High-throughput comparison of gene fitness among related bacteria

ABSTRACT: BACKGROUND: The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains to reveal differences not apparent at the gene sequence level. RESULTS: A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella Typhi Ty2 (STY1), which were then grown in rich media. The locations of 234,152 and 53,556 integration sites, respectively, were mapped by sequencing. These data were compared to similar data available for a different Ty2 strain (STY2) and essential genes identified in E. coli K-12 (ECO). Of 277 genes considered essential in ECO, all had syntenic homologs in STM1, STY1, and STY2, and all but nine genes were either devoid of Tn insertions or had very few. For three of these nine genes, part of the annotated gene lacked Tn integrations (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498.L, STM14_2872, STM14_3360.RJ, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. CONCLUSIONS: Comparisons among transposon integration profiles from different members of a species and among related species, all grown in similar conditions, identify differences in gene fitness among syntenic homologous genes. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology.     

Nitrite oxidation in the Namibian oxygen minimum zone

Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in ¹⁵N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (⩽372 nM NO₂⁻ d⁻¹) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ∼9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO₃⁻ was re-oxidized back to NO₃⁻ via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways.     

Common Loon Survival Rates and Mercury in New England and Wisconsin

Abstract: Bioaccumulation of toxic environmental mercury may affect the vital rates of piscivores such as the common loon (Gavia immer). Although immediate effects of mercury on early development or reproduction can be determined from short-term field studies or dosing experiments, long-term effects on survival for a long-lived species such as the common loon must be discerned from large, long-term observational data sets. We analyzed band-resight and mercury data for 776 adult loons in Wisconsin and New England, USA, from 1991 to 2001 to 1) estimate annual survival rates and 2) investigate the relation between mercury exposure and survival. The model-averaged estimate of apparent survival was 0.87, whereas the approximate survival rate (accounting for movement) was 0.92. We found no differences in apparent survival by geographic location or sex and no relation between survival and mercury. Power analyses showed that we were only likely to detect differences in survival ≥3%. Small differences in survival (<3%), which may be important to loon population viability, were unlikely to be detected in our dataset. (JOURNAL OF WILDLIFE MANAGEMENT 72(3):665–673; 2008)     

Soft‐tissue imprints in fossil and Recent cephalopod septa and septum formation

Several soft‐tissue imprints and attachment sites have been discovered on the inside of the shell wall and on the apertural side of the septum of various fossil and Recent ectocochleate cephalopods. In addition to the scars of the cephalic retractors, steinkerns of the body chambers of bactritoids and some ammonoids from the Moroccan and the German Emsian (Early Devonian) display various kinds of striations; some of these striations are restricted to the mural part of the septum, some start at the suture and terminate at the anterior limit of the annular elevation. Several of these features were also discovered in specimens of Mesozoic and Recent nautilids. These structures are here interpreted as imprints of muscle fibre bundles of the posterior and especially the septal mantle, blood vessels as well as the septal furrow. Most of these structures were not found in ammonoids younger than Middle Devonian. We suggest that newly formed, not yet mineralized (or only slightly), septa were more tightly stayed between the more numerous lobes and saddles in more strongly folded septa of more derived ammonoids and that the higher tension in these septa did not permit soft‐parts to leave imprints on the organic preseptum. It is conceivable that this permitted more derived ammonoids to replace the chamber liquid faster by gas and consequently, new chambers could be used earlier than in other ectocochleate cephalopods, perhaps this process began even prior to mineralization. This would have allowed faster growth rates in derived ammonoids.     

Functional redundancy of stream macroconsumers despite differences in catchment land use

1. The conversion of forested landscapes to agriculture and, increasingly, to suburban and urban development significantly affects the structure and function of both terrestrial and aquatic ecosystems. While a growing body of research is examining how biotic communities change in response to human alteration of landscapes, less is known about how these changes in community structure affect biotic interactions. 2. The objective of this study was to examine top‐down control by macroconsumers (fish and crayfish) across a human‐impacted landscape. We predicted that changes in stream macroconsumers and physicochemical characteristics associated with increased catchment development (e.g. decreased abundance of fish that are obligate benthic invertivores, increased sedimentation) would diminish top‐down control of benthic insects. We expected that effects on algal assemblages would be more variable, with increased top‐down control at sites dominated by algivorous fish and diminished control elsewhere. To test these predictions, we experimentally excluded fish and crayfish from areas of the bed of five streams whose catchments ranged from 100% to <50% forested, and examined the effects of exclusion on benthic insects and algae. 3. Despite cross‐site differences in physical, chemical and biological characteristics, the outcome of our experiments was consistent across five sites representing a range of catchment development. Across all sites, macroconsumers reduced total insect biomass, largely due to decreases in Chironomidae and Hydropsychidae larvae. Macroconsumers also affected algal assemblages, reducing chlorophyll‐a and the proportion of upright and filamentous diatoms (e.g. Melosira, Cymbella) but increasing the proportion of adnate diatoms (e.g. Achnanthes) across all sites. 4. We expected that differences in factors such as macroconsumer assemblage composition, nutrient and light availability and sedimentation would result in variable responses to macroconsumer exclusion in the five streams. Contrary to these expectations, only one response variable (ash‐free dry mass) showed a statistically significant interaction (i.e. site × exclusion) effect. Most responses to exclusion were relatively consistent, suggesting functional redundancy in assemblages of macroconsumers among the sites despite differences in catchment land use.