Changes In Beta Diversity Research Articles

Effects of snake fungal disease (ophidiomycosis) on the skin microbiome across two major experimental scales

AbstractEmerging infectious diseases are increasingly recognized as a significant threat to global biodiversity conservation. Elucidating the relationship between pathogens and the host microbiome could lead to novel approaches for mitigating disease impacts. Pathogens can alter the host microbiome by inducing dysbiosis, an ecological state characterized by a reduction in bacterial alpha diversity, an increase in pathobionts, or a shift in beta diversity. We used the snake fungal disease (SFD; ophidiomycosis), system to examine how an emerging pathogen may induce dysbiosis across two experimental scales. We used quantitative polymerase chain reaction, bacterial amplicon sequencing, and a deep learning neural network to characterize the skin microbiome of free‐ranging snakes across a broad phylogenetic and spatial extent. Habitat suitability models were used to find variables associated with fungal presence on the landscape. We also conducted a laboratory study of northern watersnakes to examine temporal changes in the skin microbiome following inoculation with Ophidiomyces ophidiicola. Patterns characteristic of dysbiosis were found at both scales, as were nonlinear changes in alpha and alterations in beta diversity, although structural‐level and dispersion changes differed between field and laboratory contexts. The neural network was far more accurate (99.8% positive predictive value [PPV]) in predicting disease state than other analytic techniques (36.4% PPV). The genus Pseudomonas was characteristic of disease‐negative microbiomes, whereas, positive snakes were characterized by the pathobionts Chryseobacterium, Paracoccus, and Sphingobacterium. Geographic regions suitable for O. ophidiicola had high pathogen loads (>0.66 maximum sensitivity + specificity). We found that pathogen‐induced dysbiosis of the microbiome followed predictable trends, that disease state could be classified with neural network analyses, and that habitat suitability models predicted habitat for the SFD pathogen.

Early-life gut microbiota assembly patterns are conserved between laboratory and wild mice

Assembly of the mammalian gut microbiota during early life is known to shape key aspects of organismal development, including immunity, metabolism and behaviour. While house mice (Mus musculus) are the major laboratory model organism for gut microbiota research, their artificial lab-based lifestyle could fundamentally alter ecological processes of microbiota assembly and dynamics, in ways that affect their usefulness as a model system. To examine this, here we directly compared patterns of gut microbiota assembly in house mice from the lab and from the wild, making use of a tractable, individually-marked wild population where we could examine patterns of gut microbiota assembly during early life. Despite lab and wild mice harbouring taxonomically distinct communities, we identify striking similarities in multiple patterns of their gut microbiota assembly. Specifically, age-related changes in both alpha and beta diversity, as well as the abundance of predominant phyla and aerotolerance of the microbiota followed parallel trajectories in both settings. These results suggest some degree of intrinsic programme in gut microbiota assembly that transcends variation in taxonomic profiles, and the genetic and environmental background of the host. They further support the notion that despite their artificial environment, lab mice can provide meaningful insights into natural microbiota ecological dynamics in early life and their interplay with host development.

Lactobacillus rhamnosus modulates murine neonatal gut microbiota and inflammation caused by pathogenic Escherichia coli

BackgroundPathogenic Escherichia coli strains produce neonatal septicemia after colonizing the neonatal gut. While the probiotic Lactobacillus rhamnosus GG (LGG) effectively reduces neonatal sepsis, LGG’s effects on the neonatal intestinal microbiota alterations and inflammation triggered by E. coli are incompletely understood. We hypothesized that LGG significantly modulates the specific neonatal gut microbial populations changes and the inflammatory response elicited by the enteral introduction of septicemia-producing E. coli. To test this hypothesis, newborn rats were pretreated orally with LGG or placebo prior to infection with the neonatal E. coli septicemia clinical isolate SCB34. Amplicon 16S rRNA gene sequencing was performed on intestinal samples. Intestinal injury and expression of inflammatory mediators and apoptosis were determined.ResultsAlpha diversity of gut microbiota was greater in SCB34-infected pups in comparison to sham-infected pups, these changes were not modified by LGG pretreatment. Beta diversity analyses also showed differences between SCB34-infected vs. uninfected pups. LGG pretreatment before SCB34 infection did not result in significant beta diversity changes compared to placebo. Moreover, individual genera and species abundance analyses by linear discriminant analysis effect size (LEfSe) showed significant changes in Gram-negative, Gram-positive, and anaerobic populations resulting from LGG pretreatment and SCB34 infection. LGG significantly suppressed the expression of inflammatory cytokines but did not attenuate SCB34-induced apoptosis or histologic injury.ConclusionsLGG modulates clinically significant microbiota features and inflammation triggered by pathogenic E. coli intestinal infection shortly after birth. This new knowledge can potentially be harnessed to design novel interventions against gut-derived neonatal sepsis.

