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Spatial Distribution of Bacterial Communities in High-Altitude Freshwater Wetland Sediment

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Spatial Distribution of Bacterial Communities in High-Altitude Freshwater Wetland Sediment Spatial distribution of bacterial communities in high-altitude freshwater wetland sediment Yong Liu, Jingxu Zhang, Lei Zhao, Xiaoling Zhang & Shuguang Xie Limnology The Japanese Society of Limnology ISSN 1439-8621 Volume 15 Number 3 Limnology (2014) 15:249-256 DOI 10.1007/s10201-014-0429-0 1 23 Your article is protected by copyright and all rights are held exclusively by The Japanese Society of Limnology. This e-offprint is for personal use only and shall not be self- archived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com”. 1 23 Author's personal copy Limnology (2014) 15:249–256 DOI 10.1007/s10201-014-0429-0 RESEARCH PAPER Spatial distribution of bacterial communities in high-altitude freshwater wetland sediment Yong Liu • Jingxu Zhang • Lei Zhao • Xiaoling Zhang • Shuguang Xie Received: 27 January 2014 / Accepted: 27 March 2014 / Published online: 12 April 2014 Ó The Japanese Society of Limnology 2014 Abstract Sediment microorganisms play a crucial role in Keywords Aquatic ecosystem Á Microbial community Á a variety of biogeochemical processes in freshwater eco- Proteobacteria Á Wetland Á Sediment Á Freshwater systems. The objective of the current study was to investi- gate the spatial distribution of sediment bacterial community structure in Luoshijiang Wetland, located in Introduction Yunnan–Kweichow Plateau (China). Wetland sediments at different sites and depths were collected. Clone library Aquatic sediment shelters a complex microbial ecosystem analysis indicates bacterial communities varied with both which is composed of high densities of viable microor- sampling site and sediment depth. A total of fourteen bac- ganisms (Martins et al. 2011). A sediment microbial terial phyla were identified in sediment samples, including community might be involved in a variety of biogeo- Proteobacteria, Acidobacteria, Actinobacteria, Armatimo- chemical processes, such as decomposition of organic nadetes, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobac- matter, methane production, nitrification, denitrification, teria, Firmicutes, Gemmatimonadetes, Nitrospirae, sulfur oxidation, sulphate reduction, phosphorus uptake/ Planctomycetes, Spirochaetes, and Verrucomicrobia. Pro- release, and iron reduction (Martins et al. 2011; Song teobacteria (mainly Betaproteobacteria and Deltaproteo- et al. 2012; Cheng et al. 2013). Sediment microbial bacteria) predominated in wetland sediments. Moreover, community structure can be influenced by many envi- the proportions of Alphaproteobacteria, Acidobacteria, ronmental factors, such as salinity, organic matter and Bacteroidetes, Gemmatimonadete, and Planctomycetes nutrients (Ye et al. 2009; Ribeiro et al. 2013), yet the were significantly correlated with chemical properties. links between sediment microbial community and envi- ronmental conditions remain largely unclear. Different environmental niches can exist in benthic sediments even on a millimeter scale (Spring et al. 2000), which can result in a spatial variation of sediment microbial com- Handling Editor: Hisaya Kojima. munity structure (Song et al. 2012; Cheng et al. 2013). In addition, sediment is a stratified habitat where substrates Electronic supplementary material The online version of this article (doi:10.1007/s10201-014-0429-0) contains supplementary and electron acceptors essential for microorganisms are material, which is available to authorized users. gradually scavenged, which also provides niches for metabolically diverse microorganisms (Zhao et al. 2008). Y. Liu Á L. Zhao However, information on the depth-related change of Yunnan Key Laboratory of Pollution Process and Management of Plateau Lake-Watershed, Kunming 650034, China sediment microbial community structure is still very limited. To date, few previous studies have investigated Y. Liu Á J. Zhang Á X. Zhang Á S. Xie (&) the depth-related change of bacterial community structure College of Environmental Sciences and Engineering, The Key in lake sediment (Zhao et al. 2008; Ye et al. 2009; Zeng Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China et al. 2009; Liu et al. 2010; Shivaji et al. 2011), and in e-mail: [email protected] reservoir sediment (Qu et al. 2008). 