Exploring bacterial pathogen community dynamics in freshwater beach sediments: A tale of two lakes

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154434/1/emi14860.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154434/2/emi14860_am.pd

Biogeochemical Characterization of Metal Behavior from Novel Mussel Shell Bioreactor Sludge Residues

Acid mine drainage (AMD) remediation commonly produces byproducts which must be stored or utilized to reduce the risk of further contamination. A mussel shell bioreactor has been implemented at a coal mine in New Zealand, which is an effective remediation option, although an accumulated sludge layer decreased efficiency which was then removed and requires storage. To understand associated risks related to storage or use of the AMD sludge material, a laboratory mesocosm study investigated the physio-chemical and biological influence in two conditions: anoxic storage (burial deep within a waste rock dump) or exposure to oxic environments (use of sludge on the surface of the mine). Solid phase characterization by Scanning Electron Microscopy (SEM) and selective extraction was completed to compare two environmental conditions (oxic and anoxic) under biologically active and abiotic systems (achieved by gamma irradiation). Changes in microbial community structure were monitored using 16s rDNA amplification and next-generation sequencing. The results indicate that microbes in an oxic environment increase the formation of oxyhydroxides and acidic conditions increase metal mobility. In an oxic and circumneutral environment, the AMD sludge may be repurposed to act as an oxygen barrier for mine tailings or soil amendment. Anoxic conditions would likely promote the biomineralization of sulfide minerals in the AMD sludge by sulfate reducing bacteria (SRB), which were abundant in the system. The anoxic conditions reduced the risk of trace metals (Zn) associated with oxides, but increased Fe associated with organic material. In summary, fewer risks are associated with anoxic burial but repurposing in an oxic condition may be appropriate under favorable conditions

Effect of COD: SO42- Ratio, HRT and Linoleic Acid Concentration on Mesophilic Sulfate Reduction: Reactor Performance and Microbial Population Dynamics

Biological sulfate (SO42-) reduction was examined in anaerobic sequential batch reactors (ASBRs) operated under different hydraulic retention times (HRTs) ranging from 12 to 36 h and COD (Chemical Oxygen Demand)/SO42- ratios of 2.4, 1.6 and 0.8. Competition between SO42- reducing bacteria (SRBs), methane producing archaea (MPAs) and homoacetogens (HACs) was examined in controls and cultures treated with linoleic acid (LA). The ASBR performance was influenced by the COD/SO42- ratio in control cultures with a SO42- reduction of 87% at a COD/SO42- ratio of 0.8. At a 12 h HRT, in both control and LA treated cultures, greater than 75% SO42- removal was observed under all the conditions examined. In control reactors operating at a 36 h HRT, high levels of MPAs belonging to Methanobacteriales and Methanosarcinales were detected; however, in comparison, under low COD/SO42- ratio and with decreasing HRT conditions, a relative increase in SRBs belonging to Desulfovibrio and Desulfatibacillum was observed. Adding 0.5 gL(-1) LA suppressed Methanobacteriales, while increasing the LA concentration to 1 gL(-1) completely suppressed MPAs with a relative increase in SRBs. HACs belonging to Bacteroidetes were observed in the control and in cultures operated at 12 h HRT with a COD/SO42- ratio of 1.6 and fed 0.5 gL(-1) LA; however, with all other LA levels (0.5 and 1.0 gL(-1)) and HRTs (12, 24 and 36 h), HACs were not detected

Improving Environmental DNA Sensitivity for Dreissenid Mussels by Targeting Tandem Repeat Regions of the Mitochondrial Genome

The recent genetic revolution through the analysis of aquatic environmental DNA (eDNA) has become a powerful tool for improving the detection of rare and/or invasive species. For the majority of eDNA studies, genetic assays are designed to target mitochondrial genes commonly referred to as “barcode” regions. However, unlike the typical structure of an animal mitochondrial genome, those for the invasive zebra and quagga mussels are greatly expanded with large extended tandem repeat regions. These sections of repeated DNA can appear hundreds of times within the genome compared to a single copy for the mitochondrial barcode genes. This higher number of target copies per mitochondrial genome presents an opportunity to increase eDNA assay sensitivity for these species. Therefore, we designed and evaluated new eDNA assays to target the extended repeat sections for both zebra and quagga mussels. These assays lower the limit of detection of genomic DNA by 100-fold for zebra mussels and 10-fold for quagga mussels. Additionally, these newly developed assays provided longer durations of detection during degradation mesocosm experiments and greater sensitivity for eDNA detection from water samples collected across western Lake Erie compared to standard assays targeting mitochondrial genes. This work illustrates how understanding the complete genomic structure of an organism can improve eDNA analysis

Improving Environmental DNA Sensitivity for Dreissenid Mussels by Targeting Tandem Repeat Regions of the Mitochondrial Genome