Regular Exercise Training Induces More Changes on Intestinal Glucose Uptake from Blood and Microbiota Composition in Leaner Compared to Heavier Individuals in Monozygotic Twins Discordant for BMI

Background/Objectives: Obesity impairs intestinal glucose uptake (GU) (intestinal uptake of circulating glucose from blood) and alters gut microbiome. Exercise improves intestinal insulin-stimulated GU and alters microbiome. Genetics influence the risk of obesity and gut microbiome. However, the role of genetics on the effects of exercise on intestinal GU and microbiome is unclear. Methods: Twelve monozygotic twin pairs discordant for BMI (age 40.4 ± 4.5 years, BMI heavier 36.7 ± 6.0, leaner 29.1 ± 5.7, 8 female pairs) performed a six-month-long training intervention. Small intestine and colonic insulin-stimulated GU was studied using [18F]FDG-PET and microbiota from fecal samples with 16s rRNA. Results: Ten pairs completed the intervention. At baseline, heavier twins had lower small intestine and colonic GU (p < 0.05). Response to exercise differed between twins (p = 0.05), with leaner twins increasing colonic GU. Alpha and beta diversity did not differ at baseline. During the intervention, beta diversity changed significantly, most prominently at the mid-point (p < 0.01). Beta diversity changes were only significant in the leaner twins when the twin groups were analyzed separately. Exercise was associated with changes at the phylum level, mainly at the mid-point (pFDR < 0.05); at the genus level, several microbes increased, such as Lactobacillus and Sellimonas (pFDR < 0.05). In type 1 analyses, many genera changes were associated with exercise, and fewer, such as Lactobacillus, were also associated with dietary sugar consumption (p < 0.05). Conclusions: Obesity impairs insulin-stimulated intestinal GU independent of genetics. Though both twin groups exhibited some microbiota changes, most changes in insulin-stimulated colon GU and microbiota were significant in the leaner twins.

12468 Loss Of Enterococcus And Faecalibacterium Associate With Polycystic Ovary Syndrome And Hirsutism In A Sample Of Hispanic Patients

Abstract Disclosure: L.A. Gonzalez-Rodriguez: Research Investigator; Self; Eli Lilly & Company. C.M. Casas Loyola: None. C.I. Martinez-Hernandez: None. L. El Musa Penna: None. J. Romaguera: None. F. Godoy-Vitorino: None. Polycystic Ovary Syndrome (PCOS) is a common endocrine disorder affecting women of reproductive age. It is characterized by symptoms such as irregular menstrual periods, excess androgen levels and polycystic ovaries. Women with PCOS often display insulin resistance independent of fat and have been associated with an increased risk of diabetes mellitus, cardiovascular disease, and mood disorders. The gut microbiota, the community of microbes living in the human gastrointestinal tract, plays a crucial role in human health and has been implicated in various diseases, including metabolic and inflammatory conditions. We aimed to characterize the gut microbiota in a sample of Hispanic women living in Puerto Rico (n=50). Of these 38 had confirmed PCOS as per Rotterdam criteria and 12 were controls. A stool sample was collected for genomic DNA extractions followed by amplification and sequencing of 16S rRNA genes (V4 region) with Illumina MiSEQ. Data analyses were performed with standard pipelines with variables sample group (PCOS vs Controls), insulin resistance assessed using HOMA-IR and hirsutism status according to modified-Ferriman Gallwey (mFG) score and controlled for age and other clinical variables. Despite there were no changes in alpha or beta diversity among the microbiota of these groups, composition was significantly different. Women with PCOS had significantly lower levels of Enterococcus species as well as Hungatella, taxa that are part of a physiologically normal gut flora. Enterococcus species contribute to the balance of the microbial community and play roles in the metabolism and immune function and are very resilient. Hungatella species are a known source of catabolic enzymes that degrade glycosaminoglycans which are important in tissue repair. These dominant taxa in controls was substituted by other taxa in PCOS. Women with prominent hirsutism had significantly lower levels of Faecalibacterium while those with insulin resistance had increased levels of Clostridium. We found that higher levels Clostridium, and lower levels of protective anti-inflammatory taxa such as Faecalibacterium or Enterococci, which are important for gut health and metabolic regulation, are linked to this metabolic disturbance. Even though this is a preliminary report, it opens potential therapeutic strategies, such as the use probiotics, and dietary modifications to modulate the gut microbiome and improve PCOS outcomes. Presentation: 6/1/2024

