Root-associated fungal community reflects host spatial co-occurrence patterns in a subtropical forest

AbstractPlant roots harbor and interact with diverse fungal species. By changing these belowground fungal communities, focal plants can affect the performance of surrounding individuals and the outcome of coexistence. Although highly host related, the roles of these root-associated fungal communities per se in host plant spatial co-occurrence is largely unknown. Here, we evaluated the host dependency of root-associated communities for 39-plant species spatially mapped throughout a 50-ha subtropical forest plot with relevant environmental properties. In addition, we explored whether the differentiation in root fungal associations among plant species can reflect their observed co-occurrence patterns. We demonstrated a strong host-dependency by discriminating the differentiation of root-associated fungal communities regardless of background soil heterogeneity. Furthermore, Random Forest modeling indicated that these nonrandom root fungal associations significantly increased our ability to explain spatial co-occurrence patterns, and to a greater degree than the relative abundance, phylogenetic relatedness, and functional traits of the host plants. Our results further suggested that plants harbor more abundant shared, “generalist” pathogens are likely segregated, while hosting more abundant unique, “specialist” ectomycorrhizal fungi might be an important strategy for promoting spatial aggregation, particularly between early established trees and the heterospecific adults. Together, we provide a conceptual and testable approach to integrate this host-dependent root fungal “fingerprinting” into the plant diversity patterns. We highlight that this approach is complementary to the classic cultivation-based scheme and can deepen our understanding of the community-level effect from overall fungi and its contribution to the pairwise plant dynamics in local species-rich communities.

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Missing checkerboards: an absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities

10.7287/peerj.preprints.531v1 ◽

2014 ◽

Author(s):

Peter Kennedy ◽

Nhu H. Nguyen ◽

Hannah Cohen ◽

Kabir G Peay

Keyword(s):

Interspecific Competition ◽

Species Interactions ◽

Community Dynamics ◽

Fungal Species ◽

Fungal Communities ◽

Positive Interactions ◽

Root Tips ◽

Host Genus ◽

Ecm Fungi ◽

Occurrence Patterns

A number of recent studies suggest that interspecific competition plays a key role in determining the structure of ectomycorrhizal (ECM) fungal communities. Despite this growing consensus, there has been limited study of ECM fungal community dynamics in abiotically stressful environments, which are often dominated by positive rather than antagonistic interactions. In this study, we examined the ECM fungal communities associated with the host genus Alnus, which live in soils high in both nitrate and acidity. The nature of ECM fungal species interactions (i.e. antagonistic, neutral, or positive) was assessed using taxon co-occurrence and sequence abundance correlational analyses. ECM fungal communities were sampled from root tips and mesh in-growth bags in three monodominant A. rubra plots and identified using Illumina-based amplification of the ITS1 gene region. We found a total of 183 ECM fungal taxa present across the plots; 16 of which were closely related to known Alnus-associated ECM fungi. Contrary to previous studies of ECM fungal communities, taxon co-occurrence analyses on both the total and Alnus-associated ECM datasets indicated that the ECM fungal communities in this system were not structured by interspecific competition. Instead the co-occurrence patterns were consistent with either random assembly or significant positive interactions. Pair-wise correlational analyses were also more consistent with neutral or positive interactions. Taken together, our results suggest that interspecific competition does not appear to determine the structure of all ECM fungal communities and that abiotic conditions may be important in determining the specific type of interaction occurring among ECM fungi.

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Missing checkerboards: an absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities

10.7287/peerj.preprints.531 ◽

2014 ◽

Author(s):

Peter Kennedy ◽

Nhu H. Nguyen ◽

Hannah Cohen ◽

Kabir G Peay

Keyword(s):

Interspecific Competition ◽

Species Interactions ◽

Community Dynamics ◽

Fungal Species ◽

Fungal Communities ◽

Positive Interactions ◽

Root Tips ◽

Host Genus ◽

Ecm Fungi ◽

Occurrence Patterns

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Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

Applied and Environmental Microbiology ◽

10.1128/aem.00905-17 ◽

2017 ◽

Vol 83 (17) ◽

Cited By ~ 40

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.

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Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges

PeerJ ◽

10.7717/peerj.4965 ◽

2018 ◽

Vol 6 ◽

pp. e4965 ◽

Cited By ~ 7

Author(s):

Mary T.H.D. Nguyen ◽

Torsten Thomas

Keyword(s):

Host Specificity ◽

Horizontal Transmission ◽

Critical Role ◽

Fungal Species ◽

Fungal Communities ◽

Sponge Species ◽

Fungal Community Composition ◽

Potential Core ◽

Community Profiling ◽

Surrounding Seawater

Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few “variable/core” fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.

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Interspecific differences in the tolerance of arbuscular mycorrhizal fungi to freezing and drying

Canadian Journal of Botany ◽

10.1139/b01-099 ◽

2001 ◽

Vol 79 (10) ◽

pp. 1161-1166 ◽

Cited By ~ 7

Author(s):

John N Klironomos ◽

Miranda M Hart ◽

Jane E Gurney ◽

Peter Moutoglis

Keyword(s):

Arbuscular Mycorrhizal Fungi ◽

Plant Species ◽

Mycorrhizal Fungi ◽

Arbuscular Mycorrhizal ◽

Fungal Species ◽

Drought Treatment ◽

Interspecific Differences ◽

The Difference ◽

One Year ◽

Arbuscular Mycorrhizal Fungal

Arbuscular mycorrhizal fungal communities in northern temperate ecosystems must function during extremes in environmental conditions. However, it is not known if arbuscular mycorrhizal fungi that co-exist in soil communities have similar tolerances to stresses such as drought and freezing. The phenology of arbuscular mycorrhizal fungi was determined over one year in a community in southern Ontario, Canada. Five fungal species from the same community were then used to inoculate five plant species, in all possible combinations, and were subjected to either a freezing treatment or a drought treatment after which new seedlings were transplanted into the treated pots. The percent colonization of roots of each plant species was measured as the difference in mean colonization from the control. Freezing reduced percent colonization in almost every case, whereas drought resulted in both increased and decreased percent colonization. Fungal species responded differently to the treatments, and there was a pronounced plant × fungus effect. These results support the hypothesis that distinct functional groups of arbuscular mycorrhizal fungi exist, and these may determine plant community structure.Key words: arbuscular mycorrhizal fungi, freezing, drying, functional diversity.

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Enumeration of Plant Species Inhabiting Oil Palm Trees (Elaeis-guineensis) at Zawlpui Plantation Site, Serchhip District, Mizoram

Science & Technology Journal ◽

10.22232/stj.2021.09.01.06 ◽

2021 ◽

Vol 9 (1) ◽

pp. 32-35

Author(s):

Lal awmpuia ◽

◽

H. Lalruatsanga ◽

Keyword(s):

Species Diversity ◽

Plant Species ◽

Oil Palm ◽

Elaeis Guineensis ◽

Vascular Plant ◽

Fungal Species ◽

Small Scale ◽

Palm Tree ◽

Palm Trees ◽

Plant Stem

A survey of plant species inhabiting oil palm trees was conducted in Zawlpui area of Serchhip district, Mizoram. The study area is a tropical potent agriculture zone, wherein small-scale business of Elaeis guineensis plantation is carried out by several farmers mainly within the gentle sloppy terrain. Oil palm with a rough bark harbors immense inhabitation by a variety plants, that rooted mostly on the debris at leaf base. Species diversity on the plant stem supposedly encourage insects and termites to establish herewith, thus causing harming to the tree. The sample stands within 400 m–800 m altitude were picked randomly. A total of 50 palm tree were accounted and all associated plants on the stem above 30 cm from the ground are all recorded. Species that cannot be identified on the site were pressed and observed at Botany Research lab, Pachhunga University College. The survey documented 38 vascular plant species which include 4 epiphytes and 1 non-vascular species of lichen, 1 bryophyte and 4 fungal species at that time. Invasive Peperomia pellucida and epiphytic pteridophytes Nephrolepis biserrata was found in most of the stand sample; however, Peperomia population decreases with the increasing elevation. Dynamics of inhabitant species diversity also correlate to location of tree. The study also established that diversity of inhabiting species was comparatively high on parts of the stem facing sunlight.

