Phylogenetic Diversity Indices Research Articles

Avian phylogenetic and functional diversity are better conserved by land‐sparing than land‐sharing farming in lowland tropical forests

Abstract The transformation of natural habitats for farming is a major driver of tropical biodiversity loss. To mitigate impacts, two alternatives are promoted: intensifying agriculture to offset protected areas (land sparing) or integrating wildlife‐friendly habitats within farmland (land sharing). In the montane and dry tropics, phylogenetic and functional diversity, which underpin evolutionary values and the provision of ecosystem functioning and services, are best protected by land sparing. A key question is how these components of biodiversity are best conserved in the more stable environments of lowland moist tropical forests. Focusing on cattle farming within the Colombian Amazon, we investigated how the occupancy of 280 bird species varies between forest and pasture spanning gradients of wildlife‐friendly features. We then simulated scenarios of land‐sparing and land‐sharing farming to predict impacts on phylogenetic and functional diversity metrics. Predicted metrics differed marginally between forest and pasture. However, community assembly varied significantly. Wildlife‐friendly pastures were inadequate for most forest‐dependent species, while phylogenetic and functional diversity indices showed minimal variation across gradients of wildlife‐friendly features. Land sparing consistently retained higher levels of Faith's phylogenetic diversity (~30%), functional richness (~20%) and evolutionarily distinct lineages (~40%) than land sharing, and did so across a range of landscape sizes. Securing forest protection through land‐sparing practices remains superior for conserving overall community phylogenetic and functional diversity than land sharing. Synthesis and applications: To minimise the loss of avian phylogenetic diversity and functional traits from farming in the Amazon, it is imperative to protect large blocks of undisturbed and regenerating forests. The intensification required within existing farmlands to make space for spared lands while meeting agricultural demand needs to be sustainable, avoiding long‐term negative impacts on soil quality and other ecosystem services. Policies need to secure the delivery of both actions simultaneously.

Phylogenetic Diversity Indices from an Affine and Projective Viewpoint

Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the evolutionary history of the species in question, which is often given in terms of a phylogenetic tree. Both rooted and unrooted phylogenetic trees can be employed, and there are close connections between the indices that are derived in these two different ways. In this paper, we introduce more general phylogenetic diversity indices that can be derived from collections of subsets (clusters) and collections of bipartitions (splits) of the given set of species. Such indices could be useful, for example, in case there is some uncertainty in the topology of the tree being used to derive a phylogenetic diversity index. As well as characterizing some of the indices that we introduce in terms of their special properties, we provide a link between cluster-based and split-based phylogenetic diversity indices that uses a discrete analogue of the classical link between affine and projective geometry. This provides a unified framework for many of the various phylogenetic diversity indices used in the literature based on rooted and unrooted phylogenetic trees, generalizations and new proofs for previous results concerning tree-based indices, and a way to define some new phylogenetic diversity indices that naturally arise as affine or projective variants of each other or as generalizations of tree-based indices.

PhyloNext: a pipeline for phylogenetic diversity analysis of GBIF-mediated data

BackgroundUnderstanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and policy development. Diversity estimates that consider the evolutionary relationships among species, such as phylogenetic diversity and phylogenetic endemicity indices, provide valuable insights into the functional diversity and evolutionary uniqueness of biological communities. These estimates are crucial for informed decision-making and effective global biodiversity management. However, the current methodologies used to generate these metrics encounter challenges in terms of efficiency, accuracy, and data integration.ResultsWe introduce PhyloNext, a flexible and data-intensive computational pipeline designed for phylogenetic diversity and endemicity analysis. The pipeline integrates GBIF occurrence data and OpenTree phylogenies with the Biodiverse software. PhyloNext is free, open-source, and provided as Docker and Singularity containers for effortless setup. To enhance user accessibility, a user-friendly, web-based graphical user interface has been developed, facilitating easy and efficient navigation for exploring and executing the pipeline. PhyloNext streamlines the process of conducting phylogenetic diversity analyses, improving efficiency, accuracy, and reproducibility. The automated workflow allows for periodic reanalysis using updated input data, ensuring that conservation strategies remain relevant and informed by the latest available data.ConclusionsPhyloNext provides researchers, conservationists, and policymakers with a powerful tool to facilitate a broader understanding of biodiversity patterns, supporting more effective conservation planning and policy development. This new pipeline simplifies the creation of reproducible and easily updatable phylogenetic diversity analyses. Additionally, it promotes increased interoperability and integration with other biodiversity databases and analytical tools.

Disease Occurrence and Climatic Factors Jointly Structure Pomelo Leaf Fungal Succession in Disturbed Agricultural Ecosystem.

For perennial plants, newly emerged organs are fresh hot spots for environmental microbes to occupy and assemble to form mature microbial communities. In the microbial community, some commensal fungi can play important roles in microbial succession, thus significantly improving host plant growth and disease resistance. However, their participating patterns in microbial assembly and succession remain largely unknown. In this study, we profiled the fungal community and found a similar fungal succession pattern of spring-emerged leaves from March to October in two pomelo orchards. Specifically, the fungal species, tracked on the old leaves, dominated the spring leaves after emergence and then decreased in relative abundance. This reduction in priority effects on the spring leaves was then followed by an increase in the number of observed species, Shannon and phylogenetic diversity indices, and the pathogen-associated fungal groups. In addition, we found that the temporal fungal succession on the spring leaves highly correlated with the disease occurrence in the orchards and with the temperature and precipitation variation from spring to summer. Of the pathogen-associated fungal groups, an increase in the relative abundance of Mycosphaerellaceae, hosting the causal agent of citrus greasy spot, correlated with the occurrence of the disease, while the relative abundance of Diaporthaceae, hosting the causal agent of melanose, was extremely low during the fungal succession. These results confirm that the two kinds of pathogen-associated fungal groups share different lifestyles on citrus, and also suggest that the study of temporal fungal succession in microbial communities can add to our understanding of the epidemiology of potential plant pathogens.

Short communication: Comparing the microbiota diversity from the core, middle part and rind of six Spanish commercial goat cheeses

The cheese core has a lower oxygen saturation and salinity and a higher acidity than the rind, but there is controversy about the incidence of such factors on the magnitude of microbial diversity. The goal of the current work was to investigate the existence of differences in α-diversity between the core, middle part, and rind of six Spanish commercial cheeses through a sequencing approach. To this end, we have collected rind, middle part, and core samples from fresh (H and M), soft semi-ripened (C and P), hard semi-ripened (B) and semi-hard aged (G) goat cheeses. After purifying deoxyribonucleic acid from these 18 samples, the V3-V4 ultravariable region of the 16S rRNA gene was sequenced. The analysis of microbial composition revealed that lactic acid bacteria from the genera Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc are predominant in all six goat cheeses. Furthermore, we identified several psychrophilic taxa often associated with the post-pasteurization contamination of refrigerated milk. Comparison of three α-diversity estimators (Chao1, Shannon and Faith's phylogenetic diversity indices) of microbiota in the core, middle part, and rind of all six goat cheeses did not reveal substantial differences, being only significant (at the nominal level) the comparison of rind vs middle part for the Shannon index (P-value = 0.031). Moreover, the construction of a dendrogram based on Aitchison distances revealed that cheese samples cluster according to their manufacturing characteristics, with a clear distinction between fresh vs semi-ripened or aged cheeses. We conclude that the magnitude of microbial α-diversity in the cheese core is similar to that in the rind despite their different physicochemical attributes. This result could be because physicochemical differences between cheese compartments are often attenuated during cheese ripening.

The robustness of phylogenetic diversity indices to extinctions

Phylogenetic diversity indices provide a formal way to apportion evolutionary history amongst living species. Understanding the properties of these measures is key to determining their applicability in conservation biology settings. In this work, we investigate some questions posed in a recent paper by Fischer et al. (Syst Biol 72(3):606–615, 2023). In that paper, it is shown that under certain extinction scenarios, the ranking of the surviving species by their Fair Proportion index scores may be the complete reverse of their ranking beforehand. Our main results here show that this behaviour extends to a large class of phylogenetic diversity indices, including the Equal-Splits index. We also provide a necessary condition for reversals of Fair Proportion rankings to occur on phylogenetic trees whose edge lengths obey the ultrametric constraint. Specific examples of rooted phylogenetic trees displaying these behaviours are given and the impact of our results on the use of phylogenetic diversity indices more generally is discussed.

Implications of gene tree heterogeneity on downstream phylogenetic analyses: A case study employing the Fair Proportion index.

Many questions in evolutionary biology require the specification of a phylogeny for downstream phylogenetic analyses. However, with the increasingly widespread availability of genomic data, phylogenetic studies are often confronted with conflicting signal in the form of genomic heterogeneity and incongruence between gene trees and the species tree. This raises the question of determining what data and phylogeny should be used in downstream analyses, and to what extent the choice of phylogeny (e.g., gene trees versus species trees) impacts the analyses and their outcomes. In this paper, we study this question in the realm of phylogenetic diversity indices, which provide ways to prioritize species for conservation based on their relative evolutionary isolation on a phylogeny, and are thus one example of downstream phylogenetic analyses. We use the Fair Proportion (FP) index, also known as the evolutionary distinctiveness score, and explore the variability in species rankings based on gene trees as compared to the species tree for several empirical data sets. Our results indicate that prioritization rankings among species vary greatly depending on the underlying phylogeny, suggesting that the choice of phylogeny is a major influence in assessing phylogenetic diversity in a conservation setting. While we use phylogenetic diversity conservation as an example, we suspect that other types of downstream phylogenetic analyses such as ancestral state reconstruction are similarly affected by genomic heterogeneity and incongruence. Our aim is thus to raise awareness of this issue and inspire new research on which evolutionary information (species trees, gene trees, or a combination of both) should form the basis for analyses in these settings.

Fungal Mycobiome of Mature Strawberry Fruits (Fragaria x ananassa Variety 'Monterey') Suggests a Potential Market Site Contamination with Harmful Yeasts.

An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to investigate the diversity of fungi associated with mature strawberries collected from a volcanic orchard and open-air market stands. Based on the Kruskal-Wallis test, no statistically significant differences were observed in both non-phylogenetic and phylogenetic alpha diversity indices. According to beta diversity analyses, significant differences in fungal communities were found between groups (orchard vs. market). Taxonomic assignment of amplicon sequence variables (ASVs) revealed 7 phyla and 31 classes. The prevalent fungal phyla were Basidiomycota (29.59-84.58%), Ascomycota (15.33-70.40%), and Fungi-phy-Insertae-sedis (0.45-2.89%). The most predominant classes among the groups were Saccharomycetes in the market group, and Microbotryomycetes and Tremellomycetes in the orchard group. Based on the analysis of microbiome composition (ANCOM), we found that the most differentially fungal genera were Hanseniaspora, Kurtzmaniella, and Phyllozyma. Endophytic yeasts Curvibasidium cygneicollum were prevalent in both groups, while Candida railenensis was detected in fruits originating only from the market. In addition, Rhodotorula graminis (relative abundance varying from 1.7% to 21.18%) and Papiliotrema flavescens (relative abundance varying from 1.58% to 16.55%) were detected in all samples regardless of origin, while Debaryomyces prosopidis was detected in samples from the market only, their relative abundance varying with the sample (from 0.80% to 19.23%). Their role in fruit quality and safety has not been yet documented. Moreover, several clinically related yeasts, such as Meyerozyma guilliermondii and Candida parapsilosis, were detected in samples only from the market. Understanding the variety and makeup of the mycobiome in ripe fruits during the transition from the orchard to the market is crucial for fruit safety after harvest.

