Shifts in Archaeaplankton Community Structure Along Ecological Gradients of Pearl Estuary Jiwen Liu1, Shaolan Yu1, Meixun Zhao2, Biyan He3,4 & Xiao-Hua Zhang1
Total Page：16
File Type：pdf, Size：1020Kb
RESEARCH ARTICLE Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary Jiwen Liu1, Shaolan Yu1, Meixun Zhao2, Biyan He3,4 & Xiao-Hua Zhang1 1College of Marine Life Sciences, Ocean University of China, Qingdao, China; 2Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China; 3State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China; and 4School of Bioengineering, Jimei University, Xiamen, China Downloaded from https://academic.oup.com/femsec/article/90/2/424/2680468 by guest on 01 October 2021 Correspondence: Xiao-Hua Zhang, College Abstract of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, The significance of archaea in regulating biogeochemical processes has led to China. Tel./fax: +86 532 82032767; an interest in their community compositions. Using 454 pyrosequencing, the e-mail: [email protected] present study examined the archaeal communities along a subtropical estuary, Pearl Estuary, China. Marine Group I Thaumarchaeota (MG-I) were predomi- Received 18 April 2014; revised 29 July nant in freshwater sites and one novel subgroup of MG-I, that is MG-Im, was 2014; accepted 31 July 2014. Final version proposed. In addition, the previously defined MG-Ia II was grouped into two published online 28 August 2014. clusters (MG-Ia II-1, II-2). MG-Ia II-1 and MG-Ik II were both freshwater- a k DOI: 10.1111/1574-6941.12404 specific, with MG-I II-1 being prevalent in the oxic water and MG-I II in the hypoxic water. Salinity, dissolved oxygen, nutrients and pH were the most Editor: Gary King important determinants that shaped the differential distribution of MG-I sub- groups along Pearl Estuary. Marine Group II Euryarchaeota (MG-II) domi- Keywords nated the saltwater sites, but their abundance was higher in surface waters. The 16S rRNA gene; 454 pyrosequencing; habitat phylogenetic patterns of MG-I subgroups and their habitat preferences provide preference; hypoxia; Marine Group I; Pearl insight into their phylogeographic relationships. These results highlight the Estuary. diversification of various ecotypes of archaea, especially of MG-I, under distinct environmental factors in Pearl Estuary, which are of great value for further exploring their ecological functions. ammonia-oxidizing archaea (AOA) (Mosier & Francis, Introduction 2008; Santoro et al., 2008; Bernhard et al., 2010) from Archaea were previously thought to be present only in freshwater to marine systems. Characterized by strong extreme environments, but since the first discovery of mixing of freshwater and saltwater with sharp salinity and Crenarchaeota in a temperate habitat (DeLong, 1992; nutrient gradients, estuaries are ideal ecosystems to eluci- Fuhrman et al., 1992), distinct archaeal lineages have date the response of different microbial phylotypes to been found in non-extreme habitats such as ocean waters, physicochemical variations. freshwater sediments, and soils (Auguet et al., 2010). Marine Group I Thaumarchaeota (MG-I) and Marine Thus, studies on structures of archaeal community and Group II Euryarchaeota (MG-II) are the most abundant their distribution patterns against environmental charac- groups of archaea in marine systems (Takai et al., 2004; teristics are essential to understand their role in ecosys- Galand et al., 2006). Members of MG-I, a major compo- tems. nent capable of aerobic ammonia oxidation (Konneke€ The significance of salinity in shaping bacterial com- et al., 2005), are widespread not only in oceans but also munity structure has been well documented (e.g. Kirch- in freshwater and soils (e.g. DeLong, 1992; Fuhrman man et al., 2005; Lozupone & Knight, 2007). et al., 1992; Schleper et al., 1997; Inagaki et al., 2003; Nevertheless, the evolutionary separation of archaeal Brown et al., 2009; Durbin & Teske, 2010; Pester et al., MICROBIOLOGY ECOLOGY MICROBIOLOGY assemblages dwelling in different salinity ranges is still 2012). Different phylogenetic ecotypes of MG-I have been elusive as few phylogenetic studies are available regarding defined previously (Massana et al., 2000; Sørensen et al., the transition of community structure of total archaea 2004; Takai et al., 2004; Durbin & Teske, 2010; Jorgensen (Crump & Baross, 2000; Galand et al., 2006, 2008) and et al., 2012), of which MG-Ia and MG-Ic are phylotypes ª 2014 Federation of European Microbiological Societies. FEMS Microbiol Ecol 90 (2014) 424–435 Published by John Wiley & Sons Ltd. All rights reserved Shifts in archaeal community structure 425 commonly retrieved from shallow and deep seawater, Corporation, Billerica, MA). The membranes were stored respectively (Massana et al., 2000; Takai et al., 2004). in liquid nitrogen onboard and at À80 °C in the lab until À However, the habitat preference of these subgroups, espe- nucleic acid extraction. Samples for nutrients (NO2 , À + 3À cially that of terrestrial ecosystems, remains largely NO3 ,NH4 and PO4 ) were analyzed with spectropho- unknown. tometric and colorimetric