Metagenomic insights into co-proliferation of Vibrio spp. and dinoflagellates Prorocentrum during a spring algal bloom in the coastal East China Sea

Kim, Daehyun Daniel; Wan, Lingling; Cao, Xiuyun; Klisarova, Daniela; Gerdzhikov, D.; Zhou, Yiyong; Song, Changchun; Yoon, Sukhwan

doi:10.1016/j.watres.2021.117625

Cited by 14 publications

(8 citation statements)

References 76 publications

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“…Arguably, bacterial taxa that are common and consistently abundant across different culturing and physiological conditions of G. balechii can be regarded as the core or stable constituents of the associated microbiome of the dinoflagellate. This notion is similar to previous work on Prorocentrum (Wang et al, 2017;Kim et al, 2021), Alexandrium spp. (Sörenson et al, 2019), and Symbiodiniacean species (Lawson et al, 2018;Nitschke et al, 2020).…”

Section: Identification Of Core (Constitutive) Component Of Gambierdi...supporting

confidence: 91%

Microbiome Associated With Gambierdiscus balechii Cultures Under Different Toxicity Conditions

Lee

Liu

et al. 2022

Front. Mar. Sci.

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Dinoflagellates, including harmful algal bloom species, are known to co-exist with and rely upon bacteria but how the microbiome changes with the physiologies of the cognate dinoflagellates is poorly understood. Here, we used 16S rRNA gene meta-barcoding to characterize the bacterial community in the cultures of Gambierdiscus balechii, a ciguatoxin-producing benthic dinoflagellate, under different nitrogen (N)-nutrient conditions and at different ciguatoxin-producing growth. The high-throughput sequencing of a total of 12 libraries generated 926,438 reads which were classified into 16 phyla. We observed a shift of the G. balechii-associated microbiome from N-replete to low-N conditions and from the early (low toxin) to the late exponential (high toxin) growth stage. Common across these conditions were species from families Rhodobacteraceae and Flavobacteriaceae. Species abundant in the low-N condition mainly included Planctomyces, Ekhidna, and Lactobacillus. Dominant or highly abundant microbial taxa in the high toxin-producing stage (N-replete, late exponential stage) were Oceanococcus and Marinoscillum. Under this condition, one Rhizobiales bacterium, Oricola, also increased in relative abundance. Our study documents the high diversity and dynamics of the G. balechii-associated microbiome, and identifies condition-specific sub-communities: the core (constitutive) microbiome that stably co-exists with G. balechii, the bacterial lineages that are responsive to N-nutrient variations, and species whose abundances are correlated with toxin content of the dinoflagellate. These findings demonstrate that particular bacterial groups are responsive to N-nutrient or toxicity changes of G. balechii and thus will be useful for further investigations on the associated microbiome’s interactions with benthic dinoflagellates and functions in the course of benthic harmful algae blooms.

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Section: Identification Of Core (Constitutive) Component Of Gambierdi...supporting

confidence: 91%

Microbiome Associated With Gambierdiscus balechii Cultures Under Different Toxicity Conditions

Lee

Liu

et al. 2022

Front. Mar. Sci.

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“…To calculate the abundance of genes and MAGs in every sample, high-quality reads were aligned with genes and MAGs with 95% identity as the threshold using Bowtie 2 (Langmead and Salzberg, 2012 ). The abundance of genes and MAGs were estimated based on reads per kilobase per million mapped reads (RPKM) (Mortazavi et al, 2008 ; Lawson et al, 2017 ; Armstrong et al, 2018 ; Pushkarev et al, 2018 ; Kim et al, 2021 ) values of metagenomic reads that mapped to each gene and MAG, where the read counts were normalized by the sequencing depth and gene length. The calculation formula of RPKM was expressed as follows (Mortazavi et al, 2008 ).…”

Section: Methodsmentioning

confidence: 99%

Changes in the Species and Functional Composition of Activated Sludge Communities Revealed Mechanisms of Partial Nitrification Established by Ultrasonication

Xue

Zheng

et al. 2022

Front. Microbiol.

