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Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance. [ABSTRACT FROM AUTHOR]

Abstract Background Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages. Results The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages. Conclusions The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.

Background: Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages. Results: The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages. Conclusions: The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated. [ABSTRACT FROM AUTHOR]

Endozoicomonas is globally the most prevalent and consistently found bacterial genus associated with Cnidaria; strains of Endozoicomonas are known to codiversify with their coral hosts, and they are widely presumed to be key mutualists. A high abundance of Endozoicomonas in corals is associated with a decreased capacity to adjust to environmental change as well as with life history trade-offs. In other marine host–microbe systems, such as clams and fish, Endozoicomonas is a known parasite and pathogen. Genomic characteristics – such as genome size and structure, and the presence of eukaryote-like proteins and effectors – do not support the view that Endozoicomonas is an obligate and exclusive coral mutualist but may suggest a diverse and potentially intracellular lifestyle, including commensalism, parasitism, or pathogenicity. Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral– Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum. [ABSTRACT FROM AUTHOR]

The marine alpha-proteobacterium Phaeobacter inhibens engages in intermittent symbioses with microalgae. The symbiosis is biphasic and concludes in a parasitic phase, during which the bacteria release algaecidal metabolites in response to algal p-coumaric acid (pCA). The cell-wide effects of pCA on P. inhibens remain unknown. Herein, we report a microarray-based transcriptomic study and find that genes related to the oxidative stress response and secondary metabolism are upregulated most, while those associated with energy production and motility are downregulated in the presence of pCA. Among genes upregulated is a previously unannotated biosynthetic gene cluster and, using a combination of gene deletions and metabolic profiling, we show that it gives rise to an unreported siderophore, roseobactin. The simultaneous production of algaecides and roseobactin in the parasitic phase allows the bacteria to take up any iron that is released from dying algal cells, thereby securing a limited micronutrient.

Microbial mutualists provide substantial benefits to hosts that feed back to enhance the fitness of the associated microbes. In many systems, beneficial microbes colonize symbiotic organs, specialized host structures that house symbionts and mediate resources exchanged between parties. Mutualisms are characterized by net benefits exchanged among members of different species, however, inequalities in the magnitude of these exchanges could result in evolutionary conflict, destabilizing the mutualism. We investigated joint fitness effects of root nodule formation, the symbiotic organ of legumes that house nitrogen-fixing rhizobia in planta. We quantified host and symbiont fitness parameters dependent on the number of nodules formed using near-isogenic Lotus japonicus and Mesorhizobium loti mutants, respectively. Empirically estimated fitness functions suggest that legume and rhizobia fitness is aligned as the number of nodules formed increases from zero until the host optimum is reached, a point where aligned fitness interests shift to diverging fitness interests between host and symbiont. However, fitness conflict was only inferred when analyzing wild-type hosts along with their mutants dysregulated for control over nodule formation. These data demonstrate that to avoid conflict, hosts must tightly regulate investment into symbiotic organs maximizing their benefit to cost ratio of associating with microbes.

Domestication has transformed hundreds of wild plant species into productive cultivars for human utility. However, cultivation practices and intense artificial selection for yield may entail a hidden cost: the disruption of interactions between plants and beneficial microbiota. Here, we synthesize theory predicting that evolutionary trade-offs, genetic costs, and relaxed selection disrupt plant-microbial symbiosis under domestication, and review the wealth of new data interrogating these predictions in crops. We describe the agronomic practices, ecological scenarios, and genomic attributes that can result in the disruption of symbiosis, and highlight new work probing its molecular basis. To improve agricultural output and sustainability, research should develop breeding methods to optimize symbiotic outcomes in crop species.

