Dieback of European Ash: What Can We Learn from the Microbial Community and Species-Specific Traits of Endophytic Fungi Associated with Ash?

2018 ◽  
pp. 229-258 ◽  
Author(s):  
Ari M. Hietala ◽  
Isabella Børja ◽  
Hugh Cross ◽  
Nina Elisabeth Nagy ◽  
Halvor Solheim ◽  
...  
Keyword(s):  
Microbial Community ◽  
Endophytic Fungi ◽  
Species Specific ◽  
European Ash

scholarly journals Evidence of within-species specialization by soil microbes and the implications for plant community diversity

2019 ◽  
Vol 116 (15) ◽  
pp. 7371-7376 ◽  
Author(s):  
Jenalle L. Eck ◽  
Simon M. Stump ◽  
Camille S. Delavaux ◽  
Scott A. Mangan ◽  
Liza S. Comita
Keyword(s):  
Microbial Community ◽  
Seed Dispersal ◽  
Plant Species ◽  
Plant Community ◽  
Plant Communities ◽  
Soil Microbial Community ◽  
Soil Microbes ◽  
Wild Plant ◽  
Soil Microbial ◽  
Species Specific

Microbes are thought to maintain diversity in plant communities by specializing on particular species, but it is not known whether microbes that specialize within species (i.e., on genotypes) affect diversity or dynamics in plant communities. Here we show that soil microbes can specialize at the within-population level in a wild plant species, and that such specialization could promote species diversity and seed dispersal in plant communities. In a shadehouse experiment in Panama, we found that seedlings of the native tree species, Virola surinamensis (Myristicaceae), had reduced performance in the soil microbial community of their maternal tree compared with in the soil microbial community of a nonmaternal tree from the same population. Performance differences were unrelated to soil nutrients or to colonization by mycorrhizal fungi, suggesting that highly specialized pathogens were the mechanism reducing seedling performance in maternal soils. We then constructed a simulation model to explore the ecological and evolutionary consequences of genotype-specific pathogens in multispecies plant communities. Model results indicated that genotype-specific pathogens promote plant species coexistence—albeit less strongly than species-specific pathogens—and are most effective at maintaining species richness when genetic diversity is relatively low. Simulations also revealed that genotype-specific pathogens select for increased seed dispersal relative to species-specific pathogens, potentially helping to create seed dispersal landscapes that allow pathogens to more effectively promote diversity. Combined, our results reveal that soil microbes can specialize within wild plant populations, affecting seedling performance near conspecific adults and influencing plant community dynamics on ecological and evolutionary time scales.

Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific

2013 ◽  
Vol 8 (8) ◽  
pp. 1755-1763 ◽  
Author(s):  
Curt R. Fischer ◽  
Benjamin P. Bowen ◽  
Chongle Pan ◽  
Trent R. Northen ◽  
Jillian F. Banfield
Keyword(s):  
Microbial Community ◽  
Stable Isotope ◽  
Hydrogen Isotope ◽  
Isotope Fractionation ◽  
Stable Isotope Probing ◽  
Species Specific

Endophytic fungi as a promising biocontrol agent to protect wheat from Fusarium graminearum head blight

Plant Disease ◽  
2021 ◽  
Author(s):  
Zachary Albert Noel ◽  
Ludmilla Roze ◽  
Mikaela Breunig ◽  
Frances Trail
Keyword(s):  
Microbial Community ◽  
Fusarium Graminearum ◽  
Endophytic Fungi ◽  
Seed Weight ◽  
Biocontrol Agent ◽  
Fungal Endophytes ◽  
In Planta ◽  
Head Blight ◽  
Species Definitions

The search for beneficial endophytes that can be part of a constructed microbial community has increased in recent years. We characterized three endophytic fungi previously isolated from wheat for their in vitro and in planta antagonism toward the Fusarium head blight pathogen, Fusarium graminearum. The endophytes were phylogenetically characterized and shown to be Alternaria destruens, Fusarium commune, and Fusarium oxysporum. Individual fungal endophytes significantly increased seed weight and lowered the accumulation of the mycotoxin deoxynivalenol compared to F. graminearum infected wheat heads without endophyte pretreatment. Investigation into the mechanism of competition in vitro showed that endophytes competitively excluded F. graminearum by pre-emptive colonization and possible inhibition over a distance. Investigations on the use of these endophytes in the field are in progress. Identification of these three endophytes highlights a common quandary in searching for beneficial microbes to use in agriculture: species definitions often do not separate individual isolates’ lifestyles. A greater understanding of the risks in using intraspecies variants for biocontrol is needed and should be examined in the context of the ecology of the individuals being investigated.

