Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities

Exploring fecal microbial activity in zoo felids of varying body mass on a similar diet

Under human care, felids are typically fed similar diets, unlike wild counterparts whose diets vary by body mass and ecology. This study evaluated fecal microbiota and fermentation products in 18 zoo felids from Pairi Daiza Zoo, Belgium, grouped by body mass: under 100 kg ("small") and over 100 kg ("large"), with 9 animals in each group. Fresh feces were collected from the rectum under anesthesia. Microbial composition was assessed via 16S rRNA gene sequencing, while the fecal volatile fatty acids were quantified using gas chromatography. At the phylum level, regardless of body mass, the gut microbiota of zoo felids was predominantly composed of Firmicutes (61.7%), Actinobacteria (16.4%) and Bacteroidetes (12.5%). At the genus level, the most abundant genus was Clostridium sensu stricto 1 (15.9%), followed by Collinsella (15.7%). Although no significant differences in microbial composition or alpha diversity were found, beta diversity showed body mass influenced overall microbial structure. Smaller felids had significantly higher acetate levels than larger felids (p < 0.01). Additionally, acetate proportions were positively correlated with Clostridium sensu stricto 13 (r = 0.6, p < 0.01) and Peptoniphilus (r = 0.5, p < 0.05). These results show particular associations between body mass and the response of the intestinal microbiome to diet, suggesting that a uniform diet may not suit all felids under human care.

Characterizing biofilm thickness, density, and microbial community composition in a full-scale hybrid membrane aerated biofilm reactor

This study examined biofilm thickness, density, and microbial composition in a full-scale MABR treating municipal wastewater, focusing on their spatial and operational variability. The MABR cassette arrangement created a thickness gradient, with biofilms in the front cassettes more than twice as thick as those at the back. Lower scouring intensity due to reduced airflow resulted in thicker biofilms. Microbial communities varied longitudinally and by operational phase, with thicker biofilms having a higher relative abundance of anaerobic microorganisms, such as fermenters and sulfur reducers, and fewer aerobic nitrifiers. Nitrosomonas were the main ammonia oxidizers, while Nitrospira and Ca. Nitrotoga dominated as nitrite oxidizers. The 16S RNA gene profiles showed strong correlations with biofilm thickness (R2 = 0.8) and nitrification rates (R2 = 0.4). Full-scale MABR biofilm characteristics have not been studied before. Study findings have practical implications for better modeling practices and improved design of future MABR facilities.

Contrasting alpha, beta, and gamma diversity in the littoral zones of mountain lakes: effects of habitat size and within-lake community structuring on bacterial biogeography

Research on microbial biogeography has revealed key patterns like the diversity-area relationship and distance-decay of similarity. However, how habitat size affects bacterial diversity in freshwater environments remains largely unclear. Here, we characterize bacterial communities in the littoral zones of 10 mountain lakes in the Sierra Nevada, CA, ranging in surface area from 0.92 to 71.72 ha. Despite significant habitat size effects on community composition, dominant bacterial phyla were shared across lakes. We found no evidence for diversity-area relationships, either in single samples (alpha diversity) or cumulative lake-level samples (within-lake gamma diversity), when accounting for environmental variation. Moreover, within-lake beta diversity showed little spatial structuring, with similar bacterial community composition across samples regardless of geographic distance. Gamma diversity did not reach saturation with our sample size, and lake size had no effect on the predicted sample size necessary to reach gamma diversity saturation. Our findings offer new insights into diversity-area dynamics and spatial structuring by investigating alpha, beta, and gamma diversity in freshwater environments. Notably, individual water samples captured much of the bacterial community, with strong correlations between alpha and gamma diversity. These results advance our understanding of microbial biogeography and inform sampling designs for characterizing bacterial diversity in freshwater ecosystems.

Eukaryotic biodiversity of sub-ice water in the marginal ice zone of the European Arctic: A multi-marker eDNA metabarcoding survey

The effects of climate change, including warming waters, loss of sea ice habitat and the resulting changes in primary production, are inducing shifts in marine communities across the Arctic Ocean. The Arctic marginal ice zone (MIZ) is a highly dynamic ecosystem and is a transition zone between pack ice and the open ocean. It is habitat for a wide range of organisms, including sympagic and pelagic taxa, all of which are affected by the changing physical dynamics of the MIZ. Here we use a multi-marker (18S rRNA V1-2 and COI Leray-XT) approach to investigate eukaryotic biodiversity of the upper water column in this understudied habitat. Environmental DNA (eDNA) was sequenced from seawater samples collected directly beneath the sea ice and at a depth of 5 m, sourced from ice floes representing different ice regimes. To explore the abiotic factors influencing under-ice diversity, we combined satellite-derived environmental data with simultaneous in situ hydrographic measurements. Our analysis identified a range of sympagic and pelagic metazoans, along with primary producers typical of the region, as well as substantial uncharacterised diversity. Alpha diversity indices were higher immediately below the ice, and community composition differed across depths and ice floe stations. We show that the properties of the meltwater stratification in the upper ocean, along with sea ice concentration and distance to the ice edge, significantly shape eukaryotic diversity and community composition. These findings highlight the effectiveness of eDNA metabarcoding for monitoring sub-ice communities and enhance our understanding of eukaryotic biodiversity in the MIZ.

Enhancing Emotional Intelligence in Autism Spectrum Disorder Through Intervention: A Systematic Review

Limitations in some emotional characteristics that are conceptualized in the definition of emotional intelligence can be seen among people with autism spectrum disorder. The main objective of this study is the analysis of the effectiveness of interventions directed to enhance emotional recognition and emotional regulation among this specific population. A systematic review was carried out in databases such as Psycinfo, WoS, SCOPUS, and PubMed, identifying a total of 572 articles, of which 29 met the inclusion criteria. The total sample included 1061 participants, mainly children aged between 4 and 13 years. The analyzed interventions focused on improving emotional recognition, with significant results in the identification of emotions such as happiness, sadness, and anger, although some showed limitations in the duration of these effects. The most used programs included training in facial recognition, virtual reality, and the use of new technologies such as robots. These showed improvements in both emotional recognition and social skills. Other types of interventions such as music therapy or the use of drama techniques were also implemented. However, a gender bias and lack of consistency between results from different cultures were observed. The conclusions indicate that, although the interventions reviewed seem effective, more research is needed to maximize their impact on the ASD population.

More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian

With amphibians still holding the record as the most threatened class of terrestrial vertebrates, their skin microbiota has been shown to play a relevant role in their survival in a fast-changing world. Yet little is known about how abiotic factors associated with different aquatic habitats impact these skin microorganisms. Here we chose the yellow-bellied toad (Bombina variegata), a small anuran that colonizes a wide range of wetland habitats, to investigate how the diversity and composition of both its bacterial and fungal skin communities vary across different habitats and with water characteristics (temperature, pH, and dissolved oxygen) of these habitats. Skin microbiota was sampled from 14 sites in the Province of Trento (Italy), including natural pools, ephemeral ponds, irrigation tanks, and farm ponds. Interestingly, the diversity of the two microbial components was also highly correlated. Close associations between both the diversity and composition of water and skin communities were noted for each habitat and sampling site, suggesting that water bodies actively contribute to the skin microbiota assemblage. In addition, water pH, temperature, and dissolved oxygen affected both bacterial and fungal diversity of skin. We confirmed the presence of Batrachochytrium dendrobatidis in skin samples of animals collected from eight waterbodies, as well as more than 60 microbial taxa previously associated with resistance to this pathogen. We concluded that both skin bacterial and fungal communities appear to be influenced by each other as well as by environmental communities and conditions, and these relationships connecting the whole ecosystem should be considered in future research concerning amphibian conservation.

