Integrated weed management with strategic tillage can maintain soil quality in continuous living cover systems

Maximizing living cover and minimizing soil disturbance with no-till are key strategies in regenerative row-crop production. Although living cover and no-till can increase beneficial soil carbon and water stable aggregates (WSA), annual crops in rotation with perennials often rely on herbicides to control weeds and terminate perennials. Integrated weed management (IWM) reduces reliance on herbicides by employing multiple weed control strategies including tillage and/or cultivation. However, many no-till growers are reluctant to implement some soil disturbance due to concerns about negative impacts on soil health. For that reason, we hypothesized that compared to continuous no-till and standard herbicides (NT-SH), a strategic inversion tillage in IWM (ST-IWM) would result in lower soil carbon and WSA in the year following the tillage event. We also hypothesized that soil carbon and WSA would not differ between the two systems when sampled after cover cropping and 2 years of perennials. We tested these hypotheses within a 6-year, diverse, dairy crop rotation initiated in 2010 in central Pennsylvania in a channery silt loam soil. The systems were compared in split-plots in a full crop entry experiment, where the six phases of the crop rotation were planted every year in a randomized complete block design, replicated four times. We compared the soil health indicators in spring 2010 prior to the start of the experiment and in 2013 and 2019 following inversion tillage (ST-IWM) or herbicide termination (NT-SH) of the perennial forage in the first year of the rotation. We also compared these indicators in the sixth year of the rotation after 3 years of annual and cover crops and 2 years of perennial forage. We sampled at two depths: 0–5 and 5–15 cm for total carbon and bulk density, 0–5 cm for labile carbon and 0–15 cm for WSA. Results indicate that despite initial smaller soil health values in the ST-IWM system following inversion tillage, all properties except labile carbon were similar to the NT-SH system in the sixth year of the rotation.

Organic fertility inputs synergistically increase denitrification-derived nitrous oxide emissions in agroecosystems

Soil fertility in organic agriculture relies on microbial cycling of nutrient inputs from legume cover crops and animal manure. However, large quantities of labile carbon (C) and nitrogen (N) in these amendments may promote the production and emission of nitrous oxide (N₂ O) from soils. Better ecological understanding of the N₂ O emission controls may lead to new management strategies to reduce these emissions. We measured soil N₂ O emission for two growing seasons in four corn-soybean-winter grain rotations with tillage, cover crop, and manure management variations typical of organic agriculture in temperate and humid North America. To identify N₂ O production pathways and mitigation opportunities, we supplemented N₂ O flux measurements with determinations of N₂ O isotopomer composition and microbiological genomic DNA abundances in microplots where we manipulated cover crop and manure additions. The N input from legume-rich cover crops and manure prior to corn planting made the corn phase the main source of N₂ O emissions, averaging 9.8 kg/ha of N₂ O-N and representing 80% of the 3-yr rotations' total emissions. Nitrous oxide emissions increased sharply when legume cover crop and manure inputs exceeded 1.8 and 4 Mg/ha (dry matter), respectively. Removing the legume aboveground biomass before corn planting to prevent co-location of fresh biomass and manure decreased N₂ O emissions by 60% during the corn phase. The co-occurrence of peak N₂ O emission and high carbon dioxide emission suggests that oxygen (O₂ ) consumption likely caused hypoxia and bacterial denitrification. This interpretation is supported by the N₂ O site preference values trending towards denitrification during peak emissions with limited N₂ O reduction, as revealed by the N₂ O δ¹⁵ N and δ¹⁸ O and the decrease in clade I nosZ gene abundance following incorporation of cover crops and manure. Thus, accelerated microbial O₂ consumption seems to be a critical control of N₂ O emissions in systems with large additions of decomposable C and N substrates. Because many agricultural systems rely on combined fertility inputs from legumes and manures, our research suggests that controlling the rate and timing of organic input additions, as well as preventing the co-location of legume cover crops and manure, could mitigate N₂ O emissions.

Fungal community shifts in soils with varied cover crop treatments and edaphic properties

Cover cropping is proposed to enhance soil microbial diversity and activity, with cover crop type affecting microbial groups in different ways. We compared fungal community compositions of bulk soils differing by cover crop treatment, season, and edaphic properties in the third year of an organic, conventionally tilled rotation of corn-soybean-wheat planted with winter cover crops. We used Illumina amplicon sequencing fungal assemblages to evaluate effects of nine treatments, each replicated four times, consisting of six single winter cover crop species, a three-species mixture, a six-species mixture, and fallow. Alpha-diversity of fungal communities was not affected by cover crop species identity, function, or diversity. Sampling season influenced community composition as well as genus-level abundances of arbuscular mycorrhizal (AM) fungi. Cover crop mixtures, specifically the three-species mixture, had distinct AM fungal community compositions, while cereal rye and forage radish monocultures had unique Core OTU compositions. Soil texture, pH, permanganate oxidizable carbon, and chemical properties including Cu, and P were important variables in models of fungal OTU distributions across groupings. These results showed how fungal composition and potential functions were shaped by cover crop treatment as well as soil heterogeneity.

