Bacterial OTUs Research Articles

A baseline of Arbutus unedo L. microbiome for future research: In vitro versus ex vitro

Arbutus unedo L. (strawberry tree) is a multipurpose Ericaceae tree with a circum-Mediterranean distribution and tolerant to abiotic and biotic stresses. The bioactive compounds and edible berries make this species attractive from an economical perspective, which causes a high demand for true to type plants. As micropropagation techniques are quite popular for the production of strawberry tree clonal plants, the characterization of its microbiome is essential, due to the possible impact in micropropagation success, including acclimatization. Thus, this study aims to identify the endophytic communities on strawberry tree plant tissues in vitro, as well as their prevalence and/or alteration upon plant acclimatization. For this purpose, the microbiome of two genotypes under micropropagation and ex vitro was identified using a culture-independent method. Bacterial OTUs were assigned to 7 phyla and 79 genera whereas only one Archaea genus was identified. The most abundant and diverse bacterial phylum was Actinobacteriota (48%) followed by Proteobacteria (43%), Firmicutes (6%) and Bacteroidota (3%). Noticeable differences in terms of composition and diversity were found when the microbiome of genotypes in vitro was compared, whereas the composition of ex vitro samples was similar. A significant higher diversity was found on both genotypes ex vitro when compared to the respective in vitro plants. This study presents the very approach into the identification and characterization of strawberry tree microbiome, including in vitro plants, using a culture-independent method. The genotype proved to be a determinant factor shaping microbiota structure. The relevance of this results for micropropagation and breeding are discussed.

PSVIII-20 Heterologous lactobacilli feed additive impact on microflora in Cobb-500 broiler laying hens

Abstract Experiment was carried out on introducing eggshells from an experimental group of laying hens of lactobacilli strains with anti-C.jejuni activity. Eggs were incubated for 21 days to obtain broiler chickens containing auto-strains of lactobacilli with anti-C.jejuni activity in the blind processes of the intestine. It should be noted that most of the incubation eggs were observed in the 2nd group, in which the eggs were laid for subsequent administration of probiotic bacteria. Check was carried out for the presence of auto-strains of lactobacilli with anti-C.jejuni activity in the intestines of broiler chickens and the timing of their persistence for 1–35 days. The objective of the study was a comparative analysis of the following DNA samples: DNA from a feed supplement containing strains of lactobacilli with anti-C.jejuni activity; DNA samples from litter of laying hens of the parent herd receiving heterologous lactobacilli as part of the feed; isolated DNA from washes from hatching eggs; DNA samples from the contents of the digestive tract of chicken embryos; DNA samples from the intestines of broiler chickens. DNA samples from groups of birds and their embryos obtained without the use of heterologous lactobacilli were used as controls. The microflora of the contents of blind processes was taken from chickens on the 22nd day and on the 35th day of growing. In total, 343 different bacterial OTUs were identified in this study, belonging to 13 types, 26 classes, 51 orders, 106 families and 172 genera. Assessment of the biodiversity of bacterial ensembles in the samples of the contents of blind processes of chickens revealed fundamental differences already at the level of growing time and type. The study was performed at the FGBOU VO “St. Petersburg State University of Veterinary Medicine» with the aid of the Russian Science Foundation Grant (Project No. 18-76-10017).

Determination of bacterial abundance and communities in the nipple drinking system of cascading cage layer houses

Water quality is critical for egg production and animal health in commercial layer housing systems. To investigate microbial contamination in nipple drinking system in layer houses, the bacterial abundance and communities in water pipes and V-troughs on different tiers (e.g., 1st, 3rd, 5th, and 7th tiers) of a layer house with 8 overlapping cage tiers were determined using qRT-PCR and 16S rRNA sequencing. The water bacterial abundance (i.e., genome 16S rDNA copy number, WBCN) in water pipes and V-troughs did not significantly differ among tiers, but they were 46.77 to 1905.46 times higher in V-troughs than that in water pipes (P < 0.05) for each tier. Illumina sequencing obtained 1,746,303 effective reads from 24 water samples in V-troughs of 4 tiers (six samples from each tier). Taxonomic analysis indicated that the 1st and 5th tiers were predominated by Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, while the 3rd and 7th tiers were predominated by Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria. The top four genera were Acinetobacter, Streptococcus, Rothia and Comamonas among measured tiers. The high bacterial abundance and bacterial OTUs of water in the V-troughs reflect poor water quality, which may adversely affect growth and health of laying hens. Therefore, it is suggested that water quality in the V-tough should be checked more frequently in commercial layer houses.

