scholarly journals Decay stages of wood and associated fungal communities characterise diversity–decomposition relationships

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu Fukasawa ◽  
Kimiyo Matsukura
Keyword(s):  
Weight Loss ◽  
Species Richness ◽  
Fungal Diversity ◽  
Wood Quality ◽  
Wood Decay ◽  
Terrestrial Ecosystems ◽  
Fungal Species ◽  
Fungal Communities ◽  
Wood Substrate ◽  
Substrate Quality

AbstractThe biodiversity–ecosystem function relationship is a central topic in ecology. Fungi are the dominant decomposers of organic plant material in terrestrial ecosystems and display tremendous species diversity. However, little is known about the fungal diversity–decomposition relationship. We evaluated fungal community assemblies and substrate quality in different stages of wood decay to assess the relationships between fungal species richness and weight loss of wood substrate under laboratory conditions. Wood-inhabiting fungal communities in the early and late stages of pine log decomposition were used as a model. Colonisation with certain species prior to inoculation with other species resulted in four-fold differences in fungal species richness and up to tenfold differences in the rate of wood substrate decomposition in both early- and late-decaying fungal communities. Differences in wood substrate quality had a significant impact on species richness and weight loss of wood and the relationships between the two, which were negative or neutral. Late communities showed significantly negative species richness–decay relationships in wood at all decay stages, whereas negative relationships in early communities were significant only in the intermediate decay stage. Our results suggest that changes in fungal communities and wood quality during wood decomposition affect the fungal diversity–decomposition relationship.

scholarly journals Forest tree species composition and abiotic site conditions drive soil fungal communities and functional groups

2021 ◽  
Author(s):  
Likulunga Emmanuel Likulunga ◽  
Carmen Alicia Rivera P&eacuterez ◽  
Dominik Schneider ◽  
Rolf Daniel ◽  
Andrea Polle
Keyword(s):  
Species Richness ◽  
Tree Species ◽  
Mycorrhizal Fungi ◽  
Fungal Diversity ◽  
Fungal Species ◽  
Douglas Fir ◽  
Fungal Communities ◽  
Site Conditions ◽  
Saprotrophic Fungi ◽  
Tree Species Composition

Soil fungi, especially the functional guilds of saprotrophic and mycorrhizal fungi, play a central role in ecosystem processes by degrading litter, mining for mineral nutrients and linking above- and belowground nutrient fluxes. Fungal community structures are influenced by abiotic habitat filters and management decisions such as tree species selection. Yet, the implications of the enrichment of temperate forests consisting of tree species in their natural range with non-native tree species on soil fungal diversity and their functional groups are unknown. Here, we studied fungal communities in 40 plots located in two regions differing in site conditions (nutrient content and soil moisture) in forests composed of European beech, Norway spruce and Douglas-fir (non-native) and mixtures of beech with either spruce or Douglas-fir. We hypothesized that fungal community structures are driven by soil resources and tree species composition, generally resulting in higher fungal diversity in mixed than in mono-specific forests. We further hypothesized that Douglas-fir has a negative effect on ectomycorrhizal fungal species richness compared to native species, whereas saprotrophic fungal richness is unaffected. We found strong separation of fungal communities between nutrient-rich and nutrient-poor sites and taxonomic divergence between beech and conifer fungal communities and an intermediate pattern in mixed forests. Mycorrhizal species richness did not vary with forest type, but the relative abundance of mycorrhizal species was lower in Douglas-fir and in mixed beech-Douglas-fir forests than in spruce or beech-spruce mixture. Conifer forests contained higher relative abundances of saprotrophic fungi than mono-specific beech forests. Among 16 abundant fungal orders in soil, two containing saprotrophic fungi (Tremellales, Hymenochaetales) were enriched in conifer forests, regardless of site conditions and tree species mixture. The other fungal orders, including those dominated by mycorrhizal fungi (Russulales, Boletales, Atheliales, Cantharellales) showed variable patterns depending on site conditions and tree species. In conclusion, Douglas-fir mono-specific or mixed forests show no loss of fungal species richness, but a shift in functional composition towards saprotrophic fungi.

scholarly journals Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

2017 ◽  
Vol 83 (17) ◽  
Author(s):  
Francesca De Filippis ◽  
Manolo Laiola ◽  
Giuseppe Blaiotta ◽  
Danilo Ercolini
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
Biological Samples ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Fungal Communities ◽  
Its2 Region ◽  
Mock Community

ABSTRACT Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes, with 16S rRNA being the gold standard for bacteria. As for fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity. After an in silico primer evaluation, we compared three amplicons (the ITS1-ITS2 region [ITS1-2], 18S ribosomal small subunit RNA, and the D1/D2 domain of the 26S ribosomal large subunit RNA), using biological samples and a mock community of common fungal species. All three targets allowed for accurate identification of the species present. Nevertheless, high heterogeneity in ITS1-2 length was found, and this caused an overestimation of the abundance of species with a shorter ITS, while both 18S and 26S amplicons allowed for more reliable quantification. We demonstrated that ITS1-2 amplicon sequencing, although widely used, may lead to an incorrect evaluation of fungal communities, and efforts should be made to promote the use of different targets in sequencing-based microbial ecology studies. IMPORTANCE Amplicon-sequencing approaches for fungi may rely on different targets affecting the diversity and abundance of the fungal species. An increasing number of studies will address fungal diversity by high-throughput amplicon sequencing. The description of the communities must be accurate and reliable in order to draw useful insights and to address both ecological and biological questions. By analyzing a mock community and several biological samples, we demonstrate that using different amplicon targets may change the results of fungal microbiota analysis, and we highlight how a careful choice of the target is fundamental for a thorough description of the fungal communities.

scholarly journals Communities of Fungi in Black Cherry Stumps and Effects of Herbicide

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1126
Author(s):  
Robert Korzeniewicz ◽  
Marlena Baranowska ◽  
Hanna Kwaśna ◽  
Gniewko Niedbała ◽  
Jolanta Behnke-Borowczyk
Keyword(s):  
Species Richness ◽  
Environmental Dna ◽  
Bioinformatic Analysis ◽  
Diversity Indices ◽  
Fungal Species ◽  
Fungal Communities ◽  
Reference Sequence ◽  
Deciduous Tree ◽  
Black Cherry ◽  
5.8S Rdna

So far, there have been no studies on fungal communities in Prunus serotina (black cherry) wood. Our objectives were to characterize fungal communities from P. serotina wood and to evaluate effects of glyphosate (Glifocyd 360 SL) used on P. serotina stumps on abundance, species richness and diversity of those communities. In August 2016, in the Podanin Forest District, stumps of black cherry trees left after felling were treated with the herbicide. Control stumps were treated with water. Wood discs were cut from the surface of the stumps in May and July–August 2017. Eight treatment combinations (2 herbicide treatments × 2 disc sizes × 2 sample times) were tested. Sub-samples were pooled and ground in an acryogenic mill. Environmental DNA was extracted with a Plant Genomic DNA Purification Kit. The ITS1, 5.8S rDNA region was used to identify fungal species, using primers ITS1FI2 5′-GAACCWGCGGARGGATCA-3′ and 5.8S 5′-CGCTGCGTT CTTCATCG-3′. The amplicons were sequenced using the Illumina system. The results were subjected to bioinformatic analysis. Sequences were compared with reference sequences from the NCBI database using the BLASTn 2.8.0 algorithm. Abundance of fungi was defined as the number of Operational Taxonomic Units (OTUs), and diversity as the number of species in a sample. Differences between the number of OTUs and taxa were analyzed using the chi-squared test (χ2). Diversity in microbial communities was compared using diversity indices. A total of 54,644 OTUs were obtained. Culturable fungi produced 49,808 OTUs (91.15%), fungi not known from culture had 2571 OTUs (4.70%), non-fungal organisms had 1333 (2.44%) and organisms with no reference sequence in NCBI, 934 OTUs (1.71%). The total number of taxa ranged from 120 to 319. Fungi in stump wood were significantly more abundant in July–August than in May, in stumps >5 cm diameter than in stumps <5 cm diameter, in glyphosate-treated than in untreated stumps when sampled in May, and in untreated than in glyphosate-treated stumps when sampled in July–August. Species richness was significantly greater in July–August than in May, and in stumps >5 cm diameter than in stumps <5 cm diameter, either treated or untreated, depending on size. Herbicides can therefore affect the abundance and diversity of fungal communities in deciduous tree wood. The greater frequency of Ascomycota in herbicide-treated than in untreated stumps indicates their greater tolerance of glyphosate.

scholarly journals Molecular Detection of Fungal Communities in the Hawaiian Marine Sponges Suberites zeteki and Mycale armata

2008 ◽  
Vol 74 (19) ◽  
pp. 6091-6101 ◽  
Author(s):  
Zheng Gao ◽  
Binglin Li ◽  
Chengchao Zheng ◽  
Guangyi Wang
Keyword(s):  
Molecular Analysis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Terrestrial Ecosystems ◽  
Fungal Species ◽  
Marine Sponges ◽  
Fungal Communities ◽  
Sponge Species ◽  
Rrna Gene ◽  
Significant Group ◽  
Marine Habitats