Impacts of host phylogeny, diet, and geography on the gut microbiome of rodents

Mammalian gut microbial communities are thought to play a variety of important roles in health and fitness, including digestion, metabolism, nutrition, immune response, behavior, and pathogen protection. Gut microbiota diversity among hosts is strongly shaped by diet as well as phylogenetic relationships among hosts. Although various host factors may influence microbial community structure, the relative contribution may vary depending on several variables, such as taxonomic scales of the species studied, dietary patterns, geographic location, and gut physiology. The present study focused on 12 species of rodents representing 3 rodent families and 3 dietary guilds (herbivores, granivores, and omnivores) to evaluate the influence of host phylogeny, dietary guild and geography on microbial diversity and community composition. Colon samples were examined from rodents that were collected from 7 different localities in Texas and Oklahoma which were characterized using 16S rRNA gene amplicon sequencing targeting the V1-V3 variable regions. The microbiota of colon samples was largely dominated by the family Porphyromonadaceae (Parabacteriodes, Coprobacter) and herbivorous hosts harbored richer gut microbial communities than granivores and omnivores. Differential abundance analysis showed significant trends in the abundance of several bacterial families when comparing herbivores and granivores to omnivores, however, there were no significant differences observed between herbivores and granivores. The gut microbiotas displayed patterns consistent with phylosymbiosis as host phylogeny explained more variation in gut microbiotas (34%) than host dietary guilds (10%), and geography (3%). Overall, results indicate that among this rodent assemblage, evolutionary relatedness is the major determinant of microbiome compositional variation, but diet and to a lesser extent geographic provenance are also influential.

Trees shape the soil microbiome of a temperate agrosilvopastoral and syntropic agroforestry system

Agroforestry systems are multifunctional land-use systems that promote soil life. Despite their large potential spatio-temporal complexity, the majority of studies that investigated soil organisms in temperate cropland agroforestry systems focused on rather non-complex systems. Here, we investigated the topsoil and subsoil microbiome of two complex and innovative alley cropping systems: an agrosilvopastoral system combining poplar trees, crops, and livestock and a syntropic agroforestry system combining 35 tree and shrub species with forage crops. Increasing soil depth resulted in a decline of bacterial and fungal richness and a community shift towards oligotrophic taxa in both agroforestry systems, which we attribute to resource-deprived conditions in subsoil. At each soil depth, the microbiome of the tree rows was compositionally distinct from the crop rows. We detected a shift towards beneficial microorganisms as well as a decline in putative phytopathogens under the trees as compared to the crop rows. Finally, based on our results on community dissimilarity, we found that compared to an open cropland without trees, spatial heterogeneity introduced by the tree rows in the agrosilvopastoral system translated into a compositionally less homogeneous soil microbiome, highlighting the potential of agroforestry to counteract the homogenization of the soil microbiome through agriculture.

Impact of Ketogenic and Mediterranean Diets on Gut Microbiota Profile and Clinical Outcomes in Drug-Naïve Patients with Diabesity: A 12-Month Pilot Study

Background/Objectives: Managing type 2 diabetes mellitus (T2DM) and obesity requires a multidimensional, patient-centered approach including nutritional interventions (NIs) and physical activity. Changes in the gut microbiota (GM) have been linked to obesity and the metabolic alterations typical of T2DM and obesity, and they are strongly influenced by diet. However, few studies have evaluated the effects on the GM of a very-low-calorie ketogenic diet (VLCKD) in patients with T2DM, especially in the mid-term and long-term. This longitudinal study is aimed at evaluating the mid-term and long-term impact of the VLCKD and Mediterranean diet (MD) on the GM and on the anthropometric, metabolic, and lifestyle parameters of 11 patients with T2DM and obesity (diabesity). This study extends previously published results evaluating the short-term (three months) impact of these NIs on the same patients. Methods: At baseline, patients were randomly assigned to either a VLCKD (KETO group) or a Mediterranean diet (MEDI group). After two months, the KETO group gradually shifted to a Mediterranean diet (VLCKD-MD), according to current VLCKD guidelines. From the fourth month until the end of the study both groups followed a similar MD. Previous published results showed that VLCKD had a more beneficial impact than MD on several variables for 3 months of NI. In this study, the analyses were extended until six (T6) and twelve months (T12) of NI by comparing data prospectively and against baseline (T0). The GM analysis was performed through next-generation sequencing. Results: Improvements in anthropometric and metabolic parameters were more pronounced in the KETO group at T6, particularly for body mass index (-5.8 vs. -1.7 kg/m2; p = 0.006) and waist circumference (-15.9 vs. -5.2 cm; p = 0.011). At T6, a significant improvement in HbA1c (6.7% vs. 5.5% p = 0.02) and triglyceride (158 vs. 95 mg/dL p = 0.04) values compared to T0 was observed only in the KETO group, which maintained the results achieved at T3. The VLCKD-MD had a more beneficial impact than the MD on the GM phenotype. A substantial positive modulatory effect was observed especially up to the sixth month of the NI in KETO due to the progressive increase in bacterial markers of human health. After the sixth month, most markers of human health decreased, though they were still increased compared with baseline. Among them, the Verrucomicrobiota phylum was identified as the main biomarker in the KETO group, together with its members Verrucomicrobiae, Akkermansiaceae, Verrucomicrobiales, and Akkermansia at T6 compared with baseline. Conclusions: Both dietary approaches ameliorated health status, but VLCKD, in support of the MD, has shown greater improvements on anthropometric and metabolic parameters, as well as on GM profile, especially up to T6 of NI.

Comparative Analysis of Protist Communities in Oilsands Tailings Using Amplicon Sequencing and Metagenomics

The Canadian province of Alberta contains substantial oilsands reservoirs, consisting of bitumen, clay and sand. Extracting oil involves separating bitumen from inorganic particles using hot water and chemical diluents, resulting in liquid tailings waste with ecotoxicologically significant compounds. Ongoing efforts aim to reclaim tailings-affected areas, with protist colonisation serving as one assessment method of reclamation progress. Oilsands-associated protist communities have mainly been evaluated using amplicon sequencing of the 18S rRNA V4 region; however, this barcode may overlook important protist groups. This study examined how community assessment methods between the V4 and V9 regions differ in representing protist diversity across four oilsands-associated environments. The V9 barcode identified more operational taxonomical units (OTUs) for Discoba, Metamonada and Amoebozoa compared with the V4. A comparative shotgun metagenomics approach revealed few eukaryotic contigs but did recover a complete Paramicrosporidia mitochondrial genome, only the second publicly available from microsporidians. Both V4 and V9 markers were informative for assessing community diversity in oilsands-associated environments and are most effective when combined for a comprehensive taxonomic estimate, particularly in anoxic environments.

Microbial diversity and community structure of microalgae (Nannochloropsis oculata) and rotifer (Brachionus plicatilis) in aquaculture by 16S rRNA amplicon-based sequencing

Live cultures, including Nannochloropsis oculata and Brachionus plicatilis, are essential in aquaculture due to its economic and nutritional value for commercial fish species. Pathogens and probiotics can be introduced to aquaculture systems by live feed, with variations in abundance influenced by environmental physicochemical parameters. To investigate this, amplicon sequencing of the V3-V4 region of the 16S rRNA was conducted using Illumina MiSeq to elucidate bacterial abundances and their variations in response to changes in physicochemical parameters in live feed cultures. Results revealed that pathogens like, Tenacibaculum, predominantly found in rotifer cultures, was inhibited under dissolved oxygen levels of 6.87-8.19 mg/L and pH levels of 8.63-9.23. Winogradskyella, mainly present on day 1 of the microalgae culture, thrived under these same conditions. Potential probiotics were also analyzed. Phaeodactylibacter, primarily found on day 1 of microalgae cultures, was favored by dissolved oxygen levels of 7.11-7.68 mg/L and pH levels of 8.63-9.23 but was inhibited by nitrite levels of 0.46-0.5 mg/L. Overall, dissolved oxygen was the key parameter modulating microbial diversity. This study shows that optimizing environmental parameters can enhance culture health by promoting probiotics and reducing harmful bacteria.

