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1. Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns [Erratum: March 2022, v.13(3)]

Author:
Susannah G. Tringe,   et al.   ; Clifton P. Bueno de Mesquita; Jinglie Zhou; Susanna Theroux;     Show all 4 Authors
Source:
Genes 2022 v.13 no.1 pp. -
ISSN:
2073-4425
Subject:
biosynthesis; byproducts; carbon; hypersalinity; isoelectric point; metagenomics; methane; new species; phosphorus; phylogeny; proteome; salt tolerance; solutes
Abstract:
... Aerobic bacteria that degrade methylphosphonates and produce methane as a byproduct have emerged as key players in marine carbon and phosphorus cycles. Here, we present two new draft genome sequences of the genus Marivita that were assembled from metagenomes from hypersaline former industrial salterns and compare them to five other Marivita reference genomes. Phylogenetic analyses suggest that bot ...
DOI:
10.3390/genes13010148

2. Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern

Author:
Susannah G. Tringe,   et al.   ; Clifton P. Bueno de Mesquita; Jinglie Zhou; Susanna M. Theroux;     Show all 4 Authors
Source:
Genes 2021 v.12 no.10 pp. -
ISSN:
2073-4425
Subject:
Methanolobus; chlorides; dimethylamine; global carbon budget; hypersalinity; methane; methane production; methanogens; new genus; organic matter; phylogeny; salt tolerance; sediments; trimethylamine; wetlands
Abstract:
... Anaerobic archaeal methanogens are key players in the global carbon cycle due to their role in the final stages of organic matter decomposition in anaerobic environments such as wetland sediments. Here we present the first draft metagenome-assembled genome (MAG) sequence of an unclassified Methanosarcinaceae methanogen phylogenetically placed adjacent to the Methanolobus and Methanomethylovorans g ...
DOI:
10.3390/genes12101609

3. Peatland microbial community responses to plant functional group and drought are depth‐dependent

Author:
Susannah G. Tringe,   et al.   ; Louis J. Lamit; Karl J. Romanowicz; Lynette R. Potvin; Jay T. Lennon; Rodney A. Chimner; Randall K. Kolka; Evan S. Kane; Erik A. Lilleskov;     Show all 9 Authors
Source:
Molecular ecology 2021 v.30 no.20 pp. 5119-5136
ISSN:
0962-1083
Subject:
Ericaceae; carbon; climate; climate change; community structure; drought; fungi; methanotrophs; microbial communities; peat; peatlands; prokaryotic cells; soil carbon; vegetation; water table
Abstract:
... Peatlands store one‐third of Earth's soil carbon, the stability of which is uncertain due to climate change‐driven shifts in hydrology and vegetation, and consequent impacts on microbial communities that mediate decomposition. Peatland carbon cycling varies over steep physicochemical gradients characterizing vertical peat profiles. However, it is unclear how drought‐mediated changes in plant funct ...
DOI:
10.1111/mec.16125

4. Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential

Author:
Susannah G. Tringe,   et al.   ; Kuno Kasak; Mikk Espenberg; Tyler L. Anthony; Alex C. Valach; Kyle S. Hemes; Whendee L. Silver; Ülo Mander; Keit Kill; Gavin McNicol; Daphne Szutu; Joseph Verfaillie; Dennis D. Baldocchi;     Show all 13 Authors
Source:
Journal of environmental management 2021 v.299 pp. 113562
ISSN:
0301-4797
Subject:
anaerobic ammonium oxidation; carbon sequestration; climate; denitrification; genes; greenhouse gases; nitrogen; nitrogen fixation; nitrous oxide; nitrous oxide production; wetland restoration; wetlands; California
Abstract:
... The concentration of nitrous oxide (N₂O), an ozone-depleting greenhouse gas, is rapidly increasing in the atmosphere. Most atmospheric N₂O originates in terrestrial ecosystems, of which the majority can be attributed to microbial cycling of nitrogen in agricultural soils. Here, we demonstrate how the abundance of nitrogen cycling genes vary across intensively managed agricultural fields and adjace ...
DOI:
10.1016/j.jenvman.2021.113562

