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publications

Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine

Published in Environmental microbiology, 2012

Thaumarchaea, which represent as much as 20% of prokaryotic biomass in the open ocean, have been linked to environmentally relevant biogeochemical processes, such as ammonia oxidation (nitrification) and inorganic carbon fixation. We have used culture-independent methods to study this group because current cultivation limitations have proved a hindrance in studying these organisms.

Recommended citation: Tully, B. J., Nelson, W. C., & Heidelberg, J. F. (2011). Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine. Environmental Microbiology, 14(1), 254–267. http://doi.org/10.1111/j.1462-2920.2011.02628.x http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02628.x/full

Prospects for the study of evolution in the deep biosphere

Published in Frontiers in microbiology, 2012

Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed.

Recommended citation: Biddle, J. F., Sylvan, J. B., Brazelton, W. J., Tully, B. J., Edwards, K. J., Moyer, C. L., et al. (2011). Prospects for the study of evolution in the deep biosphere. Frontiers in Microbiology, 2, 285. http://doi.org/10.3389/fmicb.2011.00285 http://journal.frontiersin.org/article/10.3389/fmicb.2011.00285/full

Microbial communities associated with ferromanganese nodules and the surrounding sediments

Published in Frontiers in microbiology, 2013

The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific.

Recommended citation: Tully, B. J., & Heidelberg, J. F. (2013). Microbial communities associated with ferromanganese nodules and the surrounding sediments. Frontiers in Microbiology, 4, 161. http://doi.org/10.3389/fmicb.2013.00161 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691505/

Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data

Published in Microbiome, 2014

The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble and explore the partial environmental genomes of uncultured members of the class Flavobacteria. Each of the environmental genomes represents organisms that compose less than 1% of the total microbial metagenome.

Recommended citation: Tully, B. J., Sachdeva, R., Heidelberg, K. B., & Heidelberg, J. F. (2014). Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data, Microbiome, 2(1), 1–14. http://doi.org/10.1186/2049-2618-2-34 https://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-2-34

De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape

Published in Archaea, 2015

Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in walsbyi. Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in hypersaline systems is the square archaeon, Haloquadratum Victoria, Australia, we performed a comparative genomic analysis of H. walsbyi to better understand the extent of variation between strains/subspecies.

Recommended citation: Tully, B. J., Emerson, J. B., Andrade, K., Brocks, J. J., Allen, E. E., Banfield, J. F., & Heidelberg, K. B. (2015). De NovoSequences of Haloquadratum walsbyifrom Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape. Archaea, 2015(4), 1–12. http://doi.org/10.1155/2015/875784 https://www.hindawi.com/journals/archaea/2015/875784/

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

Published in Scientific Reports, 2016

The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer.

Recommended citation: Meyer, J. L., Jaekel, U., Tully, B. J., Glazer, B. T., Wheat, C. G., Lin, H.-T., et al. (2016). A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge. Scientific Reports, 6, 22541. http://doi.org/10.1038/srep22541 http://www.nature.com/articles/srep22541?WT.feed_name=subjects_ocean-sciences

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

Published in Applied and environmental microbiology, 2016

The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses.

Recommended citation: Tully, B. J., & Heidelberg, J. F. (2016). Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments. Applied and Environmental Microbiology, 82(14), 4232–4243. http://doi.org/10.1128/AEM.01023-16 http://aem.asm.org/content/82/14/4232.short

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

Published in PeerJ, 2017

We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms.

Recommended citation: Graham, E. D., Heidelberg, J. F., & Tully, B. J. (2017). BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ, 5(Part B), e3035–19. http://doi.org/10.7717/peerj.3035 https://peerj.com/articles/3035/

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology

Published in PeerJ, 2017

Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial and archaeal genomes.

Recommended citation: Tully BJ, Sachdeva R, Graham ED, Heidelberg JF. (2017) 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology. PeerJ 5:e3558 https://doi.org/10.7717/peerj.3558 https://peerj.com/articles/3558/

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

Published in ISMEJ, 2017

Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity.