A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe–microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health. [ABSTRACT FROM AUTHOR]

Entomopathogenic fungi (EPF) represent a specialized group of microorganisms which are distinguished by their ability to infect and kill arthropods. Ophiocordyceps sinensis , a well-known and highly valued EPF species, infects the soil-dwelling larvae of Thitarodes/Hepialus (ghost moths) on the Tibetan Plateau. After the mummification of ghost moth larvae, the fungus-insect parasite complex with a fruiting body is known as Chinese cordyceps. This complex is highly esteemed as one of the most valuable traditional Asian medicines. Notably, the ghost moth larvae can survive several months after infection with O. sinensis , which makes it an exceptional model for gaining insight into the complex mechanisms in the production of Chinese cordyceps. In this review we discussed the interactions of important EPF with some key insects. Specifically, we summarized the mechanisms of EPF's mode of entry and action, uncovering the intriguing processes behind their pathogenicity. We further discussed the influence of fungal toxins on insect physiology and development, revealing the multifaceted effects that result in host mortality. Moreover, we summarized the interaction of EPF with insect's microbiota, revealing the complex dynamics that impact the pathogenic process. However, our primary focus remains on the interaction of O. sinensis with the ghost moth. Such understandings will further improve our knowledge of this complex interplay between O. sinensis and ghost moth, ultimately contributing to the improvement of Chinese cordyceps production. • Brief overview of intricate mechanisms governing how entomopathogenic fungi enter and act within their insect hosts. • Further summary of the impact of fungal metabolites on insect physiology and development. • Outline of the interaction between Ophiocordyceps sinensis and Thitarodes/Hepialus ghost moth, specifically discussing how ghost moth larva detects and responds O. sinensis , and how O. sinensis evades host immunity and survives in the host hemolymph. • Discussion of the intricate interactions between entomopathogenic fungi and insect microbiota, elucidating the complex processes that underlie pathogenicity and their implications for pest management and ethnomedicinal production, particularly Chinese cordyceps. [ABSTRACT FROM AUTHOR]

The human gut microbiome interacts with each other and the host, which has significant effects on health and disease development. Intestinal homeostasis and inflammation are maintained by the dynamic interactions between gut microbiota and the innate and adaptive immune systems. Numerous metabolic products produced by the gut microbiota play a role in mediating cross‐talk between gut epithelial and immune cells. In the event of an imbalance between the immune system and microbiota, the body becomes susceptible to infections and homeostasis is compromised. This review mainly focuses on the interplay between microbes and the immune system, such as T‐cell‐ and B‐cell‐mediated adaptive responses to microbiota and signalling pathways for effective communication between the two. We have also highlighted the role of microbes in the activation of the immune response, the development of memory cells and how the immune system determines the diversity of human gut microbiota. The review also explains the relationship of commensal microbiota and their relation to the production of immunoglobulins. [ABSTRACT FROM AUTHOR]

The opportunistic protist Acanthamoeba , which interacts with other microbes such as bacteria, fungi, and viruses, shows significant similarity in cellular and functional aspects to human macrophages. Intracellular survival of microbes in this microbivorous amoebal host may be a crucial step for initiation of infection in higher eukaryotic cells. Therefore, Acanthamoeba –microbe adaptations are considered an evolutionary model of macrophage–pathogen interactions. This paper reviews Acanthamoeba as an emerging human pathogen and different ecological interactions between Acanthamoeba and microbes that may serve as environmental training grounds and a genetic melting pot for the evolution, persistence, and transmission of potential human pathogens. Acanthamoeba , a free-living protist that is ubiquitously dispersed in the environment, is becoming an increasingly important human pathogen. Multiple factors complicate the treatment and prevention of Acanthamoeba infections such as no approved drugs against the highly resistant and dormant cyst and metabolic similarities between Acanthamoeba and mammalian cells, making finding effective and safe therapies difficult. Acanthamoeba trophozoites graze different microbes; some of the engulfed microbes evade the intracellular killing process and this may mean that Acanthamoeba acts as a predator and reservoir for pathogens. Human macrophages and Acanthamoeba have significant similarities in their ultrastructure and phagocytic processes, so Acanthamoeba -adapted microbes can become more virulent to human cells. Acanthamoeba acts as a 'genetic melting pot' where exchange of cross-species genes arises. [ABSTRACT FROM AUTHOR]

