@article {1419,
	title = {Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest.},
	journal = {ISME J},
	volume = {8},
	year = {2014},
	month = {2014 Jul},
	pages = {1548-50},
	abstract = {<p>Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.</p>
},
	keywords = {Brazil, Conservation of Natural Resources, DNA Barcoding, Taxonomic, DNA, Fungal, DNA, Ribosomal, Ecosystem, Fungi, Phylogeny, Plant Roots, Soil Microbiology, Trees, Tropical Climate},
	issn = {1751-7370},
	doi = {10.1038/ismej.2013.253},
	author = {Mueller, Rebecca C and Paula, Fabiana S and Mirza, Babur S and Rodrigues, Jorge L M and N{\"u}sslein, Klaus and Bohannan, Brendan J M}
}
@article {374,
	title = {Effects of selected root exudate components on soil bacterial communities.},
	journal = {FEMS Microbiol Ecol},
	volume = {77},
	year = {2011},
	month = {2011 Sep},
	pages = {600-10},
	abstract = {Low-molecular-weight organic compounds in root exudates play a key role in plant-microorganism interactions by influencing the structure and function of soil microbial communities. Model exudate solutions, based on organic acids (OAs) (quinic, lactic, maleic acids) and sugars (glucose, sucrose, fructose), previously identified in the rhizosphere of Pinus radiata, were applied to soil microcosms. Root exudate compound solutions stimulated soil dehydrogenase activity and the addition of OAs increased soil pH. The structure of active bacterial communities, based on reverse-transcribed 16S rRNA gene PCR, was assessed by denaturing gradient gel electrophoresis and PhyloChip microarrays. Bacterial taxon richness was greater in all treatments than that in control soil, with a wide range of taxa (88-1043) responding positively to exudate solutions and fewer (<24) responding negatively. OAs caused significantly greater increases than sugars in the detectable richness of the soil bacterial community and larger shifts of dominant taxa. The greater response of bacteria to OAs may be due to the higher amounts of added carbon, solubilization of soil organic matter or shifts in soil pH. Our results indicate that OAs play a significant role in shaping soil bacterial communities and this may therefore have a significant impact on plant growth.},
	keywords = {Bacteria, DNA, Bacterial, Molecular Sequence Data, Organic Chemicals, Phylogeny, Pinus, Plant Exudates, Plant Roots, Rhizosphere, RNA, Ribosomal, 16S, Soil, Soil Microbiology},
	issn = {1574-6941},
	doi = {10.1111/j.1574-6941.2011.01150.x},
	author = {Shi, Shengjing and Richardson, Alan E and O{\textquoteright}Callaghan, Maureen and Deangelis, Kristen M and Jones, Eirian E and Stewart, Alison and Firestone, Mary K and Condron, Leo M}
}
@article {731,
	title = {Biotechnological potential of aquatic plant-microbe interactions.},
	journal = {Curr Opin Biotechnol},
	volume = {21},
	year = {2010},
	month = {2010 Jun},
	pages = {339-45},
	abstract = {The rhizosphere in terrestrial systems is the region of soil surrounding plant roots where there is increased microbial activity; in aquatic plants, this definition may be less clear because of diffusion of nutrients in water, but there is still a zone of influence by plant roots in this environment [1]. Within that zone chemical conditions differ from those of the surrounding environment as a consequence of a range of processes that were induced either directly by the activity of plant roots or by the activity of rhizosphere microflora. Recently, there are a number of new studies related to rhizospheres of aquatic plants and specifically their increased potential for remediation of contaminants, especially remediation of metals through aquatic plant-microbial interaction.},
	keywords = {Biodegradation, Environmental, Biotechnology, Hydrogen-Ion Concentration, Plant Roots, Plants},
	issn = {1879-0429},
	doi = {10.1016/j.copbio.2010.04.004},
	author = {Stout, L and N{\"u}sslein, K}
}
@article {730,
	title = {Phytoprotective influence of bacteria on growth and cadmium accumulation in the aquatic plant Lemna minor.},
	journal = {Water Res},
	volume = {44},
	year = {2010},
	month = {2010 Sep},
	pages = {4970-9},
