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Amino acid cycling in plankton and soil microbes studied with radioisotopes: measured amino acids in soil do not reflect bioavailability

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Abstract

In radioisotope studies in plankton, bacteria turn over the nanomolar ambient concentrations of dissolved amino acids within a few hours. Uptake follows Michaelis–Menten kinetics. In contrast, within minutes the very abundant bacteria and fungi in soil take up all labeled amino acids added at nanomolar to millimolar final concentrations; uptake kinetics accordingly cannot be measured. This rapid uptake agrees with earlier findings that soil microbes exist in a starving or low-activity state but are able to keep their metabolism poised to take up amino acids as they become available. How can this rapid uptake of added amino acids be reconciled with persistent soil concentrations of 10–500 μM of total dissolved amino acids? Although respiration of added amino acid carbon has been used to deduce uptake kinetics, the data indicate that in both soil and in eutrophic natural waters constant percentages of individual amino acids are respired; this percentage varies from less than 10% of the amount taken up for basic amino acids to more than 50% for acidic amino acids. We conclude that relatively fixed internal metabolic processes control the percent of amino acid respired and that the μM concentrations of amino acid measured in water extracts from soil are unavailable to microbes. Instead, these relatively high concentrations reflect amino acids in soils that are chemically protected, hidden in pores, or released from fine roots and microbes during sample preparation.

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References

  • Alonso-Sáez L, Gasol JM, Aristegui J, Vilas JC, Vaque D, Duarte CM, Agusti S (2007) Large-scale variability in surface bacterial carbon demand and growth efficiency in the subtropical northeast Atlantic Ocean. Limnol Oceanogr 52:533–546

    Article  Google Scholar 

  • Aluwihare LI, Meador T (2008) Chemical composition of marine dissolved organic nitrogen. In: Capone DC, Bronk DA, Mulholland MR, Carpenter EJ (eds) Nitrogen in the marine environment, 2nd edn. Elsevier, Amsterdam

    Google Scholar 

  • Anraku Y (1980) Transport and utilization of amino acids by bacteria. In: Payne J (ed) Microorganisms and nitrogen sources. Wiley, New York

    Google Scholar 

  • Azam F, Hodson RE (1981) Multiphasic kinetics for d-glucose uptake by assemblages of natural marine bacteria. Mar Ecol Prog Ser 6:213–222

    Article  Google Scholar 

  • Bååth E (1994) Measurement of protein-synthesis by soil bacterial assemblages with the leucine incorporation technique. Biol Fertil Soils 7:147–153

    Article  Google Scholar 

  • Bååth E, Anderson TH (2003) Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biol Biochem 35:955–963

    Article  Google Scholar 

  • Bailey VL, Peacock AD, Smith JL, Bolton H Jr (2002) Relationships between soil microbial biomass determined by chloroform fumigation–extraction, substrate-induced respiration and phospholipid fatty acid analysis. Soil Biol Biochem 34:1385–1389

    Article  Google Scholar 

  • Bardgett RD (2005) The biology of soils: a community and ecosystem approach. Oxford University Press, Oxford

    Google Scholar 

  • Barra Caracciolo A, Grenni P, Cupo C, Rossetti S (2005) In situ analysis of native microbial communities in complex samples with high particulate loads. FEMS Microbiol Lett 253:55–58

    Article  Google Scholar 

  • Benjdia M, Rikirsch E, Muller T, Morel M, Corratge C, Chalot M, Zimmermann S, Frommer WB, Wipf D (2006) Peptide uptake in the ectomycorrhizal fungus Hebeloma cylindrosporum: characterization of two di- and tripeptide transporters (HcPTR2A and B). New Phytol 170:401–410

    Article  Google Scholar 

  • Bennett ME, Hobbie JE (1972) The uptake of glucose by Chlamydomonas sp. J Phycol 8:392–398

    Google Scholar 

  • Bertaux J, Gloger U, Schmid M, Hartmann A, Scheu S (2007) Routine fluorescence in situ hybridization in soil. J Microbiol Methods 69:451–460

    Article  Google Scholar 

  • Billen G (1984) Heterotrophic utilization and regeneration of nitrogen. In: Hobbie JE, Williams PJL (eds) Heterotrophic activity in the sea. NATO conference series. IV Marine Sciences; v 15. Plenum Press, New York

    Google Scholar 

  • Bittman S, Forge TA, Kowalenko CG (2005) Response of the bacterial and fungal biomass in a grassland soil to multi-year applications of dairy manure slurry and fertilizer. Soil Biol Biochem 37:613–623

    Article  Google Scholar 

  • Blackburn TH, Knowles R (1993) Introduction. In: Knowles R, Blackburn TH (eds) Nitrogen isotope techniques. Academic, San Diego

    Google Scholar 

  • Boddy E, Hill PW, Farrar J, Jones DL (2007) Fast turnover of low molecular weight components of the dissolved organic carbon pool of temperate grassland field soils. Soil Biol Biochem 39:827–835

    Article  Google Scholar 

  • Boschker HTS, Bertilsson SA, Dekkers EMJ, Cappenberg TE (1995) An inhibitor-based method to measure initial decomposition of naturally-occurring polysaccharides in sediments. Appl Environ Microbiol 61:2186–2192

    Google Scholar 

  • Brady NC (1974) The nature and properties of soils, 8th edn. MacMillan Publishing, Inc, New York

    Google Scholar 

  • Capone DC (2000) The marine microbial nitrogen cycle. In: Kirchman DL (ed) Microbial ecology of the oceans. Wiley-Liss, New York

    Google Scholar 

  • Carlson CA, Ducklow HW (1995) Dissolved organic carbon in the upper ocean of the central equatorial Pacific Ocean, 1992: daily and finescale vertical variations. Deep-Sea Res Part II 42:639–656

    Article  Google Scholar 

  • Chalot M, Brun A (1998) Physiology of organic nitrogen acquisition by ectomycorrhizal fungi and ectomycorrhizas. FEMS Microb Rev 22:21–44

    Article  Google Scholar 

  • Chatzinotas A, Sandaa RA, Schonhuber W, Amann R, Daae FL, Torsvik V, Zeyer J, Hahn V (1998) Analysis of broad-scale differences in microbial community composition of two pristine forest soils. Syst Appl Microbiol 21:579–587

    Article  Google Scholar 

  • Crawford CC, Hobbie JE, Webb KL (1974) The utilization of dissolved free amino acids by estuarine microorganisms. Ecology 55:551–563

    Article  Google Scholar 

  • Davis CL, Robb FT (1985) Maintenance of different mannitol uptake systems during starvation in oxidative and fermentative marine bacteria. Appl Environ Microbiol 50:743–748

    Google Scholar 

  • de Boer W, Folman LB, Summerbell RC, Boddy L (2005) Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev 29:795–811

    Article  Google Scholar 

  • De Nobili M, Contin M, Mondini C, Brookes PC (2001) Soil microbial biomass is triggered into activity by trace amounts of substrate. Soil Biol Biochem 33:1163–1170

    Article  Google Scholar 

  • del Giorgio P, Cole JJ (2000) Bacterial energetics and growth efficiency. In: Kirchman D (ed) Microbial ecology of the oceans. Wiley-Liss, New York

    Google Scholar 

  • del Giorgio P, Condon R, Bouvier T, Longnecker K, Bouvier C, Sherr E, Gasol JM (in press) Coherent patterns in bacterial growth, growth efficiency, and leucine metabolism along northeast Pacific inshore-offshore transect. Limnol Oceanogr

  • Fierer N, Strickland MS, Liptzin D, Bradford MA, Cleveland CC (2009) Global patterns in belowground communities. Ecol Lett 12:1238–1249

    Article  Google Scholar 

  • Frey SD (2007) Spatial distribution of soil organisms. In: Paul EA (ed) Soil microbiology, ecology, and biochemistry. Academic, San Diego

