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eISSN: 2083-5906
ISSN: 1230-1485
ISSN: 1230-1485
ORIGINAL RESEARCH
Comparative Assessment of 16S rRNA
and Metagenomic Sequencing for Characterizing
Microbial Communities across Mangrove
Water-Sediment Interfaces
1
Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant
Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
Submission date: 2025-04-05
Final revision date: 2025-08-01
Acceptance date: 2025-09-13
Online publication date: 2025-12-03
Publication date: 2026-10-23
Corresponding author
Pol. J. Environ. Stud. 2026;35(5):5919-5933
KEYWORDS
mangrove ecosystemmicrobial ecologyDNA sequencing methodsfunctional genehabitat-specific diversitynitrogen cycling
TOPICS
ABSTRACT
Understanding microbial communities in mangrove ecosystems presents unique methodological
challenges due to complex physicochemical gradients and varying biomass levels between water and
sediment compartments. We systematically evaluated 16S rRNA amplicon and shotgun metagenomic
sequencing approaches using the Dongzhai Port mangrove ecosystem as a model system. Metagenomic
sequencing demonstrated superior taxonomic resolution, identifying 82 phyla compared to 52 phyla
by 16S rRNA sequencing, and revealed distinct habitat-specific patterns in community structure.
Both methods consistently showed higher bacterial diversity in sediment samples, reflecting enriched
nutrient conditions and a stable physicochemical environment. While 16S rRNA sequencing effectively
captured core community structures, metagenomic analysis provided deeper insights into functional
capabilities, particularly in energy metabolism and nitrogen cycling pathways. Notably, metagenomic
sequencing uncovered unique distribution patterns of key nitrogen metabolism genes (gltB, glnA/GLUL,
gltD) between water and sediment compartments. Technical considerations, including PCR inhibition
in sediments and variable biomass in water samples, significantly influenced method performance.
Our findings provide a quantitative framework for method selection in mangrove microbiome studies,
recommending 16S rRNA sequencing for broad community surveys and metagenomic sequencing for
detailed functional analysis or rare taxa detection.
CONFLICT OF INTEREST
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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| eISSN: | 2083-5906 |
| ISSN: | 1230-1485 |
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