Publications

4857

Abstract Marine pelagic redoxclines are areas of enhanced biogeochemical cycling inhabited by distinct functional groups of prokaryotes. In this study, the diversity and abundance of archaeal and bacterial nitrifying populations throughout a pelagic redoxcline in the central Baltic Sea were examined using a suite of molecular methods. 16S rRNA/rRNA gene as well as bacterial and archaeal amoA mRNA/amoA gene fingerprints and clone libraries revealed that the putative nitrifying assemblages consisted solely of one crenarchaeotal subcluster, named GD2, which was closely related to Candidatus Nitrosopumilus maritimus. Neither distinct differences between transcript- and gene-based fingerprints nor pronounced differences in the crenarchaeotal composition throughout the whole redoxcline were detected. The abundance of this GD2 subgroup, as determined by the oligonucleotide probe Cren537 and the newly developed and more specific probe Cren679 showed that GD2 and total crenarchaeotal cell numbers were nearly identical throughout the redoxcline. The highest GD2 abundance (2.3 × 105 cells ml−1) occurred in the suboxic zone, accounting for around 26% of total prokaryotic cells. Below the chemocline, GD2 abundance was relatively stable (1.5–1.9 × 105 cells ml−1). Archaeal amoA expression was detected only in the putative nitrification zone and formed a narrow band in the suboxic layer, where ammonium, oxygen, nitrate, nitrite and phosphate concentrations were below 5 μmol l−1. To our knowledge this is the first study to show the dominance of only one crenarchaeotal nitrifying key cluster in a natural habitat. The metabolic properties and survival mechanisms present in this cluster inside and outside the nitrification zone remain to be determined.

A novel aerobic, heterotrophic bacterium, designated BiosLi39T, was isolated from the South East Pacific Ocean. Cells were Gram-negative gliding rods forming yellow colonies on marine agar. The isolate was oxidase-, catalase- and alkaline phosphatase-positive andβ-galactosidase-negative. Strain BiosLi39Tgrew at 20-37 °C (optimum 30 °C), at pH 7.0–9.0 (optimum pH 8.0) and with 20–60 g NaCl l−1(optimum 30–50 g NaCl l−1). The fatty acids (>1 %) comprised iso-C14 : 0, iso-C15 : 1G, iso-C15 : 0, anteiso-C15 : 0, C15 : 1G, C15 : 0, iso-C15 : 02-OH, iso-C16 : 1G, iso-C16 : 0, iso-C16 : 03-OH, iso-C16 : 02-OH, iso-C17 : 03-OH, C17 : 02-OH and three unidentified components with equivalent chain lengths of 17.87, 18.10 and 18.71. A significant proportion of the hydroxylated fatty acids are amide-linked. The lipid pattern indicated the presence of phosphatidylethanolamine, two unidentified aminolipids and three unidentified polar lipids. The strain contained menaquinone 7 as the sole respiratory lipoquinone and did not produce flexirubin-type pigments. The G+C content of the genomic DNA was 37.2 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain BiosLi39Twas distantly related to all of the representatives of the phylumBacteroidetes. Its closest relative wasMarinoscillum furvescensIFO 15994T, with which it shared 92.5 % 16S rRNA gene sequence similarity. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, we propose a novel genus and species,Ekhidnagen. nov., sp. nov., with type strain BiosLi39T(=DSM 19307T=CIP 109600T=OOB 398T).

Five Gram-negative, facultatively anaerobic, non-spore-forming, coccoid rod-shaped bacterial isolates were obtained from infant formula and an infant formula production environment and were investigated by use of a polyphasic taxonomic study. Biochemical tests and partialrpoBgene sequence analysis of the five isolates revealed that they formed two distinct groups in the familyEnterobacteriaceae, closely related to several species of the generaPantoeaandErwinia, which indicated a phylogenetic position within the genusPantoeaor the genusErwinia. Multilocus sequence analysis of concatenated partialatpD,gyrB,infBandrpoBgene sequences of two of the isolates suggested that they represented two novel species of the genusPantoea, phylogenetically related most closely toPantoea septica. The five isolates had general characteristics consistent with those of the genusPantoea, and DNA–DNA hybridizations between two representatives and the type strains of their phylogenetically closest relatives based on comparative 16S rRNA gene sequence analysis showed that the isolates represented two novel genospecies. These two genospecies could be differentiated from each other based on fermentation of galacturonate, sorbitol and potassium 5-ketogluconate. They could be differentiated from phylogenetically relatedPantoeaspecies based on their ability to ferment lactose and to utilizeβ-gentiobiose and raffinose, their inability to ferment or utilized-arabitol, and their inability to produce indole. On the basis of the results obtained, the five isolates are considered to represent two novel species of the genusPantoea, for which the namesPantoea gaviniaesp. nov. (type strain A18/07T=LMG 25382T=DSM 22758T) andPantoea calidasp. nov. (type strain 1400/07T=LMG 25383T=DSM 22759T) are proposed.

ABSTRACT Mealybugs (Coccoidea: Pseudococcidae) are sap-sucking plant parasites that harbor bacterial endosymbionts within specialized organs. Previous studies have identified two subfamilies, Pseudococcinae and Phenacoccinae, within mealybugs and determined the primary endosymbionts (P-endosymbionts) of the Pseudococcinae to be Betaproteobacteria (“ Candidatus Tremblaya princeps”) containing Gammaproteobacteria secondary symbionts. Here, the P-endosymbionts of phenacoccine mealybugs are characterized based on 16S rRNA from the bacteria of 20 species of phenacoccine mealybugs and four outgroup Puto species (Coccoidea: Putoidae) and aligned to more than 100 published 16S rRNA sequences from symbiotic and free-living bacteria. Phylogenetic analyses recovered three separate lineages of bacteria from the Phenacoccinae, and these are considered to be the P-endosymbionts of their respective mealybug hosts, with those from (i) the mealybug genus Rastrococcus belonging to the Bacteroidetes , (ii) the subterranean mealybugs, tribe Rhizoecini, also within Bacteroidetes , in a clade sister to cockroach endosymbionts ( Blattabacterium ), and (iii) the remaining Phenacoccinae within the Betaproteobacteria , forming a well-supported sister group to “ Candidatus Tremblaya princeps.” Names are proposed for two strongly supported lineages: “ Candidatus Brownia rhizoecola” for P-endosymbionts of Rhizoecini and “ Candidatus Tremblaya phenacola” for P-endosymbionts of Phenacoccinae excluding Rastrococcus and Rhizoecini. Rates of nucleotide substitution among lineages of Tremblaya were inferred to be significantly faster than those of free-living Betaproteobacteria . Analyses also recovered a clade of Gammaproteobacteria , sister to the P-endosymbiont lineage of aphids (“ Candidatus Buchnera aphidicola”), containing the endosymbionts of Putoidae, the secondary endosymbionts of pseudococcine mealybugs, and the endosymbionts of several other insect groups.