Combined DNA/RNA Amplicon Sequencing and Metatranscriptomics Reveals Microbial-Driven Nutrient Transformations and Core Taxa in Agriculturally Impacted Sediments

IF 2.7 4区 生物学 Q2 ENVIRONMENTAL SCIENCES
Nicholas W. Falk, Ian G. Droppo, Ken G. Drouillard, Christopher G. Weisener
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Abstract

Chronic non-point nitrogen (N) and phosphorus (P) loads reshape sediment microbial biogeochemical cycling in headwater systems, altering ecosystem function. This study integrates DNA and RNA amplicon sequencing with metatranscriptomics to examine microbial taxonomic and functional responses to nutrient inputs in lower Great Lakes watersheds, focusing on N, P, and sulphur (S) metabolism. RNA-based taxa showed a stronger correlation with metabolic functions than DNA-based taxa, highlighting RNA-based approaches as valuable tools for assessing active microbial responses to nutrients. Site-specific analyses revealed distinct microbial metabolic profiles linked to watershed fertiliser sources and seasonal variation. Inorganic fertiliser inputs were associated with tightly coupled N reduction and sulphur oxidation, driven by differential expression of dissimilatory nitrate reduction to ammonia (DNRA) and sox genes. In contrast, a manure-amended site exhibited elevated nitrosative stress and sulphur assimilation pathways, consistent with detection of ammonia-oxidising genera. The low-impact reference site demonstrated intermediate functional turnover, enhanced nitrogen fixation, and the highest microbial diversity, suggesting greater ecosystem resilience. Seasonally, functional turnover increased in fall, with fewer shared core taxa across sites compared to summer. These findings highlight the impact of chronic nutrient enrichment on site-specific microbial adaptations and underscore the importance of temporal dynamics in assessing freshwater sediment microbial communities.

Abstract Image

结合DNA/RNA扩增子测序和超转录组学揭示微生物驱动的营养转化和农业影响沉积物的核心分类群
慢性非点源氮(N)和磷(P)负荷重塑了水源系统沉积物微生物生物地球化学循环,改变了生态系统功能。本研究将DNA和RNA扩增子测序与超转录组学结合起来,研究五大湖下游流域微生物对养分输入的分类和功能反应,重点研究N, P和硫(S)代谢。与基于dna的分类群相比,基于rna的分类群与代谢功能的相关性更强,这表明基于rna的方法是评估微生物对营养物质活性反应的有价值的工具。特定地点的分析揭示了与流域肥料来源和季节变化相关的不同微生物代谢谱。无机肥料投入与氮还原和硫氧化紧密耦合相关,这是由异化硝酸盐还原氨(DNRA)和sox基因的差异表达驱动的。相比之下,经过肥料处理的位点表现出更高的亚硝化胁迫和硫同化途径,与氨氧化属的检测一致。低影响参考点表现出中等的功能转换,增强的固氮作用和最高的微生物多样性,表明更强的生态系统恢复能力。从季节上看,功能更替在秋季增加,与夏季相比,不同站点共享的核心类群较少。这些发现强调了慢性营养物富集对特定地点微生物适应的影响,并强调了时间动态在评估淡水沉积物微生物群落中的重要性。
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来源期刊
Environmental Microbiology Reports
Environmental Microbiology Reports ENVIRONMENTAL SCIENCES-MICROBIOLOGY
CiteScore
6.00
自引率
3.00%
发文量
91
审稿时长
3.0 months
期刊介绍: The journal is identical in scope to Environmental Microbiology, shares the same editorial team and submission site, and will apply the same high level acceptance criteria. The two journals will be mutually supportive and evolve side-by-side. Environmental Microbiology Reports provides a high profile vehicle for publication of the most innovative, original and rigorous research in the field. The scope of the Journal encompasses the diversity of current research on microbial processes in the environment, microbial communities, interactions and evolution and includes, but is not limited to, the following: the structure, activities and communal behaviour of microbial communities microbial community genetics and evolutionary processes microbial symbioses, microbial interactions and interactions with plants, animals and abiotic factors microbes in the tree of life, microbial diversification and evolution population biology and clonal structure microbial metabolic and structural diversity microbial physiology, growth and survival microbes and surfaces, adhesion and biofouling responses to environmental signals and stress factors modelling and theory development pollution microbiology extremophiles and life in extreme and unusual little-explored habitats element cycles and biogeochemical processes, primary and secondary production microbes in a changing world, microbially-influenced global changes evolution and diversity of archaeal and bacterial viruses new technological developments in microbial ecology and evolution, in particular for the study of activities of microbial communities, non-culturable microorganisms and emerging pathogens.
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