Microbial Ecology

Stingless bees (Meliponini) are ecologically and culturally important pollinators with a long tradition of human management in the Neotropics. Yet, little is known about how their gut microbiota vary across geographic regions or whether microbial exchange occurs with managed honey bees (Apis mellifera), which are often kept in close proximity. Using full-length 16S rRNA gene sequencing of individual bees sampled from 167 colonies, we characterized gut microbial community structure through a hierarchical, taxonomic and phylogenetic comparative framework, contrasting the microbiota of Melipona quadrifasciata and Melipona mondury with that of Apis mellifera across their shared geographic range in Brazil. The core microbiota of Melipona was dominated by Lactobacillus, Bifidobacterium, Apilactobacillus, Bombella, and Floricoccus, and showed inverse variation in relative abundance with lower-prevalence bacterial taxa. Although the core microbiota of the two stingless bee species overlapped only partially with that of Apis mellifera, they exhibited comparable alpha-diversity and beta-diversity dispersion, indicating broadly similar community assembly processes and dynamics. Nevertheless, we found that 6% of all amplicon sequence variants (ASVs) were shared between hosts, encompassing nearly all canonical honey bee "core" symbionts, indicating frequent spillover. Remarkably, several ASVs of Snodgrassella, a genus typically rare in stingless bees, reached high abundance in several M. quadrifasciata individuals and formed a deeply divergent clade ([~]96% 16S rRNA gene identity to S. alvi). These patterns are consistent with the hypothesis that human-mediated management practices, such as mixed apiaries and artificial feeding, create opportunities for microbial exchange between native and non-native bees. Together, our findings indicate that stingless bee gut microbiomes are compositionally stable yet ecologically permeable, shaped by both long-term host specificity and recent anthropogenic contact.

The gut microbiome of eusocial corbiculate bees, which include honeybees, bumblebees, and stingless bees, consists of anciently associated, host-specific bacteria that are vital for bee health. Two symbionts, Snodgrassella and Gilliamella, are ubiquitous in honeybees and bumblebees. However, their presence varies in the stingless bee clade (Meliponini), a group with pantropical distribution. They are absent or rare in the diverse genus Melipona, indicating a shift in microbiota composition in this lineage. To identify the main members of the Melipona microbiota, we combined newly collected and published data from field-collected individuals of several species. Additionally, we identified the localization of the dominant microbiota members within the gut regions of Melipona quadrifasciata anthidioides. The dominant microbiota of Melipona species includes members of the genera Bifidobacterium, Lactobacillus, Apilactobacillus, Floricoccus, and Bombella. Among these, Apilactobacillus and Bombella dominate in the crop, whereas Apilactobacillus and other members of the Lactobacillaceae dominate the ventriculus. The ileum lacks Snodgrassella or Gilliamella but contains a putative new symbiont close to Floricoccus, as well as strains of Bifidobacterium, Lactobacillaceae (including Apilactobacillus), and Bombella. The rectum is dominated by Bifidobacterium and Lactobacillus. In summary, the Melipona microbiota is compositionally distinct but shows spatial organization paralleling that of other eusocial corbiculate bees.

