Subham Mohanta, Megha Bahuguna, John David Baley, Shivika Sharma, Vikas Sharma
Microbial cellulases are an important industrial enzyme having diverse applications in biotechnology, environmental challenges, industrial products and processes. Extremophiles like thermophillic bacteria are a good source of industrially important cellulases as these can withstand industrially rigorous procedures like paper deinking, fabric material softening, bio stoning, paper and pulp, biopolishing cloth material, animal feed and juice. Identification of novel cellulases or improving them through biotechnological interventions has remained a challenge for researchers. Genetic manipulation of thermophilic bacteria for increased cellulase production or synthetic biology approaches for cellulase gene/gene cluster extraction from thermophilic bacteria and expression in appropriate hosts for improved cellulase synthesis. The classic and high-throughput technologies like genomics, metagenomics and bioinformatics could be exploited to isolate cellulase genes from a variety of thermophilic bacteria and further processing. Keeping in view the ultimate requirement of extremophilic cellulases in industries, present study is a compilation of various aspects related to extremophilic cellulases their sources, production, biotechnological interventions and challenges.
{"title":"Extremophilic Cellulases: A Comprehensive Review","authors":"Subham Mohanta, Megha Bahuguna, John David Baley, Shivika Sharma, Vikas Sharma","doi":"10.22146/jtbb.74986","DOIUrl":"https://doi.org/10.22146/jtbb.74986","url":null,"abstract":"Microbial cellulases are an important industrial enzyme having diverse applications in biotechnology, environmental challenges, industrial products and processes. Extremophiles like thermophillic bacteria are a good source of industrially important cellulases as these can withstand industrially rigorous procedures like paper deinking, fabric material softening, bio stoning, paper and pulp, biopolishing cloth material, animal feed and juice. Identification of novel cellulases or improving them through biotechnological interventions has remained a challenge for researchers. Genetic manipulation of thermophilic bacteria for increased cellulase production or synthetic biology approaches for cellulase gene/gene cluster extraction from thermophilic bacteria and expression in appropriate hosts for improved cellulase synthesis. The classic and high-throughput technologies like genomics, metagenomics and bioinformatics could be exploited to isolate cellulase genes from a variety of thermophilic bacteria and further processing. Keeping in view the ultimate requirement of extremophilic cellulases in industries, present study is a compilation of various aspects related to extremophilic cellulases their sources, production, biotechnological interventions and challenges.","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139282957","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}
Cedrela odorata L. was introduced as a possible forest restauration species in classified forests at Côte d’Ivoire. Because of its demonstrated invasive behavior in other tropical forests, this study aimed to assess the impact of Cedrela odorata on the regeneration of spontaneous plant species in tree plantations. On the base of Cedrela odorata larger tree densities, two types of forest plantation were considered: Type I (240 stems/ha) and Type II (176 stems/ha). In these plantations, plots with 0.25 ha were chosen to locate each tree with dbh ≥ 2.5 cm, in an orthonormal reference. The tree density, the basal area, the species richness, the Shannon diversity index and the rank-abundance curves were determined considering smaller and larger trees. The horizontal spatial arrangement and Ripley’s K function were performed to understand the spatial relationship between Cedrela odorata smaller trees and those of spontaneous species. The results shown lower spontaneous plant species richness (15-20 species) and diversity (1.15 - 1.43); the dominance of Cedrela odorata smaller trees (43.02 – 62.95 % of all stems). The Cedrela odorata smaller trees and those of other species have dependent spatial distributions; expressed by a spatial repulsion between the two groups up to a distance of 18 m in the most densified forest plantation. This repulsion was related to an aggregated distribution of Cedrela odorata smaller trees in plantation with higher tree density. The study suggests a 170-stems/ha (or lower) of Cedrela odorata planting density for biodiversity establishment improvement outcomes in forest plantations.
