Fungal Infection of Mantis Shrimp (Oratosquilla oratoria) Caused by Two Anamorphic Fungi Found in Japan

Stem canker and dieback are important factors that limit the longevity and reduce the yield of blueberry (Vaccinium spp.) in Chile. In this study, species of Diaporthe associated with blueberry were isolated and identified. The internal transcribed spacer (ITS) regions of ribosomal DNA of 30 isolates and the translation elongation factor 1-α (EF1-α) of 14 isolates were sequenced, analyzed, and compared with their morphological and pathological characteristics. The molecular analysis of ITS sequences by alignment with those of ex-type strains deposited in GenBank and morphological characteristics allowed the identification of Diaporthe ambigua, D. australafricana, D. neotheicola, D. passiflorae, and Diaporthe sp. 1. However, morphology alone was insufficient to identify these species. The combined analysis of ITS and EF1-α gene sequences grouped the Chilean blueberry isolates in the same five groups obtained in the ITS analysis. Pathogenicity tests conducted with attached and detached blueberry shoots (<1 year old) and stems (1 to 2 years old) confirmed that isolates of these Diaporthe spp. were pathogenic. The symptoms were reproducible and consisted of necrotic reddish-brown cankers on blueberry shoots and stems. These isolates were capable of infecting blueberry fruit, causing a soft decay, suggesting that they were tissue nonspecific and were also pathogenic on shoots of apple, grapevine, and pear. D. australafricana was the most frequently isolated species and D. ambigua, D. australafricana, and D. passiflorae were highly virulent in shoots, stems, and fruit of blueberry. This study showed that at least four species of Diaporthe are primary pathogens, capable of causing stem canker symptoms on blueberry, and this is the first report of D. ambigua, D. neotheicola, and D. passiflorae attacking this host.

The phylogenetic relationships of anastomosis groups (AG) of Rhizoctonia associated with Ceratobasidium and Thanatephorus teleomorphs were determined by cladistic analyses of internal transcribed spacer (ITS) and 28S large subunit (LSU) regions of nuclear-encoded ribosomal DNA (rDNA). Combined analyses of ITS and LSU rDNA sequences from 41 isolates representing 28 AG of Ceratobasidium and Thanatephorus supported at least 12 monophyletic groupings within Ceratobasidium and Thanatephorus. There was strong support for separation of Ceratobasidium and Thanatephorus, however, six sequences representing different AG of Ceratobasidium grouped with certain sequences within the Thanatephorus clade. Phylogenetic analysis of ITS sequence data from 122 isolates revealed 31 genetically distinct groups from Thanatephorus (21 groups) and Ceratobasidium (10 groups) that corresponded well with previously recognized AG or AG subgroups. Although phylogenetic analysis of ITS sequences provided evidence that several AG of Ceratobasidium may be more closely related with some AG from Thanatephorus, these relationships were not as strongly supported by bootstrap analysis.

The phylogenetic relationships of anastomosis groups (AG) of Rhizoctonia associated with Ceratobasidium and Thanatephorus teleomorphs were determined by cladistic analyses of internal transcribed spacer (ITS) and 28S large subunit (LSU) regions of nuclear-encoded ribosomal DNA (rDNA). Combined analyses of ITS and LSU rDNA sequences from 41 isolates representing 28 AG of Ceratobasidium and Thanatephorus supported at least 12 monophyletic groupings within Ceratobasidium and Thanatephorus. There was strong support for separation of Ceratobasidium and Thanatephorus, however, six sequences representing different AG of Ceratobasidium grouped with certain sequences within the Thanatephorus clade. Phylogenetic analysis of ITS sequence data from 122 isolates revealed 31 genetically distinct groups from Thanatephorus (21 groups) and Ceratobasidium (10 groups) that corresponded well with previously recognized AG or AG subgroups. Although phylogenetic analysis of ITS sequences provided evidence that several AG of Ceratobasidium may be more closely related with some AG from Thanatephorus, these relationships were not as strongly supported by bootstrap analysis.

Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae).

