Katie L. Duggan DiDominic, James P. Shapleigh, M. Todd Walter, Y. Samuel Wang, Matthew C. Reid, John M. Regan
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Metagenomic sequencing and bioinformatic analyses were performed on six woodchip samples (i.e., three unmilled and three milled) collected from a 10-year-old woodchip bioreactor treating agricultural tile drainage. All samples had similar DNA purity, yield, quality, and microbial diversity regardless of milling. However, when sequences were aligned against various protein libraries, our results indicated greater relative abundance of denitrification and P transformation proteins on the outside of the woodchips (unmilled), while the interior of woodchips (milled) exhibited more functional gene abundance for carbohydrate breakdown. Thus, it may be important to characterize microbial communities both within woodchips, and on woodchip surfaces, to gain a more holistic understanding of coupled biogeochemical cycles on N, P, and C in woodchip bioreactors. Based on these findings, we advise that future microbial research on woodchips (and potentially other permeable organic materials) examine both the surface biofilm and the interior organic material during initial studies. Once researchers determine where specific proteins or enzymes of interest are most prevalent, subsequent studies may then focus on either one or both aspects, as needed.</p>","PeriodicalId":15732,"journal":{"name":"Journal of environmental quality","volume":"53 5","pages":"565-576"},"PeriodicalIF":2.2000,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jeq2.20600","citationCount":"0","resultStr":"{\"title\":\"Microbial diversity and gene abundance in denitrifying bioreactors: A comparison of the woodchip surface biofilm versus the interior wood matrix\",\"authors\":\"Katie L. Duggan DiDominic, James P. Shapleigh, M. Todd Walter, Y. 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引用次数: 0
摘要
过量的氮(N)和磷(P)会导致水源富营养化。木屑生物反应器在去除农业径流中的氮方面取得了成功,但在去除磷方面却鲜为人知。木屑生物反应器是一种在农田下游安装的、装满木屑的地下盆地,用于收集和处理排水径流。本研究旨在探索生物反应器中的微生物群落,并确定研磨木屑以探测其中的微生物群落是否能揭示隐藏的微生物多样性或潜在活动。我们对从一个处理农用瓦片排水的有 10 年历史的木片生物反应器中收集的六个木片样本(即三个未研磨样本和三个已研磨样本)进行了元基因组测序和生物信息学分析。所有样本的 DNA 纯度、产量、质量和微生物多样性都很相似,与碾磨程度无关。然而,当序列与各种蛋白质库进行比对时,我们的结果表明,木片外部(未碾磨)的反硝化蛋白和P转化蛋白的相对丰度更高,而木片内部(碾磨)的碳水化合物分解功能基因丰度更高。因此,为了更全面地了解木片生物反应器中氮、磷和碳的耦合生物地球化学循环,对木片内部和木片表面的微生物群落进行特征描述可能非常重要。基于这些发现,我们建议今后对木片(可能还有其它可渗透的有机材料)进行微生物研究时,在初步研究中同时考察表面生物膜和内部有机材料。一旦研究人员确定感兴趣的特定蛋白质或酶在哪里最普遍,后续研究就可以根据需要重点研究其中一个方面或两个方面。
Microbial diversity and gene abundance in denitrifying bioreactors: A comparison of the woodchip surface biofilm versus the interior wood matrix
Excessive amounts of nitrogen (N) and phosphorus (P) can lead to eutrophication in water sources. Woodchip bioreactors have shown success in removing N from agricultural runoff, but less is known regarding P removal. Woodchip bioreactors are subsurface basins filled with woodchips installed downgradient of agricultural land to collect and treat drainage runoff. Microorganisms use the woodchips as a carbon (C) source to transform N in the runoff, with unresolved biological impacts on P. This study aims to explore microbial communities present in the bioreactor and determine whether milling woodchips to probe the microbial communities within them reveals hidden microbial diversities or potential activities. Metagenomic sequencing and bioinformatic analyses were performed on six woodchip samples (i.e., three unmilled and three milled) collected from a 10-year-old woodchip bioreactor treating agricultural tile drainage. All samples had similar DNA purity, yield, quality, and microbial diversity regardless of milling. However, when sequences were aligned against various protein libraries, our results indicated greater relative abundance of denitrification and P transformation proteins on the outside of the woodchips (unmilled), while the interior of woodchips (milled) exhibited more functional gene abundance for carbohydrate breakdown. Thus, it may be important to characterize microbial communities both within woodchips, and on woodchip surfaces, to gain a more holistic understanding of coupled biogeochemical cycles on N, P, and C in woodchip bioreactors. Based on these findings, we advise that future microbial research on woodchips (and potentially other permeable organic materials) examine both the surface biofilm and the interior organic material during initial studies. Once researchers determine where specific proteins or enzymes of interest are most prevalent, subsequent studies may then focus on either one or both aspects, as needed.
期刊介绍:
Articles in JEQ cover various aspects of anthropogenic impacts on the environment, including agricultural, terrestrial, atmospheric, and aquatic systems, with emphasis on the understanding of underlying processes. To be acceptable for consideration in JEQ, a manuscript must make a significant contribution to the advancement of knowledge or toward a better understanding of existing concepts. The study should define principles of broad applicability, be related to problems over a sizable geographic area, or be of potential interest to a representative number of scientists. Emphasis is given to the understanding of underlying processes rather than to monitoring.
Contributions are accepted from all disciplines for consideration by the editorial board. Manuscripts may be volunteered, invited, or coordinated as a special section or symposium.