Where less may be more: how the rare biosphere pulls ecosystems strings

Aanderud, 2015, Resuscitation of the rare biosphere contributes to pulses of ecosystem activity, Front Microbiol, 6, 24, 10.3389/fmicb.2015.00024

Ai, 2013, Migration and niche partitioning simultaneously increase species richness and rarity, Ecol Model, 258, 33, 10.1016/j.ecolmodel.2013.03.001

Allan, 2011, More diverse plant communities have higher functioning over time due to turnover in complementary dominant species, Proc Natl Acad Sci USA, 108, 17034, 10.1073/pnas.1104015108

Barberán, 2014, Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria, Ecol Lett, 17, 794, 10.1111/ele.12282

Baumann, 2013, Soil microbial diversity affects soil organic matter decomposition in a silty grassland soil, Biochemistry, 114, 201

Bittinger, 2014, Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing, Genome Biol, 15, 487, 10.1186/s13059-014-0487-y

Bodelier, 2013, Microbial minorities modulate methane consumption through niche partitioning, ISME J, 7, 2214, 10.1038/ismej.2013.99

Brown, 2015, Unusual biology across a group comprising more than 15% of domain bacteria, Nature, 523, 208, 10.1038/nature14486

Campbell, 2011, Activity of abundant and rare bacteria in a coastal ocean, Proc Natl Acad Sci USA, 108, 12776, 10.1073/pnas.1101405108

Chambers, 2016, Effects of salinity and inundation on microbial community structure and function in a mangrove peat soil, Wetlands, 36, 361, 10.1007/s13157-016-0745-8

Chen, 2010, When metagenomics meets stable-isotope probing: progress and perspectives, Trends Microbiol, 18, 157, 10.1016/j.tim.2010.02.002

Debroas, 2015, Evidence for an active rare biosphere within freshwater protists community, Mol Ecol, 24, 1236, 10.1111/mec.13116

Delgado-Baquerizo, 2016, Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning, J Ecol, 104, 936, 10.1111/1365-2745.12585

Dell’Anno, 2012, High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments, Environ Pollut, 167, 85, 10.1016/j.envpol.2012.03.043

Dimitriu, 2010, An evaluation of the functional significance of peat microorganisms using a reciprocal transplant approach, Soil Biol Biochem, 42, 65, 10.1016/j.soilbio.2009.10.001

Falkowski, 2008, The microbial engines that drive Earth’s biogeochemical cycles, Science, 320, 1034, 10.1126/science.1153213

Fetzer, 2015, The extent of functional redundancy changes as species’ roles shift in different environments, Proc Natl Acad Sci USA, 112, 14888, 10.1073/pnas.1505587112

Franklin, 2001, Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments, Appl Environ Microbiol, 67, 702, 10.1128/AEM.67.2.702-712.2001

Franklin, 2006, Structural and functional responses of a sewage microbial community to dilution-induced reductions in diversity, Microb Ecol, 52, 280, 10.1007/s00248-006-9033-0

Freilich, 2011, Competitive and cooperative metabolic interactions in bacterial communities, Nat Commun, 2, 589, 10.1038/ncomms1597

Fuentes, 2014, Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications, Appl Microbiol Biotechnol, 98, 4781, 10.1007/s00253-014-5684-9

Fukami, 2003, Productivity-biodiversity relationships depend on the history of community assembly, Nature, 424, 423, 10.1038/nature01785

Gagic, 2015, Improving the genetic representation of rare taxa within complex microbial communities using DNA normalization methods, Mol Ecol Res, 15, 464, 10.1111/1755-0998.12321

Garbeva, 2011, Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors, ISME J, 5, 973, 10.1038/ismej.2010.196

García-Fernández, 2004, Streamlined regulation and gene loss as adaptive mechanisms in Prochlorococcus for optimized nitrogen utilization in oligotrophic environments, Microbiol Mol Biol Rev, 68, 630, 10.1128/MMBR.68.4.630-638.2004

Garland, 1999, Survival of human-associated bacteria in prototype advanced life support systems, SAE Techical paper 1999-01-2061, American Society of Automotive Engineers, 10.4271/1999-01-2061

Gaston, 2008, Biodiversity and extinction: the importance of being common, Prog Phys Geogr, 32, 73, 10.1177/0309133308089499

Giebler, 2013, Alkane-degrading bacteria at the soil-litter interface: comparing isolates with T-RFLP-based community profiles, FEMS Microbiol Ecol, 86, 45, 10.1111/1574-6941.12097