In October 2020, fruit rot symptoms were detected on kiwifruit (Actinidia chinensis var. deliciosa 'Xuxiang') in southwestern Shaanxi (Hanzhong municipality; 107.27° E, 33.23° N) in China. Mature kiwifruit, during the harvest period, exhibited soft rot and brown lesions. The symptoms were similar than those reported for Alternaria alternata, Colletotrichum spp., Fusarium avenaceum and Rhizopus oryzae causing fruit rot on kiwifruit (Feng et al. 2019; Li et al. 2017; Kim et al. 2018; Zhao et al. 2020). The symptoms were observed in approximately 15% of the fruit in 6 kiwifruit orchards (31 ha in total). Ten samples of symptomatic tissue, approximately 1 cm2 in size, were sterilized in 2% NaOCl for 30 seconds and washed twice with sterilized water. The pathogen was isolated from all collected samples via culturing on PDA medium, containing 50 µg/mL chloramphenicol, at 28 ºC. Green powdery-like colonies were detected after 5 days (Figure 1). A total of 12 isolates were obtained via single spore isolation. Internal transcribed spacer (ITS), elongation factor 1-α (EF1-α) and RNA polymerase II subunit (RPB2) genes were amplified using ITS5/ITS4, A_EF1_F/A_EF1_R and RPB2-5F/RPB2-7cR (NJC03), or RPB2-7cF/RPB2-11aR (NJC04), primers, respectively. Eleven isolates shared the same sequences (NJC03), MZ801787 (ITS), MZ701709 (EF1-α) and MZ701707 (RPB2), while one of the isolates provided different sequences (NJC04), OK618459 (ITS), OK634020 (EF1-α) and OL331017 (RPB2). The obtained ITS sequences shared >99% homology to the ITS gene from A. flavus KU20018.4 (MT487825), the EF1-α sequences shared 100% homology to the EF1-α gene from A. flavus clinical2342 (KP054370) and the RPB2 sequences shared >99% homology to the RPB2 genes from A. flavus PW3170 (LC000581) and A. flavus NRRL3357 (XM_041293948). Molecular phylogenetic tree was constructed using MEGA7 with reference Aspergillus strains (Figure 2). Microscope observations of all isolates showed the presence of septate mycelium, circular unicellular conidia (2-4 µm diameter) and conidiophores, and agree with the morphology of A. flavus (Horn 2005). The pathogenicity of all isolates was screened using intact and wounded 'Xuxiang' kiwifruits (ten kiwifruits were used for each combination with 3 replicates), which were purchased from a local market. A 1 × 106 spores/mL (10 µL) solution of the isolates was used for the inoculation. Sterilized water was used in the control experiment. Inoculated kiwifruits were storage at 26 °C and 60% relative humidity for 10 days. Rot lesions in the wounded kiwifruits were totally covered by green mycelia, while the lesions on the intact kiwifruits were similar to the symptoms observed in the field. The pathogen was recovered and its identity was confirmed by sequence analysis of ITS, EF1-α and RPB2, fulfilling Koch's postulates. A. flavus is known to be an important fungal pathogen of corn, cotton and peanuts (Zhang et al. 2020). During recent years, A. flavus was reported to cause fruit rot on grapes (Ghuffar et al. 2020), and was identified on almond, fig, organic spelt and pistachio (Krulj et al. 2017; Ortega-Beltran et al. 2019). The presence of A. flavus in food products is an issue of global concern due to A. flavus is able to produce carcinogenic aflatoxin (Maxwell et al. 2021). As far as we know, this is the first report of A. flavus causing fruit rot on kiwifruit. This report will help to understand the distribution of A. flavus in crops and the food safety hazards that are present in China.

The powdery mildew fungus Podosphaera pannosa (Wallr.: Fr.) de Bary (syn. Sphaerotheca pannosa) is a major problem on roses worldwide. Twenty‐six monoconidial isolates of Podosphaera collected on roses and Prunus spp. in Belgium, Germany, France, Denmark, Israel and The Netherlands were characterized on the basis of differential reactions on in vitro rose genotypes and Prunus avium L. and by DNA sequence analysis of the rDNA ITS (internal transcribed spacer) region. Twenty‐four isolates were determined as P. pannosa. Amongst these, different groups could be distinguished. A first group of 18 isolates was highly virulent on rose and avirulent or very weakly virulent on P. avium. A second group of four isolates was highly virulent on both rose and P. avium. Analysis of the ITS sequence could discriminate these two groups of P. pannosa strains by a one base pair difference. Finally, two isolates of powdery mildew collected on Prunus sp. could be classified as P. pannosa based on their ITS sequence, which was identical to the ITS sequence of the isolates only highly virulent on roses. However, these two isolates were not able to infect roses. These results indicate that different strains of P. pannosa exist with varying host specificity. We demonstrated by ITS sequencing and plant reactions that the host range of P. pannosa comprises roses and Prunus spp.

