Biology subjects

Petersen, J.

Publications and source records attributed to Petersen, J..

24 records · Page 2Linked to original sources

bioRxiv2020

A Draft Reference Genome for Hirudo verbana, the Medicinal Leech

The medicinal leech, Hirudo verbana, is a powerful model organism for investigating fundamental neurobehavioral processes. The well-documented arrangement and properties of H. verbanas nervous system allows changes at the level of specific neurons or synapses to be linked to physiological and behavioral phenomena. Juxtaposed to the extensive knowledge of H. verbanas nervous system is a limited, but recently expanding, portfolio of molecular and multi-omics tools. Together, the advancement of genetic databases for H. verbana will complement existing pharmacological and electrophysiological data by affording targeted manipulation and analysis of gene expression in neural pathways of interest. Here, we present the first draft genome assembly for H. verbana, which is approximately 250 Mbp in size and consists of 61,282 contigs. Whole genome sequencing was conducted using an Illumina sequencing platform followed by genome assembly with CLC-Bio Genomics Workbench and subsequent functional annotation. Ultimately, the diversity of organisms for which we have genomic information should parallel the availability of next generation sequencing technologies to widen the comparative approach to understand the involvement and discovery of genes in evolutionarily conserved processes. Results of this work hope to facilitate comparative studies with H. verbana and provide the foundation for future, more complete, genome assemblies of the leech.

genomics↗

bioRxiv2020

RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation

We present RootPainter, a GUI-based software tool for the rapid training of deep neural networks for use in biological image analysis. RootPainter facilitates both fully-automatic and semi-automatic image segmentation. We investigate the effectiveness of RootPainter using three plant image datasets, evaluating its potential for root length extraction from chicory roots in soil, biopore counting and root nodule counting from scanned roots. We also use RootPainter to compare dense annotations to corrective ones which are added during the training based on the weaknesses of the current model.

plant biology↗

bioRxiv2019

Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments

The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans comb. nov., P. marinum comb. nov., P. flavum comb. nov. and R. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26T (= DSM 106348T = CFBP 8663T). This genome-based classification was supported by a chemotaxonomic comparison, with gradual taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium are combined with clade-specific genes to encode different strategies for detoxification and nutrition in harsh, nutrient-poor environments. Finally, we predict diagnostic phenotypes for the distinction of P. banfieldiae from other Pseudorhizobium species, including autotrophy and sensitivity to the azo dye Congo Red, which we experimentally validated.

microbiology↗

bioRxiv2019

Horizontal acquisition followed by expansion and diversification of toxin-related genes in deep-sea bivalve symbionts

Deep-sea bathymodioline mussels gain their nutrition from intracellular bacterial symbionts. Their sulfur-oxidizing (SOX) symbionts were recently shown to encode abundant toxin-related genes (TRGs) in their genomes, which may play a role in beneficial host-microbe interactions. Here, we compared TRGs in the genomes of SOX symbionts from 10 bathymodioline mussel and two sponge species to better understand their potential functions and evolutionary origins. Despite the close phylogenetic relatedness of these symbionts, the number and classes of encoded toxins varied greatly between host species. One of the TRG classes, YDs, has experienced gene expansions multiple times, suggesting that these genes are under adaptive selection. Some symbiont genomes contained secretion systems, which can play a role in host-microbe interactions. Both TRGs and secretion systems had a heterogeneous distribution, suggesting that these closely related bacteria have acquired different molecular mechanisms for interacting with the same family of animal hosts, possibly through convergent evolution.

microbiology↗

bioRxiv2019

Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems

In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared to the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to 10-fold higher compared to fluxes reported for non-symbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves contribution may boost productivity of these important blue carbon ecosystems.

ecology↗

bioRxiv2019

Diversity matters: Deep-sea mussels harbor multiple symbiont strains

Genetic diversity of closely-related free-living microbes is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Indeed, symbiont strain diversity has long assumed to be restricted in intracellular bacteria associated with animals. Here, we sequenced the metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key metabolic functions, such as the use of energy and nutrient sources, electron acceptors and viral defense mechanisms. Most strain-specific genes were expressed, highlighting their adaptive potential. We show that fine-scale diversity is pervasive in Bathymodiolus symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, not the host, feeds the symbionts.

microbiology↗