Duckweed as an Agricultural Amendment: Nitrogen Mineralization, Leaching, and Sorghum Uptake

Excessive N and P in surface waters can promote eutrophication (algae-dominated, low-O waters), which decreases water quality and aquatic life. Duckweed (Lemnaceae), a floating aquatic plant, rapidly absorbs N and P from water and its composition shows strong potential as a soil amendment. Therefore, it may be used to transfer N and P from eutrophic water bodies to agricultural fields. In this work, dried duckweed was incorporated into agricultural soil in microcosm, column, and field tests to evaluate biological N cycling, nutrient retention, and crop yield compared with compost, diammonium phosphate (DAP), and an amendment-free control. In microcosm tests, 25 ± 13% of duckweed N was mineralized, providing on average less mineral N than DAP (107 ± 21%), but more than compost (11 ± 12%). In columns, duckweed treatments leached only 2% of the N added, significantly less than DAP, which leached 60% of its N. Compared with the control, DAP leached significantly more phosphate (78%), whereas duckweed and compost treatments leached less (56 and 27%, respectively). Crop yield, as well as runoff N and P, were measured in field tests growing forage sorghum [ (L.) Moench.]. Although less total N was applied to duckweed plots than to DAP plots (75 vs. 130 kg ha, respectively), duckweed was found to retain 30% more total mineral N in a tilled agricultural field than DAP, while supporting a comparable yield. These tests indicate that duckweed may provide a sustainable source of N and P for agriculture.

Underexplored microbial metabolisms for enhanced nutrient recycling in agricultural soils

Worldwide, arable soils have been degraded through erosion and exhaustive cultivation, and substantial proportions of fertilizer nutrients are not taken up by crops. A central challenge in agriculture is to understand how soils and resident microbial communities can be managed to deliver nutrients to crops more efficiently with minimal losses to the environment. Throughout much of the twentieth century, intensive farming has caused substantial loss of organic matter and soil biological function. Today, more farmers recognize the importance of protecting soils and restoring organic matter through reduced tillage, diversified crop rotation, cover cropping, and increased organic amendments. Such management practices are expected to foster soil conditions more similar to those of undisturbed, native plant-soil systems by restoring soil biophysical integrity and re-establishing plant-microbe interactions that retain and recycle nutrients. Soil conditions which could contribute to desirable shifts in microbial metabolic processes include lower redox potentials, more diverse biogeochemical gradients, higher concentrations of labile carbon, and enrichment of carbon dioxide (CO₂) and hydrogen gas (H₂) in soil pores. This paper reviews recent literature on generalized and specific microbial processes that could become more operational once soils are no longer subjected to intensive tillage and organic matter depletion. These processes include heterotrophic assimilation of CO₂; utilization of H₂ as electron donor or reactant; and more diversified nitrogen uptake and dissimilation pathways. Despite knowledge of these processes occurring in laboratory studies, they have received little attention for their potential to affect nutrient and energy flows in soils. This paper explores how soil microbial processes could contribute to in situ nutrient retention, recycling, and crop uptake in agricultural soils managed for improved biological function.

Fe biogeochemistry in reclaimed acid mine drainage precipitates--implications for phytoremediation

At a 50-year-old coal mine drainage barrens in central Pennsylvania, USA, we evaluated the biogeochemistry of acidic, Fe(III)oxy(hydr)oxide precipitates in reclaimed plots and compared them to untreated precipitates in control areas. Reclaimed plots supported successional vegetation that became established after a one-time compost and lime treatment in 2006, while control plots supported biological crusts. Precipitates were sampled from moist yet unsaturated surface layers in an area with lateral subsurface flow of mine drainage above a fragipan. Fe(II) concentrations were three- to five-fold higher in reclaimed than control precipitates. Organically bound Fe and amorphous iron oxides, as fractions of total Fe, were also higher in reclaimed than control precipitates. Estimates of Fe-reducing and Fe-oxidizing bacteria were four- to tenfold higher in root-adherent than both types of control precipitates. By scaling up measurements from experimental plots, total Fe losses during the 5-yr following reclamation were estimated at 45 t Fe ha(-1) yr(-1).