Molecular phylogenetic relationships amongst Alternaria species and related fungi based upon analysis of nuclear ITS and mt SSU rDNA sequences

Ardisia crenata Sims, belonging to the family Myrsinaceae, has high medicinal and economic value. In July 2021,root rot disease was observed in plantations located in Ziyun (106°08'45″ E, 25°75'15″ N) and Xiuwen (106°46'53″ E, 26°54'01″ N) Counties, Guizhou Province, China, with an incidence rate of approximately 30% at fruit drop stage. The disease manifested as root softening, blackening, and phloem rot, while the aerial parts showed progressive yellowing, curling, and withering of leaves. Ultimately, the plant died. Nine symptomatic root segments were collected from fifteen infected plants, surface sterilized in 5% NaClO and 75% ethanol for 1 minute each, washed three times with sterile water, and incubated on potato dextrose agar (containing 10μg/mL of chloramphenicol) for five days at 28°C. The hyphal tip technique (Senanayake et al. 2020) was used to obtain pure cultures. Sixteen strains exhibiting similar morphological characteristics were isolated from the infected tissues. The colonies of these isolated cultures appeared white and turned light grey after 4 days. Five isolates were selected and grown on 2% water agar for 7 days for morphological characterization. Conidia were single-celled, hyaline, spindle-shaped to oval, and measured 12.04 to 19.47 µm long and 4.63 to 7.41 µm wide (n = 50). Based on these morphological features, the isolates were suspected to be Neofusicoccum parvum (Pavlic et al. 2009). For molecular identification, strain-7 was randomly selected as a representative individual to extract DNA. The internal transcribed spacer (ITS) region was amplified using primers ITS1/ITS4 (White et al. 1990). Additionally, the translation elongation factor 1-alpha (TEF1) gene was amplified using primers EF1-728F/EF1-986R (Rehner et al. 2005), and the β-tubulin (TUB2) gene was amplified using primers BT2a/BT2b (Glass et al. 1995). The sequences of strain-7 (accession number OR789487[ITS]; PV209690[TEF1]; PV209691[TUB2]) were deposited in GenBank, demonstrating a sequence homology of 99% to 100% (569/570, 265/265, 448/448) with N. parvum YBF5-1 (accession numbers PQ222752, PQ227810 and PQ227811). Based on morphological features and Neighbor-Joining method analyses of combined ITS, TEF1, and TUB2 gene sequences, strain-7 was identified as N. parvum. A pathogenicity test was performed using strain-7 by inoculating roots of 12-month-old A. crenata seedlings. The test was repeated seven times. Healthy seedlings were cut vertically with a sterile knife at 2 cm from the edge of one stem to create root damage. Spore suspensions (150 ml, 1 × 106 conidia/ml) of N. parvum were applied on the cut side, while the control group was watered with the same volume of sterile water. All plants were kept in the same glasshouse under natural conditions. After 7 days, some yellowish spots appeared on the leaf surface of some plants, with the edges turning dry and curled. The branches and leaves turned completely yellow, and the roots rotted extensively on the 14th day, whereas the control group remained asymptomatic. To satisfy Koch's postulates, N. parvum was reisolated from the inoculated plants but not from the control. N. parvum has been reported to cause leaf spot disease on Macadamia integrifolia and Vitis heyneanan in China (Li et al. 2023; Wu et al. 2015). This is the first report of N. parvum causing root rot in A. crenata in China. These findings provide a basis for the early detection of A. crenata root rot and the formulation of targeted control measures.

