We investigated the structure of bacterial communities present in livestock manure-based composting processes and evaluated the bacterial succession during the composting processes. Compost samples were derived separately from swine manure, dairy manure and sewage sludge. The structure of the bacterial community was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) using universal eubacterial primers. The genus Bacillus and related genera were mainly detected following the thermophilic composting phase of swine and dairy manure composts, and the members of the phylum Bacteroidetes were mainly detected in the cattle manure waste-based and sewage sludge compost. We recovered and sequenced limited number of the bands; however, the PCR-DGGE analysis showed that predominant diversities during the composting processes were markedly changed. Although PCR-DGGE analysis revealed the presence of different phyla in the early stages of composting, the members of the phylum Firmicutes and Bacteroidetes were observed to be one of the predominant phyla after the thermophilic phase.

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We investigated microorganisms that assimilated ammonia in lagoon treatment processes. Ammonia-assimilating microorganisms were detected by nitrogen-limited medium that contained ammonia as the sole nitrogen source. Numbers of ammonia-assimilating aerobes (log CFU/g) were 3.4, 4.8, 5.0, 4.8 and 5.0 (log CFU/mL) on the culture plate incubated at 4°C, 10°C, 15°C, 20°C and 25°C, respectively. Many isolates used ammonia in high rates when they were purely cultivated in nitrogen-limited medium added to sterilized lagoon extract. Many of them used ammonia even when they were cultivated in media containing viable microbial flora of the lagoon. Among them, enterobacteriaceae and Pseudomonas sp. were identified by analysis of 16S ribosomal DNA.

The ecology of shiga‐toxigenic Escherichia coli (STEC) is important in the animal production environment. We investigated fecal shedding of STEC in one town in Miyagi, Japan by multiplex polymerase chain reaction (PCR) targeting shiga toxin gene 1 (stx1), gene 2 (stx2) and malB promoter gene, and analyzed the PCR products of stx1 or stx2 (54 samples) by direct sequencing. Three of 46 (6.5%) beef cattle in the University Farm of Tohoku University (Kawatabi Farm) and 11 of 70 (15.7%) calves in neighboring dairy farms carried STEC. Rate of detecting genes of stx1, stx2 and stx1+2 was 3.4% (4/116), 8.6% (10/116) and 0.9% (1/116), respectively. Serotyping indicated that STEC contaminated farms at different times or through different routes. Isolates harbored no mutation among stx1, but six (Kawatabi Farm) and 38 (neighboring farms) base substitutions among stx2, respectively. The diversity of substitutions of stx2 was observed among farms or even in a farm. Phylogenic analysis revealed that STEC detected in the area were classified into three clusters by the variety of stx2. Sequence analysis of stx2 will be one of the tools for clarifying the source of outbreaks and the route of contamination of STEC.

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