Streptomyces specialis sp. nov.

A Gram-positive, non-endospore-forming bacterium (GW41-1564(T)) was isolated from soil. Comparison of 16S rRNA gene sequences showed that strain GW41-1564(T) is a member of the genus Streptomyces, exhibiting highest similarities with Streptomyces hainanensis YIM 47672(T) (97.8 %) and Streptomyces cacaoi subsp. cacaoi NBRC 12748(T) (97.5 %). Strain GW41-1564(T) could be distinguished from any other Streptomyces species with validly published names by sequence similarity values less than 97.5 %. Strain GW41-1564(T) exhibited an unusual quinone system, with the predominant compounds MK-10(H(4)) and MK-10(H(6)) and smaller amounts of MK-9(H(4)) and MK-9(H(6)). The type strain of the most closely related species, S. hainanensis YIM 47672(T), also contained an unusual quinone system composed of MK-9(H(6)) and MK-9(H(8)) in addition to MK-9(H(4)) and MK-10(H(0)), whereas the type strain of the second most closely related species, S. cacaoi NBRC 12748(T), contained a quinone system, composed of MK-9(H(6)) and MK-9(H(8)), typical of Streptomyces. The polar lipid profile of GW41-1564(T) consisted of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol and minor to trace amounts of two phosphatidylinositol mannosides and several unknown lipids, and the major fatty acids were iso-C(16 : 0,) anteiso-C(17 : 1)omega9c and anteiso-C(17 : 0). The results of physiological and biochemical tests allowed further phenotypic differentiation of strain GW41-1564(T) from the related species S. hainanensis. Strain GW41-1564(T) clearly merits species status, and we propose the name Streptomyces specialis sp. nov., with the type strain GW41-1564(T) (=DSM 41924(T) =CCM 7499(T)).

Thermophilic methanogenic Archaea in compost material: occurrence, persistence and possible mechanisms for their distribution to other environments.

Since compost is widely used as soil amendment and the fact that during the processing of compost material high amounts of microorganisms are released into the air, we investigated whether compost may act as a carrier for thermophilic methanogens to temperate soils. All eight investigated compost materials showed a clear methane production potential between 0.01 and 0.98 micromol CH(4) g dw(-1)h(-1) at 50 degrees C. Single strand conformation polymorphism (SSCP) and cloning analysis indicated the presence of Methanosarcina thermophila, Methanoculleus thermophilus, and Methanobacterium formicicum. Bioaerosols collected during the turning of a compost pile showed both a highly similar SSCP profile compared to the corresponding compost material and clear methane production during anoxic incubation in selective medium at 50 degrees C. Both observations indicated a considerable release of thermophilic methanogens into the air. To analyse the persistence of compost-borne thermophilic methanogens in temperate oxic soils, we therefore studied their potential activity in compost and compost/soil mixtures, which was brought to a meadow soil, as well as in an agricultural soil fertilised with compost. After 24h anoxic incubation at 50 degrees C, all samples containing compost showed a clear methanogenic activity, even 1 year after application. In combination with the in vitro observed resilience of the compost-borne methanogens against desiccation and UV radiation we assume that compost material acts as an effective carrier for the distribution of thermophilic methanogens by fertilisation and wind.

Nocardia acidivorans sp. nov., isolated from soil of the island of Stromboli.

A Gram-positive, non-spore-forming bacterium (strain GW4-1778(T)) was isolated from soil of the Italian island of Stromboli. 16S rRNA gene sequence similarity studies showed that strain GW4-1778(T) is a member of the genus Nocardia, most closely related to Nocardia pseudobrasiliensis (GenBank accession no. DQ659914; 98.6 %), Nocardia nova (Z36930; 98.6 %), Nocardia niigatensis (AB092563; 98.4 %), Nocardia jiangxiensis (AY639902; 98.0 %), Nocardia uniformis (Z46752; 98.0 %) and Nocardia miyunensis (AY639901; 97.8 %). Strain GW4-1778(T) could be distinguished from any other established Nocardia species by sequence similarity values of less than 97.5 %. Strain GW4-1778(T) exhibited a quinone system with the predominant compound MK-8 (H(4), omega-cycl) (99.5 %) and traces of MK-8 (H(4)), characteristic for the genus Nocardia. The polar lipid profile of strain GW4-1778(T) consisted of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides, a unknown polar lipid and trace amounts of two unknown lipids and the major fatty acids were C(15 : 0), C(16 : 0), C(17 : 1)omega8c and 10-methyl C(17 : 0). The results of DNA-DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW4-1778(T) from related species with 16S rRNA gene similarities of >97.5 %. Therefore, strain GW4-1778(T) merits species status, for which the name Nocardia acidivorans sp. nov. is proposed, with the type strain GW4-1778(T) (=CCUG 53410(T)=CIP 109315(T)=DSM 45049(T)).

Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material.

To date, composting has been regarded as an aerobic process but it has been shown that composting piles are often sources of atmospheric methane. In order to gain a more comprehensive view on the diversity of methanogenic Archaea in compost, gas chromatographical methods and molecular cloning were used to study relationships of thermophilic archaeal communities and changes in methane production potential during compost maturation. According to the thermophilic methane production potential, wide differences could be detected between differently aged compost materials. In material derived from 3- and 4-week-old piles, low and no thermophilic methane production potential, respectively, was observed at 50 degrees C. Material from a 6-week-old pile showed the maximum methane production. With compost maturation, the production slowly decreased again with 6 weeks, 8 weeks, and mature compost showing an optimum methane production potential at 60 degrees C. At 70 degrees C, only 6-week-old material showed a comparable high production of methane. The 16S rRNA-based phylogenetic surveys revealed an increase of archaeal diversity with compost maturation. In the 6-week-old material, 86% of the sequences in the archaeal 16S rRNA library had the highest sequence similarities to Methanothermobacter spp. and the remaining 14% of the clones were related to Methanosarcina thermophila. Quantification of methanogens in 6-week-old material, on the basis of the methane production rate, resulted in values of about 2x10(7) cells per gram fresh weight. In 8-week-old and mature compost material, the proportion of sequences similar to Methanothermobacter spp. decreased to 34% and 0%, respectively. The mature compost material showed the highest variation in identified sequences, although 33% could be assigned to as yet uncultured Archaea (e.g. Rice cluster I, III, and IV). Our results indicate that compost harbours a diverse community of thermophilic methanogens, with changing composition during the maturation process, presumably due to altered pile conditions. Likewise, compost may act as a potential carrier for thermophilic methanogens in temperate soils because it is widely used as a soil amendment.

Actinoplanes couchii sp. nov.

A Gram-positive bacterium, strain GW8-1761(T), was isolated from soil close to the Marmore waterfalls, Terni, Italy. 16S rRNA gene sequence similarity studies showed that strain GW8-1761(T) belonged to the genus Actinoplanes, being most closely related to Actinoplanes italicus JCM 3165(T) (98.9 %), A. rectilineatus IFO 13941(T) (98.5 %), A. palleronii JCM 7626(T) (97.8 %), A. utahensis IFO 13244(T) (97.6 %) and A. cyaneus DSM 46137(T) (97.6 %). Strain GW8-1761(T) could be distinguished from any other Actinoplanes species with validly published names by 16S rRNA gene sequence similarity values of less than 97.5 %. Chemotaxonomic data [major menaquinone MK-9(H(4)); major polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol, with phosphatidylcholine and aminoglycolipids absent; major fatty acids C(15 : 0), C(16 : 0), C(16 : 0) iso, C(17 : 1)omega8c and summed feature 3 (C(16 : 1)omega7c and/or C(15 : 0) iso 2-OH)] supported the affiliation of strain GW8-1761(T) to the genus Actinoplanes. The results of DNA-DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW8-1761(T) from the most closely related species. Strain GW8-1761(T) therefore merits species status, and we propose the name Actinoplanes couchii sp. nov., with the type strain GW8-1761(T) (=DSM 45050(T)=CIP 109316(T)).

Description of Pseudochrobactrum kiredjianiae sp. nov.

A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (strain CCUG 49584(T)), isolated from a seafood processing plant sample in New Zealand, was subjected to a polyphasic taxonomic study. On the basis of 16S rRNA and recA gene sequence similarities, the isolate was allocated to the genus Pseudochrobactrum. This was confirmed by fatty acid data (major fatty acids: C(18 : 1)omega7c and C(19 : 0) cyclo omega8c), a polar lipid profile exhibiting major characteristics of Pseudochrobactrum (phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine), quinone system Q-10 and a polyamine pattern with the predominant compounds spermidine and putrescine. DNA-DNA hybridization with the type strains of the two established species of Pseudochrobactrum and physiological and biochemical data clearly differentiated the isolate from established Pseudochrobactrum species. As a consequence, this organism represents a novel species, for which the name Pseudochrobactrum kiredjianiae sp. nov. is proposed, with the type strain CCUG 49584(T) (=CIP 109227(T)).

Thermophilic methane production and oxidation in compost.

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.