scholarly journals Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

2021 ◽  
Vol 7 (7) ◽  
pp. 565
Author(s):  
Anindita Lahiri ◽  
Brian R. Murphy ◽  
Trevor R. Hodkinson
Keyword(s):  
Community Composition ◽  
Environmental Effects ◽  
High Throughput Sequencing ◽  
Fungal Community Composition ◽  
Species Identity ◽  
Ash Dieback ◽  
Hymenoscyphus Fraxineus ◽  
Culture Independent ◽  
The Impact ◽  
Culture Dependent

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

scholarly journals Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jorge Domínguez ◽  
Manuel Aira ◽  
Keith A. Crandall ◽  
Marcos Pérez-Losada
Keyword(s):  
Sewage Sludge ◽  
Community Composition ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Wastewater Treatment Plants ◽  
Agricultural Practices ◽  
Fungal Community Composition ◽  
Earthworm Casts ◽  
Composition And Structure ◽  
Sustainable Agricultural Practices

AbstractWastewater treatment plants produce hundreds of million tons of sewage sludge every year all over the world. Vermicomposting is well established worldwide and has been successful at processing sewage sludge, which can contribute to alleviate the severe environmental problems caused by its disposal. Here, we utilized 16S and ITS rRNA high-throughput sequencing to characterize bacterial and fungal community composition and structure during the gut- and cast-associated processes (GAP and CAP, respectively) of vermicomposting of sewage sludge. Bacterial and fungal communities of earthworm casts were mainly composed of microbial taxa not found in the sewage sludge; thus most of the bacterial (96%) and fungal (91%) taxa in the sewage sludge were eliminated during vermicomposting, mainly through the GAP. Upon completion of GAP and during CAP, modified microbial communities undergo a succession process leading to more diverse microbiotas than those found in sewage sludge. Consequently, bacterial and fungal community composition changed significantly during vermicomposting. Vermicomposting of sewage resulted in a stable and rich microbial community with potential biostimulant properties that may aid plant growth. Our results support the use of vermicompost derived from sewage sludge for sustainable agricultural practices, if heavy metals or other pollutants are under legislation limits or adequately treated.

scholarly journals Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest

2016 ◽  
Vol 82 (9) ◽  
pp. 2632-2643 ◽  
Author(s):  
Hui Sun ◽  
Eeva Terhonen ◽  
Andriy Kovalchuk ◽  
Hanna Tuovila ◽  
Hongxin Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Community Composition ◽  
High Throughput ◽  
Fungal Community ◽  
Tree Species ◽  
High Throughput Sequencing ◽  
Soil Layer ◽  
Fungal Community Composition ◽  
Content Type ◽  
Boreal Peatlands

ABSTRACTBoreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (P< 0.001) and tree species (P< 0.001). The distance-based linear models analysis showed that environmental variables were significantly correlated with community structure (P< 0.04). The availability of soil nutrients (Ca [P= 0.002], Fe [P= 0.003], and P [P= 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (P< 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera ofAgaricomycotinaidentified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands.

scholarly journals Temporal and Cultivar-Specific Effects on Potato Root- and Rhizosphere Fungal Diversity

2020 ◽  
Author(s):  
Kaire Loit ◽  
Liina Soonvald ◽  
Alar Astover ◽  
Eve Runno-Paurson ◽  
Maarja Öpik ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Substantial Effect ◽  
Sampling Time ◽  
Fungal Communities ◽  
Fungal Community Composition

The rhizosphere fungal community can play an important role in determining plant growth and health. In this study, using high-throughput sequencing, we investigated the fungal diversity and community composition in the roots and rhizosphere soil of 21 potato (Solanum tuberosum L.) cultivars. The samples were collected at three different sampling points. Furthermore, we assessed the differences in both diversity and composition of pathogen and saprotroph communities. In soil and roots, the fungal richness and relative abundance of pathogens and saprotrophs were mainly affected by sampling time. However, root fungal communities were also significantly affected by cultivar. The most substantial effect of cultivar was on root pathogen diversity. Moreover, the occurrence of most pathogens strongly varied among cultivars. Soil fungal community composition was primarily determined by sampling time; whereas in roots, the primary determinant was cultivar. Our results demonstrate changes in fungal communities over the potato growing season, as well as highlight the importance of potato cultivar on root fungal communities, and emphasise their importance in plant breeding.

Diversity of fungi associated with macroalgae from an estuarine environment and description of Cladosporium rubrum sp. nov. and Hypoxylon aveirense sp. nov.

