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opencc-by-4.0Jun 2021View details →

Figure 1 in Assessment of entomopathogenic nematodes and their symbiotic bacteria to control the stink bugs Euschistus heros and Dichelops melacanthus (Heteroptera: Pentatomidae) in the soybean-corn succession system

Figure 1. Mortality (%) of Euschistus heros seven days after their exposition to 16 EPNs strains applied on sand substrate, at the rate of 140 IJs/cm² (1000 IJs/insect). Sn.: Steinernema. Ht.: Heterorhabditis. Averages followed by the same letter do not differ significantly according to the Tukey test 5%.

opencc-by-4.0Aug 2021View details →

Figure 4 in Indiscriminate ingestion of entomopathogenic nematodes and their symbiotic bacteria by Aedes aegypti larvae: a novel strategy to control the vector of Chikungunya, dengue and yellow fever

Figure 4. Melanization of Heterorhabditis bacteriophora within Aedes aegypti larvae (3rd instar). A melanized H. bacteriophora within dead Ae. aegypti larvae (a), close up picture of melanized nematode upon larval dissection (b), nematodes representing different stages of melanization recovered from one dead Ae. aegypti larvae (c). Arrows indicate melanized nematode within Ae. aegypti larvae.

opencc-by-4.0Aug 2021View details →

Figure 7 in Indiscriminate ingestion of entomopathogenic nematodes and their symbiotic bacteria by Aedes aegypti larvae: a novel strategy to control the vector of Chikungunya, dengue and yellow fever

Figure 7. Aedes aegypti larval mortality when exposed to supernatants and cell suspensions of Xenorhabdus nematophila (X. n.) and Photorhabdus laumondii (P. l.) in 24 well plates. Different uppercase or lower letters above error bars indicate statistical significance (Tukey's test p ≤ 0.05).

opencc-by-4.0Aug 2021View details →

Figure 3 in Indiscriminate ingestion of entomopathogenic nematodes and their symbiotic bacteria by Aedes aegypti larvae: a novel strategy to control the vector of Chikungunya, dengue and yellow fever

Figure 3. Different stages of Heterorhabditis bacteriophora colonization of Aedes aegypti larvae (3rd instar). H. bacteriophora within larvae at 2-day post inoculation (a), H. bacteriophora emerging out of larvae upon larval dissection at 7-day post inoculation) (b), adult H. bacteriophora within larvae along with large number of infective juveniles (IJs) released from another adult H. bacteriophora (c). Black arrows indicate adult H. bacteriophora, whereas green arrows indicate newly emerged IJs.

Fig. 5 in A symbiotic association of a boring polychaete and an echinoid from the Late Cretaceous of Germany

Fig. 5. Schematic sketch of the echinoid / polychaete interaction and the development of a Caulostrepsis boring. A. Position of the commensal polychaete on the sheltered basal side (plastron) of the echinoid, taking advantage of the hosts ciliary current and sediment resuspension due to locomotion. B. A polydorid polychaete producing an initial shallow depression on the test surface. C. The polydorid progressively deepens the excavation; the presence of a mucus−bound infill between the limbs as it is known for some Recent polydorids, is hypothetical. D. Abandoned trace and regeneration texture developed by the living echinoid skeletal tissue. The mode of penetration is based upon Söderström (1923) and Blake and Evans (1973).

Fig. 3 in A symbiotic association of a boring polychaete and an echinoid from the Late Cretaceous of Germany

Fig. 3. SEM images of a latex cast prepared from the trace−bearing plastron area of the Echinocorys ovata (Leske, 1778) echinoid (Early Maastrichtian; "Klementelvitz" quarry, Rügen Island, N Germany). A. Traces # 4–7 oriented sub−parallel to each other in close proximity to the periproct B. Lateral view of the moderately deep U−shaped trace # 12 showing a distinct regeneration texture in form of primary and miliary tubercles.

