scholarly journals Hidden Fungi: Combining Culture-Dependent and -Independent DNA Barcoding Reveals Inter-Plant Variation in Species Richness of Endophytic Root Fungi in Elymus repens

2021 ◽  
Vol 7 (6) ◽  
pp. 466
Author(s):  
Anna K. Høyer ◽  
Trevor R. Hodkinson
Keyword(s):  
Species Richness ◽  
Accurate Determination ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Grass Species ◽  
Plant Variation ◽  
Sequencing Method ◽  
Elymus Repens ◽  
Root Fungi ◽  
Culture Dependent

The root endophyte community of the grass species Elymus repens was investigated using both a culture-dependent approach and a direct amplicon sequencing method across five sites and from individual plants. There was much heterogeneity across the five sites and among individual plants. Focusing on one site, 349 OTUs were identified by direct amplicon sequencing but only 66 OTUs were cultured. The two approaches shared ten OTUs and the majority of cultured endophytes do not overlap with the amplicon dataset. Media influenced the cultured species richness and without the inclusion of 2% MEA and full-strength MEA, approximately half of the unique OTUs would not have been isolated using only PDA. Combining both culture-dependent and -independent methods for the most accurate determination of root fungal species richness is therefore recommended. High inter-plant variation in fungal species richness was demonstrated, which highlights the need to rethink the scale at which we describe endophyte communities.

scholarly journals Insights into the community structure and lifestyle of the fungal root endophytes of tomato by combining amplicon sequencing and isolation approaches with phytohormone profiling

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Andrea Manzotti ◽  
Alessandro Bergna ◽  
Meike Burow ◽  
Hans J L Jørgensen ◽  
Tomislav Cernava ◽  
...  
Keyword(s):  
Species Richness ◽  
Functional Characterization ◽  
Amplicon Sequencing ◽  
Ethylene Biosynthesis ◽  
Fungal Species ◽  
Host Genotype ◽  
Its1 Region ◽  
Tomato Seedlings ◽  
Tomato Roots

ABSTRACT Little is known about the influence of host genotype and phytohormones on the composition of fungal endophytic communities. We investigated the influence of host genotype and phytohormones on the structure of the fungal endophytic communities of tomato roots by amplicon sequencing of the ITS1 region and combined this approach with isolation and functional characterization of the isolates. A significant effect of the host genotype on the dominant fungal species was found by comparing the cultivars Castlemart and UC82B and, surprisingly, root pathogens were among the most abundant taxa. In contrast, smaller changes in the relative abundance of the dominant species were found in mutants impaired in jasmonic acid biosynthesis (def1) and ethylene biosynthesis (8338) compared to the respective wild types. However, def1 showed significantly higher species richness compared to the wild type. Analysis of the phytohormone profiles of these genotypes indicates that changes in the phytohormone balance may contribute to this difference in species richness. Assessing the lifestyle of isolated fungi on tomato seedlings revealed the presence of both beneficial endophytes and latent pathogens in roots of asymptomatic plants, suggesting that the interactions between members of the microbiome maintain the equilibrium in the community preventing pathogens from causing disease.

Correlates of pathogen species richness in the grass family

1995 ◽  
Vol 73 (S1) ◽  
pp. 42-49 ◽  
Author(s):  
Keith Clay
Keyword(s):  
Life History ◽  
Species Richness ◽  
Data Base ◽  
Native Species ◽  
Fungal Pathogens ◽  
The United States ◽  
Fungal Species ◽  
Geographical Range ◽  
Grass Species ◽  
Strong Trend

Factors contributing to the species richness of fungal pathogens infecting grasses were explored through statistical analyses of data derived from a computerized data base on fungi on plants in the United States and from grass floras. The total number of fungal species infecting each grass species, as well as numbers of smuts, rusts, and systemic clavicipitaceous fungi, were compiled. Host characteristics included grass subfamily, the number of species in the genus, geographic range, life history, and their status as native versus alien species, and crop versus noncrop species. Analyses indicated that the best predictor of pathogen species richness per host is host geographical range. Grass subfamily, life history, and status as crops or native species also were significantly correlated with pathogen load but explained less variation than host geographical range. Pathogen species richness per host showed a strong trend to increase with increasing latitude. Extensive sampling of fungal pathogens from selected grass species is needed to provide an independent measure of accuracy of the data base. Key words: biodiversity, fungi, grasses, pathogens, species richness.