2021 ◽  
Author(s):  
Tânia F. L. Vicente ◽  
Micael F. M. Gonçalves ◽  
Cláudio Brandão ◽  
Cátia Fidalgo ◽  
Artur Alves
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Type Strain ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Fungal Communities ◽  
Morphological Data ◽  
Fungal Community Composition ◽  
Culture Dependent

Fungal communities associated with macroalgae remain largely unexplored. To characterize algicolous fungal communities using culture dependent methods, macroalgae were collected from different sampling sites in the Ria de Aveiro estuary, Portugal. From a collection of 486 isolates that were obtained, 213 representative isolates were selected through microsatellite-primed PCR (MSP-PCR) fingerprinting analysis. The collection yielded 33 different genera, which were identified using the ITS region of the rDNA. The results revealed that the most abundant taxa in all collections were Acremonium-like species: Alternaria, Cladosporium, Leptobacillium and Penicillium. The fungal community composition varied with macroalgae species. Through multilocus phylogenetic analyses based on ITS, tub2, tef1-α and actA sequences, in addition to detailed morphological data, we propose Cladosporium rubrum sp. nov. (type strain=CMG 28=MUM 19.39) and Hypoxylon aveirense sp. nov. (type strain=CMG 29=MUM 19.40) as novel species.

scholarly journals Impacts of peat on nitrogen conservation and fungal community composition dynamics during food waste composting

2020 ◽  
Vol 63 (1) ◽  
Author(s):  
Zaihua He ◽  
Qiang Li ◽  
Xiaoyi Zeng ◽  
Kai Tian ◽  
Xiangshi Kong ◽  
...  
Keyword(s):  
Community Composition ◽  
Food Waste ◽  
Fungal Community ◽  
Community Dynamics ◽  
Dry Weight ◽  
Community Diversity ◽  
Ammonia Emissions ◽  
Fungal Community Composition ◽  
Nitrogen Conservation ◽  
The Impact

Abstract Peat, as a heterogeneous mixture of decaying plant debris and microbial residues, has been widely used in many fields. However, little research focused on the impact of peat addition on food waste composting. To fill this gap, a composting experiment of food waste mixed with five varying percent peat 0, 5, 10, 15, and 20% (w/w, dry weight) was designed to investigate the effect of different dosages of peat on nitrogen conservation, physiochemical parameters, and fungal community dynamics during composting. The results showed that adding peat elevated the peak temperature of composting, lowered final pH, reduced ammonia emissions and increased the final total nitrogen content. Compared to control, adding 5, 10, 15, and 20% peat decreased ammonia emissions by 1.91, 10.79, 23.73, and 18.26%, respectively, during 42 days of composting. Moreover, peat addition increased fungal community diversity especially during maturation phase. The most two abundant phyla were Basidiomycota and Ascomycota in all treatments throughout the composting process. At the end of composting, in treatments with adding 10 and 15% peat, the richest fungi were Scedosporium spp. and Coprinopsis spp., respectively. Simultaneously, canonical correlation analyses showed that pH, moisture content, and seed germination index had significant association with fungal community composition. The study also showed that fungal community and nitrogen conservation had no direct obvious relation during composting. Overall, the results suggest that the addition of peat could efficiently enhance nitrogen conservation through reduction of ammonia emissions and 15% peat addition is the optimal formula for food waste composting.

scholarly journals Host Phylogenetic Relatedness and Soil Nutrients Shape Ectomycorrhizal Community Composition in Native and Exotic Pine Plantations

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 263 ◽  
Author(s):  
Chen Ning ◽  
Gregory Mueller ◽  
Louise Egerton-Warburton ◽  
Wenhua Xiang ◽  
Wende Yan
Keyword(s):  
Host Specificity ◽  
Community Composition ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Pinus Elliottii ◽  
Pine Plantations ◽  
Fungal Communities ◽  
Spatial Distance ◽  
Fungal Community Composition ◽  
Ecm Fungi

Exotic non-native Pinus species have been widely planted or become naturalized in many parts of the world. Pines rely on ectomycorrhizal (ECM) fungi mutualisms to overcome barriers to establishment, yet the degree to which host specificity and edaphic preferences influence ECM community composition remains poorly understood. In this study, we used high-throughput sequencing coupled with soil analyses to investigate the effect of host plant identity, spatial distance and edaphic factors on ECM community composition in young (30-year-old) native (Pinus massoniana Lamb.) and exotic (Pinus elliottii Engelm.) pine plantations in China. The ECM fungal communities comprised 43 species with the majority belonging to the Thelephoraceae and Russulaceae. Most species were found associated with both host trees while certain native ECM taxa (Suillus) showed host specificity to the native P. massoniana. ECM fungi that are known to occur exclusively with Pinus (e.g., Rhizopogon) were uncommon. We found no significant effect of host identity on ECM communities, i.e., phylogenetically related pines shared similar ECM fungal communities. Instead, ECM fungal community composition was strongly influenced by site-specific abiotic factors and dispersal. These findings reinforce the idea that taxonomic relatedness might be a factor promoting ECM colonization in exotic pines but that shifts in ECM communities may also be context-dependent.