{"title":"Spatial Distribution of Cedrela Odorata Smaller Trees Affects Forest Regeneration in Exotic Tree Plantations in Central Côte d’Ivoire","authors":"B. T. A. Vroh, Abdoulaye Koné","doi":"10.22146/jtbb.84322","DOIUrl":"https://doi.org/10.22146/jtbb.84322","url":null,"abstract":"Cedrela odorata L. was introduced as a possible forest restauration species in classified forests at Côte d’Ivoire. Because of its demonstrated invasive behavior in other tropical forests, this study aimed to assess the impact of Cedrela odorata on the regeneration of spontaneous plant species in tree plantations. On the base of Cedrela odorata larger tree densities, two types of forest plantation were considered: Type I (240 stems/ha) and Type II (176 stems/ha). In these plantations, plots with 0.25 ha were chosen to locate each tree with dbh ≥ 2.5 cm, in an orthonormal reference. The tree density, the basal area, the species richness, the Shannon diversity index and the rank-abundance curves were determined considering smaller and larger trees. The horizontal spatial arrangement and Ripley’s K function were performed to understand the spatial relationship between Cedrela odorata smaller trees and those of spontaneous species. The results shown lower spontaneous plant species richness (15-20 species) and diversity (1.15 - 1.43); the dominance of Cedrela odorata smaller trees (43.02 – 62.95 % of all stems). The Cedrela odorata smaller trees and those of other species have dependent spatial distributions; expressed by a spatial repulsion between the two groups up to a distance of 18 m in the most densified forest plantation. This repulsion was related to an aggregated distribution of Cedrela odorata smaller trees in plantation with higher tree density. The study suggests a 170-stems/ha (or lower) of Cedrela odorata planting density for biodiversity establishment improvement outcomes in forest plantations.","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139289648","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}
The Glagah consortium is a mixed culture of various microalgae and bacteria isolated from Glagah Beach, Yogyakarta. Cobalamin and thiamine, which are given by symbiotic bacteria, are assumed will increase biomass. This study aimed to determine the effect of cobalamin and thiamine on microalgae biomass production in the Glagah consortium. The microalgae of Glagah consortium were cultivated for 10 days with vancomycin and gentamicin antibiotic as treatment and without antibiotics as a control. The parameters measured included the number of bacterial colonies, cobalamin and thiamine levels measured by LC-MS, chlorophyll a and b levels, cell density of microalgae and dry biomass. The highest level of cobalamin and thiamine was in the Glagah consortium without antibiotics. Cobalamin and thiamine increased in the exponential phase along with the increasing Staphylococcus sp. colonies. The Quantity of Staphylococcus sp. colonies in the exponential phase was 62.105 (cfu/mL). The level of cobalamin in the exponential phase was 2.33 µg/L and the level of thiamine in the exponential phase was 49.71 µg/L. The highest productivity dried weight biomass was 0.0134 g/L/day in the day-6th on the Glagah consortium without antibiotics. This result showed that microalgae and bacterial interaction was mutualism symbiosis involving cobalamin and thiamine that increased in the exponential phase along with the increasing Staphylococcus sp. colonies. This interaction was able to increase biomass microalgae.
