Combination Of Culture-based Methods Research Articles

Halophilomyces hongkongensis, a Novel Species and Genus in the Lulworthiaceae with Antibacterial Potential, Colonizing the Roots and Rhizomes of the Seagrass Halophila ovalis.

Seagrass serves as a quintessential reservoir for obligate marine Lulworthiaceae fungi. Our current knowledge of the mycological diversity associated with seagrass in Hong Kong remains poor. We analyzed the diversity of fungi associated with the most widely distributed seagrass species in Hong Kong Halophila ovalis (Hydrocharitaceae), using a combination of culture-based methods and high-throughput amplicon sequencing. Halophilomyces hongkongensis, a novel fungal species in a newly proposed genus within the Lulworthiaceae family, was isolated from H. ovalis roots and rhizomes. The novel fungus showed distinct morphological characteristics, while both combined 18S-28S and internal transcribed spacer (ITS) phylogenetic trees based on maximum likelihood and Bayesian methods supported its discrimination from other existing Lulworthiaceae members. The ITS2 region in the Illumina sequencing results of multiple H. ovalis compartments, water, and adjacent non-seagrass sediments revealed continuous recruitment of H. hongkongensis by H. ovalis throughout the year despite dramatically fluctuating environmental conditions, with remarkably high proportions of this taxon found in root and rhizome internal tissues, possibly indicating a strong and specialized relationship established between the Lulworthiaceae fungal partner and its seagrass host. The inhibitory abilities exhibited by H. hongkongensis against Staphylococcus aureus SA29213 and ATCC 43300 (methicillin-resistant) may imply its capacity in producing (novel) antibacterial compounds. The discovery of H. hongkongensis as the first novel Lulworthiaceae taxon in Hong Kong, along with its distributional pattern in the seagrass meadow, provides valuable insights into the systematics and ecology of this strictly marine fungal family.

Occupational exposure to inhalable pathogenic microorganisms in waste sorting

This study assessed microorganisms in personal inhalable work air samples aiming to identify potential human pathogens, and correlate exposure to adverse health outcomes in waste workers. Full-shift personal exposure was measured in six different waste sorting plants. Microbial concentrations in inhalable air samples were analysed using MALDI-TOF MS for cultivable, and next generation sequencing (NGS) for non-cultivable microorganisms. Concentrations of bacterial and fungal CFUs varied substantially within and between waste sorting plants, ranging from no identifiable organisms to a maximum concentration in the order of 105 CFU/m3. Bacillus and Staphylococcus were among the most abundant bacterial genera, whilst fungal genera were dominated by Aspergillus and Penicillium. Approximately 15% of all identified species were human pathogens classified in risk group 2, whereas 7% belonged to risk group 1. Furthermore, significant correlations between concentrations of fungi in risk group 1 and self-reported adverse symptoms, such as wheezing were identified in exposed workers. The combination of culture-based methods and NGS facilitated the investigation of infectious microbial species with potential pathophysiological properties as well as non-infectious biological agents in inhalable work air samples and thereby contributed to the risk assessment of occupational exposure in waste sorting.

Diversity and Co-Occurrence Patterns of Fungal and Bacterial Communities from Alkaline Sediments and Water of Julong High-Altitude Hot Springs at Tianchi Volcano, Northeast China.