Fig. 2 in A symbiotic association of a boring polychaete and an echinoid from the Late Cretaceous of Germany

Fig. 2. Oral surface of an Echinocorys ovata (Leske, 1778) (# MB.E 5713) featuring syn−vivo polychaete boring traces (Early Maastrichtian; "Klementelvitz" quarry, Rügen Island, N Germany). A. Overview of the well preserved oral surface with 27 Caulostrepsis isp. traces, all of which are located in the interambulacral plates of the plastron. B. Schematic sketch of the basal surface indicating the position and number of the traces and the areas enlarged in C and D. C. Close−up of several traces in close proximity of the periproct. D. Close−up of several traces illustrating their variability in length, boring depth and curvature. Note the prominent regeneration texture exhibited by all traces.

Fig. 4. A in A symbiotic association of a boring polychaete and an echinoid from the Late Cretaceous of Germany

Fig. 4. A. Recent Polydora sp. boring traces recorded in an artificial limestone substrate deployed in the Swedish Kosterfjord area during a bioerosion experiment. B. SEM image of an epoxy resin cast of an initial syn−vivo Caulostrepsis isp. boring taken from a Littorina littorea gastropod shell. C. The spionid polychaete Polydora sp. isolated from a bivalve shell. (Recent material stored at the Institute of Palaeontology, Erlangen).

Fig.1 in A symbiotic association of a boring polychaete and an echinoid from the Late Cretaceous of Germany

Fig.1. Map of Rügen Island (N Germany) in the southern Baltic Sea and the location of the chalk pit "Klementelvitz", where the Echinocorys in question was sampled in Early Maastrichtian strata.

opencc-by-4.0Sep 2024View details →

Data and analyses for Perkowski et al. (2024) manuscript accepted to AoB Plants: "Symbiotic nitrogen fixation reduces belowground biomass carbon costs of nitrogen acquisition under low, but not high, nitrogen availability"

This repository contains data and scripts for analyses and plots in Perkowski et al. (2024), titled "Symbiotic nitrogen fixation reduces belowground biomass carbon costs of nitrogen acquisition under low, but not high, nitrogen availability". v2.0 updates code and scripts per reviewer comments and is the final release prior to manuscript proofing.

opencc-by-4.0Jun 2009View details →

Figure 1 in Phylogeny-based species delimitations and the evolution of host associations in symbiotic zoanthids (Anthozoa, Zoanthidea) of the wider Caribbean region

Figure 1. Phylogeny of Caribbean symbiotic zoanthids based on the internal transcribed spacer (ITS) region of the rRNA nuclear gene. Support values are 100 pseudoreplicate maximum likelihood (ML) bootstrap values followed by three million iteration Bayesian posterior probabilities. The clades of symbiotic species are colour coded according to their host associations. The information presented in parentheses after the specimens collected for this study includes: the colour of the zoanthid, presence of Symbiodinium, host taxa, and individual identifier (which includes the collection location).

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Variation in symbiont density is linked to changes in constitutive immunity in the facultatively symbiotic coral, Astrangia poculata

Scleractinian corals are essential ecosystem engineers, forming the basis of coral reef ecosystems. However, these organisms are in decline globally, in part due to rising disease prevalence. Most corals are dependent on symbiotic interactions with single-celled algae from the family Symbiodiniaceae to meet their nutritional needs, however suppression of host immunity may be essential to this relationship. To explore immunological consequences of algal symbioses in scleractinian corals, we investigated constitutive immune activity in the facultatively symbiotic coral, Astrangia poculata. We compared immune metrics (melanin synthesis, antioxidant production, and antibacterial activity) between coral colonies of varying symbiont density. Symbiont density was positively correlated to both antioxidant activity and melanin concentration. Our results suggest that the relationship between algal symbiosis and host immunity may be more complex than originally hypothesized and highlight the need for nuanced approaches when considering these relationships.

opencc-zeroOct 2022View details →

Figure 2 in Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Figure 2. Stability of phylogenomic topologies using analyses with concatenated alignments and gene tree coalescence (A) Congruence of major class-level clades across 481 genomes including one sample for every available genus of Ascomycota and representatives of Basidiomycota (compared trees are in Data S2A, S2B, and S2C; see Star Methods). (B) Congruence of sampled lineages within Lichinomycetes based on the same two methods. Red lines indicate edges incongruent between the two methods. A complete comparison of edges is in Data S1H. (C) Gene and site phylogenetic signal for the two methodological approaches. Related to Data S1K. (D) Phylogenetic signal of three topological hypotheses of the relationship of Lichinomycetes, Lecanoromycetes, and Eurotiomycetes. Statistical differences from Gtest (withratios 1:1 and 1:1:1 respectively) isexpressedas *** p <0.001. Relatedto Data S1K.

