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Formed in 2009, the Archive Team (not to be confused with the archive.org Archive-It Team) is a rogue archivist collective dedicated to saving copies of rapidly dying or deleted websites for the sake of history and digital heritage. The group is 100% composed of volunteers and interested parties, and has expanded into a large amount of related projects for saving online and digital history.

History is littered with hundreds of conflicts over the future of a community, group, location or business that were "resolved" when one of the parties stepped ahead and destroyed what was there. With the original point of contention destroyed, the debates would fall to the wayside. Archive Team believes that by duplicated condemned data, the conversation and debate can continue, as well as the richness and insight gained by keeping the materials. Our projects have ranged in size from a single volunteer downloading the data to a small-but-critical site, to over 100 volunteers stepping forward to acquire terabytes of user-created data to save for future generations.

The main site for Archive Team is at archiveteam.org and contains up to the date information on various projects, manifestos, plans and walkthroughs.

This collection contains the output of many Archive Team projects, both ongoing and completed. Thanks to the generous providing of disk space by the Internet Archive, multi-terabyte datasets can be made available, as well as in use by the Wayback Machine, providing a path back to lost websites and work.

Our collection has grown to the point of having sub-collections for the type of data we acquire. If you are seeking to browse the contents of these collections, the Wayback Machine is the best first stop. Otherwise, you are free to dig into the stacks to see what you may find.

The Archive Team Panic Downloads are full pulldowns of currently extant websites, meant to serve as emergency backups for needed sites that are in danger of closing, or which will be missed dearly if suddenly lost due to hard drive crashes or server failures.

Collection: Archive Team: URLs

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Daniel Manter

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Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils

PLOS ONE

Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogen... more Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, often resulting in increased crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members of the soil microbiome. Here, we applied soil microbiome disruption in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on rhizosphere bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases in ways both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abu...

Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil

Illumina MiSeq is the current standard for characterizing microbial communities in soil. The Oxfo... more Illumina MiSeq is the current standard for characterizing microbial communities in soil. The Oxford Nanopore Technologies MinION sequencer is quickly gaining popularity because of the low initial cost and longer sequence reads. However, the accuracy of MinION, per base, is much lower than MiSeq (95% versus 99.9%). The effects of this difference in base-calling accuracy on taxonomic and diversity estimates remains unclear. We compared the output of short MiSeq to short and full-length MinION 16S rRNA amplicons from a mock community and agricultural soil samples. For all three methods, we found that taxonomic assignments of the mock community at both the genus and species level matched expectations with minimal deviation (genus: 80.9–90.5%; species: 70.9–85.2% Bray-Curtis similarity); however, the short MiSeq with error correction (DADA2) resulted in the correct estimate of species richness and much lower alpha diversity for soils. Several filtering strategies were tested to improve t...

Rhizosphere Ecology

Encyclopedia of Ecology, 2019

Generalist herbivorous insect modulates similar rhizosphere bacterial communities across different plant species

Authorea

Soil sterilization leads to re-colonization of a healthier rhizosphere microbiome

Rhizosphere, 2019

The Effect of Hops (Humulus lupulus L.) Extract Supplementation on Weight Gain, Adiposity and Intestinal Function in Ovariectomized Mice

Estrogen decline during menopause is associated with altered metabolism, weight gain and increase... more Estrogen decline during menopause is associated with altered metabolism, weight gain and increased risk for cardiometabolic diseases. The gut microbiota also plays a role in the development of cardiometabolic dysfunction and is also subject to changes associated with age-related hormone changes. Phytoestrogens are plant-based estrogen mimics that have gained popularity as dietary supplements for treatment or prevention of menopause-related symptoms. These compounds have the potential to both modulate and to be metabolized by the gut microbiota. Hops (Humulus lupulus L.) contain potent phytoestrogen precursors, which rely on microbial biotransformation in the gut to estrogenic forms. We supplemented ovariectomized (OVX) or sham-operated (SHAM) C57BL/6 mice, with oral estradiol (E2), a flavonoid-rich extract from hops, or a placebo carrier oil to observe effects on adiposity, inflammation, and gut bacteria composition. Hops extract and E2 protected against increased visceral adiposity...

