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. 2021 Oct 15;11(10):1093. doi: 10.3390/life11101093

Cryptic Diversity of Isaria-like Species in Guizhou, China

Wanhao Chen 1, Jiandong Liang 1, Xiuxiu Ren 1,2, Jiehong Zhao 1, Yanfeng Han 3,*, Zongqi Liang 3
Editors: Armin Mešić, Ivana Kušan
PMCID: PMC8539930  PMID: 34685462

Abstract

Many Isaria-like species have recently been moved into more appropriate genera. However, more robust molecular phylogenetic analyses are still required for Isaria-like fungi to ensure accurate taxonomic identification. We analyzed these Isaria-like strains using multi-gene phylogenetics. Cryptic diversity was discovered in several Isaria farinosa strains, and two new species, Samsoniella pseudogunnii and S. pupicola, are proposed. Our results reveal that more attention needs to be paid to cryptic intraspecific diversity across different isolates and genotypes of the Isaria-like species, some of which will need to be transferred to Samsoniella. Interestingly, S. hepiali, with a very broad host distribution, has been widely used as a medicinal and edible cordycipitoid fungus.

Keywords: cryptic diversity, intraspecific, Isaria-like, multi-gene analysis

1. Introduction

The genus Isaria was originally establish based on the species Isaria terrestris Fr. [1]. Brown and Smith [2] transferred some species described in Isaria Pers. and Spicaria Harting into Paecilomyces, which possess a conidiogenous structure similar to that of Paecilomyces variotii Bainier. de Hoog [3] redescribed the genus Isaria and chose Isaria felina (DC.) Fr. as the lectotype. Typical characteristics include denticulate conidiogenous cells without elongation that arise in clusters from subtending cells or are solitarily from undifferentiated hyphae; mostly present synnemata; and globose, ellipsoidal, or subcylindrical conidia, mostly with a rounded base [3]. Samson [4] divided the genus Paecilomyces into two sections and all entomogenous species were placed in the section Isarioidea. Hodge et al. [5] reintroduced the genus Isaria with the type species Isaria farinosa (Holmsk.) Fr. and most entomopathogenic mesophilic Paecilomyces species were transferred to Isaria (Hypocreales, Clavicipitaceae) [6,7,8].

Kepler et al. [9] proposed the rejection of Isaria in favor of Cordyceps and transferred Isaria species into Cordyceps. Mongkolsamrit et al. [10] introduced some Isaria-like species and the new genus Samsoniella Mongkols., Noisrip., Thanakitp., Spatafora, and Luangsa-ard. Chen et al. [11,12] reported four Isaria-like species: Akanthomyces araneogenus Z.Q. Liang, W.H. Chen, and Y.F. Han; Samsoniella coleopterorum W.H. Chen, Y.F. Han, and Z.Q. Liang; Samsoniella hymenopterorum W.H. Chen, Y.F. Han, and Z.Q. Liang; and Samsoniella lepidopterorum W.H. Chen, Y.F. Han, and Z.Q. Liang. Currently, many species previously placed in the genus Isaria have been transferred to more appropriate genera. However, robust molecular phylogenetic analyses are still needed for Isaria-like fungi to ensure accurate taxonomic identification with comparable results across different isolates and genotypes [10].

We previously collected many Isaria-like morphs of invertebrate-pathogenic fungi from Guizhou Province, China. Some demonstrated close phylogenetic relationships with Isaria farinosa (Holmsk.) Fr. based on the analysis of associated ITS sequences. In the present study, we applied multi-gene (ITS, LSU, RPB1, RPB2, TEF) phylogenetic analysis to reevaluate the taxonomic position of these strains, as well as the cryptic diversity among the different isolates of I. farinosa, and to describe new taxa to accommodate the cryptic diversity of Isaria-like fungi.

2. Materials and Methods

2.1. Fungal Materials and Identification

The strains used in this study were isolated from infected insect and spider specimens collected in different areas of Guizhou Province, China, including Dali Forest in Rongjiang County, Yaorenshan National Forest Park in Sandu County, Mount Fanjing in Yinjiang County, Tongmuling in Guiyang City, and Doupengshan in Duyun City. Isolation of strains was conducted as described by Chen et al. [13]. Fungal colonies emerging from specimens were isolated and cultured at 25 °C for 14 days under 12 h light/12 h dark conditions following protocols described by Zou et al. [14]. Accordingly, the living isolates were obtained. The specimens and the isolated strains were deposited in the Institute of Fungus Resources, Guizhou University (formally Herbarium of Guizhou Agricultural College; code, GZAC), Guiyang City, Guizhou, China.

Macroscopic and microscopic morphological characteristics of the fungal isolates were examined, especially for the arrangement, shape, and measurement of phialides and conidia, and also the growth rates of cultures incubated at 25 °C for 14 days were determined in Potato Dextrose Agar (PDA) (Potato powder 6%, Agar 20%, Glucose 20%, Beijing Solarbio Technology Co., Ltd., China). Hyphae and conidiogenous structures were mounted in lactophenol cotton blue or 20% lactate solution and observed with an optical microscope (OM, DM4 B, Leica, Germany).

2.2. DNA Extraction, Polymerase Chain Reaction Amplification and Nucleotide Sequencing

DNA extraction was carried out with a fungal genomic DNA extraction kit (DP2033, BioTeke Corporation) in accordance with Liang et al. [15]. The extracted DNA was stored at −20 °C. The amplification of the internal transcribed spacer (ITS) region, the large subunit ribosomal RNA (LSU) gene, the RNA polymerase II largest subunit 1 (RPB1), the RNA polymerase II largest subunit 2 (RPB2), and the translation elongation factor 1 alpha (TEF) by PCR was described by White et al. [16], Rakotonirainy et al. [17], Castlebury et al. [18], and van den Brink et al. [19], respectively. PCR reactions for five loci of all strains were performed in a total volume of 25 μL containing 12.5 μL 2× PowerTaq PCR Master Mix (Tiangen Biotech (Beijing) Co., LTD, China), 1 μL of each primer (10 μM), 1 μL of genomic DNA (20–100 ng), and 9.5 μL of sterile water. Primer sequence information is shown in Table 1. PCR products were purified and sequenced at Sangon Biotech (Shanghai) Co. The resulting sequences were submitted to GenBank (the accession number is shown in Table 2).

