Impacts of chemical gradients on microbial community structur

ISME Journal

Volumn 11, Issue 4, 2017, Pages 920-931

  Chen, Jianwei ^a,b   Hanke, Anna ^b   Tegetmeyer, Halina E ^b,c   Kattelmann, Ines ^c   Sharma, Ritin ^d,e,f   Hamann, Emmo ^a,b   Hargesheimer, Theresa ^b   Kraft, Beate ^b,g   Lenk, Sabine ^b   Geelhoed, Jeanine S ^b,h   Hettich, Robert L ^d,e   Strous, Marc ^a,b,c  

^a UNIVERSITY OF CALGARY   (Canada)

^b MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^c BIELEFELD UNIVERSITY   (Germany)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF TENNESSEE   (United States)

^f H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

^g UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^h ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

COMMUNITY STRUCTURE; DOMINANCE; ENZYME ACTIVITY; FERMENTATION; GENOMICS; LABORATORY METHOD; MARINE SEDIMENT; MICROBIAL COMMUNITY; OXIC CONDITIONS; OXYGEN CONSUMPTION; REDOX CONDITIONS; STABLE ISOTOPE; SUCCESSION;

OXYGEN;

CHEMISTRY; ECOSYSTEM; METAGENOMICS; MICROBIOLOGY; OXIDATION REDUCTION REACTION; OXYGEN CONSUMPTION; SEDIMENT;

ECOSYSTEM; GEOLOGIC SEDIMENTS; METAGENOMICS; OXIDATION-REDUCTION; OXYGEN; OXYGEN CONSUMPTION;

EID: 85009799730     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2016.175     Document Type: Article

References (56)