PHAGE Study: Effects of Supplemental Bacteriophage Intake on Inflammation and Gut Microbiota in Healthy Adults

Nutrients, 2019

The gut microbiota is increasingly recognized as an important modulator of human health. As such,... more The gut microbiota is increasingly recognized as an important modulator of human health. As such, there is a growing need to identify effective means of selectively modifying gut microbial communities. Bacteriophages, which were briefly utilized as clinical antimicrobials in the early 20th century, present an opportunity to selectively reduce populations of undesirable microorganisms. However, whether intentional consumption of specific bacteriophages affects overall gut ecology is not yet known. Using a commercial cocktail of Escherichia coli-targeting bacteriophages, we examined their effects on gut microbiota and markers of intestinal and systemic inflammation in a healthy human population. In a double-blinded, placebo-controlled crossover trial, normal to overweight adults consumed bacteriophages for 28 days. Stool and blood samples were collected and used to examine inflammatory markers, lipid metabolism, and gut microbiota. Reductions in fecal E. coli loads were observed with ...

Abundance of Bacteria, Fungi, and Sclerotinia homoeocarpa in the Thatch and Soil of Golf Courses

Phytobiomes Journal, 2018

Thatch management in turfgrass has been recommended as part of integrated pest management; howeve... more Thatch management in turfgrass has been recommended as part of integrated pest management; however, there is limited understanding of the microbial community in thatch. Previous studies on the turfgrass phytobiome mostly focused on the soil; however, culture-based studies have suggested that the thatch layer of golf courses contains higher bacterial and fungal abundances than the soil. In our study, quantitative PCR was used to investigate total abundance of bacteria, fungi, and the turfgrass pathogen, Sclerotinia homoeocarpa (causal agent of dollar spot) in the thatch and soil of three golf courses on two sampling dates. Additionally, we compared the abundance of these organisms among roughs, fairways, and putting greens, which are under different management intensities. Our results demonstrate bacterial abundance was higher in May than in September, but not consistently higher in the thatch or soil among the three golf courses or management areas. Fungi, and specifically S. homoeo...

Mitsuaria sp. and Burkholderia sp. from Arabidopsis rhizosphere enhance drought tolerance in Arabidopsis thaliana and maize (Zea mays L.)

Plant and Soil, 2017

Bacterial Microbiome and Nematode Occurrence in Different Potato Agricultural Soils

Microbial ecology, Nov 20, 2017

Pratylenchus neglectus and Meloidogyne chitwoodi are the main plant-parasitic nematodes in potato... more Pratylenchus neglectus and Meloidogyne chitwoodi are the main plant-parasitic nematodes in potato crops of the San Luis Valley, Colorado. Bacterial microbiome (16S rRNA copies per gram of soil) and nematode communities (nematodes per 200 g of soil) from five different potato farms were analyzed to determine negative and positive correlations between any bacterial genus and P. neglectus and M. chitwoodi. Farms showed differences in bacterial communities, percentage of bacterivorous and fungivorous nematodes, and numbers of P. neglectus and M. chitwoodi. The farm with the lowest population of P. neglectus and M. chitwoodi had higher abundances of the bacterial genera Bacillus spp., Arthrobacter spp., and Lysobacter spp., and the soil nematode community was composed of more than 30% of fungivorous nematodes. In contrast, the farm with higher numbers of P. neglectus and M. chitwoodi had a lower abundance of the abovementioned bacterial genera, higher abundance of Burkholderia spp., and ...

myPhyloDB: a local web server for the storage and analysis of metagenomic data

Database : the journal of biological databases and curation, 2016

myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facil... more myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of microbial community populations (e.g. 16S metagenomics data). MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g. analysis of covariance,t-tests, linear regression, differential abundance (DESeq2), and principal coordinates analysis (PCoA)) and normalization (rarefaction, DESeq2, and proportion) tools for the comparative analysis of taxonomic abundance, species richness and species diversity for projects of various types (e.g. human-associated, human gut microbiome, air, soi...

