Journal of Microbiology

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Arctic lichen Cladonia borealis-induced cell death is mediated by p53-independent activation of Caspase-9 and PARP-1 signaling in human colorectal cancer cell lines: Ju-Mi Hong, Seul Ki Min, Kyung Hee Kim, Se Jong Han, Joung Han Yim, Sojin Kim, Youn-Jung Kim, Il-Chan Kim; J. Microbiol. 2025;63(4):e2412012. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2412012

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Abstract PDF: The anti-cancer effects of Cladonia borealis (an Arctic lichen) methanol extract (CBME) on human colon carcinoma HCT116 cells were investigated for the first time. The proliferation of the HCT116 cells treated with CBME significantly decreased in a dose- and time-dependent manner. Flow cytometry results indicated that treatment with CBME resulted in significant apoptosis in the HCT116 cells. Furthermore, immunoblotting and qRT-PCR results revealed the expression of apoptosis-related marker genes and indicated a significant downregulation of the apoptosis regulator B-cell lymphoma expression and upregulation of the cleaved form of poly (ADP-ribose) polymerase as DNA repair and apoptosis regulators and central tumor suppressor p53. Therefore, CBME significantly inhibited cell proliferation by inducing apoptosis via the mitochondrial apoptotic pathway in colon carcinoma cells. Collectively, these data suggested that CBME contained one or more compounds with anti-cancer effects and could be a potential therapeutic agent. Further studies are required to identify candidate compounds and understand the mechanism of action of CBME.

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Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis: Anyeseu Park, Chanhee Lee, Jeong Yoon Lee; J. Microbiol. 2024;62(5):393-407. Published online March 7, 2024; DOI: https://doi.org/10.1007/s12275-024-00112-5

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Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.

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In Silico Intensive Analysis for the E4 Gene Evolution of Human Adenovirus Species D
Chanhee Lee, Anyeseu Park, Jeong Yoon Lee
Journal of Microbiology.2024; 62(5): 409. CrossRef

Journal Articles

Effects of Feather Hydrolysates Generated by Probiotic Bacillus licheniformis WHU on Gut Microbiota of Broiler and Common carp: Kamin Ke, Yingjie Sun, Tingting He, Wenbo Liu, Yijiao Wen, Siyuan Liu, Qin Wang, Xiaowei Gao; J. Microbiol. 2024;62(6):473-487. Published online February 29, 2024; DOI: https://doi.org/10.1007/s12275-024-00118-z

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Due to the ever-increasing demand for meat, it has become necessary to identify cheap and sustainable sources of protein for animal feed. Feathers are the major byproduct of poultry industry, which are rich in hard-to-degrade keratin protein. Previously we found that intact feathers can be digested into free amino acids, short peptides, and nano-/micro-keratin particles by the strain Bacillus licheniformis WHU in water, and the resulting feather hydrolysates exhibit prebiotic effects on mice. To explore the potential utilization of feather hydrolysate in the feed industry, we investigated its effects on the gut microbiota of broilers and fish. Our results suggest that feather hydrolysates significantly decrease and increase the diversity of gut microbial communities in broilers and fish, respectively. The composition of the gut microbiota was markedly altered in both of the animals. The abundance of bacteria with potentially pathogenic phenotypes in the gut microbial community of the fish significantly decreased. Staphylococcus spp., Pseudomonas spp., Neisseria spp., Achromobacter spp. were significantly inhibited by the feather hydrolysates. In addition, feather hydrolysates significantly improved proteolytic activity in the guts of broilers and fish. In fish, the expression levels of ZO-1 and TGF-α significantly improved after administration of feather hydrolysates. The results presented here suggest that feather hydrolysates generated by B. licheniformis WHU could be an alternative protein source in aquaculture and could exert beneficial effects on fish.

