Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia

Abstract

In this study, the combination of culture enrichments and molecular tools was used to identify bacterial guilds, plasmids and functional genes potentially important in the process of petroleum hydrocarbon (PH) decontamination in mangrove microniches (rhizospheres and bulk sediment). In addition, we aimed to recover PHdegrading consortia (PHDC) for future use in remediation strategies. The PHDC were enriched with petroleum from rhizosphere and bulk sediment samples taken from a mangrove chronically polluted with oil hydrocarbons. Southern blot hybridization (SBH) assays of PCR amplicons from environmental DNA before enrichments resulted in weak positive signals for the functional gene types targeted, suggesting that PH-degrading genotypes and plasmids were in low abundance in the rhizosphere and bulk sediments. However, after enrichment, these genes were detected and strong microniche-dependent differences in the abundance and composition of hydrocarbonoclastic bacterial populations, plasmids (IncP-1a, IncP1b, IncP-7 and IncP-9) and functional genes (naphthalene, extradiol and intradiol dioxygenases) were revealed by in-depth molecular analyses [PCR-denaturing gradient gel electrophoresis and hybridization (SBH and microarray)]. Our results suggest that, despite the low abundance of PH-degrading genes and plasmids in the environmental samples, the original bacterial composition of the mangrove microniches determined the structural and functional diversity of the PHDC enriched.

Bacterial Diversity in an Amazonian Mangrove Ecosystem

“…The represented bacterial groups are Proteobacteria, Bacterioidetes, Actinobacteria, Acidobacteria, Firmicutes, Chloroflexi, Spirochaetes, Cyanobacteria, and unclassified bacteria (Figures 5 and 6). These phyla are relatively common in the mangrove systems of southeastern Brazil (Almeida et al, 2009;Gomes et al, 2010;Santos et al, 2011;Silveira et al, 2011) and in other tropical and subtropical countries, such as India, China, Australia, and the United States (Zhang et al, 2008;Zhou et al, 2009), both aquatic and sedimentary communities Vieira et al, 2008).…”

“…With the exception of a few recent studies, little is known about the diversity and ecological function of the bacterial communities found in mangrove ecosystems (Hewson & Fuhrman, 2004;Zhang et al, 2008;Zhou et al, 2009;Gomes et al, 2010;Santos et al, 2011;Silveira et al, 2011). The present study was conducted to analyze the diversity and composition of the bacterial communities of a mangrove lake of Bragança-Pa in the eastern Amazon region.…”

Host range diversification within the IncP-1 plasmid group

“…Currently, it is recognized that the IncP-1 plasmids are ubiquitous in environmental bacteria residing in soil, sewage, marine sediments and manure (Dahlberg et al, 1997;Schlüter et al, 2007;Binh et al, 2008;Bahl et al, 2009;Gomes et al, 2010;. IncP-1 plasmids are generally considered to have a broad host range because representative plasmids of this group are able to transfer and replicate in hosts belonging to three proteobacterial subclasses, namely Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria (Schmidhauser & Helinski, 1985;De Gelder et al, 2005;Shintani et al, 2010;Yano et al, 2012).…”

Denaturing Gradient Gel Electrophoresis and Barcoded Pyrosequencing Reveal Unprecedented Archaeal Diversity in Mangrove Sediment and Rhizosphere Samples

“…Microorganisms in turn are essential for plant growth and organic matter turnover, and they use plant root exudates as a nutrient source (39,70). Little is known, however, about the impact of mangrove plants on microbial rhizosphere communities (31,32,72). The mangrove environment differs radically in many ways from typical terrestrial environments due to regular inundation with seawater and sometimes freshwater flooding (40).…”

“…The combination of PCR, more classical molecular tools, and pyrosequencing allows us to study microorganisms at an unprecedented level of detail (22,63,64). In previous studies, we applied classical molecular tools and in-depth functional microarray (32) and structural barcoded pyrosequencing (31) analyses to study the structure and functions of bacterial communities inhabiting mangrove roots. These studies suggest an important ecological role of mangrove plants in the process of selective enhancement of degrading genes and functional bacterial guilds in their complex root systems.…”