Diversity Of Phylotypes Research Articles

Comparative efficacy of essential oils against Cutibacterium acnes: effect upon strains from phylotypes with different virulence patterns

ObjectivesDespite being a commensal of human skin, Cutibacterium acnes plays an important role in the pathogenesis of Acne vulgaris, with the loss of bacterial phylotype diversity being related to disease progression. This study evaluated differences in the virulence profile of C. acnes strains from different phylotypes and investigated the possible phylotype-selective efficacy of essential oils (EOs) from Thymus x citriodorus (TC), Thymus mastichina, and Cistus ladanifer compared to Melaleuca alternifolia, focusing on both planktonic and biofilm growth forms, the latter being related with pathogenesis and treatment resistance. MethodsOne collection strain and seven clinical isolates were classified into phylotypes using multiplex-touchdown PCR. Virulence trait differences across phylotypes were evaluated by studying antibiotic resistance, biofilm formation, porphyrin production, and lipase activity. EOs were tested for minimum inhibitory/bactericidal concentrations (MIC/MBC) and effects on biofilm biomass and metabolic activity. ResultsStrains from phylotype IA1 were higher biofilm and lipase producers than phylotype II strains. Regarding EO’s efficacy, TC EO presented lower planktonic MIC values for all strains compared to the other EOs, presenting a smaller difference in MIC values across phylotypes. TC EO was able to similarly reduce biofilm biomass and metabolic activity in phylotype IA1 clinical strains, being effective at lower concentrations compared with the remaining EOs. ConclusionsNot all virulence traits were phylotype-related, highlighting the multifactorial nature of the disease. TC EO showed a relevant anti-acne potential, outperforming tea tree EO (a species with a commercial claim for Acne vulgaris) against both planktonic and biofilm forms of C. acnes.

Pro-inflammatory activity of Cutibacterium acnes phylotype IA1 and extracellular vesicles: An invitro study.

Acne is a chronic inflammatory skin condition that involves Cutibacterium acnes (C. acnes), which is classified into six main phylotypes (IA1, IA2, IB, IC, II and III). Acne development is associated with loss of C. acnes phylotype diversity, characterised by overgrowth of phylotype IA1 relative to other phylotypes. It was also shown that purified extracellular vesicles (EVs) secreted by C. acnes can induce an acne-like inflammatory response in skin models. We aimed to determine if the inflammatory profile of EVs secreted by C. acnes phylotype IA1 from an inflammatory acne lesion was different from C. acnes phylotype IA1 from normal skin, thus playing a direct role in the severity of inflammation. EVs were produced invitro after culture of two clinical strains of C. acnes phylotype IA1, T5 from normal human skin and A47 from an inflammatory acne lesion, and then incubated with either human immortalised keratinocytes, HaCaT cells, or skin explants obtained from abdominoplasty. Subsequently, quantitative PCR (qPCR) was performed for human β-defensin 2 (hBD2), cathelicidin (LL-37), interleukin (IL)-1β, IL-6, IL-8, IL-17α and IL-36γ, and ELISA for IL-6, IL-8 and IL-17α. We found that EVs produced invitro by C. acnes derived from inflammatory acne lesions significantly increased the pro-inflammatory cytokines and anti-microbial peptides at both transcriptional and protein levels compared with EVs derived from normal human skin. We show for the first time that C. acnes EVs from inflammatory acne play a crucial role in acne-associated inflammation invitro and that C. acnes phylotype IA1 collected from inflammatory acne lesion and normal skin produce different EVs and inflammatory profiles invitro.

