1. Heuer H., C.T.T. Binh, S. Jechalke, C. Kopmann, U. Zimmerling, E. Krögerrecklenfort, T.

Ledger, B. Gonzalez, E.M. Top & K. Smalla (2012). IncP-1ε plasmids are important vectors
of antibiotic resistance genes in agricultural systems: diversification driven by class 1
integron gene cassettes. Front. Microbiol. 3, 2, DOI: 10.3389/fmicb.2012.00002

2. Ding, G.-C., K. Smalla, H. Heuer & S. Kropf (2012) A new proposal for a principal
component-based test for high-dimensional data applied to the analysis of PhyloChip data.
Biom. J., 54, 94-107, DOI: 10.1002/bimj.201000164

3. Heuer, H., H. Schmitt & K. Smalla (2011) Antibiotic resistance gene spread due to manure
application on agricultural fields. Curr. Opin. Microbiol., 14, 236-243, DOI:
10.1016/j.mib.2011.04.009

4. Heuer, H., Q. Solehati, U. Zimmerling, K. Kleineidam, M. Schloter, T. Müller, A. Focks, S.

Thiele-Bruhn & K. Smalla (2011) Accumulation of sulfonamide resistance genes in arable
soils due to repeated application of manure containing sulfadiazine. Appl. Environ.
Microbiol., 77, 2527-2530, DOI: 10.1128/AEM.02577-10

5. Weinert, N., Y. Piceno, G.-C. Ding, H. Heuer, G. Berg, M. Schloter, G. Andersen & K.
Smalla (2011) PhyloChip hybridisation uncovered an enormous bacterial diversity in the
rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa.
FEMS Microbiol. Ecol. 75, 497-506, DOI: 10.1111/j.1574-6941.2010.01025.x

6. Qing-Yun, X., Y.-N. Yin,W. Yang, H. Heuer, P. Pior, J.-H Guo & K. Smalla (2011) Genetic
diversity of Ralstonia solanacearum strains from China assessed by PCR-based fingerprints
to unravel host plant and site-dependent distribution patterns. FEMS Microbiol. Ecol. 75,
507-519, DOI: 10.1111/j.1574-6941.2010.01026.x

7. Ding, G.-C., H. Heuer, S. Zühlke, M. Spiteller, G. J. Pronk, K. Heister, I. Kögel-Knabner &

K. Smalla (2010) Soil type-dependent responses to phenanthrene as revealed by determining
the diversity and abundance of polycyclic aromatic hydrocarbon ring-hydroxylating
dioxygenase genes by using a novel PCR detection system. Appl. Environ. Microbiol. 76,
4765-4771, DOI: 10.1128/AEM.00047-10

8. Heuer, H., C. T. T. Binh, C. Kopmann, U. Zimmerling, E. Krögerrecklenfort & K. Smalla

(2010) Effects of veterinary medicines introduced via manure into soil on microbial
communities. In: Interdisciplinary Studies on Environmental Chemistry—Biological
Responses to Contaminants (N. Hamamura, S. Suzuki, S. Mendo, C. M. Barroso, H. Iwata &
S. Tanabe, eds.), Terrapub, Tokyo, pp. 9-13.

9. Heuer, H., J. Ebers, N. Weinert & K. Smalla (2010) Variation in permissiveness for broad-
host-range plasmids among genetically indistinguishable isolates of Dickeya sp. from a small
field plot. FEMS Microbiol. Ecol., 73, 190-196, DOI: 10.1111/j.1574-6941.2010.00880.x

10. Weinert, N., R. Meincke, C. Gottwald, H. Heuer, M. Schloter, G. Berg & K. Smalla (2010)
Bacterial diversity on the surface of potato tubers in soil and influence of the plant genotype.
FEMS Microbiol. Ecol., 74, 114-123, DOI: 10.1111/j.1574-6941.2010.00936.x

