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Table 3 Comparison between the composition of hydrocarbon-utilizing bacterial communities in seawater and desert soil-samples determined by the culture-based method versus that determined by a modern molecular approach

From: Bias problems in culture-independent analysis of environmental bacterial communities: a representative study on hydrocarbonoclastic bacteria

Sampling sites Culture-based analysis (using a mineral medium with oil vapor as sole source of carbon and energy, detailed results in Al-Awadhi et al.2012)   Combined DGGE and band amplification analysis
  Total number of species Affiliated to the hydrocarbon-utilizing genera: Total number of DGGE bands Affiliated to the genera (hydrocarbon-utilizers are designated with the pertinent reference numbers):
Seawater
Doha 17 Psychrobacter, Oceanobacillus, Vibrio, Agarivorans, Alteromonas , Marinobacter, Stappia, Pseudoalteromonas , Microbacterium, Marinomonas, Nesiotobacter, Mycobacterium 18 Alteromonas , Candidatus 1 , Marinobacterium, Phaeobacter, Thalassobius 2 , Thalassolituus 3
Sharq 5 Alcanivorax, Stappia, Thalassospira, Nitratireductor 20 Alteromonas , Candidatus, Marinobacterium, Phaeobacter, Pseudoalteromonas , Thalassobius, Thalassolituus
Salmiyah 15 Alteromonas , Echinicola, Klebsiella, Alcanivorax, Marinomonas, Gordonia, Pseudomonas, Rhodococcus, Microbacterium, Vibrio, Marinobacter, Kocuria 17 Alteromonas , Candidatus, Marinobacterium, Phaeobacter, Pseudoalteromonas , Thalassobius, Thalassolituus
Fahaheel 9 Pseudomonas, Dietzia, Shewanella, Arthrobacter, Pseudoalteromonas , Acinetobacter, Alteromonas 20 Alteromonas , Candidatus, Marinobacterium, Phaeobacter, Pseudoalteromonas , Thalassobius, Thalassolituus
Az Zour 4 Alcanivorax, Cobetia, Pseudoalteromonas 15 Alteromonas , Candidatus, Marinobacterium, Phaeobacter, Thalassobius, Thalassolituus
Al Khiran 6 Alcanivorax, Alteromonas , Pseudoalteromonas , Cobetia 15 Alteromonas , Candidatus, Marinobacterium, Phaeobacter*, Pseudoalteromonas , Thalassobius, Thalassolituus
Desert soil
Al Abdali 7 Arthrobacter, Dietzia, Microbacterium, Streptomyces, Agrococcus 30 Bacillus, Planomicrobium 4 , Ralstonia 5 , Salinimicrobium 6 , Segetibacter 7
Sabiyah 8 Microbacterium, Dietzia, Pseudomonas, Bordetella, Roseomonas, 36 Acinetobacter, Bacillus, Burkholderia 8 , Geobacillus 9 , Halomonas 10 , Naxibacter 11 , Planomicrobium, Ralstonia
Kadma 4 Pseudomonas, Sphingomonas 47 Acinetobacter, Bacillus, Burkholderia, Curvibacter 5 , Sediminibacterium * , Halomonas, Naxibacter, Planomicrobium, Pontibacter 12 , Ralstonia, Segetibacter
Ahmadi 6 Cellulomonas, Pseudomonas, Arthrobacter, Sphingomonas 30 Acinetobacter, Bacillus, Burkholderia, Curvibacter, Naxibacter, Planomicrobium, Pontibacteter
Ash Shua’yba 12 Mycobacterium, Nocardia, Rhodococcus, Streptomyces, Bacillus 17 Bacillus, Planomicrobium, Pontibacter
Al Wafra 8 Kocuria, Streptomyces, Agrobacterium, Acinetobacter , Pseudomonas, Brevundimonas, Sphingobium 17 Acinetobacter , Bacillus , Halomonas, Naxibacter
  1. *No references were found on the hydrocarbon-degradation potential of Sediminibacterium or Phaeobacter. The superscript numbers are the reference numbers in the list recording hydrocarbonoclastic activity among species belonging to the given genera (1, Prabagaran et al. 2007;2, Teramoto et al. Teramoto et al. 2009; 3, Yakimov et al. Yakimov et al. 2004; 4, Yakimov et al. Yakimov et al. 2007; 5, Zhu et al. Zhu et al. 2010; 6, Yergeau et al. Yergeau et al. 2012; 7, Larentis et al. Larentis et al. 2009; 8; Morawski et al. 1997; 9, Arun et al. Arun et al. 2011; 10, Wang et al. Wang et al. 2007; 11, Kleinsteuber et al. Kleinsteuber et al. 2006; 12, Wan et al. Wan et al. 2011).
  2. Genera that were revealed by both approaches are in bold.