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

Al-Awadhi, Husain; Dashti, Narjis; Khanafer, Majida; Al-Mailem, Dina; Ali, Nidaa; Radwan, Samir

doi:10.1186/2193-1801-2-369

SpringerPlus

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

*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).
Genera that were revealed by both approaches are in bold.

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