M. L. Ilhamdi, Agil Al Idrus, D. Santoso, G. Hadiprayitno, M. Syazali, Ismawan Hariadi
Abstract. Ilhamdi ML, Idrus AA, Santoso D, Hadiprayitno G, Syazali M, Hariadi I. 2023. Species richness and dispersion patterns of Lepidoptera (Rhopalocera) in the Nuraksa Forest Park, Lombok, Indonesia. Biodiversitas 25: 62-70. Butterflies play an important role in maintaining the balance of ecosystems and pollinators. This study aims to analyze the species richness and dispersion patterns of butterflies from the Rhopalocera suborder in this area. The field survey was carried out from January to July 2023. The sampling site was divided into six areas. Specimens that were successfully collected using a hand net were identified at the Biological Laboratory of Mataram University. During this survey, 1576 specimens of Rhopalocera were recorded. This number consists of 47 species. Several species, such as Junonia atlites Linnaeus, 1763, Junonia almana Linnaeus, 1758, Danaus genutia Cramer, 1779, Hypolimnas misippus Linnaeus, 1764, and Amathusia phidippus Linnaeus, 1763 were found to be new records in the Nuraksa Forest Park area. The habitat types with the highest number of species are the utilization block and the traditional block, with 47 species. The habitat type with the lowest number of species is a special block with only 15 species. However, the highest species richness was found in the protection block, with an R-value of 8.09. The most dominant species is Leptosia nina Fabricius, 1793, and the least dominant is A. phidippus. Each species depicted a varying distribution in the six habitat types. According to the analysis results, it was found that the dispersion pattern of all Rhopalocera species is clustered. The research results themselves contribute to conservation and ecotourism efforts.
{"title":"Species richness and dispersion patterns of Lepidoptera (Rhopalocera) in the Nuraksa Forest Park, Lombok, Indonesia","authors":"M. L. Ilhamdi, Agil Al Idrus, D. Santoso, G. Hadiprayitno, M. Syazali, Ismawan Hariadi","doi":"10.13057/biodiv/d250108","DOIUrl":"https://doi.org/10.13057/biodiv/d250108","url":null,"abstract":"Abstract. Ilhamdi ML, Idrus AA, Santoso D, Hadiprayitno G, Syazali M, Hariadi I. 2023. Species richness and dispersion patterns of Lepidoptera (Rhopalocera) in the Nuraksa Forest Park, Lombok, Indonesia. Biodiversitas 25: 62-70. Butterflies play an important role in maintaining the balance of ecosystems and pollinators. This study aims to analyze the species richness and dispersion patterns of butterflies from the Rhopalocera suborder in this area. The field survey was carried out from January to July 2023. The sampling site was divided into six areas. Specimens that were successfully collected using a hand net were identified at the Biological Laboratory of Mataram University. During this survey, 1576 specimens of Rhopalocera were recorded. This number consists of 47 species. Several species, such as Junonia atlites Linnaeus, 1763, Junonia almana Linnaeus, 1758, Danaus genutia Cramer, 1779, Hypolimnas misippus Linnaeus, 1764, and Amathusia phidippus Linnaeus, 1763 were found to be new records in the Nuraksa Forest Park area. The habitat types with the highest number of species are the utilization block and the traditional block, with 47 species. The habitat type with the lowest number of species is a special block with only 15 species. However, the highest species richness was found in the protection block, with an R-value of 8.09. The most dominant species is Leptosia nina Fabricius, 1793, and the least dominant is A. phidippus. Each species depicted a varying distribution in the six habitat types. According to the analysis results, it was found that the dispersion pattern of all Rhopalocera species is clustered. The research results themselves contribute to conservation and ecotourism efforts.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"86 16","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140462487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract. Siblos SKV, Tabugo SR. 2023. High-throughput analysis using 16S rRNA sequencing of bacterial communities associated in selected mangrove species from Bayug Island, Iligan City, Philippines. Biodiversitas 25: 53-61. Mangrove ecosystems are recognized globally as highly productive ecosystems, that play a crucial role in carbon sequestration, erosion control, water purification, and as essential breeding grounds for diverse aquatic life. They also offer specialized ecological niches, accommodating a diverse range of organisms, including bacterial communities. This study aimed to investigate bacterial communities of Bayug Island in Iligan City, Philippines, inhabiting six mangrove species, namely Rhizophora stylosa Griffith, Rhizophora apiculata Blume, Rhizophora mucronata Lam., Sonneratia alba Sm., Ceriops tagal (Perr.) C.B.Rob., and Nypa fruticans Wurmb and their possible functions within the mangrove forests. Genomic DNA was extracted from the six pooled soil samples, and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. Six amplicon libraries, corresponding to the mangrove species were analyzed with Parallel Meta Suite software, yielding 173,270 amplicon sequence variants (ASVs) after quality control. The study identified the top five most abundant ASVs in the mangrove rhizosphere, linked to the genera Vibrio, Stenotrophomonas, Serratia, Pseudoalteromonas, and Achromobacter. Among the mangrove species, S. alba exhibited higher alpha diversity according to the Shannon index. PICRUSt analysis revealed that microorganisms are involved in biodegradation, xenobiotic metabolism, and other metabolic processes within the mangroves. These bacteria could find applications in environmental cleanup, bioremediation, waste treatment, and soil health improvement. This result contributes to the ongoing ecological restoration of mangrove forests at the research site.
