Molecular Pathogens 2024, Vol.15, No.2, 72-82 http://microbescipublisher.com/index.php/mp 74 certain substrates, to identify bacterial species (Popović et al., 2022). In a study comparing the identification results of MALDI-TOF MS and API20E, it was found that certain biochemical reactions, such as ONPG, GLU, and OX, were consistently positive for reliable identification of specific bacterial strains, highlighting the importance of biochemical tests in confirming pathogen identity before proceeding to molecular methods (Popović et al., 2022). 3.3 Molecular identification methods Molecular identification methods provide precise and reliable identification of kelp pathogens at the genetic level. Techniques such as sequencing and metagenomic analysis are commonly used. For instance, the use of Taxoblast, a pipeline for detecting contaminating sequences in the kelp genome, has revealed the presence of bacterial contaminants and hybrid sequences, indicating the importance of molecular tools in identifying and characterizing pathogens (Dittami and Corre, 2017). Additionally, metagenome-assembled genomes (MAGs) from kelp microbiomes have been reconstructed to determine the functional roles of microbial symbionts, which include potential pathogens. These MAGs provide insights into the metabolic potential and functional roles of bacteria associated with kelp, such as nutrient cycling and biofilm formation, which are crucial for understanding pathogen-host interactions (Weigel et al., 2022). Furthermore, sequencing of molecular markers like 5’COI and ITS1 has been used to investigate the diversity and host specificity of kelp endophytes, identifying various species of the genera Laminarionema and Laminariocolax that invade kelp tissues (Bernard et al., 2018). These molecular methods are indispensable for the accurate identification and understanding of kelp pathogens. 4 Genomic Analysis Techniques 4.1 DNA extraction and sequencing DNA extraction and sequencing are fundamental steps in the genomic analysis of kelp pathogens. High-throughput sequencing technologies, such as Random Subcloning Sequencing (SMS), have revolutionized the ability to analyze genomic DNA from environmental samples without prior cultivation (Jo et al., 2020). For instance, whole-genome sequencing datasets have been used to study ecto- and endosymbiotic relationships on kelp, revealing various species colonizing the kelp sporophyte (Bringloe et al., 2021). Bringloe et al. (2021) isolated and performed sequencing analysis using two molecular markers (5' COI and ITS1) on 56 endophytic strains from seven different kelp species collected from Europe, Chile, Korea, and New Zealand, uncovering the molecular diversity of these endophytes (Figure 1). Additionally, Restriction Site-Associated DNA (RAD) sequencing has been used to construct a high-density SNP linkage map for kelp, facilitating genetic research and the development of molecular tools (Zhang et al., 2015). The study from Bringloe et al., 2021 shows the scanning electron micrograph of the Nereida sp. MMG025 strain and the phylogenetic tree based on 100 single-copy genes. The electron micrograph details the cell morphology and surface structure of this strain, aiding in understanding its environmental adaptation mechanisms. The phylogenetic tree illustrates the evolutionary relationships of this strain with other related strains, revealing its precise classification within the Rhodobacteraceae family. These data provide important references for studying the genomic characteristics and ecological functions of this strain. 4.2 Genomic annotation Genome annotation involves identifying and labeling genes and other functional elements within a genome. This process is crucial for understanding the genetic composition and potential functions of kelp pathogens. For example, the annotation of the mitochondrial genome of a suspected brown algal parasite revealed many atypical features, including gene duplications and rearrangements, indicative of its parasitic lifestyle (Bringloe et al., 2021). Similarly, the annotation of the draft genome sequence of the Nereida sp. MMG025 strain isolated from giant kelp suggests that it may represent a new species, providing a resource for future microbiological and biotechnological research (Alker et al., 2022). Microscopic images show the cellular morphology and surface structures of the MMG025 strain, aiding in understanding its ecological adaptation mechanisms (Figure 2). The phylogenetic tree
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