12468 Loss Of Enterococcus And Faecalibacterium Associate With Polycystic Ovary Syndrome And Hirsutism In A Sample Of Hispanic Patients

Abstract Disclosure: L.A. Gonzalez-Rodriguez: Research Investigator; Self; Eli Lilly & Company. C.M. Casas Loyola: None. C.I. Martinez-Hernandez: None. L. El Musa Penna: None. J. Romaguera: None. F. Godoy-Vitorino: None. Polycystic Ovary Syndrome (PCOS) is a common endocrine disorder affecting women of reproductive age. It is characterized by symptoms such as irregular menstrual periods, excess androgen levels and polycystic ovaries. Women with PCOS often display insulin resistance independent of fat and have been associated with an increased risk of diabetes mellitus, cardiovascular disease, and mood disorders. The gut microbiota, the community of microbes living in the human gastrointestinal tract, plays a crucial role in human health and has been implicated in various diseases, including metabolic and inflammatory conditions. We aimed to characterize the gut microbiota in a sample of Hispanic women living in Puerto Rico (n=50). Of these 38 had confirmed PCOS as per Rotterdam criteria and 12 were controls. A stool sample was collected for genomic DNA extractions followed by amplification and sequencing of 16S rRNA genes (V4 region) with Illumina MiSEQ. Data analyses were performed with standard pipelines with variables sample group (PCOS vs Controls), insulin resistance assessed using HOMA-IR and hirsutism status according to modified-Ferriman Gallwey (mFG) score and controlled for age and other clinical variables. Despite there were no changes in alpha or beta diversity among the microbiota of these groups, composition was significantly different. Women with PCOS had significantly lower levels of Enterococcus species as well as Hungatella, taxa that are part of a physiologically normal gut flora. Enterococcus species contribute to the balance of the microbial community and play roles in the metabolism and immune function and are very resilient. Hungatella species are a known source of catabolic enzymes that degrade glycosaminoglycans which are important in tissue repair. These dominant taxa in controls was substituted by other taxa in PCOS. Women with prominent hirsutism had significantly lower levels of Faecalibacterium while those with insulin resistance had increased levels of Clostridium. We found that higher levels Clostridium, and lower levels of protective anti-inflammatory taxa such as Faecalibacterium or Enterococci, which are important for gut health and metabolic regulation, are linked to this metabolic disturbance. Even though this is a preliminary report, it opens potential therapeutic strategies, such as the use probiotics, and dietary modifications to modulate the gut microbiome and improve PCOS outcomes. Presentation: 6/1/2024

Effects of High Amylose-Resistant Starch on Gut Microbiota and Uremic Toxin Levels in Patients With Stage-G3a-G4 Chronic Kidney Disease: A Randomized Trial

ObjectiveThis study was designed to determine the effect of 16 weeks of supplementation with Hi-maize 260 resistant starch on the gut microbiota, uremic toxins (indoxyl sulfate and p-cresyl sulfate), markers of inflammation and oxidative stress along with vascular function in patients with stage G3a-G4 chronic kidney disease (CKD). Design& Methods: This was a double-blind, placebo-controlled, parallel-arm, randomized controlled trial. Sixty-eight patients with stage G3a-G4 CKD were randomized to either resistant starch with usual care or placebo and usual care. Patients attended four testing sessions: two baseline visits, and follow-up visits at 8 and 16 weeks. Fasting blood samples, resting brachial and central blood pressures, along with arterial stiffness, were collected at visits (1 or 2), and weeks 8 and 16. A stool sample was collected for analysis of microbial composition at baseline and week 16. Patients were randomized after the baseline visits. ResultsPatients receiving the resistant starch had a reduction in p-cresyl sulfate at week 16. This reduction was associated with a decrease in microbial α-diversity between baseline and week 16 (Chao1 p=0.014, Shannon p=0.017, PD p= 0.046, and Simpson p=0.017) as well as increases in Subdoligranulum (p=0.03) and Oscillospiraceae UCG 002 (p=0.02) and decreases in Bacteroides (p=0.009).There were no changes in microbial beta diversity and other biomarkers or markers of vascular function following the 16-week period Conclusion: Sixteen weeks of supplementation of resistant starch in patients with stage G3a-G4 CKD led to changes in microbial composition that were associated with a significant reduction in p-cresyl sulfate.

