scholarly journals Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Paula B. Matheus Carnevali ◽  
Adi Lavy ◽  
Alex D. Thomas ◽  
Alexander Crits-Christoph ◽  
Spencer Diamond ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Nitrogen Compound ◽  
Nitrite Reduction ◽  
Soil Microbiome ◽  
Metabolic Potential ◽  
Floodplain Soil ◽  
Core Microbiome ◽  
East River ◽  
Floodplain Soils ◽  
Nitrate And Nitrite

Abstract Background Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor. Results We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor. Conclusions The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.

scholarly journals Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

2020 ◽  
Author(s):  
Paula B. Matheus Carnevali ◽  
Adi Lavy ◽  
Alex D. Thomas ◽  
Alexander Crits-Christoph ◽  
Spencer Diamond ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Nitrite Reduction ◽  
Soil Microbiome ◽  
Watershed Scale ◽  
Metabolic Potential ◽  
Floodplain Soil ◽  
East River ◽  
Floodplain Soils ◽  
Biogeochemical Transformations ◽  
Nitrate And Nitrite

AbstractBiogeochemical exports of C, N, S and H2 from watersheds are modulated by the activity of microorganisms that function over micron scales. This disparity of scales presents a substantial challenge for development of predictive models describing watershed function. Here, we tested the hypothesis that meander-bound regions exhibit patterns of microbial metabolic potential that are broadly predictive of biogeochemical processes in floodplain soils along a river corridor. We intensively sampled floodplain soils located in the upper, middle, and lower reaches of the East River in Colorado and reconstructed 248 draft quality genomes representative at a sub-species level. Approximately one third of the representative genomes were detected across all three locations with similar levels of abundance, and despite the very high microbial diversity and complexity of the soils, ~15% of species were detected in two consecutive years. A core floodplain microbiome was enriched in bacterial capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. We did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, at the watershed scale meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations in floodplain soils. Given this, we conducted a transcriptomic analysis of the middle site. Overall, the most highly transcribed genes were amoCAB and nxrAB (for nitrification) followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Thus, widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.

scholarly journals Distinguishing Nitrous Oxide Production from Nitrification and Denitrification on the Basis of Isotopomer Abundances

2006 ◽  
Vol 72 (1) ◽  
pp. 638-644 ◽  
Author(s):  
R. L. Sutka ◽  
N. E. Ostrom ◽  
P. H. Ostrom ◽  
J. A. Breznak ◽  
H. Gandhi ◽  
...  
Keyword(s):  
Nitrogen Isotopes ◽  
Ammonia Oxidation ◽  
Nitrite Reduction ◽  
Site Preference ◽  
Ammonia Oxidizers ◽  
Site Preferences ◽  
Nitrifier Denitrification ◽  
Nitrous Oxide Production ◽  
Nitrification And Denitrification ◽  
Nitrate And Nitrite

ABSTRACT The intramolecular distribution of nitrogen isotopes in N2O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N2O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N2O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 ± 1.2‰, 32.5 ± 0.6‰, and 35.6 ± 1.4‰ for Nitrosomonas europaea, Nitrosospira multiformis, and Methylosinus trichosporium, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N2O from ammonia oxidation by N. europaea (31.4 ± 4.2‰) was similar to that produced during hydroxylamine oxidation (33.5 ± 1.2‰) and distinct from that produced during nitrifier denitrification by N. multiformis (0.1 ± 1.7‰), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N2O produced during nitrite reduction by the denitrifiers Pseudomonas chlororaphis and Pseudomonas aureofaciens (−0.6 ± 1.9‰ and −0.5 ± 1.9‰, respectively) were similar to those during nitrate reduction (−0.5 ± 1.9‰ and −0.5 ± 0.6‰, respectively), indicating no influence of either substrate on site preference. Site preferences of ∼33‰ and ∼0‰ are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N2O.

Effects of pH and alkalinity on sulfur-denitrification in a biological granular filter

1996 ◽  
Vol 34 (1-2) ◽  
pp. 355-362 ◽  
Author(s):  
Hiroaki Furumai ◽  
Hideki Tagui ◽  
Kenji Fujita
Keyword(s):  
Enrichment Culture ◽  
Nitrite Reduction ◽  
The Other ◽  
Nitrite Accumulation ◽  
Ph Dependency ◽  
Effects Of Ph ◽  
Rapid Removal ◽  
Nitrate And Nitrite ◽  
The Relationship ◽  
Biological Filters

