Candidatus Pumilisymbium abstrusum
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ABSTRACT:
PROVIDER: PRJEB77054 | ENA |
REPOSITORIES: ENA
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Project description:When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host gene expression patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We tested if RNAlater allows to preserve proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing. We used the marine gutless oligochaete Olavius algarvensis as a model for testing. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). We compared five RNAlater preserved and five flash frozen samples in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Five worms were incubated in RNAlater for 24 hours. After incubation, RNAlater was removed and samples were stored at -80°C. The remaining five worms were preserved with liquid nitrogen and stored at -80 °C immediately after preservation.
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Project description:Microbial species produce the storage biopolymer polyhydroxyalkanoate (sPHA), as a carbon and energy source. However, only bacteria and fungi are currently known to degrade microbial sPHAs, using an enzyme called PHA depolymerase (PHAD). This study shows that animals also have a PHAD that can degrade sPHA. We discovered a PHAD in the gutless oligochaete, Olavius algarvensis. These marine worms gain their nutrition by digesting their bacterial symbionts, with sPHA making up to 42% of the carbon in their dominant symbiont. In gutless oligochaetes, this sPHA-synthesizing symbiont is present in the post-genital trunk regions and absent in the head region of the worm (Ott et al., Springer 2023). Based on this previous observation, the worms were dissected to remove the head portion (“tip”) from the body (“trunk”) just above the genital pad region. Samples consisted of single worms and pools of three or five worms washed in 99% ethanol prior to dissection (n = 3 for single and pooled samples). In addition, one sample set consisted of single worms not washed with ethanol (n = 3). Dissected samples were placed in 2 ml cryo-vials, flash frozen in liquid nitrogen, and stored at -80 °C prior to protein digestion. The whole sample set was processed for proteomics.
2026-07-28 | PXD072931 | Pride
Project description:When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host protein abundance patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We replicated our experiment from PXD014591 to test if RNAlater allows preserving proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing. We used the marine gutless oligochaete Olavius algarvensis as a model for testing. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). We compared six RNAlater preserved and eight flash frozen samples in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Six worms were incubated in RNAlater for 24 hours. After incubation, RNAlater was removed and samples were stored at -80°C. Eight worms were directly flash frozen in liquid nitrogen and stored at -80 °C immediately after preservation.
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Project description:Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis
2016-02-12 | MSV000079512 | MassIVE
Project description:When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host gene expression patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We first tested if RNAlater allows to preserve proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing (see PXD014591). Second, for the data in this PRIDE submission we tested if RNAlater preserves protein expression patterns over time at room temperature. We used the marine gutless oligochaete Olavius algarvensis as a test case. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). For this dataset, we fixed a total of 33 worms and incubated them in RNAlater for up to 4 weeks. We then evaluated proteome preservation quality in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Out of this 33 samples, eleven worms were incubated for 24 hours in RNAlater at 4°C (t0), while the other worms were incubated in RNAlater at room temperature (21-23°C) for additional 24 hours (t1, 6 worms), one week (t2, 8 worms), and four weeks (t3, 8 worms). We removed RNAlater from the worms after incubation and froze the samples at -80°C.
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Project description:Phylogenetic and proteogenomic analysis of a mutualistic spirochete endosymbiont in the gutless oligochaete Olavius algarvensis
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Project description:Transcriptomes of Olavius algarvensis
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