Soil Moisture Data Assimilation to Estimate Irrigation Water Use.

Knowledge of irrigation is essential to support food security, manage depleting water resources, and comprehensively understand the global water and energy cycles. Despite the importance of understanding irrigation, little consistent information exists on the amount of water that is applied for irrigation. In this study, we develop and evaluate a new method to predict daily to seasonal irrigation magnitude using a particle batch smoother data assimilation approach, where land surface model soil moisture is applied in different configurations to understand how characteristics of remotely sensed soil moisture may impact the performance of the method. The study employs a suite of synthetic data assimilation experiments, allowing for systematic diagnosis of known error sources. Assimilation of daily synthetic soil moisture observations with zero noise produces irrigation estimates with a seasonal bias of 0.66% and a correlation of 0.95 relative to a known truth irrigation. When synthetic observations were subjected to an irregular overpass interval and random noise similar to the Soil Moisture Active Passive satellite (0.04 cm3 cm-3), irrigation estimates produced a median seasonal bias of <1% and a correlation of 0.69. When systematic biases commensurate with those between NLDAS-2 land surface models and Soil Moisture Active Passive are imposed, irrigation estimates show larger biases. In this application, the particle batch smoother outperformed the particle filter. The presented framework has the potential to provide new information into irrigation magnitude over spatially continuous domains, yet its broad applicability is contingent upon identifying new method(s) of determining irrigation schedule and correcting biases between observed and simulated soil moisture, as these errors markedly degraded performance.

Ultrastrong and Flexible Hybrid Hydrogels based on Solution Self-Assembly of Chitin Nanofibers in Gelatin Methacryloyl (GelMA).

We demonstrate ultrastrong and flexible hydrogels by self-assembling chitin nanofiber in the presence of gelatin methacryloyl. We tune the mechanical properties of the hydrogel with chitin nanofiber content and show proof-of-concept applications in engineering vascular tissue.

Solid matrix partition by fracture networks.

The geometrical properties of the matrix blocks formed by a random fracture network are investigated numerically, for a wide range of fracture shapes and for fracture densities ranging from the dilute limit to well above the threshold where the material is entirely partitioned into finite blocks. The main block characteristics are the density and volume fraction, the mean volume and surface area, and their number of faces. In the dilute limit, general expressions for these characteristics are obtained, which provide a good approximation of the numerical data for any fracture shape. In the dense regime, most properties are governed by power laws, which involve two fitted exponents independent of the fracture shape. The shape factors identified in the dilute limit remain relevant for dense networks and can be used to formulate a general model for the block characteristics, valid up to the total matrix fracturation. The transition density when this occurs is determined. It can also be used to account for the fracture shape effects in a very simple and fairly accurate general model. Beyond the transition density, the block characteristics converge as expected toward those in the space tesselation by infinite planes.

Desulfovibrio idahonensis sp. nov., sulfate-reducing bacteria isolated from a metal(loid)-contaminated freshwater sediment.

Two novel sulfate-reducing bacteria, strains CY1T and CY2, were isolated from heavy-metal-contaminated sediments of Lake Coeur d'Alene, Idaho, USA. Strains CY1T and CY2 were found to contain c-type cytochromes and to reduce sulfate, sulfite, thiosulfate, elemental sulfur, DMSO, anthraquinone disulfonate and fumarate using lactate as an electron donor. In a comparison of 16S rRNA gene sequences, CY1T and CY2 were found to be 100% identical, but only 97 and 92.4% similar, respectively, to the type strains of Desulfovibrio mexicanus and Desulfovibrio aminophilus. Unlike these species, however, CY1T was neither able to disproportionate thiosulfate nor able to use yeast extract or amino acids as electron donors. These data, considered in conjunction with differences among strain CY1T and the two related type strains in chemotaxonomy, riboprint patterns, temperature and pH optima, support recognition of a distinct and novel species within the genus Desulfovibrio, Desulfovibrio idahonensis sp. nov., with the type strain CY1T (=DSM 15450T=JCM 14124T).

Ecology of sulfate-reducing bacteria in an iron-dominated, mining-impacted freshwater sediment.