Two laboratory-scale biological filters were operated to investigate the effects of alkalinity and pH on removal of nitrate and nitrite in sulfur denitrification filter processes. The concentration of sodium bicarbonate in the feed media was changed from 120 to 240 mg/l during about 3 months in a filter (Run A). The other filter was initially fed with 300 mg/l and then with 240 mg/l (Run B). The performance of the filter was monitored by measuring pH, nitrate, nitrite, sulfate, alkalinity, and thiosulfate. Nitrate concentration in effluent rapidly decreased to lower levels within several days for both filters after inoculation of enrichment culture of sulfur denitrifiers. However there was a large difference in removal of nitrite. When rapid removal of nitrate took place, nitrite accumulation was observed and remained while the bicarbonate concentration was 120 and 150 mg/l. On the other hand the nitrite accumulation disappeared when more bicarbonate (240 and 300 mg/l) was supplied. The experimental results indicated that the nitrite accumulation was closely related to pH condition and alkalinity level in the filter. The stable data of effluent water quality for 5 cases were collected and the relationship discussed between nitrite concentration and pH in effluents. The relationship indicated a strong pH dependency on nitrite accumulation below pH of 7.4. The pH condition around 7 is not so inhibitory to biological activity. Therefore, the pH within the biofilm would be low enough to suppress the nitrite reduction by sulfur denitrifiers, while the pH in effluent was not in the inhibitory range. It was recommended to keep the pH higher than 7.4 to prevent nitrite accumulation in the sulfur denitrification filter.

scholarly journals Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

2018 ◽  
Author(s):  
Adi Lavy ◽  
David Geller McGrath ◽  
Paula B. Matheus Carnevali ◽  
Jiamin Wan ◽  
Wenming Dong ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Riparian Zone ◽  
Limited Information ◽  
Metabolic Potential ◽  
Carbon And Nitrogen ◽  
East River ◽  
Mountainous Watersheds ◽  
Geochemical Analyses ◽  
Selenium Reduction ◽  
And Function

AbstractWatersheds are important suppliers of freshwater for human societies. Within mountainous watersheds, microbial communities impact water chemistry and element fluxes as water from precipitation events discharges through soils and underlying weathered rock, yet there is limited information regarding the structure and function of these communities. Within the East River, CO watershed, we conducted a depth-resolved, hillslope to riparian zone transect study to identify factors that control how microorganisms are distributed and their functions. Metagenomic and geochemical analyses indicate that distance from the East River and proximity to groundwater and underlying weathered shale strongly impact microbial community structure and metabolic potential. Riparian zone microbial communities are compositionally distinct from all hillslope communities. Bacteria from phyla lacking isolated representatives consistently increase in abundance with increasing depth, but only in the riparian zone saturated sediments did we find Candidate Phyla Radiation bacteria. Riparian zone microbial communities are functionally differentiated from hillslope communities based on their capacities for carbon and nitrogen fixation and sulfate reduction. Selenium reduction is prominent at depth in weathered shale and saturated riparian zone sediments. We anticipate that the drivers of community composition and metabolic potential identified throughout the studied transect will predict patterns across the larger watershed hillslope system.

scholarly journals New insights into the influence of plant and microbial diversity on denitrification rates in a salt marsh

2020 ◽  
Author(s):  
Olivia U. Mason ◽  
Patrick Chanton ◽  
Loren N. Knobbe ◽  
Julian Zaugg ◽  
Behzad Mortazavi
Keyword(s):  
Microbial Community ◽  
Salt Marsh ◽  
Microbial Diversity ◽  
Ecosystem Functions ◽  
Juncus Roemerianus ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Marsh Vegetation ◽  
Core Microbiome ◽  
N Removal

AbstractCoastal salt marshes are some of the most productive ecosystems on Earth, providing numerous services such as soil carbon storage, flood protection and nutrient filtering, several of which are mediated by the sediment microbiome associated with marsh vegetation. Here, nutrient filtering (nitrate removal through denitrification) was examined by determining microbial community structure (16S rRNA gene iTag sequencing), diversity, denitrification rates and metabolic potential (assembled metagenomic sequences) in collocated patches of Spartina alterniflora (Spartina) and Juncus roemerianus (Juncus) sediments. The iTag data showed that diversity and richness in Spartina and Juncus sediment microbial communities were highly similar. However, microbial community evenness differed significantly, with the most even communities observed in Juncus sediments. Further, denitrification rates were significantly higher in Juncus compared to Spartina, suggesting oscillations in microbial abundances and in particular the core microbiome identified herein, along with plant diversity influence marsh nitrogen (N) removal. Amplicon and assembled metagenome sequences pointed to a potentially important, yet unappreciated Planctomycetes role in N removal in the salt marsh. Thus, perturbations, such as sea-level rise, that can alter marsh vegetation distribution could impact microbial diversity and may ultimately influence the ecologically important ecosystem functions the marsh sediment microbiome provides.

