FEMS Microbiology Ecology

Cover image for Vol. 90 Issue 3

Environmental Microbes


This virtual issue of FEMS Microbiology Ecology is organized to link with the April 2013 FEMS Microbiology Reviews special thematic issue on Molecular Insights into Environmental Microbes.

Cutting-edge technology for genetic and biochemical analyses are playing an increasingly important role in contributing to the understanding of microbial ecology. We have selected key papers from the archives of FEMS Microbiology Ecology to complement the topics of the eight review articles that reflect on the activity of microbes in different environments. The topics range from life in symbiosis, commensalism, and syntrophy to life in soil, lakes and oceans. Much remains to be discovered and deciphered with regards to the diversity, growth, activity and interactions of microbial communities in different habitats and their important roles in global biogeochemical cycles and ecosystem function. The application and exploitation of modern molecular methods are essential in these ecological studies. As stated in the Editorial by Hauke Henneke, Staffan Kjelleberg and Corina Brussaard: “Environmental microbes will continue to provide an immense source for the discovery of novel life styles, new biochemical reactions and pathways, and unanticipated mechanisms of gene regulation.”

The articles highlighted here represent only a small selection of the exciting studies that we have published and for additional information and inspiration please search the past issues of FEMS Microbiology Ecology.

- Ammonia oxidation and nitrogen fixation
- Microbiota of Antarctica
- Horizontal gene transfer
- Rhizobia
- Microbial synthrophy
- Genomics
- Microbe-algae interactions

Ammonia oxidation and nitrogen fixation

Trichodesmium – a widespread marine cyanobacterium with unusual nitrogen fixation properties
B. Bergman, G. Sandh, S. Lin, J. Larsson and E.J. Carpenter
FEMS Microbiology Reviews: The substantial progress related to processes and mechanisms involved in the diazotrophic biology of the cyanobacterium Trichodesmium is reviewed.

How to make a living from anaerobic ammonium oxidation
B. Kartal, N.M. de Almeida, W.J. Maalcke, H.J.M. Op den Camp, M.S.M. Jetten and J.T. Keltjens
FEMS Microbiology Reviews: Anaerobic ammonium-oxidizing (anammox) bacteria make their living from the conversion of ammonium and nitrite into dinitrogen gas using a new route. Here, current concepts on this new route are reviewed and its connection with energy (ATP) conservation and biomass formation is discussed.

Ammonia transformations and abundance of ammonia oxidizers in a clay soil underlying a manure pond.
Sher, Yonatan; Baram, Shahar; Dahan, Ofer et al.

Stimulation of thaumarchaeal ammonia oxidation by ammonia derived from organic nitrogen but not added inorganic nitrogen.
Levičnik-Höfferle, Spela; Nicol, Graeme W.; Ausec, Luka et al.
DOI: 10.1111/j.1574-6941.2011.01275.x

Effects of estuarine sediment hypoxia on nitrogen fluxes and ammonia oxidizer gene transcription.
Abell, Guy C. J.; Banks, Jo; Ross, D. Jeff et al.

Microbiota of Antarctica

Key microbial drivers in Antarctic aquatic environments
D. Wilkins, S. Yau, T.J. Williams, M.A. Allen, M.V. Brown, M.Z. DeMaere, F.M. Lauro and R. Cavicchioli
FEMS Microbiology Reviews: Antarctica is arguably the world's most important continent for influencing the Earth's climate and ocean ecosystem function, and this review puts into perspective the insight that has been and can be gained about Antarctica's aquatic microbiota by using molecular biology, and in particular, metagenomic approaches, by revealing deep insight into which microorganisms are present in cold environments, and what biogeochemical processes they perform

Shifts in coastal Antarctic marine microbial communities during and after melt water-related surface stratification.
Piquet, Anouk M. -T.; Bolhuis, Henk; Meredith, Michael P. et al.

Low cyanobacterial diversity in biotypes of the Transantarctic Mountains and Shackleton Range (80–82ºS), Antarctica.
Fernandez-Carazo R, Hodgson DA, Convey P & Wilmotte A

Microbial dynamics and flagellate grazing during transition to winter in Lakes Hoare and Bonney, Antarctica.
Thurman, Jill; Parry, Jacqueline; Hill, Philip J. et al.