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To achieve energy-efficient shortcut nitrogen removal of wastewater in the future, selective elimination of nitrite-oxidizing bacteria (NOB) while enriching ammonia-oxidizing microorganisms is a crucial step. However, the underlying mechanisms of partial nitrification are still not well understood, especially the newly discovered ultrasound-based partial nitrification. To elucidate this issue, in this study two bioreactors were set up, with one established partial nitrification by ultrasonication while the other didn't. During the operation of both reactors, the taxonomic and functional composition of the microbial community were investigated through metagenomics analysis. The result showed that during ultrasonic partial nitrification, ammonia-oxidizing archaea (AOA), Nitrososphaerales, was enriched more than ammonia-oxidizing bacteria (AOB), Nitrosomonas. The enrichment of microorganisms in the community increased the abundance of genes involved in microbial energy generation from lipid and carbohydrates. On the other hand, the abundance of NOB, Nitrospira and Nitrolancea, and Comammox Nitrospira decreased. Selective inhibition of NOB was highly correlated with genes involved in signal transduction enzymes, such as encoding histidine kinase and serine/threonine kinase. These findings provided deep insight into partial nitrification and contributed to the development of shortcut nitrification in wastewater treatment plants.

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“…To gain a more comprehensive understanding of the functional profiles of microbial communities in both aquaculture and non-aquaculture environments, our analysis specifically targeted genes encoding key enzymes linked to distinct ecosystem functions. Because less predictable is the influence of microbiota on Eutrophication of water bodies of the marine phosphorus cycle, given the patchy ecophysiological understanding of marine microbial phosphorus metabolism ( Kim et al, 2021 ). We identified genes related to phosphorus (P) metabolism in seawater by reviewing the literature.…”

Section: Resultsmentioning

confidence: 99%

Comparative metagenomic analysis of microbial community compositions and functions in cage aquaculture and its nearby non-aquaculture environments

Liu,

Wang,

et al. 2024

Front. Microbiol.

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In the context of burgeoning global aquaculture, its environmental repercussions, particularly in marine ecosystems, have gained significant attentions. Cage aquaculture, a prominent method, has been observed to significantly influence marine environments by discharging substantial amounts of organic materials and pollutants. It is also one of the important reasons for water eutrophication. This study investigated the impacts of cage aquaculture on microbial diversity and functional potential using metagenomics. Specifically, a comparison was made of the physicochemical indicators and microbial diversity between three grouper aquaculture cage nets in Lingshui Xincun Port and three nearby non-aquaculture area surface waters. We found that compared to non-aquaculture areas, the eutrophication indicators in aquaculture environments significantly increased, and the abundances of Vibrio and Pseudoalteromonas in aquaculture environments significantly rose. Additionally, microbial functional genes related to carbon, nitrogen, and sulfur metabolisms were also found to be significantly affected by aquaculture activities. The correlation analysis between microbial populations and environmental factors revealed that the abundances of most microbial taxa showed positive correlations with dissolved inorganic nitrogen, soluble reactive phosphorus, NH4+, and negative correlations with dissolved oxygen. Overall, this study elucidated the significant impacts of aquaculture-induced eutrophication on the diversity and functions of planktonic bacterial communities.

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Metagenomic insights into co-proliferation of Vibrio spp. and dinoflagellates Prorocentrum during a spring algal bloom in the coastal East China Sea

Cited by 14 publications

References 76 publications

Microbiome Associated With Gambierdiscus balechii Cultures Under Different Toxicity Conditions

Microbiome Associated With Gambierdiscus balechii Cultures Under Different Toxicity Conditions

Changes in the Species and Functional Composition of Activated Sludge Communities Revealed Mechanisms of Partial Nitrification Established by Ultrasonication

Comparative metagenomic analysis of microbial community compositions and functions in cage aquaculture and its nearby non-aquaculture environments

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