    Google Scholar 

  • Frey SD, Knorr M, Parrent J, Simpson RT (2004) Chronic nitrogen enrichment affects the structure and function of the soil microbial community in a forest ecosystem. For Ecol Manage 196:159–171

    Article  Google Scholar 

  • Fruton JS, Simmonds S (1958) General biochemistry. Wiley, New York

    Google Scholar 

  • Fuhrman J, Ferguson RL (1986) Nanomolar concentrations and rapid turnover of dissolved free amino acids in seawater: agreement between chemical and microbiological measurements. Mar Ecol Prog Ser 33:237–242

    Article  Google Scholar 

  • Gallet-Budynek A, Brzostek E, Rodgers, Talbot JM, Hyzy S, Finzi AC (2009) Intact amino acid uptake by northern hardwood and conifer trees. Oecologia 160:129–138

    Article  Google Scholar 

  • Ghazanfari MH, Rashtchian D, Kharrat R, Vossoughi S (2007) Capillary pressure estimation using statistical pore size functions. Chem Eng Technol 30:862–869

    Article  Google Scholar 

  • Guldberg LB, Finster K, Jørgensen NOG, Middelboe M, BA Lomstein (2002) Utilization of marine sedimentary dissolved organic nitrogen by native anaerobic bacteria. Limnol Oceanogr 47:1712–1722

    Article  Google Scholar 

  • Hawkes CV, DeAngelis KM, Firestone MK (2007) Root interactions with soil microbial communities and processes. In: Cardon ZC, Whitbeck JL (eds) The rhizosphere: an ecological perspective. Elsevier, Amsterdam

    Google Scholar 

  • Hobbie JE, Crawford C (1969) Respiration corrections for bacterial uptake of dissolved organic compounds in natural waters. Limnol Oceanogr 14:528–532

    Article  Google Scholar 

  • Hobbie EA, Hobbie JE (2008) Natural abundance of 15N in nitrogen-limited forests and tundra can estimate nitrogen cycling through mycorrhizal fungi: a review. Ecosystems 11:815–830

    Article  Google Scholar 

  • Hobbie EA, Wallander H (2006) Integrating ectomycorrhizal fungi into quantitative frameworks of forest carbon and nitrogen cycling. In: Gadd GM (ed) Fungi in biogeochemical cycles. Cambridge University Press, Cambridge

    Google Scholar 

  • Hobbie JE, Wright RT (1965) Bioassay with bacterial uptake kinetics: glucose in freshwater. Limnol Oceanogr 10:471–474

    Article  Google Scholar 

  • Hobbie JE, Daley RJ, Jasper S (1977) Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 33:1225–1228

    Google Scholar 

  • Hofmockel KS, Schlesinger WS, Jackson JB (2007) Effects of elevated atmospheric carbon dioxide on amino acid and NH4 +–N cycling in a temperate pine ecosystem. Glob Change Biol 13:1950–1959

    Article  Google Scholar 

  • Ingham ER, Klein DA (1984) Soil fungi: relationships between hyphal activity and staining with fluorescein diacetate. Soil Biol Biochem 16:273–278

    Article  Google Scholar 

  • Jennings DH (1995) The physiology of fungal nutrition. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Joergensen RG, Wichern F (2008) Quantitative assessment of the fungal contribution to microbial tissue in soil. Soil Biol Biochem 40:2977–2991

    Article  Google Scholar 

  • Johnson DW (1994) Nitrogen retention in forest soils. J Environ Qual 21:1–12

    Article  Google Scholar 

  • Jones DL, Hodge A (1999) Biodegradation kinetics and sorption reactions of three differently charged amino acids in soil and their effects on plant organic nitrogen availability. Soil Biol Biochem 31:1331–1342

    Article  Google Scholar 

  • Jones DL, Murphy DV (2007) Microbial response time to sugar and amino acid additions to soil. Soil Biol Biochem 39:2178–2182

    Article  Google Scholar 

  • Jones DL, Shannon D, Murphy DV, Farrar J (2004) Role of dissolved organic nitrogen (DON) in soil N cycling in grassland soils. Soil Biol Biochem 36:749–756