Soil biology for resilient, healthy soil

Journal of Soil and Water Conservation, 2015

What is a resilient, healthy soil? A resilient soil is capable of recovering from or adapting to ... more What is a resilient, healthy soil? A resilient soil is capable of recovering from or adapting to stress, and the health of the living/biological component of the soil is crucial for soil resiliency. Soil health is tightly coupled with the concept of soil quality (table 1), and the terms are frequently used interchangeably. The living component of soil or soil biota represents a small fraction (<0.05% dry weight), but it is essential to many soil functions and overall soil quality. Some of these key functions or services for production agriculture are (1) nutrient provision and cycling, (2) pest and pathogen protection, (3) production of growth factors, (4) water availability, and (5) formation of stable aggregates to reduce the risks of soil erosion and increase water infiltration (table 2). Soil resources and their inherent biological communities are the foundation for agricultural production systems that sustain the human population. The rapidly increasing human population is expanding the demand for food, fiber, feed, and fuel, which is stretching the capacity of the soil resource and contributing to soil degradation. Soil degradation decreases a soil's production capacity to directly supply human demands and decreases a soil's functional capacity to perform numerous critical services, which…

Phytopathology Journal - 97(7):850 - Abstract

A/Ci curve analysis across a range of woody plant species: influence of regression analysis parameters and mesophyll conductance

Journal of Experimental Botany, 2004

Antimicrobial Properties of an Oxidizer Produced by Burkholderia cenocepacia P525

Current Microbiology, 2014

A compound with both oxidizing properties and antibiotic properties was extracted and purified fr... more A compound with both oxidizing properties and antibiotic properties was extracted and purified from broth cultures of Burkholderia cenocepacia strain P525. A four step purification procedure was used to increase its specific activity ~400-fold and to yield a HPLC-UV chromatogram containing a single major peak. Size exclusion chromatography suggests a molecular mass of ~1,150 and UV spectroscopy suggests the presence of a polyene structure consisting of as many as six conjugated double bonds. Biological studies indicate that the compound is bacteriostatic. Enterobacter soli and E. aerogenes cells incubated with the compound exhibit a longer lag phase of growth. The bacteriostatic activity is greater at pH 3 than at pH 5. Bacteria such as B. cenocepacia strain P525 may have value in the agricultural industry as biocontrol agents.

Opinion: Why we need a National Living Soil Repository

Proceedings of the National Academy of Sciences of the United States of America, Dec 26, 2017

Influence of thawing rate and fungal infection by Rhizosphaera kalkhoffii on freezing injury in red spruce ( Picea rubens ) needles

Canadian Journal of Forest Research, 1996

ABSTRACT Red spruce (Picearubens Sarg.) decline has been observed in northeastern North America f... more ABSTRACT Red spruce (Picearubens Sarg.) decline has been observed in northeastern North America for the last 30 years. A major inciting stress involved in this decline is freezing injury of foliage. The objectives of this study were the following: (i) to examine how photosynthesis, needle electrolyte leakage, chlorophyll loss, needle reddening, needle loss and bud break respond to single freezing events down to −45 °C on 3-year-old seedlings; (ii) to test if faster thawing rates increase the amount of freezing injury; and (iii) to measure how Rhizosphaerakalkhoffii Bubák inoculations interact with freeze-injured needles. Two trials, one of 60 seedlings and one of 80 seedlings, were conducted. The second trial had half the seedlings covered with plastic bags for doubling the thawing time. Photosynthesis, as measured by gas exchange, was consistently the most sensitive measure, detecting nonvisible injury on uncovered seedlings (p &lt; 0.05) at −25 °C. Measurements detecting freezing damage on covered, slower thawing seedlings were photosynthesis, chlorophyll loss, and percent budbreak. Faster thawing rates increased the amount of injury ca. 2- to 3-fold after freezing to −35 or −45 °C for all measures. Infection by R. kalkhoffii increased 40–83% after freezing needles to −40 or −45 °C. Fungal inoculations caused ca. 40–60% reduction in photosynthesis on needles frozen to −40 or −45 °C. This study suggests that two new factors can increase freezing injury on red spruce needles: a faster thawing rate and fungal (R. kalkhoffii) infection. These results are consistent with the growing knowledge that freezing injury is a complex phenomenon in red spruce.

Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in Potato Roots

Microbial Ecology, Apr 1, 2010

In this study, we examined the bacterial endophyte community of potato (Solanum tuberosum) cultiv... more In this study, we examined the bacterial endophyte community of potato (Solanum tuberosum) cultivar/clones using two different molecular-based techniques (bacterial automated ribosomal intergenic spacer analysis (B-ARISA) and pyrosequencing). B-ARISA profiles revealed a significant difference in the endophytic community between cultivars (perMANOVA, p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001), and canonical correspondence analysis showed a significant correlation between the community structure and plant biomass (p = 0.001). Pyrosequencing detected, on average, 477 +/- 71 bacterial operational taxonomic units (OTUs, 97% genetic similarity) residing within the roots of each cultivar, with a Chao estimated total OTU richness of 1,265 +/- 313. Across all cultivars, a total of 238 known genera from 15 phyla were identified. Interestingly, five of the ten most common genera (Rheinheimera, Dyadobacter, Devosia, Pedobacter, and Pseudoxanthomonas) have not, to our knowledge, been previously reported as endophytes of potato. Like the B-ARISA analysis, the endophytic communities differed between cultivar/clones (integral-libshuff, p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001) and exhibited low similarities on both a presence/absence (0.145 +/- 0.019) and abundance (0.420 +/- 0.081) basis. Seventeen OTUs showed a strong positive (r &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; 0.600) or negative (r &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; -0.600) correlation with plant biomass, suggesting a possible link between plant production and endophyte abundance. This study represents one of the most comprehensive assessments of the bacterial endophytic communities to date, and similar analyses in other plant species, cultivars, or tissues could be utilized to further elucidate the potential contribution(s) of endophytic communities to plant physiology and production.

Antimicrobial Activity of Extracts and Select Compounds in the Heartwood of Seven Western Conifers Toward Phytophthora ramorum 1

Previously, we demonstrated that wood chips, essential oil, and four individual compounds from Al... more Previously, we demonstrated that wood chips, essential oil, and four individual compounds from Alaska yellow-cedar (Chamaecyparis nootkatensis [D. Don] Spach) heartwood strongly inhibit the germination of Phytophthora ramorum (Werres, de Cock, Man int Veld) zoospores or sporangia, and reduce hyphal growth in culture (Manter and others 2006). Essential oils from heartwood of incense cedar (Calocedrus decurrens [Torr.] Florin), western redcedar (Thuja plicata Donn ex D. Don), Port-Orford-cedar (Chamaecyparis lawsoniana [A. Murr.] Parl.), and western juniper (Juniperus occidentalis Hook.) were also tested and found to be equally active, but not investigated further until now. The objectives of this study were to: 1) test the procedure described by Kuhajek and others (2003) as a bioassay technique for P. ramorum; 2) use this bioassay with other individual compounds from yellow-cedar heartwood that were not previously tested for bioactivity toward P. ramorum; and 3) bioassay extracts and...

Do Root Exudates of Specific Winter Wheat Cultivars Recruit ACC Deaminase-Positive Bacteria?