Algal diversity in flowing waters at an acidic mine drainage "barrens" in central Pennsylvania, USA

Microscopic investigations were undertaken to decipher the diversity in the lotic algal communities from acidic waters (pH 2.4-3.2) flowing overland in sheets and channels at an acid mine drainage (AMD) barrens near Kylertown, PA, USA. Microscopic observations, supplemented with taxonomic keys, aided in identification of the dominant algae, and measurement of carbon from adjacent soils was undertaken. The unicellular protist Euglena sp. was most abundant in slower flowing waters (i.e., pool near point of emergence and surficial flow sheets), while Ulothrix sp. was most abundant in faster flowing water from the central stream channel. A diverse range of unicellular microalgae such as Chlorella, Cylindrocystis, Botryococcus, and Navicula and several filamentous forms identified as Microspora, Cladophora, and Binuclearia were also recorded. The observed high algal diversity may be related to the long duration of AMD flow at this site which has led to the development of adapted algal communities. The comparatively higher carbon content in soil materials adjacent to slower flowing water sampling locations provides evidence for the important role of algae as primary producers in this extreme environment.

Twelve testable hypotheses on the geobiology of weathering

Critical Zone (CZ) research investigates the chemical, physical, and biological processes that modulate the Earth's surface. Here, we advance 12 hypotheses that must be tested to improve our understanding of the CZ: (1) Solar-to-chemical conversion of energy by plants regulates flows of carbon, water, and nutrients through plant-microbe soil networks, thereby controlling the location and extent of biological weathering. (2) Biological stoichiometry drives changes in mineral stoichiometry and distribution through weathering. (3) On landscapes experiencing little erosion, biology drives weathering during initial succession, whereas weathering drives biology over the long term. (4) In eroding landscapes, weathering-front advance at depth is coupled to surface denudation via biotic processes. (5) Biology shapes the topography of the Critical Zone. (6) The impact of climate forcing on denudation rates in natural systems can be predicted from models incorporating biogeochemical reaction rates and geomorphological transport laws. (7) Rising global temperatures will increase carbon losses from the Critical Zone. (8) Rising atmospheric P(CO2) will increase rates and extents of mineral weathering in soils. (9) Riverine solute fluxes will respond to changes in climate primarily due to changes in water fluxes and secondarily through changes in biologically mediated weathering. (10) Land use change will impact Critical Zone processes and exports more than climate change. (11) In many severely altered settings, restoration of hydrological processes is possible in decades or less, whereas restoration of biodiversity and biogeochemical processes requires longer timescales. (12) Biogeochemical properties impart thresholds or tipping points beyond which rapid and irreversible losses of ecosystem health, function, and services can occur.

Signal processing for metagenomics: extracting information from the soup

Traditionally, studies in microbial genomics have focused on single-genomes from cultured species, thereby limiting their focus to the small percentage of species that can be cultured outside their natural environment. Fortunately, recent advances in high-throughput sequencing and computational analyses have ushered in the new field of metagenomics, which aims to decode the genomes of microbes from natural communities without the need for cultivation. Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic sequence data. Current tools and techniques are reviewed in this paper which address challenges in 1) genomic fragment annotation, 2) phylogenetic reconstruction, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology.

Characterization of Fe(II) oxidizing bacterial activities and communities at two acidic Appalachian coalmine drainage-impacted sites

We characterized the microbiologically mediated oxidative precipitation of Fe(II) from coalmine-derived acidic mine drainage (AMD) along flow-paths at two sites in northern Pennsylvania. At the Gum Boot site, dissolved Fe(II) was efficiently removed from AMD whereas minimal Fe(II) removal occurred at the Fridays-2 site. Neither site received human intervention to treat the AMD. Culturable Fe(II) oxidizing bacteria were most abundant at sampling locations along the AMD flow path corresponding to greatest Fe(II) removal and where overlying water contained abundant dissolved O(2). Rates of Fe(II) oxidation determined in laboratory-based sediment incubations were also greatest at these sampling locations. Ribosomal RNA intergenic spacer analysis and sequencing of partial 16S rRNA genes recovered from sediment bacterial communities revealed similarities among populations at points receiving regular inputs of Fe(II)-rich AMD and provided evidence for the presence of bacterial lineages capable of Fe(II) oxidation. A notable difference between bacterial communities at the two sites was the abundance of Chloroflexi-affiliated 16S rRNA gene sequences in clone libraries derived from the Gum Boot sediments. Our results suggest that inexpensive and reliable AMD treatment strategies can be implemented by mimicking the conditions present at the Gum Boot field site.

