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Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes a wide range of compounds and represents a genus of considerable industrial interest. RHA1 has one of the largest bacterial genomes sequenced to date, comprising 9,702,737 bp (67% G+C) arranged in a linear chromosome and three linear plasmids. A targeted insertion methodology was developed to determine the telomeric sequences. RHA1's 9,145 predicted protein-encoding genes are exceptionally rich in oxygenases (203) and ligases (192). Many of the oxygenases occur in the numerous pathways predicted to degrade aromatic compounds (30) or steroids (4). RHA1 also contains 24 nonribosomal peptide synthase genes, six of which exceed 25 kbp, and seven polyketide synthase genes, providing evidence that rhodococci harbor an extensive secondary metabolism. Among sequenced genomes, RHA1 is most similar to those of nocardial and mycobacterial strains. The genome contains few recent gene duplications. Moreover, three different analyses indicate that RHA1 has acquired fewer genes by recent horizontal transfer than most bacteria characterized to date and far fewer than Burkholderia xenovorans LB400, whose genome size and catabolic versatility rival those of RHA1. RHA1 and LB400 thus appear to demonstrate that ecologically similar bacteria can evolve large genomes by different means. Overall, RHA1 appears to have evolved to simultaneously catabolize a diverse range of plantderived compounds in an O₂-rich environment. In addition to establishing RHA1 as an important model for studying actinomycete physiology, this study provides critical insights that facilitate the exploitation of these industrially important microorganisms.

Corn’s ( Zea mays L.) stover is a potential nonfood, herbaceous bioenergy feedstock. A vital aspect of utilizing stover for bioenergy production is to establish sustainable harvest criteria that avoid exacerbating soil erosion or degrading soil organic carbon (SOC) levels. Our goal is to empirically estimate the minimum residue return rate required to sustain SOC levels at numerous locations and to identify which macroscale factors affect empirical estimates. Minimum residue return rate is conceptually useful, but only if the study is of long enough duration and a relationship between the rate of residue returned and the change in SOC can be measured. About one third of the Corn Stover Regional Partnership team (Team) sites met these criteria with a minimum residue return rate of 3.9 ± 2.18 Mg stover ha −1  yr −1 , n  = 6. Based on the Team and published corn-based data ( n  = 35), minimum residue return rate was 6.38 ± 2.19 Mg stover ha −1  yr −1 , while including data from other cropping systems ( n  = 49), the rate averaged 5.74 ± 2.36 Mg residue ha −1  yr −1 . In broad general terms, keeping about 6 Mg residue ha −1  yr −1 maybe a useful generic rate as a point of discussion; however, these analyses refute that a generic rate represents a universal target on which to base harvest recommendations at a given site. Empirical data are needed to calibrate, validate, and refine process-based models so that valid sustainable harvest rate guidelines are provided to producers, industry, and action agencies.

We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing gene data sets and evidence for the existence of ≈ 24,000 previously undescribed genomic loci. The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci.