Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.
Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.
复制标题
DOI：
10.1038/s41598-018-30179-1
复制
发表时间：
2018-08-06
影响因子：
4.6
通讯作者：
Creer S
中科院分区：
文献类型：
--
作者：
Nascimento FJA;Lallias D;Bik HM;Creer S
了解生物多样性在时间和空间上的变化对于评估环境变化对海底生态系统的影响至关重要。由于形态学方法的局限性，高通量测序方法在底栖真核生物群落研究中的应用迅速扩大。然而，样本大小和小尺度空间变异对评估底栖真核生物多样性的影响仍然不是很清楚。在这里，我们研究了不同样本量对后生动物和非后生动物真核生物群落组成的遗传评估的影响。因此，从5个底栖生物采样岩芯顶端2 cm的5个不同累积沉淀物体积中提取DNA作为模板，用于对18个 S的rRNA扩增片段进行ILumina MiSeq测序。样本量对后生和非后生真核生物的多样性度量都有很大影响。使用较小样本量的处理的贝塔多样性与100%采样区域的贝塔多样性显著不同。总体而言，我们的发现表明，0.2 g(占采样面积的1%)的样本量不足以解释小空间尺度上的空间异质性，并且需要相对较大比例的沉积物岩心样本来获得后生和非后生真核生物的稳健多样性测量。
Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes.
登录
查看更多内容
影响因子：
16.6
作者：
Fonseca, Vera G.;Carvalho, Gary R.;Sung, Way;Johnson, Harriet F.;Power, Deborah M.;Neill, Simon P.;Packer, Margaret;Blaxter, Mark L.;Lambshead, P. John D.;Thomas, W. Kelley;Creer, Simon
通讯作者：
Creer, Simon
EDNA水溶液的年度时间序列分析揭示了湖泊生态系统生物多样性的生态相关动力学。
影响因子：
16.6
作者：
Bista I;Carvalho GR;Walsh K;Seymour M;Hajibabaei M;Lallias D;Christmas M;Creer S
通讯作者：
Creer S
影响因子：
4.1
作者：
Chariton, Anthony A.;Ho, Kay T.;Matthews, Robin A.
通讯作者：
Matthews, Robin A.
影响因子：
6.6
作者：
Baselga, Andres;Orme, C. David L.
通讯作者：
Orme, C. David L.
影响因子：
2.7
作者：
Guardiola M;Wangensteen OS;Taberlet P;Coissac E;Uriz MJ;Turon X
通讯作者：
Turon X