Distinct microbial communities supported by iron oxidation.

Microbial biostalactites and streamers commonly grow at iron seepages in abandoned mines worldwide. This study addresses the diversity and composition of these simple prokaryotic communities, which thrive in pH ranges from 2.4 to 6.6 across six different mines. Our analysis of 85 communities reveals that a pH of approximately 3.2 is a critical threshold where alpha and beta diversity change discretely. Below this pH, the average number of ASVs per sample is 2.91 times lower than above this boundary. Autotrophs, heterotrophs, and symbionts of eukaryotes originate from nearly non-overlapping species pools in the two habitat types that differ only in pH. Communities below pH 3.2 further divide into two distinct groups, differing in diversity, taxonomic, and functional composition. Both types of communities coexist within the same stalactites, likely corresponding to zones where the capillary structure of the stalactite is either perfused or clogged. These findings indicate that microbial community structure can be significantly influenced by the intricate spatial organization of the ecosystem, rather than solely by measurable environmental parameters.

Randomised control trial indicates micronutrient supplementation may support a more robust maternal microbiome for women with antenatal depression during pregnancy

Background and AimsWe investigated the effects of high dose dietary micronutrient supplementation or placebo on the human gut microbiome in pregnant women who had moderate symptoms of antenatal depression. There is a significant absence of well-controlled clinical studies that have investigated the dynamic changes of the microbiome during pregnancy and the relationship among diet, microbiome and antenatal depression. This research is among the first to provide an insight into this area of research. MethodsThis 12 - week study followed a standard double blinded randomised placebo-controlled trial (RCT) design with either high dose micronutrients or active placebo. Matching stool microbiome samples and mood data were obtained at baseline and post-treatment, from participants between 12 and 24 weeks gestation. Stool microbiome samples from 33 participants (17 in the placebo and 16 in the treatment group) were assessed using 16s rRNA sequencing. Data preparation and statistical analysis was predominantly performed using the QIIME2 bioinformatic software tools for 16s rRNA analysis. ResultsMicrobiome community structure became increasingly heterogenous with decreased diversity during the course of the study, which was represented by significant changes in alpha and beta diversity. This effect appeared to be mitigated by micronutrient administration. There were less substantial changes at the genus level, where Coprococcus decreased in relative abundance in response to micronutrient administration. We also observed that a higher abundance of Coprococcus and higher alpha diversity correlated with higher antenatal depression scores. ConclusionsMicronutrient treatment appeared to support a more diverse (alpha diversity) and stable (beta diversity) microbiome during pregnancy. This may aid in maintaining a more resilient or adaptable microbial community, which would help protect against decreases or fluctuations that are observed during pregnancy.

PSLBII-13 Bioinformatics of rumen fluid from steers fed alfalfa-bermudagrass mixtures in the Deep South

Abstract When harvesting high-quality, high-water content forages like legumes, there is often a greater percentage of nutritive loss due to the drying process. Alternative feeding strategies like baleage provide a way to mitigate these losses. However, there is not much adoption of baleage in the Deep South. Therefore, our objective was to assess the influence of conserved forage type on rumen metabolomes of beef cattle systems in the Deep South. Three treatments including bermudagrass (Cynodon dactylon) hay, alfalfa (Medicago sativa) baleage, and alfalfa-bermudagrass baleage were supplied to four fistulated steers with a calculated daily forage allowance based on intake, body weight, and feed refusals. Each diet was allocated to one of three periods in which all four animals received the same diet due to potential feed spoilage. Each period had a 21-d adaptation period followed by a 5-d collection period to analyze rumen fluid, total fecal weight, feed intake, feed refusal, and total urine. This study integrated 16S RNA sequencing and LC-MS-based metabolomics to evaluate rumen bacterial diversity and metabolome of beef steers. Sequencing data from the rumen fluid samples were then analyzed using QIIME2. Bermudagrass hay had a reduced alpha diversity compared with alfalfa baleage (Shannon: H = 5.19, P = 0.02). Additionally, we saw a change in beta diversity (P < 0.001), measured using the unweighted UniFrac distance, between conserved forage types and distinct clustering in the PCoA analysis. The most abundant taxa in all microbial communities were from the orders Lachnospirales, Bacteroidales, and Oscillospirales. Previous analysis in this study evidenced that baleage had an increased dry matter digestibility (DMD; P = 0.02). The increase in DMD was associated with the increase in diversity of the metabolome which could influence animal health and performance. Thus, baleage can serve as a beneficial conserved forage type that mitigates the losses of high-quality forages and diversifies the gut microbiome of ruminant animals.