Fairy circles are rings of grass with centers of bare soil that are found in some arid grasslands. Above- and belowground chemical and biological attributes of fairy circles have been explored in an ongoing debate about the ultimate causes of this pattern. We studied the soil nematode communities associated with Stipagrostis fairy circles along a 900-km range in the Namib Desert of Namibia in southern Africa. Nematode abundance and diversity were highest in soils along the vegetation rings that define fairy circles and in soils in the vegetated matrix surrounding the bare circles, demonstrating the positive impact of plant-derived resources on nematode communities. In contrast, soils from the bare centers of fairy circles had lower organic matter content and were nearly defaunated, averaging only 9.9 {+/-} 1.7 nematodes 100 g-1 soil. Bacterial-feeding Acrobeloides nematodes were the only taxa over-represented in center soils in comparison to ring soils. Our results indicate that nematode communities are influenced by the unique soil environments that the fairy circle vegetation pattern generates and suggest that the soils at the centers of fairy circles are uniquely hostile habitat for soil organisms as well as plants. Co-occurrence network analysis of nematode communities elucidated relationships among the taxa. For example, the abundances of dorylaims and Nothacrobeles were positively correlated across all soil positions, suggesting they have overlapping ecological niches. In ring soils, the abundances of fungal-feeding Aphelenchoides, Ditylenchus, and Hexatylus were positively correlated, likely due to enhanced fungal communities in these plant-influenced soils. Panagrobelus demonstrated niche specialization by being negatively correlated to two other bacterial-feeding taxa (Elaphonema in matrix soils and Acrobeloides in ring soils). The co-occurrence patterns revealed by these relatively low diversity communities provide insights into the potential roles of nematode interactions as well as environmental factors in community assembly.

BackgroundMicrobiota play a crucial role in determining the ability for arthropod disease vectors to transmit pathogens. Microbial community structure can be heavily influenced by microbe-microbe interactions, host genetics and environmental factors. Here, we characterize the host population genetic structure, and bacterial and fungal communities in natural populations of the West Nile virus mosquito vector Culex tarsalis. Mosquitoes were collected and analyzed across the species range of the mosquito in the United States, where we used PoolRADSeq to quantify population genetic structure. Microbial community composition was characterized using bacterial 16S rRNA gene sequencing (V3-V4 region) and fungal ITS sequencing (ITS1 region). ResultsPoolRADSeq identified four broad genetic clusters of mosquito populations, which corresponded to previous clusters identified by microsatellite analysis and RADSeq on individual mosquitoes. Microbiome diversity grouped mosquito populations into three broad clusters, with each cluster distinctively represented by diagnostic abundant bacteria (Ralstonia, Pseudomonas, or Zymobacter/Providencia, respectively). Clustering for fungal taxa was less pronounced. Geographic distance between populations was positively correlated with microbiome community dissimilarity, and multiple environmental factors were significantly correlated with microbial species richness and diversity. ConclusionsThese results suggest that bacterial and fungal communities are geographically structured in Cx. tarsalis, interact with important environmental factors, and are partially correlated with host genetic structure. As microbiota can affect the ability for mosquitoes to transmit pathogens, understanding the factors underpinning microbiome variation across space and time has important implications for the spread of vector-borne pathogens such as WNV.

The assembly of local communities is likely to reflect the effects of local environmental factors associated with filters that act at larger spatial scales. Dissecting these multiscale effects remains a timely challenge that is particularly important for host-associated microbiomes. We investigated the relative roles of local selection (due to host species identity) and regional effects (due to water body identity) on the community structure of bacteria in the gut of tadpoles from three biogeographic areas and used graph theory and metanetwork approaches to explore and illustrate the distribution of bacteria across different ponds. The pond of origin, which represents a regional species pool of bacteria, was in general more important in shaping the gut microbiome of tadpoles than host species identity. The resulting metanetworks are modular and indicate relatively few species of bacteria occurring in more than one pond. Thus, each pond represents a relatively distinct species pool of bacteria available for community assembly of the tadpole microbiomes. Our findings indicate that microbiome community assembly in amphibian larvae, as in many other communities, is a multiscale process with important regional effects that constrain how local (i.e. host-dependent) filters act to influence microbiome community composition.Competing Interest StatementThe authors have declared no competing interest.View Full Text

Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and without microbial cycling, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse of all the planets. They have vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and contain significant stocks of sequestered carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome are scarce, especially in the Southeast Asian biodiversity hotspot. Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa, a further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be differentially abundant suggesting key roles in this microbiome, with the identified dimethylsulfoniopropionate (DMSP) metabolisers having important functions in these habitats. The majority of those identified are involved in nutrient cycling or involved in the production of compounds that promote host survival. Increasingly, blue carbon and nature-based solutions to climate change are heralded as viable mitigation steps to limit climate change, however, this is done with little to no consideration of the microbial communities that cycle sequestered carbon in these environments. Here, we examine the microbial communities present in sediment samples taken in close proximity to each tree, sediment samples represent a major sink of atmospheric carbon and understanding how the associated communities will change as climate change advances will become an increasingly important part of carbon stock assessments. Knowing what microbes are presently there is an important first step in this process.

