Abstract
Purpose
Although wetlands are one of the major ecosystems on the earth, information about the bacterial communities in different types of wetlands, especially in northeast China, has not yet been fully described. The aim of this study was to compare bacterial community compositions between sediment and water in different types of wetlands of northeast China.
Materials and methods
In this study, sediment and water samples were synchronously collected from different types of wetlands in northeast China. The bacterial communities were analyzed with Illumina MiSeq sequencing targeting the 16S rRNA gene.
Results and discussion
The results showed that the dominant phyla (relative abundance > 5%) across all sediment samples were Proteobacteria and Chloroflexi, while those across all water samples were Proteobacteria, Actinobacteria, and Bacteroidetes. Bacterial community composition was distinctly different among wetlands at the phylum and genus levels, and the indicator species for different sediment and water samples also varied greatly. The alpha diversity of bacterial community was higher in sediment samples than in water samples, and the lowest alpha diversity was detected in two coastal wetlands, both in sediment and in water samples. A heatmap analysis at the genus level and principal coordinate analysis revealed that all bacterial communities in sediment or in water samples were separated into distinct groups according to wetland type, and the communities in two coastal wetlands were highly similar to each other both in sediment and water samples, respectively. Bacterial communities in sediment were mainly affected by the available K content, followed by total C and total N, soil pH, etc., while in water, the communities were mainly affected by total P, total K, etc.
Conclusions
The results revealed that bacterial community compositions between sediment and water samples were significantly different, and the communities in two coastal wetlands were more similar than those in other wetlands. The wetland sediment samples demonstrated higher community alpha diversity than the water samples, and alpha diversity was lowest in both the sediment and water of two coastal wetlands. Moreover, bacterial communities in sediment and water were driven by different environmental factors.
Similar content being viewed by others
References
Abia ALK, Alisoltani A, Keshri J, Ubomba-Jaswa E (2018) Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use. Sci Total Environ 616:326–334
Achenbach LA, Michaelidou U, Bruce RA, Fryman J, Coates JD (2001) Dechloromonas agitata gen. nov., sp. nov. and Dechlorosoma suillum gen. nov., sp. nov., two novel environmentally dominant (per) chlorate-reducing bacteria and their phylogenetic position. Int J Syst Evol Microbiol 51:527–533
Adeloju SB, Bond AM, Briggs MH (1984) Critical evaluation of some wet digestion methods for the stripping voltammetric determination of selenium in biological-materials. Anal Chem 56:2397–2401
Alonso C, Warnecke F, Amann R, Pernthaler J (2007) High local and global diversity of Flavobacteria in marine plankton. Environ Microbiol 9:1253–1266
Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26:32–46
Barberán A, Casamayor EO (2010) Global phylogenetic community structure and β-diversity patterns in surface bacterioplankton metacommunities. Aquat Microb Ecol 59:1–10
Barns SM, Takala SL, Kuske CR (1999) Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 65:1731–1737
Barns SM, Cain EC, Sommerville L, Kuske CR (2007) Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73:3113–3116
Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. P Natl Acad Sci USA 105:10583–10588
Bouvier TC, del Giorgio PA (2002) Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries. Limnol Oceanogr 47:453–470
Bowman JP, McCuaig RD (2003) Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69:2463–2483
Bowman JP, Nichols DS (2005) Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia. Int J Syst Evol Microbiol 55:1471–1486
Brune A, Ludwig W, Schink B (2002) Propionivibrio limicola sp. nov., a fermentative bacterium specialized in the degradation of hydroaromatic compounds, reclassification of Propionibacter pelophilus as Propionivibrio pelophilus comb. nov. and amended description of the genus Propionivibrio. Int J Syst Evol Microbiol 52:441–444
