Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation

Cheng, Xinyue; Tian, Xueliang; Wang, Yunsheng; Lin, Ren-Miao; Mao, Zhenchuan; Chen, Nansheng; Xie, Bingyan

doi:10.1038/srep01869

Cited by 89 publications

(88 citation statements)

References 53 publications

(68 reference statements)

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“…Cheng et al . () showed the presence of enzymes involved xenobiotics metabolism (α‐pinene) in the genome of Serratia sp. M24T3 isolated from B. xylophilus (Proença et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Characterization of bacterial communities associated with the pine sawyer beetleMonochamus galloprovincialis, the insect vector of the pinewood nematodeBursaphelenchus xylophilus

Vicente

Nascimento

Espada

et al. 2013

FEMS Microbiol Lett

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Pine wilt disease (PWD) has a tremendous impact on worldwide forestlands, both from the environmental and economical viewpoints. Monochamus sp., a xylophagous insect from the Cerambycidae family, plays an important role in dissemination of the pinewood nematode, Bursaphelenchus xylophilus, the primary pathogenic agent of PWD. This study investigates, for the first time, the bacterial communities of Monochamus galloprovincialis collected from Portuguese Pinus pinaster trees and B. xylophilus free, using a metagenomics approach. Overall, our results show that natural bacterial communities of M. galloprovincialis are mainly composed by γ-proteobacteria, Firmicutes and Bacteroidetes, which may be a reflection of insects' feeding diet and habitat characteristics. We also report different bacterial communities' composition in the thorax and abdomen of M. galloprovincialis, with high abundance of Serratia sp. in both. Our results encourage further studies in the possible relationship between bacteria from the insect vector and B. xylophilus.

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“…Cheng et al . () showed the presence of enzymes involved xenobiotics metabolism (α‐pinene) in the genome of Serratia sp. M24T3 isolated from B. xylophilus (Proença et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Characterization of bacterial communities associated with the pine sawyer beetleMonochamus galloprovincialis, the insect vector of the pinewood nematodeBursaphelenchus xylophilus

Vicente

Nascimento

Espada

et al. 2013

FEMS Microbiol Lett

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“…Metagenomic data of nematode bacterial symbionts included the complete α-pinene degradation pathway (Cheng et al, 2013). Annotation based on KEGG revealed that the degradation pathways for limonene and pinene (map00903) and for geraniol (map00281) accounted for 2.5% of mapped metagenes.…”

Section: Databases For Pathway Analysis and A Look At Metagenomesmentioning

confidence: 99%

Microbial monoterpene transformationsâ€”a review

2014

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Isoprene and monoterpenes constitute a significant fraction of new plant biomass. Emission rates into the atmosphere alone are estimated to be over 500 Tg per year. These natural hydrocarbons are mineralized annually in similar quantities. In the atmosphere, abiotic photochemical processes cause lifetimes of minutes to hours. Microorganisms encounter isoprene, monoterpenes, and other volatiles of plant origin while living in and on plants, in the soil and in aquatic habitats. Below toxic concentrations, the compounds can serve as carbon and energy source for aerobic and anaerobic microorganisms. Besides these catabolic reactions, transformations may occur as part of detoxification processes. Initial transformations of monoterpenes involve the introduction of functional groups, oxidation reactions, and molecular rearrangements catalyzed by various enzymes. Pseudomonas and Rhodococcus strains and members of the genera Castellaniella and Thauera have become model organisms for the elucidation of biochemical pathways. We review here the enzymes and their genes together with microorganisms known for a monoterpene metabolism, with a strong focus on microorganisms that are taxonomically validly described and currently available from culture collections. Metagenomes of microbiomes with a monoterpene-rich diet confirmed the ecological relevance of monoterpene metabolism and raised concerns on the quality of our insights based on the limited biochemical knowledge.

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“…These include the transformation of proteins into forms digestible by the host12, synthesis of essential vitamins, minerals or amino acids34, priming of the host immune system56, xenobiotic degradation78, and protection against pathogens910. In higher order vertebrates, such as humans, the microbiome fulfilling these niches is extremely complex and consists of thousands of species and functions, forming an intricate web of interactions11.…”

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confidence: 99%

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

Neave

Michell

Apprill

et al. 2017

Sci Rep

197

211

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Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60-76% and 81-90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have freeliving stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

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Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation

Cited by 89 publications

References 53 publications

Characterization of bacterial communities associated with the pine sawyer beetleMonochamus galloprovincialis, the insect vector of the pinewood nematodeBursaphelenchus xylophilus

Characterization of bacterial communities associated with the pine sawyer beetleMonochamus galloprovincialis, the insect vector of the pinewood nematodeBursaphelenchus xylophilus

Microbial monoterpene transformationsâ€”a review

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

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