Forest and other upland soils are important sinks for atmospheric CH 4 , consuming 20 to 60 Tg of CH 4 per year. Consumption of atmospheric CH 4 by soil is a microbiological process. However, little is known about the methanotrophic bacterial community in forest soils. We measured vertical profiles of atmospheric CH 4 oxidation rates in a German forest soil and characterized the methanotrophic populations by PCR and denaturing gradient gel electrophoresis (DGGE) with primer sets targeting the pmoA gene, coding for the ␣ subunit of the particulate methane monooxygenase, and the small-subunit rRNA gene (SSU rDNA) of all life. The forest soil was a sink for atmospheric CH 4 in situ and in vitro at all times. In winter, atmospheric CH 4 was oxidized in a well-defined subsurface soil layer (6 to 14 cm deep), whereas in summer, the complete soil core was active (0 cm to 26 cm deep). The content of total extractable DNA was about 10-fold higher in summer than in winter. It decreased with soil depth (0 to 28 cm deep) from about 40 to 1 g DNA per g (dry weight) of soil. The PCR product concentration of SSU rDNA of all life was constant both in winter and in summer. However, the PCR product concentration of pmoA changed with depth and season. pmoA was detected only in soil layers with active CH 4 oxidation, i.e., 6 to 16 cm deep in winter and throughout the soil core in summer. The same methanotrophic populations were present in winter and summer. Layers with high CH 4 consumption rates also exhibited more bands of pmoA in DGGE, indicating that high CH 4 oxidation activity was positively correlated with the number of methanotrophic populations present. The pmoA sequences derived from excised DGGE bands were only distantly related to those of known methanotrophs, indicating the existence of unknown methanotrophs involved in atmospheric CH 4 consumption.The atmospheric concentration of CH 4 , one of the most important greenhouse gases, has increased dramatically over the past 200 years. About 80 to 90% of atmospheric CH 4 is of biogenic origin (20). The major sink is the chemical destruction by OH˙and Cl˙radicals in the troposphere and stratosphere, respectively (9, 10). However, the capacity of these atmospheric sinks may decline, since the rising concentrations of other trace gases emitted by anthropogenic activity result in a reduction of OH˙radicals in the troposphere (27).The only biological sink for CH 4 is oxidation in soil. Atmospheric CH 4 is consumed in forest, agricultural, and other upland soils. CH 4 consumption in these soils is caused by methane-oxidizing bacteria. However, the identity of these methanotrophs is still unknown. The apparent half-saturation constant (K m ) for oxidation of atmospheric CH 4 (approximately 1.8 parts per million by volume [ppmv]) in upland soils ranges from 0.8 to 280 nM (6, 7, 13, 16). However, the K m of the common type I or II methanotrophs (0.8 to 66 M), which are available in culture collections, is 1 to 3 orders of magnitude higher, and these common methanotrophs are not abl...

SummaryThe natural habitats and potential reservoirs of the nosocomial pathogen Acinetobacter baumannii are poorly defined. Here, we put forth and tested the hypothesis of avian reservoirs of A. baumannii. We screened tracheal and rectal swab samples from livestock (chicken, geese) and wild birds (white stork nestlings) and isolated A. baumannii from 3% of sampled chicken (n 5 220), 8% of geese (n 5 40) and 25% of white stork nestlings (n 5 661). Virulence of selected avian A. baumannii isolates was comparable to that of clinical isolates in the Galleria mellonella infection model. Whole genome sequencing revealed the close relationship of an antibiotic-susceptible chicken isolate from Germany with a multidrug-resistant human clinical isolate from China and additional linkages between livestock isolates and human clinical isolates related to international clonal lineages. Moreover, we identified stork isolates related to human clinical isolates from the United States. Multilocus sequence typing disclosed further kinship between avian and human isolates. Avian isolates do not form a distinct clade within the phylogeny of A. baumannii, instead they diverge into different lineages. Further, we provide evidence that A. baumannii is constantly present in the habitats occupied by storks. Collectively, our study suggests A. baumannii could be a zoonotic organism that may disseminate into livestock.

Strain K11T was isolated from activated sludge of a municipal wastewater-treatment plant. Phylogenetic analysis of the 16S rRNA gene sequence revealed that it represents a distinct line of descent within the Comamonadaceae. The novel strain was a Gram-negative, catalase- and oxidase-positive, non-motile, straight to slightly curved rod. Polyhydroxyalkanoate granules were stored intracellularly as reserve material. Colonies on agar plates were small, regular and characterized by a water-insoluble yellow pigment. Unbranched fatty acids 16 : 1ω7c, 16 : 0 and 18 : 1ω7c dominated the cellular fatty acid pattern and ubiquinone-8 (Q-8) was the major component of the respiratory lipoquinones, both traits typical of members of the Comamonadaceae. A distinguishing characteristic was the presence of the two hydroxy fatty acids 10 : 0 3-OH and 12 : 0 2-OH, each in significant amounts. The G+C content of the DNA was 59 mol%. Strain K11T was capable of aerobic chemolithoheterotrophic growth using thiosulfate as an additional substrate, but could not grow autotrophically with thiosulfate or hydrogen. Facultative anaerobic growth was possible with nitrate and nitrite as electron acceptors, but not with ferric iron, sulfate or by fermentation. The sole end product of denitrification was N2O; nitrite accumulated only transiently in small amounts. Based upon phylogenetic and phenotypic evidence, it is proposed to establish the novel taxon Ottowia thiooxydans gen. nov., sp. nov., represented by the type strain K11T (=DSM 14619T=JCM 11629T). Aquaspirillum gracile was among the phylogenetically most closely related species to strain K11T. This species has been wrongly classified, and it is proposed to reclassify it as Hylemonella gracilis gen. nov., comb. nov. The type strain is ATCC 19624T (=DSM 9158T).