{"title":"Cobalamin and Thiamine Effect on Microalgae Biomass Production in the Glagah Consortium","authors":"Tri Wahyu Setyaningrum, Arief Budiman, E. Suyono","doi":"10.22146/jtbb.81949","DOIUrl":"https://doi.org/10.22146/jtbb.81949","url":null,"abstract":"The Glagah consortium is a mixed culture of various microalgae and bacteria isolated from Glagah Beach, Yogyakarta. Cobalamin and thiamine, which are given by symbiotic bacteria, are assumed will increase biomass. This study aimed to determine the effect of cobalamin and thiamine on microalgae biomass production in the Glagah consortium. The microalgae of Glagah consortium were cultivated for 10 days with vancomycin and gentamicin antibiotic as treatment and without antibiotics as a control. The parameters measured included the number of bacterial colonies, cobalamin and thiamine levels measured by LC-MS, chlorophyll a and b levels, cell density of microalgae and dry biomass. The highest level of cobalamin and thiamine was in the Glagah consortium without antibiotics. Cobalamin and thiamine increased in the exponential phase along with the increasing Staphylococcus sp. colonies. The Quantity of Staphylococcus sp. colonies in the exponential phase was 62.105 (cfu/mL). The level of cobalamin in the exponential phase was 2.33 µg/L and the level of thiamine in the exponential phase was 49.71 µg/L. The highest productivity dried weight biomass was 0.0134 g/L/day in the day-6th on the Glagah consortium without antibiotics. This result showed that microalgae and bacterial interaction was mutualism symbiosis involving cobalamin and thiamine that increased in the exponential phase along with the increasing Staphylococcus sp. colonies. This interaction was able to increase biomass microalgae.","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139309691","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}
Rico Alexander Pratama, J. Astina, A. A. Parikesit
Type 2 diabetes mellitus (T2DM) is a global problem with increasing prevalence. The current treatments have made an immense progress with some side effects, such as drug resistance, acute kidney toxicity, and increased risk of heart attack. Banana (Musa spp.) peel comprises 40% of banana fruit contains high phenolic compounds whilst some studies have suggested a correlation between phenolic compounds and antidiabetic activity. One of the novel protein targets that has been identified as a potential anti-diabetic treatment is PTP1B (PDB ID:2NT7). Therefore, this study aimed to screen the potential PTP1B inhibitor for antidiabetic treatment from phenolic compounds in banana peel. QSAR, molecular docking, ADME-Tox, and molecular dynamics analysis were deployed to examine forty-three phenolic compounds in banana peel. Eighteen ligands were screened by QSAR analysis and eight of them had a lower binding energy than the standard (ertiprotafib) in molecular docking, with urolithin A and chrysin were the lowest. Both passed Lipinski’s rule of five, had a good intestinal absorption, and no blood-brain barrier penetration, however, their mutagenicity, carcinogenicity, and irritation to the skin and eyes were still in questions. Molecular dynamics analysis found both of them were in a stable conformation with PTP1B. This study suggested a potential of urolithin A and chrysin as PTP1B inhibitor for antidiabetic treatment. Additionally, further experimentation is required to validate this finding.
{"title":"In silico Screening of Potential Antidiabetic Phenolic Compounds from Banana (Musa spp.) Peel Against PTP1B Protein","authors":"Rico Alexander Pratama, J. Astina, A. A. Parikesit","doi":"10.22146/jtbb.83124","DOIUrl":"https://doi.org/10.22146/jtbb.83124","url":null,"abstract":"Type 2 diabetes mellitus (T2DM) is a global problem with increasing prevalence. The current treatments have made an immense progress with some side effects, such as drug resistance, acute kidney toxicity, and increased risk of heart attack. Banana (Musa spp.) peel comprises 40% of banana fruit contains high phenolic compounds whilst some studies have suggested a correlation between phenolic compounds and antidiabetic activity. One of the novel protein targets that has been identified as a potential anti-diabetic treatment is PTP1B (PDB ID:2NT7). Therefore, this study aimed to screen the potential PTP1B inhibitor for antidiabetic treatment from phenolic compounds in banana peel. QSAR, molecular docking, ADME-Tox, and molecular dynamics analysis were deployed to examine forty-three phenolic compounds in banana peel. Eighteen ligands were screened by QSAR analysis and eight of them had a lower binding energy than the standard (ertiprotafib) in molecular docking, with urolithin A and chrysin were the lowest. Both passed Lipinski’s rule of five, had a good intestinal absorption, and no blood-brain barrier penetration, however, their mutagenicity, carcinogenicity, and irritation to the skin and eyes were still in questions. Molecular dynamics analysis found both of them were in a stable conformation with PTP1B. This study suggested a potential of urolithin A and chrysin as PTP1B inhibitor for antidiabetic treatment. Additionally, further experimentation is required to validate this finding.","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139313861","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}
We reported the current distribution of Leptophryne spp. in Gede Pangrango National Park. Leptophryne cruentata was recorded in Cibodas (Cikundul waterfall and Goa Lalay), Selabintana (Cibeureum Waterfall), and Goalpara (Rasta Waterfall), whereas Leptophryne borbonica was only reported from a creek at lowland forest of Bodogol. Goa Lalay and Rasta waterfall were explicitly reported as new distribution locations of Leptophryne cruentata. It was strictly found at a higher elevation usually within reach of waterfalls that generate substantial background noise, except in Cibodas in which Leptophryne cruentata can also be found in two noisy creeks located at a fairly great distance from waterfalls (100 – 170 meters).