BackgroundThe phyllosphere is an important microbial habitat but our understanding of how plant hosts drive the composition of their associated leaf microbial communities and whether taxonomic associations between plants and phyllosphere microbes represent adaptive matching remains limited. In this study we quantify bacterial functional diversity in the phyllosphere of 17 tree species in a diverse neotropical forest using metagenomic shotgun sequencing. We ask how hosts drive the functional composition of phyllosphere communities and their turnover across tree species, using host functional traits and phylogeny. We compare functional predictions inferred from 16S gene sequencing with functions estimated from metagenomic shotgun sequencing. ResultsNeotropical tree phyllosphere communities are dominated by functions related to the metabolism of carbohydrates, amino acids and energy acquisition, along with environmental signalling pathways involved in membrane transport. While most functional variation was observed within communities, there is non-random assembly of microbial functions across host species possessing different leaf traits. Metabolic functions related to biosynthesis and degradation of secondary compounds, along with signal transduction and cell-cell adhesion were particularly important in driving the match between microbial functions and host traits. These microbial functions were also evolutionarily conserved across the host phylogeny. Functional predictions inferred from 16S gene sequences were weakly correlated with functional annotations from the same samples through metagenomic shotgun sequencing, especially for finer-scale functional annotations. ConclusionsFunctional profiling based on metagenomic shotgun sequencing offers evidence for the presence of a core functional microbiome across phyllosphere communities of neotropical trees. While functional turnover across phyllosphere communities is relatively small, the association between microbial functions and leaf trait gradients among host species supports a significant role for plant hosts as selective filters on phyllosphere community assembly. This interpretation is supported by the presence of phylogenetic signal for the microbial traits driving inter-community variation across the host phylogeny. Our comparison of functional annotations derived from 16S genes versus metagenomic shotgun sequencing suggests caution in using functions inferred from 16S genes for studying ecological dynamics in phyllosphere communities. Taken together, our results suggest that there is adaptive matching between phyllosphere microbes and their plant hosts.

Despite the low availability of nitrogen (N), the highly productive macrophyte Hydrilla verticillata (L.) is a successful invader of the littoral zones at lake Atitlan, Guatemala, with profound implications for lake ecology. To help answer the question of how Hydrilla, accompanied by the filamentous green alga Cladophora Kutzing (Ulvophyceae), sustains fast growth under conditions of N scarcity, we studied the composition and potential biogeochemical function of the associated microbiomes. We combined results from next generation sequencing of associated bacterial and fungal assemblages with traditional microscopy-based taxonomical evaluation of algae and cyanobacteria. We focused on the presence of specific N2-fixing genera and their relative importance. Data on community composition are complemented with measurements of diazotrophic activity. The results expand our knowledge of the ecophysiology of these algae-plant-microbe consortia and suggest that several levels of biological complexity should be considered to fully understand aquatic plant ecology and the process of macrophyte invasions.

Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing[≤] 81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI > 99%, interclade ANI[≤] 81%), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.