A legacy of lead and silver mining in its headwaters left Lake Coeur d'Alene, Idaho with a sediment body that is highly reduced and contains up to 100 g kg(-1) iron and a smaller fraction of chemically active sulfide phases. The dynamic character of these sulfides and their importance for the sequestering of contaminating trace elements prompted this study of the sulfate-reducing bacteria (SRB) involved in their production. We estimated parameters indicative of the distribution and activity of SRB in relation to season, site, and depth. Most probable number estimates and quantitative PCR assays of an SRB-specific functional gene, alpha-adenosine 5'-phosphosulfate reductase, indicated 10(3) to 10(6) cultivable cells and 10(5) to 10(7) gene copy numbers g(-1) dry wt sediment, respectively. Although culture-based estimates of SRB abundance correlated poorly with site, season, depth, total S, or pore water SO(4), non-culture-based estimates of SRB abundance were markedly higher at contaminated sites and positively correlated with pore water SO(4). Ex situ estimates of (35)SO(4) respiration and acid volatile sulfides abundance also showed strong among-site effects, indicating elevated sulfidogenesis at contaminated sites. These observations support the view that biogenic sulfides may act in concert with reduced iron to retain soluble metal(loid)s in the solid phase.

Desulfosporosinus lacus sp. nov., a sulfate-reducing bacterium isolated from pristine freshwater lake sediments.

A novel sulfate-reducing bacterium was isolated from pristine sediments of Lake Stechlin, Germany. This strain, STP12(T), was found to contain predominantly c-type cytochromes and to reduce sulfate, sulfite and thiosulfate using lactate as an electron donor. Although STP12(T) could not utilize elemental sulfur as an electron acceptor, it could support growth by dissimilatory Fe(III) reduction. In a comparison of 16S rRNA gene sequences, STP12(T) was 96.7 % similar to Desulfosporosinus auripigmenti DSM 13351(T), 96.5 % similar to Desulfosporosinus meridiei DSM 13257(T) and 96.4 % similar to Desulfosporosinus orientis DSM 765(T). DNA-DNA hybridization experiments revealed that strain STP12(T) shows only 32 % reassociation with the type strain of the type species of the genus, D. orientis DSM 765(T). These data, considered in conjunction with strain-specific differences in heavy metal tolerance, cell-wall chemotaxonomy and riboprint patterns, support recognition of strain STP12(T) (=DSM 15449(T)=JCM 12239(T)) as the type strain of a distinct and novel species within the genus Desulfosporosinus, Desulfosporosinus lacus sp. nov.

Biogeochemical transformations of arsenic in circumneutral freshwater sediments.

Arsenic is a wide-spread contaminant of soils and sediments, and many watersheds worldwide regularly experience severe arsenic loading. While the toxicity of arsenic to plants and animals is well recognized, the geochemical and biological transformations that alter its bioavailability in the environment are multifaceted and remain poorly understood. This communication provides a brief overview of our current understanding of the biogeochemistry of arsenic in circumneutral freshwater sediments, placing special emphasis on microbial transformations. Arsenic can reside in a number of oxidation states and complex ions. The common inorganic aqueous species at circumneutral pH are the negatively charged arsenates (H2As(V)O4(-) and Has(V)O4(2-)) and zero-charged arsenite (H3As(III)O3(0)). Arsenic undergoes diagenesis in response to both physical and biogeochemical processes. It accumulates in oxic sediments by adsorption on and/or co-precipitation with hydrous iron and manganese oxides. Burial of such sediments in anoxic/suboxic environments favors their reduction, releasing Fe(II), Mn(II) and associated adsorbed/coprecipitated As. Upward advection can translocate these cations and As into the overlying oxic zone where they may reprecipitate. Alternatively, As may be repartitioned to the sulfidic phase, forming precipitates such as arsenopyrite and orpiment. Soluble and adsorbed As species undergo biotic transformations. As(V) can serve as the terminal electron acceptor in the biological oxidation of organic matter, and the limited number of microbes capable of this transformations are diverse in their phylogeny and physiology. Fe(III)-respiring bacteria can mobilize both As(V) and As(III) bound to ferric oxides by the reductive dissolution of iron-arsenate minerals. SO4(2-)-reducing bacteria can promote deposition of As(III) as sulfide minerals via their production of sulfide. A limited number of As(III)-oxidizing bacteria have been identified, some of which couple this reaction to growth. Lastly, prokaryotic and eukaryotic microbes can alter arsenic toxicity either by coupling cellular export to its reduction or by converting inorganic As to organo-arsenical compounds. The degree to which each of these metabolic transformations influences As mobilization or sequestration in different sedimentary matrices remains to be established.

Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses.

The abundance, distribution, and phylogenetic diversity of members of the Fe(III)-reducing family Geobacteraceae were studied along a gradient of metal contaminants in Lake Coeur d'Alene, Idaho. Partial 16S rRNA gene fragments were amplified by PCR using primers directed toward conserved regions of the gene within the family Geobacteraceae. Analysis of amplicons separated by denaturing gradient gel electrophoresis (DGGE) suggested within-site variation was as great as between-site variation. Amplicons were cloned and grouped by RFLP type and DGGE migration distance and representatives were sequenced. Grouping clones with 3% or less sequence dissimilarity, 15 distinct phylotypes were identified compared to 16 distinct DGGE bands. Only 1 phylotype was recovered from all sites. This clone, B14, is most closely related to Geobacter metallireducens and constituted a greater portion of the pristine community than of the contaminated communities. A second phylotype, Q2, predominated in the contaminated communities and was notably absent from the pristine libraries. Clone Q2 presents a high degree of sequence similarity to two Geobacter spp. previously isolated from this region of Lake Coeur d'Alene. Six phylotypes were unique to the contaminated sediments, whereas two were found only in the pristine sediments. Indices of diversity (Shannon and Simpson) were consistently higher when calculated with DGGE data than when clone library data were used. Most-probable-number PCR and real-time PCR suggested that the Geobacteraceae phylotypes were spread relatively evenly across all three sites along the gradient. Our data indicate that the Geobacteraceae are diverse and abundant in Lake Coeur d'Alene sediments, regardless of metals content. These results provide insight into the ability of dissimilatory Fe(III)-reducing bacteria to colonize habitats with elevated metal concentrations, and they have important implications for the management and remediation of metal-contaminated sites.

Isolation and characterization of a novel As(V)-reducing bacterium: implications for arsenic mobilization and the genus Desulfitobacterium.

Dissimilatory arsenate-reducing bacteria have been implicated in the mobilization of arsenic from arsenic-enriched sediments. An As(V)-reducing bacterium, designated strain GBFH, was isolated from arsenic-contaminated sediments of Lake Coeur d'Alene, Idaho. Strain GBFH couples the oxidation of formate to the reduction of As(V) when formate is supplied as the sole carbon source and electron donor. Additionally, strain GBFH is capable of reducing As(V), Fe(III), Se(VI), Mn(IV) and a variety of oxidized sulfur species. 16S ribosomal DNA sequence comparisons reveal that strain GBFH is closely related to Desulfitobacterium hafniense DCB-2(T) and Desulfitobacterium frappieri PCP-1(T). Comparative physiology demonstrates that D. hafniense and D. frappieri, known for reductively dechlorinating chlorophenols, are also capable of toxic metal or metalloid respiration. DNA-DNA hybridization and comparative physiological studies suggest that D. hafniense, D. frappieri, and strain GBFH should be united into one species. The isolation of an Fe(III)- and As(V)-reducing bacterium from Lake Coeur d'Alene suggests a mechanism for arsenic mobilization in these contaminated sediments while the discovery of metal or metalloid respiration in the genus Desulfitobacterium has implications for environments cocontaminated with arsenious and chlorophenolic compounds.

Evidence for microbial Fe(III) reduction in anoxic, mining-impacted lake sediments (Lake Coeur d'Alene, Idaho).

