More Like this

1. Macrobdella decora : Old World Leech Gut Microbial Community Structure Conserved in a New World Leech

   https://doi.org/10.1128/AEM.02082-20  

   McClure, Emily Ann; Nelson, Michael C.; Lin, Amy; Graf, Joerg (April 2021, Applied and Environmental Microbiology)

   Johnson, Karyn N. (Ed.)

   ABSTRACT Leeches are found in terrestrial, aquatic, and marine habitats on all continents. Sanguivorous leeches have been used in medicine for millennia. Modern scientific uses include studies of neurons, anticoagulants, and gut microbial symbioses. Hirudo verbana , the European medicinal leech, maintains a gut community dominated by two bacterial symbionts, Aeromonas veronii and Mucinivorans hirudinis , which sometimes account for as much as 97% of the total crop microbiota. The highly simplified gut anatomy and microbiome of H. verbana make it an excellent model organism for studying gut microbial dynamics. The North American medicinal leech, Macrobdella decora , is a hirudinid leech native to Canada and the northern United States. In this study, we show that M. decora symbiont communities are very similar to those in H. verbana. We performed an extensive study using field-caught M. decora and purchased H. verbana from two suppliers. Deep sequencing of the V4 region of the 16S rRNA gene allowed us to determine that the core microbiome of M. decora consists of Bacteroides , Aeromonas, Proteocatella , and Butyricicoccus. The analysis revealed that the compositions of the gut microbiomes of the two leech species were significantly different at all taxonomic levels. The R 2 value was highest at the genus and amplicon sequence variant (ASV) levels and much lower at the phylum, class, and order levels. The gut and bladder microbial communities were distinct. We propose that M. decora is an alternative to H. verbana for studies of wild-caught animals and provide evidence for the conservation of digestive-tract and bladder symbionts in annelid models. IMPORTANCE Building evidence implicates the gut microbiome in critical animal functions such as regulating digestion, nutrition, immune regulation, and development. Simplified, phylogenetically diverse models for hypothesis testing are necessary because of the difficulty of assigning causative relationships in complex gut microbiomes. Previous research used Hirudo verbana as a tractable animal model of digestive-tract symbioses. Our data show that Macrobdella decora may work just as well without the drawback of being an endangered organism and with the added advantage of easy access to field-caught specimens. The similarity of the microbial community structures of species from two different continents reveals the highly conserved nature of the microbial symbionts in sanguivorous leeches. 

   more » « less
2. Chromosome‐level genome assembly of the aster leafhopper ( Macrosteles quadrilineatus ) reveals the role of environment and microbial symbiosis in shaping pest insect genome evolution

   https://doi.org/10.1111/1755-0998.13919  

   Vasquez, Yumary M.; Li, Zheng; Xue, Allen Z.; Bennett, Gordon M. (April 2024, Molecular Ecology Resources)

   Abstract Leafhoppers comprise over 20,000 plant‐sap feeding species, many of which are important agricultural pests. Most species rely on two ancestral bacterial symbionts,SulciaandNasuia, for essential nutrition lacking in their phloem and xylem plant sap diets. To understand how pest leafhopper genomes evolve and are shaped by microbial symbioses, we completed a chromosomal‐level assembly of the aster leafhopper's genome (ALF;Macrosteles quadrilineatus). We compared ALF's genome to three other pest leafhoppers,Nephotettix cincticeps,Homalodisca vitripennis, andEmpoasca onukii, which have distinct ecologies and symbiotic relationships. Despite diverging ~155 million years ago, leafhoppers have high levels of chromosomal synteny and gene family conservation. Conserved genes include those involved in plant chemical detoxification, resistance to various insecticides, and defence against environmental stress. Positive selection acting upon these genes further points to ongoing adaptive evolution in response to agricultural environments. In relation to leafhoppers' general dependence on symbionts, species that retain the ancestral symbiont,Sulcia, displayed gene enrichment of metabolic processes in their genomes. Leafhoppers with bothSulciaand its ancient partner,Nasuia, showed genomic enrichment in genes related to microbial population regulation and immune responses. Finally, horizontally transferred genes (HTGs) associated with symbiont support ofSulciaandNasuiaare only observed in leafhoppers that maintain symbionts. In contrast, HTGs involved in non‐symbiotic functions are conserved across all species. The high‐quality ALF genome provides deep insights into how host ecology and symbioses shape genome evolution and a wealth of genetic resources for pest control targets. 

   more » « less
3. One-step genome engineering in bee gut bacterial symbionts

   https://doi.org/10.1128/mbio.01392-24  

   Lariviere, Patrick J; Ashraf, A_H_M Zuberi; Navarro-Escalante, Lucio; Leonard, Sean P; Miller, Laurel G; Moran, Nancy A; Barrick, Jeffrey E (September 2024, mBio)

   Kaltenpoth, Martin (Ed.)