Trees diversity explains variations in biodiversity-ecosystem function relationships across environmental gradients and conservation status in riparian corridors

Riparian ecosystems are recognized as large reservoirs of biodiversity providing important ecosystem services. However, the relationship between tree species diversity and ecosystem functions and the underlying ecological mechanisms have less been studied in riparian corridors. This study assessed the effect of tree diversity (taxonomic, functional, and phylogenetic) on riparian ecosystem functions (habitat quality–HbQ and aboveground carbon–AGC) across environmental gradients (distances to stream bed) and conservation status. Data were collected from 96 inventory plots installed in a 1 km buffer zone on either side of permanent streams in the Upper Ouémé watershed in northern Benin. We employed linear mixed effects models and structural equation modeling to analyze the data. We found that ecosystem functions (HbQ, AGC) and diversity attributes including species richness (SR), Faith’s phylogenetic diversity index (PD) and community-weighted mean of maximum height (CWMHmax) were significantly lower away from the streambed than nearby. The correlation between SR and ecosystem functions was significant and positive across and within the distance gradient and conservation status. We also found that the CWMHmax was the best predictor of both ecosystem functions, and that PD mediated the effect of SR on AGC and HbQ in areas close to the streambed and in unprotected areas, respectively. Our study reveals the influence of human activities on biodiversity and ecosystem functioning relationships in riparian corridors and provides new insights into the importance of tall stature trees and species with distant lineages for the functioning of these ecosystems. Based on the variables measured and tested in this study, we argue that riparian corridor management policies should consider plant traits and phylogeny and promote wider riparian buffers for the co-benefits of biodiversity conservation and climate change mitigation.

Quantifying the difference between phylogenetic diversity and diversity indices

Phylogenetic diversity is a popular measure for quantifying the biodiversity of a collection Y of species, while phylogenetic diversity indices provide a way to apportion phylogenetic diversity to individual species. Typically, for some specific diversity index, the phylogenetic diversity of Y is not equal to the sum of the diversity indices of the species in Y. In this paper, we investigate the extent of this difference for two commonly-used indices: Fair Proportion and Equal Splits. In particular, we determine the maximum value of this difference under various instances including when the associated rooted phylogenetic tree is allowed to vary across all rooted phylogenetic trees with the same leaf set and whose edge lengths are constrained by either their total sum or their maximum value.

Alpha Diversity Indices as Indicators of the Variability of Gut Microbiota in Obese Adolescents of Different Ethnicities.

We compared alpha diversity indices of the intestinal microbiota in adolescents with obesity and normal body weight, taking into account their ethnicity. Intestinal biocenosis was studied by metasequencing of amplicon libraries of V3-V4 fragments of the 16S rRNA gene. The alpha diversity of the microbiota was assessed using classical and alternative indices. Statistically significant differences in intestinal microbiota were observed between Russians with obesity and Buryats with normal body weight, as well as between Russians with obesity and Buryats with obesity when assessing the Shannon-Weaver, Chao1 indices, Faith phylogenetic diversity index, ACE, Fisher, Gini coefficient, Margalef, and Menkhinik indices. It was shown that alpha diversity indices can be used to assess significance of differences and variability of the intestinal microbiota in multifactorial diseases such as obesity in adolescents; however, the scope of application of the criteria should be considered.

Divergent Fungal Community Dynamics of Thuja sutchuenensis in Arid Environments.

Thuja sutchuenensis Franch., an endangered species sparsely distributed in the mountainous and arid regions of southwest China, faces the critical challenge of adapting to these harsh conditions. Understanding the plant's strategies for survival and the precise roles played by soil fungal communities in this adaptation remains an area of limited knowledge. Our investigation centers on the fungal communities associated with T. sutchuenensis and their interactions with soil water content. Notably, we identified unique fungal communities in the low soil moisture group, and these communities exhibited lower coverage but higher phylogenetic diversity (PD), Chao1, and Shannon indices compared to other groups. Network analysis revealed a modular structure within the fungal communities, with key hub nodes identified, particularly in the arid group. This group demonstrated higher levels of soil saprotrophs and ectomycorrhizal fungi and a reduced presence of plant pathogens. Linear discriminant analysis highlighted the significance of genera such as Russula, Myxotrichaceae, and Sebacina, emphasizing their roles in supporting the plant in arid environments. Random forest analysis indicated that soil moisture content emerged as the primary driver in determining fungal composition and diversity and contributed to the variables of several fungal genera. Collectively, this study provides valuable insights into the fungal communities associated with T. sutchuenensis, shedding light on their adaptation to extreme arid conditions.

