Microbial Ecology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, Germany
Geomicrobiology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, Germany.
Appl Environ Microbiol. 2020 Aug 18;86(17). doi: 10.1128/AEM.01160-20.
The discovery of the novel class greatly expanded our understanding of neutrophilic, microaerophilic microbial Fe(II) oxidation in marine environments. Despite molecular techniques demonstrating their global distribution, relatively few isolates exist, especially from low-Fe(II) environments. Furthermore, the Fe(II) oxidation pathways used by remain poorly understood. Here, we present the genomes (>99% genome completeness) of two , which are the only cultivated isolates originating from typical low-Fe [porewater Fe(II), 70 to 100 μM] coastal marine sediments. The two strains share <90% average nucleotide identity (ANI) with each other and <80% ANI with any other genome. The closest relatives were strain CP-5 and strain CP-8 (96 to 98% 16S rRNA gene sequence similarity). Fe(II) oxidation of strains KV and NF is most likely mediated by the putative Fe(II) oxidase Cyc2. Interestingly, the genome of strain KV also encodes a putative multicopper oxidase, PcoAB, which could play a role in Fe(II) oxidation, a pathway found only in two other genomes ( TAG-1 and SCGC AB-602-C20). The strains show potential adaptations to fluctuating O concentrations, indicated by the presence of both - and -type cytochrome oxidases, which are adapted to low and high O concentrations, respectively. This is further supported by the presence of several oxidative-stress-related genes. In summary, our results reveal the potential Fe(II) oxidation pathways employed by these two novel chemolithoautotrophic Fe(II)-oxidizing species and the lifestyle adaptations which enable the to survive in coastal environments with low Fe(II) and regular redox fluctuations. Until recently, the importance and relevance of were mainly thought to be restricted to high-Fe(II) environments, such as deep-sea hydrothermal vents. The two novel isolates presented here originate from typical low-Fe(II) coastal marine sediments. As well as being low in Fe(II), these environments are often subjected to fluctuating O concentrations and regular mixing by wave action and bioturbation. The discovery of two novel isolates highlights the importance of these organisms in such environments, as Fe(II) oxidation has been shown to impact nutrients and trace metals. Genome analysis of these two strains further supported their lifestyle adaptation and therefore their potential preference for coastal marine sediments, as genes necessary for surviving dynamic O concentrations and oxidative stress were identified. Furthermore, our analyses also expand our understanding of the poorly understood Fe(II) oxidation pathways used by neutrophilic, microaerophilic Fe(II) oxidizers.
该新型的发现极大地扩展了我们对海洋环境中嗜中性、微需氧微生物亚铁（II）氧化的理解。尽管分子技术表明它们在全球范围内分布，但相对较少有分离株存在，特别是在亚铁（II）含量低的环境中。此外，仍然不清楚 所使用的亚铁（II）氧化途径。在这里，我们介绍了两个 的基因组（>99%的基因组完整性），它们是唯一源自典型低亚铁（II）[孔隙水亚铁（II），70 至 100μM]沿海海洋沉积物的培养分离株。这两个菌株彼此之间的平均核苷酸同一性（ANI）<90%，与任何其他 基因组的 ANI<80%。最接近的亲缘关系是 菌株 CP-5 和 菌株 CP-8（16S rRNA 基因序列相似性为 96 至 98%）。菌株 KV 和 NF 的亚铁（II）氧化很可能是由假定的亚铁（II）氧化酶 Cyc2 介导的。有趣的是，菌株 KV 的基因组还编码了一种假定的多铜氧化酶 PcoAB，它可能在亚铁（II）氧化中发挥作用，这种途径仅在另外两个 基因组（TAG-1 和 SCGC AB-602-C20）中发现。这些菌株显示出对波动的 O 浓度的潜在适应能力，这表明存在两种 - 和 - 型细胞色素 c 氧化酶，它们分别适应低氧和高氧浓度。这进一步得到了几个与氧化应激相关基因的存在的支持。总之，我们的结果揭示了这两个新型化能自养亚铁（II）氧化物种所采用的潜在亚铁（II）氧化途径，以及使 在低亚铁（II）和定期氧化还原波动的沿海环境中生存的生活方式适应。直到最近， 的重要性和相关性主要被认为仅限于高亚铁（II）环境，例如深海热液喷口。这里介绍的两个新型 分离株来自典型的低亚铁（II）沿海海洋沉积物。这些环境不仅亚铁（II）含量低，而且经常受到波动的 O 浓度和波浪作用和生物扰动引起的定期混合的影响。两个新型 分离株的发现突出了这些生物体在这些环境中的重要性，因为亚铁（II）氧化已被证明会影响营养物质和痕量金属。对这两个菌株的基因组分析进一步支持了它们的生活方式适应，因此它们可能更喜欢沿海海洋沉积物，因为鉴定出了生存所需的必要基因动态 O 浓度和氧化应激。此外，我们的分析还扩展了我们对嗜中性、微需氧亚铁（II）氧化菌所使用的亚铁（II）氧化途径的理解。