Corals and their photosynthetic endosymbiotic algae (Symbiodiniaceae) produce a strong autofluorescent signal that spans the visible to near-infrared (NIR) spectrum. However, this broad- spectrum emission hinders the use of fluorescence in situ hybridisation (FISH) for the study of bacterial heterogeneity within the different niches of corals and Symbiodiniaceae, because FISH fluorophores also fluoresce within the visible to NIR spectrum. A solution to this impediment is to use fluorescence lifetime imaging microscopy (FLIM). The ‘lifetime’ property of fluorophores is a feature that enables sample (e.g. coral/Symbiodiniaceae) autofluorescence to be distinguished from FISH-labelled bacteria. In this manner, the location of bacteria around and within Symbiodiniaceae can be quantified along with their identity and spatial distribution. Furthermore, the ‘lifetime’ of the host and associated microbe cellular autofluorescence can be analysed in terms of endogenous fluorophore composition (e.g. metabolic co-factors, aromatic amino acids) and serves as information for symbiotic versus parasitic host-microbe association.

As sequencing techniques have advanced and become cheaper in recent years, there has been a rapid increase in the number of studies conducted into the role of the microbiome in coral health, physiology, and response to environmental change. However, there is substantial variation in the methodological approaches applied. For example, DNA extraction protocols and the types of tissues sampled from the coral meta-organism are known to influence the downstream analyses of the amplified microbial communities and subsequently the interpretation of the microbiome diversity, stability and role. Studies have generally focused on whole organisms, in which the coral sampling steps homogenize the meta-organism microhabitats, however other studies targeting specific microhabitats have identified sources of variation specific to distinct compartments of the coral’s microbial landscape. Here we present a comparative analysis of methodologies optimized for the generation of coral microbiome data from the coral tissues and whole coral fragments of two commonly studied branching coral genera with distinct tissue structure. We investigate the microbiome of the imperforate Pocillopora, where the coral tissue does not penetrate through the calcium carbonate matrix, and the perforate Acropora, where the coral tissues and skeleton are interwoven throughout the coral branch. Through comparing data generated from different DNA extraction protocols using fixed coral tissues isolated from the coral skeletal structure with fixed whole coral fragments, we identify sources of variation inherent to microbial data generated from different sample types, species, and extraction protocols.

A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe–microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.

Summary: Less than a handful of cuboid and squared cells have been described in nature, which makes them a rarity. Here, we show how Candidatus Thiosymbion cuboideus, a cube-like gammaproteobacterium, reproduces on the surface of marine free-living nematodes. Immunostaining of symbiont cells with an anti-fimbriae antibody revealed that they are host-polarized, as these appendages exclusively localized at the host-proximal (animal-attached) pole. Moreover, by applying a fluorescently labeled metabolic probe to track new cell wall insertion in vivo, we observed that the host-attached pole started septation before the distal one. Similarly, Ca. T. cuboideus cells immunostained with an anti-FtsZ antibody revealed a proximal-to-distal localization pattern of this tubulin homolog. Although FtsZ has been shown to arrange into squares in synthetically remodeled cuboid cells, here we show that FtsZ may also mediate the division of naturally occurring ones. This implies that, even in natural settings, membrane roundness is not required for FtsZ function.

Colour variation in marine invertebrates is typically attributed to intraspecific variability; however, the use of molecular tools to investigate its genetic basis has uncovered many instances of cryptic speciation. The colonial ascidian Distaplia bermudensis occurs in a wide array of colour morphs, ranging from all white to a dark blue tunic with yellow siphon apertures; yet careful observations of zooid and larval morphologies have not revealed any consistent difference among these colour morphs. In this study, we sampled the 5 main colour morph groupings of D. bermudensis from Wilmington, North Carolina (USA) and sequenced fragments of the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear 18S rRNA genes. Analyses of both genes revealed the presence of two distinct genetic lineages that corresponded to unique colour morphology groupings. We further characterized symbiotic microbial communities for four samples from each lineage by high‐throughput sequencing of partial 16S rRNA genes. Each genetic lineage also harboured unique symbiont communities that differed significantly in diversity and structure. Thus, the two genetic lineages detected herein corresponded to unique colour morphs and microbial communities, indicating that two distinct species coexist under the same scientific name. Further, our study reports the utility of symbiont profiling in resolving the taxonomic status of phenotypically variable ascidian species. [ABSTRACT FROM AUTHOR]