我们报告了 Gede Pangrango 国家公园目前的 Leptophryne spp.分布情况。Leptophryne cruentata在Cibodas（Cikundul瀑布和Goa Lalay）、Selabintana（Cibeureum瀑布）和Goalpara（Rasta瀑布）都有记录，而Leptophryne borbonica仅在Bodogol低地森林的一条小溪中有报告。Goa Lalay 和 Rasta 瀑布被明确报告为 Leptophryne cruentata 的新分布地点。除了在西博达斯（Cibodas），在距离瀑布相当远（100-170 米）的两条溪流中也能发现 Leptophryne cruentata。
{"title":"Notes on The Current Distribution and Abundance of The Frog Genus Leptophryne spp. (Anura: Bufonidae) in Gede Pangrango National Park","authors":"Mohamad Isnin Noer, Ratih Tryas Intani, Priya Yuga Prasetya, Alvita Dwi Lestari, Boby Darmawan","doi":"10.22146/jtbb.84031","DOIUrl":"https://doi.org/10.22146/jtbb.84031","url":null,"abstract":"We reported the current distribution of Leptophryne spp. in Gede Pangrango National Park. Leptophryne cruentata was recorded in Cibodas (Cikundul waterfall and Goa Lalay), Selabintana (Cibeureum Waterfall), and Goalpara (Rasta Waterfall), whereas Leptophryne borbonica was only reported from a creek at lowland forest of Bodogol. Goa Lalay and Rasta waterfall were explicitly reported as new distribution locations of Leptophryne cruentata. It was strictly found at a higher elevation usually within reach of waterfalls that generate substantial background noise, except in Cibodas in which Leptophryne cruentata can also be found in two noisy creeks located at a fairly great distance from waterfalls (100 – 170 meters).","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139316261","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}
Nuzlan Rasjid, F. Y. Kurniawan, Saifa Usni Putri, Aviesta Linggabuwana, Ireneus Seno Prasojo, E. Semiarti
The most favorite ornamental crop in Indonesia is orchid which benefited as floriculture. Therefore, the quality of this crop must be improved. Biotechnology is appropriate to be used to improve the quality and quantity of orchid plants. To conduct this method, researchers must know what genes function in plant development. In Phalaenopsis orchids, the gene has been identified as homeobox genes called Phalaenopsis Orchid Homeobox1 (POH1). This research aims to conduct in silico analysis of the gene. The materials were retrieved from mRNA and amino acid databases. Then, the materials are aligned, visualized, motif location analysis, motif function discovery, phylogenetic construction, and protein 3D structural modelling. Based on mRNA and amino acid alignment, there are 4 domain regions that are conserved in POH1 and other homologous genes, such as KNOX1, KNOX2, ELK Domain, and Homeobox KN Domain, which roles as a transcription factor involved in plant development. SWISS-MODEL and ColabFold were used in protein modelling of the protein. By ColabbFold modelling, the modelling prediction uses 325 residues, higher than SWISS-MODEL in 59 residues. ColabFold validation by Ramachandra Plot depicts having the most favourite regions is 68.6%, while SWISS-MODEL is 92.3%. Another validation parameter is overall quality factor and QMEAN Score. Protein modelling by ColabFold has overall quality factor 89.252 and QMEAN Score 0.41 ± 0.05. However, SWISS-MODEL 3D prediction has overall quality factor 98.039 and QMEAN score of 0.71 ± 0.11.