Simple SummaryVolcanic hot springs are considered of particular interest in biology as precious sources of peculiar microorganisms adapted to extreme environmental conditions. The Julong high-altitude volcanic hot springs in northeast China are characterized by alkali, sulfur and metal enrichment. The microbial communities colonizing these intriguing habitats still remain completely unknown. We carried out the present study in order to shed light on the Julong hot springs fungal and bacterial community diversity, structure and interactions, and to understand the impact of pH on the microorganisms colonizing the investigated environment. We detected a large variety of typical photosynthetic, thermophilic, alkalophilic, antimicrobial-active, and sulfide- and metal-oxidizing microbial taxa representing clear links to the extreme properties of the studied environment. Results showed a striking microorganism community variation strongly influenced by pH under clearly alkaline conditions. Our analyses suggests that mutualistic relationships might be common among microorganisms coexisting in the Julong hot springs, especially for the bacterial community. This study provides new insights in the diversity and ecological interactions of microorganisms living in high-altitude volcanic hot springs and contributes to our knowledge of abiotic factors influencing the microbial community in the analyzed extreme environment. The Julong high-altitude volcanic hot springs in northeast China are of undeniable interest for microbiological studies due to their unique, extreme environmental conditions. The objective of this study was to provide a comprehensive analysis of the unexplored fungal and bacterial community composition, structure and networks in sediments and water from the Julong hot springs using a combination of culture-based methods and metabarcoding. A total of 65 fungal and 21 bacterial strains were isolated. Fungal genera Trichoderma and Cladosporium were dominant in sediments, while the most abundant fungi in hot spring water were Aspergillus and Alternaria. Bacterial communities in sediments and water were dominated by the genera Chryseobacterium and Pseudomonas, respectively. Metabarcoding analysis revealed significant differences in the microorganism communities from the two hot springs. Results suggested a strong influence of pH on the analyzed microbial diversity, at least when the environmental conditions became clearly alkaline. Our analyses indicated that mutualistic interactions may play an essential role in shaping stable microbial networks in the studied hot springs. The much more complicated bacterial than fungal networks described in our study may suggest that the more flexible trophic strategies of bacteria are beneficial for their survival and fitness under extreme conditions.

Removal of Fecal Indicators, Pathogenic Bacteria, Adenovirus, Cryptosporidium and Giardia (oo)cysts in Waste Stabilization Ponds in Northern and Eastern Australia.

Maturation ponds are used in rural and regional areas in Australia to remove the microbial loads of sewage wastewater, however, they have not been studied intensively until present. Using a combination of culture-based methods and quantitative real-time PCR, we assessed microbial removal rates in maturation ponds at four waste stabilization ponds (WSP) with (n = 1) and without (n = 3) baffles in rural and remote communities in Australia. Concentrations of total coliforms, E. coli, enterococci, Campylobacter spp., Salmonella spp., F+ RNA coliphage, adenovirus, Cryptosporidium spp. and Giardia (oo) cysts in maturation ponds were measured at the inlet and outlet. Only the baffled pond demonstrated a significant removal of most of the pathogens tested and therefore was subjected to further study by analyzing E. coli and enterococci concentrations at six points along the baffles over five sampling rounds. Using culture-based methods, we found a decrease in the number of E. coli and enterococci from the initial values of 100,000 CFU per 100 mL in the inlet samples to approximately 1000 CFU per 100 mL in the outlet samples for both bacterial groups. Giardia cysts removal was relatively higher than fecal indicators reduction possibly due to sedimentation.

Infectious cause of death determination using minimally invasive autopsies in developing countries

In developing countries, the knowledge of the microorganisms causing fatal infections is critical and could help designing and implementing more effective preventive interventions and treatment guidelines. We aimed to develop and validate protocols for microbiological analysis in post-mortem samples obtained during minimally invasive autopsy (MIA) procedures and to assess their performance. Thirty MIAs performed in adults at Maputo Central Hospital in Southern Mozambique were included in the analysis. Microbiological tests included a universal screening for HIV, hepatitis B and C viruses, Plasmodium falciparum, and bacterial/fungal culture. In addition, a variety of molecular microbiology assays guided by the histological results were performed in blood, cerebrospinal fluid and a variety of tissue samples including liver, lung and central nervous system. The combination of culture-based methods together with molecular microbiological assays led to the identification of 17 out of 19 (89.5%) of the infectious deaths. Microorganisms identified included Mycobacterium tuberculosis, Toxoplasma gondii, Pneumocystis jiroveci, Cryptococcus neoformans, hepatitis B virus, human herpesvirus 8, cytomegalovirus, Streptococcus pneumoniae, Streptococcus dysgalactiae, Ryzopus oryzae, and Acinetobacter baumannii. The combination of classical cultures, serological tests and molecular assays performed in samples obtained through MIA allows the identification of most infectious agents causing death.