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James Tiedje - Michigan State University. East Lansing, MI, US

James Tiedje James Tiedje

Distinguished Professor of Microbiology and Molecular Genetics and of Plant, Soil and Microbial Sciences | Michigan State University

East Lansing, MI, UNITED STATES

Expert in Antibiotic Resistance

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Jim Tiedje at the 2011 DOE JGI User Meeting Dr. James Tiedje SMEP Bio

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Biography

Dr. Tiedje is University Distinguished Professor of Microbiology and Molecular Genetics, and of Plant, Soil and Microbial Sciences, and is Director of the Center for Microbial Ecology at Michigan State University. His research focuses on microbial ecology, physiology and diversity, especially regarding the nitrogen cycle, biodegradation of environmental pollutants and use of molecular methods to understand microbial community structure and function. His group has discovered several microbes that biodegrade chlorinated pollutants and is using genomics to better understand microbial functions in their environment. He has served as Editor-in-Chief of Applied and Environmental Microbiology and Editor of Microbial and Molecular Biology Reviews. He has over 500 refereed publications including seven in Science and Nature. He shared the 1992 Finley Prize from UNESCO for research contributions in microbiology of international significance, is Fellow of the AAAS (The American Association for the Advancement of Science), the American Academy of Microbiology, and the Soil Science Society of America, and is a member of the U.S. National Academy of Sciences. He was President of the American Society for Microbiology and the International Society for Microbial Ecology. He received his B.S. degree from Iowa State University and his M.S. and Ph.D. degrees from Cornell University.

Industry Expertise (4)

Education/Learning Research Biotechnology Chemicals

Areas of Expertise (10)

Molecular Biology Microbial Ecology Metagenomics Soil Microbiology Denitrification Biodegradation Bioremediation Permafrost Microbiology Anaerobic Processes Antibiotic Resistance Gene Ecology

Accomplishments (1)

Finley Prize (professional)

1992-01-01

Awarded by UNESCO

Education (2)

Cornell University: Ph.D., Soil Microbiology and Biochemistry

Iowa State University: B.S., Agronomy

News (4)

Experts Sound Alarm About Antibiotics on Pig Farms

Futurity  

2016-04-14

“In the fight against the rise of antibiotic resistance, we need to understand that the use of one antibiotic or, in some cases, antibacterial disinfectants may increase the abundance of multidrug-resistant bacteria,” says study leader James Tiedje, a professor of microbiology and molecular genetics and of plant, soil, and microbial sciences at Michigan State University.

“Tracking the source of antibiotic resistance is quite complicated because antibiotic use, which increases the occurrence of resistance, is widespread, and antibiotic resistance can spread between bacteria,” he adds...

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Will Bioremediation Work At Allied? Microbial Ecologist Skeptical

WMUK 102.1  

2016-01-25

Dr. James Tiedje teaches microbial ecology at Michigan State University and has studied ways to break down PCBs for more than 20 years. He says for BioPath’s method to work, the company will first have to make sure their product can degrade these kinds of PCBs.

You see, there are more than 200 PCBs, each one with a different arrangement of chlorines. If you have, say, 50 varieties on one site, it gets complicated...

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DNA Analysis Strategy Aids in Study of Biofuel Feedstocks

Biomass Magazine  

2014-03-19

“The Great Prairie represents the largest expanse of the world’s most fertile soils, which makes it important as a reference site and for understanding the biological basis and ecosystem services of its microbial community,” said James Tiedje, distinguished professor at the Center for Microbial Ecology at Michigan State University. “It sequesters the most carbon of any soil system in the U.S. and produces large amounts of biomass annually, which is key for biofuels, food security and carbon sequestration.”...

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The Mystery of the Vanishing DDT in the Ocean Near Los Angeles

Scientific American  

2013-03-13

James Tiedje of Michigan State University said these types of chlorine-gobbling microbes “can have logarithmic growth.” The growth of their colonies starts out slowly, then reaches a point of exponential growth that transforms the entire environment.

“Some can grow up over night. There’s a number of examples where microbes in nature grow up and increase their numbers substantially and increase their rate of dechlorination,” said Tiedje, Distinguished Professor of microbiology and director of the university’s Center for Microbial Ecology...

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Journal Articles (5)

Biomass and biofuel crop effects on biodiversity and ecosystem services in the North Central US Biomass and Bioenergy

2017

Biomass cropping systems have the potential to alter the ecosystem services provided by agricultural landscapes. Depending on crop type and management, strategic incorporation of biomass cropping systems into existing agricultural landscapes could enhance a range of ecosystem services while mitigating some disservices. Here, we review the approaches and findings of eight years of research into the potential effects of a range of biomass cropping systems on ecosystem services in the North Central US. Our research was framed by an initial assessment of the abundance and distribution of multiple taxa (i.e., biodiversity) within candidate biomass cropping systems. The processes underpinning important ecosystem services in each system were then measured or modeled, related to biodiversity metrics, and used to explore the influence of management scenarios on biodiversity and ecosystem processes. We also used these data and models to develop a decision support system that allows stakeholders to consider tradeoffs and synergies under alternative landscape composition, configuration, and agronomic management. Perennial grass cropping systems provided the greatest potential to promote multiple ecosystem services. More diverse perennial grasslands that include forbs have the potential to increase pest suppression and pollination, decrease greenhouse gas emissions, and enhance grassland bird communities, but likely at the expense of biomass yield. Providing stakeholders and policymakers with information about the expected mix of ecosystem services supported by different biomass feedstock cropping systems in advance of their adoption offers the potential for informed choices to guide the implementation and management of future biomass-producing landscapes.

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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis Nucleic Acids Research

2009

The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials.

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Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy Applied and Environmental Microbiology

2007

The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (≥95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples...

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The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis Nucleic Acids Research

2005

The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp. cme. msu. edu/). RDP-II release 9.21 (August 2004) contains 101 632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, ...

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DNA recovery from soils of diverse composition Applied and Environmental Microbiology

1996

A simple, rapid method for bacterial lysis and direct extraction of DNA from soils with minimal shearing was developed to address the risk of chimera formation from small template DNA during subsequent PCR. The method was based on lysis with a high-salt extraction buffer (1.5 M NaCl) and extended heating (2 to 3 h) of the soil suspension in the presence of sodium dodecyl sulfate (SDS), hexadecyltrimethylammonium bromide, and proteinase K. The extraction method required 6 h and was tested on eight soils differing in ...

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