Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach

Huang, Xinqing; Zhu, Jianming; Cai, Zhonghua; Lao, Yong-Min; Jin, Hui; Yu, Ke; Zhang, Boya; Zhou, Jin

doi:10.1016/j.micres.2018.08.015

Cited by 26 publications

(25 citation statements)

References 78 publications

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“…The following are available online at https://www.mdpi.com/article/ 10.3390/microorganisms9061115/s1, Table S1: Bacterial genomes; Table S2: Prophages; Table S3: Phylogenomics; Table S4 [79]. The genomes of the three most abundant phages (recruiting more than 1,000 total reads) are shown on the right-hand side.…”

Section: Supplementary Materialsmentioning

confidence: 99%

Prophage Genomics and Ecology in the Family Rhodobacteraceae

et al. 2021

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Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.

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Section: Supplementary Materialsmentioning

confidence: 99%

Prophage Genomics and Ecology in the Family Rhodobacteraceae

et al. 2021

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“…There was distinct temporal heterogeneity in the main nutrient concentrations (NO 3 -, NO 2 -, NH 4 + , and PO 4 3-) throughout the HAB, and the lowest values appeared at the bloom's peak. Detailed information is given in our previous work [51]. The changes in these parameters reflect the basic ecological characteristics of the algal bloom, indicating the typical dynamic characteristics of dinoflagellates [52].…”

Section: Algal Bloom Characteristicsmentioning

confidence: 99%

“…We got 242.5 gigabases of raw reads (mean of 31,051,745 per sample) from the eight metagenomic samples. Details of the data can be found in a previous work [51]. After primary assembly, a total of 15,472,449 scaffolds (>200 bp) were obtained in the test samples.…”

Section: Metagenomic Datamentioning

confidence: 99%

“…This trend suggests that the relative abundance of Caudovirales has distinct alterations in different algal bloom stages. In addition, Caudovirales has been reported to infect a wide range of bacterial hosts, especially species in the Proteobacteria and Bacteroidetes phyla, which are dominant taxa in blooms [51]. Bacterioplankton are important microbial components of food-web fluxes [39], and they have been associated with natural plankton populations [55].…”

Section: Taxonomic Compositionmentioning

confidence: 99%

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Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

Cai

Zuo

et al. 2020

Microorganisms

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Viruses are key biogeochemical engines in the regulation of the dynamics of phytoplankton. However, there has been little research on viral communities in relation to algal blooms. Using the virMine tool, we analyzed viral information from metagenomic data of field dinoflagellate (Gymnodinium catenatum) blooms at different stages. Species identification indicated that phages were the main species. Unifrac analysis showed clear temporal patterns in virioplankton dynamics. The viral community was dominated by Siphoviridae, Podoviridae, and Myoviridae throughout the whole bloom cycle. However, some changes were observed at different phases of the bloom; the relatively abundant Siphoviridae and Myoviridae dominated at pre-bloom and peak bloom stages, while at the post-bloom stage, the members of Phycodnaviridae and Microviridae were more abundant. Temperature and nutrients were the main contributors to the dynamic structure of the viral community. Some obvious correlations were found between dominant viral species and host biomass. Functional analysis indicated some functional genes had dramatic response in algal-associated viral assemblages, especially the CAZyme encoding genes. This work expands the existing knowledge of algal-associated viruses by characterizing viral composition and function across a complete algal bloom cycle. Our data provide supporting evidence that viruses participate in dinoflagellate bloom dynamics under natural conditions.

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“…However, it is clear that AQs, along with AHLs and tetramic acids, play a role independent of quorum sensing, and can have direct consequences on microalgae growth and proliferation. Many QS signal-producing bacteria (particularly those producing AQs) have been isolated from algal blooms [22,55], an environment in which inhibiting algal growth would be a sensible strategy from the bacterium's point of view. When algae cell densities are high, such as during algal blooms, a few more dead algae does not jeopardize the bacterium's carbon source (photosynthesizing microalgae), while the lysed cells allow bacteria to capitalize on the liberated nutrients (such as N, P and Fe), especially as the bloom wanes and nutrients begin to become scarce.…”

Section: -Alkyl-4-quinolonesmentioning

confidence: 99%

How do Quorum Sensing Signals Mediate Algae–Bacteria Interactions?

Dow¹

2021

Preprint

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Quorum sensing (QS) describes a process by which bacteria can sense the local cell density of their own species, thus enabling them to coordinate gene expression and physiological processes on a community-wide scale. Small molecules called autoinducers or QS signals, which act as intraspecies signals, mediate quorum sensing. As our knowledge of QS has progressed, so too has our understanding of the structural diversity of QS signals, along with the diversity of bacteria conducting QS and the range of ecosystems in which QS takes place. It is now also clear that QS signals are more than just intraspecies signals. QS signals mediate interactions between species of prokaryotes, and between prokaryotes and eukaryotes. In recent years, our understanding of QS signals as mediators of algae–bacteria interactions has advanced such that we are beginning to develop a mechanistic understanding of their effects. This review will summarize the recent efforts to understand how different classes of QS signals contribute to the interactions between planktonic microalgae and bacteria in our oceans, primarily N-acyl-homoserine lactones, their degradation products tetramic acids, and 2-alkyl-4-quinolones. In particular, this review will discuss the ways in which QS signals alter microalgae growth and metabolism, namely as direct effectors of photosynthesis, regulators of the cell cycle, and as modulators of other algicidal mechanisms. Furthermore, the contribution of QS signals to nutrient acquisition is discussed, and finally how microalgae can modulate these small molecules to dampen their effects.

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Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach

Cited by 26 publications

References 78 publications

Prophage Genomics and Ecology in the Family Rhodobacteraceae

Prophage Genomics and Ecology in the Family Rhodobacteraceae

Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

How do Quorum Sensing Signals Mediate Algae–Bacteria Interactions?

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