Deep-sea environments have unique habitat characteristics, including extremely high hydrostatic pressure, low temperatures, and minimal light. In addition, the deep sea also has a unique energy flow and material circulation system. In this special biological environment, the species, genetic composition and ecological function diversity of deep-sea microorganisms have been improved, and the abyss is the deepest part of the deep-sea environment, which has the most special biological environment in the deep-sea and is one of the least understood marine environments by human beings so far. The abyss contains abundant microbial biomass and exhibits active organic carbon turnover characteristics, which is a "hot spot" area for organic carbon degradation in the deep sea. In the marine environment, microorganisms exist in different ways, with Particle-associated microorganisms (PA) and free-living microorganisms (FL) representing two distinct lifestyles. However, little is known about the species composition and metabolic potential of abyssal microorganisms. In this paper, we used metagenomic technology and bioinformatics analysis to study the community composition and functional characteristics of these two microorganisms in the "Challenger Deep" (water depth of 10,500 meters) in the Mariana Trench, and to find the metabolic differences caused by their different lifestyles based on their functional characteristics. The results show that the nitrogen fixation ability, extreme environment adaptability and antioxidant capacity of free microorganisms are stronger than those of epiphytic microorganisms in the abyssal environment, which provides some help for the future research on abyssal microorganisms.

Qianyi Hui. Comparison of Community Composition and Function of Particle-associated Microorganisms and Free-living Microorganisms in the Mariana Trench. Academic Journal of Environment & Earth Science (2024), Vol. 6, Issue 3: 20-29. https://doi.org/10.25236/AJEE.2024.060303.

[1] Mulder T. Gravity processes and deposits on continental slope, rise and abyssal plains. Developments in Sedimentology. 2011, 63: 125-148.

[2] Schrope M. Journey to the Bottom of the Sea. Scientific American, 2014, 310(4): 60-69.

[3] Lloyd K G, May M K, Kevorkian R T, et al. Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor. Applied and Environmental Microbiology, 2013, 79(24): 7790-7799.

[4] Fang J S, Zhang L. Exploring the deep biosphere. Science China, 2011, 54(2): 157-165.

[5] Taira K, Kitagawa S, Yamashiro T, et al. Deep and Bottom Currents in the Challenger Deep, Mariana Trench, Measured with Super-Deep Current Meters. Journal of Oceanography, 2004, 60(6): 919-926.

[6] Glud R N, Wenzhofer F, Middelboe M, et al. High rates of microbial carbon turnover in sediments in the deepest oceanic trench on Earth. Nature Geoscience, 2013, 6(4): 284-286.

[7] Luo M, Glud R N, Pan B, et al. Benthic carbon mineralization in hadal trenches: insights from in situ determination of benthic oxygen consumption. Geophysical Research Letters, 2018, 45(6): 2752-2760.

[8] Yayanos A A, Dietz A S, Van Boxtel R. Obligately Barophilic Bacterium from the Mariana Trench. Proceedings of the National Academy of Sciences of the United States of America, 1981, 78(8): 5212-5215.

[9] Kato C, Li L, Nogi Y, et al. Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 meters. Applied and environmental microbiology, 1998, 64(4): 1510-1513.

[10] Pathom-Aree W, Stach J, Ward A C, et al. Diversity of actinomycetes isolated from Challenger Deep sediment (10,898 m) from the Mariana Trench. Extremophiles, 2006, 10(3): 181-189.

[11] Eloe E A, Shulse C N, Fadrosh D W, et al. Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment. Environmental Microbiology Reports, 2011, 3(4): 449-458.

[12] Nunoura T, Hirai M, Yoshida-Takashima Y, et al. Distribution and Niche Separation of Planktonic Microbial Communities in the Water Columns from the Surface to the Hadal Waters of the Japan Trench under the Eutrophic Ocean. Frontiers in Microbiology, 2016, 7(270): 1261.

[13] Nunoura T, Takaki Y, Hirai M, et al. Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(11): 1230-1236.

[14] Tarn J, Peoples Lm, Hardy K, et al. Identification of Free-Living and Particle-Associated Microbial Communities Present in Hadal Regions of the Mariana Trench. Frontiers in Microbiology, 2016, 7: 665.

[15] Liu R L, Wang L, Liu Q F, et al. Depth-Resolved Distribution of Particle-Attached and Free-Living Bacterial Communities in the Water Column of the New Britain Trench. Frontiers in Microbiology, 2018, 9: 625.

[16] Peoples L M, Sierra D, Oladayo O, et al. Vertically distinct microbial communities in the Mariana and Kermadec trenches. PLoS ONE, 2018, 13(4): e0195102

[17] Wang Y, Gao Z M, Li J, et al. Hadal water sampling by in situ microbial filtration and fixation (ISMIFF) apparatus. Deep Sea Research Part I: Oceanographic Research Papers, 2019, 144: 132-137.

[18] Nunoura T, Nishizawa M, Hirai M, et al. Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench. Microbes and Environments, 2018, 33(2): 186-194.

[19] Hiraoka S, Hirai M, Matsui Y, et al. Microbial community and geochemical analyses of transtrench sediments for understanding the roles of hadal environments. The ISME journal, 2020, 14: 740-756.

[20] Cui G J, Li J, Gao Z M, et al. Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep. Peer J, 2019, 7: e6961.

[21] Peoples L M, Grammatopoulou E, Pombrol M, et al. Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches. Frontiers in Microbiology, 2019, 10: 347.

[22] Liu R L, Wang Z X, Wang L, et al. Bulk and active sediment prokaryotic communities in the Mariana and Mussau trenches. Frontiers in Microbiology, 2020, 11: 1521.

[23] Eloe E A, Fadrosh D W, Mark N, et al. Going Deeper: Metagenome of a Hadopelagic Microbial Community. PLoS ONE, 2011, 6(5): e20388.

[24] Liu J W, Zheng Y F, Lin H Y, et al. Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench. Microbiome, 2019, 7(1): 47.

[25] Gao Z M, Huang J M, Cui G J, et al. In situ meta-omic insights into the community compositions and ecological roles of hadal microbes in the Mariana Trench. Environmental Microbiology, 2019, 21: 4092-4108.

[26] Zhang X, Xu W, Liu Y, et al. Metagenomics Reveals Microbial Diversity and Metabolic Potentials of Seawater and Surface Sediment From a Hadal Biosphere at the Yap Trench. Frontiers in Microbiology, 2018, 9: 2402.

[27] León-Zayas R, Peoples L, Biddle J F, et al. The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1). Environmental Microbiology, 2017, 19(7): 2769-2784.

[28] León-Zayas R, Novotny M, Podell S, et al. Single Cells Within the Puerto Rico Trench Suggest Hadal Adaptation of Microbial Lineages. Applied and Environmental Microbiology, 2015, 81(24): 8265-8276.

[29] Wei Z F, Li W L, Huang J M, et al. Metagenomic studies of SAR202 bacteria at the full-ocean depth in the Mariana Trench. Deep Sea Research Part I Oceanographic Research Papers, 2020, 165: 103396.

[30] Huang J M, Wang Y. Genomic differences within the phylum Marinimicrobia: From waters to sediments in the Mariana Trench. Marine Genomics, 2019, 50: 100699.

[31] Bolger A M, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 2014, 30(15):2114-2120.

[32] Peng Y, Leung H C, Yiu S M, et al. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 2012, 28(11):1420-1428.

[33] Hyatt D, Chen G L, Locascio P F, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010, 11(1): 119.

[34] Menzel P, Ng K L, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications, 2016, 7: 11257.

[35] Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. Journal of Molecular Biology, 2016, 428(4): 726-731.

[36] Cronan J E. Assembly of Lipoic Acid on Its Cognate Enzymes: An Extraordinary and Essential Biosyn-thetic Pathway. Microbiol Mol Biol Rev. 2016; 80(2):429–450. https://doi.org/10. 1128/ MMBR. 00073-1PMID: 27074917.

[37] Cao X, Koch T, Steffens L, Finkensieper J, Zigann R, Cronan JE, et al. Lipoate-Binding Proteins and Specific Lipoate-Protein Ligases in Microbial Sulfur Oxidation Reveal an Atypical Role for an Old Cofac- tor. elife. 2018; 7:e37439. https://doi.org/10.7554/eLife.37439 PMID: 30004385.

[38] Spalding M D, Prigge ST. Lipoic Acid Metabolism in Microbial Pathogens. Microbiol Mol Biol Rev. 2010;74(2):200–228. https://doi.org/10.1128/MMBR.00008-10 PMID: 20508247.

[39] Dunn M F. Vitamin Formation from Fatty Acid Precursors. In: Geiger O, editor. Biogenesis of Fatty Acids, Lipids and Membranes. Handbook of Hydrocarbon and Lipid Microbiology. Cham: Springer Nature Switzerland AG; 2019. p. 259–271.