Subtle changes in plant diversity in the Bavarian Alps over the past eight decades.

Historical resurveys represent a unique opportunity to analyze vegetation dynamics over longer timescales than is typically achievable. Leveraging the oldest historical dataset of vegetation change in the Bavarian Alps, Germany, we address how environmental conditions, vegetation composition, and functional diversity in the calcareous grasslands of the Schachen region have changed across different elevational ranges over an 83-year timeframe. We document changes in regional average temperature and precipitation. We use indicator values (IV) for species' ecological preferences and their palatability to grazers to infer local conditions (temperature, soil moisture/fertility, and grazing regime). We further estimate changes in temporal beta-diversity and functional trait community composition between historical (1936) and contemporary (2019) surveys in two elevational (subalpine and alpine) belts. Both subalpine and alpine sites became drier; subalpine sites also became warmer with more palatable plants. Species occurrence and abundance in the Schachen region has not changed substantially over time despite changing macroclimate and local environmental conditions under anthropogenic change. Yet these grasslands have experienced several "invisible" changes in functional composition over the past 80 years. As the Schachen has become drier, species with traits related to drought tolerance and animal-based dispersal have increased in dominance. Specifically, in alpine sites, community-weighted means revealed that with low fecundity, higher potential for endo- and epizoochory (seed dispersal via animal gut and fur, respectively), higher foliar frost tolerance, and deeper dormancy increased in dominance. Similar trends were found for increasing dominance of low fecundity, epizoochorous species in subalpine sites. Vegetation data from resurveying historical plots in combination with changes in local conditions, classic biodiversity indices, and functional trait indices can provide more holistic insights into changes in the environment and potential impacts of those environmental changes on long-term plant community and functional diversity.

Comparison of the Skin Microbiota in the Periocular Region between Patients with Inflammatory Skin Diseases and Healthy Participants: A Preliminary Study.

(1) Background: Periocular or periorbital dermatitis is a common term for all inflammatory skin diseases affecting the area of skin around the eyes. The clear etiopathogenesis of periocular dermatitis is still not fully understood. Advances in molecular techniques for studying microorganisms living in and on our bodies have highlighted the microbiome as a possible contributor to disease, as well as a promising diagnostic marker and target for innovative treatments. The aim of this study was to compare the composition and diversity of the skin microbiota in the periocular region between healthy individuals and individuals affected by the specific entity of periocular dermatitis. (2) Methods: A total of 35 patients with periocular dermatitis and 39 healthy controls were enrolled in the study. After a skin swab from the periocular region was taken from all participants, DNA extraction and 16S rRNA gene amplicon sequencing using Illumina NovaSeq technology were performed. (3) Results: Staphylococcus and Corynebacterium were the most abundant bacterial genera in the microbiota of healthy skin. Analysis of alpha diversity revealed a statistically significant change (p < 0.05) in biodiversity based on the Faith's PD index between patients and healthy individuals. We did not observe changes in beta diversity. The linear discriminant analysis effect size (LEfSe) revealed that Rothia, Corynebacterium, Bartonella, and Paracoccus were enriched in patients, and Anaerococcus, Bacteroides, Porphyromonas, and Enhydrobacter were enriched in healthy controls. (4) Conclusions: According to the results obtained, we assume that the observed changes in the bacterial microbiota on the skin, particularly Gram-positive anaerobic cocci and skin commensals of the genus Corynebacterium, could be one of the factors in the pathogenesis of the investigated inflammatory diseases. The identified differences in the microbiota between healthy individuals and patients with periocular dermatitis should be further investigated.

