Page 14 - Bacci_Pagoto_etali_2015

Author's personal copy

12 Ann Microbiol (2015) 65:1–13

Bull AT, Stach JEM, Ward AC, Goodfellow M (2005) Marine Holmes AJ, Costello A, Lidstrom ME, Murrell JC (1995) Evidence that
actinobacteria: perspectives, challenges, future directions. Antonie participate methane monooxygenase and ammonia monooxygenase
Van Leeuwenhoek 87:65–79 may be evolutionarily related. FEMS Microbiol Lett 132:203–208
Cui Z, Lai Q, Dong C, Shao Z (2008) Biodiversity of polycyclic aromatic Horz H-P, Rich V, Avrahami S, Bohannan BJM (2005) Methane-
hydrocarbon-degrading bacteria from deep sea sediments of the oxidizing bacteria in a California upland grassland soil: diversity
Middle Atlantic Ridge. Environ Microbiol 10:2138–2149 and response to simulated global change. Appl Environ Microbiol
Dalmastri C, Chiarini L, Cantale C, Bevivino A, Tabacchioni S (1999) 71:2642–2652
Soil type and maize cultivar affect the genetic diversity of maize Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, Sogin ML
root-associated Burkholderia cepacia populations. Microb Ecol 38: (2008) Exploring microbial diversity and taxonomy using SSU
273–284 rRNA hypervariable tag sequencing. PLoS Genet 4:e1000255
Dohrmann AB, Kuting M, Junemann S, Jaenicke S, Schluter A, Tebbe CC Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of
(2013) Importance of rare taxa for bacterial diversity in the rhizo- metagenomic data. Genome Res 17:377–386
sphere of Bt- and conventional maize varieties. ISME J 7:37–49 Ivanova EP, Mikhailov VV (2001) A new family, Alteromonadaceae fam.
Excoffier L, Laval G, Schneider S (2007) Arlequin (version 3.0): An nov., including marine Proteobacteria of the genera Alteromonas,
integrated software package for population genetics data analysis. Pseudoalteromonas, Idiomarina,and Colwellia. Microbiology 70:
Evol Bioinforma 1:47–50 10–17
Excoffier L, Smouse PE, Quattro M (1992) Analysis of molecular vari- Jin HM, Lee HJ, Kim JM, Park MS, Lee K, Jeon CO (2011)
ance inferred from metric distances among DNA haplotypes: appli- Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy
cation to human mitochondrial DNA restriction data. Genetics 131: beach. Int J Syst Evol Bacteriol 61:1392–1396
479–491 Lee K-B, Liu C-T, Anzai Y, Kim H, Aono T, Oyaizu H (2005) The
Figueira D, Barata M (2007) Marine fungi from two sandy beaches in hierarchical system of the Alphaproteobacteria: description of
Portugal. Mycologia 99:20–23 Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and
Fuerst JA, Sagulenko E (2011) Beyond the bacterium: planctomycetes Erythrobacteraceae fam. nov. Int J Syst Evol Bacteriol 55:1907–
challenge our concepts of microbial structure and function. Nat Rev 1919
Micro 9:403–413 Ludwig B, Geisseler D, Michel K, Joergensen RG, Schulz E, Merbach I,
Gerber GK, Onderdonk AB, Bry L (2012) Inferring dynamic signatures Raupp J, Rauber R, Hu K, Niu L, Liu X (2011) Effects of fertiliza-
of microbes in complex host ecosystems. PLoS Comput Biol 8: tion and soil management on crop yields and carbon stabilization in
e1002624 soils. A review. Agron Sustain Dev 31:361–372
Giuntini E, Bazzicalupo M, Castaldini M, Fabiani A, Miclaus N, Piccolo McLachlan A, Brown A (2006) The ecology of sandy shores. Elsevier,
R, Ranalli G, Santomassimo F, Zanobini S, Mengoni A (2006) Amsterdam
Genetic diversity of dinitrogen-fixing bacterial communities in soil Mengoni A, Bazzicalupo M (2002) The statistical treatment of data and
amended with olive husks. Ann Microbiol 56:83–88 the analysis of MOlecular VAriance (AMOVA) in molecular micro-
Glavin DP, Cleaves HJ, Schubert M, Aubrey A, Bada JL (2004) New bial ecology. Ann Microbiol 52:95–101