   ABSTRACT Mechanistic understanding of interactions in many host-microbe systems, including the honey bee microbiome, is limited by a lack of easy-to-use genome engineering approaches. To this end, we demonstrate a one-step genome engineering approach for making gene deletions and insertions in the chromosomes of honey bee gut bacterial symbionts. Electroporation of linear or non-replicating plasmid DNA containing an antibiotic resistance cassette flanked by regions with homology to a symbiont genome reliably results in chromosomal integration. This lightweight approach does not require expressing any exogenous recombination machinery. The high concentrations of large DNAs with long homology regions needed to make the process efficient can be readily produced using modern DNA synthesis and assembly methods. We use this approach to knock out genes, including genes involved in biofilm formation, and insert fluorescent protein genes into the chromosome of the betaproteobacterial bee gut symbiontSnodgrassella alvi. We are also able to engineer the genomes of multiple strains ofS. alviand another species,Snodgrassella communis, which is found in the bumble bee gut microbiome. Finally, we use the same method to engineer the chromosome of another bee symbiont,Bartonella apis, which is an alphaproteobacterium. As expected, gene knockout inS. alviusing this approach isrecA-dependent, suggesting that this straightforward procedure can be applied to other microbes that lack convenient genome engineering methods. IMPORTANCEHoney bees are ecologically and economically important crop pollinators with bacterial gut symbionts that influence their health. Microbiome-based strategies for studying or improving bee health have utilized wild-type or plasmid-engineered bacteria. We demonstrate that a straightforward, single-step method can be used to insert cassettes and replace genes in the chromosomes of multiple bee gut bacteria. This method can be used for investigating the mechanisms of host-microbe interactions in the bee gut community and stably engineering symbionts that benefit pollinator health. 

   more » « less
4. A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis

   https://doi.org/10.1128/mSystems.00177-19  

   Lutz, Holly L.; Ramírez-Puebla, S. Tabita; Abbo, Lisa; Durand, Amber; Schlundt, Cathleen; Gottel, Neil R.; Sjaarda, Alexandra K.; Hanlon, Roger T.; Gilbert, Jack A.; Mark Welch, Jessica L.; et al (August 2019, mSystems)

   ABSTRACT The European common cuttlefish, Sepia officinalis , is used extensively in biological and biomedical research, yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raised S. officinalis using a combination of 16S rRNA amplicon sequencing, quantitative PCR (qPCR), and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of Vibrionaceae and Piscirickettsiaceae . The esophagus was dominated by a single ASV of the genus Vibrio . Imaging revealed bacteria in the family Vibrionaceae distributed in a discrete layer that lines the esophagus. This Vibrio was also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance, as determined by qPCR, and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly used antibiotic enrofloxacin led to a nearly 80% reduction of the dominant Vibrio ASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills were dominated by a single ASV in the family Piscirickettsiaceae , which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the Gammaproteobacteria are the major symbionts of the cuttlefish Sepia officinalis cultured from eggs in captivity and that the esophagus and gills are major colonization sites. IMPORTANCE Microbes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of Vibrio ( Aliivibrio ) fischeri in the light organ of the bobtail squid and the role of Alpha - and Gammaproteobacteria in the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genus Vibrio , as well as colonization of gills by Piscirickettsiaceae . This finding expands the range of organisms and body sites known to be associated with Vibrio and is of potential significance for understanding host-symbiont associations, as well as for understanding and maintaining the health of cephalopods in mariculture. 

   more » « less
5. Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants

   https://doi.org/10.1038/s41396-023-01490-1  

   Béchade, Benoît; Cabuslay, Christian_S; Hu, Yi; Mendonca, Caroll_M; Hassanpour, Bahareh; Lin, Jonathan_Y; Su, Yangzhou; Fiers, Valerie_J; Anandarajan, Dharman; Lu, Richard; et al (August 2023, The ISME Journal)

   Abstract While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont—Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)—and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis. 

   more » « less