Table 1.

Primers information for 5-locus DNA sequences.

Name Length Direction Sequence 5′-3′ Optimised PCR Protocols References
ITS ITS5 22 forward GGAAGTAAAAGTCGTAACAAGG (95 °C: 30 s, 51 °C: 50 s, 72 °C: 45 s) × 33 cycles [16]
ITS4 20 reverse TCCTCCGCTTATTGATATGC
LSU LROR 17 forward ACCCGCTGAACTTAAGC (94 °C: 30 s, 51 °C: 1 min, 72 °C: 2 min) × 33 cycles [17]
LR5 17 reverse TCCTGAGGGAAACTTCG
RPB1 CRPB1 20 forward CAYCCWGGYTTYATCAAGAA (94 °C: 30 s, 55 °C: 30 s, 72 °C: 1 min) × 33 cycles [18]
RPB1Cr 23 reverse CCNGCDATNTCRTTRTCCATRTA
RPB2 RPB2-5F3 20 forward GACGACCGTGATCACTTTGG (94 °C: 30 s, 54 °C: 40 s, 72 °C: 1 min 20 s) × 33 cycles [19]
RPB2-7Cr2 20 reverse CCCATGGCCTGTTTGCCCAT
TEF 983F 23 forward GCYCCYGGHCAYCGTGAYTTYAT (94 °C: 30 s, 58 °C: 1 min 20 s, 72 °C: 1 min) × 33 cycles [19]
2218R 23 reverse ATGACACCRACRGCRACRGTYTG

Table 2.

List of strains and GenBank accession numbers of sequences used in this study.

