Dataset Information

Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies.

ABSTRACT: Coelopidae (Diptera), known as kelp flies, exhibit an ecological association with beached kelp and other rotting seaweeds. This unique trophic specialization necessitates significant adaptations to overcome the limitations of an algal diet. We aimed to investigate whether the flies' microbiome could be one of these adaptive mechanisms. Our analysis focused on assessing composition and diversity of adult and larval microbiota of the kelp fly Coelopa frigida. Feeding habits of the larvae of this species have been subject of numerous studies, with debates whether they directly consume kelp or primarily feed on associated bacteria. By using a 16S rRNA metabarcoding approach, we found that the larval microbiota displayed considerably less diversity than adults, heavily dominated by only four operational taxonomic units (OTUs). Phylogenetic placement recovered the most dominant OTU of the larval microbiome, which is the source of more than half of all metabarcoding sequence reads, as an undescribed genus of Orbaceae (Gammaproteobacteria). Interestingly, this OTU is barely found among the 15 most abundant taxa of the adult microbiome, where it is responsible for less than 2% of the metabarcoding sequence reads. The other three OTUs dominating the larval microbiome have been assigned as Psychrobacter (Gammaproteobacteria), Wohlfahrtiimonas (Gammaproteobacteria), and Cetobacterium (Fusobacteriota). Moreover, we also uncovered a distinct shift in the functional composition between the larval and adult stages, where our taxonomic profiling suggests a significant decrease in functional diversity in larval samples. Our study offers insights into the microbiome dynamics and functional composition of Coelopa frigida.

SUBMITTER: Bischof PSP

PROVIDER: S-EPMC11222186 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies.

Bischof Paul S P PSP Bartolomaeus Theda U P TUP Löber Ulrike U Bleidorn Christoph C

Microbial ecology 20240703 1

Coelopidae (Diptera), known as kelp flies, exhibit an ecological association with beached kelp and other rotting seaweeds. This unique trophic specialization necessitates significant adaptations to overcome the limitations of an algal diet. We aimed to investigate whether the flies' microbiome could be one of these adaptive mechanisms. Our analysis focused on assessing composition and diversity of adult and larval microbiota of the kelp fly Coelopa frigida. Feeding habits of the larvae of this s ...[more]

PMID: 38960913

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Project description:Eukaryotic organisms evolved in a microbial world and often have intimate associations with diverse bacterial groups. Kelp, brown macroalgae in the order Laminariales, play a vital role in coastal ecosystems, yet we know little about the functional role of the microbial symbionts that cover their photosynthetic surfaces. Here, we reconstructed 79 bacterial metagenome-assembled genomes (MAGs) from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine their metabolic potential and functional roles. Despite the annual life history of bull kelp, nearly half of the bacterial MAGs were detected across multiple years. Diverse members of the kelp microbiome, spanning 6 bacterial phyla, contained genes for transporting and assimilating dissolved organic matter (DOM), which is secreted by kelp in large quantities and likely fuels the metabolism of these heterotrophic bacteria. Bacterial genomes also contained alginate lyase and biosynthesis genes, involved in polysaccharide degradation and biofilm formation, respectively. Kelp-associated bacterial genomes contained genes for dissimilatory nitrate reduction and urea hydrolysis, likely providing a reduced source of nitrogen to the host kelp. The genome of the most abundant member of the kelp microbiome and common macroalgal symbiont, Granulosicoccus, contained a full suite of genes for synthesizing cobalamin (vitamin B12), suggesting that kelp-associated bacteria have the potential to provide their host kelp with vitamins. Finally, kelp-associated Granulosicoccus contained genes that typify the aerobic anoxygenic phototrophic bacteria, including genes for bacteriochlorophyll synthesis and photosystem II reaction center proteins, making them the first known photoheterotrophic representatives of this genus. IMPORTANCE Kelp (brown algae in the order Laminariales) are foundational species that create essential habitat in temperate and arctic coastal marine ecosystems. These photosynthetic giants host millions of microbial taxa whose functions are relatively unknown, despite their potential importance for host-microbe interactions and nutrient cycling in kelp forest ecosystems. We reconstructed bacterial genomes from metagenomic samples collected from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine the functional gene content of specific members of the kelp microbiome. These bacterial genomes spanned 6 phyla and 19 families and included common alga-associated microbial symbionts such as Granulosicoccus. Key functions encoded in kelp-associated bacterial genomes included dissolved organic matter assimilation, alginate metabolism, vitamin B12 biosynthesis, and nitrogen reduction from nitrate and urea to ammonium, potentially providing the host kelp with vitamins and reduced nitrogen.

Project description:BackgroundAnchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization.ResultsWe present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family.ConclusionsAnchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.

