Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA

Zhou, Jizhong; Davey, Mary E.; Figueras, Jordi B.; Rivkina, Elizaveta; Gilichinsky, D.; Tiedje, James M.

doi:10.1099/00221287-143-12-3913

Cited by 205 publications

(130 citation statements)

References 15 publications

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“…Phylogenetic analyses of permafrost soils indicated that the majority of the clone sequences were 5-15% different from those in the current databases (Zhou et al, 1997). The results presented here enabled identification of one of the unknown genera and gave insight into its physiology and function, which remained unknown for most of the bacteria active in situ.…”

Section: Ecological Aspectsmentioning

confidence: 76%

Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic

et al. 2007

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Permafrost-affected soils of the Siberian Arctic were investigated with regard to identification of nitrite oxidizing bacteria active at low temperature. Analysis of the fatty acid profiles of enrichment cultures grown at 41C, 101C and 171C revealed a pattern that was different from that of known nitrite oxidizers but was similar to fatty acid profiles of Betaproteobacteria. Electron microscopy of two enrichment cultures grown at 101C showed prevalent cells with a conspicuous ultrastructure. Sequence analysis of the 16S rRNA genes allocated the organisms to a so far uncultivated cluster of the Betaproteobacteria, with Gallionella ferruginea as next related taxonomically described organism. The results demonstrate that a novel genus of chemolithoautotrophic nitrite oxidizing bacteria is present in polygonal tundra soils and can be enriched at low temperatures up to 171C. Cloned sequences with high sequence similarities were previously reported from mesophilic habitats like activated sludge and therefore an involvement of this taxon in nitrite oxidation in nonarctic habitats is suggested. The presented culture will provide an opportunity to correlate nitrification with nonidentified environmental clones in moderate habitats and give insights into mechanisms of cold adaptation. We propose provisional classification of the novel nitrite oxidizing bacterium as 'Candidatus Nitrotoga arctica'.

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Section: Ecological Aspectsmentioning

confidence: 76%

Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic

et al. 2007

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“…SSU rRNA genes were amplified from genomic DNA using modified primers fD1 and rP1 (Weisberg et al 1991, Zhou et al 1995. Amplification, sequencing, and sequence analysis were performed as previously described (Smith et al 1994, Strunk et al 1996, Zhou et al 1997.…”

Section: Methodsmentioning

confidence: 99%

Metal reduction at cold temperatures by Shewanella isolates from various marine environments

Stapleton¹,

Sabree²,

Palumbo³

et al. 2005

Aquat. Microb. Ecol.

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Members of the genus Shewanella capable of reducing metals and forming minerals under cold-temperature conditions were isolated from 3 distinct marine habitats (the coast of Washington State, the Puget Sound, and an iron-rich microbial mat off Hawaii). Cultures of microorganisms were isolated at 8°C on nutrient agar medium prepared in artificial seawater. Isolates in this study could use a wide variety of electron acceptors such as oxygen, nitrate, and metals, and reduce various metals coupled to the oxidation of several organic acids, glucose or hydrogen at temperatures down to 0°C. Akaganeite was reduced to either magnetite or siderite, depending on the test conditions. The geochemical profiles at the sample sites from which these strains were isolated spanned a temperature range of 1.8 to 11°C, and all showed active oxygen and nitrate reduction as well as metal reduction. This confirms previous reports that sediment microorganisms participating in biogeochemical cycles remain active at low temperatures. KEY WORDS: Biogeochemistry · Geomicrobiology · Iron reduction · Cobalt reduction · Magneite Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 38: [81][82][83][84][85][86][87][88][89][90][91] 2005 While their quantitative importance in marine sediments and water columns is not well understood, members of the genus Shewanella are commonly encountered in marine environments (Perry et al. 1993, Thamdrup et al. 2000, Brettar et al. 2002. These isolates have provided useful models for laboratory investigations on metal reduction (Nealson & Saffarini 1994, Kostka & Nealson 1995, food spoilage, barophilic growth (Kato & Nogi 2001) and, more recently, psychrophilic enzymes (Irwin et al. 2001a,b). The present study describes the isolation of members of the genus Shewanella from 3 marine environments. Specifically, strains W3-6-1 and PS-7 were used as models to investigate microbial metal reduction and mineral formation at low temperatures. MATERIALS AND METHODSSite description and sampling. Marine sediment samples were collected from a transect off the coast of Washington State (USA), at 2 locations in Puget Sound (USA) and from an iron-rich microbial mat associated with the Naha Vents on the South Rift of Loihi Seamount near Hawaii. With the exception of the vent sites, sediments were collected by box core sampling. The microbial mat sample was collected during DSRV Pisces V dive number 342 (Emerson & Moyer 2002). Each box core was sub-cored for sectioning using 7.5 and 10 cm cast-acrylic core tubes. Core sectioning took place within approximately 1 h of coring in a glove-box at ~5°C in a N 2 atmosphere. Cores were stored at ~5°C to minimize effects due to warming. Details of sample location, including geographic coordinates, are listed in Table 1.The geochemistry of the sediments was inferred from sediment pore-water distributions. Pore-water was separated from the sediments by centrifugation at 7000 rpm (>10 000 × g) for 20 min; supernatants were filtered thr...

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“…In Siberian tundra soil, it was found that over 60% of the 16S rDNA clones belonged to the Proteobacteria and 16% to the Fibrobacter division (Zhou et al, 1997). It was also found that the soil type was the dominant factor influencing the diversity of the population of culturable fluorescent Pseudomonas spp.…”

Section: The Effect Of Soilmentioning

confidence: 83%

Opening the Black Box: Understanding the Influence of Cropping Systems and Plant Communities on Bacterial and Fungal Population Dynamics

Fernando¹,

2013

Ceylon J. Sci. (Biol. Sci.)

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Since the development of agriculture 10,000 years ago, crops and the soil they grow in have interacted and affected each other"s existence. Soil microbial communities exert an important role in maintaining the health of soil and productivity of crops, and in turn, their population dynamics are influenced by agricultural systems. Researchers have attempted to assess community structure, as well as abundance, distribution, and function of species under different agricultural management systems. The effect of plants, soil, and agricultural management practices on the population dynamics of bacteria and fungi is reviewed, and methods to describe microbial communities are discussed.

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Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA

Cited by 205 publications

References 15 publications

Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic

Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic

Metal reduction at cold temperatures by Shewanella isolates from various marine environments

Opening the Black Box: Understanding the Influence of Cropping Systems and Plant Communities on Bacterial and Fungal Population Dynamics

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