	abstract = {Certain plants are known to accumulate heavy metals, and can be used in remediation of polluted soil or water. Plant-associated bacteria, especially those that are metal tolerant, may enhance the total amount of metal accumulated by the plant, but this process is still unclear. In this study, we investigated metal enhancement vs. exclusion by plants, and the phytoprotective role plant-associated bacteria might provide to plants exposed to heavy metal. We isolated cadmium-tolerant bacteria from the roots of the aquatic plant Lemna minor grown in heavy metal-polluted waters, and tested these isolates for tolerance to cadmium. The efficiency of plants to accumulate heavy metal from their surrounding environment was then tested by comparing L. minor plants grown with added metal tolerant bacteria to plants grown axenically to determine, whether bacteria associated with these plants increase metal accumulation in the plant. Unexpectedly, cadmium tolerance was not seen in all bacterial isolates that had been exposed to cadmium. Axenic plants accumulated slightly more cadmium than plants inoculated with bacterial isolates. Certain isolates promoted root growth, but overall, addition of bacterial strains did not enhance plant cadmium uptake, and in some cases, inhibited cadmium accumulation by plants. This suggests that bacteria serve a phytoprotective role in their relationship with Lemna minor, preventing toxic cadmium from entering plants.},
	keywords = {Adaptation, Physiological, Araceae, Bacteria, Biodegradation, Environmental, Cadmium, Hydrogen-Ion Concentration, Molecular Sequence Data, Plant Roots, Siderophores, Water},
	issn = {1879-2448},
	doi = {10.1016/j.watres.2010.07.073},
	author = {Stout, Lisa M and Dodova, Elena N and Tyson, Julian F and N{\"u}sslein, Klaus}
}
@article {378,
	title = {Selective progressive response of soil microbial community to wild oat roots.},
	journal = {ISME J},
	volume = {3},
	year = {2009},
	month = {2009 Feb},
	pages = {168-78},
	abstract = {Roots moving through soil induce physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. The use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies compositional changes reported earlier, including increases in chitinase- and protease-specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change compared with bulk soil in relative abundance for 7\% of the total rhizosphere microbial community (147 of 1917 taxa); the 7\% response value was confirmed by16S rRNA terminal restriction fragment length polymorphism analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared with bulk soil, but then increased in older root zones. Quantitative PCR revealed rhizosphere abundance of beta-Proteobacteria and Actinobacteria at about 10(8) copies of 16S rRNA genes per g soil, with Nitrospira having about 10(5) copies per g soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in functions observed earlier in progressively more mature rhizosphere zones.},
	keywords = {Avena sativa, Bacteria, Biodiversity, Colony Count, Microbial, Microarray Analysis, Oligonucleotide Array Sequence Analysis, Plant Roots, Polymerase Chain Reaction, RNA, Bacterial, RNA, Ribosomal, 16S, Soil Microbiology},
	issn = {1751-7370},
	doi = {10.1038/ismej.2008.103},
	author = {Deangelis, Kristen M and Brodie, Eoin L and DeSantis, Todd Z and Andersen, Gary L and Lindow, Steven E and Firestone, Mary K}
}
@article {751,
	title = {Shifts in rhizoplane communities of aquatic plants after cadmium exposure.},
	journal = {Appl Environ Microbiol},
	volume = {71},
	year = {2005},
	month = {2005 May},
	pages = {2484-92},
	abstract = {In this study we present the comparative molecular analysis of bacterial communities of the aquatic plant Lemna minor from a contaminated site (RCP) and from a laboratory culture (EPA), as well as each of these with the addition of cadmium. Plants were identified as L. minor by analysis of the rpl16 chloroplast region. Comparative bacterial community studies were based on the analyses of 16S rRNA clone libraries, each containing about 100 clones from the root surfaces of plants. Bacterial communities were compared at three phylogenetic levels of resolution. At the level of bacterial divisions, differences in diversity index scores between treatments, with and without cadmium within the same plant type (EPA or RCP), were small, indicating that cadmium had little effect. When we compared genera within the most dominant group, the beta-proteobacteria, differences between unamended and cadmium-amended libraries were much larger. Bacterial diversity increased upon cadmium addition for both EPA and RCP libraries. Analyses of diversity at the phylotype level showed parallel shifts to more even communities upon cadmium addition; that is, percentage changes in diversity indices due to cadmium addition were the same for either plant type, indicating that contamination history might be independent of disturbance-induced diversity shifts. At finer phylogenetic levels of resolution, the effects of cadmium addition on bacterial communities were very noticeable. This study is a first step in understanding the role of aquatic plant-associated microbial communities in phytoremediation of heavy metals.},
	keywords = {Araceae, Bacteria, Base Sequence, Cadmium, Molecular Sequence Data, Phylogeny, Plant Roots, RNA, Ribosomal, 16S},
	issn = {0099-2240},
	doi = {10.1128/AEM.71.5.2484-2492.2005},
	author = {Stout, Lisa M and N{\"u}sslein, Klaus}
}
