Draft Genome Sequences from Two Gram-Negative Bacteria, Serratia sp. Strain EWG9 and Leclercia sp. Strain EMC7, Isolated from the Earthworm Eisenia fetida.
Ontology highlight
ABSTRACT:
SUBMITTER: Barman P
PROVIDER: S-EPMC8852314 | biostudies-literature | 2022 Feb
REPOSITORIES: biostudies-literature
Publications
Draft Genome Sequences from Two Gram-Negative Bacteria, <i>Serratia</i> sp. Strain EWG9 and <i>Leclercia</i> sp. Strain EMC7, Isolated from the Earthworm Eisenia fetida.
Barman Partha P Mondal Nibendu N Sen Subhajit S Chatterjee Sumit S Sinha Shilpa S Ghosh Wriddhiman W Chakraborty Ranadhir R
Microbiology resource announcements 20220217 2
We present the draft genome sequences of two bacterial strains that are putatively unique species and belong to two different Gram-negative genera: <i>Serratia</i> sp. EWG9 and <i>Leclercia</i> sp. EMC7, recovered from the gut and cast, respectively, of the compost worm Eisenia fetida. ...[more]
Similar Datasets
Project description:The lumbricid earthworms (annelid family Lumbricidae) harbor gram-negative bacteria in their excretory organs, the nephridia. Comparative 16S rRNA gene sequencing of bacteria associated with the nephridia of several earthworm species has shown that each species of worm harbors a distinct bacterial species and that the bacteria from different species form a monophyletic cluster within the genus Acidovorax, suggesting that there is a specific association resulting from radiation from a common bacterial ancestor. Previous microscopy and culture studies revealed the presence of bacteria within the egg capsules and on the surface of embryos but did not demonstrate that the bacteria within the egg capsule were the same bacteria that colonized the nephridia. We present evidence, based on curing experiments, in situ hybridizations with Acidovorax-specific probes, and 16S rRNA gene sequence analysis, that the egg capsules contain high numbers of the bacterial symbiont and that juveniles are colonized during development within the egg capsule. Studies exposing aposymbiotic hatchlings to colonized adults and their bedding material suggested that juvenile earthworms do not readily acquire bacteria from the soil after hatching but must be colonized during development by bacteria deposited in the egg capsule. Whether this is due to the developmental stage of the host or the physiological state of the symbiont remains to be investigated.
| S-EPMC1352274 | biostudies-literature
Project description:In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categories. Further, 4502 contig sequences were found to map with 124 KEGG pathways. The annotated contig dataset exhibited 22 crucial neuropeptides having considerable matches to the marine annelid Platynereis dumerilii, suggesting their possible role in neurotransmission and neuromodulation. In addition, 108 human stem cell marker homologs were identified including the crucial epigenetic regulators, transcriptional repressors and cell cycle regulators, which may contribute to the neuronal and segmental regeneration. The complete functional annotation of this nerve cord transcriptome can be further utilized to interpret genetic and molecular mechanisms associated with neuronal development, nervous system regeneration and nerve cord function.
| S-EPMC5688751 | biostudies-literature
Project description:Survival of earthworms in the environment depends on their ability to recognize and eliminate potential pathogens. This work is aimed to compare the innate defense mechanisms of two closely related earthworm species, Eisenia andrei and Eisenia fetida, that inhabit substantially different ecological niches. While E. andrei lives in a compost and manure, E. fetida can be found in the litter layer in forests. Therefore, the influence of environment-specific microbiota on the immune response of both species was followed. Firstly, a reliable method to discern between E. andrei and E. fetida based on species-specific primers for cytochrome c oxidase I (COI) and stringent PCR conditions was developed. Secondly, to analyze the immunological profile in both earthworm species, the activity and expression of lysozyme, pattern recognition protein CCF, and antimicrobial proteins with hemolytic function, fetidin and lysenins, have been assessed. Whereas, CCF and lysozyme showed only slight differences in the expression and activity, fetidin/lysenins expression as well as the hemolytic activity was considerably higher in E. andrei as compared to E. fetida. The expression of fetidin/lysenins in E. fetida was not affected upon the challenge with compost microbiota, suggesting more substantial changes in the regulation of the gene expression. Genomic DNA analyses revealed significantly higher level of fetidin/lysenins (determined using universal primer pairs) in E. andrei compared to E. fetida. It can be hypothesized that E. andrei colonizing compost as a new habitat acquired an evolutionary selection advantage resulting in a higher expression of antimicrobial proteins.