Airborne microbes in five important regions of Chinese traditional distilled liquor (Baijiu) brewing: regional and seasonal variations.

Baijiu is one of the six primary distilled spirits in the world. It is produced through the solid-state fermentation of grains in the open environment, so high-quality Baijiu brewing largely depends on terrior. Environmental microbes are one of the most important factors affecting the quality, quantity, and flavors of Baijiu. As atmosphere is a pool and transport pathway for microbes from the ambient environment to Baijiu brewing ecosystems, we explored the functional microbes of Baijiu brewing in five important regions. The regions fell into two topographical types, namely, plain and river-valley. In total, 41 functional microbes were identified rich (relative abundance >0.1%) in at least one of the regions, such as the fungi of Aspergillus, Candida, Cladosporium, Debaryomyces, Penicillium, Pichia, Rhizopus, Saccharomyces, and Wickerhamomyces and the bacteria of Acetobacter, Bacillus, Clostridium, Enterobacter, Lactobacillus, Methanosarcina, Methanobacterium, Methanobrevibacter, and Pseudomonas. However, some functional bacteria (e.g., Clostridia, Gluconacetobacter, and Weissella) and fungi (e.g., Dekkera, Eurotium, Issatchenkia, Mucor, and Phoma) were not rich or were not detected in the atmosphere. Airborne microbiomes and the Phylogenetic Diversity (PD) index were significantly different between the main brewing season (winter) and the summer break in each region, except for the fungi in one region. In winter, airborne microbiomes were significantly different among almost all the regions. The relative abundance of bacterial fermentation function in each region increased from summer to winter. The relative abundances of fungal yeast function were higher in winter for the plain regions but were higher in summer for the river-valley regions. In sum, our results suggested that: (1) atmosphere was one but not the sole important source of functional microbes for Baijiu brewing and (2) microbiomes in different regions might be quite different but they could share some major functions related to Baijiu brewing.

VDR gene TaqI (rs731236) polymorphism affects gut microbiota diversity and composition in a Caucasian population.

The VDR gene is identified as a crucial host factor, influencing the gut microbiota. The current research focuses on an observational study that compares gut microbiota composition among individuals with different VDR gene TaqI polymorphisms in a Caucasian Spanish population. This study aims to elucidate the interplay between genetic variations in the VDR gene and the gut microbial composition. 87 healthy participants (57 men, 30 women), aged 18 to 48 years, were examined. Anthropometric measures, body composition, and dietary habits were assessed. VDR gene polymorphism TaqI rs731236 was determined using TaqMan assays. The V3 and V4 regions of the 16S rRNA gene were sequenced to study bacterial composition, which was analyzed using QIIME2, DADA2 plugin, and PICRUSt2. Statistical analyses included tests for normal distribution, alpha/beta diversity, ADONIS, LEfSe, and DESeq2, with established significance thresholds. No significant differences in body composition or dietary habits were observed based on VDR genotypes. Dietary intake analysis revealed no variations in energy, macronutrients, or fiber among the different VDR genotypes. Fecal microbiota analysis indicated significant differences in alpha diversity as measured by Faith's Phylogenetic Diversity index. Differential abundance analysis identified taxonomic disparities, notably in the genera Parabacteroides and Butyricimonas. Overall, this study suggests potential associations between genetic variations in the VDR gene and the composition and function of gut microbiota.

Indicators to quantify biodiversity gains for compensation and mineland rehabilitation in the Eastern Amazon.

To connect the protection of natural resources to economic development, environmental rehabilitation is a promising way to repair and compensate for impacts on biodiversity and ecosystem services. Here, we aimed to compare and select potential indicators for the success of different rehabilitating ecosystems to quantify gains in biodiversity and ecosystem services within the Impact Mitigation Hierarchy. We sampled nine environmental variables along rehabilitation chronosequences from rehabilitating (i) iron mining waste piles, (ii) sand quarries, and (iii) compensation areas in the Carajás National Forest. From that, we computed the rehabilitation status, i.e., the proportion of environmental enhancements compared to the overall rehabilitation trajectory, and statistically validated the indicators that best described the status. With a mean rehabilitation status for the oldest rehabilitation stages from waste piles, sand quarries, and compensation areas of 52, 71, and 74%, respectively, we confirmed that rehabilitation activities were able to generate considerable gains in biodiversity. In all the cases, the Shannon diversity, phylogenetic diversity and Leaf Area Index performed better than did the other indices, encouraging the increased use of these indices for upscale monitoring activities. Consistent indicators across distinct projects highlight the importance of maximizing tree diversity and canopy closure in rehabilitation projects to increase biodiversity gains within Impact Mitigation Hierarchy.

Non‐linear thresholds in the effect of area on three dimensions of diversity of herpetofauna in the West Indies

AbstractAimThe small‐island effect (SIE) describes an anomalous feature of the species–area relationship (SAR) on smaller compared to larger islands. However, previous studies on SIEs mainly focused on taxonomic diversity and overlooked phylogenetic and functional diversity. In this study, we explored SIEs in three dimensions of diversity. We expect to see the non‐linear thresholds in the effect of area on three dimensions of diversity as well as on community structures, because the dominant assembly processes vary across spatial scales.LocationThe West Indies.TaxonHerpetofauna.MethodsWe derived data on the presence/absence of 199 amphibian species on 163 islands and 614 reptile species on 748 islands in the West Indies. We built a species‐level phylogenetic tree and a species‐level functional tree to estimate six taxonomic, phylogenetic and functional diversity indices. Four community metrics on behalf of the phylogenetic and functional community structure of each island were calculated using a null modelling framework and was quantified using the standardized effect size (SES). We explored the non‐linear thresholds in the effect of area for each of the diversity indices and SES values of community metrics by comparing six piecewise regression models with a linear regression model and a null model.ResultsWe found evidence of SIEs in four diversity indices representing all three dimensions of diversity. Besides, area thresholds were also found in the phylogenetic and functional community structure for both amphibians and reptiles. Random extinction, competitive exclusion and adaptive radiation are the dominant processes structuring reptile communities on small, intermediate and large islands respectively.Main ConclusionsTo conduct a comprehensive biodiversity conservation plan concerning taxonomic, phylogenetic and functional diversity, we suggest it is necessary to explore the SIEs in various diversity indices representing all three dimensions of diversity and apply the lowest threshold value to make management strategies.

Dysbiosis of gut microbiota in patients with protein-losing enteropathy after the Fontan procedure

BackgroundThere is a lack of predictive biomarkers for the onset or activity of protein-losing enteropathy (PLE), a Fontan procedure-associated complication. Here, we aimed to identify the gut microbiota composition of patients with active PLE and investigate its relationship with PLE activity. MethodsThis multicenter case–control study involved patients who developed PLE (n = 16) after the Fontan procedure and those who did not (non-PLE; n = 20). Patients with PLE who maintained a serum albumin level of ≥3 g/dL for >1 year were included in the remissive-stage-PLE group (n = 9) and those who did not maintain this level were included in the active-PLE group (n = 7). 16S rRNA gene sequencing analysis of fecal samples was performed using QIIME2 pipeline. Alpha (Shannon and Faith's phylogenetic diversity indices) and beta diversity was assessed using principal coordinate analysis based on unweighted UniFrac distances. ResultsShannon and Faith's phylogenetic diversity indices were lower in the active-PLE group than in the remissive-stage- (q = 0.028 and 0.025, respectively) and non-PLE (q = 0.028 and 0.017, respectively) groups. Analysis of beta diversity revealed a difference in the microbiota composition between the active-PLE and the other two groups. Linear discriminant effect size analysis demonstrated differences in the relative abundance of Bifidobacterium and Granulicatella spp., and Ruminococcus torques between patients with active- and those with remissive-stage-PLE. ConclusionsGut microbiota dysbiosis was observed in patients with active PLE. Changes in the bacterial composition of the gut microbiota and decreased diversity may be associated with the severity of PLE.

