Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds

Abstract

Mangroves, as important and special ecosystems, create unique ecological environments for examining the microbial gene capacity and potential for producing bioactive compounds. However, little is known about the biogeochemical implications of microbiomes in mangrove ecosystems, especially the variations between pristine and anthropogenic mangroves. To elucidate this, we investigated the microbial taxonomic and functional shifts of the mangrove microbiomes and their potential for bioactive compounds in two different coastal mangrove ecosystems in southern China. A gene catalogue, including 87 million unique genes, was constructed, based on deep shotgun metagenomic sequencing. Differentially enriched bacterial and archaeal taxa between pristine mangroves (Guangxi) and anthropogenic mangroves (Shenzhen) were found. The Nitrospira and ammonia-oxidizing archaea, specifically, were more abundant in Shenzhen mangroves, while sulfate-reducing bacteria and methanogens were more abundant in Guangxi mangroves. The results of functional analysis were consistent with the taxonomic results, indicating that the Shenzhen mangrove microbiome has a higher abundance of genes involved in nitrogen metabolism while the Guangxi mangrove microbiome has a higher capacity for sulfur metabolism and methanogenesis. Biosynthetic gene clusters were identified in the metagenome data and in hundreds of de novo reconstructed nonredundant microbial genomes, respectively. Notably, we found different biosynthetic potential in different taxa, and we identified three high quality and novel Acidobacteria genomes with a large number of BGCs. In total, 67,278 unique genes were annotated with antibiotic resistance, indicating the prevalence and persistence in multidrug-resistant genes in the mangrove microbiome. IMPORTANCE This study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diverse mangrove regions. A large number of microbial biosynthetic gene clusters encoding novel bioactivities were found, and this can serve as a valuable resource to guide novel bioactive compound discovery for potential clinical uses.

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

“…However, this abundance may be underestimated, since the primers used in our analysis preferentially amplify bacteria, and to a lesser extent archaeal sequences. The abundance and diversity of the Archaea domain present in coastal environments have been widely reported [ 55 , 71 , 72 , 73 , 74 , 75 ]. Therefore, analyzes focused on the identification of organisms belonging to this domain are necessary, which will allow a more complete panorama of the prokaryotic communities that are part of the microbiome landscape of the Yucatan coast.…”

Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence

“…Compared with acidic soil, the microorganisms related to nitrogen fixation (e.g., Geobacter , Nitrospira , Candidatus Koribacter , and Candidatus Solibacter ) in the main modules of the network are enriched in neutral soil ( 49 , 56 , 75 , 80 , 81 ). This might indicate that waterlogging is less harmful to neutral soils than acidic soils, at least on the level of microbial functions.…”

Depth-related Variability of Biological Nitrogen Fixation and Diazotrophic Communities in Mangrove Sediments

“…Mangroves are considered as typical nitrogen-limited ecosystems [56]. Characterizing the biological nitrogen xation and diazotrophic communities is, therefore, crucial to fully elucidate the nutrient status and ecological functions of mangrove ecosystems.…”