Supralittoral isopod (Oniscidea) diversity at three ecoregions along the Colombian Caribbean: useful data for environmental management

Introduction: Terrestrial isopods (Oniscidea) play important roles in the ecological processes of the soil in tropical ecosystems and are employed as indicators of environmental impact. Despite their importance, studies on the ecology of this suborder in the Neotropics are scarce. Objective: To assess spatial changes in alpha and beta diversity of Oniscidea in the supralittoral zone across Archipiélagos Coralinos (ARCO), Magdalena (MAG), and Morrosquillo (MOR) ecoregions in the Colombian Caribbean. Methods: We conducted Direct Intuitive Searches of specimens and measured soil temperature and moisture in 19 transects with logs, leaf litter, coral remains, and decomposing plant material. Results: A total of 1 970 individuals representing 17 species were collected, with Tylidae, Halophilosciidae, and Ligiidae being the most abundant families. Alpha diversity orders were higher in ARCO than MAG and MOR ecoregions. MAG and MOR differed in observed richness. The structure of the assemblage varied in dominant species and abundances. In ARCO, the indicator species were Tylos niveus, Littorophiloscia denticulata, Halophiloscia trichoniscoides, and Ligia baudiniana; in MOR, it was Tylos marcuzzii, and in MAG, it was Littorophiloscia tropicalis. High beta diversity (&gt; 60 %), with significant differences in the assemblage structure among ecoregions, was confirmed by the NMDS, which distinctly separated each group. CCA analysis revealed a negative relationship between most species with soil temperature and moisture, with a positive relationship observed with T. marcuzzii. Conclusions: This is the first effort to describe spatial changes in the diversity of oniscideans in the supralittoral zone of the Neotropical region, providing a baseline for future studies. This information could be instrumental in identifying priority areas for conservation efforts.

Unravelling the complexities of biotic homogenization and heterogenization in the British avifauna.

Biotic homogenization is a process whereby species assemblages become more similar through time. The standard way of identifying the process of biotic homogenization is to look for decreases in spatial beta-diversity. However, using a single assemblage-level metric to assess homogenization can mask important changes in the occupancy patterns of individual species. Here, we analysed changes in the spatial beta-diversity patterns (i.e. biotic heterogenization or homogenization) of British bird assemblages within 30 km × 30 km regions between two periods (1988-1991 and 2008-2011). We partitioned the change in spatial beta-diversity into extirpation and colonization-resultant change (i.e. change in spatial beta-diversity within each region resulting from both extirpation and colonization). We used measures of abiotic change in combination with Bayesian modelling to disentangle the drivers of biotic heterogenization and homogenization. We detected both heterogenization and homogenization across the two time periods and three measures of diversity (taxonomic, phylogenetic, and functional). In addition, both extirpation and colonization contributed to the observed changes, with heterogenization mainly driven by extirpation and homogenization by colonization. These assemblage-level changes were primarily due to shifting occupancy patterns of generalist species. Compared to habitat generalists, habitat specialists had significantly (i) higher average contributions to colonization-resultant change (indicating heterogenization within a region due to colonization) and (ii) lower average contributions to extirpation-resultant change (indicating homogenization from extirpation). Generalists showed the opposite pattern. Increased extirpation-resultant homogenization within regions was associated with increased urban land cover and decreased habitat diversity, precipitation, and temperature. Changes in extirpation-resultant heterogenization and colonization-resultant heterogenization were associated with differences in elevation between regions and changes in temperature and land cover. Many of the 'winners' (i.e. species that increased in occupancy) were species that had benefitted from conservation action (e.g. buzzard (Buteo buteo)). The 'losers' (i.e. those that decreased in occupancy) consisted primarily of previously common species, such as cuckoo (Cuculus canorus). Our results show that focusing purely on changes in spatial beta-diversity over time may obscure important information about how changes in the occupancy patterns of individual species contribute to homogenization and heterogenization.