11. Kleineidam, K., S. Sharma, A. Kotzerke, H. Heuer, S. Thiele-Bruhn, K. Smalla, B. M. Wilke

& M. Schloter (2010) Effect of sulfadiazine on abundance and diversity of denitrifying
 bacteria by determining nirK and nirS genes in two arable soils. Microb. Ecol. 60, 703-707,
DOI: 10.1007/s00248-010-9691-9

12. Binh, C. T. T., H. Heuer, N. C. M. Gomes, M. Kaupenjohann & K. Smalla (2010) Similar
bacterial community structure and high abundance of sulfonamide resistance genes in field-
scale manures. In: Manure: Management, Uses and Environmental Impacts (C. S.
Dellaguardia, ed.), Nova Science Publishers, Hauppauge NY, USA, pp. 141-166. Open
access: https://www.novapublishers.com/catalog/product_info.php?products_id=16770

13. Ding, G. C., H. Heuer & K. Smalla (2010) Cultivation-independent detection of genes
present in soil bacteria. In: Handbook of soil sciences, 2nd edition (P. M. Huang, M. E.
Sumner, Y. Li, eds.), Taylor & Francis Group, London, UK.

14. Binh, C.T.T., H. Heuer, M. Kaupenjohann & K. Smalla (2009) Diverse aadA gene cassettes
on class 1 integrons introduced into soil via spread manure. Res. Microbiol. 160, 427-433,
DOI: 10.1016/j.resmic.2009.06.005

15. Weinert, N., R. Meincke, C. Gottwald, H. Heuer, N.C.M. Gomes, M. Schloter, G. Berg & K.
Smalla (2009) Molecular fingerprints reveal that the effects of genetically modified potato
plants with increased zeaxanthin content on bacterial and fungal rhizosphere communities do
not exceed natural cultivar variability. Appl. Environ. Microbiol. 75, 3859-3865.

16. Schauss, K., A. Focks, H. Heuer, A. Kotzerke, H. Schmitt, S. Thiele-Bruhn, K. Smalla, B.

Wilke, M. Matthies, W. Amelung, J. Klasmeier & M. Schloter (2009) Analysis, fate and
effects of antibiotic sulfadiazine in soil ecosystems. TrAC - Trend. Anal. Chem. 5, 612-618.

17. Heuer, H., C. Kopmann, C.T.T. Binh, E.M. Top & K. Smalla (2009) Spreading antibiotic
resistance through spread manure: characteristics of a novel plasmid type with low %G+C
content. Environ. Microbiol. 11, 937-949.

18. Schauss, K., A. Focks, S. Leininger, A. Kotzerke., H. Heuer, S. Thiele-Bruhn, S. Sharma, B.

M. Wilke, M. Matthies, K. Smalla, J. C. Munch, W. Amelung, M. Kaupenjohann, C.
Schleper & M. Schloter (2009) Dynamics and functional relevance of ammonia-oxidizing
archaea in agricultural soils. Environ. Microbiol. 11, 446-456.

19. Binh, C.T.T., H. Heuer & K. Smalla (2008) Piggery manure used for soil fertilization is a
reservoir for transferable antibiotic resistance plasmids. FEMS Microbiol. Ecol. 66, 25-37.

20. Heuer, H., Z. Abdo & K. Smalla (2008) Patchy distribution of flexible genetic elements in
bacterial populations mediates robustness to environmental uncertainty. FEMS Microbiol.
Ecol. 65, 361-371.

21. Heuer, H., A. Focks, K. Smalla, M. Spiteller, M. Matthies & M. Lamshöft (2008) Fate of
sulfadiazine administered to pigs correlated with dynamics of bacterial resistance genes in
manure and soil. Soil Biol. Biochem. 40, 1892-1900.

