Natural Microbiome Research Articles

ACHIEVEMENTS AND PERSPECTIVES OF DEVELOPMENT IN SOIL MICROBIOLOGY AT MOSCOW UNIVERSITY

The article summarizes the results of recent research by the staff of Soil Biology Department Faculty of Soil Science of Lomonosov Moscow State University in the field of assessing the genetic potential of microbial communities of soils and their application in the development of fundamental soil and environmental technologies. Promising areas of further work related to the use of the microbial potential of soils for the purpose of bioremediation territories from ecotoxicants, the development of technologies for selfpurification of soils based on the stimulation of natural communities of microorganisms, as well as the use of microbial cultures for biodegradation of petroleum products, pesticides and synthetic polymers. Another important direction is related to the development of scientific basis for the indication of biological objects in the environment and space objects. Within the framework of this direction, genomic analysis of uncultivated microorganisms from the Arctic, Antarctic and other extreme habitats is carried out, and the knowledge gained apply as a model of alien life. Another relevant direction for the Department of Soil Biology is the development of agrobiotechnologies based on the management of the natural soil microbiome, the creation of microbial preparationsstimulators of plant growth and development, microbiological ways to increase the proportion of biological nitrogen in plant nutrition, application of microbial plant endosymbionts and bioinsecticides. An equally important aspect is the search of producers of biologically active substances, such as phytohormones, antibiotics, enzymes, probiotics, hydrolytics of natural and artificial polymers. The considered areas of research in the field of soil biology are important for improving land management, environmental protection and the development of environmental technologies.

Unveiling microbial biomarkers of ruminant methane emission through machine learning.

Enteric methane from cow burps, which results from microbial fermentation of high-fiber feed in the rumen, is a significant contributor to greenhouse gas emissions. A promising strategy to address this problem is microbiome-based precision feed, which involves identifying key microorganisms for methane production. While machine learning algorithms have shown success in associating human gut microbiome with various human diseases, there have been limited efforts to employ these algorithms to establish microbial biomarkers for methane emissions in ruminants. In this study, we aim to identify potential methane biomarkers for methane emission from ruminants by employing regression algorithms commonly used in human microbiome studies, coupled with different feature selection methods. To achieve this, we analyzed the microbiome compositions and identified possible confounding metadata variables in two large public datasets of Holstein cows. Using both the microbiome features and identified metadata variables, we trained different regressors to predict methane emission. With the optimized models, permutation tests were used to determine feature importance to find informative microbial features. Among the regression algorithms tested, random forest regression outperformed others and allowed the identification of several crucial microbial taxa for methane emission as members of the native rumen microbiome, including the genera Piromyces, Succinivibrionaceae UCG-002, and Acetobacter. Additionally, our results revealed that certain herd locations and feed composition markers, such as the lipid intake and neutral-detergent fiber intake, are also predictive features for methane emissions. We demonstrated that machine learning, particularly regression algorithms, can effectively predict cow methane emissions and identify relevant rumen microorganisms. Our findings offer valuable insights for the development of microbiome-based precision feed strategies aiming at reducing methane emissions.

Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease

It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.

Assessing the potential of chitosan based coatings in modulation of bacteriome on tomato carposphere

Chitosan based edible fruit coatings are being considered today as an unconventional, ecofriendly and safe alternative of postharvest chemical treatments. The mechanism of action of chitosan coatings, like its antifungal nature or forming a barrier for transpiration and respiration, is already known. We intended to study the effect of the chitosan on natural carposphere microbiome, specifically on non-culturalable bacterial communities during storage to explore the prebiotic like nature of the chitosan based coatings. Hence the effect of coatings viz. CS (1% Chitosan), TL (Tulsi or Ocimum sanctum leaf, 1 g L-1 aqueous extract), and CS/TL mixed (2:1, 1% Chitosan and Tulsi leaf extract) was observed on coated tomato fruit. Metagenomic bacteriome analyses revealed that the untreated samples were comparatively rich epiphytic bacterial flora though the core microbiome was conserved in all the samples. Bacterial community in ripened tomato fruit (after 7 d) was mostly dominated by Acetobacter (49%) while on treatment of coatings genera like Lactobacillus, Weissella, Methylovoruse, Bacillus and Pseudomonas increased. These bacteria can act as potential bio agents in carposphere while the probiotic nature of genera as Lactobacillus or Weissella can also help in delaying the ripening of fruit. As this was a pilot study, more such studies are needed on microbial communities associated with fruits, their assembly and dynamics as well as the nature of their contribution to fruit quality and pathogen resistance during fruit ripening and storage.

Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts

Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.

Identification and Analysis of the Ankle Microbiome Using Next-Generation DNA Sequencing: An Observational Analysis.

Next-generation DNA sequencing (NGS) technologies have increased the sensitivity for detecting the bacterial presence and have been used in other areas of orthopaedics to better understand the native microbiome of various joints. This study uses NGS to determine whether (1) a unique microbiome exists in human ankle tissues, (2) if components of the ankle microbiome affect patient outcomes, and (3) whether microbes found on the skin are a normal part of the ankle microbiome. A prospective study recruited 32 patients undergoing total ankle arthroplasty (n = 23) or ankle arthrodesis (n = 9) via direct anterior approach between November 2020 and October 2021. During surgery, five layers of the ankle were swabbed: skin (n = 32), retinaculum (n = 31), tibialis anterior tendon (n = 31), joint capsule (n = 31), and distal tibia (n = 32). These swabs (N = 157) were sent to MicroGen Diagnostics (Lubbock) for NGS. Demographics, medical comorbidities, surgical indication, postoperative complications, readmission, and revision surgery rates were collected from patient records. The mean age was 60.7 (range, 19 to 85) years, and the mean follow-up duration was 10.2 (range, 4.8 to 20.6) months. Of 157 swabs sent for NGS, 19 (12.1%) indicated that bacteria were present (positive), whereas the remaining 138 (87.9%) had no bacteria present (negative). The most common organisms were Cutibacterium acnes in eight ankles (25.0%) and Staphylococcus epidermidis in two ankles (6.25%). Most bacteria were found in the retinaculum (29.6%). Complications, nonunions, infections, 90-day readmission, and revision surgery rates did not differ by NGS profile. This study found that C acnes and S epidermidis were the most common bacteria in the ankle microbiome, with C acnes being present in 25% of ankles. Complication rates did not differ between patients with or without positive bacterial DNA remnants. Thus, we concluded that a unique ankle microbiome is present in some patients, which is unique from that of the skin of the ankle. Level II, Prospective cohort study.

Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies.

The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL-1 day-1.

A Comparison of Three Artificial Rumen Systems for Rumen Microbiome Modeling

The rumen contains a complex mixture of microbes, crucial for the animal’s ability to degrade feed. Some of the feed-derived carbon is released as methane, a potent greenhouse gas, into the atmosphere. There is growing interest in reducing the loss of feed-derived carbon, making it available to the animal and improving animal productivity. Artificial rumen systems (ARSs) have been widely used to evaluate novel feed additives in terms of their ability to reduce methane production in the rumen and their effect on the rumen microbiome function prior to conducting resource-intensive animal trials. While the value of ARSs is widely acknowledged, it remains unclear which of these in vitro systems simulate the natural system most accurately. Here, we evaluated three different ARSs and compared them to in vivo rumen metrics. The results showed that all systems were capable of maintaining stable pH, redox potential, and temperature over time. The batch-style ARS simulated the rumen over 48 h. The semi-continuous ARS mimicked the volatile fatty acid profile and microbiota of the in vivo rumen for up to 120 h. Similarly, all ARSs maintained the prokaryotic and eukaryotic rumen populations over the duration of the study, with the semi-continuous ARS maintaining the natural rumen microbiome more accurately and for up to 120 h. In sum, our results suggest that three of the widely used ARSs simulate the rumen ecosystem adequately for many short-term rumen microbiome studies, with the more advanced semi-continuous ARS being more accurate when rumen simulation is extended to over 48 h.

