Microbial Nitrogen Cycling in Estuaries: From Genes to Ecosystem Processes

Damashek, Julian; Francis, Christopher A.

doi:10.1007/s12237-017-0306-2

Cited by 119 publications

(102 citation statements)

References 501 publications

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“…Ammonia oxidation has been well characterized throughout the sea, and the rates measured here are consistent with general patterns of high rates near the base of the euphotic zone (e.g., Ward ; Santoro et al ; Beman et al ) and in near‐shore/estuarine waters (e.g., Horrigan and Springer ; Bianchi et al ; Ward ; Damashek and Francis ), and are comparable to previous measurements made in Georgia coastal waters (Tolar et al , ; Liu et al ). Far less is known about oxidation of the N in DON, but recent demonstrations of thaumarchaeal oxidation of N supplied as urea and cyanate has stimulated interest in this aspect of marine DON cycling.…”

Section: Discussionsupporting

confidence: 90%

Microbial oxidation of nitrogen supplied as selected organic nitrogen compounds in the South Atlantic Bight

Damashek

Tolar

Liu

et al. 2018

Limnology & Oceanography

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Dissolved organic nitrogen (DON) can account for a large fraction of the dissolved nitrogen (N) pool in the ocean, but the cycling of marine DON is poorly understood. Recent discoveries that urea-and cyanate-N can be oxidized by some strains of Thaumarchaeota suggest that these abundant microbes may be able to access and oxidize a fraction of the DON pool. However, measurements of the oxidation of N supplied as DON compounds are scarce. Here, we compare oxidation rates of N supplied as a variety of DON compounds in samples from Georgia coastal waters, where nitrifier communities are numerically dominated by Thaumarchaeota. Our data indicate that polyamine-N is particularly amenable to oxidation compared to the other DON compounds tested. Oxidation of N supplied as putrescine (1,4-diaminobutane) was generally higher than that of N supplied as glutamate, arginine, or urea, and was consistently 5-10% of the ammonia oxidation rate. Our data also suggest that the oxidation rate of polyamine-N may increase as the length of the carbon skeleton increases. Oxidation of N supplied as putrescine, urea, and glutamate were all highest near the coast and lower further offshore, consistent with patterns of ammonia oxidation in these waters. Though it is unclear whether oxidation of polyamine-N reflects direct oxidation by Thaumarchaeota or combines remineralization and subsequent ammonia oxidation, more rapid oxidation of N from putrescine compared to amino acids or urea suggests that polyamine-N may contribute significantly to nitrification in the ocean.

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Section: Discussionsupporting

confidence: 90%

Microbial oxidation of nitrogen supplied as selected organic nitrogen compounds in the South Atlantic Bight

Damashek

Tolar

Liu

et al. 2018

Limnology & Oceanography

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“…Betaproteobacteria have a similar variation pattern, though they are often the most abundant bacteria inhabiting the upper waters of lakes (Newton et al., ). Previous studies demonstrated that Proteobacteria are involved in a variety of biogeochemical processes in aquatic ecosystems (Damashek & Francis, ; Xu et al., ; Zhang et al., ). Thus, they are more active due to a greater availability of POC and DOC at that depth, as seen in Figures d and a, which demonstrates that depth has a significant effect on their abundance in freshwater (Gattuso, Peduzzi, Pizay, & Tonolla, ).…”

Section: Resultsmentioning

confidence: 99%

“…Previous studies demonstrated that Proteobacteria are involved in a variety of biogeochemical processes in aquatic ecosystems (Damashek & Francis, 2018;Xu et al, 2014;Zhang et al, 2015).…”

Section: Spatial-temporal Variations In Bacterioplankton Community mentioning

confidence: 99%

Spatial and temporal dynamics of bacterioplankton community composition in a subtropical dammed karst river of southwestern China

Shi

Song

et al. 2019

MicrobiologyOpen

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River damming influences the hydro‐physicochemical variations in karst water; however, such disruption in bacterioplankton communities has seldom been studied. Here, three sampling sites (city‐river section, reservoir area, and outflow area) of the Ca2+–Mg2+–HCO3−–SO42− water type in the dammed Liu River were selected to investigate the bacterioplankton community composition as identified by high‐throughput 16S rRNA gene sequencing. In the dammed Liu River, thermal regimes have been altered, which has resulted in considerable spatial‐temporal differences in total dissolved solids (TDSs), oxidation‐reduction potential (Eh), dissolved oxygen (DO), and pH and in a different microenvironment for bacterioplankton. Among the dominant bacterioplankton phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria account for 38.99%–87.24%, 3.75%–36.55%, 4.77%–38.90%, and 0%–14.44% of the total reads (mean relative frequency), respectively. Bacterioplankton communities are dominated by Brevundimonas, Novosphingobium, Zymomonas, the Actinobacteria hgcIclade, the CL500‐29 marine group, Sediminibacterium, Flavobacterium, Pseudarcicella, Cloacibacterium, and Prochlorococcus. Their abundances covary with spatial‐temporal variations in hydro‐physicochemical factors, as also demonstrated by beta diversity analyses. In addition, temperature plays a pivotal role in maintaining bacterioplankton biodiversity and hydro‐physicochemical variations. This result also highlights the concept that ecological niches for aquatic bacteria in dammed karst rivers do not accidentally occur but are the result of a suite of environmental forces. In addition, bacterioplankton can alter the aquatic carbon/nitrogen cycle and contribute to karst river metabolism.

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“…These technologies have allowed the attainment of a wealth of genomic data, revealing enormous metabolic versatility within N-transforming microorganisms. Furthermore, the study of genes encoding key metabolic proteins along with rate measurements of N processes has provided important discoveries about the genomic potential of microorganisms participating in N processes, as well as their biogeography and activity in marine systems ( Table 1; Lam and Kuypers, 2011;Devol, 2015;Damashek and Francis, 2018). However, some discrepancies have been found between different studies, which may be due to the use of different methodologies (e.g., primer-based approaches versus untargeted approaches with meta-omic signatures or direct incubation experiments versus isotopic mass balance approach).…”

Section: Introductionmentioning

confidence: 99%

Processes and Microorganisms Involved in the Marine Nitrogen Cycle: Knowledge and Gaps

2019

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Nitrogen (N) is a key element for life in the oceans. It controls primary productivity in many parts of the global ocean, consequently playing a crucial role in the uptake of atmospheric carbon dioxide. The marine N cycle is driven by multiple biogeochemical transformations mediated by microorganisms, including processes contributing to the marine fixed N pool (N 2 fixation) and retained N pool (nitrification, assimilation, and dissimilatory nitrate reduction to ammonia), as well as processes contributing to the fixed N loss (denitrification, anaerobic ammonium oxidation and nitrite-dependent anaerobic methane oxidation). The N cycle maintains the functioning of marine ecosystems and will be a crucial component in how the ocean responds to global environmental change. In this review, we summarize the current understanding of the marine microbial N cycle, the ecology and distribution of the main functional players involved, and the main impacts of anthropogenic activities on the marine N cycle.

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Microbial Nitrogen Cycling in Estuaries: From Genes to Ecosystem Processes

Cited by 119 publications

References 501 publications

Microbial oxidation of nitrogen supplied as selected organic nitrogen compounds in the South Atlantic Bight

Microbial oxidation of nitrogen supplied as selected organic nitrogen compounds in the South Atlantic Bight

Spatial and temporal dynamics of bacterioplankton community composition in a subtropical dammed karst river of southwestern China

Processes and Microorganisms Involved in the Marine Nitrogen Cycle: Knowledge and Gaps

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