Bacterial Diversity and Distribution in the Holocene Sediments of a Northern Temperate Lake

Overview

Journal Microb Ecol

Specialties Environmental Health
Microbiology

Date 2007 Mar 17

PMID 17364246

Citations 7

Authors

David M Nelson

Samuel Ohene-Adjei

Feng Sheng Hu

Isaac K O Cann

Roderick I Mackie

Affiliations

Soon will be listed here.

Abstract

Sediments contain an abundance of microorganisms. However, the diversity and distribution of microorganisms associated with sediments are poorly understood, particularly in lacustrine environments. We used banding patterns from denaturing gradient gel electrophoresis (DGGE) and 16S rDNA sequences to assess the structure of bacterial communities in the Holocene sediments of a meromictic lake in Minnesota. Cluster analysis of the DGGE banding patterns indicates that the early- and middle-Holocene samples group separately from the late-Holocene samples. About 79% of the recovered bacterial sequences cluster with the alpha-, beta-, delta-, epsilon-, and gamma- Proteobacteriaceae and Firmicutes. The remaining approximately 21% lack cultured representatives. The taxonomic lineages of bacteria differ statistically among the early-, middle-, and late-Holocene samples, although the difference is smallest between early- and middle-Holocene samples. Early- and middle-Holocene samples are dominated by epsilon-Proteobacteriaceae, and late-Holocene samples are dominated by sequences from uncultured subphyla. We only recovered delta-Proteobacteriaceae in late-Holocene sediments and alpha- and gamma- Proteobacteriaceae in late- and middle-Holocene sediments. Diversity estimates derived from early-, middle-, and late-Holocene clone libraries indicate that the youngest (late-Holocene) samples had significantly greater bacterial diversity than the oldest (early-Holocene) samples, and the middle-Holocene samples contained intermediate levels of diversity. The observed patterns of diversity may be caused by increased bacterial niche-partitioning in younger sediments that contain a greater abundance of labile organic matter than older sediments.

Citing Articles

Comparing Sediment Bacterial Communities of Volcanic Lakes and Surrounding Rivers in Inner Mongolia Autonomous Region, Northeastern China.

Chao J, Li J, Gao J, Bai C, Tang X, Shao K Microorganisms. 2024; 12(7).

PMID: 39065203 PMC: 11278812. DOI: 10.3390/microorganisms12071435.

Vertical variations in microbial diversity, composition, and interactions in freshwater lake sediments on the Tibetan plateau.

Zhu X, Deng Y, Huang T, Han C, Chen L, Zhang Z Front Microbiol. 2023; 14:1118892.

PMID: 36970704 PMC: 10031068. DOI: 10.3389/fmicb.2023.1118892.

Microbial Community Structure in Arctic Lake Sediments Reflect Variations in Holocene Climate Conditions.

Moller T, van der Bilt W, Roerdink D, Jorgensen S Front Microbiol. 2020; 11:1520.

PMID: 32903319 PMC: 7396534. DOI: 10.3389/fmicb.2020.01520.

Assessment of methods to recover DNA from bacteria, fungi and archaea in complex environmental samples.

Guillen-Navarro K, Herrera-Lopez D, Lopez-Chavez M, Cancino-Gomez M, Reyes-Reyes A Folia Microbiol (Praha). 2015; 60(6):551-8.

PMID: 26014885 DOI: 10.1007/s12223-015-0403-1.

Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation.

Watanabe T, Kojima H, Fukui M Appl Environ Microbiol. 2012; 78(18):6545-9.

PMID: 22773644 PMC: 3426700. DOI: 10.1128/AEM.01349-12.

References

Coolen M, Overmann J . Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment. Appl Environ Microbiol. 1998; 64(11):4513-21. PMC: 106678. DOI: 10.1128/AEM.64.11.4513-4521.1998. View

Schloss P, Larget B, Handelsman J . Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol. 2004; 70(9):5485-92. PMC: 520927. DOI: 10.1128/AEM.70.9.5485-5492.2004. View

Whitman W, Coleman D, Wiebe W . Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A. 1998; 95(12):6578-83. PMC: 33863. DOI: 10.1073/pnas.95.12.6578. View

Schloss P, Handelsman J . Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005; 71(3):1501-6. PMC: 1065144. DOI: 10.1128/AEM.71.3.1501-1506.2005. View

Muyzer G, Smalla K . Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek. 1998; 73(1):127-41. DOI: 10.1023/a:1000669317571. View

McCracken V, Simpson J, Mackie R, Gaskins H . Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiota. J Nutr. 2001; 131(6):1862-70. DOI: 10.1093/jn/131.6.1862. View

Spring S, Schulze R, Overmann J, Schleifer K . Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes: molecular and cultivation studies. FEMS Microbiol Rev. 2000; 24(5):573-90. DOI: 10.1111/j.1574-6976.2000.tb00559.x. View

Mallet C, Basset M, Fonty G, Desvilettes C, Bourdier G, Debroas D . Microbial population dynamics in the sediments of a eutrophic lake (Aydat, France) and characterization of some heterotrophic bacterial isolates. Microb Ecol. 2004; 48(1):66-77. DOI: 10.1007/s00248-003-2017-4. View

Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M . Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol. 2005; 71(4):2162-9. PMC: 1082574. DOI: 10.1128/AEM.71.4.2162-2169.2005. View

10.

Tsai Y, Olson B . Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol. 1991; 57(4):1070-4. PMC: 182847. DOI: 10.1128/aem.57.4.1070-1074.1991. View

11.

Berthelet M, Whyte L, Greer C . Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns. FEMS Microbiol Lett. 1996; 138(1):17-22. DOI: 10.1111/j.1574-6968.1996.tb08128.x. View

12.

Coolen M, Cypionka H, Sass A, Sass H, Overmann J . Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science. 2002; 296(5577):2407-10. DOI: 10.1126/science.1071893. View

13.

Dykhuizen D . Santa Rosalia revisited: why are there so many species of bacteria?. Antonie Van Leeuwenhoek. 1998; 73(1):25-33. DOI: 10.1023/a:1000665216662. View

14.

DHondt S, Jorgensen B, Miller D, Batzke A, Blake R, Cragg B . Distributions of microbial activities in deep subseafloor sediments. Science. 2004; 306(5705):2216-21. DOI: 10.1126/science.1101155. View

15.

Dumont M, Murrell J . Stable isotope probing - linking microbial identity to function. Nat Rev Microbiol. 2005; 3(6):499-504. DOI: 10.1038/nrmicro1162. View

16.

Jurgens , Glockner , Amann , Saano , Montonen , Likolammi . Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization(1). FEMS Microbiol Ecol. 2000; 34(1):45-56. DOI: 10.1111/j.1574-6941.2000.tb00753.x. View

17.

Nelson D, Hu F, Tian J, Stefanova I, Brown T . Response of C3 and C4 plants to middle-Holocene climatic variation near the prairie-forest ecotone of Minnesota. Proc Natl Acad Sci U S A. 2004; 101(2):562-7. PMC: 327187. DOI: 10.1073/pnas.0307450100. View

18.

Nocker A, Camper A . Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide. Appl Environ Microbiol. 2006; 72(3):1997-2004. PMC: 1393219. DOI: 10.1128/AEM.72.3.1997-2004.2006. View

19.

Muyzer G, de Waal E, Uitterlinden A . Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993; 59(3):695-700. PMC: 202176. DOI: 10.1128/aem.59.3.695-700.1993. View