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Figure 1 in Geographic isolation and human-assisted dispersal in land snails: a Mediterranean story of Helix borealis and its relatives (Gastropoda: Stylommatophora: Helicidae)

Figure 1. Live individuals of the Mediterranean clade Helix species: H. cincta (A), H. borealis (B–E) and H. melanostoma (F). A, Cyprus, Kato Drys; B, Greece, Evvia, between Vassilika and Ellinika; C, Greece, Peloponnese, by Rogi near Kalavryta; D, Greece, Kefalonia: Asos; E, Greece, Peloponnese, near Sparti; F, north-western Tunisia, Kef Governorate, near Sers.

Figure 4 in Geographic isolation and human-assisted dispersal in land snails: a Mediterranean story of Helix borealis and its relatives (Gastropoda: Stylommatophora: Helicidae)

Figure 4. Detailed unrooted phylogeny of the Mediterranean clade inferred from a concatenated alignment of partial mitochondrial COI and 16S gene sequences. The tree is a 50% majority rule consensus of the posterior of a Bayesian analysis with MrBayes. Branch labels indicate SH-aLRT support values, standard bootstrap proportions from 1000 pseudoreplicates, and posterior probabilities from a Bayesian analysis, respectively. Only posterior probabilities are shown for some branches near the tips due to space constraints. Tips are labelled by isolate codes (our data) or GenBank accession numbers of 16S sequences (data from other authors) and two-letter ISO country codes; where needed for interpretation of the results, geographic origin of the sample is given, usually by the closest significant town. Red arrowheads point to samples presumed here to be taken outside of the native range of the respective species. Clade symbols and colours correspond to Figure 2. Abbreviations: anct, anctostoma; thiess, thiesseana; undesc, undescribed; valent, valentini.

opennotspecifiedDec 2021View details →

FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322). in Conlarium sichuanense sp. nov., on Ficus virens from Sichuan Province, China

FIGURE. Phylogenetic tree based on RAxML analyses of a combined LSU, ITS and SSU dataset. Bootstrap support values for ML and MP equal to or greater than 75% and PP value greater than 0.95 are in thickened. Ex-type isolates are in bold, and new taxa are indicated in red. The tree is rooted with Atractospora aquatica (S-1297) and A. aquatica (MFLU 18–2322).

opennotspecifiedDec 2021View details →

FIGURE 2 in Paraboeremia yungensis sp. nov., a new fungal species isolated from Las Yungas, South America, with promising tyrosinase production potential

FIGURE 2. Paraboeremia yungensis (LY 38.7). a. Colony on OA (front and reverse). b. Colony on MEA (front and reverse). c. Colony on PDA (front and reverse). d. Scanning electron micrograph of mature pycnidium with subtending mycelium developed on OA. e. Scanning electron micrograph of conidia covered with a mucilaginous sheath. f. Pycnidium. g. Conidiogenous cells and conidia. h. Conidia with polar guttules. Scale bars (d,f) 25 μm, (g,h) 2 μm, (e) 1 μm.

opennotspecifiedDec 2021View details →

FIGURE 1 in Paraboeremia yungensis sp. nov., a new fungal species isolated from Las Yungas, South America, with promising tyrosinase production potential

FIGURE 1. Cladogram obtained using RAxML to analyse the concatenated DNA sequence data of ITS, LSU, RPB2, and TUB2. The phylogenetic position of Paraboeremia yungensis is shown in blocks. Group support values are presented above the branches (ML bootstrap values/Bayesian posterior probabilities). Vacuiphoma bulgarica (CBS 357.84) was used as outgroup for rooting the tree in all the analyses.

opencc-by-4.0Jan 2022View details →

Complete Genome Sequence of an Aeromonas rivuli Strain Isolated from Ready-to-Eat Food - Data Files

