Complete genome sequence of Liberibacter crescens BT-1

Liberibacter crescens BT-1, a Gram-negative, rod-shaped bacterial isolate, was previously recovered from mountain papaya to gain insight on Huanglongbing (HLB) and Zebra Chip (ZC) diseases. The genome of BT-1 was sequenced at the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida. A finished assembly and annotation yielded one chromosome with a length of 1,504,659 bp and a G+C content of 35.4%. Comparison to other species in the Liberibacter genus, L. crescens has many more genes in thiamine and essential amino acid biosynthesis. This likely explains why L. crescens BT-1 is culturable while the known Liberibacter strains have not yet been cultured. Similar to Candidatus L. asiaticus psy62, the L. crescens BT-1 genome contains two prophage regions

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial signatures of the agricultural land-use. The three sites included in this study are the Broadbalk Experiment at Rothamsted Research, UK, the Everglades Agricultural Area, Florida, USA, and the Kellogg Biological Station, Michigan, USA. The effects of agricultural management on the abundance and diversity of bacteria and archaea were determined using high throughput, barcoded 16S rRNA sequencing. In addition, the relative abundance of these organisms was correlated with soil features. Two groups of microorganisms involved in nitrogen cycle were highly correlated with land use at all three sites. The ammonia oxidizing-archaea, dominated by Ca. Nitrososphaera, were positively correlated with agriculture while a ubiquitous group of soil bacteria closely related to the diazotrophic symbiont, Bradyrhizobium, was negatively correlated with agricultural management. Analysis of successional plots showed that the abundance of ammonia oxidizing-archaea declined and the abundance of bradyrhizobia increased with time away from agriculture. This observation suggests that the effect of agriculture on the relative abundance of these genera is reversible. Soil pH and NH(3) concentrations were positively correlated with archaeal abundance but negatively correlated with the abundance of Bradyrhizobium. The high correlations of Ca. Nitrososphaera and Bradyrhizobium abundances with agricultural management at three long-term experiments with different edaphoclimatic conditions allowed us to suggest these two genera as signature microorganisms for agricultural land use

Comparative genomics analysis of Liberibacter species to elucidate pathogenesis and culturability

Liberibacter crescens BT-1, a gram negative, rod-shaped bacterial isolate, was previously recovered from mountain papaya and sequenced. As L. crescens is culturable and is not a pathogen of citrus, comparative genomics of this strain with other uncultured, pathogenic Liberibacter should suggest genes involved in both phenotypes. Genomic comparison to Liberibacter sp. revealed differences in metabolic pathways and virulence genes.  Specific differences in metabolism include the inability of L. asiaticus and L. solanacearum to synthesize histidine, tryptophan, and thiamine, as well as a reduced ability to produce other amino acids. L. asiaticus and L. solanacearum possess a thiamine ABC transporter not found in L. crescens, which may compensate for the inability to synthesize thiamine.  Diversity in the flp pilus operon and metal ABC transporters were observed that may contribute to the pathogenesis of the uncultured species. These differences may contribute to variation in virulence and culturability among species. Finally, two putative prophage regions were found in L. crescens that share moderate functional similarity to the phage regions of L. asiaticus, but sequence similarity is not conserved. Additional genomic comparisons will expand our understanding of virulence and vector-interactions of the described Liberibacter sp.&nbsp

Comparative genomics analysis of Liberibacter species to elucidate pathogenesis and culturability

