scholarly journals Mycological Insights Into Wetland Fungal Communities: The Mycobiome of Camassia in the Pacific Northwest

2019 ◽  
Vol 3 (4) ◽  
pp. 286-299
Author(s):  
Gretchen Freed ◽  
Daniel Schlatter ◽  
Timothy Paulitz ◽  
Frank Dugan
Keyword(s):  
Pacific Northwest ◽  
High Throughput Sequencing ◽  
Soil Samples ◽  
Fungal Communities ◽  
Sample Type ◽  
Native Plant ◽  
Fungal Community Composition ◽  
Ephemeral Wetland ◽  
The Pacific ◽  
Wetland Habitats

Fungal communities in ephemeral wetland habitats of the Pacific Northwest (PNW) are poorly understood. Because Camassia (camas) populations are a distinctive component of native plant communities in wetland areas of the PNW, camas plant tissue, seed, and associated soil samples were taken from populations growing in wetland habitats in Oregon, Idaho, and Washington. Enumeration of fungal taxa from above- and below-ground camas tissues was accomplished using high-throughput sequencing of fungal internal transcribed spacer genes. Operational taxonomic units (OTUs) affiliated with at least 200 fungal families were found in root, tunic, leaf, rhizosphere, and proximal soil samples (n = 2,984 OTUs). Significant variation in fungal community composition was explained by sample type, habitat of origin, and their interaction. Taxa related to Cladophialophora, Cadophora, and Exophiala, believed to be dark septate endophytes, together with Penicillium, Ceratobasidium, and Ilyonectria were differentially abundant in roots compared with the rhizospheres. Seed-associated communities comprised just 127 OTUs but were highly diverse with at least 50 families detected. Comparison of communities from camas seeds, leaves, roots, and rhizospheres revealed 68 fungal taxa in common, including Alternaria, Fusarium, Selenophoma, Cladosporium, Cryptococcus, and Sporobolomyces. This study provides a baseline understanding into the composition and diversity of fungal communities associated with camas growing in wetland habitats in the PNW.

scholarly journals Differences in the endophytic fungal community and effective ingredients in root of three Glycyrrhiza species in Xinjiang, China

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11047
Author(s):  
Hanli Dang ◽  
Tao Zhang ◽  
Zhongke Wang ◽  
Guifang Li ◽  
Wenqin Zhao ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Soil Samples ◽  
Glycyrrhiza Glabra ◽  
Glycyrrhiza Uralensis ◽  
Fungal Communities ◽  
Depth Range ◽  
Fungal Community Composition ◽  
Glycyrrhiza Inflata

Background Endophytic fungi influence the quality and quantity of the medicinal plant’s bioactive compounds through specific fungus-host interactions. Nevertheless, due to the paucity of information, the composition of endophytic fungal communities and the mechanism by which effective ingredients regulate endophytic fungal communities in roots remains unclear. Methods In this study, we collected root and soil samples (depth range: 0–20, 20–40, and 40–60 cm) of three Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, and Glycyrrhiza glabra). Glycyrrhizic acid and liquiritin content were determined using high-performance liquid chromatography (HPLC), and total flavonoid content was determined using ultraviolet spectrophotometry. High-throughput sequencing technology was employed to explore the composition and diversity of the endophytic fungal community in different root segments of three Glycyrrhiza species. Furthermore, soil samples were subjected to physicochemical analyses. Results We observed that the liquiritin content was not affected by the root depth (0–20 cm, 20–40 cm, and 40–60 cm). Still, it was significantly affected by the Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, Glycyrrhiza glabra) (P < 0.05). In Glycyrrhiza root, a total of eight phyla and 140 genera were annotated so far, out of which Ascomycota and Basidiomycota phyla, and the Fusarium, Paraphoma, and Helminthosporium genera were found to be significantly dominant. Spearman correlation analysis revealed that liquiritin content was accountable for the differences in the diversity of the endophytic fungal community. Furthermore, distance-based redundancy analysis (db-RDA) showed that physicochemical properties of the soil (available potassium and ammonium nitrogen) and the root factors (liquiritin and water content) were the main contributing factors for the variations in the overall structure of the endophytic fungal community. Our results showed that the effective ingredients of Glycyrrhiza root and physicochemical properties of the soil regulated the endophytic fungal community composition and medicinal licorice diversity.

