The Nitrogen-Cycling Network of Bacterial Symbionts in the Sponge Spheciospongia vesparium

The microbes associated with sponges play important roles in the nitrogen cycle of the coral reefs ecosystem,e.g.,nitrification,denitrification,and nitrogen fixation.However,the whole nitrogen-cycling network has remained incomplete in any individual sponge holobiont.In this study,454 pyrosequencing of the 16S rRNA genes revealed that the sponge Spheciospongia vesparium from the South China Sea has a unique bacterial community(including 12 bacterial phyla),dominated particularly by the genus Shewanella(order Alteromonadales).A total of 10 functional genes,nifH,amoA,narG,napA,nirK,norB,nosZ,ureC,nrfA,and gltB,were detected in the microbiome of the sponge S.vesparium by gene-targeted analysis,revealing an almost complete nitrogen-cycling network in this sponge.Particularly,bacterial urea utilization and the whole denitrification pathway were highlighted.MEGAN analysis suggests that Proteobacteria(e.g.,Shewanella)and Bacteroidetes(e.g.,Bizionia)are probably involved in the nitrogen cycle in the sponge S.vesparium.

Nitrogen-cycling microbial community functional potential and enzyme activities in cultured biofilms with response to inorganic nitrogen availability

Biofilms mediate crucial biochemical processes in aquatic ecosystems. It was hypothesized that eutrophication may promote the growth of biofilms, resulting in larger numbers of functional genes. However, the metabolic activity and the roles of biofilms in N cycling will be affected by ambient inorganic nitrogen availability, not by the abundance of functional genes. Biofilms were cultured either with replete inorganic nitrogen(N-rep) or without exogenous inorganic nitrogen supply(N-def) in a flow incubator, and the N-cycling gene abundances(nifH, N_2 fixation; amoA, ammonia oxidation, archaea and bacteria; nirS and nirK, denitrification) and enzyme activities(nitrogenase and nitrate reductase) were analyzed. The results showed that, comparing the N-def and N-rep biofilms, the former contained lower nifH gene abundance, but higher nitrogenase activity(NA), while the latter contained higher nifH gene abundance, but lower NA. Different patterns of NA diel variations corresponded to the dynamic microbial community composition and different stages of biofilm colonization. Ammonia oxidizing bacteria(AOB), detected only in N-def biofilms, were responsible for nitrification in biofilms. N-rep biofilms contained high nirS and nirK gene abundance and high denitrification enzyme activity, but N-def biofilms contained significantly lower denitrification gene abundance and activity. In general,the strong N_2 fixation in N-def biofilms and strong denitrification in N-rep biofilms assured the balance of aquatic ecosystems. The results suggested that evaluation of the functional processes of N cycling should not only focus on genetic potential, but also on the physiological activity of biofilms.

Impacts of wastewater sludge amendments in restoring nitrogen cycle in p-nitrophenol contaminated soil

The possible impacts on nitrogen-cycle in a p-nitrophenol （PNP） polluted soil and the effectiveness of wastewater sludge amendments in restoring nitrification potential and urease activity were evaluated by an incubation study. The results indicated that PNP at 250 mg/kg soil inhibited urease activity, nitrification potential, arginine ammonification rate and heterotrophic bacteria counts to some extents. After exposure to PNP, the nitrification potential of the tested soil was dramatically reduced to zero over a period of 30 days. Based on the findings, nitrification potential was postulated as a simple biochemical indicator for PNP pollution in soils. Nitrogen-cycling processes in soils responded positively to the applications of wastewater sludges. A sludge application rate of 200 tons/ha was sufficient for successful biostimulation of these nitrogen processes. The microbial activities in sludge-amended, heavy PNP-polluted soils seemed to recover after 30–45 days, indicating the effectiveness of sludge as a useful soil amendment.

Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization

Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation.Herein,rhizospheric and bulk soils were collected from five developmental stages of soybean,which grew in soils receiving 16-year nitrogen inputs.Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR,respectively.The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions.We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure,while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes.Temporal variations in bacterial abundances increased in bulk soils,especially at the stage of soybean branching,which helps to infer underlying negative interspecies interactions.Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere,respectively.Furthermore,the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development,which may help to explain the linkages between population dynamics and functions.Overall,these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.