Taxonomic Units Research Articles

Disentangling disjunctus: an integrated analysis of the patent leather beetle, Odontotaenius disjunctus complex (Passalidae: Coleoptera) with the description of two new species

The categorical rank of species is the fundamental taxonomic unit in characterizing biodiversity, and the accurate identification of species-level lineages is vital to all fields of biological research. This is particularly true for conservation biology, where state and federal agencies make conservation assessments based on recognized species’ distribution, ecology, and demography. Currently, there are two species of bess beetle in the conterminous United States, Odontotaenius flordianus (Schuster) and O. disjunctus (Illeger). Phylogeographic studies have proposed that O. disjunctus may represent a species complex harboring cryptic diversity. This study combines multi-locus species delimitation methods and multivariate analyses of morphological characters used to distinguish O. floridanus, to assess species diversity within the O. disjunctus complex. Delimitation methods inferred four well-supported species that diverged during the Pleistocene and whose formation was driven by historical isolation associated with shifting climatic conditions. We found a correlation between increased morphological differentiation and time since divergence. We described two new species, Odontotaenius jackmanicus sp. nov., based on morphological and molecular characters, and the cryptic species, Odontotaenius cryptodisjunctus sp. nov., diagnosed exclusively on molecular characters. We propose that the morphological similarities between O. disjunctus and O. cryptodisjunctus are due to a recent speciation combined with morphological conservatism and evolutionary stasis.

Surface microlayer-mediated virome dissemination in the Central Arctic

BackgroundAquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges such as limited host availability and harsh conditions. However, due to the restricted accessibility of these ecosystems, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited.ResultsTo fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from ~60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in the Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration, followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to that of open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2–5 µm) of the melt pond was strikingly limited compared to that of open water. From the 1154 viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2% encoded for auxiliary metabolic genes (AMGs) with metabolic functions. Some AMGs like glycerol-3-phosphate cytidylyltransferase and ice-binding like proteins might serve to provide cryoprotection for the host. Prophages were often associated with SML genomes, and two active prophages of new viral genera from the Arctic SML strain Leeuwenhoekiella aequorea Arc30 were induced. We found evidence that vOTU abundance in the SML compared to that of ~60 cm depth was more positively correlated with the distribution of a vOTU across five different Arctic stations.ConclusionsThe results indicate that viruses employ elaborate strategies to endure in extreme, host-limited environments. Moreover, our observations suggest that the immediate air-sea interface serves as a platform for viral distribution in the Central Arctic.Dvb_jZZ1H7pg55rxrDSVb2Video

Dietary β-mannanase reduced post-weaning diarrhea of pigs by positively modulating gut microbiota and attenuating systemic immune responses

BackgroundAfter weaning, nursery pigs have difficulty digesting non-starch polysaccharides in their diets, which can result in growth and health problems. Among non-starch polysaccharides, β-mannan is easily found in various cereal grains that form the basis of livestock diets and interferes the digestion and utilization of nutrients. Supplementation of dietary β-mannanase in nursery diet can alleviate the negative effects on nutrient utilization efficiency caused by β-mannan and improve growth and health of pigs. This study was conducted to evaluate effects of dietary β-mannanase supplementation on growth performance, nutrient digestibility, intestinal morphology, fecal microbiota, and systemic immune responses of weaned pigs.ResultsDietary β-mannanase (MAN) improved average daily gain (P = 0.053), average daily feed intake (P < 0.05), and gain to feed ratio (P = 0.077) of pigs for 3 weeks after weaning and apparent total tract digestibility of crude protein (P = 0.060) and reduced post-weaning diarrhea (P < 0.05). The MAN did not affect the ileal morphology. Pigs fed with MAN had more diverse fecal microbiota based on the results of alpha diversity [the number of operational taxonomic units (OTUs; P = 0.061), Shannon (P = 0.071), and Simpson indices (P = 0.078)] and relative abundance of phylum Bacteroidetes (P = 0.064) and genus Prevotella (P < 0.05) than pigs fed control diet (CON). As a result of beta diversity, fecal microbiota was clustered (P < 0.05) into two distinct groups between dietary treatments. The MAN decreased (P < 0.05) packed cell volume (PCV), the number of white blood cells (WBC), C-reactive protein (CRP), tumor necrosis factor-α (TNF-α), transforming growth factor-β1 (TGF-β1), and cortisol of the pigs for 2 weeks after weaning compared with CON.ConclusionDietary β-mannanase reduced post-weaning diarrhea of pigs by positively modulating gut microbiota and attenuating systemic immune responses.