Recovery patterns of soil bacterial and fungal communities in Chinese boreal forests along a fire chronosequence

Wildfire has profound and pervasive consequences for forest ecosystems via directly altering soil physicochemical properties and modulating microbial community. In this study, we examined the changes in soil properties and microbial community composition and structure at different periods after highly severe wildfire events (44 plots, 113 samples) in the Chinese Great Khingan Mountains. We also separated charcoal from burnt soils to establish the relationship between microbial community structures in soils and charcoal. We found that wildfire only significantly altered bacterial and fungal β-diversity, but had no effect on microbial α-diversity across a 29-year chronosequence. The network analysis revealed that the complexity and connectivity of bacterial and fungal communities were significantly increased from 17 years after fire, compared with either unburnt soils or soils with recent fires (0–4 years after fire). Differential abundance analysis suggested that bacterial and fungal OTUs were enriched or depleted only during 0–4 years after fire compared with the unburnt soils. In addition, soil pH, dissolved organic C and dissolved organic N were key determinants of soil bacterial and fungal communities during 17–29 years after fire. The fire-derived charcoal provided a new niche for microbial colonization, and microbes colonized in the charcoal had a significantly different community structure from those of burnt soils. Our data suggest that soil bacterial and fungal communities changed significantly during the recovery from fire events in terms of the abundance and co-occurrence networks in the boreal forest ecosystems.

Threshold effects of soil pH on microbial co-occurrence structure in acidic and alkaline arable lands

Soil pH plays a pivotal role in shaping microbial diversity and community composition in terrestrial ecosystems. Soil microbes clearly do not exist independently and instead form complex interaction networks, but little is known about the effect of soil pH upon those microbial co-occurrence networks. In this study, 62 alkaline and 61 acidic soil samples were collected from the North China Plain to investigate the effect of soil pH on microbial co-occurrence structure. Most bacterial and fungal OTUs in acidic soils were maximally abundant at soil pH of ~5.5, while in alkaline soils the corresponding OTU abundance attainted its maximum at pH ~8.3. Unlike those OTU abundance distributions, the relationship between soil pH and the number of links between OTUs in the co-occurrence network was best fitted by convex curves, with the pH thresholds found at 5.39 for bacteria and 5.60 for fungi in acidic soils. In alkaline soils, a dip in the relationship (only for fungi) between soil pH and the links was also observed, with a pH threshold at 8.04 for bacteria and 8.28 for fungi. From the co-occurrence analysis we identified 37 core bacterial species (mainly in Actinobacteria and Proteobacteria) and 24 core fungal species (mainly in Ascomycota). Together, this study revealed the threshold effects of soil pH upon microbial co-occurrence structure and identified the core microbial species in the North China Plain. These findings provide baseline information in mediating soil microbial co-occurrence structure by adjusting soil pH and core species in croplands.

A new index of resilience applicable to external pulse-disturbances that considers the recovery of communities in the short term

Resilience is a key concept in the study of the recovery of ecosystems affected by disturbances. Currently, there are numerous indices to measure resilience, but many of them do not show the accuracy of the resilience value or the behaviour of ecological parameters in the face of disturbances. New approaches and technologies enable large amounts of information to be obtained, facilitating the proposal of new resilience indices that work consistently and intuitively for a wide variety of ecological response variables under different scenarios after pulse-disturbances. In this study, we propose and verify a new resilience index, comparing its performance with others previously published. We validated the performance of the new index using real data based on field measurements of changes in soil bacterial OTUs diversity and abundance after a wildfire. The new resilience index provided an automatic and robust functional classification of the behaviour of ecosystems after disturbances, supported by a bootstrap analysis. We identified 5 scenarios of ecosystem resilience performance according to their behaviour after a pulse-disturbance: resilient, non-resilient, recovering, rebound, and continuing.

