scholarly journals Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

2019 ◽  
Vol 3 ◽  
Author(s):  
Shunsuke Matsuoka ◽  
Yoriko Sugiyama ◽  
Hirotoshi Sato ◽  
Izumi Katano ◽  
Ken Harada ◽  
...  
Keyword(s):  
Spatial Structure ◽  
River Water ◽  
Mycorrhizal Fungi ◽  
Environmental Dna ◽  
Terrestrial Ecosystems ◽  
Rrna Gene ◽  
Terrestrial Habitats ◽  
Fungal Dna ◽  
Terrestrial Fungi ◽  
Functionally Diverse

Growing evidence has revealed high diversity and spatial heterogeneity of fungal communities in local habitats of terrestrial ecosystems. Recently, the analysis of environmental DNA has been undertaken to study the biodiversity of organisms, such as animals and plants, in both aquatic and terrestrial habitats. In the present study, we investigated fungal DNA assemblages and their spatial structure using environmental DNA metabarcoding targeting the internal transcribed spacer 1 (ITS1) region of the rRNA gene cluster in habitats across different branches of rivers in forest landscapes. A total of 1,956 operational taxonomic units (OTUs) were detected. Of these, 770 were assigned as Ascomycota, 177 as Basidiomycota, and 38 as Chytridiomycota. The river water was found to contain functionally diverse OTUs of both aquatic and terrestrial fungi, such as plant decomposers and mycorrhizal fungi. These fungal DNA assemblages were more similar within, rather than between, river branches. In addition, the assemblages were more similar between spatially closer branches. This spatial structuring was significantly associated with geographic distances but not with vegetation of the catchment area and the elevation at the sampling points. Our results imply that information on the terrestrial and aquatic fungal compositions of watersheds, and therefore their spatial structure, can be obtained by investigating the fungal DNA assemblages in river water.

scholarly journals Spatial structures of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

2019 ◽  
Author(s):  
Shunsuke Matsuoka ◽  
Yoriko Sugiyama ◽  
Hirotoshi Sato ◽  
Izumi Katano ◽  
Ken Harada ◽  
...  
Keyword(s):  
Spatial Structure ◽  
River Water ◽  
Mycorrhizal Fungi ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Terrestrial Ecosystems ◽  
Sampling Effort ◽  
Terrestrial Habitats ◽  
Fungal Dna ◽  
Terrestrial Fungi

AbstractGrowing evidence has revealed high diversity and spatial heterogeneity of fungal communities including in local habitats in terrestrial ecosystems. These findings highlight the considerable sampling effort, analysis time, and costs required for the investigation of fungal diversity over large spatial scales. Recently, the analysis of environmental DNA in river water has been undertaken to study the biodiversity of organisms, such as animals and plants, in both aquatic and terrestrial habitats. However, previous studies have not investigated the spatial structure of fungal DNA assemblages in river water. In the present study, we investigate fungal DNA assemblages and their spatial structure using environmental DNA metabarcoding in water across different branches of river over forest landscapes. The river water was found to contain both phylogenetically and functionally diverse fungal DNA, including aquatic and terrestrial fungi, such as plant decomposers and mycorrhizal fungi. These fungal DNA assemblages were more similar within, rather than between, branches. In addition, the assemblages were more similar between spatially closer branches. These results imply that information on the terrestrial and aquatic fungal compositions of watersheds, and therefore their spatial structure can be obtained by investigating the fungal DNA assemblages in river water.

scholarly journals Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding

2020 ◽  
Author(s):  
Shunsuke Matsuoka ◽  
Yoriko Sugiyama ◽  
Yoshito Shimono ◽  
Masayuki Ushio ◽  
Hideyuki Doi
Keyword(s):  
Functional Groups ◽  
Stream Water ◽  
Environmental Dna ◽  
Fungal Communities ◽  
Ecosystem Functions ◽  
Substrate Removal ◽  
Regulated Stream ◽  
Fungal Dna ◽  
Terrestrial Fungi ◽  
Forest Streams

AbstractInvestigation of the seasonal variation in the fungal community is essential for understanding biodiversity and its ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community compositions, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis, including both aquatic and terrestrial species, has been explored for its usefulness in biodiversity surveys. Examining eDNA may allow for the survey of the community over time with less disturbance to the ecosystem. In this study, we assessed whether seasonality of fungal communities can be detected with monitoring of eDNA in a flow-regulated stream in a restored forest. We conducted monthly water sampling in the stream over two years, and used DNA metabarcoding to estimate the taxonomic and functional groups of fungal eDNA in the water. The river water contained taxonomically and functionally diverse DNA from both aquatic and terrestrial fungi, such as plant decomposers, parasites, and mutualists. The DNA assemblages showed a distinct annual periodicity, meaning that the assemblages were similar to each other regardless of the year, in the same sampling season. These seasonal changes were partially explained by temperature alterations. Furthermore, the strength of the one-year periodicity may vary across functional groups. Our results suggest that forest streams act as a “natural trap” for fungal DNA and that studies of fungal DNA in stream water may provide information on the temporal variation of fungal communities inhabiting not only water but also the surrounding ecosystem.

scholarly journals Sedimentary Ancient DNA (sedaDNA) Reveals Fungal Diversity and Environmental Drivers of Community Changes throughout the Holocene in the Present Boreal Lake Lielais Svētiņu (Eastern Latvia)

2021 ◽  
Vol 9 (4) ◽  
pp. 719
Author(s):  
Liisi Talas ◽  
Normunds Stivrins ◽  
Siim Veski ◽  
Leho Tedersoo ◽  
Veljo Kisand
Keyword(s):  
Mycorrhizal Fungi ◽  
Pathogenic Fungi ◽  
Terrestrial Ecosystems ◽  
Environmental Drivers ◽  
The Holocene ◽  
Parasitic Fungi ◽  
Rapid Changes ◽  
Fungal Dna ◽  
Community Shifts ◽  
Community Changes

Fungi are ecologically important in several ecosystem processes, yet their community composition, ecophysiological roles, and responses to changing environmental factors in historical sediments are rarely studied. Here we explored ancient fungal DNA from lake Lielais Svētiņu sediment throughout the Holocene (10.5 kyr) using the ITS metabarcoding approach. Our data revealed diverse fungal taxa and smooth community changes during most of the Holocene with rapid changes occurring in the last few millennia. More precisely, plankton parasitic fungi became more diverse from the Late Holocene (2–4 kyr) which could be related to a shift towards a cooler climate. The Latest Holocene (~2 kyr) showed a distinct increase in the richness of plankton parasites, mycorrhizal, and plant pathogenic fungi which can be associated with an increased transfer rate of plant material into the lake and blooms of planktonic organisms influenced by increased, yet moderate, human impact. Thus, major community shifts in plankton parasites and mycorrhizal fungi could be utilized as potential paleo-variables that accompany host-substrate dynamics. Our work demonstrates that fungal aDNA with predicted ecophysiology and host specificity can be employed to reconstruct both aquatic and surrounding terrestrial ecosystems and to estimate the influence of environmental change.

scholarly journals Assessing high-throughput environmental DNA extraction methods for meta-barcode characterization of aquatic microbial communities

2018 ◽  
Vol 17 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Abdolrazagh Hashemi Shahraki ◽  
Subba Rao Chaganti ◽  
Daniel Heath
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput ◽  
Environmentally Friendly ◽  
Environmental Dna ◽  
Magnetic Bead ◽  
Extraction Methods ◽  
Environmental Research ◽  
Rrna Gene

Abstract The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variable community compositions. The current study developed environmentally friendly, user safe, economical, and high throughput eDNA extraction methods for mixed aquatic microbial communities and tested them using 16 s rRNA gene meta-barcoding. Five different lysis buffers including (1) cetyltrimethylammonium bromide (CTAB), (2) digestion buffer (DB), (3) guanidinium isothiocyanate (GITC), (4) sucrose lysis (SL), and (5) SL-CTAB, coupled with four different purification methods: (1) phenol-chloroform-isoamyl alcohol (PCI), (2) magnetic Bead-Robotic, (3) magnetic Bead-Manual, and (4) membrane-filtration were tested for their efficacy in extracting eDNA from recreational freshwater samples. Results indicated that the CTAB-PCI and SL-Bead-Robotic methods yielded the highest genomic eDNA concentrations and succeeded in detecting the core microbial community including the rare microbes. However, our study recommends the SL-Bead-Robotic eDNA extraction protocol because this method is safe, environmentally friendly, rapid, high-throughput and inexpensive.

scholarly journals Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

2021 ◽  
Vol 12 ◽  
Author(s):  
Larissa Frühe ◽  
Verena Dully ◽  
Dominik Forster ◽  
Nigel B. Keeley ◽  
Olivier Laroche ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Environmental Dna ◽  
Community Diversity ◽  
Rrna Gene ◽  
Local Conditions ◽  
Global Trends ◽  
Bacterial Taxon ◽  
Metabolic Properties

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

scholarly journals Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA

2021 ◽  
Author(s):  
Shunsuke Matsuoka ◽  
Yoriko Sugiyama ◽  
Mariko Nagano ◽  
Hideyuki Doi
Keyword(s):  
Dna Extraction ◽  
Environmental Dna ◽  
Operational Taxonomic Unit ◽  
Pcr Inhibition ◽  
Dna Metabarcoding ◽  
Fungal Dna ◽  
Diversity Studies ◽  
Microbial Dna ◽  
Methodological Studies ◽  
Biodiversity Analysis

Background: Environmental DNA (eDNA) metabarcoding is a rapidly expanding technique for efficient biodiversity monitoring, especially of animals. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of the DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. Methods: DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extract microbial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results [i.e., operational taxonomic unit (OTU) number and composition] of the extracted samples. Results: No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.

scholarly journals Aurantimicrobium minutum gen. nov., sp. nov., a novel ultramicrobacterium of the family Microbacteriaceae, isolated from river water

