Large Microbial Community Research Articles

Nanopore sequencing evidenced the presence of fish bacterial pathogens in the sea louse (Caligus rogercresseyi) microbiota collected from distant salmon farms in Chile

The recognized negative impacts of the ectoparasite Caligus rogercresseyi in the Chilean salmon aquaculture are primarily related to environmental and economic issues. However, recent evidence suggests a large and diverse microbial community associated with sea lice, where fish bacteria pathogens emerge as a sanitary concern. This study aimed to characterize the bacterial community associated with C. rogercresseyi, focusing on those microorganisms with potential impacts in salmon welfare. The sea lice-associated microbiota was identified using the microbial full-length16S rRNA gene sequencing by Oxford Nanopore Technology. Sea lice specimens were collected from three salmon farming zones in Los Lagos, Aysén, and Magallanes, Southern Chile. The bioinformatic analyses revealed DNA from potential pathogens inhabiting the C. rogercresseyi microbiota, representing 7.86% of the annotated sequences. Among the sampled sites, the most significant number of pathogenic bacteria DNA was found in Los Lagos (up to 23,6%), followed by Aysen (1,8%) and Magallanes (0.3%). Herein, genetic evidence from a total of 30 potential fish bacterial pathogens species were identified. Notably, fourteen Vibrio spp. were predominantly found in the Los Lagos region, while six Tenacibaculum spp. were more equally distributed among the sites. A core of five fish pathogens was observed in all farming zones, including Aliivibrio wodanis, Tenacibaculum dicentrarchi, Tenacibaculum ovolyticum, Tenacibaculum soleae, and Vibrio splendidus. Based on the reported findings, sea lice emerge as a potential reservoir for fish diseases in the aquatic environment.

Metagenomic and Recombination Analyses of Antimicrobial Resistance Genes from Recreational Waters of Black Sea Coastal Areas and Other Marine Environments Unveil Extensive Evidence for Their both Intrageneric and Intergeneric Transmission across Genetically Very Diverse Microbial Communities.

Microbial communities of marine coastal recreation waters have become large reservoirs of AMR genes (ARGs), contributing to the emergence and transmission of various zoonotic, foodborne and other infections that exhibit resistance to various antibiotics. Thus, it is highly imperative to determine ARGs assemblages as well as mechanisms and trajectories of their transmission across these microbial communities for our better understanding of the evolutionary trends of AMR (AMR). In this study, using metagenomics approaches, we screened for ARGs in recreation waters of the Black Sea coastal areas of the Batumi City (Georgia). Also, a large array of the recombination detection algorithms of the SplitsTree, RDP4, and GARD was applied to elucidate genetic recombination of ARGs and trajectories of their transmission across various marine microbial communities. The metagenomics analyses of sea water samples, obtained from across the above marine sites, could identify putative ARGs encoding for multidrug resistance efflux transporters mainly from the Major Facilitator and Resistance Nodulation Division superfamilies. The data, generated by SplitsTree (fit ≥95.619; bootstrap values ≥ 95; Phi p≤0.0494), RDP4 (p≤0.0490), and GARD, provided strong statistical evidence not only for intrageneric recombination of these ARGs, but also for their intergeneric recombination across fairly large and diverse microbial communities of marine environment. These bacteria included both human pathogenic and nonpathogenic species, exhibiting collectively the genera of Vibrio, Aeromonas, Synechococcus, Citromicrobium, Rhodobacteraceae, Pseudoalteromonas, Altererythrobacter, Erythrobacter, Altererythrobacter, Marivivens, Xuhuaishuia, and Loktanella. The above nonpathogenic bacteria are strongly suggested to contribute to ARGs transmission in marine ecosystems.

Cropping management in a livestock-pasture-crop integration modifies microbial communities, activity, and soil health score.

Understanding indicators of soil health is crucial for developing agricultural systems that are sustainable and climate resilient. Labile soil carbon (C), microbial properties, and nutrient status are all incorporated into the Haney Soil Health Tool with the goal of summarizing several indicators into one index. Monthly soil samples from an integrated crop-livestock system in Central Texas were collected from 2017 to 2019. Fields represented a range of management practices, including cover crops, no-till, rotational grazing, and a native prairie remnant. Soil samples were analyzed for total C, water-soluble C, macro- and micronutrient content and bioavailability, and phospholipid fatty acids (PLFAs). Microbial activity was determined via a 24-h CO2 incubation. Soil health score, C, and PLFAs were well correlated with each other. The greatest total PLFA (219.5nmol g-1 soil) and organic C (54.3g kg-1 soil) were found in the native prairie, and the lowest were found in the unfertilized continuous-corn system (60.5nmol PLFAs g-1 soil and 24.0g organic C kg-1 soil). Of all agroecosystems, the perennial grazing system (soil health score, 24.7) was most similar to the native prairie (soil health score, 27.4), having high soil C and a large microbial community. Of the row cropping systems, the no-till system approached the perennial systems better than the conventional till and unfertilized conventional till (soil health score, 11.1 vs. 8.0 and 5.3, respectively). This study highlights the value of perennial grass grazing in agroecosystems and appropriate best management practices. Expanding this analysis to other sites may provide additional insight.

Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data

BackgroundTime-lapse microscopy live-cell imaging is essential for studying the evolution of bacterial communities at single-cell resolution. It allows capturing detailed information about the morphology, gene expression, and spatial characteristics of individual cells at every time instance of the imaging experiment. The image analysis of bacterial "single-cell movies" (videos) generates big data in the form of multidimensional time series of measured bacterial attributes. If properly analyzed, these datasets can help us decipher the bacterial communities' growth dynamics and identify the sources and potential functional role of intra- and inter-subpopulation heterogeneity. Recent research has highlighted the importance of investigating the role of biological "noise" in gene regulation, cell growth, cell division, etc. Single-cell analytics of complex single-cell movie datasets, capturing the interaction of multiple micro-colonies with thousands of cells, can shed light on essential phenomena for human health, such as the competition of pathogens and benign microbiome cells, the emergence of dormant cells (“persisters”), the formation of biofilms under different stress conditions, etc. However, highly accurate and automated bacterial bioimage analysis and single-cell analytics methods remain elusive, even though they are required before we can routinely exploit the plethora of data that single-cell movies generate.ResultsWe present visualization and single-cell analytics using R (ViSCAR), a set of methods and corresponding functions, to visually explore and correlate single-cell attributes generated from the image processing of complex bacterial single-cell movies. They can be used to model and visualize the spatiotemporal evolution of attributes at different levels of the microbial community organization (i.e., cell population, colony, generation, etc.), to discover possible epigenetic information transfer across cell generations, infer mathematical and statistical models describing various stochastic phenomena (e.g., cell growth, cell division), and even identify and auto-correct errors introduced unavoidably during the bioimage analysis of a dense movie with thousands of overcrowded cells in the microscope's field of view.ConclusionsViSCAR empowers researchers to capture and characterize the stochasticity, uncover the mechanisms leading to cellular phenotypes of interest, and decipher a large heterogeneous microbial communities' dynamic behavior. ViSCAR source code is available from GitLab at https://gitlab.com/ManolakosLab/viscar.

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer.

Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L−1 and a phosphate content of 0.02mg.L−1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria (“Candidatus Acetothermia”) with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.

Linking the Diversity of Yeasts Inherent in Starter Cultures to Quorum Sensing Mechanism in Ethnic Fermented Alcoholic Beverages of Northeast India