Patterns of marine bacterioplankton biodiversity in the surface waters of the Scotia Arc, Southern Ocean.
Jamieson RE, Rogers AD, Billett DSM, Smale DA & Pearce DA

Horizontal gene transfer

Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria
P. Seitz and M. Blokesch
FEMS Microbiology Reviews: In this review, we summarize recent data on cues and regulatory circuits driving natural competence and transformation in representative Gram-negative bacteria.

Evidence for particle-induced horizontal gene transfer and serial transduction between bacteria.
Chiura, Hiroshi Xavier; Kogure, Kazuhiro; Hagemann, Sylvia; et al.

Monitoring horizontal antibiotic resistance gene transfer in a colonic fermentation model.
Haug, Martina C.; Tanner, Sabine A.; Lacroix, Christophe et al.

Class 1 integrons in benthic bacterial communities: abundance, association with Tn402-like transposition modules and evidence for coselection with heavy-metal resistance.
Rosewarne, Carly P.; Pettigrove, Vincent; Stokes, Hatch W. et al.

The contribution of mobile genetic elements to the evolution and ecology of Vibrios
Hazen, Tracy H.; Pan, Li; Gu, Ji-Dong et al.

Escherichia coli adapts to tetracycline resistance plasmid (pBR322) by mutating endogenous potassium transport: in silico hypothesis testing.
Hellweger FL

Rhizobia

Molecular insights into bacteroid development during Rhizobium–legume symbiosis
A.F. Haag, M.F.F. Arnold, K.K. Myka, B. Kerscher, S. Dall'Angelo, M. Zanda, P. Mergaert and G.P. Ferguson
FEMS Microbiology Reviews: Rhizobia differentiate from free-living soil bacteria to nitrogen fixing endosymbionts of legume plants requiring specific adaptations for chronic maintenance.

Genetic diversity of nodulating and non-nodulating rhizobia associated with wild soybean (Glycine soja Sieb. & Zucc.) in different ecoregions of China.
Wu, Li Juan; Wang, Hai Qing; Wang, En Tao; et al.

Most heat-tolerant rhizobia show high induction of major chaperone genes upon stress.
Alexandre, Ana; Oliveira, Solange

Microbial Syntrophy

Microbial syntrophy: interaction for the common good
B.E.L. Morris, R. Henneberger, H. Huber and C. Moissl-Eichinger
FEMS Microbiology Reviews: Many microbial communities are based on syntrophy; this obligately mutualistic, interactive exchange of metabolic products allows them to perform ecologically important, low-energy yielding but survival-ensuring chemical conversions in extreme natural and man-made nich

Evidence for anaerobic oxidation of methane in sediments of a freshwater system (Lago di Cadagno).
Schubert, Carsten J.; Vazquez, Francisco; Loesekann-Behrens, Tina et al.

Syntrophic acetate oxidation under thermophilic methanogenic condition in Chinese paddy field soil.
Rui, Junpeng; Qiu, Qiongfen; Lu, Yahai

Effects of hydrogen and acetate on benzene mineralisation under sulphate-reducing conditions.
Rakoczy, Jana; Schleinitz, Kathleen M.; Mueller, Nicolai et al.

Evidence for syntrophic butyrate metabolism under sulfate-reducing conditions in a hydrocarbon-contaminated aquifer.
Struchtemeyer, Christopher G.; Duncan, Kathleen E.; McInerney, Michael J.

Genomics

The future is now: single-cell genomics of bacteria and archaea
P.C. Blainey
FEMS Microbiology Reviews: New cultivation-independent technologies for single-cell genome sequencing are driving environmental microbial genomics farther across the tree of life and deeper into populations of bacteria and archaea.

Whole-genome amplification (WGA) of marine photosynthetic eukaryote populations.
Lepere, Cecile; Demura, Mikihide; Kawachi, Masanobu et al.

Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats.
Handl, Stefanie; Dowd, Scot E.; Garcia-Mazcorro, Jose F. et al.

Microbe-algae interactions

The seaweed holobiont: understanding seaweed–bacteria interactions

S. Egan, T. Harder, C. Burke, P. Steinberg, S. Kjelleberg and T. Thomas
FEMS Microbiology Reviews: This review discusses the diversity and ecology of seaweed (macroalgae)-associated bacteria with an emphasis on the factors that influence epiphytic community composition and function.

What we can learn from sushi: a review on seaweed–bacterial associations.
Hollants J, Leliaert F, De Clerck O & Willems A

The green macroalga Dictyosphaeria ocellata influences the structure of the bacterioplankton community through differential effects on individual bacterial phylotypes.
Sneed JM & Pohnert G

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