Methodological Approaches Frame Insights into Endophyte Richness and Community Composition
Methodological Approaches Frame Insights into Endophyte Richness and Community Composition
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方法论深入了解内生菌丰富度和群落组成
DOI：
10.1007/s00248-020-01654-y
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发表时间：
2021
影响因子：
3.6
通讯作者：
Arnold, A. Elizabeth
中科院分区：
文献类型：
--
作者：
Oita, Shuzo;Carey, Jamison;Kline, Ian;Ibáñez, Alicia;Yang, Nathaniel;Hom, Erik F.;Carbone, Ignazio;U’Ren, Jana M.;Arnold, A. Elizabeth
分离微生物对研究微生物群至关重要，但对微生物多样性和生态的洞察可能会受到顽固或不可培养的菌株的限制。无培养方法(例如，下一代测序，NGS)变得流行起来，部分原因是它们检测到比单独培养更丰富的内容。这两种方法都被广泛用于描述健康叶片(叶片内生植物)中的微真菌，但研究之间的方法学差异可能会限制对内生植物生态的大规模洞察。我们研究了温带植物群落中的内生菌，以量化某些方法因素，如收集叶片后培养和储存期的选择，如何影响关于内生菌群落的推断；这些影响在植物分类群中如何变化；以及当相同植物组织的子集用于每种植物时，培养和NGS可以如何互补。我们发现，内生菌的丰富度和组成在五种类型的培养中是一致的。来自培养和NGS的见解在很大程度上对储存期(1、5和10天)的差异很强。虽然通过培养和NGS鉴定的内生菌丰富度、组成和分类多样性明显不同，但这两种方法都揭示了寄主结构的群落。因此，只有在培养介质或储存期上不同的研究可以进行比较，以估计比单独研究更大规模的内生菌丰富度、组成和周转。我们的数据表明，更重要的是对更多的寄主物种进行采样，而不是更密集地对更少的物种进行采样，以量化给定地点的内生菌多样性，当培养和NGS配对时，对内生菌生态的最丰富见解出现。
Isolating microbes is vital to study microbiomes, but insights into microbial diversity and ecology can be constrained by recalcitrant or unculturable strains. Culture-free methods (e.g., next-generation sequencing, NGS) have become popular in part because they detect greater richness than culturing alone. Both approaches are used widely to characterize microfungi within healthy leaves (foliar endophytes), but methodological differences among studies can constrain large-scale insights into endophyte ecology. We examined endophytes in a temperate plant community to quantify how certain methodological factors, such as the choice of cultivation media for culturing and storage period after leaf collection, affect inferences regarding endophyte communities; how such effects vary among plant taxa; and how complementary culturing and NGS can be when subsets of the same plant tissue are used for each. We found that endophyte richness and composition from culturing were consistent across five media types. Insights from culturing and NGS were largely robust to differences in storage period (1, 5, and 10 days). Although endophyte richness, composition, and taxonomic diversity identified via culturing vs. NGS differed markedly, both methods revealed host-structured communities. Studies differing only in cultivation media or storage period thus can be compared to estimate endophyte richness, composition, and turnover at scales larger than those of individual studies alone. Our data show that it is likely more important to sample more host species, rather than sampling fewer species more intensively, to quantify endophyte diversity in given locations, with the richest insights into endophyte ecology emerging when culturing and NGS are paired.
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内生真菌提高切叶蚁对叶子的加工率（Atta）
影响因子：
2.2
作者：
S. V. Van Bael;M. Seid;W. Wcislo
通讯作者：
W. Wcislo
DOI：
10.1038/ismej.2012.8
发表时间：
2012-08
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
麦卢卡叶内生菌（Leptospermum scoparium）
DOI：
--
发表时间：
1998
期刊：
影响因子：
--
作者：
P. Johnston
通讯作者：
P. Johnston
影响因子：
2.5
作者：
Oono R;Lefèvre E;Simha A;Lutzoni F
通讯作者：
Lutzoni F
影响因子：
3.7
作者：
Toju H;Tanabe AS;Yamamoto S;Sato H
通讯作者：
Sato H