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Keratinous bioresources: their generation, microbial degradation, and value enhancement for biotechnological applications
Vijan Lal Vikash, Numbi Ramudu Kamini, Ganesan Ponesakki, Suresh Kumar Anandasadagopan
World Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef

The quorum sensing regulator OpaR is a repressor of polar flagellum genes in Vibrio parahaemolyticus: Renfei Lu , Junfang Sun , Yue Qiu , Miaomiao Zhang , Xingfan Xue , Xue Li , Wenhui Yang , Dongsheng Zhou , Lingfei Hu , Yiquan Zhang; J. Microbiol. 2021;59(7):651-657. Published online June 1, 2021; DOI: https://doi.org/10.1007/s12275-021-0629-3

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Abstract

Vibrio parahaemolyticus possesses two types of flagella: a single polar flagellum (Pof) for swimming and the peritrichous lateral flagella (Laf) for swarming. Expression of Laf genes has previously been reported to be regulated by the quorum sensing (QS) regulators AphA and OpaR. In the present study, we showed that OpaR, the QS regulator at high cell density (HCD), acted as a negative regulator of swimming motility and the transcription of Pof genes in V. parahaemolyticus. OpaR bound to the promoter-proximal DNA regions of flgAMN, flgMN, and flgBCDEFGHIJ within the Pof gene loci to repress their transcription, whereas it negatively regulates the transcription of flgKL-flaC in an indirect manner. Thus, this work investigated how QS regulated the swimming motility via direct action of its master regulator OpaR on the transcription of Pof genes in V. parahaemolyticus.

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Current Microbiology.2025;[Epub] CrossRef
GefB, a GGDEF domain-containing protein, affects motility and biofilm formation of Vibrio parahaemolyticus and is regulated by quorum sensing regulators
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The effect of environmental calcium on gene expression, biofilm formation and virulence of Vibrio parahaemolyticus
Xue Li, Jingyang Chang, Miaomiao Zhang, Yining Zhou, Tingting Zhang, Yiquan Zhang, Renfei Lu
Frontiers in Microbiology.2024;[Epub] CrossRef
VPA0198, a GGDEF domain-containing protein, affects the motility and biofilm formation of Vibrio parahaemolyticus and is regulated by quorum sensing associated regulators
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Antibacterial and anti-virulence potential of plant phenolic compounds against Vibrio parahaemolyticus
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The inability of Bacillus licheniformis perR mutant to grow is mainly due to the lack of PerR-mediated fur repression: Jung-Hoon Kim , Yoon-Mo Yang , Chang-Jun Ji , Su-Hyun Ryu , Young-Bin Won , Shin-Yeong Ju , Yumi Kwon , Yeh-Eun Lee , Hwan Youn , Jin-Won Lee; J. Microbiol. 2017;55(6):457-463. Published online April 22, 2017; DOI: https://doi.org/10.1007/s12275-017-7051-x

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Abstract

PerR, a member of Fur family protein, is a metal-dependent H2O2 sensing transcription factor that regulates genes in-volved in peroxide stress response. Industrially important bac-terium Bacillus licheniformis contains three PerR-like pro-teins (PerRBL, PerR2, and PerR3) compared to its close rela-tive Bacillus subtilis. Interestingly, unlike other bacteria in-cluding B. subtilis, no authentic perRBL null mutant could be established for B. licheniformis. Thus, we constructed a con-ditional perRBL mutant using a xylose-inducible promoter, and investigated the genes under the control of PerRBL. PerRBL regulon genes include katA, mrgA, ahpC, pfeT, hemA, fur, and perR as observed for PerRBS. However, there is some variation in the expression levels of fur and hemA genes be-tween B. subtilis and B. licheniformis in the derepressed state. Furthermore, katA, mrgA, and ahpC are strongly induced, whereas the others are only weakly or not induced by H2O2 treatment. In contrast to the B. subtilis perR null mutant which frequently gives rise to large colony phenotype mainly due to the loss of katA, the suppressors of B. licheniformis perR mutant, which can form colonies on LB agar, were all cata-lase-positive. Instead, many of the suppressors showed in-creased levels of siderophore production, suggesting that the suppressor mutation is linked to the fur gene. Consistent with this, perR fur double mutant could grow on LB agar without Fe supplementation, whereas perR katA double mutant could only grow on LB agar with Fe supplementation. Taken toge-ther, our data suggest that in B. licheniformis, despite the si-milarity in PerRBL and PerRBS regulon genes, perR is an essen-tial gene required for growth and that the inability of perR null mutant to grow is mainly due to elevated expression of Fur.