ABSTRACT Symbiotic microbes play a variety of fundamental roles in the health and habitat ranges of their hosts. While prokaryotes in marine sponges have been broadly characterized, the diversity of sponge-inhabiting fungi has barely been explored using molecular approaches. Fungi are an important component of many marine and terrestrial ecosystems, and they may be an ecologically significant group in sponge-microbe interactions. This study tested the feasibility of using existing fungal primers for molecular analysis of sponge-associated fungal communities. None of the eight selected primer pairs yielded satisfactory results in fungal rRNA gene or internal transcribed spacer (ITS) clone library constructions. However, 3 of 10 denaturing gradient gel electrophoresis (DGGE) primer sets, which were designed to preferentially amplify fungal rRNA gene or ITS regions from terrestrial environmental samples, were successfully amplified from fungal targets in marine sponges. DGGE analysis indicated that fungal communities differ among different sponge species (Suberites zeteki and Mycale armata) and also vary between sponges and seawater. Sequence analysis of DGGE bands identified 23 and 21 fungal species from each of the two sponge species S. zeteki and M. armata, respectively. These species were representatives of 11 taxonomic orders and belonged to the phyla of Ascomycota (seven orders) and Basidiomycota (four orders). Five of these taxonomic orders (Malasseziales, Corticiales, Polyporales, Agaricales, and Dothideomycetes et Chaetothyriomcetes incertae sedis) have now been identified for the first time in marine sponges. Seven and six fungal species from S. zeteki and M. armata, respectively, are potentially new species because of their low sequence identity (≤98%) with their references in GenBank. Phylogenetic analysis indicated sponge-derived sequences were clustered into “marine fungus clades” with those from other marine habitats. This is the first report of molecular analysis of fungal communities in marine sponges, adding depth and dimension to our understanding of sponge-associated microbial communities.

scholarly journals Fungal diversity driven by bark features affects phorophyte preference in epiphytic orchids from southern China

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lorenzo Pecoraro ◽  
Hanne N. Rasmussen ◽  
Sofia I. F. Gomes ◽  
Xiao Wang ◽  
Vincent S. F. T. Merckx ◽  
...  
Keyword(s):  
Fungal Diversity ◽  
Southern China ◽  
Fungal Species ◽  
Host Tree ◽  
Fungal Communities ◽  
Tree Bark ◽  
Orchid Species ◽  
Epiphytic Orchids ◽  
Orchid Seed ◽  
Specific Association

AbstractEpiphytic orchids exhibit varying degrees of phorophyte tree specificity. We performed a pilot study to investigate why epiphytic orchids prefer or avoid certain trees. We selected two orchid species, Panisea uniflora and Bulbophyllum odoratissimum co-occurring in a forest habitat in southern China, where they showed a specific association with Quercus yiwuensis and Pistacia weinmannifolia trees, respectively. We analysed a number of environmental factors potentially influencing the relationship between orchids and trees. Difference in bark features, such as water holding capacity and pH were recorded between Q. yiwuensis and P. weinmannifolia, which could influence both orchid seed germination and fungal diversity on the two phorophytes. Morphological and molecular culture-based methods, combined with metabarcoding analyses, were used to assess fungal communities associated with studied orchids and trees. A total of 162 fungal species in 74 genera were isolated from bark samples. Only two genera, Acremonium and Verticillium, were shared by the two phorophyte species. Metabarcoding analysis confirmed the presence of significantly different fungal communities on the investigated tree and orchid species, with considerable similarity between each orchid species and its host tree, suggesting that the orchid-host tree association is influenced by the fungal communities of the host tree bark.

scholarly journals Linking Soil Chemical Parameters and Fungal Diversity in Qatar

2020 ◽  
Author(s):  
Sakeenah Adenan ◽  
Jane Oja ◽  
Talaat Abdel-Fattah ◽  
Juha Alatalo
Keyword(s):  
Fungal Diversity ◽  
Environmental Gradients ◽  
Chemical Properties ◽  
Fungal Species ◽  
Fungal Communities ◽  
Chemical Parameters ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Study Sites ◽  
Soil Chemical Parameters

Given the vast expanse of Qatar’s dryland ecosystems, agricultural productivity and soil stability is highly dependent on the diversity of soil microbiota. The soil environment is a heterogeneous habitat shaped by various components like chemical (organic matter, salinity and nutrients) and biological (fungal diversity and vegetation) properties that form multitudes of different microhabitats. Soil microbial diversity changes along environmental gradients. It is hypothesized that a “stable” microhabitat is one that is inhabited by a large diversity of established microorganisms that are best adapted to the niche. Microorganisms like fungi serve as the underlying biological drivers for biochemical processes within the soil. The key objective of this study is to evaluate the fungal diversity and abundance present within the Qatari soil using molecular-based tools and evaluate potential relationships between the identified fungal communities with chemical properties of the habitat. We found that the composition of fungi and AMF varied between different habitats around Qatar. Despite the lack of significant differences in the measured soil chemical parameters between sampled sites, it is evident that AMF species are more abundant than compared to that of other fungal species in most of the study sites; thus, suggesting that other factors like land use may also be an essential component explaining the variation in fungal communities.