    Article  Google Scholar 

  • Jones DL, Healey JR, Willett VB, Farrar JF, Hodge A (2005a) Dissolved organic nitrogen uptake by plants—an important N uptake pathway? Soil Biol Biochem 37:413–423

    Article  Google Scholar 

  • Jones DL, Kemmitt SJ, Wright D, Cuttle SP, Bol R, Edwards AC (2005b) Rapid intrinsic rates of amino acid biodegradation in soils are unaffected by agricultural management strategy. Soil Biol Biochem 37:1267–1275

    Article  Google Scholar 

  • Jones DL, Shannon D, Junvee-Fortune T, Farrar JF (2005c) Plant capture of free amino acids is maximized under high soil amino acid concentrations. Soil Biol Biochem 37:179–181

    Article  Google Scholar 

  • Jones DL, Kielland K, Sinclair FL, Dahlgren RA, Newsham KK, Farrar JF, Murphy DV (2009) Soil organic nitrogen mineralization across a global latitudinal gradient. Glob Biogeochem Cycles 23. doi:10.1029/2008GB003250

  • Jørgensen NOG (1987) Free amino acid in lakes: concentrations and assimilation rates in relation to phytoplankton and bacterial production. Limnol Oceanogr 32:97–111

    Article  Google Scholar 

  • Kandeler E (2007) Physiological and biochemical methods for studying soil biota and their function. In: Paul EA (ed) Soil microbiology, ecology, and biochemistry. Academic, San Diego

    Google Scholar 

  • Karner M, Fuhrman JA (1997) Determination of active marine bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining. Appl Environ Microbiol 63:1208–1213

    Google Scholar 

  • Kay W, Gronlund A (1971) Transport of aromatic amino acids by Pseudomonas aeruginosa. J Bacteriol 105:1039–1046

    Google Scholar 

  • Kielland K, McFarland J, Ruess R, Olson K (2007) Rapid cycling of organic nitrogen in taiga forest soils. Ecosystems 10:360–368

    Article  Google Scholar 

  • Kirchman DL (2000) Uptake and regeneration of inorganic nutrients by marine heterotrophic bacteria. In: Kirchman DL (ed) Microbial ecology of the oceans. Wiley-Liss, New York

    Google Scholar 

  • Kirchman D, K’Nees E, Hodson R (1985) Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl Environ Microbiol 49:599–607

    Google Scholar 

  • Kleber M, Sollins P, Sutton R (2007) A conceptual model of organo-mineral interactions in soils: self-assembly of organic molecular fragments into zonal structures on mineral surfaces. Biogeochemistry 85:9–24

    Article  Google Scholar 

  • Kuzyakov Y, Blagodatskaya E, Blagodatsky S (2009) Comments on the paper by Kemmitt et al. (2008) Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass—a new perspective. [Soil Biol Biochem 40:61–73]: the biology of the Regulatory Gate. Soil Biol Biochem 41:435–439

    Google Scholar 

  • Lindahl BD, Finlay RD, Cairney JWG (2005) Enzymatic activities of mycelia in mycorrhizal fungal communities. In: Dighton J, White JF, Oudemans P (eds) The fungal community. Taylor & Francis, Boca Raton

    Google Scholar 

  • Lipson DA, Schmidt SK, Monson RK (1999) Links between microbial population dynamics and nitrogen availability in an alpine ecosystem. Ecology 80:1623–1631

    Article  Google Scholar 

  • Litchman E, Klausmeier CA, Schofield OM, Falkowski PG (2007) The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level. Ecol Lett 10:1170–1181

    Article  Google Scholar 

  • McFarland JW, Ruess RW, Kielland K, Doyle AP (2002) Cycling dynamics of NH4 + and amino acid nitrogen in soils of a deciduous boreal forest ecosystem. Ecosystems 5:775–788

    Google Scholar 

  • Morita RY (1988) Bioavailability of energy and its relationship to growth and starvation survival in nature. Can J Microbiol 34:436–441

