Microbial community assembly and evolution in subseafloor sediment

Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change in mutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.

The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement

ABSTRACT Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology. IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a large number of repetitive mobile genetic elements that obstruct genome analysis. However, these mobile elements facilitate large rearrangements that alter the order and orientation of essential protein-encoding genes, which otherwise exhibit little nucleotide sequence diversity. By comparing the complete genome assemblies from 257 isolates, we show that specific rearrangements have been conserved throughout recent evolutionary history, perhaps by eliciting changes in gene expression, which may also provide useful information for molecular epidemiology.

Complete Genome Sequences of 38 Gordonia sp. Bacteriophages

ABSTRACT We report here the genome sequences of 38 newly isolated bacteriophages using Gordonia terrae 3612 (ATCC 25594) and Gordonia neofelifaecis NRRL59395 as bacterial hosts. All of the phages are double-stranded DNA (dsDNA) tail phages with siphoviral morphologies, with genome sizes ranging from 17,118 bp to 93,843 bp and spanning considerable nucleotide sequence diversity.

MITOCHONDRIAL DNA VARIATIO OF THE RICE YELLOW STEM BORER, Scirpophaga incertulas, (LEPIDOPTERA: CRAMBIDAE) IN JAVA, INDONESIA

Scirpophaga incertulas is one of economically important rice pests in South East Asia, including Indonesia. Systematic investigation on biological characteristics of ecological races based on recently changed of agricultural practiced and environment has been conducted in order to asses knowledge on genetic variation of population of S. incertulas in Indonesia. A 685 bp segment of mitochondrialDNA COII was amplified from 42 different yellow stem borer samples from five locations in Java. The objectives of this study were to generate mitochondrial CO II  sequences for all available yellow stem borer  samples and to define haplotypes and nucleotide sequence diversity of the different yellow stem borer populations. Six different haplotypes (YSB1, YSB2, YSB3, YSB4, YSB5 and YSB6) were identified in yellow stem borer populations. The majority of the sampled individuals caried haplotype YSB2. Overall, the results of Tajima’s test statistic indicated that the population of Java was D= 0.85201, which suggests that there was no indicative of purifying selection or there was no presence of deleterious mutation segregating in the population. However, the results were not significant (P> 0:10) and additional studies are required to confirm this finding.Key words: Scirpophaga incertulas, yellow stem borer, MitochondrialDNA COIIÂ