Mitigation of Shallow Groundwater Nitrate in a Poorly Drained Riparian Area and Adjacent Cropland

Riparian ecosystems, through their unique position in the agricultural landscape and ability to influence nutrient cycles, can potentially reduce NO3 loading to surface and ground waters. The purpose of this study was to determine the fate of NO3 in shallow groundwater moving along a lateral flowpath from a grass seed cropping system through an undisturbed mixed-species herbaceous riparian area. Soil A (30–45 cm) and C horizon (135–150 cm) NO3, dissolved oxygen, and nitrous oxide concentrations were significantly higher in the cropping system than the adjacent riparian area. Nitrate concentrations in both horizons of the riparian soil were consistently at or below 0.05 mg NL-1 while cropping system concentrations ranged from 1 to 12 mg N L-1. Chloride data suggested that NO3 dilution occurred from recharge by precipitation. However, a sharp decrease in NO3/Cl ratios as water moved into the riparian area indicated that additional dilution of NO3 concentrations was unlikely. Riparian area A horizon soil water had higher dissolved organic carbon than the cropping system and when the riparian soil became saturated, available electron acceptors (O2, NO3) were rapidly reduced. Dissolved inorganic carbon was significantly higher in the riparian area than the cropping system for both horizons indicating high biological activity. Carbon limitation in the cropping system may have led to microbial respiration using primarily O2 and to a lesser degree NO3. Within 6 m of the riparian/cropping system transition, NO3 was virtually undetectable

Distributions of Extracellular Peptidases Across Prokaryotic Genomes Reflect Phylogeny and Habitat

Proteinaceous compounds are abundant forms of organic nitrogen in soil and aquatic ecosystems, and the rate of protein depolymerization, which is accomplished by a diverse range of microbial secreted peptidases, often limits nitrogen turnover in the environment. To determine if the distribution of secreted peptidases reflects the ecological and evolutionary histories of different taxa, we analyzed their distribution across prokaryotic lineages. Peptidase gene sequences of 147 archaeal and 2,191 bacterial genomes from the MEROPS database were screened for secretion signals, resulting in 55,072 secreted peptidases belonging to 148 peptidase families. These data, along with their corresponding 16S rRNA sequences, were used in our analysis. Overall, Bacteria had a much wider collection of secreted peptidases, higher average numbers of secreted peptidases per genome, and more unique peptidase families than Archaea. We found that the distribution of secreted peptidases corresponded to phylogenetic relationships among Bacteria and Archaea and often segregated according to microbial lifestyles, suggesting that the secreted peptidase complements of microbial taxa are optimized for the environmental microhabitats they occupy. Our analyses provide the groundwork for examining the specific functional role of families of secreted peptidases in relationship to the organisms and the corresponding environments in which they function

FOAM (functional ontology assignments for metagenomes):a hidden markov model (HMM) database with environmental focus

A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/

Dynamics of ammonia oxidizing archaea and bacteria populations and contributions to soil nitrification potentials

It is well known that the ratio of ammonia oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a two year wheat/fallow cycle, and adjacent uncultivated long term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P ≤ 0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomenon: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH₄⁺-availability that exist in the field.Keywords: ammonia, soil, archaea, nitrification, bacteri

Ecological consequences of the expansion of N2-fixing plants in cold biomes

Research in warm-climate biomes has shown that invasion by symbiotic dinitrogen (N2)-fixing plants can transform ecosystems in ways analogous to the transformations observed as a consequence of anthropogenic, atmospheric nitrogen (N) deposition: declines in biodiversity, soil acidification, and alterations to carbon and nutrient cycling, including increased N losses through nitrate leaching and emissions of the powerful greenhouse gas nitrous oxide (N2O). Here, we used literature review and case study approaches to assess the evidence for similar transformations in cold-climate ecosystems of the boreal, subarctic and upper montane-temperate life zones. Our assessment focuses on the plant genera Lupinus and Alnus, which have become invasive largely as a consequence of deliberate introductions and/or reduced land management. These cold biomes are commonly located in remote areas with low anthropogenic N inputs, and the environmental impacts of N2-fixer invasion appear to be as severe as those from anthropogenic N deposition in highly N polluted areas. Hence, inputs of N from N2 fixation can affect ecosystems as dramatically or even more strongly than N inputs from atmospheric deposition, and biomes in cold climates represent no exception with regard to the risk of being invaded by N2-fixing species. In particular, the cold biomes studied here show both a strong potential to be transformed by N2-fixing plants and a rapid subsequent saturation in the ecosystem's capacity to retain N. Therefore, analogous to increases in N deposition, N2-fixing plant invasions must be deemed significant threats to biodiversity and to environmental quality

Back to the future of soil metagenomics

JN was funded by a fellowship from the French MENESR.Peer reviewedPeer Reviewe

Effects of disturbance scale on soil microbial communities in the Western Cascades of Oregon

