Hough Moira, McClure Amelia, Bolduc Benjamin, Dorrepaal Ellen, Saleska Scott, Klepac-Ceraj Vanja, Rich Virginia
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States.
Department of Biological Sciences, Wellesley College, Wellesley, MA, United States.
Front Microbiol. 2020 May 15;11:796. doi: 10.3389/fmicb.2020.00796. eCollection 2020.
Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.
与植物相关的微生物群落由环境条件和植物伴生体构成，而这两者都因气候变化而发生改变。植物微生物群落的未来结构将取决于这两者各自相对重要性，而这在很大程度上尚不清楚。这种不确定性对于北极泥炭地尤为重要，随着永久冻土融化，北极泥炭地的植物群落和土壤微生物群落正在发生巨大变化，并且由于其土壤碳（C）储存，它们可能是气候变化反馈的重要来源。我们通过16S rRNA基因扩增子测序，对六种植物物种的叶际和根际微生物群落以及大块泥炭进行了表征，涵盖了永久冻土融化的整个过程（从完整的永久冻土到部分融化和完全融化阶段）。我们检验了这样一个假设，即生物过滤与环境过滤（植物物种的作用与融化定义的栖息地的作用）在构建微生物群落中的相对影响在叶际、根际和大块泥炭之间会有所不同。使用基于丰度和系统发育的方法，我们发现叶际微生物组成受植物伴生体的影响更强，栖息地的影响很小，而在根际，植物和栖息地的影响相似。基于网络的群落分析表明，关键类群表现出相似的模式，对驱动因素的反应更强。然而，与大块群落相比，植物伴生体似乎对属于与甲烷循环相关家族的生物体有更大的影响。在根际，假定的产甲烷菌受植物的影响比受栖息地的影响更强，而在叶际，假定的甲烷氧化菌受植物的影响比整个群落更强。我们得出结论，生物效应可能比环境过滤更强，但其相对重要性在不同微生物群体中有所不同。对于这个系统中的大多数微生物来说，生物过滤在地上比地下更强。然而，对于假定的甲烷循环菌来说，尽管随着融化会发生重大水文变化，但植物关联对群落组成的影响比环境更强。这表明在确定微生物与碳循环气候反馈的相关性方面植物演替动态可能与水文变化同样重要。通过划分植物过滤与环境过滤驱动微生物群落组成和功能的程度，我们可以提高预测变暖对其他正在经历类似永久冻土融化转变的北极地区碳循环影响的能力。
