scholarly journals Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12498
Author(s):  
Mauro Maver ◽  
Carmen Escudero-Martinez ◽  
James Abbott ◽  
Jenny Morris ◽  
Pete E. Hedley ◽  
...  
Keyword(s):  
Indole Alkaloid ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Host Genotype ◽  
Independent Manner ◽  
Molecular Determinants ◽  
Breeding Selection ◽  
The Impact ◽  
Soil Interface

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.

scholarly journals The indole-alkaloid gramine shapes the bacterial communities thriving at the barley root-soil interface

2020 ◽  
Author(s):  
Mauro Maver ◽  
Jenny Morris ◽  
Pete E. Hedley ◽  
Tanja Mimmo ◽  
Davide Bulgarelli
Keyword(s):  
Bacterial Communities ◽  
Soil Bacteria ◽  
Indole Alkaloid ◽  
Significant Component ◽  
Independent Manner ◽  
Bacterial Microbiota ◽  
Plant Allelochemicals ◽  
Breeding Selection ◽  
Soil Interface ◽  
Modern Varieties

AbstractThe biosynthesis of plant allelochemicals underpinning inter-organismal relationships has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but virtually absent from modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how the exogenous application of gramine impacted on the rhizosphere bacterial microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. Our investigation revealed that the application of the indole-alkaloid gramine modulates the proliferation of a subset of soil bacteria with a relatively broad phylogenetic assignment. This effect is two-pronged: a limited, but significant, component of the barley microbiota responds to gramine application in a genotype- and dosage-independent manner while at the highest dosage this secondary metabolite attenuates the host recruitment cues of the barley microbiota. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the bacterial communities inhabiting the root-soil interface.

scholarly journals Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

2019 ◽  
Author(s):  
Norma M. Morella ◽  
Francis Cheng-Hsuan Weng ◽  
Pierre M. Joubert ◽  
C. Jessica E. Metcalf ◽  
Steven Lindow ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Amplicon Sequencing ◽  
Host Genotype ◽  
Microbial Composition ◽  
Plant Host ◽  
Independent Manner ◽  
16S Amplicon Sequencing ◽  
The Impact ◽  
Plant Microbiome

AbstractThere is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across five plant genotypes for four eight-week long passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (ITS amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond.Significance StatementThere is great interest in selecting for host-associated microbiomes that confer particular functions to their host, and yet it remains unknown whether selection for a robust and stable microbiome is possible. Here, we use a microbiome passaging approach to measure the impact of host-mediated selection on the tomato phyllosphere (above ground) microbiome. We find robust community selection across replicate lines that is shaped by plant host genotype in early passages, but changes in a genotype-independent manner in later passages. Work such as ours is crucial to understanding the general principles governing microbiome assembly and adaptation, and is widely applicable to both sustainable agriculture and microbiome-related medicine.

scholarly journals Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR

2021 ◽  
Author(s):  
Annemarie Siebert ◽  
Katharina Hofmann ◽  
Lena Staib ◽  
Etienne V. Doll ◽  
Siegfried Scherer ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Dna Extraction ◽  
Raw Milk ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Microbiome Analysis ◽  
Eukaryotic Dna ◽  
Selective Lysis ◽  
The Impact

Abstract The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. Key points • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.

scholarly journals Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

2021 ◽  
Vol 12 ◽  
Author(s):  
Charles S. Cockell ◽  
Bettina Schaefer ◽  
Cornelia Wuchter ◽  
Marco J. L. Coolen ◽  
Kliti Grice ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Granitic Rocks ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Deep Subsurface ◽  
Cell Biomass ◽  
Colonization Potential ◽  
The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

scholarly journals Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon

2019 ◽  
Vol 7 (8) ◽  
pp. 233 ◽  
Author(s):  
Shruti Gupta ◽  
Jorge Fernandes ◽  
Viswanath Kiron
Keyword(s):  
Atlantic Salmon ◽  
Intestinal Microbiota ◽  
Amplicon Sequencing ◽  
Study Groups ◽  
Oxolinic Acid ◽  
Rrna Gene ◽  
Farmed Fish ◽  
Bacterial Phyla ◽  
Microbial Profile ◽  
The Impact

The intestinal microbiota of certain farmed fish are often exposed to antimicrobial substances, such as antibiotics, that are used to prevent and treat bacterial diseases. Antibiotics that kill or inhibit the growth of harmful microbes can rapidly alter intestinal microbial diversity and composition, with potential effects on the host health. In this study, we have elucidated the impact of two antibiotics, florfenicol and oxolinic acid, by employing a high-throughput 16S rRNA gene amplicon sequencing technique on the distal and mid intestinal microbial communities of Atlantic salmon (Salmo salar). For this, Atlantic salmon were offered diets with or without antibiotics. We then investigated the bacterial communities in the intestinal mucus of the fish. Our results showed that antibiotic exposure shifts the intestinal microbial profile differentially. In addition, the bacterial compositions of the control and antibiotic-fed groups were significantly different. Antibiotic feeding altered the composition and abundance of the dominant bacterial phyla, namely Proteobacteria, Actinobacteria, Firmicutes, Spirochaetes, Bacteroidetes, Tenericutes, and Thermotogae. The bacterial association network analysis also indicated the differential pattern of co-occurrence of bacteria in the three study groups. The results regarding the differences in the structure and association of the intestinal microbiota of Atlantic salmon after florfenicol and oxolinic acid feeding can be employed to attenuate the adverse effects of antibiotic feeding on fish.