scholarly journals Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10060
Author(s):  
Meng Wang ◽  
Samina Noor ◽  
Ran Huan ◽  
Congling Liu ◽  
JiaYi Li ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Culture Collection ◽  
Medium Composition ◽  
Microbial Culture ◽  
Bacterial Strains ◽  
Marine Microbes ◽  
Natural Systems ◽  
Operational Taxonomic Units ◽  
The Impact ◽  
Culture Dependent

Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.

scholarly journals The impact of ash dieback on veteran trees in southwestern Sweden

2021 ◽  
Vol 27 (1) ◽  
Author(s):  
Vikki Bengtsson ◽  
Anna Stenström ◽  
C. Philip Wheater ◽  
Karin Sandberg
Keyword(s):  
Key Words ◽  
Mortality Rates ◽  
Ash Dieback ◽  
Hymenoscyphus Fraxineus ◽  
Veteran Trees ◽  
Significant Difference ◽  
Ash Trees ◽  
Dieback Disease ◽  
The Impact ◽  
First Time

Ash dieback (Hymenoscyphus fraxineus) is a fungal disease which affects ash throughout Sweden.  Monitoring to study of the impact of ash dieback on veteran trees was undertaken in southwest Sweden in 2009, 2011, 2013, 2015, and 2020. The study found that 94.5% of the ash trees observed were affected by ash dieback disease in 2020 compared with 62% in 2009.  70 of the studied ash trees have died (21%) since the monitoring began. In 2009 there was no relationship between girth and ash dieback, but in 2020 the correlation between girth and the impact of ash dieback was statistically significant. In 2020, also for the first time during monitoring, the ash trees in the shade were significantly more affected by ash dieback, compared with trees standing in the open. This difference was not detected in 2013 or 2015. The effect of ash dieback on pollarded trees has varied between the years studied, but in 2020 there is no longer any significant difference between the pollarded and the non-pollarded ash trees.  There was however a significant difference in the mortality rates between the groups of trees, with ash trees pollarded in more recent times having the highest mortality. Therefore, the recommendation in relation to veteran trees with ash dieback is that all pruning on veteran ash trees should be avoided. Pollarding should only be done on ash pollards that are in a regular cutting cycle and are not showing any symptoms of ash dieback.  If possible, clear around old ash trees if they are in shaded conditions. Given that there are relatively few studies on the impact of ash dieback on veteran ash trees, the results of this study should also be relevant outside of Sweden and for the management of ash trees in non-woodland situations. Key words: Ash dieback, pollards, veteran trees, Hymenoscyphus fraxineus, ash

scholarly journals Contrasting Patterns and Drivers of Soil Fungal Communities between Two Ecosystems Divided by the Treeline

2021 ◽  
Vol 9 (11) ◽  
pp. 2280
Author(s):  
Xueying Wang ◽  
Guixiang Li ◽  
Yuxin Zhang ◽  
Keming Ma
Keyword(s):  
Climate Change ◽  
Community Composition ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Montane Forest ◽  
Fungal Communities ◽  
Formation Mechanisms ◽  
Fungal Community Composition ◽  
Soil Fungal Community ◽  
Soil Fungal Community Composition

The treeline is a sensitive region of the terrestrial ecosystem responding to climate change. However, studies on the composition and formation mechanisms of soil fungal communities across the treeline are still lacking. In this study, we investigated the patterns of soil fungal community composition and interactions among functional guilds above and below the treeline using Illumina high-throughput sequencing and ecological network analysis. The results showed that there were significant differences in the soil environment and soil fungal community composition between the two ecosystems above and below the treeline. At the local scale of this study, geographic distance and environmental factors affected the composition of the soil fungal community. Soil temperature was an important environmental predictor of soil fungal community composition. Species in soil fungal communities in the subalpine meadow were more closely related to each other compared to those in the montane forest. Furthermore, the soil fungal community in montane forest was more stable. Our findings contribute to a better understanding of how mountain ecological functions respond to global climate change.

Sign in / Sign up

Export Citation Format

Share Document