The Integrative Conjugative Element clc (ICEclc) of Pseudomonas aeruginosa JB2

Integrative conjugative elements (ICE) are a diverse group of chromosomally integrated, self-transmissible mobile genetic elements (MGE) that are active in shaping the functions of bacteria and bacterial communities. Each type of ICE carries a characteristic set of core genes encoding functions essential for maintenance and self-transmission, and cargo genes that endow on hosts phenotypes beneficial for niche adaptation. An important area to which ICE can contribute beneficial functions is the biodegradation of xenobiotic compounds. In the biodegradation realm, the best-characterized ICE is ICEclc, which carries cargo genes encoding for ortho-cleavage of chlorocatechols (clc genes) and aminophenol metabolism (amn genes). The element was originally identified in the 3-chlorobenzoate-degrader Pseudomonas knackmussii B13, and the closest relative is a nearly identical element in Burkholderia xenovorans LB400 (designated ICEclc-B13 and ICEclc-LB400, respectively). In the present report, genome sequencing of the o-chlorobenzoate degrader Pseudomonas aeruginosa JB2 was used to identify a new member of the ICEclc family, ICEclc-JB2. The cargo of ICEclc-JB2 differs from that of ICEclc-B13 and ICEclc-LB400 in consisting of a unique combination of genes that encode for the utilization of o-halobenzoates and o-hydroxybenzoate as growth substrates (ohb genes and hyb genes, respectively) and which are duplicated in a tandem repeat. Also, ICEclc-JB2 lacks an operon of regulatory genes (tciR-marR-mfsR) that is present in the other two ICEclc, and which controls excision from the host. Thus, the mechanisms regulating intracellular behavior of ICEclc-JB2 may differ from that of its close relatives. The entire tandem repeat in ICEclc-JB2 can excise independently from the element in a process apparently involving transposases/insertion sequence associated with the repeats. Excision of the repeats removes important niche adaptation genes from ICEclc-JB2, rendering it less beneficial to the host. However, the reduced version of ICEclc-JB2 could now acquire new genes that might be beneficial to a future host and, consequently, to the survival of ICEclc-JB2. Collectively, the present identification and characterization of ICEclc-JB2 provides insights into roles of MGE in bacterial niche adaptation and the evolution of catabolic pathways for biodegradation of xenobiotic compounds

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4

Abstract Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding phenanthrene degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3’ end a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Determination of the complete genome sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH biodegradation that may shape the process in the environment.http://deepblue.lib.umich.edu/bitstream/2027.42/134560/1/40793_2015_Article_41.pd

Impacts of Edaphic Factors on Communities of Ammonia-Oxidizing Archaea, Ammonia-Oxidizing Bacteria and Nitrification in Tropical Soils

<div><p>Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (<i>ca.</i> 10⁵ to 10⁶ copies archaeal <i>amoA</i> g⁻¹ soil), but AOB levels were low and bacterial <i>amoA</i> was infrequently detected. AOA abundance showed a significant negative correlation (<i>p</i><0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by <i>amoA</i> terminal restriction fragment (TRF) analysis, differed significantly between soils (<i>p</i><0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (<i>p</i><0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (<i>p</i><0.01). In clone libraries, phylotypes of archaeal <i>amoA</i> (predominantly <i>Nitrososphaera</i>) and bacterial <i>amoA</i> (predominanatly <i>Nitrosospira</i>) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (<i>p</i><0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity.</p></div

BEST Variables explaining variation between soils in bacterial <i>amoA</i> MspI terminal restriction fragment profiles^a.

a<p>Variables included in correlation indicated by “X”. Abbreviations: P = Phosphorus; K = Potassium; S = Sulphur; B = Boron; Mn = Manganese; Fe = Iron, Cu = Copper; Al = Aluminium; Na, Sodium; BD, Bulk Density; OC, Organic Carbon.</p

Neighbor joining consensus tree of bacterial AmoA phylotypes.

<p>Colored branches indicate the <i>Nitrosomonas</i> cluster (green) and <i>Nitrosospira</i> cluster (blue). Boot strap values are indicated at nodes. Values in red are cluster designations following the classification of Avrahami et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089568#pone.0089568-Avrahami1" target="_blank">[48]</a> based on amino acid alignment of bacterial AmoA.</p

Box and whisker plots of gene abundance determined by qPCR.

<p>Panel A, Archaeal <i>amoA</i>; Panel B, Archaeal 16S rRNA; Panel C, Bacterial 16S rRNA. Symbol colors correspond to soil types: red, sandy loam; blue, silty loam; green, clay. Soil name abbreviations are: A, Arena; B, Brasso; E, Ecclesville; P, Piarco; R, River Estate; S, St. Augustine; T, Talparo; W, Princes Town.</p

Nitrification Potential^a.

a<p>N = NO₃-N+NO₂-N, <i>p</i><0.001, LSD (5%) = 0.17, SEM = 0.06.</p

Soil Elemental Properties^a.

a<p>Abbreviations: P = Phosphorus; K = Potassium; Ca = Calcium; Mg = Magnesium; S = Sulphur; Zn = Zinc, B = Boron;</p><p>Mn = Manganese; Fe = Iron, Cu = Copper; Al = Aluminium; Na = Sodium.</p

Principle coordinate plot of archaeal <i>amoA</i> clone libraries (Panel A) and bacterial <i>amoA</i> clone libraries (Panel B).

<p>Symbol colors correspond to soil pH: red, acidic (pH<6); green, circum-neutral (pH 6.2, 6.6), blue, alkaline (pH 7.8, 8.2), purple, multiple pH. Letters indicate soil names that are abbreviated as: A, Arena; B, Brasso; E, Ecclesville; P, Piarco; R, River Estate; S, St. Augustine; T, Talparo; W, Princes Town.</p

Map of Trinidad showing distribution of the soil series analyzed and the sampling locations.

<p>Map of Trinidad showing distribution of the soil series analyzed and the sampling locations.</p