scholarly journals Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Tess E. Brewer ◽  
Emma L. Aronson ◽  
Keshav Arogyaswamy ◽  
Sharon A. Billings ◽  
Jon K. Botthoff ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
The United States ◽  
Soil Profiles ◽  
Growth Strategies ◽  
Surface Soils ◽  
Wide Range ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

ABSTRACT While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments. IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.

scholarly journals Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons

2019 ◽  
Author(s):  
Tess E. Brewer ◽  
Emma L. Aronson ◽  
Keshav Arogyaswamy ◽  
Sharon A. Billings ◽  
Jon K. Botthoff ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Depth ◽  
Soil Microbial Communities ◽  
Soil Profiles ◽  
Growth Strategies ◽  
Surface Soils ◽  
Wide Range ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities ◽  
The U.S

AbstractWhile most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the U.S. to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.ImportanceSoil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the U.S., we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored distinct communities compared to the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising amount of novel microbes with unique adaptations to oligotrophic subsurface conditions.

scholarly journals Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

GCB Bioenergy ◽  
2015 ◽  
Vol 8 (2) ◽  
pp. 481-494 ◽  
Author(s):  
Ederson da C. Jesus ◽  
Chao Liang ◽  
John F. Quensen ◽  
Endang Susilawati ◽  
Randall D. Jackson ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Cropping Systems ◽  
Soil Microbial Communities ◽  
The United States ◽  
Upper Midwest ◽  
Soil Microbial

scholarly journals Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales

2013 ◽  
Vol 79 (9) ◽  
pp. 2906-2913 ◽  
Author(s):  
Orin C. Shanks ◽  
Ryan J. Newton ◽  
Catherine A. Kelty ◽  
Susan M. Huse ◽  
Mitchell L. Sogin ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Dna Sequences ◽  
The United States ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Untreated Sewage ◽  
Wide Range ◽  
Taxonomic Groups

ABSTRACTMicrobial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups withinFirmicutes,Bacteroidetes,Actinobacteria, andProteobacteria. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States.

The Politics of Precaution

2012 ◽  
Author(s):  
David Vogel
Keyword(s):  
United States ◽  
Animal Feed ◽  
The United States ◽  
Hazardous Substances ◽  
Risk Regulation ◽  
Scientific Certainty ◽  
European Public ◽  
Wide Range ◽  
Regulatory Controls ◽  
Milk Hormones

This book examines the politics of consumer and environmental risk regulation in the United States and Europe over the last five decades, explaining why America and Europe have often regulated a wide range of similar risks differently. It finds that between 1960 and 1990, American health, safety, and environmental regulations were more stringent, risk averse, comprehensive, and innovative than those adopted in Europe. But since around 1990 global regulatory leadership has shifted to Europe. What explains this striking reversal? This book takes an in-depth, comparative look at European and American policies toward a range of consumer and environmental risks, including vehicle air pollution, ozone depletion, climate change, beef and milk hormones, genetically modified agriculture, antibiotics in animal feed, pesticides, cosmetic safety, and hazardous substances in electronic products. The book traces how concerns over such risks—and pressure on political leaders to do something about them—have risen among the European public but declined among Americans. The book explores how policymakers in Europe have grown supportive of more stringent regulations while those in the United States have become sharply polarized along partisan lines. And as European policymakers have grown more willing to regulate risks on precautionary grounds, increasingly skeptical American policymakers have called for higher levels of scientific certainty before imposing additional regulatory controls on business.

Microbial communities associated with honey bees in Brazil and in the United States

2021 ◽  
Author(s):  
Denise de Oliveira Scoaris ◽  
Frederic Mendes Hughes ◽  
Milton Adolfo Silveira ◽  
Jay Daniel Evans ◽  
Jeffery Stuart Pettis ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Honey Bees ◽  
The United States

Expansion of Groundnut ringspot virus Host and Geographic Ranges in Solanaceous Vegetables in Peninsular Florida

2011 ◽  
Vol 12 (1) ◽  
pp. 34 ◽  
Author(s):  
Craig G. Webster ◽  
William W. Turechek ◽  
H. Charles Mellinger ◽  
Galen Frantz ◽  
Nancy Roe ◽  
...  
Keyword(s):  
United States ◽  
The United States ◽  
Vegetable Production ◽  
Viral Pathogen ◽  
Geographic Ranges ◽  
First Report ◽  
Geographic Spread ◽  
Wide Range ◽  
Production Areas ◽  
Solanaceous Plants

To the best of our knowledge, this is the first report of GRSV infecting tomatillo and eggplant, and it is the first report of GRSV infecting pepper in the United States. This first identification of GRSV-infected crop plants in commercial fields in Palm Beach and Manatee Counties demonstrates the continuing geographic spread of the virus into additional vegetable production areas of Florida. This information indicates that a wide range of solanaceous plants is likely to be infected by this emerging viral pathogen in Florida and beyond. Accepted for publication 27 June 2011. Published 25 July 2011.

The Relations Between the Navy and the Foreign Service

1939 ◽  
Vol 33 (2) ◽  
pp. 283-291
Author(s):  
Clark H. Woodward
Keyword(s):  
United States ◽  
The United States ◽  
Government Agencies ◽  
National Defense ◽  
International Affairs ◽  
Proper Position ◽  
Foreign Service ◽  
Wide Range ◽  
National Emergency ◽  
The Relationship

In the conduct of foreign policy and the participation of the United States in international affairs, the relation between the Navy and the Foreign Service is of vital importance, but often misunderstood. The relationship encompasses the very wide range of coördination and coöperation which should and must exist between the two interdependent government agencies in peace, during times of national emergency, and, finally, when the country is engaged in actual warfare. The relationship involves, as well, the larger problem of national defense, and this cannot be ignored if the United States is to maintain its proper position in world affairs.

Small Screen, Big Feels

2020 ◽  
Author(s):  
Melissa Ames
Keyword(s):  
United States ◽  
The United States ◽  
Presidential Debates ◽  
Audience Studies ◽  
The Walking Dead ◽  
Wide Range ◽  
In Series ◽  
Fear And Anxiety ◽  
Small Screen ◽  
Network Era

While television has always played a role in recording and curating history, shaping cultural memory, and influencing public sentiment, the changing nature of the medium in the post-network era finds viewers experiencing and participating in this process in new ways. They skim through commercials, live tweet press conferences and award shows, and tune into reality shows to escape reality. This new era, defined by the heightened anxiety and fear ushered in by 9/11, has been documented by our media consumption, production, and reaction. In Small Screen, Big Feels, Melissa Ames asserts that TV has been instrumental in cultivating a shared memory of emotionally charged events unfolding in the United States since September 11, 2001. She analyzes specific shows and genres to illustrate the ways in which cultural fears are embedded into our entertainment in series such as The Walking Dead and Lost or critiqued through programs like The Daily Show. In the final section of the book, Ames provides three audience studies that showcase how viewers consume and circulate emotions in the post-network era: analyses of live tweets from Shonda Rhimes's drama, How to Get Away with Murder (2010--2020), ABC's reality franchises, The Bachelor (2002--present) and The Bachelorette (2003--present), and political coverage of the 2016 Presidential Debates. Though film has been closely studied through the lens of affect theory, little research has been done to apply the same methods to television. Engaging an impressively wide range of texts, genres, media, and formats, Ames offers a trenchant analysis of how televisual programming in the United States responded to and reinforced a cultural climate grounded in fear and anxiety.

Zines, Half-Lives, and Afterlives: On the Temporalities of Social and Political Change

PMLA ◽  
2011 ◽  
Vol 126 (1) ◽  
pp. 140-150 ◽  
Author(s):  
Janice Radway
Keyword(s):  
United States ◽  
Science Fiction ◽  
Special Interest ◽  
Political Change ◽  
The United States ◽  
Alternative Press ◽  
Wide Range ◽  
Do It Yourself ◽  
Mainstream Society ◽  
The 1960S

The term zine is a recent variant of fanzine, a neologism coined in the 1930s to refer to magazines self-published by Aficionados of science fiction. Until zines emerged as digital forms, they were generally defined as handmade, noncommercial, irregularly issued, small-run, paper publications circulated by individuals participating in alternative, special-interest communities. Zines exploded in popularity during the 1980s when punk music fans adopted the form as part of their do-it-yourself aesthetic and as an outsider way to communicate among themselves about punk's defiant response to the commercialism of mainstream society. In 1990, only a few years after the first punk zines appeared, Mike Gunderloy made a case for the genre's significance in an article published in the Whole Earth Review, one of the few surviving organs of the 1960s alternative press in the United States. He celebrated zines' wide range of interests and the oppositional politics that generated their underground approach to publication.

scholarly journals Sources: Oil: A Cultural and Geographic Encyclopedia of Black Gold

2015 ◽  
Vol 54 (4) ◽  
pp. 83
Author(s):  
Paul MacLennan
Keyword(s):  
United States ◽  
International Relations ◽  
The United States ◽  
Monetary Value ◽  
Wide Range ◽  
To Come ◽  
The Individual ◽  
As Effects

In the winter of 2015, as this review is being written, the price of gasoline is plummeting in the United States and what this will mean for the individual, community, and country for the immediate future but also in years to come is unknown. There are a wide range of implications in politics, economics, and international relations as well as effects on what the individual pays for everyday groceries. It is therefore important that libraries provide their communities with the resources that include information and discussion on how energy and its monetary value interact with society.

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