Phylogenetic Lineages Research Articles

The Pangenome of Gram-Negative Environmental Bacteria Hides a Promising Biotechnological Potential.

Secondary metabolites (SMs) from environmental bacteria offer viable solutions for various health and environmental challenges. Researchers are employing advanced bioinformatic tools to investigate less-explored microorganisms and unearth novel bioactive compounds. In this research area, our understanding of SMs from environmental Gram-negative bacteria lags behind that of its Gram-positive counterparts. In this regard, Pedobacter spp. have recently gained attention, not only for their role as plant growth promoters but also for their potential in producing antimicrobials. This study focuses on the genomic analysis of Pedobacter spp. to unveil the diversity of the SMs encoded in their genomes. Among the 41 genomes analyzed, a total of 233 biosynthetic gene clusters (BGCs) were identified, revealing the potential for the production of diverse SMs, including RiPPs (27%), terpenes (22%), hybrid SMs (17%), PKs (12%), NRPs (9%) and siderophores (6%). Overall, BGC distribution did not correlate with phylogenetic lineage and most of the BGCs showed no significant hits in the MIBiG database, emphasizing the uniqueness of the compounds that Pedobacter spp. can produce. Of all the species examined, P. cryoconitis and P. lusitanus stood out for having the highest number and diversity of BGCs. Focusing on their applicability and ecological functions, we investigated in greater detail the BGCs responsible for siderophore and terpenoid production in these species and their relatives. Our findings suggest that P. cryoconitis and P. lusitanus have the potential to produce novel mixtures of siderophores, involving bifunctional IucAC/AcD NIS synthetases, as well as carotenoids and squalene. This study highlights the biotechnological potential of Pedobacter spp. in medicine, agriculture and other industries, emphasizing the need for a continued exploration of its SMs and their applications.

One size does not fit all - Trehalose metabolism by Clostridioides difficile is variable across the five phylogenetic lineages.

Clostridioides difficile, the leading cause of antibiotic-associated diarrhoea worldwide, is a genetically diverse species which can metabolise a number of nutrient sources upon colonising a dysbiotic gut environment. Trehalose, a disaccharide sugar consisting of two glucose molecules bonded by an α 1,1-glycosidic bond, has been hypothesised to be involved in the emergence of C. difficile hypervirulence due to its increased utilisation by the RT027 and RT078 strains. Here, growth in trehalose as the sole carbon source was shown to be non-uniform across representative C. difficile strains, even though the genes for its metabolism were induced. Growth in trehalose reduced the expression of genes associated with toxin production and sporulation in the C. difficile R20291 (RT027) and M120 (RT078) strains in vitro, suggesting an inhibitory effect on virulence factors. Interestingly, the R20291 TreR transcriptional regulatory protein appeared to possess an activator function as its DNA-binding ability was increased in the presence of its effector, trehalose-6-phosphate. Using RNA-sequencing analysis, we report the identification of a putative trehalose metabolism pathway which is induced during growth in trehalose: this has not been previously described within the C. difficile species. These data demonstrate the metabolic diversity exhibited by C. difficile which warrants further investigation to elucidate the molecular basis of trehalose metabolism within this important gut pathogen.

Falsirhodobacter algicola sp. nov., a member of the Rhodobacteraceae isolated from the marine red algae Grateloupia sp.

A Gram-negative, pale yellow-pigmented, non-flagellated, motile, rod-shaped and aerobic bacterium, designated strain PG104T, was isolated from red algae Grateloupia sp. collected from the coastal area of Pohang, Republic of Korea. Growth of strain PG104T was observed at 15-35 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.5-8.0) and in the presence of 0-8.0 % (w/v) NaCl (optimum, 5.0 %). The predominant fatty acids included C17 : 0, C18 : 0, 11-methyl C18 : 1 ω7c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and the major respiratory quinone was Q-10. Polar lipids included phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain PG104T formed a phylogenetic lineage with members of the genus Falsirhodobacter and exhibited 16S rRNA gene sequence similarities of 97.1 and 96.6 % to Falsirhodobacter deserti W402T and Falsirhodobacter halotolerans JA744T, respectively. The complete genome of strain PG104T consisted of a single circular chromosome of approximately 2.8 Mbp with five plasmids. Based on polyphasic taxonomic data, strain PG104T represents a novel species in the genus Falsirhodobacter, for which the name Falsirhodobacter algicola sp. nov. is proposed. The type strain of Falsirhodobacter algicola is PG104T (=KCTC 82230T=JCM 34380T).

