Community-level physiological profiling (CLPP) analyses from very diverse environments are frequently used with the aim of characterizing the metabolic versatility of whole environmental bacterial communities. While the limitations of the methodology for the characterization of whole communities are well known, we propose that CLPP combined with high-throughput sequencing and qPCR can be utilized to identify the copiotrophic, fast-growing fraction of the bacterial community of soil environments, where oligotrophic taxa are usually dominant. In the present work we have used this approach to analyze samples of litter and soil from a coniferous forest in the Czech Republic using BIOLOG GN2 plates. Monosaccharides and amino acids were utilized significantly faster than other C substrates, such as organic acids, in both litter and soil samples. Bacterial biodiversity in CLPP wells was significantly lower than in the original community, independently of the carbon source. Bacterial communities became highly enriched in taxa that typically showed low abundance in the original soil, belonging mostly to the Gammaproteobacteria and the genus Pseudomonas, indicating that the copiotrophic strains, favoured by the high nutrient content, are rare in forest litter and soil. In contrast, taxa abundant in the original samples were rarely found to grow at sufficient rates under the CLPP conditions. Our results show that CLPP is useful to detect copiotrophic bacteria from the soil environments and that bacterial growth is substrate specific.

Laboratory of Environmental Microbiology Institute of Microbiology of the CAS Prague Czech Republic

Zobrazit více v PubMed

Myneni RB, Dong J, Tucker CJ, Kaufmann RK, Kauppi PE, Liski J et al. (2001) A large carbon sink in the woody biomass of Northern forests. Proceedings of the National Academy of Sciences of the United States of America 98: 14784–14789. 10.1073/pnas.261555198 PubMed DOI PMC

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31: 814–821. 10.1038/nbt.2676 PubMed DOI PMC

Grayston SJ, Wang S, Campbell C, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biology & Biochemistry 30: 369–378.

Collins B, McArthur JV, Sharitz RR (2004) Plant effects on microbial assemblages and remediation of acidic coal pile runoff in mesocosm treatment wetlands. Ecological Engineering 23: 107–115.

Lyons MM, Ward JE, Gaff H, Hicks RE, Drake JM, Dobbs FC (2010) Theory of island biogeography on a microscopic scale: organic aggregates as islands for aquatic pathogens. Aquatic Microbial Ecology 60: 1–13.

Mastrogianni A, Papatheodorou EM, Monokrousos N, Menkissoglu-Spiroudi U, Stamou GP (2014) Reclamation of lignite mine areas with Triticum aestivum: The dynamics of soil functions and microbial communities. Applied Soil Ecology 80: 51–59.

Lladó S, Žifčáková L, Větrovský T, Eichlerová I, Baldrian P (2016a) Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition. Biology and Fertility of Soils 52: 251–260.

Baldrian P, Voříšková J, Dobiášová P, Merhautová V, Lisá L, Valaskova V (2011) Production of extracellular enzymes and degradation of biopolymers by saprotrophic microfungi from the upper layers of forest soil. Plant and Soil 338: 111–125.

Cummings SP (2010) Bioremediation methods and protocols. University of Northumbria, Newcastle-upon-Tyne, UK: Humana Press.

Bochner BR (1989) Sleuthing out bacterial identities. Nature 339: 157–158. 10.1038/339157a0 PubMed DOI

Garland JL, Mills AL (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Applied and Environmental Microbiology 57: 2351–2359. PubMed PMC

Liu B, Li Y, Zhang X, Wang J, Gao M (2015) Effects of chlortetracycline on soil microbial communities: Comparisons of enzyme activities to the functional diversity via Biolog EcoPlates™. European Journal of Soil Biology 68: 69–76.

Mangalassery S, Mooney SJ, Sparkes DL, Fraser WT, Sjögersten S (2015) Impacts of zero tillage on soil enzyme activities, microbial characteristics and organic matter functional chemistry in temperate soils. European Journal of Soil Biology 68: 9–17.

Konopka A, Oliver L, Turco RF (1998) The use of carbon substrate utilization patterns in environmental and ecological microbiology. Microbial Ecology 35: 103–115. PubMed

Smalla K, Wachtendorf U, Heuer H, Liu W, Forney L (1998) Analysis of BIOLOG GN substrate utilization patterns by microbial communities. Applied and Environmental Microbiology 64: 1220–1225. PubMed PMC

Gamo M, Shoji T (1998) A method of profiling microbial communities based on a most-probable-number assay that uses BIOLOG plates and multiple sole carbon sources. Applied and Environmental Microbiology 65: 4419–4424. PubMed PMC

Preston-Mafham J, Boddy L, Randerson PF (2002) Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles—a critique. FEMS Microbiology Ecology 42: 1–14. 10.1111/j.1574-6941.2002.tb00990.x PubMed DOI

Weber KP, Gehder M, Legge RL (2008) Assessment of changes in the microbial community of constructed wetland mesocosms in response to acid mine drainage exposure. Water Res 42: 180–188. 10.1016/j.watres.2007.06.055 PubMed DOI

Pierce ML, Ward JE, Dobbs FC (2014) False positives in Biolog EcoPlates and MT2 MicroPlates caused by calcium. J Microbiol Methods 97: 20–24. 10.1016/j.mimet.2013.12.002 PubMed DOI