    Article  Google Scholar 

  • Morita RY (1997) Bacteria in oligotrophic environments: starvation-survival lifestyle. Chapman and Hall, N.Y, p 529

    Google Scholar 

  • Näsholm TA, Ekblad A, Nordin A, Giesler R, Hogberg M, Hogberg P (1998) Boreal forest plants take up organic nitrogen. Nature 392:914–916

    Article  Google Scholar 

  • Näsholm T, Kielland K, Ganeteg U (2009) Uptake of organic nitrogen by plants. New Phytol 182:31–48

    Article  Google Scholar 

  • Neff JC, Chapin FS, Vitousek PM (2003) Breaks in the cycle: dissolved organic nitrogen in terrestrial ecosystems. Front Ecol Environ 1:205–211

    Article  Google Scholar 

  • Nissen H, Nissen P, Azam F (1984) Multiphasic uptake of d-glucose by an oligotrophic marine bacterium. Mar Ecol Prog Ser 16:155–160

    Article  Google Scholar 

  • Nordin A, Schmidt IK, Shaver GR (2004) Nitrogen uptake by arctic soil microbes and plants in relation to soil nitrogen supply. Ecology 85:955–962

    Article  Google Scholar 

  • Norton JM, Firestone MK (1991) Metabolic status of bacteria and fungi in the rhizosphere of ponderosa pine seedlings. Appl Environ Microbiol 17:1161–1167

    Google Scholar 

  • Panikov NS, Blagodatsky SA, Blagodatskaya JV, Glagolev MV (1992) Determination of microbial mineralization activity in soil by modified Wright and Hobbie method. Biol Fertil Soils 14:280–287

    Article  Google Scholar 

  • Parsons TR, Strickland JDH (1962) On the production of particulate organic carbon by heterotrophic processes in sea water. Deep-Sea Res 8:211–222

    Google Scholar 

  • Poretsky RS, Sun SL, Mou XZ, Moran MA (2010) Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon. Environ Microbiol 12:616–627

    Article  Google Scholar 

  • Raven JA, Wollenweber B, Handley LL (1992) A comparison of ammonium and nitrate as nitrogen-sources for photolithotrophs. New Phytol 121(1):19–32

    Article  Google Scholar 

  • Rousk J, Demaling LA, Bååth E (2009) Contrasting short-term antibiotic effects on respiration and bacterial growth compromises the validity of the selective respiratory inhibition technique to distinguish fungi and bacteria. Microb Ecol 58:75–85

    Article  Google Scholar 

  • Schimel JP, Bennett J (2004) Nitrogen mineralization: challenges of a changing paradigm. Ecology 85:591–602

    Article  Google Scholar 

  • Smith EM, del Giorgio PA (2003) Low fractions of active bacteria in natural aquatic communities? Aquat Microb Ecol 31:203–208

    Article  Google Scholar 

  • Sollins P, Kramer MG, Swanston C, Lajtha K, Filley T, Aufdenkampe AK, Wagai R, Bowden RD (2009) Sequential density fractionation across soils of contrasting mineralogy: evidence for both microbial and mineral controlled soil organic matter stabilization. Biogeochemistry 96:209–231

    Article  Google Scholar 

  • Sorensen PL, Michelsen A, Jonasson S (2008) Ecosystem partitioning of 15N-glycine after long-term climate and nutrient manipulations, plant clipping and addition of labile carbon in a subarctic heath tundra. Soil Biol Biochem 40:2344–2350

    Article  Google Scholar 

  • van Hees PAW, Johansson E, Jones DL (2008) Dynamics of simple carbon compounds in two forest soils as revealed by soil solution concentrations and biodegradation kinetics. Plant Soil 310:11–23

    Article  Google Scholar 

  • Vincent WF, Goldman CR (1980) Evidence for algal heterotrophy in Lake Tahoe, California-Nevada. Limnol Oceanogr 25:89–99

    Article  Google Scholar 

  • Vinolas LC, Vallejo VR, Jones DL (2001) Control of amino acid mineralization and microbial metabolism by temperature. Soil Biol Biochem 33:1137–1140