{"title":"In Silico Analysis of Phalaenopsis Orchid Homeobox1 (POH1) Functional Gene for Shoot Development in Phalaenopsis Orchid","authors":"Nuzlan Rasjid, F. Y. Kurniawan, Saifa Usni Putri, Aviesta Linggabuwana, Ireneus Seno Prasojo, E. Semiarti","doi":"10.22146/jtbb.83934","DOIUrl":"https://doi.org/10.22146/jtbb.83934","url":null,"abstract":"The most favorite ornamental crop in Indonesia is orchid which benefited as floriculture. Therefore, the quality of this crop must be improved. Biotechnology is appropriate to be used to improve the quality and quantity of orchid plants. To conduct this method, researchers must know what genes function in plant development. In Phalaenopsis orchids, the gene has been identified as homeobox genes called Phalaenopsis Orchid Homeobox1 (POH1). This research aims to conduct in silico analysis of the gene. The materials were retrieved from mRNA and amino acid databases. Then, the materials are aligned, visualized, motif location analysis, motif function discovery, phylogenetic construction, and protein 3D structural modelling. Based on mRNA and amino acid alignment, there are 4 domain regions that are conserved in POH1 and other homologous genes, such as KNOX1, KNOX2, ELK Domain, and Homeobox KN Domain, which roles as a transcription factor involved in plant development. SWISS-MODEL and ColabFold were used in protein modelling of the protein. By ColabbFold modelling, the modelling prediction uses 325 residues, higher than SWISS-MODEL in 59 residues. ColabFold validation by Ramachandra Plot depicts having the most favourite regions is 68.6%, while SWISS-MODEL is 92.3%. Another validation parameter is overall quality factor and QMEAN Score. Protein modelling by ColabFold has overall quality factor 89.252 and QMEAN Score 0.41 ± 0.05. However, SWISS-MODEL 3D prediction has overall quality factor 98.039 and QMEAN score of 0.71 ± 0.11.","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139318402","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}
S. Suyono, Imey Tamara Indivia, R. S. Resmisari, Fitriyah Fitriyah, Didik Wahyudi
This study uses morphological characteristics and RAPD markers to evaluate the polyploidization of synthetic porang. Seeds of triploid porang (2n=2x=26) were soaked in the different colchicine concentrations for 24 hours. After colchicine treatment, the porang seeds were planted to an MS medium that contained 2.2 µM of 6-benzylaminopurine (BAP), then, 40 days after planting in the MS media, the morphology and molecular of synthetic polyploid porang were characterized. For DNA extraction, a total of 100 mg of young leaves of porang plantlet was collected. One way Anova followed by the Duncan test (95%) was performed for phenotypic characterization. The number of different alleles, number of effective alleles, Shannon's information index, diversity, and unbiased diversity were assessed for genetic diversity. Synthetic polyploid porang has a higher total shoot, root, and wider leaves than normal porang. Polyploidy induction also successfully increased the genetic diversity of porang, and the genetic diversity will increase porang adaptability and sustainability of porang cultivation.