scholarly journals Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Alejandra Hernandez-Agreda ◽  
William Leggat ◽  
Pim Bongaerts ◽  
César Herrera ◽  
Tracy D. Ainsworth
Keyword(s):  
Microbial Community ◽  
Core Microbiome ◽  
Functional Roles ◽  
Individual Level ◽  
Coral Microbiome ◽  
Coral Holobiont ◽  
Environmentally Responsive ◽  
The Individual ◽  
Species Specific ◽  
Responsive Community

ABSTRACTStudies of the coral microbiome predominantly characterize the microbial community of the host species as a collective, rather than that of the individual. This ecological perspective on the coral microbiome has led to the conclusion that the coral holobiont is the most diverse microbial biosphere studied thus far. However, investigating the microbiome of the individual, rather than that of the species, highlights common and conserved community attributes which can provide insights into the significance of microbial associations to the host. Here, we show there are consistent characteristics between individuals in the proposed three components of the coral microbiome (i.e., “environmentally responsive community,” “resident or individual microbiome,” and “core microbiome”). We found that the resident microbiome of a photoendosymbiotic coral harbored <3% (∼605 phylotypes) of the 16S rRNA phylotypes associated with all investigated individuals of that species (“species-specific microbiome”) (∼21,654 phylotypes; individuals fromPachyseris speciosa[n= 123],Mycedium elephantotus[n= 95], andAcropora aculeus[n= 91] from 10 reef locations). The remaining bacterial phylotypes (>96%) (environmentally responsive community) of the species-specific microbiome were in fact not found in association with the majority of individuals of the species. Only 0.1% (∼21 phylotypes) of the species-specific microbiome of each species was shared among all individuals of the species (core microbiome), equating to ∼3.4% of the resident microbiome. We found taxonomic redundancy and consistent patterns of composition, structure, and taxonomic breadth across individual microbiomes from the three coral species. Our results demonstrate that the coral microbiome is structured at the individual level.IMPORTANCEWe propose that the coral holobiont should be conceptualized as a diverse transient microbial community that is responsive to the surrounding environment and encompasses a simple, redundant, resident microbiome and a small conserved core microbiome. Most importantly, we show that the coral microbiome is comparable to the microbiomes of other organisms studied thus far. Accurately characterizing the coral-microbe interactions provides an important baseline from which the functional roles and the functional niches within which microbes reside can be deciphered.

scholarly journals Emergence Shapes the Structure of the Seed Microbiota

2014 ◽  
Vol 81 (4) ◽  
pp. 1257-1266 ◽  
Author(s):  
Matthieu Barret ◽  
Martial Briand ◽  
Sophie Bonneau ◽  
Anne Préveaux ◽  
Sophie Valière ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Practical Applications ◽  
Bacterial Marker ◽  
Species Specific ◽  
Diversity Studies

ABSTRACTSeeds carry complex microbial communities, which may exert beneficial or deleterious effects on plant growth and plant health. To date, the composition of microbial communities associated with seeds has been explored mainly through culture-based diversity studies and therefore remains largely unknown. In this work, we analyzed the structures of the seed microbiotas of different plants from the family Brassicaceae and their dynamics during germination and emergence through sequencing of three molecular markers: the ITS1 region of the fungal internal transcribed spacer, the V4 region of 16S rRNA gene, and a species-specific bacterial marker based on a fragment ofgyrB. Sequence analyses revealed important variations in microbial community composition between seed samples. Moreover, we found that emergence strongly influences the structure of the microbiota, with a marked reduction of bacterial and fungal diversity. This shift in the microbial community composition is mostly due to an increase in the relative abundance of some bacterial and fungal taxa possessing fast-growing abilities. Altogether, our results provide an estimation of the role of the seed as a source of inoculum for the seedling, which is crucial for practical applications in developing new strategies of inoculation for disease prevention.

scholarly journals Novel Approach to Quantitative Detection of Specific rRNA in a Microbial Community, Using Catalytic DNA

2005 ◽  
Vol 71 (8) ◽  
pp. 4879-4884 ◽  
Author(s):  
Hikaru Suenaga ◽  
Rui Liu ◽  
Yuko Shiramasa ◽  
Takahiro Kanagawa
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Bacterial Species ◽  
Quantitative Detection ◽  
Catalytic Function ◽  
Novel Approach ◽  
Specific Manner ◽  
Novel Method ◽  
Species Specific ◽  
Wastewater Treatment Systems

ABSTRACT We developed a novel method for the quantitative detection of the 16S rRNA of a specific bacterial species in the microbial community by using deoxyribozyme (DNAzyme), which possesses the catalytic function to cleave RNA in a sequence-specific manner. A mixture of heterogeneous 16S rRNA containing the target 16S rRNA was incubated with a species-specific DNAzyme. The cleaved target 16S rRNA was separated from the intact 16S rRNA by electrophoresis, and then their amounts were compared for the quantitative detection of target 16S rRNA. This method was used to determine the abundance of the 16S rRNA of a filamentous bacterium, Sphaerotilus natans, in activated sludge, which is a microbial mixture used in wastewater treatment systems. The result indicated that this DNAzyme-based approach would be applicable to actual microbial communities.

