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

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

Abstract Wastewater 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 in processing sewage sludge, which can contribute to alleviate the severe environmental problems caused by their 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 community composition and diversity changed significantly during both vermicomposting processes. Most of the bacterial and fungal taxa in the sewage sludge were eliminated during vermicomposting, mainly through the GAP. 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.

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.

scholarly journals The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet

2020 ◽  
Author(s):  
Tahliyah S. Mims ◽  
Qusai Al Abdullah ◽  
Justin D. Stewart ◽  
Sydney P. Watts ◽  
Catrina T. White ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Genetic Background ◽  
Dietary Exposure ◽  
Fungal Communities ◽  
Metabolic Adaptation ◽  
Fungal Community Composition ◽  
Metabolic Outcomes ◽  
Metabolic Biomarkers

ABSTRACTObjectiveAs an active interface between the host and their diet, the gut bacteriome influences host metabolic adaptation. However, the contribution of gut fungi to host metabolic outcomes is not yet understood. Therefore, we aimed to determine if host metabolic response to an ultra-processed diet reflects gut fungal community composition.DesignWe compared jejunal fungi and bacteria from 72 healthy mice with the same genetic background but different starting mycobiomes before and after 8 weeks on an ultra-processed or standardized diet using 16S and internal transcribed spacer region 2 ribosomal RNA sequencing. We measured host body composition using magnetic resonance imaging, examined changes in metabolically active host tissues and quantified serum metabolic biomarkers.ResultsGut fungal communities are highly variable between mice, differing by vendor, age and sex. After exposure to an ultra-processed diet for 8 weeks, persistent differences in fungal community composition strongly associate with differential deposition of body mass in male mice compared to mice on standardized diet. Fat deposition in the liver, genomic adaptation of metabolically active tissues and serum metabolic biomarkers are correlated with alterations in fungal diversity and community composition. Variation in fungi from the genera Thermomyces and Saccharomyces most strongly associate with increased weight gain.ConclusionsIn the gut of healthy mice, host-microbe metabolic interactions strongly reflect variability in fungal communities. Our results confirm the importance of luminal fungal communities to host metabolic adaptation to dietary exposure. Gut fungal communities may represent a therapeutic target for the prevention and treatment of metabolic disease.Graphical AbstractIn BriefWhat is already known about this subject?Gut bacterial communities have evolved to influence the metabolic outcomes of the host in mammals. Evidence from across the lifespan suggests that differences in composition of these communities is associated with energy consumption. However, gut microbial communities, while often equated to bacteria, are diverse, multi-kingdom ecologies and limited information is available for the role of other kingdoms of life, such as fungi.What are the new findings?Gut fungal communities, collectively termed the mycobiome, are less diverse and abundant than bacterial communities in the gastrointestinal tract. This study identifies the considerable influence of the environment and dietary exposure on the composition of jejunal fungal communities in healthy mice with the same genetic background. After exposure to processed diet, differences in fungal community composition in male mice were strongly correlated with persistent differences body composition and markers of metabolic tone.How might it impact on clinical practice in the foreseeable future?These results verify that the baseline metabolic tone of health mice strongly reflects the ecological complexity of the gastrointestinal mycobiome. Variation in the composition of gut fungal communities is likely an underappreciated source of experimental and clinical variability in metabolic studies. Gastrointestinal fungi are likely a target for prevention and treatment of metabolic disease.

scholarly journals Drivers of Ectomycorrhizal Fungal Community Structure Associated with Pinus sylvestris var. mongolica Differ at Regional vs. Local Spatial Scales in Northern China

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 323
Author(s):  
Mishan Guo ◽  
Guanglei Gao ◽  
Guodong Ding ◽  
Ying Zhang
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Phosphorus Content ◽  
Regional Scale ◽  
Northern China ◽  
Local Scale ◽  
Stand Age ◽  
Organic Carbon Content ◽  
Fungal Community Composition ◽  
Composition And Structure

Pinus sylvestris var. mongolica, a widely planted tree species, is facing long-lasting, unresolved degradation in desertified Northern China. Ectomycorrhizal fungi (EMF) are closely related to the stand status, because they substantially participate in ecological processes of terrestrial forest ecosystems. EMF may be key to solving the introduction recession. Therefore, we performed DNA sequencing of P. sylvestris root samples from plantations and natural forests as control to characterize the EMF from semi-arid and dry sub-humid regions, using ITS Illumina sequencing and conventional soil physicochemical index determination. The results indicated that (1) the dominant EMF genera were Suillus, Rhizopogon, and Wilcoxina in the Hulunbuir, Mu Us, and Horqin Sandy Lands, respectively. Their dominance retained with stand ageing. (2) Plantation EM fungal diversity differs significantly among the three sandy lands and was significantly lower than in natural forest. The diversity varied with stand age, showing distinct trends at the local scale. (3) At the regional scale, the mean annual sunshine times and the soil organic carbon content affect EMF diversity. The community composition and structure were more characterized by temperature and precipitation. At the local scale, besides the soil organic carbon content, the EM fungal community composition and structure were correlated with total nitrogen and phosphorus content (Hulunbuir), the total phosphorus content (Mu Us), and the pH and total soil porosity (Horqin). The EM fungal community composition and structure have the obvious geographical distribution variation; they were strongly correlated with the meteorological elements and soil nutrients at the regional scale. At the local scale, they were jointly driven by stand age and soil properties. This improved information contributes to increasing the understanding of the interaction between EMF and forest ecosystems and guides sustainable forest management of degraded P. sylvestris plantations.