{"title":"Induction of Synthetic Polyploids of Porang (Amorphophallus muelerri Blume) and Assessment of Its Genetic Variability Using Morphological Data and RAPD Molecular Marker","authors":"S. Suyono, Imey Tamara Indivia, R. S. Resmisari, Fitriyah Fitriyah, Didik Wahyudi","doi":"10.22146/jtbb.82238","DOIUrl":"https://doi.org/10.22146/jtbb.82238","url":null,"abstract":"This study uses morphological characteristics and RAPD markers to evaluate the polyploidization of synthetic porang. Seeds of triploid porang (2n=2x=26) were soaked in the different colchicine concentrations for 24 hours. After colchicine treatment, the porang seeds were planted to an MS medium that contained 2.2 µM of 6-benzylaminopurine (BAP), then, 40 days after planting in the MS media, the morphology and molecular of synthetic polyploid porang were characterized. For DNA extraction, a total of 100 mg of young leaves of porang plantlet was collected. One way Anova followed by the Duncan test (95%) was performed for phenotypic characterization. The number of different alleles, number of effective alleles, Shannon's information index, diversity, and unbiased diversity were assessed for genetic diversity. Synthetic polyploid porang has a higher total shoot, root, and wider leaves than normal porang. Polyploidy induction also successfully increased the genetic diversity of porang, and the genetic diversity will increase porang adaptability and sustainability of porang cultivation.","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"1979 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139320541","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}
This study aims to determine the use of vertical stratification of mangrove vegetation by bird species in the mangrove ecosystem of Nusa Lembongan. The study was conducted at seven mangrove ecosystem sites, in April-July 2021. Observation of the number of birds in each vegetation strata was carried out using the point count method. The association of the use of vegetation strata by bird species was carried out by Detrended correspondence analysis (DCA) statistical test. The results showed that total of 32 species are found in the mangrove ecosystem of Nusa Lembongan which belong to 26 families. There is a strong association between bird species and the vertical strata of vegetation. The species of birds associated with pure mangrove vegetation are; strata I, namely Amaurornis phoenicurus (Pennant,1769), Ardea purpurea Linnaeus, 1766, Sterna bergii M.H.K.Lichtenstein, 1823, Passer domesticus (Linnaeus, 1758), and Pycnonotus aurigaster (Vieillot, 1818); strata II are Todiramphus chloris (Boddaert, 1783), Todirhamphus sanctus (Vigors and Horsfield, 1827), Alcedo coerulescens Vieillot, 1818 and Butorides striata (Linnaeus, 1758); strata III are Hypothymis azurea (Boddaert, 1783), Lanius schach Linnaeus, 1758, Merops philippinus Linnaeus, 1767, Nectarinia jugularis Linnaeus, 1766 and Gerygone sulphurea Wallace, 1864; strata IV are Collocalia linchi Horsfield & F.Moore,1854, Oriolus chinensis Linnaeus, 1766, Hirundo tahitica Gmelin,1789 and Pycnonotus goiaver (Scopoli, 1786). The bird species associated with mixed mangrove and dryland vegetation are strata I, namely species Turnix suscitator (J.F.Gmelin, 1789), Acridotheres javanicus Cabanis, 1851, Anthreptes malacensis (Scopoli, 1786), Passer domesticus (Linnaeus,1758), Pycnonotus aurigaster (Vieillot, 1818), Spilopelia chinensis (Scopoli, 1786) and Geopelia striata (Linnaeus, 1766); strata II, namely Alcedo coerulescens Vieillot, 1818, Zosterops chloris Bonaparte, 1850, Todirhamphus sanctus (Vigors and Horsfield,1827) and Todiramphus chloris (Boddaert, 1783); strata III, namely Anthreptes malacensis (Scopoli,1786), Cacomantis merulinus (Scopoli,1786), Hypothymis azurea (Boddaert,1783), Copsychus saularis (Linnaeus,1758), Nectarinia jugularis Linnaeus, 1766, Gerygone sulphurea Wallace, 1864 and Merops philippinus Linnaeus,1767; strata IV, namely Collocalia linchi Horsfield & F.Moore,1854, Hirundo tahitica Gmelin,1789 and Corvus sp. Factors influencing strata preference by birds are resources, both food and space, as well as the bioecological characteristics of the birds themselves.
