Metaproteomics of soils from semiarid environment: Functional and phylogenetic information obtained with different protein extraction methods

Singleton, 2003, The potential of soil protein-based methods to indicate metal contamination, Appl Soil Ecol, 23, 25, 10.1016/S0929-1393(03)00004-0

Benndorf, 2007, Functional metaproteome analysis of protein extracts from contaminated soil and groundwater, ISME J, 1, 224, 10.1038/ismej.2007.39

Chourey, 2010, Direct cellular lysis/protein extraction protocol for soil metaproteomics, J Proteome Res, 9, 6615, 10.1021/pr100787q

VerBerkmoes, 2009, Functional analysis of natural microbial consortia using community proteomics, Nat Rev Microbiol, 7, 196, 10.1038/nrmicro2080

Siggins, 2012, Exploring mixed microbial community functioning: recent advances in metaproteomics, FEMS Microbiol Ecol, 80, 265, 10.1111/j.1574-6941.2011.01284.x

Morris, 2010, Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction, ISME J, 4, 673, 10.1038/ismej.2010.4

Sowell, 2011, Environmental proteomics of microbial plankton in a highly productive coastal upwelling system, ISME J, 5, 856, 10.1038/ismej.2010.168

Keiblinger, 2012, Soil metaproteomics — comparative evaluation of protein extraction protocols, Soil Biol Biochem, 54, 14, 10.1016/j.soilbio.2012.05.014

Hettich, 2013, Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities, Anal Chem, 85, 4203, 10.1021/ac303053e

Becher, 2013, Metaproteomics to unravel major microbial key players in leaf litter and soil environments: challenges and perspectives, Proteomics, 13, 2895, 10.1002/pmic.201300095

Bastida, 2009, Soil metaproteomics: a review of an emerging environmental science. Significance, methodology and perspectives, Eur J Soil Sci, 60, 845, 10.1111/j.1365-2389.2009.01184.x

Whiffen, 2007, Polyphenolic compounds interfere with quantification of protein in soil extracts using the Bradford method, Soil Biol Biochem, 39, 691, 10.1016/j.soilbio.2006.08.012

Kanerva, 2013, Comparison of extractants and applicability of MALDI-TOF-MS in the analysis of soil proteinaceous material from different types of soil, Org Geochem, 56, 1, 10.1016/j.orggeochem.2012.12.003

Williams, 2010, Metaproteomic characterization of a soil microbial community following carbon amendment, Soil Biol Biochem, 42, 1148, 10.1016/j.soilbio.2010.03.021

Bastida, 2012, Feasibility of a cell separation-proteomic based method for soils with different edaphic properties and microbial biomass, Soil Biol Biochem, 45, 136, 10.1016/j.soilbio.2011.10.017

Burns, 1982, Enzyme activity in soil: location and a possible role in microbial ecology, Soil Biol Biochem, 14, 423, 10.1016/0038-0717(82)90099-2

Nannipieri, 1990, Ecological significance of the biological activity in soils, 293

Nannipieri, 1996, Humus and enzyme activity, 293

Masciandaro, 2008, Comparison of extraction methods for recovery of extracellular β-glucosidase, Soil Biol Biochem, 40, 2156, 10.1016/j.soilbio.2008.05.001

1991

García, 1994, Microbial activity in soils under Mediterranean environmental conditions, Soil Biol Biochem, 26, 1185, 10.1016/0038-0717(94)90142-2

Bastida, 2006, Microbiological degradation index of soils in a semiarid climate, Soil Biol Biochem, 38, 3463, 10.1016/j.soilbio.2006.06.001

Giagnoni, 2011, Extraction of microbial proteome from soil: potential and limitations assessed through a model study, Eur J Soil Sci, 62, 74, 10.1111/j.1365-2389.2010.01322.x

Guitian, 1976

Bremmer, 1978, Urease activity in soils, 149

Yeomans, 1989, A rapid and precise method four routine determination of organic carbon in soil, Commun Soil Sci Plant Anal, 19, 1467, 10.1080/00103628809368027

Guerlava, 1998, Comparison of different methods of cell lysis and protein measurements in Clostridium perfringens: application to the cell volume determination, Curr Microbiol, 36, 131, 10.1007/PL00006756

Keller, 2002, Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search, Anal Chem, 74, 5383, 10.1021/ac025747h

Nesvizhskii, 2003, A statistical model for identifying proteins by tandem mass spectrometry, Anal Chem, 75, 4646, 10.1021/ac0341261

Roberts, 2008, Critical evaluation of methods for determining total protein in soil solution, Soil Biol Biochem, 40, 1485, 10.1016/j.soilbio.2008.01.001

Bonmatí, 1998, Protease extraction from soil by sodium pyrophosphate and chemical characterization of the extracts, Soil Biol Biochem, 14, 2113, 10.1016/S0038-0717(98)00089-3

Bastida, 2012, Effects of organic amendments on soil carbon fractions, enzyme activity and humus–enzyme complexes under semi-arid conditions, Eur J Soil Biol, 53, 94, 10.1016/j.ejsobi.2012.09.003

Smith, 2011, Fate of prions in soil: a review, J Environ Qual, 40, 449, 10.2134/jeq2010.0412

Connon, 2007, Bacterial diversity in hyperarid Atacama Desert soils, J Geophys Res, 112, G04S17, 10.1029/2006JG000311

Neilson, 2012, Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile, Extremophiles, 16, 553, 10.1007/s00792-012-0454-z

Bastida, 2013, Phylogenetic and functional changes in the microbial community of long-term restored soils under semiarid climate, Soil Biol Biochem, 65, 12, 10.1016/j.soilbio.2013.04.022

Ben-David, 2010, Assessment of the spatial distribution of soil microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using combined PLFA and DGGE analyses, FEMS Microbiol Ecol, 76, 492, 10.1111/j.1574-6941.2011.01075.x

Aguirre-Garrido, 2012, Bacterial community structure in the rhizosphere of three cactus species from semi-arid highlands in central Mexico, Antonie Van Leeuwenhoek, 101, 891, 10.1007/s10482-012-9705-3

Hortal, 2013, Soil microbial community under a nurse-plant species changes in composition, biomass and activity as the nurse grows, Soil Biol Biochem, 64, 139, 10.1016/j.soilbio.2013.04.018

Belnap, 2003

Lin, 2013, Metaproteomic analysis of ratoon sugarcane rhizospheric soil, BMC Microbiol, 13, 135, 10.1186/1471-2180-13-135

Badger, 2013, CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution, J Exp Bot, 54, 609, 10.1093/jxb/erg076

Burns, 2013, Soil enzymes in a changing environment: current knowledge and future directions, Soil Biol Biochem, 58, 216, 10.1016/j.soilbio.2012.11.009