Publications

4378

AbstractNonulosonic acids (NulOs) are a family of acidic carbohydrates with a nine-carbon backbone, which include different related structures, such as sialic acids. They have mainly been studied for their relevance in animal cells and pathogenic bacteria. Recently, sialic acids have been discovered as important compound in the extracellular matrix of virtually all microbial life and in “CandidatusAccumulibacter phosphatis”, a well-studied polyphosphate-accumulating organism, in particular. Here, bioaggregates highly enriched with these bacteria (approx. 95% based on proteomic data) were used to study the production of NulOs in an enrichment of this microorganism. Fluorescence lectin-binding analysis, enzymatic quantification, and mass spectrometry were used to analyze the different NulOs present, showing a wide distribution and variety of these carbohydrates, such as sialic acids and bacterial NulOs, in the bioaggregates. Phylogenetic analysis confirmed the potential of “Ca. Accumulibacter” to produce different types of NulOs. Proteomic analysis showed the ability of “Ca. Accumulibacter” to reutilize and reincorporate these carbohydrates. This investigation points out the importance of diverse NulOs in non-pathogenic bacteria, which are normally overlooked. Sialic acids and other NulOs should be further investigated for their role in the ecology of “Ca. Accumulibacter” in particular, and biofilms in general.Key Points“Ca.Accumulibacter” has the potential to produce a range of nonulosonic acids.Mass spectrometry and lectin binding can reveal the presence and location of nonulosonic acids.Role of nonulosonic acid in non-pathogenic bacteria needs to be studied in detail.

AbstractAquatic environments with high levels of dissolved ferrous iron and low levels of sulfate serve as an important systems for exploring biogeochemical processes relevant to the early Earth. Boreal Shield lakes, which number in the tens of millions globally, commonly develop seasonally anoxic waters that become iron rich and sulfate poor, yet the iron–sulfur microbiology of these systems has been poorly examined. Here we use genome-resolved metagenomics and enrichment cultivation to explore the metabolic diversity and ecology of anoxygenic photosynthesis and iron/sulfur cycling in the anoxic water columns of three Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel “Candidatus Chlorobium canadense”, encoded the cyc2 gene that is associated with photoferrotrophy among cultured Chlorobia members, along with genes for phototrophic sulfide oxidation. One environmental genome bin also encoded cyc2. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in “Ca. Chlorobium canadense”. Genomic potential for phototrophic sulfide oxidation was more commonly detected than cyc2 among environmental genome bins of Chlorobia, and metagenome and cultivation data suggested the potential for cryptic sulfur cycling to fuel sulfide-based growth. Overall, our results provide an important basis for further probing the functional role of cyc2 and indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have underexplored photophysiology pertinent to understanding Earth’s early microbial communities.

Abstract The African citrus triozid (ACT) Trioza erytreae (Del Guercio) (Hemiptera: Triozidae) and the Asian citrus psyllid (ACP) Diaphorina citri (Kuwayama) (Hemiptera: Liviidae) are primary vectors of the ‘ Candidatus ’ Liberibacter spp. ACT is associated with ‘ Candidatus Liberibacter africanus’ (CLaf) causal agent of the African citrus greening disease (ACGD), whereas ACP vectors ‘ Candidatus Liberibacter asiaticus’ (CLas) and ‘ Candidatus Liberibacter americanus’ (CLam), the Asian and the American strains, respectively, associated with huanglongbing. A preliminary survey in Kenyan citrus groves after the invasion of ACP had revealed that lime‐green sticky traps (Asacp) were not effective in detecting and monitoring ACT and ACP. Therefore, this study compared eight differently coloured double‐sided sticky traps to evaluate, which colour was most effective for detecting ACT and ACP, particularly at low densities. The traps were coded Red, Blue, Asgreen1, GLMgreen, Asacp, Asyellow, White, and Black. Asyellow and GLMgreen traps captured more ACTs and ACPs than any other trap type. However, since there was no clear difference in the efficiency of Asyellow and GLMgreen in trapping ACP, any of the two trap types would be useful in the presence of both pests. Among the eight traps, Asyellow and GLMgreen traps are potentially promising options for monitoring and detecting the pests in areas where they coexist. Our findings will guide biosecurity agencies in decision‐making and designing ecologically friendly integrated pest management (IPM) strategies for citrus greening vectors in Africa as well as serve as an early warning to safeguard against pests' invasion into unaffected areas.

A novel Gram-stain-negative, non-endospore-forming, motile, and aerobic bacterial strain, M105T, was isolated from coral Porites lutea, and was subjected to a polyphasic taxonomic study. Global alignment based on 16S rRNA gene sequences indicated that M105T shares the highest sequence identity of 94.5 % with Aliikangiella marina GYP-15T. The average nucleotide identity (ANI) and average amino acid identity (AAI) between M105T and A. marina GYP-15T was 69.8 and 71.6 %, respectively. On the basis of the results of phenotypic, chemotaxonomic, phylogenetic, phylogenomic, and comparative genomic analyses, it is concluded that M105T should represent a novel species in the genus Aliikangiella , for which the name Aliikangiella coralliicola sp. nov. is proposed. The type strain is M105T (=MCCC 1K03773T= KCTC 72442T). Furthermore, the family Kangiellaceae was classified into two families on the basis of phylogenetic, phylogenomic, polar lipid profile and motility variations. The novel family Pleioneaceae fam. nov. is proposed to accommodate the genera Aliikangiella and Pleionea .

Summary Cyanobacteria of the genus Synechococcus are major contributors to global primary productivity and are found in a wide range of aquatic ecosystems. This Synechococcus collective (SC) is metabolically diverse, with some lineages thriving in polar and nutrient‐rich locations and others in tropical or riverine waters. Although many studies have discussed the ecology and evolution of the SC, there is a paucity of knowledge on its taxonomic structure. Thus, we present a new taxonomic classification framework for the SC based on recent advances in microbial genomic taxonomy. Phylogenomic analyses of 1085 cyanobacterial genomes demonstrate that organisms classified as Synechococcus are polyphyletic at the order rank. The SC is classified into 15 genera, which are placed into five distinct orders within the phylum Cyanobacteria: (i) Synechococcales ( Cyanobium , Inmanicoccus , Lacustricoccus gen. Nov., Parasynechococcus , Pseudosynechococcus , Regnicoccus , Synechospongium gen. nov., Synechococcus and Vulcanococcus ); (ii) Cyanobacteriales ( Limnothrix ); (iii) Leptococcales ( Brevicoccus and Leptococcus ); (iv) Thermosynechococcales ( Stenotopis and Thermosynechococcus ) and (v) Neosynechococcales ( Neosynechococcus ). The newly proposed classification is consistent with habitat distribution patterns (seawater, freshwater, brackish and thermal environments) and reflects the ecological and evolutionary relationships of the SC.

The classDeltaproteobacteriacomprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylumProteobacteria, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the classDeltaproteobacteriaencompassingBdellovibrio-like predators was recently reclassified into a separate proteobacterial class, theOligoflexia. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classesDeltaproteobacteriaandOligoflexiain the phylumProteobacteria. Instead, the great majority of currently recognized members of the classDeltaproteobacteriaare better classified into four novel phylum-level lineages. We propose the namesDesulfobacterotaphyl. nov. andMyxococcotaphyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the classOligoflexiarepresent a separate phylum for which we propose the nameBdellovibrionotaphyl. nov. based on priority in the literature and general recognition of the genusBdellovibrio. Desulfobacterotaphyl. nov. includes the taxa previously classified in the phylumThermodesulfobacteria, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in theThermodesulfobacteriarather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phylaMyxococcotaandBdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.