A spatial matrix factorization method to characterize ecological assemblages as a mixture of unobserved sources: An application to fish eDNA surveys

Abstract Understanding how ecological assemblages vary in space and time is essential for advancing our knowledge of biodiversity dynamics and ecosystem functioning. Metabarcoding of environmental DNA (eDNA) is an efficient method for documenting biodiversity changes in both marine and terrestrial ecosystems. However, current methods fail to detect and display the biodiversity structure within and between eDNA samples limiting ecological and biogeographical interpretations. We present a spatial matrix factorization method that identifies optimal eDNA sample assemblages—called pools—assuming that taxonomic unit composition is based on a fixed number of unknown sources. These sources, in turn, represent taxonomic units sharing similar habitat properties or characteristics. The method aims to reduce the multi‐taxa composition structure into a low number of dimensions defined by these sources. This method is inspired by admixture analysis in population genetics. Using a marine fish eDNA survey on 263 sampling stations detecting 2888 molecular operational taxonomic units (MOTUs), we apply this method to analyse the biogeography and mixing patterns of fish assemblages at regional and large scales. At large scale, our analysis reveals six primary pools of fish samples characterized by distinct biogeographic patterns, with some mixtures between these pools. We identify pools composed of unique sources, corresponding to distinct and more isolated regions such as the Mediterranean and Scotia Seas. We also identify pools composed of a greater mix of sources, corresponding to geographically connected areas, such as tropical regions. Additionally, we identify the taxa underpinning the formation of each pool. In the regional analysis of Mediterranean eDNA samples, our method successfully identifies different pools, allowing the detection of not only geographic gradients but also human‐induced gradients corresponding to protection levels. Spatial matrix factorization adds a new method in community ecology, where each sample is considered as a mixture of K unobserved sources, to assess the dissimilarity of ecological assemblages revealing environmental and human‐induced gradients. Beyond the study of fish eDNA samples, this method has the potential to shed new light on any biodiversity survey and provide new bioindicators of global change.

Shedding light on some dark branches: The under‐appreciated diversity of gymnosome pteropods and their coiled thecosome prey in the Neotropics

AbstractHoloplanktonic organisms are thought to have enormous populations sizes, expansive geographic ranges, and low species diversity. Previous work suggests that pelagic gastropods are no exception to this generalization. However, most of these data are derived from temperate species, whereas the bulk of pteropod diversity occurs in the tropics. Here, we present DNA barcode data for COI focused on the under‐studied limacinoid, gymnosome, and pseudothecosome pteropods collected from the coastal waters of Panama. We applied four molecular species delimitation approaches to determine the number of operational taxonomic units (OTUs) identifiable from our sequences and all data available from Barcode of Life Database (BOLD) and GenBank and compared these to the Barcode Index Number generated by the BOLD. Assemble Species by Automatic Partitioning (ASAP), Poisson Tree Processes (PTP), Bayesian Poisson Tree Processes (bPTP), and Generalized Mixed Yule Coalescent (GMYC) methods generally gave congruent results and suggest that pteropod diversity in the tropics is significantly underrepresented both in DNA sequence databases and in the number of named OTUs. Of 42 specimens collected and sequenced, we recovered 16 OTUs, only one of which belonged to an OTU already represented in sequence databases. Neighbor‐joining trees including the previously published sequences show that in all three groups morphospecies can include genetically divergent lineages. Many very divergent (&gt;15% from nearest neighbor) taxa are also still represented by only a single sequence, suggesting that there is a large amount of cryptic or pseudo‐cryptic diversity still to be described. To aid this future endeavor, we include some preliminary 16S data derived from new pteropod‐specific primers.

Influence of decades-long irrigation with secondary treated wastewater on soil microbial diversity, resistome dynamics, and antibiotrophy development

In arid and semi-arid regions, the use of treated wastewater (TWW) for irrigation is gaining ground to alleviate pressure on natural water sources. Despite said treatment, the existing methods fail to eliminate potentially dangerous contaminants. As such, this study assessed the impact of long-term TWW irrigation (5 and 25 years) on soil physicochemical properties and bacterial resistance to heavy metals (Pb, Cu, Cd) and antibiotics (tetracycline and amoxicillin). The results revealed heightened salinity and conductivity and reduced pH in irrigated soils. TWW induces harmful effects by reducing microbial density and size, leading to the disappearance of sensitive populations. Conversely, resilient populations, which mainly utilize antibiotics as a carbon source, have adapted. Metagenomic 16S amplicon sequencing analysis demonstrated a shift, notably reducing Actinobacteria, Bacteroidetes, and Firmicutes while increasing Acidobacteriota and Patescibacteria in treated soils. Operational Taxonomic Units affiliated with either Halomonadacea, or Saccharimonadacea and Vicinamibacteracea, were defined as indicators of the absence or presence of TWW contamination, respectively. We conclude that TWW irrigation significantly increases bacterial resistance to heavy metals, whereas the impact of antibiotics is nuanced, with antibiotrophy leveraging lower concentrations in treated soils.

Potentially Pathogenic Vibrio spp. in Algal Wrack Accumulations on Baltic Sea Sandy Beaches

The Vibrio bacteria known to cause infections to humans and wildlife have been largely overlooked in coastal environments affected by beach wrack accumulations from seaweed or seagrasses. This study presents findings on the presence and distribution of potentially pathogenic Vibrio species on coastal beaches that are used for recreation and are affected by red-algae-dominated wrack. Using species-specific primers and 16S rRNA gene amplicon sequencing, we identified V. vulnificus, V. cholerae (non-toxigenic), and V. alginolyticus, along with 14 operational taxonomic units (OTUs) belonging to the Vibrio genus in such an environment. V. vulnificus and V. cholerae were most frequently found in water at wrack accumulation sites and within the wrack itself compared to sites without wrack. Several OTUs were exclusive to wrack accumulation sites. For the abundance and presence of V. vulnificus and the presence of V. cholerae, the most important factors in the water were the proportion of V. fucoides in the wrack, chl-a, and CDOM. Specific Vibrio OTUs correlated with salinity, water temperature, cryptophyte, and blue-green algae concentrations. To better understand the role of wrack accumulations in Vibrio abundance and community composition, future research should include different degradation stages of wrack, evaluate the link with nutrient release, and investigate microbial food-web interactions within such ecosystems, focusing on potentially pathogenic Vibrio species that could be harmful both for humans and wildlife.

Integrative taxonomic revision of the grasshopper genera Parapetasia Bolívar, 1884, and Loveridgacris Rehn, 1954 (Orthoptera, Pyrgomorphidae), with description of a new species of Loveridgacris

The taxonomic status of the Pyrgomorphid genera Parapetasia Bolívar, 1884, and Loveridgacris Rehn, 1954 is complex and challenging. Here, we use a combination of morphological, distributional, and genetic data to revise the two genera and provide new information on their diversity. We describe a new species, Loveridgacris tectiferussp. nov., from Tanzania and formally resurrect the status of Parapetasia rammei as a valid species within Parapetasia, resulting in two species in Parapetasia (P. femorata and P. rammei) and two in Loveridgacris (L. impotens and L. tectiferussp. nov.). We also sequenced the COI and 16S genes of 10 Pyrgomorphidae species and provided the first phylogeny of the group. Our data show that all species are clearly distinct and represent molecular operational taxonomic units (mOTUs), with the exceptions of L. impotens and L. tectiferussp. nov., which are morphologically clearly distinct but for which the concatenated sequence alignments of the two individual gene datasets (COI and 16S) do not provide sufficient information. In addition, high interspecific distances were found between Parapetasia and Loveridgacris. Moreover, the complete mitogenomes of L. impotens and L. tectiferussp. nov. were sequenced using next-generation sequencing technology. The total lengths of the assembled mitogenomes were 15,592 bp and 15,737 bp, representing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one D-loop region, respectively. To aid in identification, we present a key for the two genera, including a key to species. This study provides insights into the morphology, distribution, and phylogeny of Pyrgomorphidae in Africa.

Seasonal variations of microbial communities and viral diversity in fishery-enhanced marine ranching sediments: insights into metabolic potentials and ecological interactions

BackgroundThe ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.ResultsThe current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation - denitrification - S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts.ConclusionsThis finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation.DRyDF7ykR-XALqAtu34uZtVideo

The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments.

Accurate knowledge of the microbiota collected from surfaces in food processing environments is important for food quality and safety. This study assessed discrepancies in taxonomic composition and alpha and beta diversity values generated from eight different bioinformatic workflows for the analysis of 16S rRNA gene sequences extracted from the microbiota collected from surfaces in dairy processing environments. We found that the microbiota collected from environmental surfaces varied widely in density (0-9.09 log10 CFU/cm2) and Shannon alpha diversity (0.01-3.40). Consequently, depending on the sequence analysis method used, characterization of low-abundance genera (i.e., below 1% relative abundance) and the number of genera identified (114-173 genera) varied considerably. Some low-abundance genera, including Listeria, varied between the amplicon sequence variant (ASV) and operational taxonomic unit (OTU) methods. Centered log-ratio transformation inflated alpha and beta diversity values compared to rarefaction. Furthermore, the ASV method also inflated alpha and beta diversity values compared to the OTU method (P < 0.05). Therefore, for sparse, uneven, low-density data sets, the OTU method and rarefaction are better for taxonomic and ecological characterization of surface microbiota.IMPORTANCECulture-dependent environmental monitoring programs are used by the food industry to identify foodborne pathogens and spoilage biota on surfaces in food processing environments. The use of culture-independent 16S rRNA amplicon sequencing to characterize this surface microbiota has been proposed as a tool to enhance environmental monitoring. However, there is no consensus on the most suitable bioinformatic analyses to accurately capture the diverse levels and types of bacteria on surfaces in food processing environments. Here, we quantify the impact of different bioinformatic analyses on the results and interpretation of 16S rRNA amplicon sequences collected from three cultured dairy facilities in New York State. This study provides guidance for the selection of appropriate 16S rRNA analysis procedures for studying environmental microbiota in dairy processing environments.

Impact of periodontal therapy on oral bacterial composition in individuals diagnosed with advanced periodontal disease.

Introduction. Negative changes in the microbial composition have been extensively studied in individuals with periodontal disease.Gap Statement. The changes in the oral microbiota after treating this disease are still unknown.Aim. We sought to elucidate the distinctive traits of salivary microbiota in individuals displaying healthy gums and those with severe periodontitis (SP) and examine the influence of periodontal therapy.Methodology. Periodontal pocket depths were examined to determine disease severity. The presence and quantity of oral Helicobacter pylori (associated with periodontal disease) were determined. Sequencing of 16S ribosomal DNA and bioinformatic analyses were performed to assess oral bacterial compositions in patients.Results. Sequencing analysis of 16S ribosomal DNA revealed a significant reduction in the abundance of operational taxonomic units (OTUs) and Chao1 and Abundance coverage-based estimator(ACE) indices in the oral cavities of individuals with SP compared to those of the healthy controls. However, these parameters showed significant recovery after appropriate treatment severe periodontitis after treatment (TSP). Additionally, the levels of harmful Bacillales and Spirochetes significantly increased, whereas the presence of beneficial Euryarchaeota significantly decreased in the SP group. The TSP group exhibited considerably augmented abundances of Burkholderiaceae and Veillonella, while noteworthy reductions in the pathogenic microbiota (Clostridia, Fusobacteria and Spirochaetes) were noticed compared to those of the SP group. Functionally, these modified OTUs were extensively implicated in 41 metabolic pathways.Conclusion. Our study demonstrates that nonsurgical periodontal therapy can effectively reduce the diversity of the oral microbiota, thereby potentially enhancing the treatment efficacy in patients with periodontal disease.