In this review, the relevance of diversity of yeasts and their interactive association in household ethnic fermentation are discussed. The longstanding traditional household fermentation practice involves preparation of fermented product such as alcoholic beverages from various indigenous agricultural products with the help of microorganisms cultivated from local environment and perpetuated for hundreds of years through generations indoctrinating an indigenous knowledge system. Northeast India is known for its rich physiographic and geo-demographic diversity and is home to several ethnicities who follow unique practices of household traditional fermentation. The diversity of yeasts present within the microbial inoculum used for fermentation by different indigenous communities has been keenly studied and reported to be unique in spite of their common source for starter substrates.Saccharomycesyeasts are primarily involved in alcoholic fermentation, whereas non-Saccharomycesyeasts, which are reportedly confined to a particular geographical region, have been reported to contribute toward the final outcome of fermentation produce. During fermentation, interaction among these large microbial communities and their resulting physiological expression within the fermentation micro-environment is believed to affect the final quality of the product. Mechanism of quorum sensing plays an important role in these interactions in order to maintain proportionality of different yeast populations wherein the quorum sensing molecules not only regulate population density but also effectively aid in enhancement of alcoholic fermentation. Additionally, various secondary metabolites, which are secreted as a result of inter-species interactions, have been found to affect the quality of beverages produced. This review concludes that diverse species of yeasts and their interaction within the fermentation micro-environment influence the sustainability and productivity of household ethnic fermentation.

Identification and Phylogenetic Analyses of Anaerobic Sulfidogenic Bacteria in Two Algerian Oilfield Water Injection Samples

Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon. For the first time, sulfidogenic communities in injection waters of two Algerian oilfields, Tin Fuin Tabankort (IT3) and Stah (IS2) were examined using the 16S rRNA gene cloning and sequencing approach. Water samples were inoculated into selective medium for sulfate-reducing bacteria and incubated under anaerobic conditions at 45 °C. The total number of culturable sulfidogenic microorganisms in the samples obtained from the two sampled waters (IT3 and IS2) was 2.4 × 105 cells/mL and 3.9 × 104 cells/mL, respectively. Scanning electron microscopy analyses showed different morphological forms reflecting the diversity of sulfidogenic communities. 16S rRNA gene sequencing and phylogenetic diversity analyses revealed that both water reservoirs harbor large amounts of anaerobic bacteria. However, a majority of all the sequences analyzed (e.g., 34% in the IS2 and 84% in the IT3 samples) were not assigned to any known bacterial group, suggesting that subsurface waters harbor very large sulfidogenic anaerobic microbial communities of as yet undescribed bacterial phyla. Proteobacteria were found to be the most dominant phylum in the IS2 sample (49%); however, no Proteobacteria were detected at the IT3 production well. The Firmicutes phylum (10%) was detected in the two water samples, whereas Bacteroidetes phylum (7%) was retrieved only in IT3. The most abundant related genera were: Desulfotomaculum, Porphyrobacter, Hyphomicrobium, Acidocella, Comamonas, Ramlibacter, Pseudomonas, Enterobacter and Flavitalea. No shared operational taxonomic units were observed among the two samples analyzed, demonstrating the uniqueness of each subsurface water well. This study demonstrates the diversity of the sulfidogenic bacteria that might play a critical role in the souring mediated corrosion of metallic oilfield pipelines. This information could help oilfield companies develop better anticorrosion treatments and strategies.

Intestinal microbiota and kidney diseases.

Large microbial communities reside in the gut as an endogenous organ and interact with the host physiology through symbiotic relationships, affecting health. Recent advances in high-throughput sequencing techniques have made it possible to better understand these complex microbial communities and their effects on hosts. Animal and clinical studies have provided considerable evidence to show that the microbiota plays an important role in chronic kidney disease, acute kidney injury, nephrolithiasis, and kidney transplantation by altering the functions of the intestinal barrier, regulating local and systemic inflammation, controlling production of metabolic components, and affecting immune responses. Although the exact mechanism underlying the microbial shift and its impact on disease progression remains uncertain, the kidney-gut interaction clearly plays a significant role in onset and progression of kidney disease and, therefore, holds promise as a therapeutic target. Here, we review recent literature pertaining to the bidirectional relationship between microbes and humans in various kidney diseases and discuss the future direction of microbial research in nephrology.

The interplay between Trichuris and the microbiota.

