Stormwater in Silver Bow and Blacktail Creeks: Implications for the Microbial Community

Silver Bow and Blacktail Creeks are the headwaters of the Clark Fork River and are impacted by historic mining activities in the area. Although metal concentrations of runoff into the creeks are monitored and reported in previous studies, the composition and diversity of microbial communities are unknown. We seek to identify the microbial communities present and investigate changes in community structure due to stormwater impact, thereby determining and monitoring the overall environmental health of the system. We sampled five sites in Silver Bow and Blacktail Creeks in Butte, MT for chemical and biological analyses during high stormwater flow events. Water samples were collected for analysis of major anions and cations, metal concentrations, dissolved inorganic and organic carbon and carbon isotopes and hydrogen and oxygen isotopes in water. In situ measurements of pH, temperature and dissolved oxygen were taken at the time of sampling. Redox sensitive species - total dissolved sulfide, dissolved silica and ferrous iron - were measured using wet chemical tests and field spectrophotometry. Concurrent biological samples were collected for microbial identification and diversity (DNA), activity (protein), quantity (cell counts) and culturing. Overall microbial results are in progress, but water chemistry data provide clues about microbial habitats available in the creeks. Results upstream in Butte will be compared to downstream areas such as Durant Canyon and the Warm Springs Settling Ponds. The relationship between water chemistry, microbes, and overall ecosystem health can be characterized by deciphering how water chemistry affects microbial activity and vice versa

Computed tomographic morphometry of tympanic bulla shape and position in brachycephalic and mesaticephalic dog breeds

Anatomic variations in skull morphology have been previously described for brachycephalic dogs; however there is little published information on interbreed variations in tympanic bulla morphology. This retrospective observational study aimed to (1) provide detailed descriptions of the computed tomographic (CT) morphology of tympanic bullae in a sample of dogs representing four brachycephalic breeds (Pugs, French Bulldogs, English Bulldog, and Cavalier King Charles Spaniels) versus two mesaticephalic breeds (Labrador retrievers and Jack Russell Terriers); and (2) test associations between tympanic bulla morphology and presence of middle ear effusion. Archived head CT scans for the above dog breeds were retrieved and a single observer measured tympanic bulla shape (width:height ratio), wall thickness, position relative to the temporomandibular joint, and relative volume (volume:body weight ratio). A total of 127 dogs were sampled. Cavalier King Charles Spaniels had significantly flatter tympanic bullae (greater width:height ratios) versus Pugs, English Bulldogs, Labrador retrievers, and Jack Russell terriers. French Bulldogs and Pugs had significantly more overlap between tympanic bullae and temporomandibular joints versus other breeds. All brachycephalic breeds had significantly lower tympanic bulla volume:weight ratios versus Labrador retrievers. Soft tissue attenuating material (middle ear effusion) was present in the middle ear of 48/100 (48%) of brachycephalic breeds, but no significant association was found between tympanic bulla CT measurements and presence of this material. Findings indicated that there are significant interbreed variations in tympanic bulla morphology, however no significant relationship between tympanic bulla morphology and presence of middle ear effusion could be identified

Use of high throughput sequencing to observe genome dynamics at a single cell level

With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions. Here, we sequenced several genomes of Escherichia coli from colonies obtained after chemical mutagenesis and observed a strikingly nonrandom distribution of the induced mutations. These include long stretches of exclusively G to A or C to T transitions along the genome and orders of magnitude intra- and inter-genomic differences in mutation density. Whereas most of these observations can be explained by the known features of enzymatic processes, the others could reflect stochasticity in the molecular processes at the single-cell level. Our results demonstrate how analysis of the molecular records left in the genomes of the descendants of an individual mutagenized cell allows for genome-scale observations of fixation and segregation of mutations, as well as recombination events, in the single genome of their progenitor.Comment: 22 pages, 9 figures (including 5 supplementary), one tabl

Rabbit Creek: Geochemistry of an Alkaline Deeply Sourced Hot Spring with Abundant Microbial Mats

The Rabbit Creek hot springs in Yellowstone National Park are located along the edge of the Mallard Lake Dome in the Midway Geyser Basin. The principal source, Rabbit Creek hot spring, contains high concentrations of arsenic and antimony relative to hot springs throughout the area. This study investigates the water chemistry of the Rabbit Creek hot spring outflow, geologic explanations for the distinct differences in hot spring compositions of the area, and the implications for the abundant thermophilic microbial mats present in the outflow. The distribution of the microbial mats may be related to the concentrations of arsenic and antimony throughout the outflow. In addition, changes in the microbial mats related to temperature and sulfide concentrations are discussed. This study aids in our understanding of the hot springs in the Rabbit Creek area and of the potential effects of the Mallard Lake Dome on the Midway Geyser Basin

