Cite this paper:
LIU Hongmei, WANG Bin, HU Xiaoke. Sediment bacterial communities are more complex in coastal shallow straits than in oceanic deep straits[J]. HaiyangYuHuZhao, 2018, 36(5): 1643-1654

Sediment bacterial communities are more complex in coastal shallow straits than in oceanic deep straits

LIU Hongmei1, WANG Bin2, HU Xiaoke2
1 School of Ocean, Yantai University, Yantai 264003, China;
2 Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
Abstract:
Straits are ideal models to investigate the bacterial community assembly in complex hydrological environments. However, few studies have focused on bacterial communities in them. Here, comparable bacterial communities in costal shallow Bohai Strait (BS) and oceanic deep Fram Strait (FS) were studied. The Shannon and Chao1 indices were both higher in BS than in FS. The relative abundances of the classes Deltaproteobacteria and Bacilli and the family Halieaceae were higher in BS than in FS, in contrast to the families OM1_clade and JTB255_marine_benthic_group, revealing typical characteristics of bacterial communities in coastal and oceanic regions. Cluster analysis based on the Bray-Curtis index showed that samples were clustered by depth layer in FS and BS, indicating that structures of bacterial communities would differ with increasing water depth in straits. Additionally, the cluster relationships among samples in abundant and rare communities were both similar to those in entire communities. However, the dissimilarities among samples showed a descending order as rare communities, entire communities and abundant communities. Network analysis indicated that the BS network was obviously more complex than the FS network. Filamentous bacteria Desulfobulbaceae exhibited high degree values in BS but not in FS, indicating key roles of Desulfobulbaceae in the BS. Our study provides different and common evidences for understanding microbial ecology in coastal shallow and oceanic deep straits.
Key words:    bacterial communities|Bohai Strait|Fram Strait|currents|microbial ecological network   
Received: 2017-05-04   Revised:
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References:
Barberan A, Bates S T, Casamayor E O, Fierer N. 2014. Using network analysis to explore co-occurrence patterns in soil microbial communities (vol 6, pg 343, 2012). ISME J., 8(4):952.
Bienhold C, Zinger L, Boetius A, Ramette A. 2016. Diversity and biogeography of bathyal and abyssal seafloor bacteria.PLoS One, 11(1):e0148016, https://doi.org/10.1371/journal.pone.0148016.
Bowman J P. 2006. The marine clade of the family flavobacteriaceae:the genera aequorivita, arenibacter, cellulophaga, croceibacter, formosa, gelidibacter, gillisia, maribacter, mesonia, muricauda, polaribacter, psychroflexus, psychroserpens, robiginitalea, salegentibacter, tenacibaculum, ulvibacter, vitellibacter and zobellia. In:Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E eds. The Prokaryotes:Volume 7:Proteobacteria:Delta, Epsilon Subclass.Springer, New York. p.677-694.
Buttigieg P L, Ramette A. 2014. Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments(HAUSGARTEN, Fram Strait). Frontiers in Microbiology, 5:660, https://doi.org/10.3389/fmicb.2014.00660.
Campbell B J, Kirchman D L. 2013. Bacterial diversity, community structure and potential growth rates along an estuarine salinity gradient. The ISME Journal, 7(1):210-220, https://doi.org/10.1038/ismej.2012.93.
Chaffron S, Rehrauer H, Pernthaler J, von Mering C. 2010. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Research, 20(7):947-959, https://doi.org/10.1101/gr.104521.109.
Coutinho F H, Meirelles P M, Moreira A P B, Paranhos R P, Dutilh B E, Thompson F L. 2015. Niche distribution and influence of environmental parameters in marine microbial communities:a systematic review. PeerJ, 3:e1008, https://doi.org/10.7717/peerj.1008.
Coveley S, Elshahed M S, Youssef N H. 2015. Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA). PeerJ, 3:e1182, https://doi.org/10.7717/peerj.1182.
Doblin M A, van Sebille E. 2016. Drift in ocean currents impacts intergenerational microbial exposure to temperature. Proceedings of the National Academy of Sciences of the United States of America, 113(20):5 700-5 705, https://doi.org/10.1073/pnas.1521093113.
Faust K, Raes J. 2012. Microbial interactions:from networks to models. Nature Reviews Microbiology, 10(8):538-550, https://doi.org/10.1038/nrmicro2832.
Flynn J M, Brown E A, Chain F J J, MacIsaac H J, Cristescu M E. 2015. Toward accurate molecular identification of species in complex environmental samples:testing the performance of sequence filtering and clustering methods.Ecology and Evolution, 5(11):2 252-2 266, https://doi.org/10.1002/ece3.1497.
Freilich S, Kreimer A, Meilijson I, Gophna U, Sharan R, Ruppin E. 2010. The large-scale organization of the bacterial network of ecological co-occurrence interactions.Nucleic Acids Research, 38(12):3 857-3 868, https://doi.org/10.1093/nar/gkq118.
Fuhrman J A, Cram J A, Needham D M. 2015. Marine microbial community dynamics and their ecological interpretation. Nature Reviews Microbiology, 13(3):133-146, https://doi.org/10.1038/nrmicro3417.
Gilbert J A, Steele J A, Caporaso J G, Steinbruck L, Reeder J, Temperton B, Huse S, McHardy A C, Knight R, Joint I, Somerfield P, Fuhrman J A, Field D. 2012. Defining seasonal marine microbial community dynamics. ISME J., 6(2):298-308, https://doi.org/10.1038/ismej.2011.107.
Gong J, Shi F, Ma B, Dong J, Pachiadaki M, Zhang X L, Edgcomb V P. 2015. Depth shapes α-and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems. Environmental Microbiology, 17(10):3 722-3 737, https://doi.org/10.1111/1462-2920.12763.
Hibbing M E, Fuqua C, Parsek M R, Peterson S B. 2010.Bacterial competition:surviving and thriving in the microbial jungle. Nature Reviews Microbiology, 8(1):15-25, https://doi.org/10.1038/nrmicro2259.
Itoi S, Uchida J, Takanashi S, Narita T, Abe K, Naya S, Sugita H. 2014. The clam Meretrix lamarckii (Bivalvia:Veneridae) is a rich repository of marine lactic acid bacterial strains. Annals of Microbiology, 64(3):1 267-1 274, https://doi.org/10.1007/s13213-013-0771-1.
Jacob M, Soltwedel T, Boetius A, Ramette A. 2013.Biogeography of deep-sea benthic bacteria at regional scale (LTER HAUSGARTEN, Fram Strait, Arctic). PLoS One, 8(9):e72779, https://doi.org/10.1371/journal.pone.0072779.
Kozich J J, Westcott S L, Baxter N T, Highlander S K, Schloss P D. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq illumina sequencing platform. Applied and Environmental Microbiology, 79(17):5 112-5 120, https://doi.org/10.1128/AEM.01043-13.
Li A C, Qiao L L, Wan X Q, Ma W W. 2016. Distribution, flux and seasonal variation of suspended particulate matters in the Bohai Strait. Oceanologia et Limnologia Sinica, 47(2):310-318. (in Chinese with English abstract)
Li W, Gao K S. 2012. A marine secondary producer respires and feeds more in a high CO2 ocean. Marine Pollution Bulletin, 64(4):699-703, https://doi.org/10.1016/j.marpolbul.2012.01.033.
Li Y F, Wolanski E, Zhang H. 2015. What processes control the net currents through shallow straits? A review with application to the Bohai Strait, China. Estuarine, Coastal and Shelf Science, 158:1-11, https://doi.org/10.1016/j.ecss.2015.03.013.
Lin M, Liu Y H, Chen W W, Wang H, Hu X K. 2014. Use of bacteria-immobilized cotton fibers to absorb and degrade crude oil. International Biodeterioration & Biodegradation, 88:8-12, https://doi.org/10.1016/j.ibiod.2013.11.015.
Liu J W, Liu X S, Wang M, Qiao Y L, Zheng Y F, Zhang X H. 2015. Bacterial and archaeal communities in sediments of the North Chinese marginal seas. Microbial Ecology, 70(1):105-117, https://doi.org/10.1007/s00248-014-0553-8.
Liu Y H, Hu X K, Liu H. 2016. Industrial-scale culturing of the crude oil-degrading marine Acinetobacter sp. strain HC8-3S. International Biodeterioration & Biodegradation, 107:56-61, https://doi.org/10.1016/j.ibiod.2015.11.007.
Lupatini M, Suleiman A K A, Jacques R J S, Antoniolli Z I, de Siqueira Ferreira A, Kuramae E E, Roesch L F W. 2014.Network topology reveals high connectance levels and few key microbial genera within soils. Frontiers in Environmental Science, 2:10, https://doi.org/10.3389/fenvs.2014.00010.
Lynch M D J, Neufeld J D. 2015. Ecology and exploration of the rare biosphere. Nature Reviews Microbiology, 13(4):217-229, https://doi.org/10.1038/nrmicro3400.
Madigan M T, Martinko J M, Bender K S, Buckley D H, Stahl D A, Brock T. 2014. Brock Biology of Microorganisms. 14th edn. Pearson Benjamin Cummings, San Francisco.
