bluuebunny/crossref_metadata_2025 huggingface dataset:
Better choice of the type of specimen used for untargeted metagenomic sequencing in the diagnosis of periprosthetic joint infections
Authors: He Renke , Wang Qiaojie , Wang Jin , Tang Jin , Shen Hao , Zhang Xianlong
Published: May 2021

Aims

As a proven and comprehensive molecular technique, metagenomic next-generation sequencing (mNGS) has shown its potential in the diagnosis of pathogens in patients with periprosthetic joint infection (PJI), using a single type of specimen. However, the optimal use of mNGS in the management of PJI has not been explored. In this study, we evaluated the diagnostic value of mNGS using three types of specimen with the aim of achieving a better choice of specimen for mNGS in these patients.

Methods

In this prospective study, 177 specimens were collected from 59 revision arthroplasties, including periprosthetic tissues, synovial fluid, and prosthetic sonicate fluid. Each specimen was divided into two, one for mNGS and one for culture. The criteria of the Musculoskeletal Infection Society were used to define PJI (40 cases) and aseptic failure (19 cases).

Results

The sensitivity and specificity of mNGS in the diagnosis of PJI were 95% and 94.7%, respectively, for all types of specimen. The sensitivity and specificity were 65% and 100%, respectively, for periprosthetic tissues, 87.5% and 94.7%, respectively, for synovial fluid, and 92.5% and 94.7%, respectively, for prosthetic sonicate fluid. The mNGS of prosthetic sonicate fluid outperformed that for other types of specimen in the rates of detection of pathogens (84.6%), sequencing reads (> ten-fold) and the rate of genome coverage (> five-fold).

Conclusion

mNGS could serve as an accurate diagnostic tool in the detection of pathogens in patients with a PJI using three types of specimen. Due to its superior perfomance in identifying a pathogen, mNGS of prosthetic sonicate fluid provides the most value and may partly replace traditional tests such as bacteriological culture in these patients. Cite this article: Bone Joint J 2021;103-B(5):923–930.
Particulate Matter Concentrations and Emission Rates at Two Retrofitted Manure-Belt Layer Houses
Authors: Knight Reyna M. , Tong Xinjie , Zhao Lingying , Manuzon Roderick B. , Darr Matthew J. , Heber Albert J. , Ni Ji-Qin
Published: May 2021

Highlights

Annual average PM10 (daily) and PM2.5 (hourly) concentrations of 509 ±203 and 43.3 ±36.1 µg m-3, respectively.

Significant seasonal and diurnal variations in PM concentrations; higher in colder seasons and during daytime.

Annual average PM10 (daily) and PM2.5 (hourly) emission rates of 17.9 ±9.6 and 1.41 ±1.53 mg d-1 hen-1, respectively.

Significant diurnal variations in PM emission rates but inconsistent seasonal variations; higher during daytime.

Abstract. Particulate matter (PM) concentration and emission rate information is needed to assess air quality concerns and environmental impacts related to egg production. Many egg layer buildings were retrofitted from high-rise to manure-belt houses over the past few decades. However, no studies have reported these PM data for the retrofitted layer houses. In this study, concentrations and emission rates of PM10 and PM2.5 were continuously monitored for 12 months at two commercial retrofitted manure-belt layer houses in the Midwestern U.S. The average daily mean PM10 and average hourly mean PM2.5 concentrations in the houses were 509 ±203 µg m-3 and 43.3 ±36.1 µg m-3, respectively. Significant seasonal and diurnal variations in PM concentrations were observed, with higher concentrations in colder seasons and during daytime. The average daily mean PM10 and average hourly mean PM2.5 emission rates from the two houses were 17.9 ±9.6 mg d-1 hen-1 and 1.41 ±1.53 mg d-1 hen-1, respectively. There were no consistent patterns in seasonal variations. Significant diurnal variations were also observed for PM emission rates, with higher PM emission rates observed during daytime. The PM concentrations were significantly correlated with ambient temperature, ventilation rate, bird age, egg production, daily mortality, and feed conversion ratio, while PM emission rates were significantly correlated with ambient temperature, bird age, bird mass, egg mass, and ventilation rate. Keywords: Diurnal variation, Dust, Egg production, PM, Poultry, Seasonal variation.
Impact of Dairy Wastewater Irrigation and Manure Application on Soil Structural and Water-Holding Properties
Authors: Pinkerton Taylor C. , Assi Amjad T. , Pappa Valentini A. , Kan Eunsung , Mohtar Rabi H.
Published: May 2021

Highlights

Quantitative evaluation was performed of dairy waste on soil water-holding capacity.

Considering the soil variability on a farm is significant for management practices.

Soil aggregate structure plays a pivotal role in studying the impact of waste reuse.

