Publications

4525

Appendix 9, Section E of the International Code of Nomenclature of Prokaryotes provides guidelines on how to form adjectival specific and subspecific epithets that reflect the geographical location where the organism was found or studied. It does not mention ways of naming genera after geographical locations. We here propose emendation of Appendix 9 with the recommendations on how to form such names. Comments on the implementation of the current wording of Appendix 9, Section E are also made.

Abstract Background Phloem limited non-culturable bacteria Candidatus Liberibacter asiaticus (CLas) affects the worldwide citrus production through causing citrus Huanglongbing (HLB). Despite the efficient colonization of citrus endophyte in the phloem as same niche as CLas pathogen, citrus microbiome manipulation and recruitment as well as citrus defense mechanisms in the presence of indigenous citrus endophyte against this pathogen are still unknown.Results Endophyte-mediated microbiome manipulation may potentially play a significant role in restoration of disease suppressive endophytic microbiome in vascular pathogen affected diseased plants and positively influence the citrus defense. For this, citrus endophyte Bacillus subtilis L1-21 was introduced in CLas-infected citrus groves for one year and pathogen reduction from 105 to 10 copies/gram/leaves was recorded. Resident bacterial community composition in diseased host dramatically changed after introduction of B. subtilis L1-21 and positive enrichment of certain bacteria was recorded in diseased citrus host. These enrichments were predominantly driven by high and low relative abundance of Bacillus and CLas pathogen respectively, after one year of endophyte application. Moreover, endophyte application resulted in citrus defence gene induction against CLas pathogen and demonstrated key resistance genes (PR-1, PR-4, RPS5, RBOHD) in endophyte-pathogen interaction pathway in infected citrus. Upon introduction of B. subtilis L1-21 in the diseased citrus plants, we identified high level of up-regulated genes (> 2-fold) involved in defense pathway (padj < 0.05) underpinning the fundamental defense mechanisms.Conclusion Thorough evaluation of disease suppressive mechanism of endophyte against pathogen requires further exploration. However, introduction of B. subtilis L1-21 restructured citrus microbiome by regulating key bacterial communities which might help plant to control this pathogen. In addition, we highlight advanced insights regarding activation of multiple disease resistance and secondary metabolites encoding genes in endophyte treated HLB-infected citrus plants showing potential resistance against CLas pathogen. Conclusively, endophyte-mediated manipulation could play decisive role in restoration of microbiome to positively influence the citrus defense.

Abstract We investigated microbial methane oxidation in the water column of two connected but hydrodynamically contrasting basins of Lake Lugano, Switzerland. Both basins accumulate large amounts of methane in the water column below their chemoclines, but methane oxidation efficiently prevents methane from reaching surface waters. Here we show that in the meromictic North Basin water column, a substantial fraction of methane was eliminated through anaerobic methane oxidation (AOM) coupled to nitrite reduction by Candidatus Methylomirabilis. Incubations with 14CH4 and concentrated biomass from this basin showed enhanced AOM rates with nitrate (+62%) and nitrite (+43%). In the more dynamic South Basin, however, aerobic methanotrophs prevailed, Ca. Methylomirabilis was absent in the anoxic water column, and no evidence was found for nitrite-dependent AOM. Here, the duration of seasonal stratification and anoxia seems to be too short, relative to the slow growth rate of Ca. Methylomirabilis, to allow for the establishment of anaerobic methanotrophs, in spite of favorable hydrochemical conditions. Using 16 S rRNA gene sequence data covering nearly ten years of community dynamics, we show that Ca. Methylomirabilis was a permanent element of the pelagic methane filter in the North Basin, which proliferated during periods of stable water column conditions and became the dominant methanotroph in the system. Conversely, more dynamic water column conditions led to a decline of Ca. Methylomirabilis and induced blooms of the faster-growing aerobic methanotrophs Methylobacter and Crenothrix. Our data highlight that physical (mixing) processes and ecosystem stability are key drivers controlling the community composition of aerobic and anaerobic methanotrophs.