Strong Saharan Dust Deposition Events Alter Microbial Diversity and Composition in Sediments of High-Mountain Lakes of Sierra Nevada (Spain)

Mediterranean high-mountain lakes are being increasingly affected by strong Saharan dust deposition events. However, the ecological impacts of these severe atmospheric episodes remain largely unknown. We examined the effects of a strong Saharan dust intrusion to the Iberian Peninsula in 2022 on the physicochemical parameters and prokaryotic communities in sediments of nine high-mountain lakes of Sierra Nevada (Spain) located above 2800 m.a.s.l and in different orientations (north vs. south). A previous year (2021), with lower Saharan dust deposition with respect to 2022, was used for interannual comparisons. The strong dust deposition to the high-mountain lakes resulted in a significant increase in sediment nutrient availability which was linked to changes in the composition of prokaryotic communities. Decreases in alpha diversity and changes in beta diversity of prokaryotic communities were mainly observed in lakes located in the south compared to the north orientation likely because the former was more affected by the atmospheric dust deposition episode. Dust intrusion to the high-mountain lakes resulted in significant changes in the relative abundance of specific genera involved in important nutrient cycling processes such as phosphate solubilization, nitrogen fixation, nitrification, and denitrification. Saharan dust deposition also increased predicted microbial functionality in all lakes. Our findings show that severe atmospheric dust inputs to remote high-mountain lakes of Sierra Nevada can have significant biogeochemical and biodiversity consequences through changes in nutrient availability and prokaryotic communities in sediments of these freshwater ecosystems. This information contributes to understanding how Mediterranean high-mountain lakes of Sierra Nevada face strong intrusions of Saharan dust and their ecological consequences.

The Brominated Flame Retardant Hexabromocyclododecane Causes Systemic Changes in Polyunsaturated Fatty Acid Incorporation in Mouse Lipids.

Brominated flame retardants are used in many household products to reduce flammability, but often leach into the surrounding environment over time. Hexabromocyclododecane (HBCD) is one brominated flame retardant detected in human blood across the world. HBCD exposure can result in neurological problems and altered lipid metabolism, but to date the two remain unlinked. As lipids constitute ∼50% of brain dry weight, lipid metabolism plays a critical role in neuronal function and homeostasis. To determine the effect of HBCD exposure on brain lipid metabolism, young adult male C57BL/6 mice were exposed to 1 mg/kg HBCD every 3 days for 28 days. Major lipid classes were found to change across brain regions, including the membrane glycerolipids phosphatidylcholine and phosphatidylethanolamine, and sphingolipids such as hexosylceramide. In addition, saturated, monounsaturated, and polyunsaturated fatty acids were enriched within brain lipid species. To understand the source of the brain lipidomic alterations, the blood and liver lipidomes and the cecal microbiome were evaluated. The liver and blood demonstrated changes amongst multiple lipid classes, including triacylglycerol suppression, as well as altered esterified fatty acid content. Significant alterations were also detected in the cecal microbiome, with decreases in the Firmicutes to Bacteriodetes ratio, changes in beta diversity, and pathway alterations associated with metabolic pathways and amino acid biosynthesis. These data demonstrate that HBCD can induce lipidomic alterations across brain regions and organs and supports a potential role of the microbiome in these alterations.

Effects of dietary zinc on the gut microbiome and resistome of the gestating cow and neonatal calf

Zinc is an essential trace element required in the diet of all species. While the effects of zinc have been studied in growing calves, little is known about the effect of zinc on the microbiota of the gestating cow or her neonatal calf. Understanding factors that shape the gut health of neonatal animals and evaluating the effect of dietary supplements in adult gestating animals is important in promoting animal health and informing feeding practices. The aims of this study were to determine the effect of dietary zinc on the microbiota and resistome of the gestating cow and calf. Gestating cows received standard (40 ppm) or high (205 ppm) dietary zinc levels from dry off to calving. Fecal samples were collected from cows upon enrollment and at calving and from neonatal calves. Fecal samples underwent 16S rRNA sequencing and a subset also underwent shotgun metagenomic sequencing. The effect of zinc supplementation on the diversity and composition of the cow and calf microbiome and resistome was assessed. Alpha and beta diversity and composition of the microbiota were significantly altered over time but not by treatment in the cows, with alpha diversity decreasing and 14 genera found at significantly higher relative abundances at calving compared to enrollment. Levels of 27 antimicrobial resistance genes significantly increased over time. Only a small number of taxa were differentially expressed at calving in treatment and control groups, including Faecalibacterium, Bacteroides, Turicibacter, and Bifidobacterium pseudolongum. No effect of the dam’s treatment group was observed on the diversity or composition of the neonatal calf microbiota. The calf resistome, which was relatively rich and diverse compared to the cow, was also unaffected by the dam’s treatment group. The impact of high levels of dietary zinc thus appeared to be minimal, with no observed changes in alpha or beta diversity, and few changes in the relative abundance of a small number of taxa and antimicrobial resistance genes.