The Montseny brook newt, Calotriton arnoldi, is a Critically Endangered amphibian species endemic to the Montseny Massif in Catalonia, Northeastern Spain. Due to population declines and threats to its natural habitat, an ex-situ breeding program was initiated in 2007. A key goal of the program is to ensure the survival of captive-bred individuals after reintroduction, which in amphibians heavily relies on the specimens microbiome being capable of protecting them from environmental microorganisms, especially considering the global Chytridiomycosis pandemic caused by the fungi Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). This study aims to characterize the microbiome of wild and captive specimens of Calotriton arnoldi, to identify differences in microbiome composition, and to determine their potential impact on captive-bred individuals upon reintroduction. Up to 7,438 ASVs (Amplicon Sequence Variants) were identified from 138 samples from 21 and 61 wild and captive-bred individuals, respectively. Results indicate that wild populations from different subspecies have significantly different microbiome composition, as do wild and captive-bred groups from the same subspecies. Additionally, dissimilarities in microbiome variability were only found within each subspecies, between wild and captive-bred groups. In terms of composition, certain bacteria were identified as potential markers for both wild and captive environments. Enhancing microbiome variability might improve the survival prospects of reintroduced specimens. Thus, exposing captive specimens to a more natural environment while in captivity or a soft-release procedure could potentially mitigate the absence of exposure to other bacteria and potential pathogens from their native environment.

Stingless bees are globally important social corbiculate bees, fulfilling critical pollination roles in many ecosystems; however, their gut microbiota, especially fungal communities, are not well characterized to date. We collected 121 bee samples from two species, Tetragonula carbonaria and Austroplebeia australis, across a distance of 1,200 km of eastern Australia, and analysed their gut microbiomes. We found that the gut bacterial richness of T. carbonaria was influenced by geography (latitude and longitude) and positively correlated to an established fitness indicator in insects; namely, host forewing length/size that relates to flight capacity of stingless bees. We characterized the core microbiomes of the two bees and found that they consisted of the bacterial taxa Snodgrassella, Lactobacillus, Acetobacteraceae and Bombella, and the fungal taxa Didymellaceae, Monocilium mucidum, Malassezia restricta and Aureobasidium pullulans. Both host species identity and management (wild or managed) significantly influenced the gut microbial diversity and composition, and similarity between colonies declined as the geographical distance between them increased. This result was also supported by our co-existing network analyses. Overall, we have thoroughly analysed stingless bee gut microbiomes, and provided novel evidence that T. carbonaria bees with larger wings or from more southern populations have higher microbial diversity in their guts. Originality-Significance StatementBeneficial interactions between insects and their microbial symbionts are pivotal for their fitness. In this study, we analysed the gut microbiomes of two stingless bee species, Tetragonula carbonaria and Austroplebeia australis, that are widespread and important pollinators in Australia. We characterized their gut microbiomes and detected a significant positive correlation between gut bacterial richness and host forewing size for T. carbonaria; the first time that gut microbial diversity has been linked to a morphological trait in stingless bees. Furthermore, we found that host species identity, management type (wild or managed) and geography all significantly influenced bee gut microbial diversity and composition, and were able to describe both bacterial and fungal core microbial taxa. This study reveals novel understandings of stingless bee gut microbiomes and provides the basis for utilizing microbial strategies to maintain colony health.

BackgroundThe interactions between the host organism and the microbiota play an important role in the hosts survival, influencing its physiology and adaptation. The Antarctic, due to its extreme living conditions, is a unique region for studying such interactions. However, research on the microbiomes of Antarctic terrestrial and freshwater invertebrates remains limited, especially with regard to the regions sole endemic insect, Belgica antarctica. Our aim was to study the B. antarctica microbiome collected from different substrates and from varying ornithogenic influence levels. MethodsA total of 330 B. antarctica larvae and moss substrates were sampled at three sites with different ornithogenic impact, followed by DNA extraction using Qiagen kits. The V3-V4 region of bacterial 16S rRNA was amplified by PCR and sequenced on the Illumina NovaSeq platform, followed by bioinformatic processing in QIIME2 for OTU clustering, taxonomic classification, and diversity analysis. Further analysis and visualization was performed in R, Python and GraphPad Prism. ResultsAmplicon sequencing revealed rich microbial diversity, with NMDS demonstrating clear clustering of samples according to their origin (insects vs substrate) and ornithogenic influence level. Comparative analysis revealed that the vast majority of OTUs associated with B. antarctica (ca. 95%) were shared with substrates, whereas the insect-specific fraction was small, highly variable, and partially influenced by moss species. Ornithogenic influence significantly structured the symbiotic microbiota in both insects and substrates, reducing microbial diversity and altering the relative abundance of major bacterial taxa. Overall, substrate type and ornithogenic impact are significant factors influencing microbial community structure, while insect-specific taxa formed only a minor, heterogeneous component of this midge microbiome. Additionally, the Wolbachia infection was detected in B. antarctica larvae for the first time. ConclusionThe substrate that B. antarctica inhabits, as well as ornithogenic influence, play a significant role in the shaping of the species microbiome. This Antarctic chironomid also maintains a core microbial community. The detection of Wolbachia in B. antarctica is the first evidence of this endosymbiont in Antarctica.