Aroma and bacterial communities dramatically change with storage of fresh white truffle Tuber magnatum

White truffles are highly valuable, but the aroma is susceptible to change with storage. How volatile composition and microbiome of Tuber magnatum evolve by storage time is poorly understood. Changes in bacterial community and volatile compounds of T. magnatum fruiting bodies with storage time at 23 °C were investigated. Truffles (21 fruiting bodies) were collected from different sites in Italy, Hungary, and Croatia. Single fruiting bodies were subsampled at four time points (day (D)0, 3, 6, and 9). Gas chromatography-mass spectrometry and microbiome composition using PCR-high throughput sequencing were used to analyse the volatiles and bacterial communities, respectively. Spoilage compounds atypical of truffles increased with storage time. Likewise, bacterial communities changed with storage time; families belonging to Xanthobacteraceae dominated at D0 and gradually evolved to more Rhizobiaceae and Pseudomonadaceae by D3 and D6, and finally with more prominent Xanthomonadaceae and Burkholderiaceae at D9. Overall, storage time had increased the diversity of bacterial communities. The microbiome and volatile data were correlated using regularised canonical correlation analysis and determined correlations between 2-methylisoborneol and five bacterial OTUs. Potential candidate bacteria and their volatile metabolites can serve as markers for truffle spoilage. The results highlighted the mechanisms by which the degradation of expensive truffles occur.

Geography, Host Genetics, and Cross-Domain Microbial Networks Structure the Skin Microbiota of Fragmented Brazilian Atlantic Forest Frog Populations.

The host‐associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon‐based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co‐occurrence networks; and (3) co‐occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). While bacterial alpha diversity varied by both site type and host MHC IIB genotype, microeukaryotic alpha diversity varied only by site type. However, bacteria and microeukaryote composition showed variation according to both site type and host MHC IIB genotype. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions may occur among domains. Lastly, anti‐Bd bacteria were not broadly negatively co‐associated with the fungal microbiome and were positively associated with potential amphibian parasites. Our findings emphasize the importance of considering both domains in microbiome research and suggest that for effective probiotic strategies for amphibian disease management, considering potential interactions among all members of the microbiome is crucial.

Characterization of gut microbiome in mice model of depression with divergent response to escitalopram treatment

Depression is a common and heterogeneous mental disorder. Although several antidepressants are available to treat the patients with depression, the factors which could affect and predict the treatment response remain unclear. Here, we characterize the longitudinal changes of microbial composition and function during escitalopram treatment in chronic unpredictable mild stress (CUMS) mice model of depression based on 16 S rRNA sequencing and metabolomics. Consequently, we found that escitalopram (ESC) administration serves to increase the alpha-diversity of the gut microbiome in ESC treatment group. The microbial signatures between responder (R) and non-responder (NR) groups were significantly different. The R group was mainly characterized by increased relative abundances of genus Prevotellaceae_UCG-003, and depleted families Ruminococcaceae and Lactobacillaceae relative to NR group. Moreover, we identified 15 serum metabolites responsible for discriminating R and NR group. Those differential metabolites were mainly involved in phospholipid metabolism. Significantly, the bacterial OTUs belonging to family Lachnospiraceae, Helicobacteraceae, and Muribaculaceae formed strong co-occurring relationships with serum metabolites, indicating alternations of gut microbiome and metabolites as potential mediators in efficiency of ESC treatment. Together, our study demonstrated that the alterations of microbial compositions and metabolic functions might be relevant to the different response to ESC, which shed new light in uncovering the mechanisms of differences in efficacy of antidepressants.

Targeted 16S rRNA gene and ITS2 amplicon sequencing of leaf and spike tissues of Piper longum identifies new candidates for bioprospecting of bioactive compounds.

Piper longum (also known as Indian long pepper) is widely used in Ayurvedic, Siddha and Unani medicine systems. The principle bioactive compound of this plant is piperine, which mainly accumulates in the fruits called spikes. The report of piperine production by endophytic microbes isolated from Piper sp., motivated us to investigate the endophytic microbial diversity associated with the spikes vis-à-vis leaves (which contain negligible levels of piperine). This is the first report to use metagenomics approach to unravel the endophytic microbial diversity in P. longum. Our results indicate that 2, 56, 631 bacterial OTUs and 1090 fungal OTUs were picked cumulatively from both the tissues. Although bacterial and fungal endophytes occupy the same niche, remarkable differences exist in their diversity and abundance. For instance, the most abundant bacterial genera in spikes were Nocardioides and Pseudonocardia (Phylum Actinobacteria; reported to produce bioactive compounds); while, in leaves were Larkinella and Hymenobacter (Phylum Bacteriodetes). Likewise, the fungal endophytes, Periconia, Cladosporium and Coniothyrium (which have been earlier reported to produce commercially important metabolites including piperine), were also present in high abundance in spikes, in comparison to leaves. Further, the results of PICRUSt analysis reveal the high metabolic potential of spike-associated bacteria for secondary metabolism, namely biosynthesis of alkaloids (including pyridine/piperidine), terpenes, flavonoids and antibiotics. Therefore, our findings indicate that the endophytes abundant or unique in spikes could be explored for bioprospecting of novel/commercially important metabolites; an approach that has both ecological and economical benefits.