209 Prevalence of Antimicrobial Resistance Genes and Mobile Genetic Elements in the Swine Gut Microbiome

Abstract Antimicrobial resistance (AMR) is one of the most pressing threats to public health. It contributes to over a million deaths a year currently and by 2050 it is expected to cause more annual death than cancer. The swine industry has taken important steps to address the AMR crisis by phasing out the use of antimicrobial growth promoters. Nonetheless, the use of antimicrobials for controlling infectious diseases on swine farms remains high, particularly during the nursery stage of pig production. This has raised concerns about the potential role of the swine industry in the emergence and spread of antimicrobial resistance genes (ARGs) capable of conferring resistance to medically important antimicrobials. While traditionally ARGs have been studied in the context of pathogens, there is growing evidence that the natural microbiome of humans and animals can also serve as a significant reservoir of ARGs. Of particular importance is the association of ARGs with different classes of mobile genetic elements (MGEs) which can facilitate the horizontal transfer of genes among commensal bacteria and pathogens. In this study, we evaluated the diversity and distribution of ARGs and their associated MGEs in the swine gut microbiome. To achieve this, we isolated and sequenced the whole genomes of 130 unique bacterial isolates from stool, digesta, and mucosa of healthy adult sows and their piglets. Screening of genomes for the presence of ARGs was performed using the Resistance Gene Identifier (RGI) and Comprehensive Antibiotic Resistance Database (CARD), resulting in the identification of 323 ARGs across 117 genomes. Among these, genes predicted to confer resistance against tetracycline, lincosamide, beta-lactams, and fluoroquinolone were the most prevalent across all genomes. Importantly, we observed that several strictly anaerobic species belonging to gut-specific lineages including Lachnospiraceae, Megasphaeraceae, and Desulfovibrionaceae contained large ARGs pools spanning more than five different classes of antimicrobials. Further, we screened the flanking regions of ARGs for the presence of signature genes of MGEs including recombinases, phage integrases and capsids, and type IV secretion system. A total of 60 ARGs were identified to be associated with different classes of MGEs, including integrative and conjugative elements (ICEs; n = 30), bacteriophages (n = 8), integrative mobile elements (IMEs; n = 6), and plasmids (n = 3). Overall, our study highlights that ARGs, including those conferring resistance to medically important antimicrobials, are prevalent across different lineages of the swine gut microbiota. The association of the identified ARGs with MGEs warrants further in vitro experiments to evaluate the risk of transmission of resistance to zoonotic pathogens capable of infecting humans and animals.

Characterizing the Native Microbiome Using Next-Generation Sequencing of Bilateral ‘Aseptic’ Knees

BackgroundNext generation sequencing (NGS) has proven ability to identify organisms beyond those identified through traditional culture-based techniques in cases of suspected prosthetic joint infection. However, there is concern that some microorganisms identified may represent the natural joint microbiome rather than pathogenic agents. This work sought to evaluate the presence of microorganisms identified with NGS in bilateral native, presumed “aseptic” knees with osteoarthritis. MethodsThere were 40 patients undergoing primary unilateral (30) or bilateral (10) total knee arthroplasty enrolled prospectively. During surgery, samples of fluid and tissue were obtained from operative knees, and joint fluid was obtained from nonoperative knees. Samples were sent for NGS analysis and processed according to manufacturer protocols. Patient age, body mass index, comorbidities, prior history of injections, and grade of arthritis were evaluated for association with positive NGS results. ResultsThere were 3 of 80 samples (3.8%) that demonstrated positive NGS. There were two of these that had multiple microorganisms identified (1 knee with 4 microorganisms; 1 knee with 2 microorganisms). An additional 2 samples had positive NGS results below the manufacturer's threshold for reporting. The most common organism identified was Cutibacterium acnes, present in 2 of the 3 positive samples. No patient baseline characteristics were associated with positive NGS results. ConclusionsSome native knee joints with osteoarthritis have positive microorganisms identified with NGS. The presence of microorganisms in the native knee has important implications for better understanding the native joint microbiome as well as utilization of NGS in cases of suspected prosthetic joint infection.

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

BackgroundViruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes.ResultsWe identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth.ConclusionTaken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.2RJdjcjTGzDNGfvgvrWr_YVideo

Nature-Based Solution to Eliminate Cyanotoxins in Water Using Biologically Enhanced Biochar.

