Sequencing of environmental DNA (eDNA) for community analysis (i.e., eDNA metabarcoding) is already well established and applied in molecular microbial ecology. However, molecular methods for use in soil animal studies require further development before high-throughput sequencing can be considered a reliable technique in community ecology. To aid in this effort, we compare primers that target two frequently used genetic markers, mitochondrial cytochrome oxidase (COI) and ribosomal 18S genes, to determine their utility in broad soil animal eDNA studies. DNA was analyzed from individually identified invertebrates to test the efficiency of the primer sets in successfully targeting animal DNA and identification through sequencing. Primers were also tested for amplification of faunal genes from forest soil and leaf litter eDNA. Targeting the 18S gene resulted in the most successful amplification and correct identification of a wide range of individual invertebrate taxa, and was the most reliable primer set for use in eDNA analysis of invertebrate communities spanning several phyla. In contrast, the selected COI primers were inefficient in identifying a wide range of invertebrates, and amplified mostly bacterial sequences from eDNA.

Microbial communities within the soil of Laurentian Great Lakes coastal wetlands drive biogeochemical cycles and provide several other ecosystem services. However, there exists a lack of understanding of how microbial communities respond to nutrient gradients and human activity in these systems. This research sought to address the lack of understanding through exploration of relationships among nutrient gradients, microbial community diversity, and microbial networks. Significant differences in microbial community structure were found among coastal wetlands within the western basin of Lake Erie and all other wetlands studied (three regions within Saginaw Bay and one region in the Beaver Archipelago). These diversity differences coincided with higher nutrient levels within the Lake Erie region. Site-to-site variability also existed within the majority of the regions studied, suggesting site-scale heterogeneity may impact microbial community structure. Several subnetworks of microbial communities and individual community members were related to chemical gradients among wetland regions, revealing several candidate indicator communities and taxa that may be useful for Great Lakes coastal wetland management. This research provides an initial characterization of microbial communities among Great Lakes coastal wetlands and demonstrates that microbial communities could be negatively impacted by anthropogenic activities.

Heavy metal concentrations within freshwater systems can increase as a result of anthropogenic inputs, which in turn can influence microbial community composition and community function. In this study, lake sediments collected from two historically heavy metal impacted geographical regions [Poyang Lake, People's Republic of China (PRC), and sites adjacent to the Muskegon Watershed, MI (USA)] were analyzed for total and available heavy metals (Cd, Cr, Cu, Pb, and Zn), as well as microbial community structure using highthroughput sequencing technology. In PRC tributaries leading into Poyang Lake, Zn was found to be the most available metal species. In USA sites, available Cd was higher in Mona Lake sites than alternate USA sites. In both regions, results indicate a weak influence of metals on microbial alpha and beta diversity, but strong positive and negative correlations of available heavy metals with specific taxonomic groups of bacteria and archaea. Further, individual metal species impacted microbial groups and operational taxonomic units differently, suggesting that individual metal species are important in determining which microbial groups and species prevail under heavy metal stress, particularly in the case of bioavailable metals. In PRC, several taxonomic groups were correlated positively with Zn, including Actinobacteria, Bacteroidetes, Proteobacteria, and Verrucomicrobia. Geobacter and Pedosphaerales were both correlated positively to Cr in the same sites, while other correlations with microbial groups were negative. In sites from the USA, Deltaproteobacteria were correlated positively with Cd, while Betaproteobacteria were negatively correlated, suggesting that Cd resistance may differ at the level of Class within Proteobacteria. This study highlights the importance of analyzing available metals when examining the impact of this disturbance on microbial community structure within aquatic sediments.

Microbial communities within the soil of Laurentian Great Lakes coastal wetlands drive biogeochemical cycles and provide several other ecosystems services. However, there exists a lack of understanding of how microbial communities respond to nutrient gradients and human activity in these systems. This research sought to address the lack of understanding through exploration of relationships between nutrient gradients, microbial community diversity, and microbial networks. Significant differences in microbial community structure were found among coastal wetlands within the western basin of Lake Erie and all other wetlands studied (three regions within Saginaw Bay and one region in the Beaver Archipelago). These diversity differences coincided with higher nutrient levels within the Lake Erie region. Site-to-site variability also existed within the majority of the regions studied, suggesting site-scale heterogeneity may impact microbial community structure. Several subnetworks of microbial communities and individual community members were related to chemical gradients among wetland regions, revealing several candidate indicator communities and taxa which may be useful for Great Lakes coastal wetland management. This research provides an initial characterization of microbial communities among Great Lakes coastal wetlands and demonstrates that microbial communities could be negatively impacted by anthropogenic activities.

Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island.