method for estimating bacterial cell abundances in natural samples Mengoni A, Pini F, Huang L-N, Shu W-S, Bazzicalupo M (2009) Plant-
by use of sublimation. Appl Environ Microbiol 70:5923–5928 by-plant variations of bacterial communities associated with leaves
Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, Fernandes AD, of the nickel-hyperaccumulator Alyssum bertolonii Desv. Microb
MacPhee R, Reid G (2010) Microbiome profiling by illumina Ecol 58:660–667
sequencing of combinatorial sequence-tagged PCR products. Mengoni A, Tatti E, Decorosi F, Viti C, Bazzicalupo M, Giovannetti L
PLoS ONE 5:e15406 (2005) Comparison of 16S rRNA and 16S rDNA T-RFLP ap-
Gobet A, Böer SI, Huse SM, Van Beusekom JEE, Quince C, Sogin ML, proaches to study bacterial communities in soil microcosms treated
Boetius A, Ramette A (2012) Diversity and dynamics of rare and of with chromate as perturbing agent. Microb Ecol 50:375–384
resident bacterial populations in coastal sands. ISME J 6:542–553 Misic C, Fabiano M (2005) Enzymatic activity on sandy beaches of the
Gorbushina AA, Broughton WJ (2009) Microbiology of the atmosphere- Ligurian Sea (NW Mediterranean). Microb Ecol 49:513–522
rock interface: How biological interactions and physical stresses Mizrahi-Man O, Davenport ER, Gilad Y (2013) Taxonomic classification
modulate a sophisticated microbial ecosystem. Annu Rev of bacterial 16S rRNA genes using short sequencing reads: evalua-
Microbiol 63:431–450 tion of effective study designs. PLoS ONE 8:e53608
Green-Garcìa AM, Engel AS (2012) Bacterial diversity of siliciclastic Mudryk ZJ (2005) Occurrence and distribution antibiotic resistance of
sediments in a Thalassia testudinum meadow and the implications heterotrophic bacteria isolated from a marine beach. Mar Pollut Bull
for Lucinisca nassula chemosymbiosis. Estuar Coast Shelf Sci 112: 50:80–86
153–161 Musat N, Werner U, Knittel K, Kolb S, Dodenhof T, van Beusekom JEE,
Haaijer SCM, Ji K, Van Niftrik L, Hoischen A, Speth DR, Jetten MSM, de Beer D, Dubilier N, Amann R (2006) Microbial community
Sinninghe Damsté JS, Op Den Camp HJM (2013) A novel marine structure of sandy intertidal sediments in the North Sea, Sylt-
nitrite-oxidizing Nitrospira species from Dutch coastal North Sea Rømø Basin, Wadden Sea. Syst Appl Microbiol 29:333–348
water. Front Microbiol 4:60 Pastorelli R, Landi S, Trabelsi D, Piccolo R, Mengoni A, Bazzicalupo M,
Hallberg K, Hedrich S, Johnson D (2011) Acidiferrobacter thiooxydans Pagliai M (2011) Effects of soil management on structure and
gen. nov. sp. nov.; an acidophilic, thermo-tolerant, facultatively activity of denitrifying bacterial communities. Appl Soil Ecol 49:
anaerobic iron- and sulfur-oxidizer of the family 49–58
Ectothiorhodospiraceae. Extremophiles 15:271–279 Pini F, Frascella A, Santopolo L, Bazzicalupo M, Biondi E, Scotti C,
Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statis- Mengoni A (2012) Exploring the plant-associated bacterial commu-
tics software package for education and data analysis. Palaeontol nities in Medicago sativa L. BMC Microbiol 12:78
Electron 41:9 Pukall R, Buntefuss D, Fruhling A, Rohde M, Kroppenstedt RM,
Head KH (1984) Manual of soil laboratory testing. Vol 1: soil classifica- Burghardt J, Lebaron P, Bernard L, Stackebrandt E (1999)
tion and compaction tests. ELE International Ltd, London Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing mem-
Hill TCJ, Walsh KA, Harris JA, Moffett BF (2003) Using ecological ber of the α-Proteobacteria. Int J Syst Bacteriol 49:513–519
diversity measures with bacterial communities. FEMS Microbiol Rich JJ, Heichen RS, Bottomley PJ, Cromack K, Myrold DD (2003)
Ecol 43:1–11 Community composition and functioning of denitrifying bacteria