Root exudates are important for establishing plant-microbial associations because they are chemic... more Root exudates are important for establishing plant-microbial associations because they are chemical signals that promote chemotaxis, initiate symbiotic interactions, and/or act as substrates promoting the growth of some microbes. We hypothesize that root exudates are utilized by winter wheat to recruit ACC deaminase positive (ACC+) bacteria. These bacteria degrade the “stress” ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), and promote plant growth under drought stress. Our previous studies have found that the abundance, diversity, and species composition of these bacteria vary under different wheat cultivars in Colorado, possibly in response to different root exudate profiles. In this study, we characterized the root exudate profiles of two contrasting wheat cultivars, Ripper and RonL, and measured the response of ACC+ bacteria to exudates and exudate fractions added to soil. Root exudates of Ripper and RonL were collected under hydroponic growth conditions over a ...

Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils

PLOS ONE

Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogen... more Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, often resulting in increased crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members of the soil microbiome. Here, we applied soil microbiome disruption in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on rhizosphere bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases in ways both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abu...

Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil

Illumina MiSeq is the current standard for characterizing microbial communities in soil. The Oxfo... more Illumina MiSeq is the current standard for characterizing microbial communities in soil. The Oxford Nanopore Technologies MinION sequencer is quickly gaining popularity because of the low initial cost and longer sequence reads. However, the accuracy of MinION, per base, is much lower than MiSeq (95% versus 99.9%). The effects of this difference in base-calling accuracy on taxonomic and diversity estimates remains unclear. We compared the output of short MiSeq to short and full-length MinION 16S rRNA amplicons from a mock community and agricultural soil samples. For all three methods, we found that taxonomic assignments of the mock community at both the genus and species level matched expectations with minimal deviation (genus: 80.9–90.5%; species: 70.9–85.2% Bray-Curtis similarity); however, the short MiSeq with error correction (DADA2) resulted in the correct estimate of species richness and much lower alpha diversity for soils. Several filtering strategies were tested to improve t...

Rhizosphere Ecology

Encyclopedia of Ecology, 2019

Generalist herbivorous insect modulates similar rhizosphere bacterial communities across different plant species

Authorea

Soil sterilization leads to re-colonization of a healthier rhizosphere microbiome

Rhizosphere, 2019

The Effect of Hops (Humulus lupulus L.) Extract Supplementation on Weight Gain, Adiposity and Intestinal Function in Ovariectomized Mice

Estrogen decline during menopause is associated with altered metabolism, weight gain and increase... more Estrogen decline during menopause is associated with altered metabolism, weight gain and increased risk for cardiometabolic diseases. The gut microbiota also plays a role in the development of cardiometabolic dysfunction and is also subject to changes associated with age-related hormone changes. Phytoestrogens are plant-based estrogen mimics that have gained popularity as dietary supplements for treatment or prevention of menopause-related symptoms. These compounds have the potential to both modulate and to be metabolized by the gut microbiota. Hops (Humulus lupulus L.) contain potent phytoestrogen precursors, which rely on microbial biotransformation in the gut to estrogenic forms. We supplemented ovariectomized (OVX) or sham-operated (SHAM) C57BL/6 mice, with oral estradiol (E2), a flavonoid-rich extract from hops, or a placebo carrier oil to observe effects on adiposity, inflammation, and gut bacteria composition. Hops extract and E2 protected against increased visceral adiposity...

PHAGE Study: Effects of Supplemental Bacteriophage Intake on Inflammation and Gut Microbiota in Healthy Adults

Nutrients, 2019

The gut microbiota is increasingly recognized as an important modulator of human health. As such,... more The gut microbiota is increasingly recognized as an important modulator of human health. As such, there is a growing need to identify effective means of selectively modifying gut microbial communities. Bacteriophages, which were briefly utilized as clinical antimicrobials in the early 20th century, present an opportunity to selectively reduce populations of undesirable microorganisms. However, whether intentional consumption of specific bacteriophages affects overall gut ecology is not yet known. Using a commercial cocktail of Escherichia coli-targeting bacteriophages, we examined their effects on gut microbiota and markers of intestinal and systemic inflammation in a healthy human population. In a double-blinded, placebo-controlled crossover trial, normal to overweight adults consumed bacteriophages for 28 days. Stool and blood samples were collected and used to examine inflammatory markers, lipid metabolism, and gut microbiota. Reductions in fecal E. coli loads were observed with ...

