Epp Schmidt Dietrich J, Kotze David Johan, Hornung Erzsébet, Setälä Heikki, Yesilonis Ian, Szlavecz Katalin, Dombos Miklós, Pouyat Richard, Cilliers Sarel, Tóth Zsolt, Yarwood Stephanie
Department of Environmental Science and Technology, University of Maryland, College Park, College Park, MD, United States.
Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland.
Front Microbiol. 2019 Oct 10;10:2330. doi: 10.3389/fmicb.2019.02330. eCollection 2019.
Urbanization results in the systemic conversion of land-use, driving habitat and biodiversity loss. The "urban convergence hypothesis" posits that urbanization represents a merging of habitat characteristics, in turn driving physiological and functional responses within the biotic community. To test this hypothesis, we sampled five cities (Baltimore, MD, United States; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa) across four different biomes. Within each city, we sampled four land-use categories that represented a gradient of increasing disturbance and management (from least intervention to highest disturbance: reference, remnant, turf/lawn, and ruderal). Previously, we used amplicon sequencing that targeted bacteria/archaea (16S rRNA) and fungi (ITS) and reported convergence in the archaeal community. Here, we applied shotgun metagenomic sequencing and QPCR of functional genes to the same soil DNA extracts to test convergence in microbial function. Our results suggest that urban land-use drives changes in gene abundance related to both the soil N and C metabolism. Our updated analysis found taxonomic convergence in both the archaeal and bacterial community (16S amplicon data). Convergence of the archaea was driven by increased abundance of ammonia oxidizing archaea and genes for ammonia oxidation (QPCR and shotgun metagenomics). The proliferation of ammonia-oxidizers under turf and ruderal land-use likely also contributes to the previously documented convergence of soil mineral N pools. We also found a higher relative abundance of methanogens (amplicon sequencing), a higher relative abundance of gene sequences putatively identified as Ni-Fe hydrogenase and nickel uptake (shotgun metagenomics) under urban land-use; and a convergence of gene sequences putatively identified as contributing to the nickel transport function under urban turf sites. High levels of disturbance lead to a higher relative abundance of gene sequences putatively identified as multiple antibiotic resistance protein marA and multidrug efflux pump mexD, but did not lead to an overall convergence in antibiotic resistance gene sequences.
城市化导致土地利用的系统性转变，推动栖息地丧失和生物多样性减少。“城市趋同假说”认为，城市化代表着栖息地特征的融合，进而驱动生物群落内部的生理和功能反应。为了验证这一假说，我们在四个不同生物群落中对五个城市（美国马里兰州巴尔的摩市；芬兰赫尔辛基市和拉赫蒂市；匈牙利布达佩斯市；南非波切夫斯特鲁姆市）进行了采样。在每个城市中，我们对四种土地利用类别进行了采样，这些类别代表了干扰和管理程度不断增加的梯度（从最少干预到最高干扰：参照地、残留地、草皮/草坪和杂草丛生地）。此前，我们使用靶向细菌/古菌（16S rRNA）和真菌（ITS）的扩增子测序，并报道了古菌群落的趋同现象。在这里，我们将鸟枪法宏基因组测序和功能基因的定量聚合酶链反应应用于相同的土壤DNA提取物，以测试微生物功能的趋同情况。我们的结果表明，城市土地利用驱动了与土壤氮和碳代谢相关的基因丰度变化。我们更新后的分析在古菌和细菌群落（16S扩增子数据）中均发现了分类学趋同现象。古菌的趋同是由氨氧化古菌丰度的增加以及氨氧化基因（定量聚合酶链反应和鸟枪法宏基因组学）驱动的。草皮和杂草丛生地土地利用条件下氨氧化菌的增殖可能也促成了先前记录的土壤矿质氮库的趋同现象。我们还发现，在城市土地利用条件下，产甲烷菌的相对丰度较高（扩增子测序），假定为镍铁氢化酶和镍摄取的基因序列的相对丰度较高（鸟枪法宏基因组学）；并且在城市草皮地点，假定为参与镍转运功能的基因序列出现了趋同现象。高度干扰导致假定为多重抗生素抗性蛋白marA和多药外排泵mexD的基因序列相对丰度较高，但并未导致抗生素抗性基因序列的总体趋同。