The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models

The colonization of land by descendants of charophyte green algae marked a turning point in Earth history that enabled the development of the diverse terrestrial ecosystems we see today. Early land plants diversified into three gametophyte-dominant lineages, namely the hornworts, liverworts, and mosses, collectively known as bryophytes, and a sporophyte-dominant lineage, the vascular plants, or tracheophytes. In recent decades, the prevailing view of evolutionary relationships among these four lineages has been that the tracheophytes were derived from a bryophyte ancestor. However, recent phylogenetic evidence has suggested that bryophytes are monophyletic, and thus that the first split among land plants gave rise to the lineages that today we recognize as the bryophytes and tracheophytes. We present a phylogenetic analysis of chloroplast protein-coding data that also supports the monophyly of bryophytes. This newly compiled data set consists of 83 chloroplast genes sampled across 30 taxa that include chlorophytes and charophytes, including four members of the Zygnematophyceae, and land plants, that were sampled following a balanced representation of the main bryophyte and tracheophyte lineages. Analyses of non-synonymous site nucleotide data and amino acid translation data result in congruent phylogenetic trees showing the monophyly of bryophytes, with the Zygnematophyceae as the charophyte group most closely related to land plants. Analyses showing that bryophytes and tracheophytes evolved separately from a common terrestrial ancestor have profound implications for the way we understand the evolution of plant life cycles on land and how we interpret the early land plant fossil record.This work was supported by FCT (Portuguese Foundation for Science and Technology) through project grant PTDC/BIA-EVF/1499/2014 to CC and national funds through project UIDB/04326/2020, and from the operational programs CRESC Algarve 2020 and COMPETE 2020 through projects EMBRC.PT ALG-01-0145-FEDER-022121 and BIODATA.PT ALG-01-0145-FEDER-022231.info:eu-repo/semantics/publishedVersio

An archaeal origin of eukaryotes supports only two primary domains of life

The discovery of the Archaea and the proposal of the three-domains ‘universal’ tree, based on ribosomal RNA and core genes mainly involved in protein translation, catalysed new ideas for cellular evolution and eukaryotic origins. However, accumulating evidence suggests that the three-domains tree may be incorrect: evolutionary trees made using newer methods place eukaryotic core genes within the Archaea, supporting hypotheses in which an archaeon participated in eukaryotic origins by founding the host lineage for the mitochondrial endosymbiont. These results provide support for only two primary domains of life—Archaea and Bacteria—because eukaryotes arose through partnership between them

The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models

Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.UIDB/04326/2020, PTDC/BIA-EVF/1499/2014, EMBRC.PT ALG-01-0145-FEDER-022121, BIODATA.PT ALG-01-0145-FEDER-022231info:eu-repo/semantics/publishedVersio

Lack of Evidence for an Association between Iridovirus and Colony Collapse Disorder

Colony collapse disorder (CCD) is characterized by the unexplained losses of large numbers of adult worker bees (Apis mellifera) from apparently healthy colonies. Although infections, toxins, and other stressors have been associated with the onset of CCD, the pathogenesis of this disorder remains obscure. Recently, a proteomics study implicated a double-stranded DNA virus, invertebrate iridescent virus (Family Iridoviridae) along with a microsporidium (Nosema sp.) as the cause of CCD. We tested the validity of this relationship using two independent methods: (i) we surveyed healthy and CCD colonies from the United States and Israel for the presence of members of the Iridovirus genus and (ii) we reanalyzed metagenomics data previously generated from RNA pools of CCD colonies for the presence of Iridovirus-like sequences. Neither analysis revealed any evidence to suggest the presence of an Iridovirus in healthy or CCD colonies

Standard methods for Apis mellifera anatomy and dissection

An understanding of the anatomy and functions of internal and external structures is fundamental to many studies on the honey bee Apis mellifera. Similarly, proficiency in dissection techniques is vital for many more complex procedures. In this paper, which is a prelude to the other papers of the COLOSS BEEBOOK, we outline basic honey bee anatomy and basic dissection techniques