Parasitic worms are amongst the most common pathogens to infect humans and have a long-established history of inflicting disease in their hosts. There is a large body of evidence that states intestine-dwelling helminths ensure their survival by influencing the host immune response against them. In recent years, it has become apparent that the large and diverse microbial communities that exist in the gastrointestinal (GI) tract of the host and within the parasite itself have a pivotal role in worm survival and persistence. Using a variety of mouse models (including laboratory, germ-free and rewilded mice), there have been new insights into how bacteria and worms interact with each other; this includes the discovery that Trichuris is unable to hatch and/or infect their host in the absence of bacteria, and that these worms contain a Trichuris-specific gut microbiota. These interactions are determined in part by the capacity of the host, gut microbiota and worms to communicate via metabolites such as butyrate, which are microbially derived and have known immunoregulatory properties. By exploring the contribution of gut bacteria to worm infections and the intricate relationship that exists between them, an exciting and emerging field in whipworm parasitology is established.

Drift dynamics in microbial communities and the effective community size.

The structure and diversity of all open microbial communities are shaped by individual births, deaths, speciation and immigration events; the precise timings of these events are unknowable and unpredictable. This randomness is manifest as ecological drift in the population dynamics, the importance of which has been a source of debate for decades. There are theoretical reasons to suppose that drift would be imperceptible in large microbial communities, but this is at odds with circumstantial evidence that effects can be seen even in huge, complex communities. To resolve this dichotomy we need to observe dynamics in simple systems where key parameters, like migration, birth and death rates can be directly measured. We monitored the dynamics in the abundance of two genetically modified strains of Escherichia coli, with tuneable growth characteristics, that were mixed and continually fed into 10 identical chemostats. We demonstrated that the effects of demographic (non-environmental) stochasticity are very apparent in the dynamics. However, they do not conform to the most parsimonious and commonly applied mathematical models, where each stochastic event is independent. For these simple models to reproduce the observed dynamics we need to invoke an 'effective community size', which is smaller than the census community size.

Chemistry of Microbial Life in Phyllosphere: A Review

The phyllosphere is associated with a diverse community of microorganisms. The association of phyllosphere microbes and host plant affects the both health and function of plant. The phyllosphere supports a huge diversity of microbes. Phyllospheric microbes mostly include bacteria and fungi, work as mutualists and promote the plant growth and make them tolerant to various environmental stresses. They use the plant as habitat for their own growth and reproduction. The little informations are known about the colonization of pathogenic and beneficial bacteria in the phyllosphere across the whole plant life-cycle which limits our abilities to understand the role of phyllospheric microbes in plant performance. The phyllosphere is actually the habitat of microbes provided by the aboveground parts of plants. It supports a large and complex microbial community on global scale. This review covers all information about the diversity, source, nature and composition of microbial life in phyllosphere.

The magic world of whiskey microbiota

Modern metagenomics techniques in combination with next generation sequencing are increasingly used for research of numerous environments inhabited by diverse microbiota. In the present study we focused on a rather unusual environment for their growth, a forgotten bottle of blended Scotch whiskey. Whiskey is a world-known popular spirit, traditionally produced in a series of steps comprising malting of barley, fermenting the malt to an alcoholic wort, distilling and at least 3-year long maturation in oak casks, followed by filtration. In the process, notably in the fermentation, microorganisms play a crucial role. However, we were primarily interested in potential microbiological and chemical changes that might have taken place over the years while the half-empty whiskey bottle was left open. We found that only a very low number of aerobic mesophilic bacteria survived in it while the ethanol content decreased from 40 % to approximately 30 %. Interestingly, the metagenomics analysis showed there was a large and diverse microbial community present in the forgotten whiskey. Among the most abundant microorganisms were members of human commensal microbiota, some potentially disease-causing and also food spoiling bacteria, in particular genus Pseudomonas. Surprisingly, we even found a non-negligible number of typically environmental bacterial species.