{"title":"High-throughput analysis using 16S rRNA sequencing of bacterial communities associated in selected mangrove species from Bayug Island, Iligan City, Philippines","authors":"S. Siblos, S. Tabugo","doi":"10.13057/biodiv/d250107","DOIUrl":"https://doi.org/10.13057/biodiv/d250107","url":null,"abstract":"Abstract. Siblos SKV, Tabugo SR. 2023. High-throughput analysis using 16S rRNA sequencing of bacterial communities associated in selected mangrove species from Bayug Island, Iligan City, Philippines. Biodiversitas 25: 53-61. Mangrove ecosystems are recognized globally as highly productive ecosystems, that play a crucial role in carbon sequestration, erosion control, water purification, and as essential breeding grounds for diverse aquatic life. They also offer specialized ecological niches, accommodating a diverse range of organisms, including bacterial communities. This study aimed to investigate bacterial communities of Bayug Island in Iligan City, Philippines, inhabiting six mangrove species, namely Rhizophora stylosa Griffith, Rhizophora apiculata Blume, Rhizophora mucronata Lam., Sonneratia alba Sm., Ceriops tagal (Perr.) C.B.Rob., and Nypa fruticans Wurmb and their possible functions within the mangrove forests. Genomic DNA was extracted from the six pooled soil samples, and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. Six amplicon libraries, corresponding to the mangrove species were analyzed with Parallel Meta Suite software, yielding 173,270 amplicon sequence variants (ASVs) after quality control. The study identified the top five most abundant ASVs in the mangrove rhizosphere, linked to the genera Vibrio, Stenotrophomonas, Serratia, Pseudoalteromonas, and Achromobacter. Among the mangrove species, S. alba exhibited higher alpha diversity according to the Shannon index. PICRUSt analysis revealed that microorganisms are involved in biodegradation, xenobiotic metabolism, and other metabolic processes within the mangroves. These bacteria could find applications in environmental cleanup, bioremediation, waste treatment, and soil health improvement. This result contributes to the ongoing ecological restoration of mangrove forests at the research site.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"82 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140462515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yuli S. Fitriana, Eko Sulistyadi, Rizki Kurnia Tohir, Mhd Muhajir Hasibuan, Farid Rifaie, Ibnu Maryanto, Arie Mulia Lubis, M. F. Rifqi
Abstract. Fitriana YS, Sulistyadi E, Tohir RK, Hasibuan MM, Rifaie F, Maryanto I, Lubis AM, Rifqi MF. 2024. Population study of long-tailed macaque (Macaca fascicularis) on Deli Island, Banten, Indonesia. Biodiversitas 25: 144-150. Understanding the distribution and population dynamics of primate species is essential for practical conservation efforts. However, such information is often unavailable, even for species whose populations appear abundant. The long-tailed macaque (Macaca fascicularis Raffles, 1821) is a species with a wide range in Southeast Asia, including Sumatra, Java, Kalimantan, Bali, Lombok, and Lesser Sunda in Indonesia. However, comprehensive data on population density across its Indonesian distribution area still needs to be improved. To address this knowledge gap, we conducted a thorough survey and study to estimate the population density of long-tailed macaques on Deli Island, located in Banten Province. Long-tailed macaques were introduced to Deli Island between 1989 and 1990 with a total of 1000 males and 10,000 females. To date, a total of 9,500 individuals have been harvested from this island in the period 1991-2010. We employed the line transect distance sampling (LTDS) method with a perpendicular distance approach that covered all habitat types throughout the island. Our findings revealed that the population density of long-tailed macaques on Deli Island is approximately five individuals per hectare, with an estimated total population of 4,860. The data pertaining to age structure and sex ratio is notably limited, primarily due to challenges in identification caused by dense vegetation. To address these limitations and acquire a more comprehensive understanding, additional research is essential for the accurate determination of the age structure and sex ratio on the island. Our study provides crucial baseline data for conserving this species. We recommend implementing a systematic survey encompassing the entire distribution range of the long-tailed macaque across Indonesia. Such an initiative will be instrumental in assessing its threat status and laying out a comprehensive plan for conservation efforts.