Ever since the publication of the seminal paper by Lynn Margulis in 1967 proposing the theory of the endosymbiotic origin of organelles, the study of the symbiotic relationships between unicellular eukaryotes and prokaryotes has received ever-growing attention by microbiologists and evolutionists alike. While the evolutionary significance of the endosymbiotic associations within protists has emerged and is intensively studied, the impact of these relationships on human health has been seldom taken into account. Microbial endosymbioses involving human eukaryotic pathogens are not common, and the sexually transmitted obligate parasite Trichomonas vaginalis and the free-living opportunistic pathogen Acanthamoeba represent two unique cases in this regard, to date. The reasons of this peculiarity for T. vaginalis and Acanthamoeba may be due to their lifestyles, characterized by bacteria-rich environments. However, this characteristic does not fully explain the reason why no bacterial endosymbiont has yet been detected in unicellular eukaryotic human pathogens other than in T. vaginalis and Acanthamoeba, albeit sparse and poorly investigated examples of morphological identification of bacteria-like microorganisms associated with Giardia and Entamoeba were reported in the past. In this review article we will present the body of experimental evidences revealing the profound effects of these examples of protist/bacteria symbiosis on the pathogenesis of the microbial species involved, and ultimately their impact on human health.

Insects share an intimate relationship with their gut microflora and this symbiotic association has developed into an essential evolutionary outcome intended for their survival through extreme environmental conditions. While it has been clearly established that insects, with very few exceptions, associate with several microbes during their life cycle, information regarding several aspects of these associations is yet to be fully unraveled. Acquisition of bacteria by insects marks the onset of microbial symbiosis, which is followed by the adaptation of these bacterial species to the gut environment for prolonged sustenance and successful transmission across generations. Although several insect–microbiome associations have been reported and each with their distinctive features, diversifications and specializations, it is still unclear as to what led to these diversifications. Recent studies have indicated the involvement of various evolutionary processes operating within an insect body that govern the transition of a free-living microbe to an obligate or facultative symbiont and eventually leading to the establishment and diversification of these symbiotic relationships. Data from various studies, summarized in this review, indicate that the symbiotic partners, i.e., the bacteria and the insect undergo several genetic, biochemical and physiological changes that have profound influence on their life cycle and biology. An interesting outcome of the insect-microbe interaction is the compliance of the microbial partner to its eventual genome reduction. Endosymbionts possess a smaller genome as compared to their free-living forms, and thus raising the question what is leading to reductive evolution in the microbial partner. This review attempts to highlight the fate of microbes within an insect body and its implications for both the bacteria and its insect host. While discussion on each specific association would be too voluminous and outside the scope of this review, we present an overview of some recent studies that contribute to a better understanding of the evolutionary trajectory and dynamics of the insect-microbe association and speculate that, in the future, a better understanding of the nature of this interaction could pave the path to a sustainable and environmentally safe way for controlling economically important pests of crop plants.

Ever since the publication of the seminal paper by Lynn Margulis in 1967 proposing the theory of the endosymbiotic origin of organelles, the study of the symbiotic relationships between unicellular eukaryotes and prokaryotes has received ever-growing attention by microbiologists and evolutionists alike. While the evolutionary significance of the endosymbiotic associations within protists has emerged and is intensively studied, the impact of these relationships on human health has been seldom taken into account. Microbial endosymbioses involving human eukaryotic pathogens are not common, and the sexually transmitted obligate parasite Trichomonas vaginalis and the free-living opportunistic pathogen Acanthamoeba represent two unique cases in this regard, to date. The reasons of this peculiarity for T. vaginalis and Acanthamoeba may be due to their lifestyles, characterized by bacteria-rich environments. However, this characteristic does not fully explain the reason why no bacterial endosymbiont has yet been detected in unicellular eukaryotic human pathogens other than in T. vaginalis and Acanthamoeba , albeit sparse and poorly investigated examples of morphological identification of bacteria-like microorganisms associated with Giardia and Entamoeba were reported in the past. In this review article we will present the body of experimental evidences revealing the profound effects of these examples of protist/bacteria symbiosis on the pathogenesis of the microbial species involved, and ultimately their impact on human health. [ABSTRACT FROM AUTHOR]