PSI-10 Effects of a Moderate and Aggressive Implant Strategy on the Rumen Microbial Community in Steers

Abstract The effects of growth-promoting implant strategies have been well-defined in research for their ability to impact growth performance in beef cattle. Production-relevant microbiomes in the rumen have also been associated with growth traits. However, the role of implant strategies on the rumen microbiome is not understood. The objective was to determine if varying doses of implant hormones cause gain-associated ruminal microbial community shifts. To assess this, a completely randomized design was used and 336 fall-born steers from the germplasm evaluation population between 450–470 days of age at the U.S. Meat Animal Research Center (Clay Center, NE) were divided into two treatment groups: 1) a moderate implant strategy of Revalor-IS (80 mg trenbolone acetate, 16 mg estradiol) followed by Revalor-S (120 mg trenbolone acetate, 24 mg estradiol) and 2) an aggressive implant strategy of Revalor-IS followed by Revalor-200 (200 mg trenbolone acetate, 20 mg estradiol). Steers were fed the same diet (57.0% dry-rolled corn, 30% wet distiller’s grains with solubles, 8.0% alfalfa hay, 4.25% supplement, and 0.75% urea, DM basis). Body weights were collected once per month with initial weights of 439.8 ± 43.1 kg. After implants were administered for 84 days, rumen content was collected via orogastric tubing. Samples were sequenced targeting bacterial V1-V3 16S rRNA gene regions, V3-V4 for archaea, and partial 18S rRNA gene of protozoa. Sequences were processed in R utilizing Phyloseq and analyzed with DESeq2 to test differential abundances. Production data between implant strategies were analyzed using a mixed model ANOVA (SASv9.4, Cary, NC). Alpha- and beta-diversity between strategies did not differ for bacteria, archaea, or protozoa (P &amp;gt; 0.05). Average daily gain was different (P = 0.01; 1.72 vs 1.66 ± 0.02 kg, aggressive vs moderate, respectively); however, large microbial community shifts were not associated implant strategy. USDA is an equal opportunity provider and employer.

Oral microbiota and dental caries data from monozygotic and dizygotic twin children

There are recent studies which aimed to detect the inheritance on the etiology of dental caries exploring oral composition. We present data on the oral microbiota and its relation with dental caries and other factors in monozygotic (MZ) and dizygotic (DZ) twin children. Following clinical investigation, DNA samples were collected and isolated from saliva of 198 patients (49 MZ and 50 DZ twins) with an average age of 9.7 ± 2.7 years. Salivary bacterial microbiota analysis was performed using high throughput amplicon sequencing method targeting V3-V4 region of the 16S rRNA gene. A total of 8,297,859 raw reads corresponding to 41,908 reads per sample were obtained on average. The QIIME2-deblur workflow was used for 16S rRNA amplicon analysis. Microbiome similarity analyses between twins (based on Bray-Curtis dissimilarity, weighted and unweighted Unifrac distances) showed that monozygotic twins share more bacterial microbial content compared to dizygotic twins. This is a large microbial community dataset of MZ and DZ twins with or without dental findings which can be further used for children oral microbiome profile explorations.

Balancing the hydrogen books.

Abiotic sources of H2 in the lithosphere outweigh the sinks, with the balance potentially being available to a large microbial community.

Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology.

Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species–species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.

Peculiar attenuation of soil toluene at contaminated coking sites

In the soil of contaminated coking sites, polycyclic aromatic hydrocarbons (PAHs) and benzene, toluene, ethylbenzene and xylene (BTEX) are typical indicator compounds. Generally, PAHs are enriched in the topsoil layer. BTEX, with higher water solubilities and lower organic carbon-water partitioning coefficients (Koc), are distributed deeper than PAHs. However, current models have employed predictions using single compounds to mimic the migration of BTEX at contaminated coking sites. Such models have not considered the influence of the upper soil layer, where PAHs are enriched. An attempt to fill this gap was made by setting up a control soil column experiment in this study. One column was filled with undisturbed soil (column #1) and the other with PAH-contaminated soil (column #2) to simulate the theoretical and actual surface soil layers, respectively. The results showed that in column #2, the toluene gas concentration of the headspace and time required to reach steady state were notably greater than those in column #1. High-throughput sequencing revealed that there were large microbial community structure differences between the two soil columns throughout the experiment, while some genera that degrade toluene with high efficiency emerged noteworthily in column #2. This implied that the upper soil layer enriched with PAHs was conducive to the degradation of toluene vapor. Applying this finding to human health exposure assessment of toluene suggests that the potential exposure level should be reduced from the current predicted level given the unanticipated attenuation at contaminated coking sites.