Gobet, 2012, Diversity and dynamics of rare and of resident bacterial populations in coastal sands, ISME J, 6, 542, 10.1038/ismej.2011.132

Griffiths, 2001, An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities, Soil Biol Biochem, 33, 1713, 10.1016/S0038-0717(01)00094-3

Griffiths, 2004, The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil, Microb Ecol, 47, 104, 10.1007/s00248-002-2043-7

Gudelj, 2010, An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure, Ecol Lett, 13, 1073, 10.1111/j.1461-0248.2010.01507.x

Guss, 2011, Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis, ISME J, 5, 20, 10.1038/ismej.2010.88

Hajishengallis, 2011, Low-abundance biofilm species orchestrates inflammatory periodontal disease through the commensal microbiota and complement, Cell Host Microbe, 10, 497, 10.1016/j.chom.2011.10.006

Haruta, 2009, Intertwined interspecies relationships: approaches to untangle the microbial network, Environ Microbiol, 11, 2963, 10.1111/j.1462-2920.2009.01956.x

Hausmann, 2016, Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms, ISME J, 10, 2365, 10.1038/ismej.2016.42

Hedlund, 2014, Impact of single-cell genomics and metagenomics on the emerging view of extremophile ‘microbial dark matter’, Extremophiles, 18, 865, 10.1007/s00792-014-0664-7

Helliwell, 2013, Widespread decay of vitamin-related pathways: coincidence or consequence?, Trends Genet, 29, 469, 10.1016/j.tig.2013.03.003

Hernandez-Raquet, 2013, Impact of microbial diversity depletion on xenobiotic degradation by sewage-activated sludge, Environ Microbiol Rep, 5, 588, 10.1111/1758-2229.12053

Herrera, 1989, Pollinator abundance, morphology, and flower visitation rate - analysis of the quantity component in a plant-pollinator system, Oecologia, 80, 241, 10.1007/BF00380158

Hol, 2010, Reduction of rare soil microbes modifies plant-herbivores interactions, Ecol Lett, 13, 292, 10.1111/j.1461-0248.2009.01424.x

Hol, 2015, Context dependency and saturating effects of loss of rare soil microbes on plant productivity, Front Plant Sci, 6, 485, 10.3389/fpls.2015.00485

Hol, 2015, Non-random species loss in bacterial communities reduces antifungal volatile production, Ecology, 96, 2042, 10.1890/14-2359.1

Hua, 2015, Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics, ISME J, 9, 1280, 10.1038/ismej.2014.212

Jimenez, 2014, Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion, Appl Microbiol Biotechnol, 98, 2789, 10.1007/s00253-013-5253-7

Jousset, 2009, Predators promote defence of rhizosphere bacterial populations by selective feeding on non-toxic cheaters, ISME J, 3, 666, 10.1038/ismej.2009.26

Jousset, 2013, Evolutionary history predicts the stability of cooperation in microbial communities, Nat Commun, 4, 2573, 10.1038/ncomms3573

Kummerli, 2010, Molecular and regulatory properties of a public good shape the evolution of cooperation, Proc Natl Acad Sci USA, 107, 18921, 10.1073/pnas.1011154107

Leitão, 2016, Rare species contribute disproportionately to the functional structure of species assemblages, Proc R Soc Lond Ser B Biol Sci, 283, 20160084, 10.1098/rspb.2016.0084

Li, 2008, Simultaneous analysis of microbial identity and function using NanoSIMS, Environ Microbiol, 10, 580, 10.1111/j.1462-2920.2007.01478.x

Locey, 2016, Scaling laws predict global microbial diversity, Proc Natl Acad Sci USA, 113, 5970, 10.1073/pnas.1521291113

Low-Décarie, 2015, Community rescue in experimental metacommunities, Proc Natl Acad Sci USA, 112, 14307, 10.1073/pnas.1513125112

Loy, 2010, Geomicrobiology: Molecular and Environmental Perspective, 127, 10.1007/978-90-481-9204-5_6

Lynch, 2015, Ecology and exploration of the rare biosphere, Nat Rev Microbiol, 13, 217, 10.1038/nrmicro3400

Lyons, 2005, Rare species and ecosystem functioning, Conserv Biol, 19, 1019, 10.1111/j.1523-1739.2005.00106.x

Mallon, 2015, Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities, Ecology, 96, 915, 10.1890/14-1001.1

Matos, 2005, Effects of microbial community diversity on the survival of Pseudomonas aeruginosa in the wheat rhizosphere, Microb Ecol, 49, 257, 10.1007/s00248-004-0179-3