摘要Fitriana YS, Sulistyadi E, Tohir RK, Hasibuan MM, Rifaie F, Maryanto I, Lubis AM, Rifqi MF.2024.印度尼西亚万丹省德利岛长尾猕猴种群研究。Biodiversitas 25: 144-150.了解灵长类物种的分布和种群动态对实际保护工作至关重要。然而，即使是种群数量看似丰富的物种，也往往无法获得此类信息。长尾猕猴（Macaca fascicularis Raffles，1821 年）在东南亚分布广泛，包括印度尼西亚的苏门答腊岛、爪哇岛、加里曼丹岛、巴厘岛、龙目岛和小巽他岛。然而，印尼分布区内种群密度的综合数据仍有待改进。为了填补这一知识空白，我们在万丹省的德利岛上进行了一次全面的调查和研究，以估计长尾猕猴的种群密度。长尾猕猴于1989年至1990年间被引入德利岛，当时共引进了1000只雄性长尾猕猴和10,000只雌性长尾猕猴。1991-2010 年间，该岛共捕获了 9,500 只长尾猕猴。我们采用了线段距离取样法（LTDS），以垂直距离取样的方法覆盖了全岛的所有栖息地类型。我们的研究结果表明，德利岛上长尾猕猴的种群密度约为每公顷五只，估计总种群数量为 4,860 只。有关年龄结构和性别比例的数据明显有限，这主要是由于茂密的植被给识别带来了困难。为了解决这些局限性并获得更全面的了解，必须开展更多研究，以准确确定岛上的年龄结构和性别比例。我们的研究为保护该物种提供了重要的基础数据。我们建议对长尾猕猴在整个印度尼西亚的分布范围进行系统调查。这一举措将有助于评估长尾猕猴的威胁状况，并为保护工作制定全面计划。
{"title":"Population study of long-tailed macaque (Macaca fascicularis) on Deli Island, Banten, Indonesia","authors":"Yuli S. Fitriana, Eko Sulistyadi, Rizki Kurnia Tohir, Mhd Muhajir Hasibuan, Farid Rifaie, Ibnu Maryanto, Arie Mulia Lubis, M. F. Rifqi","doi":"10.13057/biodiv/d250114","DOIUrl":"https://doi.org/10.13057/biodiv/d250114","url":null,"abstract":"Abstract. Fitriana YS, Sulistyadi E, Tohir RK, Hasibuan MM, Rifaie F, Maryanto I, Lubis AM, Rifqi MF. 2024. Population study of long-tailed macaque (Macaca fascicularis) on Deli Island, Banten, Indonesia. Biodiversitas 25: 144-150. Understanding the distribution and population dynamics of primate species is essential for practical conservation efforts. However, such information is often unavailable, even for species whose populations appear abundant. The long-tailed macaque (Macaca fascicularis Raffles, 1821) is a species with a wide range in Southeast Asia, including Sumatra, Java, Kalimantan, Bali, Lombok, and Lesser Sunda in Indonesia. However, comprehensive data on population density across its Indonesian distribution area still needs to be improved. To address this knowledge gap, we conducted a thorough survey and study to estimate the population density of long-tailed macaques on Deli Island, located in Banten Province. Long-tailed macaques were introduced to Deli Island between 1989 and 1990 with a total of 1000 males and 10,000 females. To date, a total of 9,500 individuals have been harvested from this island in the period 1991-2010. We employed the line transect distance sampling (LTDS) method with a perpendicular distance approach that covered all habitat types throughout the island. Our findings revealed that the population density of long-tailed macaques on Deli Island is approximately five individuals per hectare, with an estimated total population of 4,860. The data pertaining to age structure and sex ratio is notably limited, primarily due to challenges in identification caused by dense vegetation. To address these limitations and acquire a more comprehensive understanding, additional research is essential for the accurate determination of the age structure and sex ratio on the island. Our study provides crucial baseline data for conserving this species. We recommend implementing a systematic survey encompassing the entire distribution range of the long-tailed macaque across Indonesia. Such an initiative will be instrumental in assessing its threat status and laying out a comprehensive plan for conservation efforts.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"208 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140462456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract. Chotimah, Soffan A, Joko T. 2024. Diversity of universal stress protein in Enterobacteriales and its reduced expressions on Pectobacterium brasiliense after manuka honey treatment. Biodiversitas 25: 49-52. Universal stress proteins (Usps) support the survival of an organism by increasing their expressions under stress conditions, which include nutritional deficiencies, heat shock, and antibiotics. However, the expression of uspA in Staphylococcus aureus decreased after manuka honey exposure. Manuka honey also inhibits the growth of Pectobacterium brasiliense, although its effect on the usp gene of this soft-rot pathogen has never been studied. This study aimed to determine the diversity of Usps in P. brasiliense and their orthologs from Enterobacteriales using phylogenetic analysis. The effects of manuka honey on usp gene expressions were also investigated using quantitative real-time polymerase chain reaction and pathogenicity assay of P. brasiliense on Chinese cabbage. The results revealed that the UspA, UspB, and UspE of P. brasiliense had the closest similarity to those of P. carotovorum. By contrast, UspG had the closest similarity to P. polaris. The usp gene expressions were downregulated by 5, 16, 10, and 62% in 5% (w/v) manuka honey treatment. When tested on Chinese cabbage, P. brasiliense treated with manuka honey caused smaller lesion symptoms than those in the control treatment. This reduced virulence of P. brasiliense may be related to the reduced expression of usp genes triggered by manuka honey.