Recommended citation: Tully BJ, Wheat CG, Glazer BT, Huber JA. (2017) A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. The ISME Journal 12, 1-16 https://doi.org/10.1038/ismej.2017.187 https://www.nature.com/articles/ismej2017187

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

Published in Scientific Data, 2018

Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to reconstruct 2,631 draft genomes with an estimated completion of ≥50% were generated (1,491 draft genomes >70% complete; 603 genomes >90% complete).

Recommended citation: Tully BJ, Graham ED, Heidelberg JF. (2018) The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Scientific Data 5(170203), 1-18 https://doi.org/10.1038/sdata.2017.203 https://www.nature.com/articles/sdata2017203

Nitrogen Cycling of Active Bacteria within Oligotrophic Sediment of the Mid-Atlantic Ridge Flank

Published in Geomicrobiology Journal, 2018

Microbial ecology within oligotrophic marine sediment is poorly understood, yet is critical for understanding geochemical cycles. Here, 16S rRNA sequences from RNA and DNA inform the structure of active and total microbial communities in oligotrophic sediment on the western flank of the Mid-Atlantic Ridge.

Recommended citation: Reese BK, Zinke LA, Sobol MS, LaRowe DE, Orcutt BN, Zhang X, Jaekel U, Wang F, Dittmar T, Defforey D, Tully B, Paytan A, Sylvan JB, Amend JP, Edwards KJ & Girguis P (2018) Nitrogen Cycling of Active Bacteria within Oligotrophic Sediment of the Mid-Atlantic Ridge Flank, Geomicrobiology Journal, https://doi.org/10.1080/01490451.2017.1392649 https://www.tandfonline.com/doi/full/10.1080/01490451.2017.1392649

Potential for primary productivity in a globally-distributed bacterial phototroph

Published in ISMEJ, 2018

Aerobic anoxygenic phototrophs (AAnPs) are common in marine environments and are associated with photoheterotrophic activity. To date, AAnPs that possess the potential for carbon fixation have not been identified in the surface ocean. Using the Tara Oceans metagenomic dataset, we have identified draft genomes of nine bacteria that possess the genomic potential for anoxygenic phototrophy, carbon fixation via the Calvin-Benson-Bassham cycle, and the oxidation of sulfite and thiosulfate.

Recommended citation: Graham ED, Heidelberg JF, Tully BJ. (2018) Potential for primary productivity in a globally-distributed bacterial phototroph. ISME J 350, 1–6 https://doi.org/10.1038/s41396-018-0091-3 https://www.nature.com/articles/s41396-018-0091-3

Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns

Published in Nature Communcations, 2019

250 environmental Marine Group II Euryarchaea genomes shed light on the physiological potential and ecology of a diverse and abundant marine heterotroph.

Recommended citation: Tully BJ. (2019) Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns. Nature Communications 10:271, 1–12 https://doi.org/10.1038/s41467-018-07840-4 https://www.nature.com/articles/s41467-018-07840-4

talks

teaching

Introduction to Bioinformatics

Published in Stanford University, Workshop, 2015

Designed 2-day workshop to provide introduction to an environmental microbiology metagenomic workflow. Topics: Unix, Sequence quality control, Experimental design, Sequence assembly, Genome binning, Gene annotation, Phylogenetic analysis. Participation of 12 C-DEBI researchers. Additional information, including resources, can be found here

ECOGEO Introduction to Environmental ‘Omics

Published in University of Hawaii, Workshop, 2016

Working with Drs. Elisha Wood-Charlson and Edward Delong at the University of Hawaii, Monoa, the workshop was expanded and developed to accommodate additional attendees and lecturers for the ECOGEO Research Coordination Network meeting. Approximately 40 researchers of various academic levels, including graduate students, postdoctoral researchers, and junior faculty, attended the workshop. Recorded lectures, documentation, and a full version of the virtual Linux environment is available via the EarthCube ECOGEO webpage