Seasonal Changes in an Alpine Soil Bacterial Community in the Colorado Rocky Mountains

ABSTRACT The period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. The large winter microbial community begins to turn over rapidly, releasing nutrients to plants. Past studies have shown that the soil microbial community in alpine dry meadows of the Colorado Rocky Mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. However, little specific information exists on the diversity of the alpine bacterial community or how it changes during this ecologically important period. We constructed clone libraries of 16S ribosomal DNA from alpine soil collected in winter, spring, and summer. We also cultivated bacteria from the alpine soil and measured the seasonal abundance of selected cultured isolates in hybridization experiments. The uncultured bacterial communities changed between seasons in diversity and abundance within taxa. The Acidobacterium division was most abundant in the spring. The winter community had the highest proportion of Actinobacteria and members of the Cytophaga/Flexibacter/Bacteroides (CFB) division. The summer community had the highest proportion of the Verrucomicrobium division and of β-Proteobacteria. As a whole,α -Proteobacteria were equally abundant in all seasons, although seasonal changes may have occurred within this group. A number of sequences from currently uncultivated divisions were found, including two novel candidate divisions. The cultured isolates belonged to the α-, β-, and γ-Proteobacteria, the Actinobacteria, and the CFB groups. The only uncultured sequences that were closely related to the isolates were from winter and spring libraries. Hybridization experiments showed that actinobacterial and β-proteobacterial isolates were most abundant during winter, while the α- andγ -proteobacterial isolates tested did not vary significantly. While the cultures and clone libraries produced generally distinct groups of organisms, the two approaches gave consistent accounts of seasonal changes in microbial diversity.

[1]  P. Hugenholtz,et al.  Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives , 2001, Applied and Environmental Microbiology.

[2]  D. Bossio,et al.  Determinants of Soil Microbial Communities: Effects of Agricultural Management, Season, and Soil Type on Phospholipid Fatty Acid Profiles , 1998, Microbial Ecology.

[3]  N. Pace,et al.  Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring , 1998, Journal of bacteriology.

[4]  Richard A. Silverman,et al.  Probability Theory: A Concise Course , 1977 .

[5]  R. Amann,et al.  Combined Use of 16S Ribosomal DNA and 16S rRNA To Study the Bacterial Community of Polychlorinated Biphenyl-Polluted Soil , 2001, Applied and Environmental Microbiology.

[6]  P. Hobbs,et al.  Seasonal changes in soil microbial communities along a fertility gradient of temperate grasslands , 1999 .

[7]  A. Chao,et al.  Stopping rules and estimation for recapture debugging with unequal failure rates , 1993 .

[8]  R. Monson,et al.  LINKS BETWEEN MICROBIAL POPULATION DYNAMICS AND NITROGEN AVAILABILITY IN AN ALPINE ECOSYSTEM , 1999 .

[9]  A. Ulrich,et al.  Diversity of grass-associated Microbacteriaceae isolated from the phyllosphere and litter layer after mulching the sward; polyphasic characterization of Subtercola pratensis sp. nov., Curtobacterium herbarum sp. nov. and Plantibacter flavus gen. nov., sp. nov. , 2002, International journal of systematic and evolutionary microbiology.

[10]  E. Stackebrandt,et al.  Verrucomicrobium spinosum, a Eubacterium Representing an Ancient Line of Descent , 1987 .

[11]  N. Pace.  A molecular view of microbial diversity and the biosphere. , 1997, Science.

[12]  A. Chao.  Nonparametric estimation of the number of classes in a population , 1984 .

[13]  J. Fuhrman,et al.  Microbial Desulfurization of a Crude Oil Middle-Distillate Fraction: Analysis of the Extent of Sulfur Removal and the Effect of Removal on Remaining Sulfur , 1999, Applied and Environmental Microbiology.

[14]  J. Fuhrman,et al.  Combined Microautoradiography–16S rRNA Probe Technique for Determination of Radioisotope Uptake by Specific Microbial Cell Types In Situ , 1999, Applied and Environmental Microbiology.

[15]  Christopher W. Schadt,et al.  Seasonal Dynamics of Previously Unknown Fungal Lineages in Tundra Soils , 2003, Science.

[16]  W. Liesack,et al.  Evidence for unlinked rrn operons in the Planctomycete Pirellula marina , 1989, Journal of bacteriology.

[17]  J. Imhoff,et al.  Phylogenetic Diversity of Numerically Important Arctic Sea-Ice Bacteria Cultured at Subzero Temperature , 2002, Microbial Ecology.

[18]  Timothy R. Seastedt,et al.  TOPOGRAPHIC PATTERNS OF ABOVE‐ AND BELOWGROUND PRODUCTION AND NITROGEN CYCLING IN ALPINE TUNDRA , 1998 .

[19]  Robert K. Colwell,et al.  Estimating terrestrial biodiversity through extrapolation. , 1994, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[20]  A. S. Raghubanshi,et al.  Microbial biomass acts as a source of plant nutrients in dry tropical forest and savanna , 1989, Nature.

[21]  Y. Kosako,et al.  Acidobacterium capsulatum gen. nov., sp. nov.: An acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment , 2005, Current Microbiology.

[22]  David A. Wardle,et al.  CONTROLS OF TEMPORAL VARIABILITY OF THE SOIL MICROBIAL BIOMASS: A GLOBAL-SCALE SYNTHESIS , 1998 .

[23]  Arctic and Alpine Biodiversity: Patterns, Causes and Ecosystem Consequences , 1995, Ecological Studies.

