Biodiv Sci ›› 2013, Vol. 21 ›› Issue (4): 421-432. DOI: 10.3724/SP.J.1003.2013.12052
Special Issue: 微生物多样性专辑
• Orginal Article • Previous Articles Next Articles
Lijuan Ren1,2, Dan He1,2, Peng Xing1, Yujing Wang1,2, Qinglong Wu1,*()
Received:
2013-02-27
Accepted:
2013-05-20
Online:
2013-07-20
Published:
2013-07-29
Contact:
Wu Qinglong
Lijuan Ren,Dan He,Peng Xing,Yujing Wang,Qinglong Wu. Bacterial diversity and ecological function in lake water bodies[J]. Biodiv Sci, 2013, 21(4): 421-432.
Fig. 1 The interpretation of the relationship between bacterial community similarity and environmental gradients and geographic distances under four perspectives of meta- community hypothesis (revised from Logue et al., 2008)
1 | Adams HE, Crump BC, Kling GW (2010) Temperature controls on aquatic bacterial production and community dynamics in arctic lakes and streams.Environmental Microbiology, 12, 1319-1333. |
2 | Affronti LF, Marshall HG (1994) Using frequency of dividing cells in estimating autotrophic picoplankton growth and productivity in the Chesapeake Bay.Hydrobiologia, 284, 193-203. |
3 | Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation.Microbiological Reviews, 59, 143-169. |
4 | Baas-Becking LGM (1934) Geobiologie of Inleiding tot de Milieukunde. WP Van Stockum & Zoon, The Hague, The Netherlands. (in Dutch) |
5 | Beijerinck MW (1913) De Infusies en de Ontdekking der Backteriën. Jaarboek van de Koninklijke Aakademie voor Wetenschappen. Müller. Amsterdam, The Netherlands. (in Dutch) |
6 | Bouvy M, Bettarel Y, Bouvier C, Domaizon I, Jacquet S, Floc’h L, Montanié H, Mostajir B, Sime-Ngando T, Torréton JP, Vidussi F, Bouvier T (2011) Trophic interactions between viruses, bacteria and nanoflagellates under various nutrient conditions and simulated climate change. Environmental Microbiology, 13, 1842-1857. |
7 | Brendan Logue J, Lindström ES (2008) Biogeography of bacterioplankton in inland waters.Freshwater Reviews, 1, 99-114. |
8 | Chase JM, Amarasekare P, Cottenie K, Gonzalez A, Holt RD, Holyoak M, Hoopes MF, Leibold MA, Loreau M, Mouquet NM, Shurin JB, Tilman D (2005) Competing theories for competitive metacommunities. In: Metacommunities: Spatial Dynamics and Ecological Communities (eds Holyoak M, Leibold MA, Holt RD), pp. 335-354. The University of Chicago Press, Chicago and London. |
9 | Chirwa EN, Wang YT (2000) Simultaneous chromium (VI) reduction and phenol degradation in an anaerobic consortium of bacteria.Water Research, 34, 2376-2384. |
10 | Cohan FM (2002) What are bacterial species? Annual Reviews in Microbiology, 56, 457-487. |
11 | Crump BC, Kling GW, Bahr M, Hobbie JE (2003) Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source.Applied and Environmental Microbiology, 69, 2253-2268. |
12 | Curtis TP, Sloan WT (2004) Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology.Current Opinion in Microbiology, 7, 221-226. |
13 | Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proceedings of the National Academy of Sciences, USA, 99, 10494-10499. |
14 | Daufresne M, Lengfellner K, Sommer U (2009) Global warming benefits the small in aquatic ecosystems. Proceedings of the National Academy of Sciences, USA, 106, 12788-12793. |
15 | Di Siervi M, Mariazzi AA, Donadelli JL (1995) Bacterioplankton and phytoplankton production in a large patagonian reservoir (República Argentina).Hydrobiologia, 297, 123-129. |
16 | Dziallas C, Grossart HP (2011) Temperature and biotic factors influence bacterial communities associated with the cyanobacterium Microcystis sp.Environmental Microbiology, 13, 1632-1641. |
17 | Eiler A, Bertilsson S (2004) Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes.Environmental Microbiology, 6, 1228-1243. |
18 | Fenchel TOM, Finlay BJ (2004) The ubiquity of small species: patterns of local and global diversity.BioScience, 54, 777-784. |
19 | Ferber LR, Levine SN, Lini A, Livingston GP (2004) Do cyanobacteria dominate in eutrophic lakes because they fix atmospheric nitrogen? Freshwater Biology, 49, 690-708. |
20 | Forbes SA (1887) The lake as a microcosm. Bulletin Science Association of Peoria, Illinois, 1887, 77-87. |
21 | Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL, Brown JH (2008) A latitudinal diversity gradient in planktonic marine bacteria. Proceedings of the National Academy of Sciences, USA, 105, 7774-7778. |
