The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity

Bog ecosystems fulfil important functions in Earth's carbon and water turnover. While plant communities and their keystone species Sphagnum have been well studied, less is known about the microbial communities associated with them. To study our hypothesis that bog plants share an essential core of their microbiome despite their different phylogenetic origins, we analysed four plant community plots with 24 bryophytes, vascular plants and lichen species in two Alpine bogs in Austria by 16S rDNA amplicon sequencing followed by bioinformatic analyses. The overall bog microbiome was classified into 32 microbial phyla, while Proteobacteria (30.8%), Verrucomicrobia (20.3%) and Planctomycetes (15.1%) belonged to the most abundant groups. Interestingly, the archaeal phylum Euryarcheota represented 7.2% of total microbial abundance. However, a high portion of micro-organisms remained unassigned at phylum and class level, respectively. The core microbiome of the bog vegetation contained 177 operational taxonomic units (OTUs) (150 526 seq.) and contributed to 49.5% of the total microbial abundance. Only a minor portion of associated core micro-organisms was host specific for examined plant groups (5.9–11.6%). Using our new approach to analyse plant–microbial communities in an integral framework of ecosystem, vegetation and microbiome, we demonstrated that bog vegetation harboured a core microbiome that is shared between plants and lichens over the whole ecosystem and formed a transkingdom metacommunity. All micro- and macro-organisms are connected to keystone Sphagnum mosses via set of microbial species, for example Burkholderia bryophila which was found associated with a wide spectrum of host plants and is known for a beneficial plant–microbe interaction.

沼泽生态系统在地球碳循环与水循环中发挥着关键功能。尽管学界已对植物群落及其关键物种泥炭藓属（Sphagnum）开展了充分研究，但针对与之共生的微生物群落的认知仍较为匮乏。为验证我们的假说——尽管沼泽植物具有不同的系统发育起源，但它们共享一套核心微生物组，我们针对奥地利两处高山沼泽中的4个植物群落样地展开了分析：共涵盖24种苔藓植物、维管植物与地衣物种，实验先采用16S核糖体DNA（16S rDNA）扩增子测序，随后辅以生物信息学分析。整体沼泽微生物组可划分为32个微生物门，其中丰度最高的类群为变形菌门（Proteobacteria，占比30.8%）、疣微菌门（Verrucomicrobia，占比20.3%）与浮霉菌门（Planctomycetes，占比15.1%）。值得注意的是，古菌门下的广古菌门（Euryarcheota）占总微生物丰度的7.2%。但仍有较高比例的微生物分别无法在门与纲水平被归类。沼泽植被的核心微生物组包含177个操作分类单元（operational taxonomic units, OTUs），对应150526条序列，其丰度占总微生物丰度的49.5%。仅占较小比例的核心共生微生物对所研究的植物类群具有宿主特异性（占比5.9%~11.6%）。我们依托全新的分析方法，在生态系统、植被与微生物组的整合框架下研究植物-微生物群落，结果表明：整个生态系统中的沼泽植被均拥有一套共享于植物与地衣之间的核心微生物组，并由此形成了跨王国元群落。所有微型与大型微生物均通过一系列微生物物种与关键物种泥炭藓属（Sphagnum）苔藓建立联系，例如嗜泥炭伯克霍尔德菌（Burkholderia bryophila）：该菌已被发现可与多种宿主植物共生，且因具有有益的植物-微生物互作特性而为人熟知。