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Research Support, Non-U.S. Gov'ts

Surface Display Expression of Bacillus licheniformis Lipase in Escherichia coli Using Lpp’OmpA Chimera: Jae-Hyung Jo , Chan-Wook Han , Seung-Hwan Kim , Hyuk-Jin Kwon , Hyune-Hwan Lee; J. Microbiol. 2014;52(10):856-862. Published online August 27, 2014; DOI: https://doi.org/10.1007/s12275-014-4217-7

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Abstract

The lipase from Bacillus licheniformis ATCC14580 was displayed on the cell surface of Escherichia coli using Lpp’OmpA as the anchoring protein. The expressed Lpp’OmpA-lipase fusion protein has a molecular weight of approximately 35 kDa, which was confirmed by SDS-PAGE and western blot analysis. The Lpp’OmpA-lipase fusion protein was located on the cell surface, as determined by immunofluorescence confocal microscopy and flow cytometry. The enzyme activity of the surface-displayed lipase showed clear halo around the colony. The cell surface-displayed lipase showed the highest activity of 248.12 ± 9.42 U/g (lyophilized cell) at the optimal temperature of 37°C and pH 8.0. The enzyme exhibited the highest activity toward the substrate p-nitrophenyl caprylate (C8). These results suggest that E. coli, which displayed the lipase on its surface, could be used as a whole cell biocatalyst.

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NOTE] Isolation and Characterization of Histamine-Producing Bacteria from Fermented Fish Products: Jin Seok Moon , So-Young Kim , Kyung-Ju Cho , Seung-Joon Yang , Gun-Mook Yoon , Hyun-Ju Eom , Nam Soo Han; J. Microbiol. 2013;51(6):881-885. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3333-0

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Abstract

Histamine is mainly produced by microorganisms that are found in fermented foods, and is frequently involved in food poisoning. Two histamine-producing bacteria were isolated from fermented fish products, anchovy sauce, and sand lance sauce by using a histidine decarboxylating medium. The species were identified as Bacillus licheniformis A7 and B. coagulans SL5. Multiplex PCR analysis showed the presence of the conserved histidine decarboxylase (hdc) gene in the chromosome of these bacteria. B. licheniformis A7 and B. coagulans SL5 produced the maximum amount of histamine (22.3±3.5 and 15.1±1.5 mg/L, respectively). As such, they were determined to be potential histamine-producing bacteria among the tested cultures.

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Detailed Modes of Action and Biochemical Characterization of endo-Arabinanase from Bacillus licheniformis DSM13: Jung-Mi Park , Myoung-Uoon Jang , Jung-Hyun Kang , Min-Jeong Kim , So-Won Lee , Yeong Bok Song , Chul-Soo Shin , Nam Soo Han , Tae-Jip Kim; J. Microbiol. 2012;50(6):1041-1046. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2489-3

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Abstract: An endo-arabinanase (BLABNase) gene from Bacillus licheniformis DSM13 was cloned and expressed in Escherichia coli, and the biochemical properties of its encoded enzyme were characterized. The BLABNase gene consists of a single open reading frame of 987 nucleotides that encodes 328 amino acids with a predicted molecular mass of about 36 kDa. BLABNase exhibited the highest activity against debranched α-(1,5)-arabinan in 50 mM sodium acetate buffer (pH 6.0) at 55°C. Enzymatic characterization revealed that BLABNase hydrolyzes debranched or linear arabinans with a much higher activity than branched arabinan from sugar beet. Enzymatic hydrolysis pattern analyses demonstrated BLABNase to be a typical endo-(1,5)-α-L-arabinanase (EC 3.2.1.99) that randomly cleaves the internal α-(1,5)-linked L-arabinofuranosyl residues of a branchless arabinan backbone to release arabinotriose mainly, although a small amount of arabino-oligosaccharide intermediates is also liberated. Our results indicated that BLABNase acts preferentially along with the oligosaccharides longer than arabinopentaose, thus enabling the enzymatic production of various arabinooligosaccharides.

Identification of a New Bacillus licheniformis Strain Producing a Bacteriocin-Like Substance: Yaoqi Guo , Zhanqiao Yu , Jianhua Xie , Rijun Zhang; J. Microbiol. 2012;50(3):452-458. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2051-3

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20 Scopus

Abstract: The emergence of antibiotic resistance has spurred a great number of studies for development of new antimicrobials in the past decade. The purpose of this study was to screen environmental samples for Bacillus strains producing potent antimicrobial agents. A new strain, which showed strong antimicrobial activity against Staphylococcus aureus and Salmonella enterica ser. Pullorum, was isolated from soil and designated as B116. This new isolate was identified as Bacillus licheniformis by morphological, biochemical and genetic analyses. The production of bacteriocin-like substance (BLS) started at early exponential phase and achieved highest level at early stationary phase. The BLS was precipitated by ammonium sulfate and its molecular mass was determined as ~4 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Culture supernatant of the new isolate exhibited antimicrobial activity against both Gram-positive and Gram-negative bacteria, including Bacillus cereus, Staphylococcus aureus, Listeria monocytogenes, Micrococcus luteus, Escherichia coli, and Salmonella spp. The BLS was resistant to heat, acid and alkaline treatment. Activity of the BLS was totally lost after digestion by pronase and partially lost after digestion by papain and lipase. The new isolate and relevant BLS are potentially useful in food and feed applications.