The impact of raw material form and starter culture inoculation on bacterial communities and metabolites in fermented anchovy sauce

This study explored the dynamics of anchovy sauce fermentation and investigated how the raw material form and the use of starter cultures affect bacterial and metabolite profiles. Using a comprehensive approach, we examined the fermentation process using anchovies in two forms (whole and ground) and three different starter cultures. The use of ground anchovies resulted in an accelerated fermentation process for anchovy sauce; however, the increased diversity of bacterial phylotypes and altered accumulation of biogenic amines were observed. Inoculation of starter cultures resulted in a shift from spontaneous to controlled fermentation, highlighting their ability to regulate bacterial communities. Despite a slightly reduced fermentation rate, inoculation with Tetragenococcus halophilus was shown to be a potent method for reducing biogenic amines and affecting metabolite profiles. As the industry strives to balance fermentation speed and quality, our research could provide insights for improving the efficiency, safety, and quality of anchovy sauce production.

Genetic diversity of culturable fungi associated with scleractinian corals in the Gulf of Thailand

Abstract Coral reefs are one of the most biodiverse marine ecosystems. Diverse microbes are associated with corals, including zooxanthellae, protists, prokaryotes, and viruses. This study aimed to investigate the genetic diversity of the culturable fungi associated with scleractinian corals in the Gulf of Thailand. Ribosomal DNA sequence analysis and morphological analysis of 130 fungal isolates revealed a high diversity of fungal phylotypes from three coral species: Pavona decussata, Pocillopora damicornis and Porites lutea. Ascomycota was the most abundant fungal phylum. The predominant orders included Eurotiales, Cladosporiales, Hypocreales, Mycosphaerellales, and Diaporthales. There were eight orders of the Basidiomycota dominated by Polyporales, Hymenochaetales, Agaricales, and Wallemiales. A principal component analysis was performed to compare abundance and correlation between the fungal communities, sampling locations and coral species. The results showed that the dissimilarity of fungal communities corresponded to geographic localities. On the other hand, there was a considerable overlap between the fungal communities of different coral species. The results from this research provide information on the diversity and ecology of the fungal communities associated with scleractinian corals in the Gulf of Thailand.

Coordination and divergence in community assembly processes across co-occurring microbial groups separated by cell size.

Setting the pace of life and constraining the role of members in food webs, body size can affect the structure and dynamics of communities across multiple scales of biological organization (e.g., from the individual to the ecosystem). However, its effects on shaping microbial communities, as well as underlying assembly processes, remain poorly known. Here, we analyzed microbial diversity in the largest urban lake in China and disentangled the ecological processes governing microbial eukaryotes and prokaryotes using 16S and 18S amplicon sequencing. We found that pico/nano-eukaryotes (0.22-20 μm) and micro-eukaryotes (20-200 μm) showed significant differences in terms of both community composition and assembly processes even though they were characterized by similar phylotype diversity. We also found scale dependencies whereby micro-eukaryotes were strongly governed by environmental selection at the local scale and dispersal limitation at the regional scale. Interestingly, it was the micro-eukaryotes, rather than the pico/nano-eukaryotes, that shared similar distribution and community assembly patterns with the prokaryotes. This indicated that assembly processes of eukaryotes may be coupled or decoupled from prokaryotes' assembly processes based on eukaryote cell size. While the results support the important influence of cell size, there may be other factors leading to different levels of assembly process coupling across size classes. Additional studies are needed to quantitatively parse the influence of cell size versus other factors as drivers of coordinated and divergent community assembly processes across microbial groups. Regardless of the governing mechanisms, our results show that there are clear patterns in how assembly processes are coupled across sub-communities defined by cell size. These size-structured patterns could be used to help predict shifts in microbial food webs in response to future disturbance.

Recent advances in understanding inflammatory acne: Deciphering the relationship between Cutibacterium acnes and Th17 inflammatory pathway.

