Applied Microbiology and Biotechnology

ABSTRACT Methylglyoxal (MG) is a cytotoxic, nonenzymatic by-product of glycolysis that readily glycates proteins and DNA, resulting in carbonyl stress. Glyoxalase I and II (GloA and GloB) sequentially convert MG into d -lactic acid using glutathione (GSH) as a cofactor. The glyoxalase system is essential for the mitigation of MG-induced carbonyl stress, preventing subsequent cell death, and recycling GSH for maintenance of cellular redox poise. All pathogenic liberibacters identified to date are uncultured, including “ Candidatus Liberibacter asiaticus,” a psyllid endosymbiont and causal agent of the severely damaging citrus disease “huanglongbing.” In silico analysis revealed the absence of gloA in “ Ca . Liberibacter asiaticus” and all other pathogenic liberibacters. Both gloA and gloB are present in Liberibacter crescens , the only liberibacter that has been cultured. L. crescens GloA was functional in a heterologous host. Marker interruption of gloA in L. crescens appeared to be lethal. Key glycolytic enzymes were either missing or significantly downregulated in “ Ca . Liberibacter asiaticus” compared to (cultured) L. crescens . Marker interruption of sut , a sucrose transporter gene in L. crescens , decreased its ability to take up exogenously supplied sucrose in culture. “ Ca . Liberibacter asiaticus” lacks a homologous sugar transporter but has a functional ATP/ADP translocase, enabling it to thrive both in psyllids and in the sugar-rich citrus phloem by (i) avoiding sucrose uptake, (ii) avoiding MG generation via glycolysis, and (iii) directly importing ATP from the host cell. MG detoxification enzymes appear to be predictive of “ Candidatus ” status for many uncultured pathogenic and environmental bacteria. IMPORTANCE Discovered more than 100 years ago, the glyoxalase system is thought to be present across all domains of life and fundamental to cellular growth and viability. The glyoxalase system protects against carbonyl stress caused by methylglyoxal (MG), a highly reactive, mutagenic and cytotoxic compound that is nonenzymatically formed as a by-product of glycolysis. The uncultured alphaproteobacterium “ Ca . Liberibacter asiaticus” is a well-adapted endosymbiont of the Asian citrus psyllid, which transmits the severely damaging citrus disease “huanglongbing.” “ Ca . Liberibacter asiaticus” lacks a functional glyoxalase pathway. We report here that the bacterium is able to thrive both in psyllids and in the sugar-rich citrus phloem by (i) avoiding sucrose uptake, (ii) avoiding (significant) MG generation via glycolysis, and (iii) directly importing ATP from the host cell. We hypothesize that failure to culture “ Ca . Liberibacter asiaticus” is at least partly due to its dependence on host cells for both ATP and MG detoxification.

AbstractCultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, ‘Candidatus Reconcilibacillus cellulovorans’, possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the ‘Ca. Reconcilibacillus cellulovorans’ multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.

AbstractChallenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.

Summary A novel candidate species of the liberibacter genus, ‘ Candidatus Liberibacter brunswickensis’ ( CL br), was identified in the Australian eggplant psyllid, Acizzia solanicola . This is the first discovery of a species belonging to the liberibacter genus in Australia and the first report of a liberibacter species in the psyllid genus Acizzia . This new candidate liberibacter species has not been associated with plant disease, unlike other psyllid‐vectored species in the genus including ‘ Candidatus Liberibacter asiaticus ’ ( CL as), ‘ Candidatus Liberibacter africanus’ ( CL af) and ‘ Ca . Liberibacter solanacearum’ ( CL so). This study describes novel generic liberibacter genus primers, used to screen Australian psyllids for the presence of microflora that may confound diagnosis of exotic pathogens. CL br forms a unique clade in the liberibacter genus based on phylogenetic analysis of the 16S ribosomal ribonucleic acid ( rRNA ) region and multilocus sequence analysis ( MLSA ) of seven highly conserved genes, dnaG , gyrB , mutS , nusG , rplA , rpoB and tufB . The MLSA mapping approach described in this article was able to discriminate between two ‘ Ca . Liberibacter’ species within a metagenomic data set and represents a novel approach to detecting and differentiating unculturable species of liberibacter. Further, CL br can confound the Li et al . (2006) quantitative PCR ( qPCR ) diagnostic tests for CL as and CL af.