scholarly journals Global diversity and biogeography of the Zostera marina mycobiome

2021 ◽  
Author(s):  
Cassandra L. Ettinger ◽  
Laura E. Vann ◽  
Jonathan A. Eisen
Keyword(s):  
Fungal Community ◽  
Community Assembly ◽  
Zostera Marina ◽  
High Throughput Sequencing ◽  
Marine Fungi ◽  
Marine Ecosystem ◽  
Fungal Community Composition ◽  
Functional Roles ◽  
Functional Guilds ◽  
The Many

Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens or endophytes in global ecosystems. Here we characterize the distribution of fungi associated with the seagrass, Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S ribosomal RNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested amplicon sequence variants (ASVs) were plant-selected or dispersal-limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak, but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The Z. marina core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp. and Saccharomyces sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds, that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses. Importance Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass, Zostera marina, across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases, that general knowledge of seagrass-associated fungi and marine fungi generally is lacking. This work serves as an important foundational step towards future work investigating the functional ramifications of fungi in the marine ecosystem.

scholarly journals Global diversity and biogeography of the Zostera marina mycobiome

2020 ◽  
Author(s):  
Cassandra L. Ettinger ◽  
Laura E. Vann ◽  
Jonathan A. Eisen
Keyword(s):  
Fungal Community ◽  
Community Assembly ◽  
Zostera Marina ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Marine Fungi ◽  
Its Region ◽  
Global Distribution ◽  
Rrna Gene ◽  
Fungal Community Composition

AbstractSeagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens or endophytes in global ecosystems. Here we characterize the distribution of fungi associated with the seagrass, Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S ribosomal RNA gene, we first measured fungal community composition and diversity, then we tested hypotheses of neutral community assembly theory and the degree to which deviations suggested amplicon sequence variants (ASVs) were plant-selected or dispersal-limited, and finally we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. Our results show that the fungal community is significantly different between sites and follows a weak, but significant pattern of distance decay. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome. The Z. marina core leaf and root mycobiomes are dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp. and Saccharomyces sp. A few ASVs (e.g. Lobulomyces sp.) appear restricted to one or a handful of locations (e.g. possibly due to local adaptation, deterministic dispersal limitation or seasonal bloom events), while others (e.g. Saccharomyces sp.) are more ubiquitous across all locations suggesting a true global distribution and possible plant-selection. Fungal guilds associated with Z. marina were only weakly identified (10.12% of ITS region and 3.4% 18S rRNA gene ASV guild assignments were considered highly probable) including wood saprotrophs, ectomycorrhizal fungi, endophytic fungi and plant pathogens. Our results are similar to those found for other seagrass species. It is clear from the many unclassified fungal ASVs and fungal functional guilds, that our knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses.

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.

Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities

Botany ◽  
2014 ◽  
Vol 92 (4) ◽  
pp. 303-311 ◽  
Author(s):  
Steven W. Kembel ◽  
Rebecca C. Mueller
Keyword(s):  
Host Plant ◽  
Tropical Forests ◽  
Fungal Community ◽  
Tree Species ◽  
High Throughput Sequencing ◽  
Plant Traits ◽  
Fungal Species ◽  
Fungal Communities ◽  
Fungal Community Composition ◽  
Individual Tree

The aerial surface of plants, known as the phyllosphere, represents a widespread and diverse habitat for microbes, but the fungal communities colonizing the surface of leaves are not well characterized, and how these communities are assembled on hosts is unknown. We used high-throughput sequencing of fungal communities on the leaves of 51 tree species in a lowland tropical rainforest in Panama to examine the influence of host plant taxonomy and traits on the fungi colonizing the phyllosphere. Fungal communities on leaves were dominated by the phyla Ascomycota (79% of all sequences), Basidiomycota (11%), and Chytridiomycota (5%). Host plant taxonomic identity explained more than half of the variation in fungal community composition across trees, and numerous host functional traits related to leaf morphology, leaf chemistry, and plant growth and mortality were significantly associated with fungal community structure. Differences in fungal biodiversity among hosts suggest that individual tree species support unique fungal communities and that diverse tropical forests also support a large number of fungal species. Similarities between phyllosphere and decomposer communities suggest that fungi inhabiting living leaves may have significant roles in ecosystem functioning in tropical forests.

scholarly journals High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem

2021 ◽  
Vol 8 ◽  
Author(s):  
Raquel Ríos-Castro ◽  
Alejandro Romero ◽  
Raquel Aranguren ◽  
Alberto Pallavicini ◽  
Elisa Banchi ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Coastal Upwelling ◽  
Marine Ecosystem ◽  
Environmental Dna ◽  
Functional Roles ◽  
Molecular Approaches ◽  
Eukaryotic Microorganisms ◽  
Causative Agents ◽  
Veterinary Importance ◽  
Water Fractions

The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.

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 Plant host and drought shape the root associated fungal microbiota in rice

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7463 ◽  
Author(s):  
Beatriz Andreo-Jimenez ◽  
Philippe Vandenkoornhuyse ◽  
Amandine Lê Van ◽  
Arvid Heutinck ◽  
Marie Duhamel ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Microbiota Composition ◽  
Plant Genotype ◽  
Drought Adaptation ◽  
Fungal Community Composition ◽  
Plant Host ◽  
Drought Period ◽  
Fungal Microbiota

Background and Aim Water is an increasingly scarce resource while some crops, such as paddy rice, require large amounts of water to maintain grain production. A better understanding of rice drought adaptation and tolerance mechanisms could help to reduce this problem. There is evidence of a possible role of root-associated fungi in drought adaptation. Here, we analyzed the endospheric fungal microbiota composition in rice and its relation to plant genotype and drought. Methods Fifteen rice genotypes (Oryza sativa ssp. indica) were grown in the field, under well-watered conditions or exposed to a drought period during flowering. The effect of genotype and treatment on the root fungal microbiota composition was analyzed by 18S ribosomal DNA high throughput sequencing. Grain yield was determined after plant maturation. Results There was a host genotype effect on the fungal community composition. Drought altered the composition of the root-associated fungal community and increased fungal biodiversity. The majority of OTUs identified belonged to the Pezizomycotina subphylum and 37 of these significantly correlated with a higher plant yield under drought, one of them being assigned to Arthrinium phaeospermum. Conclusion This study shows that both plant genotype and drought affect the root-associated fungal community in rice and that some fungi correlate with improved drought tolerance. This work opens new opportunities for basic research on the understanding of how the host affects microbiota recruitment as well as the possible use of specific fungi to improve drought tolerance in rice.

scholarly journals Insights into the Fungal Community and Functional Roles of Pepper Rhizosphere Soil under Plastic Shed Cultivation

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 432
Author(s):  
Shi Yao ◽  
Xiaona Li ◽  
Hu Cheng ◽  
Kaining Sun ◽  
Xin Jiang ◽  
...  
Keyword(s):  
Fungal Community ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Crop Productivity ◽  
Fungal Communities ◽  
Functional Roles ◽  
Rhizosphere Soils ◽  
Soil Microbial ◽  
Fungal Community Structure ◽  
Abundance Variation

The rhizosphere fungal community is essential for determining plant health and improving crop productivity. The fungal community structure and functional roles in the plastic shed soils were explored using high throughput sequencing and FUNGuild in this study. The fungal community structures shifted between the rhizosphere and non-rhizosphere soils. The greatest abundance variation was observed for the rare fungal members with relative abundances <0.1%. In the rhizosphere soil of pepper, the abundance of the genera Purpureocillium, Metacorgyceps, Arthrobotrys, Cephalotheca, and Scedosporium increased significantly, among which, Purpureocillium, Arthrobotrys and Metacorgyceps exhibited biocontrol characteristics. Co-occurrence network analysis revealed different interactions of fungal communities in the rhizosphere and non-rhizosphere soils, both of which were dominated by low abundance members. More positive correlation was identified among the rare members, the fungal pathotroph functions and phthalate acid ester in the rhizosphere soil. This study highlights the important niche of the rare fungal members in soil microbial ecology under plastic shed cultivation.

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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