Insects share an intimate relationship with their gut microflora and this symbiotic association has developed into an essential evolutionary outcome intended for their survival through extreme environmental conditions. While it has been clearly established that insects, with very few exceptions, associate with several microbes during their life cycle, information regarding several aspects of these associations is yet to be fully unraveled. Acquisition of bacteria by insects marks the onset of microbial symbiosis, which is followed by the adaptation of these bacterial species to the gut environment for prolonged sustenance and successful transmission across generations. Although several insect–microbiome associations have been reported and each with their distinctive features, diversifications and specializations, it is still unclear as to what led to these diversifications. Recent studies have indicated the involvement of various evolutionary processes operating within an insect body that govern the transition of a free-living microbe to an obligate or facultative symbiont and eventually leading to the establishment and diversification of these symbiotic relationships. Data from various studies, summarized in this review, indicate that the symbiotic partners, i.e., the bacteria and the insect undergo several genetic, biochemical and physiological changes that have profound influence on their life cycle and biology. An interesting outcome of the insect-microbe interaction is the compliance of the microbial partner to its eventual genome reduction. Endosymbionts possess a smaller genome as compared to their free-living forms, and thus raising the question what is leading to reductive evolution in the microbial partner. This review attempts to highlight the fate of microbes within an insect body and its implications for both the bacteria and its insect host. While discussion on each specific association would be too voluminous and outside the scope of this review, we present an overview of some recent studies that contribute to a better understanding of the evolutionary trajectory and dynamics of the insect-microbe association and speculate that, in the future, a better understanding of the nature of this interaction could pave the path to a sustainable and environmentally safe way for controlling economically important pests of crop plants. [ABSTRACT FROM AUTHOR]

ABSTRACT Accidental oil spills from shipping and during extraction can threaten marine biota, particularly coral reef species which are already under pressure from anthropogenic disturbances. Marine sponges are an important structural and functional component of coral reef ecosystems; however, despite their ecological importance, little is known about how sponges and their microbial symbionts respond to petroleum products. Here, we use a systems biology-based approach to assess the effects of water-accommodated fractions (WAF) of crude oil, chemically enhanced water-accommodated fractions of crude oil (CWAF), and dispersant (Corexit EC9500A) on the survival, metamorphosis, gene expression, and microbial symbiosis of the abundant reef sponge Rhopaloeides odorabile in larval laboratory-based assays. Larval survival was unaffected by the 100% WAF treatment (107 μg liter−1 polycyclic aromatic hydrocarbon [PAH]), whereas significant decreases in metamorphosis were observed at 13% WAF (13.9 μg liter−1 PAH). The CWAF and dispersant treatments were more toxic, with decreases in metamorphosis identified at 0.8% (0.58 μg liter−1 PAH) and 1.6% (38 mg liter−1 Corexit EC9500A), respectively. In addition to the negative impact on larval settlement, significant changes in host gene expression and disruptions to the microbiome were evident, with microbial shifts detected at the lowest treatment level (1.6% WAF; 1.7 μg liter−1 PAH), including a significant reduction in the relative abundance of a previously described thaumarchaeal symbiont. The responsiveness of the R. odorabile microbial community to the lowest level of hydrocarbon treatment highlights the utility of the sponge microbiome as a sensitive marker for exposure to crude oils and dispersants. IMPORTANCE Larvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the ecological importance of sponges, uncontrolled hydrocarbon releases from shipping accidents or production could affect sponge recruitment, which would have concomitant consequences for reef ecosystem function. Author Video: An author video summary of this article is available.

