Environmental Genomics Study Of Archaea In Dajiuhu Peatland

Peat is a marsh product which is formed by the complete or partial mineralization of plant residues,and it also plays an important role in the global carbon cycle.Though the peat covers the 3%soil areas compared with global land,it is the most effective natural carbon sink on earth which can store 30%global soil carbon sink.Peatland release CO2 and CH4 to atmosphere by slow function of organic matter decomposing,and it has also received extensive attention as a source of methane.Methanogens,inhabiting boreal peatland,are dominated by Methanomicrobiales and Methanosarcinales,which are affiliated with Euryarchaeota.Moreover,Thaumarchaeota,Crenarchaeota and Bathyarchaeota are also discovered in this environment.At present,the pure colony and genome information of archaea is rare and absent,especially the most abundant Bathyarchaeota which have few reports on metabolic pathways and ecological functions.In this case,the understanding of the archaea's ecological niche in the biogeochemical cycle of peatlands is seriously restricted.In this study,archaeal communities of nucleotide sequences of the Dajiuhu Peatland,Shennongjia were characterized based on comparison with other peatlands in the global scope.Subsequently those features were verified by high-throughput sequencing.Metagenome sequencing and genome bining technology had been used to explore ecological function and ecological adaptation mechanism of archaea at the community level,and it also excavated the metabolic pathways and evolutionary characteristics of archaea at individual level.With the help of these methods,it had opened our horizons for understanding the elements circulation involved in archaea on the earth.The main progress of this paper is as follows:1)Bathyarchaeota was the most abundant taxa in Dajiuhu peatland,and the methanogenic archaea occupied less abundance.Organic content,total organic carbon,pH and water content had significant effect on the distribution of archaea.Re-annotation of cloning sequence indicated that the sedimentary samples of the Dajiuhu didn't have methanogenic archaea and the abundance of Bathyarchaeota was most abundant.And the results of high-throughput sequencing found the abundance of Bathyarchaeota was 92.1%in the Dajiuhu sedimentary samples,and abundance of methanogenic archaea was lower than 0.2%.The Bathyarchaeota could be split into13 subgroups,MCG5b?38.5%?,MCG20?23.9%?and MCG6?11.4%?were top four abundant subgroups.The diversity analysis of high-throughput sequencing data shown that the Dajiuhu sedimentary samples had low archaea diversity,and decreased with depth.The copies number of archaea 16S rRNA gene ranged from 10⁵ to 10⁷copies/g in the Dajiuhu sedimentary samples,the largest value was the middle of the core,the least in the bottom.Both phylogenetic method and taxonomic approach show that organic matter,total organic carbon and water content had significant influence on archaeal community.2)Archaea participated in the complete degradation process of plant polymers to CO₂ and CH₄ and had multiple anti-reverse mechanisms in peatland.Bathyarchaeota had the function of fixing nitrogen and hydrolyzing polysaccharide.In total Archaea occupied the 9.7%of total gene abundance according to metagenomics,the relative abundance increased with depth.Euryarchaeota was the most abundance taxa,while the Bathyarchaeota took account of 2.9%.The results of16S rRNA gene analysis found that the abundance of Bathyarchaeota was higher than Euryarchaeota and Thaumarchaeota.The KEGG annotation showed that archaea included 15 genes of carbon fixation such as Calvin cycle and reductive tricarboxylic acid pathway,6 genes mediating nitrogen fixation and 6 genes assimilating phosphate from environment.It also contained cellulose,hemicellulose and pectinase which fragemented plant polymers into organic small moleculars,and multiple enzymes and produce CO₂ and CH₄ by anaerobic respiration of nitrate,nitrite and sulfate reduction.In addition,these resistance genes of antibiotics,oxidative stress,acidic adaption and heavy metal contribute archaea to adapting peat habitat.Bathyarchaeota had nifU gene,carbohydrate-active enzymes CE1 and CBM44,it meant that Bathyarchaeota participated in the nitrogen fixation and cellulose degradation process in the peatland environment.3)The Bathyarchaeota in Dajiuhu peatland contains functions such as carbon fixation,propionic acid degradation,and nitrite reduction,and with the characteristics of eukaryotes evolutionary.We finally obtained 5 high-quality genomes of Bathyarchaeota by genomic bining method.The five Bathyarchaeota MAGs kept distant phylogentic relationship with reference database with the average nucleotide identity 58.58%-72.02%.The 5MAG were classified into MCG5b,MCG6,MCG9,MCG10 and MCG13 according to phylogenetic tree of 16S rRNA gene.These MAGs were characterized with genome size of 1.22-3.08 M,coding genes of 1296–3218.Using KEGG database for function annotation,we found that these MAGs have nearly complete Wood-Ljungdhl pathway except MCR gene,indicating these Bathyarhaeota fix atmosphere CO₂ by this pathway.Complete metabolic pathway of propionic and various carbohydrate hydrolases,such as alpha-,beta-galactosidase,glacosidase and endo-1,4-beta-mannosidase,meaning Bathyarchaeota keep mutualism with acid-forming bacteria or degrade plant polymer.The discovery of nitrite reductase indicated their anaerobic respiration using nitrite.In addition,some Eukaryotic signature proteins were uncovered in these genomes,such as putative DNA polymerase epsilon,Eukaryotic-type Topoisomerase,putative homologs of Eukaryotic ribosomal protein L22e,ESCRT machinery,Ubiquitin modifier systems and trafficking system related protein.The above studies explored the composition,ecological function,habitat adaptability and evolutionary characteristics of archaeal communities in the Dajiuhu peatlands based the perspective of molecular biology.It is found that the Bathyarchaeota is the main group of peat deposits in Dajiuhu.Archaea in Dajiuhu peatlands not only degrades plant residues,anaerobic and fermentatively metabolizes small organic molecules,but also assimilates carbon,nitrogen and phosphorus to increase peat biomass.Bathyarchaeota has the ability to hydrolyze extracellular proteins and polysaccharides.It also has the function of degrading propionic acid and reducing nitrite,and has the evolutionary characteristics of eukaryotic organisms.The above researches give insight into biogeochemical processes in peatlands.