scholarly journals Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate

2014 ◽  
Vol 80 (6) ◽  
pp. 1810-1820 ◽  
Author(s):  
Puja Jasrotia ◽  
Stefan J. Green ◽  
Andy Canion ◽  
Will A. Overholt ◽  
Om Prakash ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
Fungal Community ◽  
Ph Gradient ◽  
Fungal Communities ◽  
Rrna Genes ◽  
Acidic Ph ◽  
Watershed Scale ◽  
Subsurface Environment ◽  
Fungal Isolates ◽  
Groundwater Samples

ABSTRACTThe objective of this study was to characterize fungal communities in a subsurface environment cocontaminated with uranium and nitrate at the watershed scale and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semiquantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylumAscomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH <4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genusConiochaeta, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylumAscomycotaand within a single genus of theBasidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide underin situacidic pH conditions.

scholarly journals One-time Nitrogen Fertilization Shifts Switchgrass Soil Microbiomes within a Context of Larger Spatial and Temporal Variation

2019 ◽  
Author(s):  
Huaihai Chen ◽  
Zamin K. Yang ◽  
Dan Yip ◽  
Reese H. Morris ◽  
Steven J. Lebreux ◽  
...  
Keyword(s):  
Temporal Variation ◽  
Fungal Community ◽  
Temporal Variability ◽  
N Fertilization ◽  
Fungal Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Spatial And Temporal Variation ◽  
Vertical Heterogeneity ◽  
Over Time

AbstractSoil microbiome responses to short-term nitrogen (N) inputs within the context of existing spatio-temporal variability remain uncertain. Here, we examined soil bacterial and fungal communities pre/post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha-1 as NH4NO3) for the first time since planting. Soils were collected at two depths, 0-5 and 5-15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions, and soil metagenomic analysis. Baseline assessment prior to fertilization revealed no pre-existing differences in either bacterial or fungal communities across plots. The one-time N fertilization increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12-22 % of the variation in bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. Thus, variability within the field might override the changes induced by N addition. Continued analyses of these trends over time with fertilization and management are needed to understand whether these transient effects change over time.

scholarly journals Local Adaptation to Soil Hypoxia Determines the Structure of an Arbuscular Mycorrhizal Fungal Community in Roots from Natural CO2Springs

2011 ◽  
Vol 77 (14) ◽  
pp. 4770-4777 ◽  
Author(s):  
Irena Maček ◽  
Alex J. Dumbrell ◽  
Michaela Nelson ◽  
Alastair H. Fitter ◽  
Dominik Vodnik ◽  
...  
Keyword(s):  
Fungal Community ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Small Subunit ◽  
Fungal Communities ◽  
Rrna Genes ◽  
Soil Conditions ◽  
Small Subunit Rrna ◽  
Fungal Community Composition ◽  
Environmental Selection

ABSTRACTThe processes responsible for producing and maintaining the diversity of natural arbuscular mycorrhizal (AM) fungal communities remain largely unknown. We used natural CO2springs (mofettes), which create hypoxic soil environments, to determine whether a long-term, directional, abiotic selection pressure could change AM fungal community structure and drive the selection of particular AM fungal phylotypes. We explored whether those phylotypes that appear exclusively in hypoxic soils are local specialists or widespread generalists able to tolerate a range of soil conditions. AM fungal community composition was characterized by cloning, restriction fragment length polymorphism typing, and the sequencing of small subunit rRNA genes from roots of four plant species growing at high (hypoxic) and low (control) geological CO2exposure. We found significant levels of AM fungal community turnover (β diversity) between soil types and the numerical dominance of two AM fungal phylotypes in hypoxic soils. Our results strongly suggest that direct environmental selection acting on AM fungi is a major factor regulating AM fungal communities and their phylogeographic patterns. Consequently, some AM fungi are more strongly associated with local variations in the soil environment than with their host plant's distribution.

scholarly journals Bacteria Respond Stronger Than Fungi Across a Steep Wood Ash-Driven pH Gradient

2021 ◽  
Vol 4 ◽  
Author(s):  
Carla Cruz-Paredes ◽  
Toke Bang-Andreasen ◽  
Søren Christensen ◽  
Flemming Ekelund ◽  
Tobias G. Frøslev ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Fungal Community ◽  
Environmental Parameters ◽  
Wood Ash ◽  
Ph Gradient ◽  
Fungal Communities ◽  
Ph Effects ◽  
Fungal Community Composition ◽  
Plantation Forests