Species Strain No. Host/ Substratum GenBank Accession No.
ITS LSU RPB1 RPB2 TEF
Akanthomyces aculeatus HUA 772 Lepidoptera; Sphingidae - KC519370 - - KC519366
A. attenuates CBS 402.78 Leaf litter (Acer saccharum) - AF339565 EF468888 EF468935 EF468782
A. coccidioperitheciatus NHJ 6709 Araneae (Spider) - EU369042 EU369067 - EU369025
A. farinosa CBS 541.81 - AY624180 MF416553 MF416655 MF416449 JQ425686
A. tuberculatus BCC 16819 Lepidoptera (Adult moth) - GQ249987 - - GQ250037
A. tuberculatus OSC 111002 Lepidoptera - DQ518767 DQ522384 - DQ522338
Ascopolyporus polychrous P.C. 546 Plant - DQ118737 DQ127236 - DQ118745
A. villosus ARSEF 6355 Plant - AY886544 DQ127241 - DQ118750
Beauveria bassiana ARSEF 1564 Lepidoptera; Arctiidae - - HQ880833 HQ880905 HQ880974
B. brongniartii ARSEF 617 Coleoptera; Scarabaeidae - AB027381 HQ880854 HQ880926 HQ880991
B. brongniartii BCC 16585 Coleoptera (Anomala cuprea) JN049867 JF415967 JN049885 JF415991 JF416009
B. caledonica ARSEF 2567 Soil - AF339520 HQ880889 HQ880961 EF469057
Bionectria ochroleuca AFTOL-ID187 - - DQ862027 - DQ862013 DQ862029
B. vericulosa HMAS 183151 Plant HM050304 HM050302 - - -
Blackwellomyces cardinalis OSC 93609 Lepidoptera; Tineidae (Larva) - AY184962 DQ522370 - DQ522325
B. cardinalis OSC 93610 Lepidoptera; Tineidae (Larva) - AY184963 EF469088 - EF469059
B. pseudomilitaris NBRC 101409 Lepidoptera (Larva) - JN941393 JN992482 - -
B. pseudomilitaris NBRC 101410 Lepidoptera (Larva) - JN941394 JN992481 - -
Calcarisporium arbuscula CBS 221.73 - AY271809 - - - -
C. arbuscula CBS 900.68 Hymenomycetes (Agarics sp.) KT945003 KX442598 - KX442597 KX442596
C. cordycipiticola CGMCC 3.17904 Cordycipitaceae (Cordyceps militaris) KT945001 KX442604 - KX442607 KX442605
C. cordycipiticola CGMCC 3.17905 Cordycipitaceae (Cordyceps militaris) KT944999 KX442599 - KX442594 KX442593
C. xylariicola HMAS 276836 Xylariaceae (Xylaria sp.) KX442603 KX442601 - KX442606 KX442595
Calonectria ilicicola CBS 190.50 Plant GQ280605 GQ280727 - KM232307 AY725726
Cephalosporium curtipes CBS 154.61 Uredinales (Hemileia vastatrix) AJ292404 AF339548 - EF468947 EF468802
Claviceps fusiformis ATCC 26019 Poaceae JN049817 - - - DQ522320
Clonostachys rosea GJS 90-227 Plant - AY489716 - - AY489611
Cocoonihabitus sinensis HMAS 254523 Saturniidae (Cocoon) KY924870 KY924869 - - -
C. sinensis HMAS 254524 Saturniidae (Cocoon) MF687395 MF687396 - - -
Cordyceps amoene-rosea CBS 107.73 Coleoptera (Pupa) MH860646 MH872342 MF416651 - -
C. bifusispora EFCC 5690 Lepidoptera (Pupa) - EF468806 EF468854 EF468909 EF468746
C. cateniannulata CBS 152.83 Coleoptera (Adult) NR_111169 NG_067333 - - -
C. cateniobliqua CBS 153.83 Lepidoptera (Adoxophyesprivatana) NR_111170 - - - JQ425688
C. cf. farinosa OSC 111004 Lepidoptera (Pupa) - EF468840 EF468886 - EF468780
C. coleopterorum CBS 110.73 Coleoptera (Larva) AY624177 JF415988 JN049903 JF416006 JF416028
C. farinosa CBS 111113 - - MF416554 MF416656 MF416450 MF416499
C. fumosorosea CBS 107.10 - - MF416556 MF416659 MF416453 MF416502
C. militaris OSC 93623 Lepidoptera (Pupa) - AY184966 DQ522377 AY545732 DQ522332
Dactylonectria alcacerensis CBS 129087 Plant (Vitis vinifera) JF735333 KM231629 - - JF735819
Elaphocordyceps ophioglossoides NBRC106332 - JN943322 JN941409 - - -
E. paradoxa NBRC 106958 - JN943324 JN941411 - - -
Engyodontium aranearum CBS 309.85 Araneae (Spider) - AF339526 DQ522387 DQ522439 DQ522341
Epichloë typhina ATCC 56429 Poaceae (Festuca rubra) JN049832 U17396 - DQ522440 AF543777
Flammocladiella aceris CPC 24422 Plant (Acer platanoides) KR611883 KR611901 - - -
Flavocillium bifurcatum YFCC 6101 Noctuidae (Larva) - MN576781 MN576841 MN576897 MN576951
Fusarium circinatum CBS 405.97 - U61677 - - JX171623 KM231943
F. subluratum CBS 189.34 Soil HQ897830 KM231680 - - -
Gelasinospora tetrasperma AFTOL-ID 1287 - - DQ470980 - DQ470932 DQ471103
Gibellula longispora NHJ 12014 Araneae (Spider) - - EU369055 - EU369017
G. pulchra NHJ 10808 Araneae (Spider) - EU369035 EU369056 - EU369018
G. ratticaudata ARSEF 1915 Araneae (Spider) - DQ518777 DQ522408 - DQ522360
Haptocillium sinense CBS 567.95 Nematode AJ292417 AF339545 - - -
Harposporium harposporiferum ARSEF 5472 - - NG_060621 - - -
Hevansia arachnophile NHJ 10469 Araneae (Spider) - EU369031 EU369047 - EU369008
H. cinerea NHJ 3510 Araneae (Spider) - - EU369048 - EU369009
H. nelumboides BCC 41864 Araneae (Spider) JN201871 JN201873 - - JN201867
H. novoguineensis NHJ 11923 Araneae (Spider) - EU369032 EU369052 - EU369013
Hyperdermium pulvinatum P.C. 602 Hemiptera (Scale insect) - DQ118738 DQ127237 - DQ118746
Hydropisphaera erubescens ATCC 36093 - - AF193230 - AY545731 DQ518174
H. peziza GJS 92-101 Plant (Bark) - AY489730 - - AY489625
Hypocrea americana AFTOL-ID 52 - DQ491488 AY544649 - - DQ471043
H. lutea ATCC 208838 On decorticated conifer wood - AF543791 - DQ522446 AF543781
H. rufa DAOM JBT1003 - JN942883 JN938865
H. discoidea BCC 8237 - JN049840 DQ384937 - DQ452461 DQ384977
Hypomyces polyporinus ATCC 76479 - - AF543793 - - AF543784
Isaria farinosa CEP 004 Soil JN998783 - - - JN998763
I. farinosa CEP 005 Soil JN998784 - - - JN998764
I. farinosa CEP 029 Trialeurodes vaporariorum JN998785 - - - JN998765
I. farinosa OSC 111005 Lepidoptera (Pupa) - DQ518772 DQ522394 - DQ522348
I. farinosa OSC 111006 Lepidoptera (Pupa) - EF469080 EF469094 - EF469065
I. farinosa OSC 111007 Lepidoptera (Pupa) - DQ518773 DQ522395 DQ522449 DQ522349
Lecanicillium antillanum CBS 350.85 Hymenomycetes (Agaric sp.) - AF339536 DQ522396 DQ522450 DQ522350
L. attenuatum CBS 402.78 Leaf litter of Acer saccharum - AF339565 EF468888 EF468935 EF468782
L. aranearum CBS 726.73a Arachnida (Spider) - AF339537 EF468887 EF468934 EF468781
L. fusisporum CBS 164.70 Hymenomycetes (Coltricia perennis) - AF339549 EF468889 - EF468783
L. psalliotae CBS 367.86 Puccinia graminis - KM283800 - - KM283823
L. lecanii CBS101247 Hemiptera (Coccus viridis) JN049836 KM283794 - KM283859 DQ522359
Leptobacillium chinense LC 1345 submerged wood - JQ410322 - - -
L. coffeanum CDA 734 Plant (Coffea arabica) - MF066032 - - -
Liangia sinensis YFCC 3103 Fungi (Beauveria yunnanensis) - MN576782 MN576842 MN576898 MN576952
L. sinensis YFCC 3104 Fungi (Beauveria yunnanensis) - MN576783 MN576843 MN576899 MN576953
Metapochonia goniodes CBS 891.72 Fungi AJ292409 AF339550 DQ522401 DQ522458 DQ522354
Myrotheciomyces corymbiae CPC 33206 Plant (Corymbia variegata) NR_160351 NG_064542 - - -
