Ecological and functional capabilities of an uncultured Kordia sp.

Royo-Llonch, Marta; Sánchez, Pablo; González, José M.; Pedrós‐Alió, Carlos; Acinas, Silvia G.

doi:10.1016/j.syapm.2019.126045

Cited by 6 publications

(4 citation statements)

References 87 publications

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“…Previous studies reported ecological succession of bacterial clades with members such as Flavobaceriaceae and Rhodobacteraceae in late August and September 2010 14,15 . Kordia, member of the Flavobaceriaceae family, was recently assessed at the pangenomic level 48 , revealing that Kordia's core pangenome comprised a large fraction of cell wall and membrane biogenesis genes, peptidase and TBDR encoding genes. At t4 for the dispersants-only treatment, Kordia showed an increased transcriptional activity of TBDR, glyoxylate shunt, membrane biogenesis and peptidase biosynthesis ( Figure 3B, Supplementary Figures 4 and 5), matching previous descriptions of Kordia as an active player in niche colonization 48 .…”

Section: Discussionmentioning

confidence: 99%

“…Kordia, member of the Flavobaceriaceae family, was recently assessed at the pangenomic level 48 , revealing that Kordia's core pangenome comprised a large fraction of cell wall and membrane biogenesis genes, peptidase and TBDR encoding genes. At t4 for the dispersants-only treatment, Kordia showed an increased transcriptional activity of TBDR, glyoxylate shunt, membrane biogenesis and peptidase biosynthesis ( Figure 3B, Supplementary Figures 4 and 5), matching previous descriptions of Kordia as an active player in niche colonization 48 . Colwellia signatures in the K2015 metatranscriptome indicated an opportunistic behavior that arose from the chemical exposure regime and time.…”

Section: Discussionmentioning

confidence: 99%

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ColwelliaandMarinobactermetapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities

Peña-Montenegro

Kleindienst

Allen

et al. 2020

Preprint

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Over 7 million liters of Corexit EC9500A and EC9527A were applied to the Gulf of Mexico in response to the Deepwater Horizon oil spill. The impacts of dispersants remain under debate and negative, positive, and inconclusive impacts have been reported. Here, metatrancriptomics was applied in the context of metapangenomes to microcosms that simulated environmental conditions comparable to the hydrocarbon-rich 1,100 m deep plume. Within this microcosm study, negative effects of dispersants on microbial hydrocarbon degradation were previously reported based on activity measurements and geochemical data. Transcriptional enrichment of Colwellia, a potential dispersant degrader, followed variable time-dependent trajectories due to interactions between oil, dispersants, and nutrients. The Colwellia metapangenome captured a mixture of environmental responses linked to the Colwellia psychrerythraea 34H genome and to the genomes of other members of the Colwellia genus. The activation of genes involved in lipid degradation, nitrogen metabolism, and membrane composition under oil or nutrient availability, suggested an opportunistic growth strategy for Colwellia. In contrast, transcripts of Marinobacter, a natural hydrocarbon degrader, increased only in oil treatments. Marinobacter transcripts largely recruited to the accessory metapangenome of Marinobacter sp. C18, the closest genomic reference. A complex response involving carbon and lipid metabolism, chemotaxis and a type IV secretion system suggested active energy-dependent processes in Marinobacter. These findings highlight chemistry-dependent responses in the metabolism of key hydrocarbon-degrading bacteria and underscore that dispersant-driven selection could temper the ability of the community to respond to hydrocarbon injection.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

ColwelliaandMarinobactermetapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities

Peña-Montenegro

Kleindienst

Allen

et al. 2020

Preprint

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“…According to the in silico predictions made by the reports of Silva et al ( 6 , 29 ) and in this study, several novel compounds from diverse classes are yet to be unveiled from this genus. Members of the genus Kordia , in their turn, play a vital role in the marine carbon cycle since they feed on phytoplankton particles and possess algicidal activities, contributing to the control of phytoplankton blooms ( 36 ). Despite their relevant roles in nature, knowledge of secondary metabolites typically produced by Kordia species is acutely scarce, if non-existent.…”

Section: Discussionmentioning

confidence: 99%

Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon

Silva,

Nabhan Homsi,

Keller-Costa

et al. 2023

mSystems

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Flavobacteriaceae spp. are key players in global biogeochemical cycling and are known for their versatile carbohydrate and peptide catabolism. However, it is currently unknown whether secondary metabolism traits underlie their broad range of occurrence across the earth’s biomes. We examined 2,680 genomes to unveil an unprecedented phylogenetic signal dictating natural product biosynthesis diversification within the Flavobacteriaceae family. The distribution of secondary metabolite biosynthetic gene clusters (BGCs) across genomes usually follows macroevolutionary, genus-specific patterns. Noticeably, 88.6% of the observed BGCs were inferred to lead to the biosynthesis of likely novel natural products. We found an unanticipated, large diversity of taxon-specific BGCs encoding carotenoid and flexirubin pigments, the vast majority of which awaiting formal description. In particular, Aquimarina and Kordia spp. possessed large genomes, versatile catabolic traits, and a repertoire of BGCs possibly encoding drug-inspiring polyketides, non-ribosomal peptides, or post-translationally modified peptides. Using a machine learning approach (feature selection), we reveal that marine and non-marine Flavobacteriaceae genomes are differentially enriched in CAZymes and peptidases with distinct functionalities and molecular targets. IMPORTANCE This is the most comprehensive study performed thus far on the biosynthetic potential within the Flavobacteriaceae family. Our findings reveal intertwined taxonomic and natural product biosynthesis diversification within the family. We posit that the carbohydrate, peptide, and secondary metabolism triad synergistically shaped the evolution of this keystone bacterial taxon, acting as major forces underpinning the broad host range and opportunistic-to-pathogenic behavior encompassed by species in the family. This study further breaks new ground for future research on select Flavobacteriaceae spp. as reservoirs of novel drug leads.

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“…Some pioneer studies have explored the pangenomes of uncultured Prochlorococcus (Kashtan et al 2014;Thompson et al 2019), SAR11 lineages (Grote et al 2012;Haro-Moreno et al 2020;Thrash et al 2014;Tsementzi et al 2016), or uncultured Bacteroidetes relatives of Kordia sp. (Royo-Llonch et al 2020a).…”

Section: Delineation Of Ecological Meaningful Units Of Uncultured Mic...mentioning

confidence: 99%

Towards a Global Perspective of the Marine Microbiome

Acinas

Sebastián

Ferrera

2022

The Microbiomes of Humans, Animals, Plants, and the Environment

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Marine microbes play fundamental roles in nutrient cycling and climate regulation at a planetary scale. The field of marine microbial ecology has experienced major breakthroughs following the application of high-throughput sequencing and cultureindependent methodologies that have pushed the exploration of the marine microbiome to an unprecedented scale. This chapter overviews how the advances in gene-and genome-centric approaches as well as in culturing and single cell physiological methodologies in conjunction with global oceanographic circumnavigation expeditions and long-term time series are fueling our understanding of the biogeography, temporal dynamics, functional diversity, and evolutionary processes of microbial populations. We discuss how the joint effort of all those integrative approaches will help to boost our knowledge of the marine microbiome to reach a predictive understanding of how it is going to evolve in future scenarios.

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Ecological and functional capabilities of an uncultured Kordia sp.

Cited by 6 publications

References 87 publications

ColwelliaandMarinobactermetapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities

ColwelliaandMarinobactermetapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities

Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon

Towards a Global Perspective of the Marine Microbiome

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