Biogeochemistry of metalliferous peats: sulfur speciation and depth distributions of dsrAB genes and Cd, Fe, Mn, S, and Zn in soil cores

Spatial relationships between concentrations of Cd, Fe, Mn, S, and Zn and bacterial genes for dissimilatory sulfate reduction were studied in soils of the Manning peatland region in western New York. Peat cores were collected within a field exhibiting areas of Zn phytotoxicity, and pH and elemental concentrations were determined with depth. The oxidation states of S were estimated using S-XANES spectroscopy. Soil microbial community DNA was extracted from peat soils for ribosomal RNA intergenic spacer analysis (RISA) of diversity profiles with depth. To assess the presence of sulfate-reducing microorganisms (SRM), DNA extracts were also used as templates for PCR detection of dsrAB genes coding for dissimilatory (bi)-sulfite reductase. Elemental distributions, S redox speciation, and detection of dsrAB genes varied with depth and water content. The pH of peat soils increased with depth. The highest concentrations of Zn, Cd, and S occurred at intermediate depths, whereas Mn concentrations were highest in the topmost peat layers. Iron showed a relatively uniform distribution with depth. Concentrations of redox sensitive elements, S and Mn, but not Fe, seemed to respond to variations in water content and indicated vertical redox stratification in peat cores where topmost peats were typically acidic and oxidizing and deeper peats were typically circumneutral and reducing. Even then, S-XANES analyses showed that surface peats contained >50% of the total S in reduced forms while deep peats contained generally <5% of the total S in oxidized forms. While bacterial RISA profiles of the peats were diverse, dsrAB gene detection followed redox stratification chemistry closely. For the most part, dsrAB genes were detected in deeper peats, where S accumulation was evident, while they were not detected in topmost peat layers where Mn accumulation indicated oxic conditions. Combined chemical, spectroscopic, and microbiological analyses indicated that prolonged exposure to dry-wet cycles resulted in the formation of two redox-stratified zones with distinct chemical and microbiological signatures within peat cores of the Manning peatland region. As illustrated in this study, changes in redox conditions affect bacterial community composition and downward mobility of toxic elements, which has implications for water contamination and the design of metal remediation strategies.

Using minced horseradish roots and peroxides for the deodorization of swine manure: a pilot scale study

Enzymes that have proven to be capable of removing toxic compounds from water and soil may also be useful in the deodorization of animal manures. Considering that pork production in the US is a $40-billion industry with over half a million workers, odor control to protect air quality in the neighboring communities must be considered an essential part of managing livestock facilities. This pilot scale (20-120 L) study tested the use of minced horseradish (Armoracia rusticana L.) roots (1:10 roots to swine slurry ratio), with calcium peroxide (CaO(2) at 34 mM) or hydrogen peroxide (H(2)O(2) at 68 mM), to deodorize swine slurry taken from a 40,000-gallon storage pit at the Pennsylvania State University's Swine Center. Horseradish is known to contain large amounts of peroxidase, an enzyme that, in the presence of peroxides, can polymerize phenolic odorants and thus reduce the malodor. Twelve compounds commonly associated with malodor (seven volatile fatty acids or VFAs, three phenolic compounds and two indolic compounds) were used as odor indicators. Their concentration in swine slurry before and after treatment was determined by gas chromatography (GC) to assess the deodorization effect. The pilot scale testing demonstrated a complete removal of phenolic odorants (with a detection limit of 0.5 mg L(-1)) from the swine slurry, which was consistent with our previous laboratory experiments using 30-mL swine slurry samples. Horseradish could be recycled (reused) five times while retaining significant reduction in the concentration of phenolic odorants. In view of these findings, inexpensive plant materials, such as horseradish, represent a promising tool for eliminating phenolic odorants from swine slurry.

Biological hydrogen production by Clostridium acetobutylicum in an unsaturated flow reactor

A mesophilic unsaturated flow (trickle bed) reactor was designed and tested for H2 production via fermentation of glucose. The reactor consisted of a column packed with glass beads and inoculated with a pure culture (Clostridium acetobutylicum ATCC 824). A defined medium containing glucose was fed at a flow rate of 1.6 mL/min (0.096 L/h) into the capped reactor, producing a hydraulic retention time of 2.1 min. Gas-phase H2 concentrations were constant, averaging 74 +/- 3% for all conditions tested. H2 production rates increased from 89 to 220 mL/hL of reactor when influent glucose concentrations were varied from 1.0 to 10.5 g/L. Specific H2 production rate ranged from 680 to 1270 mL/g glucose per liter of reactor (total volume). The H2 yield was 15-27%, based on a theoretical limit by fermentation of 4 moles of H2 from 1 mole of glucose. The major fermentation by-products in the liquid effluent were acetate and butyrate. The reactor rapidly (within 60-72 h) became clogged with biomass, requiring manual cleaning of the system. In order to make long-term operation of the reactor feasible, biofilm accumulation in the reactor will need to be controlled through some process such as backwashing. These tests using an unsaturated flow reactor demonstrate the feasibility of the process to produce high H2 gas concentrations in a trickle-bed type of reactor. A likely application of this reactor technology could be H2 gas recovery from pre-treatment of high carbohydrate-containing wastewaters.