Abundance of Bacteria, Fungi, and Sclerotinia homoeocarpa in the Thatch and Soil of Golf Courses

Phytobiomes Journal, 2018

Thatch management in turfgrass has been recommended as part of integrated pest management; howeve... more Thatch management in turfgrass has been recommended as part of integrated pest management; however, there is limited understanding of the microbial community in thatch. Previous studies on the turfgrass phytobiome mostly focused on the soil; however, culture-based studies have suggested that the thatch layer of golf courses contains higher bacterial and fungal abundances than the soil. In our study, quantitative PCR was used to investigate total abundance of bacteria, fungi, and the turfgrass pathogen, Sclerotinia homoeocarpa (causal agent of dollar spot) in the thatch and soil of three golf courses on two sampling dates. Additionally, we compared the abundance of these organisms among roughs, fairways, and putting greens, which are under different management intensities. Our results demonstrate bacterial abundance was higher in May than in September, but not consistently higher in the thatch or soil among the three golf courses or management areas. Fungi, and specifically S. homoeo...

Mitsuaria sp. and Burkholderia sp. from Arabidopsis rhizosphere enhance drought tolerance in Arabidopsis thaliana and maize (Zea mays L.)

Plant and Soil, 2017

Bacterial Microbiome and Nematode Occurrence in Different Potato Agricultural Soils

Microbial ecology, Nov 20, 2017

Pratylenchus neglectus and Meloidogyne chitwoodi are the main plant-parasitic nematodes in potato... more Pratylenchus neglectus and Meloidogyne chitwoodi are the main plant-parasitic nematodes in potato crops of the San Luis Valley, Colorado. Bacterial microbiome (16S rRNA copies per gram of soil) and nematode communities (nematodes per 200 g of soil) from five different potato farms were analyzed to determine negative and positive correlations between any bacterial genus and P. neglectus and M. chitwoodi. Farms showed differences in bacterial communities, percentage of bacterivorous and fungivorous nematodes, and numbers of P. neglectus and M. chitwoodi. The farm with the lowest population of P. neglectus and M. chitwoodi had higher abundances of the bacterial genera Bacillus spp., Arthrobacter spp., and Lysobacter spp., and the soil nematode community was composed of more than 30% of fungivorous nematodes. In contrast, the farm with higher numbers of P. neglectus and M. chitwoodi had a lower abundance of the abovementioned bacterial genera, higher abundance of Burkholderia spp., and ...

myPhyloDB: a local web server for the storage and analysis of metagenomic data

Database : the journal of biological databases and curation, 2016

myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facil... more myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of microbial community populations (e.g. 16S metagenomics data). MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g. analysis of covariance,t-tests, linear regression, differential abundance (DESeq2), and principal coordinates analysis (PCoA)) and normalization (rarefaction, DESeq2, and proportion) tools for the comparative analysis of taxonomic abundance, species richness and species diversity for projects of various types (e.g. human-associated, human gut microbiome, air, soi...

