skip to main content

Explore Research Products in the NSF-PAR

  • NSF Public Access
  • Search Results
  • Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer
Title: Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer
Abstract

To what extent multi-omic techniques could reflectin situmicrobial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3−g−1dry soil d−1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+ → NH2OH → NO → NO2- → NO3−) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteriaNitrosomonasandNitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.

  more » « less
Award ID(s):
1831599 1831582
NSF-PAR ID:
10153774
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ;
Publisher / Repository:
Nature Publishing Group
Date Published:
Journal Name:
Scientific Reports
Volume:
9
Issue:
1
ISSN:
2045-2322
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ( , ISME Communications)
    null (Ed.)
    Abstract Nitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N 2 O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N 2 O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N 2 O yields between 0.18 and 0.41 ng N 2 O–N per µg NO x –N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil. 
    more » « less
  2. ; ; ; ; ; ( , Global Biogeochemical Cycles)
    Abstract

    Marine oxygen deficient zones are dynamic areas of microbial nitrogen cycling. Nitrification, the microbial oxidation of ammonia to nitrate, plays multiple roles in the biogeochemistry of these regions, including production of the greenhouse gas nitrous oxide (N2O). We present here the results of two oceanographic cruises investigating nitrification, nitrifying microorganisms, and N2O production and distribution from the offshore waters of the Eastern Tropical South Pacific. On each cruise, high‐resolution measurements of ammonium ([NH4+]), nitrite ([NO2−]), and N2O were combined with15N tracer‐based determination of ammonia oxidation, nitrite oxidation, nitrate reduction, and N2O production rates. Depth‐integrated inventories of NH4+and NO2−were positively correlated with one another and with depth‐integrated primary production. Depth‐integrated ammonia oxidation rates were correlated with sinking particulate organic nitrogen flux but not with primary production; ammonia oxidation rates were undetectable in trap‐collected sinking particulate material. Nitrite oxidation rates exceeded ammonia oxidation rates at most mesopelagic depths. We found positive correlations between archaealamoAgenes and ammonia oxidation rates and betweenNitrospina‐like 16S rRNA genes and nitrite oxidation rates. N2O concentrations in the upper oxycline reached values of >140 nM, even at the western extent of the cruise track, supporting air‐sea fluxes of up to 1.71 μmol m−2 day−1. Our results suggest that a source of NO2−other than ammonia oxidation may fuel high rates of nitrite oxidation in the offshore Eastern Tropical South Pacific and that air‐sea fluxes of N2O from this region may be higher than previously estimated.

     
    more » « less
  3. ; ; ; ; ; ; ; ; ; ; et al ( , Ecosphere)
    Abstract

    The conversion of native ecosystems to residential ecosystems dominated by lawns has been a prevailing land‐use change in the United States over the past 70 years. Similar development patterns and management of residential ecosystems cause many characteristics of residential ecosystems to be more similar to each other across broad continental gradients than that of former native ecosystems. For instance, similar lawn management by irrigation and fertilizer applications has the potential to influence soil carbon (C) and nitrogen (N) pools and processes. We evaluated the mean and variability of total soil C and N stocks, potential net N mineralization and nitrification, soil nitrite (NO2−)/nitrate (NO3−) and ammonium (NH4+) pools, microbial biomass C and N content, microbial respiration, bulk density, soil pH, and moisture content in residential lawns and native ecosystems in six metropolitan areas across a broad climatic gradient in the United States: Baltimore, MD (BAL); Boston, MA (BOS); Los Angeles, CA (LAX); Miami, FL (MIA); Minneapolis–St. Paul, MN (MSP); and Phoenix, AZ (PHX). We observed evidence of higher N cycling in lawn soils, including significant increases in soil NO2−/NO3−, microbial N pools, and potential net nitrification, and significant decreases in NH4+pools. Self‐reported yard fertilizer application in the previous year was linked with increased NO2−/ NO3−content and decreases in total soil N and C content. Self‐reported irrigation in the previous year was associated with decreases in potential net mineralization and potential net nitrification and with increases in bulk density and pH. Residential topsoil had higher total soil C than native topsoil, and microbial biomass C was markedly higher in residential topsoil in the two driest cities (LAX and PHX). Coefficients of variation for most biogeochemical metrics were higher in native soils than in residential soils across all cities, suggesting that residential development homogenizes soil properties and processes at the continental scale.

