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      The role of microorganisms at different stages of ecosystem development for soil formation

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      Biogeosciences
      Copernicus GmbH

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          Abstract

          <p><strong>Abstract.</strong> Soil formation is the result of a complex network of biological as well as chemical and physical processes. The role of soil microbes is of high interest, since they are responsible for most biological transformations and drive the development of stable and labile pools of carbon (C), nitrogen (N) and other nutrients, which facilitate the subsequent establishment of plant communities. Forefields of receding glaciers provide unique chronosequences of different soil development stages and are ideal ecosystems to study the interaction of bacteria, fungi and archaea with their abiotic environment. In this review we give insights into the role of microbes for soil development. The results presented are based on studies performed within the Collaborative Research Program DFG SFB/TRR 38 (<a href="http://www.tu-cottbus.de/ecosystem"_target="blank">http://www.tu-cottbus.de/ecosystem</a> ) and are supplemented by data from other studies. The review focusses on the microbiology of major steps of soil formation. Special attention is given to the development of nutrient cycles on the formation of biological soil crusts (BSCs) and on the establishment of plant–microbe interactions.</p>

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          Microbial diversity and function in soil: from genes to ecosystems.

          Soils sustain an immense diversity of microbes, which, to a large extent, remains unexplored. A range of novel methods, most of which are based on rRNA and rDNA analyses, have uncovered part of the soil microbial diversity. The next step in the era of microbial ecology is to extract genomic, evolutionary and functional information from bacterial artificial chromosome libraries of the soil community genomes (the metagenome). Sophisticated analyses that apply molecular phylogenetics, DNA microarrays, functional genomics and in situ activity measurements will provide huge amounts of new data, potentially increasing our understanding of the structure and function of soil microbial ecosystems, and the interactions that occur within them. This review summarizes the recent progress in studies of soil microbial communities with focus on novel methods and approaches that provide new insight into the relationship between phylogenetic and functional diversity.
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            Uptake of organic nitrogen by plants.

            Languishing for many years in the shadow of plant inorganic nitrogen (N) nutrition research, studies of organic N uptake have attracted increased attention during the last decade. The capacity of plants to acquire organic N, demonstrated in laboratory and field settings, has thereby been well established. Even so, the ecological significance of organic N uptake for plant N nutrition is still a matter of discussion. Several lines of evidence suggest that plants growing in various ecosystems may access organic N species. Many soils display amino acid concentrations similar to, or higher than, those of inorganic N, mainly as a result of rapid hydrolysis of soil proteins. Transporters mediating amino acid uptake have been identified both in mycorrhizal fungi and in plant roots. Studies of endogenous metabolism of absorbed amino acids suggest that L- but not D-enantiomers are efficiently utilized. Dual labelled amino acids supplied to soil have provided strong evidence for plant uptake of organic N in the field but have failed to provide information on the quantitative importance of this process. Thus, direct evidence that organic N contributes significantly to plant N nutrition is still lacking. Recent progress in our understanding of the mechanisms underlying plant organic N uptake may open new avenues for the exploration of this subject.
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              The mycorrhiza helper bacteria revisited.

              In natural conditions, mycorrhizal fungi are surrounded by complex microbial communities, which modulate the mycorrhizal symbiosis. Here, the focus is on the so-called mycorrhiza helper bacteria (MHB). This concept is revisited, and the distinction is made between the helper bacteria, which assist mycorrhiza formation, and those that interact positively with the functioning of the symbiosis. After considering some examples of MHB from the literature, the ecological and evolutionary implications of the relationships of MHB with mycorrhizal fungi are discussed. The question of the specificity of the MHB effect is addressed, and an assessment is made of progress in understanding the mechanisms of the MHB effect, which has been made possible through the development of genomics. Finally, clear evidence is presented suggesting that some MHB promote the functioning of the mycorrhizal symbiosis. This is illustrated for three critical functions of practical significance: nutrient mobilization from soil minerals, fixation of atmospheric nitrogen, and protection of plants against root pathogens. The review concludes with discussion of future research priorities regarding the potentially very fruitful concept of MHB.
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                Author and article information

                Journal
                Biogeosciences
                Biogeosciences
                Copernicus GmbH
                1726-4189
                2013
                June 18 2013
                : 10
                : 6
                : 3983-3996
                Article
                10.5194/bg-10-3983-2013
                36632968
                b39b1876-548b-4e36-971d-2a049299c0cb
                © 2013

                https://creativecommons.org/licenses/by/3.0/

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