Fungal and prokaryotic activities in the Marine subsurface biosphere at Peru Margin and canterbury basin inferred from RNA-based analyses and microscopy

Frontiers in Microbiology

Volumn 7, Issue JUN, 2016, Pages

  Pachiadaki, Maria G ^a,c   Rédou, Vanessa ^b   Beaudoin, David J ^a   Burgaud, Gaëtan ^b   Edgcomb, Virginia P ^a  

^a WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

^b UNIVERSITÉ DE BREST   (France)

^c BIGELOW LABORATORY FOR OCEAN SCIENCES   (United States)

Author keywords

Calcofluor white; DNA; Fungi; ITAG; Metatranscriptome; MRNA; RRNA operon; Sediment

Indexed keywords

CARRIER PROTEINS AND BINDING PROTEINS; CONTIG; FUNGAL RNA; METATRANSCRIPTOME; RIBOSOME RNA; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ANTIBIOTIC RESISTANCE; ARTICLE; BIOSPHERE; CELL MOTILITY; CONIDIUM; DEEP SEA; DNA EXTRACTION; FUNGAL DETECTION; FUNGAL GENE; FUNGUS IDENTIFICATION; FUNGUS SPORE; GENE EXPRESSION; MARINE ENVIRONMENT; MARINE SPECIES; MARINE SUBSURFACE BIOSPHERE; METAGENOMICS; MICROBIAL DIVERSITY; MICROBIAL METABOLISM; MICROSCOPY; NONHUMAN; PERU; PROKARYOTE; REVERSE TRANSCRIPTION; RNA ANALYSIS; SEQUENCE ANALYSIS; TAXONOMIC IDENTIFICATION; UNITED KINGDOM;

EID: 84979999727     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2016.00846     Document Type: Article

References (89)

1. Adeyemi, A. O. (2009). Bioaccumulation of arsenic in fungi. Am. J. Environ. Sci. 5, 364-370. doi: 10.3844/ajessp.2009.364.370
2. Alberti, A., Belser, C., Engelen, S., Bertrand, L., Orvain, C., Brinas, L., et al. (2014). Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data. BMC Genomics 15:912. doi: 10.1186/1471-2164-15-912
3. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410. doi: 10.1016/S0022-2836(05)80360-2
4. Amend, A. (2014). From dandruffto deep-sea vents: Malassezia-like Fungi are ecologically hyper-diverse. PLoS Pathog. 10:e1004277. doi: 10.1371/journal.ppat.1004277
5. Baker, B. J., Saw, J. H., Lind, A. E., Lazar, C. S., Hinrichs, K.-U., Teske, A. P., et al. (2016). Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea. Nat. Microbiol. 1, 16002. doi: 10.1038/NMICROBIOL.2016.2
6. Bass, D., Howe, A., Brown, N., Barton, H., Demidova, M., Michelle, H., et al. (2007). Yeast forms dominate fungal diversity in the deep oceans. Pros. R. Soc. B 274, 3069-3077. doi: 10.1098/rspb.2007.1067
7. Bengston, S., Ivarsson, M., Astolfo, A., Belivanova, V., Broman, C., Marone, F., et al. (2014). Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts. Geobology 12, 489-496. doi: 10.1111/gbi.12100
8. Biddle, J. F., Fitz-Gibbon, S., Schuster, S. C., Brenchley, J. E., and House, C. H. (2008). Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc. Natl. Acad. Sci. U.S.A. 105, 10583-10588. doi: 10.1073/pnas.0709942105
9. Bolger, A. M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120. doi: 10.1093/bioinformatics/btu170170
10. Borneman, J., and Hartin, R. J. (2000). PCR primers that amplify fungal rRNA genes from environmental samples. Appl. Environ. Microbiol. 66, 4356-4360. doi: 10.1128/AEM.66.10.4356-4360.2000
11. Burdige, D. J. (2007). Preservation of organic matter in marine sediments: controls, mechanisms, and an imbalance in sediment organic carbon budgets. Chem. Rev. 107, 467-485. doi: 10.1021/cr050347q
12. Burgaud, G., Arzur, D., Durand, L., Cambon-Bonavita, M. A., and Barbier, G. (2010). Marine culturable yeasts in deep-sea hydrothermal vents: species richness and association with fauna. FEMS Microbiol. Ecol. 73, 121-133. doi: 10.1111/j.1574-6941.2010.00881.x
13. Burgaud, G., Le Calvez, T., Arzur, D., Vandenkoornhuyse, P., and Barbier, G. (2009). Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents. Environ. Microbiol. 11, 1588-1600. doi: 10.1111/j.1462-2920.2009.01886.x
14. Burgaud, G., Thi Minh Hu, N., Arzur, D., Coton, M., Perrier-Cornet, J. M., Jebbar, M., et al. (2015). Effects of hydrostatic pressure on yeasts isolated from deep-sea hydrothermal vents. Res. Microbiol. 166, 700-709. doi: 10.1016/j.resmic.2015.07.005
15. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336. doi: 10.1038/nmeth.f.303
16. Cernansky, S., Urík, M., Ševc, J., and Hiller, E. (2007). Biosorption of arsenic and cadmium from aqueous solutions. Afr. J. Biotechnol. 6, 1932-1934
17. Chung, Y. J., and Saier, M. H. (2002). Overexpression of the Escherichia coli sugE gene confers resistance to a narrow range of quaternary ammonium compounds. J. Bacteriol. 184, 2543-2545. doi: 10.1128/JB.184.9.2543-2545.2002
18. Ciobanu, M. C., Burgaud, G., Dufresne, A., Breuker, A., Redou, V., Maamar, S. B., et al. (2014). Microorganisms persist at record depths in the subseafloor of the Canterbury Basin. ISME J. 8, 1370-1380. doi: 10.1038/ismej.2013.250
19. Conesa, A., Gotz, S., Garcia-Gomez, J. M., Terol, J., Talon, M., and Robles, M. (2005). Blast2GO: a universal tool for annottion, visualization and nalysis in functional genomics research. Bioinformatics 21, 3674-3676. doi: 10.1093/bioinformatics/bti610