Forest type modulates mammalian responses to megafires

Although considered an evolutionary force responsible for shaping ecosystems and biodiversity, fires’ natural cycle is being altered by human activities, increasing the odds of destructive megafire events. Here, we show that forest type modulates the responses of terrestrial mammals, from species to assemblage level, to a catastrophic megafire in the Brazilian Pantanal. We unraveled that mammalian richness was higher 1 year after fire passage compared to a pre-fire condition, which can be attributed to habitat modification caused by wildfires, attracting herbivores and open-area tolerant species. We observed changes in assemblage composition between burned/unburned sites, but no difference in mammalian richness or relative abundance. However, by partitioning the effects of burned area proportion per forest type (monospecific vs. polyspecific), we detected differential responses of mammals at several levels of organization, with pronounced declines in species richness and relative abundance in monospecific forests. Eighty-six percent of the species presented moderate to strong negative effects on their relative abundance, with an overall strong negative effect for the entire assemblage. Wildfires are predicted to be more frequent with climate and land use change, and if events analogous to Pantanal-2020 become recurrent, they might trigger regional beta diversity change, benefitting open-area tolerant species.

Amplicon-based metagenomics to study the effect of coir age and wood biochar on microbiome in relation to strawberry yield

In the UK, strawberry is mostly grown in coconut coir substrate under protection. Coir substrate is usually used only for one or two cropping seasons because the continuous reuse of coir without any treatment leads to yield decline. In this study, we investigated the changes in bacterial and fungal communities in strawberry roots and bulk coir in relation to (i) the coir substrate age (cropping seasons) and (ii) oak or beech biochar amendment at planting. Coir age did not affect fungal/bacterial alpha (within-sample) diversity but affected beta (between-sample) diversity. Amendment with either oak or beech biochar did not lead to significant changes in either alpha or beta diversity for both fungi and bacteria, but it did alter the relative abundance of 13 fungal ASVs. This study identified six bacterial and 20 fungal ASVs with a significant positive linear relationship with coir age and also eight bacterial and 22 fungal ASVs with a significant negative linear relationship with coir age. Notably, the observed strawberry yield decline in reused coir substrate could be associated with a generalist root pathogen, Ilyonectria destructans (ex. Cylindrocarpon destructans), of which the abundance increased annually by 225% and 426% in strawberry root and bulk coir, respectively. Future research is needed to confirm the role of I. destructans in reused coir on strawberry plant health and fruit productivity and then to identify management strategies for yield decline mitigation.

Assessing the potential of nematode metabarcoding for benthic monitoring of offshore oil platforms

Environmental DNA metabarcoding is gaining momentum as a time and cost-effective tool for biomonitoring and environmental impact assessment. Yet, its use as a replacement for the conventional marine benthic monitoring based on morphological analysis of macrofauna is still challenging. Here we propose to study the meiofauna, which is much better represented in sediment DNA samples. We focus on nematodes, which are the most numerous and diverse group of meiofauna. Our aim is to assess the potential of nematode metabarcoding to monitor impacts associated with offshore oil platform activities. To achieve this goal, we used nematode-optimized marker (18S V1V2-Nema) and universal eukaryotic marker (18S V9) region to analyse 252 sediment DNA samples collected near three offshore oil platforms in the North Sea. For both markers, we analysed changes in alpha and beta diversity in relation to distance from the platforms and environmental variables. We also defined three impact classes based on selected environmental variables that are associated with oil extraction activities and used random forest classifiers to compare the predictive performance of both datasets. Our results show that alpha- and beta-diversity of nematodes varies with the increasing distance from the platforms. The variables directly related to platform activity, such as Ba and THC, strongly influence the nematode community. The nematode metabarcoding data provide more robust predictive models than eukaryotic data. Furthermore, the nematode community appears more stable in time and space, as illustrated by the overlap of nematode datasets obtained from the same platform three years apart. A significative negative correlation between distance and Shannon diversity also advocates for higher performance of the V1V2-Nema over the V9. Overall, these results suggest that the sensitivity of nematodes is higher compared to the eukaryotic community. Hence, nematode metabarcoding has the potential to become an effective tool for benthic monitoring in marine environment.