Liberibacter crescens BT-1, a gram negative, rod-shaped bacterial isolate, was previously recovered from mountain papaya and sequenced. As L. crescens is culturable and is not a pathogen of citrus, comparative genomics of this strain with other uncultured, pathogenic Liberibacter should suggest genes involved in both phenotypes. Genomic comparison to Liberibacter sp. revealed differences in metabolic pathways and virulence genes.  Specific differences in metabolism include the inability of L. asiaticus and L. solanacearum to synthesize histidine, tryptophan, and thiamine, as well as a reduced ability to produce other amino acids. L. asiaticus and L. solanacearum possess a thiamine ABC transporter not found in L. crescens, which may compensate for the inability to synthesize thiamine.  Diversity in the flp pilus operon and metal ABC transporters were observed that may contribute to the pathogenesis of the uncultured species. These differences may contribute to variation in virulence and culturability among species. Finally, two putative prophage regions were found in L. crescens that share moderate functional similarity to the phage regions of L. asiaticus, but sequence similarity is not conserved. Additional genomic comparisons will expand our understanding of virulence and vector-interactions of the described Liberibacter sp.&nbsp

The Effect of Tillage System and Crop Rotation on Soil Microbial Diversity and Composition in a Subtropical Acrisol

Agricultural management alters physical and chemical soil properties, which directly affects microbial life strategies and community composition. The microbial community drives important nutrient cycling processes that can influence soil quality, cropping productivity and environmental sustainability. In this research, a long-term agricultural experiment in a subtropical Acrisol was studied in south Brazil. The plots at this site represent two tillage systems, two nitrogen fertilization regimes and three crop rotation systems. Using Illumina high-throughput sequencing of the 16S rRNA gene, the archaeal and bacterial composition was determined from phylum to species level in the different plot treatments. The relative abundance of these taxes was correlated with measured soil properties. The P, Mg, total organic carbon, total N and mineral N were significantly higher in the no-tillage system. The microbial diversity was higher in the no-tillage system at order, family, genus and species level. In addition, overall microbial composition changed significantly between conventional tillage and no-tillage systems. Anaerobic bacteria, such as clostridia, dominate in no-tilled soil as well as anaerobic methanogenic archaea, which were detected only in the no-tillage system. Microbial diversity was higher in plots in which only cereals (oat and maize) were grown. Soil management influenced soil biodiversity on Acrisol by change of composition and abundance of individual species

KEGG pathway indicating the extent of Folate Biosynthesis in <i>Liberibacter</i> species.

<p>All genomes lack alkaline phosphatase (EC 3.1.3.1.). This pathway is further incomplete in Ca. Liberibacter asiaticus, which has lost several enzymes for the production of Dihydrofolate (DHF).</p

Genomic coverage of SEED subsystems.

<p>The total number of genes annotated in each SEED subsystem is shown. The number of subsystem genes identified in each studied genome is shown in bold, with the percent-coverage in parenthesis. Additional manual curation, independent of RAST, is not reflected in this table.</p

Comparative Genomics of Cultured and Uncultured Strains Suggests Genes Essential for Free-Living Growth of <i>Liberibacter</i>

<div><p>The full genomes of two uncultured plant pathogenic <i>Liberibacter</i>, <i>Ca</i>. Liberibacter asiaticus and <i>Ca</i>. Liberibacter solanacearum, are publicly available. Recently, the larger genome of a closely related cultured strain, <i>Liberibacter crescens</i> BT-1, was described. To gain insights into our current inability to culture most <i>Liberibacter</i>, a comparative genomics analysis was done based on the RAST, KEGG, and manual annotations of these three organisms. In addition, pathogenicity genes were examined in all three bacteria. Key deficiencies were identified in <i>Ca</i>. L. asiaticus and <i>Ca</i>. L. solanacearum that might suggest why these organisms have not yet been cultured. Over 100 genes involved in amino acid and vitamin synthesis were annotated exclusively in <i>L. crescens</i> BT-1. However, none of these deficiencies are limiting in the rich media used to date. Other genes exclusive to <i>L. crescens</i> BT-1 include those involved in cell division, the stringent response regulatory pathway, and multiple two component regulatory systems. These results indicate that <i>L. crescens</i> is capable of growth under a much wider range of conditions than the uncultured <i>Liberibacter</i> strains. No outstanding differences were noted in pathogenicity-associated systems, suggesting that <i>L. crescens</i> BT-1 may be a plant pathogen on an as yet unidentified host.</p></div