Draft Genome Sequences of Propionibacterium acnes Type Strain ATCC6919 and Antibiotic-Resistant Strain HL411PA1.

Propionibacterium acnes is a major skin commensal and is associated with acne vulgaris, the most common skin disease. Here we report the draft genome sequences of two P. acnes strains, the type strain ATCC6919 and an antibiotic-resistant strain, HL411PA1

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results

Characterizing environmentally assisted crack initiation and short crack growth

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Unique molecular and functional features of extramedullary hematopoietic stem and progenitor cell reservoirs in humans

Rare hematopoietic stem and progenitor cell (HSPC) pools outside the bone marrow (BM) contribute to blood production in stress and disease but remain ill-defined. Although non-mobilized peripheral blood (PB) is routinely sampled for clinical management, the diagnosis and monitoring potential of PB HSPCs remains untapped, as no healthy PB HSPC baseline has been reported. Here we comprehensively delineate human extramedullary HSPC compartments comparing spleen, PB and mobilized PB (mPB) to BM using single-cell RNA-seq and/or functional assays. We uncover HSPC features shared by extramedullary tissues and others unique to PB. First, in contrast to actively dividing BM HSPCs, we find no evidence of substantial ongoing hematopoiesis in extramedullary tissues at steady state, but report increased splenic HSPC proliferative output during stress erythropoiesis. Second, extramedullary stem cells/multipotent progenitors (HSC/MPPs) from spleen, PB and mPB share a common transcriptional signature and increased abundance of lineage-primed subsets compared to BM. Third, healthy PB HSPCs display a unique bias towards erythroid-megakaryocytic differentiation. At HSC/MPP level, this is functionally imparted by a subset of phenotypic CD71+ HSC/MPPs, exclusively producing erythrocytes and megakaryocytes, highly abundant in PB but rare in other adult tissues. Finally, the unique erythroid-megakaryocytic-skewing of PB is perturbed with age, in essential thrombocythemia and in beta-thalassemia. Collectively, we identify extramedullary lineage-primed HSPC reservoirs that are non-proliferative in situ and report involvement of splenic HSPCs during demand-adapted hematopoiesis. Our data also establish aberrant composition and function of circulating HSPCs as potential clinical indicators of BM dysfunction

Unique molecular and functional features of extramedullary hematopoietic stem and progenitor cell reservoirs in humans.

Rare hematopoietic stem and progenitor cell (HSPC) pools outside the bone marrow (BM) contribute to blood production in stress and disease but remain ill-defined. Although nonmobilized peripheral blood (PB) is routinely sampled for clinical management, the diagnosis and monitoring potential of PB HSPCs remain untapped, as no healthy PB HSPC baseline has been reported. Here we comprehensively delineate human extramedullary HSPC compartments comparing spleen, PB, and mobilized PB to BM using single-cell RNA-sequencing and/or functional assays. We uncovered HSPC features shared by extramedullary tissues and others unique to PB. First, in contrast to actively dividing BM HSPCs, we found no evidence of substantial ongoing hematopoiesis in extramedullary tissues at steady state but report increased splenic HSPC proliferative output during stress erythropoiesis. Second, extramedullary hematopoietic stem cells/multipotent progenitors (HSCs/MPPs) from spleen, PB, and mobilized PB share a common transcriptional signature and increased abundance of lineage-primed subsets compared with BM. Third, healthy PB HSPCs display a unique bias toward erythroid-megakaryocytic differentiation. At the HSC/MPP level, this is functionally imparted by a subset of phenotypic CD71+ HSCs/MPPs, exclusively producing erythrocytes and megakaryocytes, highly abundant in PB but rare in other adult tissues. Finally, the unique erythroid-megakaryocytic-skewing of PB is perturbed with age in essential thrombocythemia and β-thalassemia. Collectively, we identify extramedullary lineage-primed HSPC reservoirs that are nonproliferative in situ and report involvement of splenic HSPCs during demand-adapted hematopoiesis. Our data also establish aberrant composition and function of circulating HSPCs as potential clinical indicators of BM dysfunction

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; referees: 1 approved, 2 approved with reservations]

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results

A manager’s guide to using eDNA metabarcoding in marine ecosystems

Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications

Microbial community diversity, function, and succession in California’s Mediterranean habitats

