Publications

4859

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.

AbstractStrategies to increase the production rate of chicken for human consumption alter the natural process of microbial colonisation and the nutritional performance of the animal. The lack of sufficient reference genomes limits the interpretation of sequencing data and restrain the study of complex functions. In this study, 43 strains obtained from crop, jejunum and ileum of chicken were isolated, characterised and genome analysed to observe their metabolic profiles, adaptive strategies and to serve as future references. Eight isolates represent new species that colonise the upper gut intestinal tract and present consistent adaptations that enable us to predict their ecological role, expanding our knowledge on the adaptive functions. Molecular characterisation confirmed the classification ofClostridium anaeroviscerissp. nov. (DSM 113860= LMG 32675),Clostridium butanolproducens(DSM 115076= LMG 32878),Ligilactobacillus hohenheimiussp. nov. (DSM 113870= LMG 32876),Limosilactobacillus gallussp. nov. (DSM 113833 =LMG 32623),Limosilactobacillus aviumsp. nov. (DSM 113849= LMG 32671), Limosilactobacillus pullumsp. nov. (DSM 115077 =LMG 32877),Limosilactobacillus digestussp. nov. (DSM113835= LMG 32625) andLimosilactobacillus difficilesp. nov. (DSM 114195= LMG 32875). Strains ofLimosilactobacilluswere found to be more abundant in the crop, whileLigilactobacillusdominated the ileal digesta. Isolates from crop encode a high number of glycosidases specialized in complex polysaccharides compared to strains isolated from jejunum and ileum. These results represent the first approach for the isolation and detection of bacteria from the chicken’s upper digestive tract and describe the functional diversity of bacteria inhabiting these regions, improving the potential handling of chicken microbiota with biotechnological applications.

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 The ammonia monooxygenase (AMO) is a key enzyme in ammonia‐oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper‐containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co‐oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well‐established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia‐oxidizing archaeon ‘ Candidatus Nitrosocosmicus franklandus C13’. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants ( K i ) for methane and methanol were 2.2 and 20 μM, respectively, concentrations which are environmentally relevant and orders of magnitude lower than those previously reported for ammonia‐oxidizing bacteria. Furthermore, we demonstrate that a specific suite of proteins is upregulated and downregulated in ‘ Ca. Nitrosocosmicus franklandus C13’ in the presence of methane or methanol, which provides a foundation for future studies into metabolism of one‐carbon (C1) compounds in ammonia‐oxidizing archaea.

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.