Microbes and Climate Change: a Research Prospectus for the Future.

Climate change is the most serious challenge facing humanity. Microbes produce and consume three major greenhouse gases-carbon dioxide, methane, and nitrous oxide-and some microbes cause human, animal, and plant diseases that can be exacerbated by climate change. Hence, microbial research is needed to help ameliorate the warming trajectory and cascading effects resulting from heat, drought, and severe storms.

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 (N O) from soils. Better ecological understanding of the N O emission controls may lead to new management strategies to reduce these 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.

Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome.

Soil surface consortia are easily observed and sampled, allowing examination of their interactions with soil microbiomes. Here, we present metatranscriptomic sequences from Dark Green 1 (DG1), a cyanobacterium-based soil surface consortium, in the presence and absence of an underlying soil microbiome and/or urea.

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.

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.

Electrochemically active microorganisms from an acid mine drainage-affected site promote cathode oxidation in microbial fuel cells.

The limited database of acidophilic or acidotolerant electrochemically active microorganisms prevents advancements on microbial fuel cells (MFCs) operated under low pH. In this study, three MFCs were used to enrich cathodic biofilms using acid mine drainage (AMD) sediments as inoculum. Linear sweep voltammetry showed cathodic current plateaus of 5.

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.

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.

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.

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.

Removal of odors from Swine wastewater by using microbial fuel cells.

A single-chamber microbial fuel cell (MFC) was used to reduce 10 chemicals associated with odors by 99.76% (from 422 +/- 23 mug/ml) and three volatile organic acids (acetate, butyrate, and propionate) by >99%. The MFC produced a maximum of 228 mW/m(2) and removed 84% of the organic matter in 260 h.

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.

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.

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.

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.

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).

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.

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.

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.

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.