Using terminal restriction fragment length polymorphism (T-RFLP) analysis to assess microbial community structure in compost systems

Food Waste Composting and Microbial Community Structure Profiling

Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. Rotting discharges methane, causing greenhouse effect and adverse health effects due to pathogenic microorganisms or toxic leachates that reach agricultural land and water system. As a solution, composting is implemented to manage and reduce food waste in line with global sustainable development goals (SDGs). This review compiles input on the types of organic composting, its characteristics, physico-chemical properties involved, role of microbes and tools available in determining the microbial community structure. Composting types: vermi-composting, windrow composting, aerated static pile composting and in-vessel composting are discussed. The diversity of microorganisms in each of the three stages in composting is highlighted and the techniques used to determine the microbial community structure during composting such as biochemical identification, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), terminal restriction fragment length polymorphism (T-RFLP) and single strand-conformation polymorphism (SSCP), microarray analysis and next-generation sequencing (NGS) are discussed. Overall, a good compost, not only reduces waste issues, but also contributes substantially to the economic and social sectors of a nation.

Changes in global trends in food waste composting: Research challenges and opportunities

Increasing food waste (FW) generation has put significant pressure on the environment and has increased the global financial costs of its appropriate management. Among the traditional organic waste recycling technologies (i.e., incineration, landfilling and anaerobic digestion), composting is an economically feasible and reliable technology for FW recycling regardless of its technical flaws and social issues. The global scenario of FW generation, technical advancement in FW composting and essential nutrient recovery from organic waste with waste recycling are discussed in this article. Recent research on various strategies to improve FW composting, including co-composting, the addition of organic/inorganic additives, the mitigation of gaseous emission, and microbiological variations are comprehensively explained. Subsequently, it is shown that the performing FW composting in an existing mechanical facility can improve organic waste degradation and produce value-added mature compost to save on costs and increase the technological feasibility and viability of FW composting to some extent.

Composting of food wastes: Status and challenges

This review analyses the main challenges of the process of food waste composting and examines the crucial aspects related to the quality of the produced compost. Although recent advances have been made in crucial aspects of the process, such composting microbiology, improvements are needed in process monitoring. Therefore, specific problems related to food waste composting, such as the presence of impurities, are thoroughly analysed in this study. In addition, environmental impacts related to food waste composting, such as emissions of greenhouse gases and odours, are discussed. Finally, the use of food waste compost in soil bioremediation is discussed in detail.

Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function

Cystic fibrosis (CF) is a genetic disease resulting in chronic polymicrobial infections of the airways and progressive decline in lung function. To gain insight into the underlying causes of severe lung diseases, we aimed at comparing the airway microbiota detected in sputum of CF patients with stable lung function (S) versus those with a substantial decline in lung function (SD). Microbiota composition was investigated by using culture-based and culture-independent methods, and by performing multivariate and statistical analyses. Culture-based methods identified some microbial species associated with a worse lung function, i.e. Pseudomonas aeruginosa, Rothia mucilaginosa, Streptococcus pneumoniae and Candida albicans, but only the presence of S. pneumoniae and R. mucilaginosa was found to be associated with increased severe decline in forced expiratory volume in 1 second (FEV₁). Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis revealed a higher bacterial diversity than that detected by culture-based methods. Molecular signatures with a statistically significant odds ratio for SD status were detected, and classified as Pseudomonas, Burkholderia and Shewanella, while for other Terminal Restriction Fragments (T-RFs) no species assignation was achieved. The analysis of T-RFLP data using ecological biodiversity indices showed reduced Evenness in SD patients compared to S ones, suggesting an impaired ecology of the bacterial community in SD patients. Statistically significant differences of the ecological biodiversity indices among the three sub-groups of FEV₁ (normal/mild vs moderate vs severe) were also found, suggesting that the patients with moderate lung disease experienced changes in the airway assembly of taxa. Overall, changes in CF airway microbial community associated with a severe lung function decline were detected, allowing us to define some discriminatory species as well as some discriminatory T-RFs that represent good candidates for the development of predictive biomarkers of substantial decline in lung function.

Ammonia-oxidizing bacteria and archaea in sediments of the Gulf of Mexico

The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of the Gulf of Mexico was examined. Using polymerase chain reaction primers designed to specifically target the archaeal ammonia monooxygenase-subunit (amoA) gene and bacterial amoA gene, we found AOA and AOB to be present in all three sampling sites. Archaeal amoA libraries were dominated by a few widely distributed Nitrosopumilus-like sequence types, whereas AOB diversity showed significant variation in both richness and community composition. Majority of the bacterial amoA sequences recovered belong to Betaproteobacteria and very few belong to Gammaproteobacteria. Results suggest that water depth and nutrient availability were identified as potential drivers that affected the selection of the AOA and AOB communities. Besides influencing the abundance of individual taxa, these environmental factors also had an impact on the overall richness of the overall AOA and AOB communities. The richness and diversity of AOA and AOB genes were higher at the shallowest sediments (100 m depth) and the deepest sediments (1300 m depth). The reduced diversity in the deepest sediments could be explained by much lower nutrient availability.

Validating T-RFLP as a sensitive and high-throughput approach to assess bacterial diversity patterns in human anterior nares

While recent works aimed to thoroughly characterize the bacterial community of the human anterior nares of a few candidates, this work sought to analyse a greater cross-section by sampling 100 volunteers. After optimizing and validating the method of terminal restriction fragment length polymorphism against six previously pyrosequenced samples, abundant species could be discriminated and their relative abundances measured in a high-throughput manner. The 100 volunteers could be statistically clustered into 12 groups, where two-thirds of volunteers shared more than 40% similarity in respect to their bacterial community structure, while the remaining third clustered into smaller groups being dominated by Dolosigranulum pigrum, Moraxella spp. or Staphylococcus aureus. Moraxella spp. was present predominantly in women rather than in men. The use of network analysis charting bacterial ecological co-occurrences revealed new evidence of likely positive associations between some core human nasal species. So, in the age of post 'omics' and 'deep sequencing', there is still a place for these well-tried and well-tested methods that can offer a rapid, reproducible and economical alternative, whereby also yielding valuable new information.