Myrothecium inundatum IMI 158855 Hymenomycetes (Russula nigricans) - AY489731 - - AY489626
M. roridum ATCC 16297 Soil - AY489708 - - AY489603
M. verrucaria ATCC 9095 Plant (Gossypium sp.) - AY489713 - - AY489608
Nectira cinnabarina CBS 125165 Plant (Aesculus sp.) HM484548 HM484562 - KM232402 HM484527
N. nigrescens CBS 125148 Plant (Dicotyledonous tree) HM484707 HM484720 - KM232403 HM484672
Nectriopsis violacea CBS 424.64 Fungi (Fuligo sp.) - AY489719 - - -
Neobarya parasitica Marson s/n Fungi (Bertia moriformis) KP899626 KP899626 - - -
Neonectria candida CBS 151.29 Plant (Malus sylvestris) JF735313 AY677333 - - JF735791
N. faginata CBS 217.67 - HQ840385 HQ840382 - DQ789797 JF268746
N. neomacrispora CBS 118984 - HQ840388 HQ840379 - DQ789810 JF268754
N. ramulariae CBS 182.36 - HM054157 HM042435 - DQ789793 HM054092
Neurospora crassa ICMP 6360 - AY681193 AY681158 - - -
Niesslia exilis CBS 560.74 - - AY489720 - - AY489614
Ophiocordyceps heteropoda EFCC 10125 Cicadidae (Tibicen bihamatus) JN049852 EF468812 - EF468914 EF468752
O. sinensis EFCC 7287 Lepidoptera (Ghostmoth) JN049854 EF468827 - EF468924 EF468767
O. stylophor OSC 111000 Insect (Larvae) JN049828 DQ518766 - DQ522433 DQ522337
Peethambara spirostriata CBS 110115 Plant (Theobroma cacao) - AY489724 - EF692516 AY489619
Purpureocillium lilacinum CBS 284.36 Soil - AY624227 EF468898 EF468941 EF468792
P. lilacinum CBS 431.87 Nematoda (Meloidogyne sp.) HQ842812 EF468844 EF468897 EF468940 EF468791
Rosasphaeria moravica LMM - JF440985 - - JF440986 JF440987
Roumegueriella rufula GJS 91-64 - - EF469082 - EF469116 EF469070
R. rufula CBS 346.85 - - DQ518776 - DQ522461 DQ522355
Samsoniella alboaurantium CBS 240.32 Lepidoptera (Pupa) - JF415979 JN049895 JF415999 JF416019
S. alboaurantium CBS 262.58 Soil - AB080087 MF416654 MF416448 MF416497
S. alpina YFCC 5818 Hepialidae (Hepialus baimaensis) - MN576809 MN576869 MN576923 MN576979
S. alpina YFCC 5831 Hepialidae (Hepialus baimaensis) - MN576810 MN576870 MN576924 MN576980
S. antleroides YFCC 6016 Noctuidae (Larvae) - MN576803 MN576863 MN576917 MN576973
S. antleroides YFCC 6113 Noctuidae (Larvae) - MN576804 MN576864 MN576918 MN576974
S. aurantia TBRC 7271 Lepidoptera - MF140728 MF140791 MF140818 MF140846
S. aurantia TBRC 7272 Lepidoptera - MF140727 - MF140817 MF140845
S. aurantia DY10951 Lepidoptera (Pupa) MZ827667 MZ827827 - - MZ855229
S. aurantia DY10952 Lepidoptera (Pupa) MZ827666 MZ827084 - - MZ855230
S. cardinalis YFCC 5830 Limacodidae (Pupa) - MN576788 MN576848 MN576902 MN576958
S. cardinalis YFCC 6144 Limacodidae (Pupa) - MN576786 MN576846 MN576900 MN576956
S. coleopterorum A19501 Curculionidae (Snout beetle) MT626376 - MT642600 MN101585 MN101586
S. coleopterorum A19502 Curculionidae (Snout beetle) MT626625 - MT642603 MN101587 MT642602
S. cristata YFCC 6021 Saturniidae (Pupa) - MN576791 MN576851 MN576905 MN576961
S. cristata YFCC 6023 Saturniidae (Pupa) - MN576792 MN576852 MN576906 MN576962
S. hepiali ICMM 82-2 Fungi (Ophiocordyceps sinensis) - MN576794 MN576854 MN576908 MN576964
S. hepiali ICMM Cs-4 Fungi (Ophiocordycepssinensis) - MN576799 MN576859 MN576913 MN576969
S. hepiali YFCC 661 Fungi (Ophiocordycepssinensis) - MN576795 MN576855 MN576909 MN576965
S. hepiali YJ06171 Formicidae MZ831866 MZ831868 MZ855241 - MZ855235
S. hepiali YJ06172 Formicidae MZ831867 MZ831873 - - MZ855236
S. hymenopterorum A19521 Vespidae (Bee) MN128224 - MT642601 MT642604 MN101588
S. hymenopterorum A19522 Vespidae (Bee) MN128081 - MN101589 MN101590 MN101591
S. inthanonensis TBRC 7915 Lepidoptera (Pupa) MF140761 - MF140790 MF140815 MF140849
S. inthanonensis TBRC 7916 Lepidoptera (Pupa) MF140760 - MF140789 MF140814 MF140848
S. kunmingensis YHH 16002 Lepidoptera (Pupa) - MN576802 MN576862 MN576916 MN576972
S. lanmaoa YFCC 6148 Lepidoptera (Pupa) - MN576789 MN576849 MN576903 MN576959
S. lanmaoa YFCC 6193 Lepidoptera (Pupa) - MN576790 MN576850 MN576904 MN576960
S. lepidopterorum DL10071 Lepidoptera (Pupa) MN128076 - MN101592 MN101593 MN101594
S. lepidopterorum DL10072 Lepidoptera (Pupa) MN128084 - - MT642605 MT642606
S. pseudogunii GY407201 Lepidoptera (Larvae) MZ827470 MZ827010 - MZ855239 MZ855233
S. pseudogunii GY407202 Lepidoptera (Larvae) MZ831863 MZ831865 - MZ855240 MZ855234
S. pupicola DY101681 Lepidoptera (Pupa) MZ827085 MZ827009 - MZ855237 MZ855231
S. pupicola DY101682 Lepidoptera (Pupa) MZ827008 MZ827635 - MZ855238 MZ855232
S. ramose YFCC 6020 Limacodidae (Pupa) - MN576805 MN576865 MN576919 MN576975
S. tortricidae YFCC 6013 Limacodidae (Pupa) - MN576807 MN576867 MN576921 MN576977
S. tortricidae YFCC 6131 Limacodidae (Pupa) - MN576806 MN576866 MN576920 MN576976
S. yunnanensis YFCC 1527 Limacodidae (Pupa) - MN576812 MN576872 MN576926 MN576982
S. yunnanensis YFCC 1824 Limacodidae (Pupa) - MN576813 MN576873 MN576927 MN576983
Sarocladium bacillisporum CBS 425.67 Soil NR_145039 MH870718 - - -
S. dejongiae CBS 144929 Soil NR_161153 NG_067854 - - -
S. implicatum CBS 959.72 Soil HG965023 MH878470 - - -
S. subulatum CBS 217.35 Soil MH855652 NG_070566 - - -
S. terricola CBS 243.59 Soil MH857853 MH869389 - - -
Shimizuomyces paradoxus EFCC 6279 Smilacaceae (Smilax sieboldii) JN049847 EF469084 - EF469117 EF469071
Simplicillium lamellicola CBS 116.25 Hymenomycetes (Agaricus bisporus) AJ292393 MH866307 - DQ522462 DQ522356
S. lanosoniveum CBS 101267 Uredinales (Hemileia vastatrix) - AJ292395 - DQ522463 DQ522357
S. lanosoniveum CBS 704.86 Uredinales (Hemileia vastatrix) AJ292396 AF339553 - DQ522464 DQ522358
Sordaria fimicola AFTOL-ID 216 - DQ518178 - - - DQ518175
Sphaerostilbella aureonitens GJS74-87 - FJ442633 HM466683 - FJ442763 -
S. berkeleyana GJS82-274 - - U00756 - - AF543783
Stachybotrys chlorohalonata DAOM 235557 - JN942888 JN938870 - - -
S. eucylindrospora ATCC 18851 - JN942887 JN938869 - - -
Stephanonectria keithii GJS92-133 Plant (Bark) - AY489727 - - AY489622
Tilachlidium brachiatum CBS 363.97 Hymenomycetes (Agaricus sp.) KM231838 KM231719 - KM232414 KM231975
T. brachiatum CBS 506.67 Hymenomycetes (Hypholoma fasciculare) KM231839 HQ232177 - KM232415 KM231976
Tolypocladium inflatum SCALT1007-002 Sclerotium KC963032 - - - -
Trichoderma aggresivum CBS 100525 - - JN939837 - JQ014130 -
T. viride GJS89-127 Plant (Bark) - AY489726 - - AY489621
Trichothecium roseum DUCC 502 Plant (Solanum lycopersicum) JN937590 JX458860 - - -
Valetoniellopsis laxa GJS 96-174 - - AY015635 - AY015638 -

2.3. Sequence Alignment and Phylogenetic Analyses

Lasergene software (version 6.0, DNASTAR) was applied for the assembling and editing of DNA sequence in this study. The ITS, LSU, RPB1, RPB2, and TEF sequences were downloaded from GenBank, based on Kepler et al. [9], Mongkolsamrit et al. [10,19], Chen et al. [12], Wang et al. [20], and others selected on the basis of BLAST algorithm-based searches in GenBank (Table 2). A single gene data set was aligned and edited by MAFFT v7.037b [21] and MEGA6 [22]. Combined sequences of ITS, LSU, RPB1, RPB2, and TEF were performed by SequenceMatrix v.1.7.8 [23]. The combined datasets (ITS+LSU+RPB2+TEF) and (ITS+LSU+RPB1+RPB2+TEF) were used to determine the family placement of those strains in Hypocreales and the taxonomic position of strains and the cryptic diversity among the different isolates of I. farinosa in Cordycipitaceae

The combined genes were both analyzed using the Bayesian inference (BI) and maximum likelihood (ML) methods. For BI, the model was selected for Bayesian analysis by ModelFinder [24] in the software PhyloSuite [25]. A Markov Chain Monte Carlo (MCMC) algorithm was used to generate phylogenetic trees with Bayesian probabilities using MrBayes v.3.2 [26] for the combined sequence datasets. The Bayesian analysis resulted in 20,001 trees after 10,000,000 generations. The first 4000 trees, representing the burn-in phase of the analyses, were discarded, while the remaining 16,001 trees were used for calculating posterior probabilities in the majority rule consensus tree. After the analysis was finished, each run was examined using the program Tracer v1.5 [27] to determine burn-in, confirming that both runs had converged. ML analyses were constructed with RAxMLGUI [28]. The GTRGAMMA model was used for all partitions, in accordance with recommendations in the RAxML manual against the use of invariant sites.

3. Results

3.1. Phylogenetic Analyses

Gelasinospora tetrasperma Dowding, Neurospora crassa Shear and B.O. Dodge, and Sordaria fimicola (Roberge ex Desm.) Ces. and De Not. were used as the outgroup in analysis 1 (Figure 1) (to determine the family placement of those strains in Hypocreales). Purpureocillium lilacinum (Thom) Luangsa-ard, Houbraken, Hywel-Jones, and Samson was used as the outgroup in analysis 2 (Figure 2) (to determine the taxonomic position of strains and the cryptic diversity among the different isolates of I. farinosa in Cordycipitaceae). The concatenated sequences of analysis 1 and 2 included 77 and 62 taxa, respectively, and consisted of 2396 (ITS, 620; LSU, 712; RPB2, 510; and TEF, 554) and 3309 (ITS, 554; LSU, 677; RPB1, 533; RPB2, 671; and TEF, 874) characters with gaps, respectively.

Figure 1.

Figure 1

Phylogenetic placement of the new Isaria-like strains in the order of Hypocreales based on multigene dataset (ITS, LSU, RPB2m and TEF). Statistical support values (≥50%/0.5) are shown at the nodes for ML bootstrap support/BI posterior probabilities.