Dissimilatory iron reduction and odor indicator abatement by biofilm communities in swine manure microcosms

Animal waste odors arising from products of anaerobic microbial metabolism create community relations problems for livestock producers. We investigated a novel approach to swine waste odor reduction: the addition of FeCl(3), a commonly used coagulant in municipal wastewater treatment, to stimulate degradation of odorous compounds by dissimilatory iron-reducing bacteria (DIRB). Two hypotheses were tested: (i) FeCl(3) is an effective source of redox-active ferric iron (Fe(3+)) for dissimilatory reduction by bacteria indigenous to swine manure, and (ii) dissimilatory iron reduction results in significant degradation of odorous compounds within 7 days. Our results demonstrated that Fe(3+) from FeCl(3) was reduced biologically as well as chemically in laboratory microcosms prepared with prefiltered swine manure slurry and limestone gravel, which provided pH buffering and a substrate for microbial biofilm development. Addition of a 1-g liter(-1) equivalent concentration of Fe(3+) from FeCl(3), but not from presynthesized ferrihydrite, caused initial, rapid solids flocculation, chemical Fe(3+) reduction, and E(h) increase, followed by a 2-day lag period. Between 2 and 6 days of incubation, increases in Fe(2+) concentrations were accompanied by significant reductions in concentrations of volatile fatty acids used as odor indicators. Increases in Fe(2+) concentrations between 2 and 6 days did not occur in FeCl(3)-treated microcosms that were sterilized by gamma irradiation or amended with NaN(3), a respiratory inhibitor. DNA sequences obtained from rRNA gene amplicons of bacterial communities in FeCl(3)-treated microcosms were closely related to Desulfitobacterium spp., which are known representatives of DIRB. Use of iron respiration to abate wastewater odors warrants further investigation.

Physicochemical characteristics of animal and municipal wastes decomposed in arid soils

The application of anaerobically processed animal manure to maintain adequate levels of organic matter in arid soils is becoming a common practice. The purpose of this study was to characterize two farm manure products as compared with municipal waste compost (MWC). The anaerobic processing to obtain a biogas manure (BM) product was much faster (25 d) than the aerobic composting of farmyard manure (FYM) (90 d). Drying by three different methods (solar-drying, vacuum-drying at 45 degrees C, and freeze-drying) did not affect the quality of BM. Based on the chemical characteristics, FYM and BM products were comparable, and, containing less ash (30%) and heavy metals (50 mg Pb kg(-1)), seemed superior to MWC that contained 65% ash and 108 mg Pb kg(-1). On the other hand, MWC had higher C content (69.9%), lower acidity (15.04 mol kg(-1)), and higher exothermic peaks (300-460 degrees C) than BM and FYM (50% C, 20 mol kg(-1), and 275-450 degrees C, respectively), thus showing a greater extent of humification. Also, when the organic materials were incubated with arid soils and monitored for mean residence times (MRT), MWC was slightly more resistant to decomposition (MRT 175-180 d) than BM or FYM (MRT 161-166 d). The observed differences, however, were too small to dismiss any of the products as a valuable material for land applications to improve soil quality. In view of the results obtained, MWC may be considered an adequate substitute for BM or FYM, whenever the latter are in short supply.

Deodorization of swine manure using minced horseradish roots and peroxides

Public concerns about offensive odors from livestock manures are on the rise and so is the pressure to develop practical ways to reduce the odors. The use of minced horseradish (Armoracia rusticanaL) roots (1:10 w/v plant tissue to swine slurry ratio), with calcium peroxide (CaO2 at 26 or 34 mM) or hydrogen peroxide (H2O2 at 34, 52, or 68 mM) for the deodorization of swine manure, was evaluated through a series of laboratory experiments. The principle underlying this deodorization method is the oxidation of odorants by the concerted action of horseradish peroxidase (present in the plant tissue) and peroxide that serves as an electron acceptor, followed by polymerization of phenolic odorants with a possible copolymerization or adsorption of other odorant compounds. The deodorization effect was assessed by a human panel and gas chromatography (GC). In the case of the GC method, 12 compounds commonly associated with malodor (7 volatile fatty acids or VFAs, 3 phenolic compounds, and 2 indolic compounds) were used as odor indicators. Malodor assessment of the treated slurry by a human panel indicated a 50% reduction in odor intensity. GC results showed 100% removal of all phenolic odorants without reoccurrence for at least 72 h. In view of these data, using plant materials as enzyme carriers and peroxides as electron acceptors emerges as an effective approach to phenolic odor control in animal manure.