Bacterial phylotypes associated with rock-dwelling Umbilicaria Lichens from Arctic/Subarctic areas in North America and Northern Europe

AbstractThe diversity of bacteria associated with lichens has received increasing attention. However, studies based on next-generation sequencing of microbiomes have not yet been conducted in the Arctic and Subarctic regions. In this study, rock-dwelling lichens belonging to the Umbilicariaceae family were sampled from the Arctic and Subarctic biological zones. The primary research purpose was to undertake a comparative investigation of the bacterial composition and diversity, identify potential indicators, and explore their potential metabolic pathways. 18S rRNA gene sequences of the fungal partner belonging to the genus Umbilicaria (Ascomycota) and the algal partner affiliated with the lineage Trebouxia (Chlorophyta). Comparing Umbilicaria spp. with a previous study in the Antarctic zone, the fungal partners were more inclined to cluster by sampling region. Operational taxonomic units (OTUs) were established based on a predetermined similarity threshold for V3-V4 sequences, which were ascribed to 19 bacterial phyla, and ten of them were consistently present in all samples. The most distinct zonal indicator genera based on OTU frequencies from Arctic and Subarctic lichens were Capsulimonas (Armatimonadota) and Jatrophihabitans (Actinomycota), respectively. Although the Subarctic zone had higher biodiversity and species richness based on alpha-diversity, the beta-diversity showed that the main species of bacterial communities were not significantly different, and the predictions of metabolic pathways based on the bacterial microbiome in lichen samples from the two zones were similar. These findings provide evidence that the geographical and/or bioclimatic environment and the different lichen-forming fungal species mainly and partially influence bacterial microbiomes and metabolic pathways.

Systematics and Phylogeny of Myxomycetes: Yesterday, Today, Tomorrow

Myxomycetes are amoeboid fungus-like organisms (Amoebozoa) with a unique life cycle characterized by a great morphological diversity of fruiting bodies. Due to the similarity of these structures to the fruiting bodies of some representatives of Ascomycota and Basidiomycota, myxomycetes have been classified as fungi since the first known scientific description in 1654. Only in the XIX century, when their life cycle was studied, the difference of this group from fungi became clear. During the same period, microscopic structures of fruiting bodies, as well as ornamentation of the spore surface, began to be considered as diagnostic features. Due to this, in the period from the end of XIX to the middle of XX century, a rather stable system was formed. However, as further studies have shown, both macro- and micromorphological characters are often quite variable, depend on environmental conditions, and often result from a convergent evolution, which causes difficulties in defining species and taxonomic units of higher ranks. Since the first decade of the 21st century, thanks to the development of molecular genetic methods and accumulation of data on nucleotide sequences of marker genes together with the improvement of microscopic studies, it has been possible to obtain data on the evolutionary relationships of different groups of myxomycetes. A milestone in this process was the publication of the first phylogenetic system of myxomycetes in 2019. This work was the starting point for a number of studies on the relationships of different groups of myxomycetes at a lower taxonomic level. Thus, there has been a surge in the number of studies that bring us closer to constructing a natural system. The latest iteration of the myxomycete system, incorporating all modifications and enhancements as of June 2024, is presented.

Effect of conservation agriculture on soil fungal diversity in rice-wheat-greengram cropping system in eastern Indo-Gangetic plains of South Asia.

Conservation agriculture (CA) is emerging as an eco-friendly and sustainable approach to food production in South Asia. CA, characterized by reduced tillage, soil surface cover through retaining crop residue or raising cover crops, and crop diversification, enhances crop production and soil fertility. Fungal communities in the soil play a crucial role in nutrient recycling, crop growth, and agro-ecosystem stability, particularly in agricultural crop fields. This study investigates the impact of seven combinations of tillage and crop residue management practices of agricultural production systems, including various tillage and crop residue management practices, on soil fungal diversity. Using the Illumina MiSeq platform, fungal diversity associated with soil was analysed. The results show that the partial CA-based (pCA) production systems had the highest number of unique operational taxonomic units (OTUs) (948 OTUs) while the conventional production system had the lowest number (665 OTUs). The major fungal phyla identified in the topsoil (0-15 cm) were Ascomycota, Basidiomycota, and Mortierellomycota, with their abundance varying across different tillage-cum-crop establishment (TCE) methods. Phylum Ascomycota was dominant in CA-based management treatments (94.9±0.62), followed by the partial CA (pCA)-based treatments (91.0 ± 0.37). Therefore, CA-based production systems play a crucial role in shaping soil fungal diversity, highlighting their significance for sustainable agricultural production.

Investigating the evolution of green algae with a large transcriptomic data set.