Mining-impacted sediments of Lake Coeur d'Alene, Idaho, contain more than 10% metals on a dry weight basis, approximately 80% of which is iron. Since iron (hydr)oxides adsorb toxic, ore-associated elements, such as arsenic, iron (hydr)oxide reduction may in part control the mobility and bioavailability of these elements. Geochemical and microbiological data were collected to examine the ecological role of dissimilatory Fe(III)-reducing bacteria in this habitat. The concentration of mild-acid-extractable Fe(II) increased with sediment depth up to 50 g kg(-1), suggesting that iron reduction has occurred recently. The maximum concentrations of dissolved Fe(II) in interstitial water (41 mg liter(-1)) occurred 10 to 15 cm beneath the sediment-water interface, suggesting that sulfidogenesis may not be the predominant terminal electron-accepting process in this environment and that dissolved Fe(II) arises from biological reductive dissolution of iron (hydr)oxides. The concentration of sedimentary magnetite (Fe(3)O(4)), a common product of bacterial Fe(III) hydroxide reduction, was as much as 15.5 g kg(-1). Most-probable-number enrichment cultures revealed that the mean density of Fe(III)-reducing bacteria was 8.3 x 10(5) cells g (dry weight) of sediment(-1). Two new strains of dissimilatory Fe(III)-reducing bacteria were isolated from surface sediments. Collectively, the results of this study support the hypothesis that dissimilatory reduction of iron has been and continues to be an important biogeochemical process in the environment examined.

Systematic changes in gene expression patterns following adaptive evolution in yeast.

Culturing a population of Saccharomyces cerevisiae for many generations under conditions to which it is not optimally adapted selects for fitter genetic variants. This simple experimental design provides a tractable model of adaptive evolution under natural selection. Beginning with a clonal, founding population, independently evolved strains were obtained from three independent cultures after continuous aerobic growth in glucose-limited chemostats for more than 250 generations. DNA microarrays were used to compare genome-wide patterns of gene expression in the evolved strains and the parental strain. Several hundred genes were found to have significantly altered expression in the evolved strains. Many of these genes showed similar alterations in their expression in all three evolved strains. Genes with altered expression in the three evolved strains included genes involved in glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation, and metabolite transport. These results are consistent with physiological observations and indicate that increased fitness is acquired by altering regulation of central metabolism such that less glucose is fermented and more glucose is completely oxidized.

Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment.

When microbes evolve in a continuous, nutrient-limited environment, natural selection can be predicted to favor genetic changes that give cells greater access to limiting substrate. We analyzed a population of baker's yeast that underwent 450 generations of glucose-limited growth. Relative to the strain used as the inoculum, the predominant cell type at the end of this experiment sustains growth at significantly lower steady-state glucose concentrations and demonstrates markedly enhanced cell yield per mole glucose, significantly enhanced high-affinity glucose transport, and greater relative fitness in pairwise competition. These changes are correlated with increased levels of mRNA hybridizing to probe generated from the hexose transport locus HXT6. Further analysis of the evolved strain reveals the existence of multiple tandem duplications involving two highly similar, high-affinity hexose transport loci, HXT6 and HXT7. Selection appears to have favored changes that result in the formation of more than three chimeric genes derived from the upstream promoter of the HXT7 gene and the coding sequence of HXT6. We propose a genetic mechanism to account for these changes and speculate as to their adaptive significance in the context of gene duplication as a common response of microorganisms to nutrient limitation.

Nosocomial acquisition of multiresistant Acinetobacter baumannii: risk factors and prognosis.

To identify risk factors for and prognostic indicators of the nosocomial acquisition of multiresistant Acinetobacter baumannii in an intensive care unit, we prospectively studied 40 patients: 13 who were infected with this organism and 27 who were colonized. Isolates were identified by pulsed-field gel electrophoresis; the infected/colonized patients were compared with 348 noninfected, noncolonized patients by logistic regression analysis and with matched historical controls in a cohort study. The severity of illness (evaluated by the APACHE II score; P < .05) and previous infection (P < .001) were retained as independent risk factors for acquiring A. baumannii. Logistic regression analysis selected a high APACHE II score (P < .01) and the acquisition of A. baumannii (P < .01) as factors independently associated with death. The acquisition of A. baumannii was associated not only with high mortality but also with a length of stay on the intensive care unit in excess of that due to the underlying disease alone; specifically, the attributable mortality was 25%, with a risk ratio for death of 2.0 (95% confidence interval, 1.11-3.62), and the duration of stay for infected/colonized patients was 10.3 days longer than that for controls (P < .001).