{"title":"Birds Species on Vertical Stratification of Mangrove Vegetation Nusa Lembongan, Bali Indonesia","authors":"I. K. Ginantra, Ketut Muksin, M. Joni","doi":"10.22146/jtbb.78394","DOIUrl":"https://doi.org/10.22146/jtbb.78394","url":null,"abstract":"This study aims to determine the use of vertical stratification of mangrove vegetation by bird species in the mangrove ecosystem of Nusa Lembongan. The study was conducted at seven mangrove ecosystem sites, in April-July 2021. Observation of the number of birds in each vegetation strata was carried out using the point count method. The association of the use of vegetation strata by bird species was carried out by Detrended correspondence analysis (DCA) statistical test. The results showed that total of 32 species are found in the mangrove ecosystem of Nusa Lembongan which belong to 26 families. There is a strong association between bird species and the vertical strata of vegetation. The species of birds associated with pure mangrove vegetation are; strata I, namely Amaurornis phoenicurus (Pennant,1769), Ardea purpurea Linnaeus, 1766, Sterna bergii M.H.K.Lichtenstein, 1823, Passer domesticus (Linnaeus, 1758), and Pycnonotus aurigaster (Vieillot, 1818); strata II are Todiramphus chloris (Boddaert, 1783), Todirhamphus sanctus (Vigors and Horsfield, 1827), Alcedo coerulescens Vieillot, 1818 and Butorides striata (Linnaeus, 1758); strata III are Hypothymis azurea (Boddaert, 1783), Lanius schach Linnaeus, 1758, Merops philippinus Linnaeus, 1767, Nectarinia jugularis Linnaeus, 1766 and Gerygone sulphurea Wallace, 1864; strata IV are Collocalia linchi Horsfield & F.Moore,1854, Oriolus chinensis Linnaeus, 1766, Hirundo tahitica Gmelin,1789 and Pycnonotus goiaver (Scopoli, 1786). The bird species associated with mixed mangrove and dryland vegetation are strata I, namely species Turnix suscitator (J.F.Gmelin, 1789), Acridotheres javanicus Cabanis, 1851, Anthreptes malacensis (Scopoli, 1786), Passer domesticus (Linnaeus,1758), Pycnonotus aurigaster (Vieillot, 1818), Spilopelia chinensis (Scopoli, 1786) and Geopelia striata (Linnaeus, 1766); strata II, namely Alcedo coerulescens Vieillot, 1818, Zosterops chloris Bonaparte, 1850, Todirhamphus sanctus (Vigors and Horsfield,1827) and Todiramphus chloris (Boddaert, 1783); strata III, namely Anthreptes malacensis (Scopoli,1786), Cacomantis merulinus (Scopoli,1786), Hypothymis azurea (Boddaert,1783), Copsychus saularis (Linnaeus,1758), Nectarinia jugularis Linnaeus, 1766, Gerygone sulphurea Wallace, 1864 and Merops philippinus Linnaeus,1767; strata IV, namely Collocalia linchi Horsfield & F.Moore,1854, Hirundo tahitica Gmelin,1789 and Corvus sp. Factors influencing strata preference by birds are resources, both food and space, as well as the bioecological characteristics of the birds themselves.","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139322307","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}
Apriliana Pratiwi, Anggiresti Kinasih, Maura Indria Meidianing, F. Y. Kurniawan, E. Semiarti
In silico biology is considered as an effective and applicable approach to initiate various research, such as biodiversity taxonomical conservation. Phylogenetic analysis using in silico taxonomy method for orchid species can provide data on genetic diversity and evolutionary relationships. One particular method that can be used to evaluate specific targets of gene loci in the taxonomic study is DNA barcoding. This research was conducted to determine the specific target locus gene using matK, rbcL, rpoC1, and nrDNA markers for DNA barcoding of the Coelogyne genus with in silico approach using phylogenetic analysis. All marker sequences were collected from the NCBI website and analysed using several softwares and methods, namely Clustal X for sample sequence alignment and MEGA 11 for phylogenetic tree construction and analysis. The results showed that the gene locus in Coelogyne recommended was the nrDNA gene locus. Phylogenetic analysis revealed that the use of the nrDNA gene locus was able to separate 17 Coelogyne species with two outgroup species, namely Cymbidium and Vanilla, then followed with ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) while the other gene loci, namely maturase K (matK) and polymerase beta' subunit (rpoC1) provided a visual phylogenetic tree in which the two outgroup species entered into the same clade as the Coelogyne species. Thus, the results of this study can be used as a reference to support the Coelogyne breeding and conservation program.