[40] Liao D F, Chen J W, Xie P, Zhu Z Q, Xu R. Studies on the antioxidation effects of alpha-lipoic acid and dihydrolipoic acid. Journal of East China Normal University: Natural Science, 2007(2): 87–92, 136.

[41] Cronan J E. Biotin and lipoic acid: synthesis, attachment, and regulation. EcoSal Plus, 2008, 3(1): 10.1128. DOI:10.1128/ecosalplus.3.6.3.5.

[42] Jordan S W, Cronan J E. The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein: protein transferase. Journal of Bacteriology, 2003, 185(5): 1582-1589. DOI:10.1128/JB. 185.5. 1582-1589.2003.

[43] Cronan J E. The structure of lipoyl synthase, a remarkable enzyme that performs the last step of an extraordinary biosynthetic pathway. Biochemical Journal, 2014, 464(1): e1-e3. DOI: 10. 1042/ bj20141061.

[44] Morris T W, Reed K E, Cronan J E. Lipoic acid metabolism in Escherichia coli: the lplA and lipB genes define redundant pathways for ligation of lipoyl groups to apoprotein. Journal of Bacteriology, 1995, 177(1): 1-10. DOI:10.1128/jb.177.1.1-10.1995.

[45] Kim D J, Kim K H, Lee H H, Lee S J, Ha J Y, Yoon H J, Suh S W. Crystal structure of lipoate-protein ligase A bound with the activated intermediate: insights into interaction with lipoyl domains. The Journal of Biological Chemistry, 2005, 280(45): 38081-38089. DOI:10.1074/jbc. M507284200.

[46] Harding T. S. History of trehalose, its discovery and methods of p reparation. Sugar. 1923, 25: 476–478.

[47] Jiang Xirui, Huo Xingyun, Huang Jihong, Sun Zhongtao. Biofermentation technology. Beijing: China Light Industry Press. 2016, 326-327.

[48] Koch E M. Koch: The p resence of trehalose in yeast. Marine Genomics. 1925, 61: 570–572.

[49] Elbein A. D. The metabolism of a, a - trehalose. Ad2 vances in Carbohydrate Chemistry and Biochemistry. 1974, 30: 227–256.

[50] Yuan Qinsheng. Progress in the application research of alginate. Food and Drugs. 2005, 7 (4): 1-3.

[51] Xu J Y, Mao Y P. Microbiology Letters. From typical nitrifying bacteria to full-process ammonia-oxidizing microorganisms: discovery and research progress. Microbiology Letters, 2019, 46(4): 202-213.

[52] Hong Y G, He X, Wu J P, et al. Research progress on carbon and nitrogen biogeochemical cycle driven by Marine ammonia-oxidizing archaea. Journal of the University of Chinese Academy of Sciences, 2020, 37(4): 433-441.

[53] Gao J F, Fan X Y, Pan K L, et al. Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter. Scientific Reports, 2016, 6: 38785.

[54] Walker C B, De La Torre J R, Klotz M G, et al. Nitrosopumilusmaritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(19): 8818-8823.

[55] Tourna M, Stieglmeier M, Spang A, et al. Nitrososphaeraviennensis, an ammonia oxidizing archaeon from soil.Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(20): 8420-8425.

[56] Yu S L, Qiao Y L, Han Y Q, et al. Differencesbetween ammonia-oxidizing microorganisms in phylogeny and physiological ecology. Microbiology China, 2015, 42(12): 2457-2465.

[57] Verhamme D T, Prosser J I, Nicol G W. Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. The ISME Journal, 2011, 5(6): 1067-1071.

[58] Liu R L, Wang L, Wei Y L, et al. The hadal biosphere: Recent insights and new directions. Deep-Sea Research Part II: Topical Studies in Oceanography, 2018, 155: 11-18.

[59] Jamieson A J, Fujii T, Mayor D J, et al. Hadal trenches: the ecology of the deepest places on Earth. Trends in Ecology and Evolution, 2010, 25(3): 190-197.

[60] Wang H L, Guo A Y. An Introduction to Metagenome Databases of Environmental Microbiology. Biotechnology Bulletin, 2015, 31(11): 78-88.  

[61] Choo Kwang Raymond. Pesticide Pollution Affects the Functional Diversity of Soil Microbial Community. Academic Journal of Environmental Biology, 2020, 1(2): 44-53.