scholarly journals Effect of Salinity on the Gut Microbiome of Pike Fry (Esox lucius)

2020 ◽  
Vol 10 (7) ◽  
pp. 2506
Author(s):  
Tomasz Dulski ◽  
Roman Kujawa ◽  
Martyna Godzieba ◽  
Slawomir Ciesielski
Keyword(s):  
Gut Microbiome ◽  
High Salinity ◽  
Fish Farming ◽  
Amplicon Sequencing ◽  
Good Alternative ◽  
Control Group ◽  
Rrna Gene ◽  
Microbiological Analysis ◽  
Early Life Stages ◽  
The Impact

The increasing popularity of pike in angling and fish farming has created a need to increase pike production. However, intensive pike farming is subject to limitations due to diseases and pathogens. Sodium chloride (NaCl) could be a good alternative to chemotherapeutics, especially for protecting the fish against pathogens and parasites at early life stages. However, the impact of high salinity on the symbiotic bacteria inhabiting freshwater fish is still unclear. Therefore, our objective was to analyze the gut microbiome to find possible changes caused by salinity. In this study, the influence of 3‰ and 7‰ salinity on pike fry was investigated. High-throughput 16S rRNA gene amplicon sequencing was used to profile the gut microbiome of the fish. It was found that salinity had a statistically significant influence on pike fry mortality. Mortality was highest in the 7‰ salinity group and lowest in the 3‰ group. Microbiological analysis indicated that Proteobacteria and Actinobacteria predominated in the pike gut microbiome in all examined groups, followed by lower percentages of Bacteroidetes and Firmicutes. There were no statistically significant differences in the percent abundance of bacterial taxa between the control group and groups with a higher salinity. Our results suggest that salinity influences the gut microbiome structure in pike fry, and that 3‰ salinity may be a good solution for culturing pike at this stage in their development.

scholarly journals Half-Elemental Diet Shifts the Human Intestinal Bacterial Compositions and Metabolites: A Pilot Study with Healthy Individuals

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Jun Miyoshi ◽  
Daisuke Saito ◽  
Mio Nakamura ◽  
Miki Miura ◽  
Tatsuya Mitsui ◽  
...  
Keyword(s):  
Pilot Study ◽  
Gut Microbiota ◽  
Dietary Habits ◽  
Elemental Diet ◽  
Amplicon Sequencing ◽  
Short Chain Fatty Acids ◽  
Rrna Gene ◽  
Healthy Individuals ◽  
The Impact ◽  
Time Point

Background and Aim. Half-elemental diet (ED) (900 kcal/day of ED) has clinical efficacy to treat Crohn’s disease (CD). However, the underlying mechanisms of how the ED exerts its efficacy remain unclear. Alterations of the gut microbiota, known as dysbiosis, have been reported to play a role in CD pathogenesis. Many variables including diet affect the gut microbiota. We hypothesized that half-ED has the potential to change the gut microbiota composition and functions leading to anti-inflammatory actions. Given that inflammation can be a confounding factor affecting the intestinal microbiota, we aimed to test our hypothesis among healthy individuals in this pilot study. Methods. This prospective study included four healthy volunteers. The subjects continued their dietary habits for 2 weeks after the registration of the study and then started half-ED replacing 900 kcal of the regular diet with ED (time point 1, T1). The subjects continued half-ED for 2 weeks (T2). After the withdrawal of ED, subjects resumed their original dietary habits for 2 weeks (T3). Fecal samples were collected from all subjects at all time points, T1-3. Fecal DNA and metabolites were extracted from the samples. We performed 16S rRNA gene amplicon sequencing and metabolomic analysis to examine the bacterial compositions and intestinal metabolites. Results. There were differences in the gut bacterial compositions and metabolites at each time point as well as overtime changing patterns between subjects. Several bacteria and metabolites including short-chain fatty acids and bile acids altered significantly across the subjects. The bacterial membership and intestinal metabolites at T3 were different from T1 in all subjects. Conclusions. Half-ED shifts the gut bacterial compositions and metabolites. The changes varied with each individual, while some microbes and metabolites change commonly across individuals. The impact of half-ED may persist even after the withdrawal. This trial is registered with UMIN ID: 000031920.

scholarly journals Preliminary insights into the impact of primary radiochemotherapy on the salivary microbiome in head and neck squamous cell carcinoma

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Christina Kumpitsch ◽  
Christine Moissl-Eichinger ◽  
Jakob Pock ◽  
Dietmar Thurnher ◽  
Axel Wolf
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Treatment Options ◽  
Well Being ◽  
Amplicon Sequencing ◽  
Neck Squamous Cell Carcinoma ◽  
Rrna Gene ◽  
The Impact