Burton TM, Uzarski DG (2009) Biodiversity in protected coastal wetlands along the west coast of Lake Huron. Aquat Ecosyst Health 12:63–76
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R (2010a) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266–267
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Tumbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010b) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336
Carignan V, Villard MA (2002) Selecting indicator species to monitor ecological integrity: a review. Environ Monit Assess 78:45–61
Casas V, Rohwer F (2007) Phage metagenomics. Methods Enzymol 421:259–268
Chen X, Feng SG, Zhang HX, Wang YF, Bai ZH, Gu LK (2011) Investigation of bacterial community diversity in water of Zoige alpine wetland. Acta Ecol Sin 31:205–211
Corteselli EM, Aitken MD, Singleton DR (2017) Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds. Int J Syst Evol Microbiol 67:311–318
Davidsson TE, Stepanauskas R, Leonardson L (1997) Vertical patterns of nitrogen transformations during infiltration in two wetland soils. Appl Environ Microbiol 63:3648–3656
De Cáceres M, Legendre P, Moretti M (2010) Improving indicator species analysis by combining groups of sites. Oikos 119:1674–1684
De Carvalho CC, Da Fonseca MMR (2005) The remarkable Rhodococcus erythropolis. Appl Microbiol Biotehnol 67:715–726
DeLong EF, Karl DM (2005) Genomic perspectives in microbial oceanography. Nature 437:336–342
Dufrêne M, Legendre P (1997) Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol Monogr 67:345–366
Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, Palenik BP, Paulsen IT, de Marsac NT, Wincker P, Dossat C, Ferriera S, Johnson J, Post AF, Hess WR, Partensky F (2008) Unravelling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol 9:R90
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998
Fahrbach M, Kuever J, Meinke R, Kämpfer P, Hollender J (2006) Denitratisoma oestradiolicum gen. nov., sp. nov., a 17 β-oestradioldegrading, denitrifying betaproteobacterium. Int J Syst Evol Microbiol 56:1547–1552
Fang L, Chen L, Liu Y, Tao W, Zhang ZZ, Liu HY, Tang Y (2015) Planktonic and sedimentary bacterial diversity of Lake Sayram in summer. Microbiologyopen 4:814–825
Feng BW, Li XR, Wang JH, Hu ZY, Meng H, Xiang LY, Quan ZX (2009) Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea. FEMS Microbiol Ecol 70:236–248
Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364
Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325–338
Guo XP, Lu DP, Niu ZS, Feng JN, Chen YR, Tou FY, Liu M, Yang Y (2018) Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China. Mar Pollut Bull 126:141–149
Gutknecht JLM, Goodman RM, Balser TC (2006) Linking soil process and microbial ecology in freshwater wetland ecosystems. Plant Soil 289:17–34
Hartman WH, Richardson CJ, Vilgalys R, Bruland GL (2008) Environmental and anthropogenic controls over bacterial communities in wetland soils. P Natl Acad Sci USA 105:17842–17847
He T, Guan W, Luan ZY, Xie SG (2015) Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment. Appl Microbiol Biotechnol 100:1479–1488
Jackson ML (1958) Soil chemical analysis. Prentice Hall, Englewood Cliffs
Jackson EF, Jackson CR (2008) Viruses in wetland ecosystems. Freshw Biol 53:1214–1227
Jing RY, Liu JJ, Yu ZH, Liu XB, Wang GH (2014) Phylogenetic distribution of the capsid assembly protein gene (g20) of cyanophages in paddy floodwaters in northeast China. PLoS One 9:e88634
Jones DL, Willett VB (2006) Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil. Soil Biol Biochem 38:991–999
Junk WJ, An S, Finlayson CM, Gopal B, Květ J, Mitchell SA, Mitsch WJ, Robarts RD (2013) Current state of knowledge regarding the world’s wetlands and their future under global climate change: a synthesis. Aquat Sci 75:151–167
Kasalický V, Jezbera J, Hahn MW, Šimek K (2013) The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLoS One 8:e58209
Keller JK (2011) Wetlands and the global carbon cycle, what might the simulated past tell us about the future? New Phytol 192:789–792
Kolukirik M, Ince O, Cetecioglu Z, Celikkol S, Ince BK (2011) Spatial and temporal changes in microbial diversity of the Marmara Sea sediments. Mar Pollut Bull 62:2384–2394
Kostanjsek R, Lapanje A, Drobne D, Svetlana Perovic S, Perovic A, Zidar P, Štrus J, Hollert H, Karaman G (2005) Bacterial community structure analyses to assess pollution of water and sediments in the Lake Shkodra/Skadar, Balkan Peninsula. Environ Sci Pollut Res 12:361–368
