Understanding the implicit effects of 16S rRNA gene databases on microbial bioindicator studies

IF 4.1 2区环境科学与生态学 Q1 MARINE & FRESHWATER BIOLOGY

Aquatic Toxicology Pub Date : 2025-03-30 DOI:10.1016/j.aquatox.2025.107351

Vitória da Silva Pereira Domingues, Lucy Seldin, Diogo Jurelevicius

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引用次数: 0

Abstract

Analysis of the presence and the abundance of microorganisms related to diseases can be used to monitor marine environmental health. Our study evaluated the interference of taxonomic databases (SILVA, Greengenes v13.8, Greengenes2, and RDP) to monitor the distribution of bacterial genera potentially related to diseases in marine organisms (BGPRDs) from low- (Dois Rios Beach-DR), medium- (Abraão Beach-AB) and high (Guanabara Bay-GB) impacted marine environments. The frequency, richness, diversity, and composition of BGPRDs present in DR, AB and GB were significantly influenced by the different databases (p < 0.05). Consequently, the analyses revealed that the use of different databases resulted in controversial results regarding the distribution of BGPRDs in the DR, AB and GB. While Greengenes v13.8 and RDP showed that GB had the highest frequency of BGPRDs (p < 0.05), analysis based on Greengenes2 and SILVA revealed a greater frequency of BGPRDs in AB (p < 0.05). Additionally, there was no congruence of BGPRDs detected by each taxonomic database in DR, AB and GB. In highly-impacted GB, Arcobacter was the main BGPRD obtained with the Greengenes2 and RDP databases, whereas Synechococcus and Alteromonas represented the main BGPRD according to the Greengenes v13.8 and SILVA databases, respectively. Our results showed we cannot determine the exact composition and abundance of BGPRDs in low-, medium- and highly-impacted marine environments. These findings emphasize the critical influence of database choice on microbial community characterization and its implications for effective environmental monitoring and management strategies. Interestingly, alpha diversity indices of BGPRDs obtained from DR, AB and GB were consistent among the different databases and showed greater congruence than did the frequency, richness, distribution and abundance of BGPRDs. The use of diversity indices of BGPRDs can be an alternative to overcome the limitations caused by the bias of taxonomic annotations for biomonitoring marine environments.

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了解16S rRNA基因数据库在微生物生物指标研究中的隐性作用

分析与疾病有关的微生物的存在和丰度可用于监测海洋环境健康。本研究评估了SILVA、Greengenes v13.8、Greengenes2和RDP等分类数据库对低（Dois Rios Beach-DR）、中（abra o Beach-AB）和高（Guanabara Bay-GB）影响海洋生物（BGPRDs）中可能与疾病相关的细菌属分布的干扰。在DR、AB和GB中存在的BGPRDs的频率、丰富度、多样性和组成受到不同数据库的显著影响(p <；0.05)。因此，分析显示，使用不同的数据库导致了关于BGPRDs在DR、AB和GB分布的有争议的结果。而Greengenes v13.8和RDP显示，GB的BGPRDs频率最高(p <；0.05)，基于Greengenes2和SILVA的分析显示AB中BGPRDs的频率更高(p <；0.05)。此外，在DR、AB和GB的各个分类数据库中检测到的BGPRDs没有一致性。在高度受影响的GB中，根据Greengenes2和RDP数据库获得的BGPRD主要为Arcobacter，而根据Greengenes v13.8和SILVA数据库获得的BGPRD主要为聚球菌和Alteromonas。我们的研究结果表明，我们无法确定低、中、高影响海洋环境中BGPRDs的确切组成和丰度。这些发现强调了数据库选择对微生物群落特征的关键影响及其对有效环境监测和管理策略的影响。有趣的是，从DR、AB和GB中获得的BGPRDs的α多样性指数在不同数据库中是一致的，其一致性大于BGPRDs的频率、丰富度、分布和丰度。利用生物多样性指数可以克服海洋生物环境监测中分类学注释的偏倚所带来的局限性。

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来源期刊

Aquatic Toxicology 环境科学-毒理学

CiteScore

7.10

自引率

4.40%

发文量

250

审稿时长

56 days

期刊介绍： Aquatic Toxicology publishes significant contributions that increase the understanding of the impact of harmful substances (including natural and synthetic chemicals) on aquatic organisms and ecosystems. Aquatic Toxicology considers both laboratory and field studies with a focus on marine/ freshwater environments. We strive to attract high quality original scientific papers, critical reviews and expert opinion papers in the following areas: Effects of harmful substances on molecular, cellular, sub-organismal, organismal, population, community, and ecosystem level; Toxic Mechanisms; Genetic disturbances, transgenerational effects, behavioral and adaptive responses; Impacts of harmful substances on structure, function of and services provided by aquatic ecosystems; Mixture toxicity assessment; Statistical approaches to predict exposure to and hazards of contaminants The journal also considers manuscripts in other areas, such as the development of innovative concepts, approaches, and methodologies, which promote the wider application of toxicological datasets to the protection of aquatic environments and inform ecological risk assessments and decision making by relevant authorities.