Abstract Squamous cell carcinoma is the most common type of throat cancer. Treatment options comprise surgery, radiotherapy, and/or chemo(immuno)therapy. The salivary microbiome is shaped by the disease, and likely by the treatment, resulting in side effects caused by chemoradiation that severely impair patients’ well-being. High-throughput amplicon sequencing of the 16S rRNA gene provides an opportunity to investigate changes in the salivary microbiome in health and disease. In this preliminary study, we investigated alterations in the bacterial, fungal, and archaeal components of the salivary microbiome between healthy subjects and patients with head and neck squamous cell carcinoma before and close to the end point of chemoradiation (“after”). We enrolled 31 patients and 11 healthy controls, with 11 patients providing samples both before and after chemoradiation. Analysis revealed an effect on the bacterial and fungal microbiome, with a partial antagonistic reaction but no effects on the archaeal microbial community. Specifically, we observed an individual increase in Candida signatures following chemoradiation, whereas the overall diversity of the microbial and fungal signatures decreased significantly after therapy. Thus, our study indicates that the patient microbiome reacts individually to chemoradiation but has potential for future optimization of disease diagnostics and personalized treatments.

scholarly journals Host Species Determines the Composition of the Prokaryotic Microbiota in Phlebotomus Sandflies

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 428
Author(s):  
Christos Papadopoulos ◽  
Panagiotis A. Karas ◽  
Sotirios Vasileiadis ◽  
Panagiota Ligda ◽  
Anastasios Saratsis ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Host Species ◽  
Archaeal Community ◽  
Amplicon Sequencing ◽  
Structural Effect ◽  
Rrna Gene ◽  
Host Genotype ◽  
Operational Taxonomic Units ◽  
Phlebotomine Sandflies ◽  
Leishmania Spp

Phlebotomine sandflies are vectors of the humans’ and mammals’ parasite Leishmania spp. Although the role of gut microbiome in the biological cycle of insects is acknowledged, we still know little about the factors modulating the composition of the gut microbiota of sandflies. We tested whether host species impose a strong structural effect on the gut microbiota of Phlebotomus spp. Sandflies were collected from the island of Leros, Greece, and classified to P. papatasi, P. neglectus, P. tobbi, and P. similis, all being negative to Leishmania spp. The prokaryotic gut microbiota was determined via 16S rRNA gene amplicon sequencing. Phlebotomus species supported distinct microbial communities (p < 0.001). P. papatasi microbiota was the most distinct over-dominated by three Spiroplasma, Wolbachia and Paenibacillus operational taxonomic units (OTUs), while another Wolbachia OTU prevailed in P. neglectus. Conversely, the microbiota of P. tobbi and P. similis was composed of several less dominant OTUs. Archaea showed low presence with the dominant OTUs belonging to methanogenic Euryarcheota, ammonia-oxidizing Thaumarcheota, and Nanoarchaeota. We provide first insights into the composition of the bacterial and archaeal community of Phlebotomus sandflies and showed that, in the absence of Leishmania, host genotype is the major modulator of Phlebotomus sandfly gut microbiota.

scholarly journals Influence of light on particulate organic matter utilization by attached and free-living marine bacteria

2019 ◽  
Author(s):  
Laura Gomez-Consarnau ◽  
David M. Needham ◽  
Peter K. Weber ◽  
Jed A. Fuhrman ◽  
Xavier Mayali
Keyword(s):  
Microbial Community ◽  
Amplicon Sequencing ◽  
Time Of Day ◽  
Rrna Gene ◽  
Free Living ◽  
Isotope Incorporation ◽  
The Pacific ◽  
C And N ◽  
N Incorporation ◽  
The Impact

While the impact of light on primary productivity in aquatic systems has been studied for decades, the role light plays in the degradation of photosynthetically-produced biomass is less well understood. We investigated the patterns of light-induced particle breakdown and bacterial assimilation of detrital C and N using13C and15N labeled freeze-thawed diatom cells incubated in laboratory microcosms with a marine microbial community freshly-collected from the Pacific Ocean. Particles incubated in the dark resulted in increased bacterial counts and dissolved organic carbon concentrations compared to those incubated in the light. Light also influenced the attached and free-living microbial community structure as detected by 16S rRNA gene amplicon sequencing. For example, bacterial taxa from the Sphingobacteriia were enriched on dark-incubated particles and taxa from the family Flavobacteriaceae and the genus Pseudoalteromonas were numerically enriched on particles in the light. Isotope incorporation analysis by phylogenetic microarray and NanoSIMS (a method called Chip-SIP) identified free-living and attached microbial taxa able to incorporate N and C from the particles. Some taxa, including members of the Flavobacteriaceae and Cryomorphaceae, exhibited increased isotope incorporation in the light, suggesting the use of photoheterotrophic metabolisms. In contrast, some members of Oceanospirillales and Rhodospirillales showed decreased isotope incorporation in the light, suggesting that their heterotrophic metabolism, particularly when occurring on particles, might increase at night or may be inhibited by sunlight. These results show that light influences particle degradation and C and N incorporation by attached bacteria, suggesting that the transfer between particulate and free-living phases are likely affected by external factors that change with the light regime, such as time of day, depth and season.

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