A metagenomic snapshot of metabolic potentials in wintertime eutrophic sediments of Lake Taihu inferred from metagenome-assembled genomes.

IF 5.8 2区生物学 Q2 MICROBIOLOGY

Frontiers in Microbiology Pub Date : 2026-09-28 eCollection Date: 2026-01-01 DOI:10.3389/fmicb.2026.1929411

Qi Wei, Yajie Li, Aidong Ruan

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Abstract

Introduction: Understanding the metabolic potential of microbial communities in eutrophic lake sediments at the genome-resolved level is essential for predicting nutrient cycling and stress responses in contaminated freshwater ecosystems.

Methods: In this study, we reconstructed 206 dereplicated metagenome-assembled genomes (MAGs) from sediment cores collected across four regions of Lake Taihu.

Results: These dereplicated MAGs spanned 34 classified phyla and 72 classified genera, with 97.6% unclassified at the species level, indicating substantial genomic novelty. The cyanobacterial MAGs harbored diverse secondary metabolite biosynthetic gene clusters, suggesting a genomic basis for potential adaptive traits. Across all dereplicated MAGs, the highest biosynthetic potential for secondary metabolites was observed in Chloroflexota and Pseudomonadota. Putative antibiotic resistance genes were predominantly represented by glycopeptide resistance determinants (vanT/vanW) and resistance-nodulation-division (RND) efflux pumps, which together accounted for 86.1% of the detected resistome. Additionally, 490 predicted horizontal gene transfer (HGT) events were identified, with transferred genes being most prevalent in energy metabolism (12.4%), translation (10.8%), and transcriptional regulation (7.2%).

Discussion: This genome-resolved survey provides a foundation for understanding the metabolic and genomic potential of sediment microbiomes in eutrophic freshwater systems.

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太湖冬季富营养化沉积物代谢势的宏基因组分析。

在基因组解析水平上了解富营养化湖泊沉积物中微生物群落的代谢潜力，对于预测受污染淡水生态系统的养分循环和应激反应至关重要。方法：在本研究中，我们从太湖四个地区的沉积物岩心中重建了206个去复制的宏基因组组装基因组（MAGs）。结果：这些去重复的mag跨越了34个分类门和72个分类属，其中97.6%的mag在种水平上未分类，表明了大量的基因组新颖性。蓝藻MAGs拥有多种次生代谢物生物合成基因簇，表明潜在的适应性状具有基因组基础。在所有去复制的mag中，氯氟藻和假单胞藻的次生代谢物的生物合成潜力最高。推定的抗生素耐药基因主要为糖肽耐药决定因素（vanT/vanW）和耐药-结瘤-分裂（RND）外排泵，共占检测到的耐药组的86.1%。此外，共鉴定出490个可预测的水平基因转移（HGT）事件，其中转移基因在能量代谢（12.4%）、翻译（10.8%）和转录调控（7.2%）中最为普遍。讨论：这项基因组解析调查为了解富营养化淡水系统中沉积物微生物组的代谢和基因组潜力提供了基础。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Frontiers in Microbiology MICROBIOLOGY-

CiteScore

7.70

自引率

9.60%

发文量

4837

审稿时长

14 weeks

期刊介绍： Frontiers in Microbiology is a leading journal in its field, publishing rigorously peer-reviewed research across the entire spectrum of microbiology. Field Chief Editor Martin G. Klotz at Washington State University is supported by an outstanding Editorial Board of international researchers. This multidisciplinary open-access journal is at the forefront of disseminating and communicating scientific knowledge and impactful discoveries to researchers, academics, clinicians and the public worldwide.