| S-EPMC3815151 | biostudies-literature
Project description:The present article reports the complete draft genome annotation of earthworm Eisenia fetida, obtained from the manuscript entitled "Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm E. fetida" (Zwarycz et al., 2015) and provides the data on the repetitive elements, protein coding genes and noncoding RNAs present in the genome dataset of the species. The E. fetida protein coding genes were predicted from AUGUSTUS gene prediction and subsequently annotated based on their sequence similarity, Gene Ontology (GO) functional terms, InterPro domains, Clusters of Orthologous Groups (COGs) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways information. The genome wide comparison of orthologous clusters and phylogenomic analysis of the core genes were performed to understand the events of genome evolution and genomic diversity between E. fetida and its related metazoans. In addition, the genome dataset was screened to identify the crucial stem cell markers, regeneration specific genes and immune-related genes and their functionally enriched GO terms were predicted from Fisher׳s enrichment analysis. The E. fetida genome annotation data containing the GFF (general feature format) annotation file, predicted coding gene sequences and translated protein sequences were deposited to the figshare repository under the DOI: https://doi.org/10.6084/m9.figshare.6142322.v1.
| S-EPMC6126081 | biostudies-literature
Project description:Timing and scope of genomic expansion within Annelida: evidence from Hoxeobox genes in the genome of the earthworm Eisenia fetida
| PRJEB10048 | ENA
Project description:The earthworm Eisenia fetida is one of the most used species in standardized soil ecotoxicity tests. Endpoints such as survival, growth and reproduction are ecologically relevant but provide little mechanistic insight into the toxicity pathways, especially at the molecular level. To better understand toxicological modes of action and to facilitate the development of molecular biomarkers, we have obtained 30,245 unique EST sequences from E. fetida and have designed a novel microarray with 15,119 60-mer oligonucleotide probes. These probes target the unique non-redundant EST sequences identified in E. fetida. Using this array we have profiled gene expression of E. fetida after exposure to CL-20, a cage cyclic nitramine previously found exhibiting reversible neurotoxicity to worms. Worms were exposed for 6 days to CL-20. Half of the exposed worms were allowed to recover in a clean environment for 7 days. Electrophysiological analysis showed that the conduction velocity of worm medial giant nerve fiber was significantly decreased after 6-d exposure to CL-20, and that giant nerve fiber function was restored at the end of the 7-d recovery period. Total RNA samples isolated from four treatment groups (6 replicates per group), i.e., 6-d control, 6-d exposed, 13-d control and 6-d exposed with 7-d recovery, were analyzed using the new 15K oligo array. Bioinformatics and statistical analyses have identified specific neurological pathways affected by CL-20 and recovery of these pathways after CL-20 removal. These results provide significant insights on the CL-20 toxic mode of action and how earthworms can recover from chemical stressors.
2009-10-14 | GSE18536 | GEO
Project description:Increasing attention has been paid to the toxicity and hazards of antibiotics on non-target organisms in soil ecosystems because redundant antibiotics in the excretion of treated animals are being brought into the soil by way of manure and sewage irrigation. In order to understand the toxic mechanisms of antibiotics in soil ecosystems, the earthworm Eisenia fetida was exposed to 500 mg kg-1 of oxytetracycline (OTC) as a typical antibiotic for 7, 14 and 21 days. The total proteins of E. fetida in each treatment were separated by two-dimensional gel electrophoresis and differential expressed proteins were identified by MALDI-TOF/TOF-MS. A total of 30 proteins were successfully identified and divided into four categories based on the function. It was surprisingly found that more than 50% of identified proteins belong to the actin family, and all of them were down-regulated more than 2.0-fold. In the meantime, the fibrinolytic enzymes, an important protease with plasminogen activator activity, were suppressed in the last two weeks. The validations in the mRNA level were performed using RT-PCR. However, due to the incomplete genome sequence of E. fetida, we failed to identify more proteins response to OTC stress. This study may provide a new insight into the discovery of novel biomarkers for continuous-poured and low-toxicity pollutants.
