Changes in the microbial community structure are observed in individuals with intestinal inflammatory disorders. These changes are often characterized by a depletion of obligate anaerobic bacteria, whereas the relative abundance of facultative anaerobic Enterobacteriaceae increases. The mechanisms by which the host response shapes the microbial community structure, however, remain unknown. We show that nitrate generated as a by-product of the inflammatory response conferred a growth advantage to the commensal bacterium Escherichia coli in the large intestine of mice. Mice deficient for inducible nitric oxide synthase (iNOS) did not support growth of E. coli by nitrate respiration, suggesting that nitrate generated during inflammation was host-derived. Thus the inflammatory host response selectively enhances growth of commensal Enterobacteriaceae by generating electron acceptors for anaerobic respiration.

The contribution of various bacterial surface functional groups to adhesion at hematite and ZnSe surfaces was examined using attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy. When live Shewanella oneidensis, Pseudomonas aeruginosa, and Bacillus subtilis cells were introduced to a horizontal hematite (alpha-Fe(2)O(3))-coated internal reflection element (IRE), FTIR peaks emerged corresponding to bacterial phosphate group binding. These IR peaks were not observed when bacteria were introduced to the uncoated ZnSe IRE. When cells were added to colloidal suspensions of alpha-Fe(2)O(3) at pH 7, spectra included peaks corresponding to P-OFe and nu(COOH), the latter being attributed to bridging of carboxylate at mineral surface OH groups. Selected model organic compounds with P-containing functionalities (phenylphosphonic acid [PPA], adenosine 5'-monophosphate [AMP], 2'-deoxyadenyl(3'-->5')-2'-deoxyadenosine [DADA], and deoxyribonucleic acid [DNA]) produce spectra with similar peaks corresponding to P-OFe when adsorbed to alpha-Fe(2)O(3). The data indicate that both terminal phosphate/phosphonate and phosphodiester groups, either exuded from the cell or present as surface biomolecules, are involved in bacterial adhesion to Fe-oxides through formation of innersphere Fe-phosphate/phosphonate complexes.

Studies have shown that pyrolysis method and temperature are the key factors influencing biochar chemical and physical properties; however, information on the nature of biochar feedstocks is more accessible to consumers, making feedstock a better measure for selecting biochars. This study characterizes physical and chemical properties of commercially available biochars and investigates trends in biochar properties related to feedstock material to develop guidelines for biochar use. Twelve biochars were analyzed for physical and chemical properties. Compiled data from this study and from the literature (n = 85) were used to investigate trends in biochar characteristics related to feedstock. Analysis of compiled data reveals that despite clear differences in biochar properties from feedstocks of algae, grass, manure, nutshells, pomace, and wood (hard- and softwoods), characteristic generalizations can be made. Feedstock was a better predictor of biochar ash content and C/N ratio, but surface area was also temperature dependent for wood-derived biochar. Significant differences in ash content (grass and manure > wood) and C/N ratio (softwoods > grass and manure) enabled the first presentation of guidelines for biochar use based on feedstock material.

Biologically catalyzed Mn(II) oxidation produces biogenic Mn-oxides (BioMnO(x)) and may serve as one of the major formation pathways for layered Mn-oxides in soils and sediments. The structure of Mn octahedral layers in layered Mn-oxides controls its metal sequestration properties, photochemistry, oxidizing ability, and topotactic transformation to tunneled structures. This study investigates the impacts of cations (H(+), Ni(II), Na(+), and Ca(2+)) during biotic Mn(II) oxidation on the structure of Mn octahedral layers of BioMnO(x) using solution chemistry and synchrotron X-ray techniques. Results demonstrate that Mn octahedral layer symmetry and composition are sensitive to previous cations during BioMnO(x) formation. Specifically, H(+) and Ni(II) enhance vacant site formation, whereas Na(+) and Ca(2+) favor formation of Mn(III) and its ordered distribution in Mn octahedral layers. This study emphasizes the importance of the abiotic reaction between Mn(II) and BioMnO(x) and dependence of the crystal structure of BioMnO(x) on solution chemistry.

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Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA viral diversity in biochar-amended agricultural soils at the preplanting and harvesting stages of a tomato growing season via paired total metagenomes and viral size fraction metagenomes (viromes). Size fractionation prior to DNA extraction reduced sources of nonviral DNA in viromes, enabling the recovery of a vaster richness of viral populations (vOTUs), greater viral taxonomic diversity, broader range of predicted hosts, and better access to the rare virosphere, relative to total metagenomes, which tended to recover only the most persistent and abundant vOTUs. Of 2961 detected vOTUs, 2684 were recovered exclusively from viromes, while only three were recovered from total metagenomes alone. Both viral and microbial communities differed significantly over time, suggesting a coupled response to rhizosphere recruitment processes and/or nitrogen amendments. Viral communities alone were also structured along an 18 m spatial gradient. Overall, our results highlight the utility of soil viromics and reveal similarities between viral and microbial community dynamics throughout the tomato growing season yet suggest a partial decoupling of the processes driving their spatial distributions, potentially due to differences in dispersal, decay rates, and/or sensitivities to soil heterogeneity.

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