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Fungal Community Analysis and Biodeterioration of Waterlogged Wooden Lacquerware from the Nanhai No. 1 Shipwreck

Applied Sciences ◽

10.3390/app10113797 ◽

2020 ◽

Vol 10 (11) ◽

pp. 3797

Author(s):

Yin Jia ◽

Liuyu Yin ◽

Fengyu Zhang ◽

Mei Wang ◽

Mingliang Sun ◽

...

Keyword(s):

Fusarium Solani ◽

High Throughput Sequencing ◽

Environmental Parameters ◽

Community Analysis ◽

Fungal Species ◽

Potato Dextrose Agar ◽

Fungal Communities ◽

Cellulolytic Enzymes ◽

Biocidal Products

To avoid the lacquerware of the Nanhai No. 1 shipwreck from being corroded by microorganisms and to improve the knowledge on microbial ecology of the wood lacquers, we conducted a series of tests on the two water samples storing the lacquerware and colonies on the surface of the lacquerware. The high-throughput sequencing detected dominant fungal communities. After that, the fungal strains were isolated and then identified by amplification of ITS- 18S rRNA. Then the activity of ligninolytic and cellulolytic enzymes was detected on potato dextrose agar (PDA) plates with 0.04% (v/v) guaiacol and carboxymethyl cellulose (CMC) agar plates. Finally, we tested the biocide susceptibility of these fungi. Penicillium chrysogenum (NK-NH3) and Fusarium solani (NK- NH1) were the dominant fungi in the sample collected in April 2016 and June 2017. What is more, both showed activity of ligninolytic and cellulolytic enzymes. Four biocidal products (Preventol® D7, P91, BIT 20N, and Euxyl® K100) inhibited the growth of the fungal species in vitro effectively. In further research, the microbial community and environmental parameters in the museum should be monitored to assess the changes in the community and to detect potential microbial outbreaks.

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Communities of Fungi in Black Cherry Stumps and Effects of Herbicide

Plants ◽

10.3390/plants9091126 ◽

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.

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Host specialization and species richness of fruit flies (Diptera: Tephritidae) in a New Guinea rain forest

Journal of Tropical Ecology ◽

10.1017/s0266467404002044 ◽

2005 ◽

Vol 21 (1) ◽

pp. 67-77 ◽

Cited By ~ 26

Author(s):

Vojtech Novotny ◽

Anthony R. Clarke ◽

Richard A. I. Drew ◽

Solomon Balagawi ◽

Barbara Clifford

Keyword(s):

Papua New Guinea ◽

Plant Species ◽

Rain Forest ◽

New Guinea ◽

Fruit Fly ◽

Fruit Flies ◽

Host Specialization ◽

Area 5 ◽

Local Species ◽

Single Genus

Frugivorous dacine fruit flies were studied in a lowland tropical rain forest in Papua New Guinea to determine their host specificity, abundance, and the number of species attacking various plant species. Plant species hosted 0–3 fruit fly species at median (1–3 quartile) densities of 1 (0–17) fruit flies per 100 fruits. Fruit flies were mostly specialized to a single plant family (83% species) and within each family to a single genus (88% species), while most of the species (66%) were able to feed on >1 congeneric plant species. Only 30 from the 53 studied plant species were colonized by fruit flies. The plant–fruit fly food web, including these 30 plant species and the total of 29 fruit fly species feeding on them, was divided into 14 compartments, each including 1–8 plant species hosting mutually disjunct assemblages of fruit flies. This structure minimizes indirect interactions among plant species via shared herbivores. The local species pool was estimated at 152±32 (±SE) fruit fly species. Forty per cent of all taxonomically described species known from Papua New Guinea were reared or trapped in our study area. Such a high proportion indicates low beta-diversity of fruit flies. Steiner traps were highly efficient in sampling the lure-responsive fruit fly species as they re-collected 84% of all species trapped in the same area 5 y before. Fruit fly monitoring by these traps is a cheap, simple and efficient method for the study of spatial and temporal changes in rain-forest communities.

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