Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms
Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms
复制标题
DOI：
10.1038/s41564-019-0449-y
复制
发表时间：
2019-08-01
影响因子：
28.3
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
--
作者：
Diamond, Spencer;Andeer, Peter F.;Banfield, Jillian F.
土壤微生物活动驱动碳和氮循环，是大气微量气体周转的重要决定因素，但大多数土壤由代谢能力未知的微生物主导。即使是土壤中最丰富的细菌之一酸杆菌，也仍然缺乏特征，并且对Verrucomicrobia， gemmatimonadees， Chloroflexi和Rokubacteria等群体的功能研究不足。在这里，我们解析了来自地中海草原土壤生态系统的60个宏基因组和20个蛋白质组数据集，并从18个门中恢复了793个近乎完整的微生物基因组，约占检测到的微生物总数的三分之一。重要的是，这使得广泛的基于基因组学的代谢预测成为可能。来自多个以前未被研究的类别的酸杆菌具有编码用于复杂碳水化合物降解的大型酶补体的基因组。另外，大多数微生物编码碳水化合物酯酶，从果胶和木聚糖等聚合物中剥离容易获得的甲基和乙酰基，形成甲醇和乙酸，这可以解释基因组中C-1代谢和乙酸利用的高发性。在三种土壤深度、自然和修正降雨条件下收集的样品中，微生物丰度分别表明深层和浅层土壤中无机氮代谢和碳降解的统计学相关性更高。在延长的春季降雨条件下，这种分配减少，表明长期气候变化可以同时影响碳和氮循环。总体而言，通过利用自然和实验梯度与基因组分解代谢谱，我们将缺乏先前基因组表征的微生物与复杂的碳、碳- 1、硝酸盐和氨转化中的特定作用联系起来，并限制影响其在土壤中分布的因素。
Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C-1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C-l , nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.