Four New Species of Pseudephedrus (Hymenoptera, Braconidae, Aphidiinae) from Chile with a Key to Species Identification.

The following work consists of the description of four new species of the genus Pseudephedrus Starý (Aphidiinae), endemic to South America, associated with endemic callaphidid aphid hosts. The descriptions of the new species are based on new samples from Chile and Argentina. The new species described here are as follows: Pseudephedrus staryi sp.n., which is morphologically very close to the already described P. chilensis Starý, with clear apomorphies; P. pubescens sp.n., which presents a setose scutellum, P. flava sp.n. and P. patagonicus sp.n. which have distinct, very elongated, and crenulated petioles representing synapomorphies and probably form separate phylogenetic lineages within Pseudephedrus. All hosts are aphids from the genus Neuquenaphis Blanchard, with varying degrees of diet specialization. From our field and laboratory observations, we hypothesize that, since attempts to sample parasitoids using sweep nets were much more successful than sampling from collected aphids, and since we found mummified aphids only on the ground among the fallen leaves under the trees, Neuquenaphis aphids fall to the ground showing a dropping behaviour as a defence against natural enemies after being stung by parasitoids. This makes rearing from live aphids very unsuccessful and could help explain why it has been difficult to collect and describe species. We supplement the distribution of Pseudephedrus from South America and present a key for the identification of all species based on their morphology.

Atypically Shaped Setae in Gall Mites (Acariformes, Eriophyoidea) and Mitogenomics of the Genus Leipothrix Keifer (Eriophyidae).

The setae in Eriophyoidea are filiform, slightly bent and thickened near the base. Confocal microscopy indicates that their proximal and distal parts differ in light reflection and autofluorescence. Approximately 50 genera have atypically shaped setae: bifurcated, angled or swollen. These modifications are known in the basal part of prosomal setae u', ft', ft″, d, v, bv, ve, sc and caudal setae h2. We assessed the distribution of atypically shaped setae in Eriophyoidea and showed that they are scattered in different phylogenetic lineages. We hypothesized that the ancestral setae of eriophyoid mites were bifurcated before later simplifying into filiform setae. We also proposed that hypo-furcating setae are a synapomorphy that unites Eriophyoidea with Nematalycidae. We analyzed four new mitochondrial genomes of Leipothrix, the largest genus with bifurcated d, and showed that it is monophyletic and has a unique mitochondrial gene order with translocated trnK. We exclude Cereusacarus juniperensisn. comb. Xue and Yin, 2020 from Leipothrix and transfer five Epitrimerus spp. to Leipothrix: L. aegopodii (Liro 1941) n. comb., L. femoralis (Liro 1941) n. comb., L. geranii (Liro 1941) n. comb., L. ranunculi (Liro 1941) n. comb., and L. triquetra (Meyer 1990) n. comb.

Phylogeny and taxonomy of the genera of Erysiphaceae, part 4: Erysiphe (the “Uncinula lineage”)