1. Albert DB, Martens CS. (1997). Determination of lowmolecular- weight organic acid concentrations in seawater and pore-water samples via HPLC. Mar Chem 56: 27-37.
2. Billerbeck M, Werner U, Polerecky L, Walpersdorf E, DeBeer D, Huettel M. (2006). Surficial and deep pore water circulation governs spatial and temporal scales of nutrient recycling in intertidal sand flat sediment. Mar Ecol Prog Ser 326: 61-76.
3. Bolger AM, Lohse M, Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
4. Bordel S. (2010). Steepest entropy increase is justified by information theory. the relations between Ziegler's principle, Onsager's formalism and Prigogine's principle. Phys A Stat Mech Appl 389: 4564-4570.
5. Canfield DE, Steward FJ, Thamdrup B, De Brabandere L, Dalsgaart T, Delong EF et al. (2010). A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast. Science 330: 1375-1378.
6. Chen F, Xia Q, Ju L-K. (2003). Aerobic denitrification of Pseudomonas aeruginosa monitored by online NAD(P)H fluorescence. Appl Environ Microbiol 69: 6715-6722.
7. Crabtree HG. (1928). The carbohydrate metabolism of certain pathological overgrowths. Biochem J 22: 1289-1298.
8. Dalsgaard T, Bak F. (1994). Nitrate reduction in a sulfatereducing bacterium, desulfovibrio desulfuricans, isolated from rice paddy soil: sulfide inhibition, kinetics, and regulation. Appl Environ Microbiol 60: 291-297.
9. Diaz-Ruiz R, Rigoulet M, Devin A. (2011). The Warburg and Crabtree effects: on the origin of cancer cell energy metabolism and of yeast glucose repression. Biochim Biophys Acta 1807: 568-576.
10. Eddy SR. (2008). A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol 4: e1000069.
11. Edgar RC. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
12. Fan L, McElroy K, Thomas T. (2012). Reconstruction of ribosomal RNA genes from metagenomic data. PLoS One 7: e39948.
13. Fenchel T, King GM, Blackburn TH. (2012). Transport mechanisms. In: Blackburn TFMKH (ed). Bacterial Biogeochemistry. Academic Press: Boston, MA, USA, pp 35-47.
14. Fenchel TM, Jørgensen BB. (1977). Detritus food chains of aquatic ecosystems: the role of bacteria. In: Alexander M (ed). Advances in Microbial Ecology. Plenum Press: New York, NY, USA, pp 1-58.
15. Gao H, Schreiber F, Collins G, Jensen MM, Kostka JE, Lavik G et al. (2010). Aerobic denitrification in permeable Wadden Sea sediments. ISME J 4: 417-426.
16. Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ. (2015). Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone. ISME J 9: 2682-2696.
17. Hanke A, Hamann E, Sharma R, Geelhoed JS, Hargesheimer T, Kraft B et al. (2014). Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Front Microbiol 5: 231.
18. Hawley AK, Brewer HM, Norbeck AD, Paša-Tolić L, Hallam SJ. (2014). Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. Proc Natl Acad Sci USA 111: 11395-11400.
19. Heijnen JJ, Van Loosdrecht MCM, Tijhuis L. (1992). A black box mathematical model to calculate auto- and heterotrophic biomass yields based on Gibbs energy dissipation. Biotechnol Bioeng 40: 1139-1154.
20. Honisch U, Zumft WG. (2003). Operon structure and regulation of the nos gene region of Pseudomonas stutzeri, encoding an ABC-Type ATPase for maturation of nitrous oxide reductase. J Bacteriol 185: 1895-1902.
21. Jensen MM, Petersen J, Dalsgaard T, Thamdrup B. (2009). Pathways, rates, and regulation of N2 production in the chemocline of an anoxic basin, Mariager Fjord, Denmark. Mar Chem 113: 102-113.
22. Jünemann S. (1997). Cytochrome bd terminal oxidase. Biochim Biophys Acta 1321: 107-127.
23. Kamyshny A, Ekeltchik I, Gun J, Lev O. (2006). Method for the determination of inorganic polysulfide distribution in aquatic systems. Anal Chem 78: 2631-2639.
24. Khardenavis AA, Kapley A, Purohit HJ. (2007). Simultaneous nitrification and denitrification by diverse Diaphorobacter sp. Appl Microbiol Biotechnol 77: 403-409.
25. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M et al. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41: e1.
26. Kraft B, Tegetmeyer HE, Sharma R, Klotz MG, Ferdelman TG, Hettich RL et al. (2014). The environmental controls that govern the end product of bacterial nitrate respiration. Science 345: 676-679.
27. Kuivila KM, Murray JW, Devol AH. (1990). Methane production in the sulfate-depleted sediments of two marine basins. Geochim Cosmochim Acta 54: 403-411.
28. Little AEF, Robinson CJ, Peterson SB, Raffa KF, Handelsman J. (2008). Rules of engagement: interspecies interactions that regulate microbial communities. Annu Rev Microbiol 62: 375-401.
29. Llobet-Brossa E, Rosselló-Mora R, Amann R. (1998). Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl Environ Microbiol 64: 2691-2696.
30. Lowry OH, Rosebrough NJ, Farr AL, Randall RJ. (1951). Protein measurement with the Folin phenol reagent. J Biol Chem 193: 265-275.
31. Newman DK, Banfield JF. (2002). Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems. Science 296: 1071-1077.
32. Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. (2011).Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 75: 361-422.
33. Oremland RS, Capone DG, Stolz JF, Fuhrman J. (2005). Whither or wither geomicrobiology in the era of "community metagenomics". Nat Rev Microbiol 3: 572-578.
34. Pernthaler A, Pernthaler J, Amann R. (2004). Sensitive multi-color fluorescence in situ hybridization for the identification of environmental microorganisms. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans AD, van Elsas JD (eds). Molecular Microbial Ecology Manual. Kluwer Academic Press: Dordrecht, The Netherlands, pp 2613-2627.
35. Pitcher RS, Watmough NJ. (2004). The bacterial cytochrome cbb3 oxidases. Biochim Biophys Acta 1655: 388-399.
36. Richards FA. (1965). Anoxic basins and fjords. Chemical Oceanography. Academic Press: London, UK.
37. Robertson LA, Cornelisse R, De Vos P, Hadioetomo R, Kuenen JG. (1989). Aerobic denitrification in various heterotrophic nitrifiers. Antonie Van Leeuwenhoek 56: 289-299.
38. Rodriguez J, Lema J, Kleerebezem R. (2008). Energy-based models for environmental biotechnology. Trends Biotechnol 26: 366-374.
39. Schloss PD, Westcott SL, Ryabin T, Hall JR, Harmann M, Hollister EB et al. (2009). Introducing mothur: opensource, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
40. Schulz HN, Jørgensen BB. (2001). Big bacteria. Annu Rev Microbiol 55: 105-137.
41. Schreiber F, Littmann S, Lavik G, Escrig S, Meibom A, Kuypers MMM et al. (2016). Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments. Nat Microbiol 1: 16055.
42. Seemann T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics 30: 2068-2069.
43. Smith CJ, Nedwell DB, Dong LF, Osborn AM. (2007). Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Appl Environ Microbiol 73: 3612-3622.
44. Stewart FJ, Ulloa O, DeLong EF. (2012). Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ Microbiol 14: 23-40.
45. Stolper DA, Revsbech NP, Canfield DE. (2010). Aerobic growth at nanomolar oxygen concentrations. Proc Natl Acad Sci USA 107: 18755-18760.
46. Strohm TO, Griffin B, Zumft WG, Schink B. (2007). Growth yields in bacterial denitrification and nitrate ammonification. Appl Environ Microbiol 73: 1420-1424.
47. Strous M, Kraft B, Bisdorf R, Tegetmeyer HE. (2012). The binning of metagenomic contigs for microbial physiology of mixed cultures. Front Microbiol 3: 410.
48. Su JF, Zhang K, Huang TL, Wen G, Guo L, Yang SF. (2015). Heterotrophic nitrification and aerobic denitrification at low nutrient condition by a newly isolated bacterium, Acinetobacter sp. SYF26. Microbiology 161: 829-837.
49. Takaya N, Catalan-Sakairi MAB, Sakaguchi Y, Kato I, Zhou Z, Shoun H. (2003). Aerobic denitrifying bacteria that produce low levels of nitrous oxide. Appl Environ Microbiol 69: 3152-3157.
50. Temudo MF, Poldermans R, Kleerebezem R, Van Loosdrecht MCM. (2008). Glycerol fermentation by (open) mixed cultures: a chemostat study. Biotechnol Bioeng 100: 1088-1098.
51. Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, Aris JP et al. (2005). Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet 37: 630-635.
52. Van Eck GR. (1966). Plysiological and chemical test for drinking water. NEN 1056 IV 2. Nederlandse Normalisatie Instituut Rijswijk: Rijswijk, The Netherlands.
53. Warburg O. (1956). On the origin of cancer cells. Science 123: 309-314.
54. Woodcock S, Van der Gast CJ, Bell T, Lunn M, Curtis TP, Head IM et al. (2007). Neutral assembly of bacterial communities. FEMS Microbiol Ecol 62: 171-180.
55. Yan J, Haaijer SCM, Op den Camp HJM, van Niftrik L, Stahl DA, Könneke M, Rush D et al. (2012). Mimicking the oxygen minimum zones: stimulating interaction of aerobic archaeal and anaerobic bacterial ammonia oxidizers in a laboratory-scale model system. Environ Microbiol 14: 3146-3158.
56. Zhou J, Bruns MA, Tiedje JM. (1996). DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316-322.