Little is known about the extent or pattern of environmental fecal contamination among households using low-cost, on-site sanitation facilities, or what role environmental contamination plays in the transmission of diarrheal disease. A microbial survey of fecal contamination and selected diarrheal pathogens in soil (n = 200), surface (n = 120), and produce samples (n = 24) was conducted in peri-urban Bagamoyo, Tanzania, among 20 households using private pit latrines. All samples were analyzed for E. coli and enterococci. A subset was analyzed for enterovirus, rotavirus, norovirus GI, norovirus GII, diarrheagenic E. coli, and general and human-specific Bacteroidales fecal markers using molecular methods. Soil collected from the house floor had significantly higher concentrations of E. coli and enterococci than soil collected from the latrine floor. There was no significant difference in fecal indicator bacteria levels between households using pit latrines with a concrete slab (improved sanitation) versus t...

Fecal Contamination and Diarrheal Pathogens on Surfaces and in Soils among Tanzanian Households with and without Improved Sanitation

Approaches for the cultivation-independent analysis of microbial communities are summarized as meta’omics, which predominantly includes metagenomic, -transcriptomic, -proteomic and -metabolomic studies. These have shown that endophytic, root-associated and soil fungal communities are strongly shaped by associated plant species. The impact of plant identity on the composition of its litter-associated fungal community remains to be disentangled from the impact of litter chemistry. The composition of the plant community also shapes the fungal community. Most strikingly, adjacent plant species may share mycorrhizal symbionts even if the plants usually have different types of mycorrhizal fungi associated with them (ectomycorrhizal, ericoid and arbuscular mycorrhizal fungi). Environmental parameters weakly explain fungal community composition globally, and their effect is inconsistent at local and regional scales. Decrease in similarity among communities with increasing distance (i.e. distance decay) has been reported from local to global scales. This pattern is only exceptionally caused by spatial dispersal limitation of fungal propagules, but mostly due to the inability of the fungi to establish at the particular locality (i.e. environmental filtering or competitive exclusion). Fungal communities usually undergo pronounced seasonal changes and also differ between consecutive years. This indicates that development of the communities is usually not solely cyclic. Meta’omic studies challenge the classical view of plant litter decomposition. They show that mycorrhizal and (previously) endophytic fungi may be involved in plant litter decomposition and only partly support the idea of a succession from an Ascomycota to a Basidiomycota-dominated community. Furthermore, vertical separation of saprotrophic and mycorrhizal species in soil and sequential degradation from easily accessible to ‘recalcitrant’ plant compounds, such as lignin, can probably not be generalized. The current models of litter decomposition may therefore have to be eventually refined for certain ecosystems and environmental conditions. To gain deeper insights into fungal ecology, a meta’omic study design is outlined which focuses on environmental processes, because fungal communities are usually taxonomically diverse, but functionally redundant. This approach would initially identify dynamics of chemical shifts in the host and/or substrate by metametabolomics. Detected shifts would be subsequently linked to microbial activity by correlation with metatranscriptomic and/or metaproteomic data. A holistic trait-based approach might finally identify factors shaping taxonomic composition in communities against the dynamics of the environmental process(es) they are involved in.

Plant-associated fungal communities in the light of meta’omics

Isotope ratio mass spectrometry as a tool for source inference in forensic science: A critical review

Detection of bacterial gene expression in soil emerged in the early 1990s and provided information on bacterial responses in their original soil environments. As a key procedure in the detection, extraction of bacterial RNA from soil has attracted much interest, and many methods of soil RNA extraction have been reported in the past 20 years. In addition to various RT-PCR-based technologies, new technologies for gene expression analysis, such as microarrays and high-throughput sequencing technologies, have recently been applied to examine bacterial gene expression in soil. These technologies are driving improvements in RNA extraction protocols. In this mini-review, progress in the extraction of bacterial RNA from soil is summarized with emphasis on the major difficulties in the development of methodologies and corresponding strategies to overcome them.

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Extraction of Bacterial RNA from Soil: Challenges and Solutions

Developments in forensic mass spectrometry tend to follow, rather than lead, the developments in other disciplines. Examples of techniques having forensic potential born independently of forensic applications include ambient ionization, imaging mass spectrometry, isotope ratio mass spectrometry, portable mass spectrometers, and hyphenated chromatography-mass spectrometry instruments, to name a few. Forensic science has the potential to benefit enormously from developments that are funded by other means, if only the infrastructure and personnel existed to adopt, validate, and implement the new technologies into casework. Perhaps one unique area in which forensic science is at the cutting edge is in the area of chemometrics and the determination of likelihood ratios for the evaluation of the weight of evidence. Such statistical techniques have been developed most extensively for ignitable-liquid residue analyses and isotope ratio analysis. This review attempts to capture the trends, motivating forces, and likely impact of developing areas of forensic mass spectrometry, with the caveat that none of this research is likely to have any real impact in the forensic community unless: (a) The instruments developed are turned into robust black boxes with red and green lights for positives and negatives, respectively, or (b) there are PhD graduates in the workforce who can help adopt these sophisticated techniques.

Marianne E. Dietz

Papers

Forensic utility of isotope ratio analysis of the explosive urea nitrate and its precursors

Forensic utility of carbon isotope ratio variations in PVC tape backings.

Evaluation of commercial RNA extraction kits for the isolation of viral MS2 RNA from soil