22 | Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, de Peer YV, Vandamme P, Thompson FL, Swings J (2005) Re-evaluating prokaryotic species.Nature Reviews Microbiology, 3, 733-739. |
23 | Glöckner FO, Zaichikov E, Belkova N, Denissova L, Pernthaler J, Pernthaler A, Amann R (2000) Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Applied and Environmental Microbiology, 66, 5053-5065. |
24 | Grossart HP (2010) Ecological consequences of bacterioplankton lifestyles: changes in concepts are needed. Environmental Microbiology Reports, 2, 706-714. |
25 | Hahn MW (2003) Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones.Applied and Environmental Microbiology, 69, 5248-5254. |
26 | Hahn MW, Höfle MG (2001) Grazing of protozoa and its effect on populations of aquatic bacteria.FEMS Microbiology Ecology, 35, 113-121. |
27 | Hahn MW, Lang E, Tarao M, Brandt U (2011) Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake.International Journal of Systematic and Evolutionary Microbiology, 61, 781-787. |
28 | Hamersley MR, Woebken D, Boehrer B, Schultze M, Lavik G, Kuypers MMM (2009) Water column anammox and denitrification in a temperate permanently stratified lake (Lake Rassnitzer, Germany).Systematic and Applied Microbiology, 32, 571-582. |
29 | Hanski I, Gilpin M (1991) Metapopulation dynamics: brief history and conceptual domain.Biological Journal of the Linnean Society, 42, 3-16. |
30 | Hanson MA, Butler MG (1994) Responses of plankton, turbidity, and macrophytes to biomanipulation in a shallow prairie lake.Canadian Journal of Fisheries and Aquatic Sciences, 51, 1180-1188. |
31 | Hollibaugh JT, Wong PS, Bano N, Pak SK, Prager EM, Orrego C (2001) Stratification of microbial assemblages in Mono Lake, California, and response to a mixing event. Hydrobiologia, 466, 45-60. |
32 | Holyoak M, Leibold MA, Mouquet NM, Holt RD, Hoopes MF (2005) Metacommunities: a framework for large-scale community ecology. In: Metacommunities: Spatial Dynamics and Ecological Communities (eds Holyoak M, Leibold MA, Holt RD), pp. 1-31. The University of Chicago Press, Chicago and London. |
33 | Hubbell SP (2001) The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press, Princeton, NJ. |
34 | Humayoun SB, Bano N, Hollibaugh JT (2003) Depth distribution of microbial diversity in Mono Lake, a meromictic soda lake in California.Applied and Environmental Microbiology, 69, 1030-1042. |
35 | Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, Sogin ML (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.PLoS Genetics, 4, e1000255. |
36 | Jaspers E, Overmann J (2004) Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Applied and Environmental Microbiology, 70, 4831-4839. |
37 | Jezberová J, Jezbera J, Brandt U, Lindström ES, Langenheder S, Hahn MW (2010) Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogenous 2000 km2 area.Environmental Microbiology, 12, 658-669. |
38 | Jurasinski G, Retzer V, Beierkuhnlein C (2009) Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity.Oecologia, 159, 15-26. |
39 | Jürgens K, Güde H (1994) The potential importance of grazing-resistant bacteria in planktonic systems.Marine Ecology Progress Series, 112, 169-188. |
40 | Keirn MA, Brezonik PL (1971) Nitrogen fixation by bacteria in Lake Mize, Florida, and in some lacustrine sediments.Limnology and Oceanography, 16, 720-731. |
41 | Kent AD, Yannarell AC, Rusak JA, Triplett EW, McMahon KD (2007) Synchrony in aquatic microbial community dynamics.The ISME Journal, 1, 38-47. |
42 | Langenheder S, Lindström ES, Tranvik LJ (2006) Structure and function of bacterial communities emerging from different sources under identical conditions.Applied and Environmental Microbiology, 72, 212-220. |
43 | Lawton JH (1999) Are there general laws in ecology? Oikos, 84, 177-192. |
44 | Leibold MA, Holyoak M, Mouquet N, Amarasekare P, Chase JM, Hoopes MF, Holt RD, Shurin JB, Law R, Tilman D, Loreau M, Gonzalez A (2004) The metacommunity concept: a framework for multi-scale community ecology.Ecology Letters, 7, 601-613. |
45 | Lindström ES, Forslund M, Algesten G, Bergström AK (2006) External control of bacterial community structure in lakes.Limnology and Oceanography, 51, 339-342. |
46 | Lindström ES, Kamst-Van Agterveld MP, Zwart G (2005) Distribution of typical freshwater bacterial groups is associated with pH, temperature, and lake water retention time.Applied and Environmental Microbiology, 71, 8201-8206. |
