Molecular Ecology of nifH Genes and Transcripts Along a Chronosequence in Revegetated Areas of the Tengger Desert

Abstract

The colonization and succession of diazotrophs are essential for the development of organic soil layers in desert. We examined the succession of diazotrophs in the well-established revegetated areas representing a chronosequence of 0 year (control), 22 years (restored artificially since 1981), 57 years (restored artificially since 1956), and more than 100 years (restored naturally) to determine the community assembly and active expression of diazotrophs. The pyrosequencing data revealed that Alphaproteobacteria-like diazotrophs predominated in the topsoil of our mobile dune site, while cyanobacterial diazotrophs predominated in the revegetated sites. The cyanobacterial diazotrophs were primarily composed of the heterocystous genera Anabaena, Calothrix, Cylindrospermum, Nodularia, Nostoc, Trichormus, and Mastigocladus. Almost all the nifH sequences belonged to the Cyanobacteria phylum (all the relative abundance values >99.1 %) at transcript level and all the active cyanobacterial diazotrophs distributed in the families Nostocaceae and Rivulariaceae. The most dominant active cyanobacterial genus was Cylindrospermum in all the samples. The rank abundance and community analyses demonstrated that most of the diazotrophic diversity originated from the "rare" species, and all the DNA-based diazotrophic libraries were richer and more diverse than their RNA-based counterparts in the revegetated sites. Significant differences in the diazotrophic community and their active population composition were observed among the four research sites. Samples from the 1981-revegetating site (predominated by cyanobacterial crusts) showed the highest nitrogenase activity, followed by samples from the naturally revegetating site (predominated by lichen crusts), the 1956-revegetating site (predominated by moss crusts), and the mobile dune site (without crusts). Collectively, our data highlight the importance of nitrogen fixation by the primary successional desert topsoil and suggest that the N2-fixing cyanobacteria are the key diazotrophs to the nitrogen budget and the development of topsoil in desert, which is critical for the succession of the degraded terrestrial ecosystems.

Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs

“…rRNA-based studies [33,[48][49][50][51]. Here we directly tracked nifH-defined communities, because nifH gene may provide better insight into the diversity and composition of the communities that are capable of nitrogen fixation in an environment than those extrapolated from16S rRNA data.…”

Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils

“…Relationships between diazotroph communities and N fixation rates have been investigated in many terrestrial ecosystems, including temperate forest soils ( Rosch et al, 2002 ; Yeager et al, 2005 ), wetlands ( Moseman et al, 2009 ), desert systems ( Yeager et al, 2004 ; Wang et al, 2016 ), grasslands ( Tu et al, 2016 ), and agricultural lands ( Pereira e Silva et al, 2013 ). Despite the fact that tropical forest ecosystems maintain considerable biological N fixation to balance the large potential N losses, this process and the microbial community involved in it remain poorly investigated in these soils ( Cusack et al, 2009 ; Reed et al, 2010 ; Mirza et al, 2014 ).…”

Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs

“…rRNA-based studies [33,[48][49][50][51]. However, our nifH sequence analysis revealed a higher alphadiversity in the active (based on RNA) than in the total (based on DNA) communities of PADs (Fig.…”