Acne vulgaris is a common chronic inflammatory skin disease of the pilosebaceous units. Four factors contribute to acne: hyperseborrhea and dysseborrhea, follicular hyperkeratinisation, skin microbiome dysbiosis and local immuno-inflammation. Recent key studies have highlighted a better understanding of the important role of Cutibacterium acnes (C.acnes) in the development of acne. Three major findings in the last decade include: (1) the ability of C.acnes to self-organize in a biofilm associated with a more virulent activity, (2) the loss of the C.acnes phylotype diversity and (3) the central role of the Th17 pathway in acne inflammation. Indeed, there is a close link between C.acnes and the activation of the Th17 immuno-inflammatory pathway at the initiation of acne development. These mechanisms are directly linked to the loss of C.acnes phylotype diversity during acne, with a predominance of the pro-pathogenic phylotype IA1. This specifically contributes to the induction of the Th17-mediated immuno-inflammatory response involving skin cells, such as keratinocytes, monocytes and sebocytes. These advancements have led to new insights into the underlying mechanisms which can be harnessed to develop novel treatments and diagnostic biomarkers. A major disadvantage of traditional treatment with topical antibiotics is that they induce cutaneous dysbiosis and antimicrobial resistance. Thus, future treatments would no longer aim to 'kill' C.acnes, but to maintain the skin microbiota balance allowing for tissue homeostasis, specifically, the restoration of C.acnes phylotype diversity. Here, we provide an overview of some of the key processes involved in the pathogenesis of acne, with a focus on the prominent role of C.acnes and the Th17-inflammatory pathways involved.

Change in Cutibacterium acnes phylotype abundance and improvement of clinical parameters using a new dermocosmetic product containing Myrtus communis and Celastrol enriched plant cell culture extracts in patients with acne vulgaris.

Acne is a multifactorial chronic inflammatory disease of the pilosebaceous unit, where Cutibacterium acnes plays a main role. Recent papers demonstrated that specific C.acnes phylotypes were correlated with the severity of inflammatory acne and reported a specific loss of C.acnes phylotype diversity in this context. The aim of this exploratory study was to evaluate the efficacy of a new dermocosmetic product containing Myrtus communis and Celastrol-enriched plant cell culture extracts on C.acnes phylotype abundance and clinical parameters in subjects with mild to moderate acne vulgaris. Cutibacterium acnes phylotype diversity was evaluated by single-locus sequence typing sequencing on the nonlesional areas of the forehead, that is, areas excluding inflammatory lesions (papules and pustules) on day 1 (D1) and after 56 days (D57) of twice daily application of the dermocosmetic product on the whole face. Clinical efficacy on acne was also assessed by acne lesion counting and Global Evaluation Acne (GEA) score on D1 and D57. Our study confirmed the link between the presence of some C.acnes phylotypes and acne severity. The dermocosmetic cream was linked to a positive impact on C.acnes phylotypes: a significant decrease in pro-pathogen phylotype IC and increase in nonpathogen phylotype IB were observed in the nonlesional areas of acne on D57 compared to D1. In parallel, the clinical results showed a significant decrease in inflammatory and comedonal acne lesions and a significant improvement in the acne severity according to the GEA score. This study showed that the application of a new dermocosmetic product containing M.communis and Celastrol-enriched plant cell culture extracts was linked to a change in the C.acnes phylotype abundance and an improvement in acne severity.

Implications of Escherichia coli community diversity in free-ranging Australian pinniped pups.

Escherichia coli is a widely studied bacterium, commonly used as an indicator of faecal contamination. Investigations into the structure and diversity of E. coli in free-ranging wildlife species has been limited. The objective of this study was to characterise intra-individual and inter-species E. coli phylotype and B2 sub-type diversity in free-ranging Australian pinniped pups, to determine whether a single E. coli colony is representative of the phylotype and B2 sub-type diversity in these hosts. Faecal samples were collected from free-ranging Australian fur seal (Arctocephalus pusillus doriferus), Australian sea lion (Neophoca cinerea) and long-nosed fur seal (Arctocephalus forsteri) pups from three breeding colonies between 2018 and 2021. Faecal swabs from thirty randomly selected pups (n=10 from each species) were cultured and ten E. coli colonies were selected from each culture based on morphology and separation between colonies on agar plates. Molecular screening techniques were utilised to assign isolates to phylotypes and B2 sub-types. There was no significant difference (p>0.05) in either intra-individual or inter-species E. coli phylotype and B2 sub-type diversity. The B2 phylotype was the most dominant, with 78% of isolates (n=234) assigned to this phylotype. Host factors (species, weight [kg] and standard length [cm]) did not significantly affect phylotype diversity. The absence of intra-individual and inter-species differences in E. coli diversity at a phylotype level suggests that a single E. coli colony could be used as an indicator of overall diversity of E. coli at a phylotype level in A. p. doriferus, N. cinerea and A. forsteri pups. These findings can be used to simplify and improve the efficiency of sampling protocols for ongoing monitoring of human-associated E. coli phylotypes in free-ranging pinniped populations.

