Marine heterotrophic bacteria associated with Prochlorococcus sp. RSP50
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA805060 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18079769_1.fastq.gz | Fastqsanger.gz | |||
| SRR18079769_2.fastq.gz | Fastqsanger.gz | |||
| SRR18079770_1.fastq.gz | Fastqsanger.gz | |||
| SRR18079770_2.fastq.gz | Fastqsanger.gz | |||
| SRR18079771_1.fastq.gz | Fastqsanger.gz |
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Project description:Macroalgae contribute substantially to primary production in coastal ecosystems. Their biomass, mainly consisting of polysaccharides, is cycled into the environment by marine heterotrophic bacteria (MHB), using largely uncharacterized mechanisms. In Zobellia galactanivorans, we discovered and characterized the complete catabolic pathway for carrageenans, major cell wall polysaccharides of red macroalgae, providing a model system for carrageenan utilization by MHB. We further demonstrate that carrageenan catabolism relies on a multifaceted carrageenan-induced regulon, including a non-canonical polysaccharide utilization locus (PUL) and several distal genes. The genetic structure of the carrageenan utilization system is well conserved in marine Bacteroidetes, but modified in other MHB phyla. The core system is completed by additional functions which can be assumed by non-orthologous genes in different species. This complex genetic structure is due to multiple evolutionary events including gene duplications and horizontal gene transfers. These results allow for an extension on the definition of bacterial PUL-mediated polysaccharide digestion.
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Project description:Influence of the constant full-spectrum light and short-to-long wavelengths of the visible spectrum (red, green and blue lights) and the significance of 12 h photoperiod was tested on heterotrophic marine flavobacteria Siansivirga zeaxanthinifaciens CC-SAMT-1T. RNA-seq analysis revealed remarkable qualitative and quantitative variations in terms of gene expression in CC-SAMT-1T with respect to incident lights. While blue light illumination stimulated expression of genes involved in inorganic carbon metabolism, green˗red lights largely upregulated the genes participating in high-molecular-weight (HMW) organic carbon metabolism. Constant full-spectrum light also displayed the upregulation of genes involved in the metabolism of HMW organic carbon. Thus, the short-to-long wavelengths of visible light and the 12 h photoperiod most likely to play a key role in the marine carbon cycle by tuning heterotrophic bacterial metabolism.
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Project description:Examining the impact of short term exposure to HDPE and PVC plastic leachates on gene transcription in Prochlorococcus cultures in vitro
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Project description:Prochlorococcus is found throughout the euphotic zone in the oligotrophic open ocean. Deep mixing and sinking in aggregates or while attached to particles can, however, transport cells below this sunlit zone, depriving them of light for extended periods of time and influencing their circulation via ocean currents. Viability of these cells over extended periods of darkness could shape the ecology and evolution of the Prochlorococcus collective. We have shown that when co-cultured with a heterotrophic microbe and subjected to repeated periods of extended darkness, Prochlorococcus cells develop a heritable dark-tolerant phenotype – through an apparent epigenetic mechanism – such that they survive longer periods of darkness. Here we examine this adaptation at the level of physiology and metabolism in co-cultures of dark-tolerant and parent strains of Prochlorococcus, each grown with the heterotroph Alteromonas under diel light:dark conditions. The relative abundance of Alteromonas is higher in dark-tolerant than parental co-cultures, while dark tolerant Prochlorococcus cells are also larger, contain less chlorophyll, and are less synchronized to the light:dark cycle. Meta-transcriptome analysis of the cultures further suggests that dark-tolerant co-cultures undergo a coupled shift in which Prochlorococcus uses more organic carbon and less photosynthesis, and Alteromonas uses more organic acids and fewer sugars. Collectively, the data suggest that dark adaptation involves a loosening of the coupling between Prochlorococcus metabolism and the light:dark cycle and a strengthening of the coupling between the carbon metabolism of Prochlorococcus and Alteromonas.
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Project description:Marine picocyanobacteria are ubiquitous primary producers across the world's oceans, and play a key role in the global carbon cycle. Recent evidence stemming from in situ investigations have shown that picocyanobacteria are able to sink out of the euphotic zone to depth, which has traditionally been associated with larger, mineral ballasted cells. The mechanisms behind the sinking of picocyanobacteria remain a point of contention, given that they are too small to sink on their own. To gain a mechanistic understanding of the potential role of picocyanobacteria in carbon export, we tested their ability to form "suspended" (5-60 μm) and "visible" (ca. > 0.1 mm) aggregates, as well as their production of transparent exopolymer particles (TEP)-which are a key component in the formation of marine aggregates. Additionally, we investigated if interactions with heterotrophic bacteria play a role in TEP production and aggregation in Prochlorococcus and Synechococcus by comparing xenic and axenic cultures. We observed TEP production and aggregation in batch cultures of axenic Synechococcus, but not in axenic Prochlorococcus. Heterotrophic bacteria enhanced TEP production as well as suspended and visible aggregate formation in Prochlorococcus, while in Synechococcus, aggregation was enhanced with no changes in TEP. Aggregation experiments using a natural plankton community dominated by picocyanobacteria resulted in aggregation only in the presence of the ballasting mineral kaolinite, and only when Synechococcus were in their highest seasonal abundance. Our results point to a different export potential between the two picocyanobacteria, which may be mediated by interactions with heterotrophic bacteria and presence of ballasting minerals. Further studies are needed to clarify the mechanistic role of bacteria in TEP production and aggregation of these picocyanobacteria.
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Project description:Organic substrate transfer between photoautotrophic and heterotrophic microbes in the surface ocean is a central but poorly understood process in the global carbon cycle. This study developed a co-culture system of marine diatom Thalassiosira pseudonana and heterotrophic bacterium Ruegeria pomeroyi, and addressed diel changes in phytoplankton endometabolite production using nuclear magnetic resonance (NMR) and bacterial metabolite consumption using gene expression. Here we deposit data for NMR analysis from the study. Samples were collected every 6 hours over two days under a diel light cycle. During the course of the study, we observed an increase in some phytoplankton endometabolites presumably due to the effects of the associated bacteria. We introduced an additional experiment and tested this possibility by comparing phytoplankton endometabolite accumulation between axenic treatments and bacteria coculture treatments.
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Project description:Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. However, the high complexity of in situ ecosystems renders it difficult to study these interactions. Two-member co-culture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of co-cultivation. The associated heterotrophic bacterial assembly mostly constituted five classes including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria. The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes from the co-culture system were reconstructed inclusive of Synechococcus and the five dominant heterotrophic bacterial populations. The only primary producer of the co-culture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TBDT, glycoside hydrolase, and peptidases proteins. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low molecular weight DOM, including Flavobacteria metabolism byproducts, through ABC, TRAP, and TTT transport systems. Polysaccharide-utilization loci present in the flavobacterial genomes encoded similar trans-membrane protein complexes as Sus/cellulosome and may influence their lifestyle preferences and close associations with phytoplankton. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking also contributed to the maintenance of the Synechococcus / heterotroph co-culture system and the interactions shaping the system.
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Project description:metagenome-assembled genomes of heterotrophic marine thaumarchaea
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