Codonopsis javanica, a Campanulaceae herb endemic to Guizhou, is locally called "Tudangshen", its root is used in medicine to fortify spleen-qi, moisten the lung and arrest cough, and promote lactation. In June 2023, root rot of C. javanica was observed in a cultivation field in Xiuwen County (106°46'48" E, 26°53'59" N), Guizhou Province, with the estimated disease incidence ranging from 20% to 50%. The initial symptoms were light brown spots on the surface of the root, and the spots were brown or black in severe cases, and the lower end of the root and the rhizome were rotted. The aboveground portions of the leaves exhibited yellowing and wilting, followed by withering and death. The diseased root tissue (5 mm × 5 mm) was cut and disinfected with 75 % alcohol for 15 s, 5 % sodium hypochlorite treatment for 1 min, followed by three rinses with sterile distilled water. After drying, the samples were transferred onto Potato Dextrose Agar (PDA) and incubated at 28 °C in darkness for 3-5 days. Through hyphal tip culture methodology (Senanayake et al. 2020), 12 strains with similar morphology were obtained. The colonies were white to purplish red. The fungus produced two types of conidia: microconidia and macroconidia. The microconidia were ovate, without septa or 1-2 septa, and the size was 4.98-9.22 × 1.88-3.65 μm. The macroconidia were sickle-shaped, slightly curved, 1-4 septa, and the size was 21.55-37.92 × 3.10-6.50 μm. Chlamydospores were subspherical to spherical. Based on these morphological features, the isolates were suspected to be Fusarium oxysporum (Leslie et al. 2006). For molecular confirmation of the morphological identification, strain ZPJ1 was randomly selected as a representative isolate for DNA extraction. The primers ITS1/ITS4, EF1-F6/R6, and RPB2-5F/RPB2-7cR were used to amplify three genomic DNA regions including the internal transcribed spacer (ITS)(Crous et al. 2021), translation elongation factor 1-alpha (EF1)(Moslemi et al. 2017), and RNA polymerase II second largest subunit (RPB2)(Xiang et al. 2025). The sequences of ZPJ1 (accession numbers PV750775, PV759349, and PV759350 for ITS, EF1 and RPB2, respectively) were deposited in GenBank, demonstrating a sequence homology of 99 % to 100 % (546/546, 702/705, 974/978) with F. oxysporum (accession numbers PP596264, MN892354, MN457466). Based on morphological features and maximum likelihood method analyses of combined ITS, EF1, and RPB2 gene sequences, strain ZPJ1 was identified as F. oxysporum. Pathogenicity experiments were conducted in a greenhouse with a temperature ranging from 24 to 27 °C and a relative humidity of 80 %. Root wounding was performed on potted C. javanica seedlings (n = 5, 1-year-old) using a sterile needle. A spore suspension (150 mL, 1 × 106 conidia/mL) of strain ZPJ1 was inoculated onto the wounds, with an equal volume of sterile water used as the control. After 18 days, all inoculated plants developed characteristic root rot symptoms, while the plants in the control group remained healthy and did not show any symptoms of root rot disease. F. oxysporum was successfully reisolated from the symptomatic roots and identified by the morphology and the molecular methods de-scribed above, meeting Koch’s postulates. Based on current understanding, this is the first report of F. oxysporum causing root rot in C. javanica in China. These findings provide a basis for the early detection of C. javanica root rot caused by F. oxysporum and the formulation of targeted control measures.