     
    more » « less
  4. ; ; ; ; ; ( , mSphere)
    ABSTRACT Ammonia availability due to chloramination can promote the growth of nitrifying organisms, which can deplete chloramine residuals and result in operational problems for drinking water utilities. In this study, we used a metagenomic approach to determine the identity and functional potential of microorganisms involved in nitrogen biotransformation within chloraminated drinking water reservoirs. Spatial changes in the nitrogen species included an increase in nitrate concentrations accompanied by a decrease in ammonium concentrations with increasing distance from the site of chloramination. This nitrifying activity was likely driven by canonical ammonia-oxidizing bacteria (i.e., Nitrosomonas ) and nitrite-oxidizing bacteria (i.e., Nitrospira ) as well as by complete-ammonia-oxidizing (i.e., comammox) Nitrospira -like bacteria. Functional annotation was used to evaluate genes associated with nitrogen metabolism, and the community gene catalogue contained mostly genes involved in nitrification, nitrate and nitrite reduction, and nitric oxide reduction. Furthermore, we assembled 47 high-quality metagenome-assembled genomes (MAGs) representing a highly diverse assemblage of bacteria. Of these, five MAGs showed high coverage across all samples, which included two Nitrosomonas, Nitrospira, Sphingomonas , and Rhizobiales -like MAGs. Systematic genome-level analyses of these MAGs in relation to nitrogen metabolism suggest that under ammonia-limited conditions, nitrate may be also reduced back to ammonia for assimilation. Alternatively, nitrate may be reduced to nitric oxide and may potentially play a role in regulating biofilm formation. Overall, this study provides insight into the microbial communities and their nitrogen metabolism and, together with the water chemistry data, improves our understanding of nitrogen biotransformation in chloraminated drinking water distribution systems. IMPORTANCE Chloramines are often used as a secondary disinfectant when free chlorine residuals are difficult to maintain. However, chloramination is often associated with the undesirable effect of nitrification, which results in operational problems for many drinking water utilities. The introduction of ammonia during chloramination provides a potential source of nitrogen either through the addition of excess ammonia or through chloramine decay. This promotes the growth of nitrifying microorganisms and provides a nitrogen source (i.e., nitrate) for the growth for other organisms. While the roles of canonical ammonia-oxidizing and nitrite-oxidizing bacteria in chloraminated drinking water systems have been extensively investigated, those studies have largely adopted a targeted gene-centered approach. Further, little is known about the potential long-term cooccurrence of complete-ammonia-oxidizing (i.e., comammox) bacteria and the potential metabolic synergies of nitrifying organisms with their heterotrophic counterparts that are capable of denitrification and nitrogen assimilation. This study leveraged data obtained for genome-resolved metagenomics over a time series to show that while nitrifying bacteria are dominant and likely to play a major role in nitrification, their cooccurrence with heterotrophic organisms suggests that nitric oxide production and nitrate reduction to ammonia may also occur in chloraminated drinking water systems. 
    more » « less
  5. ; ; ; ; ; ; ; ; ; ( , Proceedings of the National Academy of Sciences)

    Reactive nitrogen oxides (NOy; NOy= NO + NO2+ HONO) decrease air quality and impact radiative forcing, yet the factors responsible for their emission from nonpoint sources (i.e., soils) remain poorly understood. We investigated the factors that control the production of aerobic NOyin forest soils using molecular techniques, process-based assays, and inhibitor experiments. We subsequently used these data to identify hotspots for gas emissions across forests of the eastern United States. Here, we show that nitrogen oxide soil emissions are mediated by microbial community structure (e.g., ammonium oxidizer abundances), soil chemical characteristics (pH and C:N), and nitrogen (N) transformation rates (net nitrification). We find that, while nitrification rates are controlled primarily by chemoautotrophic ammonia-oxidizing archaea (AOA), the production of NOyis mediated in large part by chemoautotrophic ammonia-oxidizing bacteria (AOB). Variation in nitrification rates and nitrogen oxide emissions tracked variation in forest communities, as stands dominated by arbuscular mycorrhizal (AM) trees had greater N transformation rates and NOyfluxes than stands dominated by ectomycorrhizal (ECM) trees. Given mapped distributions of AM and ECM trees from 78,000 forest inventory plots, we estimate that broadleaf forests of the Midwest and the eastern United States as well as the Mississippi River corridor may be considered hotspots of biogenic NOyemissions. Together, our results greatly improve our understanding of NOyfluxes from forests, which should lead to improved predictions about the atmospheric consequences of tree species shifts owing to land management and climate change.

     
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email