Cite this paper:
HOU Qinghua, FANG Zhou, ZHU Qingmei, DONG Hongpo. Microbial diversity in Huguangyan Maar Lake of China revealed by high-throughput sequencing[J]. HaiyangYuHuZhao, 2019, 37(4): 1245-1257

Microbial diversity in Huguangyan Maar Lake of China revealed by high-throughput sequencing

HOU Qinghua, FANG Zhou, ZHU Qingmei, DONG Hongpo
Guangdong Province Key Laboratory for Coastal Ocean Variation and Disaster Prediction, College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524088, China
Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high-throughput sequencing method. We found significant differences between the microbial community compositions of the water and the sediment. The sediment samples contained more diverse Bacteria and Archaea than did the water samples. Actinobacteria, Betaproteobacteria, Cyanobacteria, and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria, Anaerolineae, Nitrospira, and Dehalococcoidia were the major bacterial groups in the sediment. As for Archaea, Woesearchaeota (DHVEG-6), unclassified Archaea, and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water, whereas the Miscellaneous Crenarchaeotic Group, Thermoplasmata, and Methanomicrobia were significantly more abundant in the sediment. Interactions between Bacteria and Archaea were common in both the water column and the sediment. The concentrations of major nutrients (NO3-, PO43-, SiO32- and NH4+) shaped the microbial population structures in the water. At the higher phylogenetic levels including phylum and class, many of the dominant groups were those that were also abundant in other lakes; however, novel microbial populations (unclassified) were often seen at the lower phylogenetic levels. Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs.
Key words:    Huguangyan Maar Lake|high-throughput sequencing|microbial diversity   
Received: 2018-02-08   Revised: 2018-06-12
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Aguirre-Garrido J F, Ramírez-Saad H C, Toro N, MartínezAbarca F. 2016. Bacterial diversity in the soda saline crater lake from Isabel Island, Mexico. Microbial Ecology, 71(1):68-77.
Amato K R, Yeoman C J, Kent A, Righini N, Carbonero F, Estrada A. Rex Gaskins H, Stumpf R M, Yildirim S, Torralba M, Gillis M, Wilson B A, Nelson K E, White B A, Leigh S R. 2013. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. The ISME Journal, 7(7):1 344-1 353.
Asami H, Aida M, Watanabe K. 2005. Accelerated sulfur cycle in coastal marine sediment beneath areas of intensive shellfish aquaculture. Applied and Environmental Microbiology, 71(6):2 925-2 933.
Carlsson P, Caron D A. 2001. Seasonal variation of phosphorus limitation of bacterial growth in a small lake. Limnology and Oceanography, 46(1):108-120.
Casamayor E O, Triadó-Margarit X, Castañeda C. 2013.Microbial biodiversity in saline shallow lakes of the Monegros Desert, Spain. FEMS Microbiology Ecology, 85(3):503-518.
Castelle C J, Wrighton K C, Thomas B C, Hug L A, Brown C T, Wilkins M J. Frischkorn K R, Tringe S G, Singh A, Markillie L M, Taylor R C, Williams K H, Banfield J F. 2015. Genomic expansion of domain Archaea highlights roles for organisms from new Phyla in anaerobic carbon cycling. Current Biology, 25(6):690-701.
Clingenpeel S, Macur R E, Kan J J, Inskeep W P, Lovalvo D, Varley J., Mathur E, Nealson K, Gorby Y, Jiang H, LaFracois T, McDermott T R. 2011. Yellowstone Lake:high-energy geochemistry and rich bacterial diversity.Environmental Microbiology, 13(8):2 172-2 185.
Durbin A M, Teske A. 2012. Archaea in organic-lean and organic-rich marine subsurface sediments:an environmental gradient reflected in distinct phylogenetic lineages. Frontiers in Microbiology, 3:168,
Fillol M, Auguet J C, Casamayor E O, Borrego C M. 2016.Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage. The ISME Journal, 10(3):665-677.
Ghylin T W, Garcia S L, Moya F, Oyserman B O, Schwientek P, Forest K T, Mutschler J, Dwulit-Smith J, Chan L K, Martinez-Garcia M, Sczyrba A, Stepanauskas R, Grossart H P, Woyke T, Warnecke F, Malmstrom R, Bertilsson S, McMahon K D. 2014. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. The ISME Journal, 8(12):2 503-2 516.
Glissman K, Chin K J, Casper P, Conrad R. 2004. Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow:effect of temperature.Microbial Ecology, 48(3):389-399.
Haller L, Tonolla M, Zopfi J, Peduzzi R, Wildi W, Poté J. 2011.Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels(Lake Geneva, Switzerland). Water Research, 45(3):1 213-1 228.
Hug L A, Thomas B C, Sharon I, Brown C T, Sharma R, Hettich R L, Wilkins M J, Williams K H, Singh A, Banfield J F. 2016. Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages. Environmental Microbiology, 18(1):159-173.
Inskeep W P, Jay Z J, Macur R E, Clingenpeel S, Tenney A, Lovalvo D, Beam J P, Kozubal M A, Shanks W C, Morgan L A, Kan J J, Gorby Y, Yooseph S, Nealson K. 2015.
Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake:geochemical controls on microbial community structure and function. Frontiers in Microbiology, 6:1 044,
Kan J J, Clingenpeel S, Dow C L, McDermott T R, Macur R E, Inskeep W P, Nealson K H. 2016. Geochemistry and mixing drive the spatial distribution of free-living archaea and bacteria in Yellowstone Lake. Frontiers in Microbiology, 7:210,
Kou W B, Zhang J, Lu X X, Ma Y T, Mou X Z, Wu L. 2016.Identification of bacterial communities in sediments of Poyang Lake, the largest freshwater lake in China.SpringerPlus, 5:401,
Lazar C S, Biddle J F, Meador T B, Blair N, Hinrichs K U, Teske A P. 2015. Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA). Environmental Microbiology, 17(7):2 228-2 238.
Lindh M V, Lefébure R, Degerman R, Lundin D, Andersson A, Pinhassi J. 2015. Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment. Ambio, 44(S3):S402-S412.
Lloyd K G, Schreiber L, Petersen D G, Kjeldsen K U, Lever M A, Steen A D, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jorgensen B B. 2013. Predominant archaea in marine sediments degrade detrital proteins.Nature, 496(7444):215-218.
Lovalvo D, Clingenpeel S R, McGinnis S, Macur R E, Varley J D, Inskeep W P, Glime J, Nealson K, McDermott T R. 2010. A geothermal-linked biological oasis in Yellowstone Lake, Yellowstone National Park, Wyoming. Geobiology, 8(4):327-336.
Lovley D R, Phillips E J P, Lonergan D J, Widman P K. 1995.Fe(Ⅲ) and S0 reduction by Pelobacter carbinolicus.Applied and Environmental Microbiology, 61(6):2 132-2 138.
Lozupone C, Knight R. 2005. UniFrac:a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology, 71(12):8 228-8 235.
Meng J, Xu J, Qin D, He Y, Xiao X, Wang F P. 2014. Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses.The ISME Journal, 8(3):650-659.
Parkes R J, Webster G, Cragg B A, Weightman A J, Newberry C J, Ferdelman T G, Kallmeyer Jens, Jørgensen B B, Aiello I W, Fry J C. 2005. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature, 436(7094):390-394.
Paul D, Kumbhare S V, Mhatre S S, Chowdhury S P, Shetty S A, Marathe N P, Bhute S, Shouche Y S. 2016. Exploration of microbial diversity and community structure of Lonar lake:the only hypersaline meteorite crater lake within basalt rock. Frontiers in Microbiology, 6:1 553,
Percent S F, Frischer M E, Vescio P A, Duffy E B, Milano V, McLellan M, Stevens B M, Boylen C W, NierzwickiBauer S A. 2008. Bacterial community structure of acidimpacted lakes:what controls diversity?. Applied and Environmental Microbiology, 74(6):1 856-1 868.
Salcher M M, Pernthaler J, Posch T. 2010. Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake.Limnology and Oceanography, 55(2):846-856.
Schloss P D, Gevers D, Westcott S L. 2011. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One, 6:e27310.
Schwarz J I K, Eckert W, Conrad R. 2007. Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel). Systematic and Applied Microbiology, 30(3):239-254.
Sirisena K A, Ramirez S, Steele A, Glamoclija M. 2018.Microbial diversity of hypersaline sediments from lake Lucero Playa in white sands national monument, New Mexica, USA. Microbial Ecology, 76(2):404-418.
Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M, Kamagata Y. 2005. Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivationbased techniques. Applied and Environmental Microbiology, 71(4):2 162-2 169.
Vila-Costa M, Barberan A, Auguet J C, Sharma S, Moran M A, Casamayor E O. 2013. Bacterial and archaeal community structure in the surface microlayer of high mountain lakes examined under two atmospheric aerosol loading scenarios. FEMS Microbiology Ecology, 84(2):387-397.
Warnecke F, Amann R, Pernthaler J. 2004. Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environmental Microbiology, 6(3):242-253.
Wolfe A P, Vinebrooke R D, Michelutti N, Rivard B, Das B. 2006. Experimental calibration of lake-sediment spectral reflectance to chlorophyll a concentrations:methodology and paleolimnological validation. Journal of Paleolimnology, 36(1):91-100.
Wu X D, Zhang Z H, Xu X M, Shen J. 2012. Asian summer monsoonal variations during the Holocene revealed by Huguangyan maar lake sediment record.Palaeogeography, Palaeoclimatology, Palaeoecology, 323-325:13-21.
Xing P, Hahn M W, Wu Q L. 2009. Low taxon richness of bacterioplankton in high-altitude lakes of the eastern Tibetan plateau, with a predominance of Bacteroidetes and Synechococcus spp. Applied and Environmental Microbiology, 75(22):7 017-7 025.
Yancheva G, Nowaczyk N R, Mingram J, Dulski P, Schettler G, Negendank J F W, Liu J Q, Sigman D M, Peterson L C, Haug G H. 2007. Influence of the intertropical convergence zone on the East Asian monsoon. Nature, 445(7123):74-77.
Ye W J, Liu X L, Lin S Q, Tan J, Pan J L, Li D T, Yang H. 2009.The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu.FEMS Microbiology Ecology, 70(2):263-276.
Zhang J X, Yang Y Y, Zhao L, Li Y Z, Xie S G, Liu Y. 2015.Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes. Applied Microbiology and Biotechnology, 99(7):3 291-3 302.
Zhang R, Wu Q L, Piceno Y M, Desantis T Z, Saunders F M, Andersen G L, Liu W T. 2013. Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis. FEMS Microbiology Ecology, 86(2):277-287.