123 Author's personal copy 250 Limnology (2014) 15:249–256 Wetlands play a number of eco-environmental roles. To Laboratories). The same amount of DNA from triplicate date, the structures of microbial communities in wetland soils samples was pooled together for clone library analysis. and sediments have been extensively investigated (Jiang Bacterial 16S rRNA genes were amplified using primers et al. 2013; Peralta et al. 2013), which has contributed to our 27F (50-GAGTTTGATCMTGGCTCAG-30) and 1492R understanding of the complex biological processes within (50-GGTTACCTTGTTACGACTT-30) according to the wetland ecosystems. However, the depth-related change of literature (Zhang et al. 2012a). PCR products were cloned bacterial community structure in wetland sediment remains into pMD19-T vector (Takara Corp, Japan) with ampicillin unclear. Moreover, little is known about bacterial commu- selection and blue/white screening. The clones containing nities in freshwater wetland sediment and their spatial vari- correct sizes were sequenced at SinoGenoMax Co., Ltd. ation (Wang et al. 2012). Information on sediment bacterial In this study, partial 16S rRNA gene sequences (about community structure in high-altitude freshwater wetlands is 800 bp) were used for analyses. The Ribosomal Database still lacking. The Luoshijiang Wetland is a freshwater wet- Project analysis tool ‘‘classifier’’ (http://rdp.cme.msu.edu/ land in the Yunnan-Kweichow Plateau. The freshwater classifier/classifier.jsp) was applied to determine the taxo- wetland is adjacent to the Rrhai Lake, the second largest nomic identity of the sequence obtained in this study high-altitude lake in Yunnan Province (China). It covers an (Wang et al. 2007). Principal components analysis (PCA) area of about 1 km2 with an elevation of about 2,056 m. using the software package CANOCO for Windows 4.5 Annual mean air temperature and annual precipitation in the was performed on a correlation matrix composed of the local region were 15.7 °C, and 1,000–1,200 mm, respec- relative abundances of the identified bacterial groups from tively (Zhang et al. 2013). In the present study, the objective eight individual sediment samples, to explore the vari- was to investigate the spatial distribution of sediment bac- ability of bacterial community composition. In addition, terial community structure in Luoshijiang Wetland. Pearson’s correlation analysis of the identified bacterial groups with chemical parameters was performed using SPSS 20.0 software. The bacterial sequences obtained in Materials and methods this study were submitted to GenBank under accession numbers KF247431–KF247993. Sampling sites and sample collection Wetland sediment samples were collected in triplicate using a Results core sampler at four different sites in Luoshijiang Wetland: A (25°5702500N–100°0600600E, no vegetation zone), B (5°5701200 Phylum composition N–100°0505900E, reed-planted zone), C (25°570400N– 100°0600000E, densely water-lily-planted zone), and D A total of 66, 84, 77, 72, 59, 75, 66 and 64 bacterial (25°5605500N–100°0505900E, sparsely water-lily-planted sequences were retrieved from samples AU, AL, BU, BL, zone). The schematic representation of the sampling sites and CU, CL, DU and DL, respectively. The rarefaction curves the environmental conditions of the water body measured for each bacterial clone library did not level off (Fig. S1). directly above the sediment at the time of sampling has been The percentage of coverage for each sample ranged roughly described in detail in a previous study (Zhang et al. 2013). between 50 and 60 % (data not shown). These results For each site, sediment samples were sliced into layers. suggested that further sequencing would result in more During this study, the upper layer (0–5 cm) and the lower operational taxonomic units (OTUs). Bacterial community layer (10–15 cm) were used for further analysis. The upper compositions of the eight sediment samples are shown in layer and lower layer sediments in sampling sites A–D Fig. 1. Unclassified bacterial sequences had a very high were referred to as samples AU and AL, BU and BL, CU proportion (28.8–40.6 %) in samples BL, DU and DL, but and CL, and DU and DL, respectively. were less abundant in other samples. In this study, a total of ? Total organic carbon (TOC), ammonium nitrogen (NH4 - 14 known phyla were identified in these samples, including N), total nitrogen (TN), available phosphorus (AP), and total Proteobacteria, Acidobacteria, Actinobacteria, Armatimo- phosphorus (TP) contents of the sediments were 2.01–6.17, nadetes, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobac- 0.11–0.36, 0.22–2.44, 0.01–0.05, and 0.25–0.73 g/kg, teria, Firmicutes, Gemmatimonadetes, Nitrospirae, respectively (Table S1). Planctomycetes, Spirochaetes, and Verrucomicrobia, while only Proteobacteria
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