22. Hammesfahr, U., H. Heuer, B. Manzke, K. Smalla & S. Thiele-Bruhn (2008) Impact of the
antibiotic sulfadiazine and pig manure on the microbial community structure in agricultural
soils. Soil Biol. Biochem. 40, 1583-1591.
23. Kotzerke, A., S. Sharma, K. Schauss, H. Heuer, S. Thiele-Bruhn, K. Smalla, B.M.Wilke &
M. Schloter (2008) Alterations in soil microbial activity and N-transformation processes due
to sulfadiazine loads in pig-manure. Environ. Pollut. 153, 315-322.

24. Binh, C. T. T., H. Heuer, N. C. M. Gomes, A. Kotzerke, M. Fulle, B.-M. Wilke, M. Schloter
& K. Smalla (2007) Short-term effects of amoxicillin on bacterial communities in manured
soil. FEMS Microbiol. Ecol. 62, 290-302.

25. Heuer, H. & K. Smalla (2007) Horizontal gene transfer between bacteria. Environ. Biosafety
Res. 6, 3-13.

26. Heuer, H., Y.-N. Yin, Q.-Y. Xue, K. Smalla & J.-H. Guo (2007) Repeat domain diversity of
avrBs3/pthA-like genes in Ralstonia solanacearum strains and association with host
preferences in the field. Appl. Environ. Microbiol. 73, 4379-4384.

27. Smalla, K., M. Oros-Sichler, A. Milling, H. Heuer, S. Baumgarte, R. Becker, G. Neuber, S.

Kropf, A. Ulrich & C. C. Tebbe (2007) Bacterial diversity of soils assessed by DGGE, T-
RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: Do the different
methods provide similar results? J. Microbiol. Methods 69, 470–479.

28. Heuer, H. & K. Smalla (2007) Manure and sulfadiazine synergistically increased bacterial
antibiotic resistance in soil at least over two months. Environ. Microbiol. 9, 657-666.

29. Heuer, H., R. E. Fox & E. M. Top (2007) Frequent conjugative transfer accelerates
adaptation of a broad-host-range plasmid to an unfavourable Pseudomonas putida host.
FEMS Microbiol. Ecol. 59, 738-748.

30. Oros-Sichler, M., R. Costa, H. Heuer & K. Smalla (2007) Molecular fingerprinting
techniques to analyze soil microbial communities. In: Modern Soil Microbiology, 2nd edition
(J. D. van Elsas, J. K. Jansson, J. T. Trevors, eds.) CRC Press, Boca Raton, USA, Chap. 14,
pp. 355-386.

31. Kropf, S., A. Lux, M. Eszlinger, H. Heuer & K. Smalla (2006) Comparison of independent
samples of high-dimensional data by pairwise distance measures. Biom. J. 48, 1-12.

32. Smalla, K., A. S. Haines, K. Jones, E. Krögerrecklenfort, H. Heuer, M. Schloter, C. M.

Thomas (2006) Increased abundance of IncP-1 plasmids and mercury resistance genes in
mercury polluted river sediments - first discovery of IncP-1 plasmids with a complex mer
transposon as sole accessory element. Appl. Environ. Microbiol. 72, 7253-7259.

33. Smalla, K. & H. Heuer (2006) How to assess the abundance and diversity of mobile genetic
elements (MGE) in soil bacterial communities? In: Soil Biology, Vol. 8 - Nucleic acids and
proteins in soil (P. Nannipieri & K. Smalla, eds.), Springer-Verlag, Berlin, Heidelberg, pp.
313-330.

34. Nikolakopoulou, T. L., S. Egan, L. S. van Overbeek, G. Guillaume, H. Heuer, E. M.

Wellington, J. D. van Elsas, J. M. Collard, K. Smalla & A. D. Karagouni (2005) PCR
detection of oxytetracycline resistance genes otr(A) and otr(B) in tetracycline-resistant
Streptomycete isolates from diverse habitats. Curr. Microbiol. 51, 211-216.
35. Schlüter, A., H. Heuer, R. Szczepanowski, S. M. Poler, S. Schneiker, A. Pühler & E. M. Top
(2005) Plasmid pB8 is closely related to the prototype IncP-1β plasmid R751 but transfers
poorly to Escherichia coli and carries a new transposon encoding a small multidrug
resistance efflux protein. Plasmid 54, 135-148.