We live on a predominantly microbial planet. I it is estimated that more than a billion microorganisms can live in a gram of soil. Microorganisms comprise the largest pool of genetic diversity on the planet and drive global biogeochemical cycles. Since microbial ecology is intimately associated with environment, changes in environmental conditions can have profound effects on the microbial diversity and function of microbial communities. In this dissertation I study; 1) the relationship between environmental heterogeneity and microbial diversity, 2) the relationship between the environment, microbial diversity, and microbial functional traits, and 3) microbial secession related to changing environmental conditions during anaerobic decomposition.Chapter 1Annual grassland invasions can increase environmental heterogeneity and reduce the biological diversity of plants and animals. There is a generally positive relationship between environmental heterogeneity and biodiversity, and more specifically, soil heterogeneity is known to influence plant diversity. Here I test if the diversity of soil microorganisms, like that of plants, displays a positive relationship with soil environmental heterogeneity. Specifically, I test to see if invasive annual grasses lead to reductions in soil heterogeneity and microbial alpha- and beta- diversity. I sampled the soil profile across invasive annual grassland, oak woodland, and coastal sage scrub habitat and characterized environmental heterogeneity (soil percent carbon, nitrogen, water content, total dissolved solids, and pH in addition to litter percent carbon, nitrogen and C:N), alpha and beta diversity. I found that invasive annual grassland habitat has greater soil environmental homogeneity than native woody habitats throughout the soil profile. Annual grassland communities have lower alpha-, but not beta-, diversity than native woody species. Patterns of alpha diversity with depth differ between grassland and woody habitat, and although not significant, woody habitats have higher community heterogeneity. Alpha diversity and beta diversity show positive relationships with several measures of environmental heterogeneity, suggesting that like plants, soil microbial diversity increases with environmental heterogeneity. Annual grassland invasions into native woody habitats reduce soil microbial diversity. This is particularly true in deep soil communities.Chapter 2 Plant invasions frequently alter ecosystem processes in part because they modify soil microbial communities. These communities decompose the bulk of terrestrial organic matter by producing and releasing extracellular enzymes. California's native Mediterranean habitats (e.g. Oak woodland and coastal sage scrub) are invaded by annual grasses and are converted to invasive annual grasslands. I investigated the relationship between extracellular enzyme activities and microbial community composition in these habitats by examining 1) how extracellular enzyme activities differed between native and invasive habitats, 2) whether changes in microbial community correlate with changes in extracellular activity, and 3) if the composition of bacterial phyla that contain genes for extracellular enzymes differ between habitats. I found that annual grassland enzyme activities are much different from those of woody habitat, and the differences in enzyme activities between habitats generally declined with depth as did enzyme activities. There was also a strong correlation between community composition and extracellular enzyme activity. This correlation was not influenced by soil environmental variables. The relative abundance of phyla with genes for extracellular enzymes were similar between habitats and those genes are contained in distinct assemblages of phyla. Habitat change through annual grassland invasion modifies soil communities and their functions thought out the soil profile. Future studies on the effects of annual grassland invasion on ecosystem processes in deep soil are needed to fully understand the consequences of these invasions.Chapter 3. Natural tar seeps are the source of millions of fossils from animals that became entrapped, died and were decomposed over the millennia. The microbial communities responsible for the anaerobic decomposition of these entrapped animals are not known. However, microbial communities likely play a role in the rapid time to skeletonization of animal components submerged in tar. I hypothesized that high energy animal tissue would support fast growing taxa and support lower microbial diversity, and that microbial succession across different locations in the tar environment and animal tissue decay would resemble known patterns of microbial decomposition in similar habits. I sampled different locations in a tar seep and also bobcat limbs that were experimentally submerged in the seep and left to decay until skeletonization. Microbial communities were characterized using 16S rDNA sequencing of the V4 region. I found that decay communities had lower diversity than tar environment communities and that microbial succession proceeded similarly to that in analogous habitats. The addition of animal tissue into this tar seep appeared to lead to rapid microbial community succession. This microbial succession likely affected the rate of decomposition of this tissue. Future experiments are required to understand the role of microbial succession in determining the rate of decomposition and time to skeletonization in tar environments

rCRUX: A rapid and versatile tool for generating metabarcoding reference libraries in R

Abstract The sequencing revolution requires accurate taxonomic classification of DNA sequences. The key to making accurate taxonomic assignments is curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa than are currently curated by professional staff. Thus, there is a growing need for an easy‐to‐implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like its predecessor, relies on sequence homology and PCR primer compatibility instead of keyword searches to avoid limitations of user‐defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user‐defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI)‐formatted nt database using a taxonomic rank‐based stratified random sampling approach (blast_seeds()). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer‐specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple‐to‐use tool for the generation of curated, comprehensive reference databases for user‐defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly

Draft Genome Sequences of Propionibacterium acnes Type Strain ATCC6919 and Antibiotic-Resistant Strain HL411PA1.

Propionibacterium acnes is a major skin commensal and is associated with acne vulgaris, the most common skin disease. Here we report the draft genome sequences of two P. acnes strains, the type strain ATCC6919 and an antibiotic-resistant strain, HL411PA1