Abstract. The livestock sector contributes about 40% of global agricultural output and uses over 30% of total feed-crop land. The sector’s continuing growth has led to increased technology and larger-scale, commercialized agriculture, and it correlates to growth in by-products and waste, which can compromise the environment and human health. Although organic manure is an excellent soil fertilizer whose nutrient content increases crop yield, untreated and/or overapplied manure pollutes local water resources and can alter soil aggregate structure, potentially affecting soil health and available water. Proper livestock waste management is essential for sustainable food production. Waste reuse strategies exist, with goals such as minimizing freshwater consumption, improving food production, and contributing to energy production, However, each strategy has tradeoffs in environmental, energy, or monetary costs. This study provides a quantitative approach to evaluating waste impact on soil health and helps to better manage irrigation practices and water supply gaps in arid and semi-arid areas by better understanding how management practices affect physical soil health. The TypoSoil apparatus was used to measure and analyze the hydrostructural parameters (water-holding capacity and soil structure) of fine sandy loam (A horizon) and sandy clay (B horizon). Soils from the Texas A&M AgriLife Research Dairy (Stephenville, Texas) were collected and compared with control (untouched) soils. Waste (manure, bedding materials, wash water) was separated into liquid (passed through a natural lagoon treatment process) and solid components (applied as fertilizer). Approximately half the wastewater was reused as wash water, the remainder for irrigation. Although the soil varied substantially between sample locations, a statistically significant difference existed between the control and manure/wastewater applications in both the A and B horizons. Both applications improved plant-available water (AW) in the A horizon (40% and 30%, respectively) but deteriorated AW in the B horizon (25% and 30%). Thus, dairy farm waste is a viable source for agricultural use. Keywords: Available water capacity, Pedostructure, Soil health, Soil shrinkage curve, Soil water characteristic curve.
DNA barcoding of the tidal swamp rice (Oryza sativa) landraces from South Kalimantan, Indonesia
Authors: Mursyidin Dindin Hidayatul , Nazari Yudhi Ahmad , BADRUZSAUFARI Badruzsaufari , Masmitra Muhammad Ridho Dinta
Published: May 2021

Abstract. Mursyidin DH, Nazari YA, Badruzsaufari, Masmitra MRD. 2021. DNA barcoding of the tidal swamp rice (Oryza sativa) landraces from South Kalimantan, Indonesia. Biodiversitas 22: 1593-1599. The tidal swamp rice (Oryza sativa L.) landraces of the South Kalimantan, Indonesia, has been known for hundred years ago with a better adaptation to the local conditions, such as acidity, salinity, and metals contamination. However, the genetic insight of these landraces has not fully understood. Here, the rbcL region of tidal swamp rice from this region was successfully sequenced, aligned, analyzed, and deposited into the GenBank with accession numbers of MT818188–MT818201. The multiple alignments of these sequences showing a barcoding motif with eight mutation or polymorphic sites with both substitutions (transition-transversion) and indels (insertion-deletion). Based on this marker, the tidal swamp rice has a low genetic diversity, only 0.086. However, the UPGMA and maximum likelihood (ML) analyses revealed that this germplasm was grouped into five and twoclusters or clades, respectively. In this case, Bayar Putih is closely related to Siam Panangah and farthest from Lemo. This information might help to develop conservation and breeding programs of the tidal swamp rice landraces in the future.
Characterization of Sardinella fimbriata and Clarias gariepinus bones
Authors: Tun Mohd Rosidi Wan Norasiah , Mohd Arshad Nurainni , Mohtar Nor Fazliyana
Published: May 2021

Abstract. Rosidi WNATM, Arshad NM, Mohtar NF. 2021. Characterization of Sardinella fimbriata and Clarias gariepinus bones. Biodiversitas 22: 1621-1626. Calcium is one of the most important minerals required by the human body, which can be directly consumed from milk or any dietary supplement. This study was carried out to determine the calcium content in Fringescale sardinella (Sardinella fimbriata) and catfish (Clarias gariepinus) bones and compare their suitability for human consumption. Fish bones were cleaned, boiled, dried, and ground into powder. Bones from both species were white in color and odorless after drying. The protein content of S. fimbriata was measured to be 20.40 ± 1.61%, while for C. gariepinus it was 19.47 ± 0.61%. Ash content of S. fimbriata and C. gariepinus bones was 62.32 ± 0.08% and 67.9 ± 0.25%, respectively. S. fimbriata bone exhibited 16.4 ± 0.15% moisture, higher than C. gariepinus (7.71 ± 0.14%). The lipid content of S. fimbriata was 0.77 ± 0.17% and for C. gariepinus it was 3.56 ± 0.9%. The solubility of S. fimbriata bone was 23.67 ± 2.65%, higher than that of in C. gariepinus bone (9.02 ± 2.19%). The calcium content found in S. fimbriata and C. gariepinus bones were 4.96 ± 0.13 µg/g and 4.79 ± 0.06 µg/g, respectively. S. fimbriata bone exhibited higher solubility than that of C. gariepinus and was more suitable for human consumption. Overall findings have suggested the calcium from fish bones that may replace commercial calcium in the market, thus meeting the requirements of food safety standards.
Architectural and physical properties of fungus comb from subterranean termite Macrotermes gilvus (Isoptera: Termitidae) mound
Authors: Kusumawardhani Dina , Nandika Dodi , Karlinasari Lina , ARINANA ARINANA , BATUBARA IRMANIDA
Published: May 2021

Abstract. Kusumawardhani DT, Nandika D, Karlinasari L, Arinana, Batubara I. 2021. Architectural and physical properties of fungus comb from subterranean termite Macrotermes gilvus (Isoptera: Termitidae) mound. Biodiversitas 22: 1627-1634. Subterranean termite Macrotermes gilvus Hagen (Isoptera; Termitidae) is the most widely distributed termite species in Indonesia. This termite species has a unique habit of making fungus comb inside their nest. The fungus comb is a growth substrate for Termitomyces fungi, which provides a nutrient source for the termite. However, there is a lack of scientific information regarding the architecture and physical properties of fungus combs of M. gilvus. A study was conducted to determine the architecture and physical properties of fungus combs of M. gilvus found in Yanlappa Experimental Forest, Bogor, West Java Province, Indonesia. The fungus combs were collected from six of twenty-two nests of M. gilvus found in the rectangular sample plot (150 x 250 m) in the area. The results showed that the fungus comb of M. gilvus was brain-shaped with 44.17 ± 7.36 cm3 in volume and had burrows that interconnected from the surface (6.20 ± 1.06 mm in diameter) to the base of the fungus comb structure (4.32 ± 0.91 mm in diameter). The burrows were interconnected with each other to support cross-ventilation in the fungus comb. White nodules of Termitomyces fungi were found in the fungus comb. Architecturally, the fungus comb consisted of two structural parts, namely fresh comb on the upper part and old comb on the lower part of the fungus comb. The fresh comb possessed a larger volume (48.33 ± 2.89 cm3) and smoother texture (177.88-977.50 nm) than the old comb (40.00 ± 8.66 cm3, 407.49-6762.62 nm). The fresh comb had a larger volume (48.33 ± 2.89 cm3) than the old comb (40.00 ± 8.66 cm3). It was also found a smoother texture in the fresh comb (177.88-977.50 nm) than in the old comb (407.49-6762.62 nm). In terms of color, the fresh comb was darker (reddish) than the old comb (yellowish white). In addition, the density of the old comb was higher (0.87 ± 0.11 g/cm3) than the fresh comb (0.77 ± 0.13 g/cm3) so that the old comb was able to function as a strong foundation for fungus comb.
Combination of plant growth-promoting bacteria and botanical pesticide increases organic red rice yield and reduces the Leptocorisa acuta population
Authors: Hoesain Mohammad , Prastowo Sigit , SUHARTO Suharto , Pradana Ankardiansyah Pandu , Asyiah Iis Nur , Alfarizy Fariz Kustiawan , Adiwena Muh
Published: May 2021

Abstract. Hoesain M, Prastowo S, Suharto, Pradana AP, Asyiah IN, Alfarizy FK, Adiwena M. 2021. Combination of plant growth-promoting bacteria and botanical pesticide increases organic red rice yield and reduces the Leptocorisa acuta population. Biodiversitas 22: 1686-1694. Organic red rice production faces similar constraints as conventional rice production, namely pest attacks, especially rice earhead bugs (Leptocorisa acuta). The use of synthetic chemical inputs is also not allowed in organic red rice production. This problem can be overcome with the application of botanical pesticides, but the use of botanical pesticides do not promote plant growth. As a solution, a combination formula of plant growth-promoting bacteria and botanical pesticides is required. This study aimed to examine the effectiveness of a combination of plant growth-promoting bacteria with botanical pesticides in increasing the growth and yield of organic red rice plants and reducing the rice earhead bug population. The research was conducted on organic agricultural land in Jember Regency, Indonesia. The research began with the extraction of botanical pesticides from the leaves of Azadirachta indica, Aglaia odorata, and Ageratum conyzoides using 96% ethanol. The bacterial isolates obtained and characterized in previous studies were tested for their compatibility and cell viability in the combination formula. The field experiment was conducted with 8 treatments, 3 replications, and each replication consisted of 150 rice plants. The randomization pattern followed a randomized block design pattern. The results showed that all bacteria were compatible when combined with 20% botanical pesticides. In addition, cell viability at 3 months of storage decreased, but not significantly. In the organic rice growth variable, all combinations of bacteria with botanical pesticides showed good performance to increase the plant growth. Increased plant growth occurred in the number of tillers, plant height, and the number of productive panicles. Furthermore, yield variables, fresh seed weight per panicle, dry seed weight per panicle, and weight of 1000 seeds also increased significantly after being treated with a combination of plant growth-promoting bacteria and botanical pesticides. The decline in the rice earhead bug population also occurred in all plants treated using botanical pesticides either singly or in combination. The best treatments in this study were BS01 and PD01, which showed consistent results. This study provides information that the combination of plant growth-promoting bacteria and botanical pesticides is compatible, does not cause a high number decrease of bacterial cells at a shelf-life of 3 months, and can stimulate the growth and yield of organic red rice, and can suppress rice earhead bug populations.
Agronomic characteristics of 30 promising lines of aromatic, red, and black rice and their antioxidant and cytotoxic effects in some cancer cells
Authors: LIMBONGAN YUSUF , RAMADHAN RICO , SHIMIZU KUNIYOSHI , Tangkearung Enos
Published: May 2021

Abstract. Limbongan Y, Ramadhan R, Shimizu K, Arung ET. 2021. Agronomic characteristics of 30 promising lines of aromatic, red, and black rice and their antioxidant and cytotoxic effects in some cancer cells. Biodiversitas 22: 1695-1700. In our effort to increase rice production, some activities were done such as increased land production, rice planting patterns, and crossbreeding some rice with the special characteristic. We have cross-bred aromatic rice with red rice and black rice. These activities resulted in thirty lines of rice varieties. The thirty lines of rice variation were extracted with ethanol and evaluated the extracts for their phytochemicals, antioxidant activity, and cytotoxicity effect on cancer cell lines (MCF-7, HeLa, and OVK-18). The phytochemicals of thirty lines variation of rice showed variation in their contents. The line of F2BA201 extracts showed the strongest in antioxidant with IC50 2.43 ?g/mL while Vitamin C was 32.93 ?g/mL. The line of F2LD20 extracts displayed potent inhibition with value of 40.2% against OVK-18 cancer cells while 5FU as positive control revealed percentage inhibition with value of 21.2%. Based on the results, the thirty line rice variations exhibited antioxidant and anti-cancer potential.
Application of selected teak clone and organic fertilizer to accelerate rehabilitation of lowland forest in Java, Indonesia
Authors: HARDIWINOTO SURYO , ARDIANSYAH FIQRI , Widiyatno Widiyatno
Published: May 2021

Abstract. Hardiwinoto S, Ardiansyah F, Widiyatno. 2021. Application of selected teak clone and organic fertilizer to accelerate rehabilitation of lowland forest of Java, Indonesia. Biodiversitas 22: 1750-1756. Lowland forest in Java Island Indonesia is dominated by teak forest. However, for some decades, the forest has degraded and decreased teak wood production. Rehabilitation of the degraded forest is needed to accelerate the forest land cover. Vegetative propagation of selected clones is one of the techniques used in the asexual reproduction of plants to maintain superior genetics from ancestors to their offspring. In addition, adding organic fertilizer can improve the chemical and physical properties of degraded sites. In this study, vegetative propagation techniques of selected teak clones and addition of organic fertilizer were used to rehabilitate the degraded forest. The objectives of the research were to determine the best propagation technique and appropriate dosage of organic fertilizer toward the early growth of clonal teak plantations. The results showed that the height and diameter parameters did not significantly differ for vegetative propagation and interaction with organic fertilizer dosage (P > 0.05). However, the dosage of organic fertilizer significantly increased the DBH of the teak (P < 0.05), although the height parameter did not significantly differ among dosages of organic fertilizer (P > 0.05). The best dosage of organic fertilizer was 5 kg/individual, under which the average growth in height and diameter of teak at 14 months was 3.79 and 5.60 cm, respectively. This suggests that vegetative propagation of selected teak clones and addition of 5 kg/individual organic fertilizer could be implemented to support the successful rehabilitation of degraded forests.
Antimicrobial activity and GC-MS analysis of bioactive constituents of Aspergillus fumigatus 269 isolated from Sungai Pinang Hot Spring, Riau, Indonesia
Authors: Octarya Zona , NOVIANTY RIRYN , SURAYA NABELLA , SARYONO SARYONO
Published: May 2021

Abstract. Octarya Z, Novianty R, Suraya N, Saryono. 2021. Antimicrobial activity and GC-MS analysis of bioactive constituents of Aspergillus fumigatus 269 isolated from Sungai Pinang Hot Spring, Riau, Indonesia. Biodiversitas 22: 1839-1845. A total of 16 isolates of thermophilic fungi originating from hot springs in Riau and West Sumatra have been tested for their antimicrobial ability against pathogenic microbes Candida albicans, Staphylococcus aureus, and Escherichia coli. The antimicrobial test was carried out by using the disk diffusion method. Molecular identification of the most potential isolate (LBKURCC269) was carried out by amplifying the ITS (Internal transcribed spacer) sequence on rDNA using universal primer ITS-4 and ITS-5. ITS sequence results showed that LBKURCC269 has a 99% similarity to Aspergillus fumigatus. Ethyl acetate extract of LBKURCC269 (Aspergillus fumigatus 269) showed good antimicrobial activities against three pathogenic microbes tested with the inhibition of 17 mm, 13 mm, and 13 mm against Staphylococcus aureus, Candida albicans, and Escherichia coli, respectively. There were 24 identified chemical compounds in ethyl acetate extract. The major compounds were eicosane, eicosane 2-methyl, phenol, 2,6-bis(1,1-dimethyl ethyl)-4-methyl, hexadecane 2, and 11-octadecenoic acid, methyl ester. These findings suggest that thermophilic fungi isolated from hot springs could serve as reservoirs for new bioactive compounds of industrial and medical importance.
The activity budgets of captive orangutan (Pongo pygmaeus) in two different Indonesian zoos
Authors: Dalimunthe Nurzaidah Putri , Alikodra Hadi Sukadi , Iskandar Entang , Utami-Atmoko Sri Suci
Published: May 2021

Abstract. Dalimunthe NP, Alikodra HS, Iskandar E, Atmoko SSU. 2021. The activity budgets of captive orangutan (Pongo pygmaeus) in two different Indonesian zoos. Biodiversitas 22: 1912-1919. In nature, orangutans spent most of the activity budgets for foraging. It is presumed that orangutan in captivity carries out different activities. This study aimed to investigate the activity of Bornean Orangutan (Pongo pygmaeus) in different zoos with different types of cage according to their design, enrichments, and diets. It was conducted at two different Indonesian zoos, namely Ragunan Zoo (TMR) and Taman Safari Indonesia (TSI). The study used a total of 11 orangutans. From each zoo, orangutan individuals from each zoo and each age and sex class (adult male, adult female, and juvenile/juvenile) were used in the present study. The activity budgets were compared between age-sexual classes, cage types, and weekday-holiday categories. Environmental enrichment analysis was also used. The total observation time in this study for each individual was 4,500 minutes. The adult male had more resting activity than other groups, while the juvenile group showed a higher percentage of social, moving, and feeding activities. It was also observed that there were different activity budgets between individuals in a separate cage and week-holiday groups. Overall, it was assumed that the difference in orangutan activity budgets was influenced by cage types, individual arrangements, and environmental enrichment. Meanwhile, a juvenile showed a higher percentage of enrichment using. Enrichment was influenced by cage type and individual arrangement.
Morphological characteristics of Phaius spp. orchids from Indonesia
Authors: Hartati Sri , SAMANHUDI Samanhudi , Manurung Ida Rumia , CAHYONO ONGKO
Published: May 2021

Abstract. Hartati S, Samanhudi, Manurung IR, Cahyono O. 2021. Morphological characteristics of Phaius spp. orchids from Indonesia. Biodiversitas 22: 1991-1995. Orchid is one of the ornamental plants with great economic value in various communities. Characterization and grouping of several orchid species can be used in breeding efforts to obtain hybrid with the desired traits. This study is aimed to characterize the morphological appearance of Phaius orchids and to cluster the species based on their similarity in morphological characteristics. Five species of Phaius (P. tankervilleae, P. indigoferus, P. montanus, P. amboinensis, and P. callosus) of the collection of the Bogor Botanical Garden were observed based on 30 morphological characters including the characters of stems, pseudobulbs, leaves and flowers. The data obtained were converted into binary data and computed using the Numerical Taxonomy and Multivariate Analysis System (NTSYS) Spc 2.02 program to produce dendrogram. The results show that based on the morphological characterization of the five species of Phaius spp., they have similarities from 63% to 80%. Among the five Phaius species, P. amboinensis, P. tankervilleae, and P. montanus had 80% similarity and can be used as parents for crossing.
Compendium of plants used for preparation of traditional alcoholic beverages by four major ethnic communities of Assam, northeast India
Authors: Borah Dipankar , GOGOI TRIDIP , SARMA JINTU , BORAH PUNAM JYOTI , GOHAIN BICHITRA , MILI CHIRANJIB , UPADHYAYA ANKUR , BASUMATARY JENIMA , NEOG KASTURI , WANGPAN TONLONG , TANGJANG SUMPAM
Published: May 2021

Abstract. Borah D, Gogoi T, Sarma J, Borah PJ, Gohain B, Mili C, Upadhyaya A, Basumatary J, Neog K, Wangpan T, Tangjang S. 2021. Compendium of plants used for preparation of traditional alcoholic beverages by different major ethnic communities of Assam, Northeast India. Biodiversitas 22: 2019-2031. This paper deals with the ethnobotanical research on the preparation of traditional alcoholic beverages by Ahom, Bodo, Karbi and Mishing ethnic communities of Assam, India. Along with the information on preparation, the plant species associated with the preparation of alcoholic beverages are also recorded. Field investigations were conducted to cover 32 villages of six districts of Assam, India. The data was generated from 202 respondents using participatory rural appraisal tools including semi-structured questionnaires and personal interviews. The plant species were collected, identified and submitted in the Herbarium of Rajiv Gandhi University, Arunachal Pradesh, India. The study recorded 129 plants falling under 107 genera and 54 families which are exclusively used for the preparation of alcoholic beverages by the studied communities. The study confirmed that the association of traditional alcoholic beverages with their rich indigenous knowledge.. The finding also revealed varied forms of protocol followed by these tribes to prepare traditional liquors and the starter cakes for brewing of alcohol were prepared locally. However, the Mishing tribe was known to prepare unique rice beer known as Po:ro apong, as the preparation technique and extraction process of this liquor was slightly different. Distillation of alcohol was also observed in all the communities except the Ahom. The rich traditional knowledge of brewing alcohol and the plant species used in the process were worth documenting considering the on-going alteration of traditional society with the modernization.
Traditional market, social relations, and diversity of edible plants traded in Beringharjo Market, Yogyakarta, Indonesia
Authors: ISKANDAR Budiawati Supangkat , Iskandar Johan , Mulyanto Dede , Alfian Rahman Latif , SUROSO Suroso
Published: May 2021

Abstract. Iskandar BS, Iskandar J, Mulyanto D, Alfian RL, Suroso. 2021. Traditional market, social relations, and diversity of edible plants traded in Beringharjo Market, Yogyakarta, Indonesia. Biodiversitas 22: 2012-2024. Although the modern markets have rapidly developed in many cities of Indonesia in the last decades, the urban traditional markets still exist in Indonesia, including Beringharjo Market, Yogyakarta. This study illustrated the story and social relation activities, biodiversity of edible plants traded, and market chain system of edible plant supplies from rural areas to Beringharjo Market. The study was conducted between February and March 2019. The method used in this study was qualitative data with an ethnobotanical approach. Some field techniques, including plant surveys and deep interviews with competent informants, were employed to collect the primary data. The result of this study showed that historically the economic activities of Beringharjo Market had been existing very a long time at least documented in 1758, while the market building was constructed by the Sultanate of Yogyakarta Palace, Sri Sultan Hamengku Buwono VIII in 1925. Like other traditional markets in Indonesia, the Beringharjo Market has played an important role in developing local economic activities, as the main place for the transaction of various edible plants and meeting for many ethnics, making the important as center of biocultural diversity at the local level. An ethnobotanical survey revealed that 93 edible plant species belonging to 37 families with a total of 159 landraces were commonly traded. The Beringharjo Market has traditionally traded a high diversity of edible plants that are supplied from local farmers productions of Yogyakarta and Central Java. Therefore, this traditional market has an important role in enhancing local economic development and contributing to promoting and conserving local plant diversity in this region.
Carbon emissions as impact of mangrove degradation: A case study on the Air Telang Protected Forest, South Sumatra, Indonesia (2000-2020)
Authors: Eddy Syaiful , Milantara Noril , Basyuni Mohammad
Published: May 2021

Abstract. Eddy S, Milantara N, Basyuni M. 2021. Carbon emissions as impact of mangrove degradation: A case study on the Air Telang Protected Forest, South Sumatra, Indonesia (2000-2020). Biodiversitas 22: 2142-2149. Massive degradation in ATPF occurs due to anthropogenic activities that have converted this area into a coconut plantation, fishpond, settlement, and agriculture. The purpose of this study was to describe changes in land cover and the amount of CO2 emission in ATPF and its causes during the 2000-2020 period using remote sensing data. Data from remote sensing were used to obtain area, classification and land cover change in each period; meanwhile, carbon stock, emissions, and CO2 sequestration were obtained from the analysis using LUMENS software. The results showed that the emissions resulting from land conversion in ATPF during the 2000-2020 period were much greater than sequestration. Net emissions of 1,928,076.56 tons of CO2-eq with an annual emission rate of 96,403.83 tons of CO2-eq/year. The largest source of emissions came from the conversion of primary forest, coconut plantation and secondary forest to open areas; while the source of sequestration comes from the formation of primary and secondary forests. There need to be restoration and conservation efforts in this area by the government and the community to restore the function of ATPF as a coastal protection forest. This research is the first study to examine land cover changes in mangrove forests using data analysis methods with LUMENS.
Review: Fruit collapse and heart rot disease in pineapple: Pathogen characterization, ultrastructure infections of plant and cell mechanism resistance
Authors: Cano Reinoso Diego Mauricio , Soesanto Loekas , Kharisun Kharisun , Wibowo Condro
Published: May 2021

Abstract. Cano-Reinoso DM, Soesanto L, Kharisun, Wibowo C. 2021. Review: Fruit collapse and heart rot disease: Pathogen characterization, ultrastructure infections of plant and cell mechanism resistance. Biodiversitas 22: 2477-2488. Fruit collapse and bacterial heart rot are diseases in pineapple caused by Erwinia chrysanthemi (later classified as Dickeya zeae) which are increasingly prevalent in the last decade, causing devastating production loss in pineapple cultivation. Yet, comprehensive knowledge to tackle such diseases is limited, understandably due to the relatively new emerge of the diseases. Here, we review the causes of bacterial heart rot and fruit collapse, stages of infection, typical symptoms and the occurrence of resistance mechanisms in plants. In pineapple, the fruit collapse is noticeable by the release of juice and gas bubbles, also the shell of the fruit that turns into olive-green. Meanwhile, bacterial heart rot is characterized by water-soaked zones on the leaves, the formation of brown streaks on the lamina and in the mesophyll, and light-brown exudate in the blisters. The most common means of penetration into the host plant used by this type of pathogen is through plant natural openings, injuries and wounds, and entire surfaces. Concurrently, plants and fruits develop disease-resistant mechanisms to inhibit infection growth under this pathogenic attack. These mechanisms can be divided into hypersensitive reactions, locally acquired resistance, and systematic acquired resistance. In addition, pathological infections produce an interaction of the cell wall with pectolytic enzymes. Understanding the membrane breakdown process carried out by these enzymes has become critical to a pineapple protection plan. This review suggests that future research to tackle fruit collapse and bacterial heart rot can be focused on disease-resistant mechanisms, and their effects on the cell wall status with an enzymatic characterization.
Isolation and characterization of N-fixing and IAA producing rhizobacteria from two rice field agro-ecosystems in South Sulawesi, Indonesia
Authors: Haerani Nining , SYAM’UN ELKAWAKIB , RASYID BURHANUDDIN , HARING FERANITA
Published: May 2021

Abstract. Haerani N, Syam’un E, Rasyid B, Feranita. 2021. Isolation and characterization of N-fixing and IAA producing rhizobacteria from two rice field agro-ecosystems in South Sulawesi, Indonesia. Biodiversitas 22: 2497-2503. Nitrogen-fixing bacteria that live in the rhizosphere are microorganisms that can increase N availability for rice plants in a non-symbiotic manner. Nitrogen-fixing bacteria also support growth through the production of growth hormones. These abilities are mainly influenced by the environment and their association with plants. This research aims to determine the microbial characteristics from two different rice fields agro-ecosystems (rainfed and irrigated) in South Sulawesi. Bacteria isolated from the rhizosphere soil of rice in six districts were cultured and isolated using Burk's N-free media for screening purposes. A total of 20 isolates were observed for their morphological and biochemical properties, determined their ability to fix nitrogen and produce IAA. The results showed that all isolates could grow on nitrogen-free media, in which 13 isolates were isolated from rainfed rice fields, and 7 isolates were from irrigated rice fields with various physical and biochemical properties, all other qualities tested also varied. NG4 isolate from Gowa Regency (rainfed rice field) produced the highest nitrogen (0.157%), and NB13 isolate from Barru (rainfed rice field) had the highest concentration of growth hormone (IAA) (1,835 mg L-1). All isolates obtained from rainfed rice fields showed a better ability to fix nitrogen and produce growth hormone than those from irrigated rice fields. Bacteria isolates from rainfed rice fields have higher biofertilizers and biostimulant capacity to develop environmentally-friendly rice cultivation.
Potency of secondary metabolites of Trichoderma asperellum and Pseudomonas fluorescens in the growth of cocoa plants affected by vascular streak dieback
Authors: SIMAMORA MANIPPO , BASYUNI MOHAMMAD , Lisnawita Lisnawita
Published: May 2021

Abstract. Simamora M, Basyuni M, Lisnawita. 2021. Potency of secondary metabolites of Trichoderma asperellum and Pseudomonas fluorescens in the growth of cocoa plants affected by vascular streak dieback. Biodiversitas 22: 2542-2547. Vascular streak dieback (VSD) is the main disease in cocoa caused by Oncobasidium theobromae. Using secondary metabolites of Trichoderma asperellum and Pseudomonas fluorescens is one of the methods to control disease in cocoa plants. The aim of this research is to evaluate the potency of secondary metabolites of T. asperellum and P. fluorescens to control VSD and study its effect on the growth of cocoa plants. The study used a non-factorial, completely randomized design (CRD) with eight treatments and four replications. The secondary metabolites were applied every week for ten times. The results showed that the secondary metabolites of T. asperellum and P. fluorescens were effective in controlling VSD. The combination of organic fertilizer and secondary metabolite of P. fluorescens and T. asperellum as found to be the best treatment to increase cocoa growth and the number of shoots increased by 43.58 shoots
Incorporation of pectin during biosynthesis of bacterial cellulose by Gluconacetobacter xylinus InaCC B404: Possibility for producing green food packaging
Authors: Agustin Sukmiyati , Wahyuni Endang Tri , Suparmo Suparmo , Supriyadi Supriyadi , Cahyanto Muhammad Nur
Published: May 2021

Abstract. Agustin S, Wahyuni ET, Suparmo, Supriyadi, Cahyanto MN. 2021. Incorporation of pectin during biosynthesis of bacterial cellulose by Gluconacetobacter xylinus InaCC B404: Possibility for producing green food packaging. Biodiversitas 22: 2548-2553. Bacterial cellulose-pectin biocomposite is developed as a potential environmentally friendly food packaging material. The objective of this research was to investigate the effects of pectin supplementation to the growth medium of Gluconacetobacter xylinus on the properties of the biocomposite produced. Pectin was added into the growth medium at different concentrations, i.e.: 0.1, 0.2 and 0.3% (w/v). The bacterial cellulose-pectin biocomposites produced were analyzed for structure, mechanical strength, crystallinity, morphology, color and opacity. FTIR analysis suggested that interaction between bacterial cellulose and pectin was hydrogen bonding. Generally, pectin addition decreased the crystallinity, tensile strength, tear strength and lightness of biocomposite produced. The tensile and tear strength of bacterial cellulose-pectin biocomposites were in the range of 23.05-25.72 MPa and 13.30-15.72 g/?m respectively, comparable to those conventional non-biodegradable plastics such as high-density polyethylene and low-density polyethylene with opacity much lower than HDPE. These results suggesting the possibility of cellulose-pectin biocomposite as semi-translucent green food packaging.
Genetic diversity and morphological responses of Capsicum annuum varieties under aluminum stress
Authors: ANDRIYANI ANDRIYANI , Jadid Nurul
Published: May 2021

Abstract. Andriyani, Jadid N. 2021. Genetic diversity and morphological responses of Capsicum annuum varieties under aluminum stress. Biodiversitas 22: 2576-2582. Capsicum annuum is one of the most cultivated vegetable crops in the world. Its fruit contains various beneficial metabolites which possess antioxidant activities. Fertilizers play important role to increase plant productivity. However, excessive use of fertilizers could harm the environment. Heavy metals, including aluminum (Al), contamination have been reported to negatively affect plant production and inhibit root growth. C. annuum var Ciko, Lingga, Lembang1, and Tanjung2 are commonly cultivated in Indonesia. However, the genetic diversity of those plants and their responses to Al stress condition are still unknown. Therefore, our study aimed to analyze the genetic diversity of four C. annuum cultivars and to observe their morphological responses under Al stress conditions. The genetic diversity was analyzed using five universal inter-simple sequence repeat (ISSR) primers. Our results showed that the PIC values ranged from 0 (primer 825) to 0.6375 (Primer 9). The UPGMA phylogenetic construction also demonstrated that the cv. Lembang1 is closely related to the cv Lingga. Meanwhile, cv Tanjung 2 is closely related to the cv. Ciko. Each cultivar also performed different morphological responses under Al stress conditions. Our data showed that Al affected significantly root growth but not affected their plant height. Aluminum at 100 ppm significantly decreased root length of cv. Lingga
Novel chitinolytic bacteria from the shrimp shell processing waste
Authors: Masri Mashuri , SUKMAWATY EKA , ADITIA LASINRANG
Published: May 2021

Abstract. Masri M, Sukmawaty E, Aditia L. 2021. Novel chitinolytic bacteria from the shrimp shell processing waste. Biodiversitas 22: 2672-2681. Chitinase is an enzyme that hydrolyzes chitin (?-1,4 Nsetyl-D-glucosamine polymer). Several types of microorganisms produce chitinase that contributes to basic science and application. The role of chitinase enzyme is widely utilized in various fields, such as health as an anti-tumor agent and agriculture as biological control agents in plant disease caused by fungus. The purpose of this study was to isolate novel chitinolytic bacteria from shrimp shell waste in Makassar, Indonesia, using the scatter plate method on chitin agar selective media incubated at 37°C for 3 days. The clear zone formation around the colony was marked as an indicator of chitinase activity performed by the certain isolate. Selection was carried out by recycling all isolates on chitin agar media, which were incubated at 37°C for 3 days and measured the chitinolytic index. Two of ten isolates produced the highest chitinolytic index, namely, KLA-2 (45) and KLA-4 (15) isolates. The molecular identification results showed that the KLA-2 and KLA-4 isolates were Lysinibacillus fusiformis strain WH22 and Brevibacillus reuszeri strain CMB-15, respectively. Therefore, novel chitinolytic bacteria that can produce chitinase enzyme from shrimp shell waste are L. fusiformis and B. reuszeri
Proteomic approach: Identification of Nephotettix virescens vector protein transmitting the tungro virus in rice
Authors: SENOAJI WASIS , Rahardjo Bambang Tri , Tarno Hagus
Published: May 2021

Abstract. Senoaji W, Rahardjo BT, Tarno H. 2021. Proteomic approach: Identification of Nephotettix virescens vector protein transmitting the tungro virus in rice. Biodiversitas 22: 2750-2755. As a vector of tungro virus, Nephotettix virescens is one primary pest in rice cultivars. Associated Rice Tungro Spherical Virus provides a helper component for Rice Tungro Bacilliform Virus acquisition produced the severe symptoms in rice. The vector proteins encoded by the virus become a poorly understood transmission of plant viruses, particularly in semi-persistent mechanisms. It is essential to develop new molecules to interrupt the transmission mechanism of plant viruses by insect vectors. This study aimed to detect the helper proteins in vectors with proteomics. Protein separation was performed using SDS-PAGE, and then was identified by the Liquid Chromatography-Mass Spectrometry (LC-MS/MS) to find the candidate proteins. The result showed that actin was identified in N. virescens as responsible protein that related to transmitting tungro viruses into the plant.
Genetic analysis on grain physical characteristics and grain color from the crosses of black × white rice genotypes
Authors: Nurhidayah Siti , BADIARAJA PANJI HANDOKO , HARYANTO HERU TOTOK AGUNG D. , DEWI PRITA SARI
Published: May 2021

Abstract. Nurhidayah S, Firmansyah E, Haryanto TAD, Dewi PS. 2021. Genetic studies of grain physical characteristics and grain color from the crosses of black × white rice genotypes. Biodiversitas 22: 2763-2772. This study was conducted to investigate genetic variance, cytoplasmic maternal effect, gene action, and broad-sense heritability of grain physical characteristics and grain color from crosses of black × white rice genotypes (Oryza sativa). Genetic studies were conducted using F2 generations from the crosses of black × white rice genotypes and their reciprocal crosses. The plant materials consisted of seven black rice genotypes (PH2, PH3, PH4, PH5, PH6, PH7, and PH8), three commercial white rice varieties (Inpari 13, Inpari 18, and Inpari 19),  a total of 30 F2 generations, and their reciprocal crosses. There are four-grain physical traits examined: grain length, grain width, grain thickness, and grain color. The result showed that maternal cytoplasmic effect was present in most F2 generations and their reciprocal crosses. The characters of grain length, grain width, and grain thickness are controlled by polygene with additive action. Based on the results of the Chi-Square Test, the grain color did not follow the expected 1: 2: 1 ratio for incomplete dominance involving monogenic traits. Broad sense heritability for grain length, grain width, and grain thickness are varied from low to medium for a cross of black rice genotypes × Inpari 19, and low to high for the crosses of black rice genotypes × Inpari 13 and black rice genotypes × Inpari 18.
Freshwater vertebrates monitoring in Maninjau Lake, West Sumatra, Indonesia using environmental DNA
Authors: ROESMA DEWI IMELDA , DJONG HON TJONG , JANRA MUHAMMAD NAZRI , AIDIL DYTA RABBANI
Published: May 2021

Abstract. Roesma DI, Tjong DH, Janra MN, Aidil DR. 2021. Freshwater vertebrates monitoring in Maninjau Lake, West Sumatra, Indonesia using environmental DNA. Biodiversitas 22: 2794-2802. Environmental DNA (eDNA) is one of the DNA sources without directly disturbing the organisms. The eDNA potentially an effective method with next-generation sequencing (NGS) that can read all DNA in parallel at one sequential run. Maninjau Lake in West Sumatra has experienced a decline the species richness, thus monitor biodiversity with the non-invasive method is needed. This study aimed to apply eDNA for monitoring freshwater vertebrates in Maninjau Lake. The eDNA was collected from water samples using the filter membrane to DNA isolation and sequencing with the NGS technique from Illumina. The eDNA method detected 150 vertebrate individuals and consists of 92 Actinopterygii fishes, three chondrichthyes fishes, 11 amphibians, seven reptiles, ten aves, and 27 mammals. Among all individuals were detected, only 11% known present in Maninjau Lake, while the others (89%) are native species to other countries. The fishes were detected living in Maninjau Lake by the eDNA method, i.e., Cyprinidae (Carassius auratus and Cyprinus carpio), Cichlidae (Oreochromis niloticus), and Poeciliidae (Gambusia affinis and Xiphophorus maculatus). Bias results in this study to be influenced by various factors i.e., possibility of contamination, poor DNA quality, the bias results during molecular processes, and not available the complete sequences databases to assigned into the correct taxa, especially fish species in Maninjau Lake. The eDNA method for monitoring biodiversity should consider the increase of sampling sites, replication samples, and the availability of sequences database in Genbank, NCBI
Short Communication: Allometric model to estimate bifoliate leaf area and weight of kaffir lime (Citrus hystrix)
Authors: Budiarto Rahmat , Poerwanto Roedhy , Santosa Edi , Efendi Darda , Agusta Andria
Published: May 2021

Abstract. Budiarto R, Poerwanto R, Santosa E, Efendi D, Agusta A. 2021. Short Communication: Allometric model to estimate bifoliate leaf area and weight of kaffir lime (Citrus hystrix). Biodiversitas 22: 2815-2820. Leaf is an economically important plant organ harvested from kaffir lime (Citrus hystrix DC.) for flavor and fragrance. This study aimed to formulate and validate regression models to estimate the leaf area (LA) and leaf weight (LW) of bifoliate kaffir lime leaf. There were 220 bifoliate leaves collected from 22 individual plants planted on Bogor. Bifoliate C. hystrix leaf consisted of upper main leaflets and winged petiole as lower secondary leaflet. All leaves were pooled and then grouped randomly into two subgroups for model formulation and validation, respectively. Linear, zero intercepts linear, exponential, logarithmic, polynomial, zero intercept polynomial and power regressions were used to properly estimate LA and LW. There was 63 formula obtained from nine predictors following seven regression models. Selected nine formulas with the highest R2 plus a stepwise formula were further tested for validation. Stepwise always showed the highest R2 followed by total of leaf ,length (TL) both on LA and LW estimation. However, the stepwise seemed to be more complicated and time wasted than TL regression model. Thus, our recommendation models for non-destructive and simple estimation in C. hystrix bifoliate leaf were LA = 0.1997 (TL)2 + 0.4571 (TL) and LW = 0.0067 (TL)2 + 0.0065 (TL), respectively.