Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

Biological nitrogen fixation is a major factor contributing to microbial primary productivity in the open ocean. The current view depicts a few cyanobacterial diazotrophs as the most relevant marine nitrogen fixers, whereas heterotrophic diazotrophs are more diverse and considered to have lower impacts on the nitrogen balance. Here, we used 891 Tara Oceans metagenomes to create a manually curated, non-redundant genomic database corresponding to free-living, as well as filamentous, colony-forming, particle-attached and symbiotic bacterial and archaeal populations occurring in the surface of five oceans and two seas. Notably, the database provided the genomic content of eight cyanobacterial diazotrophs including Trichodesmium populations and a newly discovered population similar to Richelia, as well as 40 heterotrophic bacterial diazotrophs organized into three main functional groups that considerably expand the known diversity of abundant marine nitrogen fixers compared to previous genomic surveys. Critically, these 48 populations may account for more than 90% of cells containing known nifH genes and occurring in the sunlit ocean, suggesting that the genomic characterization of the most abundant marine diazotrophs may be nearing completion. The newly identified heterotrophic bacterial diazotrophs are widespread, express their nifH genes in situ, and co-occur under nitrate-depleted conditions in large size fractions where they might form aggregates providing the low-oxygen microenvironments required for nitrogen fixation. Most significantly, we found heterotrophic bacterial diazotrophs to be more abundant than cyanobacterial diazotrophs in most metagenomes from the open oceans and seas. This large-scale environmental genomic survey emphasizes the considerable potential of heterotrophs in the marine nitrogen balance.

Diversity and distribution of nitrogen fixation genes in the oxygen minimum zones of the world oceans

Diversity and community composition of nitrogen (N) fixing microbes in the three main oxygen minimum zones (OMZs) of the world ocean were investigated using operational taxonomic unit (OTU) analysis of nifH clone libraries. Representatives of three of the four main clusters of nifH genes were detected. Cluster I sequences were most diverse in the surface waters, and the most abundant OTUs were affiliated with Alpha- and Gammaproteobacteria. Cluster II, III, and IV assemblages were most diverse at oxygen-depleted depths, and none of the sequences were closely related to sequences from cultivated organisms. The OTUs were biogeographically distinct for the most part – there was little overlap among regions, between depths, or between cDNA and DNA. In this study of all three OMZ regions, as well as from the few other published reports from individual OMZ sites, the dominance of a few OTUs was commonly observed. This pattern suggests the dynamic response of the components of the overall diverse assemblage to variable environmental conditions. Community composition in most samples was not clearly explained by environmental factors, but the most abundant OTUs were differentially correlated with the obvious variables, temperature, salinity, oxygen, and nitrite concentrations. Only a few cyanobacterial sequences were detected. The prevalence and diversity of microbes that harbor nifH genes in the OMZ regions, where low rates of N fixation are reported, remains an enigma.

Diversity and distribution of Nitrogen Fixation Genes in the Oxygen Minimum Zones of the World Oceans

Diversity and community composition of nitrogen fixing microbes in the three main oxygen minimum zones (OMZs) of the world ocean were investigated using operational taxonomic unit (OTU) analysis of nifH clone libraries. Representatives of the all four main clusters of nifH genes were detected. Cluster I sequences were most diverse in the surface waters and the most abundant OTUs were affiliated with Alpha- and Gammaproteobacteria. Cluster II, III, IV assemblages were most diverse at oxygen depleted depths and none of the sequences were closely related to sequences from cultivated organisms. The OTUs were biogeographically distinct for the most part – there was little overlap among regions, between depths or between cDNA and DNA. Only a few cyanobacterial sequences were detected. The prevalence and diversity of microbes that harbour nifH genes in the OMZ regions, where low rates of N fixation are reported, remains an enigma.

Changes in Acetylene Reduction Activities and nifH Genes Associated with Field-Grown Sweet Potatoes with Different Nursery Farmers and Cultivars

Sweet potato cultivars obtained from different nursery farmers were cultivated in an experimental field from seedling-stage to harvest, and the acetylene reduction activity (ARA) of different parts of the plant as well as the nifH genes associated with the sweet potatoes were examined. The relationship between these parameters and the plant weights, nitrogen contents, and natural abundance of 15N was also considered. The highest ARA was detected in the tubers and in September. Fragments of a single type of nitrogenase reductase gene (nifH) were amplified, and most of them had similarities with those of Enterobacteriaceae in γ-Proteobacteria. In sweet potatoes from one nursery farm, Dickeya nifH was predominantly detected in all of the cultivars throughout cultivation. In sweet potatoes from another farm, on the other hand, a transition to Klebsiella and Phytobacter nifH was observed after the seedling stage. The N2-fixing ability contributed to plant growth, and competition occurred between autochthonous and allochthonous bacterial communities in sweet potatoes.

Genetic diversity and symbiotic efficiency difference of endophytic rhizobia of Medicago sativa

Research on rhizobium diversity has paved the way for diversification of rhizobial germplasm resources. Seventy-three endophytic bacterial isolates were collected from seven tissues of five alfalfa cultivars in three geographic locations in Gansu, China. Restriction fragment length polymorphism (RFLP) fingerprinting of 16S rRNA and analysis of concatenated sequence of three housekeeping genes (atpD, glnII, and recA) and two symbiotic genes (nodC and nifH) were used for strain identification. Results showed that the endophytic strains were genetically diverse at different taxonomic levels, and Ensifer meliloti (31) and Agrobacterium radiobacter (12) are common Medicago sativa endophytic bacteria in Gansu, China. The nifH genes (97%–98% sequence identity) of E. meliloti strains were more diverse than the nodC genes (99%–100% sequence identity), even though the strains evolved from a common ancestor. The degree of dispersion of symbiotic phenotypes of E. meliloti strains on M. sativa ‘Gannong No. 3’, ‘Gannong No. 9’, and ‘Qingshui’ was much less than that on M. sativa ‘Longzhong’ and ‘WL168HQ’. This suggested that the symbiotic efficiency of E. meliloti strains on the former three alfalfa cultivars was similar but on the latter two was discrepant. Their symbiotic efficiency differed primarily according to alfalfa cultivars and, to a lesser extent, to the tested strains, indicating the difference in the sensitivity of different alfalfa cultivars to rhizobial strains.