Biodiversity Data Journal : Taxonomic Paper
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Taxonomic Paper
Sporidesmiella lignicola sp. nov., a new hyphomycetous fungus from freshwater habitats in China
expand article infoXiao-Hong Li, Yu-Lin Liu§, Hai-Yan Song|, Dian-Ming Hu‡,, Yang Gao, Hai-Jing Hu, Jian-Ping Zhou
‡ Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang, China
§ Jiangxi Environmental Engineering Vocational College, Ganzhou, China
| Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, China
¶ College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
Open Access

Abstract

Background

Freshwater fungi, growing on submerged wood, can promote the degradation of organisms and the reuse of rotten wood energy and play key roles in freshwater ecosystems. Here, a new hyphomycetous fungus, Sporidesmiella lignicola, was isolated and identified from submerged wood samples collected in a small stream in Jiangxi Province, south-eastern China.

New information

The new taxon was studied, based on morphological characters and phylogenetic analyses combined with LSU, ITS, TEF1α and RPB2 sequences data. Sporidesmiella lignicola was morphologically characterised by its pink colonies on PDA medium in prophase, macronematous, mononematous, solitary, brown, septate, unbranched, straight or slightly flexuous conidiophores with holoblastic, polyblastic, integrated, terminal, pale brown conidiogenous cells and cylindrical, narrowly clavate, broadly obovoid to cuneiform, 3–4-distoseptate, olivaceous brown or brown conidia with rounded apex. A phylogenetic tree was constructed, based on the combination of LSU, ITS, TEF1α and RPB2 sequences data.

Keywords

freshwater fungi, lignicolous fungi, hyphomycetes, taxonomy

Introduction

The genus Sporidesmiella was introduced by Kirk to accommodate two newly-described species and four new combinations from Sporidesmium, with Sporidesmiella claviformis as the type species (Kirk 1982). Sporidesmiella was commonly characterised by having clavate or obovoid to cuneate conidia, with a few distosepta, rounded or coronate at the apex, seceding schizolytically from monoblastic, integrated, terminal, annellidic or rarely sympodially extending conidiogenous cells. Ma et al. (2012) revised Sporidesmiella and accepted 26 species, based on the characters of proliferations of conidiogenous cells and conidial shape, size range and septation. Subsequently, 12 additional taxa have been added to Sporidesmiella, based on morphological characters, i.e. S. curtiphora (Monteiro et al. 2014), S. bawanglingensis and S. nanlingensis (Ma et al. 2015), S. mammillata (Heredia et al. 2015), S. physconiicola (Zhurbenko et al. 2015), S. guangdongensis and S. jiangxiensis (Ma 2016a), S. lushanensis and S. jiulianshanensis (Ma 2016b), S. novae-zelandiae (Hernández-Restrepo et al. 2018), S. corniformis (Ai et al. 2019) and S. suttonii (Kirk 2019). Recently, Luo et al. (2019) introduced a new species S. aquatica from freshwater habitats. Dong et al. (2021) reported a new species S. obovioidia from submerged wood. Up to now, 40 species have been accepted in Sporidesmiella.

So far, the molecular data of Sporidesmiella are relatively few; there are DNA sequences of only five species deposited in NCBI, i.e. S. aquatic, S. fusiformis, S. hyalosperma, S. novae-zelandiae and S. obovoidia. Therefore, most Sporidesmiella species have not been subjected to molecular phylogenetic analysis. Shenoy et al. (2006) classified Sporidesmiella fusiformis in the Melanommataceae according to the phylogenies with the combined LSU nu-rDNA and RPB2 dataset. Luo et al. (2019), Crous et al. (2020) and Dong et al. (2021) accommodated S. aquatic, S. hyalosperma, S. novae-zelandiae and S. obovoidia within Junewangiaceae, based on the combination of LSU, ITS, TEF1α and RPB2 sequences data. Therefore, as Sporidesmiella was suspected to be polyphyletic, the molecular data of the type species S. claviformis are in need of analysis.

Based on investigations of freshwater fungi in Jiangxi Province (Hu et al. 2012a, Huang et al. 2016, Hu et al. 2016, Song et al. 2018, Song et al. 2020), we reported a new species of Sporidesmiella, collected on submerged wood from freshwater habitats in Jiangxi Province. It was described and illustrated as Sporidesmiella lignicola, based on phylogenetic evidence of combined LSU, ITS, TEF1α and RPB2 sequence data and morphological characters.

Materials and methods

Samples collection

Submerged wood samples were collected randomly from a stream in Xinfeng County, Ganzhou City, Jiangxi Province, China. The samples were taken to the laboratory in zip-lock bags and incubated in moist plastic boxes.

Specimen examination

Fruiting bodies or colonies were examined following the method of Hu et al. (2012a) using a Nikon dissecting microscope. Samples were examined and photographed using a Nikon (Ni) compound microscope with differential interference contrast (DIC) (Hu et al. 2016). The fungal specimens were deposited in the Herbarium of Fungi, Jiangxi Agricultural University (HFJAU), Nanchang, China.

Single spore isolation and cultivation

The fungal colonies on the rotten wood were picked up and placed in 200 μl sterile water to make a suspension, then the suspension was evenly spotted on potato dextrose agar (PDA), then cultured in a 28℃ incubator. The spore germination was observed every 12 hours and recorded. The germinating single spore was transfered to new PDA medium with a sterile needle under aseptic conditions and then cultured in a 28℃ incubator to obtain the pure strain.

DNA extraction, PCR amplification and sequencing

DNA was extracted from the pure cultures with the CTAB method, following Doyle and Doyle (1987). Four gene regions, LSU, ITS, TEF1α and RPB2 were amplified using the primer pairs LR0R/LR5, ITS1/ITS4, EF1-983F/EF1-2218R and RPB2-5F/RPB2-7cR, respectively (Vilgalys and Hester 1990, White et al. 1990, Liu et al. 1999). The amplification was performed following the method described by Hu et al. (2012b). The PCR products were examined using 1% agarose electrophoresis gels, stained with GelRed and purified and sequenced with the same primers at Tsingke Biotechnology Co. Ltd.

Phylogenetic analyses

Four novel sequences (OK091615, MZ613187, OK323223, OK323222) from the new taxon, together with reference sequences obtained from GenBank (Table 1), were aligned with MAFFT version 7 (https://mafft.cbrc.jp/alignment/software/, Katoh and Standley 2013). The ML analyses were conducted with RAxML v. 7.2.6 (Stamatakis and Alachiotis 2010), using a GTRGAMMA substitution model with 1000 bootstrap replicates. The robustness of the analyses was evaluated by bootstrap support (MLBS).

Table 1.

Taxa used in this study and their GenBank accession numbers. Ex-type strains are in bold; newly-generated sequences are highlighted with underline.

Abbreviation: MFLU: the Herbarium of Mae Fah Luang University, Chiang Rai, Thailand; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Rai, Thailand; HFJAU: Herbarium of Fungi, Jiangxi Agricultural University, Nanchang, China; CBS: Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands; HSAUP: Herbarium of Department of Plant Pathology, Shandong Agricultural University, Taian, China; HMAS: Mycological Herbarium, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Dali University Culture Collection, Yunnan, China; JAUCC: Jiangxi Agricultural University Culture Collection, Nanchang, China. KUMCC: Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China; CPC: Culture collection of Pedro Crous, housed at CBS.

Taxon

Voucher/Culture

GenBank accession numbers

LSU

ITS

TEF1α

RPB2

Botryotinia fuckeliana

AFTOL-ID 59T

AY544651

DQ491491

DQ471045

DQ247786

Dictyosporella aquatica

CBS H-22127T

KT241022

_

_

_

Dictyosporella chiangmaiensis

MFLUCC 17-2345T

MW287765

MW286491

_

_

Dictyosporella ellipsoidea

MFLUCC 18-1042T

MW287758

_

_

_

Dictyosporella guizhouensis

MFLU 18-1505T

MK593605

MK593606

_

_

Dictyosporella guizhouensis

MFLUCC 18-1232

MW287760

MW286487

MW396646

_

Dictyosporella hydei

IFRDCC 3075T

MG813161

_

_

_

Dictyosporella thailandensis

MFLUCC 15-0985T

MF374364

MF374355

MF370958

MF370952

Junewangia aquatic

HFJAU 0700T

MG213737

MG213738

_

_

Junewangia globulosa

CBS 126093

MH875535

MH864078

_

_

Junewangia lamma

HSAUPH 4695

KU751883

KU999971

_

_

Junewangia lamma

HMAS 44438

KU751882

KU999961

_

_

Junewangia queenslandica

HSAUPmyr 7722

KX033575

KU999984

_

_

Junewangia sphaerospora

HSAUPmyr 4733

KX033572

KU999981

_

_

Junewangia thailandica

MFLU 15-2682T

MW287762

_

_

_

Sporidesmiella aquatica

DLUCC 1339

MK849844

_

MN194035

MN124524

Sporidesmiella aquatic

DLUCC 0777T

MK849843

MK828692

MN194034

_

Sporidesmiella hyalosperma

DLUCC 1518

MK849842

MK828691

MN194033

MN124523

Sporidesmiella hyalosperma

KUMCC 15-0431

MK849841

MK828690

MN194032

MN124522

Sporidesmiella hyalosperma

S-1320

MK849840

MK828689

_

MN124521

Sporidesmiella hyalosperma

MFLUCC 18-1312

MK849839

MK828688

MN194031

MN124520

Sporidesmiella hyalosperma

MFLUCC 18-1013

MW287773

MW286499

MW396654

MW504070

Sporidesmiella lignicola

JAUCC 3436T

OK091615

MZ613187

OK323223

OK323222

Sporidesmiella novae-zelandiae

DLUCC 0951

MK849847

MK828695

MN194037

MN124526

Sporidesmiella novae-zelandiae

S-048

MK849846

MK828694

_

_

Sporidesmiella novae-zelandiae

DLUCC 1256

MK849845

MK828693

MN194036

MN124525

Sporidesmiella obovoidia

MFLUCC 17-2372T

MW287766

MW286492

_

_

Sporidesmium appendiculatum

MFLU 18-0981T

MW287774

MW286500

_

_

Sporidesmium chiangmaiense

MFLUCC 18-0999T

MW287771

MW286497

_

_

Sporidesmium dulongense

MFLUCC 17-0116T

MH795817

MH795812

MH801191

MH801190

Sporidesmium lageniforme

DLUCC 0880T

MK849782

MK828640

MN194044

MN124533

Sporidesmium melaleucae

CPC 32936

MH327854

MH327818

_

_

Sporidesmium melaleucae

CPC 32707T

MH327853

MH327817

_

_

Sporidesmium pyriformatum

MFLUCC 15-0627

KX710143

KX710148

MF135663

MF135650

Sporidesmium pyriformatum

MFLUCC 15-0620T

KX710141

KX710146

MF135662

MF135649

The multilocus sequences were concatenated with PhyloSuite v. 1.2.2 (Zhang et al. 2020). The concatenated aligned datasets were analysed separately using Maximum Likelihood (ML) and Bayesian Inference (BI). ModelFinder (Kalyaanamoorthy et al. 2017) was used to select the best-fit model using AICc criterion. The best-fit model according to AICc was GTR+F+I+G4. Bayesian Inference phylogenies were inferred using MrBayes 3.2.6 (Ronquist et al. 2012) under partition model (2 parallel runs, 2,000,000 generations), in which the initial 25% of sampled data were discarded as burn-in. Modification of the final phylogenetic tree was done in FigTree v. 1.4.3 and Adobe Illustrator CS6.

Taxon treatment

Sporidesmiella lignicola X.H. Li, H.Y. Song & D.M. Hu, sp. nov.

Material    Download as CSV 
Holotype:
  1. scientificName:
    Sporidesmiella lignicola
    ; acceptedNameUsage:
    Sporidesmiella lignicola X.H. Li, H.Y. Song & D.M. Hu, 2021, sp. nov.
    ; taxonID:
    urn:lsid:biosci.ohio-state.edu:osuc_names:275502
    ; parentNameUsage:
    Sporidesmiella P.M. Kirk 1982
    ; kingdom:
    Fungi
    ; phylum:
    Ascomycota
    ; class:
    Dothideomycetes
    ; order:
    Pleosporales
    ; family:
    Junewangiaceae
    ; taxonRank:
    species
    ; verbatimTaxonRank:
    species
    ; genus:
    Sporidesmiella
    ; specificEpithet:
    lignicola
    ; scientificNameAuthorship:
    X.H. Li, H.Y. Song & D.M. Hu
    ; continent:
    Asia
    ; country:
    China
    ; stateProvince:
    Jiangxi
    ; county:
    Xinfeng
    ; municipality:
    Ji'an
    ; locality:
    Jinji Forest Farm
    ; verbatimElevation:
    305 m
    ; locationRemarks:
    label transliteration: "Jiangxi, Jinji Forest Farm, 2020.7.7, Li Xiao-Hong"; [江西赣州市信丰县金鸡林场,2020年7月7日,李小红]
    ; verbatimCoordinates:
    25.4732 N, 115.2048 E
    ; decimalLatitude:
    25.4732
    ; decimalLongitude:
    115.2048
    ; georeferenceProtocol:
    label
    ; samplingProtocol:
    collecting
    ; eventDate:
    07/07/2021
    ; habitat:
    Freshwater
    ; individualCount:
    1
    ; recordedBy:
    Xiao-Hong Li
    ; identifiedBy:
    Xiao-Hong Li and Dian-Ming Hu
    ; dateIdentified:
    2020
    ; type:
    PhysicalObject
    ; language:
    en
    ; rightsHolder:
    Dian-Ming Hu
    ; institutionID:
    HFJAU 10001 (Dried culture with conidia)
    ; collectionID:
    FF019
    ; institutionCode:
    the Herbarium of Fungi, Jiangxi Agricultural University (HFJAU)
    ; collectionCode:
    Fungi
    ; ownerInstitutionCode:
    the Herbarium of Fungi, Jiangxi Agricultural University (HFJAU)
    ; basisOfRecord:
    PreservedSpecimen

Description

Saprobic on decaying wood submerged in freshwater habitats. Colonies effuse, hairy, pale brown. Mycelium mostly superficial, partly immersed, consisting of unbranched, septate, smooth, thick-walled, brown to dark brown hyphae. Sexual morph: Undetermined. Asexual morph: Conidiophores 110–150 × 3–7 μm (mean = 124.6 × 4.2, n = 20), macronematous, mononematous, solitary, pale brown, smooth at the bottom and verrucose at the apex, septate, unbranched, straight or slightly flexuous. Conidiogenous cells 15–26 × 2–5 μm (mean = 22.4 × 4, n = 20), holoblastic, polyblastic, integrated, terminal, pale brown, cylindrical. Conidia 18–26 × 7–11 μm (mean = 21 × 8.9, n = 20), acrogenous, dry, cylindrical, narrowly clavate, obovoid to broadly obovoid to cuneiform, truncate at the base, rounded or rarely coronate at the apex, 2–3-distoseptate, pale olivaceous to olivaceous brown or brown, smooth. Conidial session schizolytic (Fig. 1).

Figure 1.  

Sporidesmiella lignicola (HFJAU 10001, Holotype) a Colony on wood; b, c Conidiophores; d Conidiophores with production of conidia; eg Conidia; h, i Colony on PDA for 21 days (left-front, right-reverse). Scale bars: a = 125 µm, b–c = 12.5 µm, d–g = 10 µm, h–i = 1.5 cm.

Culture characteristics: On PDA, colony reaching 12 mm in 21 days at 28°C, pink from above, pink-grey from below, surface rough, dry, with loose mycelium and irregular edge. After half a year, the colony produces spores. The hyphae penetrate into the PDA medium, the surface colour becomes brown to dark brown, raised with white in the middle, reverse of culture pale brown to dark brown, with entire and regular edge. Mycelium composed of septate, pale brown, unbranched, smooth hyphae. Conidiophores macronematous, solitary, cylindrical, straight or slightly flexuous, septate, brown, smooth, thick-walled, 37–54 × 3.5–5.5 μm (mean = 46.5 × 4.6, n = 20). Conidiogenous cells holoblastic, polyblastic, integrated, terminal, pale brown, cylindrical, 10–26 × 3–7 μm (mean = 27.1 × 4.6, n = 20), slightly enlarged towards the apex. Conidia acrogenous, cylindrical, broadly obovoid to cuneiform, truncate at the base, rounded at the apex, 3–4-distoseptate, brown to pale olivaceous brown, smooth, 18–28 × 8–12 μm (mean = 22.3 × 9.6, n = 20) (Fig. 2).

Figure 2.  

a–b, e Conidiophores with production of conidia; c–d Conidiophores; f–i Conidia; j Colony on PDA after 6 months (left-front, right-reverse). Scale bars: a–d = 25 µm, e–i = 10 µm, d–g = 10 µm.

Etymology

The specific epithet “lignicola” (Latin) meaning ‘‘growing on wood’’.

Ecology

Saprophyte on wood submerged in a small stream.

Notes

Sporidesmiella lignicola is characterised by being cylindrical, broadly obovoid to cuneiform, truncate at the base, rounded at the apex, 3–4-distoseptate, pale olivaceous brown to brown, smooth, which is consistent with the characteristics of Sporidesmiella. Sporidesmiella lignicola is similar to S. obovoidia and S. hyalosperma in having polyblastic conidiogenous cells and obovoid, 3–4-distoseptate, brown conidia (Luo et al. 2019, Dong et al. 2021). However, S. lignicola differs from other species in having longer and verrucose conidiophores (Table 2). In addition, the colonies of S. lignicola are pink from above, pink-grey from below, characteristics which were not observed in the other two species (Fig. 3, Table 2).

Table 2.

Comparisons of Sporidesmiella lignicola and similar species.

Species

Conidiophores (µm)

Conidiogenous cell (µm)

Conidia

Colour of cultures

References

Shape

Colour

Size (µm)

S. hyalosperma

Smooth, 90–110 × 3.5–4.7

35–48 × 4–4.5

obovoid or broadly clavate

olivaceous brown

18.5–25 × 8–10.5

reddish-brown from above and below

Dong et al. 2021

S. lignicola

Verrucose at the apex, 110150 × 37

1526 × 25

broadly obovoid to cuneiform

brown or olivaceous brown

1826 × 711

pink from above, pink-grey from below

This paper

S. obovoidia

Smooth, 80–125 × 3.5–4.5

10–40 × 3–4

mostly obovoid or broadly clavate

brown or olivaceous brown

20–25 × 9–11.5

grey-dark brown from above, black from below

Dong et al. 2021

Figure 3.  

Comparisons of colonies on PDA (left-front, right-reverse) in Sporidesmiella lignicola and similar species. a S. hyalosperma; b S. obovoidia; c S. lignicola.

Based on a BLAST of NCBI’s GenBank nucleotide database, the most similar sequence was Sporidesmiella obovoidia. The nucleotide comparison between S. lignicola and S. obovoidia showed differences of 10 and 4 nucleotides in ITS and LSU sequence data, respectively (Fig. 4, Fig. 5), which supported them to be different species (Jeewon and Hyde 2016).

Figure 4.  

The specific base differences between S. lignicola and S. obovoidia in ITS. Different base pairs have been marked on specific sites, and the same base is omitted.

Figure 5.  

The specific base differences between S. lignicola and S. obovoidia in LSU. Different base pairs have been marked on specific sites, and the same base is omitted.

Unfortunately, the strain could not be successfully activated due to improper operation during preservation. When the original culture was retained for 6 months, the sporulation of mycelium could be observed under the microscope (Fig. 2). We deposited the dried culture as specimens (HFJAU 10001) of this species.

Analysis

Phylogenetic analyses

The analysed dataset comprised 35 taxa retrieved from GenBank and we selected Botryotinia fuckeliana (AFTOL-ID 59) as the outgroup taxon (Table 1). Partial nucleotide sequences of LSU (844bp), ITS (598bp), TEF1α (881bp), RPB2 (1059bp) and, for a total of 3382 characters including gaps, were used to determine the phylogenetic placement of the new taxon. The generated ML and Bayesian trees were similar in topology and the best scoring RAxML tree is presented in Fig. 6.

Figure 6.  

Phylogenetic tree inferred from a Maximum Likelihood analysis, based on a concatenated alignment of LSU, ITS, TEF1α and RPB2 sequences of 35 strains representing Sporidesmiella species and other similar species. Bootstrap support values (ML) for Maximum Likelihood higher than 80% and Bayesian posterior probabilities (PP) greater than 0.80 are given at the nodes as ML/PP. The root of this tree is Botryotinia fuckeliana. Ex-type strains are in bold; new species are highlighted in red.

The phylogenetic tree demonstrated that the new taxon (Sporidesmiella lignicola), together with species of S. obovoidia, S. hyalosperma, S. aquatica and S. novae-zelandiae, formed a distinct clade representing the genus Sporidesmiella with strong bootstrap support (100% MLBS, 1.00 PP). Additionally, in our phylogenetic analysis, the three genera Dictyosporella, Junewangia and Sporidesmiella constituted a well-supported clade with strong ML and BYPP bootstrap support (100% MLBS, 1.00 PP), which is in accordance with Luo et al. (2019) and Dong et al. (2021). Sporidesmiella lignicola appeared closely related to S. obovoidia and S. hyalosperma. Although S. lignicola (JAUCC 3436) clustered together in S. obovoidia (MFLUCC 17-2372) with high support (88% MLBS, 1.00 PP), they are not phylogenetically identical.

Discussion

Kirk (1982) established the genus Sporidesmiella with S. claviformis as the type species, which had accommodated 40 species before this study. This study introduced Sporidesmiella lignicola as a new hyphomycetous fungus from freshwater habitats. In our phylogenetic analysis, S. lignicola clustered in Sporidesmiella, together with Dictyosporella and Junewangia forming a well-supported clade representing Junewangiaceae.

Many species of Sporidesmiella are found on decaying leaves, wood, bark, dead branches, cane and culms. At present, only three species have been found on submerged wood. Our research provides a new freshwater fungus found on submerged wood for Sporidesmiella and we provide four new sequences data, enriching the molecular database of Sporidesmiella.

As a decomposer, lignicolous freshwater fungi play an important role in freshwater ecosystem and material cycles in nature. They are also important biological resources, which have great application potential. Lignicolous freshwater fungi are a great treasure of resources to be developed. Many unknown species are waiting for us to understand and explore.

Acknowledgements

Funds for research were provided by the National Natural Science Foundation of China (NSFC 32070023 and NSFC 32060014), the Key Projects of Youth Fund of Jiangxi Science and Technology Department of China (20192ACBL21017), Natural Science Foundation of Education Department of Jiangxi Province of China (GJJ190168).

References