Soil pH is probably the most important variable explaining bacterial richness and community composition locally as well as globally. In contrast, pH effects on fungi appear to be less pronounced, but also less studied. Here we analyze the community responses of bacteria and fungi in parallel over a local extreme pH gradient ranging from 4 to 8. We established the pH gradient by applying strongly alkaline wood ash in dosages of 0, 3, 9, 15, 30, and 90 t ha–1 to replicated plots in a Picea abies plantation and assessed bacterial and fungal community composition using high throughput amplicon sequencing 1 year after ash application. At the same time, the experiment investigated if returning wood ash to plantation forests pose any immediate threats for the microbial communities. Among the measured environmental parameters, pH was by far the major driver of the microbial communities, however, bacterial and fungal communities responded differently to the pH increment. Whereas both bacterial and fungal communities showed directional changes correlated with the wood ash-induced increase in pH, the bacterial community displayed large changes at wood ash dosages of 9 and 15 t ha–1 while only higher dosages (&gt;30 t ha–1) significantly changed the fungal community. The results confirm that fungi are less sensitive to pH changes than bacteria but also that fertilizing plantation forests with wood ash, viewed through the lens of microbial community changes, is a safe management at standard dosages (typically 3 t ha–1).

Experimentally altered rainfall regimes and host root traits affect grassland arbuscular mycorrhizal fungal communities

2019 ◽  
Author(s):  
Coline Deveautour ◽  
Suzanne Donn ◽  
Sally Power ◽  
Kirk Barnett ◽  
Jeff Powell
Keyword(s):  
Fungal Community ◽  
Community Assembly ◽  
Root Length ◽  
Specific Root Length ◽  
Root Traits ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Rainfall Regime ◽  
Precipitation Regimes ◽  
Rainfall Regimes

Future climate scenarios predict changes in rainfall regimes. These changes are expected to affect plants via effects on the expression of root traits associated with water and nutrient uptake. Associated microorganisms may also respond to these new precipitation regimes, either directly in response to changes in the soil environment or indirectly in response to altered root trait expression. We characterised arbuscular mycorrhizal (AM) fungal communities in an Australian grassland exposed to experimentally altered rainfall regimes. We used Illumina sequencing to assess the responses of AM fungal communities associated with four plant species sampled in different watering treatments and evaluated the extent to which shifts were associated with changes in root traits. We observed that altered rainfall regimes affected the composition but not the richness of the AM fungal communities, and we found distinctive communities in the increased rainfall treatment. We found no evidence of altered rainfall regime effects via changes in host physiology because none of the studied traits were affected by changes in rainfall. However, specific root length was observed to correlate with AM fungal richness, while concentrations of phosphorus and calcium in root tissue and the proportion of root length allocated to fine roots were correlated to community composition. Our study provides evidence that climate change and its effects on rainfall may influence AM fungal community assembly, as do plant traits related to plant nutrition and water uptake. We did not find evidence that host responses to altered rainfall drive AM fungal community assembly in this grassland ecosystem.

Temporal dynamics of mycorrhizal fungal communities and co-associations with grassland plant communities following experimental manipulation of rainfall

2019 ◽  
Author(s):  
Coline Deveautour ◽  
Sally Power ◽  
Kirk Barnett ◽  
Raul Ochoa-Hueso ◽  
Suzanne Donn ◽  
...  
Keyword(s):  
Community Composition ◽  
Plant Community ◽  
Plant Communities ◽  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Temporal Dynamics ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Plant Responses ◽  
Rainfall Regimes

Climate models project overall a reduction in rainfall amounts and shifts in the timing of rainfall events in mid-latitudes and sub-tropical dry regions, which threatens the productivity and diversity of grasslands. Arbuscular mycorrhizal fungi may help plants to cope with expected changes but may also be impacted by changing rainfall, either via the direct effects of low soil moisture on survival and function or indirectly via changes in the plant community. In an Australian mesic grassland (former pasture) system, we characterised plant and arbuscular mycorrhizal (AM) fungal communities every six months for nearly four years to two altered rainfall regimes: i) ambient, ii) rainfall reduced by 50% relative to ambient over the entire year and iii) total summer rainfall exclusion. Using Illumina sequencing, we assessed the response of AM fungal communities sampled from contrasting rainfall treatments and evaluated whether variation in AM fungal communities was associated with variation in plant community richness and composition. We found that rainfall reduction influenced the fungal communities, with the nature of the response depending on the type of manipulation, but that consistent results were only observed after more than two years of rainfall manipulation. We observed significant co-associations between plant and AM fungal communities on multiple dates. Predictive co-correspondence analyses indicated more support for the hypothesis that fungal community composition influenced plant community composition than vice versa. However, we found no evidence that altered rainfall regimes were leading to distinct co-associations between plants and AM fungi. Overall, our results provide evidence that grassland plant communities are intricately tied to variation in AM fungal communities. However, in this system, plant responses to climate change may not be directly related to impacts of altered rainfall regimes on AM fungal communities. Our study shows that AM fungal communities respond to changes in rainfall but that this effect was not immediate. The AM fungal community may influence the composition of the plant community. However, our results suggest that plant responses to altered rainfall regimes at our site may not be resulting via changes in the AM fungal communities.