Molecular assessment of inoculated and indigenous bacteria in biofilms from a pilot-scale perchlorate-reducing bioreactor

Bioremediation of perchlorate-contaminated groundwater can occur via bacterial reduction of perchlorate to chloride. Although perchlorate reduction has been demonstrated in bacterial pure cultures, little is known about the efficacy of using perchlorate-reducing bacteria as inoculants for bioremediation in the field. A pilot-scale, fixed-bed bioreactor containing plastic support medium was used to treat perchlorate-contaminated groundwater at a site in Southern California. The bioreactor was inoculated with a field-grown suspension of the perchlorate-respiring bacterium Dechlorosoma sp. strain KJ and fed groundwater containing indigenous bacteria and a carbon source amendment. Because the reactor was flushed weekly to remove accumulated biomass, only bacteria capable of growing in biofilms in the reactor were expected to survive. After 26 days of operation, perchlorate was not detected in bioreactor effluent. Perchlorate remained undetected by ion chromatography (detection limit 4 mug L(-1)) during 6 months of operation, after which the reactor was drained. Plastic medium was subsampled from top, middle, and bottom locations of the reactor for shipment on blue ice and storage at -80 degrees C prior to analysis. Microbial community DNA was extracted from successive washes of thawed biofilm material for PCR-based community profiling by 16S-23S ribosomal intergenic spacer analysis (RISA). No DNA sequences characteristic of strain KJ were recovered from any RISA bands. The most intense bands yielded DNA sequences with high similarities to Dechloromonas spp., a closely related but different genus of perchlorate-respiring bacteria. Additional sequences from RISA profiles indicated presence of representatives of the low G+C gram-positive bacteria and the Cytophaga-Flavobacterium-Bacteroides group. Confocal scanning laser microscopy and fluorescence in situ hybridization (FISH) were also used to examine biofilms using genus-specific 16S ribosomal RNA probes. FISH was more sensitive than RISA profiling in detecting possible survivors from the initial inoculum. FISH revealed that bacteria hybridizing to Dechlorosoma probes constituted <1% of all cells in the biofilms examined, except in the deepest portions where they represented 3-5%. Numbers of bacteria hybridizing to Dechloromonas probes decreased as biofilm depth increased, and they were most abundant at the biofilm surface (23% of all cells). These spatial distribution differences suggested persistence of low numbers of the inoculated strain Dechlorosoma sp. KJ in parts of the biofilm nearest to the plastic medium, concomitant with active colonization or growth by indigenous Dechloromonas spp. in the biofilm exterior. This study demonstrated the feasibility of post hoc analysis of frozen biofilms following completion of field remediation studies.

H2-Producing bacterial communities from a heat-treated soil inoculum

Hydrogen gas (approximately 60% H(2)) was produced in a continuous flow bioreactor inoculated with heat-treated soil, and fed synthetic wastewater containing glucose (9.5 g l(-1)). The pH in the bioreactor was maintained at 5.5 to inhibit consumption of H(2) by methanogens. The objective of this study was to characterize bacterial communities in the reactor operated under two different hydraulic retention times (HRTs of 30-h and 10-h) and temperatures (30 degrees C and 37 degrees C). At 30-h HRT, the H(2) production rate was 80 ml h(-1) and yield was 0.91 mol H(2)/mol glucose. At 10-h HRT, the H(2) production rate was more than 5 times higher at 436 ml h(-1), and yield was 1.61 mol H(2)/mol glucose. Samples were removed from the reactor under steady-state conditions for PCR-based detection of bacterial populations by ribosomal intergenic spacer analysis (RISA). Populations detected at 30-h HRT were more diverse than at 10-h HRT and included representatives of Bacillaceae, Clostridiaceae, and Enterobacteriaceae. At 10-h HRT, only Clostridiaceae were detected. When the temperature of the 10-h HRT reactor was increased from 30 degrees C to 37 degrees C, the steady-state H(2) production rate increased slightly to 463 ml h(-1) and yield was 1.8 mol H(2)/mol glucose. Compared to 30 degrees C, RISA fingerprints at 37 degrees C from the 10-h HRT bioreactor exhibited a clear shift from populations related to Clostridium acidisoli (subcluster Ic) to populations related to Clostridium acetobutylicum (subcluster Ib).