Trichomonas vaginalis is an anaerobic protist, responsible for the most prevalent non-viral sexually transmitted infection in humans. One of the most intriguing aspects of T. vaginalis pathobiology is the complex relationship with intracellular microbial symbionts: a group of dsRNA viruses belonging to family of Totiviridae (T. vaginalis virus), and eubacteria belonging to the Mycoplasma genus, in particular M ycoplasma hominis. Both microorganisms seem to strongly influence the lifestyle of T. vaginalis , suggesting a role of the symbiosis in the high variability of clinical presentation and sequelae during trichomoniasis. In the last few years many aspects of this unique symbiotic relationship have been investigated: M. hominis resides and replicates in the protozoan cell, and T. vaginalis is able to pass the bacterial infection to both mycoplasma-free protozoan isolates and human epithelial cells; M. hominis synergistically upregulates the proinflammatory response of human monocytes to T. vaginalis. Furthermore, the influence of M. hominis over T. vaginalis metabolism and physiology has been characterized. The identification of a novel species belonging to the class of Mollicutes (Candidatus Mycoplasma girerdii) exclusively associated to T. vaginalis opens new perspectives in the research of the complex series of events taking place in the multifaceted world of the vaginal microbiota, both under normal and pathological conditions. [ABSTRACT FROM AUTHOR]

The studied area is in the buffer zone of the Northwest Biosphere, in the Peruvian northwest. In this place, traditional agriculture is practiced in the riverbed during the flood time. After the rainy season, when the flood reduces, between April and June, crops are cultivated. The soil is translocated from the slope, were the Prosopis trees grow. The hypothesis is that the soil used for traditional agriculture includes more nitrogen and phosphorus, on the basis of the microbial and fungi symbiosis characteristic for the Fabaceae family. This soil will be removed by the flood. The study was conducted in Jaguay Negro, where the soil was transported from the slope, and in Casitas, where the agriculture uses soil from the gully. Interviews and soil fertility were analyzed. The result shows nitrogen and phosphorus in a middle level, which, as for the dry ecosystem, has a positive influence for the symbioses. This practice of orillado can be interpreted as a form of ecological agriculture since it uses the microbial symbiosis and mycorrhizal fungi. The orillado can be interesting as a resilient response from the local population to the Climate Change. [ABSTRACT FROM AUTHOR]

DPANN archaea are an enigmatic superphylum that are difficult to isolate and culture in the laboratory due to their specific culture conditions and apparent ectosymbiotic lifestyle. Here, we successfully isolated and cultivated a coculture system of a novel Nanobdellota archaeon YN1 and its host Sulfurisphaera ohwakuensis YN1HA. We characterized the coculture system by complementary methods, including metagenomics and metabolic pathway analysis, fluorescence microscopy, and high-resolution electron cryo-tomography (cryoET). We show that YN1 is deficient in essential metabolic processes and requires host resources to proliferate. CryoET imaging revealed an enormous attachment organelle present in the YN1 envelope that forms a direct interaction with the host cytoplasm, bridging the two cells. Together, our results unravel the molecular and structural basis of ectosymbiotic relationship between YN1 and YN1HA. This research broadens our understanding of DPANN biology and the versatile nature of their ectosymbiotic relationships., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Summary: Fungal symbioses are ubiquitous in plants, but their effects have mostly been studied in seed plants. This study aimed to assess the diversity of fungal endophyte effects in a bryophyte and identify factors contributing to the variability of outcomes in these interactions. Fungal endophyte cultures and axenic liverwort clones were isolated from wild populations of the liverwort, Marchantia polymorpha. These collections were combined in a gnotobiotic system to test the effects of fungal isolates on the growth rates of hosts under laboratory conditions. Under the experimental conditions, fungi isolated from M. polymorpha ranged from aggressively pathogenic to strongly growth‐promoting, but the majority of isolates caused no detectable change in host growth. Growth promotion by selected fungi depended on nutrient concentrations and was inhibited by coinoculation with multiple fungi. The M. polymorpha endophyte system expands the resources for this model liverwort. The experiments presented here demonstrate a wealth of diversity in fungal interactions even in a host reported to lack standard mycorrhizal symbiosis. In addition, they show that some known pathogens of vascular plants live in M. polymorpha and can confer benefits to this nonvascular host. This highlights the importance of studying endophyte effects across the plant tree of life. [ABSTRACT FROM AUTHOR]

Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3–V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334–26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.