36. Heuer, H., R. Szczepanowski, S. Schneiker, A. Pühler, E. M. Top & A. Schlüter (2004) The
complete sequences of plasmids pB2 and pB3 provide evidence for a recent ancestor of the
IncP-1β group without any accessory genes. Microbiology - SGM 150, 3591-3599.

37. Kropf, S., H. Heuer, M. Grüning & K. Smalla (2004) Significance test for comparing
complex microbial community fingerprints using pairwise similarity measures. J. Microbiol.
Methods 57, 187-195.

38. Smalla, K., H. Heuer, A. Milling, M. Götz, M. Schloter, J. Lottmann & G. Berg (2004) Are
microbial communities affected by genetically modified plants? In: Aspects of Applied
Biology Vol. 74, GM crops – ecological dimensions (H. F. van Emden & A. J. Gray, eds.),
The Association of Applied Biologists, Wellesbourne, Warwick, UK.

39. Schönfeld, J., H. Heuer, J. D. van Elsas & K. Smalla (2003) Specific and sensitive detection
of Ralstonia solanacearum in soil on the basis of PCR amplification of fliC fragments. Appl.
Environ. Microbiol. 69, 7248–7256.

40. Schlüter, A., H. Heuer, R. Szczepanowski, L. J. Forney, C. M. Thomas, A. Pühler & E. M.

Top (2003) The 64,508 bp IncP-1β antibiotic multiresistance plasmid pB10 isolated from a
wastewater treatment plant provides evidence for recombination between members of
different branches of the IncP-1β group. Microbiology - SGM 149, 3139–3153.

41. Heim, S., M. Ferrer, H. Heuer, D. Regenhardt, M. Nimtz & K. N. Timmis (2003) Proteome
reference map of Pseudomonas putida strain KT2440 for genome expression profiling:
distinct responses of KT2440 and Pseudomonas aeruginosa strain PAO1 to iron deprivation
and a new form of superoxide dismutase. Environ. Microbiol. 5, 1257-1269.

42. Regenhardt, D., H. Heuer, S. Heim, D. U. Fernandez, C. Strömpl, E. R. B. Moore & K. N.

Timmis (2002) Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440.
Environ. Microbiol. 4, 912-915.

43. Overbeek L. S. van, E. M. H. Wellington, S. Egan, K. Smalla, H. Heuer, J.-M. Collard, G.

Guillaume, A. D. Karagouni, T. L. Nikolakopoulou & J. D. van Elsas (2002) Prevalence of
streptomycin-resistance genes in bacterial populations in European habitats. FEMS
Microbiol. Ecol. 42, 277-288.

44. Heuer, H., E. Krögerrecklenfort, S. Egan, L. van Overbeek, G. Guillaume, T. L.

Nikolakopoulou, E. M. H. Wellington, J. D. van Elsas, J.-M. Collard, A. D. Karagouni & K.
Smalla (2002) Gentamicin resistance genes in environmental bacteria: Prevalence and
transfer. FEMS Microbiol. Ecol. 42, 289-302.

45. Heuer, H., R. M. Kroppenstedt, J. Lottmann, G. Berg & K. Smalla (2002) Effects of T4
lysozyme release from transgenic potato roots on bacterial rhizosphere communities are
negligible relative to natural factors. Appl. Environ. Microbiol. 68, 1325-1335.
46. Smalla, K., G. Wieland, A. Buchner, A. Zock, J. Parzy, S. Kaiser, N. Roskot, H. Heuer & G.
Berg (2001). Bulk and rhizosphere soil bacterial communities studied by denaturing gradient
gel electrophoresis: Plant-dependent enrichment and seasonal shifts revealed. Appl. Environ.
Microbiol. 67, 4742-4751.