Geographic variation and core microbiota composition of Anastrepha ludens (Diptera: Tephritidae) infesting a single host across latitudinal and altitudinal gradients

Anastrepha ludens is a pestiferous tephritid fly species exhibiting extreme polyphagy. It develops optimally in hosts rich in sugar but low nitrogen content. We studied the geographical influence on the composition of A. ludens's larval and newly emerged adult gut microbiota in altitudinal (0-2,000 masl) and latitudinal (ca. 800 km from 17° to 22°N latitude) transects along the coastline of the state of Veracruz, Mexico. In the 16 collection sites, we only collected Citrus x aurantium fruit (238 samples of A. ludens larvae and adults, plus 73 samples of pulp) to control for host effect, hypothesizing that there exists a conserved core microbiota that would be dominated by nitrogen-fixing bacteria. We found that latitude triggered more significant changes in the gut microbiota than altitude. Northern and southernmost samples differed the most in microbiota composition, with a trade-off between Acetobacteraceae and Rhizobiaceae driving these differences. As hypothesized, the core microbiota in each sampling site, contained the functional group of nitrogen-fixing bacteria. We conclude that A. ludens larvae can acquire multiple diazotrophic symbionts along its wide distribution range where it infests fruit with a high C:N ratio in the pulp.

Asynchronous patterns in soil bacterial diversity and functional potentials along an alpine altitudinal gradient

Introduction

Altitudinal changes in soil bacterial diversity, composition, biotic interactions, and function are prevalent. However, the overall patterns and associations among these dimensions remain unclear, particularly in vulnerable alpine mountain ecosystems.

Methods

Here, we investigated soil bacterial communities along a high-altitude gradient to elucidate patterns and associations in taxonomic and phylogenetic diversity, co-occurrence networks, and functional potentials.

Results

We observed increasing altitudinal trends in bacterial richness and phylogenetic diversity, along with significant differences in taxonomic and phylogenetic composition across altitudes. The connectivity component of the co-occurrence network properties showed a negative association with altitude. We also observed high redundancy in functional potentials, resulting in insignificant variation in functional diversity along the altitudinal gradient. However, the strength of functional diversity varied based on the interaction between network connectivity and phylogenetic diversity. Additionally, functional dissimilarity was more closely associated with phylogenetic rather than taxonomic dissimilarity or differences in network properties, highlighting the role of phylogenetic lineages in functional redundancy.

Discussion

This study characterizes the altitudinal distribution of soil bacteria and explores their covariations, enhancing our understanding of soil bacterial diversity and functional potentials along altitudinal gradients and providing valuable insights for predicting community changes and improving alpine ecosystem conservation.

Associations Between Gut Microbiota Diversity and a Host Fitness Proxy in a Naturalistic Experiment Using Threespine Stickleback Fish

The vertebrate gut microbiota is a critical determinant of organismal function, yet whether and how gut microbial communities affect host fitness under natural conditions remains largely unclear. We characterised associations between a fitness proxy-individual growth rate-and bacterial gut microbiota diversity and composition in threespine stickleback fish introduced to large semi-natural ponds. We detected a 63% higher richness of bacterial taxa (α-diversity) in the guts of high-fitness fish compared to low-fitness fish, which might be driven by stronger bacterial dispersal among high-fitness fish according to the fit of a neutral community model. Further, microbial communities of high-fitness fish were more similar to one another (i.e., exhibited lower β-diversity) than those of low-fitness fish. The lower β-diversity found to be associated with higher host fitness is consistent with the Anna Karenina principle-that there are fewer ways to have a functional microbiota than a dysfunctional microbiota. Our study links differences in α- and β-diversity to a fitness-related trait in a vertebrate species reared under naturalistic conditions and our findings provide a basis for functional tests of the fitness consequences of host-microbiota interactions.

Biodegradation of poly(butylene adipate terephthalate) and poly(vinyl alcohol) within aquatic pathway

Understanding the environmental fate of biodegradable plastics in aquatic systems is crucial, given the alarming amount of plastic waste and microplastic particles transported through aquatic pathways. In particular, there is a need to analyze the biodegradation of commercialized biodegradable plastics upon release from wastewater treatment plants into natural aquatic systems. This study investigates the biodegradation behaviors of poly(butylene adipate terephthalate) (PBAT) and poly(vinyl alcohol) (PVA) in wastewater, freshwater, and seawater. Biodegradation of PBAT and PVA assessed through biochemical oxygen demand (BOD) experiments and microcosm tests revealed that the type of aquatic system governs the biodegradation behaviors of each plastic, with the highest biodegradation rate achieved in wastewater for both PBAT and PVA (25.6 and 32.2 % in 30 d, respectively). Plastic release pathway from wastewater into other aquatic systems simulated by sequential incubation in different microcosms suggested that PBAT exposed to wastewater and freshwater before reaching seawater was more prone to degradation than when directly exposed to seawater. On the other hand, PVA displayed comparable biodegradation rate regardless of whether it was directly exposed to seawater or had passed through other environments beforehand. Metagenome amplicon sequencing of 16S rRNA genes revealed distinct community shifts dependent on the type of plastics in changing environments along the simulated aquatic pathway. Several bacterial species putatively implicated in the biodegradation of PBAT and PVA are discussed. Our findings underscore the significant influence of pollution routes on the biodegradation of PBAT and PVA, highlighting the potential for wastewater treatment to facilitate rapid degradation compared to direct exposure to pristine aquatic environments.

In-hospital areas with distinct maintenance and staff/patient traffic have specific microbiome profiles, functions, and resistomes

Hospitals are subject to strict microbial control. Stringent cleaning and confinement measures in hospitals lead to a decrease in microbial diversity, but an increase in resistance genes. Given the rise of antimicrobial resistances and healthcare-associated infections, understanding the hospital microbiome and its resistome is crucial. This study compared the microbiome and resistome at different levels of confinement (CL) within a single hospital. Using amplicon sequencing, shotgun metagenomics, and genome/plasmid reconstruction, we demonstrate that microbial composition differs in a stable way between the CLs and that the most restrictive confinement level CL1 had the lowest microbial but the highest functional diversity. This CL also exhibited a greater abundance of functions related to virulence, disease, defense, and stress response. Comparison of antibiotic resistance also showed differences among CLs in terms of the selection process and specific mechanisms for antimicrobial/antibiotic resistance. The resistances found in the samples of CL1 were mostly mediated via antibiotic efflux pumps and were mainly located on chromosomes, whereas in the other, less restrictive CL antibiotic resistances were more present on plasmids. This could be of particular importance for patient-related areas (CL2), as the potential spread of antibiotic resistances could be a major concern in this area. Our results show that there are differences in the microbiome and resistome even within a single hospital, reflecting room utilization and confinement. Since restrictive confinement selects for resistant microorganisms, strategies are required to deepen our understanding of dynamic processes of microbiome and resistome within hospital environments.

IMPORTANCE

Effective measures to combat antibiotic resistances and healthcare-associated infections are urgently needed, including optimization of microbial control. However, previous studies have indicated that stringent control can lead to an increase in the resistance capacities of microbiomes on surfaces. This study adds to previous knowledge by focusing on the conditions in a single hospital, resolving the microbiomes and their resistomes in three different confinement levels (CL): operating room, patient-related areas, and non-patient-related areas. We were able to identify stable key taxa; profiled the capacities of taxa, functions, and antimicrobial resistances (AMR); and reconstruct genomes and plasmids in each CL. Our results show that the most restrictive CL indeed had the highest functional diversity, but that resistances were mostly encoded on chromosomes, indicating a lower possibility of resistance spread. However, clever strategies are still required to strike a balance between microbial control and selective pressures in environments where patients need protection.

Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning

Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.

