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标准的过滤方法可能会显著扭曲对浮游微生物多样性的估计。

Standard filtration practices may significantly distort planktonic microbial diversity estimates.

作者信息

Padilla Cory C, Ganesh Sangita, Gantt Shelby, Huhman Alex, Parris Darren J, Sarode Neha, Stewart Frank J

机构信息

School of Biology, Georgia Institute of Technology Atlanta, GA, USA.

出版信息

Front Microbiol. 2015 Jun 2;6:547. doi: 10.3389/fmicb.2015.00547. eCollection 2015.

Abstract

Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size) and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40 to 60% of prefilter datasets at low volumes (0.05-0.5 L) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes, and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold). Taxon richness (97% similarity clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

摘要

通过过滤对生物量进行分级分离是浮游微生物采样的标准方法。目前尚不清楚过滤后的生物量的分类组成如何随样品体积而变化。我们使用来自海洋氧含量最低区域的海水,对孔径为1.6μm的预过滤器和下游0.2μm过滤器上0.05至5L样品体积的生物量的16S rRNA基因组成进行了定量分析。两个过滤级分中均发生了显著的群落变化,且在预过滤器群落中最为明显。与弧菌目匹配的序列在低样品体积(0.05 - 0.5L)时占预过滤器数据集的约40%至60%,而在高样品体积时降至不到5%,而诸如着色菌目和嗜盐硫杆菌目等类群则呈现相反趋势,从少量占比增加到在高样品体积时成为优势分类群。通常与海洋颗粒相关的类群,包括δ-变形菌纲、浮霉菌门和拟杆菌门的成员,是随样品体积增加幅度最大的类群之一(增加4至27倍)。分类单元丰富度(97%相似度聚类)也随样品体积显著变化,且根据过滤级分的不同方向相反,这突出了群落复杂性估计中的潜在偏差。这些数据引发了人们对使用过滤分级分离进行水生微生物多样性定量比较研究的担忧,例如在自由生活和与颗粒相关的群落之间的比较。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4be1/4451414/13be2c2c99ac/fmicb-06-00547-g0001.jpg

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