Rhizospheric soil fungal community patterns of Duchesnea indica in response to altitude gradient in Yunnan, southwest China

2020 ◽  
Vol 66 (5) ◽  
pp. 359-367
Author(s):  
Arslan Jamil ◽  
Jun-Yu Yang ◽  
Dai-Fa Su ◽  
Jiang-Yun Tong ◽  
Shan-Yan Chen ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Altitudinal Gradient ◽  
Rhizosphere Soil ◽  
Fungal Community Composition ◽  
Altitude Gradient ◽  
Community Patterns ◽  
Composition And Structure ◽  
Soil Fungal Community ◽  
Duchesnea Indica

The magnitude of the impact of altitude gradient on microbial community and diversity has been studied in recent decades. Whereas bacteria have been the focus of most studies, fungi have been given relatively less attention. As a vital part of the macro- and microscopic ecosystem, rhizosphere fungi play a key role in organic matter decomposition and relative abundance of plant species and have an impact on plant growth and development. Using Duchesnea indica as the host plant, we examined the rhizosphere soil fungal community patterns across the altitude gradient in 15 sites of Yunnan province by sequencing the fungal ITS2 region with the Illumina MiSeq platform. We determined the fungal community composition and structure. We found that, surprisingly, rhizosphere soil fungal diversity of D. indica increased with altitudinal gradient. There was a slight difference in diversity between samples from high- and medium-altitude sites, with medium-altitude sites having the greater diversity. Furthermore, the rhizosphere soil fungal community composition and structure kept changing along the altitudinal gradient. Taxonomic results showed that the extent of phylum diversity was greatest at high-altitude sites, with Ascomycota, Basidiomycota, Zygomycota, and Glomeromycota as the most dominant fungal phyla.

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.

scholarly journals Machine learning for exploring microbial inter-kingdom associations in Cystic Fibrosis and Bronchiectasis

2022 ◽  
Author(s):  
Leah Cuthbertson ◽  
Jonathan Ish-horowicz ◽  
Imogen Felton ◽  
Phillip James ◽  
Elena Turek ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cystic Fibrosis ◽  
Community Composition ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Disease Status ◽  
Fungal Disease ◽  
Rrna Gene ◽  
Fungal Community Composition

Background: Cystic fibrosis (CF) and non-CF bronchiectasis (BX) are lung diseases characterised by severe chronic infections. Fungal and bacterial components of infection are both recognized. Recent molecular investigation of sputum from patients with CF and BX has revealed a complex mycobiome. However, little is known about how fungal and bacterial organisms interact or whether the interactions impact on disease outcomes. Methods: Quantitative PCR and next generation sequencing of ITS2 and 16S rRNA gene was carried out on 107 patients with CF and BX and defined clinical fungal infection status. Fungal and bacterial communities were explored using supervised and unsupervised machine learning to understand associations between fungal and bacterial communities and their relationship to disease. Results: Fungal and bacterial communities both had significantly higher biomass and lower diversity in CF compared to BX patients. Random forest modelling demonstrated that the fungal and bacterial communities were distinct between CF and BX patients. Within the CF group, bacterial communities contained no predictive signal for fungal disease status. Neither bacterial nor fungal community composition were predictive of the presence of CF pulmonary exacerbation (CFPE). Intra-kingdom correlations were far stronger than those between the two kingdoms. Dirichlet mixture components analysis identified two distinct clusters of bacteria related to the relative abundance of Pseudomonas. Fungal community composition contained no predictive signal for bacterial clusters. Conclusions: Clear changes in diversity were observed between patients with different clinical disease status. Although our results demonstrate that bacterial community composition differs in the presence of fungal disease, no direct relationship between bacterial and fungal OTUs was found.

scholarly journals Major Differences in the Diversity of Mycobiomes Associated with Wheat Processing and Domestic Environments: Significant Findings from High-Throughput Sequencing of Fungal Barcode ITS1

2019 ◽  
Vol 16 (13) ◽  
pp. 2335 ◽  
Author(s):  
Erika Yashiro ◽  
Dessislava Savova-Bianchi ◽  
Hélène Niculita-Hirzel
Keyword(s):  
Community Composition ◽  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Dust Exposure ◽  
Fungal Community Composition ◽  
Exposed Population ◽  
Rural And Urban ◽  
Occupationally Exposed ◽  
Domestic Environments

Occupational exposure to grain dust is associated with both acute and chronic effects on the airways. However, the aetiology of these effects is not completely understood, mainly due to the complexity and variety of potentially causative agents to which workers are exposed during cereals process. In this study, we characterized the mycobiome during different steps of wheat processing—harvesting, grain unloading and straw handling—and compared it to mycobiomes of domestic environments—rural and urban. To do so, settled dust was collected at a six month interval for six weeks in the close proximity of 142 participants, 74 occupationally exposed to wheat dust—freshly harvested or stored—and 68 not occupationally exposed to it. Fungal community composition was determined in those samples by high-throughput sequencing of the primary fungal barcode marker internal transcribed spacer 1 (ITS1). The comparison of different mycobiomes revealed that fungal richness, as well as their composition, was much higher in the domestic environment than at the workplace. Furthermore, we found that the fungal community composition strongly differed between workplaces where workers handled freshly harvested wheat and those where they handled stored wheat. Indicator species for each exposed population were identified. Our results emphasize the complexity of exposure of grain workers and farmers and open new perspectives in the identification of the etiological factors responsible for the respiratory pathologies induced by wheat dust exposure.

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