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Metagenomic and Proteomic Analyses of a Mangrove Microbial J. Microbiol. Biotechnol. (2016), 26(12), 2127–2137 http://dx.doi.org/10.4014/jmb.1607.07025 Research Article Review jmb Metagenomic and Proteomic Analyses of a Mangrove Microbial Community Following Green Macroalgae Enteromorpha prolifera Degradation S Yijing Wu1, Chao Zhao1,2*, Zheng Xiao1, Hetong Lin1, Lingwei Ruan3, and Bin Liu1,4 1College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R. China 2Department of Chemistry, University of California, Davis, CA 95616, USA 3Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, P.R. China 4National Engineering Research Center of Juncao, Fuzhou 350002, P.R. China Received: July 11, 2016 Revised: August 7, 2016 A mangrove microbial community was analyzed at the gene and protein levels using Accepted: August 10, 2016 metagenomic and proteomic methods with the green macroalgae Enteromorpha prolifera as the substrate. Total DNA was sequenced on the Illumina HiSeq 2000 PE-100 platform. Two- dimensional gel electrophoresis in combination with liquid chromatography tandem mass First published online spectrometry was used for proteomic analysis. The metagenomic data revealed that the orders August 24, 2016 Pseudomonadales, Rhizobiales, and Sphingomonadales were the most prevalent in the *Corresponding author mangrove microbial community. By monitoring changes at the functional level, proteomic Phone: +86-591-83530197; analyses detected ATP synthase and transporter proteins, which were expressed mainly by Fax: +86-591-83530197; members of the phyla Proteobacteria and Bacteroidetes. Members of the phylum E-mail: [email protected] Proteobacteria expressed a high number of sugar transporters and demonstrated specialized and efficient digestion of various glycans. A few glycoside hydrolases were detected in S upplementary data for this members of the phylum Firmicutes, which appeared to be the main cellulose-degrading paper are available on-line only at http://jmb.or.kr. bacteria. This is the first report of multiple “omics” analysis of E. prolifera degradation. These results support the fact that key enzymes of glycoside hydrolase family were expressed in pISSN 1017-7825, eISSN 1738-8872 large quantities, indicating the high metabolic activity of the community. Copyright© 2016 by The Korean Society for Microbiology Keywords: Enteromorpha prolifera, mangrove, degrading community, metagenomics, proteomics and Biotechnology Introduction easily hydrolyzable carbohydrate and low lignin contents, enabling enzymes access to these substrates and achieve an Global energy demand is increasing, creating problems efficient hydrolysis rate [7, 33]. such as energy security, resources depletion, environmental Enteromorpha (Ulva) prolifera (Muell.) J. Agardh (Chlorophyta, degradation, and climate change, which are expected to Ulvales), which is distributed worldwide in the intertidal increase over the next decades. Biomass is considered a zone of the sea, is the dominant species of green tide sustainable renewable energy source. The biofuel potential (Fig. 1). Enteromorpha prolifera (EP) caused the world’s in marine biomass is more than 100 EJ/year and significantly largest transregional macroalgal bloom in the Yellow Sea of higher than the values for land biomass (22 EJ/year) [7]. China. The massive green tide covered 600 km2, and more Third-generation algae-based biofuel feedstock, seaweed, than one million tons of green alga were cleaned from the and microalgae are considered to have potential for biofuel beach and coast [26]. In addition, Ireland, France, Italy, and production. Algae biomass shows higher yields and Japan suffered from massive Ulva (Enteromorpha) green rates, higher photosynthetic efficiency, and lower land tides on the shoreline. EP dry matter is mainly composed of requirements [1]. Furthermore, macroalgae have greater approximately 45% water-soluble carbohydrate, 15% crude December 2016 ⎪ Vol. 26⎪ No. 12 2128 Wu et al. role in the determination of microbial function in a variety of environments [45, 48-50]. The use of two-dimensional gel electrophoresis (2-DE) in combination with liquid chromatography (LC)-mass spectrometry (MS)/MS approaches has become widely used in recent studies. Recently, with the availability of extensive metagenomic sequences from various marine microbial communities, metaproteomics has attracted considerable attention in the marine biology field to answer a variety of questions. This method can also be used to determine specific features of mixed marine Fig. 1. Green tide of Enteromorpha prolifera in coastal waters of the Yellow Sea near Qingdao, China, in August 2014. samples and overall microbial ecosystem function. The biodegradation of different terrestrial biomasses with microbial communities has been well-documented [3], fiber, and 14% crude protein [22]. E. prolifera is a high- but the EP-degrading microbial communities from mangrove valued biomass rich in complex carbohydrate and fiber ecosystems are largely unknown. A better understanding contents. One critical step in biofuel development is of the EP-degrading bacterial communities can facilitate determining the most favorable conditions for enzymatic the development of the algal biofuels industry. The use saccharification to hydrolyze the biomass to fermentable of metagenomics and proteomics may play a key role sugars. The saccharification of EP can be advantageous in determining the molecular mechanisms by which when EP is treated with a mixture of effective enzymes. microorganisms attack and degrade the green macroalgae However, the polysaccharides present in EP have not been (Fig. 2). Therefore, the purpose of this study was to investigate fully characterized [53] and the complex structures are an EP-degrading community from mangrove sediment difficult to degrade. Mangrove ecosystems are very using an Illumina HiSeq 2000 sequencing system and LC- important for both maintaining and improving biological MS/MS. Our results provide insights into the biodegradation environments [25]. The humid subtropical climate fosters of green macroalgae. microbial diversity in mangrove sediments, and the microorganisms that thrive in mangrove environments are Materials and Methods a valuable source of novel enzymes. Metagenomics is a powerful approach for determining Enrichment of EP-Degrading Microbial Community the structure, diversity, gene content, and functional Green macroalgae EP was collected from a beach (N36°03’, composition of microbial communities. It also provides E120°20’) in Qingdao, China (Fig. 1). The soil sediments were insight into the large number of uncultured microbes [9]. sampled from a typical mangrove protection zone in the Dongzhai Next-generation sequencing (NGS), known as high- Port of Haikou, China. The mangrove sediment samples were enriched with the EP powders as the sole source of carbon and throughput sequencing, plays a key role in the analysis of energy. An EP-degrading enrichment culture was obtained and shotgun sequencing-based metagenomics [16]. The four named DZ21. The community studied was capable of digesting commercially available NGS platforms (Illumina/Solexa, the green macroalgae. The EP-degrading samples after degradation, 454/Roche, ABI/SOLiD, and Helicos BioSciences) have coated with a gold sputter coating, were dried for scanning provided unprecedented opportunities for functional genomic electron microscopic (SEM) observation (JSM-6380, Japan). research based on their ability to generate hundreds of megabases of data [32, 36]. The Illumina/Solexa Genome Total DNA Isolation and Sequencing DNA on the Illumina Analyzer is the most widely used sequencing platform in HiSeq 2000 PE-100 Platform the field and currently dominates the NGS market [31]. Total microbial genomic DNA of the EP-degrading community Illumina constructed longer and more accurate contigs and was extracted as previously described [42]. The DNA concentration scaffolds than other platforms did, and is a more appropriate was determined with a NanoDrop 2000 Spectrophotometer and then analyzed by gel electrophoresis. A highly pure (A /A = approach for metagenomic surveys [27, 30, 37]. 260 280 1.8) and large amount of total genomic DNA (200-360 ng/μl) was Metaproteomics is a new field within the “omics” generated (Fig. S1). Total DNA from the bacterial community was sciences that attempts to identify all proteins expressed in a sheared to produce a DNA fragment library for whole-genome given ecosystem. Metaproteomic studies play an important shotgun sequencing according to the manufacturer’s instructions J. Microbiol. Biotechnol. Omics Analysis of Enteromorpha prolifera-Degrading Community 2129 Fig. 2. Schematic overview of the application of metagenomics and proteomics to study the Enteromorpha prolifera-degrading microbial community. from the TruSeq DNA sample preparation kit (Illumina, USA). contigs were used for further analysis. DNA sequencing was performed on an Illumina HiSeq 2000 sequencer, which generated 100 bp paired-end (PE) raw reads. Gene Prediction in Non-Redundant Microbial Gene Sets of Metagenomes Statistics of Sequencing Data De Novo Assembly of Illumina MetaGeneMark was used to predict open reading frames GA Short Reads (ORFs) from the assembly contigs as well as merging contigs from The obtained raw sequences were submitted to NCBI’s Sequence the sample. Next, BLAST was used to align the predicted ORFs. A Read Archive (SRA). The metagenomic sequences were deposited pair of genes with
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