Molecular Characterization of the Archaeal Community in an Amazonian Wetland Soil and Culture-Dependent Isolation of Methanogenic Archaea

Abstract

Tropical wetlands are the major natural source of methane released into the atmosphere, producing about 60% of all natural emissions. The great wetland areas of the Amazon basin are the largest source of methane in this region, contributing an estimated 5% of the total emissions from the world's flooded areas. However, despite the important role that methanogenic archaea play in these environments, there have been few studies on the composition of their archaeal communities. In this survey, four 16S rRNA archaeal clone libraries from different depths were constructed to examine the archaeal community in an Amazon wetland soil. A total of 599 clones were used to perform diversity and phylogenetic analyses. A broad, diverse archaeal community was found at the site, with the diversity decreasing as the depth increased (Shannon index range: 2.40-1.94). Phylogenetic analysis revealed sequences belonging to two archaeal phyla, with 65% classified as Crenarchaeota and 35% classified as Euryarchaeota. Within the Euryarchaeota group, most sequences were clustered into the Methanococci and Methanomicrobia classes, two groups of methanogens. Based on the abundance of methanogenic organisms, culture-dependent isolation was used to isolate these organisms. To enhance the growth of methanogenic archaea, a modified atmosphere (H 2 :CO 2 = 80:20) was established combined with an anoxic environment for 18 months. Among the isolates, OPEN ACCESSDiversity 2010, 2 1027 the genera Methanosarcina and Methanobacterium were detected throughout the anaerobic in vitro cultivation, indicating a possible role for these organisms in methane production. In conclusion, these exploratory molecular and culture-dependent approaches enhance our understanding of the archaeal community and methanogenic archaea living in wetland soils of the eastern Amazon and their role in methane production.

Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil

“…This variation of nutrients may explain the significant difference between 10 and 40 cm depths. Along with our findings, several studies have also demonstrated that the microbial structure responds to different depths in soils [39][40][41][42]. Arrows indicate correlation between the chemical parameters and sample community structure.…”

Genetic and Functional Diversities of Microbial Communities in Amazonian Soils Under Different Land Uses and Cultivation

“…In Eastern Amazon wetland soils Archaeal community was characterized by 16S rRNA gene libraries and by isolation of methanogenic Archaea (Pazinato et al, 2010). Archaeal diversity decreased with depth and the most of sequences belonging to Crenarchaeota, Methanosarcina and Metahnobacteriam genera were isolated from the sites.…”

Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

“…In this context, Brazil has been slowing down deforestation by trying to make better use of already cleared land (Tollefson, 2010). However, the establishment of policies for the sustainable use of land in the Amazon region requires considering not only the diversity of flora and fauna but also the aspects of microbial ecology and biogeochemistry represented in this region as well (Piccolo et al, 1994;Borneman & Triplett, 1997;Moraes et al, 2002;Cenciani et al, 2009;Chaves et al, 2009;Jesus et al, 2009;O'Neill et al, 2009;Pazinato et al, 2010).…”