scholarly journals Microbial community analysis of a UASB reactor and application of an evolutionary algorithm to enhance wastewater treatment and biogas production

2015 ◽  
Author(s):  
◽  
Abimbola Motunrayo Enitan
Keyword(s):  
Microbial Community ◽  
Biogas Production ◽  
Methanogenic Archaea ◽  
Granular Sludge ◽  
Full Scale ◽  
Uasb Reactor ◽  
Brewery Wastewater ◽  
Effluent Quality ◽  
Ch4 Production ◽  
Species Specific

Anaerobic digestion, a proven and highly efficient biological process for treating industrial wastewater and biogas generation is an underutilized technology in South Africa. Some of the industries that have on-site anaerobic reactors tend to face problems in operating these reactors due to poor understanding of the process and implementation of the technology. This has resulted in high pollutant loads in their final effluents and low energy recovery. In this study, an on-site full–scale upflow anaerobic sludge blanket (UASB) reactor treating brewery wastewater was extensively monitored in order to evaluate the efficiency in terms of effluent quality, biogas production and microbial structure. Furthermore, developed and adopted kinetic models were used to optimize the performance of the full–scale UASB reactor using a combined Pareto differential evolution (CPMDE) algorithm. A preliminary analysis of the raw wastewater has shown that the wastewater produced from the brewery industry was high in organic matter with a total chemical oxygen demand (COD) between 1096.41 to 8926.08 mg/L. The average removal efficiency of COD from the UASB reactor after treatment was 79% with a methane (CH4) production of 60-69% at temperature ranges of 28-32˚C and hydraulic retention time (HRT) of 12 h within the optimal pH range for anaerobic bacteria (6.6 and 7.3) under various organic loading rates. However, the results also showed an increase in total suspended solids (TSS), nitrogen (N2), ammonia (NH3) and orthophosphate concentrations when comparing the influent to the effluent, which indicated the necessity for further optimization of the reactor condition in order to reduce these effluent parameters to acceptable standards and to increase CH4 production. In order to optimize the process, a thorough understanding of microbial interaction was essential. A combination of different molecular techniques viz., fluorescence in–situ hybridization (FISH), polymerase chain reaction (PCR) and quantitative real-time PCR (QPCR) were employed to understand the microbial community structure of the granular sludge samples using species specific primers and probes. The results revealed that the dominance of diverse groups of eubacteria belonging to phyla Proteobacteria, Firmicutes and Chloroflexi and an uncultured candidate division WS6 with four different orders of methanogenic Archaea viz., Methanomicrobiales, Methanococcales, Methanobacteriales and Methanosarcinales belonging to hydrogenotrophic and aceticlastic methanogens were within the reactor samples. Quantification of the 16S rDNA copies of eubacteria and methanogenic Archaea using species-specific primers further confirmed the spatial distribution of these microorganisms within the different compartments of the reactor where, the upper compartments were dominated by eubacteria and the lower compartments by methanogenic Archaea. The concentration of Archaea per nanogram of DNA was much higher (96.28%) than eubacteria (3.78%) in lower compartments, while, the eubacteria concentration increased to 98.34% in upper compartments with a decrease in Archaea quantity (1.66%). A modified kinetic methane generation model (MMGM) was developed on the basis of mass balance principles with respect to substrate (COD) degradation and the endogenous decay rate to predict CH4 production efficiency of the reactor. Furthermore, a Stover–Kincannon kinetic model was adopted with the aim of predicting the final effluent quality in terms of COD concentration and model coefficients were determined using the data collected from the full–scale reactor. Thereafter, a model-based multi-objective optimization was carried out using the CPMDE algorithm with three–objective functions namely; maximization of volumetric CH4 production rate; minimization of effluent substrate concentration and minimization of biomass washout, in order to increase the overall efficiency of the UASB reactor. Important decision variables and constraints related to the process were set for the optimization. A set of non-dominated solutions with high CH4 production rates of between 2.78 and 5.06 L CH4/g COD/day at low biomass washout concentrations were obtained at almost constant solution for the effluent COD concentration. A high COD removal efficiency (85-87%) at ~30-31˚C and 8-9 h HRT was obtained for the multi-objective optimization problem formulated. This study could significantly contribute towards optimization of a full–scale UASB reactor treating brewery wastewater for better effluent quality and biogas production. Knowledge on the activity and performance of microbial community present in the granular sludge taken from the full–scale UASB reactor would contribute significantly to future optimization strategies of the reactor. In addition, optimization using an evolutionary algorithm under different operational conditions would help to save both time and resources wasted in operating anaerobic bioreactors.

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