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Research on the micro-ecology of nitrogen cycling bacteria in sediments of Lake Taihu

YUE Dong-Mei,TIAN Meng,SONG Wei,XIAO Lin,YANG Liu-Yan,

微生物学通报 , 2011,
Abstract: The amount and distribution of nitrogen cycling bacteria in sediments of Meiliang Bay and Gonghu Bay of Lake Taihu were studied by FISH analysis. The amount of archaea decreased along the sediment depth, however, its ratio to total microorganisms increased. The amount of Ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in Meiliang Bay was higher than that in Gonghu Bay although the amount of both bacteria decreased along the sediment depth. Our results indicated that the existence of aquatic macrophyte in Gonghu Bay might affiliate transformation of nitrogen. Crenarchaeota was universally detected in surface sediments and overnumbered AOB, which indicated that it might play an important role in nitrogen cycling.
Response of the Abundance of Key Soil Microbial Nitrogen-Cycling Genes to Multi-Factorial Global Changes  [PDF]
Ximei Zhang, Wei Liu, Michael Schloter, Guangming Zhang, Quansheng Chen, Jianhui Huang, Linghao Li, James J. Elser, Xingguo Han
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0076500
Abstract: Multiple co-occurring environmental changes are affecting soil nitrogen cycling processes, which are mainly mediated by microbes. While it is likely that various nitrogen-cycling functional groups will respond differently to such environmental changes, very little is known about their relative responsiveness. Here we conducted four long-term experiments in a steppe ecosystem by removing plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and manipulating some of their combinations. We quantified the abundance of seven nitrogen-cycling genes, including those for fixation (nifH), mineralization (chiA), nitrification (amoA of ammonia-oxidizing bacteria (AOB) or archaea (AOA)), and denitrification (nirS, nirK and nosZ). First, for each gene, we compared its sensitivities to different environmental changes and found that the abundances of various genes were sensitive to distinct and different factors. Overall, the abundances of nearly all genes were sensitive to nitrogen enrichment. In addition, the abundances of the chiA and nosZ genes were sensitive to plant functional group removal, the AOB-amoA gene abundance to phosphorus enrichment when nitrogen was added simultaneously, and the nirS and nirK gene abundances responded to watering. Second, for each single- or multi-factorial environmental change, we compared the sensitivities of the abundances of different genes and found that different environmental changes primarily affected different gene abundances. Overall, AOB-amoA gene abundance was most responsive, followed by the two denitrifying genes nosZ and nirS, while the other genes were less sensitive. These results provide, for the first time, systematic insights into how the abundance of each type of nitrogen-cycling gene and the equilibrium state of all these nitrogen-cycling gene abundances would shift under each single- or multi-factorial global change.
Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California  [PDF]
J. M. Beman,Victoria J. Bertics
Frontiers in Microbiology , 2012, DOI: 10.3389/fmicb.2012.00263
Abstract: Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation–reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation) are active and actively coupled to one another – yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O2, N H 4 + , and N O 3 ? ) profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock (BR) and within Catalina Harbor (CH), oxygen penetration (0.24–0.5 cm depth) and the abundance of amoA genes (up to 9.30 × 107 genes g–1) varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in BR cores, and CH cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer) demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated CH sediments, where it may be carried out by either or both ammonia-oxidizing archaea and bacteria.
The role of continental shelves in nitrogen and carbon cycling  [PDF]
K. Fennel
Ocean Science Discussions (OSD) , 2010,
Abstract: Continental shelves play a key role in the cycling of nitrogen and carbon. Here the physical transport and biogeochemical transformation processes affecting the fluxes into and out of continental shelf systems are reviewed, and their role in the global cycling of both elements is discussed. Uncertainties in observation-based estimates of nitrogen and carbon fluxes mostly result from uncertainties in the shelf-open ocean exchange of organic and inorganic matter, which is hard to quantify based on observations alone, but can be inferred from biogeochemical models. Model-based nitrogen and carbon budgets are presented for the Northwestern North Atlantic continental shelf. Results indicate that shelves are an important sink for fixed nitrogen and a source of alkalinity, but are not much more efficient in exporting organic carbon to the deep ocean than the adjacent open ocean for the shelf region considered.
Microbial nitrogen cycling on the Greenland Ice Sheet
J. Telling, M. Stibal, A. M. Anesio, M. Tranter, I. Nias, J. Cook, C. Bellas, G. Lis, J. L. Wadham, A. Sole, P. Nienow,A. Hodson
Biogeosciences (BG) & Discussions (BGD) , 2012,
Abstract: Nitrogen inputs and microbial nitrogen cycling were investigated along a 79 km transect into the Greenland Ice Sheet (GrIS) during the main ablation season in summer 2010. The depletion of dissolved nitrate and production of ammonium (relative to icemelt) in cryoconite holes on Leverett Glacier, within 7.5 km of the ice sheet margin, suggested microbial uptake and ammonification respectively. Positive in situ acetylene assays indicated nitrogen fixation both in a debris-rich 100 m marginal zone and up to 5.7 km upslope on Leverett Glacier (with rates up to 16.3 μmoles C2H4 m 2 day 1). No positive acetylene assays were detected > 5.7 km into the ablation zone of the ice sheet. Potential nitrogen fixation only occurred when concentrations of dissolved and sediment-bound inorganic nitrogen were undetectable. Estimates of nitrogen fluxes onto the transect suggest that nitrogen fixation is likely of minor importance to the overall nitrogen budget of Leverett Glacier and of negligible importance to the nitrogen budget on the main ice sheet itself. Nitrogen fixation is however potentially important as a source of nitrogen to microbial communities in the debris-rich marginal zone close to the terminus of the glacier, where nitrogen fixation may aid the colonization of subglacial and moraine-derived debris.
