Integrated molecular approaches for fermented food microbiome research

peer-reviewedMolecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment—especially diet and nutrition—in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.Horizon 202

Microhabitats Shape Bacterial Community Composition, Ecosystem Function, and Genome Traits

This dissertation helps to integrate bacteria into the broader field of ecology by investigating bacterial community composition and diversity as it relates to ecosystem function in microhabitats within freshwater systems of the Great Lakes Region. Here, I combine field- and laboratory-based measurements of observational data collected from three major types of lake ecosystems: inland lakes, a freshwater estuary (Muskegon Lake), and a Great Lake (Lake Michigan). First, to determine the primary controls on lake bacterial community composition, I assessed the influence of lake layer (i.e. stratification), lake productivity, and particle-association on the bacterial community across 11 inland lakes with varying productivity in Southwestern Michigan. I found that particle-association very strongly structures freshwater bacterial community composition. Second, I studied a freshwater estuarine lake, Muskegon Lake, which has a large spatio-temporal variation in bacterial heterotrophic productivity, to test whether there was an association between heterotrophic production and bacterial biodiversity (defined as the number of taxa and taxon abundance). I specifically focused on two co-occurring freshwater habitats that my first chapter showed to be populated by very distinct communities: particle-associated and free-living. Positive biodiversity-heterotrophic productivity relationships were found only in particles. Third, I performed a genome-based analysis of free-living specialists, particle-associated bacterial specialists, and generalists to characterize the genomic architecture and genetic traits that are associated with adaptations to these specific habitats. The genomes of particle-associated specialist bacteria were about twice the size of the genomes of free-living specialists and generalists, which had streamlined genomes. Fourth, to identify the bacterial taxa driving heterotrophic productivity across the large set of lake samples, I found that high nucleic acid (i.e., HNA) functional groups identified by flow cytometry can serve as a proxy for freshwater bacterial heterotrophic productivity, whereas low nucleic acid (i.e., LNA) functional groups cannot. Then, I used a machine learning approach to identify bacterial taxa associated with HNA and LNA. This allowed me to identify the bacterial taxa, which were often members of the Phylum Bacteroidetes, that are associated heterotrophic productivity. Finally, I investigated patterns of lake specificity and phylogenetic conservation of taxonomic groups. Throughout my dissertation, I found that there was very deep (Class to Phylum-level) phylogenetic conservation of which bacteria lived in which habitats, but not of what bacterial taxa contributed to HNA and LNA functional groups, and thus heterotrophic productivity. Positive biodiversity-heterotrophic productivity relationships only existed in particle-associated, and not free-living communities, and communities composed of more phylogenetically related organisms were more productive per-capita. These differences in biodiversity-ecosystem function relationships may in part be explained by particle-associated bacteria having larger genomes, higher nitrogen content, and more unique genes that provide the potential for niche complementarity. The taxa that drove HNA and LNA cell numbers, and by proxy heterotrophic productivity, were lake and time-specific and indicated that taxa could switch between the two functional groups. Overall, my dissertation elucidates the ecological and evolutionary effects of microhabitat structure on bacterial communities and genomes in natural systems.PHDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/147651/1/marschmi_1.pd

Winter moth adaptation to climate change:Genetic changes in thermal plasticity of embryonic development rate

Timing of winter moth egg hatching shows rapid genetic adaptation to climate change. The reaction norm of egg development rate versus temperature has shifted up compared to 10 years ago. This later hatching for a given temperature has led to a better match with timing of their food source, young oak leaves. To identify the genes underlying the genetic adaptation of winter moth egg hatching, we used an evo-eco-devo approach: eggs collected from the field were used in a split-brood experiment. At different times during development, we measured embryonic development in, and obtained transcriptomes of, eggs before and after transfer to a colder or warmer temperature compared to a baseline. Stages of embryonic development in the winter moth were determined by imagining eggs using epifluorescence microscopy. These images were then used to map the thermal sensitivity of winter moth embryonic development over time, enabling us to focus on the transcriptomes taken during thermally sensitive stages of development. Ultimately, we aim to compare the genes identified this way with genes that show changes in allele frequency over the past 20 years, using our DNA record of four natural populations that adapted to climate change. As winter moths are one of the few species showing genetic adaptation under climate change, this study of winter moth embryonic development can advance our understanding of the genetic basis of adaptive evolutionary change in a natural population