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4072-4079 ◽  
Author(s):  
Ryosuke Nakai ◽  
Tomoya Baba ◽  
Hironori Niki ◽  
Miyuki Nishijima ◽  
Takeshi Naganuma
Keyword(s):  
River Water ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
High Sequence Similarity ◽  
The Family ◽  
Western Japan ◽  
Unidentified Species ◽  
Diamino Acid ◽  
Ph Range

A Gram-stain-positive, aerobic, non-motile, curved (selenoid), rod-shaped actinobacterium, designated KNCT, was isolated from the 0.2 μm-filtrate of river water in western Japan. Cells of strain KNCT were ultramicrosized (0.04–0.05 μm3). The strain grew at 15–37 °C, with no observable growth at 10 °C or 40 °C. The pH range for growth was 7–9, with weaker growth at pH 10. Growth was impeded by the presence of NaCl at concentrations greater than 1 %. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KNCT showed relatively high sequence similarity (97.2 %) to Alpinimonas psychrophila Cr8-25T in the family Microbacteriaceae. However, strain KNCT formed an independent cluster with cultured, but as-yet-unidentified, species and environmental clones on the phylogenetic tree. The major cellular fatty acids were anteiso-C15 : 0 (41.0 %), iso-C16 : 0 (21.8 %), C16 : 0 (18.0 %) and anteiso-C17 : 0 (12.9 %), and the major menaquinones were MK-11 (71.3 %) and MK-12 (13.6 %). The major polar lipids were phosphatidylglycerol and two unknown glycolipids. The cell-wall muramic acid acyl type was acetyl. The peptidoglycan was B-type, and contained 3-hydroxyglutamic acid, glutamic acid, aspartic acid, glycine, alanine and lysine, with the latter being the diagnostic diamino acid. The G+C content of the genome was unusually low for actinobacteria (52.1 mol%), compared with other genera in the family Microbacteriaceae. Based on the phenotypic characteristics and phylogenetic evidence, strain KNCT represents a novel species of a new genus within the family Microbacteriaceae, for which the name Aurantimicrobium minutum gen. nov., sp. nov. is proposed. The type strain of the type species is KNCT ( = NBRC 105389T = NCIMB 14875T).

scholarly journals Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Shingo Miyauchi ◽  
Enikő Kiss ◽  
Alan Kuo ◽  
Elodie Drula ◽  
Annegret Kohler ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Transposable Elements ◽  
Genome Sequencing ◽  
Mycorrhizal Fungi ◽  
Large Scale ◽  
Terrestrial Ecosystems ◽  
Pathogenic Species ◽  
Fungal Genomes ◽  
Induced Genes

Abstract Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

Retrieval of nearly complete 16S rRNA gene sequences from environmental DNA following 16S rRNA-based community fingerprinting

2005 ◽  
Vol 7 (5) ◽  
pp. 670-675 ◽  
Author(s):  
Manfred G. Hofle ◽  
Sebastien Flavier ◽  
Richard Christen ◽  
Julia Botel ◽  
Matthias Labrenz ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Environmental Dna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Community Fingerprinting

scholarly journals Further evidence for fungivory in the Lower Devonian (Lochkovian) of the Welsh Borderland, UK

PalZ ◽  
2020 ◽  
Vol 94 (4) ◽  
pp. 603-618
Author(s):  
Dianne Edwards ◽  
Lindsey Axe ◽  
Jennifer L. Morris ◽  
Lynne Boddy ◽  
Paul Selden
Keyword(s):  
Carbon Cycling ◽  
Lower Devonian ◽  
Terrestrial Ecosystems ◽  
Lower Surface ◽  
Early Devonian ◽  
Faecal Pellets ◽  
Terrestrial Invertebrates ◽  
Terrestrial Animal ◽  
Complete Digestion ◽  
Terrestrial Fungi

Abstract The recent demonstrations that widespread mid-Palaeozoic Prototaxites and other nematophytes had fungal affinities indicate that terrestrial fungi were important elements in carbon cycling in the Early Devonian. Here, we provide evidence for their participation in the recycling of nutrients by early terrestrial invertebrates. Evidence is in the form of coprolites, both those associated with nematophytes or containing their fragmentary remains. Cylindrical coprolites consistently associated with fungal mats are placed in a new ichnospecies, Bacillafaex myceliorum. Their contents are granular to amorphous, suggestive of complete digestion of the ingested hyphae, with the inference of possession of chitinases in the digestive tracts of the consumers. A further single example comprises a cluster of cylindrical bodies attached to the lower surface of a Nematothallus fragment. Here, homogenisation was less complete, with traces of hyphae remaining. Terrestrial animal fossils have not been found at the locality, but scorpions, pseudoscorpions, Opiliones, mites, centipedes (carnivores) and millipedes, and Collembola (detritivores) have been recorded from the slightly younger Rhynie cherts. Studies of fungivory in extant arthropods have concentrated on Collembola and, to a lesser extent, mites, but their faecal pellets are much smaller than the fossil examples. Millipedes, based on body size and faeces of extant forms, are considered more realistic producers, but little is known about fungal feeding in these animals. Regardless of the affinities of the producers, the diversity in morphology, sizes, aggregations, and composition of nematophyte-containing examples suggests that fungivory was an important component of carbon cycling in early terrestrial ecosystems.

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