The Diversity and Co-occurrence Patterns of N2-Fixing Communities in a CO2-Enriched Grassland Ecosystem

Abstract

Diazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems.

Biogeographic patterns of soil diazotrophic communities across six forests in the North America

“…The dominance of a few nifH OTUs was also previously observed in a grassland ecosystem, where the 15 most abundant OTUs accounted for 67.8% of the total captured nifH sequences in that ecosystem (Tu et al . ). Third, consistent with what has been observed for macrocommunities such as plant and animal communities, rainforests were found to have nifH OTU richness values twice that observed for temperate forest ecosystems.…”

Enhancing Non-symbiotic N2 Fixation in Agriculture

“…New research using molecular techniques will reveal the true diversity of diazotrophic bacteria in agricultural and natural ecosystems and their potential to be used as inoculants in agricultural systems. Additionally, co-occurrence network analysis using nifH sequence data indicated the presence of complex co-occurrence patterns in the free-living diazotrophs than that known in symbiotic diazotrophs [202]. Such novel insights in to the ecology of diazotrophs may lead to development of inoculant mixtures that promote overall N 2 fixation.…”

Distinct Network Interactions in Particle-Associated and Free-Living Bacterial Communities during a Microcystis aeruginosa Bloom in a Plateau Lake

“…The RMT-based approach is a widely used and robust tool for network construction and has been successfully used to construct various networks, including gene regulatory networks (Zhou et al, 2010; Lin et al, 2011, 2013), functional molecular ecological networks (Zhou et al, 2010) and phylogenetic molecular ecological networks (Zhou et al, 2011; Tu et al, 2016). To construct reliable co-occurrence ecological networks, the RMT-based network method was used (Deng et al, 2015), and only OTUs observed in at least 8 of the 12 samples were used for subsequent network analyses.…”

“…Culture-independent molecular technology has developed rapidly in recent years and has been acknowledged as a feasible approach to study complex microbial communities. Emerging high-throughput sequencing technologies can provide a comprehensive understanding of the specific microbial species that live and thrive in various environments (Logares et al, 2014), and network-based approaches have been successfully used to evaluate the influence of environmental disturbances on the whole community (Raes and Bork, 2008; Zhou et al, 2010) and analyze microbial interactions in diverse habitats, including marine (Wang Y. et al, 2015), soil (Tu et al, 2015), acid mine drainage (Kuang et al, 2016) and groundwater environments (Deng et al, 2015). However, relevant research on microbial interactions during algal blooms is still limited, especially for the relationship between algae and associated bacteria.…”