Nitrate and nitrite reduction by ferrous iron minerals in polluted groundwater: Isotopic characterization of batch experiments

2020 ◽  
Vol 548 ◽  
pp. 119691
Author(s):  
Rosanna Margalef-Marti ◽  
Raúl Carrey ◽  
José Antonio Benito ◽  
Vicenç Marti ◽  
Albert Soler ◽  
...  
Keyword(s):  
Ferrous Iron ◽  
Nitrite Reduction ◽  
Batch Experiments ◽  
Iron Minerals ◽  
Isotopic Characterization ◽  
Nitrate And Nitrite

Indole degrading of ammonia oxidizing bacteria isolated from swine wastewater treatment system

2009 ◽  
Vol 59 (12) ◽  
pp. 2405-2410 ◽  
Author(s):  
Ping Li ◽  
Lei Tong ◽  
Kun Liu ◽  
Yanhong Wang ◽  
Yanxin Wang
Keyword(s):  
Wastewater Treatment ◽  
Biochemical Analysis ◽  
Ammonia Oxidation ◽  
Treatment System ◽  
Swine Wastewater ◽  
Ammonia Oxidizing Bacteria ◽  
16S Rdna Gene ◽  
Wastewater Treatment System ◽  
Nitrate And Nitrite ◽  
Physiological And Biochemical

Three new strains named LPA11, LPB11 and LPC24 were isolated to investigate the patterns of indole degradation and ammonia oxidation in swine wastewater from different parts of a swine wastewater treatment system by the direct spreading plate method. These three isolates were all identified as Pseudomonas putida based on 16S-rDNA gene sequences, main physiological and biochemical analysis. They were capable of decomposing 1.0 mM indole completely in 10, 16 and 18 days respectively. According to the results of HPLC and GC/MS, the possible pathway for the degradation was via oxindole, isatin and anthranilic acid. The three bacteria were capable of oxidizing ammonia, and the strains LPA11 and LPC24 were capable of effectively reducing nitrate and nitrite.

Nitrate and Nitrite Reduction

1980 ◽  
pp. 115-168 ◽  
Author(s):  
LEONARD BEEVERS ◽  
RICHARD H. HAGEMAN
Keyword(s):  
Nitrite Reduction ◽  
Nitrate And Nitrite

scholarly journals Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Dan Naylor ◽  
Sarah Fansler ◽  
Colin Brislawn ◽  
William C. Nelson ◽  
Kirsten S. Hofmockel ◽  
...  
Keyword(s):  
Amplicon Sequencing ◽  
Low Complexity ◽  
Soil Extract ◽  
Soil Microbiome ◽  
Functional Modules ◽  
Anaerobic Conditions ◽  
Metabolic Potential ◽  
16S Rrna Amplicon Sequencing ◽  
Alternative Approach ◽  
Reduced Complexity

ABSTRACT The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Here, we developed an alternative approach in which the complex soil microbiome was broken into components (“functional modules”), based on metabolic capacities, for individual characterization. We hypothesized that reproducible, low-complexity communities that represent functional modules could be obtained through targeted enrichments and that, in combination, they would encompass a large extent of the soil microbiome diversity. Enrichments were performed on a starting soil inoculum with defined media based on specific carbon substrates, antibiotics, alternative electron acceptors under anaerobic conditions, or alternative growing conditions reflective of common field stresses. The resultant communities were evaluated through 16S rRNA amplicon sequencing. Less permissive modules (anaerobic conditions, complex polysaccharides, and certain stresses) resulted in more distinct community profiles with higher richness and more variability between replicates, whereas modules with simple substrates were dominated by fewer species and were more reproducible. Collectively, approximately 27% of unique taxa present in the liquid soil extract control were found across functional modules. Taxa that were underrepresented or undetected in the source soil were also enriched across the modules. Metatranscriptomic analyses were carried out on a subset of the modules to investigate differences in functional gene expression. These results demonstrate that by dissecting the soil microbiome into discrete components it is possible to obtain a more comprehensive view of the soil microbiome and its biochemical potential than would be possible using more holistic analyses. IMPORTANCE The taxonomic and functional diversity inherent to the soil microbiome complicate assessments of the metabolic potential carried out by the community members. An alternative approach is to break down the soil microbiome into reduced-complexity subsets based on metabolic capacities (functional modules) prior to sequencing and analysis. Here, we demonstrate that this approach successfully identified specific phylogenetic and biochemical traits of the soil microbiome that otherwise remained hidden from a more top-down analysis.

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