Sugary kefir beverage is produce by fermenting raw sugar solution with kefir grains, the latter consisting of polysaccharide and microorganisms. This beverage, with great consumption in countries such as USA, Japan, France, and Brazil, represents a promising market to functional cultured drinks. This paper reviews the microbial diversity and interaction, kinetics, safety, and bioactivities of sugary kefir fermentation. The literature reviewed here demonstrates that sugary kefir possesses a similar microbial association relative to traditional milk kefir fermentation, especially among lactic acid bacteria and yeast species, such as Lactobacillus , Leuconostoc, Kluyveromyces , Pichia, and Saccharomyces . However, a selective pressure at species level is generally observed, as, for example, the stimulation of Saccharomyces species metabolism, leading to a high content of alcohol in the final product. This also seems to stimulate the growth of acetic acid bacteria that benefit of increased ethanol production to acetic acid metabolism. Existing reports have suggested important bioactivities associated with sugary kefir beverage consumption, such as antimicrobial, antiedematogenic, anti-inflammatory, antioxidant, cicatrizing, and healing activities. Other alternative non-dairy substrates, such as fruits, vegetables, and molasses, have also been tested for adaptation of kefir grains and production of functional beverages with distinct sensory characteristics. This diversification is of crucial importance for the production of new probiotic products to provide people with special needs (lactose intolerance) and vegan consumers. [ABSTRACT FROM AUTHOR]

Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3-V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334-26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity. [ABSTRACT FROM AUTHOR]

Modern day endodontics is undergoing a massive change with the introduction of new molecular based techniques for microbial identification. This review focuses on the microbiota in untreated and root-filled canals. It will also describe briefly the recent developments in microbial identification and the mechanisms by which certain species of microbes are able to invade and establish themselves in the root canal.

Herbicide tolerance in crops and weeds is considered to be monotrophic, i.e. determined by the relative susceptibility of the physiological process targeted and the plant's ability to metabolise and detoxify the agrochemical. A growing body of evidence now suggests that endophytes, microbes that inhabit plant tissues and provide a range of growth, health and defence enhancements, can contribute to other types of abiotic and biotic stress tolerance. The current evidence for herbicide tolerance being bitrophic, with both free-living and plant-associated endophytes contributing to tolerance in the host plant, has been reviewed. We propose that endophytes can directly contribute to herbicide detoxification through their ability to metabolise xenobiotics. In addition, we explore the paradigm that microbes can 'prime' resistance mechanisms in plants such that they enhance herbicide tolerance by inducing the host's stress responses to withstand the downstream toxicity caused by herbicides. This latter mechanism has the potential to contribute to the growth of non-target-site-based herbicide resistance in weeds. Microbial endophytes already contribute to herbicide detoxification in planta, and there is now significant scope to extend these interactions using synthetic biology approaches to engineer new chemical tolerance traits into crops via microbial engineering. © 2015 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Intraspecific variation in dietary breadth can influence important ecological and evolutionary processes, yet the mechanisms generating this variation are usually unknown. Maternally transmitted bacterial symbionts frequently infect insect herbivores, and many have been shown to mediate key ecological interactions. For polyphagous herbivores, infection with particular symbionts is often strongly correlated with feeding on particular plant species, suggesting that facultative symbionts might directly determine herbivore food plant specificity. However, previous tests of this hypothesis have returned inconsistent results, providing little empirical support for a causal relationship between facultative symbiont infection and dietary breadth., Here, we investigate whether heritable facultative symbionts mediate dietary breadth in the polyphagous aphid, Aphis craccivora. We first determined that asexual clones of the aphid differ dramatically in performance across two leguminous food plants, locust and alfalfa, and could be considered biotypes with distinct ecological characteristics. The heritable symbiont Arsenophonus is strongly associated with locust-origin aphids., We created experimental lines that share aphid genotypes but differed with respect to Arsenophonus infection status, and compared performance across three food plant species. Naturally Arsenophonus-infected clones performed 2-4× better on locust and up to 75% worse on two alternate plant species than uninfected controls, clearly demonstrating that Arsenophonus promotes specialization on locust. In both laboratory and field experiments, uninfected locust- and alfalfa-origin clones exhibited similar and modest performance on locust, indicating that the 'locust-associated biotype' would not exist without Arsenophonus., We also hypothesized that moving Arsenophonus, via transinfection, to an alfalfa-origin lineage would improve performance on locust and serve to expand dietary breadth. Indeed, transinfection doubled aphid performance on locust and halved aphid performance on alfalfa. However, because this aphid lineage naturally performs better on alfalfa, the transinfected symbiont functionally equalized aphid performance between locust and alfalfa, making the alfalfa biotype more generalized. Thus, the same symbiont can either reduce or expand dietary breadth, depending on host genotype., Our results unequivocally demonstrate that symbiont gain or loss can instantaneously and substantially change the topology of food plant use in a polyphagous insect, modifying diet in ways that potentially influence the insect's ecological niche, evolutionary trajectory and pest status. [ABSTRACT FROM AUTHOR]