47 | Logares R, Bråte J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K (2009) Infrequent marine-freshwater transitions in the microbial world. Trends in Microbiology, 17, 414-422. |
48 | Logue JB, Bürgmann H, Robinson CT (2008) Progress in the ecological genetics and biodiversity of freshwater bacteria.BioScience, 58, 103-113. |
49 | Loreau M, Mouquet N, Holt RD (2003) Meta-ecosystems: a theoretical framework for a spatial ecosystem ecology. Ecology Letters, 6, 673-679. |
50 | MacArthur RH, Wilson EO(1967) The Theory of Island Biogeography. Princeton University Press, Princeton, New Jersey. |
51 | Magnuson JJ, Benson BJ, Kratz TK (1990) Temporal coherence in the limnology of a suite of lakes in Wisconsin, USA.Freshwater Biology, 23, 145-159. |
52 | Magnuson JJ, Kratz TK, Benson BJ (2006) Long-term Dynamics of Lakes in the Landscape: term Ecological Research North Temperate Lakes. Oxford University Press, USA. |
53 | Martiny JBH, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Øvreås L, Reysenbach AL, Smith VH, Staley JT (2006) Microbial biogeography: putting microorganisms on the map.Nature Reviews Microbiology, 4, 102-112. |
54 | Mathes J, Arndt H (1994) Biomass and composition of protozooplankton in relation to lake trophy in north German lakes.Aquatic Microbial Ecology, 8, 357-375. |
55 | Nakano SI, Ishii N, Manage PM, Kawabata ZI (1998) Trophic roles of heterotrophic nanoflagellates and ciliates among planktonic organisms in a hypereutrophic pond. Aquatic Microbial Ecology, 16, 153-161. |
56 | Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S (2011) A guide to the natural history of freshwater lake bacteria.Microbiology and Molecular Biology Reviews, 75, 14-49. |
57 | Pérez MT, Sommaruga R (2006) Differential effect of algal- and soil-derived dissolved organic matter on alpine lake bacterial community composition and activity.Limnology and Oceanography, 51, 2527-2537. |
58 | Pomeroy LR, Wiebe WJ (2001) Temperature and substrates as interactive limiting factors for marine heterotrophic bacteria.Aquatic Microbial Ecology, 23, 187-204. |
59 | Rashidan KK, Bird DF (2001) Role of predatory bacteria in the termination of a cyanobacterial bloom.Microbial Ecology, 41, 97-105. |
60 | Reche I, Pulido-Villena E, Morales-Baquero R, Casamayor EO (2005) Does ecosystem size determine aquatic bacterial richness? Ecology, 86, 1715-1722. |
61 | Rheinheimer G (1980) Aquatic Microbiology, 2nd edn. Wiley, New York. |
62 | Riemann L, Winding A (2001) Community dynamics of free-living and particle-associated bacterial assemblages during a freshwater phytoplankton bloom.Microbial Ecology, 42, 274-285. |
63 | Rogozin DY, Zykov VV, Degermendzhi AG (2012) Ecology of purple sulfur bacteria in the highly stratified meromictic Lake Shunet (Siberia, Khakassia) in 2002-2009.Microbiology, 81, 727-735. |
64 | Rosenzweig ML (1995) Species Diversity in Space and Time. Cambridge University Press, Cambridge, UK. |
65 | Ross JL, Boon PI, Ford P, Hart BT (1997) Detection and quantification with 16S rRNA probes of planktonic methylotrophic bacteria in a floodplain lake.Microbial Ecology, 34, 97-108. |
66 | Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes.FEMS Microbiology Reviews, 25, 39-67. |
67 | Schloss PD (2009) A high-throughput DNA sequence aligner for microbial ecology studies.PLoS ONE, 4, e8230. |
68 | Schloss PD, Westcott SL (2011) Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis.Applied and Environmental Microbiology, 77, 3219-3226. |
69 | Shchur LA, Aponasenko AD, Lopatin VN, Makarskaya GV (2002) Functional characteristics of bacterioplankton with reference to its aggregation in water bodies of different types.Biology Bulletin of the Russian Academy of Sciences, 29, 431-436. |
70 | Šimek K, Chrzanowski TH (1992) Direct and indirect evidence of size-selective grazing on pelagic bacteria by freshwater nanoflagellates.Applied and Environmental Microbiology, 58, 3715-3720. |
71 | Simon M, Wünsch C (1998) Temperature control of bacterioplankton growth in a temperate large lake.Aquatic Microbial Ecology, 16, 119-130. |
72 | Sorokin DY, Kuenen JG, Muyzer G (2011) The microbial sulfur cycle at extremely haloalkaline conditions of soda lakes.Frontiers in Microbiology, 2, 44. |
73 | Spijkerman E, Coesel PFM (1998) Alkaline phosphatase activity in two planktonic desmid species and the possible role of an extracellular envelope.Freshwater Biology, 39, 503-513. |