33563 Change in Cutibacterium acnes phylotype diversity and improvement of clinical parameters using a new dermocosmetic product containing Myrtus communis and Celastrol-enriched plant cell culture extracts in patients with acne vulgaris

Introduction: Cutibacterium acnes, the main bacterial species of the pilosebaceous unit, plays a major role in acne. Recent papers demonstrated that specific C acnes phylotypes were correlated with the severity of inflammatory acne and reported a specific loss of C acnes phylotype diversity in this context. Objectives: The aim of the study was to evaluate the efficacy of a new dermocosmetic product containing Myrtus communis and Celastrol-enriched plant cell culture extracts on C acnes phylotype abundance and clinical parameters in subjects with mild to moderate acne vulgaris. Materials/methods: Efficacy on C. acnes phylotype diversity was evaluated by single-locus sequence typing sequencing after 57 days of twice daily application of the product. Clinical parameters of acne and product tolerance were also assessed. Results: Our study confirmed the link between the presence of some C. acnes phylotypes and acne. At day 57, the product had a positive impact on C. acnes phylotypes: a significant decrease of propathogen phylotype IC and increased of nonpathogen phylotype IB were observed. In parallel, the clinicals results showed a significant decrease of inflammatory and total acne lesions, and a significant improvement of global acne evaluation score. The tolerance of the product was assessed very good. Conclusion: This study showed the topic modulation of C. acnes phylotype diversity by this new dermocosmetic product containing Myrtus communis and Celastrol enriched plant cell culture extracts associated with a significant clinical efficacy.

553 Change in c. acnes phylotype abundance and improvement of clinical parameters using a new dermocosmetic product containing myrtus communis and celastrol enriched plant cell culture extracts in patients with acne vulgaris

Introduction: Cutibacterium acnes (C. acnes), the main bacterial species of the pilosebaceous unit, plays a major role in acne. Recent papers demonstrated that specific C. acnes phylotypes were correlated with the severity of inflammatory acne and reported a specific loss of C. acnes phylotype diversity in this context. Objectives: The aim of the study was to evaluate the efficacy of a new dermocosmetic product containing Myrtus communis and Celastrol enriched plant cell culture extracts on C. acnes phylotype abundance and clinical parameters in subjects with mild to moderate acne vulgaris.

Phylotype diversity within soil fungal functional groups drives ecosystem stability.

Soil fungi are fundamental to plant productivity, yet their influence on the temporal stability of global terrestrial ecosystems, and their capacity to buffer plant productivity against extreme drought events, remain uncertain. Here we combined three independent global field surveys of soil fungi with a satellite-derived temporal assessment of plant productivity, and report that phylotype richness within particular fungal functional groups drives the stability of terrestrial ecosystems. The richness of fungal decomposers was consistently and positively associated with ecosystem stability worldwide, while the opposite pattern was found for the richness of fungal plant pathogens, particularly in grasslands. We further demonstrated that the richness of soil decomposers was consistently positively linked with higher resistance of plant productivity in response to extreme drought events, while that of fungal plant pathogens showed a general negative relationship with plant productivity resilience/resistance patterns. Together, our work provides evidence supporting the critical role of soil fungal diversity to secure stable plant production over time in global ecosystems, and to buffer against extreme climate events.

