A microfluidic platform for the simultaneous quantification of methanogen populations in anaerobic digestion processes.

Methanogens are a diverse group of archaea that play a critical role in the global carbon cycle. The lack of appropriate molecular tools to simultaneously quantify numerous methanogenic taxa, however, has largely limited our ability to study these communities in a wide variety of habitats, such as anaerobic digesters (ADs). In this study, 34 probe-based quantitative PCR (qPCR) assays were designed to target all known methanogenic genera within the archaeal phylum Euryarchaeota. These qPCR assays were adapted to a high-throughput microfluidic platform, which allowed for the simultaneous detection and absolute quantification of numerous taxa in a single run. The resulting microfluidic qPCR (MFQPCR) platform was successfully used to decipher structure-function relationships among methanogenic communities in four laboratory-scale digesters exposed to a transient organic overload. Twelve of the 34 genera targeted in the MFQPCR were detected in the ADs, similar to results obtained using high-throughput sequencing. The MFQPCR platform and conventional qPCR assays also generated similar quantitative results. The MFQPCR tool developed here will help optimize AD technologies for efficient waste treatment and enhanced biogas production and can facilitate studies that will increase our understanding of methanogenic communities in other environments.

Water and sediment act as reservoirs for microbial taxa associated with invasive dreissenid mussels.

Zebra mussels (Dreissena polymorpha) are invasive, filter-feeding, bivalves that have disrupted the ecology of thousands of freshwater biomes across North America. Due to their efficient filter-feeding activity, zebra mussels (ZMs) and other bivalves are extensively used to detect chemical contamination in waterways. In this study, we evaluated whether water and sediment serve as major sources of ZM tissue-associated microbiota, and whether ZMs serve as a reservoir for potentially pathogenic microbes in aquatic systems. High-throughput DNA sequencing of 16S rRNA gene was done to characterize the microbial community structure in 472 environmental samples, comprising ZMs, sediment, and the water column, collected from 15 lakes during the summer and fall months. Sequence analyses, done using the SourceTracker program, predicted that water and sediment contributed up to 91 and 86%, respectively, to the structure of microbiota within ZMs, and that mussels from the same site showed nearly identical source microbiota profiles. The relatively high local source contribution suggests that the microbiota in ZM tissue has the potential to reflect biological contamination and this phenomenon can be used to monitor microbial water quality. A preferential enrichment of several taxa was also observed in ZM tissues, including potential pathogenic groups such as Aeromonas, Enterobacteriaceae, and Pseudomonas. Taken together, our results contribute to an improved understanding of ZMs as a sentinel species in aquatic habitats and its potential impact to water quality management.

Association between submerged aquatic vegetation and elevated levels of Escherichia coli and potential bacterial pathogens in freshwater lakes.

Fecal indicator bacteria such as Escherichia coli have been reported to persist and potentially grow in a wide variety of secondary habitats, such as water, beach sand, sediment, periphyton and some algae. However, little is known about their association with submerged macrophytes and how this may influence water quality. In this study, we examined the association of E. coli and potential bacterial pathogens with Eurasian watermilfoil (EWM), an invasive, submerged, macrophyte that has spread across thousands of lakes in North America. EWM samples were collected from 10 lakes in Minnesota, once a month, for six consecutive months from early summer to late fall. Microbiota associated with EWM were examined using membrane filtration, quantitative PCR targeting various bacterial pathogens and host-associated marker genes, and high-throughput DNA sequencing. E. coli densities were generally elevated on EWM samples, and peaked during warmer months. Moreover, our results showed that EWM could serve as a temporal source for transmission of microbiota to the water column. Several potential pathogenic groups, including Aeromonas, Enterobacteriaceae, and Clostridium were present in significantly greater relative abundance on EWM than in water, and waterfowl was predicted to be the major source of fecal contamination. These findings have water quality implications with respect to the potential for submerged macrophytes to harbor and disperse E. coli and other bacterial pathogens in a large number of waterbodies.

Spatial and temporal characterization of epiphytic microbial communities associated with Eurasian watermilfoil: a highly invasive macrophyte in North America.

Bacterial communities that inhabit the surface of aquatic plants are thought to play a critical role in relation to host fitness and function. However, little is known about their structure and dynamics in comparison with those of bacterioplankton. In this study, we performed a comprehensive spatial and temporal characterization of epibacterial communities associated with Eurasian watermilfoil (EWM; Myriophyllum spicatum), an invasive macrophyte, which has established itself in thousands of lakes across North America. EWM samples were collected from 10 lakes in Minnesota, once a month, for six consecutive months, along with surrounding water and sediment. High-throughput DNA sequencing analyses, performed on all samples (n = 522) using the Illumina platform, indicated that EWM-associated epibacterial communities were distinct from those found in water and sediment. EWM-specific microbiota was comprised of operational taxonomic units classified to the families Rhodobacteraceae, Comamonadaceae, Cyanobacteria Subsection I Family I, Aeromonadaceae, Planctomycetaceae, Sphingomonadaceae and Verrucomicrobiaceae. In addition, several identified taxa were overrepresented in EWM samples when compared to water and sediment. Amongst all the environmental factors examined, water temperature had the greatest influence on epibacterial community structure. Our findings suggest that EWM harbor specific, but temporally adapted, epibacterial communities that are potentially involved in host-microbe interactions.