Soil biology for resilient, healthy soil

Journal of Soil and Water Conservation, 2015

What is a resilient, healthy soil? A resilient soil is capable of recovering from or adapting to ... more What is a resilient, healthy soil? A resilient soil is capable of recovering from or adapting to stress, and the health of the living/biological component of the soil is crucial for soil resiliency. Soil health is tightly coupled with the concept of soil quality (table 1), and the terms are frequently used interchangeably. The living component of soil or soil biota represents a small fraction (<0.05% dry weight), but it is essential to many soil functions and overall soil quality. Some of these key functions or services for production agriculture are (1) nutrient provision and cycling, (2) pest and pathogen protection, (3) production of growth factors, (4) water availability, and (5) formation of stable aggregates to reduce the risks of soil erosion and increase water infiltration (table 2). Soil resources and their inherent biological communities are the foundation for agricultural production systems that sustain the human population. The rapidly increasing human population is expanding the demand for food, fiber, feed, and fuel, which is stretching the capacity of the soil resource and contributing to soil degradation. Soil degradation decreases a soil's production capacity to directly supply human demands and decreases a soil's functional capacity to perform numerous critical services, which…

Phytopathology Journal - 97(7):850 - Abstract

A/Ci curve analysis across a range of woody plant species: influence of regression analysis parameters and mesophyll conductance

Journal of Experimental Botany, 2004

Antimicrobial Properties of an Oxidizer Produced by Burkholderia cenocepacia P525

Current Microbiology, 2014

A compound with both oxidizing properties and antibiotic properties was extracted and purified fr... more A compound with both oxidizing properties and antibiotic properties was extracted and purified from broth cultures of Burkholderia cenocepacia strain P525. A four step purification procedure was used to increase its specific activity ~400-fold and to yield a HPLC-UV chromatogram containing a single major peak. Size exclusion chromatography suggests a molecular mass of ~1,150 and UV spectroscopy suggests the presence of a polyene structure consisting of as many as six conjugated double bonds. Biological studies indicate that the compound is bacteriostatic. Enterobacter soli and E. aerogenes cells incubated with the compound exhibit a longer lag phase of growth. The bacteriostatic activity is greater at pH 3 than at pH 5. Bacteria such as B. cenocepacia strain P525 may have value in the agricultural industry as biocontrol agents.

Opinion: Why we need a National Living Soil Repository

Proceedings of the National Academy of Sciences of the United States of America, Dec 26, 2017

Influence of thawing rate and fungal infection by Rhizosphaera kalkhoffii on freezing injury in red spruce ( Picea rubens ) needles

Canadian Journal of Forest Research, 1996

ABSTRACT Red spruce (Picearubens Sarg.) decline has been observed in northeastern North America f... more ABSTRACT Red spruce (Picearubens Sarg.) decline has been observed in northeastern North America for the last 30 years. A major inciting stress involved in this decline is freezing injury of foliage. The objectives of this study were the following: (i) to examine how photosynthesis, needle electrolyte leakage, chlorophyll loss, needle reddening, needle loss and bud break respond to single freezing events down to −45 °C on 3-year-old seedlings; (ii) to test if faster thawing rates increase the amount of freezing injury; and (iii) to measure how Rhizosphaerakalkhoffii Bubák inoculations interact with freeze-injured needles. Two trials, one of 60 seedlings and one of 80 seedlings, were conducted. The second trial had half the seedlings covered with plastic bags for doubling the thawing time. Photosynthesis, as measured by gas exchange, was consistently the most sensitive measure, detecting nonvisible injury on uncovered seedlings (p &lt; 0.05) at −25 °C. Measurements detecting freezing damage on covered, slower thawing seedlings were photosynthesis, chlorophyll loss, and percent budbreak. Faster thawing rates increased the amount of injury ca. 2- to 3-fold after freezing to −35 or −45 °C for all measures. Infection by R. kalkhoffii increased 40–83% after freezing needles to −40 or −45 °C. Fungal inoculations caused ca. 40–60% reduction in photosynthesis on needles frozen to −40 or −45 °C. This study suggests that two new factors can increase freezing injury on red spruce needles: a faster thawing rate and fungal (R. kalkhoffii) infection. These results are consistent with the growing knowledge that freezing injury is a complex phenomenon in red spruce.

Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in Potato Roots

Microbial Ecology, Apr 1, 2010

In this study, we examined the bacterial endophyte community of potato (Solanum tuberosum) cultiv... more In this study, we examined the bacterial endophyte community of potato (Solanum tuberosum) cultivar/clones using two different molecular-based techniques (bacterial automated ribosomal intergenic spacer analysis (B-ARISA) and pyrosequencing). B-ARISA profiles revealed a significant difference in the endophytic community between cultivars (perMANOVA, p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001), and canonical correspondence analysis showed a significant correlation between the community structure and plant biomass (p = 0.001). Pyrosequencing detected, on average, 477 +/- 71 bacterial operational taxonomic units (OTUs, 97% genetic similarity) residing within the roots of each cultivar, with a Chao estimated total OTU richness of 1,265 +/- 313. Across all cultivars, a total of 238 known genera from 15 phyla were identified. Interestingly, five of the ten most common genera (Rheinheimera, Dyadobacter, Devosia, Pedobacter, and Pseudoxanthomonas) have not, to our knowledge, been previously reported as endophytes of potato. Like the B-ARISA analysis, the endophytic communities differed between cultivar/clones (integral-libshuff, p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001) and exhibited low similarities on both a presence/absence (0.145 +/- 0.019) and abundance (0.420 +/- 0.081) basis. Seventeen OTUs showed a strong positive (r &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; 0.600) or negative (r &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; -0.600) correlation with plant biomass, suggesting a possible link between plant production and endophyte abundance. This study represents one of the most comprehensive assessments of the bacterial endophytic communities to date, and similar analyses in other plant species, cultivars, or tissues could be utilized to further elucidate the potential contribution(s) of endophytic communities to plant physiology and production.

Antimicrobial Activity of Extracts and Select Compounds in the Heartwood of Seven Western Conifers Toward Phytophthora ramorum 1

Previously, we demonstrated that wood chips, essential oil, and four individual compounds from Al... more Previously, we demonstrated that wood chips, essential oil, and four individual compounds from Alaska yellow-cedar (Chamaecyparis nootkatensis [D. Don] Spach) heartwood strongly inhibit the germination of Phytophthora ramorum (Werres, de Cock, Man int Veld) zoospores or sporangia, and reduce hyphal growth in culture (Manter and others 2006). Essential oils from heartwood of incense cedar (Calocedrus decurrens [Torr.] Florin), western redcedar (Thuja plicata Donn ex D. Don), Port-Orford-cedar (Chamaecyparis lawsoniana [A. Murr.] Parl.), and western juniper (Juniperus occidentalis Hook.) were also tested and found to be equally active, but not investigated further until now. The objectives of this study were to: 1) test the procedure described by Kuhajek and others (2003) as a bioassay technique for P. ramorum; 2) use this bioassay with other individual compounds from yellow-cedar heartwood that were not previously tested for bioactivity toward P. ramorum; and 3) bioassay extracts and...

Do Root Exudates of Specific Winter Wheat Cultivars Recruit ACC Deaminase-Positive Bacteria?

Root exudates are important for establishing plant-microbial associations because they are chemic... more Root exudates are important for establishing plant-microbial associations because they are chemical signals that promote chemotaxis, initiate symbiotic interactions, and/or act as substrates promoting the growth of some microbes. We hypothesize that root exudates are utilized by winter wheat to recruit ACC deaminase positive (ACC+) bacteria. These bacteria degrade the “stress” ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), and promote plant growth under drought stress. Our previous studies have found that the abundance, diversity, and species composition of these bacteria vary under different wheat cultivars in Colorado, possibly in response to different root exudate profiles. In this study, we characterized the root exudate profiles of two contrasting wheat cultivars, Ripper and RonL, and measured the response of ACC+ bacteria to exudates and exudate fractions added to soil. Root exudates of Ripper and RonL were collected under hydroponic growth conditions over a ...