scholarly journals Improved strategies to efficiently isolate thermophilic, thermotolerant, and heat-resistant fungi from compost and soil

2021 ◽  
Vol 20 (3) ◽  
pp. 325-339
Author(s):  
Frederick Witfeld ◽  
Dominik Begerow ◽  
Marco Alexandre Guerreiro
Keyword(s):  
Elevated Temperatures ◽  
Fungal Species ◽  
Dna Barcodes ◽  
Heat Shock Treatment ◽  
Isolation And Identification ◽  
Heat Resistant ◽  
Heat Stable ◽  
Promising Source ◽  
Culture Dependent ◽  
Selection Of

AbstractThermophilic, thermotolerant and heat-resistant fungi developed different physiological traits, enabling them to sustain or even flourish under elevated temperatures, which are life-hostile for most other eukaryotes. With the growing demand of heat-stable molecules in biotechnology and industry, the awareness of heat-adapted fungi as a promising source of respective enzymes and biomolecules is still increasing. The aim of this study was to test two different strategies for the efficient isolation and identification of distinctly heat-adapted fungi from easily accessible substrates and locations. Eight compost piles and ten soil sites were sampled in combination with different culture-dependent approaches to describe suitable strategies for the isolation and selection of thermophilous fungi. Additionally, an approach with a heat-shock treatment, but without elevated temperature incubation led to the isolation of heat-resistant mesophilic species. The cultures were identified based on morphology, DNA barcodes, and microsatellite fingerprinting. In total, 191 obtained isolates were assigned to 31 fungal species, from which half are truly thermophilic or thermotolerant, while the other half are heat-resistant fungi. A numerous amount of heat-adapted fungi was isolated from both compost and soil samples, indicating the suitability of the used approaches and that the richness and availability of those organisms in such environments are substantially high.

scholarly journals Culture-Independent and Culture-Dependent Characterization of the Black Soldier Fly Gut Microbiome Reveals a Large Proportion of Culturable Bacteria with Potential for Industrial Applications

2021 ◽  
Vol 9 (8) ◽  
pp. 1642
Author(s):  
Dorothee Tegtmeier ◽  
Sabine Hurka ◽  
Sanja Mihajlovic ◽  
Maren Bodenschatz ◽  
Stephanie Schlimbach ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Amplicon Sequencing ◽  
Industrial Applications ◽  
Culture Collection ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Culturable Bacteria ◽  
Black Soldier Fly ◽  
Culture Independent ◽  
Culture Dependent

Black soldier fly larvae (BSFL) are fast-growing, resilient insects that can break down a variety of organic substrates and convert them into valuable proteins and lipids for applications in the feed industry. Decomposition is mediated by an abundant and versatile gut microbiome, which has been studied for more than a decade. However, little is known about the phylogeny, properties and functions of bacterial isolates from the BSFL gut. We therefore characterized the BSFL gut microbiome in detail, evaluating bacterial diversity by culture-dependent methods and amplicon sequencing of the 16S rRNA gene. Redundant strains were identified by genomic fingerprinting and 105 non-redundant isolates were then tested for their ability to inhibit pathogens. We cultivated representatives of 26 genera, covering 47% of the families and 33% of the genera detected by amplicon sequencing. Among these isolates, we found several representatives of the most abundant genera: Morganella, Enterococcus, Proteus and Providencia. We also isolated diverse members of the less-abundant phylum Actinobacteria, and a novel genus of the order Clostridiales. We found that 15 of the isolates inhibited at least one of the tested pathogens, suggesting a role in helping to prevent colonization by pathogens in the gut. The resulting culture collection of unique BSFL gut bacteria provides a promising resource for multiple industrial applications.

