Publications

4982

Incidence and severity of Huanglongbing (HLB) disease were assessed in Apr. 2010 among eight citrus cultivars representing diverse scion types growing in commercial groves in Florida's Indian River region, an area with a high incidence of HLB. In each grove, 20 trees of each cultivar were rated for visual HLB symptoms and leaves were collected for quantitative polymerase chain reaction quantification of Candidatus Liberibacter asiaticus (CLas), the presumptive causal agent of HLB. There was a strong correlation between HLB rating and CLas titer (titer represented by Ct, r2 = 0.37 and 0.40, for whole tree and leaf sample, respectively, both with P < 0.0001) across all cultivars and groves. Although incidence and severity of HLB varied considerably among the groves, scion-specific differences were apparent, even when analyses excluded potentially confounding grove effects. ‘Temple’ tangor showed the most consistently low incidence of HLB symptoms and CLas titer; in contrast, ‘Murcott’ tangor and ‘Minneola’ tangelo had the highest incidence of HLB symptoms and highest CLas titer. These results suggest useful resistance to HLB with reduced symptoms and reduced CLas titer may be found in conventional scion cultivars and further work is needed to assess this potential and its commercial value.

An aerobic, saccharolytic, obligately thermophilic, motile, non-spore-forming bacterium, strain T49T, was isolated from geothermally heated soil at Hell’s Gate, Tikitere, New Zealand. On the basis of 16S rRNA gene sequence similarity, T49T is the first representative of a new class in the newly described phylum Armatimonadetes, formerly known as candidate division OP10. Cells of strain T49T stained Gram-negative and were catalase-positive and oxidase-negative. Cells possessed a highly corrugated outer membrane. The major fatty acids were 16 : 0, i17 : 0 and ai17 : 0. The G+C content of the genomic DNA was 54.6 mol%. Strain T49T grew at 50–73 °C with an optimum temperature of 68 °C, and at pH 4.7–5.8 with an optimum growth pH of 5.3. A growth rate of 0.012 h−1 was observed under optimal temperature and pH conditions. The primary respiratory quinone was MK-8. Optimal growth was achieved in the absence of NaCl, although growth was observed at NaCl concentrations as high as 2 % (w/v). Strain T49T was able to utilize mono- and disaccharides such as cellobiose, lactose, mannose and glucose, as well as branched or amorphous polysaccharides such as starch, CM-cellulose, xylan and glycogen, but not highly linear polysaccharides such as crystalline cellulose or cotton. On the basis of its phylogenetic position and phenotypic characteristics, we propose that strain T49T represents a novel bacterial genus and species within the new class Chthonomonadetes classis nov. of the phylum Armatimonadetes. The type strain of Chthonomonas calidirosea gen. nov., sp. nov. is T49T ( = DSM 23976T = ICMP 18418T).

A sustainable option for nitrogen removal is the anaerobic ammonium-oxidizing (anammox) process in which ammonium is oxidized to nitrogen gas with nitrite as electron acceptor. Application of this process, however, is limited by the availability of anammox biomass. In this study, two Brocadia-like anammox phylotypes were successfully enriched, detected and identified from an activated sludge taken from a domestic wastewater treatment plant (Minas Gerais, Brazil) employing a Sequencing Batch Reactor (SBR). The dominant phylotype was closely related to ‘Candidatus Brocadia sinica’, but one clone seemed to represent a novel species for which we propose the name ‘Candidatus Brocadia brasiliensis’. Based on Fluorescence in situ hybridization (FISH) analysis, this enrichment led to a relative population size of 52.7% (±15.6) anammox bacteria after 6 months of cultivation. The cultivation process can be divided into three phases: phase 1 (approximately 25 days) was characterized by heterotrophic denitrification metabolism, phase 2 was the propagation phase and phase 3 (from the 87th day onwards), in which significant anammox activity was detected. A long-term performance of the SBR showed a near perfect removal of nitrite based on the influent NO2−-N concentration of 61–95 mg L−1. The average ammonia removal efficiency was 90% with the influent NH4+-N concentration of 55–82 mg L−1. Therefore, anammox cultivation and enrichment from activated sludge was possible under a controlled environment within 3 months.

ABSTRACT Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, “ Candidatus Nitrosopumilus koreensis” MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite.

Nitrification is a fundamental component of the global nitrogen cycle and leads to significant fertilizer loss and atmospheric and groundwater pollution. Nitrification rates in acidic soils (pH < 5.5), which comprise 30% of the world's soils, equal or exceed those of neutral soils. Paradoxically, autotrophic ammonia oxidizing bacteria and archaea, which perform the first stage in nitrification, demonstrate little or no growth in suspended liquid culture below pH 6.5, at which ammonia availability is reduced by ionization. Here we report the discovery and cultivation of a chemolithotrophic, obligately acidophilic thaumarchaeal ammonia oxidizer, “ Candidatus Nitrosotalea devanaterra,” from an acidic agricultural soil. Phylogenetic analysis places the organism within a previously uncultivated thaumarchaeal lineage that has been observed in acidic soils. Growth of the organism is optimal in the pH range 4 to 5 and is restricted to the pH range 4 to 5.5, unlike all previously cultivated ammonia oxidizers. Growth of this organism and associated ammonia oxidation and autotrophy also occur during nitrification in soil at pH 4.5. The discovery of Nitrosotalea devanaterra provides a previously unsuspected explanation for high rates of nitrification in acidic soils, and confirms the vital role that thaumarchaea play in terrestrial nitrogen cycling. Growth at extremely low ammonia concentration (0.18 nM) also challenges accepted views on ammonia uptake and metabolism and indicates novel mechanisms for ammonia oxidation at low pH.

ABSTRACT “ Candidatus Liberibacter asiaticus” is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of “ Ca . Liberibacter” associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes ( hyv I and hyv II ) were identified in the prophage regions of the Psy62 “ Ca. Liberibacter asiaticus” genome. Sequence analyses of the hyv I and hyv II genes in 35 “ Ca. Liberibacter asiaticus” DNA isolates collected globally revealed that the hyv I gene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, while hyv II contains up to 2 NITRs and 4 partial repeats and shares homology with hyv I . Frequent deletions or insertions of these repeats within the hyv I and hyv II genes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of “ Ca. Liberibacter asiaticus” bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single “ Ca. Liberibacter asiaticus”-infected sample. This is the first evidence of different “ Ca. Liberibacter asiaticus” populations coexisting in a single HLB-affected sample. The Florida “ Ca. Liberibacter asiaticus” isolates contain both hyv I and hyv II , while all other global “ Ca. Liberibacter asiaticus” isolates contain either one or the other. Interclade assignments of the putative Hyv I and Hyv II proteins from Florida isolates with other global isolates in phylogenetic trees imply multiple “ Ca. Liberibacter asiaticus” populations in the world and a multisource introduction of the “ Ca. Liberibacter asiaticus” bacterium into Florida.