Pyrosequencing Investigation into the Bacterial Community in Permafrost Soils along the China-Russia Crude Oil Pipeline (CRCOP)

Abstract

The China-Russia Crude Oil Pipeline (CRCOP) goes through 441 km permafrost soils in northeastern China. The bioremediation in case of oil spills is a major concern. So far, little is known about the indigenous bacteria inhabiting in the permafrost soils along the pipeline. A pilot 454 pyrosequencing analysis on the communities from four selected sites which possess high environment risk along the CRCOP is herein presented. The results reveal an immense bacterial diversity than previously anticipated. A total of 14448 OTUs with 84834 reads are identified, which could be assigned into 39 different phyla, and 223 families or 386 genera. Only five phyla sustain a mean OTU abundance more than 5% in all the samples, but they altogether account for 85.08% of total reads. Proteobacteria accounts for 41.65% of the total OTUs or 45% of the reads across all samples, and its proportion generally increases with soil depth, but OTUs numerically decline. Among Proteobacteria, the abundance of Beta-, Alpha-, Delta- and Gamma- subdivisions average to 38.7% (2331 OTUs), 37.5% (2257 OTUs), 10.35% (616 OTUs), and 6.21% (374 OTUs), respectively. Acidobacteria (esp. Acidobacteriaceae), Actinobacteria (esp. Intrasporangiaceae), Bacteroidetes (esp. Sphingobacteria and Flavobacteria) and Chloroflexi (esp. Anaerolineaceae) are also very common, accounting for 8.56% (1237 OTUs), 7.86% (1136 OTUs); 7.35% (1063 OTUs) and 8.27% (1195 OTUs) of total libraries, respectively. The ordination analysis indicates that bacteria communities in the upper active layer cluster together (similar), while bacterial consortia from the lower active layer and permafrost table scatter (less similar). The abundance of Rhodococcus (12 OTUs), Pseudomonas (71 OTUs) and Sphingomonas (87 OTUs) is even less (<0.01%). This effort to profile the background diversity may set the first stage for better evaluating the bacterial dynamics in response to accidental oil spills.

A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities

“…The available nitrogen showed a positive correlation to Bacteroidetes, Planctomycetes, Firmicutes, and Crenarchaeota, while it had the negative correlation to Proteobacteria and Gemmatimonadetes. The most dominant bacteria in the greenhouse-based vegetable land were Proteobacteria, which was in agreement with a summary report for several soils [29]. The members of Proteobacteria cover enormous morphological and metabolic diversity, playing a crucial role in the global carbon, nitrogen and sulphur cycles [30].…”

“…Among Proteobacteria, the relative abundance of Gamma-, Alpha-, Beta-, and Delta-subdivisions averaged to 38.73 % (2489 OTUs), 26.51 % (1745 OTUs), 21.23 % (1398 OTUs), and 13.42 % (883 OTUs), respectively. However, the Epsilonproteobacteria only accounted for 0.002 % OTUs of the total OTUs, which was a very small proportion compared with other reports [29]. The second predominant phylum of Actinobacteria showed an obviously increasing trend with the elevated application of N fertilizer.…”

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

“…After hydrocarbon pollution, bacteria from several genera, including Gordonia and Rhodococcus (Actinobacteria), Sphingomonas, Acinetobacter, and Pseudomonas (Proteobacteria), and Bacillus and Exiguobacterium (Firmicutes) are usually enriched (5)(6)(7)(8). However, the magnitude and dynamics of microbial community shifts are dependent on the environment (e.g., soil type, freshwater, and seawater), pollution time, hydrocarbon composition (e.g., different crude distillates and specific hydrocarbon), and remediation treatment (9)(10)(11)(12).…”

Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation

“…This observation contradicts many previous investigations in which Proteobacteria were frequently identified as the most abundant phylum in oil-contaminated environments. For instance, Proteobacteria was identified as the most dominant phylum in Algerian oilfield injection waters (Lenchi et al 2013), an oilcontaminated mangrove (Dos Santos et al 2011), and permafrost soils along the China-Russia crude oil pipeline (Yang et al 2012). In this study, Proteobacteria exhibited a relatively low relative abundance in some samples, including sites CQ5, JS1, JS2, JS4, XJ6, and XJ7.…”

“…Bacterial communities were also investigated in permafrost soils along the China-Russia crude oil pipeline by pyrosequencing. The results revealed an immensely higher microbial diversity than anticipated (Yang et al 2012). These pyrosequencing-based studies demonstrated that highthroughput sequencing provide a more complete picture of indigenous microbial communities than traditional molecular techniques.…”