Performance and microbial characterization of aerobic granular sludge in a sequencing batch reactor performing simultaneous nitrification, denitrification and phosphorus removal with varying C/N ratios.

The mechanism and effect of C/N ratios on the aerobic granules simultaneous nitrification, denitrification and phosphorus removal (SNDPR) system are still unclear. The reactor performance and microbial community dynamics of the system were investigated under variable C/N ratios (20, 10 and 5). The COD, TP and NH4+-N removal remained unaffected with variable C/N ratios. The decreased C/N ratio of five strongly influenced the nitrogen removal. Further investigations revealed that Candidatus_Accumulibacter, Acinetobacter, Candidatus_Competibacter were the predominant genera. Classification of key groups involved in nitrogen and phosphorus removal indicated the lowest C/N ratio resulting in a large microbial community shift. This study might contribute to the application of SNDPR system for the treatment of wastewater. Different C/N ratios led to shift on the microbial community and the dominant was phosphorus-accumulating bacteria. The nitrogen removal efficiency decreased while the removal of COD, TP and NH4+-N remained remarkable with the decreased C/N ratios.

The Role of Bacterial Biofilms in Dental Caries and Periodontal and Peri-implant Diseases: A Historical Perspective

Over the last hundred years, groundbreaking research in oral microbiology has provided a broad and deep understanding about the oral microbiome, its interactions with our body, and how the community can affect our health, be protective, or lead to the development of dental diseases. During this exciting journey, hypotheses were proposed, and concepts were established, discarded, and later revisited from updated perspectives. Dental plaque, previously considered a polymicrobial community of unspecific pathogenicity, is recognized as microbial biofilms with healthy, cariogenic, or periodontopathogenic profiles, resulting from specific ecologic determinants and host factors. The “one pathogen, one disease” paradigm of oral infections has been replaced by a holistic concept of a microbial community as the entity of pathogenicity. Cutting-edge technology can now explore large microbial communities related to different clinical conditions, which has led to finding several novel disease-associated species and potential pathobionts and pathobiomes. This vast amount of data generated over time has widened our view of the etiology of caries and periodontal and peri-implant diseases and has promoted updated strategies to treat and prevent the oral diseases.

Microbiomes and Pathogen Survival in Crop Residues, an Ecotone Between Plant and Soil

The negative contribution of crop residues as a source of inoculum for plant diseases is well established. However, microbial ecologists have long reported positive effects of residues on the stability of agrosystems and conservation tillage practices have become increasingly widespread. Most studies have suggested that large microbial communities should be taken into account in plant disease management, but we know little about their ecological interaction with pathogens in the crop residue compartment. This review focuses on microbiomes associated with residues within the context of other microbial habitats in cereal-producing agroecosystems such as phyllosphere or rhizosphere. We connected residue microbiome with the survival of residue-borne fungal plant pathogens, thus combining knowledge in microbial ecology and epidemiology, two disciplines still not sufficiently connected. We provide an overview of the impact of residues on cereal disease epidemics and how dynamic interactions between microbial communities of nonburied residues during their degradation, along with soil and multitude of abiotic factors, can contribute to innovative disease management strategies, including next-generation microbiome-based biocontrol strategies. Starting from the classical but still relevant view of crop residues as a source of pathogen inoculum, we first consider possibilities for limiting the amount of residues on the soil surface to reduce the pathogen pressure. We then describe residues as a transient half-plant/half-soil compartment constituting a key fully fledged microbial ecosystem: in other words, an ecotone which deserves special attention. We focus on microbial communities, the changes in these communities over time and the factors influencing them. Finally, we discuss how the interactions between the microbial communities and the pathogens present on residues could be used: identification of keystone taxa and beneficial assemblages, then preservation of these taxa by adapted agronomic practices or development of synthetic communities, rather than the introduction of a single exogenous biocontrol species designed as a treatment product. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .