فهرست مطالب t. kajita

The unique positioning of mangrove ecosystems between land and sea makes them vital in the nitrogen cycle. The role of nitrification in the nitrogen cycle is important to provide nitrogen compounds readily absorbed by mangrove plants. Nevertheless, the nitrification process and nitrifying bacteria in mangrove areas have yet to be comprehensively understood. The primary objective of this study is to provide comprehensive analysis of nitrifying bacteria in mangrove sediments by conducting a systematic review. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses method is used as a guide to help report reviews systematically and has a flow chart to show the process of selecting relevant studies. Data collection was carried out by utilizing 6 databases and journal search engines including Scopus, PubMed, ResearchGate, Google Scholar, and Springer in order to achieve more comprehensive findings. This study employed the widely recognized and commonly used technique of defining the review's scope in a focused manner by first identifying the population, intervention, comparison, and outcome. This study identified 358 studies, and 31 studies were included in the review after screening. Based on the screening results, research on nitrifying bacteria in mangrove sediments is geographically limited to several countries such as Indonesia, Vietnam, Thailand, China, Mexico, the United States, India, and Saudi Arabia. This study vealed that there is a high level of diversity among nitrifying bacteria in mangrove sediment, with five distinct groups identified: ammonia oxidizing bacteria, nitrite oxidizing bacteria, anammox bacteria, and comammox bacteria, a recently identified group. In carrying out changes in nitrogen compounds, nitrifying bacteria use functional genes from different steps of the nitrification process, such as nitrogenase, ammonia monooxygenase subunit A, nitrite oxidoreductase alpha subunit, nitrate reductase alpha chain, nitrite reductase, nitric oxide reductase, nitrous oxide reductase, hydrazine synthase, hydrazine oxidoreductase and hydroxylamine oxidoreductase genes. Ammonia-oxidizing bacteria were the predominant group in general, but various nitrifying bacteria groups were distributed diversely across different mangrove environments. This study also indicated the vegetation type and the distribution of nitrifying bacteria in mangrove sediments. The depth of these sediments typically varies from 0 to 60 centimeters, with most samples taken at a depth of 0 to 20 centimeters. The type of vegetation at the sampling location is dominated by species of Kandelia candel, Avicennia marina, Kandelia obovata, and Rhizophora mangle. Limitations regarding research on nitrifying bacteria in mangrove sediments provide opportunities for in-depth study. This comprehensive review provides an in-depth overview of the variety and spread of nitrifying bacteria, highlighting their role in nitrogen cycling and emphasizing the potential for discovering new nitrifying bacteria in mangrove sediments.

Mangrove forests in North Sumatra and Aceh are concentrated on the east coast of Sumatra Island. Mangrove habitats are highly productive, diversified, and ecologically and commercially significant ecosystems. However, they are vulnerable to both anthropogenic and natural hazards. The identification of coastal ecosystem species, such as mangrove and coastal forests, is very important in conserving and using the biodiversity of coastal ecosystems, which appears to be hindered by a lack of taxonomic and molecular expertise. This study aimed to address the lack of reference deoxyribonucleic acid barcodes from mangroves in North Sumatra and Aceh and assess the effectiveness of four deoxyribonucleic acid barcoding methods in terms of primer universality, successful identification rate, barcoding gap and species-tree inference, and then phylogenetic tree construction.

This study focused on selecting the main regions where mangroves are predominantly distributed in the provinces of North Sumatra and Aceh: Percut Sei Tuan and Deli Serdang mangrove areas, Pulau Sembilan and Lubuk Kertang of Langkat mangrove areas in North Sumatra, and Langsa mangrove areas in Aceh. The genomic deoxyribonucleic acid of mangrove plants was isolated from fresh leaf material using the Geneaid genomic deoxyribonucleic acid mini kit. Based on the guidance provided by the International Union for Biological Barcoding with four molecular sequences, deoxyribonucleic acid barcodes were chosen for amplification: chloroplast ribulose 1,5-bisphosphate carboxylase/oxygenase, maturase-K, transfer ribonucleic acid for histidine–photosystem II reaction center protein A, and nuclear genome internal transcribed spacer. The Tamura 3-parameter + Gamma method in molecular evolutionary genetics analysis X software was used to measure and describe the genetic distances between different species and within the same species. The construction of phylogenetic trees was carried out using the molecular evolutionary genetics analysis X from ribulose 1,5-bisphosphate carboxylase/oxygenase, transfer ribonucleic acid for histidine–photosystem II reaction center protein A, Internal transcribed spacer, and maturase-K barcodes based on the bootstrap analysis conducted using 100 permutations.

This study showed that the primers ribulose 1,5-bisphosphate carboxylase/oxygenase, transfer ribonucleic acid for histidine–photosystem II reaction center protein A, internal transcribed spacer, and maturase-K had the highest success rates during amplification, which could be strong barcodes for enhancing taxonomic clarification and gaining insights into phylogenetic relationships. The primers ribulose 1,5-bisphosphate carboxylase/oxygenase, transfer ribonucleic acid for histidine–photosystem II reaction center protein A, internal transcribed spacer, and maturase-K had the highest success rates during amplification. The success rate for the ribulose 1,5-bisphosphate carboxylase/oxygenase gene was the highest (90% percent), followed by (86 percent), transfer ribonucleic acid for histidine–photosystem II react percent ion center protein Ainternal transcribed spacer (75 percent), and maturase-K (57 Percent). The significant differences were as follows: inter- and intraspecific genetic distance (probability (p) <0.001), maturase-K (probability = 0.0001), combination maturase-K + photosystem II reaction center protein A (probability = 0.0008), maturase-K + ribulose 1,5-bisphosphate carboxylase/oxygenase (probability = 0.0008), maturase-K + internal transcribed spacer (probability = 0.0003), ribulose 1,5-bisphosphate carboxylase/oxygenase + internal transcribed spacer (probability = 0.0002), photosystem II reaction center protein A + internal transcribed spacer (probability = 7.051e-05), and three combined markers maturase-K + photosystem II reaction center protein A + internal transcribed spacer (probability = 0.0007). It is noteworthy that the maturase-K barcode could construct the clustering and differentiate the mangrove species based on family and not from sites. The ribulose 1,5-bisphosphate carboxylase/oxygenase barcode showed that members of Rhizophoraceae (Bruguiera parviflora, Rhizophora apiculata, and Rhizophora stylosa), Ptiredeacea (Acrostichum aureum), and Scyphiphora hydrophyllaceae from Rubiaceae existed in one branch.

This study provided a reference database both molecularly and taxonomically to strengthen biodiversity assessment and monitor mangrove forests. This database can be used to clarify the results of deoxyribonucleic acid barcodes for morphological and biochemical identification in the eastern coast of Sumatra.