Korean winter hazel (Corylopsis coreana) is an endemic species of the South Korea (Seo et al. 2016; Kim et al. 2021), which is cultivated as an ornamental plant in this country, but also in China and Japan (Yoon et al. 2016). In July 2022, typical symptoms of a rust disease were observed on C. coreana at Jirisan National Park (35°22'07.7"N 127°34'57.7"E) in Namwon, South Korea. Spermogonia were epiphyllous, densely grouped, pale brown or orange-yellow, round, and 0.23 - 0.38 × 0.19 - 0.41 mm in size. Aecia were hypophyllous, mostly densely grouped, yellow or pale orange, resembling small wart-like galls, and 0.04 - 0.06 × 0.89 - 1.68 mm in size. Aeciospores were hyaline, mostly angularly globose, ellipsoid or oblong-ellipsoid, and 17.8 - 25.2 × 15 - 26.5 μm (average 19.2 × 19.1 μm; n=50) in size. Aeciospore walls were echinulate-verrucose, and 1.1 - 2.2 µm (average 1.7 µm; n=50) in thickness. In December 2022, dark brown telia were observed on the lower surface of Sasa borealis leaves near C. coreana. Telia were mostly scattered but often compacted, brown to dark brown, round, and 1.5 - 1.95 × 1.24 - 1.55 mm in size. Teliospores were either one- or two-celled with a long tapering apex, and light brown to brown in color. One-celled teliospores were globose, and 95.1 - 186.5 × 20.5 - 36.4 μm (average 136.4 × 27.7 μm; n=50) in size. Two-celled teliospores were ellipsoid-cylindrical, and 111.4 - 180.3 × 13.5 - 32.6 μm (average 149 × 21.1 μm; n=50) in size. Side walls of teliospores were golden and 2.2 - 5.5 µm thick (average 3.5 µm; n=50), and pedicels were hyaline, measuring 150 - 300 μm long. Uredinial stage was not observed. Disease symptomology and pathogen morphology were mostly consistent with that of Puccinia sasicola reported in Japan (Hino. 1955). For phylogenetic analysis, genomic DNA was extracted from the aeciospores collected from C. coreana and the teliospores collected from S. borealis. The internal transcribed spacer (ITS) rDNA and the large subunit (LSU) rDNA regions were amplified using ITS5u/ITS4rust (Pfunder and Schürch 2001) and LRust1R/LRust3 (Beenken et al. 2012) primers, respectively. Both sequences were identical for the spores collected from the two different hosts. The sequences were deposited in GenBank (PP171665, PP174211 [ITS], PP171709, PP174356 [LSU]). A GenBank BLAST search revealed 89.53% and 96.78% similarity with Puccinia kusanoi (KX610657) and Puccinia sp. (MT7298241) for ITS and LSU sequences, respectively. In maximum-likelihood phylogenetic analysis of ITS and LSU sequences, the isolates from C. coreana and S. borealis formed a separate clade from other Puccinia species. To test Koch's postulates, leaf disks with telia from S. borealis were directly attached to the adaxial surface of six healthy C. coreana leaves with tape. As controls, healthy S. borealis leaf disks were attached to the adaxial surface of six C. coreana leaves. After four weeks, four inoculated leaves developed small yellow wart-like galls on the abaxial surface, while the control leaves remained symptom-free. The isolates obtained from the inoculated leaves had identical sequences to the original isolate. There are no publicly available sequences for P. sasicola, nor did we find any sequences that match our Puccinia samples. Nevertheless, based on morphological characteristics and life cycle, our isolates closely matched with the previous description of P. sasicola by Hino (1955). To our knowledge, this is the first report of P. sasicola causing leaf rust in C. coreana in South Korea.

이 연구는 Alternaria속 균류 중에서 분생포자의 형태가 유사하여 분류, 동정이 매우 어려운 소형의 포자를 형성하는 11종의 Alternaria의 종간 유연관계와 분류체계를 확립하기 위하여 공시균들의 ribosomal DNA의 ITS 및 미토콘드리아 small submit 영역의 염기서열 분석, 그리고 URP primer에 의한 핵산지문분석을 실시하였다. 소형의 포자를 형성하는 11종 Alternaria속의 rDNA internal transcribed spacer(ITS) 영역과 미토콘드리아 small submit rDNA 의 염기서열을 분석하였던 바 A. infectoria를 제외한 10종의 Alternaria에서 100%의 상동성을 나타내었다. 이는 공시한 10종의 Alternaria가 유전적으로 매우 근연의 관계에 있음을 나타내며, 이 marker는 공시균들의 종구분에 이용할 수 없음을 나타내는 것이다. URP primer 10종을 공시하여 소형의 포자를 형성하는 Alternaria 균류의 핵산지문분석을 실시한 결과, 개개의 primer 로는 종간의 구분이 불가능하였으나 여러개의 primer를 종합하여 UPGMA분석을 실시할 경우 비록 종간 유사도는 높았디만 각각의 종은 독립된 cluster를 형성하여 종간 구별이 가능하였다. 자리공에서 분리한 Alternaria sp.는 URP-PCR 핵산지문 분석 결과 다른 Alternaria 종들과 차이가 인정됨으로 이 균은 미기록인 신종의 Alternaria로 사료되었다. A.infectoria는 다른 Alternaria 종들과 ITS 분석 및 URP-PCR 핵산지문분석에서 큰 차이를 보임으로서 뚜렷이 구별되는 종으로 판단되었다. To establish taxonomic system of morphologically similar species of small-spored Alternaria, phylogenetic analysis of internal transcribed spacer (ITS 1, ITS 2 and 5.8S rDNA) and mitochondrial small subunit (mt SSU) rDNA sequences and URP-PCR fingerprinting analysis from 11 species ofAlternaria were performed. Phylogenetic analysis of ITS and mt SSU rDNA sequences revealed that 10 out of 11 species of the smallspored Alternaria were phylogenetically identical with a bootstrap value of 100%. A. infectoria only was phylogenetically differentiated from the other species. The results suggest that the 10 small-spored Alternaria species are very closely related evolutionally and the markers can not be used for differentiation of the smallspored Alternaria species. URP-PCR fingerprinting analysis from eleven species of smallspored Alternaria using 10 URP primers showed that it was possible to differentiate the species, although genetic similarities were found among the species. The Alternaria sp. from common pokeweed could be distinguished from other species by URP-PCR analysis, and it was considered as a new species. A. infectoria could be easily distinguished from the other 10 species by phylogenetic analysis of ITS and mt SSU rDNA sequences and the URPPCR fingerprinting analysis.