{"title":"In Silico Approach for DNA Barcoding using Phylogenetic Analysis of Coelogyne spp. based on the matK, rpoC1, rbcL and nrDNA Markers","authors":"Apriliana Pratiwi, Anggiresti Kinasih, Maura Indria Meidianing, F. Y. Kurniawan, E. Semiarti","doi":"10.22146/jtbb.73130","DOIUrl":"https://doi.org/10.22146/jtbb.73130","url":null,"abstract":"In silico biology is considered as an effective and applicable approach to initiate various research, such as biodiversity taxonomical conservation. Phylogenetic analysis using in silico taxonomy method for orchid species can provide data on genetic diversity and evolutionary relationships. One particular method that can be used to evaluate specific targets of gene loci in the taxonomic study is DNA barcoding. This research was conducted to determine the specific target locus gene using matK, rbcL, rpoC1, and nrDNA markers for DNA barcoding of the Coelogyne genus with in silico approach using phylogenetic analysis. All marker sequences were collected from the NCBI website and analysed using several softwares and methods, namely Clustal X for sample sequence alignment and MEGA 11 for phylogenetic tree construction and analysis. The results showed that the gene locus in Coelogyne recommended was the nrDNA gene locus. Phylogenetic analysis revealed that the use of the nrDNA gene locus was able to separate 17 Coelogyne species with two outgroup species, namely Cymbidium and Vanilla, then followed with ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) while the other gene loci, namely maturase K (matK) and polymerase beta' subunit (rpoC1) provided a visual phylogenetic tree in which the two outgroup species entered into the same clade as the Coelogyne species. Thus, the results of this study can be used as a reference to support the Coelogyne breeding and conservation program.","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139324494","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}
Wiwin Maisyaroh, Luchman Hakim, S. Sudarto, J. Batoro
Gumuk is a unique landscape in Jember Regency resulting from the eruption of Mount Raung that can provide ecosystem services through its ecological functions. Increased mining activity in Gumuk and land-use changes can lead to a decline in biodiversity and affect ecosystem services. This study aims to determine the diversity of herbaceous in the Gumuk ecosystem. Conducted in January - March 2021 in Ledokombo District, Jember Regency. The spatial distribution of Gumuk was carried out using GIS. Herbaceous sampling was carried out using 2x2 plots on three types of Gumuk utilisation, namely mixed gardens, sand mining, and stone mining. The results showed that there were 136 Gumuk in Ledokombo District. One hundred twenty herbaceous species (49 families) were found in all types of Gumuk. Mixed gardens have the highest species diversity (109 species, 49 families) compared to other types. Digitaria sanguinalis (L.) Scop. has high dominance in all types. Species dominance showed a moderate category for all types of Gumuk (D = 0.07). Community complexity in all types was in the high class (D' = 0.90) and species diversity was in the high class (H’ = 3.25). Evenness index € was different in the three types of Gumuk; in mixed gardens, the evenness of species was lower (0.23) than the other two types.
{"title":"Herbaceous Diversity in the Gumuk Ecosystem in Ledokombo District-Jember Regency with Varied Land Use Type","authors":"Wiwin Maisyaroh, Luchman Hakim, S. Sudarto, J. Batoro","doi":"10.22146/jtbb.77888","DOIUrl":"https://doi.org/10.22146/jtbb.77888","url":null,"abstract":"Gumuk is a unique landscape in Jember Regency resulting from the eruption of Mount Raung that can provide ecosystem services through its ecological functions. Increased mining activity in Gumuk and land-use changes can lead to a decline in biodiversity and affect ecosystem services. This study aims to determine the diversity of herbaceous in the Gumuk ecosystem. Conducted in January - March 2021 in Ledokombo District, Jember Regency. The spatial distribution of Gumuk was carried out using GIS. Herbaceous sampling was carried out using 2x2 plots on three types of Gumuk utilisation, namely mixed gardens, sand mining, and stone mining. The results showed that there were 136 Gumuk in Ledokombo District. One hundred twenty herbaceous species (49 families) were found in all types of Gumuk. Mixed gardens have the highest species diversity (109 species, 49 families) compared to other types. Digitaria sanguinalis (L.) Scop. has high dominance in all types. Species dominance showed a moderate category for all types of Gumuk (D = 0.07). Community complexity in all types was in the high class (D' = 0.90) and species diversity was in the high class (H’ = 3.25). Evenness index € was different in the three types of Gumuk; in mixed gardens, the evenness of species was lower (0.23) than the other two types.","PeriodicalId":52402,"journal":{"name":"Journal of Tropical Biodiversity and Biotechnology","volume":"134 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139335448","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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