BackgroundThe Gorgonian coral, Eunicella singularis, is one of the main components of Mediterranean marine animal forests, whose canopies play a key role in Mediterranean sublittoral ecosystems due to their capacity to provide shelter, food, and nursery ground to several species. Like other gorgonian species, E. singularis faces environmental threats with potential repercussions on the associated biodiversity. This photophilic octocoral, spanning the Western Mediterranean, Adriatic, and Aegean Seas at depths of 10-70m, engages in symbiosis with Symbiodiniaceae dinoflagellates, thereby influencing their resilience in nutrient-poor habitats. However, mesophotic populations ([~]60m depth) are characterized by very low Symbiodiniaceae density, prompting questions regarding metabolic adaptations. The associations of corals with specific bacteria that differ from those in the surrounding seawater suggest a role in host health and physiology. In particular, in mesophotic colonies, bacteria may perform activities that Symbiodinium typically carries out in shallow colonies. Here, we applied metagenomics techniques to analyze the changes in the microbiome of Eunicella singularis with depth, analyzing DNA samples from shallow (12m) and mesophotic (57m) colonies in the Northwestern Mediterranean Sea. ResultsHigh-coverage metagenomes (ca. 80 Gb per sample) were generated from E. singularis colony samples. We observed significant changes in the relative abundance of prokaryotic and microbial eukaryotic symbionts with depth. Mesophotic samples exhibited higher levels of symbiotic prokaryotes, dominated by Endozoicomonas and Bermanella, whereas shallow samples were enriched with the symbiotic dinoflagellate Symbiodiniaceae. The metabolic potential of the microbiome also varied with depth. The shallow microbiome showed a prevalence of photosynthesis and carbon fixation pathways. In turn, the mesophotic microbiome exhibited a higher abundance of metabolic functions related to vitamin biosynthesis, energy metabolism, especially carbon metabolism, as well as pathways associated with carbohydrates, amino acids, and cofactors. ConclusionsOur results indicate that the structure and metabolic function of the microbiome of Eunicella singularis change with depth. In the absence of symbiotic dinoflagellates, associated bacteria seem to use different sources of carbon, in addition to cycling nutrients and vitamins, which could influence coral health. These findings gain significance in the context of global change, as shifts in oceanic conditions may affect the coral microbiome.

