Micromonospora: An important microbe for biomedicine and potentially for biocontrol and biofuels

Micromonospora species have long been recognized as important sources of antibiotics and also for their unusual spores. However, their involvement in plant-microbe associations is poorly understood although several studies demonstrate that Micromonospora species function in biocontrol, plant growth promotion, root ecology, and in the breakdown of plant cell wall material. Our knowledge of this generally understudied group of actinomycetes has been greatly advanced by the increasing number of reports of their associations with plants, by the deployment of DNA cloning and molecular systematics techniques, and by the recent application of whole genome sequencing. Efforts to annotate the genomes of several Micromonospora species are underway. This information will greatly augment our knowledge of these versatile microorganisms.     

Starving the soil of plant inputs for 50 years reduces abundance but not diversity of soil bacterial communities

If soil communities rely on plant-derived carbon, is biodiversity lost when this primary source is removed? Soil microbial and mesofaunal communities at the Rothamsted Highfield site were compared under a mixed grass sward, arable rotation and a section maintained as a bare-fallow for the past 50 years by regular tillage. Organic matter reserves have been degraded and microbial and mesofaunal numbers and mite diversity have declined in this unique bare-fallow site, where fresh carbon inputs have been drastically reduced. However, it supports a species-rich metabolically active bacterial community of similar diversity to that in soil maintained as grass sward. Thus in contrast to soil mesofauna, bacterial diversity (but not abundance) is apparently independent of plant inputs.     

Estriolum Treatment in the Bitch: A Risk for Uterine Infection?

Purulent vaginal discharge in a bitch in which ovariohysterectomy has been performed is often caused by inflammation of the uterine stump. The inflammation is due to either cystic endometrial hyperplasia (CEH) induced primarily by progesterone from remnant ovarian tissue or exogenous progestagens, or it is due to the presence of unabsorbed suture material. This report describes a 9-year-old Irish setter with hemopurulent vaginal discharge and non-pruritic symmetrical alopecia, which had undergone ovariohysterectomy 3.5 years ago and which had been treated with estriolum daily for the past 2.5 years because of urinary incontinence. Vaginoscopy revealed hemopurulent discharge throughout the vagina and vestibule. Cytological examination of ultrasound-guided fine-needle aspiration biopsies of a large mass in the hypogastricum, which appeared to be the uterine cervical stump, revealed septic purulent inflammation. The concentration of plasma progesterone was low and the concentration of plasma 17-ß oestradiol did not increase after gonadotrophin-releasing hormone administration. No remnant ovarian tissue was found by abdominal ultrasonography, laparotomy, or histological examination of mesovarian pedicles. Laparotomy revealed uterine stump empyema. Histological examination of the surgically removed mass excluded both CEH and unabsorbed suture material as the cause of the stump empyema. Instead, it is hypothesized that the long-term treatment with estriolum was a causative factor. This suggests that bitches treated with estriolum should be examined regularly.     

Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment

Dried soil samples from many sources have been stored in archives world-wide over the years, but there has been little research on their value for studying microbial populations. Samples collected since 1843 from the Broadbalk field experiment on crop nutrition at Rothamsted have been used to document changes in the structure and composition of soils as agricultural practices evolve, also offering an invaluable record of environmental changes from the pre- to post-industrial era in the UK. To date, the microbial communities of these soils have not been studied, in part due to the well-documented drop in bacterial culturability in dried soils. However, modern molecular methods based on PCR amplification of DNA extracted directly from soil do not require bacterial cells to be viable or intact and may allow investigations into the legacy of bacteria that were present at the time of sample collection.

In a preliminary study, to establish if dried soils can provide a historical record of bacterial communities, samples from the Broadbalk soil archive dating back to 1868 were investigated and plots treated with either farmyard manure (FYM) or inorganic fertilizer (NPK) were compared. As anticipated, the processes of air-drying and milling greatly reduced bacterial viability whilst DNA yields declined less and may be preserved by desiccation. A higher proportion of culturable bacteria survived the archiving process in the FYM soil, possibly protected by the increased soil organic matter. The majority of surviving bacteria were firmicutes, whether collected in 2003 or in 1914, but a wide range of genera was detected in DNA extracted from the samples using PCR and DGGE of 16S rRNA genes. Analysis of DGGE band profiles indicated that the two plots maintained divergent populations. Sequence analysis of bands excised from DGGE gels, from a sample collected in 1914, revealed DNA from - and β-proteobacteria as well as firmicutes. PCR using primers specific for ammonia oxidizing bacteria showed similar band profiles across the two treatments in recently collected samples, however older samples from the NPK plot showed greater divergence. Primers specific for the genus Pseudomonas were designed and used in real-time quantitative PCR to indicate that archived soil collected in 1868 contained 10-fold less pseudomonad DNA than fresh soil, representing around 10⁵ genomes g⁻¹ soil. Prior to milling, dramatically less pseudomonad DNA was extracted from recently collected air-dried soil from the NPK compared to the FYM plot; otherwise, the two plots followed similar trends. Overall bacterial abundance, diversity and survival during the archiving process differed in the two soils, possibly due to differences in clay and soil organic matter content. Nevertheless, the results demonstrate that air-dried soils can protect microbial DNA for more than 150 years and offer an invaluable resource for future research.