Microbial adaptation to a changeable environment: cell-cell interactions mediate physiological and genetic differentiation.

Recent work by Magnuson, Solomon and Grossman(1) adds to a growing body of evidence indicating that microorganisms possess sophisticated signaling systems that enable them to sense and respond to environmental challenges. Typically, this response results in morphological, physiological and even genetic differentiation, paralleling that observed among higher organisms. These signaling systems may be interpreted as adaptations that maximize the reproductive potential of a population.

Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli.

Populations of Escherichia coli initiated with a single clone and maintained for long periods in glucose-limited continuous culture, become polymorphic. In one population, three clones were isolated and by means of reconstruction experiments were shown to be maintained in stable polymorphism, although they exhibited substantial differences in maximum specific growth rates and in glucose uptake kinetics. Analysis of these three clones revealed that their stable coexistence could be explained by differential patterns of the secretion and uptake of two alternative metabolites acetate and glycerol. Regulatory (constitutive and null) mutations in acetyl-coenzyme A synthetase accounted for different patterns of acetate secretion and uptake seen. Altered patterns in glycerol uptake are most likely explained by mutations which result in quantitative differences in the induction of the glycerol regulon and/or structural changes in glycerol kinase that reduce allosteric inhibition by effector molecules associated with glycolysis. The evolution of resource partitioning, and consequent polymorphisms which arise may illustrate incipient processes of speciation in asexual organisms.

Regulation of fitness in yeast overexpressing glycolytic enzymes: responses to heat shock and nitrogen starvation.

Current models based on the analysis of linear metabolic pathways at steady-state predict that large increases over wild type in the activity of one enzyme will not alter an organism's fitness. This prediction is tested at steps in a highly branched pathway under two conditions known to alter steady-state: heat shock and nitrogen starvation. Saccharomyces cerevisiae transformants overproducing 1 of 4 enzymes in glycolysis (hexokinase B, phosphoglucose isomerase, phosphofructokinase, or pyruvate kinase) were subjected to heat shock in both exponential and stationary phases of growth. In neither phase does enzyme overexpression alter heat shock sensitivity. When starved for nitrogen in acetate medium, transformants overproducing hexokinase, phosphoglucose isomerase, and phosphofructokinase sporulate at the same rate and with the same frequency as cells harbouring only the plasmid vector. Current models therefore correctly predict the relationship between activity and components of fitness for 3 of 4 enzymes. By contrast, cells overexpressing pyruvate kinase sporulate poorly. This defect is not observed among cells transformed with a plasmid containing a Tn5 disrupted copy of the PYK gene. These findings are consistent with reports that implicate the PYK locus in yeast cell cycle control and suggest that it may be challenging to model relations between fitness and activity for multifunctional proteins.

Regulation of fitness in yeast overexpressing glycolytic enzymes: parameters of growth and viability.

Current models predict that large increases over wild-type in the activity of one enzyme will not alter an organism's fitness. This prediction is tested in Saccharomyces cerevisiae through the use of a high copy plasmid that bears one of the following: hexokinase B (HEXB), phosphoglucose isomerase (PGI), phosphofructokinase (PFKA and PFKB), or pyruvate kinase (PYK). Transformants containing these plasmids demonstrate a four to ten-fold increase in enzyme specific activity over either the parent strain or transformants containing the plasmid alone. Haploid and diploid transformants derived from independent backgrounds were grown on both fermentable and non-fermentable carbon sources and evaluated for several components of fitness. These include growth rate under non-limiting conditions, maximum stationary phase density, and viability in extended batch culture. Cell viability is not affected by overproduction of these enzymes. Growth rate and stationary phase density do not differ significantly among strains that overexpress HEXB, PGI or contain the vector alone. PFKA, B transformants show reduced growth rate on glucose in one background only. For these loci the current model is confirmed. By contrast, when grown on glucose, yeast overexpressing PYK demonstrate reduced growth rate and increased stationary phase density in both backgrounds. These effects are abolished in cells containing plasmids with a Tn5 disrupted copy of the PYK gene. Our results are consistent with reports that the PYK locus may exert control over the yeast cell cycle and suggest that it will be challenging to model relations between fitness and activity for multifunctional proteins.