Elexacaftor-tezacaftor-ivacaftor decreases pseudomonas abundance in the sinonasal microbiome in cystic fibrosis.

Chronic rhinosinusitis (CRS) is common in individuals with cystic fibrosis (CF) and is marked by chronic inflammation and episodes of infection that negatively impact quality of life. Several studies have shown that elexacaftor-tezacaftor-ivacaftor (ETI) improves symptoms and examination findings in CF-CRS. The current study determines the effect of ETI on the sinonasal microbiota in CF. Sinonasal samples were collected under endoscopic visualization before and after starting ETI. Samples were subjected to 16S amplicon sequencing and sequences were processed with the QIIME2 pipeline with subsequent analysis using the vegan R-package. Twenty-nine individual baseline samples and 23 sample pairs pre-/post-ETI were available. At baseline, the cohort had samples dominated by Staphylococcus, and alpha diversity was lower than that of a published reference set of individuals without sinonasal disease. Individuals with prior sinus surgery had lower alpha diversity as measured by Shannon Index, Observed Richness, and Faith's phylogenetic diversity Index. Beta diversity differed between individuals with and without allergic rhinitis, with higher Staphylococcus abundance in those with allergic rhinitis. No change in alpha or beta diversity was seen after a median of 9 months on ETI. With ETI, the Pseudomonas genus and the genus containing Burkholderia decreased in samples containing these taxa at baseline. Pseudomonas abundance decreased with treatment as measured by qPCR. Core sinonasal microbiome members Staphylococcus, Corynebacterium, and Streptococcus were unchanged, while Moraxella increased with ETI. Treatment with ETI leads to a reduction in Pseudomonas abundance within the sinonasal microbiome of individuals with Pseudomonas at baseline.

Microbiome Analysis of Organic and Conventional Chickens Processed Using Whole Carcass Enrichment and Rinse Methods

Investigating the chicken microbiome is important to establish control measures for pathogens to protect consumers. This study aimed at evaluating the comparative efficiency of human pathogen detection through 16S rRNA sequencing of organic and conventional chickens processed using whole carcass enrichment (WCE) and rinse (WCR) methods. Organic and conventional whole broiler carcasses (n = 31) were vigorously shaken with 500 mL buffered peptone water (BPW). For the rinse method, a 30 mL aliquot was mixed with 30 mL of BPW. The rest of the sample, including the carcass, was used for the enrichment method. All samples were incubated at 37°C for 24 h. The samples were divided into five groups [Negative Control: only BPW without chicken (n = 5), Organic-Rinsed (n = 7), -Enriched (n = 8), Conventional-Rinsed (n = 7), and -Enriched (n = 9)]. Fifty milliliters of each sample were subjected to DNA extraction followed by 16S rRNA sequencing. Proteobacteria and Firmicutes predominated the microbiota of both conventional and organic chickens, followed by low abundances of Bacteroidetes and Fusobacterium. While the abundance of Proteobacteria and Firmicutes remained unchanged in organic chicken irrespective of the methods used, a noticeable shift in the Proteobacteria and Firmicutes ratio (59%:39% in rinsed to 38%:60% in enriched) was observed in conventional chicken. Furthermore, the choice of method did not yield any differences in Abundance-Based Coverage Estimator, and Jackknife, among conventional and organic chickens but resulted in a statistically significant difference in the Shannon, Simpson, Chao1, and phylogenetic diversity indices (p < 0.05). The relative abundance of Salmonella and Campylobacter was less than 0.1%. The results suggested the WCE method provides a broad range of information on the chicken microbiome.

Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts.

Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.