ABSTRACT This is the fourth contribution within an ongoing series dedicated to the phylogeny and taxonomy of powdery mildews. This particular installment undertakes a comprehensive evaluation of a group previously referred to as the “Uncinula lineage” within Erysiphe. The genus Erysiphe is too large to be assessed in a single paper; thus, the treatment of Erysiphe is split into three parts, according to phylogenetic lineages. The first paper, presented here, discusses the most basal lineage of Erysiphe and its relationship to allied basal genera within tribe Erysipheae (i.e., Brasiliomyces and Salmonomyces). ITS+28S analyses are insufficient to resolve the basal assemblage of taxa within the Erysipheae. Therefore, phylogenetic multilocus examinations have been carried out to better understand the evolution of these taxa. The results of our analyses favor maintaining Brasiliomyces, Bulbomicroidium, and Salmonomyces as separate genera, at least for the interim, until further phylogenetic multilocus data are available for additional basal taxa within the Erysipheae. The current analyses also confirmed previous results that showed that the “Uncinula lineage” is not exclusively composed of Erysiphe species of sect. Uncinula but also includes some species that morphologically align with sect. Erysiphe, as well as species that had previously been assigned to Californiomyces and Typhulochaeta. Numerous sequences of Erysiphe species from the “Uncinula lineage” have been included in the present phylogenetic analyses and were confirmed by their position in well-supported species clades. Several species have been sequenced for the first time, including Erysiphe clintonii, E. couchii, E. geniculata, E. macrospora, and E. parvula. Ex-type sequences are provided for 16 taxa including E. nothofagi, E. trinae, and E. variabilis. Epitypes are designated and ex-epitype sequences are added for 18 taxa including Erysiphe carpophila, E. densa, and U. geniculata var. carpinicola. The new species Erysiphe canariensis is described, and the new names E. hosagoudarii and E. pseudoprunastri and the new combination E. ampelopsidis are introduced.

TWO LINEAGES OF ORIBATID MITES MORPHOLOGICALLY CORESPOND TO THE CIRCUMPOLAR SPECIES <i>AMERONOTHRUS NIGROFEMORATUS</i> (ACARI, ORIBATIDA) BUT DIFFER GENETICALLY AS DISTINCT SPECIES ARE REVEALED ON THE KOLGUEV ISLAND

Until recently, data on the genetic characteristics of the oribatid mite Ameronothrus nigrofemoratus have been reported only from the Northern Canada. Analysis of the partial cytochrome oxidase I gene (COI) mtDNA sequence of the mites from Kolguev Island that morphologically correspond to this species has revealed two highly divergent phylogenetic lineages of A. nigrofemoratus (divergence of 7%), neither of which was found on the Canadian coast. One lineage differs by four COI amino acid substitutions from North American A. nigrofemoratus. This corresponds to the degree of difference between A. nigrofemoratus and its sister species A. lineatus.

A generic monograph of the Hyacinthaceae subfamily Urgineoideae

Taxonomy and systematics and specifically the generic circumscription of the Hyacinthaceae subfamily Urgineoideae have been a matter of controversy in recent decades. Widely contrasting taxonomic treatments have been proposed, ranging from systems comprising only two genera (including a morphologically very variable Drimia covering nearly the whole subfamily) to about 20 genera based mainly on preliminary phylogenetic studies supporting recognition of traditionally accepted and morphologically distinct genera such as Litanthus, Schizobasis, Tenicroa, and Thuranthos. All previous studies covered only a limited diversity and distribution of the subfamily, precluding comprehensive insight into the evolution of the diversity within the subfamily. Based on detailed morphological, phylogenetic, and biogeographic studies in Urgineoideae, covering its whole distribution range and most of the currently known species, we present a new taxomic treatment of the subfamily focusing on the circumscription of genera. Our analyses revealed 31 phylogenetic lineages corroborating unique syndromes of morphological characters linked to well-defined biogeographic patterns. These lineages are interpreted as well-defined genera. An identification key to the genera is provided to facilitate further taxonomic work in Urgineoideae and morphological descriptions of the accepted genera are presented. Two new genera, Spirophyllos gen. nov. and Zulusia gen. nov., are described to accommodate newly revealed phylogenetic lineages from northwestern and southeastern Africa, respectively. Further, a complete list of taxa included in the accepted genera is presented, providing details on typification, and the 50 new combinations, and one new name required to appropriately accomodate taxa in the new taxonomic treatment.

Phylogenetic relatedness enhances the understanding of soil microbial coexistence in alpine wetlands of the Tibetan Plateau