Response of dry grassland vegetation to fluctuations in weather conditions: a 9-year case study in Prague (Czech Republic)

Biologia ◽  
2011 ◽  
Vol 66 (5) ◽  
Author(s):  
Jiří Dostálek ◽  
Tomáš Frantík
Keyword(s):  
Species Richness ◽  
Czech Republic ◽  
Weather Conditions ◽  
Grass Species ◽  
Individual Species ◽  
Weather Variability ◽  
Grassland Vegetation ◽  
Dry Grassland ◽  
Local Climate ◽  
The Impact

AbstractThe extreme habitats of dry grasslands are suitable for investigations of the response of vegetation to local climate changes. The impact of weather variability on the dynamics of a plant community in a dry grassland was studied. Correlations were found between different functional groups of species and individual species and weather variability. During a 9-year study in five nature reserves in Prague (Czech Republic), the following responses of dry grassland vegetation to weather conditions were observed: (i) wetter conditions, especially in the winter, affected the dominance and species richness of perennial grass species and the decline of rosette plants; (ii) the year-to-year higher temperatures in the winter produced a decline in the dominance of short graminoids and creeping forbs; (iii) spring drought adversely impacted the overall abundance, especially the abundance of dicotyledonous species, and the species richness. However, these relationships may be manifested in different ways in different locations, and in some cases the vegetation of different locations may respond to weather conditions in opposite manners.

scholarly journals Seasonal Diversity of Arbuscular Mycorrhizal Fungi in Mangroves of Goa, India

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
James D’Souza ◽  
Bernard Felinov Rodrigues
Keyword(s):  
Species Richness ◽  
Mycorrhizal Fungi ◽  
Monsoon Season ◽  
Arbuscular Mycorrhizal ◽  
Fungal Spore ◽  
Fungal Species ◽  
Spore Density ◽  
Species Variation ◽  
Fungal Community Composition ◽  
Mangrove Plant

Seasonal dynamics of arbuscular mycorrhizal (AM) fungal community composition in three common mangrove plant species, namely, Acanthus ilicifolius, Excoecaria agallocha, and Rhizophora mucronata, from two sites in Goa, India, were investigated. In all three species variation in AM fungal spore density was observed. Maximum spore density and AM species richness were recorded in the premonsoon season, while minimum spore density and richness were observed during monsoon season at both sites. A total of 11 AM fungal species representing five genera were recorded. Acaulospora laevis was recorded in all seasons at both sites. Multivariate analysis revealed that season and host coaffected AM spore density and species richness with the former having greater influence than the latter.

scholarly journals Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

2017 ◽  
Vol 83 (17) ◽  
Author(s):  
Francesca De Filippis ◽  
Manolo Laiola ◽  
Giuseppe Blaiotta ◽  
Danilo Ercolini
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
Biological Samples ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Fungal Communities ◽  
Its2 Region ◽  
Mock Community

ABSTRACT Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes, with 16S rRNA being the gold standard for bacteria. As for fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity. After an in silico primer evaluation, we compared three amplicons (the ITS1-ITS2 region [ITS1-2], 18S ribosomal small subunit RNA, and the D1/D2 domain of the 26S ribosomal large subunit RNA), using biological samples and a mock community of common fungal species. All three targets allowed for accurate identification of the species present. Nevertheless, high heterogeneity in ITS1-2 length was found, and this caused an overestimation of the abundance of species with a shorter ITS, while both 18S and 26S amplicons allowed for more reliable quantification. We demonstrated that ITS1-2 amplicon sequencing, although widely used, may lead to an incorrect evaluation of fungal communities, and efforts should be made to promote the use of different targets in sequencing-based microbial ecology studies. IMPORTANCE Amplicon-sequencing approaches for fungi may rely on different targets affecting the diversity and abundance of the fungal species. An increasing number of studies will address fungal diversity by high-throughput amplicon sequencing. The description of the communities must be accurate and reliable in order to draw useful insights and to address both ecological and biological questions. By analyzing a mock community and several biological samples, we demonstrate that using different amplicon targets may change the results of fungal microbiota analysis, and we highlight how a careful choice of the target is fundamental for a thorough description of the fungal communities.

scholarly journals The Interior Surfaces of Wooden Barrels Are an Additional Microbial Inoculation Source for Lambic Beer Production

2018 ◽  
Vol 85 (1) ◽  
Author(s):  
J. De Roos ◽  
D. Van der Veken ◽  
L. De Vuyst
Keyword(s):  
Microbial Community ◽  
Amplicon Sequencing ◽  
Microbial Inoculation ◽  
Culture Independent ◽  
Pressure Water ◽  
Cleaning Procedures ◽  
Environmental Air ◽  
Beer Production ◽  
Different Characteristics ◽  
Culture Dependent