Project description:Phylogenetic relationships within the oestroid subclades Rhinophorinae (Calliphoridae) and Polleniidae were reconstructed for the first time, applying a Sanger sequencing approach using the two protein-coding nuclear markers CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase; 1794 bp) and MCS (molybdenum cofactor sulfurase; 2078 bp). Three genera of Polleniidae and nineteen genera of Rhinophorinae were analyzed together with a selection of taxa representing the major lineages of Oestroidea (non-rhinophorine Calliphoridae, Oestridae, Sarcophagidae, Tachinidae). The selected markers provide good resolution and moderate to strong support of the distal branches, but weak support for several deeper nodes. Polleniidae (cluster flies) emerge as monophyletic and their sister-group relationship to Tachinidae is confirmed. Morinia Robineau-Desvoidy as currently circumscribed emerges as paraphyletic with regard to Melanodexia Williston, and Pollenia Robineau-Desvoidy is the sister taxon of the Morinia-Melanodexia clade. We propose a classification with two subfamilies, Moriniinae Townsend (including Morinia, Melanodexia, and Alvamaja Rognes), and Polleniinae Brauer & Bergenstamm (including Pollenia, Dexopollenia Townsend, and Xanthotryxus Aldrich). Anthracomyza Malloch and Nesodexia Villeneuve are considered as Oestroidea incertae sedis pending further study. Rhinophorinae (woodlouse flies) emerge as monophyletic and sister to a clade composed of (Ameniinae + (Ameniinae + Phumosiinae)), and a tribal classification is proposed with the subfamily divided into Rhinophorini Robineau-Desvoidy, 1863 and Phytonini Robineau-Desvoidy, 1863 (the Stevenia-group and the Phyto-group of authors, respectively). Oxytachina Brauer & Bergenstamm, 1891, stat. rev. is resurrected to contain nine Afrotropical rhinophorine species currently assigned to genus Rhinomorinia Brauer & Bergenstamm, 1891: Oxytachina approximata (Crosskey, 1977) comb. nov., O. atra (Bischof, 1904) comb. nov., O. bisetosa (Crosskey, 1977) comb. nov., O. capensis (Brauer & Bergenstamm, 1893) comb. nov., O. scutellata (Crosskey, 1977) comb. nov., O. setitibia (Crosskey, 1977) comb. nov., O. verticalis (Crosskey, 1977) comb. nov., O. vittata Brauer & Bergenstamm, 1891, and O. xanthocephala (Bezzi, 1908) comb. nov.

Project description:The world Rhinophoridae are catalogued, recognising 33 genera and 177 species. Nomenclatural information is provided for all genus-group and species-group names, including lists of synonyms and name-bearing type data. Species distributions are recorded by country. A key to the world genera is presented. Four new genera are erected to accommodate five new species, which do not fit within any of the current generic concepts in Rhinophoridae, according to the results of a morphology-based phylogenetic analysis: Marshallicona Cerretti & Pape with type species Marshallicona quitu Cerretti & Pape, gen. et sp. nov. (Ecuador); Maurhinophora Cerretti & Pape with type species Maurhinophora indoceanica Cerretti & Pape, gen. et sp. nov. (Mauritius); Neotarsina Cerretti & Pape with type species Neotarsina caraibica Cerretti & Pape, gen. et sp. nov. (Trinidad and Tobago) and Neotarsina andina Cerretti & Pape, sp. nov. (Peru); Kinabalumyia Cerretti & Pape with type species Kinabalumyia pinax Cerretti & Pape, gen. et sp. nov. (Malaysia, Sabah). The genus Aporeomyia Pape & Shima (type species Aporeomyia antennalis Pape & Shima), originally assigned to Tachinidae, is here reassigned to Rhinophoridae based on a reassessment of the homologies of the male terminalia. The following five species-group names, which were previously treated as junior synonyms or nomina dubia, are recognised as valid species names: Acompomintho caucasica (Villeneuve, 1908), stat. rev. [from nomen dubium to valid species]; Acompomintho sinensis (Villeneuve, 1936), stat. rev. [from nomen dubium to valid species]; Stevenia bertei (Rondani, 1865), stat. rev. [from nomen dubium to valid species]; Stevenia sardoa Villeneuve, 1920, stat. rev. [from junior synonym of Rhinophora deceptoria Loew, 1847 to valid species]; Stevenia subalbida (Villeneuve, 1911), stat. rev. [from junior synonym of Rhinophora deceptoria Loew, 1847 to valid species]. Reversal of precedence is invoked for the following case of subjective synonymy to promote stability in nomenclature: Rhinophora lepida (Meigen, 1824), nomen protectum, and Musca parcus Harris, 1780: 144, nomen oblitum. New generic and specific synonymies are proposed for the following two names: Mimodexia Rohdendorf, 1935, junior synonym of Tromodesia Rondani, 1856, syn. nov. and Ptilocheta tacchetti Rondani, 1865, junior synonym of Stevenia obscuripennis (Loew, 1847), syn. nov. The following new combinations are proposed: Acompomintho sinensis (Villeneuve, 1936), comb. nov. [transferred from Tricogena Robineau-Desvoidy, 1830]; Tromodesia guzari (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia intermedia (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia lindneriana (Rohdendorf, 1961), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia magnifica (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia obscurior (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia pallidissima (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia setiventris (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935] and Tromodesia shachrudi (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935].

Dataset Information

Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies.

Publications

Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies.

Similar Datasets

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