Cd immobilization and soil quality under Fe–modified biochar in weakly alkaline soil

Cost–effective and environment–friendly implementation techniques are critical to the success of remediation in large–scale cadmium (Cd) contaminated agricultural soil. Field experiments were conducted to investigate the effect of Fe–modified biochar on Cd bioavailability in soils and uptake by maize (Zea mays L.), soil aggregate distribution and stability, and microbial community composition in weakly alkaline Cd–contaminated soil. Results showed that Fe–modified biochar optimized the structure and stability of soil aggregates. Moreover, the content of soil organic carbon increased by 6.59%–20.36% when compared with the control groups. However, DTPA–Cd concentration under the treatment of Fe–modified biochar was suffered by 37.74%–41.65% reduction in contrast with CK, and the significant decrease (P < 0.05) was obtained at 0.5% Fe–modified biochar. Moreover, sequential extraction procedures showed that the acid soluble and reducible states of Cd was converted into oxidizable and residual form. The addition of Fe–modified biochar inhibited Cd accumulation in maize, being 41.31%–76.64% (Zhengdan 958), 38.19%–70.95% (Liyu 86) and 52.30%–59.95% (Sanbei 218) reduction, respectively, in contrast with CK. The activity of catalase, urease and alkaline phosphatase in soil increased gradually with the addition of Fe–modified biochar. The enhancement in the number of soil bacterial OTUs and the values of Shannon, Chao1, ACE index indicated that Fe–modified biochar promoted the richness and diversity of bacterial communities. Therefore, the improvements of soil environment and biological quality indicated that Fe–modified biochar should be an alternative agent on remediation of Cd–contaminated soils.

Total and Metabolically Active Microbial Community of Aerobic Granular Sludge Systems Operated in Sequential Batch Reactors: Effect of Pharmaceutical Compounds.

Two aerobic granular sludge (AGS) sequential batch reactors were operated at a mild (15 °C) temperature for 180 days. One of those bioreactors was exposed to a mixture of diclofenac, naproxen, trimethoprim, and carbamazepine. The AGS system, operating under pressure from emerging contaminants, showed a decrease in COD, BOD5, and TN removal capacity, mainly observed during the first 100 days, in comparison with the removal ratios detected in the control bioreactor. After an acclimatisation period, the removal reached high-quality effluent for COD and TN, close to 95% and 90%, respectively. In the steady-state period, trimethoprim and diclofenac were successfully removed with values around 50%, while carbamazepine and naproxen were more recalcitrant. The dominant bacterial OTUs were affected by the presence of a mixture of pharmaceutical compounds, under which the dominant phylotypes changed to OTUs classified among the Pseudomonas, Gemmobacter, and Comamonadaceae. The RT-qPCR and qPCR results showed the deep effects of pharmaceutical compounds on the number of copies of target genes. Statistical analyses allowed for linking the total and active microbial communities with the physico-chemical performance, describing the effects of pharmaceutical compounds in pollution degradation, as well as the successful adaptation of the system to treat wastewater in the presence of toxic compounds.

Microbial Diversity of Adult Aedes aegypti and Water Collected from Different Mosquito Aquatic Habitats in Puerto Rico.

Mosquitoes, the major vectors of viruses like dengue, are naturally host to diverse microorganisms, which play an important role in their development, fecundity, immunity, and vector competence. The composition of their microbiota is strongly influenced by the environment, particularly their aquatic larval habitat. In this study, we used 2×300 bp 16s Illumina sequencing to compare the microbial profiles of emerging adult Aedes aegypti mosquitoes and the water collected from common types of aquatic habitat containers in Puerto Rico, which has endemic dengue transmission. We sequenced 141 mosquito and 46 water samples collected from plastic containers, septic tanks, discarded tires, underground trash cans, tree holes, or water meters. We identified 9 bacterial genera that were highly prevalent in the mosquito microbiome, and 77 for the microbiome of the aquatic habitat. The most abundant mosquito-associated bacterial OTUs were from the families Burkholderiaceae, Pseudomonadaceae, Comamonadaceae, and Xanthomonadaceae. Microbial profiles varied greatly between mosquitoes, and there were few major differences explained by container type; however, the microbiome of mosquitoes from plastic containers was more diverse and contained more unique taxa than the other groups. Container water was significantly more diverse than mosquitoes, and our data suggest that mosquitoes filter out many bacteria, with Alphaproteobacteria in particular being far more abundant in water. These findings provide novel insight into the microbiome of mosquitoes in the region and provide a platform to improve our understanding of the fundamental mosquito-microbe interactions.