[24]  S. K. Schmidt,et al.  Nitrogen Mineralization and Microbial Biomass Nitrogen Dynamics in Three Alpine Tundra Communities , 1995 .

[25]  B H Olson,et al.  Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction , 1992, Applied and environmental microbiology.

[26]  F. Rainey,et al.  Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil , 1997, Applied and environmental microbiology.

[27]  P. Hugenholtz,et al.  Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. , 2003, International journal of systematic and evolutionary microbiology.

[28]  Tim Tolker-Nielsen,et al.  Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region , 1998 .

[29]  W. Whitman,et al.  Molecular and Culture-Based Analyses of Prokaryotic Communities from an Agricultural Soil and the Burrows and Casts of the Earthworm Lumbricus rubellus , 2002, Applied and Environmental Microbiology.

[30]  M. McClelland,et al.  DNA rehybridization during PCR: the 'Cot effect' and its consequences. , 1996, Nucleic acids research.

[31]  Andrew P. Martin.  Phylogenetic Approaches for Describing and Comparing the Diversity of Microbial Communities , 2002, Applied and Environmental Microbiology.

[32]  K. Schleifer,et al.  Detection and in situ identification of representatives of a widely distributed new bacterial phylum. , 1997, FEMS microbiology letters.

[33]  R. Monson,et al.  Carbon availability and temperature control the post-snowmelt decline in alpine soil microbial biomass , 2000 .

[34]  Martin F. Polz,et al.  Bias in Template-to-Product Ratios in Multitemplate PCR , 1998, Applied and Environmental Microbiology.

[35]  E. Smit,et al.  Diversity and Seasonal Fluctuations of the Dominant Members of the Bacterial Soil Community in a Wheat Field as Determined by Cultivation and Molecular Methods , 2001, Applied and Environmental Microbiology.

[36]  A. Chao,et al.  Estimating the Number of Classes via Sample Coverage , 1992 .

[37]  T. Lueders,et al.  Evaluation of PCR Amplification Bias by Terminal Restriction Fragment Length Polymorphism Analysis of Small-Subunit rRNA and mcrA Genes by Using Defined Template Mixtures of Methanogenic Pure Cultures and Soil DNA Extracts , 2003, Applied and Environmental Microbiology.

[38]  Diverse, yet-to-be-cultured members of the Rubrobacter subdivision of the Actinobacteria are widespread in Australian arid soils. , 2000, FEMS microbiology ecology.

[39]  R. Monson,et al.  SOIL AMINO ACID UTILIZATION AMONG SPECIES OF THE CYPERACEAE: PLANT AND SOIL PROCESSES , 1999 .

[40]  D. Lipson,et al.  The unexpected versatility of plants: organic nitrogen use and availability in terrestrial ecosystems , 2001, Oecologia.

[41]  P. Janssen,et al.  Improved Culturability of Soil Bacteria and Isolation in Pure Culture of Novel Members of the Divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia , 2002, Applied and Environmental Microbiology.

[42]  J. Tiedje,et al.  THE VERNAL DAM: PLANT-MICROBE COMPETITION FOR NITROGEN IN NORTHERN HARDWOOD FORESTS' , 1990 .

[43]  M. Cottrell,et al.  Natural Assemblages of Marine Proteobacteria and Members of the Cytophaga-Flavobacter Cluster Consuming Low- and High-Molecular-Weight Dissolved Organic Matter , 2000, Applied and Environmental Microbiology.

[44]  J. Klironomos.  Feedback with soil biota contributes to plant rarity and invasiveness in communities , 2002, Nature.

[45]  Philip Hugenholtz,et al.  Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity , 1998, Journal of bacteriology.

[46]  W. Liesack,et al.  Characterization and Identification of Numerically Abundant Culturable Bacteria from the Anoxic Bulk Soil of Rice Paddy Microcosms , 1999, Applied and Environmental Microbiology.

[47]  John Dunbar,et al.  Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning , 1999, Applied and Environmental Microbiology.

[48]  Masataka Watanabe,et al.  Succession of Bacterial Community Structure along the Changjiang River Determined by Denaturing Gradient Gel Electrophoresis and Clone Library Analysis , 2002, Applied and Environmental Microbiology.

[49]  J. Schimel.  Ecosystem Consequences of Microbial Diversity and Community Structure , 1995 .

[50]  C. Kuske,et al.  Wide Distribution and Diversity of Members of the Bacterial Kingdom Acidobacterium in the Environment , 1999, Applied and Environmental Microbiology.

[51]  J. Kreft,et al.  Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds , 2004, Archives of Microbiology.

[52]  C. Schadt,et al.  Changes in Soil Microbial Community Structure and Function in an Alpine Dry Meadow Following Spring Snow Melt , 2002, Microbial Ecology.

[53]  A. Willems,et al.  A New Species of Devosia That Forms a Unique Nitrogen-Fixing Root-Nodule Symbiosis with the Aquatic Legume Neptunia natans (L.f.) Druce , 2002, Applied and Environmental Microbiology.

[54]  R. Monson,et al.  An empirical model of amino acid transformations in an alpine soil , 2001 .

[55]  K. Pregitzer,et al.  Compositional and functional shifts in microbial communities due to soil warming , 1997 .

[56]  Michel Loève,et al.  Probability Theory I , 1977 .

[57]  E. Stackebrandt,et al.  Proposal for a New Hierarchic Classification System, Actinobacteria classis nov. , 1997 .