Winter moth adaptation to climate change:Genetic changes in thermal plasticity of embryonic development rate

Timing of winter moth egg hatching shows rapid genetic adaptation to climate change. The reaction norm of egg development rate versus temperature has shifted up compared to 10 years ago. This later hatching for a given temperature has led to a better match with timing of their food source, young oak leaves. To identify the genes underlying the genetic adaptation of winter moth egg hatching, we used an evo-eco-devo approach: eggs collected from the field were used in a split-brood experiment. At different times during development, we measured embryonic development in, and obtained transcriptomes of, eggs before and after transfer to a colder or warmer temperature compared to a baseline. Stages of embryonic development in the winter moth were determined by imagining eggs using epifluorescence microscopy. These images were then used to map the thermal sensitivity of winter moth embryonic development over time, enabling us to focus on the transcriptomes taken during thermally sensitive stages of development. Ultimately, we aim to compare the genes identified this way with genes that show changes in allele frequency over the past 20 years, using our DNA record of four natural populations that adapted to climate change. As winter moths are one of the few species showing genetic adaptation under climate change, this study of winter moth embryonic development can advance our understanding of the genetic basis of adaptive evolutionary change in a natural population

Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration

Mining of mineral resources produces substantial volumes of crushed rock based wastes that are characterised by poor physical structure and hydrology, unstable geochemistry and potentially toxic chemical conditions. Recycling of these substrates is desirable and can be achieved by blending waste with native soil to form a 'novel substrate' which may be used in future landscape restoration. However, these post-mining substrate based 'soils' are likely to contain significant abiotic constraints for both plant and microbial growth. Effective use of these novel substrates for ecosystem restoration will depend on the efficacy of stored topsoil as a potential microbial inoculum as well as the subsequent generation of key microbial soil functions originally apparent in local pristine sites. Here, using both marker gene and shotgun metagenome sequencing, we show that topsoil storage and the blending of soil and waste substrates to form planting substrates gives rise to variable bacterial and archaeal phylogenetic composition but a high degree of metabolic conservation at the community metagenome level. Our data indicates that whilst low phylogenetic conservation is apparent across substrate blends we observe high functional redundancy in relation to key soil microbial pathways, allowing the potential for functional recovery of key belowground pathways under targeted management

Microbial biodiversity contributes to soil carbon release : a case study on fire disturbed boreal forests

Microbial biodiversity plays the dominant role in soil carbon emissions in fire-disturbed boreal forests. Microbial communities often possess enormous diversity, raising questions about whether this diversity drives ecosystem functioning, especially the influence of diversity on soil decomposition and respiration. Although functional redundancy is widely observed in soil microorganisms, evidence that species occupy distinct metabolic niches has also emerged. In this paper, we found that apart from the environmental variables, increases in microbial diversity, notably bacterial diversity, lead to an increase in soil C emissions. This was demonstrated using structural equation modelling (SEM), linking soil respiration with naturally differing levels of soil physio-chemical properties, vegetation coverage, and microbial diversity after fire disturbance. Our SEMs also revealed that models including bacterial diversity explained more variation of soil CO2 emissions (about 45%) than fungal diversity (about 38%). A possible explanation of this discrepancy is that fungi are more multifunctional than bacteria and, therefore, an increase in fungal diversity does not necessarily change soil respiration. Further analysis on functional gene structure suggested that bacterial and fungal diversities mainly explain the potential decomposition of recalcitrant C compare with that of labile C. Overall, by incorporating microbial diversity and the environmental variables, the predictive power of models on soil C emission was significantly improved, indicating microbial diversity is crucial for predicting ecosystem functions.Peer reviewe