Ecology, Evolution, Behavior and Systematics

Summary Gold ore processing uses cyanide ( CN − ), which often results in large volumes of thiocyanate‐ ( SCN − ) contaminated wastewater requiring treatment. Microbial communities can degrade SCN − and CN − , but little is known about their membership and metabolic potential. Microbial‐based remediation strategies will benefit from an ecological understanding of organisms involved in the breakdown of SCN − and CN − into sulfur, carbon and nitrogen compounds. We performed metagenomic analysis of samples from two laboratory‐scale bioreactors used to study SCN − and CN − degradation. Community analysis revealed the dominance of Thiobacillus spp., whose genomes harbour a previously unreported operon for SCN − degradation. Genome‐based metabolic predictions suggest that a large portion of each bioreactor community is autotrophic, relying not on molasses in reactor feed but using energy gained from oxidation of sulfur compounds produced during SCN − degradation. Heterotrophs, including a bacterium from a previously uncharacterized phylum, compose a smaller portion of the reactor community. Predation by phage and eukaryotes is predicted to affect community dynamics. Genes for ammonium oxidation and denitrification were detected, indicating the potential for nitrogen removal, as required for complete remediation of wastewater. These findings suggest optimization strategies for reactor design, such as improved aerobic/anaerobic partitioning and elimination of organic carbon from reactor feed.

Abstract Methylotrophic planktonic bacteria fulfill a particular role in the carbon cycle of lakes via the turnover of single-carbon compounds. We studied two planktonic freshwater lineages (LD28 and PRD01a001B) affiliated with Methylophilaceae (Betaproteobacteria) in Lake Zurich, Switzerland, by a combination of molecular and cultivation-based approaches. Their spatio-temporal distribution was monitored at high resolution (n=992 samples) for 4 consecutive years. LD28 methylotrophs constituted up to 11 × 107 cells l−1 with pronounced peaks in spring and autumn–winter, concomitant with blooms of primary producers. They were rare in the warm water layers during summer but abundant in the cold hypolimnion, hinting at psychrophilic growth. Members of the PRD01a001B lineage were generally less abundant but also had maxima in spring. More than 120 axenic strains from these so far uncultivated lineages were isolated from the pelagic zone by dilution to extinction. Phylogenetic analysis separated isolates into two distinct genotypes. Isolates grew slowly (μmax=0.4 d−1), were of conspicuously small size, and were indeed psychrophilic, with higher growth yield at low temperatures. Growth was enhanced upon addition of methanol and methylamine to sterile lake water. Genomic analyses of two strains confirmed a methylotrophic lifestyle with a reduced set of genes involved in C1 metabolism. The very small and streamlined genomes (1.36 and 1.75 Mb) shared several pathways with the marine OM43 lineage. As the closest described taxa (Methylotenera sp.) are only distantly related to either set of isolates, we propose a new genus with two species, that is, ‘Candidatus Methylopumilus planktonicus’ (LD28) and ‘Candidatus Methylopumilus turicensis’ (PRD01a001B).

The phenotypic and genotypic characteristics of four Bordetella hinzii-like strains from human respiratory specimens and representing nrdA gene sequence based genogroups 3, 14 and 15 were examined. In a 16S rRNA gene sequence based phylogenetic tree, the four strains consistently formed a single coherent lineage but their assignment to the genus Bordetella was equivocal. The respiratory quinone, polar lipid and fatty acid profiles generally conformed to those of species of the genus Bordetella and were characterized by the presence of ubiquinone 8, of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several aminolipids, and of high percentages of C16 : 0, cyclo-C17 : 0 and summed feature 2, as major chemotaxonomic marker molecules, respectively. The DNA G+C content was about 66 mol%, which corresponded with that of the high-percentage DNA G+C content genera of the family Alcaligenaceae including the genus Bordetella. DNA–DNA hybridization experiments revealed the presence of three distinct genomospecies and thus confirmed phenotypic differences as revealed by means of extensive biochemical characterization. We therefore propose to formally classify Bordetella genogroups 3, 14 and 15 as Bordetella bronchialis sp. nov. (type strain LMG 28640T = AU3182T = CCUG 56828T), Bordetella sputigena sp. nov. (type strain LMG 28641T = CCUG 56478T) and Bordetella flabilis sp. nov. (type strain LMG 28642T = AU10664T = CCUG 56827T). In addition, we propose to reclassify Achromobacter sediminum into the novel genus Verticia, as Verticia sediminum, gen. nov., comb. nov., on the basis of its unique phylogenetic position, its marine origin and its distinctive phenotypic, fatty acid and polar lipid profile.