Microbial nitrogen cycling on the Greenland Ice Sheet  [PDF]
J. Telling,M. Stibal,A. M. Anesio,M. Tranter
Biogeosciences Discussions , 2011, DOI: 10.5194/bgd-8-10423-2011
Abstract: Microbial nitrogen cycling was investigated along a 79 km transect into the Greenland Ice Sheet (GrIS) in early August 2010. The depletion of dissolved nitrate and production of ammonium (relative to icemelt) in cryoconite holes within 7.5 km of the ice sheet margin suggested microbial uptake and ammonification respectively. Nitrogen fixation (<4.2 μmoles C2H4 m 2 day 1 to 16.3 μmoles C2H4 m 2 day 1) was active in some cryoconite holes at sites up to 5.7 km from the ice sheet margin, with nitrogen fixation inversely correlated to concentrations of inorganic nitrogen. There may be the potential for the zone of nitrogen fixation to progressively extend further into the interior of the GrIS as the melt season progresses as reserves of available nitrogen are depleted. Estimated annual inputs of nitrogen from nitrogen fixation along the transect were at least two orders of magnitude lower than inputs from precipitation, with the exception of a 100 m long marginal debris-rich zone where nitrogen fixation could potentially equal or exceed that of precipitation. The average estimated contribution of nitrogen fixation to the nitrogen demand of net microbial growth at sites along the transect ranged from 0% to 17.5%.
Metagenomic Profiling of a Microbial Assemblage Associated with the California Mussel: A Node in Networks of Carbon and Nitrogen Cycling  [PDF]
Catherine A. Pfister,Folker Meyer,Dionysios A. Antonopoulos
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010518
Abstract: Mussels are conspicuous and often abundant members of rocky shores and may constitute an important site for the nitrogen cycle due to their feeding and excretion activities. We used shotgun metagenomics of the microbial community associated with the surface of mussels (Mytilus californianus) on Tatoosh Island in Washington state to test whether there is a nitrogen-based microbial assemblage associated with mussels. Analyses of both tidepool mussels and those on emergent benches revealed a diverse community of Bacteria and Archaea with approximately 31 million bp from 6 mussels in each habitat. Using MG-RAST, between 22.5–25.6% were identifiable using the SEED non-redundant database for proteins. Of those fragments that were identifiable through MG-RAST, the composition was dominated by Cyanobacteria and Alpha- and Gamma-proteobacteria. Microbial composition was highly similar between the tidepool and emergent bench mussels, suggesting similar functions across these different microhabitats. One percent of the proteins identified in each sample were related to nitrogen cycling. When normalized to protein discovery rate, the high diversity and abundance of enzymes related to the nitrogen cycle in mussel-associated microbes is as great or greater than that described for other marine metagenomes. In some instances, the nitrogen-utilizing profile of this assemblage was more concordant with soil metagenomes in the Midwestern U.S. than for open ocean system. Carbon fixation and Calvin cycle enzymes further represented 0.65 and 1.26% of all proteins and their abundance was comparable to a number of open ocean marine metagenomes. In sum, the diversity and abundance of nitrogen and carbon cycle related enzymes in the microbes occupying the shells of Mytilus californianus suggest these mussels provide a node for microbial populations and thus biogeochemical processes.
Amino-acid cycling drives nitrogen fixation
C L Bishop
Genome Biology , 2003, DOI: 10.1186/gb-spotlight-20030422-04
Abstract: Ludwig et al. examined amino-acid cycling in pea bacteriods by the mutation of two ABC-type amino-acid transporters with broad specificity - aap and bra. Single mutants resulted in a 40-70% reduction in rates of amino-acid uptake by pea nodules. No difference in pea growth was observed in the presence of the mutant bacteriods, however. A double aapbra mutant was also capable of amino-acid synthesis, but phenotypic observations suggested that the plants were unable to fix nitrogen. Further analysis established that the plants were capable of reducing nitrogen in the presence of the aapbra mutants, but that the plants could not acquire ammonium. The authors propose that plants provide bacteriods with amino acids via Aap and/or Bra; in turn, bacteriods can shut down ammonium assimilation. To obtain amino acids the bacteriods secrete ammonium to the plant - thus allowing amino-acid synthesis to occur.The authors conclude that "the interaction between the symbiotic partners is far more complex than hitherto realized: each has evolved a complete metabolic dependence on the other."

Kang Demeng,Chen Liding,

环境科学学报 , 1991,
Abstract: The biogeochemical cycling of nitrogen in the environment of China has been investigated.The cycling of nitrogen was modelled based on the processes such as plant uptake,dry and wet deposition,leaching,mineralization-immobilization,denitrification,and volatilization.The flux and reservoir contents of nitrogen in atmosphere, hydrosphere, lithosphere and biosphere was predicted accordingly.
Nitrogen cycling in sub-oxic water colmns
Dalsgaard,Tage; Thamdrup,Bo; Mark Jensen,Marlene;
Gayana (Concepción) , 2006, DOI: 10.4067/S0717-65382006000300004
Abstract: the current knowledge about nitrogen removal processes in suboxic water columns will be reviewed. the most recent development in the understanding of these processes is the documentation of anaerobic ammonium oxidation with nitrite (anammox) in these areas, and the balance between the traditional denitrification and anammox will be in focus.
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