Publications

4366

AbstractAimTo quantify current and predict future distribution of the citrus greening pathogens “Candidatus Liberibacter asiaticus” (Las) in Africa and “Candidatus Liberibacter africanus” (Laf) globally.LocationAfrica.MethodsThree species distribution models (MaxEnt, BIOCLIM and Boosted Regression Trees) were used to predict the current and future potential distribution of Las in Africa, and the potential global distribution of Laf, using long‐term bioclimatic variables. Two climate change scenarios (moderate and extreme) were employed to determine how future climate alterations may affect the potential distribution of Las in Africa. Presence data from global reports of Las, as well as the new positional points obtained in this survey, were used to predict the habitat suitability of the pathogen in Africa, while the presence data points of Laf were used to predict the global habitat suitability. Testing data comprised 25% of the presence only points.ResultsConsensus of the three models predicted a potential distribution of Las in large areas of Western, Eastern and sub‐Saharan Africa. North Africa was mostly unsuitable for Las, except for the northern fringes. The potential distribution of Laf included South and Central America, Asia and Australia. In Europe, the United Kingdom and the Iberian Peninsula showed marginal suitability for Laf. The projections under the future climate change scenarios showed an increase in the Laf habitat suitability hotspots under the extreme scenario.Main conclusionsThis study highlights the potential establishment and distribution in Africa of Las‐associated Huanglongbing and globally for Laf‐associated with African citrus greening disease. The ensemble modelling approach for the distribution of plant pathogens is a valuable tool for the development of strategies for crop protection. These results constitute an early alert for citrus‐producing regions that should inform strategies for surveillance and preventive management against the invasion and spread of this destructive disease.

A novel endophytic actinobacterium, designated strain EGI 650086T, was isolated from the roots of Anabasis elatior (C.A.Mey.) Schischk. collected in Xinjiang, north-west China. The taxonomic position of the strain was investigated using a polyphasic taxonomic approach. Growth occurred at 15–40 °C, pH 6.0–8.0 and in the presence of 0–6 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence and concatenation of 22 protein marker genes revealed that strain EGI 650086T formed a monophyletic clade within the genus Amycolatopsis and shared the highest sequence similarities with Amycolatopsis nigrescens JCM 14717T (97.1 %) and Amycolatopsis sacchari DSM 44468T (97.0 %). Sequence similarities with type strains of other species of the genus Amycolatopsis were less than 97.0 %. The average nucleotide identity and DNA–DNA hybridization values between strain EGI 650086T and the reference strains were 78.1–79.8 % and 22.1–23.0 %, respectively. The genome of strain EGI 650086T was 10.9 Mb, with a DNA G+C content of 70.1 mol%. The diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. The major whole-cell sugars contained arabinose, galactose, glucose and ribose. The predominant menaquinones were MK-9 (H4) and MK-9 (H2). Major fatty acids were iso-C16 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The polar lipid profile of strain EGI 650086T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phospholipids, an unknown glycolipid and an unknown lipid. Polyphasic taxonomic characteristics indicated that strain EGI 650086T represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis anabasis sp. nov. is proposed. The type strain is EGI 650086T (=KCTC 49044T=CGMCC 4.7188T).

Summary ‘ Candidatus Liberibacter asiaticus ’ is a fastidious bacterium and a putative agent of citrus greening disease (a.k.a., huanglongbing, HLB), a significant agricultural disease that affects citrus fruit quality and tree health. In citrus, ‘ Ca. L. asiaticus ’ is phloem limited. Lack of culture tools to study ‘ Ca. L. asiaticus ’ complicates analysis of this important organism. To improve understanding of ‘ Ca. L. asiaticus ’–host interactions including parameters that affect ‘ Ca. L. asiaticus ’ replication, methods suitable for screening pathogen responses to physicochemical and nutritional variables are needed. We describe a leaf disc‐based culture assay that allows highly selective measurement of changes in ‘ Ca. L. asiaticus ’ DNA within plant tissue incubated under specific physicochemical and nutritional conditions. qPCR analysis targeting the hypothetical gene CD16‐00155 (strain A4) allowed selective quantification of ‘ Ca. L. asiaticus ’ DNA content within infected tissue. ‘ Ca. L. asiaticus ’ DNA replication was observed in response to glucose exclusively under microaerobic conditions, and the antibiotic amikacin further enhanced ‘ Ca. L. asiaticus ’ DNA replication. Metabolite profiling revealed a moderate impact of ‘ Ca. L. asiaticus ’ on the ability of leaf tissue to metabolize and respond to glucose.

A novel obligately anaerobic, thermophilic and formate-utilizing bacterium K32T was isolated from Shengli oilfield of China. Cells were straight rods (0.4–0.8 µm × 2.5–8.0 µm), Gram-stain-positive, non-spore-forming and slightly motile. Optimum growth occurred with pH of 7 and 0.5 g l–1 NaCl under temperature of 55–60 °C. Nitrate could be reduced into nitrite, syntrophic formate oxidation to methane and carbon dioxide occurred when co-culturing strain K32T and Methanothermobacter thermautotrophicus ΔH. The main cellular fatty acids were iso-C15 : 0 (24.0 %), anteiso-C15 : 0 (21.7 %), C16 : 0 (12.7 %) and C14 : 0 (10.8 %), and the main polar lipid was phosphatidylglycerol. The G+C content of the genomic DNA was 46.3 mol%. The 16S rRNA gene sequence of K32T shared ≤90.4 % of sequence similarity to closest type strains of Desulfitibacter alkalitolerans , Calderihabitans maritimus and members of the genus Moorella . Based on the phenotypic, biochemical and genotypic characterization, Zhaonella formicivorans gen. nov., sp. nov. is proposed with K32T (=CCAM 584T =DSM 107278T=CGMCC1.5297T) as the type strain, which is the first representative of Zhaonellaceae fam. nov. In addition, the order Thermoanaerobacterales and family Peptococcaceae were reclassified, and three novel families in the novel order of Moorellales ord. nov. were also proposed.

In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of nonmethane alkane activation by noncanonical methyl-coenzyme M reductase enzymes and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.