摘要.Chotimah, Soffan A, Joko T. 2024.肠杆菌中通用应激蛋白的多样性及其在麦卢卡蜂蜜处理后对巴西果胶杆菌的表达减少。Biodiversitas 25: 49-52.通用应激蛋白（Usps）在营养缺乏、热休克和抗生素等应激条件下会增加表达量，从而支持生物体的生存。然而，在接触麦卢卡蜂蜜后，金黄色葡萄球菌中 uspA 的表达量减少。麦卢卡蜂蜜还能抑制巴西果胶杆菌的生长，但它对这种软腐病原体的 usp 基因的影响却从未被研究过。本研究旨在利用系统发育分析法确定巴西栉水母中 Usps 的多样性及其与肠杆菌的同源物。此外，还利用实时定量聚合酶链式反应和大白菜上 P. brasiliense 的致病性实验研究了麦卢卡蜂蜜对 usp 基因表达的影响。研究结果表明，P. brasiliense 的 UspA、UspB 和 UspE 与 P. carotovorum 的相似度最高。相比之下，UspG 与 P. polaris 的相似度最高。在 5%（w/v）麦卢卡蜂蜜处理中，usp 基因表达分别下调了 5%、16%、10% 和 62%。在大白菜上进行试验时，用麦卢卡蜂蜜处理的巴西痢疾杆菌造成的病害症状比对照组小。P. brasiliense 的毒性降低可能与麦卢卡蜂蜜引发的 usp 基因表达减少有关。
{"title":"Diversity of universal stress protein in Enterobacteriales and its reduced expressions on Pectobacterium brasiliense after manuka honey treatment","authors":"Chotimah Chotimah, Alan Soffan, Tri Joko","doi":"10.13057/biodiv/d250106","DOIUrl":"https://doi.org/10.13057/biodiv/d250106","url":null,"abstract":"Abstract. Chotimah, Soffan A, Joko T. 2024. Diversity of universal stress protein in Enterobacteriales and its reduced expressions on Pectobacterium brasiliense after manuka honey treatment. Biodiversitas 25: 49-52. Universal stress proteins (Usps) support the survival of an organism by increasing their expressions under stress conditions, which include nutritional deficiencies, heat shock, and antibiotics. However, the expression of uspA in Staphylococcus aureus decreased after manuka honey exposure. Manuka honey also inhibits the growth of Pectobacterium brasiliense, although its effect on the usp gene of this soft-rot pathogen has never been studied. This study aimed to determine the diversity of Usps in P. brasiliense and their orthologs from Enterobacteriales using phylogenetic analysis. The effects of manuka honey on usp gene expressions were also investigated using quantitative real-time polymerase chain reaction and pathogenicity assay of P. brasiliense on Chinese cabbage. The results revealed that the UspA, UspB, and UspE of P. brasiliense had the closest similarity to those of P. carotovorum. By contrast, UspG had the closest similarity to P. polaris. The usp gene expressions were downregulated by 5, 16, 10, and 62% in 5% (w/v) manuka honey treatment. When tested on Chinese cabbage, P. brasiliense treated with manuka honey caused smaller lesion symptoms than those in the control treatment. This reduced virulence of P. brasiliense may be related to the reduced expression of usp genes triggered by manuka honey.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"119 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140462220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hiksa Maulana Saputra, N. Maryana, Pudjianto Pudjianto
Abstract. Saputra HM, Maryana N, Pudjianto. 2023. Parasitoid of coffee berry borer, Hypothenemus hampei Ferrari (Coleoptera: Curculionidae) at Bogor District, West Java, Indonesia. Biodiversitas 24: 6447-6453. The coffee berry borer (CBB), Hypothenemus hampei Ferrari (Coleoptera: Curculionidae), is an essential pest of coffee plants that can cause loss and decrease in the quality of coffee berries. Parasitoids were expected to affect the presence of coffee berry borer in the ecosystem as one of its natural enemies. This study aimed to identify and describe the parasitoid of CBB in Bogor District, West Java, Indonesia. The study was conducted from June 2022 to January 2023 on three coffee cultivation located in three sub-districts in Bogor District, i.e., Cijeruk, Dramaga, and Sukamakmur. This study collected attacked coffee berries by CBB from coffee cultivation that kept the coffee berry until the parasitoids emerged and the parasitoids were identified; the morphological characters and descriptions of parasitoids CBB were presented. Ten species of Hymenopteran parasitoids belonging to five families were found. These parasitoids were Microgastrinae, Mendesellinae (Braconidae), Trissolcus sp. (Scelionidae), Anagyrus sp., Marxella sp., Procheiloneurus sp., Pararhopella sp., Parablastothrix sp. (Encyrtidae), Pronotalia sp. (Eulophidae), and Pteromalus sp. (Pteromalidae). The parasitoids of CBB in Bogor District were quite diverse, but their abundance was low.
