Fungi associated with seagrass Enhalus acoroides in Puttalam Lagoon, Sri Lanka: Discovery of two new species (Neodevriesia zeylanica and Neooccultibambusa zeylanica (Dothideomycetes)) and taxonomic validation of Halophilomyces (Sordariomycetes)
Abstract
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
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Figure 10| Species name | Strain/voucher no. | GenBank accession number | ||
|---|---|---|---|---|
| ITS | LSU | |||
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| MUM 19.27T |
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| NA |
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| CPC 19833T |
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| CBS 118285T |
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| CBS 130602T |
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| OUCMBI110119T |
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| OUCMBI101247 |
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| CBS 145064T |
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| NA |
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| CPC 23534T |
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| CBS 145553T |
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| NA |
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| LWHHK-7T |
| NA | NA |
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| CBS 128217T |
| NA | NA |
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| OUCMBI101249T |
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| OUCMBI141254 |
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| CPC 15382T |
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| CAP1371 |
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| CBS 148320 T |
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| CBS 122898T |
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| CPC 14403T |
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| FMR 18825T |
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| NA |
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| NFCCI 4382 |
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| CBS 48137T |
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| CBS 145084T |
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| CCFEE 5672T |
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| SFC20250301-M047T |
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| CPC 25044T |
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| NA |
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| CPC 25086T |
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| NA |
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| CBS 129527T |
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| CCFEE 6202T |
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| PL127 |
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| NA |
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| NA |
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| NA |
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| CBS 149461T |
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| CBS 145568T |
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| NA |
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| CPC 19782T |
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| CCFEE 5681T |
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| CBS 118302 | NA |
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| CPC 19948T |
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| NA |
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| CBS 122379T |
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| CBS 146019T |
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| CBS 145065T |
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| NA |
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| CBS 128219T |
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| NA |
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| NA |
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| Species name | Strain/voucher no. | GenBank accession number | ||||
|---|---|---|---|---|---|---|
| ITS | LSU | SSU | ||||
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| ZHKUCC 23-0664T |
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| ZHKUCC 23-0665 |
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| MFLUCC 17-2070T |
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| MFLUCC 21-0008T |
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| CGMCC 3.20403T |
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| GZCC 21-0185 |
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| CGMCC 3.28689T |
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| NA | NA |
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| GUCC 24-0060T |
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| BRIP 72515d |
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| NA | NA | NA |
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| KUMCC 17-0030T |
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| NA |
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| MFLUCC 20-0016 |
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| X135 |
| NA | NA | NA | NA | |
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| MFLUCC 12-0559T |
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| KUNCC 24-18351T |
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| KUNCC 24-18353 |
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| MFLUCC 16-0643 | NA |
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| CGMCC 3.20404T |
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| GZCC 21-0184 |
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| KUMCC 17-0179T |
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| MFLUCC 16-0274T |
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| CGMCC 3.20405 |
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| GZCC 21-0181 |
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| NA | NA |
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| NA | NA |
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| NA | NA |
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| MFLUCC 17-2061T |
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| MFLUCC 17-2073T |
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| MFLUCC 13-0855T |
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| MFLUCC 16-0380T | NA |
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| MFLUCC 11-0127T |
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| NA |
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| GZCC 16-0117T | NA |
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| HKAS 102151T |
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| GZCC 16-0116T | NA |
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| MFLUCC 11-0502T |
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| NA | NA |
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| CBS 141480 |
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| MGC |
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| NA |
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| MFLUCC 11-0182T |
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| NA |
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| MFLUCC 11-0621T |
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| NA | NA | NA |
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| MFLUCC 11-0179T |
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| MFLU 19-0690T | NA |
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| CBS 138873T |
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| NA | NA | NA |
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| CBS 141481T |
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| TB |
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| NA |
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| TB2 |
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| NA |
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| JCM 14775T |
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| NA | NA |
| Species name | Strain/voucher no. | GenBank accession number | ||
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| ITS | LSU | SSU | ||
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| JF 08139 | NA |
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| NBRC105256 | NA |
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| NBRC105256 | NA |
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| MF819T | NA |
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| FCUL280207CF9 |
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| FCUL170907CP5 |
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| HOMAR1 |
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| HOMAR2 |
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| HOMAR3 |
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| HOMAR4 |
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| AFTOL_ID_413 |
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| JK4322 | NA |
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| KMPB150 | NA |
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| KMPB82 | NA |
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| SUMCC H-08001T | NA |
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| MFLUCC 17-0392T | NA |
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| GR78 | NA |
| NA |
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| PRM 924377 | NA |
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| HPa15 | NA |
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| HPa16 | NA |
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| HPa50 | NA |
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| HPa51 | NANA |
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| TRä3137AT | NA |
| NA |
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| NA |
| NA | |
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| JK4686 |
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| TRä3137A |
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| NTOU3841 | NA |
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| NTOU3847 | NA |
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| Species name | Strain/Voucher No. | GenBank accession number | ||
|---|---|---|---|---|
| ITS | LSU | SSU | ||
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| CBS 125414T |
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| MF46 | NA |
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| NBRC 105256 | NA |
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| MF819T | NA |
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| CCF 3788T |
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| CCF 3787 |
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| HOMAR2T |
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| NBRC 33069 | NA |
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| ATCC 56663T | NA | NA |
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| NBRC 32499 | NA |
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| MF 836T | NA |
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| GR78 | NA |
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| MUT 5430T |
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| MUT 5422T |
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| MUT 435T |
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| CBS 208.64T |
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| NA |
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| MUT 5417T |
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| MUT 5261T |
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| HPa3T |
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| HPa50 |
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| BBH 16759T | NA |
| NA |
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| J.K. 4686 | NA |
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| CBS 153577T |
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| CBS 153576 |
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| CBS 153646 |
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| CBS 153624 |
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| CBS 153625 |
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| NA |
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| NA |
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| FCUL280207CP1 |
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| NBRC 32137T |
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| CMG 65T |
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Taxonomy
TopicsPlant Pathogens and Fungal Diseases · Marine and coastal plant biology · Microbial Natural Products and Biosynthesis
Introduction
Fungi are ubiquitous microorganisms found in a variety of environments, often quite challenging for life (Gostinčar et al. 2023). Marine habitats provide important niches for different groups of fungi and fungus-like taxa (Wijayawardene et al. 2022) and are currently reported to harbor ca. 2,253 species (https://www.marinefungi.org/ fide Jones et al. 2019; accession date 11 November 2025).
Given this situation, fungi from different marine substrates, such as algae, seaweed, seagrasses, and marine sponges, have been characterized both taxonomically and biochemically. On a global scale, many studies are available on seagrass-inhabiting fungal endophytes (e.g., Panno et al. 2013). Rajakaruna et al. (2024) discussed the importance of exploring seagrass-associated fungi, especially in understudied geographical regions, which can be rich in novel taxa that are useful in the pharmaceutical industry. To the best of our knowledge, no previous studies have been conducted in Sri Lanka, a biodiversity-rich country with the potential for high fungal diversity but an understudied geographic location. Since Sri Lanka belongs to the Indo-Pacific bioregion and is considered a biodiversity hotspot, investigating seagrass-associated fungi has the potential to discover new fungi with useful bioactivities.
In this study, we collected Enhalus acoroides (Linnaeus f.) Royle, 1839 samples from three sampling sites in shallow coastal waters of nearby localities near Kalpitiya, Puttalam Lagoon, Sri Lanka. Ten endophytic fungal strains have been isolated from healthy leaves, roots, and rhizomes using the surface sterilization method. According to the BLAST results of ITS sequence data, these strains belong to four different genera: viz., Neodevriesia (in Neodevriesiaceae, Mycosphaerellales) and Neooccultibambusa (in Occultibambusaceae, Pleosporales) in the class Dothideomycetes, and Thalassodendromyces (in Lulworthiaceae, Lulworthiales) and Halophilomyces (in Lulworthiaceae, Lulworthiales) in the class Sordariomycetes. Based on multi-locus phylogenetic analyses, we introduce two new species, i.e., Neodevriesia zeylanica Wijayaw. et al. and Neooccultibambusa zeylanica Wijayaw. et al., and two new country and host records (i.e., Neodevriesia saximollicula D.S. Paiva and Thalassodendromyces purpureus Vohník & Réblová).
Furthermore, two strains are confirmed as Halophilomyces hongkongensis Xiao Wang et al., the type species of Halophilomyces Xiao Wang et al. (Wang et al. 2024). However, Halophilomyces hongkongensis is invalidly published (Art. 40.7), and, being the type, Halophilomyces is also invalid. In this study, we validate Halophilomyces hongkongensis (based on the newly isolated strains) by providing a new name, Halophilomyces zeylanica Wijayaw. et al., and designating a new holotype and ex-type.
Materials and methods
Sample collection
The Enhalus acoroides (L.f.) Royle seagrass plants were collected on two occasions during low tide (23 August and 26 October 2023) from three sampling sites in shallow coastal waters of Puttalam Lagoon (8°08'38.80"N, 79°44'11.86"E; 8°13'09.90"N, 79°45'01.63"E; and 8°14'52.83"N, 79°46'17.80"E). The sampling sites were separated by an average distance of approximately 8.2 km. Enhalus acoroides was identified at the sampling site by its unique, long, ribbon-like leaves; rhizomes covered with fibrous bristles; and cord-like roots (Fig. 1). Three whole plants were collected from each sampling site. All plants were manually uprooted while snorkeling. The collected plants were washed thoroughly at the respective sampling site with seawater to remove debris and brought to the laboratory in plastic containers along with seawater. The lids of the containers were kept open, and the plants were maintained in submerged conditions until processing.
Morphological and reproductive features of Enhalus acoroides. A–C. Growth habit and submerged canopy in the natural habitat; D. Complete shoot with scale; E. Rhizome showing persistent black fibers and roots; F. Opened fruit; G. Female flower; H–I. Mature bristly fruit.
Fungal isolation
In the laboratory, the leaves, roots, and rhizomes of undamaged plants from each sampling site were separated and washed thoroughly with seawater. Before surface sterilization, the tissues were cut into manageable segments. For leaf segments, surface sterilization was carried out according to Devarajan et al. (2002) and Venkatachalam et al. (2015) by rinsing with 70% ethanol for 5 s, immersing in 4% sodium hypochlorite for 60 s, and rinsing with sterile distilled water. Due to the higher microbial load and surface contaminants associated with underground tissues, a modified sterilization protocol was applied for roots and rhizomes, involving rinsing with 70% ethanol for 15 s, immersion in 4% sodium hypochlorite for 60 s, followed by rinsing with sterile distilled water. After surface sterilization, the tissue segments were blotted dry using sterile filter paper. An imprint of each tissue segment was made on the surface of the Potato Dextrose Agar (PDA) plate to verify the efficacy of the surface sterilization protocol. Following the imprint, the edges of each segment were trimmed, and the remaining tissue was divided into six segments. These were plated on 9 cm diameter PDA plates amended with ciprofloxacin (150 mgL^-1^). Another set of tissue segments, similarly surface-sterilized, was plated on PDA prepared using undiluted seawater (filtered through Whatman No. 1 filter paper) collected from the same lagoon.
Cultures were incubated for 45 days at room temperature (29 °C). The culture plates were monitored periodically, and the endophytic fungi growing out from the tissue segments were subcultured onto fresh PDA medium. All resulting isolates were purified using the hyphal tip purification technique (Senanayake et al. 2020). Each isolate was assigned a unique code corresponding to its host tissue (leaf, root, or rhizome), sampling site, and the specific isolation medium used (standard PDA or seawater PDA). Pure cultures were maintained for further morphological and molecular characterization.
Morphological characterization
Mycelial plugs (6 mm) from 7-day-old cultures grown on PDA were transferred to new plates containing PDA, Malt Extract Agar (MEA), PDA prepared using seawater, and Enhalus acoroides-infused medium. The cultures were incubated for 14 days at 25 °C (±1 °C). At the end of the incubation period, photographs of colonies were taken using a Canon EOS REBEL T7 (Canon Inc., Tokyo, Japan). To determine the growth rate, radial growth measurements were taken by averaging the two perpendicular diameters for each colony (Hendricks et al. 2017). The colony characteristics, including color, form, margin, elevation, zonation, and sporulation, were recorded for each medium type.
Slide cultures were prepared to observe microscopic features. The microscopic features of fungal isolates were observed under a Nikon ECLIPSE Ci upright microscope (Nikon, Tokyo, Japan) and a Nikon SMZ18 stereomicroscope (Nikon, Tokyo, Japan), and measurements of microscopic features were made using ImageJ software. At least 30 measurements were taken for each microscopic structure. The illustrated figures were processed using Adobe Photoshop CS6 software (Adobe Systems, San Jose, CA, USA).
Techniques used for sporulation of cultures
To induce sporulation in the fungal isolates, several nutritional and environmental methods were employed. Nutritional stress was applied by subculturing isolates onto half-strength media, specifically 1/2 Potato Dextrose Agar (PDA) and 1/2 Soya-Wheat Agar (SW). To simulate host-specific conditions, E. acoroides tissue extract was incorporated into the media, and sterilized E. acoroides tissue segments were embedded in the agar to serve as a natural lignocellulosic scaffold. Mechanical stimulation was provided via the toothpick method to facilitate mycelial attachment and development of fruiting bodies. Physical stressors included a cold shock treatment at 4 °C for 24 hours and ultraviolet (UV) irradiation for 5 seconds. All cultures were subsequently incubated under a standard 12-hour light/dark cycle and monitored for the development of reproductive structures.
Herbarium specimens (including dried cultures) and living culture depositions
Newly generated cultures were deposited in the culture collection of the University of Colombo (UOCCC) and the Rajarata University Fungal Culture Collection
(RUFCC). Dried cultures were deposited as herbarium specimens in the Rajarata University Fungarium (RUSLH).
Registration of novel taxa
Index Fungorum Registration Identifiers were obtained for the new species and newly validated species, as mentioned in Index Fungorum (2025).
Fungal genomic DNA extraction, PCR amplification, and sequencing
Fresh mycelia were scraped from fungal cultures grown on PDA and transferred into 1.5 mL microcentrifuge tubes. DNA extraction followed a laboratory-developed protocol based on Al-Samarrai and Schmid (2000). Fungal cultures were grown in Potato Dextrose Broth (PDB) at 28 °C for 7 days. The mycelia were harvested by centrifugation to remove excess liquid and homogenized in 500 µL of preheated SDS-containing extraction buffer, followed by incubation at 65 °C. DNA was purified using potassium acetate and chloroform:isoamyl alcohol (24:1) and precipitated with ice-cold isopropanol. The resulting DNA pellets were washed with 70% ethanol, resuspended in TE buffer, and stored at −20 °C. DNA quality and concentration were assessed using 1% agarose gel electrophoresis and a NanoDrop 1000 spectrophotometer. Polymerase chain reaction (PCR) amplifications were performed using the following primer pairs: ITS1F/ITS4 for the internal transcribed spacer region (ITS, including 5.8S rDNA); NS1/NS4 for the nuclear ribosomal small subunit (SSU, 18S rDNA) (White et al. 1990; Gardes and Bruns 1993); and LR0R/LR5 for the nuclear ribosomal large subunit (LSU, 28S rDNA) (Vilgalys and Hester 1990).
The reaction was performed in a final volume of 25 µL DNA template containing 12.5 μL of 2 × GoTaq Green Master Mix (Promega, USA), 2.5 μL of each primer (10 µM), 5.5 μL of nuclease-free water, and 2 μL of genomic DNA template (50 ng/µL). PCR amplifications were carried out using the T100 Thermal Cycler (Bio-Rad, USA) with an initial denaturation step at 94 °C for 5 min, followed by 35 cycles of denaturation at 94 °C for 1 min, annealing for 1 min, and extension at 72 °C for 1 min, with a final extension at 72 °C for 10 min. The annealing temperatures were optimized for each gene locus as follows: ITS, 48 °C; LSU, 48 °C; and SSU, 55 °C. All products were visualized by agarose gel electrophoresis (1% gel, 100 V, 30 min) stained with ethidium bromide. The PCR products were sequenced at Genelabs Medical, Sri Jayawardenepura Kotte, Sri Lanka, and Macrogen Inc., South Korea.
Phylogenetic analyses
Forward and reverse sequences of the newly generated isolates were assembled using BioEdit (Hall 2004). The resulting consensus sequences were submitted to the NCBI database for BLAST searches to identify the closest taxonomic relatives (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch). Additional sequences for the phylogenetic analyses in this study were obtained from recent literature and downloaded from GenBank (https://www.ncbi.nlm.nih.gov/WebSub/?form=history&tool=-genbank). The single-gene sequences were aligned using MAFFT v. 7 (Katoh and Standley 2013) (https://mafft.cbrc.jp/alignment/server), and ambiguous sites were trimmed using trimAl v.1.2rev59 (Capella-Gutiérrez et al. 2009). Subsequently, the trimmed single-gene alignments were merged into a single FASTA file using Matrix 1.9 (Vaidya et al. 2011). Finally, the FASTA format was converted to PHYLIP and NEXUS formats using AliView for the maximum likelihood (ML) and Bayesian inference (BI) analyses, respectively.
Maximum likelihood (ML) analysis was performed using RAxML-HPC2 on XSEDE (v. 8.2.12) via the CIPRES Science Gateway v. 3.3 (http://www.phylo.org/portal2), using the GTRGAMMA substitution model with 1,000 bootstrap replicates (Stamatakis et al. 2008; Stamatakis 2014). Bayesian analyses were conducted using MrBayes 3.2.7a, and the best model for each dataset was evaluated using MrMTgui (Ronquist et al. 2012; Ma 2016). Six simultaneous Markov chains were run for 1 million generations, and trees were sampled every 100^th^ generation. The final trees were visualized in FigTree v. 1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/) (Rambaut 2012) and formatted using Adobe Illustrator CS v. 5. All newly generated sequences were deposited in GenBank, and the sequence alignments and phylogenetic trees were deposited in TreeBASE (Tables 1–4).
Results
Phylogenetic analysis
Multi-gene analyses for Neodevriesia s.str.
A phylogram was generated from an ML analysis of Neodevriesia based on combined ITS, LSU, and rpb2 sequence data of 43 taxa (including the new isolates), which comprised 2569 base pairs (ITS = 538, LSU = 858, and rpb2 = 1171) (TreeBASE Submission ID 32494) (The rpb2 locus was included to improve topology and resolution. A separate analysis of the ITS locus was performed to confirm the topology, which was similar to the multi-locus tree; the single-gene tree is provided as Suppl. material 1). The tree is rooted with Teratosphaeria complicata (CPC14535T). The best-scoring RAxML tree, with a final likelihood value of −12909.069600, is presented. The matrix contained 766 distinct alignment patterns with 46.42% undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.242017, C = 0.256467, G = 0.288928, T = 0.212588; substitution rates: AC = 1.492415, AG = 1.850180, AT = 1.203640, CG = 1.238011, CT = 5.009471, GT = 1.000000; gamma distribution shape parameter α = 0.310960.
In the phylogenetic tree (Fig. 2), our two new strains (UOCCC 251201 and UOCCC 251209) formed a sister clade with Neodevriesia saximollicula (PL127, MUM 2348) with 100% ML and 1.00 BYPP statistical support. Moreover, two other new isolates (UOCCC 251202 and UOCCC 251210) formed a distinct lineage to Neodevriesia shakazului (CPC 19782) with high statistical support (92% ML and 0.99 BYPP).
RAxML tree based on a combined dataset of partial ITS, LSU, and rpb2 DNA sequence analyses. Bootstrap support values for ML ≥ 60% and Bayesian posterior probabilities (BYPP) ≥ 0.9 are shown as ML/BI above the nodes. Type materials are indicated by the superscript “T” while newly generated sequences are shown in red.
Multi-gene analyses for Neooccultibambusa s.str.
A phylogram was generated from an ML analysis (using a concatenated dataset of ITS, LSU, SSU, rpb2, and tef1*-α* regions), which comprised 4374 characters with gaps (ITS = 531, LSU = 865, SSU = 1020, rpb2 = 1004, and tef1*-α* = 950) (TreeBASE Submission ID 32486) (The tef1*-α* locus was included to achieve better topology and resolution, following Hyde et al. (2018). A separate analysis of the ITS locus was carried out to confirm the topology, which was similar to the multi-locus tree. The single-gene tree is provided as Suppl. material 2). Ohleria modesta (CBS 141480, MGC) was used as the outgroup taxon. The best-scoring RAxML tree, with a final likelihood value of −24372.732742, is presented. The matrix had 1482 distinct alignment patterns, with 25.54% undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.246671, C = 0.252028, G = 0.270378, T = 0.230922; substitution rates: AC = 2.086124, AG = 5.211652, AT = 1.764318, CG = 1.722822, CT = 11.447364, GT = 1.000000; gamma distribution shape parameter α = 0.563581.
In the phylogenetic tree (Fig. 3), our new strains (UOCCC 251207, UOCCC 251213, UOCCC 251208, and UOCCC 251214) formed a sister clade with Neooccultibambusa kaiyangensis (CGMCC 3.20404 and GZCC 21-0184), N. chiangraiensis (MFLUCC 12-0559), and N. coffeae (KUNCC 24-18353 and KUNCC 2418351), with 75% ML value support.
RAxML tree based on a combined dataset of partial ITS, LSU, SSU, rpb2, and tef1-α DNA sequence analyses. Bootstrap support values for ML ≥ 60% and Bayesian posterior probabilities (BYPP) ≥ 0.9 are shown as ML/BI above the nodes. Type materials are indicated by the superscript “T” while newly generated sequences are shown in red.
Multi-gene analyses for Halophilomyces s.str.
A phylogram was generated from an ML analysis based on combined ITS, LSU, and SSU sequence data of 37 taxa, which comprised 2457 base pairs (ITS = 534, LSU = 887, and SSU = 1034) (TreeBASE Submission ID 32493). The tree is rooted with Achroceratosphaeria potamia (JF 08139) and Pisorisporium cymbiforme (PRM 924377). The best-scoring RAxML tree, with a final likelihood value of −8938.534084, is presented. The matrix had 628 distinct alignment patterns, with 24.65% undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.250520, C = 0.237936, G = 0.291273, T = 0.220271; substitution rates: AC = 1.442542, AG = 2.593080, AT = 0.854251, CG = 2.008941, CT = 6.565557, GT = 1.000000; gamma distribution shape parameter α = 0.678649.
In the phylogenetic tree (Fig. 4), the new strains (UOCCC 251203 and UOCCC 251211) clustered with Halophilomyces hongkongensis (HOMAR1, HOMAR2, HOMAR3, and HOMAR4) with 100% ML value support.
RAxML tree based on a combined dataset of partial ITS, LSU, and SSU DNA sequence analyses. Bootstrap support values for ML ≥ 60% and Bayesian posterior probabilities (BYPP) ≥ 0.9 are shown as ML/BI above the nodes. Type materials are indicated by the superscript “T” while newly generated sequences are shown in red.
Multi-gene analyses for Thalassodendromyces s.str.
A phylogram was generated from an ML analysis (based on combined ITS, LSU, and SSU sequence data), and 35 strains were included in the sequence analysis, which comprised 3178 characters (ITS = 431, LSU = 879, and SSU = 1343; TreeBASE Submission ID 32490). Achroceratosphaeria potamia (CBS 125414) was used as the outgroup taxon. The tree topology of the ML analysis was similar to that of the BI analysis. The best-scoring RAxML tree, with a final likelihood value of −14387.797340, is presented. The matrix had 945 distinct alignment patterns, with 22.00% undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.241245, C = 0.251235, G = 0.298972, and T = 0.208549; substitution rates: AC = 1.675090, AG = 2.751572, AT = 1.215209, CG = 1.798431, CT = 6.092003, and GT = 1.000000; gamma distribution shape parameter α = 0.736186.
In the phylogenetic tree (Fig. 5), two new isolates (UOCCC 2512006 and UOCCC 251212) clustered with Thalassodendromyces purpureus (CBS 153625, CBS 153577, CBS 153624, CBS 153576, and CBS 153646) with 100% ML and 1.00 BYPP value support.
RAxML tree based on a combined dataset of partial ITS, LSU, and SSU DNA sequence analyses. Bootstrap support values for ML ≥ 60% and Bayesian posterior probabilities (BYPP) ≥ 0.9 are shown as ML/BI above the nodes. Type materials are indicated by the superscript “T” while newly generated sequences are shown in red.
Taxonomy
Dothideomycetes O.E. Erikss. & Winka
Mycosphaerellales P.F. Cannon
Neodevriesiaceae Quaedvl. & Crous
Neodevriesia
Taxon classificationFungiCapnodialesDothideomycetes
Quaedvl. & Crous, Persoonia 33: 24 (2014)
717B61C9-886C-5791-8D24-9B10225D3F1C
Notes.
The genus Neodevriesia was introduced by Quaedvlieg et al. (2014) to accommodate devriesia-like species that are phylogenetically distinct from Devriesia s.str. Currently, the genus comprises 36 species (Species Fungorum 2025; accessed 6 December 2025) and is reported from a broad range of habitats under different ecological conditions (e.g., **1)**N. cladophorae M.M. Wang & W. Li from marine algae (Cladophora sp.) fide Wang et al. 2017; **2)**N. queenslandica (Crous, R.G. Shivas & McTaggart) Crous from leaves of Scaevola taccada), worldwide.
In this study, four strains of Neodevriesia were collected from Enhalus acoroides. Multi-locus phylogenetic analyses confirmed that two strains (UOCCC 251201 and UOCCC 251209) belong to N. saximollicula (Fig. 2). The other two strains formed a distinct lineage within Neodevriesia s.str. in our phylogenetic analysis; thus, we introduce Neodevriesia zeylanica Wijayaw. et al.
Neodevriesia
saximollicula
Taxon classificationFungiCapnodialesDothideomycetes
D.S. Paiva, Fungal Systematics and Evolution 15: 66 (2024)
8D0FEFBE-BC7D-52CB-BD4B-7CF462E857B3
Index Fungorum: IF852927
Culture characteristics.
Colonies on PDA velvety, irregular in shape, convex, reached 14–16 mm diam. after 14 days at 25 °C; grayish black center with black margin in forward view; reverse black. Colonies on Enhalus acoroides-infused PDA looked identical to those observed on PDA, with a slightly decreased radial growth, reaching 11–13 mm at 25 °C in 14 days of incubation.
Neodevriesia saximollicula (UOCCC 251201 and UOCCC 251209). A. Forward and B. Reverse views of colony morphology of two-week-old cultures grown at 25 °C on PDA; C. Forward and D. Reverse views of 14-day-old cultures on seagrass-infused PDA; E–G. Heavily branched, septate hyphae. Scale bars: 50 μm (E–G).
Micromorphology.
Hyphae 1.5–4 μm wide, heavily branched, septate, smooth, hyaline to olivaceous brown; no sporulation observed. Occasionally, thick-walled hyphal knots observed.
Material examined.
Sri Lanka • North Western Province, Puttalam District, Kalpitiya, Puttalam Lagoon, endophytic in healthy leaves of Enhalus acoroides, 23 August 2023, O. Rajakaruna & S. Udagedara, living culture numbers, UOCCC 251201 = UOCCC 251209.
Notes.
Paiva et al. (2025) introduced Neodevriesia saximollicula from stone artworks in Aveiro, Portugal. In their phylogenetic analyses (based on ITS and LSU), Neodevriesia saximollicula formed a separate, monophyletic clade within Neodevriesia s.str. In our phylogenetic analyses based on ITS, LSU, and rpb2 sequence data (Fig. 2), new strains UOCCC 251201 = UOCCC 251209 grouped with MUM 23.48 (ex-type) and PL127 of Neodevriesia saximollicula with high statistical support (100% ML and 1.00 BYPP in BI analyses, respectively). Hence, we identified UOCCC 251201 and UOCCC 251209 as Neodevriesia saximollicula.
To the best of our knowledge, this is the first report of Neodevriesia saximollicula from a marine or aquatic environment, specifically from the leaves of Enhalus acoroides. In addition, this is the first report of the genus Neodevriesia and N. saximollicula from Sri Lanka.
Neodevriesia
zeylanica
Taxon classificationFungiCapnodialesDothideomycetes
Wijayaw., Rajakaruna, L.S. Han & K.G.S.U. Ariyaw. sp. nov.
8FBD72D4-B13C-58F8-A245-CE8D657B9747
Index Fungorum: IF904758
Etymology.
The species epithet ‘zeylanica’ refers to the old name of Sri Lanka, ‘Ceylon.’
Culture characteristics.
Colonies on PDA reached 6 diam. after 14 days at 25 °C, exhibiting extremely slow, uniform radial growth. Colonies were velvety with flat elevation, irregular outline, with undulate margin; grayish black in forward view, dark black in reverse. Colonies on Enhalus acoroides-infused PDA appeared identical to those on standard PDA.
Neodevriesia zeylanica (UOCCC 251202 and UOCCC 251210). A. Forward and B. Reverse views of colony characteristics of two-week-old cultures grown at 25 °C on PDA; C. Sparsely branched, hyaline to pale brown hyphae; D, E. Irregularly branched, chlamydospore-like structures in chains. Scale bars: 50 µm (C–E).
Micromorphology.
Hyphae septate, branched, initially pale brown, differentiating into dark brown, thick-walled moniliform chains composed of globose to ellipsoidal cells constricted at the septa, eventually forming heavily melanized intercalary chlamydospore-like cells in chains, 100–500 μm long, 2–5 μm thick; no conidia observed.
Typification.
Sri Lanka • North Western Province, Puttalam District, Kalpitiya, Puttalam Lagoon, endophytic in healthy leaves of Enhalus acoroides, 23 August 2023, O. Rajakaruna & S. Udagedara, En71 (holotypeRUSLH/247, dried culture; ex-typeUOCCC 251202).
Additional material examined.
Sri Lanka • North Western Province, Puttalam District, Kalpitiya, Puttalam Lagoon, endophytic in healthy leaves of Enhalus acoroides, 23 August 2023, O. Rajakaruna & S. Udagedara, En71, living culture, En71a = UOCCC 251210.
Notes.
In the phylogenetic tree, the new isolates clustered with Neodevriesia shakazului (CPC 19782, ex-type) with high statistical support (92% ML and 0.99 BYPP in Bayesian analyses, respectively). Based on pairwise nucleotide comparisons, UOCCC 251202 and UOCCC 251210 diverged from Neodevriesia shakazului (CPC 19782, ex-type) by 19/533 bp (3.5%) in ITS and 15/827 bp (1.8%) in LSU. Our isolates failed to sporulate, except for some chlamydospore-like cells in linear chains. Although different techniques were used (see Materials and methods), we were unable to compare the microscopic morphological characteristics. Hence, based on the phylogenetic analyses (Fig. 2) and base pair differences, we introduce our isolates as a new species in Neodevriesia s.str., namely N. zeylanica.
Pleosporales Luttr. ex M.E. Barr
Occultibambusaceae D.Q. Dai & K.D. Hyde
Neooccultibambusa
Taxon classificationFungiPleosporalesOccultibambusaceae
Doilom & K.D. Hyde, Fungal Diversity 82: 126 (2016) [2017]
7CEF10EC-2BFF-5AE0-B8D6-946DC27BE6F0
Notes.
The genus Neooccultibambusa was introduced by Doilom et al. (2017) from dead culms of Bambusoideae in Thailand, with a sexual morph (cylindrical to subcylindrical unitunicate asci and fusiform ascospores with 1–3 transverse septa) and chlamydospores forming in culture. Later, the genus was reported with hyphomycetous asexual morphs (Hyde et al. 2018). Currently, the genus comprises seven species and has been reported from China (Guizhou and Yunnan Provinces), Italy, and Thailand (Jayasiri et al. 2016; Hyde et al. 2018; Yu et al. 2021; Lu et al. 2025). In this study, we collected two strains of Neooccultibambusa from Enhalus acoroides; multi-locus phylogenetic studies confirmed that these strains represent a novel species. Hence, we introduce Neooccultibambusa zeylanica.
Neooccultibambusa
zeylanica
Taxon classificationFungiPleosporalesOccultibambusaceae
Wijayaw., Rajakaruna, L.S. Han & K.G.S.U. Ariyaw. sp. nov.
7BDC355E-C750-531A-9970-8B4A281D9290
Index Fungorum: IF904759
Etymology.
The species epithet ‘zeylanica’ refers to the old name of Sri Lanka, ‘Ceylon.’
Culture characteristics.
Colonies on PDA velvety, circular with an undulate margin, raised, umbonate, attaining 16 mm diam. after 14 days at 25 °C; surface grey at center, white toward margin; reverse black. Colonies on Enhalus acoroides-infused PDA are similar.
Neooccultibambusa zeylanica (UOCCC 251207 and UOCCC 251213). A. Forward and B. Reverse views of colony morphology of two-week-old cultures grown at 25 °C on PDA; C. Microscopic features observed from 14-day-old cultures illustrating loosely interwoven, sparsely branched, hyaline to pale brown hyphae; D. Long, thin, septate hyphae; E. Irregularly branched, septate hyphae with chlamydospore-like cells with thickened, smooth cell walls. Scale bars: 100 µm (C); 50 µm (D, E).
Micromorphology.
Hyphae 1–2 μm wide, profusely branched, septate, smooth-walled, with globose to subglobose or irregular, intercalary, chlamydospore-like structures, 5–30 × 2–5 μm (x̄ = 18 × 3.5 μm diam., n = 30), smooth-walled cells, hyaline to olivaceous.
Typification.
Sri Lanka • North Western Province, Puttalam District, Kalpitiya, Puttalam Lagoon, endophytic in healthy leaves of Enhalus acoroides, 23 August 2023, O. Rajakaruna & S. Udagedara, En 42 (holotypeRUSLH/248, dried culture; ex-typeUOCCC 251207).
Additional material examined.
Sri Lanka • North Western Province, Puttalam District, Kalpitiya, Puttalam Lagoon, endophytic of healthy leaves of Enhalus acoroides, 23 August 2023, O. Rajakaruna & S. Udagedara, En 42, living culture En 42a = UOCCC 251213; Ibid., living culture En 54a = En 54.
Notes.
Our new strains of Neooccultibambusa are accommodated within Neooccultibambusa s.str. as a separate clade (Fig. 3), thus introducing Neooccultibambusa zeylanica sp. nov. here. Neooccultibambusa zeylanica cultures failed to produce any defined microscopic spore-like structures in culture, although different techniques were used for sporulation. Hence, we could not compare its morphological characteristics with those of other members of the genus. Therefore, the introduction of this novel taxon is based solely on molecular differences between the ex-type of the new species and its closely related species.
Sordariomycetes O.E. Erikss. & Winka
Lulworthiales Kohlm., Spatafora & Volkm.-Kohlm.
Lulworthiaceae Kohlm., Spatafora & Volkm.-Kohlm.
Halophilomyces
Taxon classificationFungiPleosporalesLulworthiaceae
Xiao Wang, L. Pecoraro & H.B. Liu ex Wijayaw. & P.M. Kirk
D699A0FD-6E0F-5F26-8428-DB951E54E725
Index Fungorum: IF904724
***=***Halophilomyces Xiao Wang, L. Pecoraro & H.B. Liu, J. Fungi 10 (7, no. 474): 10 (2024) (Nom. Inval. Art. 40.7); Index Fungorum Registration Identifier IF854689.
Type species.
Halophilomyces zeylanica Wijayaw., Rajakaruna, D.J. Bhat, P.M. Kirk & K.G.S.U. Ariyaw., sp. nov.
Endophytic on seagrass species Halophila ovalis and Enhalus acoroides. Hyphae with abundant loop-like structures. Chlamydospores in basipetal chains. Conidia generally increasing in size from base to apex. Solitary conidia present, 1–4-septate, deeply constricted at septa, coiled to spiral, dark brown, smooth-walled (Wang et al. 2024; this study).
Notes.
Wang et al. (2024) introduced Halophilomyces (type species: H. hongkongensis) from the roots and rhizomes of Halophila ovalis (Hydrocharitaceae), a seagrass species in Hong Kong, China. However, H. hongkongensis (the type species of Halophilomyces) is invalid (Art. 40.7 (Shenzhen)); thus, the genus is correspondingly invalid.
In this study, we isolated H. hongkongensis from healthy leaves of Enhalus acoroides. Morphologically, the new isolates resemble the original description (as in Wang et al. 2024) and phylogenetically reside in the same clade as H. hongkongensis (Fig. 4).
Halophilomyces
zeylanica
Taxon classificationFungiPleosporalesLulworthiaceae
Wijayaw., Rajakaruna, D.J. Bhat, P.M. Kirk & K.G.S.U. Ariyaw. sp. nov.
BF288BC9-FB01-5968-84E8-7F89D291FECB
Index Fungorum: IF904723
= Halophilomyces hongkongensis Xiao Wang, L. Pecoraro & H.B. Liu, J. Fungi 10 (7, no. 474): 10 (2024) (Nom. inval., Art. 40.7 (Shenzhen)); Index Fungorum Registration Identifier IF854690.
Etymology.
The species epithet ‘zeylanica’ refers to the old name of Sri Lanka, ‘Ceylon.’
Culture characteristics.
Surface cottony, filamentous, round in shape with raised margin. Colonies cultured on PDA reaching 52–55 mm diam. at 25 °C after 14 days, forming dense areal mycelium with partly submerged hyphae, white to olive at center; white at edges in forward view; reverse black with white margin.
Micromorphology.
Mycelium partly superficial, partly immersed, composed of 3.3–3.9 μm wide, septate, branched, pale brown to olivaceous brown, smooth hyphae, with abundant hyphal loops. Conidiophores reduced to conidiogenous cells. Conidiogenous cells micronematous to semi-macronematous, holoblastic. Conidia acrogenous, solitary to catenate, 1–4-septate, deeply constricted at septa, coiled to spiral when in chains, dark brown, smooth-walled, 24–54 μm diam. (x̄ = 32.2 diam., n = 30), globose to subglobose, with apical cell 14–25 µm, basal cell 9–22 µm. Single-celled conidia 9–30 μm diam. (x̄ = 22.1 μm diam., n = 30), present, rarely found; Chlamydospores in chains, 5–8-celled, intercalary in hyphae, with cells ellipsoidal to globose, 14–21 μm diam., olivaceous brown, smooth.
Halophilomyces zeylanica (UOCCC 251203 and UOCCC 251211). A. Submerged leaf canopy of Enhalus acoroides; B. Forward; C. Reverse views of colony morphology of two-week-old cultures grown at 25 °C on PDA; D. Overall view of the mycelia; E. Branched, septate hyphae; F–H. Multicellular mature conidia; I. Single-cell mature conidia; J. Loop structures formed by the hyphae; K, L. Multicellular chlamydospores. Scale bars: 50 μm (C–K).
Typification.
Sri Lanka • North Western Province, Puttalam District, Kalpitiya, Puttalam Lagoon, endophytic in healthy leaves of Enhalus acoroides, 23 August 2023, O. Rajakaruna & S. Udagedara (holotypeRUSLH/249, dried culture; ex-typeUOCCC 251203).
Additional material examined.
Sri Lanka • North Western Province, Puttalam District, Kalpitiya, Puttalam Lagoon, endophytic in healthy leaves of Enhalus acoroides, 23 August 2023, O. Rajakaruna & S. Udagedara, living culture EN 39a = UOCCC 251211.
Notes.
Phylogenetically, the new collections (UOCCC 251203 and UOCCC 251211) formed a sister clade with Halophilomyces hongkongensis (HOMAR1, HOMAR2, HOMAR3, and HOMAR4) with 100% ML support. The new isolates have only four base pair differences in the ITS locus compared to the ex-type of H. hongkongensis and no differences in the LSU and SSU loci. Conidial dimensions of the new collections resemble those described in Wang et al. (2024). Hence, we confirm that our new strains belong to Halophilomyces hongkongensis (Fig. 4).
Wang et al. (2024), in the original publication that introduced Halophilomyces and H. hongkongensis, did not designate a holotype for the type species; thus, both the type species and the genus are invalid (Art. 40.1 (Index Fungorum 2025). Here, we designate our new collection (the dried culture) as the new holotype RUSLH/249 and deposit a new living culture (UOCCC 251203) as the ex-type. Thus, we validate the genus with a new Index Fungorum Registration Identifier and provide a new name for Halophilomyces hongkongensis, namely Halophilomyces zeylanica, with a new Index Fungorum Registration Identifier.
Thalassodendromyces
Taxon classificationFungiPleosporalesLulworthiaceae
Vohník & Réblová, IMA Fungus 16 (e157688): 22 (2025)
0D0E6369-ECAF-5D48-9602-894CAC7BB9BF
Notes.
Réblová et al. (2025) introduced Thalassodendromyces purpureus (the type species of Thalassodendromyces) from surface-sterilized roots of the seagrass Thalassodendron ciliatum from Mauritius.
Thalassodendromyces
purpureus
Taxon classificationFungiPleosporalesLulworthiaceae
Vohník & Réblová, IMA Fungus 16 (e157688): 22 (2025)
ECF72D09-F356-5C06-BD40-9B7964A8D972
Index Fungorum: IF858635
Culture characteristics.
Filamentous, flat, filiform in margin, with colonies on seawater-supplemented PDA attaining 60–63 mm diam. after 14 days at 25 °C, with no growth observed on Enhalus acoroides extract-amended PDA or standard PDA after 30 days at 25 °C (three replicates), partly superficial and partly submerged, olivaceous brown center, lighter at the edges in forward view; reverse olivaceous with lighter margin.
Thalassodendromyces purpureus (UOCCC 251206 and UOCCC 251212). A. Rhizome of Enhalus acoroides; B. Forward; C. Reverse views of colony morphology of two-week-old cultures at 25 °C on seawater-supplemented PDA; D, E. Two-week-old colonies on seagrass-infused PDA showing no growth; F. Branched, septate hyphae; G, H. Young chlamydospores in chains; I. Mature chlamydospores in chains. Scale bars: 50 μm (F–I).
Micromorphology.
Hyphae 5–6 μm wide, septate, smooth, olivaceous to brown, chlamydospores in chains, cells ellipsoidal, brown in color. The length of the chlamydospores varies between 13–30 × 7–14 μm (x̄ = 21.2 × 10.8 µm, n = 10).
Material examined.
Sri Lanka • North Western Province, Puttalam District, Kalpitiya, Puttalam Lagoon, endophytic in healthy rhizomes of Enhalus acoroides, 23 August 2023, O. Rajakaruna & S. Udagedara, living cultures, En13 = UOCCC 251206, UOCCC 251212.
Notes.
Our new strains (UOCCC 2512006 and UOCCC 251212) cluster with the ex-type of Thalassodendromyces purpureus (CBS 153577) and other putative strains with high statistical support (Fig. 5). In the original description, Réblová et al. (2025) did not observe chlamydospores or any other microscopic characteristics. However, our newly isolated strains produced chlamydospores in chains on seawater-supplemented PDA, but no growth was observed on standard PDA.
To our knowledge, this is the first report of Thalassodendromyces purpureus from Enhalus acoroides and the first record of both the genus and species from Sri Lanka.
Discussion
Seagrasses are a group of flowering plants that have fully adapted to a submerged lifestyle and are reported from shallow marine waters (Hemminga and Duarte 2000; Larkum et al. 2006, 2018). They have been reported as monospecific or multispecific meadows and spread over a larger surface area, covering the seabed (Duarte 2001; Short et al. 2016). The mycobiome associated with different seagrass species has been explored in different studies (e.g., Ettinger and Eisen 2019; Hurtado-McCormick et al. 2019), but further studies based on modern screening techniques (such as high-throughput sequencing) are essential to understand fungal diversity, particularly from biodiversity-rich, understudied regions such as the Sri Lankan seas (Rajakaruna et al. 2024).
Sri Lanka is a biodiversity-rich country, yet its marine fungal diversity remains poorly documented (Wijayawardene et al. 2023). In this study, we selected Enhalus acoroides, a common seagrass species in the Kalpitiya Lagoon, Puttalam District, Sri Lanka, to recover culturable filamentous fungi. In total, ten different endophytic strains were isolated from healthy leaves, roots, and rhizomes using the surface sterilization method.
Four strains were identified as members of Neodevriesia s.str., and multilocus phylogenetic analyses confirmed that they represent two different species. Neodevriesia saximollicula was identified as a first report from Enhalus acoroides in Sri Lanka. Originally, Neodevriesia saximollicula was reported from a terrestrial habitat; therefore, this is the first report of this species from a marine habitat. Neodevriesia zeylanica was introduced to accommodate two other strains of Neodevriesia s.str., which formed a distinct clade in the phylogenetic analyses. Previously, four members of Neodevriesia s.str., viz., N. aestuarina (from Ria de Aveiro in Portugal fide Crous et al. 2020), N. grateloupiae (from marine algae in China fide Wang et al. 2017), and N. manglicola Devadatha et al. (from mangroves fide Yuan et al. 2020), were isolated from marine environments. Herein, we report two more species of Neodevriesia (i.e., Neodevriesia saximollicula and N. zeylanica) from marine habitats, of which N. zeylanica is new to science. Furthermore, this is the first report of the genus Neodevriesia from Sri Lanka.
In this study, we also introduce a new member of Neooccultibambusa s.str., i.e., N. zeylanica, from Enhalus acoroides in Sri Lanka. Members of Neooccultibambusa have been predominantly reported from terrestrial habitats (e.g., Doilom et al. 2017; Lu et al. 2025). Hence, this is the first report of a member of this genus from an aquatic habitat, particularly from a marine environment. Moreover, this is the first report of the genus from Enhalus acoroides (thus a new host record) and a new record from Sri Lanka (a new geographical record).
The genus Halophilomyces was introduced by Wang et al. (2024) with Halophilomyces hongkongensis as the type species. We isolated two strains of Halophilomyces hongkongensis in this study, and both strains were phylogenetically and morphologically confirmed. However, Wang et al. (2024) did not designate a type specimen for Halophilomyces hongkongensis; therefore, the species remained invalid. The generic name is also regarded as invalid because its type species is invalid (Index Fungorum 2025). Since the new strains are identical to Halophilomyces hongkongensis, we designated the dried culture as the holotype and provided a new name, H. zeylanica. Consequently, H. hongkongensis becomes a synonym of H. zeylanica. The new name was registered in Index Fungorum and obtained a new identifier. Since the type species is validly published here, the genus also becomes valid. We registered the name Halophilomyces Xiao Wang, L.Pecoraro & H.B.Liu ex Wijayaw. & P.M.Kirk in Index Fungorum and obtained a new identifier.
In this study, we isolated Thalassodendromyces purpureus (the type species of Thalassodendromyces fideRéblová et al. 2025) from Enhalus acoroides in Sri Lanka. The genus is monotypic and has only been reported from the roots of the seagrass Thalassodendron ciliatum in Mauritius. As far as we know, this is the first report of Thalassodendromyces purpureus from Enhalus acoroides (a new host record) and from Sri Lanka (a new country record).
This study confirms that the underexplored Sri Lankan marine habitats are rich in fungal diversity. All the species we isolated were slow growers and thus highly susceptible to contamination by common fungal epiphytes (such as Aspergillus spp. and Penicillium spp.) and bacteria. Hence, future studies should be planned using highly selective media (Réblová et al. 2025). Furthermore, it is necessary to focus on identifying unculturable fungi from the mycobiome of seagrasses in understudied regions such as Sri Lanka.
Supplementary Material
XML Treatment for Neodevriesia
XML Treatment for Neodevriesia saximollicula
XML Treatment for Neodevriesia zeylanica
XML Treatment for Neooccultibambusa
XML Treatment for Neooccultibambusa zeylanica
XML Treatment for Halophilomyces
XML Treatment for Halophilomyces zeylanica
XML Treatment for Thalassodendromyces
XML Treatment for Thalassodendromyces purpureus
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