Climate change induces shifts in coastal Baltic Sea surface water microorganism stress and photosynthesis gene expression

The world's oceans are challenged by climate change linked warming with typically highly populated coastal areas being particularly susceptible to these effects. Many studies of climate change on the marine environment use large, short-term temperature manipulations that neglect factors such as long-term adaptation and seasonal cycles. In this study, a Baltic Sea 'heated' bay influenced by thermal discharge since the 1970s from a nuclear reactor (in relation to an unaffected nearby 'control' bay) was used to investigate how elevated temperature impacts surface water microbial communities and activities. 16S rRNA gene amplicon based microbial diversity and population structure showed no difference in alpha diversity in surface water microbial communities, while the beta diversity showed a dissimilarity between the bays. Amplicon sequencing variant relative abundances between the bays showed statistically higher values for, e.g., Ilumatobacteraceae and Burkholderiaceae in the heated and control bays, respectively. RNA transcript-derived activities followed a similar pattern in alpha and beta diversity with no effect on Shannon's H diversity but a significant difference in the beta diversity between the bays. The RNA data further showed more elevated transcript counts assigned to stress related genes in the heated bay that included heat shock protein genes dnaKJ, the co-chaperonin groS, and the nucleotide exchange factor heat shock protein grpE. The RNA data also showed elevated oxidative phosphorylation transcripts in the heated (e.g., atpHG) compared to control (e.g., atpAEFB) bay. Furthermore, genes related to photosynthesis had generally higher transcript numbers in the control bay, such as photosystem I (psaAC) and II genes (psbABCEH). These increased stress gene responses in the heated bay will likely have additional cascading effects on marine carbon cycling and ecosystem services.

Local environment shapes milk microbiomes while evolutionary history constrains milk macronutrients in captive cercopithecine primates

Milk is a complex biochemical fluid that includes macronutrients and microbiota, which, together, are known to facilitate infant growth, mediate the colonization of infant microbiomes, and promote immune development. Examining factors that shape milk microbiomes and milk-nutrient interplay across host taxa is critical to resolving the evolution of the milk environment. Using a comparative approach across four cercopithecine primate species housed at three facilities under similar management conditions, we test for the respective influences of the local environment (housing facility) and host species on milk (a) macronutrients (fat, sugar, and protein), (b) microbiomes (16S rRNA), and (c) predicted microbial functions. We found that milk macronutrients were structured according to host species, while milk microbiomes and predicted function were strongly shaped by the local environment and, to a lesser extent, host species. The milk microbiomes of rhesus macaques (Macaca mulatta) at two different facilities more closely resembled those of heterospecific facility-mates compared to conspecifics at a different facility. We found similar, facility-driven patterns of microbial functions linked to physiology and immune modulation, suggesting that milk microbiomes may influence infant health and development. These results provide novel insight into the complexity of milk and its potential impact on infants across species and environments.

Host ecotype and rearing environment are the main drivers of threespine stickleback gut microbiota diversity in a naturalistic experiment

Host-microbiota interactions play a critical role in the hosts' biology, and thus, it is crucial to elucidate the mechanisms that shape gut microbial communities. We leveraged threespine stickleback fish (Gasterosteus aculeatus) as a model system to investigate the contribution of host and environmental factors to gut microbiota variation. These fish offer a unique opportunity for experiments in naturalistic conditions; we reared benthic and limnetic ecotypes from three different lakes in experimental ponds, allowing us to assess the relative effects of shared environment (pond), geographic origin (lake-of-origin), trophic ecology and genetics (ecotype) and biological sex on gut microbiota α- and β-diversity. Host ecotype had the strongest influence on α-diversity, with benthic fish exhibiting higher diversity than limnetic fish, followed by the rearing environment. β-diversity was primarily shaped by rearing environment, followed by host ecotype, indicating that environmental factors play a crucial role in determining gut microbiota composition. Furthermore, numerous bacterial orders were differentially abundant across ponds, underlining the substantial contribution of environmental factors to gut microbiota variation. Our study illustrates the complex interplay between environmental and host ecological or genetic factors in shaping the stickleback gut microbiota and highlights the value of experiments conducted under naturalistic conditions for understanding gut microbiota dynamics.

Warming increases the compositional and functional variability of a temperate protist community

Phototrophic protists are a fundamental component of the world's oceans by serving as the primary source of energy, oxygen, and organic nutrients for the entire ecosystem. Due to the high thermal seasonality of their habitat, temperate protists could harbour many well-adapted species that tolerate ocean warming. However, these species may not sustain ecosystem functions equally well. To address these uncertainties, we conducted a 30-day mesocosm experiment to investigate how moderate (12 °C) and substantial (18 °C) warming compared to ambient conditions (6 °C) affect the composition (18S rRNA metabarcoding) and ecosystem functions (biomass, gross oxygen productivity, nutritional quality - C:N and C:P ratio) of a North Sea spring bloom community. Our results revealed warming-driven shifts in dominant protist groups, with haptophytes thriving at 12 °C and diatoms at 18 °C. Species responses primarily depended on the species' thermal traits, with indirect temperature effects on grazing being less relevant and phosphorus acting as a critical modulator. The species Phaeocystis globosa showed highest biomass on low phosphate concentrations and relatively increased in some replicates of both warming treatments. In line with this, the C:P ratio varied more with the presence of P. globosa than with temperature. Examining further ecosystem responses under warming, our study revealed lowered gross oxygen productivity but increased biomass accumulation whereas the C:N ratio remained unaltered. Although North Sea species exhibited resilience to elevated temperatures, a diminished functional similarity and heightened compositional variability indicate potential ecosystem repercussions for higher trophic levels. In conclusion, our research stresses the multifaceted nature of temperature effects on protist communities, emphasising the need for a holistic understanding that encompasses trait-based responses, indirect effects, and functional dynamics in the face of exacerbating temperature changes.

Efficacy of Essential Oil Vapours in Reducing Postharvest Rots and Effect on the Fruit Mycobiome of Nectarines

Nectarines can be affected by many diseases, resulting in significant production losses. Natural products, such as essential oils (EOs), are promising alternatives to pesticides to control storage rots. This work aimed to test the efficacy of biofumigation with EOs in the control of nectarine postharvest diseases while also evaluating the effect on the quality parameters (firmness, total soluble solids, and titratable acidity) and on the fruit fungal microbiome. Basil, fennel, lemon, oregano, and thyme EOs were first tested in vitro at 0.1, 0.5, and 1.0% concentrations to evaluate their inhibition activity against Monilinia fructicola. Subsequently, an in vivo screening trial was performed by treating nectarines inoculated with M. fructicola, with the five EOs at 2.0% concentration by biofumigation, performed using slow-release diffusers placed inside the storage cabinets. Fennel, lemon, and basil EOs were the most effective after storage and were selected to be tested in efficacy trials using naturally infected nectarines. After 28 days of storage, all treatments showed a significant rot reduction compared to the untreated control. Additionally, no evident phytotoxic effects were observed on the treated fruits. EO vapors did not affect the overall quality of the fruits but showed a positive effect in reducing firmness loss. Metabarcoding analysis showed a significant impact of tissue, treatment, and sampling time on the fruit microbiome composition. Treatments were able to reduce the abundance of Monilinia spp., but basil EO favored a significant increase in Penicillium spp. Moreover, the abundance of other fungal genera was found to be modified.