    Article  Google Scholar 

  • Vonk JA, Middelburg JJ, Stapel J, Bouma TJ (2008) Dissolved organic nitrogen uptake by seagrasses. Limnol Oceanogr 53:542–548

    Article  Google Scholar 

  • Wallenstein MD, Weintraub MN (2008) Emerging tools for measuring and modeling the in situ activity of soil extracellular enzymes. Soil Biol Biochem 40:2098–2106

    Article  Google Scholar 

  • Wanek W, Mooshammer M, Blöchl A, Hanreich A, Richter A (2010) Determination of gross rates of amino acid production and immobilization in decomposing leaf litter by a novel 15N isotope pool dilution technique. Soil Biol Biochem 42:1293–1302

    Article  Google Scholar 

  • Warren CR (2009) Does nitrogen concentration affect relative uptake rates of nitrate, ammonium, and glycine? J Plant Nutr Soil Sci 172:224–229

    Article  Google Scholar 

  • White DC (1995) Chemical ecology: possible linkage between macro- and microbial ecology. Oikos 74:177–184

    Article  Google Scholar 

  • Whitman WB, Coleman DC, Wiebe W (1998) Perspective: prokaryotes—the unseen majority. Proc Natl Acad Sci 95:6578–6583

    Article  Google Scholar 

  • Williams PJL (1970) Heterotrophic utilization of dissolved organic compounds in the sea. J Mar Biol Assoc UK 50:859–870

    Article  Google Scholar 

  • Williams PJL (2000) Heterotrophic bacteria and the dynamics of dissolved organic matter. In: Kirchman DL (ed) Microbial ecology of the oceans. Wiley-Liss, New York, Chichester

    Google Scholar 

  • Wright RT (1974) Mineralization of organic solutes by heterotrophic bacteria. In: Colwell RR, Morita RY (eds) The effect of the ocean environment on microbial activities. University Park Press, Baltimore

    Google Scholar 

  • Wright RT, Hobbie JE (1966) Use of glucose and acetate by bacteria and algae in aquatic ecosystems. Ecology 47:447–464

    Article  Google Scholar 

  • Xu L, Baldocchi DD, and Tang J (2004) How soil moisture, rain pulses, and growth alter the response of ecosystem respiration to temperature. Glob Biogeochem Cycles 18 GB4002, doi:10.1029/2004GB002281

  • Yu Z, Zhang Q, Kraus TEC, Dahlgren RA, Anastasio C, Zasoski RJ (2002) Contribution of amino compounds to dissolved organic nitrogen in forest soils. Biogeochemistry 61:173–198

    Article  Google Scholar 

  • Zarda B, Hahn D, Chatzinotas A, Schonhuber W, Neef A, Amann RI, Zeyer J (1997) Analysis of bacterial community structure in bulk soil by in situ hybridization. Arch Microbiol 168:185–192

    Article  Google Scholar 

  • Zubkov MV, Tarran GA, Mary I, Fuchs BM (2008) Differential microbial uptake of dissolved amino acids and amino sugars in surface waters of the Atlantic Ocean. J Plankton Res 30:211–220

    Article  Google Scholar 

  • Zvyagintsev DG (2001) Composition and functioning of a complex of soil microorganisms. Eurasian Soil Sci 34:S65–S73

    Google Scholar 

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Acknowledgments

This work was supported by the National Science Foundation Office of Polar Programs 0612598 and National Science Foundation Division of Environmental Biology 0614266 and 0423385. We thank Hugh Ducklow, Jim Tang, Zoe Cardon, Mirko Lunau, and Xelu Morán for comments. Helpful comments from reviewers pointed out a number of publications and concepts to consider.

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Hobbie, J.E., Hobbie, E.A. Amino acid cycling in plankton and soil microbes studied with radioisotopes: measured amino acids in soil do not reflect bioavailability. Biogeochemistry 107, 339–360 (2012). https://doi.org/10.1007/s10533-010-9556-9

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