Magurran A E. 2003. Measuring Biological Diversity. WileyBlackwell, Oxford.
Maruyama A, Honda D, Yamamoto H, Kitamura K, Higashihara T. 2000. Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov. International Journal of Systematic and Evolutionary Microbiology, 50(2):835-846, https://doi.org/10.1099/00207713-50-2-835.
Molloy S. 2014. Environmental microbiology:disentangling syntrophy. Nature Reviews Microbiology, 12(1):7, https://doi.org/10.1038/nrmicro3194.
Nemergut D R, Schmidt S K, Fukami T, O'Neill S P, Bilinski T M, Stanish L F, Knelman J E, Darcy J L, Lynch R C, Wickey P, Ferrenberg S. 2013. Patterns and processes of microbial community assembly. Microbiology and Molecular Biology Reviews, 77(3):342-356, https://doi.org/10.1128/MMBR.00051-12.
Pan H Q, Hu J C. 2015. Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment. Marine Genomics, 23:55-57, https://doi.org/10.1016/j.margen.2015.05.003.
Pedrós-Alió C. 2012. The rare bacterial biosphere. Annual Review of Marine Science, 4:449-466, https://doi.org/10.1146/annurev-marine-120710-100948.
Piontek J, Sperling M, Nöthig E M, Engel A. 2015. Multiple environmental changes induce interactive effects on bacterial degradation activity in the Arctic Ocean.Limnology and Oceanography, 60(4):1 392-1 410, https://doi.org/10.1002/lno.10112.
Pontarp M, Canbäck B, Tunlid A, Lundberg P. 2012.Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe. Microbial Ecology, 64(1):8-17, https://doi.org/10.1007/s00248-011-0005-7.
Schloss P D, Westcott S L, Ryabin T, Hall J R, Hartmann M, Hollister E B, Lesniewski R A, Oakley B B, Parks D H, Robinson C J, Sahl J W, Stres B, Thallinger G G, Van Horn D J, Weber C F. 2009. Introducing mothur:open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75(23):7 537-7 541, https://doi.org/10.1128/AEM.01541-09.
Shao L, Li X J, Geng J H, Pang X, Lei Y C, Qiao P J, Wang L L, Wang H B. 2007. Deep water bottom current deposition in the northern South China Sea. Science in China Series D:Earth Sciences, 50(7):1 060-1 066, https://doi.org/10.1007/s11430-007-0015-y.
Signori C N, Thomas F, Enrich-Prast A, Pollery R C G, Sievert S M. 2014. Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula. Frontiers in Microbiology, 5:647, https://doi.org/10.3389/fmicb.2014.00647.
Singh R, Paul D, Jain R K. 2006. Biofilms:implications in bioremediation. Trends in Microbiology, 14(9):389-397, https://doi.org/10.1016/j.tim.2006.07.001.
Spring S, Scheuner C, Göker M, Klenk H P. 2015. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Frontiers in Microbiology, 6:281, https://doi.org/10.3389/fmicb.2015.00281.
Sunagawa S, Coelho L P, Chaffron S, Kultima J R, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende D R, Alberti A, Cornejo-Castillo F M, Costea P I, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol J M, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos B T, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan M B, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas S G, Bork P, Boss E, Bowler C, Follows M, Karp-Boss L, Krzic U, Reynaud E G, Sardet C, Sieracki M, Velayoudon D. 2015. Structure and function of the global ocean microbiome. Science, 348(6237):1 261 359, https://doi.org/10.1126/science.1261359.
Yoshida M, Yoshida-Takashima Y, Nunoura T, Takai K. 2015. Identification and genomic analysis of temperate Pseudomonas bacteriophage PstS-1 from the Japan trench at a depth of 7000 m. Research in Microbiology, 166(9):668-676, https://doi.org/10.1016/j.resmic.2015.05.001.
Zhang X M, Liu W, Schloter M, Zhang G M, Chen Q S, Huang J H, Li L H, Elser J J, Han X G. 2013. Response of the abundance of key soil microbial nitrogen-cycling genes to multi-factorial global changes. PLoS One, 8(10):e76500, https://doi.org/10.1371/journal.pone.0076500.
Zhou J Z, Deng Y, Luo F, He Z L, Yang Y F. 2011a. Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2. mBio, 2(4):e00122-11, https://doi.org/10.1128/mBio.00122-11.
Zhou J Z, Wu L Y, Deng Y, Zhi X Y, Jiang Y H, Tu Q C, Xie J P, Van Nostrand J D, He Z L, Yang Y F. 2011b. Reproducibility and quantitation of amplicon sequencingbased detection. The ISME Journal, 5(8):1 303-1 313, https://doi.org/10.1038/ismej.2011.11.