Tree diversity and functional leaf traits drive herbivore-associated microbiomes in subtropical China.

Herbivorous insects acquire microorganisms from host plants or soil, but it remains unclear how the diversity and functional composition of host plants contribute to structuring herbivore microbiomes. Within a controlled tree diversity setting, we used DNA metabarcoding of 16S rRNA to assess the contribution of Lepidoptera species and their local environment (particularly, tree diversity, host tree species, and leaf traits) to the composition of associated bacterial communities. In total, we obtained 7,909 bacterial OTUs from 634 caterpillar individuals comprising 146 species. Tree diversity was found to drive the diversity of caterpillar‐associated bacteria both directly and indirectly via effects on caterpillar communities, and tree diversity was a stronger predictor of bacterial diversity than diversity of caterpillars. Leaf toughness and dry matter content were important traits of the host plant determining bacterial species composition, while leaf calcium and potassium concentration influenced bacterial richness. Our study reveals previously unknown linkages between trees and their characteristics, herbivore insects, and their associated microbes, which contributes to developing a more nuanced understanding of functional dependencies between herbivores and their environment, and has implications for the consequences of plant diversity loss for trophic interactions.

Predicting spatial patterns of soil bacteria under current and future environmental conditions

Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.

Nutrient resource availability mediates niche differentiation and temporal co-occurrence of soil bacterial communities

Nutrient resource availability is a crucial environmental factor in determining soil bacterial community assembly. However, the effects of nutrient availability on niche differentiation and temporal co-occurrence patterns of bacterial communities remain elusive. Here, we retrieved sequencing datasets (105 amplicon samples of bacterial 16S rRNA genes and 60 bacterial metagenomic samples) from a laboratory incubation experiment and a coastal wetland study, to elucidate the effects of nutrient availability on niche differentiation and co-occurrence patterns of bacterial communities. Niche differentiation within bacterial communities, indicated by nearest taxon index and niche breadth of bacterial communities, did not significantly correlate with nutrient availability gradients in either environment, even though deterministic processes dominated bacterial community assembly. Network analyses revealed that co-occurrence patterns of bacterial OTUs over incubation time changed across nutrient availability gradients, and were likely to be mediated by environmental selection. There were more co-occurrences of metabolic genes under higher nutrient levels. This study revealed the non-significant correlation between nutrient availability gradients and niche differentiation within bacterial communities, not only in a natural environment but also in a laboratory modified environment where the nutrient availability gradient was the sole environmental variable. These findings boost the understanding of bacterial community assembly along environmental nutrient availability gradients.

Microbiome diversity of cotton aphids (Aphis gossypii) is associated with host alternation

Aphids are infected by a series of bacteria that can help them survive on specific host plants. However, the associations between aphids and these bacteria are not clear, and the bacterial communities in many aphid species are poorly characterized. Here, we investigated the bacterial communities of cotton aphids (Aphis gossypii) on 2 representative winter host plants and transferred to 3 summer host plants by 16S rDNA sequencing using the Illumina MiSeq platform. Our results revealed that the bacterial communities varied among cotton aphids on hibiscus, cotton aphids on pomegranate, cotton aphids on cotton transferred from hibiscus, cotton aphids on muskmelon transferred from hibiscus, cotton aphids on cucumber transferred from hibiscus,. The diversity and richness of the bacterial communities were significantly higher in aphids on muskmelon and aphids on cucumber than in the other treatments. There were two main factors influencing the distribution of internal bacterial OTUs revealed by principal component analysis, including the differences among Punicaceae, Malvaceae and Cucurbitaceae. There were 28 bacterial communities with significant differences between two arbitrary treatments, which could be grouped into 6 main clusters depending on relative abundance. Moreover, our results indicated that in addition to the obligate endosymbiont Buchnera, with a dominant position (> 52%), A. gossypii also harbored 3 facultative endosymbiotic bacteria (Serratia, Arsenophonus, and Wolbachia) and 3 possibly symbiotic bacteria (Acinetobacter, Pantoea, and Flavobacterium). There were several correspondences between the symbiotic bacteria in cotton aphids and the specific host plants of the aphids. This study provides a better understanding of the interactions among symbiotic bacteria, aphids and host plants, suggesting that the selection pressure on aphid bacterial communities is likely to be exerted by the species of host plants.