47. Gomes, N. C. M., H. Heuer, J. Schönfeld, R. Costa, L. Mendonca-Hagler & K. Smalla

(2001) Bacterial diversity of the rhizosphere of maize (Zea mays) grown in tropical soil
studied by temperature gradient gel electrophoresis. Plant Soil 232, 167-180.

48. Heuer, H., G. Wieland, J. Schönfeld, A. Schönwälder, N. C. M. Gomes & K. Smalla (2001)
Bacterial community profiling using DGGE or TGGE analysis. Environmental Molecular
Microbiology: Protocols and Applications (P. A. Rochelle, ed.), Horizon Scientific Press,
Norwich, UK, pp. 177-190.

49. Smalla, K., E. Krögerrecklenfort, H. Heuer, et al. (2000) PCR-based detection of mobile
genetic elements in total community DNA. Microbiology - SGM 146, 1256-1257.

50. Smalla, K., H. Heuer, A. Götz, D. Niemeyer, E. Krögerrecklenfort & E. Tietze (2000)
Exogenous isolation of antibiotic resistance plasmids from piggery manure slurries: a high
prevalence and diversity of IncQ-like plasmids revealed. Appl. Environ. Microbiol. 66,
4854-4862.

51. Lottmann, J., H. Heuer, J. de Vries, A. Mahn, K. Düring, W. Wackernagel, K. Smalla & G.
Berg (2000) Establishment of introduced antagonistic bacteria in the rhizosphere of
transgenic potatoes and their effect on the bacterial community. FEMS Microbiol. Ecol. 33,
41-49.

52. Lin, M., K. Smalla, H. Heuer & J. D. van Elsas (2000) Effect of an Alcaligenes faecalis
inoculant strain on bacterial communities in flooded soil microcosms planted with rice
seedlings. Appl. Soil Ecol. 15, 211-225.

53. De Vries, J., A. Mahn, K. Düring, I. Broer, J. Lottmann, G. Berg, H. Heuer, K. Smalla, I.
Arendholtz & W. Wackernagel (2000) Prüfung von Resistenz und umweltrelevanten
Auswirkungen beim Freilandanbau transgener T4-Lysozymkartoffeln. In: Biologische
Sicherheitsforschung bei Freilandversuchen mit transgenen Organismen und
anbaubegleitendes Monitoring (J. Schiemann, ed.), Jülich: Forschungszentrum,
Zentralbibliothek, pp. 49-64.

54. Smalla, K., F. Gebhard & H. Heuer (2000) Antibiotika-Resistenzgene als Marker in
gentechnisch veränderten Pflanzen – Gefahr durch horizontalen Gentransfer?
Nachrichtenblatt des Deutschen Pflanzenschutzdienstes 52, 62-68.

55. Lottmann, J., H. Heuer, K. Smalla & G. Berg (2000) Beneficial bacteria in the underground
organs of potato (Solanum tuberosum L.). In: Advances in Verticillium research and disease
management (Tjamos EC, Rowe C, Heale JB & Fravel DR, eds), APS Press, St. Paul,
Minnesota, USA, pp. 264-268.

56. Heuer, H., K. Hartung, G. Wieland, I. Kramer & K. Smalla (1999) Polynucleotide probes
that target a hypervariable region of 16S rRNA genes to identify bacterial isolates
corresponding to bands of community fingerprints. Appl. Environ. Microbiol.65, 1045-1049.
57. Lottmann, J., H. Heuer, K. Smalla & G. Berg (1999) Influence of transgenic T4-lysozyme-
producing potato plants on potentially beneficial plant-associated bacteria. FEMS Microbiol.
Ecol. 29, 365-377.

58. Brim, H., H. Heuer, E. Krögerrecklenfort, M. Mergeay & K. Smalla (1999) Characterization
of the bacterial community of a zinc polluted soil. Can. J. Microbiol. 45, 326-338.

59. Heuer, H. & K. Smalla (1999) Bacterial phyllosphere communities of Solanum tuberosum L.
and T4-lysozyme producing variants. FEMS Microbiol. Ecol. 28, 357-371.

60. Lottmann, J., H. Heuer, K. Smalla & G. Berg (1999) Characterization of antifungal bacteria
from the rhizosphere and geocaulosphere of transgenic T4-lysozyme-expressing potato
plants. Bulletin of the Polish Academy of Science 47, 77-84.

61. Dybas, M. J., M. Barcelona, S. Bezborodnikov, S. Davies, L. Forney, H. Heuer, O. Kawka,

T. Mayotte, L. Sepulveda-Torres, K. Smalla, M. Sneathen, J. Tiedje, T.Voice, D. C.
Wiggert, M. E. Witt & C. S. Criddle (1998) Pilot-scale evaluation of bioaugmentation for in-
situ remediation of a carbon tetrachloride-contaminated aquifer. Environ. Sci. & Technol. 32,
3598-3611.

62. Engelen, B., K. Meinken, F. von Wintzingerode, H. Heuer, H.-P. Malkomes & H. Backhaus
(1998) Monitoring impact of a pesticide treatment on bacterial soil communities by
metabolic and genetic fingerprinting in addition to conventional testing procedures. Appl.
Environ. Microbiol. 64, 2814-2821.

63. Smalla, K., U. Wachtendorf, H. Heuer, W.-T. Liu & L. Forney (1998) Analysis of BIOLOG
GN substrate utilization patterns by microbial communities. Appl. Environ. Microbiol. 64,
1220-1225.

64. Smalla, K. & H. Heuer (1998) Effekte transgener T4-Lysozym produzierender

Kartoffellinien auf Bakteriengemeinschaften der Rhizosphäre im Freilandversuch. In:
Freisetzungsbegleitende Sicherheitsforschung mit gentechnisch veränderten Pflanzen und
Mikroorganismen (J. Schiemann, ed.), Braunschweig, Jülich, BEO (Projektträger Biologie,
Energie, Umwelt des BMBF), pp. 81-90.

65. Glimm, E., H. Heuer, B. Engelen, K. Smalla & H. Backhaus (1997) Statistical comparisons
of community catabolic profiles. J. Microbiol. Methods 30, 71-80.

66. Heuer, H. & K. Smalla (1997) Evaluation of community level catabolic profiling using
BIOLOG GN microplates to study microbial community changes in potato phyllosphere. J.
Microbiol. Methods 30, 49-61.

67. Heuer, H., M. Krsek, P. Baker, K. Smalla & E. M. H. Wellington (1997) Analysis of
actinomycete communities by specific amplification of 16S rDNA and gel electrophoretic
separation in denaturing gradients. Appl. Environ. Microbiol. 63, 3233-3241.

68. Heuer, H. & K. Smalla (1997) Application of denaturing gradient gel electrophoresis and
temperature gradient gel electrophoresis for studying soil microbial communities. In:
Modern Soil Microbiology (J. D. van Elsas, E. M. H. Wellington, J. T. Trevors, eds.),
Marcel Dekker, New York, USA, pp. 353-373.
69. Heuer, H., K. Hartung, B. Engelen & K. Smalla (1995) Studies on microbial communities
associated with potato plants by Biolog and TGGE patterns. Mededelingen Faculteit
Landbouwkundige en Toegepaste Biol. Wetenschappen Univ. Gent 60(4b), 2639-2645.

70. Heuer, H. & G. Auling (1995) Möglichkeiten der Sicherheitsprüfung von gentechnisch
modifizierten Mikroorganismen (GEMMO) in Modell-Ökosystemen. Forschungsbericht
10802097, Texte 4/95, ISSN 0722-186X, Umweltbundesamt, Berlin.

71. Heuer, H., D. F. Dwyer, K. N. Timmis & I. Wagner-Döbler (1995) Efficacy in aquatic
microcosms of a genetically engineered Pseudomonad applicable for bioremediation.
Microb. Ecol. 29, 203-220.