Dual stressors of infection and warming can destabilize host microbiomes

Climate change is causing extreme heating events and intensifying infectious disease outbreaks. Animals harbour microbial communities, which are vital for their survival and fitness under stressful conditions. Understanding how microbiome structures change in response to infection and warming may be important for forecasting host performance under global change. Here, we evaluated alterations in the microbiomes of several wild Caenorhabditis elegans isolates spanning a range of latitudes, upon warming temperatures and infection by the parasite Leucobacter musarum. Using 16S rRNA sequencing, we found that microbiome diversity decreased, and dispersion increased over time, with the former being more prominent in uninfected adults and the latter aggravated by infection. Infection reduced dominance of specific microbial taxa, and increased microbiome dispersion, indicating destabilizing effects on host microbial communities. Exposing infected hosts to warming did not have an additive destabilizing effect on their microbiomes. Moreover, warming during pre-adult development alleviated the destabilizing effects of infection on host microbiomes. These results revealed an opposing interaction between biotic and abiotic factors on microbiome structure. Lastly, we showed that increased microbiome dispersion might be associated with decreased variability in microbial species interaction strength. Overall, these findings improve our understanding of animal microbiome dynamics amidst concurrent climate change and epidemics. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Responses of vascular plant fine roots and associated microbial communities to whole-ecosystem warming and elevated CO2 in northern peatlands

Warming and elevated CO2 (eCO2) are expected to facilitate vascular plant encroachment in peatlands. The rhizosphere, where microbial activity is fueled by root turnover and exudates, plays a crucial role in biogeochemical cycling, and will likely at least partially dictate the response of the belowground carbon cycle to climate changes. We leveraged the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, to explore the effects of a whole-ecosystem warming gradient (+0°C to 9°C) and eCO2 on vascular plant fine roots and their associated microbes. We combined trait-based approaches with the profiling of fungal and prokaryote communities in plant roots and rhizospheres, through amplicon sequencing. Warming promoted self-reliance for resource uptake in trees and shrubs, while saprophytic fungi and putative chemoorganoheterotrophic bacteria utilizing plant-derived carbon substrates were favored in the root zone. Conversely, eCO2 promoted associations between trees and ectomycorrhizal fungi. Trees mostly associated with short-distance exploration-type fungi that preferentially use labile soil N. Additionally, eCO2 decreased the relative abundance of saprotrophs in tree roots. Our results indicate that plant fine-root trait variation is a crucial mechanism through which vascular plants in peatlands respond to climate change via their influence on microbial communities that regulate biogeochemical cycles.

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert

We describe the metagenome composition, community functional annotation, and prokaryote diversity in calcareous stromatolites from a dry stream bed of the San Felipe Creek in the Anza Borrego Desert. Analyses show a community capable of nitrogen fixation, assimilatory nitrate reduction, biofilm formation, quorum sensing, and potential thick-walled akinete formation for desiccation resistance.

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

Co-occurrence network analysis reveals the alterations of the skin microbiome and metabolome in adults with mild to moderate atopic dermatitis

Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence. Staphylococcus species, especially S. aureus, were significantly increased in AD patients. Metabolomic profiles were also different between the groups. Dipeptide derivatives are more abundant in ADL, which may be related to skin inflammation. Co-occurrence network analysis of the microbiome and metabolomics data revealed higher co-occurrence of metabolites and bacteria in healthy ADNL compared to ADL. S. aureus co-occurred with dipeptide derivatives in ADL, while phytosphingosine-derived compounds showed co-occurrences with commensal bacteria, for example, Paracoccus sp., Pseudomonas sp., Prevotella bivia, Lactobacillus iners, Anaerococcus sp., Micrococcus sp., Corynebacterium ureicelerivorans, Corynebacterium massiliense, Streptococcus thermophilus, and Roseomonas mucosa, in healthy and ADNL groups. Therefore, these findings provide valuable insights into how AD affects the human skin metabolome and microbiome.IMPORTANCEThis study provides valuable insight into changes in the skin microbiome and associated metabolomic profiles in an adult population with mild to moderate atopic dermatitis. It also identifies new therapeutic targets that may be useful for developing personalized treatments for individuals with atopic dermatitis based on their unique skin microbiome and metabolic profiles.

Interindividual differences in aronia juice tolerability linked to gut microbiome and metabolome changes-secondary analysis of a randomized placebo-controlled parallel intervention trial

BACKGROUND

Aronia melanocarpa is a berry rich in polyphenols known for health benefits. However, the bioavailability of polyphenols has been questioned, and the individual taste acceptance of the fruit with its specific flavor varies. We recently observed substantial differences in the tolerability of aronia juice among healthy females, with half of the individuals tolerating aronia juice without complaints. Given the importance of the gut microbiome in food digestion, we investigated in this secondary analysis of the randomized placebo-controlled parallel intervention study (ClinicalTrials.gov registration: NCT05432362) if aronia juice tolerability was associated with changes in intestinal microbiota and bacterial metabolites, seeking for potential mechanistic insights into the impact on aronia polyphenol tolerance and metabolic outcomes.

RESULTS

Forty females were enrolled for this 6-week trial, receiving either 100 ml natural aronia juice (verum, V) twice daily or a polyphenol-free placebo (P) with a similar nutritional profile, followed by a 6-week washout. Within V, individuals were categorized into those who tolerated the juice well (Vt) or reported complaints (Vc). The gut microbiome diversity, as analyzed by 16S rRNA gene-based next-generation sequencing, remained unaltered in Vc but changed significantly in Vt. A MICOM-based flux balance analysis revealed pronounced differences in the 40 most predictive metabolites post-intervention. In Vc carbon-dioxide, ammonium and nine O-glycans were predicted due to a shift in microbial composition, while in Vt six bile acids were the most likely microbiota-derived metabolites. NMR metabolomics of plasma confirmed increased lipoprotein subclasses (LDL, VLDL) post-intervention, reverting after wash out. Stool samples maintained a stable metabolic profile.

CONCLUSION

In linking aronia polyphenol tolerance to gut microbiota-derived metabolites, our study explores adaptive processes affecting lipoprotein profiles during high polyphenol ingestion in Vt and examines effects on mucosal gut health in response to intolerance to high polyphenol intake in Vc. Our results underpin the importance of individualized hormetic dosing for beneficial polyphenol effects, demonstrate dynamic gut microbiome responses to aronia juice, and emphasize personalized responses in polyphenol interventions.

Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses

Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.

IMPORTANCE

Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.

Markers of fertility in reproductive microbiomes of male and female endangered black-footed ferrets (Mustela nigripes)

Reproductive microbiomes contribute to reproductive health and success in humans. Yet data on reproductive microbiomes, and links to fertility, are absent for most animal species. Characterizing these links is pertinent to endangered species, such as black-footed ferrets (Mustela nigripes), whose populations show reproductive dysfunction and rely on ex-situ conservation husbandry. To understand microbial contributions to animal reproductive success, we used 16S rRNA amplicon sequencing to characterize male (prepuce) and female (vaginal) microbiomes of 59 black-footed ferrets at two ex-situ facilities and in the wild. We analyzed variation in microbiome structure according to markers of fertility such as numbers of viable and non-viable offspring (females) and sperm concentration (males). Ferret vaginal microbiomes showed lower inter-individual variation compared to prepuce microbiomes. In both sexes, wild ferrets harbored potential soil bacteria, perhaps reflecting their fossorial behavior and exposure to natural soil microbiomes. Vaginal microbiomes of ex-situ females that produced non-viable litters had greater phylogenetic diversity and distinct composition compared to other females. In males, sperm concentration correlated with varying abundances of bacterial taxa (e.g., Lactobacillus), mirroring results in humans and highlighting intriguing dynamics. Characterizing reproductive microbiomes across host species is foundational for understanding microbial biomarkers of reproductive success and for augmenting conservation husbandry.

The probiotic SLAB51 as agent to counteract BPA toxicity on zebrafish gut microbiota -liver-brain axis

A plethora of studies have so far described the toxic effects of bisphenol A (BPA) on organism health, highlighting the urgent need to find new strategies not only to reduce the presence of this toxicant but also to counteract its adverse effects. In this context, probiotics emerged as a potential tool since they promote organism welfare. Using a multidisciplinary approach, this study explores the effects of SLAB51 dietary administration to counteract BPA toxicity using zebrafish as a model. Adult males and females were maintained under standard conditions (control group; C), exposed for 28 days via the water to an environmental relevant dose of BPA (10 μg/L; BPA), dietary treated with SLAB51 (109 CFU/g of body weight; P) and co-treated with BPA plus SLAB51 (BPA + P). In the gut, exposure to BPA resulted in altered architecture in both males and females, with females also experiencing an increase of pathogenic bacterial species. Co-administration of BPA + P led to the restoration of normal gut architecture, favored beneficial bacteria colonization, and decreased the abundance of pathogenic species. In the liver, male BPA exposure led to steatosis and glycogen depletion, which was partially mitigated by SLAB51 co-administration. In contrast, in females exposed to BPA, the lack of steatosis along with the greater glycogen depletion, suggested an increase in energy demand as supported by the metabolomic phenotype. The analysis of liver metabolites in BPA + P males revealed increased levels of anserine and reduced levels of glutamine, which could lie behind the counteraction of the brain histopathological damage caused by BPA. In BPA + P females, a reduction of retinoic acid was found in the liver, suggesting an increase in retinoids responsible for BPA detoxification. Overall, these results demonstrate that SLAB51 exerts its beneficial effects on the gut microbiota-brain-liver axis through distinct molecular pathways, effectively mitigating the pleiotropic toxicity of BPA.