Two Gram-negative, oxidase-positive rods (strains BSB 9.5T and BSB 41.8T) isolated from wastewater were studied using a polyphasic approach. 16S rRNA gene sequence comparisons demonstrated that both strains cluster phylogenetically within the family Comamonadaceae: the two strains shared 99·9 % 16S rRNA gene sequence similarity and were most closely related to the type strains of Hydrogenophaga palleronii (98·5 %) and Hydrogenophaga taeniospiralis (98·0 %). The fatty acid patterns and substrate-utilization profiles displayed similarity to the those of the five Hydrogenophaga species with validly published names, although clear differentiating characteristics were also observed. The two strains showed DNA–DNA hybridization values of 51 % with respect to each other. No close similarities to any other Hydrogenophaga species were detected in hybridization experiments with the genomic DNAs. On the basis of these results, two novel Hydrogenophaga species, Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov. are proposed, with BSB 9.5T (=DSM 15341T=CIP 108119T) and BSB 41.8T (=DSM 15342T=CIP 108118T) as the respective type strains.

Methane cycling within compost heaps has not yet been investigated in detail. We show that thermophilic methane oxidation occurred after a lag phase of up to one day in 4-week old, 8-week old and mature (>10-week old) compost material. The potential rate of methane oxidation was between 2.6 and 4.1 micromol CH4(gdw)(-1)h(-1). Profiles of methane concentrations within heaps of different ages indicated that 46-98% of the methane produced was oxidised by methanotrophic bacteria. The population size of thermophilic methanotrophs was estimated at 10(9) cells (gdw)(-1), based on methane oxidation rates. A methanotroph (strain KTM-1) was isolated from the highest positive step of a serial dilution series. This strain belonged to the genus Methylocaldum, which contains thermotolerant and thermophilic methanotrophs. The closest relative organism on the basis of 16S rRNA gene sequence identity was M. szegediense (>99%), a species originally isolated from hot springs. The temperature optimum (45-55 degrees C) for methane oxidation within the compost material was identical to that of strain KTM-1, suggesting that this strain was well adapted to the conditions in the compost material. The temperatures measured in the upper layer (0-40 cm) of the compost heaps were also in this range, so we assume that these organisms are capable of effectively reducing the potential methane emissions from compost.

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Anoxic soils, such as flooded rice fields, are major sources of the greenhouse gas CH(4) while oxic upland soils are major sinks of atmospheric CH(4). Nevertheless, CH(4) is also consumed in rice fields where up to 90% of the produced CH(4) is oxidized in a narrow oxic zone around the rice roots and in the soil surface layer before it escapes into the atmosphere. After 1 day drainage of rice field soil, CH(4) oxidation was detected in the top 2-mm soil layers, but after 8 days drainage the zone of CH(4) oxidation extended to 8 mm depth. Simultaneously, the potential for CH(4) production decreased, but some production was still detectable after 8 days drainage throughout the soil profile. The vertical distribution of the methanotrophic community was also monitored after 1 and 8 days drainage using denaturing gradient gel electrophoresis after PCR amplification with primer sets targeting two regions on the 16S rRNA gene that are relatively specific for methylotrophic alpha- and gamma-Proteobacteria, and targeting two functional genes encoding subunits of key enzymes in all methanotrophs, i.e. the genes for the particulate methane monooxygenase (pmoA) and the methanol dehydrogenase (mxaF). Drainage stimulated the methanotrophic community. Eight days after drainage, new methanotrophic populations appeared and a distinct methanotrophic community developed. The population structure of type I and II methanotrophs was differently affected by drainage. Type II methanotrophs (alpha-Proteobacteria) were present throughout the soil core directly after drainage (1 day), and the community composition remained largely unchanged with depth. Only two new type II populations appeared after 8 days of drainage. Drainage had a more pronounced impact on the type I methanotrophic community (gamma-Proteobacteria). Type I populations were not or only weakly detected 1 day after drainage. However, after 8 days of drainage, a large diversity of type I methanotrophs were detected, altough they were not evenly distributed throughout the soil core but dominated at different depths. A distinct type I community structure had developed within each soil section between 0 and 20 mm soil depth, indicating the widening of suitable habitats for methanotrophs in the rice field soil within 1 week of drainage.