74 | Teske A, Ramsing NB, Habicht K, Fukui M, Küver J, Jørgensen BB, Cohen Y (1998) Sulfate-reducing bacteria and their activities in cyanobacterial mats of Solar Lake (Sinai, Egypt).Applied and Environmental Microbiology, 64, 2943-2951. |
75 | Torrey MS, Lee GF (1975) Nitrogen fixation in Lake Mendota, Madison, Wisconsin.Limnology and Oceanography, 21, 365-378. |
76 | Torsvik V, Øvreås L, Thingstad TF (2002) Prokaryotic diversity: magnitude, dynamics, and controlling factors.Science, 296, 1064-1066. |
77 | Villaescusa JA, Casamayor EO, Rochera C, Velázquez D, Chicote Á, Quesada A, Camacho A (2010) A close link between bacterial community composition and environmental heterogeneity in maritime Antarctic lakes.International Microbiology, 13, 67-77. |
78 | Vincent WF, Downes MT (1981) Nitrate accumulation in aerobic hypolimnia: relative importance of benthic and planktonic nitrifiers in an oligotrophic lake.Applied and Environmental Microbiology, 42, 565-573. |
79 | Wang J, Yang D, Zhang Y, Shen J, van der Gast C, Hahn MW, Wu Q (2011) Do patterns of bacterial diversity along salinity gradients differ from those observed for macroorganisms? PLoS ONE, 6, e27597. |
80 | Warnecke F, Sommaruga R, Sekar R, Hofer JS, Pernthaler J (2005) Abundances, identity, and growth state of Actinobacteria in mountain lakes of different UV transparency.Applied and Environmental Microbiology, 71, 5551-5559. |
81 | Weinbauer MG, Hornák K, Jezbera J, Nedoma J, Dolan JR, Šimek K (2006) Synergistic and antagonistic effects of viral lysis and protistan grazing on bacterial biomass, production and diversity.Environmental Microbiology, 9, 777-788. |
82 | Whitby CB, Saunders JR, Pickup RW, McCarthy AJ (2001) A comparison of ammonia-oxidiser populations in eutrophic and oligotrophic basins of a large freshwater lake.Antonie van Leeuwenhoek, 79, 179-188. |
83 | Whittaker RH (1960) Vegetation of the Siskiyou mountains, Oregon and California.Ecological Monographs, 30, 279-338. |
84 | Whittaker RH (1972) Evolution and measurement of species diversity.Taxon, 21, 213-251. |
85 | Wu QL, Boenigk J, Hahn MW (2004) Successful predation of filamentous bacteria by a nanoflagellate challenges current models of flagellate bacterivory.Applied and Environmental Microbiology, 70, 332-339. |
86 | Wu QL, Hahn MW (2006a) High predictability of the seasonal dynamics of a species-like Polynucleobacter population in a freshwater lake. Environmental Microbiology, 8, 1660-1666. |
87 | Wu QL, Hahn MW (2006b) Differences in structure and dynamics of Polynucleobacter communities in a temperate and a subtropical lake, revealed at three phylogenetic levels.FEMS Microbiology Ecology, 57, 67-79. |
88 | Wu QL, Zwart G, Schauer M, Kamst-van Agterveld MP, Hahn MW (2006) Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China.Applied and Environmental Microbiology, 72, 5478-5485. |
89 | Wu QL, Zwart G, Wu J, Kamst-van Agterveld MP, Liu S, Hahn MW (2007) Submersed macrophytes play a key role in structuring bacterioplankton community composition in the large, shallow, subtropical Taihu Lake, China.Environmental Microbiology, 9, 2765-2774. |
90 | Yannarell AC, Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Applied and Environmental Microbiology, 71, 227-239. |
91 | Young KD (2006) The selective value of bacterial shape. Microbiology and Molecular Biology Reviews, 70, 660-703. |
92 | Zeng J, Bian YQ, Xing P, Wu QL (2012) Macrophyte species drive the variation of bacterioplankton community composition in a shallow freshwater lake.Applied and Environmental Microbiology, 78, 177-184. |
93 | Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F, Han SK (2002) Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers.Aquatic Microbial Ecology, 28, 141-155. |
94 | Zwart G, Van Hannen EJ, Kamst-van Agterveld MP, Van der Gucht K, Lindström ES, Van Wichelen J, Lauridisen T, Han SK, Declerck S (2003) Rapid screening for freshwater bacterial groups by using reverse line blot hybridization.Applied and Environmental Microbiology, 69, 5875-5883. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||
Copyright © 2022 Biodiversity Science
Editorial Office of Biodiversity Science, 20 Nanxincun, Xiangshan, Beijing 100093, China
Tel: 010-62836137, 62836665 E-mail: biodiversity@ibcas.ac.cn