This dataset contains input and intermediate files of the bcgTree analysis described in the Schwartz et al. MRA manuscript entitled “Complete Genome Sequence of an Aeromonas rivuli Strain Isolated from Ready-to-Eat Food”. <table> <tbody> <tr> <td> File name </td> <td> Description </td> </tr> <tr> <td> ‘Aeromonadaceae identifier’.fa </td> <td> Amino acid FASTA file of the translated CDS sequences of a strain X (bcgTree input file) </td> </tr> <tr> <td> full_alignment.concat.fa </td> <td> Alignment of the concatenated amino acid sequences of 107 single-copy core genes that is used for phylogenetic tree calculation in bcgTree (bcgTree intermediate file) </td> </tr> </tbody> </table>   In the bcgTree files, the Aeromonadaceae sequences were named/abbreviated as follows: <table> <tbody> <tr> <td> Sequence name in the bcgTree file </td> <td> Description </td> </tr> <tr> <td> AAZUK01-1 </td> <td> Tolumonas lignilytica BRL6-1 </td> </tr> <tr> <td> Aeromonas-caviae </td> <td> Aeromonas caviae NCTC 12244 </td> </tr> <tr> <td> Aeromonas-dhakensis </td> <td> Aeromonas dhakensis CIP 107500 </td> </tr> <tr> <td> Aeromonas-hydrophila </td> <td> Aeromonas hydrophila ATCC 7966 </td> </tr> <tr> <td> Aeromonas-rivuli </td> <td> Aeromonas rivuli DSM 22539 </td> </tr> <tr> <td> Aeromonas-rivuli-20-VB00005 </td> <td> Aeromonas rivuli 20-VB00005 </td> </tr> <tr> <td> Aeromonas-veronii </td> <td> Aeromonas veronii CECT 4257 </td> </tr> <tr> <td> CP001616-1 </td> <td> Tolumonas auensis DSM 9187 </td> </tr> <tr> <td> JACHGR01-1 </td> <td> Tolumonas osonensis DSM 22975 </td> </tr> </tbody> </table>

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Data from: Habitat isolation reduces intra- and interspecific biodiversity and stability

Fragmentation is predicted to reduce biodiversity and stability by increasing habitat isolation and impeding dispersal among patches. These effects may manifest at both the interspecific and intraspecific levels, yet few studies have simultaneously explored dispersal effects across levels of organization. We used field mesocosm experiments to examine how habitat isolation (in the form of dispersal rate) alters inter- and intraspecific stability and diversity in local zooplankton communities. We observed effects of increasing dispersal rate at both the intra- and interspecific levels. Increasing dispersal increased local species diversity and reduced mean temporal variability of populations. At the intraspecific level, Daphnia pulex clonal diversity was enhanced by dispersal and mean temporal variability of clone abundances through time was reduced.

opencc-zeroJan 2022View details →

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Genetic diversity, differentiation and historical origin of the isolated population of rooksCorvus frugilegusin Iberia

Current bird populations in southern temperate latitudes often represent relicts of glacial refugia from which northern populations expanded as the climate became suitable following the last glacial maximum, 18 000 years before present. Alternatively, these southern populations could be the result of the fragmentation of large distributions and other processes not related to glaciations, like recent recolonization from northern populations and human impact in historical times. Here, we investigate the origin of a small, isolated population of rooks Corvus frugilegus in north-western Iberia. We use genetic data from mitochondrial sequence markers and seven microsatellite loci to assess levels of genetic diversity, structure and gene flow among extant populations in Iberia and its broad distribution across western Europe. Microsatellite markers revealed the existence of two genetic clusters corresponding to Iberia and the remaining European populations, respectively. Haplotype networks based on mtDNA markers revealed a marked star-like phylogenetic pattern and evidence of a recent population expansion in northern Europe, but not in the Iberian population. Our results suggest that contemporary gene flow between Iberia and western Europe is restricted, and that breeding recruitment over recent generations in the Iberian population is local. The results are consistent with a relatively recent post-glacial colonization of Europe and western Siberia by rooks surviving the last glacial maximum in an Iberian refugium, and likely from refugia in other southern peninsulas. The unique ecological features and genetic differentiation of the Iberian rooks underscore the importance of ensuring the long-term conservation of this declining population.

opencc-zeroJan 2022View details →

FIGURE 5. Secondary structures for the D1–D1 in Porphyrosiphon annulatus sp. nov. (Oscillatoriales, Cyanobacteria) isolated on moist soil in Suwon, Republic of Korea

FIGURE 5. Secondary structures for the D1–D1ʹ helix (A–G) and Box-B helix (H–N) in conserved regions of the 16S–23S ITS. (A, H) Microcoleus vaginatus, (B, I) M. autumnalis, (C, J) Kamptonema formosum, (D, K) Anagnostidinema carotinosum, (E, L), A. pseudacutissimum, (F, M) Geitlerinema splendidum, (G, N) Porphyrosiphon annulatus. Species in bold represents our studied organism.

FIGURE 4 in Porphyrosiphon annulatus sp. nov. (Oscillatoriales, Cyanobacteria) isolated on moist soil in Suwon, Republic of Korea

FIGURE 4. Phylogenetic relationships of cyanobacteria species within the genus Porphyrosiphon inferred from partial 16S rRNA gene sequences with Bayesian analysis. A 16S sequence of Gloeobacter violaceus was included as an outgroup. Additional Maximum-Likelihood (ML) and Neighbor-Joining (NJ) trees showed similar topology of the present Bayesian tree. Their bootstrap proportions (BP) were incorporated into the tree. The first, second and third numbers at the nodes display BP (> 50%) in ML, NJ and posterior probabilities (PP;> 0.90) in Bayesian analysis, respectively. Branch lengths are proportional to the scale given. Species in bold represents our studied organism.

FIGURE 3 in Porphyrosiphon annulatus sp. nov. (Oscillatoriales, Cyanobacteria) isolated on moist soil in Suwon, Republic of Korea

FIGURE 3. Transmission electron micrographs of Porphyrosiphon annulatus strain (FBCC-A260). (A, B) Thylakoids appeared in longitudinal section, (C, D) Radial thylakoid arrangement showed in cross section; cw: cell wall, sh: sheath, th: thylakoids.

FIGURE 2 in Porphyrosiphon annulatus sp. nov. (Oscillatoriales, Cyanobacteria) isolated on moist soil in Suwon, Republic of Korea

FIGURE 2. Microphotographs of Porphyrosiphon annulatus the raw (A–C) and culture samples (D–J) from the reference strain (FBCC-A260). (A–B) Yellowish-brown and blue-green filaments, (C) Transversely annular lamellations in the sheath (arrow), (D) Colony of trichomes (sheath initially colorless and later yellow-brown or pink), (E, F) Longitudinal lamellations in the sheath (arrow), (G–I) Transversely annular lamellations in the sheath (arrows), (J) Two trichomes within a sheath; Scale bars = (A–C, E–J) 10 µm, (D) 50 µm.

FIGURE 1 in Porphyrosiphon annulatus sp. nov. (Oscillatoriales, Cyanobacteria) isolated on moist soil in Suwon, Republic of Korea

FIGURE 1. Map showing site in the Mt. Gwanggyo, Republic of Korea. (A) The aerial view (A red circle is collection site), (B) The habitat of a collection site.

Fig. 4 in Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)

Fig. 4. Presence of known haem-dependent and manganese-dependent catalase encoding genes in five reference genomes of the genus Latilactobacillus and AMBP162T. Analysis was done by comparing the four known catalase genes from lactic acid bacteria against all predicted proteins from the six Latilactobacillus genomes using BLASTp.

Fig. 2 in Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)

Fig. 2. Core genome phylogenetic tree of the genus Latilactobacillus. Genes were predicted with Prodigal version 2.6.3 [33] and core genes were determined, aligned and concatenated with SCARAP version 7cd24ba [16]. 662 strict core genes were found. Columns with one or more gaps were trimmed from the alignment with trimAl version 1.4.rev15 [34]. A maximum-likelihood phylogeny was inferred with IQ-Tree version 1.6.11 [31], using the LG+F+I+G4 amino acid substitution model. Bootstrap support was determined with the SH-aLRT test with 1000 replicates and the UFboot test with 1000 replicates. Branches with an SH-aLRT support of at least 80% and UFboot support of at least 95% were considered reliable and were indicated with a dark blue dot. The tree was visualized with ggtree version 3.0.2 [32].

Fig. 3 in Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa)

Fig. 3. Light microscope image at ×1000 magnification of Gram-stained cells of AMBP162T grown for 24 h at 30 °C in de Man–Rogosa–Sharpe broth, shaking at 200 r.p.m.

Fig. 2 in Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum

Fig. 2. Whole genome sequence phylogeny of MMM721T, ISU324, PIG517 and all publicly available genomes on the PATRIC genome database as of November 2020. The tree is rooted by Eggerthia catenaformis OT569. Only bootstrap values>50% are noted for branch nodes. The PATRIC genome IDs are noted in parentheses after the strain name.

Fig. 1 in Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum

Fig. 1. (a) Transmission electron microscope image of MMM721T cells. Bar, 1 Μm. (b) Scanning electron microscope image of MMM721T cells. Bar, 2 Μm. Cells were cultured in BHIGL for 24 h at 42 °C prior to fixation and visualization.

Fig. 2. A in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 2. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among five novel Limosilactobacillus species, six L. reuteri subspecies and other recognized species in the genus Limosilactobacillus. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].

Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].