Changes of soil bacterial community structure at the secondary successional stages in the Pinus yunnanensis forest.

Soil bacterial diversity is a key factor for the maintanence of forest ecosystem function. Soil bacterial community would change along forest succession. We analyzed the variations of soil bacterial diversity and community composition at different successional stages in the Pinus yunnanensis forest, which would help understand the mechanism underlying forest restoration. We investigated soil bacterial diversity, community composition, and effect factors at different successional stages (including coniferous forest, mixed coniferous and broadleaf forest, and evergreen broadleaf forest) using Illumina Hiseq platform. The results showed that OTUs, Chao1 index, Ace index, and Shannon index of soil bacterial community decreased with the process of secondary succession. The highest soil bacterial total OTUs, richness, and complexity appeared at early successional stage. Soil bacterial community composition varied across different stages, with the mixed coniferous and broadleaf forest showing largest variation. Proteobacteria and Acidobacteria were common dominant phyla at secondary successional stages. Actinobacteria, Chloroflexi, and Patescibacteria were dominant phyla at the early successional stage, the abundance of which decreased with successional process in the P. yunnanensis forest. Proteobacteria and WPS-2 increased with the succession. Soil pH and tree species richness were key factors in driving soil bacterial community structure. The soil bacterial diversity decreased with forest succession, while the variations of soil bacterial community composition became larger.

Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale

BackgroundThe plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between microbiota composition and plant health. Here we investigated landscape scale rhizosphere microbial assembly processes in oilseed rape (OSR), the UK’s third most cultivated crop by area and the world's third largest source of vegetable oil, which suffers from yield decline associated with the frequency it is grown in rotations. By including 37 conventional farmers’ fields with varying OSR rotation frequencies, we present an innovative approach to identify microbial signatures characteristic of microbiomes which are beneficial and harmful to the host.ResultsWe show that OSR yield decline is linked to rotation frequency in real-world agricultural systems. We demonstrate fundamental differences in the environmental and agronomic drivers of protist, bacterial and fungal communities between root, rhizosphere soil and bulk soil compartments. We further discovered that the assembly of fungi, but neither bacteria nor protists, was influenced by OSR rotation frequency. However, there were individual abundant bacterial OTUs that correlated with either yield or rotation frequency. A variety of fungal and protist pathogens were detected in roots and rhizosphere soil of OSR, and several increased relative abundance in root or rhizosphere compartments as OSR rotation frequency increased. Importantly, the relative abundance of the fungal pathogen Olpidium brassicae both increased with short rotations and was significantly associated with low yield. In contrast, the root endophyte Tetracladium spp. showed the reverse associations with both rotation frequency and yield to O. brassicae, suggesting that they are signatures of a microbiome which benefits the host. We also identified a variety of novel protist and fungal clades which are highly connected within the microbiome and could play a role in determining microbiome composition.ConclusionsWe show that at the landscape scale, OSR crop yield is governed by interplay between complex communities of both pathogens and beneficial biota which is modulated by rotation frequency. Our comprehensive study has identified signatures of dysbiosis within the OSR microbiome, grown in real-world agricultural systems, which could be used in strategies to promote crop yield.9LHMp6srYAP4ntBATPUdWaVideo abstract

Fecal Microbiota Transplant from Human to Mice Gives Insights into the Role of the Gut Microbiota in Non-Alcoholic Fatty Liver Disease (NAFLD).

Non-alcoholic fatty liver diseases (NAFLD) are associated with changes in the composition and metabolic activities of the gut microbiota. However, the causal role played by the gut microbiota in individual susceptibility to NAFLD and particularly at its early stage is still unclear. In this context, we transplanted the microbiota from a patient with fatty liver (NAFL) and from a healthy individual to two groups of mice. We first showed that the microbiota composition in recipient mice resembled the microbiota composition of their respective human donor. Following administration of a high-fructose, high-fat diet, mice that received the human NAFL microbiota (NAFLR) gained more weight and had a higher liver triglycerides level and higher plasma LDL cholesterol than mice that received the human healthy microbiota (HR). Metabolomic analyses revealed that it was associated with lower and higher plasma levels of glycine and 3-Indolepropionic acid in NAFLR mice, respectively. Moreover, several bacterial genera and OTUs were identified as differently represented in the NAFLR and HR microbiota and therefore potentially responsible for the different phenotypes observed. Altogether, our results confirm that the gut bacteria play a role in obesity and steatosis development and that targeting the gut microbiota may be a preventive or therapeutic strategy in NAFLD management.