ABSTRACTTraditional lambic beer production takes place through wort inoculation with environmental air and fermentation and maturation in wooden barrels. These wooden casks or foeders are possible additional inoculation sources of microorganisms for lambic worts. To date, however, these lambic barrels have been examined only with culture-dependent techniques, thereby missing a portion of the microorganisms present. Moreover, the effects of the cleaning procedures (involving high-pressure water and/or fumigation) and the barrel type on the microbial community structures of the interior surfaces of wooden lambic barrels were unclear. The culture-dependent plating and culture-independent amplicon sequencing of swab samples obtained from the interior surfaces of different wooden casks and foeders used for traditional lambic beer production in Belgium revealed that the microbial compositions of these surfaces differed statistically throughout the barrel-cleaning procedures applied. At the end of the cleaning procedures, amplicon sequencing still detected fermentation- and maturation-related microorganisms, although only a few colonies were still detectable using culture-dependent methods. It is possible that some of the surviving microorganisms were missed due to the presence of many of these cells in a viable but not culturable state and/or engrained deeper in the wood. These surviving microorganisms could act as an additional inoculation source, besides brewery air and brewery equipment, thereby helping to establish a stable microbial community in the wort to diminish batch-to-batch variations in fermentation profiles. Furthermore, the microbial compositions of the interior barrel surfaces differed statistically based on the barrel type, possibly reflecting different characteristics of the lambic barrels in terms of age, wood thickness, and wood porosity.IMPORTANCEAlthough the coolship step is generally regarded as the main contributor to the spontaneous inoculation by environmental air of fresh worts for lambic beer production, it is known that microorganisms often associate with specific surfaces present in a brewery. However, knowledge about the association of microorganisms with the interior surfaces of wooden lambic barrels is limited. To clarify the role of casks and foeders as additional microbial inoculation sources, it was important to determine the influence of the barrel characteristics and the cleaning procedures on the microbial communities of the interior barrel surfaces. Moreover, this helped to elucidate the complex spontaneous lambic beer fermentation and maturation process. It will allow further optimization of the lambic beer production process, as well as the wooden-barrel-cleaning procedures applied.

scholarly journals Factors influencing early restoration progress of a Eucalyptus tereticornis open forest on former agricultural land.

2012 ◽  
Vol 18 (4) ◽  
pp. 263 ◽  
Author(s):  
Tom Lewis ◽  
David Taylor ◽  
Scott Swift ◽  
Valerie Debuse
Keyword(s):  
Species Richness ◽  
Plant Regeneration ◽  
Woody Plant ◽  
Agricultural Land ◽  
Livestock Grazing ◽  
Grass Species ◽  
Eucalyptus Tereticornis ◽  
Mature Trees ◽  
Litter Biomass ◽  
Open Forest

We monitored an area that was revegetated with the goal of restoring a Eucalyptus tereticornis open forest on former agricultural land in central, eastern Queensland. Revegetation involved: (1) planting 60 ha of previously cleared and heavily grazed land with eight local trees species; and (2) removing cattle grazing to encourage natural regeneration in areas where some mature trees remained. We compared the revegetation site to native pasture that had also been previously cleared, with only scattered paddock trees remaining, and continued to be managed for livestock production (an area similar to the revegetation site, prior to planting) and a remnant forest (reference area). Nine years since revegetation began there was some evidence that the revegetated site was diverging from pasture in terms of understorey plant composition, sapling density and topsoil C and N. There was little divergence in terms of plant species richness (native, introduced, grass, forb and woody plant richness), herbaceous biomass and woody plant regeneration. Some monitoring plots were subject to fire (prescribed fire and or wildfire) over the period of monitoring. With increasing time since fire, the richness of native species, introduced species and grass species (both native and introduced) declined, and forb and grass species richness declined with increasing litter biomass, suggesting that the occurrence of fire and the associated removal of litter biomass has a positive influence on herbaceous diversity in this ecosystem. Woody plant regeneration persisted through lignotubers at the revegetation site and at the pasture, but this regeneration was stunted at the pasture presumably due to livestock grazing. Hence areas of former E. tereticornis forest showed promising regenerative capacity where mature trees remained and where livestock grazing was removed.

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