Effects of Herbicide, Tillage, and Grass Seeding on Wild Chervil (Anthriscus sylvestris)

2011 ◽  
Vol 4 (3) ◽  
pp. 326-331 ◽  
Author(s):  
Timothy W. Miller ◽  
Danielle E. D'Auria
Keyword(s):  
Pacific Northwest ◽  
Weed Management ◽  
Dry Weight ◽  
Integrated Weed Management ◽  
Native Plant ◽  
Forage Production ◽  
Perennial Weed ◽  
Native Plant Species ◽  
Herbicide Treatment ◽  
The Pacific

AbstractWild chervil is an invasive biennial or short-lived perennial weed introduced into North America that negatively impacts forage production and degrades habitat for native plant species. A 2-yr study using prebloom mowing followed by combinations of herbicide, tillage, and grass seeding was conducted in the Pacific Northwest to identify an effective integrated weed management strategy for this species. By 2 mo after herbicide treatment (MAHT), wild chervil control with glyphosate + ammonium sulfate (AMS) and clopyralid was 83 and 73%, respectively. Tillage with or without herbicide pretreatment resulted in 92 to 98% wild chervil control at 2 MAHT, whereas herbicide without tillage gave only 45% control across all treatments. Tillage with or without subsequent grass seeding reduced wild chervil density four-fold compared to herbicide alone at 9 MAHT. Herbicide + tillage + grass seeding resulted in similar wild chervil cover (1 to 5% cover) as herbicide + tillage (1 to 6% cover) without subsequent grass seeding. Wild chervil biomass at 1 yr after herbicide treatment (YAHT) was reduced to 487 kg ha−1 (439 lb ac−1) with herbicide + tillage compared to 4,256 kg ha−1 for herbicide treatment alone. Herbicide + tillage + grass seeding increased grass dry weight at 1 YAHT from 201 kg ha−1 for herbicide + tillage to 1,575 kg ha−1, compared to 351 kg ha−1 in herbicide-only plots.

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 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 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.

Analysis of the structure of bacterial and fungal communities in disease suppressive and disease conducive tobacco-planting soils in China

Soil Research ◽  
2020 ◽  
Vol 58 (1) ◽  
pp. 35
Author(s):  
Lin Gao ◽  
Rui Wang ◽  
Jiaming Gao ◽  
Fangming Li ◽  
Guanghua Huang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Soil Samples ◽  
Fungal Communities ◽  
Sequencing Technology ◽  
Operational Taxonomic Units ◽  
Tobacco Cultivation ◽  
Bacteria And Fungi ◽  
Disease Suppressive Soil ◽  
Conducive Soil

To clarify the differences between microbial communities resident in disease suppressive soil (DSS) and disease conducive soil (DCS) in tobacco cultivation, representative soil samples were collected from tobacco plantations in Shengjiaba, China, and the structure and diversity of the resident bacterial and fungal communities were analysed using high-throughput sequencing technology. Our results showed a greater number of operational taxonomic units associated with bacteria and fungi in DSS than in DCS. At the phylum level, abundances of Chloroflexi, Saccharibacteria, Firmicutes, and Planctomycetes in DSS were lower than in DCS, but abundance of Gemmatimonadetes was significantly higher. Abundances of Zygomycota and Chytridiomycota were higher in DSS than DCS, but abundance of Rozellomycota was significantly lower. At the genus level, abundances of 18 bacterial and nine fungal genera varied significantly between DSS and DCS. Relative abundances of Acidothermus, Microbacterium, Curtobacterium, and Colletotrichum were higher in DCS than DSS. The Shannon and Chao1 indices of DSS microbial communities were higher than those of DCS communities. High microbial diversity reduces the incidence of soil-borne diseases in tobacco plantations and promotes the formation of DSSs.

scholarly journals Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay

2021 ◽  
Author(s):  
Sebastian Martinez
Keyword(s):  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Fungal Community Composition ◽  
Bacterial Phyla ◽  
New Crops ◽  
Operational Taxonomic Units ◽  
Rotation System ◽  
Long Term Experiment ◽  
Well Differentiated ◽  
The Impact

Rice is an important crop in Uruguay associated mostly with livestock production in a rice and pasture rotation system since the 1920s. However, in recent years there has been interest in intensifying the production in some of these systems to satisfy market demands and increase income. Intensification occurs by augmenting the rice frequency in the rotation, including new crops like sorghum and soybean, or shortening the pasture phase. A long-term experiment was established in 2012 in the main rice producing area of Uruguay with the objective to study the impact of intensification in rice rotations. After the first cycle of rotation soils from seven rotation phases were sampled and microbial communities were studied by means of high-throughput sequencing of Illumina NovaSeq 6000. Archaeal/bacterial and fungal community composition were studied (16S rRNA and 18S gene regions) detecting 3662 and 807 bacterial and fungal Operational Taxonomic Units (OTUs), respectively. Actinobacteria, Firmicutes and Proteobacteria were the most common bacterial phyla. Among them, only Proteobacteria differed significantly between rotations. Although most fungal OTUs were unidentified, Ascomycota, Basidiomycota and Mucoromycota were the most abundant fungal classes within identified taxa. Bacterial communities differed between rotations forming three groups according to the percentage of rice in the system. Fungal communities clustered in four groups, although not well differentiated, and mostly associated with the antecessor crop. Only P and C:N varied between rotations among soil physicochemical variables after six years, and individual bacterial OTUs appeared weakly influenced by P, pH, Mg and fungal OTUs by P. The results suggest that after six years, bacteria/archaeal communities were influenced by the time with rice in the rotation, and fungal communities were more influenced by the antecessor crop. More studies are needed to associate fungal communities with certain rotational or environmental variables. Some taxa were associated with a particular rotation, and some bacterial taxa were identified as biomarkers. Fungal indicator taxa were not identified at the species level for any rotation.

scholarly journals Responses of Soil Fungal Communities to Lime Application in Wheat Fields in the Pacific Northwest

2021 ◽  
Vol 12 ◽  
Author(s):  
Chuntao Yin ◽  
Daniel C. Schlatter ◽  
Duncan R. Kroese ◽  
Timothy C. Paulitz ◽  
Christina H. Hagerty
Keyword(s):  
Pacific Northwest ◽  
Fungal Community ◽  
Fungal Diversity ◽  
Soil Depth ◽  
Fungal Communities ◽  
Agricultural Practice ◽  
The Pacific ◽  
Soil Fungal Community ◽  
Lime Application ◽  
The Impact

Liming is an effective agricultural practice and is broadly used to ameliorate soil acidification in agricultural ecosystems. Our understanding of the impacts of lime application on the soil fungal community is scarce. In this study, we explored the responses of fungal communities to liming at two locations with decreasing soil pH in Oregon in the Pacific Northwest using high-throughput sequencing (Illumina MiSeq). Our results revealed that the location and liming did not significantly affect soil fungal diversity and richness, and the impact of soil depth on fungal diversity varied among locations. In contrast, location and soil depth had a strong effect on the structure and composition of soil fungal communities, whereas the impact of liming was much smaller, and location- and depth-dependent. Interestingly, families Lasiosphaeriaceae, Piskurozymaceae, and Sordariaceae predominated in the surface soil (0–7.5 cm) and were positively correlated with soil OM and aluminum, and negatively correlated with pH. The family Kickxellaceae which predominated in deeper soil (15–22.5 cm), had an opposite response to soil OM. Furthermore, some taxa in Ascomycota, such as Hypocreales, Peziza and Penicillium, were increased by liming at one of the locations (Moro). In conclusion, these findings suggest that fungal community structure and composition rather than fungal diversity responded to location, soil depth and liming. Compared to liming, location and depth had a stronger effect on the soil fungal community, but some specific fungal taxa shifted with lime application.

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