Analysis of Competition in Soil among 2,4-Dichlorophenoxyacetic Acid-Degrading Bacteria

Competition among indigenous and inoculated 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria was studied in a native Kansas prairie soil following 2,4-D additions. The soil was inoculated with four different 2,4-D-degrading strains at densities of 10(3) cells per g of soil; the organisms used were Pseudomonas cepacia DBO1(pJP4) and three Michigan soil isolates, strain 745, Sphingomonas paucimobilis 1443, and Pseudomonas pickettii 712. Following 2,4-D additions, total soil DNA was extracted and analyzed on Southern blots by using a tfdA gene probe which detected three of the strains and another probe that detected the fourth strain, S. paucimobilis 1443, which belongs to a different class of 2,4-D degraders. P. cepacia DBO1(pJP4), a constructed strain, outcompeted the other added strains and the indigenous 2,4-D-degrading populations. The S. paucimobilis population was the secondary dominant population, and strain 745 and P. pickettii were not detected. Relative fitness coefficients determined in axenic broth cultures predicted the outcome of competition in soil for some but not all strains. Lag time was shown to be a principal determinant of competitiveness among the strains, but the lag times were significantly reduced in mixed broth cultures, which changed the competitive outcome. Plasmids containing the genes for the 2,4-D pathway were important determinants of competitiveness since plasmid pKA4 in P. cepacia DBO1 resulted in the slower growth characteristic of its original host, P. pickettii, rather than the rapid growth observed when this strain harbors pJP4

Genetic and Phenotypic Diversity of 2,4-Dichlorophenoxyacetic Acid (2,4-D)-Degrading Bacteria Isolated from 2,4-D-Treated Field Soils

Forty-seven numerically dominant 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria were isolated at different times from 1989 through 1992 from eight agricultural plots (3.6 by 9.1 m) which were either not treated with 2,4-D or treated with 2,4-D at three different concentrations. Isolates were obtained from the most dilute positive most-probable-number tubes inoculated with soil samples from the different plots on seven sampling dates over the 3-year period. The isolates were compared by using fatty acid methyl ester (FAME) profiles, chromosomal patterns obtained by PCR amplification of repetitive extragenic palindromic (REP) sequences, and hybridization patterns obtained with probes for the tfd genes of plasmid pJP4 and a probe (Spa probe) that detects a distinctly different 2,4-D-degrading isolate, Sphingomonas paucimobilis (formerly Pseudomonas paucimobilis). A total of 57% of the isolates were identified to the species level by the FAME analysis, and these isolates were strains of Sphingomonas, Pseudomonas, or Alcaligenes species. Hybridization analysis revealed four groups. Group I strains, which exhibited sequence homology with tfdA, -B, -C, and -D genes, were rather diverse, as determined by both the FAME analysis and the REP-PCR analysis. Group II, which exhibited homology only with the tfdA4 gene, was a small group and was probably a subset of group I. All group I and II strains had plasmids. Hybridization analysis revealed that the tfd genes were located on plasmids in 75% of these strains and on the chromosome or a large plasmid in the other 25% of the strains. One strain exhibited tfdA and -B hybridization associated with a plasmid band, while tfdC and -D hybridized with the chromosomal band area. The group III strains exhibited no detectable homology to tfd genes but hybridized to the Spa probe. The members of this group were tightly clustered as determined by both the FAME analysis and the REP-PCR analysis, were distinctly different from group I strains as determined by the FAME analysis, and had very few plasmids; this group contained more of the 47 isolates than any other group. The group III strains were identified as S. paucimobilis. The group IV strains, which hybridized to neither the tfd probe nor the Spa probe, were as diverse as the group I strains as determined by the FAME and REP-PCR analyses. Most of group IV strains could not be identified by the FAME analysis. Strains belonging to groups I and III were more frequently recovered from soils that had greater field exposure to 2,4-D, suggesting that they were the best competitors for 2,4-D under field conditions. The selection regimen which we used led to two successful but dissimilar groups; the members of one group were similar at the plasmid level but not at the organism level, and the members of the other group were similar at the organism level. Since the members of the latter group are ecologically successful and degradative genes unlike tfd genes, they deserve more attention

