Ecological Patterns Of Ammonia Or Methane Oxidizing Microorganisms In Global Oceans

Ammonia oxidation and methane oxidation are very important steps in nitrogen and carbon cycles. Up to now, global patterns of related functional microorganisms were analyzed based on PCR amplified sequences in public databases. However, the coverage of "universal" primers cause biases, which may miss many important microorganisms especially uncultured microorganisms. With the development of high-throughput sequencing technology, the metagenome and metatranscriptome sequencing become more popular in analysing various environmental samples. In this study we will mining metagenome and metatranscriptome datasets from CAMERA database and analysis ecological patterns of ammonia or methane oxidizing microorganisms in global oceans.56553 amoA or pmoA amino acid reference sequences were grouped using Usearch clustering at a 90% sequence identity and obtained 373 representative sequences. Then these sequences were searched against the CAMERA database with tBLASTn program. After screening, duplicating and removing low quality sequences, we obtained 885 reads from metagenome and 14972 reads from metatranscriptome, which came from 105 global samples (including 85 metagenome samples and 20 metatranscriptome samples).Ammonia oxidizing archaea were widely distributed in the ocean, which were detected from 96% of the ocean samples, these samples including coastal, surface open ocean, deep open ocean, hydrothermal vents and Symbiont. Four of five phylogenetic lineages of ammonia oxidizing archaea were found and Nitrosopumilis cluster was the dominate cluster. In 18 Nitrosopumilis subclusters, Nitrosopumilus subcluster 13 was shown as the highest relative abundance one. Ammonia oxidizing bacteria was distributed in coastal and open ocean, its relative abundance and activity was significantly lower than that of ammonia oxidizing archaea. We detected ammonia oxidizing bacteria in 10 high latitude polar ocean samples and it suggest that ammonia oxidizing bacteria have a certain adaptability to the cold environment. Due to the emission of methane from seafloor and hydrothermal vents, methane oxidizing bacteria were detected in deep open ocean and hydrothermal vents. Comparing the relative content of functional genes in metagenome and metatranscriptome datasets, we can know that ammonia oxidizing archaea are more active in coastal compared with deep open ocean. NMDS and Mantel test confirmed that depth, latitude, oxygen, ammonia and temperature were significantly correlated with the distribution of ammonia oxidizing archaea. Primer amoA-2R was normally used for ammonia oxidizing bacteria (β-proteobacteria), but there are 53% C mismatch,37% A mismatch in position 7 and 94% T mismatch in position 13, so it need modification, but it depends more experiments to validate in the future.