scholarly journals Effects of rhizosphere fungi on the chemical composition of fruits of the medicinal plant Cinnamomum migao endemic to southwestern China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jingzhong Chen ◽  
Xiaolong Huang ◽  
Bingli Tong ◽  
Deng Wang ◽  
Jiming Liu ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Fungal Community ◽  
Small Population ◽  
Biologically Active ◽  
Fungal Communities ◽  
Chemical Components ◽  
Rhizosphere Fungi ◽  
Medicinal Value ◽  
Main Driver ◽  
Fungal Populations

Abstract Background This study examined how rhizosphere fungi influence the accumulation of chemical components in fruits of a small population species of Cinnamomum migao. Results Ascomycota and Basidiomycota were dominant in the rhizosphere fungal community of C. migao. Pestalotiopsis and Gibellulopsis were associated with α-Terpineol and sabinene content, and Gibellulopsis was associated with crude fat and carbohydrate content. There were significant differences in rhizosphere fungal populations between watersheds, and there was no obvious change between fruiting periods. Gibberella, Ilyonectria, Micropsalliota, and Geminibasidium promoted sabinene accumulation, and Clitocybula promoted α-Terpineol accumulation. Conclusion The climate-related differentiation of rhizosphere fungal communities in watershed areas is the main driver of the chemical composition of C. migao fruit. The control of the production of biologically active compounds by the rhizosphere fungal community provides new opportunities to increase the industrial and medicinal value of the fruit of C. migao.

Do fungi and bacteria respond similar across a steep local pH gradient?

2021 ◽  
Author(s):  
Rasmus Kjoller ◽  
Carla Cruz-Paredes
Keyword(s):  
Community Composition ◽  
Soil Ph ◽  
Wood Ash ◽  
Ph Gradient ◽  
Fungal Communities ◽  
Ph Effects ◽  
Fungal Community Composition ◽  
Ph Gradients ◽  
Field Samples ◽  
Bacterial Richness

&lt;p&gt;Soil pH is consistently recorded as the single most important variable explaining bacterial richness and community composition locally as globally. Bacterial richness responds to soil pH in a bell-shaped pattern, highest in soils with near-neutral pH, while lower diversity is found in soil with pH &gt;8 and &lt;4.5. Also, community turnover is strongly determined by pH for bacteria. In contrast, pH effects on fungi is apparently less pronounced though also much less studied compared to bacteria. Still, pH appears to be a significant determinant for fungal communities but typically not the most important. Rarely are bacterial and fungal communities co-analyzed from the same field samples taken across pH gradients. Here we analyze the community responses of fungi and bacteria in parallel over an extreme pH gradient ranging from pH 4 to 8 established by applying strongly alkaline wood ash to replicated plots in a Picea abies plantation. Bacterial and fungal community composition were assessed by amplicon-based meta-barcoding. Bacterial richness were not significantly affected by pH, while fungal richness and a-diversity were stimulated with higher pH. We found that both, bacterial and fungal communities increasingly deviated from the untreated plots with increasing amount of wood ash though fungal communities were more resistant to changes than bacterial. Soil NH&lt;sub&gt;4&lt;/sub&gt;, NO&lt;sub&gt;3&lt;/sub&gt; and pH significantly correlated with the NMDS pattern for both bacterial and fungal communities. In the presentation we will discuss resistance versus sensitivity of different fungal functional guilds towards higher pH as well as the underlying factors explaining the community changes.&lt;/p&gt;

scholarly journals Highlighting the Crude Oil Bioremediation Potential of Marine Fungi Isolated from the Port of Oran (Algeria)

Diversity ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 196 ◽  
Author(s):  
Ahlem Maamar ◽  
Marie-Elisabeth Lucchesi ◽  
Stella Debaets ◽  
Nicolas Nguyen van Long ◽  
Maxence Quemener ◽  
...  
Keyword(s):  
Species Richness ◽  
Carbon Source ◽  
Crude Oil ◽  
Marine Environment ◽  
Marine Fungi ◽  
Oil Pollution ◽  
Fungal Communities ◽  
Contaminated Site ◽  
Fungal Isolates ◽  
Seawater Samples

