Advancing Marker-Gene-Based Methods for Prokaryote-Mediated Multifunctional Redundancy: Exploring Random and Non-Random Extinctions in a Catchment

IF 2.8 2区生物学 Q2 ECOLOGY

Freshwater Biology Pub Date : 2025-03-16 DOI:10.1111/fwb.70020

Wan-Hsuan Cheng, Takeshi Miki, Motohiro Ido, Kinuyo Yoneya, Kazuaki Matsui, Taichi Yokokawa, Hiroki Yamanaka, Shin-ichi Nakano

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引用次数: 0

Abstract

Multifunctional redundancy, which measures the extent of loss in multiple ecosystem functions with decreasing biodiversity, stands as a crucial index for evaluating ecosystem resilience to environmental changes. Previous studies have assessed functional redundancy by evaluating the overlap in multiple traits or functions among taxonomic units, but quantifying these experimentally for each taxonomic unit is challenging and resource-intensive, especially for microorganisms. In this study, we aimed to refine the estimation of multifunctional redundancy in prokaryotic communities using a marker-gene-based methodology.
We used the bioinformatic tool, PICRUSt2, to predict KEGG ortholog (KO) composition for each Amplicon Sequence Variant (ASV) of the 16S rRNA gene and assessed community-wide KO richness as a metric of genomic multifunctionality. Additionally, we introduced a refined regression on KO richness vs. ASV richness curves, providing a reliable estimate of the power-law exponent within computational time constraints, serving as the multifunctional redundancy index. To quantify variations between different species extinction scenarios, we incorporated various non-random extinction scenarios alongside a random one. Finally, to elucidate potential mechanisms contributing to the variations in multifunctional redundancy, we applied our refined methodology to the prokaryote community in Lake Biwa and four of its inlet rivers.
Our refined marker-gene-based methodology for quantifying multifunctional redundancy was effectively validated using experimentally quantified phenotypic multifunctionality. Our application to the Lake Biwa catchment revealed spatio-temporal variations in multifunctional redundancy.
Our analysis demonstrated lower redundancy in Lake Biwa compared to its inlet rivers, aiding in prioritising conservation targets and inferring distinct community assembly processes.
Future directions include a deeper exploration of KO composition information for detailed multifunctionality quantification and the refinement of extinction scenarios. This study demonstrates the promising integration of bioinformatic functional prediction and modelling biodiversity loss, offering a valuable tool for effective ecosystem management.

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推进基于标记基因的原核生物介导的多功能冗余方法：探索流域随机和非随机灭绝

多功能冗余是衡量生态系统多种功能随着生物多样性的减少而丧失的程度，是评价生态系统适应环境变化能力的重要指标。以前的研究通过评估分类单元之间多个性状或功能的重叠来评估功能冗余，但对每个分类单元进行实验量化是具有挑战性和资源密集型的，特别是对于微生物。在这项研究中，我们旨在使用基于标记基因的方法来改进原核生物群落中多功能冗余的估计。我们使用生物信息学工具PICRUSt2预测了16S rRNA基因的每个扩增子序列变体（ASV）的KEGG同源物（KO）组成，并评估了社区范围内KO丰富度作为基因组多功能性的度量。此外，我们引入了对KO丰富度和ASV丰富度曲线的精细回归，在计算时间限制内提供幂律指数的可靠估计，作为多功能冗余指数。为了量化不同物种灭绝情景之间的差异，我们将各种非随机灭绝情景与随机灭绝情景结合起来。最后，为了阐明多功能冗余变化的潜在机制，我们将改进的方法应用于琵琶湖及其四条入口河流的原核生物群落。我们改进的基于标记基因的多功能冗余量化方法通过实验量化表型多功能性得到了有效验证。我们对琵琶湖流域的应用揭示了多功能冗余的时空变化。我们的分析表明，与进口河流相比，琵琶湖的冗余度较低，这有助于确定保护目标的优先顺序，并推断出不同的群落组装过程。未来的方向包括对KO成分信息进行更深入的探索，以进行详细的多功能量化和对灭绝情景的改进。该研究表明，生物信息学功能预测与生物多样性丧失建模相结合，为有效的生态系统管理提供了有价值的工具。

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来源期刊

Freshwater Biology 生物-海洋与淡水生物学

CiteScore

5.90

自引率

3.70%

发文量

162

审稿时长

2 months

期刊介绍： Freshwater Biology publishes papers on all aspects of the ecology of inland waters, including rivers and lakes, ground waters, flood plains and other freshwater wetlands. We include studies of micro-organisms, algae, macrophytes, invertebrates, fish and other vertebrates, as well as those concerning whole systems and related physical and chemical aspects of the environment, provided that they have clear biological relevance. Studies may focus at any level in the ecological hierarchy from physiological ecology and animal behaviour, through population dynamics and evolutionary genetics, to community interactions, biogeography and ecosystem functioning. They may also be at any scale: from microhabitat to landscape, and continental to global. Preference is given to research, whether meta-analytical, experimental, theoretical or descriptive, highlighting causal (ecological) mechanisms from which clearly stated hypotheses are derived. Manuscripts with an experimental or conceptual flavour are particularly welcome, as are those or which integrate laboratory and field work, and studies from less well researched areas of the world. Priority is given to submissions that are likely to interest a wide range of readers. We encourage submission of papers well grounded in ecological theory that deal with issues related to the conservation and management of inland waters. Papers interpreting fundamental research in a way that makes clear its applied, strategic or socio-economic relevance are also welcome. Review articles (FRESHWATER BIOLOGY REVIEWS) and discussion papers (OPINION) are also invited: these enable authors to publish high-quality material outside the constraints of standard research papers.