Growth of Cupriavidus metallidurans CH34 in the presence of basalt. Cupriavidus metallidurans CH34

The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Yet the genetics of biological rock weathering are unknown. For the first time, we apply a DNA microarray to investigate the genes involved in weathering by the heavy metal resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium sequesters iron in the ferrous state (FeII); therefore, not requiring siderophores. Instead an energy efficient process involving upregulation of large porins is employed concomitantly with genes associated with biofilm formation. We hypothesise that rock weathering is induced by changes in chemical equilibrium at the microbe-mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal resistant genes. Volcanic environments are analogous to some of the earliest environments on Earth. These results not only elucidate the mechanisms by which microorganisms might have sequestered nutrients on the early Earth but they also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity. Overall design: Cultures of Cupriavidus metallidurans CH34 were grown in Tris buffered medium MM284 media (with iron), MM284 without iron and MM284 without iron with sterilized basalt at 25 rpm, 30°C until mid-log phase. RNA was extracted from the cells. Three biological replicates of both samples were differentially labeled (resp. Cy3 and Cy5) and hybridized to three CH34 60-mer oligonucleotide glass-spotted microarray carrying three technical repeats.

火山矿物风化对全球硅酸盐风化收支具有重要贡献，进而影响二氧化碳固存与气候调控。玄武岩在硅酸盐风化过程中贡献了全球超过30%的二氧化碳固存量。然而，生物岩石风化的遗传机制目前仍不明确。本研究首次采用DNA微阵列（DNA microarray）技术，探究耐重金属菌株嗜金属贪铜菌（Cupriavidus metallidurans）CH34参与岩石风化的相关基因，重点研究其铁固存过程。研究结果表明，该菌株以亚铁形态（FeII）固存铁元素，因此无需分泌铁载体。取而代之的是，该菌采用了一种节能的代谢途径：上调大型孔蛋白的表达，并同步激活与生物膜形成相关的基因。我们提出假说：微生物-矿物界面的化学平衡改变会诱导岩石风化，进而降低铁的饱和状态；同时本研究证实，玄武岩中低浓度的金属会诱导耐重金属基因的表达。火山环境与地球早期的部分原始环境具有相似性。本研究结果不仅阐明了早期地球微生物固存营养物质的潜在机制，同时也解释了在人类活动造成工业污染生境之前，多重耐重金属基因的演化起源。实验设计：将嗜金属贪铜菌（Cupriavidus metallidurans）CH34分别接种于三种培养基中：添加铁元素的三羟甲基氨基甲烷（Tris）缓冲培养基MM284、不含铁元素的MM284培养基，以及不含铁元素但添加灭菌玄武岩的MM284培养基，于30℃、25 rpm条件下培养至对数生长中期。随后提取细胞总RNA。两组样本各设置3次生物学重复，分别用Cy3和Cy5进行差异标记后，与搭载3次技术重复的CH34 60聚体寡核苷酸玻璃点样微阵列进行杂交。