20. Damare, S., and Raghukumar, C. (2008). Fungi and Macroaggregation in deep-Sea sediments. Microbiol. Ecol. 56, 168-177. doi: 10.1007/s00248-007-9334-y
21. Damon, C., Lehembre, F., Oger-Desfeux, C., Luis, P., Ranger, J., Fraissinet-Tachet, L., et al. (2012). Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS ONE 7:e28967. doi: 10.1371/journal.pone.0028967
22. Dekov, V. M., Bindi, L., Burgaud, G., Petersen, S., Asael, D., Rédou, V., et al. (2013). Inorganic and biogenic As-sulfide precipitation at seafloor hydrothermal fiels. Mar. Geol. 342, 28-38. doi: 10.1016/j.margeo.2013.06.006
23. Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461. doi: 10.1093/bioinformatics/btq461
24. Edgcomb, V. P., Beaudoin, D., Gast, R., Biddle, J., and Teske, A. (2011). Marine subsurface eukaryotes: the fungal majority. Environ. Microbiol. 13, 172-183. doi: 10.1111/j.1462-2920.2010.02318.x
25. Fernandes, P., Domitrovic, T., Kao, C. M., and Kurtenbach, E. (2004). Genomic expression pattern in Saccharomyces cerevisiae cells in response to high hydrostatic pressure. FEBS Lett. 556, 153-160. doi: 10.1016/S0014-5793(03)01396-6
26. Flores, G. E., Campbell, J. H., Kirshtein, J. D., Steinberg, J. I., Seewald, J. S., Tivey, M. K., et al. (2011). Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge. Environ. Microbiol. 13, 2158-2171. doi: 10.1111/j.1462-2920.2011.02463.x
27. Frias-Lopez, J., Shi, Y., Tyson, G. W., Coleman, M. L., Schuster, S. C., Chisholm, S. W., et al. (2008). Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. U.S.A. 105, 3805-3810. doi: 10.1073/pnas.0708897105
28. Fulthorpe, C. S., Hoyanagi, K., Blum, P., and the Expedition (317)Scientists (2011). "Site U1352, "in Proceedings of the Integrated Ocean Drilling Program 317, (Tokyo: Integrated Ocean Drilling Program Management International, Inc). doi: 10.2204/iodp.proc.317.104.2011
29. Gadanho, M., and Sampaio, J. P. (2005). Occurrence and diversity of yeasts in the mid-atlantic ridge hydrothermal fields near the azores archipelago. Microb. Ecol. 50, 408-417. doi: 10.1007/s00248-005-0195-y
30. Goffin, C., and Ghuysen, J.-M. (1998). Multimodular penicillin-binding proteins: an enigmatic family of orthologs and paralogs. Microb. Mol. Biol. Rev. 62, 1079-1093
31. Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., et al. (2011). Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644-652. doi: 10.1038/nbt.1883
32. Hoehler, T. M., and Jørgensen, B. B. (2013). Microbial life under extreme energy limitation. Nature Rev. Microbiol. 11, 83-94. doi: 10.1038/nrmicro2939
33. Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M. L., Larimer, F. W., and Hauser, L. J. (2010). Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11:119. doi: 10.1186/1471-2105-11-119
34. Ivarsson, M., Bengston, S., Skogby, H., Belivanova, V., and Maronc, F. (2013). Fungal colonies in open fractures of subseafloor basalt. Geo-Mar. Lett. 33, 233-243. doi: 10.1007/s00367-013-0321-7
35. Ivarsson, M., Broman, C., Gustafsson, H., and Holm, N. G. (2015). Biogenic mn-oxides in subseafloor basalts. PLoS ONE 10:e0128863. doi: 10.1371/journal.pone.0128863
36. Jebaraj, C. S., Raghukumar, C., Behnke, A., and Stoeck, T. (2010). Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiol. Ecol. 71, 399-412. doi: 10.1111/j.1574-6941.2009.00804.x
37. Jørgensen, B. B. (2011). Deep subseafloor microbial cells on physiological standby. Proc. Natl. Acad. Sci. U.S.A. 108, 18193-18194. doi: 10.1073/pnas.1115421108
38. Jørgensen, B. B., and Boetius, A. (2007). Feast and famine-microbial life in the deep-sea bed. Nature Rev. 5, 770-781