A combination ofDekkera bruxellensisandGluconacetobacter intermediusis used as a model system to emulate the microbial symbiosis between yeast and acetic acid bacteria in kombucha, and to study glucuronic acid (GlcUA) production in this system. In the current study, the addition ofLactobacillus caseiand variations in the fermentative conditions, such as sucrose concentration, temperature and duration, were examined to evaluate their effects on GlcUA formation. Results showed thatL. caseiacts as a supporter species and stimulated GlcUA production in the kombucha symbiosis model to levels 54.1% greater than in the control. Varying the fermentation parameters also affected GlcUA production. Therefore, the range of each factor value was screened and restricted to achieve a higher amount of target acid, as it was 5–15%, 25–31°C, 3–7 days, and 5–7 units in sucrose concentration, temperature, fermentation time and initial pH value, respectively. These findings are an important step for optimizing GlcUA production by this model system. [ABSTRACT FROM AUTHOR]

A combination of Dekkera bruxellensis and Gluconacetobacter intermedius is used as a model system to emulate the microbial symbiosis between yeast and acetic acid bacteria in kombucha, and to study glucuronic acid (GlcUA) production in this system. In the current study, the addition of Lactobacillus casei and variations in the fermentative conditions, such as sucrose concentration, temperature and duration, were examined to evaluate their effects on GlcUA formation. Results showed that L. casei acts as a supporter species and stimulated GlcUA production in the kombucha symbiosis model to levels 54.1% greater than in the control. Varying the fermentation parameters also affected GlcUA production. Therefore, the range of each factor value was screened and restricted to achieve a higher amount of target acid, as it was 5-15%, 25-31°C, 3-7 days, and 5-7 units in sucrose concentration, temperature, fermentation time and initial pH value, respectively. These findings are an important step for optimizing GlcUA production by this model system. [ABSTRACT FROM AUTHOR]

The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0-9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community. [ABSTRACT FROM AUTHOR]

Cockroaches are a group of insects that evolved early in geological time. Because of their antiquity, they for the most part display generalized behavior and physiology and accordingly have frequently been used as model insects to examine physiological and biochemical mechanisms involved with water balance, nutrition, reproduction, genetics, and insecticide resistance. As a result, a considerable amount of information on these topics is available. However, there is much more to be learned by employing new protocols, microchemical analytical techniques, and molecular biology tools to explore many unanswered questions. [ABSTRACT FROM AUTHOR]

The authors explore the physiological role of aryl hydrocarbon receptor (AhR) resulting from various AhR ligands and the multiplicity of AhR-expressing cells in host-microbial symbiosis in mammals. They describe the role of AhR in immune homeostasis and autoimmunity. They also discuss the significance of the interaction between the enzyme indoleamine-2,3-dioxygenase 1 (IDO1) and AhR in the context of autoimmune diseases.