The recent genetic revolution through the analysis of aquatic environmental DNA (eDNA) has become a powerful tool for improving the detection of rare and/or invasive species. For the majority of eDNA studies, genetic assays are designed to target mitochondrial genes commonly referred to as “barcode” regions. However, unlike the typical structure of an animal mitochondrial genome, those for the invasive zebra and quagga mussels are greatly expanded with large extended tandem repeat regions. These sections of repeated DNA can appear hundreds of times within the genome compared to a single copy for the mitochondrial barcode genes. This higher number of target copies per mitochondrial genome presents an opportunity to increase eDNA assay sensitivity for these species. Therefore, we designed and evaluated new eDNA assays to target the extended repeat sections for both zebra and quagga mussels. These assays lower the limit of detection of genomic DNA by 100-fold for zebra mussels and 10-fold for quagga mussels. Additionally, these newly developed assays provided longer durations of detection during degradation mesocosm experiments and greater sensitivity for eDNA detection from water samples collected across western Lake Erie compared to standard assays targeting mitochondrial genes. This work illustrates how understanding the complete genomic structure of an organism can improve eDNA analysis

16S rRNA gene based analysis of the microbial diversity and hydrogen production in three mixed anaerobic cultures

To explore of role of microbial diversity and its functionality in commercial bioreactors, three anaerobic microbial communities from Ontario, Canada were characterized using 16S rRNA gene-based, clone library sequencing and terminal restriction fragment length polymorphism (T-RFLP) and compared with the hydrogen (H-2) and methane yields. The T-RFLP method showed more operational taxonomic units than the clone library sequence analysis; however, the two methods showed similar dominant species and relative diversity while Spearman\u27s Rank correlation coefficient (r) values ranged from 0.82 to 0.91. The Chao 1 and Shannon-Wiener indices revealed that the cultures samples have highly diverse microbial communities. Comparatively, cultures from a municipal wastewater treatment plant (CA) showed more diversity than those from facilities treating effluents from a baby food processor and a brewery. Even though culture CA has the highest microbial diversity, low H-2 and methane production yield was attributed to the presence of sulphate reducers, propionate producers and a low percentage of methanogens. This study confirms that the selection of the source of mixed anaerobic cultures plays an important role in H-2 and methane production. Crown Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved

Metabarcoding of native and invasive species in stomach contents of Great Lakes fishes.

As aquatic invasive species (AIS) proliferate worldwide, a better understanding of their roles in invaded habitats is needed to inform management and introduction prevention strategies and priorities. Metabarcoding of stomach content DNA (scDNA) shows considerable promise in such regard. We thus metabarcoded scDNA from two non-native fish species (alewife (Alosa pseudoharengus) and rainbow smelt (Osmerus mordax)), and three native ones (bloater (Coregonus hoyi), ninespine stickleback (Pungitius pungitius), and slimy sculpin (Cottus cognatus)). Fishes (N = 376) were sampled in spring 2009 and 2010 from 73-128 m depths at three Lake Michigan sites. Four mitochondrial cytochrome oxidase 1 (CO1) primer sets designed to target five potential AIS prey, and a universal aquatic invertebrate CO1 primer set targeting both native and AIS prey were used. Quality controlled prey amplicons were matched to three AIS prey: Bythotrephes longimanus (mean percent frequency occurrence, all samples = 7%), Cercopagis pengoi (5%), and Dreissena rostriformis bugensis (11%). Neither invasive prey Dreissena polymorpha nor Hemimysis anomala were detected. Native prey Leptodiaptomus sicilis, Limnocalanus macrurus, and Mysis diluviana were relatively common in scDNA (respective mean percent occurrences, all samples: 48%, 25%, 42%). Analysis of variation in prey occurrences for sample site, predator species, sample year, sample depth, and predator total length (TL) indicated site and predator species were most important. However, B. longimanus occurrence in scDNA depended upon predator TL, perhaps indicative of its unique defensive spine limiting susceptibility to predation until fishes exceed species-specific gape-based limitations. Our analysis of native and invasive prey species indicated possible indirect AIS impacts such as native predators switching their diet due to AIS-driven losses of preferred native prey. Metabarcoding demonstrated that AIS are integrated components of the offshore Lake Michigan food web, with both native and non-native predators, and both invasive and native prey are affecting species interactions across multiple trophic levels

Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome

Abstract Background While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation. Results We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes. Conclusions Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstrac

Production of L (+) lactic acid by Lactobacillus delbrueckii immobilized in functionalized alginate matrices

The role of functionalized alginate gels as immobilized matrices in production of L (+) lactic acid by Lactobacillus delbrueckii was studied. L. delbrueckii cells immobilized in functionalized alginate beads showed enhanced bead stability and selectivity towards production of optically pure L (+) lactic acid in higher yields (1.74Yp/s) compared to natural alginate. Palmitoylated alginate beads revealed 99% enantiomeric selectivity (ee) in production of L (+) lactic acid. Metabolite analysis during fermentation indicated low by-product (acetic acid, propionic acid and ethanol) formation on repeated batch fermentation with functionalized immobilized microbial cells. The scanning electron microscopic studies showed dense entrapped microbial cell biomass in modified immobilized beads compared to native alginate. Thus the methodology has great importance in large-scale production of optically pure lactic acid