Metabolic Potential And Ecological Function Of Chloroflexi In The Sediment Of The Mariana Trench

The deep-sea harbors around 75% of the prokaryotic biomass and more than half of the prokaryotic production of the global ocean,and it is a key site for organic matter(OM)remineralization and long-term storage in the biosphere.The hadal trenches are the deepest part of the ocean,accounting for 1-2% of benthic area and 45% of vertical depth of the ocean,and they are important component of the deep ocean.However,the hadal zone is one of the least explored marine habitats on earth.Organic matter content and microbial carbon turnover rates are significantly higher at hadal trench sediments compared with abyssal plain site,making the hadal trenches “hot spots” for microbial colonization and organic matter deposition in the deep ocean.Multiple sources of OM inputs combined with frequent OM remobilization due to special topographies,tectonic activities and intra-trench currents,lead to a great heterogeneity and fluctuation of OM in the hadal trenches.Hadal trench microorganisms therefore have to employ special metabolic strategies to cope with the variable OM conditions to ensure their survival and function.Bacteria of the phylum Chloroflexi are dominant members in the global deep ocean.Previous studies revealed that Chloroflexi from deep-sea waters harbor genes involved in degradation of organocarbon and organosulfur compounds,and those for metabolisms of recalcitrant compounds such as cyclic alkanes and aromatic compounds.However,currently,little is known about the metabolic potential of Chloroflexi living in hadal sediments,and their metabolic strategy to cope with the varied OM supply in the hadal trenches is still unknown.In this study,we employed a metagenomic methodology to fill the knowledge gap on metabolism of Chloroflexi that are living in surface sediments of the Mariana Trench.The objectives are to(1)analyze the phylogeny of hadal Chloroflexi;(2)explore the distribution of hadal Chloroflexi in the hadal sediments and other ecosystems worldwide;and(3)explore for the first time the metabolic potential of Chloroflexi in hadal sediments and their metabolic strategies to cope with the varied OM conditions.As the first part of this Msc thesis,we construct a metagenomic analysis pipeline in which the metagenomic raw data were trimmed,quality controlled,assembled and highquality metagenomic assembled genomes(MAGs)were reconstructed by Binning.The MAGs were further dereplicated and functional annotation and metabolic network reconstruction were performed against various functional databases.A total of 62 Chloroflexi MAGs were recovered from the nine metagenomes from surface sediments of the Mariana Trench(0-10 cm),and 17 representative MAGs were selected after dereplication.Phylogenomic analysis showed that the MAGs belonged to the classes Anaerolineae,Dehalococcoidia,and they represent six novel species,four novel genera and one novel family in the orders SM23-28-2,SAR202,UBA2963,UBA1151,UBA3495 and Anaerolineales.In addition,one MAG was found to represent a novel order of the class Dehalococcoidia.Mapping of the MAGs against the 16 S r RNA and 16 S r RNA gene libraries constructed from the same sediment samples confirmed that the recovered MAGs represent major members of Chloroflexi in the hadal sediment of the Mariana Trench.The global distribution of recovered MAGs was evaluated by read recruitments against58 metagenomes derived from different natural habitats,including seawater and surface sediments from different depths of the open ocean,sediments of mud volcanos,deep-sea oil spilling sites,deep subseafloors,coastal regions,rivers and salt-lakes,as well as several soil samples.The results suggest that the majority of the MAGs(except order SM23-28-2)have recruited reads from metagenomes derived from surface sediments and seawaters of worldwide deep oceans.However,MAGs from different orders showed apparent preferences in their distributions in different deep-sea habitats.MAGs from the order UBA3495 showed high recruitment values in both deep seawater and sediment metagenomes.In contrast to UBA3495,MAGs from the orders Anaerolineales,SAR202,UBA2963,UBA1151 and the novel order showed higher recruit values in metagenomes from deep-sea sediments compared to those from seawater.The MAGs of the order SM23-28-2 only matched with the reads from sediment metagenomes of the Mariana Trench,indicating a potential endemism for the Mariana Trench.Genome annotation of the MAGs was performed against the KEGG,COG,CAZy and PROKKA databases.The recovered MAGs showed potentials for organo-heterotrophic metabolisms capable of utilizing a wide range of OM.In addition,our results advance the existing knowledge by reporting the pathways for the complete degradation of phthalate and benzoate to CO2 by hadal sediment Chloroflexi,and is the first time to show that deep-sea Chloroflexi harbor pathways to completely degrade fluorene,biphenyl and 4-chlorobiphenyl.In this study,we further revealed for the first time the complete or near complete pathways for hydrolytic and oxidative degradation of multiple types of organohalides in hadal trench Chloroflexi.These findings suggest a significant role of Chloroflexi in driving the biogeochemical cycles of carbon,sulfur and halogen in the deep ocean.In addition to the capacities of metabolizing a wide range of organic matter with different recalcitrancy,the recovered MAGs harbor genes encoding key enzymes for the formation of at least one type of intracellular energy storage compound.Moreover,all of the MAGs harbor the metabolism regulating modules such as lrp gene encoding the leucineresponsive regulatory protein(LRP),suggesting the potential for rapid response to changes of nutrient conditions.These metabolic features were consistent with a potentially “feast and famine” metabolic strategy,which allows the hadal Chloroflexi to modify their metabolic mode in response to the changes on quality and quantity of organic matter in the environment,which may provide advantages for the Chloroflexi to survive and adapt to the varied nutrient conditions in the hadal trenches and other deep-sea habitats.This study expands the knowledge on metabolic processes in deep-ocean Chlorolfexi,and highlights their significance in deep-sea carbon,sulfur and halogen cycles.The metabolic plasticity likely provides Chloroflexi with advantages for the survival under variable and heterogenic OM inputs in the deep ocean.The results of this research are important for understanding microbial processes occurring in the hadal zone,and lay a foundation for revealing the biogeochemical cycling mechanisms in the deep sea.