Figure 2.

Figure 2

Phylogenetic placement of the new strains in Cordycipitaceae, based on multigene dataset (ITS, LSU, RPB1, RPB2, and TEF). Statistical support values (≥50%/0.5) are shown at the nodes for ML bootstrap support/BI posterior probabilities.

Analysis 1: The selected models for BI analysis were GTR+F+I+G4 parameters for partition ITS and LSU+RPB2, and GTR+F+G4 parameters for partition TEF. The final value of the highest scoring tree was –37,321.078127, which was obtained from an ML analysis of the dataset (ITS+LSU+RPB2+TEF). The parameters of the general time reversible (GTR) model used to analyze the dataset were estimated using the following frequencies: A = 0.230263, C = 0.272892, G = 0.280445, and T = 0.216401; substitution rates AC = 1.451341, AG = 2.441940, AT = 1.532513, CG = 1.182477, CT = 5.701598, and GT = 1.000000; as well as the gamma distribution shape parameter α = 0.381402. In the phylogenetic tree (Figure 1), both analyses of ML and BI trees were largely congruent, and strongly supported in most branches. DY10951, DY10952, DY101681, DY101682, GY407201, GY407202, YJ06171, and YJ06172 strains had a close relationship with Cordyceps Fr., Akanthomyces Lebert, and Simplicillium W. Gams and Zare, and clustered into Cordycipitaceae.

Analysis 2: The selected models for BI analysis were GTR+F+I+G4 parameters for partition ITS+LSU+RPB2+TEF and GTR+F+G4 parameters for partition RPB1. The final value of the highest scoring tree was –31,206.916701, which was obtained from an ML analysis of the dataset (ITS+LSU+RPB1+RPB2+TEF). The parameters of the general time reversible (GTR) model used to analyze the dataset were estimated using the following frequencies: A = 0.238319, C = 0.279080, G = 0.271674, and T = 0.210926; substitution rates AC = 1.120096, AG = 2.745044, AT = 0.784066, CG = 0.934312, CT = 6.322628, and GT = 1.000000; as well as the gamma distribution shape parameter α = 0.308970. In the phylogenetic tree (Figure 2), both analyses of ML and BI trees were largely congruent, and strongly supported in most branches. The new strains were all clustered within the genus Samsoniella. GY407201 and GY407202 strains clustered with Samsoniella coleopterorum W.H. Chen, Y.F. Han, and Z.Q. Liang in a subclade. DY10951 and DY10952 strains clustered with Samsoniella aurantia Mongkols., Noisrip., Thanakitp., Spatafora, and Luangsa-ard in a subclade. DY101681 and DY101682 strains had a close relationship with Samsoniella alboaurantia (G. Sm.) Mongkols., Noisrip., Thanakitp., Spatafora, and Luangsa-ard; Samsoniella alpina H. Yu, Y.B. Wang, Y. Wang, and Zhu L. Yang; and Samsoniella cardinalis H. Yu, Y.B. Wang, Y. Wang, Q. Fan, and Zhu L. Yang. YJ06171 and YJ06172 strains clustered with Isaria farinosa (Holmsk.) Fr. in a subclade and had close relationship with Samsoniella hepiali (Q.T. Chen and R.Q. Dai ex R.Q. Dai, X.M. Li, A.J. Shao, Shu F. Lin, J.L. Lan, Wei H. Chen, and C.Y. Shen) H. Yu, R.Q. Dai, Y.B. Wang, Y. Wang, and Zhu L. Yang.

3.2. Taxonomy

3.2.1. Samsoniella pseudogunnii W.H. Chen, Y.F. Han, J.D. Liang, and Z.Q. Liang, sp. nov.

MycoBank No.: MB840999

Etymology: referring to similar morphology with Keithomyces neogunnii.

Holotype: CHINA, Guizhou, Guiyang, Tongmuling (N26°23’, E106°40’). On a larva (Lepidoptera), 1 April 2019, Wanhao Chen, GZAC GY40720 (holotype), ex-type living cultures, GY407201, GY407202.

Description: Colonies on PDA, 4.1–4.3 cm diam. after 14 d at 25°C, white, consisting of a basal felt and cottony, floccose hyphal overgrowth, reverse yellowish. Prostrate hyphae smooth, septate, hyaline, 1.0–1.3 μm diam. Erect conidiophores usually arises from aerial hyphae. Phialides are solitary or in whorls of two to nine. Phialides 6.8–11.0 × 2.2–2.4 μm, with a cylindrical basal portion, tapering into a short distinct neck. Conidia in chains, hyaline, fusiform, one-celled, 2.8–3.2 × 1.7–2.1 μm. Chlamydospores and sexual state were not observed. Sizes and shapes of phialides and conidia are similar in culture and on natural substratum.

Known distribution: Tongmuling, Guiyang, Guizhou Province, China.

Notes: Samsoniella pseudogunnii was identified as belonging to Samsoniella based on the phylogenetic analyses (Figure 2) and has a close relationship with S. coleopterorum. However, Samsoniella pseudogunnii (Figure 3) has longer phialide, larger conidia, and its larva host belongs to the order Lepidoptera.

Figure 3.

Figure 3

Samsoniella pseudogunnii (A) infected larva (Lepidoptera) (B,C) culture plate, showing the front (B) and the reverse (C) of the colony, cultured on PDA medium (DI) phialides solitary, conidia adhering ellipsoidal slimy head and conidia (J) conidia. Scale bars: 10 mm (B,C), 10 μm (DJ).

3.2.2. Samsoniella Pupicola W.H. Chen, Y.F. Han, J.D. Liang, and Z.Q. Liang, sp. nov.

MycoBank No.: MB841003

Etymology: referring to its pupa-inhabitor.

Holotype: CHINA, Guizhou, Qiannan Buyi and Miao Autonomous Prefecture, Duyun City (26°21′24.71″ N, 107°22′48.22″ E). On a pupa (Lepidoptera), 1 October 2019, Wanhao Chen, GZAC DY10168 (holotype), ex-type living cultures, DY101681, DY101682.

Description: Colonies on PDA, 2.3–2.4 cm diam. after 14 d at 25°C, white, consisting of a basal felt and cottony, floccose hyphal overgrowth, reverse yellowish. Prostrate hyphae smooth, septate, hyaline, 1.2–2.2 μm diam. Erect conidiophores usually arise from aerial hyphae. Phialides are solitary or in whorls of two to nine. Phialides 7.0–9.2 × 2.5–3.3 μm, with a cylindrical basal portion, tapering into a short distinct neck. Conidia in chains, hyaline, fusiform, one-celled, 2.5–3.3 × 2.2–2.6 μm. Chlamydospores and sexual state were not observed. Sizes and shapes of phialides and conidia are similar in culture and on natural substratum.

Known distribution: Duyun City, Qiannan Buyi and Miao Autonomous Prefecture, Guizhou Province, China.

Additional specimens examined: CHINA, Guizhou, Qiandongnan Miao and Dong Autonomous Prefecture, Rongjiang County (26°01′58.70″ N, 108°24′48.06″ E), on a lepidopteran pupa, 1 October 2018, W.H. Chen, GZAC DL1014.

Notes: Samsoniella pupicola was identified as belonging to Samsoniella, based on the phylogenetic analyses (Figure 2) and has a close relationship with S. alboaurantium, S. alpina, and S. cardinalis. However, S. pupicola (Figure 4) is distinguished from S. alboaurantium by having larger fusiform conidia, distinguished from S. alpina by having white colony and fusiform conidia, and distinguished from S. cardinalis by having shorter phialides.

Figure 4.

Figure 4

Samsoniella pupicola (A) infected pupa (Lepidoptera) (B,C) culture plate, showing the front (B) and the reverse (C) of the colony, cultured on PDA medium (DJ) phialides solitary, conidia adhering ellipsoidal slimy head and conidia (K) conidia. Scale bars: 10 mm (B,C), 10 μm (DK).

3.2.3. Samsoniella aurantia Mongkols., Noisrip., Thanakitp., Spatafora, and Luangsa-ard, Mycologia 110(1): 249

Description: Colonies on PDA, 3.7–4.2 cm diam. after 14 d at 25°C, white, consisting of a basal felt and cottony, floccose hyphal overgrowth, pale green and pale pink in the middle of the colony, reverse yellowish and pale brown in the middle. Prostrate hyphae smooth, septate, hyaline, 1.3–2.6 μm diam. Erect conidiophores usually arise from aerial hyphae. Phialides are solitary or in whorls of two to ten. Phialides 3.6–7.7 × 1.3–1.6 μm, with a cylindrical basal portion, tapering into a short distinct neck. Conidia in chains, hyaline, fusiform, occasionally cylindrical, one-celled, 2.6–3.9 × 1.7–2.2 μm. Chlamydospores and sexual state were not observed. Sizes and shapes of phialides and conidia are similar in culture and on natural substratum.

Specimens examined: CHINA, Guizhou, Qiannan Buyi and Miao Autonomous Prefecture, Duyun City (26°21′24.71″ N, 107°22′48.22″ E). On a pupa (Lepidoptera), 1 October 2019, Wanhao Chen, GZAC DY1095, living cultures, DY10951, DY10952.

Note: DY10951 and DY10952 strains were identified as belonging to Samsoniella, based on the phylogenetic analyses (Figure 2), and clustered with Samsoniella aurantia in a clade. The characteristics of DY10951 and DY10952 (Figure 5) strains are similar to that of S. aurantia, which had fusiform conidia (2–4 × 1–2 μm) and larger phialide (5–13 × 2–3 μm). Besides, the pairwise dissimilarities of ITS sequences show no difference within 554 bp between DY10951 and S. aurantia. Thus, molecular phylogenetic results and morphologically based conclusions support the idea that DY10951 and DY10952 strains were S. aurantia.

Figure 5.

Figure 5

Samsoniella aurantia (A) infected pupa (Lepidoptera) (B,C) culture plate, showing the front (B) and the reverse (C) of the colony, cultured on PDA medium (DJ) phialides solitary, conidia adhering ellipsoidal slimy head and conidia (K) conidia. Scale bars: 10 mm (B,C), 10 μm (DK).

3.2.4. Samsoniella hepiali (Q.T. Chen, and R.Q. Dai ex R.Q. Dai, X.M. Li, A.J. Shao, Shu F. Lin, J.L. Lan, Wei H. Chen, and C.Y. Shen) H. Yu, R.Q. Dai, Y.B. Wang, Y. Wang, and Zhu L. Yang, Fungal Diversity 103: 31

Description: Colonies on PDA, 5.8–5.9 cm diam. after 14 d at 25°C, white, consisting of a basal felt and cottony, floccose hyphal overgrowth, reverse yellowish. Prostrate hyphae smooth, septate, hyaline, 1.1–1.8 μm diam. Erect conidiophores usually arise from aerial hyphae. Phialides are solitary or in whorls of two to eight. Phialides 6.0–7.8 × 1.5–1.8 μm, with a cylindrical basal portion, tapering into a short distinct neck. Conidia in chains, hyaline, fusiform, one-celled, 2.1–2.5 × 0.9–1.6 μm. Chlamydospores and sexual state were not observed. Sizes and shapes of phialides and conidia are similar in culture and on natural substratum.

Specimens examined: CHINA, Guizhou, Tongren City, Yinjiang (N 27°55′17.1″, E 108°41′25.2″), on an ant, 1 October 2019, Wanhao Chen, GZAC YJ0617, DY1044, living cultures, YJ06171, YJ06172.