Solanum muricatum, known as pepino or melon pear, is a species of evergreen shrub grown for its sweet edible fruits, which was introduced in Yunnan about 20 years ago. Since 2019 to now, serious blight disease was observed on foliages, haulms and fruits of pepino plants in Shilin (25°N, 103°E), which is the biggest pepino production area in China. The symptomatic blighted plants showed water-soaked and brown foliar lesions, haulm brown necrosis, black-brown and rotting fruits, and overall plant decline. The samples with typical disease symptoms were collected for pathogen isolation. After surface sterilization, disease samples were cut into small pieces and placed on rye sucrose agar medium amended with both 25 mg/liter rifampin and 50 mg/liter ampicillin, then incubated in the dark at 25℃ for 3 to 5 days. White fluffy colonies of mycelia that grew from the edge of diseased tissues were further purified and subcultured on rye agar plates. All purified isolates were identified as Phytophthora spp. based on morphological characteristics (Fry 2008). Sporangiophores were nodular and sympodial branches with swellings at the points where sporangia were attached. Sporangia that were hyaline and the average size were 22×40 μm were formed on the tip of sporangiophores and appeared as subspherical, ovoid, ellipsoid or lemon shaped with half-papillate on the spire. Mature sporangia were easilly detached from sporangiophores. For pathogenicity tests, healthy leaves, haulms and fruits of pepino were inoculated with 1×104 cfu/ml zoospore suspension of Phytophthora islolate (RSG2101), and controls were treated with sterile distilled water, respectively. After 5 to 7 days postinoculation, all Phytophthora-inoculated leaves and haulms showed water-soaked and brown lesions with white mold layer, fruits showed dark-brown firm lesions which got expanded and rotted the entire fruit. The symptoms were same as those occurred in natural fields. In contrast, no disease symptoms appeared in the control tissues. Phytophthora isolates could be reisolated and showed same morphological characteristics from the infected tissues of leaves, haulms, and fruits, sufficing Koch's postulates. Two common molecular targets of the internal transcribed spacer (ITS) region of ribosomal DNA and partial cytochrome c oxidase subunit II (CoxII) of the Phytophthora isolate (RSG2101) were amplified and sequenced with primers ITS1/ITS4 and FM75F/FM78R (Kroon et al. 2004). The ITS and CoxII sequence data were deposited in GenBank under accession numbers OM671258 and OM687527, respectively. Blastn analysis of both ITS and CoxII sequences showed 100% identity with isolates of P. infestans (MG865512, MG845685, AY770731 and DQ365743, respectively). Phylogenetic analysis also indicated that RSG2101 isolate and known P. infestans isolates localized in the same evolutionary branch based on sequences of ITS and CoxII, respectively. Based on these results, the pathogen was identified as P. infestans. It is known that P. infestans infection of pepino occurrs in Latin America and then it was recorded in other parts of the world such as New Zeeland and India (Hill, 1982; Abad and Abad,1997; Mohan et al. 2000).To our knowledge, this is the first report of late blight on pepino caused by P. infestans in China, which will be helpful to develop efficient blight management strategies on pepino.