methods (Dai et al., 2006; Han The wide distribution of MG-I subgroups raises the et al., 2012). question of the driving forces of such distribution. Depth was considered a predominant factor in the structure of Nucleic acid extraction and high-throughput archaeal assemblages (Brown et al., 2009; Hu et al., sequencing 2011). Dissolved oxygen (DO) was also an important determinant, as a species of MG-I, Nitrosopumilus mariti- Community DNA was extracted using the method Downloaded from https://academic.oup.com/femsec/article/90/2/424/2680468 by guest on 01 October 2021 mus (Konneke€ et al., 2005), was found to grow under described by Yin et al. (2013) with a modified step to fully aerobic conditions, whereas some specific ecotypes maximize the DNA output, in which a Fast Prep-24 of AOA could tolerate DO concentration near 1 lM Homogenization System (MP Biomedicals, Irvine, CA) (Erguder et al., 2009). Therefore, the adaptations and was used to intensify cell lysis at maximum speed for growth responses of different MG-I subgroups to low DO 40 s. DNA integrity was checked on a 1% (w/v) conditions should be investigated further. Compared with agarose gel. Amplification of archaeal 16S rRNA gene the widely studied MG-I, the distribution pattern of MG- was conducted using barcode and adaptor added pri- II remains largely unknown. mer 344F (50-ACGGGGYGCAGCAGGCGCGA-30) and The archaeal ecology of subtropical estuaries remains 915R (50-GTGCTCCCCCGCCAATTCCT-30) (Casamayor elusive. Pearl Estuary, a typical subtropical estuary in et al., 2002). A 20 lL PCR reaction included 4 lLof59 China, receives discharges from four eastern outlets, FastPfu Buffer, 2 lL of 2.5 mM deoxynucleoside triphos- Humen, Jiaomen, Hongqimen and Hengmen (Support- phate (dNTP) mix, 0.8 lL of each primer (5 lM), 0.4 lL ing Information, Fig. S1) (PRWRC/PRRCC, 1991), and of TransStart Fastpfu DNA Polymerase (TransGen), 1 lL is subject to hypoxia caused by excessive anthropogenic of template DNA and 11 lL of double-distilled H2O. A inputs in both the upstream and downstream areas triplicate PCR reaction was performed and PCR products (Yin et al., 2004; Dai et al., 2006). The archaeal com- were purified with an AxyPrepDNA Gel Extraction Kit munity distribution along gradients of various environ- (Axygen, Hangzhou, China) and quantified using a mental factors of Pearl Estuary has not been Quant-iT PicoGreen double-stranded DNA assay systematically investigated. To gain an insight into the (Invitrogen, Carlsbad, CA). The amplicons from each environmental and geochemical controls on archaeal reaction mixture were pooled in equimolar ratios based community composition and to test whether archaea on concentration and subject to emulsion PCR to are adapted to different environments such as salinity generate amplicon libraries, as recommended by 454 Life and DO gradients, 454 pyrosequencing of the archaeal Sciences. Sequencing was conducted on a Roche Genome 16S rRNA gene along Pearl Estuary was performed in Sequencer FLX Titanium platform at Majorbio this study. Our study highlights that different MG-I Bio-Pharm Technology Co. Ltd. (Shanghai, China). subgroups evolved to accommodate different environ- ments. Sequence processing and operational taxonomic unit (OTU) assignment Materials and methods All the sequence analysis processes followed the pipeline of MOTHUR (Schloss et al., 2009). All reads completely Sampling matching the barcodes were retained as well as reads with a Surface and bottom water samples of six sites along the maximum single mismatch to the primers. Reads were then salinity gradient of Pearl Estuary (Fig. S1) were collected trimmed by removing the sequencing adaptor, barcodes during 16 July to 12 August, 2012. P01, P03 and P07 rep- and primer sequences. Reads shorter than 200 base pairs, resented the sites located in the upstream freshwater with an average quality score lower than 25 and with any region, and A08, C2 and F412 the sites situated in the ambiguous bases were further removed. Chimeric downstream saltwater region. Samples were collected with sequences were identified and removed using UCHIME a Sealogger CTD (SBE 25, Sea-Bird Co.) rosette water (Edgar et al., 2011). After quality control, the average sampler. One liter of water samples for nucleic acid was length of the reads was 490 bp. The selected reads were prefiltered through 3-mm-pore size filters before collec- compared with the SILVA v111 16S rRNA gene reference tion on 0.22-lm polycarbonate membranes (Millipore database (http://www.arb-silva.de) and taxonomically FEMS Microbiol Ecol 90 (2014) 424–435 ª 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved 426 J. Liu et al. assigned using a 3% distance level at 80% confidence tively, in the following analysis) from six sites were exam- threshold. ined. Environmental factors changed vertically in the The representative read of each of the top 50 OTUs saltwater sites, but remained consistent in the freshwater obtained was blasted against the National Center for Bio- sites (Table 1). The average water depth, ranging from 3 technology Information (NCBI, http://www.ncbi.nlm.nih.