Soil microorganisms, spanning diverse phylogenetic lineages, form complex ecological networks wherein various species coexist and contribute to multiple ecosystem services. While microbial networks facilitate the understanding of their coexistence and functions in soils, the influence of phylogenetic relatedness among soil microbes themselves on these networks remains largely unknown.To address this knowledge gap, we conducted a comprehensive survey of soil bacteria and archaea in twenty alpine wetlands on the Tibetan Plateau, characterized by wide edaphic and climatic heterogeneity. Through network and phylogenetic analyses, we evaluated the complexity of network associations and their dependence on phylogenetic relatedness.Our findings revealed consistencies and discrepancies between phylogenetic relatedness and network associations within soil bacterial and archaeal communities. Specifically, in bacterial networks, both positive and negative complexity were significantly associated with mean phylogenetic distance, whereas in archaeal networks, only negative complexity correlated with mean phylogenetic distance. Even after accounting for the effects of environmental factors, we observed that phylogenetic relatedness still explained variations in the complexities of bacterial and archaeal associations. Furthermore, a multi-threshold analysis indicated that network complexity exhibited phylogenetic signals in both bacterial and archaeal networks, albeit within different associated distance classes, suggesting distinct coexistence mechanisms of soil bacteria and archaea driven by niche and fitness trade-offs.Overall, our findings underscore the importance of incorporating phylogenetic information when studying microbial communities in complex soil habitats and demonstrate that phylogenetic relatedness crucially shapes coexistence outcomes among soil microbes.

Presence of Aspergillus fumigatus with the TR34/L98H Cyp51A mutation and other azole-resistant aspergilli in the air of a zoological park

Antifungal-resistant fungi, including Aspergillus fumigatus and other Aspergillus species, pose an urgent threat to human and animal health. Furthermore, the environmental route of azole resistance selection due to the widespread use of azole fungicides in crop protection and other applications is a major public health issue. Although environmental surveillance of fungi is frequently performed in many zoological parks and wildlife rehabilitation centers, the antifungal susceptibility of recovered isolates is only rarely analyzed, which precludes a clear assessment of the threat posed by these fungi to captive animals. In this study, we assessed the presence of airborne azole-resistant Aspergillus spp., including the so-called ‘cryptic species’ (i.e., species which are phenotypically similar to more well-known aspergilli but clearly constitute different phylogenetic lineages) in a zoological park located in the city of Madrid, Spain. In general, our results revealed a low prevalence A. fumigatus and cryptic aspergilli with decreased susceptibility to azoles. However, we detected an A. fumigatus isolate with the TR34/L98H mutation in the gene encoding the lanosterol 14α-demethylase (Cyp51A), consisting of a tandem repeat of 34 base pairs in the promoter region and a lysine to histidine substitution at codon 98. Notably, this TR34/L98H mutation has been linked to the environmental route of azole resistance selection, thus highlighting the ‘One Health’ dimension of the emerging problem of antifungal resistance. In this context, continuous environmental surveillance of azole-resistant aspergilli in zoological parks and other similar animal facilities is recommended.

The divergence of mutation rates and spectra across the Tree of Life.

Owing to advances in genome sequencing, genome stability has become one of the most scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological, the mutation rate (per nucleotide site per generation) ranges over three orders of magnitude among species and several-fold within individual phylogenetic lineages. Within all major organismal groups, mutation rates scale negatively with the effective population size of a species and with the amount of functional DNA in the genome. This relationship is most parsimoniously explained by the drift-barrier hypothesis, which postulates that natural selection typically operates to reduce mutation rates until further improvement is thwarted by the power of random genetic drift. Despite this constraint, the molecular mechanisms underlying DNA replication fidelity and repair are free to wander, provided the performance of the entire system is maintained at the prevailing level. The evolutionary flexibility of the mutation rate bears on the resolution of several prior conundrums in phylogenetic and population-genetic analysis and raises challenges for future applications in these areas.

Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emended description of the genus Alkalicoccobacillus Joshi et al. 2022.

A Gram-stain-positive alkali-tolerant and strictly aerobic bacterium, designated strain P16T, was isolated from a marine red alga, Porphyridium cruentum, in the Yellow Sea, Republic of Korea. Cells were motile rods with peritrichous flagella and exhibited catalase and oxidase activities. The optimal growth of strain P16T was observed to occur at 30 °C and pH 8.0 and in the presence of 2.0 % (w/v) NaCl. Menaquinone-7 was identified as the sole respiratory quinone. Strain P16T contained anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major cellular fatty acids and polar lipids, respectively. The G+C content of strain P16T was 40.8 mol%. Strain P16T was most closely related to Shouchella plakortidis P203T, Shouchella gibsonii DSM 8722T and Alkalicoccobacillus murimartini LMG 21005T with 98.1, 98.1 and 98.0 % 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strain P16T, S, plakortidis, S. gibsonii and A. murimartini formed a single phylogenetic lineage cluster, and genomic relatedness analyses showed that they are different species. Based on phylogenetic, phenotypic, chemotaxonomic and molecular features, strain P16T represents a novel species of the genus Alkalicoccobacillus, for which the name Alkalicoccobacillus porphyridii sp. nov. is proposed. The type strain is P16T (=KACC 19520T=JCM 32931T). In addition, S. plakortidis and S. gibsonii are reclassified as Alkalicoccobacillus plakortidis comb. nov. (type strain P203T=DSM 19153T=NCIMB 14288T) and Alkalicoccobacillus gibsonii comb. nov. (type strain PN-109T=ATCC 700164T=DSM 8722T=KCCM 41407T), respectively.

Drivers of plant community (in)stability along a sea–inland gradient

Abstract Global change pressures are highlighting the need to better understand the mechanisms driving the temporal stability of natural communities under different environmental conditions. There is ample evidence that species richness helps communities to withstand environmental fluctuations and stabilise over time. However, it is still debated whether richness promotes stability through the diversity of species functional traits, phylogenetic lineages and ecological strategies in the community or because of the likelihood of including stable species. Furthermore, it is unclear whether the positive effect of diversity on stability is maintained in conditions of strong environmental fluctuations (e.g. frequent disturbances and stress). To address these questions, we analysed long‐term monitoring data of 84 permanent plots in coastal dune plant communities distributed along a gradient of natural stress and disturbance, with communities closer to the sea subject to greater stress and more frequent disturbances. Specifically, we used structural equation models to disentangle the relative influence of the environmental gradient and the different diversity components (species richness, functional and phylogenetic diversity; SR, FD and PD), as well as of the dominant ecological strategy (captured by species lifespan) on community stability, through their effect on two key stability mechanisms (population stability and species asynchrony). We found that the sea–inland environmental gradient was the main driver of stability mechanisms. Stress and disturbance decreased both population stability and species asynchrony, but also reduced species richness, which thus exerted a stabilising effect only on the communities in more favourable environmental conditions. Surprisingly, we did not find an effect of FD and PD on community stability, neither directly nor via asynchrony. However, the dominance of perennial species mitigated the instability generated by stress and disturbance. Perennial species were on average more stable than annuals and displayed a wider range of species fluctuations, including compensatory dynamics among species (i.e. asynchrony). Synthesis: Overall, our results highlight the importance of accounting for the environmental context when examining mechanisms of community stability. Species richness remains a useful direct predictor of community stability. Species ecological strategies, like the acquisitive–conservative trade‐off connected to lifespan, however, should also be routinely considered as drivers of both population stability and compensatory dynamics.

Comparable ectomycorrhizal fungal species richness but low species similarity among native Abies alba and alien Abies grandis from provenance trials in Poland

Our study contributes to the understanding of the diversity of ectomycorrhizal fungal (ECMF) communities of native A. alba and alien A. grandis in provenance trials situated in lowland and montane regions in Poland (Central Europe). Ectomycorrhizal fungi were identified directly from field-collected root tips using PCR- and Sanger-sequencing-based methods. We found that the studied fir species had relatively high and comparable ECMF species richness (66 and 69 fungal taxa on A. grandis and A. alba, respectively). Twenty-six taxa were associated with both hosts and 83 taxa were found uniquely on one or the other fir species. The ECMF community composition and structure of A. alba and A. grandis differed substantially both at the species and the phylogenetic lineage levels. Soil parameters such as total nitrogen, magnesium and potassium content and C/N ratio appeared moderately but significantly correlated with the ECMF community assembly of both firs. The provenance of the host tree species did not appear to be a strong factor in structuring the ECMF communities. This was found despite the low number of common ECMF species and relatively high number of unique species among the individual provenances of both fir species. The results of the study suggest that locally based specificity in host–fungal communities is likely a contributing factor in the outcome of provenance trials. We posit that much insight into the role of tree provenances in shaping ECMF communities will be gained by further exploring this area of research. On the surveyed experimental forest sites of A. alba and A. grandis, fungal species of conservation concern – particularly those that were endangered and rare – have been reported. Our findings imply that tree species planted outside their natural range serve as ecologically important species because they may act as an excellent reservoir of ECMF diversity, a factor of importance in functioning forest ecosystems.

Genome analysis of clinical genotype Vibrio vulnificus isolated from seafood in Mangaluru Coast, India provides insights into its pathogenicity

Vibrio vulnificus an opportunistic human pathogen native to marine/estuarine environment, is one of the leading causes of death due to seafood consumption and exposure of wounds to seawater worldwide. The present study involves the whole genome sequence analysis of an environmental strain of V. vulnificus (clinical genotype) isolated from seafood along the Mangaluru coast of India. The sequenced genome data was subjected to in-silico analysis of phylogeny, virulence genes, antimicrobial resistance determinants, and secretary proteins using suitable bioinformatics tools. The sequenced isolate had an overall genome length of 4.8 Mb and GC content of 46% with 4400 coding DNA sequences. The sequenced strain belongs to a new sequence type (Multilocus sequence typing) and was also found to branch with a phylogenetic lineage that groups the most infectious strains of V. vulnificus. The seafood isolate had complete genes involved in conferring serum resistance yet showed limited serum resistance. The study identified several genes against the antibiotics that are commonly used in their treatment, highlighting the need for alternative treatments. Also, the secretory protein analysis revealed genes associated with major pathways like ABC transporters, two-component systems, quorum sensing, biofilm formation, cationic antimicrobial peptide (CAMP) resistance, and others that play a critical role in the pathogenesis of the V. vulnificus. To the best of our knowledge, this is the first report of a detailed analysis of the genomic information of a V. vulnificus isolated from the Indian subcontinent and provides evidence that raises public health concerns about the safety of seafood.

Speciation on the Roof of the World: Parallel Fast Evolution of Cryptic Mole Vole Species in the Pamir-Alay-Tien Shan Region.

Speciation is not always accompanied by morphological changes; numerous cryptic closely related species were revealed using genetic methods. In natural populations of Ellobius tancrei (2n = 54-30) and E. alaicus (2n = 52-48) of the Pamir-Alay and Tien Shan, the chromosomal variability due to Robertsonian translocations has been revealed. Here, by comprehensive genetic analysis (karyological analyses as well as sequencing of mitochondrial genes, cytb and COI, and nuclear genes, XIST and IRBP) of E. alaicus and E. tancrei samples from the Inner Tien Shan, the Alay Valley, and the Pamir-Alay, we demonstrated fast and independent diversification of these species. We described an incompletely consistent polymorphism of the mitochondrial and nuclear markers, which arose presumably because of habitat fragmentation in the highlands, rapid karyotype changes, and hybridization of different intraspecific varieties and species. The most intriguing results are a low level of genetic distances calculated from mitochondrial and nuclear genes between some phylogenetic lines of E. tancrei and E. alaicus, as well significant species-specific chromosome variability in both species. The chromosomal rearrangements are what most clearly define species specificity and provide further diversification. The "mosaicism" and inconsistency in polymorphism patterns are evidence of rapid speciation in these mammals.

How Do Prebiotics Affect Human Intestinal Bacteria?-Assessment of Bacterial Growth with Inulin and XOS In Vitro.

Prebiotics are believed to exhibit high specificity in stimulating the growth or activity of a limited number of commensal microorganisms, thereby conferring health benefits to the host. However, the mechanism of action of prebiotics depends on multiple factors, including the composition of an individual's gut microbiota, and is therefore difficult to predict. It is known that different bacteria can utilize inulin and xylooligosaccharides (XOS), but an overview of which bacteria in the human gut may be affected is lacking. Detailed knowledge of how bacterial growth is affected by prebiotics is furthermore useful for the development of new synbiotics, which combine a living microorganism with a selective substrate to confer a health benefit to the host. Hence, we developed a statistical model to compare growth in vitro among typical human gut bacteria from different phylogenetic lineages. Based on continuous observation of the optical density (OD600), we compare maximal growth rates (rmax), maximal attained OD600 (ODmax), and area under the growth curve (AUC) of bacteria grown on inulin or XOS. The consideration of these three parameters suggests strain-specific preferences for inulin or XOS and reveals previously unknown preferences such as Streptococcus salivarius growth on XOS.

Vibrio vulnificus mutation rate: an in vitro approach.

Vibrio vulnificus is a multi-host pathogenic species currently subdivided into five phylogenetic lineages (L) plus one pathovar with the ability to infect fish due to a transmissible virulence plasmid. This plasmid (or a fragment of it) has been transmitted between lineages within the species, contributing to the evolution of V. vulnificus. This study aimed to provide an experimental approximation to the V. vulnificus mutation rate by determining spontaneous mutation rates from bacterial cultures of representants of the different lineages by whole-genome sequencing. To this purpose, synonymous SNP differences, i.e., spontaneous mutation not subjected to the evolutive forces, between initial and final culture after serial growth were evaluated and used for mutation rate calculation.

Commentary on: dominance and subordination in the smooth dogfish, Mustelus canis (Allee & Dickenson, 1954)

Abstract In, 1954, Warder C. Allee and Joshua C. Dickinson decided to establish that “dominance-subordination” hierarchies are present in the Chondrichthyan phylogenetic line. To do so, they confined sixteen fished smooth dogfish (Mustelus canis) in tanks and observed their behaviour. They found neither competition over food, in spite of starving the animals for up to six days at times, nor any clear example of aggression, though it is through aggressive actions that such hierarchies are, by definition, established. They therefore used collision avoidance to support their hypothesis that the sharks had established a rigid size-dependent dominance-subordinate hierarchy, and claimed to have established that such hierarchies are present in Chondrichthyans. However, ethological studies since then have not identified the hierarchies in elasmobranchs that this study claims to be present, but they have found that smaller sharks tend to avoid colliding with larger individuals, which is the simplest explanation for their observations.

Complex origin, evolution, and diversification of non-canonically organized OVATE-OFP and OVATE-Like OFP gene pair across Embryophyta

Ovate Family Proteins (OFP) is a plant-specific gene family of negative transcriptional regulators. Till-date, a handful of in-silico studies have provided glimpses into family size, expansion patterns, and genic features across all major plant lineages. A major lacuna exists in understanding origin of organisation complexity of members such as those arranged in a head-to-head manner which may lead to transcriptional co-regulation via a common bi-directional promoter. To address this gap, we investigated the origin, organization and evolution of two head-to-head arranged gene pairs of homologs of AtOFP2-AtOFP17, and, AtOFP4-AtOFP20 across Archaeplastida. The ancestral forms of AtOFP2, AtOFP4, AtOFP17, and AtOFP20 are likely to have evolved in last common ancestors of Embryophyta (land plants) given their complete absence in Rhodophyta and Chlorophyta. The OFP gene family originated and expanded in Bryophyta, including protein variants with complete (OVATE-OFP) or partial (OVATE-Like OFP) OVATE domain; with head-to-head organization present only in Spermatophyta (gymnosperms and angiosperms). Ancestral State Reconstruction revealed the origin of head-to-head organized gene pair in gymnosperms, with both genes being OVATE-OFP (homologs of AtOFP2/4). Phylogenetic reconstruction and copy number analysis suggests the presence of a single copy of the head-to-head arranged pair of OFP2/4 (OVATE)-OFP17/20 (OVATE-Like) in all angiosperms except Brassicaceae, and a duplication event in last common ancestor of core Brassicaceae approximately 32–54 MYA leading to origin of AtOFP2-AtOFP17 and AtOFP4-AtOFP20 as paralogs. Synteny analysis of genomic regions harbouring homologs of AtOFP2-AtOFP17, AtOFP4-AtOFP20 and AtOFP2/4-AtOFP17/20 across angiosperms suggested ancestral nature of AtOFP2-AtOFP17 gene pair. The present study thus establishes the orthology and evolutionary history of two non-canonically organised gene pairs with variation in their OVATE domain. The non-canonical organisation, atleast in Brassicaceae, has the potential of generating complex transcriptional regulation mediated via a common bi-directional promoter. The study thus lays down a framework to understand evolution of gene and protein structure, transcriptional regulation and function across a phylogenetic lineage through comparative analyses.