{"title":"Parasitoid of coffee berry borer, Hypothenemus hampei Ferrari (Coleoptera: Curculionidae) at Bogor District, West Java, Indonesia","authors":"Hiksa Maulana Saputra, N. Maryana, Pudjianto Pudjianto","doi":"10.13057/biodiv/d241206","DOIUrl":"https://doi.org/10.13057/biodiv/d241206","url":null,"abstract":"Abstract. Saputra HM, Maryana N, Pudjianto. 2023. Parasitoid of coffee berry borer, Hypothenemus hampei Ferrari (Coleoptera: Curculionidae) at Bogor District, West Java, Indonesia. Biodiversitas 24: 6447-6453. The coffee berry borer (CBB), Hypothenemus hampei Ferrari (Coleoptera: Curculionidae), is an essential pest of coffee plants that can cause loss and decrease in the quality of coffee berries. Parasitoids were expected to affect the presence of coffee berry borer in the ecosystem as one of its natural enemies. This study aimed to identify and describe the parasitoid of CBB in Bogor District, West Java, Indonesia. The study was conducted from June 2022 to January 2023 on three coffee cultivation located in three sub-districts in Bogor District, i.e., Cijeruk, Dramaga, and Sukamakmur. This study collected attacked coffee berries by CBB from coffee cultivation that kept the coffee berry until the parasitoids emerged and the parasitoids were identified; the morphological characters and descriptions of parasitoids CBB were presented. Ten species of Hymenopteran parasitoids belonging to five families were found. These parasitoids were Microgastrinae, Mendesellinae (Braconidae), Trissolcus sp. (Scelionidae), Anagyrus sp., Marxella sp., Procheiloneurus sp., Pararhopella sp., Parablastothrix sp. (Encyrtidae), Pronotalia sp. (Eulophidae), and Pteromalus sp. (Pteromalidae). The parasitoids of CBB in Bogor District were quite diverse, but their abundance was low.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"45 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140490663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mariana Febrilianti Resilinda Putri, Irfan Alias Kendek, F. J. Wibisono, M. Effendi, Dadik Rahardjo, W. Tyasningsih, E. N. Ugbo
Abstract. Putri MFR, Kendek IA, Wibisono FJ, Effendi MH, Rahardjo D, Tyasningsih W, Ugbo EN. 2023. Molecular detection of iron gene on multidrug resistant avian fecal Escherichia coli isolated from broiler on traditional markets, Surabaya, Indonesia. Biodiversitas 24: 6454-6460. Avian Fecal Escherichia coli (AFEC) is the cause of colibacillosis, which often infects the poultry industry throughout the world. The virulence gene influences the iroN factor, which causes systemic infections in poultry. This research aimed to determine Multidrug Resistance (MDR) in AFEC obtained from traditional markets in Surabaya. There were 96 cloacal swab samples from broiler chickens. The samples were isolated and identified using culture media in the form of Eosin Methylene Blue Agar (EMBA), gram stain, Triple Sugar Iron Agar (TSIA), Sulfide Indole Motility (SIM), Simmons Citrate Agar (SCA), Voges Proskauer (MR-VP) indole and methyl test; detection of multidrug resistance using Mueller-Hinton Agar (MHA) media. The results of the isolation and identification of Escherichia coli bacteria in this study showed that 60.4% of the isolates were positive for Escherichia coli. Escherichia coli is resistant to tetracycline antibiotics by 56%, ciprofloxacin by 55%, antibiotics aztreonam 29%, kanamycin 20%, and chloramphenicol 18%. The multidrug resistance test result on Escherichia coli was 25.8%. The PCR test results for the iroN gene were 40%. Therefore, there are MDR and iroN genes in avian fecal Escherichia coli in Surabaya traditional markets; APEC with iroN gene poses the potential to affect public health.
{"title":"Molecular detection of iron gene on multidrug resistant avian fecal Escherichia coli isolated from broiler on traditional markets, Surabaya, Indonesia","authors":"Mariana Febrilianti Resilinda Putri, Irfan Alias Kendek, F. J. Wibisono, M. Effendi, Dadik Rahardjo, W. Tyasningsih, E. N. Ugbo","doi":"10.13057/biodiv/d241207","DOIUrl":"https://doi.org/10.13057/biodiv/d241207","url":null,"abstract":"Abstract. Putri MFR, Kendek IA, Wibisono FJ, Effendi MH, Rahardjo D, Tyasningsih W, Ugbo EN. 2023. Molecular detection of iron gene on multidrug resistant avian fecal Escherichia coli isolated from broiler on traditional markets, Surabaya, Indonesia. Biodiversitas 24: 6454-6460. Avian Fecal Escherichia coli (AFEC) is the cause of colibacillosis, which often infects the poultry industry throughout the world. The virulence gene influences the iroN factor, which causes systemic infections in poultry. This research aimed to determine Multidrug Resistance (MDR) in AFEC obtained from traditional markets in Surabaya. There were 96 cloacal swab samples from broiler chickens. The samples were isolated and identified using culture media in the form of Eosin Methylene Blue Agar (EMBA), gram stain, Triple Sugar Iron Agar (TSIA), Sulfide Indole Motility (SIM), Simmons Citrate Agar (SCA), Voges Proskauer (MR-VP) indole and methyl test; detection of multidrug resistance using Mueller-Hinton Agar (MHA) media. The results of the isolation and identification of Escherichia coli bacteria in this study showed that 60.4% of the isolates were positive for Escherichia coli. Escherichia coli is resistant to tetracycline antibiotics by 56%, ciprofloxacin by 55%, antibiotics aztreonam 29%, kanamycin 20%, and chloramphenicol 18%. The multidrug resistance test result on Escherichia coli was 25.8%. The PCR test results for the iroN gene were 40%. Therefore, there are MDR and iroN genes in avian fecal Escherichia coli in Surabaya traditional markets; APEC with iroN gene poses the potential to affect public health.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"175 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140501352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
E. S. Kusmintarsih, Hanan Hassan Alsheikh Mahmoud, M. H. Sastranegara, Hamdan Syakuri, Agus Nuryanto, T. B. Ambarningrum
Abstract. Kusmintarsih ES, Mahmoud HHA, Sastranegara MH, Syakuri H,Nuryanto A, Ambarningrum TB. 2023. Barcoding of ornamental freshwater shrimp, Neocaridina denticulata (De Haan, 1844) from the aquatic ornamental market in Purbalingga, Central Java, Indonesia. Biodiversitas 24: 3601-3608. Indonesia is one of the world’s leading aquatic ornamental shrimps producers and exports. One of the aquatic ornament shrimp species is a Neocaridina denticulate (De Haan, 1844). There is a wide range of colors including red, bright red, yellow, orange, green, blue, violet, black, and color combinations. It is a landlocked Atydiae family species comprising31 species and subspecies. Due to taxonomic difficulties, this species is continually under revision, and the validation of a few species is currently questionable and uncertain for the relationships among the various colors of N. denticulata. The Cytochrome Oxidase gene I (CO1) gene sequences of mitochondrial DNA were used for species DNA barcoding studies. This study aimed to validate the taxonomic status of different colors of N. denticulata species using the mitochondrial DNA or mtDNA Cytochrome oxidase (CO1) gene sequences. Neighbour Joining trees were constructed based on 545 bp of CO1 gene from white, black, red, yellow, blue colors, and their combination. Several sequences were derived from GenBank for relevant species from different countries and the outgroup. The result showed that all samples are homolog, even to N. denticulata from China NC_023823.1.
