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Author: Bill Nelson3
Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia
Energy and Material Processing, Microbial Community Dynamics, Adaptive Responses

Abstract (Expand)

To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. … Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9x to 2,700x) within the metagenomic data set.

Authors: W. C. Nelson, Y. Maezato, Y. W. Wu, M. F. Romine, S. R. Lindemann

Date Published: 23rd Oct 2015

Publication Type: Not specified

Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a
Energy and Material Processing, Microbial Community Dynamics, Adaptive Responses

Abstract (Expand)

The genome of the unicellular cyanobacterium Thermosynechococcus sp. strain NK55a, isolated from the Nakabusa hot spring, Nagano Prefecture, Japan, comprises a single, circular, 2.5-Mb chromosome. The … genome is predicted to contain 2,358 protein-encoding genes, including genes for all typical cyanobacterial photosynthetic and metabolic functions. No genes encoding hydrogenases or nitrogenase were identified.

Authors: S. Stolyar, , V. Thiel, L. P. Tomsho, N. Pinel, , , , S. Haruta, S. C. Schuster, D. A. Bryant,

Date Published: 1st Feb 2014

Publication Type: Not specified

Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach.
Microbial Community Dynamics

Abstract (Expand)

The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy … and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species' abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.

Authors: S. R. Lindemann, J. M. Mobberley, J. K. Cole, L. M. Markillie, R. C. Taylor, E. Huang, W. B. Chrisler, H. S. Wiley, M. S. Lipton, W. C. Nelson, J. K. Fredrickson, M. F. Romine

Date Published: No date defined

Publication Type: Not specified

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