Figure 3 in Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Figure 3. Lifestyle diversity of Lichinomycetes (A) Stegobium paniceum beetle host of Symbiotaphrinabuchneri (photo by Nikolai Vladimirov). (B) Candelina submexicana, a lichen from rocks in Mexico. (C) Sarea resinae, a fungus on conifer resin in boreal forests. (D) Geoglossum glabrum, an earth-tongue of Sphagnum bogs (photo by Jozef Pavlík). (E) Chaenotheca chrysocephala, a ''pin lichen'' of ancient forests. (F) Pycnora praestabilis, a lichen on wood in the Alps. (G) Vezdaea aestivalis, a lichen on plant detritus in the Rocky Mountains. (H) Piccolia ochrophora, a lichen on poplar bark in British Columbia, Canada. (I) Lichina confinis, a lichen on seashore rocks in western Scotland. Photos by the authors except where indicated.

Figure S1 in Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Figure S1. Ancestral node reconstruction of CAZymes putatively degrading cellulose, lignin and pectin. Relatedto Figure 1. Ancestral nodes are display as letters in the tree, with colored stars referring the three nodes that were included in the PCA analyses: MRCA Lichinomycetes in blue; MRCA Lichinomycetes + Lecanoromycetes and Eurotiomycetes in green; and the MRCA of Arthoniomycetes and Dothideomycetes + Lichinomycetes, Lecanoromycetes and Eurotiomycetes in orange. Color is scaled per CAZyme. Columns with an asterisk did not converge at the ancestral state estimation (convergence =1).

Figure 1 in Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Figure 1. Position of newly sampled early-diverging lineages in a maximum likelihood reconstruction of 115 Ascomycota genomes based on 1,292 concatenated loci Dating based on the program LSD2 with six fossils, showing confidence interval bars (see Star Methods). Newly generated genomes are indicated by bold text; underlying highlighting indicates ascomycotan classes in which these lineages have been placed until now. Single asterisk = lineages classified in ''orphan'' classes; double asterisk = additionally sampled putatively early-diverging lineages. Genome size, GC content, number of genes, tRNAs, CAZy classes, Pfams, and BGCs based on de novo annotations of all genomes. Voucher data on newly sequenced genomes are in Table S1; expanded background data on genome assemblies and annotations are found in Table S2 and Data S1L and S1Mand on CAZyme and BGC annotations in Data S1O and S1P. An underlying tree with 481 taxa is in Data S2B and S2D, an expanded CAZyme heat map with node dating is in Figure S1, and underlying CAZyme and BGC data are in Data S2E and S2F.

opencc-by-4.0Mar 2023View details →

Supplemental Files for "A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis"