While over hundreds of terrestrial fungal genera have been shown to play important roles in the biodegradation of hydrocarbons, few studies have so far focused on the fungal bioremediation potential of petroleum in the marine environment. In this study, the culturable fungal communities occurring in the port of Oran in Algeria, considered here as a chronically-contaminated site, have been mainly analyzed in terms of species richness. A collection of 84 filamentous fungi has been established from seawater samples and then the fungi were screened for their ability to utilize and degrade crude oil. A total of 12 isolates were able to utilize crude oil as a unique carbon source, from which 4 were defined as the most promising biodegrading isolates based on a screening test using 2,6-dichlorophenol indophenol as a proxy to highlight their ability to metabolize crude oil. The biosurfactant production capability was also tested and, interestingly, the oil spreading and drop-collapse tests highlighted that the 4 most promising isolates were also those able to produce the highest quantity of biosurfactants. The results generated in this study demonstrate that the most promising fungal isolates, namely Penicillium polonicum AMF16, P. chrysogenum AMF47 and 2 isolates (AMF40 and AMF74) affiliated to P. cyclopium, appear to be interesting candidates for bioremediation of crude oil pollution in the marine environment within the frame of bioaugmentation or biostimulation processes.

scholarly journals Water-Covered Depth with the Freeze–Thaw Cycle Influences Fungal Communities on Rice Straw Decomposition

Agriculture ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1113
Author(s):  
Xiaolong Lin ◽  
Zongmu Yao ◽  
Xinguang Wang ◽  
Shangqi Xu ◽  
Chunjie Tian ◽  
...  
Keyword(s):  
Community Structure ◽  
Rice Straw ◽  
Fungal Community ◽  
Fungal Communities ◽  
Straw Decomposition ◽  
Freeze Thaw ◽  
Fungal Community Structure ◽  
Thaw Cycle ◽  
Freeze Thaw Cycle ◽  
Rice Straw Decomposition

Rice is a staple food for the world’s population. However, the straw produced by rice cultivation is not used sufficiently. Returning rice straw to the field is an effective way to help reduce labor and protect the soil. This study focused on the effect of water-covered depth with the freeze–thaw cycle on rice straw decomposition and the soil fungal community structure in a field in Northeast China. The field and controlled experiments were designed, and the fungal ITS1 region was tested by high-throughput sequencing for analyzing the fungal communities in this study. The results showed that water coverage with the freeze–thaw cycle promoted the decomposition of rice straw and influenced the fungal community structure; by analyzing the network of the fungal communities, it was found that the potential keystone taxa were Penicillium, Talaromyces, Fusarium, and Aspergillus in straw decomposition; and the strains with high beta-glucosidase, carboxymethyl cellulase, laccase, lignin peroxidase, and manganese peroxidase could also be isolated in the treated experiment. Furthermore, plant pathogenic fungi were found to decrease in the water-covered treatment. We hope that our results can help in rice production and straw return in practice.

scholarly journals Long-term Effects of Mixed Planting on Arbuscular Mycorrhizal Fungal Communities in the Roots and Soils of Juglans mandshurica Plantations

2020 ◽  
Author(s):  
Li Ji ◽  
Yan Zhang ◽  
Yuchun Yang ◽  
Lixue Yang ◽  
Na Yang ◽  
...  
Keyword(s):  
Fungal Community ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Soil Samples ◽  
Fungal Communities ◽  
Juglans Mandshurica ◽  
Mixed Plantations ◽  
Mixed Plantation ◽  
Unique Otus

Abstract Background: Establishing mixed plantations is an effective way to improve soil fertility and increase forest productivity. Arbuscular mycorrhizal (AM) fungi are obligate symbiotic fungi that can promote mineral nutrient absorption and regulate intraspecific and interspecific competition in plants. However, the effects of mixed plantations on the community structure and abundance of AM fungi are still unclear. Illumina MiSeq sequencing was used to investigate the AM fungal community in the roots and soils of pure and mixed plantations (Juglans mandshurica × Larix gmelinii). The objective of this study is to compare the differential responses of the root and rhizosphere soil AM fungal communities of Juglans mandshurica to long-term mixed plantation management.Results: Glomus and Paraglomus were the dominant genera in the root samples, accounting for more than 80% of the sequences. Compared with that in the pure plantation, the relative abundance of Glomus was higher in the mixed plantation. Glomus, Diversispora and Paraglomus accounted for more than 85% of the sequences in the soil samples. The relative abundances of Diversispora and an unidentified genus of Glomeromycetes were higher and lower in the pure plantation, respectively. The Root_P samples (the roots in the pure plantation) had the highest number of unique OTUs (operational taxonomic units), which belonged mainly to an unidentified genus of Glomeromycetes, Paraglomus, Glomus and Acaulospora. The number of unique OTUs detected in the soil was lower than that in the roots. In both the root and soil samples, the forest type did not have a significant effect on AM fungal diversity, but the Sobs value and the Shannon, Chao1 and Ace indices of AM fungi in the roots were significantly higher than those in the soil.Conclusions: Mixed forest management had little effect on the AM fungal community of Juglans mandshurica roots and significantly changed the community composition of the soil AM fungi, but not the diversity.

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