Suppression of arbuscular mycorrhizal fungi aggravate the negative interactive effects of warming and nitrogen addition on soil bacterial and fungal diversity and community composition

2021 ◽  
Author(s):  
Xue Yang ◽  
Meng Yuan ◽  
Jixun Guo ◽  
Lianxuan Shi ◽  
Tao Zhang
Keyword(s):  
Species Richness ◽  
Arbuscular Mycorrhizal Fungi ◽  
Plant Species ◽  
Mycorrhizal Fungi ◽  
Fungal Diversity ◽  
Arbuscular Mycorrhizal ◽  
Plant Species Richness ◽  
Fungal Communities ◽  
N Addition ◽  
Soil Bacterial

We examined the impacts of warming, nitrogen (N) addition and suppression of arbuscular mycorrhizal fungi (AMF) on soil bacterial and fungal richness and community composition in a field experiment. AMF root colonization and the concentration of an AMF-specific phospholipid fatty acid (PLFA) were significantly reduced after the application of the fungicide benomyl as a soil drench. Warming and N addition had no independent effects but interactively decreased soil fungal richness, while warming, N addition and AMF suppression together reduced soil bacterial richness. Soil bacterial and fungal species diversity was lower with AMF suppression, indicating that AMF suppression have negative effect on microbial diversity. Warming and N addition decreased the net loss of plant species and the plant species richness, respectively. AMF suppression reduced plant species richness and the net gain of plant species but enhanced the net loss of plant species. Structural equation modeling (SEM) demonstrated that the soil bacterial community responded to the increased soil temperature (ST) induced by warming and the increased soil available N (AN) induced by N addition through changes in AMF colonization and plant species richness; ST directly affected the bacterial community, but AN affected both the soil bacterial and fungal communities via AMF colonization. In addition, higher mycorrhizal colonization increased the plant species richness by increasing the net gains in plant species under warming and N addition. IMPORTANCE Arbuscular mycorrhizal fungi (AMF) can influence the composition and diversity of plant communities. Previous studies have shown that climate warming and N deposition reduce the effectiveness of AMF. However, how AMF affects soil bacterial and fungal communities under these global change drivers are still poorly understood. A 4-year field study revealed that AMF suppression decreased bacterial and fungal diversity irrespective of warming or N addition, while AMF suppression interacted with warming or N addition to reduce bacterial and fungal richness. In addition, bacterial and fungal community compositions were determined by mycorrhizal colonization which was regulated by soil AN and ST. These results suggest that AMF suppression can aggravate the severe losses to native soil microbial diversity and functioning caused by global changes and thus AMF plays a vital role in maintaining belowground ecosystem stability in the future.

scholarly journals Fungal Community Responses to Past and Future Atmospheric CO2Differ by Soil Type

2014 ◽  
Vol 80 (23) ◽  
pp. 7364-7377 ◽  
Author(s):  
Andrew C. Procter ◽  
J. Christopher Ellis ◽  
Philip A. Fay ◽  
H. Wayne Polley ◽  
Robert B. Jackson
Keyword(s):  
Species Richness ◽  
Relative Abundance ◽  
Fungal Community ◽  
Decomposition Rate ◽  
Soil Type ◽  
Clay Soil ◽  
Sandy Loam ◽  
Fungal Species ◽  
Fungal Communities ◽  
Black Clay