How important is food structure when cats eat mice?

Feeding whole prey to felids has shown to benefit their gastrointestinal health. Whether this effect is caused by the chemical or physical nature of whole prey is unknown. Fifteen domestic cats, as a model for strict carnivores, were either fed minced mice (MM) or whole mice (WM), to determine the effect of food structure on digestibility, mean urinary excretion time (MUET) of 15N, intestinal microbial activity and fermentation products. Faeces samples were collected after feeding all cats a commercially available extruded diet (EXT) for 10 d before feeding for 19 d the MM and WM diets with faeces and urine collected from day 11 to 15. Samples for microbiota composition and determination of MUET were obtained from day 16 to 19. The physical structure of the mice diet (minced or not) did not affect large intestinal fermentation as total SCFA and branched-chain fatty acid (BCFA), and most biogenic amine (BA) concentrations were not different (P > 0·10). When changing from EXT to the mice diets, the microbial community composition shifted from a carbolytic (Prevotellaceae) to proteolytic (Fusobacteriaceae) profile and led to a reduced faecal acetic to propionic acid ratio, SCFA, total BCFA (P < 0·001), NH3 (P = 0·04), total BA (P < 0·001) and para-cresol (P = 0·08). The results of this study indicate that food structure within a whole-prey diet is less important than the overall diet type, with major shifts in microbiome and decrease in potentially harmful fermentation products when diet changes from extruded to mice. This urges for careful consideration of the consequences of prey-based diets for gut health in cats.

Gut Microbiota Uniqueness Is Associated with Lake Size, a Proxy for Diet Diversity, in Stickleback Fish

AbstractOrganismal divergence can be driven by differential resource use and adaptation to different trophic niches. Variation in diet is a major factor shaping the gut microbiota, which is crucial for many aspects of their hosts' biology. However, it remains largely unknown how host diet diversity affects the gut microbiota, and it could be hypothesized that trophic niche width is positively associated with gut microbiota diversity. To test this idea, we sequenced the 16S ribosomal RNA gene from intestinal tissue of 14 threespine stickleback populations from lakes of varying size on Vancouver Island, Canada, that have been shown to differ in trophic niche width. Using lake size as a proxy for trophic ecology, we found evidence for higher gut microbiota uniqueness among individuals from populations with broader trophic niches. While these results suggest that diet diversity might promote gut microbiota diversity, additional work investigating diet and gut microbiota variation of the same host organisms will be necessary. Yet our results motivate the question of how host population diversity (e.g., ecological, morphological, genetic) might interact with the gut microbiota during the adaptation to ecological niches.

Waste not, want not: revisiting the analysis that called into question the practice of rarefaction

In 2014, McMurdie and Holmes published the provocatively titled "Waste not, want not: why rarefying microbiome data is inadmissible." The claims of their study have significantly altered how microbiome researchers control for the unavoidable uneven sequencing depths that are inherent in modern 16S rRNA gene sequencing. Confusion over the distinction between the definitions of rarefying and rarefaction continues to cloud the interpretation of their results. More importantly, the authors made a variety of problematic choices when designing and analyzing their simulations. I identified 11 factors that could have compromised the results of the original study. I reproduced the original simulation results and assessed the impact of those factors on the underlying conclusion that rarefying data is inadmissible. Throughout, the design of the original study made choices that caused rarefying and rarefaction to appear to perform worse than they truly did. Most important were the approaches used to assess ecological distances, the removal of samples with low sequencing depth, and not accounting for conditions where sequencing effort is confounded with treatment group. Although the original study criticized rarefying for the arbitrary removal of valid data, repeatedly rarefying data many times (i.e., rarefaction) incorporates all the data. In contrast, it is the removal of rare taxa that would appear to remove valid data. Overall, I show that rarefaction is the most robust approach to control for uneven sequencing effort when considered across a variety of alpha and beta diversity metrics.IMPORTANCEOver the past 10 years, the best method for normalizing the sequencing depth of samples characterized by 16S rRNA gene sequencing has been contentious. An often cited article by McMurdie and Holmes forcefully argued that rarefying the number of sequence counts was "inadmissible" and should not be employed. However, I identified a number of problems with the design of their simulations and analysis that compromised their results. In fact, when I reproduced and expanded upon their analysis, it was clear that rarefaction was actually the most robust approach for controlling for uneven sequencing effort across samples. Rarefaction limits the rate of falsely detecting and rejecting differences between treatment groups. Far from being "inadmissible", rarefaction is a valuable tool for analyzing microbiome sequence data.

Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize

Intercropping has the potential to improve plant nutrition as well as crop yield. However, the exact mechanism promoting improved nutrient acquisition and the role the rhizosphere microbiome may play in this process remains poorly understood. Here, we use a peanut/maize intercropping system to investigate the role of root-associated microbiota in iron nutrition in these crops, combining microbiome profiling, strain and substance isolation and functional validation. We find that intercropping increases iron nutrition in peanut but not in maize plants and that the microbiota composition changes and converges between the two plants tested in intercropping experiments. We identify a Pseudomonas secreted siderophore, pyoverdine, that improves iron nutrition in glasshouse and field experiments. Our results suggest that the presence of siderophore-secreting Pseudomonas in peanut and maize intercropped plays an important role in iron nutrition. These findings could be used to envision future intercropping practices aiming to improve plant nutrition.

Biogeographic survey of soil bacterial communities across Antarctica

BACKGROUND

Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.

RESULTS

Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.

CONCLUSIONS

Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.

Phytoplankton ecology in the early years of a boreal oil sands end pit lake

BACKGROUND

Base Mine Lake (BML) is the first full-scale end pit lake for the oil sands mining industry in Canada. BML sequesters oil sands tailings under a freshwater cap and is intended to develop into a functional ecosystem that can be integrated into the local watershed. The first stage of successful reclamation requires the development of a phytoplankton community supporting a typical boreal lake food web. To assess the diversity and dynamics of the phytoplankton community in BML at this reclamation stage and to set a baseline for future monitoring, we examined the phytoplankton community in BML from 2016 through 2021 using molecular methods (targeting the 23S, 18S, and 16S rRNA genes) and microscopic methods. Nearby water bodies were used as controls for a freshwater environment and an active tailings pond.

RESULTS

The phytoplankton community was made up of diverse bacteria and eukaryotes typical of a boreal lake. Microscopy and molecular data both identified a phytoplankton community comparable at the phylum level to that of natural boreal lakes, dominated by Chlorophyta, Cryptophyta, and Cyanophyta, with some Bacillariophyta, Ochrophyta, and Euglenophyta. Although many of the same genera were prominent in both BML and the control freshwater reservoir, there were differences at the species or ASV level. Total diversity in BML was also consistently lower than the control freshwater site, but consistently higher than the control tailings pond. The phytoplankton community composition in BML changed over the 5-year study period. Some taxa present in 2016-2019 (e.g., Choricystis) were no longer detected in 2021, while some dinophytes and haptophytes became detectable in small quantities starting in 2019-2021. Different quantification methods (qPCR analysis of 23S rRNA genes, and microscopic estimates of populations and total biomass) did not show a consistent directional trend in total phytoplankton over the 5-year study, nor was there any consistent increase in phytoplankton species diversity. The 5-year period was likely an insufficient time frame for detecting community trends, as phytoplankton communities are highly variable at the genus and species level.

CONCLUSIONS

BML supports a phytoplankton community composition somewhat unique from control sites (active tailings and freshwater lake) and is still changing over time. However, the most abundant genera are typical of natural boreal lakes and have the potential to support a complex aquatic food web, with many of its identified major phytoplankton constituents known to be primary producers in boreal lake environments.

