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.
Highlights
Mangroves are coastal estuarine ecosystems covering 60–70% of the coastlines in the tropics and subtropics [1], and they have an estimated economic value of 2000 to 9000 USD per hectare per year [2]
Three samples from mangrove sediments were obtained on January 2017 (21.121251 N, −90.074685 W) inside “El Palmar” natural reserve
Mangrove roots (MR) samples are sediments that were collected directly over roots; mangrove tree area (MA) samples are sediments collected close to roots but not directly over them; anrd mangrove water channel (MC) samples are sediments collected in a nearby water channel with a constant flow of water and not obviously influenced by mangrove roots (Figure S1)
Summary
Mangroves are coastal estuarine ecosystems covering 60–70% of the coastlines in the tropics and subtropics [1], and they have an estimated economic value of 2000 to 9000 USD per hectare per year [2]. Mangroves act as barriers against erosion by the wind and ocean waves, and create an important buffer zone between the land and ocean [3,4] These tidal forests are highly productive environments with robust microbial communities, which play a crucial role in supporting the local food chain. Descriptions of the biotechnological potential of mangrove microbial communities through the use of genome mining is scarce, and little research has focused on identifying genes involved in the biosynthesis of medically and industrially relevant compounds from these sediments [29,30,31,32]. 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 [33,34,35]
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