Climate change and high eutrophication levels of freshwater sources are increasing the occurrence and intensity of toxic cyanobacterial blooms in drinking water supplies. Conventional water treatment struggles to eliminate cyanobacteria/cyanotoxins, and expensive tertiary treatments are needed. To address this, we have designed a sustainable, nature-based solution using biochar derived from waste coconut shells. This biochar provides a low-cost porous support for immobilizing microbial communities, forming biologically enhanced biochar (BEB). Highly toxic microcystin-LR (MC-LR) was used to influence microbial colonization of the biochar by the natural lake-water microbiome. Over 11 months, BEBs were exposed to microcystins, cyanobacterial extracts, and live cyanobacterial cells, always resulting in rapid elimination of toxins and even a 1.6-1.9 log reduction in cyanobacterial cell numbers. After 48 h of incubation with our BEBs, the MC-LR concentrations dropped below the detection limit of 0.1 ng/mL. The accelerated degradation of cyanotoxins was attributed to enhanced species diversity and microcystin-degrading microbes colonizing the biochar. To ensure scalability, we evaluated BEBs produced through batch-scale and continuous-scale pyrolysis, while also guaranteeing safety by maintaining toxic impurities in biochar within acceptable limits and monitoring degradation byproducts. This study serves as a proof-of-concept for a sustainable, scalable, and safe nature-based solution for combating toxic algal blooms.

Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut

Probiotics often acquire potentially adaptive mutations in vivo, gaining new functional traits through gut selection. While both the host and microbiome can contribute to probiotics’ genetic evolution, separating the microbiome and the host’s contribution to such selective pressures remains challenging. Here, we introduced germ-free (GF) and specific pathogen-free (SPF) mouse models to track how probiotic strains, i.e., Lactiplantibacillus plantarum HNU082 (Lp082) and Bifidobacterium animalis subsp. lactis V9 (BV9), genetically evolved under selection pressures derived from host factors alone and both host and microbial ecological factors. Notably, compared to the genome of a probiotic strain before consumption, the host only elicited <15 probiotic mutations in probiotic genomes that emerged in the luminal environment of GF mice, while a total of 840 mutations in Lp082 mutants and 21,579 mutations in BV9 were found in SPF mice, <0.25% of those derived from both factors that were never captured by other experimental evolution studies, indicating that keen microbial competitions exhibited the predominant evolutionary force in shaping probiotic genetic composition (>99.75%). For a given probiotic, functional genes occurring in potentially adaptive mutations induced by hosts (GF mice) were all shared with those found in mutants of SPF mice. Collectively, the native microbiome consistently drove a more rapid and divergent genetic evolution of probiotic strains in seven days of colonization than host factors did. Our study further laid a theoretical foundation for genetically engineering probiotics for better gut adaptation through in vitro artificial gut ecosystems without the selection pressures derived from host factors.

Microbial activities along a 20 million-year-old pristine oil reservoir

Studies on oil reservoir microbiology typically take samples from producing reservoirs and sample fluids that have been pumped to the surface. This comes with problems since producing oil reservoirs are affected by production processes leading to changes in environmental conditions and the natural microbiome. Hence, pumped samples do not display an unaltered picture of the spatial distribution and composition of the microorganisms in the reservoir. We took 13 samples from a freshly drilled sediment core of a pristine, heavily biodegraded oil reservoir in the North Sea. Core samples originated from above, within, and below the reservoir. 16S rRNA gene amplicon sequencing of the microbiome revealed distinct differences between sediments and formation water, indicating that studies on microbiomes from formation water alone are not necessarily representative for the microbial processes in an oil reservoir. Fluorescence microscopy showed that microorganisms live in small microcolonies on the sediment surface. CT-scanning with image analysis visualized the water phase distribution inside the reservoir sediments and clearly indicated water-filled voids that might be habitable for microorganisms, enlarging the surface for potential biodegradation. Employing microcosm experiments and reverse isotope labelling, we were able to determine the first degradation rates measured from cores above, within, and below a reservoir ranging from no activity up to 1 mM CO2/(gsediment x year), Results indicate significant degradation potential from autochthonous microorganisms in the reservoir above the water-contact-zone. Evading the general issues of produced oil samples for studying microbiomes results in a more realistic picture of an oil reservoir unaffected by production artefacts.

Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities.