Journal Article

Chitinase Production by Bacillus thuringiensis and Bacillus licheniformis: Their Potential in Antifungal Biocontrol: Eman Zakaria Gomaa; J. Microbiol. 2012;50(1):103-111. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1343-y

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136 Scopus

Abstract: Thirty bacterial strains were isolated from the rhizosphere of plants collected from Egypt and screened for production of chitinase enzymes. Bacillus thuringiensis NM101-19 and Bacillus licheniformis NM120-17 had the highest chitinolytic activities amongst those investigated. The production of chitinase by B. thuringiensis and B. licheniformis was optimized using colloidal chitin medium amended with 1.5% colloidal chitin, with casein as a nitrogen source, at 30°C after five days of incubation. An enhancement of chitinase production by the two species was observed by addition of sugar substances and dried fungal mats to the colloidal chitin media. The optimal conditions for chitinase activity by B. thuringiensis and B. licheniformis were at 40°C, pH 7.0 and pH 8.0, respectively. Na+, Mg2+, Cu2+, and Ca2+ caused enhancement of enzyme activities whereas they were markedly inhibited by Zn2+, Hg2+, and Ag+. In vitro, B. thuringiensis and B. licheniformis chitinases had potential for cell wall lysis of many phytopathogenic fungi tested. The addition of B. thuringiensis chitinase was more effective than that of B. licheniformis in increasing the germination of soybean seeds infected with various phytopathogenic fungi.

Research Support, Non-U.S. Gov'ts

Isolation and Characterization of a Reducing Polyketide Synthase Gene from the Lichen-Forming Fungus Usnea longissima: Yi Wang , Jung A Kim , Yong Hwa Cheong , Yogesh Joshi , Young Jin Koh , Jae-Seoun Hur; J. Microbiol. 2011;49(3):473-480. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0362-4

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15 Scopus

Abstract: The reducing polyketide synthases found in filamentous fungi are involved in the biosynthesis of many drugs and toxins. Lichens produce bioactive polyketides, but the roles of reducing polyketide synthases in lichens remain to be clearly elucidated. In this study, a reducing polyketide synthase gene (UlPKS3) was isolated and characterized from a cultured mycobiont of Usnea longissima. Complete sequence information regarding UlPKS3 (6,519 bp) was obtained by screening a fosmid genomic library. A UlPKS3 sequence analysis suggested that it contains features of a reducing fungal type I polyketide synthase with β-ketoacyl synthase (KS), acyltransferase (AT), dehydratase (DH), enoyl reductase (ER), ketoacyl reducatse (KR), and acyl carrier protein (ACP) domains. This domain structure was similar to the structure of ccRads1, which is known to be involved in resorcylic acid lactone biosynthesis in Chaetomium chiversii. The results of phylogenetic analysis located UlPKS3 in the clade of reducing polyketide synthases. RT-PCR analysis results demonstrated that UlPKS3 had six intervening introns and that UlPKS3 expression was upregulated by glucose, sorbitol, inositol, and mannitol.

Evaluation of Antagonistic Activities of Bacillus subtilis and Bacillus licheniformis Against Wood-Staining Fungi: In Vitro and In Vivo Experiments: Natarajan Velmurugan , Mi Sook Choi , Sang-Sub Han , Yang-Soo Lee; J. Microbiol. 2009;47(4):385-392. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-009-0018-9