Use of Gene Probes to Aid in Recovery and Identification of Functionally Dominant 2,4-Dichlorophenoxyacetic Acid-Degrading Populations in Soil

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) was applied to soils in microcosms, and degradation was monitored after each of five repeated additions. Total DNAs were isolated from soil bacterial communities after each 2,4-D treatment. The DNA samples were analyzed on slot blots and Southern blots by using a tfdA gene probe subcloned from plasmid pJP4 and a Spa probe derived from a different 2,4-D-degrading isolate, a Sphingomonas paucimobilis strain. 2,4-D applied to soil was quickly degraded by indigenous microbial populations. As determined by slot blot analyses of DNA from a Michigan soil, the increase in hybridization signal in response to 2,4-D treatments was greater with the Spa probe than with the tfdA probe. In contrast, the DNA from a Saskatchewan soil exhibited an increase in hybridization signal with the tfdA probe. This indicated that a population with 2,4-D-degradative gene sequences different from the tfdA gene sequence was dominant in the Michigan site, but not in the Saskatchewan site. A Southern blot analysis of DNA from Michigan soil showed that the dominant 2,4-D-degrading population was S. paucimobilis 1443. A less dominant 2,4-D-degrading population was detected with the tfdA probe; further analysis revealed that this population was a Pseudomonas pickettii 712. These gene probe analyses revealed that an important population carrying out 2,4-D degradation was not detected when the canonical tfdA gene probe was used. After a series of new strains were isolated, we identified a probe to detect and identify the dominant members of this new group

Genome sequences of Burkholderia sp. Strains CCGE1002 and H160, isolated from legume nodules in Mexico and Brazil.

The genome sequences of Burkholderia sp. strains CCGE1002 from Mexico and H160 from Brazil, isolated from legume nodules, are reported. Their gene contents in relation to plant-microbe interactions and xenobiotic degradation are discussed

Simple transfer functions for calculating benthic fixed nitrogen losses and C:N:P regeneration ratios in global biogeochemical models

Empirical transfer functions are derived for predicting the total benthic nitrate loss(LNO3) and the net loss of dissolved inorganic nitrogen (LDIN) in marine sediments,equivalent to sedimentary denitrification. The functions are dynamic vertically integratedsediment models which require the rain rate of particulate organic carbon to the seafloor(RRPOC) and a proposed new variable(O2-NO3)bw (bottom water O2 concentration minus NO3-concentration) as the only input parameters. Applied globally to maps of RRPOC and(O2-NO3)bw on a 1° x 1° spatial resolution, the models predict a NO3- drawdown of 196 Tg yr-1 (LNO3)of which 153 – 155 Tg yr-1 is denitrified to N2 (LDIN). This is in good agreement with previous estimates using very different methods. Our approach implicitly accounts for fixed N loss via anammox, such that our findings do not support the idea that the relatively recent discovery of anammox in marine sediments might require current estimates of the global benthic marine N budget to be revised. The continental shelf (0 – 200 m) accounts for >50% of global LNO3 and LDIN, with slope (200 – 2000 m) and deep-sea (>2000 m) sediments contributing ca. 30% and 20%, respectively. Denitrification in high-nitrate/low-oxygen regions such as oxygen minimum zones is significant (ca. 15 Tg N yr-1; 10% of global) despite covering only 1% of the seafloor. The data are used to estimate the net fluxes of nitrate (18 Tg N yr-1) and phosphate(27 Tg P yr-1) across the sediment-water interface. The benthic fluxes strongly deviate from Redfield composition, with globally averaged N:P, N:C and C:P values of 8.3, 0.067 and 122, respectively, indicating world-wide fixed N losses (by denitrification) relative to C and P. The transfer functions are designed to be coupled dynamically to general circulation models to better predict the feedback of sediments on pelagic nutrient cycling and dissolved O2 distributions

