We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).

/pdf/construction-of-escherichia-coli-k-12-in-frame-single-gene-4c68fx6pb1.pdf

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.

▪ Abstract Local habitat and biological diversity of streams and rivers are strongly influenced by landform and land use within the surrounding valley at multiple scales. However, empirical associations between land use and stream response only varyingly succeed in implicating pathways of influence. This is the case for a number of reasons, including (a) covariation of anthropogenic and natural gradients in the landscape; (b) the existence of multiple, scale-dependent mechanisms; (c) nonlinear responses; and (d) the difficulties of separating present-day from historical influences. Further research is needed that examines responses to land use under different management strategies and that employs response variables that have greater diagnostic value than many of the aggregated measures in current use. In every respect, the valley rules the stream.      H.B.N. Hynes (1975)

http://deq.idaho.gov/media/525804-Landscapes_Riverscapes_Influence_landuse_stream_ecosystems_Allan_2004.pdf

Landscapes and Riverscapes: The Influence of Land Use on Stream Ecosystems

Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development.

Microbial Biofilms: from Ecology to Molecular Genetics

Interpretation of X-ray Powder Diffraction Patterns . By H. Lipson and H. Steeple. Pp. viii + 335 + 3 plates. (Mac-millan: London; St Martins Press: New York, May 1970.) £4.

X-Ray Diffraction

Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems: A global assessment.

(Alnus rubra Bong.) in southeast Alaska R. K. KIMBIRAUSKAS, R. W. MERRITT, M. S. WIPFLI, & P. HENNON Michigan State University, Department of Entomology, 243 Natural Science Building, East Lansing, MI 48824 USGS Alaska Cooperative Fish and Wildlife Research Unit, Institute of Artic Biology, 209 Irving I Building, University of Alaska, Fairbanks, AK 99775-7020 USDA Forest Service, Pacific Northwest Research Station, Juneau Forestry Sciences Laboratory 2770 Sherwood Lane, Suite 2A, Juneau, AK 99801-8545

Headwater macroinvertebrate community response to riparian red alder (Alnus rubra Bong.) in southeast Alaska

The black flies (Simuliidae) of North America

Seasonal abundance of immature Coquillettidia perturbans was studied at 3 sites in south-central Michigan in 1987 and 1988. A modified boat bilge pump and funnel separators proved to be good sampling and sorting devices. Pupae were found in late May to early July, first and second instars were most abundant in July and August, while third and fourth instars were present year-round. Overall, larvae were most numerous in August and September, indicating that Cq. perturbans has a single generation per year in Michigan, with midsummer to fall as the main period of larval development, and with third and fourth larval instars as overwintering stages. Parasitism of Cq. perturbans larvae by a previously undiscovered mermithid nematode was documented at 2 sites in late summer.

Sampling, seasonal abundance, and mermithid parasitism of larval Coquillettidia perturbans in south-central Michigan.

We examined microbial respiration and carbon/nitrogen content of decomposing leaf material in microcosms used for growth studies of the treehole mosquito, Aedes triseriatus. Leaf material originated from birch and oak trees exposed to conditions of shade/sun and elevated/ambient levels of CO2. Microbial respiration as measured by CO2 production was generally greatest on birch leaves grown under shaded conditions, however, ANOVA indicated possible light X CO2 interactions. There were also strong interactions between species of leaf and CO2 levels, but oak leaves grown under elevated CO2 supported significantly higher microbial respiration rates than oak leaves grown in an ambient CO2 atmosphere. Birch leaves grown under elevated CO2 also generally supported higher rates of microbial respiration. However, light effects were much more pronounced and birch leaves grown under full sun and elevated CO2 conditions supported relatively low microbial respiration. Microbial respiration varied inversely with leaf carbon:nitrogen ratio and directly with nitrogen content across treatments, however, initial carbon and nitrogen content of leaf material was not a consistent predictor of microbial respiration. In general, mosquito production paralleled microbial respiration, suggesting a tight link between the two trophic levels. These data indicate that interactions between available light and CO2 on parent plant material could have variable, species-dependent effects on microorganisms and secondary consumers in aquatic, detritus-based systems.

https://www.nrs.fs.fed.us/pubs/gtr/gtr_ne214/gtr_ne214_089.pdf

Richard W. Merritt

Papers

Headwater macroinvertebrate community response to riparian red alder (Alnus rubra Bong.) in southeast Alaska

The black flies (Simuliidae) of North America

Sampling, seasonal abundance, and mermithid parasitism of larval Coquillettidia perturbans in south-central Michigan.

Effects of elevated CO2 and shade on the decomposition of senesced tree foliage: impacts on microbial activity

The Role of Aquatic Organisms in Forensic Investigations