Note: YJ06171 and YJ06172 strains were identified as belonging to Samsoniella, based on the phylogenetic analyses (Figure 2), and clustered with Samsoniella hepiali in a clade. The characteristics of YJ06171 and YJ06172 (Figure 6) strains were very closely linked with S. hepiali, which had fusiform or oval conidia (1.8–3.3 × 1.4–2.2 μm) and larger phialide (3.5–13.6 × 1.3–2.1 μm). Besides, the pairwise dissimilarities of LSU sequences show no difference within 677 bp between YJ06171 and S. hepiali. Thus, molecular phylogenetic results and morphologically based conclusions supported the idea that YJ06171 and YJ06172 strains were S. hepiali.

Figure 6.

Figure 6

Samsoniella hepiali (A) infected ant (Formicidae) (B,C) culture plate, showing the front (B) and the reverse (C) of the colony, cultured on PDA medium (DJ) phialides solitary, conidia adhering ellipsoidal slimy head and conidia (N) conidia. Scale bars: 10 mm (B,C), 10 μm (DN).

4. Discussion

The taxonomic delimitation of Isaria was originally based on morphological characteristics. However, Isaria shares many morphological characters with other genera in Hypocreales, which has resulted in a turbulent taxonomic history [10,29]. D’Alessandro et al. [30] noted that the morphological characteristics used to classify the genus Isaria frequently do not resolve new isolates into clearly defined species and need additional molecular markers in phylogenetic analyses. In the present study, Isaria-like strains collected from Guizhou Province, China, and previously identified by morphological characteristics, were reanalyzed using multi-gene (ITS, LSU, RPB1, RPB2, TEF) phylogenetic methodology. We proposed two new species of Samsoniella in this study.

The species Isaria farinosa is a well-known entomopathogenic fungi with worldwide distribution and a wide host range [31]. Kepler et al. [9] transferred Isaria farinosa to the genus Cordyceps as C. farinosa (Holmsk.) Kepler, B. Shrestha, and Spatafora based on a phylogenetic analysis of the CBS 111113 strain. We analyzed several strains of Isaria farinosa in the present study. Some properly belonged in the genus Samsoniella. CEP 004, CEP 005, CEP 029, YJ06171, and YJ06172 strains were identified as S. hepiali. Strains DY10951 and DY10952 were identified as S. aurantia. OSC 111005 and OSC 111006 strains were identified as new species but are absent in delineating morphological characteristics. Our results reveal cryptic diversity present in Isaria farinosa (now treated as Cordyceps farinosa) and illustrated that more attention should be paid on cryptic intraspecific diversity across different fungi isolates and genotypes.

The genus Samsoniella was established for the typical species S. inthanonensis Mongkolsamrit, Noisripoom, Thanakitpipattana, Spatafora, and Luangsa-ard, and two other species (S. alboaurantia (G. Sm.) Mongkols., Noisrip., Thanakitp., Spatafora, and Luangsa-ard and S. aurantia Mongkols., Noisrip., Thanakitp., Spatafora, and Luangsa-ard) [10]. Samsoniella species all have Isaria-like morphological characteristics, and cluster in an independent clade with close relationship to the genus Akanthomyces. The species S. alboaurantia was established based on two strains, CBS 240.32 and CBS 262.58, which previously belonged to Isaria farinosa (originally designated Paecilomyces farinosus (Holmsk.) A.H.S. Br. and G. Sm.) [10]. Lin et al. [32] revised the taxonomy of some Isaria-like strains originally identified as Isaria farinosa by morphological characteristics using multi-gene phylogenetic analysis. All the strains were identified as Samsoniella hepiali (Q.T. Chen and R.Q. Dai ex R.Q. Dai, X.M. Li, A.J. Shao, Shu F. Lin, J.L. Lan, Wei H. Chen, and C.Y. Shen) H. Yu, R.Q. Dai, Y.B. Wang, Y. Wang, and Zhu L. Yang. In the present study, YJ06171 and YJ06172 strains were also identified as Samsoniella hepiali. Our results revealed that more isolates and genotypes, originally designated as Isaria, will need to be transferred to Samsoniella.

Samsoniella hepiali (otherwise known as Paecilomyces hepiali) is isolated from a field collection of natural Ophiocordyceps sinensis insect–fungi complex [33], and is widely used as a medicinal and edible cordycipitoid fungus, creating a great economic value [20]. Lin et al. [32] reported six isolates of Samsoniella hepiali from Anhui Province, China, which were isolated from leafhopper, larva, and cicada. CEP 004, CEP 005, CEP 029 strains from Buenos Aires, Argentina, were isolated from whitefly and soil [30]. YJ06171 and YJ06172 strains from Guizhou Province, China were isolated from ant. It is interesting that Samsoniella hepiali and its hosts are widely distributed in China and Argentina. This result will help us to assess the extent and distribution of genetic diversity of Samsoniella hepiali on a large scale, understand its biology and demographic history, and guide biodiversity conservation programs.

Acknowledgments

We thank Steven M. Thompson for editing the English text of a draft of this manuscript.

Author Contributions

Resources, W.C., J.L. and X.R.; data curation, W.C.; writing—original draft preparation, W.C., J.L., X.R.; writing—review and editing, J.L., Y.H.; review and editing, J.Z., Z.L.; funding acquisition, W.C., J.L., X.R., J.Z., Y.H. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by National Natural Science Foundation of China (31860002, 32060011), High-level Innovative Talents Training Object in Guizhou Province (Qiankehepingtairencai [2020]6005), Science and Technology Foundation of Guizhou Province (Qiankehejichu [2020]1Y060), Program of Innovative Scientific and technological Talent Team of Guizhou Province (2020-5010), Guizhou Science and Technology Support Project (Qiankehezhicheng [2019]2776), The Youth Science and Technology Talent Growth project from Guizhou Provincial Department of Education ([2018]389).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare no conflict of interest.

Footnotes

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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