The colonization of land by plants approximately 450-500 million years ago (Mya) is one of the most important events in the history of life on Earth. Land plants, hereafter referred to as "embryophytes," comprise the foundation of every terrestrial biome, making them an essential lineage for the origin and maintenance of biodiversity. The embryophytes form a monophyletic clade within one of the two major phyla of the green algae (Viridiplantae), the Streptophyta. Estimates from fossil data and molecular clock analyses suggest the Streptophyte algae (Charophytes) diverged from the other main phylum of green algae, the Chlorophyta, as much as 1500 Mya. Here we present a phylogenetic analysis using transcriptomic and genomic data of 62 green algae and embryophyte operational taxonomic units, 31 of which were assembled de novo for this project. We have focused on identifying the charophyte lineage that is sister to embryophytes, and show that the Zygnematophyceae have the strongest support, followed by the Charophyceae. Furthermore, we have examined amino acid and codon usage across the tree and determined these data broadly follow the phylogenetic tree. We concluded by searching the data set for protein domains and gene families known to be important in embryophytes. Many of these domains and genes have homologous sequences in the charophyte lineages, giving insight into the processes that underlay the colonization of the land by plants. This provides new insights into green algal diversification, identifies previously unknown attributes of genome evolution within the group, and shows how functional mechanisms have evolved over time.

Oral Microbiota Development in the First 60 Months: A Longitudinal Study.

Childhood is considered crucial in the establishment of future oral microbiota. However, the precise period of oral microbiota development remains unclear. This study aimed to identify the progression of oral microbiota formation in children. We longitudinally investigated the salivary microbiota of 54 children across 13 time points from 1 wk to 60 mo (5 y) old and their parents at 2 time points as a representative sample of the adult microbiota. Using next-generation sequencing, we obtained 10,000 gene sequences of the 16s rRNA V1-V2 region for each sample. The detection rate in children of 110 operational taxonomic units commonly detected in more than 85% of mothers and fathers, defined as the main constituent bacteria, was 25% at 1 wk old, increased to 80% between 6 and 18 mo old, and reached approximately 90% by 36 mo old. Early main constituent bacteria detected at 1 wk old were limited to Streptococcus, Rothia, and Gemella. At 6 to 18 mo old, the detection rates of various main constituent bacteria, including Neisseria, Haemophilus, and Fusobacterium, increased. UniFrac distance analysis showed that the oral microbiota of children approached that of adults at 6 to 18 mo old. In the weighted UniFrac distance index, unlike the unweighted index, there were no significant changes in children between 36 and 60 mo old from adults, and microbiota formation at 60 mo old was sufficiently advanced to be included within the range of adult individual differences. Our findings suggest that the initial 36 mo, particularly the period from 6 to 18 mo old, consists of a time window for oral microbiota maturation. In addition, the development of microbiota during this period may be critical for future oral disease prevention.

The Systematics and Phylogeny of Myxomycetes: Yesterday, Today, and Tomorrow.

Abstract-Myxomycetes are amoeboid fungus-like organisms (Amoebozoa) with a unique life cycle characterized by a great morphological diversity of fruiting bodies. Due to the similarity of these structures to the fruiting bodies of some representatives of Ascomycota and Basidiomycota, myxomycetes have been classified as fungi since the first known scientific description in 1654. Only in the 19th century, when their life cycle was studied, did the difference of this group from fungi become clear. During the same period, microscopic structures of fruiting bodies, as well as ornamentation of the spore surface, began to be considered as diagnostic features. Due to this, in the period from the end of the 19th to the middle of the 20th century, a rather stable system was formed. However, as further studies have shown, both macro- and micromorphological characters are often quite variable, depend on environmental conditions, and often result from convergent evolution, which causes difficulties in defining species and taxonomic units of higher ranks. Since the first decade of the 21st century, due to the development of molecular genetic methods and the accumulation of data on nucleotide sequences of marker genes together with the improvement of microscopic studies, it has been possible to obtain data on the evolutionary relationships of different groups of myxomycetes. A milestone in this process was the publication of the first phylogenetic system of myxomycetes in 2019. This work was the starting point for a number of studies on the relationships between different groups of myxomycetes at a lower taxonomic level. Thus, there has been a surge in the number of studies that bring us closer to constructing a natural system.

What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case Study.

