Fitness tradeoffs are often assumed by evolutionary theory, yet little is known about the frequency of fitness tradeoffs during stress adaptation. Even less is known about the genetic factors that confer these tradeoffs and whether alternative adaptive mutations yield contrasting tradeoff dynamics. We addressed these issues using 114 clones of Escherichia coli that were evolved independently for 2,000 generations under thermal stress (42.2°C). For each clone, we measured their fitness relative to the ancestral clone at 37°C and 20°C. Tradeoffs were common at 37°C but more prevalent at 20°C, where 56% of clones were outperformed by the ancestor. We also characterized the upper and lower thermal boundaries of each clone. All clones shifted their upper boundary to at least 45°C; roughly half increased their lower niche boundary concomitantly, representing a shift of thermal niche. The remaining clones expanded their thermal niche by increasing their upper limit without a commensurate increase of lower limit. We associated these niche dynamics with genotypes and confirmed associations by engineering single mutations in the rpoB gene, which encodes the beta subunit of RNA polymerase, and the rho gene, which encodes a termination factor. Single mutations in the rpoB gene exhibit antagonistic pleiotropy, with fitness tradeoffs at 18°C and fitness benefits at 42.2°C. In contrast, a mutation within the rho transcriptional terminator, which defines an alternative adaptive pathway from that of rpoB, had no demonstrable effect on fitness at 18°C. This study suggests that two different genetic pathways toward high-temperature adaptation have contrasting effects with respect to thermal tradeoffs.RNA polymerase | Rho factor | genotype-phenotype associations | experimental evolution D espite the centrality of adaptation to evolution, surprisingly little is known about the diversity of mutations that contribute to adaptation or about their phenotypic and fitness effects (1). There are, in fact, only a few well-known examples linking genotype, phenotype, and adaptation in nature (2-4). In nature, this connection is often complicated by factors such as varying selection pressures or underlying genetic heterogeneities. Although the task is difficult, the general inability to connect phenotype to genotype in the context of environmental adaptation has been a major failing in the field of evolution (5).Experimental evolution provides a more tractable approach to study relationships among fitness, genotype, and phenotype (5, 6). Here we explore these relationships based on our recent, large-scale evolutionary experiment (7). The experiment began with an ancestral strain of Escherichia coli B that was inoculated into ∼115 independent replicates. Each replicate was grown at high temperature (42.2°C) for 2,000 generations. At the end of the experiment, fitness was measured at 42.2°C for a single clone from each of 114 lineages; on average, fitness increased ∼40% during the yearlong experiment.We sequenced the genome of these 114 clones, ...

The evolutionary history and ecological differentiation of the genus Exiguobacterium was characterized within natural communities from the Cuatro Cienegas Basin, Mexico. Exiguobacterium comprises both halophilic and alkaliphilic bacteria that are abundant among the aquatic systems of the Cuatro Cienegas Basin. We obtained complete sequences of the 16srRNA gene and partial sequences of four housekeeping genes (citC, rpoB, recA and hsp70) in 183 Exiguobacterium isolates retrieved from distinct aquatic systems. We defined three main phylogroups that are closely related to marine and thermophilic species of the genus. These phylogroups were neither specific to a given aquatic system nor to a particular salinity. Phylogenetic reconstruction indicated the presence of several small clusters within the phylogroups. These clusters consisted of isolates predominantly retrieved from sediment or water. Unifrac and AdaptML analyses confirmed this observation, pointing towards a clear pattern of differentiation linked to either sediment or water habitats. Our results are in line with the concept that niche differentiation is one of the main factors shaping prokaryotic populations and leading to evolutionary divergence.

Nine Gram-negative, rod-shaped, non-spore-forming isolates with identical or very similar repetitive-sequence-based PCR profiles were recovered from an evaporative lagoon in Mexico. In the present study, a polyphasic approach was undertaken to determine the taxonomic status of nine isolates recovered from an evaporative lagoon in the Churince system, a hydrological system in the Cuatro Ciénegas valley in Coahuila, Mexico (26 u 50.8309 N 102 u 09.3359 W).A large collection of bacterial isolates was obtained from surface water samples collected at two different points (10 m apart) in the lagoon referred to as Laguna Grande. Water samples (15 ml) from each site were collected in sterile BD Falcon vials (BD Biosciences) and 200 ml from each sample was inoculated on glutamate/starch/phenol red (GSP) agar plates (Kielwein, 1971). The GSP medium had the following composition (g l 21): sodium L-(+)-glutamate, 10.0; starch (soluble), 20.0; potassium dihydrogen phosphate, 2.0; magnesium sulfate, 0.5; phenol red, 0.36; agar-agar, 12.0). Incubation was performed at 29 u C for 48 h. Colonies grown on different GSP plates were purified by subculture on Luria-Bertani (LB) agar (1 % tryptone, 0.5 % yeast extract, 1 % NaCl and 1.5 % agar) plates and the cultures were maintained at 280 u C in LB broth (1 % tryptone, 0.5 % yeast extract and 1 % NaCl) with 20 % (w/v) glycerol prior to analysis.The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA sequences of strains 1NT and 3N are EU791281 and EU791282, respectively.A figure showing a pulsed-field electrophoresis gel of novel strains described in this work and type and reference strains of known Pseudomonas species is available with the online version of this paper.