| S-EPMC9076484 | biostudies-literature
Project description:BackgroundEisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR.ResultsA total of 3144 good quality ESTs (GenBank dbEST accession number EH669363-EH672369 and EL515444-EL515580) were obtained from the raw clone sequences after cleaning. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, and Caenorhabditis elegans. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2.ConclusionThe ESTMD containing the sequence and annotation information of 4032 E. fetida ESTs is publicly accessible at http://mcbc.usm.edu/estmd/.
| S-EPMC2099499 | biostudies-literature
Project description:BackgroundExplosive compounds such as TNT and RDX are recalcitrant contaminants often found co-existing in the environment. In order to understand the joint effects of TNT and RDX on earthworms, an important ecological and bioindicator species at the molecular level, we sampled worms (Eisenia fetida) exposed singly or jointly to TNT (50 mg/kg soil) and RDX (30 mg/kg soil) for 28 days and profiled gene expression in an interwoven loop designed microarray experiment using a 4k-cDNA array. Lethality, growth and reproductive endpoints were measured.ResultsSublethal doses of TNT and RDX had no significant effects on the survival and growth of earthworms, but significantly reduced cocoon and juvenile counts. The mixture exhibited more pronounced reproductive toxicity than each single compound, suggesting an additive interaction between the two compounds. In comparison with the controls, we identified 321 differentially expressed transcripts in TNT treated worms, 32 in RDX treated worms, and only 6 in mixture treated worms. Of the 329 unique differentially expressed transcripts, 294 were affected only by TNT, 24 were common to both TNT and RDX treatments, and 3 were common to all treatments. The reduced effects on gene expression in the mixture exposure suggest that RDX might interact in an antagonistic manner with TNT at the gene expression level. The disagreement between gene expression and reproduction results may be attributed to sampling time, absence of known reproduction-related genes, and lack of functional information for many differentially expressed transcripts. A gene potentially related to reproduction (echinonectin) was significantly depressed in TNT or RDX exposed worms and may be linked to reduced fecundity.ConclusionsSublethal doses of TNT and RDX affected many biological pathways from innate immune response to oogenesis, leading to reduced reproduction without affecting survival and growth. A complex interaction between mixtures of RDX and TNT was observed at the gene expression level that requires further study of the dynamics of gene expression and reproductive activities in E. fetida. These efforts will be essential to gain an understanding of the additive reproductive toxicity between RDX and TNT.
| S-EPMC2386057 | biostudies-literature
Project description:Biochar is the degradation-resistant product generated by the pyrolysis of organic materials and is produced for the intended use of land application in order to promote carbon sequestration and soil improvement. However, despite the many potential benefits biochar application offers, it is important to quantify any ecological impacts that may result from soil amendment in order to avoid potentially causing negative effects upon soil biota which are crucial in the many ecosystem services provided by soil. Any impacts on earthworms in particular are important to evaluate because of their pivotal role in organic matter breakdown, nutrient cycling and soil formation. In this study, we conducted a series of ecotoxicological assays to determine lethal and sublethal (avoidance, mass change and moisture content) effects of heavy biochar applications that reflect levels that may be used in soil restoration efforts. Two earthworm species, Eisenia fetida, an epigeic species, and Lumbricus terrestris, an anecic species, were utilised as test organisms. Two types of biochar, produced from wheat straw and rice husk feedstocks, respectively, were applied to OECD artificial soil and to a natural soil (Kettering loam) at rates of up to 20% w/w. The influence of biochar application on soil porewater chloride, fluoride and phosphate concentrations was also assessed. The biochar applications induced only a subtle level of avoidance behaviour while effects on survival over a 4-week exposure period were inconsistent. However, death and physical damage to some individual earthworms at high biochar application rates were observed, the mechanisms and processes leading to which should be investigated further. Earthworm development (mean mass change over time) proved to be a more sensitive measure, revealing negative effects on L. terrestris at 10% and 20% (w/w) wheat biochar applications in OECD soil and at 20% (w/w) applications of both biochars in Kettering loam. The moisture content of E. fetida remained remarkably consistent across all treatments (~ 82%), indicating that this is not a sensitive measure of effects. The high rates of biochar application resulted in increased chloride (2 to 3-fold) and phosphate (100-fold) concentrations in simulated soil porewaters, which has important implications for soil fertility and production but also for environmental management.
| S-EPMC7423795 | biostudies-literature