39. Jørgensen, B. B., and Marshall, I. (2016). Slow microbial life in the seabed. Annu. Rev. Mar. Sci. 8, 311-332. doi: 10.1146/annurev-marine-010814-015535
40. Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., and D'Hondt, S. (2012). Global distribution of microbial abundance and biomass in subseafloor sediment. Proc. Natl. Acad. Sci. U.S.A. 109, 16213-16216. doi: 10.1073/pnas.1203849109
41. Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., et al. (2010). Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform. 11, 40-79. doi: 10.1093/bib/bbp043
42. Kielbasa, S. M., Wan, R., Sato, K., Horton, P., and Frith, M. C. (2011). Adaptive seeds tame genomic sequence comparison. Genome Res. 21, 487-493. doi: 10.1101/gr.113985.110
43. Kling, J. (2014). Fresh from the biotech pipeline-2013. Nat. Biotechnol. 32, 121-124. doi: 10.1038/nbt.2811
44. Koch, A. L. (2000). Penicillin binding proteins, beta-lactams, and lactamases: offensives, attacks, and defensive countermeasures. Crit. Rev. Microbiol. 26, 205-220. doi: 10.1080/10408410091154228
45. Konwar, K. M., Hanson, N. W., Bhatia, M. P., Kim, D., Wu, S. J., Hahn, A. S., et al. (2015). MetaPathways v2.5: quantitative functional, taxonomic and usability improvements. Bioinformatics 32, 3345-3347. doi: 10.1093/bioinformatics/btv361
46. Konwar, K. M., Hanson, N. W., Page, A. P., and Hallam, S. J. (2013). MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. BMC Bioinformatics 14:202. doi: 10.1186/1471-2105-14-202
47. Lai, X., Cao, L., Tan, H., Fang, S., Huang, Y., and Zhou, S. (2007). Fungal communities from methane hydrate-bearing deep-sea marine sediments in South China Sea. ISME J. 1, 756-762. doi: 10.1038/ismej.2007.51
48. Le Calvez, T., Burgaud, G., Mahé, S., Barbier, G., and Vandenkoornhuyse, P. (2009). Fungal diversity in deep-sea hydrothermal ecosystems. Appl. Environ. Microbiol. 75, 6415-6421. doi: 10.1128/AEM.00653-09
49. Li, H., and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595. doi: 10.1093/bioinformatics/btp698
50. Lloyd, K. G., Schreiber, L., Petersen, D. G., Kjeldsen, K. U., Lever, M. A., Steen, A. D., et al. (2013). Predominant archaea in marine sediments degrade detrital proteins. Nature 496, 215-218. doi: 10.1038/nature12033
51. López-García, P., Vereshchaka, A., and Moreira, D. (2007). Eukaryotic diversity associated with carbonates and fluidseawater interface in Lost City hydrothermal field. Environ. Microbiol. 9, 546-554. doi: 10.1111/j.1462-2920.2006.01158.x
52. Magoc, T., and Salzberg, S. (2011). FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963. doi: 10.1093/bioinformatics/btr507
53. Mouton, M., Postma, F., Wilsenach, J., and Botha, A. (2012). Diversity and characterization of culturable fungi from marine sediment collected from St. Helena Bay, South Africa. Microb. Ecol. 64, 311-319. doi: 10.1007/s00248-012-0035-9
54. Nagahama, T., Hamamoto, M., Nakase, T., and Horikoshi, K. (2001). Rhodotorula lamellibrachii sp. nov., a new yeast species from a tubeworm collected at the deep-sea floor in Sagami Bay and its phylogenetic analysis. Antonie van Leeuwenhoek 80, 317-323. doi: 10.1023/A:1013043301388
55. Nagahama, T., Takahashi, E., Nagano, Y., Abdel-Wahab, M. A., and Miyazaki, M. (2011). Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane coldseep sediments. Environ. Microbiol. 13, 2359-2370. doi: 10.1111/j.1462-2920.2011.02507.x
56. Nagano, Y., Nagahama, T., Hatada, Y., Nunoura, T., Takami, H., Miyazaki, J., et al. (2010). Fungal diversity in deep-sea sediments-the presence of novel fungal groups. Fung. Ecol. 3, 316-325. doi: 10.1016/j.funeco.2010.01.002