Microbiome diversity and composition in mammals is affected by the hosts environment and has been linked to important immune and physiological host functions, yet most of these data come from the gut microbiome. Research on the oral and hair microbiome in nonhuman primates has been far less common, and information from wild primates is even rarer. These overlooked patterns of environmental effects on microbial communities across the body may have important implications for a range of host functions. Therefore, in this study we characterized the gut, oral, and hair microbiomes across nine different captive and wild lemur species: Eulemur collaris, Eulemur coronatus, Eulemur mongoz, Lemur catta, Microcebus griseorufus, Microcebus murinus, Propithecus coquereli, Propithecus verreauxi, and Varecia rubra. We explored how host environment affects the microbiome diversity of these three body regions using 16S rRNA sequencing and found significant differences in microbiome composition, diversity, and environmental influence across body regions. The oral microbiome was least diverse and most resilient to different environmental effects; conversely, the hair microbiome was both most diverse and most labile. Differentially abundant bacterial taxa across oral, gut, and hair microbiota may also reflect selective regimes unique to each body region. These results emphasize the importance of accounting for body region when conducting microbiome studies. ImportanceAn organisms microbiome plays important roles in a wide variety of the host animals physiological functions, yet how these microbial communities in body regions beyond the gut are affected by the hosts environment is not clearly understood. We therefore analyzed how the oral, gut, and hair microbiomes of nine lemur species (genera Eulemur, Lemur, Microcebus, Propithecus, and Varecia) varied across wild and captive environments. We found that host environment affected the microbiomes of each body region in distinct ways, with the oral microbiome appearing conserved and more resilient to environmental effects, particularly compared to the diverse and widely variable hair microbiome. To our knowledge, this study is the most comprehensive multi-body-region analysis of the lemur microbiome to date. Our results demonstrate that the environment does not have a universal effect on the microbiome across body regions, but is instead mediated by body-region specific factors.

The composition of the microbiome is shaped by both environment and host genetic background in most organisms, but in the mosquito Aedes aegypti the role of host genetics in shaping the microbiome is poorly understood. Previously, we had shown that four lines of Ae. aegypti harbored different microbiomes when reared in the same insectary under identical conditions. To determine whether these lines differed from each other across time and in different environments, we characterized the microbiome of the same four lines of Ae. aegypti reared in the original insectary and at another institution. While it was clear that the environment influenced the microbiomes of these lines, we did still observe distinct differences in the microbiome between lines within each insectary. Clear differences were observed in alpha diversity, beta diversity, and abundance of specific bacterial taxa. To determine if the line specific differences in the microbiome were maintained across environments, pair-wise differential abundances of taxa was compared between insectaries. Lines were most similar to other lines from the same insectary than to the same line reared in a different insectary. Additionally, relatively few differentially abundant taxa identified between pairs of lines were shared across insectaries, indicating that line specific properties of the microbiome are not conserved across environments, or that there were distinct microbiota within each insectary. Overall, these results demonstrate that mosquito line can shape the microbiome across microbially- diverse environments and host by microbe interactions affecting microbiome composition and abundance is dependent on environmentally available bacteria. Author SummaryThe mosquito microbiome plays a critical role in shaping interactions with human pathogens. The factors that contribute to shaping the composition of the mosquito microbiome are of high importance due to its role in pathogen interactions and the successful development of control strategies. In other organisms, both host genetics and environment shape the microbiome composition, but the role of host genetics in shaping the mosquito microbiome is less clear. Previously, we have shown that different lines of Aedes aegypti harbor different microbiomes when reared in the same environment. We were curious to see if these differences could still be detected after further generations in the same insectary and across environments in a different insectary. We found that found that the microbiome differed between these lines in each insectary indicating an element of both host genetic background and environment play a role in establishing the microbiome. Our results indicate that different genetic backgrounds of Ae. aegypti will interact with their environment differently to shape their microbiome, which could potentially influence interactions with human pathogens and/or the effectiveness of control strategies. More broadly, our results are of interest for the ecology of host-microbe interactions.