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29 Scopus

Abstract: The antifungal activity of bacterial strains Bacillus subtilis EF 617317 and B. licheniformis EF 617325 was demonstrated against sapstaining fungal cultures Ophiostoma flexuosum, O. tetropii, O. polonicum, and O. ips in both in vitro and in vivo conditions. The crude active supernatant fractions of 7 days old B. subtilis and B. licheniformis cultures inhibited the growth of sapstaining fungi in laboratory experiments. Thermostability and pH stability of crude supernatants were determined by series of experiments. FT-IR analysis was performed to confirm the surface structural groups of lipoproteins present in the crude active supernatant. Partial purification of lipopeptides present in the crude supernatant was done by using Cellulose anion exchange chromatography and followed by Sephadex gel filtration chromatography. Partially purified compounds significantly inhibited the sapstaining fungal growth by in vitro analysis. The lipopeptides responsible for antifungal activity were identified by electrospray ionization mass spectrometry after partial purification by ion exchange and gel filtration chromatography. Four major ion peaks were identified as m/z 1023, 1038, 1060, and 1081 in B. licheniformis and 3 major ion peaks were identified as m/z 1036, 1058, and 1090 in B. subtilis. In conclusion, the partially purified lipopeptides may belong to surfactin and iturin family. In vivo analysis for antifungal activity of lipopeptides on wood was conducted in laboratory. In addition, the potential of extracts for fungal inhibition on surface and internal part of wood samples were analyzed by scanning electron microscopy.

Lichen Flora around the Korean Antarctic Scientific Station, King George Island, Antarctic: Ji Hee Kim , In-Young Ahn , Soon Gyu Hong , Mikhail Andreev , Kwang-Mi Lim , Mi Jin Oh , Young Jin Koh , Jae-Seoun Hur; J. Microbiol. 2006;44(5):480-491.; DOI: https://doi.org/2450 [pii]

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Abstract: As part of the long-term monitoring projects on Antarctic terrestrial vegetation in relation to global climate change, a lichen floristical survey was conducted around the Korean Antarctic Station (King Sejong Station), which is located on Barton Peninsula, King George Island, in January and February of 2006. Two hundred and twenty-five lichen specimens were collected and sixty-two lichen species in 38 genera were identified by morphological characteristics, chemical constituents, TLC analysis and ITS nucleotide sequence analysis.

Highland Macrolichen Flora of Northwestern Yunnan, China: Jae-Seoun Hur , Li-Song Wang , Soon-Ok Oh , Gyoung Hee Kim , Kwang-Mi Lim , Jae-Sung Jung , Young Jin Koh; J. Microbiol. 2005;43(3):228-236.; DOI: https://doi.org/2222 [pii]

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Abstract: Fifty-six species in 36 genera of macrolichens are reported from the Zhongdian area, northwest Yunnan, China during the lichenological expedition for highland macrolichen survey in June, 2004. More than 60% of these species have not been reported in South Korea. All of the 182 collected specimens are deposited in the Korean Lichen Research Institute (KoLRI) at Sunchon National University in Korea, and some of them are duplicated in the lichen herbarium, Crytogamic Herbarium, Kunming Institute of Botany, Academia Sinica (KUN-L) in China. This is the first report on the macrolichen flora in the visited areas.

Introduction of Saxicolous Lichens Distributed in Coastal Rocks of U-do Islet in Jeju, Korea: Hyung-Yeel Kahng , Byoung-Jun Yoon , Sung-Hyun Kim , Duck-Ja Shin , Jae-Seoun Hur , Hyun-Woo Kim , Eui-Sung Kang , Kye-Heon Oh , Young Jin Koh; J. Microbiol. 2004;42(4):292-298.; DOI: https://doi.org/2108 [pii]

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Abstract: This study reports, for the first time, the ivestigation of the distribution of Korean saxicolous lichens in the coastal rocks of U-do islet, which is known as an unpolluted zone in Jeju. More than thirty lichens were obtained and investigated from the coastal rocks frequently contacted by seawater. A molecular analysis using PCR amplification of the rRNA ITS regions revealed the coastal rock lichens could be placed into 8 families and 14 genera, Ramalinaceae (Bacidia, Ramalina), Physciaceae (Buellia, Dirinaria, Phaeophyscia, Physcia, Pyxine), Lecanoraceae (Candelaria, Lecanora), Parmeliaceae (Xanthoparmelia), Graphidaceae (Graphis), Pertusariaceae (Pertusaria), Rhizocarpaceae (Rhizocarpon), and Teloschistaceae (Caloplaca), showing a diversity of lichens, with foliose (flat leaf-like), crustose (crust-like), and fruticose (miniature shrub-like) life forms might be distributed in the coastal rocks. These findings suggested the possibility that the lichens identified in the present work might be resistant to a salty environment.

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