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed to ensure reliable taxonomic unit recovery. This study aims to provide those guidelines for a fungal metabarcoding context and to apply them to a case study of ectomycorrhizae in the decaying bark of Fagus sylvatica. We introduce the eNano pipeline to test two standard metabarcoding approaches: (1) Reference-based mapping leveraging UNITE's species hypothesis system (SH approach); (2) Constructing 98% OTUs (OTU approach). Our results demonstrate that both approaches are effective with Nanopore data. When using a reference database, we recommend strict mapping criteria rather than Phred-based filtering. Leveraging the SH-system further enhances reproducibility and facilitates cross-study communication. For the 98% OTUs, filtering reads at ≥Q25 is recommended. Our case study reveals that the decay gradient is a primary determinant of community composition and that specific mycorrhizal fungi colonize decaying bark. Complementing our metabarcoding results with root tip morphotypification, we identify Laccaria amethystina and Tomentella sublilacina as key ectomycorrhizae of saplings on decaying logs. These findings demonstrate that Nanopore sequencing can provide valuable ecological insights and support its broader use in fungal metabarcoding as read quality continues to improve.

Improvement in Microbiota Recovery Using Cas-9 Digestion of Mānuka Plastid and Mitochondrial DNA

Understanding host-microbe interactions in planta is an expanding area of research. Amplicon sequencing of the 16S rRNA gene is a powerful and common method to study bacterial communities associated with plants. However, the co-amplification of mitochondrial and plastid 16S rRNA genes by universal primers impairs the sensitivity and performance of 16S rRNA sequencing. In 2020, a new method, Cas-16S-seq, was reported in the literature to remove host contamination for profiling the microbiota in rice, a well-studied domestic plant, by engineering RNA-programmable Cas9 nuclease in 16S rRNA sequencing. For the first time, we tested the efficiency and applicability of the Cas-16S-seq method on foliage, flowers, and seed of a non-domesticated wild plant for which there is limited genomic information, Leptospermum scoparium (mānuka). Our study demonstrated the efficiency of the Cas-16S-seq method for L. scoparium in removing host contamination in V4-16S amplicons. An increase of 46% in bacterial sequences was found using six guide RNAs (gRNAs), three gRNAs targeting the mitochondrial sequence, and three gRNAs targeting the chloroplast sequence of L. scoparium in the same reaction. An increase of 72% in bacterial sequences was obtained by targeting the mitochondrial and chloroplast sequences of L. scoparium in the same sample at two different steps of the library preparation (DNA and 1st step PCR). The number of OTUs (operational taxonomic units) retrieved from soil samples was consistent when using the different methods (Cas-16S-seq and 16S-seq) indicating that the Cas-16S-seq implemented for L. scoparium did not introduce bias to microbiota profiling. Our findings provide a valuable tool for future studies investigating the bacterial microbiota of L. scoparium in addition to evaluating an important tool in the plant microbiota research on other non-domesticated wild species.

Ectomycorrhizal fungal community response to warming and rainfall reduction differs between co-occurring temperate-boreal ecotonal Pinus saplings.

Understanding the responses of ectomycorrhizal (ECM) fungi and their tree hosts to warming and reduced soil water availability under realistic future climate scenarios is essential, yet few studies have investigated how combined global change stressors impact ECM fungal community richness and composition as well as host performance. In this study, we leveraged a long-term factorial warming (ambient, + 1.7 ºC, + 3.2 ºC) and rainfall reduction (ambient, 30% reduced rainfall) experiment in northern Minnesota, USA to investigate the responses of two congeneric hosts with varying drought tolerances and their associated ECM fungal communities to a gradient of soil moisture induced by a combination of warming and rainfall reduction. Soil drying had host-specific effects; the less drought tolerant Pinus strobus had decreased stem growth and lower ECM fungal community richness (fewer ECM fungal Operational Taxonomic Units, OTUs), while the more drought tolerant Pinus banksiana experienced no decline in stem growth but had an altered ECM fungal community composition under drier, warmer soils. Taken together, the results of this study suggest that the combined effects of warming and decreased precipitation will largely be additive in terms of their impact on host performance and ECM fungal community richness, but that drier and warmer soil conditions may also differentially impact specific ECM fungal genera independently of host performance.