Aurantivirga profunda gen. nov., sp. nov., isolated from deep-seawater, a novel member of the family Flavobacteriaceae

Song, Jaeho; Choi, Jae‐Suk; Im, Mihye; Joung, Yochan; Yoshizawa, Susumu; Cho, Jang-Cheon; Kogure, Kazuhiro

doi:10.1099/ijsem.0.000662

Cited by 19 publications

(11 citation statements)

References 33 publications

(40 reference statements)

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“…There, they would accumulate attached to the remaining particles or switching to a free-living lifestyle, explaining the highest recruitments at the free-living fraction of meso- and bathypelagic waters. It must be considered, however, that proteorhodopsins have been found in the deep sea (Tang et al, 2015; Yoshizawa et al, 2015) and that both presence and expression of proteorhodopsin genes were detected in the Arctic Ocean during the Polar night (Nguyen et al, 2015), suggesting that proteorhodopsins may have an unknown function in dark waters.…”

Section: Discussionmentioning

confidence: 99%

Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

et al. 2017

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Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms.

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Section: Discussionmentioning

confidence: 99%

Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

et al. 2017

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“…An opposite trend was followed by the reads classified as members of the genera Aurantivirga, and, with a markedly lower abundance, by the reads affiliated to Clade Ia, OM60 (NOR5) clade, Alcanivorax, Marinobacter and Halomonas (Figure 9B). Aurantivirga is a member of Flavobacteriaceae whose type strain, Aurantivirga profunda, has been isolated in the deep-sea waters of the Pacific Ocean (Song et al, 2015). Our data show that the ASVs belonging to Aurantivirga are abundant in the RSOW area (on average 4.7 %) and become substantially lower in the coastal area of TNB (0.7 %, adj.p<0.01).…”

Section: Differential Distribution Of Key Bacterial Genera In the Ross Sea Surface Watersmentioning

confidence: 70%

Bacterioplankton Diversity and Distribution in Relation to Phytoplankton Community Structure in the Ross Sea surface waters

Cordone

d’Errico

et al. 2021

Preprint

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Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community. Exchange of exudates, metabolism by-products and cofactors between the phytoplankton and the bacterioplankton communities drive a series of complex interactions affecting the micronutrient availability and co-limitation, as well as nutrient uptakes in Antarctic waters. Yet, the number of studies reporting the simultaneous diversity of the phytoplankton and bacterioplankton in Antarctic waters are limited. Here we report data on the bacterial diversity in relation to phytoplankton community in the surface waters of the Ross Sea during the austral summer 2017. Our results show partially overlapping bacterioplankton communities between the stations located in the Terra Nova Bay coastal waters and the Ross Sea open waters, suggesting that the two communities are subjected to different drivers. We show that the rate of diversity change between the two locations is influenced by both abiotic (salinity and the nitrogen to phosphorus ratio) and biotic (phytoplankton community structure) factors. Our data provides new insight into the coexistence of the bacterioplankton and phytoplankton in Antarctic waters.

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“…Particularly interesting is the fact that the Order Flavobacteriales, although presenting ASVs in both treatments, displayed a much higher significant enrichment in the L-DOM than in the H + L-DOM niche. For example, some ASVs belonging to the genus Tenacibaculum (ASV6 and ASV9), a component of deep marine bacterial communities (Song et al, 2015), were unique in the L-DOM treatment. Bacteria belonging to Tenacibaculum are assumed to be important in the degradation of polymeric organic matter (Zheng et al, 2020) because of their ability to produce hydrolytic enzymes (Cottrell and Kirchman, 2000;Giovannoni and Rappé, 2000).…”

Section: Diversity and Community Composition Selection In Response Tomentioning

confidence: 99%

“…Similarly, the genus Aurantivirga was associated to L-DOM treatment. Bacteria belonging to this genus were described in the deep ocean as chemoheterotrophic and aerobic bacteria (Song et al, 2015), and were found to be quite abundant during the course of incubations from natural blooms (Reintjes et al, 2020), when the supply of lowmolecular-weight products from hydrolysis was larger. These evolving dominances of certain bacterial taxa depending on the different size-fraction incubations may likely imply that different microbial organisms may have diverse capabilities on the decomposition of DOM according to its molecular size.…”

Section: Diversity and Community Composition Selection In Response Tomentioning

confidence: 99%

Changes in Activity and Community Composition Shape Bacterial Responses to Size-Fractionated Marine DOM

et al. 2020

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To study the response of bacteria to different size-fractions of naturally occurring dissolved organic matter (DOM), a natural prokaryotic community from North Atlantic mesopelagic waters (1000 m depth) was isolated and grown in (i) 0.1-μm filtered seawater (CONTROL), (ii) the low-molecular-weight (<1 kDa) DOM fraction (L-DOM), and (iii) the recombination of high- (>1 kDa) and low-molecular-weight DOM fractions (H + L-DOM), to test the potential effect of ultrafiltration on breaking the DOM size continuum. Prokaryotic abundance and leucine incorporation were consistently higher in the H + L-DOM niche than in the L-DOM and CONTROL treatments, suggesting a different interaction with each DOM fraction and the disruption of the structural DOM continuum by ultrafiltration, respectively. Rhodobacterales (Alphaproteobacteria) and Flavobacteriales (Bacteroidetes) were particularly enriched in L-DOM and closely related to the colored DOM (CDOM) fraction, indicating the tight link between these groups and changes in DOM aromaticity. Conversely, some other taxa that were rare or undetectable in the original bacterial community were enriched in the H + L-DOM treatment (e.g., Alteromonadales belonging to Gammaproteobacteria), highlighting the role of the rare biosphere as a seed bank of diversity against ecosystem disturbance. The relationship between the fluorescence of protein-like CDOM and community composition of populations in the H + L-DOM treatment suggested their preference for labile DOM. Conversely, the communities growing on the L-DOM niche were coupled to humic-like CDOM, which may indicate their ability to degrade more reworked DOM and/or the generation of refractory substrates (as by-products of the respiration processes). Most importantly, L- and/or H + L-DOM treatments stimulated the growth of unique bacterial amplicon sequence variants (ASVs), suggesting the potential of environmental selection (i.e., changes in DOM composition and availability), particularly in the light of climate change scenarios. Taken together, our results suggest that different size-fractions of DOM induced niche-specialization and differentiation of mesopelagic bacterial communities.

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Aurantivirga profunda gen. nov., sp. nov., isolated from deep-seawater, a novel member of the family Flavobacteriaceae

Cited by 19 publications

References 33 publications

Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

Bacterioplankton Diversity and Distribution in Relation to Phytoplankton Community Structure in the Ross Sea surface waters

Changes in Activity and Community Composition Shape Bacterial Responses to Size-Fractionated Marine DOM

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