ABSTRACTSoils sequester and release substantial atmospheric carbon, but the contribution of fungal communities to soil carbon balance under rising CO2is not well understood. Soil properties likely mediate these fungal responses but are rarely explored in CO2experiments. We studied soil fungal communities in a grassland ecosystem exposed to a preindustrial-to-future CO2gradient (250 to 500 ppm) in a black clay soil and a sandy loam soil. Sanger sequencing and pyrosequencing of the rRNA gene cluster revealed that fungal community composition and its response to CO2differed significantly between soils. Fungal species richness and relative abundance of Chytridiomycota (chytrids) increased linearly with CO2in the black clay (P< 0.04,R2> 0.7), whereas the relative abundance of Glomeromycota (arbuscular mycorrhizal fungi) increased linearly with elevated CO2in the sandy loam (P= 0.02,R2= 0.63). Across both soils, decomposition rate was positively correlated with chytrid relative abundance (r= 0.57) and, in the black clay soil, fungal species richness. Decomposition rate was more strongly correlated with microbial biomass (r= 0.88) than with fungal variables. Increased labile carbon availability with elevated CO2may explain the greater fungal species richness and Chytridiomycota abundance in the black clay soil, whereas increased phosphorus limitation may explain the increase in Glomeromycota at elevated CO2in the sandy loam. Our results demonstrate that soil type plays a key role in soil fungal responses to rising atmospheric CO2.

scholarly journals Agarwood wound locations provide insight into the association between fungal diversity and volatile compounds in Aquilaria sinensis

2019 ◽  
Vol 6 (7) ◽  
pp. 190211 ◽  
Author(s):  
Juan Liu ◽  
Xiang Zhang ◽  
Jian Yang ◽  
Junhui Zhou ◽  
Yuan Yuan ◽  
...  
Keyword(s):  
Fungal Diversity ◽  
Chemical Properties ◽  
Fungal Species ◽  
Fungal Communities ◽  
Strongly Correlated ◽  
Resolution Time ◽  
Aquilaria Sinensis ◽  
Flight Mass Spectrometry ◽  
Insight Into ◽  
Wound Tissue

The aim of the present study was to investigate the effect of wound location on the fungal communities and volatile distribution of agarwood in Aquilaria sinensis . Two-dimensional gas chromatography with high-resolution time-of-flight mass spectrometry revealed 60 compounds from the NIST library, including 25 sesquiterpenes, seven monoterpenes, two diterpenes, nine aromatics, nine alkanes and eight others. Of five agarwood types, Types IV and II contained the greatest number and concentration of sesquiterpenes, respectively. The fungal communities of the agarwood were dominated by the phylum Ascomycota and were significantly affected by the type of wound tissue. Community richness indices (observed species, Chao1, PD whole tree, ACE indices) indicated that Types I and IV harboured the most and least species-rich fungal communities, and the fungal communities of Types V, I, III and IV/II were dominated by Lasiodiplodia , Hydnellum , Phaeoisaria and Ophiocordyceps species, respectively. Correlations between fungal species and agarwood components revealed that the chemical properties of A. sinensis were associated with fungal diversity. More specifically, the dominant fungal genera of Types V, I and III ( Lasiodiplodia , Hydnellum and Phaeoisaria , respectively) were strongly correlated with specific terpenoid compounds. The finding that wound location affects the fungal communities and volatile distribution of agarwood provides insight into the formation of distinct agarwood types.

scholarly journals Fungal diversity in selected coastal mangrove ecosystems in East Berbice Corentyne, Guyana, South America

2021 ◽  
Vol 17 (1) ◽  
pp. 138-146
Author(s):  
Wazim R Sharif ◽  
Phillip NB Da Silva
Keyword(s):  
Species Richness ◽  
Fungal Diversity ◽  
Species Abundance ◽  
Environmental Parameters ◽  
Diversity Indices ◽  
Mangrove Ecosystem ◽  
Fungal Species ◽  
Fruiting Bodies ◽  
Mangrove Ecosystems ◽  
Study Sites

There is limited data on the fungal diversity in mangrove ecosystems in Guyana. This study investigated fungal diversity during the dry season in three selected coastal mangrove ecosystems along the Corentyne Coast of East Berbice, Guyana. Sampling was conducted within randomly established 50 m x 50 m plots containing 20 mini transects of length 12.5 m x 10 m in the overwash mangrove ecosystem at each of six study sites within the three study locations. Samples retrieved from the study plots included leaf, bark, soil and fruiting bodies. These were placed into separate bags and labelled appropriately. Environmental parameters were recorded at each study plot. Fruiting bodies were used to identify macrofungal species, and the leaf, bark and soil were used to prepare cultures from which microfungal samples were identified. The species that were identified were used to compile a checklist of fungal species, and diversity indices were calculated. A total of thirty (30) species were recorded, nine (9) of which were microfungi identified from the cultured samples and twenty-one (21) species were identified from macrofungal fruiting bodies retrieved at the study sites. The results further revealed that an increase in pH and salinity and a decrease in temperature resulted in an increase in species richness. Tidal activity also appeared to reduce species richness. Aspergillus, Rhizopus and Trichoderma were the dominant species at the three study sites with high relative species abundance. There also appeared to be some instances of substrate specificity.

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