57. Olaniran, A. O., Balgobind, A., and Pillay, B. (2013). Bioavailability of heavy metals in soil: impact on microbial biodegradation of organic compounds and possible improvement strategies. Int. J. Mol. Sci. 14, 10197-10228. doi: 10.3390/ijms140510197
58. Oliveira, A., and Pampulha, M. E. (2006). Effects of long-term heavy metal contamination on soil microbial characteristics. J. Biosci. Bioeng. 102, 157-161. doi: 10.1263/jbb.102.157
59. Orcutt, B. N., LaRowe, D. E., Biddle, J. F., Colwell, F. S., Glazer, B. T., Reese, B. K., et al. (2013). Microbial activity in the marine deep biosphere: progress and prospects. Front. Microbiol. 4:189. doi: 10.3389/fmicb.2013.00189
60. Orsi, W., Edgcomb, V. P., Christman, G. D., and Biddle, J. F. (2013a). Gene expression in the deep biosphere. Nature 499, 205-208. doi: 10.1038/nature12230
61. Orsi, W., Biddle, J., and Edgcomb, V. P. (2013b). Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces. PLoS ONE 8:e56335. doi: 10.1371/journal.pone.0056335
62. Parkes, J., Cragg, B., and Wellsbury, P. (2000). Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol. J. 8, 11-28. doi: 10.1007/PL00010971
63. Parkes, R. J., Cragg, B., Roussel, E., Webseter, G., Weightman, A., and Sass, H. (2014). A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere:geosphere interactions. Mar. Geol. 352, 409-425. doi: 10.1016/j.margeo.2014.02.009
64. Parkes, R. J., Webster, G., Cragg, B. A., Weightman, A. J., Newberry, C. J., Ferdelman, T. G., et al. (2005). Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436, 390-394. doi: 10.1038/nature03796
65. Pittner, F., Tovarova, I. I., Komitskaya, E. Y., Khokhlov, A. S., and Hoffmann-Ostenhof, O. (1979). Myo-inositol-1-phosphate synthase from Streptomyces griseus (studies on the biosynthesis of cyclitols, XXXVIII). Mol. Cell. Biochem. 25, 43-46
66. Pruitt, K. D., Tatusova, T., and Maglott, D. R. (2005). NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33, D501-D504. doi: 10.1093/nar/gki025
67. Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596. doi: 10.1093/nar/gks1219
68. Ravikumar, S., Williams, G. P., Shanthy, S., Gracelin, N. A., Babu, S., and Parimala, P. S. (2007). Effect of heavy metals (Hg and Zn) on the growth and phosphate solubilising activity in halophilic phosphobacteria isolated from Manakudi mangrove. J. Environ. Biol. 28, 109-114
69. Raychoudhury, R., Sen, R., Cai, Y., Sun, Y., Lietze, V. U., Boucias, D. G., et al. (2013). Comparative metatranscriptomic signatures of wood and paper feeding in the gut of the termite Reticulitermes flavipes (Isoptera: Rhinotermitidae). Insect Mol. Biol. 22, 155-171. doi: 10.1111/imb.12011
70. Rédou, V., Ciobanu, M. C., Pachiadaki, M. G., Edgcomb, V., Alain, K., Barbier, G., et al. (2014). In-depth analyses of deep subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities at record-breaking depths. FEMS Microbiol. Ecol. 90, 908-921. doi: 10.1111/1574-6941.12447
71. Rédou, V., Navarri, M., Meslet-Cladière, L., Barbier, G., and Burgaud, G. (2015). Species richness and adaptation of marine fungi from deep-subseafloor. Appl. Environ. Microb. 81, 3571-3583. doi: 10.1128/AEM.04064-14
72. Reyes, C., Lloyd, J. R., and Saltikov, C. W. (2008). "Geomicrobiology of iron and arsenic in aNoxic sediments, "in Arsenic Contamination of Groundwater: Mechanism, Analysis, and Remediation, ed. S. Ahuja (New York, NY: John Wiley and Sons, Inc), 123-146