Summary To date, six candidate genera of anaerobic ammonium‐oxidizing (anammox) bacteria have been identified, and numerous studies have been conducted to understand their ecophysiology. In this study, we examined the physiological characteristics of an anammox bacterium in the genus ‘ C andidatus   J ettenia’. Planctomycete KSU ‐1 was found to be a mesophilic (20–42.5°C) and neutrophilic ( pH 6.5–8.5) bacterium with a maximum growth rate of 0.0020 h −1 . Planctomycete KSU ‐1 cells showed typical physiological and structural features of anammox bacteria; i.e. 29 N 2 gas production by coupling of 15 NH 4 + and 14 NO 2 − , accumulation of hydrazine with the consumption of hydroxylamine and the presence of anammoxosome. In addition, the cells were capable of respiratory ammonification with oxidation of acetate. Notably, the cells contained menaquinone‐7 as a dominant respiratory quinone. Proteomic analysis was performed to examine underlying core metabolisms, and high expressions of hydrazine synthase, hydrazine dehydrogenase, hydroxylamine dehydrogenase, nitrite/nitrate oxidoreductase and carbon monoxide dehydrogenase/acetyl‐ CoA synthase were detected. These proteins require iron or copper as a metal cofactor, and both were dominant in planctomycete KSU ‐1 cells. On the basis of these experimental results, we proposed the name ‘ C a . J ettenia caeni’ sp. nov. for the bacterial clade of the planctomycete KSU ‐1.

A novel anoxygenic photoheterotrophic member of the phylum Acidobacteria , Chloracidobacterium thermophilum strain B sp. nov., was isolated from a cyanobacterial enrichment culture derived from microbial mats associated with Octopus Spring, Yellowstone National Park, WY. C. thermophilum sp. nov. was a Gram-stain-negative rod (diameter, approximately 0.8–1.0 µm; variable length, approximately 2.5 µm), which formed greenish-brown liquid suspension cultures. It was a moderately thermophilic microaerophile and grew in a defined medium at 51 °C (Topt; range 44 to 58 °C) and in the pH range 5.5 to 9.5 (pHopt = ~7.0). The DNA G+C content was 61.3 mol%, and phylogenetic analysis, based on the 16S rRNA sequence, showed that C. thermophilum sp. nov. belongs to subdivision 4 ( Acidobacteriaceae ) of the Acidobacteria . C. thermophilum sp. nov. was unable to synthesize branched-chain amino acids, l-lysine, and vitamin B12, which were required for growth. Although the organism lacked genes/enzymes for autotrophic carbon fixation, bicarbonate was required. Growth was stimulated by other amino acids and 2-oxoglutarate. Cells produced chlorosomes containing a diverse mixture of bacteriochlorophyll (BChl) c derivatives, and additionally, synthesized BChl a P, Chl a PD, and Zn-BChl a′P, which occurred in type-1 homodimeric reaction centres. The carotenoids included echinenone, canthaxanthin, lycopene, γ-carotene and β-carotene. C. thermophilum sp. nov. produced iso-diabolic acid as its major fatty acid and synthesized three hopanoids (diploptene, bacteriohopanetetrol and bacteriohopanetetrol cyclitol ether). Based upon its phenotypic and genotypic properties, the name Chloracidobacterium thermophilum gen. nov., sp. nov. is proposed for this isolate; the type strain is C. thermophilum strain BT (ATCC BAA-2647 = JCM 30199).