Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
Department of Botany, University of Wisconsin-Madison, Madison, WI, USA.
Ann Bot. 2022 Jul 19;130(1):65-75. doi: 10.1093/aob/mcac060.
Canyon stream beds in the hyperarid Atacama Desert surprisingly harbour magnificent groves of endemic giant horsetail wetland plants, Equisetum xylochaetum. Our previous metagenomic study of eukaryotes closely associated with this plant indicated that the microbiome included prokaryotes that might likewise influence host success and environment. We explored this possibility by using the metagenomic sequence to characterize prokaryote taxa and functional genes present in the microbiome of E. xylochaetum sampled from remote sites differing in the degree of anthropogenic disturbance. We focused on biogeochemical functions known to be important in wetland ecosystems.
To ensure that analyses were conducted on microbes most closely associated with plants, we extracted DNA from well-washed plant organs whose microbial biofilms were revealed with scanning electron microscopy. To assess the benefits of longer sequences for taxonomic and gene classifications, results of analyses performed using contigs were compared with those obtained with unassembled reads. We employed methods widely used to estimate genomic coverage of single taxa for genomic analysis to infer relative abundances of taxa and functional genes.
Key functional bacterial genera (e.g. Hydrogenophaga, Sulfuritalea and Rhodoferax) inferred from taxonomic and functional gene analysis of contigs - but not unassembled reads - to occur on surfaces of (or within) plants at relatively high abundance (>50× genomic coverage) indicated roles in nitrogen, sulfur and other mineral cycling processes. Comparison between sites revealed impacts on biogeochemical functions, e.g. reduced levels of the nifH gene marker under disturbance. Vanadium nitrogenases were more important than molybdenum nitrogenases, indicated by both functional genes and taxa such as Rhodomicrobium and Phaeospirillum inferred from contigs but not unassembled reads.
Our contig-based metagenomic analyses revealed that microbes performing key wetland biogeochemical functions occur as tightly adherent biofilms on the plant body, not just in water or sediments, and that disturbance reduces such functions, providing arguments for conservation efforts.
在极度干旱的阿塔卡马沙漠中，峡谷溪流床出人意料地拥有壮丽的本地巨型木贼湿地植物群落，即木贼属 xylochaetum。我们之前对与这种植物密切相关的真核生物的宏基因组研究表明，微生物组包括可能同样影响宿主成功和环境的原核生物。我们通过使用宏基因组序列来描述从受人为干扰程度不同的偏远地点采集的木贼属 xylochaetum 微生物组中的原核生物分类群和功能基因，探索了这种可能性。我们专注于在湿地生态系统中已知很重要的生物地球化学功能。
为确保分析是在与植物最密切相关的微生物上进行，我们从经过充分清洗的植物器官中提取 DNA，并用扫描电子显微镜揭示其微生物生物膜。为了评估长序列对分类和基因分类的好处，我们比较了使用连续序列进行分析的结果与使用未组装读取进行分析的结果。我们采用广泛用于估计单类群基因组覆盖度的方法来推断分类群和功能基因的相对丰度。
从连续序列的分类和功能基因分析推断出的关键功能细菌属（例如氢噬菌属、硫代硫酸盐和红杆菌属）-但不是未组装的读取-在相对较高的丰度（>50×基因组覆盖度）下出现在（或存在于）植物表面或内部，表明它们在氮、硫和其他矿物质循环过程中发挥作用。对不同地点的比较表明，生物地球化学功能受到了影响，例如在受到干扰时，nifH 基因标记的水平降低。通过功能基因和从连续序列推断出的分类群（如红微菌属和黄单胞菌属），而非未组装的读取，表明钒氮酶比钼氮酶更为重要。
我们基于连续序列的宏基因组分析表明，执行关键湿地生物地球化学功能的微生物作为紧密附着的生物膜存在于植物体上，而不仅仅存在于水中或沉积物中，并且干扰会降低这些功能，为保护工作提供了依据。
