zhao, Xianfeng; Zhao, Zhihui; Zhang, Honglian; Huang, Xiaoping; Xu, Weiqing; Yuchun, Shen; Lan, Wensheng

doi:10.1007/s10646-021-02391-9

Cited by 7 publications

(4 citation statements)

References 30 publications

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“…This result was consistent with a study on fresh hairtails from different regions that reported that Psychrobacter , Thermus and Oceanisphaera were the dominant bacteria in samples from Nantong, while a wide variety of bacterial genera were found in samples from Zhoushan ( Qiankun et al, 2018 ). Another study of water areas produced similar results, with samples from the western part of Shenzhen containing more Proclococcus and samples from the eastern part of Shenzhen containing more Chlorella ( Zhang et al, 2021 ). This results showed that there were differences in microorganisms of diseased potato tubers in different ecological regions which may be related to the local natural environment.…”

Section: Discussionmentioning

confidence: 61%

Comparative Analysis of Microbial Community Diversity and Dynamics on Diseased Tubers During Potato Storage in Different Regions of Qinghai China

et al. 2022

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Effective storage of potatoes is very important for the food industry. Given the problems involving rotten potatoes and low quality during storage, harvested potatoes from the main potato-producing areas in the Qinghai Plateau were treated by selection and air drying (Group “A”) and the others were stored directly as controls (Group “C”). Then, the microbial community structure and diversity of diseased potato tubers from four main production areas were analyzed by high-throughput sequencing technology in different storage stages. The results showed that the community composition and diversity of microbes in different regions and storage periods were different, and the dominant fungi in diseased potato tubers were Boeremia in Huangyuan (HY), Maying (MY) and Zhongling (ZL) and Apiotrichum in Huangzhong (HZ) at the genus level. The dominant bacterial genus was Pseudomonas, but its abundance varied in samples from different regions and storage periods. In the analysis of indicator species, there were some common species and endemic species in each region and period, and the period with the largest number of different species was the third period. Among the four storage periods, the region with the largest number of different species was HZ. Some fungi, especially Fusarium and other potato pathogens, were more abundant in control Group “C” than in treatment Group “A.” In the diversity analysis, the α diversity of fungi in Group “C” was higher than that in Group “A,” but the α diversity of bacteria in Group “A” was higher than that in Group “C,” and there was no obvious regularity with storage time. The β diversity varied significantly among different regions. In addition, through functional prediction analysis, it was found that a plant pathogen was one of the main nutritional types of fungi, which indicated that treatment by selection and drying could significantly reduce phytopathogenic microbe and other microorganisms and could be used as an effective measure for potato storage compared with the prevention and control by drugs that can cause environmental pollution. Further analysis of co-occurrence network showed that pathogenic fungi Fusarium was negatively correlated with pathogenic bacteria Erwinia, and there is also a negative correlation between pathogens and antagonistic microorganisms indicated that there were various symbiotic relationships among microorganisms in diseased potatoes. This study may provide a theoretical basis for biological control of potato cellar diseases and the maintenance of potato quality during long-term storage.

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Section: Discussionmentioning

confidence: 61%

Comparative Analysis of Microbial Community Diversity and Dynamics on Diseased Tubers During Potato Storage in Different Regions of Qinghai China

et al. 2022

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“…At the genus level, the presence of Alteromonas, Synechococcus , Candidatus Actinomarina , and NS5 marine group in all stations (Figure 5A,B ) together with the hydrocarbon quantification (Table 3 ) suggest that the water column of the YS does not show signs of oil pollution. Previous studies have reported that Candidatus Actinomarina , NS5 marine group and Synechococcus are representative genera of coastal areas with low pollution concentrations (Caruso, 2020 ; Zhang et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon‐degrading microorganisms

Valencia‐Agami,

Cerqueda‐García,

Gamboa‐Muñoz

et al. 2024

Environ Microbiol Rep

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This study assessed the bacterioplankton community and its relationship with environmental variables, including total petroleum hydrocarbon (TPH) concentration, in the Yucatan shelf area of the Southern Gulf of Mexico. Beta diversity analyses based on 16S rRNA sequences indicated variations in the bacterioplankton community structure among sampling sites. PERMANOVA indicated that these variations could be mainly related to changes in depth (5 to 180 m), dissolved oxygen concentration (2.06 to 5.93 mg L−1), and chlorophyll‐a concentration (0.184 to 7.65 mg m3). Moreover, SIMPER and one‐way ANOVA analyses showed that the shifts in the relative abundances of Synechococcus and Prochlorococcus were related to changes in microbial community composition and chlorophyll‐a values. Despite the low TPH content measured in the studied sites (0.01 to 0.86 μL L−1), putative hydrocarbon‐degrading bacteria such as Alteromonas, Acinetobacter, Balneola, Erythrobacter, Oleibacter, Roseibacillus, and the MWH‐UniP1 aquatic group were detected. The relatively high copy number of the alkB gene detected in the water column by qPCR and the enrichment of hydrocarbon‐degrading bacteria obtained during lab crude oil tests exhibited the potential of bacterioplankton communities from the Yucatan shelf to respond to potential hydrocarbon impacts in this important area of the Gulf Mexico.

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“…In addition to pathogen detection, NGS technologies have helped to dissect the aquatic microbial community composition as a proxy for microbial water quality assessment in various water environments, e.g., rivers and sediments, drinking water distribution systems, fish farming ponds, lakes, recreational water, rainwater, natural wetlands, marine, estuaries, coastal waters, reservoirs, lagoons, and hot springs, under varied exogenous impacts (e.g., miscellaneous pollution from fecal contamination, fertilizing and mining, WWTP discharge, landfill leachate, anthropogenic activities, and environmental variabilities) [151][152][153][154][155][156][157][158][159][160][161][162][163][164][165]. Furthermore, the dynamic changes in microbial diversity under a variety of anthropogenic, geographic, seasonal, and climatic impacts can also be assessed using the NGS approach to elucidate the observed spatiotemporal variabilities [156,162,[166][167][168][169][170][171].…”

Section: Droplet Digital Pcr (Ddpcr)mentioning

confidence: 99%

Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality

Paruch

2022

IJERPH

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Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.

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High-throughput sequencing reveals the spatial distribution variability of microbial community in coastal waters in Shenzhen

Cited by 7 publications

References 30 publications

Comparative Analysis of Microbial Community Diversity and Dynamics on Diseased Tubers During Potato Storage in Different Regions of Qinghai China

Comparative Analysis of Microbial Community Diversity and Dynamics on Diseased Tubers During Potato Storage in Different Regions of Qinghai China

Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon‐degrading microorganisms

Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality

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