A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure

Abstract

Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments’ microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from “El Palmar” harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of “El Palmar” microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases’ biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from “El Palmar”, and show the impact selective media had on the composition of communities of actinobacteria.

Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications

“…However, there may be a bias in the status of the antiSMASH database, with NRPS (23%), PKS (17%), and terpene synthases (12%) being the most abundant BGCs from the total of 172,395 BGCs from 24,776 unique species/strains present in this pipeline (Moghaddam et al, 2021). A high BGC and SM diversity was found in the Polac sinkhole sediment, higher than the 10 BGC types reported for mangrove sediments that lie very close to Polac and that were studied using cultivation-dependent metagenomes (Marfil-Santana et al, 2021); of those BGC types, eight were found in our metagenomes, including terpenes and NRPS. That study reported 23 SMs of which 8 were detected in Polac's MAGs.…”

“…BGCs are a grouping of all genes responsible for the assembly of secondary metabolites (SMs) (also known as natural products) (Medema et al, 2015 ), which play roles within their host as defense molecules, virulence factors, or give them survival advantage, additionally, they are of medical and biotechnological importance (Ceniceros et al, 2017 ; Letzel et al, 2013 ). To identify BGCs, various computational tools have been developed (Blin et al, 2019 ; van Heel et al, 2018 ; Ziemert et al, 2012 ), and the process is commonly called “genome mining.” BGC identification using genome mining has significantly increased in recent years leading to the exploration of diverse microbial environments such as marine microbial mats (Chen, Wong, et al, 2020 ), lakes (Chen, Chiang, et al, 2021 ; Cuadrat et al, 2018 ), the Arctic Ocean (Rego et al, 2021 ), marine sediments (Bruce et al, 2022 ), mangrove sediments (Marfil‐Santana et al, 2021 ), and marine sponges (Storey et al, 2020 ). These searches are providing an understanding of microbial ecological and evolutionary processes in these environments and are revealing the potential they have as sources of natural products.…”

Diversity and bioprospection of Gram-positive bacteria derived from a Mayan sinkhole

“…Sediment samples were resuspended 1:10 in sterilized water from Pol-Ac. Thereafter, serial dilutions up to 10 − 7 were prepared and streaked onto A1 agar plates (10 g L − 1 starch, 4 g L − 1 yeast extract, 2 g L − 1 peptone, 16 g L − 1 agar) [32] containing either sterile marine water from Sisal, Yucatán (A1 m agar plates) or sterile sinkhole water from Pol-Ac. All plates were incubated at 27°C for 1 to 2 weeks.…”

Insights into the phylogenetic diversity, biological activities, and biosynthetic potential of mangrove rhizosphere Actinobacteria from Hainan Island

“…Encoding a wealth of biosynthetic gene clusters (BGCs) makes Actinobacteria well-known producers of diverse secondary metabolites (Kamjam et al, 2017 ; Matsumoto and Takahashi, 2017 ; Singh et al, 2021 ). Among these gene clusters, polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes are the most commonly used to assess the natural product potential of a community due to their involvement in the biosynthesis of numerous bioactive compounds through multifunctional pathways (Marfil-Santana et al, 2021 ). Polyketides (PKs) such as erythromycin and rapamycin are encoded in type I polyketide synthase (PKS-I), and tetracycline and doxorubicin are assembled using type II polyketide synthase (PKS-II) gene clusters (Seow et al, 1997 ; Hertweck et al, 2007 ; Gontang et al, 2010 ; Kharel et al, 2012 ; Rao et al, 2016 ).…”