Aerobic Hydrocarbon-Degrading Alphaproteobacteria: Sphingomonadales

Kertesz, Michael A.; Kawasaki, Akitomo

doi:10.1007/978-3-319-60053-6_9-1

Cited by 9 publications

(9 citation statements)

References 132 publications

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“…Within each of the lifestyle categories the taxonomic assignation of the ASVs was phylogenetically diverse (Figure 1b), but there were notable differences in how these ASVs contributed to each category in the rDNA and the RNA pool. FL-ls assemblages in the rDNA were largely represented by sequences of the putatively chemolithotrophic Crenarchaeota [48] and SAR324 [14], and by Chloroflexi (mostly SAR202), Marinimicrobia and the Alphaproteobacteria Sphingomonadales, which may have the ability to use recalcitrant compounds [15, 49, 50]. In contrast, in the rRNA pool, Sphingomonadales took over and accounted for half of the reads (Figure 1b).…”

Section: Resultsmentioning

confidence: 99%

The quality of dissolved organic matter shapes the biogeography of the active bathypelagic microbiome

Sebastián

Sánchez

Salazar

et al. 2021

Preprint

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The bathypelagic ocean (1000-4000 m depth) is the largest aquatic biome on Earth but it is still largely unexplored. Due to its prevalent low dissolved organic carbon concentrations, most of the prokaryotic metabolic activity is assumed to be associated to particles. The role of free-living prokaryotes has thus been mostly ignored, except that of some chemolithoautotrophic lineages. Here we used a global bathypelagic survey of size-fractionated metagenomic and 16S (genes and transcripts) data and performed a differential abundance analysis to explore the functional traits of the different prokaryotic life-strategies, their contribution to the active microbiome, and the role that the quality of the dissolved organic matter (DOM) plays in driving this contribution. We found that free-living prokaryotes have limited capacity to uplift their metabolism in response to environmental changes and display comparatively lower growth rates than particle associated prokaryotes, but are responsible for the synthesis of vitamins in the bathypelagic. Furthermore, their contribution to the active prokaryotic microbiome increased towards waters depleted of labile DOM, which represented a large fraction of the tropical and subtropical ocean sampled stations. This points to a relevant yet overlooked role of free-living prokaryotes in DOM cycling in the vast bathypelagic desert.

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Section: Resultsmentioning

confidence: 99%

The quality of dissolved organic matter shapes the biogeography of the active bathypelagic microbiome

Sebastián

Sánchez

Salazar

et al. 2021

Preprint

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“…The Order Rickettsiales is represented by the genus Rickettsia , which is a symbiont of Eukaryota and can induce disease in humans [ 85 ]. Sphingomonadales ( Sphingomonas , Novosphingobium , Sphingobium , Sphingopyxis and Erythrobacter ) are common aerobic bacteria isolated from a wide range of environments, including temperate and polar soils, marine sediments and plant surfaces and tissues [ 86 ].…”

Section: Resultsmentioning

confidence: 99%

Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae

et al. 2021

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L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as infectious agents causing allergies and as potential vectors of pathogens and microrganisms. In spite of the close bacteria–nematode relationship very little is known of the anisakids microbiota. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of anisakids when the L3 larvae migrate through the muscles. As a consequence, the bacterial inoculum will be spread, with potential effects on the quality of the fish, and possible clinical effects cannot be discarded. A total of 2,689,113 16S rRNA gene sequences from a total of 113 L3 individuals obtained from fish captured along the FAO 27 fishing area were studied. Bacteria were taxonomically characterized through 1803 representative operational taxonomic units (OTUs) sequences. Fourteen phyla, 31 classes, 52 orders, 129 families and 187 genera were unambiguously identified. We have found as part of microbiome an average of 123 OTUs per L3 individual. Diversity indices (Shannon and Simpson) indicate an extraordinary diversity of bacteria at an OTU level. There are clusters of anisakids individuals (samples) defined by the associated bacteria which, however, are not significantly related to fish hosts or anisakid taxa. This suggests that association or relationship among bacteria in anisakids, exists without the influence of fishes or nematodes. The lack of relationships with hosts of anisakids taxa has to be expressed by the association among bacterial OTUs or other taxonomical levels which range from OTUs to the phylum level. There are significant biological structural associations of microbiota in anisakid nematodes which manifest in clusters of bacteria ranging from phylum to genus level, which could also be an indicator of fish contamination or the geographic zone of fish capture. Actinobacteria, Aquificae, Firmicutes, and Proteobacteria are the phyla whose abundance value discriminate for defining such structures.

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“…The relative abundance of Sphingomonas was less than 1% in 1-year and more than 1.4% in 14-year treatments, showing an increase with CC. Other studies have shown that Sphingomonas was a nutrient-poor nanobacterium, which could adapt to heterotrophic growth under conditions of nutrient depletion ( Kämpfer et al, 2002 ; Delmotte et al, 2009 ; Williams et al, 2009 ; Sharma et al, 2010 ; Kertesz et al, 2017 ). In this paper, the increase of Sphingomonas indicates that after 14 years of continuous cultivation, the rhizosphere soil presented a state of nutrient depletion.…”

Section: Discussionmentioning

confidence: 99%

Metabolomics and Microbiomics Reveal Impacts of Rhizosphere Metabolites on Alfalfa Continuous Cropping

et al. 2022

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Alfalfa long-term continuous cropping (CC) can pose a serious threat to alfalfa production. However, the mechanism of alfalfa CC obstacle is unclear as of today. Our preliminary study showed that the main factors of CC obstacle were not the lack of nutrients or water in alfalfa rhizosphere soils. Further, we evaluated physic-chemical property, microbial population structure, and metabolite differences of alfalfa rhizosphere soils with CC for 1, 7, and 14 years based on analysis of metabolomics and microbiomics. Four phenolic acid metabolites, including p-coumaric acid, ferulic acid, vanillic acid, and p-hydroxybenzoic acid, were found to have significant differences among different CC years, which may be the key factors of CC obstacle. Among them, p-coumaric acid and ferulic acid could significantly decrease the germination rate of alfalfa seeds by 21.11 and 16.67% at the concentration of 100 μg/mL and the height (root length) of alfalfa seedlings by 21% (32.9%) and 13.72% (16.45%). Moreover, these metabolites could effectively promote the growth of some pathogenic fungi, causing alfalfa root rot. Among them, p-coumaric acid obviously and significantly aggravated the occurrence of alfalfa root rot. With the increase of CC years, soil microbial community changed from fungi to bacteria; fungi decreased by 10.83%, fungi increased by 8.08%, and beneficial microorganisms decreased with the increase of CC years. Field analysis and experimental verification showed that the above results were consistent with that of CC obstacle in the field. Among the key metabolites, the autotoxicity of p-coumaric acid was the strongest. This study fully proved that the continuous accumulation of autotoxic substances in alfalfa rhizosphere was the key factor causing alfalfa CC obstacles.

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Aerobic Hydrocarbon-Degrading Alphaproteobacteria: Sphingomonadales

Cited by 9 publications

References 132 publications

The quality of dissolved organic matter shapes the biogeography of the active bathypelagic microbiome

The quality of dissolved organic matter shapes the biogeography of the active bathypelagic microbiome

Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae

Metabolomics and Microbiomics Reveal Impacts of Rhizosphere Metabolites on Alfalfa Continuous Cropping

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