@article {1417,
	title = {Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities.},
	journal = {Mol Ecol},
	volume = {23},
	year = {2014},
	month = {2014 Jun},
	pages = {2988-99},
	abstract = {<p>Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale.</p>
},
	keywords = {Agriculture, Carbon Cycle, Ecosystem, Genes, Bacterial, Genes, Fungal, Genetic Variation, Metagenome, Multigene Family, Nitrogen Cycle, Oligonucleotide Array Sequence Analysis, Soil Microbiology, Trees, Tropical Climate},
	issn = {1365-294X},
	doi = {10.1111/mec.12786},
	author = {Paula, Fabiana S and Rodrigues, Jorge L M and Zhou, Jizhong and Wu, Liyou and Mueller, Rebecca C and Mirza, Babur S and Bohannan, Brendan J M and N{\"u}sslein, Klaus and Deng, Ye and Tiedje, James M and Pellizari, Vivian H}
}
@article {1422,
	title = {Identification and characterization of a NaCl-responsive genetic locus involved in survival during desiccation in Sinorhizobium meliloti.},
	journal = {Appl Environ Microbiol},
	volume = {79},
	year = {2013},
	month = {2013 Sep},
	pages = {5693-700},
	abstract = {<p>The Rhizobiaceae are a bacterial family of enormous agricultural importance due to the ability of its members to fix atmospheric nitrogen in an intimate relationship with plants. Their survival as naturally occurring soil bacteria in agricultural soils as well as popular seed inocula is affected directly by drought and salinity. Survival after desiccation in the presence of NaCl is enabled by underlying genetic mechanisms in the model organism Sinorhizobium meliloti 1021. Since salt stress parallels a loss in water activity, the identification of NaCl-responsive loci may identify loci involved in survival during desiccation. This approach enabled identification of the loci asnO and ngg by their reduced ability to grow on increased NaCl concentrations, likely due to their inability to produce the osmoprotectant N-acetylglutaminylglutamine (NAGGN). In addition, the mutant harboring ngg::Tn5luxAB was affected in its ability to survive desiccation and responded to osmotic stress. The desiccation sensitivity may have been due to secondary functions of Ngg (N-acetylglutaminylglutamine synthetase)-like cell wall metabolism as suggested by the presence of a d-alanine-d-alanine ligase (dAla-dAla) domain and by sensitivity of the mutant to \&beta;-lactam antibiotics. asnO::Tn5luxAB is expressed during the stationary phase under normal growth conditions. Amino acid sequence similarity to enzymes producing \&beta;-lactam inhibitors and increased resistance to \&beta;-lactam antibiotics may indicate that asnO is involved in the production of a \&beta;-lactam inhibitor.</p>
},
	keywords = {Desiccation, DNA Transposable Elements, Gene Expression Regulation, Bacterial, Gene Knockout Techniques, Genes, Bacterial, Genetic Loci, Microbial Viability, Mutagenesis, Insertional, Osmotic Pressure, Sinorhizobium meliloti, Sodium Chloride, Stress, Physiological},
	issn = {1098-5336},
	doi = {10.1128/AEM.01037-13},
	author = {Vriezen, Jan A C and de Bruijn, Frans J and N{\"u}sslein, Klaus}
}
@article {748,
	title = {Distribution of extensive nifH gene diversity across physical soil microenvironments.},
	journal = {Microb Ecol},
	volume = {51},
	year = {2006},
	month = {2006 May},
	pages = {441-52},
	abstract = {The diversity of nitrogen-fixing bacteria is well described for aquatic environments; however, terrestrial analyses remain mostly biased to rhizobial plant-microbe associations. We maximized the level of resolution for this study through the use of nucleotide sequence information extracted from a series of soil microenvironments, ranging from macroaggregates at 2000 microm to the clay fraction at < 75 microm in diameter. In addition, we attempted to create an overview of the distribution of terrestrial nitrogen fixers across such microenvironments by combining culture-independent techniques with a suite of natural soil environments from uniquely different origins. Soil diazotroph diversity was analyzed phylogenetically for 600 terrestrial nifH sequences from 12 midsized clone libraries based on microenvironments of three separate soils across a global scale. Statistical analyses of nifH gene clone libraries were used to estimate coverage, establish degrees of sequence overlap, and compare cluster distributions. These analyses revealed an extensive diversity in a tropical (19 phylotypes) and an arctic soil (17 phylotypes), and moderate diversity in a temperate soil (11 phylotypes). Within each soil, comparisons across aggregate size fractions delineated nifH gene cluster shifts within populations and degrees of sequence overlap that ranged from significantly different (arctic, tropical) to significantly similar (temperate). We suggest that this is due to population separation across aggregates of different size classes, which results from differences in the temporal stability of aggregates as niches for microbial communities. This study not only provides new knowledge of the arrangement of diazotrophic communities at the soil microscale, but it also contributes to the underrepresented knowledge of soil nifH sequences in the public databases.},
	keywords = {Bacteria, Base Sequence, DNA Primers, Genes, Bacterial, Multigene Family, Oxidoreductases, Phylogeny, Polymerase Chain Reaction, Soil Microbiology},
	issn = {0095-3628},
	doi = {10.1007/s00248-006-9044-x},
	author = {Izquierdo, Javier A and N{\"u}sslein, Klaus}
}