Background. The term “DNA barcode” is used extensively in molecular taxonomy. Basically, this technique is based on the use of a DNA sequence (about 400–800 bp) as a standard to identify and determine the species relation of organisms quickly and accurately. Therefore, DNA barcodes not only help taxonomists in classifying and identifying species, but also improve their ability to control, understand and utilize biodiversity. In this study, the authors conducted identification of samples of Anoectochilus setaceus Blume collected in Thanh Hoa through the isolated sequence of ITS gene regions.Materials and methods. Total DNA was extracted from young leaves of A. setaceus samples using CTAB method. The ITS gene segment was amplified by PCR and sequenced. This genetic sequence was analyzed, compared and used to establish a phylogenetic tree using BioEdit, BLAST and DNASTAR programs.Results and conclusion. We isolated 4 sequences of the ITS gene region in 4 A. setaceus samples collected at Xuan Lien and Pu Luong of Thanh Hoa province; the ITS gene region was 667 nucleotide long. The findings identified the samples as the same species and showed 99% similarity to the ITS gene sequence of A. roxburghii (Wall.) Lindl. published in GenBank, GQ328774. This study also demonstrates that the method employing internal transcribed spacer (ITS) sequences is an effective tool to identify A. setaceus taxa.

We present the first characterization of fungal community diversity of natural mixed-species biofilms on artificial marine reefs. Four artificial reefs in the Mississippi (MS) Sound, USA, representing low-profile (underwater) and high-profile (periodically air-exposed) conditions were sampled every 3 months over a 23-month period to investigate changes in fungal diversity within reef biofilms. Fungal presence was assessed via PCR amplification of the internal transcribed spacer (ITS) region of fungal ribosomal DNA, and by terminal restriction fragment length polymorphism (T-RFLP) analysis of fungal ITS regions – the latter being used to track variation in fungal community structure with respect to season, location, and reef profile type. Fungal communities were also characterized taxonomically through both morphological identification and phylogenetic comparisons of ITS gene sequences, with 36 fungal genera cultured from reef biofilms. Using a multivariate statistical approach, significant temporal and spatial differences in fungal biofilm communities were detected. High-profile reefs differed significantly in biofilm fungal community composition across the 10 sampling periods. This assessment of marine fungal biofilm communities over time provides novel insights into the fungal diversity present on artificial reefs in an understudied region, the north-central Gulf of Mexico.

The 16S-23S rDNA internal transcribed spacer (ITS) of Roseobacter denitrificans, Roseobacter litoralis, Ruegeria algicola and strains of the recently described species Antarctobacter heliothermus and Roseovarius tolerans were analysed in order to examine DNA sequence variations and to draw conclusions about inter- and intraspecific relationships. A. heliothermus included four strains with an ITS fragment length of 1092 bp. Roseovarius tolerans was described on the basis of eight strains. Five of these harboured two ITS fragments of different lengths (959 and about 1100 bp), while the others had one fragment of either 1083 bp (two strains) or 1165 bp (one strain). ITS lengths of the related species Roseobacter denitrificans, Roseobacter litoralis and Ruegeria algicola were found to be 980, 984 and 1158 bp, respectively. Phylogenetic analyses of the DNA sequences allowed species affiliation of strains with sequence length differences of > 200 bp and recognition of relationships based on a well-supported ITS tree. The strains of A. heliothermus and Roseovarius tolerans each formed a monophyletic branch and they were separated from each other by Ruegeria algicola. This species was now clearly separated from Roseobacter denitrificans and Roseobacter litoralis, which corresponded to the new genus affiliation of Ruegeria algicola. These data were additionally supported by analyses of the structure, relative position and order of genes for tRNA(Ile) and tRNA(Ala) found within the ITS of each strain. Comparative DNA sequence analyses of ITS and 16S rDNA revealed limitations, on species and strain levels, with respect to the phylogenetic resolution of the 16S rDNA due to the limited number of informative (variable) sites, while ITS sequence analyses provided more variable and sufficiently conserved positions to discriminate between strains and to reconstruct their taxonomic relationships.