cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p91wvuxo
title: Ken Pierce's Legacy Field Notebooks and Annotated Aerial Photographs, Geological, and Topographical Maps from Across the Western United States 1963-2021 (ver. 2.0, January 2024)

description: Ken Pierce was a Research Geologist with the U.S. Geological Survey for over 55 years and authored numerous scientific papers, geologic maps, and field trip guides. This data release contains digital scans of 44 field notebooks authored by Ken Pierce or his collaborators. Information contained in these notebooks provided much of the underpinning of Ken Pierce's research on the glacial and geomorphological history of Yellowstone National Park and surrounding areas.
DOI: 10.6084/m9.figshare.25016084
title: Data S4 - host_plant_filtering_stats.xlsx

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016084.v1
title: Data S4 - host_plant_filtering_stats.xlsx

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016087
title: Data S3 - multiqc_reads_posthostandplant.html

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016087.v1
title: Data S3 - multiqc_reads_posthostandplant.html

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016090
title: Data S2 - fastqc_rawreads_postfastp.zip

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016090.v1
title: Data S2 - fastqc_rawreads_postfastp.zip

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016117
title: Data S6 - full_vs_bac_assembly_statistics.xlsx

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016096
title: Data S1 - fastqc_rawreads.zip

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016096.v1
title: Data S1 - fastqc_rawreads.zip

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016099.v1
title: Data S5 - metaspades_assembly_statistics.zip

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016117.v1
title: Data S6 - full_vs_bac_assembly_statistics.xlsx

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.6084/m9.figshare.25016099
title: Data S5 - metaspades_assembly_statistics.zip

description: Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut bacterial phylotypes dominate communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, cease to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Furthermore, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees and other low-microbial abundance systems.
DOI: 10.17630/0f7a7c71-26f5-4346-9bf1-3da33e354721
title: Solving decision problems in finitely presented groups via generalized small cancellation theory (thesis data)

description: The data set contains the implementation of the algorithms from the thesis in the Computer Algebra System MAGMA. See ReadMe.txt for more information.