Supplemental files for "A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis". This data is linked to the bioRxiv pre-print doi: https://doi.org/10.1101/2022.10.19.511543, an updated version of which is in press at G3: Genes|Genomes|Genetics, and corresponds to the NCBI BioProject PRJNA885267 and NCBI BioSample SAMN31081226.   Nuclear genome assembly Rhizophagus_irregularis_DAOM197198_assembly.fasta   Illumina and Illumina+Nanopore gene annotations Rhizophagus_irregularis_DAOM197198_Illumina+ONT_curated.gff3 Rhizophagus_irregularis_DAOM197198_Illumina_curated.gff3   Illumina and Illumina+Nanopore functional gene annotations Rhizophagus_irregularis_DAOM197198_annotations_Illumina+ONT.txt Rhizophagus_irregularis_DAOM197198_annotations_Illumina.txt   Illumina and Illumina+Nanopore CDS sequences Rhizophagus_irregularis_DAOM197198_cds-transcripts_Illumina+ONT_curated.fa Rhizophagus_irregularis_DAOM197198_cds-transcripts_Illumina_curated.fa   Illumina and Illumina+Nanopore mRNA sequences Rhizophagus_irregularis_DAOM197198_mrna-transcripts_Illumina+ONT_curated.fa Rhizophagus_irregularis_DAOM197198_mrna-transcripts_Illumina_curated.fa   Illumina and Illumina+Nanopore protein sequences Rhizophagus_irregularis_DAOM197198_proteins_Illumina+ONT_curated.fa Rhizophagus_irregularis_DAOM197198_proteins_Illumina_curated.fa   GO terms for g:Profiler Rhizophagus_irregularis_DAOM197198_Illumina+ONT_GOterms.gmt *Or use token gp__xfGY_dQeI_yx4   Repetitive and transposable element library and annotation Rhizophagus_irregularis_DAOM197198_curatedrepeatlibrary.fasta Rhizophagus_irregularis_DAOM197198_repeatmasker.out Rhizophagus_irregularis_DAOM197198_repeats.gff3   DNA methylome (sequenced from spores) Rhizophagus_irregularis_DAOM197198_mCG_mods_frequency.tsv   Poly(A) signal and tail sequences Rhizophagus_irregularis_DAOM197198_pasa_polyAsite_analysis.out Rhizophagus_irregularis_DAOM197198_pasa_polyAsites.fasta   Small RNA annotation Rhizophagus_irregularis_DAOM197198_sRNA.gff3 Rhizophagus_irregularis_DAOM197198_sRNA.tsv   Mitochondrial genome assembly and annotation Rhizophagus_irregularis_DAOM197198_mtDNA.fasta Rhizophagus_irregularis_DAOM197198_mtDNA.gff   R. irregularis phylostratigraphy Rhizophagus_irregularis_DAOM197198_1432141_phyloranks.tsv Rhizophagus_irregularis_DAOM197198_1432141_high-confidence_phyloranks.tsv   Mucoromycota fungi phylostratigraphy Disdec1_101101_phyloranks.tsv Geopyr1_50956_phyloranks.tsv Gigmar1_4874_phyloranks.tsv Morel2_1314771_phyloranks.tsv Phybl2_4837_phyloranks.tsv Radspe1_64574_phyloranks.tsv   Fatty acid synthase phylogeny FAS_genes_muscle5_msa.fa (alignments) FAS_genes.raxml.support (ML tree)

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Symbiotic microbiota vary with breeding group membership in a highly social joint-nesting bird

Symbiotic microbes affect the health, fitness, and behavior of their animal hosts, and can even affect the behavior of non-hosts. Living in groups presents numerous benefits and challenges to social animals, including exposure to symbiotic microbes, which can mediate both cooperation and competition. In social mammals, individuals from the same social group tend to share more similar microbes, and this social microbiome, the microbial community of all hosts in the same social group, can shape the benefits and costs of group living. In contrast, little is known about the social microbiome of group-living birds. We tested the predictions that communally breeding smooth-billed anis (Crotophaga ani) belonging to the same breeding group share more similar microbes and that microbial community composition differs between body regions. To test this, we used 16S rRNA gene sequencing to characterize the preen gland and body feather microbiota of adult birds from 16 breeding groups at a long-term study site in southwestern Puerto Rico. As predicted, individuals from the same breeding group shared more similar microbiota than non-group members and preen gland and body feathers harboured distinct microbial communities. Future research will evaluate whether this social microbiome affects the behavior of group living birds.

opencc-zeroApr 2023View details →

opencc-by-4.0Apr 2023View details →

Transcriptomes for Ranitomeya imitator and R. variabilis: Evidence for a Parabasalian Gut Symbiote in Egg-Feeding Poison Frog Tadpoles in Peru

This dataset contains the assembled transcriptomes for our paper. The three assemblies are for Ranitomeya imitator, R. variabilis, and a merged assembly of the two species. For methodological details, see the published manuscript.