Kato Shingo, Ohkuma Moriya, Powell Deborah H, Krepski Sean T, Oshima Kenshiro, Hattori Masahira, Shapiro Nicole, Woyke Tanja, Chan Clara S
Department of Geological Sciences, University of Delaware, Newark DE, USA ; Japan Collection of Microorganisms, RIKEN BioResource Center Tsukuba, Japan.
Japan Collection of Microorganisms, RIKEN BioResource Center Tsukuba, Japan.
Front Microbiol. 2015 Nov 13;6:1265. doi: 10.3389/fmicb.2015.01265. eCollection 2015.
Neutrophilic microaerophilic iron-oxidizing bacteria (FeOB) are thought to play a significant role in cycling of carbon, iron and associated elements in both freshwater and marine iron-rich environments. However, the roles of the neutrophilic microaerophilic FeOB are still poorly understood due largely to the difficulty of cultivation and lack of functional gene markers. Here, we analyze the genomes of two freshwater neutrophilic microaerophilic stalk-forming FeOB, Ferriphaselus amnicola OYT1 and Ferriphaselus strain R-1. Phylogenetic analyses confirm that these are distinct species within Betaproteobacteria; we describe strain R-1 and propose the name F. globulitus. We compare the genomes to those of two freshwater Betaproteobacterial and three marine Zetaproteobacterial FeOB isolates in order to look for mechanisms common to all FeOB, or just stalk-forming FeOB. The OYT1 and R-1 genomes both contain homologs to cyc2, which encodes a protein that has been shown to oxidize Fe in the acidophilic FeOB, Acidithiobacillus ferrooxidans. This c-type cytochrome common to all seven microaerophilic FeOB isolates, strengthening the case for its common utility in the Fe oxidation pathway. In contrast, the OYT1 and R-1 genomes lack mto genes found in other freshwater FeOB. OYT1 and R-1 both have genes that suggest they can oxidize sulfur species. Both have the genes necessary to fix carbon by the Calvin-Benson-Basshom pathway, while only OYT1 has the genes necessary to fix nitrogen. The stalk-forming FeOB share xag genes that may help form the polysaccharide structure of stalks. Both OYT1 and R-1 make a novel biomineralization structure, short rod-shaped Fe oxyhydroxides much smaller than their stalks; these oxides are constantly shed, and may be a vector for C, P, and metal transport to downstream environments. Our results show that while different FeOB are adapted to particular niches, freshwater and marine FeOB likely share common mechanisms for Fe oxidation electron transport and biomineralization pathways.
嗜中性微需氧铁氧化细菌（FeOB）被认为在淡水和富铁海洋环境中的碳、铁及相关元素循环中发挥着重要作用。然而，由于培养困难和缺乏功能基因标记，嗜中性微需氧FeOB的作用仍知之甚少。在此，我们分析了两种淡水嗜中性微需氧形成柄状的FeOB，即淡水栖铁柄菌OYT1和铁柄菌菌株R-1的基因组。系统发育分析证实，它们是β-变形菌纲中的不同物种；我们描述了菌株R-1，并提出了球状淡水栖铁柄菌这一名称。我们将这些基因组与两种淡水β-变形菌和三种海洋ζ-变形菌FeOB分离株的基因组进行比较，以寻找所有FeOB共有的机制，或者只是形成柄状的FeOB所共有的机制。OYT1和R-1的基因组均含有与cyc2的同源物，cyc2编码一种已被证明能在嗜酸FeOB氧化亚铁硫杆菌中氧化铁的蛋白质。这种c型细胞色素在所有七种微需氧FeOB分离株中都存在，这进一步证明了其在铁氧化途径中的普遍作用。相比之下，OYT1和R-1的基因组缺乏在其他淡水FeOB中发现的mto基因。OYT1和R-1都有表明它们可以氧化硫物种的基因。两者都有通过卡尔文-本森-巴斯姆途径固定碳所需的基因，而只有OYT1有固定氮所需的基因。形成柄状的FeOB共享xag基因，这些基因可能有助于形成柄的多糖结构。OYT1和R-1都形成了一种新型生物矿化结构，即比其柄小得多的短杆状羟基氧化铁；这些氧化物会不断脱落，可能是碳、磷和金属向下游环境运输的载体。我们的结果表明，虽然不同的FeOB适应特定的生态位，但淡水和海洋FeOB可能在铁氧化电子传递和生物矿化途径方面具有共同机制。