BackgroundRecent evidence suggests that soil microbial communities can regulate plant community dynamics. In addition, the drought tolerance of plants can be enhanced by soil microbes. So far, few studies have assessed the variation in the microbiome of specific plant species along environmental gradients. Yet understanding these dynamics is essential to improve predictions of plant-soil feedbacks and the consequences of ongoing climate changes. Here we characterized the soil microbiome of two co-occurring Mediterranean oaks along a precipitation gradient, using amplicon sequencing of phylogenetic marker genes for prokaryotes and fungi. Additionally, we identified tree-specific and locally-specific microbes potentially responsible for tree community dynamics. ResultsWe show that two co-occurring, evergreen Mediterranean oak species harbor distinct microbiomes along a precipitation gradient. The soil microbial diversity increased along the precipitation gradient, for prokaryotic and {beta} diversity and for fungal {beta} diversity. Quercus ilex harbored richer fungal communities than Quercus suber, and host-specific taxa more often belonged to fungi than to prokaryotes. Notably, the microbial communities at the dry end of the precipitation gradient harbored more locally-specific prokaryotic and fungal taxa than the microbial communities with a higher diversity, at the wet end of the gradient, suggesting higher specialization in drier areas. ConclusionsEven congeneric tree species, belonging to the same functional group, can harbor distinct and specific soil microbiomes. These microbiomes become more similar and consist of more specialized taxa under drier compared with wetter conditions. With this, our study offers a step towards a better understanding of the context-dependency of plant-soil feedbacks by going beyond and {beta} diversities and focusing on specialized taxa potentially driving community changes along environmental gradients. We hope that our study will stimulate future research assessing the importance of context-dependency of interactions between plants and soil communities in a changing world.

Sex, age, diet, stress, and social environment have all been shown to influence the gut microbiota. In several mammals, including humans, increased stress is related to decreasing gut microbial diversity and may differentially impact specific taxa. Recent evidence from gorillas shows fecal glucocorticoid metabolite concentration (FGMC) did not significantly explain gut microbial diversity, but it was significantly associated with the abundance of the family Anaerolineaceae. These patterns have yet to be examined in other primates, like bonobos (Pan paniscus). We compared FGMC to 16S rRNA amplicons for 201 bonobo fecal samples collected across five months to evaluate the impact of stress, measured with FGMC, on the gut microbiota. Alpha diversity measures (Chaos and Shannons indexes) were not significantly related to FGMC. FGMC explained 0.08% of the variation in beta diversity for Jensen-Shannon and 1.27% for weighted UniFrac but was not significant for unweighted UniFrac. We found that genus SHD-231, a member of the family Anaerolinaceae had a significant positive relationship with FGMC. These results suggest that bonobos are relatively similar to gorillas in alpha diversity and family Anaerolinaceae responses to FGMC, but different from gorillas in beta diversity. Members of the family Anaerolinaceae may be differentially affected by FGMC across great apes. FGMC appears to be context dependent and may be species-specific for alpha and beta diversity but this study provides an example of consistent change in two African apes. Thus, the relationship between physiological stress and the gut microbiome may be difficult to predict, even among closely related species. Graphical Abstract: See PDF Legend: We compared the bonobo gut microbiota to fecal glucocorticoid metabolite concentrations (FGMC). FGMC did not explain alpha diversity, but FGMC explained [~]1.5% of the variation in beta diversity.

BackgroundBrown algae (Phaeophyceae) are essential species in coastal ecosystems where they form kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology. The bacterial microbial partners of brown algae have received far more attention than microbial eukaryotes. To our knowledge, this is the first study to investigate brown algal-associated eukaryotes (the eukaryome) using broadly targeting pan-eukaryotic primers and high throughput sequencing (HTS). Using this approach, we aimed to unveil the eukaryome of seven large common brown algal species. We also aimed to assess whether these macroalgae harbour novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome, based on taxonomic affiliation and phylogenetic placement. ResultsOur sequence dataset was dominated by brown algal reads, from the host species and potential symbionts. We also detected a broad taxonomic diversity of eukaryotes in the brown algal holobiomes, with OTUs taxonomically assigned to ten of the eukaryotic major Kingdoms or supergroups. A total of 265 microeukaryotic and epi-endophytic operational taxonomic units (OTUs) were defined, using 97% similarity cut off during clustering, and were dominated by OTUs assigned to stramenopiles, Alveolata and Fungi. Almost one third of the OTUs we detected have not been found in previous molecular environmental surveys, and represented potential novel eukaryotic diversity. This potential novel diversity was particularly prominent in phylogenetic groups comprising heterotrophic and parasitic organisms, such as labyrinthulids and oomycetes, Cercozoa, and Amoebozoa. ConclusionsOur findings provide important baseline data for future studies of seaweed-associated microorganisms, and demonstrate that microeukaryotes and epi-endophytic eukaryotes should be considered as an integral part of brown algal holobionts. The potential novel eukaryotic diversity we found and the fact that the vast majority of macroalgae in marine habitats remain unexplored, demonstrates that brown algae and other seaweeds are potentially rich sources for a large and hidden diversity of novel microeukaryotes and epi-endophytes.

Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict the species responses to environmental change. We used reciprocal gardens planted with distinct regional Andropogon gerardii ecotypes adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotype effect highlighted active microbial recruitment in the rhizosphere driven by ecotype or plant genetic background. Our data also suggest that ecotypes were more successful in recruiting rhizosphere community members unique to their local homesites, supporting the "home field advantage" hypothesis. These unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Further, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced effects of plant ecotypes on the rhizosphere microbiome recruitment. Our results should facilitate expanded studies on understanding the complexity of plant host interactions with local soil microbes and identification of functional potential of recruited microbes. Our study has the potential to aid in predicting ecosystem responses to climate change and the impact of management on restoration practices. ImportanceIn this study, we used reciprocal gardens located across a sharp precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional Andropogon gerardii ecotypes. We used16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though the location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site". We found evidence for "home field advantage" interactions between the host and associated rhizobiomes, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study provides insights into the understanding of factors effecting the plant adaptation, improving management strategies, and predicting of the future landscape under the changing climate.

It is known that animal-associated microbiomes form indispensable relationships with hosts and are responsible for many functions important for host-survival. Next-gen driven approaches documenting the remarkable diversity of microbiomes have burgeoned, with amphibians too, benefiting from such treatments. The microbiome of Gymnophiona (caecilians), one of the three amphibian orders, constituting of 3% of amphibians, however, remains almost unknown. The present study aims to address this knowledge gap through analysis of the microbiome of Ichthyophis bannanicus. As these caecilian larvae are aquatic and hence exposed to a greater propensity for bacterial microbiomic interchange, we hypothesize that bacterial phyla would overlap between gut and skin. Further, from the host-specificity patterns observed in other vertebrate taxa, we hypothesize that Gymnophiona have different dominant gut bacterial microbiomes at a higher taxonomic level when compared to the larvae of the other two amphibian orders (Anura and Caudata). We used 16S rRNA gene amplicon sequencing based on Illumina Nova sequencing platform to characterize and compare the gut (represented by faecal samples) and skin microbiome of I. bannanicus larvae (N = 13), a species distributed across South-East-Asia and the only caecilian species occurring in China. We compared our gut microbiome results with published anuran and caudate larval microbiomes. For I. bannanicus, a total of 4,053 operational taxonomic units (OTU) across 13 samples were detected. Alpha-diversity indices were significant between gut and skin samples. Non-metric multidimensional scaling analysis suggest that gut and skin samples each contained a distinct microbiome at OTU level. We record significant differences between the bacterial phyla of gut and skin samples in larvae of I. bannanicus. The study provides an overview of gut and skin bacterial microbiomes of a caecilian, while highlighting the major differences between larval microbiomes of the three amphibian orders. We find a partial overlap of gut bacterial microbiomes at phylum level for the three orders; however, the relative abundance of the dominant phyla is distinct. The skin and gut microbiomes are distinct with little overlap of species, highlighting that gut-skin axis is weak. This in turn suggests that many of the microbial species on skin and gut are functionally specialized to those locations. We also show that the skin microbiome is more diverse than the gut microbiome at species level; however, a reason for this could be a portion of the gut microbiome not being represented in faecal samples. These first microbiome information from a caecilian lay the foundation for comparative studies of the three amphibian orders.