To gain a better understanding of how rapidly microbial communities respond to different magnitudes of perturbation that mimic minor or catastrophic disturbances. Two montane sites in the western Cascade Mountains of Oregon with adjacent areas of forest and meadow vegetation were studied. A reciprocal transplant experiment evaluated both minor (soil cores remaining in the same vegetation type) or more severe disturbance (soil cores transferred to a different vegetation type). The biomass and composition of the bacterial and fungal communities were measured for 2 years following the establishment of the experiment. Minor disturbance (coring) had little impact on microbial biomass but transferring between vegetation type showed greater fungal biomass in soil incubated in the forest environment. The composition of bacterial communities was not influenced by coring but responded strongly to transfers between vegetation sites, changing to reflect their new environment after 2 years. Fungal community composition responded somewhat to coring, probably from disrupting mycorrhizal fungal hyphae, but more strongly to being transferred to a new environment. The response of the microbial community to major disturbance was rapid, showing shifts reflective of their new environment within 2 years, suggesting that microbial communities have the capacity to quickly adjust to catastrophic disturbances.Keywords: Bacteria, Forest soil, Reciprocal transfer, FungiKeywords: Bacteria, Forest soil, Reciprocal transfer, Fung

Nano-scale investigation of the association of microbial nitrogen residues with iron (hydr)oxides in a forest soil O-horizon

Amino sugars in fungal cell walls (such as chitin) represent an important source of nitrogen (N) in many forest soil ecosystems. Despite the importance of this material in soil nitrogen cycling, comparatively little is known about abiotic and biotic controls on and the timescale of its turnover. Part of the reason for this lack of information is the inaccessibility of these materials to classic bulk extraction methods. To address this issue, we used advanced visualization tools to examine transformation pathways of chitin-rich fungal cell wall residues as they interact with microorganisms, soil organic matter and mineral surfaces. Our goal was to document initial micro-scale dynamics of the incorporation of ¹³C- and ¹⁵N-labeled chitin into fungi-dominated microenvironments in O-horizons of old-growth forest soils. At the end of a 3-week incubation experiment, high-resolution secondary ion mass spectrometry imaging of hyphae-associated soil microstructures revealed a preferential association of ¹⁵N with Fe-rich particles. Synchrotron-based scanning transmission X-ray spectromicroscopy (STXM/NEXAFS) of the same samples showed that thin organic coatings on these soil microstructures are enriched in aliphatic C and amide N on Fe (hydr)oxides, suggesting a concentration of microbial lipids and proteins on these surfaces. A possible explanation for the results of our micro-scale investigation of chemical and spatial patterns is that amide N from chitinous fungal cell walls was assimilated by hyphae-associated bacteria, resynthesized into proteinaceous amide N, and subsequently concentrated onto Fe (hydr)oxide surfaces. If confirmed in other soil ecosystems, such rapid association of microbial N with hydroxylated Fe oxide surfaces may have important implications for mechanistic models of microbial cycling of C and N.This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/geochimica-et-cosmochimica-acta

Use of aliphatic n-alkynes to discriminate soil nitrification activities of ammonia-oxidizing thaumarchaea and bacteria

Ammonia (NH₃)-oxidizing bacteria (AOB) and thaumarchaea (AOA) co-occupy most soils, yet no short-term growth-independent method exists to determine their relative contributions to nitrification in situ. Microbial monooxygenases differ in their vulnerability to inactivation by aliphatic n-alkynes, and we found that NH₃ oxidation by the marine thaumarchaeon Nitrosopumilus maritimus was unaffected during a 24-h exposure to ≤20 μM concentrations of 1-alkynes C₈ and C₉. In contrast, NH₃ oxidation by two AOB (Nitrosomonas europaea and Nitrosospira multiformis) was quickly and irreversibly inactivated by 1 μM C₈ (octyne). Evidence that nitrification carried out by soilborne AOA was also insensitive to octyne was obtained. In incubations (21 or 28 days) of two different whole soils, both acetylene and octyne effectively prevented NH₄⁺-stimulated increases in AOB population densities, but octyne did not prevent increases in AOA population densities that were prevented by acetylene. Furthermore, octyne-resistant, NH₄⁺-stimulated net nitrification rates of 2 and 7 μg N/g soil/day persisted throughout the incubation of the two soils. Other evidence that octyne-resistant nitrification was due to AOA included (i) a positive correlation of octyne-resistant nitrification in soil slurries of cropped and noncropped soils with allylthiourea-resistant activity (100 μM) and (ii) the finding that the fraction of octyne-resistant nitrification in soil slurries correlated with the fraction of nitrification that recovered from irreversible acetylene inactivation in the presence of bacterial protein synthesis inhibitors and with the octyne-resistant fraction of NH₄⁺-saturated net nitrification measured in whole soils. Octyne can be useful in short-term assays to discriminate AOA and AOB contributions to soil nitrification.This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Society for Microbiology and can be found at: http://aem.asm.org/