Phillips RP, Finzi AC, Bernhardt ES (2011) Enhanced root exudation induces microbial feedbacks to N cycling in a pine forest under long-term CO2 fumigation. Ecol Lett 14: 187–194. 10.1111/j.1461-0248.2010.01570.x PubMed DOI

Högberg P, Nordgren A, Buchmann N, Taylor AFS, Ekblad A, Högberg MN et al. (2001) Large-scale forest girdling shows that current photosynthesis drives soil respiration. Nature 411: 789–792. 10.1038/35081058 PubMed DOI

Baldrian P (2017) The Forest Microbiome: Diversity, Complexity and Dynamics. FEMS Microbiology Reviews 41: fuw040. PubMed

Baldrian P, Merhautova V, Cajthaml T, Petrankova M, Snajdr J (2010) Small-scale distribution of extracellular enzymes, fungal, and bacterial biomass in Quercus petraea forest topsoil. Biology and Fertility of Soils 46: 717–726.

Kuzyakov Y, Blagodatskaya E (2015) Microbial hotspots and hot moments in soil: Concept & review. Soil Biology and Biochemistry 83: 184–199.

Baldrian P, Kolarik M, Stursova M, Kopecky J, Valaskova V, Větrovský T et al. (2012) Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. Isme Journal 6: 248–258. 10.1038/ismej.2011.95 PubMed DOI PMC

Žifčaková L, Větrovský T, Howe A, Baldrian P (2016) Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter. Environ Microbiol 18: 288–301. 10.1111/1462-2920.13026 PubMed DOI

Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J (2008) Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Applied and Environmental Microbiology 74: 2902–2907. 10.1128/AEM.02161-07 PubMed DOI PMC

Wilmotte A, Auwera G, Wachter R (1993) Structure of the 16S ribosomal RNA of the termophilic cyanobacterium chlorogloeopsis HTF (Mastigocladus laminosus HTF) strain PCC7518, and phylogenetic analysis. FEBS 317: 96–100. PubMed

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N et al. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6: 1621–1624. 10.1038/ismej.2012.8 PubMed DOI PMC

Větrovský T, Baldrian P (2013a) Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED. Biology and Fertility of Soils 49: 1027–1037.

Aronesty E (2013) Comparison of sequencing utility programs. The Open Bioinformatics Journal 7: 1–8.

Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460–2461. 10.1093/bioinformatics/btq461 PubMed DOI

Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10: 996–998. 10.1038/nmeth.2604 PubMed DOI

Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y et al. (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42: D633–642. 10.1093/nar/gkt1244 PubMed DOI PMC

Větrovský T, Baldrian P (2013b) The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses. Plos One 8. PubMed PMC

Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M et al. (2008) The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386 10.1186/1471-2105-9-386 PubMed DOI PMC

Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88: 1354–1364. PubMed

Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6: 1007–1017. 10.1038/ismej.2011.159 PubMed DOI PMC

Ernebjerg M, Kishony R (2012) Distinct growth strategies of soil bacteria as revealed by large-scale colony tracking. Appl Environ Microbiol 78: 1345–1352. 10.1128/AEM.06585-11 PubMed DOI PMC

Fierer N, Barberan A, Laughlin DC (2014) Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities. Front Microbiol 5: 614 10.3389/fmicb.2014.00614 PubMed DOI PMC

Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3: 442–453. 10.1038/ismej.2008.127 PubMed DOI PMC

Carson JK, Campbell L, Rooney D, Clipson N, Gleeson DB (2009) Minerals in soil select distinct bacterial communities in their microhabitats. FEMS Microbiol Ecol 67: 381–388. 10.1111/j.1574-6941.2008.00645.x PubMed DOI

Carson JK, Gonzalez-Quinones V, Murphy DV, Hinz C, Shaw JA, Gleeson DB (2010) Low pore connectivity increases bacterial diversity in soil. Appl Environ Microbiol 76: 3936–3942. 10.1128/AEM.03085-09 PubMed DOI PMC

Urbanová M, Kopecky J, Valašková V, Sagova-Marecková M, Elhottová D, Kyselková M, et al. (2011) Development of bacterial community during spontaneous succession on spoil heaps after brown coal mining. FEMS Microbiol Ecol 78: 59–69. 10.1111/j.1574-6941.2011.01164.x PubMed DOI

Garcia-Fraile P, Benada O, Cajthaml T, Baldrian P, Llado S (2016) Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation. Appl Environ Microbiol 82: 560–569. PubMed PMC

Lladó S, Benada O, Cajthaml T, Baldrian P, García-Fraile P (2016b) Silvibacterium bohemicum gen. nov. sp. nov., an acidobacterium isolated from coniferous soil in the Bohemian Forest National Park. Syst Appl Microbiol 39: 14–19. PubMed

Starke R, Kermer R, Ullmann-Zeunert L, Baldwin IT, Seifert J, Bastida F, et al. (2016) Bacteria dominate the short-term assimilation of plant-derived N in soil. Soil Biology and Biochemistry 96: 30–38.

Biodiversity and Metabolic Potential of Bacteria in Bulk Soil from the Peri-Root Zone of Black Alder (Alnus glutinosa), Silver Birch (Betula pendula) and Scots Pine (Pinus sylvestris)

High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by "Candidatus Phytoplasma prunorum"

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change