The Experts below are selected from a list of 270 Experts worldwide ranked by ideXlab platform
Katherine C Goldfarb - One of the best experts on this subject based on the ideXlab platform.
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differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance
Frontiers in Microbiology, 2011Co-Authors: Katherine C Goldfarb, Ulas Karaoz, China A Hanson, Clark A Santee, Mark A Bradford, Kathleen K Treseder, Matthew D Wallenstein, Eoin L BrodieAbstract:Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.
Hong Kum Lee - One of the best experts on this subject based on the ideXlab platform.
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dasania marina gen nov sp nov of the order Pseudomonadales isolated from arctic marine sediment
Journal of Microbiology, 2007Co-Authors: Yoo Kyung Lee, Soon Gyu Hong, Hyun Hee Cho, Kyeung Hee Cho, Hong Kum LeeAbstract:An obligately aerobic bacterium, strain KOPRI 20902T, was isolated from a marine sediment in Ny-Arlesund, Spitsbergen Islands, Norway. Cells were irregular rods and motile with polar monotrichous flagellum. The optimum growth temperature was 17-22 degrees . Cells grew best in pH 7.0-10.0 and 3-4% sea salts (corresponding to 2.3-3.1% NaCl). The novel strain required Ca2+ or Mg2+ in addition to NaCl for growth. Sequence analysis of 16S rRNA gene revealed that the Arctic isolate is distantly related with established species (<92.4% sequence similarity) and formed a monophyletic group with Cellvibrio, which formed a distinct phylogenetic lineage in the order Pseudomonadales. Predominant cellular fatty acids [C16:1 omega7c/15:0 iso 2OH (45.3%), C16:0 (18.4%), ECL 11.799 (11.2%), C10:0 3OH (10.4%)]; DNA G+C content (37.0 mol%); nitrate reduction to nitrogen; absence of aesculin hydrolysis, N-acetyl-beta-glucosaminidase and esterase; no assimilation of arabinose, galactose, glucose, lactose, maltose, and trehalose differentiated the strain from the genus Cellvibrio. Based on the phylogenetic and phenotypic characteristics, Dasania marina gen. nov., sp. nov. is proposed in the order Pseudomonadales. Strain KOPRI 20902T (=KCTC 12566T=JCM 13441T) is the type strain of Dasania marina.
John T Wertz - One of the best experts on this subject based on the ideXlab platform.
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ventosimonas gracilis gen nov sp nov a member of the gammaproteobacteria isolated from cephalotes varians ant guts representing a new family ventosimonadaceae fam nov within the order Pseudomonadales
International Journal of Systematic and Evolutionary Microbiology, 2016Co-Authors: Jonathan Y Lin, William J Hobson, John T WertzAbstract:Cephalotes 'turtle' ants are known to harbor a core group of gut symbionts, including members belonging to the Gammaproteobacteria. Here, we describe the cultivation and characterization of strain CV58T, a novel member of the Gammaproteobacteria order Pseudomonadales isolated from the guts of the ant Cephalotes varians. Strain CV58T was rod-shaped, Gram-stain-negative, non-motile and formed pale-yellow colonies on trypticase soy agar. Optimum growth occurred under an atmosphere of 4-20 % (v/v) O2. Growth was possible for strain CV58Tat NaCl concentrations of 0-1.5 % (w/v), temperatures of 23-40 °C, and pH values of 5.5-8.5. The G+C content of the genomic DNA was 54.9 mol% and the major fatty acids were C18 : 1ω7c, C16 : 0, C16 : 1ω7c/C16 : 1ω6c, C12 : 0 and C12 : 03OH. The only respiratory quinone detected was ubiquinone-9 (Q-9) and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on phylogenetic analysis of the 16S rRNA gene sequence, strain CV58T shared an 88.3 % nucleotide identity with its closest cultivated neighbor, Pseudomonas putida R43. We believe that this, combined with the housekeeping gene phylogeny, differences in phenotypic characteristics and cellular fatty acid compositions of other cultivated members indicates that strain CV58T represents a novel species occupying a novel genus and family within the order Pseudomonadales. Thus, we propose the name Ventosimonadaceae fam nov., followed by Ventosimonas gracilis gen. nov., sp. nov., to classify strain CV58T (=NCIMB 15011T =DSM 100910T).
Luc Dendooven - One of the best experts on this subject based on the ideXlab platform.
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molecular characterization of soil bacterial communities in contrasting zero tillage systems
Plant and Soil, 2010Co-Authors: Javier A Cejanavarro, Flor N Rivera, Leonardo Patinozuniga, Anton Vilasanjurjo, R. Marsch, Bram Govaerts, Luc DendoovenAbstract:It is well known that agricultural practices change the physical and chemical characteristics of soil. As a result, microbial populations can also be affected. The aim of this study was to analyze the effect on soil bacterial communities of zero tillage (ZT) under maize monoculture (MM) with crop residue removal (-R) (MM/-R treatment), compared to a ZT system under wheat monoculture (WW) with crop retention (+R) (WW/+R treatment). Phylogenetic analysis was used to characterize soil bacterial communities. Phylogenetic groups found exclusively in MM/-R were Caldilineales, Chromatiales, Oscillatoriales, Legionellales, Nitrosomonadales and unclassified ∂-Proteobacteria, while Bacillales, Burkholderiales, Pseudomonadales and Rubrobacteriales were found only in WW/+R. Sequences of bacteria related to fluorescent Pseudomonas sp. were detected only in WW/+R. Acidobacteria, a largely unknown group of bacteria, were the dominant group in both treatments with a relative proportion of 0.703 and 0.517 for MM/+R and WW/-R respectively. It was found that zero tillage with removal of crop residue in soil cultivated with a monoculture of maize strongly reduced microbial diversity (H = 3.30; D = 0.9040) compared to soil where crop residue was retained in a wheat zero tillage situation (H = 4.15; D = 0.9848).
Eoin L Brodie - One of the best experts on this subject based on the ideXlab platform.
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differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance
Frontiers in Microbiology, 2011Co-Authors: Katherine C Goldfarb, Ulas Karaoz, China A Hanson, Clark A Santee, Mark A Bradford, Kathleen K Treseder, Matthew D Wallenstein, Eoin L BrodieAbstract:Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.