摘要Kusmintarsih ES, Mahmoud HHA, Sastranegara MH, Syakuri H,Nuryanto A, Ambarningrum TB.2023.来自印度尼西亚中爪哇 Purbalingga 水生观赏市场的淡水观赏虾 Neocaridina denticulata（De Haan，1844 年）的条形码。Biodiversitas 24: 3601-3608。印度尼西亚是世界领先的水生观赏虾生产国和出口国之一。其中一种水生观赏虾是Neocaridina denticulate（De Haan，1844年）。它有多种颜色，包括红色、鲜红色、黄色、橙色、绿色、蓝色、紫色、黑色以及各种颜色的组合。它是 Atydiae 科的内陆种，包括 31 个种和亚种。由于分类上的困难，该物种仍在不断修正中，目前对一些物种的验证尚存在疑问，也无法确定 N. denticulata 各种颜色之间的关系。线粒体 DNA 的细胞色素氧化酶基因 I（CO1）基因序列被用于物种 DNA 条形码研究。本研究旨在利用线粒体 DNA 或 mtDNA 细胞色素氧化酶（CO1）基因序列验证不同颜色的牙鲆物种的分类地位。根据白色、黑色、红色、黄色、蓝色及其组合的 545 bp CO1 基因构建了邻接树。从 GenBank 中提取了不同国家相关物种和外群的多个序列。结果表明，所有样本都是同源的，甚至与中国的 N. denticulata NC_023823.1 也是同源的。
{"title":"Barcoding of ornamental freshwater shrimp, Neocaridina denticulata (De Haan, 1844) from the aquatic ornamental market in Purbalingga, Central Java, Indonesia","authors":"E. S. Kusmintarsih, Hanan Hassan Alsheikh Mahmoud, M. H. Sastranegara, Hamdan Syakuri, Agus Nuryanto, T. B. Ambarningrum","doi":"10.13057/biodiv/d240714","DOIUrl":"https://doi.org/10.13057/biodiv/d240714","url":null,"abstract":"Abstract. Kusmintarsih ES, Mahmoud HHA, Sastranegara MH, Syakuri H,Nuryanto A, Ambarningrum TB. 2023. Barcoding of ornamental freshwater shrimp, Neocaridina denticulata (De Haan, 1844) from the aquatic ornamental market in Purbalingga, Central Java, Indonesia. Biodiversitas 24: 3601-3608. Indonesia is one of the world’s leading aquatic ornamental shrimps producers and exports. One of the aquatic ornament shrimp species is a Neocaridina denticulate (De Haan, 1844). There is a wide range of colors including red, bright red, yellow, orange, green, blue, violet, black, and color combinations. It is a landlocked Atydiae family species comprising31 species and subspecies. Due to taxonomic difficulties, this species is continually under revision, and the validation of a few species is currently questionable and uncertain for the relationships among the various colors of N. denticulata. The Cytochrome Oxidase gene I (CO1) gene sequences of mitochondrial DNA were used for species DNA barcoding studies. This study aimed to validate the taxonomic status of different colors of N. denticulata species using the mitochondrial DNA or mtDNA Cytochrome oxidase (CO1) gene sequences. Neighbour Joining trees were constructed based on 545 bp of CO1 gene from white, black, red, yellow, blue colors, and their combination. Several sequences were derived from GenBank for relevant species from different countries and the outgroup. The result showed that all samples are homolog, even to N. denticulata from China NC_023823.1.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139356237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tanapat Bamrungpanichtavorn, Sunisa Ungwiwatkul, P. Boontanom, Aiya Chantarasiri
Abstract. Bamrungpanichtavorn T, Ungwiwatkul S, Boontanom P, Chantarasiri A. 2023. Diversity and cellulolytic activity of cellulase-producing bacteria isolated from the soils of two mangrove forests in Eastern Thailand. Biodiversitas 24: 3891-3902. The Southeast Asian countries hold the largest proportion of the world's mangrove area. Mangrove forests are a potential source for the isolation of economic microbial enzymes. Cellulases are a widely used microbial enzyme for cellulose degradation in various industries. Therefore, this study aimed to isolate, genetically identify, and enzymatically characterize cellulase-producing bacteria from the soils of two mangrove forests in Eastern Thailand. Twenty-six cellulase-producing bacteria were isolated and subsequently genotyped by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis of the 16S rRNA genes. Thirteen different RFLP patterns were obtained and genetically analyzed into six bacterial genera comprising Aeromonas, Bacillus, Chryseobacterium, Lysinibacillus, Pseudomonas, and Vibrio. The Bacillus species were the predominant cellulase-producing bacteria in the study sites. Moreover, the cellulase-producing Chryseobacterium and Lysinibacillus had hardly ever been reported. The Bacillus sp. strain RY08B was the most active cellulase-producing bacterium with 1.510±0.060 U/mL of CMCase activity. The optimum temperature and pH for the CMCase activity were determined to be 50°C at a pH of 7.0 with a thermal stability range of 25-50°C at a pH of 7.0. This bacterium could be applied in several environmentally friendly industries requiring mild conditions for their production processes.
{"title":"Diversity and cellulolytic activity of cellulase-producing bacteria isolated from the soils of two mangrove forests in Eastern Thailand","authors":"Tanapat Bamrungpanichtavorn, Sunisa Ungwiwatkul, P. Boontanom, Aiya Chantarasiri","doi":"10.13057/biodiv/d240728","DOIUrl":"https://doi.org/10.13057/biodiv/d240728","url":null,"abstract":"Abstract. Bamrungpanichtavorn T, Ungwiwatkul S, Boontanom P, Chantarasiri A. 2023. Diversity and cellulolytic activity of cellulase-producing bacteria isolated from the soils of two mangrove forests in Eastern Thailand. Biodiversitas 24: 3891-3902. The Southeast Asian countries hold the largest proportion of the world's mangrove area. Mangrove forests are a potential source for the isolation of economic microbial enzymes. Cellulases are a widely used microbial enzyme for cellulose degradation in various industries. Therefore, this study aimed to isolate, genetically identify, and enzymatically characterize cellulase-producing bacteria from the soils of two mangrove forests in Eastern Thailand. Twenty-six cellulase-producing bacteria were isolated and subsequently genotyped by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis of the 16S rRNA genes. Thirteen different RFLP patterns were obtained and genetically analyzed into six bacterial genera comprising Aeromonas, Bacillus, Chryseobacterium, Lysinibacillus, Pseudomonas, and Vibrio. The Bacillus species were the predominant cellulase-producing bacteria in the study sites. Moreover, the cellulase-producing Chryseobacterium and Lysinibacillus had hardly ever been reported. The Bacillus sp. strain RY08B was the most active cellulase-producing bacterium with 1.510±0.060 U/mL of CMCase activity. The optimum temperature and pH for the CMCase activity were determined to be 50°C at a pH of 7.0 with a thermal stability range of 25-50°C at a pH of 7.0. This bacterium could be applied in several environmentally friendly industries requiring mild conditions for their production processes.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"67 2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139356209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nevlya Mia Safitri, Fanany Wuri Prastiwi, Syifa Salsabila, Yogi Feriawan, Alif Brilianto, W. D. Nugroho
Abstract. Safitri NM, Prastiwi FW, Salsabila S, Feriawan Y, Brilianto A, Nugroho WD. 2023. Anatomical characteristics of the leaning stem in Pinus merkusii seedling. Biodiversitas 24: 3796-3802. Pinus merkusii Jungh. & de Vriese is one of the tropical conifer species. The species formed reaction wood called compression wood (CW) when the stem grows in an abnormal position. CW in stem wood is frequently found to cause several problems for utilization in the use of its products. However, there are few studies on the anatomical characteristics of reaction wood in tropical conifer. This study aimed to observe the differences in anatomical characteristics between compression (CW) and opposite (OW) woods in leaning the stem of P. merkusii seedlings and their anatomical differences compared to normal wood (NW). Approx. 1-year-old P. merkusii seedlings from a nursery in Trenggalek, East Java, Indonesia, that were naturally bent or tilted were used in the study. Anatomical characteristics of wood, namely the dimension of tracheids, rays, resin canals, and the proportion of cells were observed in the study. The results showed that CW of P. merkusii seedlings formed a rounded tracheid shape and intercellular space. The differences between CW and OW in P. merkusii seedlings were significant in terms of height of ray cells, tracheid proportion, and resin canal proportion. However, tracheid length, tracheid diameter, tracheid wall thickness, resin canal diameter and frequency, rays frequency, and ray proportion were not significantly different compared to OW and NW.