Biological hydrogen production using a membrane bioreactor

A cross-flow membrane was coupled to a chemostat to create an anaerobic membrane bioreactor (MBR) for biological hydrogen production. The reactor was fed glucose (10,000 mg/L) and inoculated with a soil inoculum heat-treated to kill non-spore-forming methanogens. Hydrogen gas was consistently produced at a concentration of 57-60% in the headspace under all conditions. When operated in chemostat mode (no flow through the membrane) at a hydraulic retention time (HRT) of 3.3 h, 90% of the glucose was removed, producing 2200 mg/L of cells and 500 mL/h of biogas. When operated in MBR mode, the solids retention time (SRT) was increased to SRT = 12 h producing a solids concentration in the reactor of 5800 mg/L. This SRT increased the overall glucose utilization (98%), the biogas production rate (640 mL/h), and the conversion efficiency of glucose-to-hydrogen from 22% (no MBR) to 25% (based on a maximum of 4 mol-H(2)/mol-glucose). When the SRT was increased from 5 h to 48 h, glucose utilization (99%) and biomass concentrations (8,800 +/- 600 mg/L) both increased. However, the biogas production decreased (310 +/- 40 mL/h) and the glucose-to-hydrogen conversion efficiency decreased from 37 +/- 4% to 18 +/- 3%. Sustained permeate flows through the membrane were in the range of 57 to 60 L/m(2) h for three different membrane pore sizes (0.3, 0.5, and 0.8 microm). Most (93.7% to 99.3%) of the membrane resistance was due to internal fouling and the reversible cake resistance, and not the membrane itself. Regular backpulsing was essential for maintaining permeate flux through the membrane. Analysis of DNA sequences using ribosomal intergenic spacer analysis indicated bacteria were most closely related to members of Clostridiaceae and Flexibacteraceae, including Clostridium acidisoli CAC237756 (97%), Linmingia china AF481148 (97%), and Cytophaga sp. MDA2507 AF238333 (99%). No PCR amplification of 16s rRNA genes was obtained when archaea-specific primers were used.

Perchlorate reduction by a novel chemolithoautotrophic, hydrogen-oxidizing bacterium

Water treatment technologies are needed that can remove perchlorate from drinking water without introducing organic chemicals that stimulate bacterial growth in water distribution systems. Hydrogen is an ideal energy source for bacterial degradation of perchlorate as it leaves no organic residue and is sparingly soluble. We describe here the isolation of a perchlorate-respiring, hydrogen-oxidizing bacterium (Dechloromonas sp. strain HZ) that grows with carbon dioxide as sole carbon source. Strain HZ is a Gram-negative, rod-shaped facultative anaerobe that was isolated from a gas-phase anaerobic packed-bed biofilm reactor treating perchlorate-contaminated groundwater. The ability of strain HZ to grow autotrophically with carbon dioxide as the sole carbon source was confirmed by demonstrating that biomass carbon (100.9%) was derived from CO2. Chemolithotrophic growth with hydrogen was coupled with complete reduction of perchlorate (10 mM) to chloride with a maximum doubling time of 8.9 h. Strain HZ also grew using acetate as the electron donor and chlorate, nitrate, or oxygen (but not sulphate) as an electron acceptor. Phylogenetic analysis of the 16S rRNA sequence placed strain HZ in the genus Dechloromonas within the beta subgroup of the Proteobacteria. The study of this and other novel perchlorate-reducing bacteria may lead to new, safe technologies for removing perchlorate and other chemical pollutants from drinking water.

Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacterial in compost biofilter enrichments

The gasoline additive MTBE, methyl tert-butyl ether, is a widespread and persistent groundwater contaminant. MTBE undergoes rapid mineralization as the sole carbon and energy source of bacterial strain PM1, isolated from an enrichment culture of compost biofilter material. In this report, we describe the results of microbial community DNA profiling to assess the relative dominance of isolate PM1 and other bacterial strains cultured from the compost enrichment. Three polymerase chain reaction (PCR)-based profiling approaches were evaluated: denaturing gradient gel electrophoresis (DGGE) analysis of 230 bp 16S rDNA fragments; thermal gradient gel electrophoresis (TGGE) analysis of 575 bp 16S rDNA fragments; and non-denaturing polyacrylamide gel electrophoresis of 300-1,500 bp fragments containing 16S/23S ribosomal intergenic transcribed spacer (ITS) regions. Whereas all three DNA profiling approaches indicated that PM1-like bands predominated in mixtures from MTBE-grown enrichments, ITS profiling provided the most abundant and specific sequence data to confirm strain PM1's presence in the enrichment. Moreover, ITS profiling did not produce non-specific PCR products that were observed with T/DGGE. A further advantage of ITS community profiling over other methods requiring restriction digestion (e.g. terminal restriction fragment length polymorphisms) was that it did not require an additional digestion step or the use of automated sequencing equipment. ITS bands, excised from similar locations in profiles of the enrichment and PM1 pure culture, were 99.9% identical across 750 16S rDNA positions and 100% identical across 691 spacer positions. BLAST comparisons of nearly full-length 16S rDNA sequences showed 96% similarity between isolate PM1 and representatives of at least four different genera in the Leptothrix subgroup of the beta-Proteobacteria (Aquabacterium, Leptothrix, Rubrivivax and Ideonella). Maximum likelihood and parsimony analyses of 1,249 nucleotide positions supported isolate PM1's position in a separate lineage within the Leptothrix subgroup.

Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils

Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within Nitrosospira cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes for Nitrosospira cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the Nitrosospira cluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.

Functional Gene Hybridization Patterns of Terrestrial Ammonia-Oxidizing Bacteria

Abstract The biochemical pathway and genetics of autotrophic ammonia oxidation have been studied almost exclusively in Nitrosomonas europaea. Terrestrial autotrophic ammonia-oxidizing bacteria (AAOs), however, comprise two distinct phylogenetic groups in the beta-Proteobacteria, the Nitrosomonas and Nitrosospira groups. Hybridization patterns were used to assess the potential of functional probes in non-PCR-based molecular analysis of natural AAO populations and their activity. The objective of this study was to obtain an overview of functional gene homologies by hybridizing probes derived from N. europaea gene sequences ranging in size from 0.45 to 4.5 kb, and labeled with 32P to Southern blots containing genomic DNA from four Nitrosospira representatives. Probes were specific for genes encoding ammonia monooxygenase (amoA and amoB), hydroxylamine oxidoreductase (hao), and cytochrome c-554 (hcy). These probes produced hybridization signals, at low stringency (30 degreesC), with DNA from each of the four representatives; signals at higher stringency (42 degreesC) were greatly reduced or absent. The hybridization signals at low stringency ranged from 20 to 76% of the total signal obtained with N. europaea DNA. These results indicate that all four functional genes in the ammonia oxidation pathway have diverged between the Nitrosomonas and Nitrosospira groups. The hao probe produced the most consistent hybridization intensities among the Nitrosospira representatives, suggesting that hao sequences would provide the best probes for non-PCR-based molecular analysis of terrestrial AAOs. Since N. europaea can also denitrify, an additional objective was to hybridize genomic DNA from AAOs with probes for Pseudomonas genes involved in denitrification. These probes were specific for genes encoding heme-type dissimilatory nitrite reductase (dNir), Cu-type dNir, and nitrous oxide reductase (nosz). No hybridization signals were observed from probes for the heme-type dNir or nosz, but Nitrosospira sp. NpAV and Nitrosolobus sp. 24-C hybridized, under low-stringency conditions, with the Cu-type dNir probe. These results indicate that AAOs may also differ in their mechanisms and capacities for denitrification.

DNA recovery from soils of diverse composition

A simple, rapid method for bacterial lysis and direct extraction of DNA from soils with minimal shearing was developed to address the risk of chimera formation from small template DNA during subsequent PCR. The method was based on lysis with a high-salt extraction buffer (1.5 M NaCl) and extended heating (2 to 3 h) of the soil suspension in the presence of sodium dodecyl sulfate (SDS), hexadecyltrimethylammonium bromide, and proteinase K. The extraction method required 6 h and was tested on eight soils differing in organic carbon, clay content, and pH, including ones from which DNA extraction is difficult. The DNA fragment size in crude extracts from all soils was > 23 kb. Preliminary trials indicated that DNA recovery from two soils seeded with gram-negative bacteria was 92 to 99%. When the method was tested on all eight unseeded soils, microscopic examination of indigenous bacteria in soil pellets before and after extraction showed variable cell lysis efficiency (26 to 92%). Crude DNA yields from the eight soils ranged from 2.5 to 26.9 micrograms of DNA g-1, and these were positively correlated with the organic carbon content in the soil (r = 0.73). DNA yields from gram-positive bacteria from pure cultures were two to six times higher when the high-salt-SDS-heat method was combined with mortar-and-pestle grinding and freeze-thawing, and most DNA recovered was of high molecular weight. Four methods for purifying crude DNA were also evaluated for percent recovery, fragment size, speed, enzyme restriction, PCR amplification, and DNA-DNA hybridization. In general, all methods produced DNA pure enough for PCR amplification. Since soil type and microbial community characteristics will influence DNA recovery, this study provides guidance for choosing appropriate extraction and purification methods on the basis of experimental goals.