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes

Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change

The Rho GDI Rdi1 regulates Rho GTPases by distinct mechanisms

© 2008 by The American Society for Cell Biology. Under the License and Publishing Agreement, authors grant to the general public, effective two months after publication of (i.e.,. the appearance of) the edited manuscript in an online issue of MBoC, the nonexclusive right to copy, distribute, or display the manuscript subject to the terms of the Creative Commons–Noncommercial–Share Alike 3.0 Unported license (http://creativecommons.org/licenses/by-nc-sa/3.0).The small guanosine triphosphate (GTP)-binding proteins of the Rho family are implicated in various cell functions, including establishment and maintenance of cell polarity. Activity of Rho guanosine triphosphatases (GTPases) is not only regulated by guanine nucleotide exchange factors and GTPase-activating proteins but also by guanine nucleotide dissociation inhibitors (GDIs). These proteins have the ability to extract Rho proteins from membranes and keep them in an inactive cytosolic complex. Here, we show that Rdi1, the sole Rho GDI of the yeast Saccharomyces cerevisiae, contributes to pseudohyphal growth and mitotic exit. Rdi1 interacts only with Cdc42, Rho1, and Rho4, and it regulates these Rho GTPases by distinct mechanisms. Binding between Rdi1 and Cdc42 as well as Rho1 is modulated by the Cdc42 effector and p21-activated kinase Cla4. After membrane extraction mediated by Rdi1, Rho4 is degraded by a novel mechanism, which includes the glycogen synthase kinase 3β homologue Ygk3, vacuolar proteases, and the proteasome. Together, these results indicate that Rdi1 uses distinct modes of regulation for different Rho GTPases.Deutsche Forschungsgemeinschaf

Long-term effects of cropping system on N2O emission potential

The potential for N2O emissions outside the main growing season may be influenced by long-term effects of cropping system. This was investigated by collecting intact soil cores (100 cm3, 0-4 cm depth) under winter wheat in three organic cropping systems and a conventional reference within a long-term crop rotation experiment. Average annual inputs of C in crop residues and manure ranged from 1.7 to 3.3 Mg ha-1. A simulated freeze-thaw cycle resulted in a flush of CO2 during the first 48 h, which could be mainly from microbial sources. Other samples were adjusted to approximately –10, -30 or –100 hPa and amended with excess 15NO3- prior to freezing and thawing. Denitrification was the main source of N2O during a 72-h incubation at 22C, as judged from N2O and total 15N evolution. Although the input of C in the conventionally managed cropping system was significantly less than in the organic cropping systems, it showed higher N2O evolution at all three matric potentials. Estimates of relative gas diffusivity (DP/D0) in soil from the four cropping systems indicated that C input affected soil aeration. Soil from the two cropping systems with highest C input showed N2O evolution at DP/D0 in excess of 0.02, which is normally considered a threshold for development of anaerobic sites in the soil, presumably because the oxygen demand was also high. The study shows that cropping system affects both soil gas diffusivity and C availability, and that both characteristics significantly influence the N2O emission potential

Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock

Shewanellae are microbial models for environmental stress response; however, the sequential expression of mechanisms in response to stress is poorly understood. Here we experimentally determine the response mechanisms of Shewanella amazonensis SB2B during sodium chloride stress using a novel liquid chromatography and accurate mass-time tag mass spectrometry time-course proteomics approach. The response of SB2B involves an orchestrated sequence of events comprising increased signal transduction associated with motility and restricted growth. Following a metabolic shift to branched chain amino acid degradation, motility and cellular replication proteins return to pre-perturbed levels. Although sodium chloride stress is associated with a change in the membrane fatty acid composition in other organisms, this is not the case for SB2B as fatty acid degradation pathways are not expressed and no change in the fatty acid profile is observed. These findings suggest that shifts in membrane composition may be an indirect physiological response to high NaCl stress