Transferable plasmids play a critical role in shaping the functions of microbial communities. Previous studies suggested multiple mechanisms underlying plasmid persistence and abundance. Here, we focus on the interplay between heterogeneous community partitioning and plasmid fates. Natural microbiomes often experience partitioning that creates heterogeneous local communities with reduced population sizes and biodiversity. Little is known about how population partitioning affects the plasmid fate through the modulation of community structure. By modeling and experiments, we show that heterogeneous community partitioning can paradoxically promote the persistence of a plasmid that would otherwise not persist in a global community. Among the local communities created by partitioning, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance by serving as a local plasmid haven. Our results provide insights into plasmid maintenance and suggest a generalizable approach to modulate plasmid persistence for engineering and medical applications.

Identification and Analysis of the Ankle Microbiome Using Next-Generation DNA Sequencing: An Observational Analysis

Category: Ankle; Basic Sciences/Biologics Introduction/Purpose: Next-generation DNA sequencing (NGS) technologies have increased the sensitivity of bacterial cultures and has been used in other areas of orthopaedics to better understand the native microbiome of various joints. This study uses NGS to determine whether (1) a unique microbiome exists in human ankle tissues, (2) if components of the ankle microbiome impact patient outcomes, and (3) whether microbes found on the skin are a normal part of the ankle microbiome. Methods: A prospective study recruited 32 patients undergoing total ankle arthroplasty (TAA, n=23) or ankle arthrodesis via an anterior approach (n=9) during 2020-2021 with one of two fellowship-trained foot and ankle surgeons at an academic medical center. During the operation, the surgeon would swab five layers of the ankle for analysis at a CLIA-licensed molecular diagnostic laboratory: skin (n=32), retinaculum (n=31), tibialis anterior tendon (n=31), joint capsule (n=31), and distal tibia (n=32). Demographics, medical comorbidities, surgical indication, postoperative complications, and readmission and reoperation rates were collected from patient records. Results: Of the 157 swabs sent for NGS, 19 (12.1%) indicated 27 bacteria were present (positive), while the remaining 138 (87.9%) had no bacteria present (negative). The most common organisms were Cutibacterium acnes, present in 11 ankles (34.4%), and Staphylococcus epidermidis, present in 3 ankles (9.4%). The most bacteria were found in the retinaculum (29.6%). No PROM nor follow-up duration was associated with the presence of bacteria, or the number of bacteria or affected layers. Similarly, complication (positive=18.2%, negative=23.8%; p=1.000), nonunion (positive=0.0%, negative=28.6%; p=1.000), infection (positive=0.0%, negative=4.8%; p=1.000), 90-day readmission (positive=0.0%, negative=4.8%; p=1.000), and reoperation (positive=0.0%, negative=4.8%; p=1.000) rates did not differ if a subject’s NGS profile was positive or negative. Conclusion: This study found that C. acnes and S. epidermidis were most commonly found in the ankle microbiome, with C. acnes being present in 34% of ankles. There was no difference in complication rates between patient with and without positive bacterial cultures following TAA or ankle arthrodesis.

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

BackgroundMicrobiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes.ResultsOur results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities. Host plant genetic variation also exerted a stronger effect on core prokaryotic communities than on non-core prokaryotic communities in each microhabitat of two Miscanthus species. From rhizosphere soils to root endophytes, prokaryotic co-occurrence network stability increased, but fungal co-occurrence network stability decreased. Furthermore, we found root endophytic microbial communities in two Miscanthus species were more strongly driven by deterministic processes rather than stochastic processes. Root-enriched prokaryotic OTUs belong to Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, and [Saprospirae] both in two Miscanthus species, while prokaryotic taxa enriched in the rhizosphere soil are widely distributed among different phyla.ConclusionsWe provide empirical evidence that host genetic variation plays important roles in root-associated microbiome in Miscanthus. The results of this study have implications for future bioenergy crop management by providing baseline data to inform translational research to harness the plant microbiome to sustainably increase agriculture productivity.7yeh-8ahY_T_UpG1ho_dZsVideo

Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing

Multi-omic analyses can provide information on the potential for activity within a microbial community but often lack specificity to link functions to cell, primarily offer potential for function or rely on annotated databases. Functional assays are necessary for understanding in situ microbial activity to better describe and improve microbiome biology. Targeting enzyme activity through activity-based protein profiling enhances the accuracy of functional studies. Here, we introduce a pipeline of coupling activity-based probing with fluorescence-activated cell sorting, culturing, and downstream activity assays to isolate and examine viable populations of cells expressing a function of interest. We applied our approach to a soil microbiome using two activity-based probes to enrich for communities with elevated activity for lignocellulose-degradation phenotypes as determined by four fluorogenic kinetic assays. Our approach efficiently separated and identified microbial members with heightened activity for glycosyl hydrolases, and by expanding this workflow to various probes for other function, this process can be applied to unique phenotype targets of interest.

Invasive plant species interact with drought to shift key functions and families in the native rhizosphere

Background and aimsInteractions between species invasions and climate change have the potential to drive changes in plant communities more than either factor alone. One pathway through which these effects can occur is via changes to the rhizosphere microbial community. Invasive plants can alter these microbial communities affecting natives’ abilities to compete with invaders. At the same time, climate change is leading to more frequent extreme wet and dry events. Understanding the response of plant communities to these combined global change drivers requires a comprehensive approach that assesses the relationship between plant competition and belowground rhizosphere microbial community responses.MethodsHere we use a field experiment in a California grassland with a set of six native annual forbs (i.e., wildflowers) and three invasive annual grasses to test how competition with invasive plants alters both identity and function in the native rhizosphere microbiome, and whether competition between these groups interacts with rainfall to amplify or ameliorate microbial shifts.ResultsMetagenomics of rhizosphere communities revealed that drought combined with competition from invaders altered a higher number of functions and families in the native rhizosphere compared to invasive competition alone or drought alone. Watering combined with invasion led to fewer shifts.ConclusionThis suggests invasion-driven shifts in the microbial community may be involved in weakening natives’ ability to cope with climate change, especially drought. Understanding the role of the microbial community under invasion and climate change may be critical to mitigating the negative effects of these interacting global change drivers on native communities.Graphical abstractUnderstanding plant community response to global change drivers requires a comprehensive approach that assesses the relationship between plant competition and belowground rhizosphere microbial community responses. (a) In this work, we use a field experiment in a California grassland with a set of native forbs (purple) and invasive grasses (teal) to assess the combined effects of competition and water availability (drought, control, watered) on the rhizosphere microbiome. (b) Drought combined with competition from invaders altered the relative abundance of 36 functions (white) and 22 microbial families (blue) in the native rhizosphere compared to the effects of competition (3 functions, 16 families) or drought alone on natives (not shown: 5 functions, 0 families). (c) Additionally, regardless of watering treatment, invasive grasses sourced more of the taxonomic community in native-invasive mixes and this was exacerbated during drought. Overall, these results suggest invasion-driven shifts in the microbiome may be involved in weakening natives’ ability to cope with climate change, especially drought.

Glyphosate effect on biofilms formation, mutagenesis and stress response of E. сoli

Glyphosate is the most widely used herbicide in the world. There is still no complete clarity about the degree of its genotoxicity and mutagenicity. In addition, its effect on bacterial biofilms, the main life form of soil microbial communities, has not been adequately studied. Toxicity and mutagenicity, as well as changes in the bacterial biofilm biomass, physiological activity, and the number of living cells in its composition in the presence of glyphosate were assessed using the Escherichia coli model. To assess damage to cellular components under the action of this pesticide, luminescent whole-cell bacterial lux-biosensors were used. Changes in the level of mutagenesis were studied by the method of rifampicin mutants. High integral toxicity of glyphosate, the average level of increased oxidative stress and protein damage were shown with the help of bacterial biosensors. All the studied concentrations of the pesticide completely or partially suppress the matrix and structure of the E. coli CDC F-50 biofilm formation, as well as the bacterial cells metabolic activity in the biofilm. At the concentrations of 6.7 and 0.67 g/L, glyphosate suppresses mutagenesis, probably due to general suppression of metabolism, and at the concentration of 0.0067 g/L, it enhances mutagenesis by six times compared with the spontaneous level. Suppression of bacterial biofilms formation, toxic effects on microorganisms, and mutagenesis enhancement by glyphosate can lead to negative consequences for natural microbiomes.