Maternal breast milk microbiota and immune markers in relation to subsequent development of celiac disease in offspring

The potential impact of the composition of maternal breast milk is poorly known in children who develop celiac disease (CD). The aim of our study was to compare the microbiota composition and the concentrations of immune markers in breast milk from mothers whose offspring carried the genetic predisposition to CD, and whether they did or did not develop CD during follow-up for the first 3 years of life. Maternal breast milk samples [CD children (n = 6) and healthy children (n = 18)] were collected 3 months after delivery. Enzyme-linked immunosorbent assays were used to measure TGF-β1, TGF-β2, sIgA, MFG-E8 and sCD14. For microbiota analysis, next generation (Illumina) sequencing, real-time PCR and denaturing gradient gel electrophoresis were used. Phylotype abundance and the Shannon ‘H’ diversity index were significantly higher in breast milk samples in the CD group. There was higher prevalence of the phyla Bacteroidetes and Fusobacteria, the classes Clostridia and Fusobacteriia, and the genera Leptotrichia, Anaerococcus, Sphingomonas, Actynomyces and Akkermansia in the CD group. The immunological markers were differently associated with some Gram-negative bacterial genera and species (Chryseobacterium, Sphingobium) as well as Gram-positive species (Lactobacillusreuteri, Bifidobacteriumanimalis). In conclusion, the microbiota in breast milk from mothers of genetically predisposed offspring who presented CD showed a higher bacterial phylotype abundance and diversity, as well as a different bacterial composition, as compared with the mothers of unaffected offspring. These immune markers showed some associations with bacterial composition and may influence the risk for development of CD beyond early childhood.

Polylysine dendrigraft is able to differentially impact Cutibacterium acnes strains preventing acneic skin.

With a view to reducing the impact of Cutibacteriumacnes (C.acnes) on acne vulgaris, it now appears interesting to modify the balance between acneic and non-acneic strains of C.acnes using moderate approach. In the present study, we identified that a G2 dendrigraft of lysine dendrimer (G2 dendrimer) was able to modify membrane fluidity and biofilm formation of a C.acnes acneic strain (RT5), whereas it appeared no or less active on a C.acnes non-acneic strain (RT6). Moreover, skin ex vivo data indicated that the G2 is able to decrease inflammation (IL1α and TLR-2) and improve skin desquamation after of C.acnes acneic strains colonization. Then, in vivo data confirmed, after C.acnes quantification by metagenomic analysis that the G2 cream after 28days of treatment was able to increase the diversity of C.acnes strains versus placebo cream. The data also showed a modification of the balance expression between C.acnes phylotype IA1 and phylotype II abundances. Taken together, the results confirm the interest of using soft compounds in cosmetic product for modifying phylotype abundances and diversity of C.acnes strains could be a new strategy for prevent acne vulgaris outbreak.

Environmental gradients and physical barriers drive the basin‐wide spatial structuring of Mediterranean Sea and adjacent eastern Atlantic Ocean prokaryotic communities

AbstractThe Mediterranean Sea is a miniature ocean divided by the Sicily Strait into two basins with a marked west to east trophic gradient and separated of the nearby eastern Atlantic Ocean by the Strait of Gibraltar. Here, we test the hypothesis that these physical and environmental barriers favor the development of specific prokaryotic assemblages, leading to changes in community structure both in the vertical and horizontal spatial scales. By analyzing taxonomic and phylogenetic diversity using amplicon sequence variants (ASVs) of the 16S rRNA gene, we show that there is indeed marked vertical segregation of prokaryotic groups, similar to that found in other areas of the ocean, but also a clear horizontal structuring among the two Mediterranean basins and the adjacent Atlantic waters. Prokaryotic diversity increased with depth and toward the Atlantic, whereas the easternmost stations displayed more phylogenetically diverse phylotypes, despite harboring globally less diverse communities. Basin‐indicator taxa (ASVs) accounted for a large fraction of the community (between 50% and 80%) in each of the basins at the surface and bathypelagic layers, being associated with different environmental variables. The existence of biogeographic and environmental barriers in the Mediterranean Sea is likely related to the trophic gradient at the surface and the isolation of water bodies in depth due to the Gibraltar and Sicily straits. Our work highlights the importance of studying microbial regional biogeography and provides the basis for future studies on the impact of this regionalization in the function of Mediterranean Sea prokaryotic communities.

Diversity and flexibility of algal symbiont community in globally distributed larger benthic foraminifera of the genus Amphistegina

BackgroundUnderstanding the specificity and flexibility of the algal symbiosis-host association is fundamental for predicting how species occupy a diverse range of habitats. Here we assessed the algal symbiosis diversity of three species of larger benthic foraminifera from the genus Amphistegina and investigated the role of habitat and species identity in shaping the associated algal community.ResultsWe used next-generation sequencing to identify the associated algal community, and DNA barcoding to identify the diatom endosymbionts associated with species of A. lobifera, A. lessonii, and A. radiata, collected from shallow habitats (< 15 m) in 16 sites, ranging from the Mediterranean Sea to French Polynesia. Next-generation sequencing results showed the consistent presence of Ochrophyta as the main algal phylum associated with all species and sites analysed. A significant proportion of phylotypes were classified as Chlorophyta and Myzozoa. We uncovered unprecedented diversity of algal phylotypes found in low abundance, especially of the class Bacillariophyta (i.e., diatoms). We found a significant influence of sites rather than host identity in shaping algal communities in all species. DNA barcoding revealed the consistent presence of phylotypes classified within the order Fragilariales as the diatoms associated with A. lobifera and A. lessonii, while A. radiata specimens host predominately diatoms of the order Triceratiales.ConclusionsWe show that local habitat is the main factor influencing the overall composition of the algal symbiont community. However, host identity and the phylogenetic relationship among hosts is relevant in shaping the specific endosymbiont diatom community, suggesting that the relationship between diatom endosymbiont and hosts plays a crucial role in the evolutionary history of the genus Amphistegina. The capacity of Amphistegina species to associate with a diverse array of diatoms, and possibly other algal groups, likely underpins the ecological success of these crucial calcifying organisms across their extensive geographic range.

Effect of land use changes on soil microbial enzymatic activity and soil microbial community composition on Maryland's Eastern Shore

We compared microbial enzymatic activity and community composition in small, undisturbed, family cemetery soils and surrounding agricultural fields or suburban lawns to determine the effect of land use changes on soil biology. We collected soil from seven sites in Wicomico County, Maryland monthly for one year. Fluorescein diacetate (FDA) hydrolysis and dehydrogenase activity were significantly greater in the cemetery soils compared to field soils (agricultural and lawn) 63% and 30% of the time, respectively. Much less frequently the field soils had significantly higher microbial activity compared to the cemetery soils (10% of sample pairs for both FDA and dehydrogenase). FDA activity measurements were highest in the spring and lowest in late summer at all seven sites, while no seasonal variation was evident for dehydrogenase activity. Dominant bacterial phyla in the soils were similar between field and cemetery sites with the exception of Gemmatimonadetes having higher relative abundance in fields. Fourteen genera differed in relative abundance between cemeteries and fields, and the relative abundance of these genera correlated with soil pH, organic matter, and phosphorus levels. There was no difference in phylotype richness or diversity between fields and cemetery soils. Based on FDA hydrolysis, microbial activity is greater in cemetery soils, providing evidence to suggest land use changes have altered the biological properties of these soils.

Pathogenic and genetic variability of Ralstonia solanacearum strains from the Philippines

AbstractIn the Philippines, bacterial wilt caused by Ralstonia solanacearum is one of the most important diseases affecting vegetables and banana. In this study, 89 strains of R. solanacearum isolated from various hosts were screened for their biovar, phylotype, pathogenicity, and genetic diversity. Foreign strains were included for comparison with these Philippine strains. Results of the biochemical and multiplex‐PCR tests divided the Philippine strains into five biovars (1, 2, 3, 4, and N2) and three phylotypes (I, II, and IV). Three potato strains belonged to biovar N2/phylotype IV. Pathogenicity tests divided the strains into five pathogenicity types based on their virulence in tomato, potato, eggplant, sweet pepper, and tobacco. Strains classified as biovar N2 were weakly pathogenic to potato (pathogenicity type III) and almost all strains isolated from banana were not pathogenic to the test plants except potato (pathogenicity type V). The results of AFLP analysis divided the strains into four clusters. Cluster 1 was composed of strains isolated from solanaceous crops, ginger (Zingiber officinale), and Morus sp. from the Philippines and other Asian countries. Cluster 2 grouped the potato strains (biovar N2) from the Philippines and Japan and blood disease bacterium strains from Indonesia. Cluster 3 contained the local and foreign strains isolated from potato (biovar 2) and banana (biovar 1). Cluster 4 consisted only of the tomato strain from the USA.

High diversity of Vibrio spp. associated with different ecological niches in a marine aquaria system and description of Vibrio aquimaris sp. nov

The aim of the study was to characterise the diversity and niche-specific colonization of Vibrio spp. in a marine aquaria system by a cultivation-dependent approach. A total of 53 Vibrio spp. isolates were cultured from different ecological niches in a marine aquarium including microplastic (MP) and sandy sediment particles (12 weeks after added sterile to the system), detritus, and the surrounding aquarium water. Based on the 16S rRNA gene sequence phylogeny and multilocus sequence analysis (MLSA) the isolates were assigned to seven different phylotypes. Six phylotypes were identified by high probability to the species level. The highest phylotype diversity was cultured from detritus and water (six out of seven phylotypes), while only two phylotypes were cultured from MP and sediment particles. Genomic fingerprinting indicated an even higher genetic diversity of Vibrio spp. at the strain (genotype) level. Again, the highest diversity of genotypes was recovered from detritus and water while only few partially particle-type specific genotypes were cultured from MP and sediment particles. Phylotype V-2 formed an independent branch in the MLSA tree and could not be assigned to a described Vibrio species. Isolates of this phylotype showed highest 16S rRNA gene sequence similarity to type strains of Vibrio japonicus (98.5%) and Vibrio caribbeanicus (98.4%). A representative isolate, strain THAF100T, was characterised by a polyphasic taxonomic approach and Vibrio aquimaris sp. nov., with strain THAF100T (=DSM 109633T=LMG 31434T=CIP 111709T) as type strain, is proposed as novel species.

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

ABSTRACTTrue fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

Candidatus Amarolinea and Candidatus Microthrix Are Mainly Responsible for Filamentous Bulking in Danish Municipal Wastewater Treatment Plants.

Filamentous bulking is a common serious operational problem leading to deteriorated sludge settling that has long been observed in activated sludge biological wastewater treatment systems. A number of bacterial genera found therein possess filamentous morphology, where some have been shown to be implicated in bulking episodes (e.g., Ca. Microthrix), the impact of many others is still not clear. In this study we performed a survey of 17 Danish municipal wastewater treatment plants (WWTPs) with nutrient removal using 16S rRNA amplicon sequencing over a period of 13 years, where all known filamentous bacteria from 30 genera were analyzed. The filamentous community constituted on average 13 ± 6%, and up to 43% of total read abundance with the same genera common to all plants. Ca. Microthrix and several genera belonging to phylum Chloroflexi were among the most abundant filamentous bacteria. The effect of filamentous bacteria on sludge settling properties was analyzed using measurements of the diluted sludge volume index (DSVI). Strong positive correlations with DSVI were observed only for Ca. Microthrix and Ca. Amarolinea, the latter being a novel, recently characterized genus belonging to the phylum Chloroflexi. The bulking potential of other filamentous bacteria was not significant despite their presence in many plants. Low phylogenetic diversity was observed for both Ca. Microthrix and Ca. Amarolinea, making physiological characterization of individual species and potential development of control strategies more feasible. In this study we show that, despite the high diversity of filamentous phylotypes in Danish WWTPs, only few of them were responsible for severe bulking episodes.