Microbes and microplastics: Community shifts along an urban coastal contaminant gradient

Plastic substrates introduced to the environment during the Anthropocene have introduced new pathways for microbial selection and dispersal. Some plastic-colonising microorganisms have adapted phenotypes for plastic degradation (selection), while the spatial transport (dispersal) potential of plastic colonisers remains controlled by polymer-specific density, hydrography and currents. Plastic-degrading enzyme abundances have recently been correlated with concentrations of plastic debris in open ocean environments, making it critical to better understand colonisation of hydrocarbon degraders with plastic degradation potential in urbanised watersheds where plastic pollution often originates. We found that microbial colonisation by reputed hydrocarbon degraders on microplastics (MPs) correlated with a spatial contaminant gradient (New York City/Long Island waterways), polymer types, temporal scales, microbial domains and putative cell activity (DNA vs. RNA). Hydrocarbon-degrading taxa enriched on polyethylene and polyvinyl chloride substrates relative to other polymers and were more commonly recovered in samples proximal to New York City. These differences in MP colonisation could indicate phenotypic adaptation processes resulting from increased exposure to urban plastic runoff as well as differences in carbon bioavailability across polymer types. Shifts in MP community potential across urban coastal contaminant gradients and polymer types improve our understanding of environmental plastic discharge impacts toward biogeochemical cycling across the global ocean.

The bladder microbiota is not significantly altered by intravesical BCG therapy

INTRODUCTION

Bladder microbiota dysbiosis has been associated with several urological disorders. However, dysbiosis markers in bladder cancer have not been identified and little is known about the effect of Bacillus Calmette-Guérin (BCG) intravesical therapy on the bladder microbiota. In this study, we compared the bladder microbiota of patients with non-muscle-invasive bladder cancer (NMIBC) undergoing BCG therapy to nononcological controls. We also longitudinally analyzed the impact of BCG therapy on the bladder microbiota of NMIBC patients and addressed whether bladder microbiota is associated with BCG efficacy.

METHODS

We collected catheterized urine samples from males with intermediate/high-risk NMIBC (cancer group, n = 32) or benign prostatic hyperplasia (control group, n = 41). The cancer group also provided urine samples during and after BCG induction. We used 16S rRNA gene sequencing to characterize the bladder microbiota. Bladder microbiota parameters, such as diversity and taxonomic composition, were compared between groups and associated with clinicopathological data and BCG efficacy.

RESULTS

We observed no significant differences between the bladder microbiota of NMIBC patients and controls. BCG intravesical instillations did not significantly alter the bladder microbiota of NMIBC patients, and BCG was rarely detected in the bladder during and after BCG therapy. Microbiota diversity and overall composition before BCG induction did not influence disease persistence at 3 months. However, higher abundance of Lactobacillus, Streptococcus, and Cutibacterium in the pre-BCG bladder microbiota was associated with BCG effectiveness.

CONCLUSION

We were unable to identify markers of bladder microbiota dysbiosis among male NMIBC patients. Moreover, we demonstrated for the first time using longitudinally collected samples that BCG cannot persist in the bladder microbiota nor significantly alter its diversity and composition. The associations found between bladder microbes and BCG efficacy highlight the potential of microbial-based therapeutic and risk-stratification strategies in the intermediate/high-risk NMIBC setting.

Longitudinal analysis at three oral sites links oral microbiota to clinical outcomes in allogeneic hematopoietic stem-cell transplant

IMPORTANCE

The oral cavity is the ultimate doorway for microbes entering the human body. We analyzed oral microbiota dynamics in allogeneic hematopoietic stem-cell transplant recipients and showed that microbiota injury and recovery patterns were highly informative on transplant complications and outcomes. Our results highlight the importance of tracking the recipient's microbiota changes during allogeneic hematopoietic stem-cell transplant to improve our understanding of its biology, safety, and efficacy.

Connecting the multiple dimensions of global soil fungal diversity

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

Characterization of the Bacterial Composition of 47 Fermented Foods in Sweden

Fermentation has long been utilized to preserve and enhance the flavor and nutritional value of foods. Recently, fermented foods have gained popularity, reaching new consumer groups due to perceived health benefits. However, the microbial composition of many fermented foods re-mains unknown. Here, we characterized the bacterial composition, diversity, and richness of 47 fermented foods available in Sweden, including kombucha, water kefir, milk kefir, yogurt, plant-based yogurt alternatives, kimchi, sauerkraut, and fermented vegetables. Via 16S rRNA gene sequencing, we identified 2497 bacteria (amplicon sequence variants). The bacterial composition was strongly associated with the type of fermented food, and lactic acid bacteria and/or acetic acid bacteria dominated most samples. However, each fermented food had a unique composition, with kombucha and water kefir having the highest diversity across and within samples. Few bacteria were abundant in multiple foods and food groups. These were Streptococcus thermophilus in yogurts and plant-based yoghurts; Lactococcus lactis in milk kefirs and one water kefir; and Lactiplantibacillus plantarum in kimchi, sauerkraut, and fermented cucumber. The broad range of fermented foods included in this study and their diverse bacterial communities warrant further investigation into the implications of microbial compositions for product traits and potential impact on human health.

Association of Subjective and Objective Measures of Sleep With Gut Microbiota Composition and Diversity in Older Men: The Osteoporotic Fractures in Men Study

BACKGROUND

Growing evidence suggests bidirectional links between gut microbiota and sleep quality as shared contributors to health. Little is known about the relationship between microbiota and sleep among older persons.

METHODS

We used 16S rRNA sequencing to characterize stool microbiota among men (n = 606, mean [standard deviation] age = 83.9 [3.8]) enrolled in the Osteoporotic Fractures in Men (MrOS) study from 2014 to 2016. Sleep was assessed concurrently by a questionnaire (Pittsburgh Sleep Quality index [PSQI]), and activity monitor to examine timing (acrophase) and regularity of patterns (F-statistic). Alpha diversity was measured using Faith's phylogenetic diversity (PD). Beta diversity was calculated with robust Aitchison distance with matrix completion (RPCA) and phylogenetic-RPCA (PRPCA). Their association with sleep variables was tested with partial distance-based redundancy analysis (dbRDA). Predictive-ratio biomarkers associated with sleep measurements were identified with CoDaCoRe.

RESULTS

In unadjusted analyses, men with poor sleep (PSQI >5) tended to have lower alpha diversity compared to men with normal sleep (Faith's PD, beta = -0.15; 95% confidence interval [CI]: -0.30 to 0.01, p = .06). Sleep regularity was significantly associated with RPCA and PRPCA, even after adjusting for site, batch, age, ethnicity, body mass index, diabetes, antidepressant and sleep medication use, and health behaviors (RPCA/PRPCA dbRDA; p = .033/.002). In taxonomic analysis, ratios of 7:6 bacteria for better regularity (p = .0004) and 4:7 for worse self-reported sleep (p = .005) were differentially abundant: some butyrate-producing bacteria were associated with better sleep characteristics.

CONCLUSIONS

Subjective and objective indicators of sleep quality suggest that older men with better sleep patterns are more likely to harbor butyrate-producing bacteria associated with better health.