73. Richards, T. A., Leonard, G., Mahé, F., del Campo, J., Romac, S., Jones, M. D., et al. (2015). Molecular diversity and distribution of marine fungi across 130 European environmental samples. Proc. R. Soc. B 282, 20152243. doi: 10.1098/rspb.2015.2243
74. Schrenk, M. O., Huber, J. A., and Edwards, K. J. (2010). Microbial provinces in the subseafloor. Annu. Rev. Mar. Sci. 2, 279-304. doi: 10.1146/annurev-marine-120308-081000
75. Sebat, J. L., Paszczynski, A. J., Cortese, M. S., and Crawford, R. L. (2001). Antimicrobial properties of Pyridine-2, 6-dithiocarboxylic acid, a metal chelator produced by Pseudomonas spp. Appl. Environ. Microb. 67, 3934-3942. doi: 10.1128/AEM.67.9.3934-3942.2001
76. Shi, W., and Sun, H. (2002). Type IV pilus-dependent motility and its possible role in bacterial pathogenesis. Infect. Immun. 70, 1-4. doi: 10.1128/IAI.70.1.1-4.2002
77. Shipboard Scientific Party (2003). "Controls on microbial communities in deeply buried sediments, eastern equatorial pacific and peru margin: covering leg 201 of the cruises of the drilling vessel joides resolution, "in Proceedings of the Ocean Drilling Program Initial Report, College Station, TX, 1-81
78. Simonato, F., Campanaro, S., Lauro, F. M., Vezzi, A., D'Angelo, M., Vitulo, N., et al. (2006). Piezophilic adaptation: a genomic point of view. J. Biotechnol. 126, 11-25. doi: 10.1016/j.jbiotec.2006.03.038
79. Singh, P., Raghukumar, C., Verma, P., and Shouche, Y. (2011). Fungal community analysis in the deep-sea sediments of the Central Indian Basin by culture-independent approach. Microb. Ecol. 61, 507-517. doi: 10.1007/s00248-010-9765-8
80. Sohlberg, E., Bomberg, M., Miettinen, H., Nyyssönen, M., Salavirta, H., Vikman, M., et al. (2015). Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland. Front. Microbiol. 6:573. doi: 10.3389/fmicb.2015.00573
81. Srivastava, S., and Goyal, P. (2010). Novel Biomaterials: Decontamination of Toxic Metals from Wastewater. New York, NY: Springer-Verlag
82. Stewart, F. J., Ottesen, E. A., and DeLong, E. F. (2010). Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J. 4, 896-907. doi: 10.1038/ismej.2010.18
83. Stock, A., Breiner, H. W., Pachiadaki, M., Edgcomb, V., Filker, S., La Cono, V., et al. (2012). Microbial eukaryote life in the new hypersaline deep-sea basin Thetis. Extremophiles 16, 21-34. doi: 10.1007/s00792-011-0401-4
84. Takagi, H., Motohashi, K., Miyamoto, T., Shin-Ya, K., Furihata, K., and Seto, H. (2005). Studies on terpoenoids produced by Actinomycetes. J. Antibiot. 58, 275-278. doi: 10.1038/ja.2005.33
85. Tamas, M. J., Sharma, S., Ibstedt, S., Jacobson, T., and Christen, P. (2014). Heavy metals and metalloids as a cause for protein misfolding and aggregation. Biomolecules 4, 252-267. doi: 10.3390/biom4010252
86. Thaler, A. D., Van Dover, C. L., and Vilgalys, R. (2012). Ascomycete phylotypes recovered from a Gulf of Mexico methane seep are identical to an uncultured deep-sea fungal clade from the Pacific. Fungal Ecol. 5, 270-273. doi: 10.1016/j.funeco.2011.07.002
87. Tsementzi, D., Poretsky, R., Rodriguez-R, L. M., Luo, C., and Konstantinidis, K. T. (2014). Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities. Environ. Microbiol. Rep. 6, 640-655. doi: 10.1111/1758-2229.12180
88. Xu, W., Pang, K. L., and Luo, Z. H. (2014). High fungal diversity and abundance recovered in the deep-sea sediments of the pacific ocean. Microbial. Ecol. 68, 688-698. doi: 10.1007/s00248-014-0448-8
89. Zhang, T., Fei Wang, N., Qin Zhang, Y., Yu Liu, H., and Yan Yu, L. (2015). Diversity and distribution of fungal communities in the marine sediments of Kongsfjorden, Svalbard (High Arctic). Sci. Rep. 5:14524. doi: 10.1038/srep14524