Kozak A, Celewicz-Goldyn S, Kuczyńska-Kippen N (2019) Cyanobacteria in small water bodies: the effect of habitat and catchment area conditions. Sci Total Environ 646:1578–1587
Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120
Lee YJ, Romanek CS, Wiegel J (2007) Clostridium aciditolerans sp. nov., an acid-tolerant spore-forming anaerobic bacterium from constructed wetland sediment. Int J Syst Evol Microbiol 57:311–315
Lefèvre CT, Frankel RB, Abreu F, Lins U, Bazylinski DA (2011) Culture-independent characterization of a novel, uncultivated magnetotactic member of the Nitrospirae phylum. Environ Microbiol 13:538–549
Li P, Li SN, Zhang Y, Cheng HM, Zhou HL, Qiu LG, Diao XP (2018) Seasonal variation of anaerobic ammonium oxidizing bacterial community and abundance in tropical mangrove wetland sediments with depth. Appl Soil Ecol 130:149–158
Liu JJ, Zheng CY, Song CC, Guo SD, Liu XB, Wang GH (2014) Conversion from natural wetlands to paddy field alters the composition of soil bacterial communities in Sanjiang Plain, Northeast China. Ann Microbiol 64:1395–1403
Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. P Natl Acad Sci USA 104:11436–11440
Mao DH, Wang ZM, Luo L, Ren CY, Jia MM (2016) Monitoring the evolution of wetland ecosystem pattern in northeast China from 1990 to 2013 based on remote sensing. J Nat Resour 31:1253–1263 (in Chinese)
Mausbach MJ, Parker WB (2001) Background and history of the concept of hydric soils. In: Richardson JL, Vepraskas MJ (eds) Wetland soils: genesis, hydrology, landscapes, and classification. CRC, Florida, pp 19–33
Mcbride MJ, Liu W, Lu X, Zhu X, Zhang W (2014) The family Cytophagaceae. In: Rosenberg E et al (eds) The prokaryotes. Springer, Berlin, pp 577–593
McJannet D, Wallace J, Keen R, Hawdon A, Kemei J (2012) The filtering capacity of a tropical riverine wetland: I. Water balance. Hydrol Process 26:40–52
Mehlich A (1984) Mehlich 3 soil test extractant: a modification of Mehlich 2 extractant. Commun Soil Sci Plan 15:1409–1416
Milligan GW (1985) Cluster-analysis for researchers-Romesburg, Hc. J Classif 2:133–137
Miranda KM, Espey MG, Wink DA (2001) A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite. Nitric Oxide-Biol Ch 5:62–71
Mitsch WJ, Gosselink JG (2007) Wetlands. Wiley, New Jersey
Nally RM, Fleishman E (2004) A successful predictive model of species richness based on indicator species. Conserv Biol 18:646–654
Nedashkovskaya OI, Kim SB, Lee KH, Mikhailov VV, Bae KS (2005) Gillisia mitskevichiae sp. nov., a novel bacterium of the family Flavobacteriaceae, isolated from sea water. Int J Syst Evol Microbiol 55:321–323
Niederberger TD, Sohm JA, Gunderson TE, Parker AE, Tirindelli J, Capone DG, Carpenter EJ, Cary SC (2015) Microbial community composition of transiently wetted Antarctic Dry Valley soils. Front Microbiol 6:9
Olsen SR, Cole CV, Watanabe FS, Dean LA (1954) Estimation of available phosphorus in soils by extraction with sodium bicarbonate. United States Department of Agriculture, Washington
Partensky F, Blanchot J, Vaulot D (1999) Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review. In: Charpy L, Larkum AWD (eds) Marine cyanobacteria. Musée Oceanographique, Monaco, pp 457–476
Perkins TL, Clements K, Baas JH, Jago CF, Jones DL, Malham SK, McDonald JE (2014) Sediment composition influences spatial variation in the abundance of human pathogen indicator bacteria within an estuarine environment. PLoS One 9:e112951
Pommier T, Canback B, Riemann L, Bostrom KH, Simu K, Lundberg P, Tunlid A, Hagstrom A (2007) Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 16:867–880
Price MN, Dehal PS, Arkin AP (2009) Fast tree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650
R Development Core Team (2016) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
Roh SW, Lee M, Lee HW, Yim KJ, Heo SY, Kim N, Yoon C, Nam YD, Kim JY, Hyun DW, Bae JW, Jeong JB, Kang H, Kim D (2013) Gillisia marina sp. nov., from seashore sand, and emended description of the genus Gillisia. Int J Syst Evol Microbiol 63:3640–3645
Sadaie T, Sadaie A, Takada M, Hamano K, Ohnishi J, Ohta N, Matsumoto K, Sadaie Y (2007) Reducing sludge production and the domination of Comamonadaceae by reducing the oxygen supply in the wastewater treatment procedure of a food-processing factory. Biosci Biotechnol Biochem 71:791–799
Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y (2003) Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53:1843–1851
Sergeev VN, Gerasimenko LM, Zavarzin GA (2002) The proterozoic history and present state of cyanobacteria. Microbiology 71:623–637
Sun L, Toyonaga M, Ohashi A, Matsuura N, Tourlousse DM, Meng XY, Meng X, Tamaki H, Hanada S, Cruz R, Yamaguchi T, Sekiguchi Y (2016) Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous, anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi. Int J Syst Evol Microbiol 66:988–996
Tripathi BM, Kim M, Singh D, Lee-Cruz L, Lai-Hoe A, Ainuddin AN, Go R, Rahim RA, Husni MH, Chun J, Adams JM (2012) Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too. Microb Ecol 64:474–484
Van Trappen S, Vandecandelaere I, Mergaert JS, Swings J (2004) Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a microbial mat in Lake Fryxell, Antarctica. Int J Syst Evol Microbiol 54:445–448
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267
Wang GH, Asakawa S, Kimura M (2011) Spatial and temporal changes of cyanophage communities in paddy field soils as revealed by the capsid assembly protein gene g20. FEMS Microbiol Ecol 76:352–359
Wang Y, Sheng HF, He Y, Wu JY, Jiang YX, Tam NFY, Zhou HW (2012) Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags. Appl Environ Microbiol 78:8264–8271
Wang L, Liu XS, Yu SL, Shi XC, Wang XL, Zhang XH (2017) Bacterial community structure in intertidal sediments of Fildes Peninsula, maritime Antarctica. Polar Biol 40:339–349
Weelink SA, Van Doesburg W, Saia FT, Rijpstra WIC, Röling WFM, Smidt H, Stams AJM (2009) A strictly anaerobic betaproteobacterium Georgfuchsia toluolica gen. nov., sp. nov. degrades aromatic compounds with Fe (III), Mn (IV) or nitrate as an electron acceptor. FEMS Microbiol Ecol 70:575–585
Wiegel J, Tanner R, Rainey FA (2006) An introduction to the family Clostridiaceae. In: Dworkin W, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes, 3rd edn. Springer, New York, pp 654–678
Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56:1331–1340
Yannarell AC, Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 71:227–239
Ye WJ, Liu XL, Lin SQ, Tan J, Pan JL, Li DT, Yang H (2009) The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu. FEMS Microbiol Ecol 70:263–276
Zehr JP, Ward BB (2002) Nitrogen cycling in the ocean: new perspectives on processes and paradigms. Appl Environ Microbiol 68:1015–1024
Zhang H, Chang YQ, Zheng WS, Chen GJ, Du ZJ (2017) Salinimicrobium flavum sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 67:4083–4088
Zhang HH, Wang Y, Chen SN, Zhao ZF, Feng J, Zhang ZH, Lu KY, Jia JY (2018) Water bacterial and fungal community compositions associated with urban lakes, Xi’an, China. Int J Environ Res Public Health 15:469
Zhang HH, Feng J, Chen SN, Zhao ZF, Li BQ, Wang Y, Jia JY, Li SL, Wang Y, Yan MM, Lu KY, Hao HY (2019) Geographical patterns of nirS gene abundance and nirS-type denitrifying bacterial community associated with activated sludge from different wastewater treatment plants. Microb Ecol 77:304–316
Zhao X, Li DY, Xu SH, Guo ZH, Zhang Y, Man L, Jiang BH, Hu XM (2017) Clostridium guangxiense sp. nov. and Clostridium neuense sp. nov., two phylogenetically closely related hydrogen-producing species isolated from lake sediment. Int J Syst Evol Microbiol 67:710–715
Zhou ZC, Meng H, Liu Y, Gu JD, Li M (2017) Stratified bacterial and archaeal community in mangrove and intertidal wetland mudflats revealed by high throughput 16S rRNA gene sequencing. Front Microbiol 8:2148
Zubkov MV, Fuchs BM, Archer SD, Kiene RP, Amann R, Burkill PH (2001) Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ Microbiol 3:304–311
Funding
This work was supported by grants from the National Natural Science Foundation of China (41571246) and National Key Research and Development Program of China (2017YFD0200604).
Author information
Authors and Affiliations
Corresponding author
Additional information
Responsible editor: Haihan Zhang
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(DOCX 533 kb)
Rights and permissions
About this article
Cite this article
Sun, Y., Li, X., Liu, J. et al. Comparative analysis of bacterial community compositions between sediment and water in different types of wetlands of northeast China. J Soils Sediments 19, 3083–3097 (2019). https://doi.org/10.1007/s11368-019-02301-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11368-019-02301-x