Ecosystem type drives soil eukaryotic diversity and composition in Europe

Soil eukaryotes play a crucial role in maintaining ecosystem functions and services, yet the factors driving their diversity and distribution remain poorly understood. While many studies focus on some eukaryotic groups (mostly fungi), they are limited in their spatial scale. Here, we analyzed an unprecedented amount of observational data of soil eukaryomes at continental scale (787 sites across Europe) to gain further insights into the impact of a wide range of environmental conditions (climatic and edaphic) on their community composition and structure. We found that the diversity of fungi, protists, rotifers, tardigrades, nematodes, arthropods, and annelids was predominantly shaped by ecosystem type (annual and permanent croplands, managed and unmanaged grasslands, coniferous and broadleaved woodlands), and higher diversity of fungi, protists, nematodes, arthropods, and annelids was observed in croplands than in less intensively managed systems, such as coniferous and broadleaved woodlands. Also in croplands, we found more specialized eukaryotes, while the composition between croplands was more homogeneous compared to the composition of other ecosystems. The observed high proportion of overlapping taxa between ecosystems also indicates that DNA has accumulated from previous land uses, hence mimicking the land transformations occurring in Europe in the last decades. This strong ecosystem-type influence was linked to soil properties, and particularly, soil pH was driving the richness of fungi, rotifers, and annelids, while plant-available phosphorus drove the richness of protists, tardigrades, and nematodes. Furthermore, the soil organic carbon to total nitrogen ratio crucially explained the richness of fungi, protists, nematodes, and arthropods, possibly linked to decades of agricultural inputs. Our results highlighted the importance of long-term environmental variables rather than variables measured at the time of the sampling in shaping soil eukaryotic communities, which reinforces the need to include those variables in addition to ecosystem type in future monitoring programs and conservation efforts.

Peat loss collocates with a threshold in plant-mycorrhizal associations in drained peatlands encroached by trees

Drainage-induced encroachment by trees may have major effects on the carbon balance of northern peatlands, and responses of microbial communities are likely to play a central mechanistic role. We profiled the soil fungal community and estimated its genetic potential for the decay of lignin and phenolics (class II peroxidase potential) along peatland drainage gradients stretching from interior locations (undrained, open) to ditched locations (drained, forested). Mycorrhizal fungi dominated the community across the gradients. When moving towards ditches, the dominant type of mycorrhizal association abruptly shifted from ericoid mycorrhiza to ectomycorrhiza at c. 120 m from the ditches. This distance corresponded with increased peat loss, from which more than half may be attributed to oxidation. The ectomycorrhizal genus Cortinarius dominated at the drained end of the gradients and its relatively higher genetic potential to produce class II peroxidases (together with Mycena) was positively associated with peat humification and negatively with carbon-to-nitrogen ratio. Our study is consistent with a plant-soil feedback mechanism, driven by a shift in the mycorrhizal type of vegetation, that potentially mediates changes in aerobic decomposition during postdrainage succession. Such feedback may have long-term legacy effects upon postdrainage restoration efforts and implication for tree encroachment onto carbon-rich soils globally.

Gut microbiota parallelism and divergence associated with colonisation of novel habitats

An organism's gut microbiota can change in response to novel environmental conditions, in particular when colonisation of new habitats is accompanied by shifts in the host species' ecology. Here, we investigated the gut microbiota of three lizard species (A. inornata, H. maculata and S. cowlesi) from their ancestral-like habitat in the Chihuahuan desert and two colonised habitats with contrasting geological and ecological compositions: the White Sands and Carrizozo lava flow. The host species and the lizards' environment both shape gut microbiota composition, but host effects were overall stronger. Further, we found evidence that colonisation of the same environment by independent host species led to parallel changes of the gut microbiota, whereas the colonisation of two distinct environments by the same host species led to gut microbiota divergence. Some of the gut microbiota changes that accompanied the colonisation of the White Sands were associated with shifts in diet (based on diet information from previous studies), which is congruent with the general observation that trophic ecology has a strong effect on gut microbiota composition. Our study provides insights into how shifts in host ecology accompanying colonisation of novel environments can affect gut microbiota composition and diversity.

Equine sinusitis aetiology is linked to sinus microbiome by amplicon sequencing

BACKGROUND

Information regarding the microbiome in sinusitis using genetic sequencing is lacking and more-in-depth understanding of the microbiome could improve antimicrobial selection and treatment outcomes for cases of primary sinusitis.

OBJECTIVES

To describe sinus microbiota in samples from horses with sinusitis and compare microbiota and the presence of antimicrobial resistance genes between primary, dental-related and other secondary causes of sinusitis.

STUDY DESIGN

Retrospective case series.

METHODS

Records of equine sinusitis from 2017 to 2021 were reviewed and historical microbial amplicon sequence data were obtained from clinical diagnostic testing of sinus secretions. Following bioinformatic processing of bacterial and fungal sequence data, the sinus microbiota and importance of sinusitis aetiology among other factors were investigated from the perspectives of alpha diversity (e.g., number of operational taxonomic units [OTUs], Hill1 Diversity), beta diversity, and differentially abundant taxa. Quantitative PCR allowed for comparisons of estimated bacterial abundance and detection rate of common antibiotic resistance-associated genes. In a smaller subset, longitudinal analysis was performed to evaluate similarity in samples over time.

RESULTS

Of 81 samples analysed from 70 horses, the bacterial microbiome was characterised in 66, and fungal in five. Only sinusitis aetiology was shown to significantly influence microbiome diversity and composition (p < 0.05). Dental-related sinusitis (n = 44) was associated with a significantly higher proportion of obligate anaerobic bacteria, whereas primary sinusitis (n = 12) and other (n = 10) groups were associated with fewer bacteria and higher proportions of facultative anaerobic and aerobic genera. Antimicrobial resistance genes and fungal components were exclusively identified in dental-related sinusitis.

MAIN LIMITATIONS

Retrospective nature, incomplete prior antimicrobial administration data.

CONCLUSIONS

Molecular characterisation in sinusitis identifies microbial species which may be difficult to isolate via culture, and microbiome profiling can differentiate sinusitis aetiology, which may inform further treatment, including antimicrobial therapy.

Grapevines escaping trunk diseases in New Zealand vineyards have a distinct microbiome structure

Grapevine trunk diseases (GTDs) are a substantial challenge to viticulture, especially with a lack of available control measures. The lack of approved fungicides necessitates the exploration of alternative controls. One promising approach is the investigation of disease escape plants, which remain healthy under high disease pressure, likely due to their microbiome function. This study explored the microbiome of grapevines with the disease escape phenotype. DNA metabarcoding of the ribosomal internal transcribed spacer 1 (ITS1) and 16S ribosomal RNA gene was applied to trunk tissues of GTD escape and adjacent diseased vines. Our findings showed that the GTD escape vines had a significantly different microbiome compared with diseased vines. The GTD escape vines consistently harbored a higher relative abundance of the bacterial taxa Pseudomonas and Hymenobacter. Among fungi, Aureobasidium and Rhodotorula were differentially associated with GTD escape vines, while the GTD pathogen, Eutypa, was associated with the diseased vines. This is the first report of the link between the GTD escape phenotype and the grapevine microbiome.

Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient

INTRODUCTION

The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica.

METHODS

We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons.

RESULTS AND DISCUSSION

Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.

Water quality determines protist taxonomic and functional group composition in a high-altitude wetland of international importance

Alpine wetland is a natural laboratory for studying the Earth's third polar ecosphere. Protist communities are key components of wetland ecosystems which are extremely vulnerable to environmental change. It is of great importance to study the protist community in relation to environment, which might be the key to understand the ecosystem of the alpine wetlands under global change. In this study, we investigated the composition of protist communities across the Mitika Wetland, a unique alpine wetland hosting tremendous endemic diversity. Using 18S rRNA gene high-throughput sequencing, we evaluated how protist taxonomic and functional group composition is structured by seasonal climate and environmental variation. We found a high relative abundance of Ochrophyta, Ciliophora, and Cryptophyta, each of which showcased a unique spatial pattern in the wet and dry seasons. The proportion of consumers, parasites and phototrophs groups were stable among the functional zones and also between the seasons, with consumers dominating communities in terms of richness, while phototrophic taxa dominated in terms of relative abundance. Protist and each functional group were rather regulated by deterministic than stochastic processes, with water quality having a strong control on communities. Salinity and pH were the most important environmental factors at shaping protistan community. The protist co-occurrence network dominated by the positive edge indicating the communities resisted extreme environmental conditions through close cooperation, and more consumers were determined as the keystones in wet season and more phototrophic taxa in dry season. Our results provided the baseline of the protist taxonomic and functional group composition in the highest wetland, and highlighted environmental selections drive protist distribution, implying the alpine wetland ecosystem are sensitive to climate changes and human activities.