Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling
Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling
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DOI：
10.1128/aem.00546-21
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发表时间：
2020-06
影响因子：
4.4
通讯作者：
S. Karthikeyan;Luis H. Orellana;E. Johnston;J. Hatt;F. Löffler;Héctor L. Ayala-del-Rı́o;G. González;K. Konstantinidis
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文献类型：
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作者：
S. Karthikeyan;Luis H. Orellana;E. Johnston;J. Hatt;F. Löffler;Héctor L. Ayala-del-Rı́o;G. González;K. Konstantinidis
热带雨林是大气二氧化碳最大的陆地汇，也是氧化亚氮排放的最大自然源，这两种温室气体对气候至关重要。通过独立于培养的方法直接或间接地影响植物生长，对这些通量做出贡献的雨林土壤微生物群落仍然很少被描述。摘要 热带雨林微生物群落的系统发育和功能多样性以及这些微生物群落与温带微生物群落的差异仍然鲜为人知，但与来自热带的一氧化二氮 (N2O) 等温室气体通量的增加直接相关。为了缩小这些知识差距，我们分析了波多黎各卢基洛实验森林 (LEF) 四个地点的复制鸟枪宏基因组，这些宏基因组代表不同的生命区域和海拔梯度。与温带草原或农业土壤相比，这些土壤具有独特的微生物群落组成和较低的物种多样性。与整体不同的群落组成相比，热带森林和温带土壤之间 N2O 还原酶 (nosZ) 的相对丰度和核苷酸序列高度相似。然而，热带土壤中呼吸性一氧化氮还原酶（norB）的含量是热带土壤的两倍，这可能与其排放更多的氧化亚氮有关。固氮 (nifH) 在雨林中的相对丰度也高于温带土壤，即每种土壤类型中分别有 20% 和 0.1% 至 0.3% 的细菌基因组含有该基因。最后，与温带土壤不同，LEF 土壤在前 0 至 30 厘米的深度内几乎没有表现出分层，约 45% 的群落组成差异仅由位置来解释。总的来说，这些结果增进了我们对热带雨林土壤群落的空间多样性和代谢能力的理解，并应有助于未来对这些生态系统的生态研究。重要性 热带雨林是大气中二氧化碳的最大陆地汇和氧化亚氮排放的最大自然源，这两种温室气体对气候至关重要。通过独立于培养的方法直接或间接地影响植物生长，对这些通量做出贡献的雨林土壤微生物群落仍然很少被描述。为了缩小这一知识差距，本研究将鸟枪法宏基因组学应用于从波多黎各雨林内三个不同生命带中选取的样本。这些结果增进了我们对雨林土壤微生物群落多样性的理解，并有助于未来对这些关键生态系统的自然或人为扰动的研究。
Tropical rainforests are the largest terrestrial sinks of atmospheric CO2 and the largest natural source of N2O emissions, two greenhouse gases that are critical for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. ABSTRACT The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Toward closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N2O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N2O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ∼45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems. IMPORTANCE Tropical rainforests are the largest terrestrial sinks of atmospheric CO2 and the largest natural source of N2O emissions, two greenhouse gases that are critical for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from three distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.