5. Hidden diversity in the oomycete genus Olpidiopsis is a potential hazard to red algal cultivation and conservation worldwide

Author:
Susannah G. Tringe,   et al.   ; Yacine Badis; Tatyana A. Klochkova; Janina Brakel; Paola Arce; Martin Ostrowski; Gwang Hoon Kim; Claire M.M. Gachon;     Show all 8 Authors
Source:
European journal of phycology 2020 v.55 no.2 pp. 162-171
ISSN:
1469-4433
Subject:
Bangia; DNA barcoding; Olpidiopsis; Porphyra; Pyropia yezoensis; algae culture; biogeography; biosecurity; crops; cultivars; economic crises; fauna; financial economics; genetic markers; horticulture; indigenous species; industry; macroalgae; marine environment; microbiome; monitoring; pathogens; risk; thallus; trade; virulence; Korean Peninsula; Scotland
Abstract:
... Marine species of the oomycete genus Olpidiopsis that infect cultivated red macroalgae, most notably Pyropia spp., are one of the main causes of economic loss in the Asian seaweed industry. We recently described novel Olpidiopsis species infecting red algae in Scotland, and thus hypothesized that this genus is more abundant and widespread than previously recognized. Here, we show that the eukaryot ...
DOI:
10.1080/09670262.2019.1664769

6. Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor

Author:
Susannah G. Tringe,   et al.   ; Xinwei Mao; Benoit Stenuit; Julien Tremblay; Ke Yu; Lisa Alvarez-Cohen;     Show all 6 Authors
Source:
Water research 2019 v.158 pp. 146-156
ISSN:
0043-1354
Subject:
Dehalococcoides mccartyi; dechlorination; enrichment culture; enzymes; ethylene; genes; organochlorine compounds; ribosomal RNA; transcriptomics; vinyl chloride
Abstract:
... A trichloroethene (TCE)-dechlorinating community (CANAS) maintained in a completely mixed flow reactor was established from a semi-batch enrichment culture (ANAS) and was monitored for 400 days at a low solids retention time (SRT) under electron acceptor limitation. Around 85% of TCE supplied to CANAS (0.13 mmol d−1) was converted to ethene at a rate of 0.1 mmol d−1, with detection of low producti ...
DOI:
10.1016/j.watres.2019.04.038
PubMed:
31035191
PubMed Central:
PMC7053656

7. Meta-omics survey of [NiFe]-hydrogenase genes fails to capture drastic variations in H2-oxidation activity measured in three soils exposed to H2

Author:
Susannah G. Tringe,   et al.   ; Mondher Khdhiri; Sarah Piché-Choquette; Julien Tremblay; Philippe Constant;     Show all 5 Authors
Source:
Soil biology & biochemistry 2018 v.125 pp. 239-243
ISSN:
0038-0717
Subject:
Populus; agricultural land; bacteria; case studies; genes; hydrogen; land use; metagenomics; oxidation; physicochemical properties; population size; soil; soil microorganisms; soil sampling; surveys; transcriptomics
Abstract:
... Inferences on soil biogeochemical processes based on metagenomic profiles is a challenging task due to enormous diversity of soil microbes and the fragile linkage between gene abundance and functioning. Here we used the biological sink of H₂ as a case study to test the hypothesis that [NiFe]-hydrogenase gene distribution and expression profiles explain variations in H₂ oxidation rate measured in s ...
DOI:
10.1016/j.soilbio.2018.07.020

8. High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

Author:
Susannah G. Tringe,   et al.   ; Jizhong Zhou; Zhili He; Yunfeng Yang; Ye Deng; Lisa Alvarez-Cohen;     Show all 6 Authors
Source:
mBio 2015 v.6 no.1 pp. e02288-14
ISSN:
2150-7511
Subject:
genes; high-throughput nucleotide sequencing; metagenomics; microbial communities; phylogeny; screening; soil; soil microorganisms
Abstract:
... Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic scr ...
DOI:
10.1128/mBio.02288-14
PubMed:
25626903
PubMed Central:
PMC4324309

9. Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils

Author:
Susannah G Tringe,   et al.   ; M A Wadud Khan; Brendan J M Bohannan; Klaus Nüsslein; James M Tiedje; Eloi Parlade; Albert Barberán; Jorge L M Rodrigues;     Show all 8 Authors
Source:
FEMS microbiology ecology 2018 v.95 no.2 pp. -
ISSN:
1574-6941
Subject:
biochemical pathways; deforestation; denitrification; ecological function; ecosystems; land use change; microbial communities; nitrification; nitrogen cycle; pastures; physicochemical properties; ribosomal RNA; sequence analysis; soil chemical properties; soil physical properties; temperature; topology; tropical forests
Abstract:
... Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to de ...
DOI:
10.1093/femsec/fiy230
PubMed:
30481288
PubMed Central:
PMC6294608

10. Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains

Author:
Susannah G. Tringe,   et al.   ; José F. Cobo-Díaz; Antonio J. Fernández-González; Pablo J. Villadas; Nicolás Toro; Manuel Fernández-López;     Show all 6 Authors
Source:
Forests 2017 v.8 no.10 pp. -
ISSN:
1999-4907
Subject:
Actinobacteria; Bacteroidetes; Nitrospirae; Proteobacteria; Quercus pyrenaica; Verrucomicrobia; altitude; carbon nitrogen ratio; community structure; developmental stages; forest canopy; forest soils; forests; functional diversity; metagenomics; methane; microbial communities; microbiome; mountains; nitrogen metabolism; phylogeny; rhizosphere; soil pH; sulfur; trees
Abstract:
... Altitude significantly affects vegetation growth and distribution, including the developmental stages of a forest. We used shotgun Illumina sequencing to analyze microbial community composition and functional potential in melojo-oak (Quercus pyrenaica Willd.) rhizospheric soil for three different development stages along an altitudinal gradient: (a) a low altitude, non-optimal site for forest main ...
DOI:
10.3390/f8100390

11. Patterns and drivers of fungal community depth stratification in Sphagnum peat

Author:
Susannah G. Tringe,   et al.   ; Louis J. Lamit; Karl J. Romanowicz; Lynette R. Potvin; Adam R. Riveres; Kanwar Singh; Jay T. Lennon; Evan S. Kane; Erik A. Lilleskov;     Show all 9 Authors
Source:
FEMS microbiology ecology 2017 v.93 no.7 pp. -
ISSN:
0168-6496
Subject:
Ericaceae; Sphagnum; carbon; community structure; drought; endophytes; fungal communities; mycorrhizal fungi; oxidation; peat; peatlands; population density; quantitative polymerase chain reaction; saprotrophs; soil depth; soil pore water; stratigraphy; water table
Abstract:
... Peatlands store an immense pool of soil carbon vulnerable to microbial oxidation due to drought and intentional draining. We used amplicon sequencing and quantitative PCR to 1) examine how fungi are influenced by depth in the peat profile, water table (WT) and plant functional group (PFG) at the onset of a multi-year mesocosm experiment, and 2) test if fungi are correlated with abiotic variables o ...
Handle:
10113/5763096
DOI:
10.1093/femsec/fix082

12. Conversion of Amazon rainforest to agriculture alters community traits of methane‐cycling organisms

Author:
Susannah G. Tringe,   et al.   ; Kyle M. Meyer; Ann M. Klein; Jorge L. M. Rodrigues; Klaus Nüsslein; Babur S. Mirza; James M. Tiedje; Brendan J. M. Bohannan;     Show all 8 Authors
Source:
Molecular ecology 2017 v.26 no.6 pp. 1547-1556
ISSN:
0962-1083
Subject:
cattle; environmental impact; genes; land use change; life history; metagenomics; methane; methane production; methanogens; methanotrophs; pastures; rain forests; soil; tropical forests; Amazonia
Abstract:
... Land use change is one of the greatest environmental impacts worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it i ...
DOI:
10.1111/mec.14011
CHORUS:
10.1111/mec.14011
Chorus Open Access:
10.1111/mec.14011

13. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

Author:
Susannah G. Tringe,   et al.   ; Devin Coleman‐Derr; Damaris Desgarennes; Citlali Fonseca‐Garcia; Stephen Gross; Scott Clingenpeel; Tanja Woyke; Gretchen North; Axel Visel; Laila P. Partida‐Martinez;     Show all 10 Authors
Source:
new phytologist 2016 v.209 no.2 pp. 798-811
ISSN:
0028-646X
Subject:
Agave; abiotic stress; arid zones; biofuels; biogeography; feedstocks; fungal communities; fungi; leaves; microbiome; phyllosphere; phylogeny; plant growth; rhizosphere; soil sampling; xerophytes; North America
Abstract:
... Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semi ...
DOI:
10.1111/nph.13697
PubMed:
26467257
PubMed Central:
PMC5057366

14. Tackling soil diversity with the assembly of large, complex metagenomes

Author:
Susannah G. Tringe,   et al.   ; Adina Chuang Howe; Janet K. Jansson; Stephanie A. Malfatti; James M. Tiedje; C. Titus Brown;     Show all 6 Authors
Source:
Proceedings of the National Academy of Sciences of the United States of America 2014 v.111 no.13 pp. 4904-4909
ISSN:
0027-8424
Subject:
Escherichia coli; biochemical pathways; biodiversity; corn; data collection; databases; genes; metagenomics; microbial communities; prairie soils; proteins; sequence analysis; Iowa
Abstract:
... The large volumes of sequencing data required to sample deeply the microbial communities of complex environments pose new challenges to sequence analysis. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires substantial computational resources. We combine two preassembly filtering approaches—digital normalization and partitioning—to generate previou ...
DOI:
10.1073/pnas.1402564111
PubMed:
24632729
PubMed Central:
PMC3977251

15. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

Author:
Susannah G. Tringe,   et al.   ; Maggie R. Wagner; Derek S. Lundberg; Devin Coleman‐Derr; Jeffery L. Dangl; Thomas Mitchell‐Olds; John Klironomos;     Show all 7 Authors
Source:
Ecology letters 2014 v.17 no.6 pp. 717-726
ISSN:
1461-023X
Subject:
Arabidopsis; Boechera stricta; environmental factors; flowering; microbial communities; phenology; phenotypic plasticity; selection intensity; soil; soil microorganisms
Abstract:
... Plant phenology is known to depend on many different environmental variables, but soil microbial communities have rarely been acknowledged as possible drivers of flowering time. Here, we tested separately the effects of four naturally occurring soil microbiomes and their constituent soil chemistries on flowering phenology and reproductive fitness of Boechera stricta, a wild relative of Arabidopsis ...
DOI:
10.1111/ele.12276
PubMed:
24698177
PubMed Central:
PMC4048358

16. Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions

Author:
Susannah G. Tringe,   et al.   ; Shaomei He; Stephanie A. Malfatti; Jack W. McFarland; Frank E. Anderson; Amrita Pati; Marcel Huntemann; Julien Tremblay; Tijana Glavina del Rio; Mark P. Waldrop; Lisamarie Windham-Myers;     Show all 11 Authors
Source:
mBio 2015 v.6 no.3 pp. e00066-15
ISSN:
2150-7511
Subject:
Archaea; bacteria; carbon; carbon dioxide; carbon sequestration; climate; community structure; correlation; ecosystems; genes; genetic markers; greenhouse gas emissions; greenhouse gases; hydrology; land management; methane; methane production; methanogens; methanotrophs; microbial communities; models; peat; phylogeny; prediction; river deltas; roots; subsidence; wetlands; California
Abstract:
... Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial com ...
DOI:
10.1128/mBio.00066-15
PubMed:
25991679
PubMed Central:
PMC4442139

17. Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle

Author:
Susannah G. Tringe,   et al.   ; Erin D. Scully; Scott M. Geib; Kelli Hoover; Ming Tien; Kerrie W. Barry; Tijana Glavina del Rio; Mansi Chovatia; Joshua R. Herr; John E. Carlson; Pedro Lagerblad Oliveira;     Show all 11 Authors
Source:
PloS one v.8 no.9 pp. -
ISSN:
1932-6203
Subject:
Anoplophora glabripennis; Isoptera; biopolymers; cellulases; cellulose; control methods; digestion; genes; glycosides; heartwood; hemicellulose; herbivores; hindgut; insects; larvae; lignin; lignocellulose; metagenomics; microbial communities; microorganisms; midgut; nutrients; peroxidases; pests; sugars; trees; xylanases
Abstract:
... The Asian longhorned beetle (Anoplophora glabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A . glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose ...
DOI:
10.1371/journal.pone.0073827
PubMed:
24023907
PubMed Central:
PMC3762729

18. Enriching for direct regulatory targets in perturbed gene-expression profiles

Author:
Susannah G Tringe,   et al.   ; Andreas Wagner; Stephanie W Ruby;     Show all 3 Authors
Source:
Genome biology 2004 v.5 no.4 pp. 833
ISSN:
1474-760X
Subject:
algorithms; gene overexpression; genes; mutants
Abstract:
... Here we build on a previously proposed algorithm to infer direct regulatory relationships using gene-expression profiles from cells in which individual genes are deleted or overexpressed. The updated algorithm can process networks containing feedback loops, incorporate positive and negative regulatory relationships during network reconstruction, and utilize data from double mutants to resolve ambi ...
DOI:
10.1186/gb-2004-5-4-r29
PubMed:
15059262
PubMed Central:
PMC395788

19. Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

Author:
Susannah G. Tringe,   et al.   ; Margret E. Berg Miller; Carl J. Yeoman; Nicholas Chia; Florent E. Angly; Robert A. Edwards; Harry J. Flint; Raphael Lamed; Edward A. Bayer; Bryan A. White;     Show all 10 Authors
Source:
Environmental microbiology 2012 v.14 no.1 pp. 207-227
ISSN:
1462-2912
Subject:
gene transfer; seeds; microbial communities; Proteobacteria; DNA; carbohydrates; surveys; bacteriophages; metagenomics; genotype; Firmicutes; ecosystems; rumen fluids; amino acid metabolism; metabolomics
Abstract:
... Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus‐enriched metagenomes ...
DOI:
10.1111/j.1462-2920.2011.02593.x
PubMed:
22004549

20. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Author:
Susannah G. Tringe,   et al.   ; Robert M. Bowers; Nikos C. Kyrpides; Ramunas Stepanauskas; Miranda Harmon-Smith; Devin Doud; T. Reddy B.K.; Frederik Schulz; Jessica Jarett; Adam R. Rivers; Emiley A. Eloe-Fadrosh; Natalia N. Ivanova; Alex Copeland; Alicia Clum; Eric D. Becraft; Rex R. Malmstrom; Bruce Birren; Mircea Podar; Peer Bork; George M. Weinstock;     Show all 20 Authors
Source:
Nature Biotechnology 2017 v.35 no.8 pp. 725-731
ISSN:
1546-1696
Subject:
Archaea; bacteria; biotechnology; genetic markers; genome; information; metagenomics; nucleotide sequences; standards and grades
Abstract:
... We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the minimum information about any (x) sequence (MIxS). The standards are the minimum information about a single amplified genome (MISAG) and the minimum information about a metagenome-assembled genome (MIMAG), including (but not limited to) asse ...
Handle:
10113/5801851
DOI:
10.1038/nbt.3893
PubMed:
28787424
PubMed Central:
PMC6436528