摘要Safitri NM, Prastiwi FW, Salsabila S, Feriawan Y, Brilianto A, Nugroho WD.2023.梅花松幼苗倾斜茎的解剖特征。Biodiversitas 24: 3796-3802.Pinus merkusii Jungh. & de Vriese 是热带针叶树种之一。当茎干以不正常的位置生长时，该树种会形成称为压缩木（CW）的反应木。茎木中的 CW 经常被发现会给其产品的使用带来一些问题。然而，有关热带针叶树反应木解剖特征的研究很少。本研究旨在观察梅花杉幼苗茎干倾斜时压缩木（CW）和反向木（OW）的解剖学特征差异，以及它们与正常木（NW）的解剖学差异。研究使用了印度尼西亚东爪哇 Trenggalek 苗圃中自然弯曲或倾斜的约 1 年树龄的 P. merkusii 树苗。研究中观察了木材的解剖特征，即管胞、射线、树脂管的尺寸和细胞的比例。结果表明，P. merkusii幼苗的CW形成了圆形的气管形状和细胞间隙。在射线细胞高度、气管比例和树脂管比例方面，P. merkusii幼苗的CW和OW差异显著。然而，气管长度、气管直径、气管壁厚度、树脂管直径和频率、射线频率和射线比例与 OW 和 NW 相比差异不显著。
{"title":"Anatomical characteristics of the leaning stem in Pinus merkusii seedling","authors":"Nevlya Mia Safitri, Fanany Wuri Prastiwi, Syifa Salsabila, Yogi Feriawan, Alif Brilianto, W. D. Nugroho","doi":"10.13057/biodiv/d240717","DOIUrl":"https://doi.org/10.13057/biodiv/d240717","url":null,"abstract":"Abstract. Safitri NM, Prastiwi FW, Salsabila S, Feriawan Y, Brilianto A, Nugroho WD. 2023. Anatomical characteristics of the leaning stem in Pinus merkusii seedling. Biodiversitas 24: 3796-3802. Pinus merkusii Jungh. & de Vriese is one of the tropical conifer species. The species formed reaction wood called compression wood (CW) when the stem grows in an abnormal position. CW in stem wood is frequently found to cause several problems for utilization in the use of its products. However, there are few studies on the anatomical characteristics of reaction wood in tropical conifer. This study aimed to observe the differences in anatomical characteristics between compression (CW) and opposite (OW) woods in leaning the stem of P. merkusii seedlings and their anatomical differences compared to normal wood (NW). Approx. 1-year-old P. merkusii seedlings from a nursery in Trenggalek, East Java, Indonesia, that were naturally bent or tilted were used in the study. Anatomical characteristics of wood, namely the dimension of tracheids, rays, resin canals, and the proportion of cells were observed in the study. The results showed that CW of P. merkusii seedlings formed a rounded tracheid shape and intercellular space. The differences between CW and OW in P. merkusii seedlings were significant in terms of height of ray cells, tracheid proportion, and resin canal proportion. However, tracheid length, tracheid diameter, tracheid wall thickness, resin canal diameter and frequency, rays frequency, and ray proportion were not significantly different compared to OW and NW.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"93 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139356249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
K. Rozana, S. Prabaningtyas, Dimas Ricko Widyatama
Abstract. Rozana K, Prabaningtyas S, Widyatama DR. 2023. Distribution and biodegradation analysis of polyvinyl chloride microplastic by indigenous bacteria isolated from Supit Urang Landfill, Malang, Indonesia. Biodiversitas 24: 3853-3859. Microplastic waste is one of the most common forms of environmental pollution. Indonesia is the world's fourth largest contributor of plastic waste. One type of plastic that accumulates in the environment is Polyvinyl Chloride (PVC). Various attempts or methods have been developed to reduce PVC plastic waste, one of which is with the help of using indigenous bacteria. This research is essential in determining the best optimization method for PVC biodegradation agents through molecular and bioinformatic approaches. Indigenous bacteria were isolated from Supit Urang Landfill, Malang City, with three dilution levels (10-4, 10-5, and 10-6). The three highest isolates were taken for further biodegradation tests for 30 days and were identified based on the 16S rRNA gene. Then, the BLAST results were made into a phylogenetic tree to determine the kinship of each species. The isolation results obtained 17 bacterial isolates, selected by initial biodegradation screening for 10 days. Isolate K4 has a degradation percentage of 1.61±0.007379%. While isolates K4 and K15 have a biodegradation potential of 3.04±0.001861%. and 1.90±0.005576%. The BLAST results showed that K4 isolate had a 99% similarity to Staphylococcus capitis, K14 had a 99% similarity to Bacillus subtilis, and K15 had a 100% similarity to Acinetobacter pittii.
{"title":"Distribution and biodegradation analysis of polyvinyl chloride microplastic by indigenous bacteria isolated from Supit Urang Landfill, Malang, Indonesia","authors":"K. Rozana, S. Prabaningtyas, Dimas Ricko Widyatama","doi":"10.13057/biodiv/d240724","DOIUrl":"https://doi.org/10.13057/biodiv/d240724","url":null,"abstract":"Abstract. Rozana K, Prabaningtyas S, Widyatama DR. 2023. Distribution and biodegradation analysis of polyvinyl chloride microplastic by indigenous bacteria isolated from Supit Urang Landfill, Malang, Indonesia. Biodiversitas 24: 3853-3859. Microplastic waste is one of the most common forms of environmental pollution. Indonesia is the world's fourth largest contributor of plastic waste. One type of plastic that accumulates in the environment is Polyvinyl Chloride (PVC). Various attempts or methods have been developed to reduce PVC plastic waste, one of which is with the help of using indigenous bacteria. This research is essential in determining the best optimization method for PVC biodegradation agents through molecular and bioinformatic approaches. Indigenous bacteria were isolated from Supit Urang Landfill, Malang City, with three dilution levels (10-4, 10-5, and 10-6). The three highest isolates were taken for further biodegradation tests for 30 days and were identified based on the 16S rRNA gene. Then, the BLAST results were made into a phylogenetic tree to determine the kinship of each species. The isolation results obtained 17 bacterial isolates, selected by initial biodegradation screening for 10 days. Isolate K4 has a degradation percentage of 1.61±0.007379%. While isolates K4 and K15 have a biodegradation potential of 3.04±0.001861%. and 1.90±0.005576%. The BLAST results showed that K4 isolate had a 99% similarity to Staphylococcus capitis, K14 had a 99% similarity to Bacillus subtilis, and K15 had a 100% similarity to Acinetobacter pittii.","PeriodicalId":8801,"journal":{"name":"Biodiversitas Journal of Biological Diversity","volume":"72 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139356394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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