# Dataset on ecological health and microbial communities of coastal aquaculture ponds from surrounding region of Sundarban mangroves

## TL;DR

This study provides a dataset on the ecological health and microbial communities of aquaculture ponds near the Sundarbans mangroves using environmental DNA analysis.

## Contribution

The paper presents the first eDNA-based high-throughput sequencing assessment of aquaculture ponds near the Sundarbans mangroves.

## Key findings

- IMA ponds showed ideal conditions for shrimp aquaculture with no hypoxic conditions.
- Proteobacteria, Bacillariophyta, and Chlorophyta were predominant in the microbial communities.
- Functional gene profiles indicated pathways for nutrient metabolism and aromatic compound degradation.

## Abstract

Integrated Mangrove Aquaculture (IMA) and Sustainable Aquaculture in Mangrove Ecosystem Fisheries (SAIME) are key activities undertaken across coastal regions globally to meet growing demand for brackish-water aquaculture products through sustainable practices. An in-depth biomonitoring study was conducted to map the ecological health of IMA and non-IMA aquaculture ponds in the surrounding region of the Indian Sundarbans mangroves located along the northeast coast of Bay of Bengal. Surface water samples were collected from six aquaculture ponds, four IMA (IMA_C1, IMA_C3, IMA_DB1, and IMA_DB4) and two non-IMA (C6_NM and DB5_NM) in the month of October 2022, for characterizing niche-specific biological communities using the environmental DNA (eDNA) approach. During sampling, in-situ environmental parameters were recorded. Mangrove litter-derived phenolics (tannic and gallic acids) and dissolved nutrients were estimated using a UV–Vis spectrophotometer, while dissolved organic carbon (DOC) was measured with the elemental analyzer. Metal and metalloid concentrations were determined by inductively coupled plasma mass spectrometry approach (ICP–MS). IMA ponds showed ideal conditions for shrimp aquaculture, with pH ranging from 7.913 to 8.633 and dissolved oxygen (DO) between 5.32 and 6.03 mg/L, indicating no hypoxic conditions despite higher concentrations of phenolics. High-throughput sequencing (HTS) based on Oxford Nanopore Technologies (ONT) sequencing chemistry was undertaken on the MinION platform, revealing the predominance of Proteobacteria among prokaryotes and Bacillariophyta as well as Chlorophyta among eukaryotes from extracted eDNA in each studied pond. Additionally, members of the family Cyprinidae were also detected, reflecting the biodiversity of fish population in these ponds. Functional gene profiling indicated signatures associated with nitrogen, phosphorus, sulphur, potassium and iron acquisition and metabolism, along with pathways related to aromatic compound degradation. Overall, dissolved nutrients, dissolved organic carbon (DOC), metal and metalloid ion concentrations as well as structure and functional profiles of biological communities provide a comprehensive basis for evaluating the ecological health of aquaculture ponds. This study generates important baseline information for long-term monitoring and represents the first eDNA-based high-throughput sequencing assessment of IMA and non-IMA aquaculture ponds from surface water in close proximity to the Sundarbans mangrove.