McMurdie, 2014, Waste not, want not: why rarefying microbiome data is inadmissible, PLoS Comp Biol, 10, e1003531, 10.1371/journal.pcbi.1003531

Mee, 2014, Syntrophic exchange in synthetic microbial communities, Proc Natl Acad Sci USA, 111, 2149, 10.1073/pnas.1405641111

Meyer, 2007, The effects of competition and predation on diversification in a model adaptive radiation, Nature, 446, 432, 10.1038/nature05599

Mouillot, 2013, Rare species support vulnerable functions in high diversity ecosystems, PLoS Biol, 11, 11, 10.1371/journal.pbio.1001569

Musat, 2008, A single-cell view on the ecophysiology of anaerobic phototrophic bacteria, Proc Natl Acad Sci USA, 105, 17861, 10.1073/pnas.0809329105

Narisawa, 2008, Coexistence of antibiotic-producing and antibiotic-sensitive bacteria in biofilms is mediated by resistant bacteria, Appl Environ Microbiol, 74, 3887, 10.1128/AEM.02497-07

Nemergut, 2011, Global patterns in the biogeography of bacterial taxa, Environ Microbiol, 13, 135, 10.1111/j.1462-2920.2010.02315.x

Nipperess, 2013, The mean and variance of phylogenetic diversity under rarefaction, Methods Ecol Evol, 4, 566, 10.1111/2041-210X.12042

Nuccio, 2016, Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass, Ecology, 97, 1307, 10.1890/15-0882.1

Panaud, 2016, Horizontal transfers of transposable elements in eukaryotes: the flying genes, C R Biol, 339, 296, 10.1016/j.crvi.2016.04.013

Pedrós-Alió, 2007, Dipping into the rare biosphere, Science, 315, 192, 10.1126/science.1135933

Pester, 2010, A ‘rare biosphere’ microorganism contributes to sulfate reduction in a peatland, ISME J, 4, 1591, 10.1038/ismej.2010.75

Peter, 2011, Function-specific response to depletion of microbial diversity, ISME J, 5, 351, 10.1038/ismej.2010.119

Philippot, 2013, Loss in microbial diversity affects nitrogen cycling in soil, ISME J, 7, 1609, 10.1038/ismej.2013.34

Podar, 2007, Targeted access to the genomes of low-abundance organisms in complex microbial communities, Appl Environ Microbiol, 73, 3205, 10.1128/AEM.02985-06

Portillo, 2013, Cell size distributions of soil bacterial and archaeal taxa, Appl Environ Microbiol, 79, 7610, 10.1128/AEM.02710-13

Rabinowitz, 1981, The Biological Aspects of Rare Plant Conservation, 205

Reid, 2011, The Rare Biosphere, 1

Rodrigues, 2013, Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities, Proc Natl Acad Sci USA, 110, 988, 10.1073/pnas.1220608110

Rodriguez-Valera, 2009, Explaining microbial population genomics through phage predation, Nat Rev Microbiol, 7, 828, 10.1038/nrmicro2235

Rousk, 2009, Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization, Appl Environ Microbiol, 75, 1589, 10.1128/AEM.02775-08

Russell, 2014, Nature’s microbiome: introduction, Mol Ecol, 23, 1225, 10.1111/mec.12676

Salonius, 1981, Metabolic capabilities of forest soil microbial-populations with reduced species-diversity, Soil Biol Biochem, 13, 1, 10.1016/0038-0717(81)90094-8

Sanchez, 2004, A previously unexposed forest soil microbial community degrades high levels of the pollutant 2,4,6-trichlorophenol, Appl Environ Microbiol, 70, 7567, 10.1128/AEM.70.12.7567-7570.2004

Schadt, 2015, Comment on “Global diversity and geography of soil fungi”, Science, 348, 1438, 10.1126/science.aaa4269

Schluter, 2015, Adhesion as a weapon in microbial competition, ISME J, 9, 139, 10.1038/ismej.2014.174

Shade, 2014, Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity, Mbio, 5, e01371, 10.1128/mBio.01371-14

Sogin, 2006, Microbial diversity in the deep sea and the underexplored “rare biosphere”, Proc Natl Acad Sci USA, 103, 12115, 10.1073/pnas.0605127103

Soliveres, 2016, Locally rare species influence grassland ecosystem multifunctionality, Philos Trans R Soc Lond Ser B Biol Sci, 371, 20150269, 10.1098/rstb.2015.0269

Stecher, 2013, Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle, FEMS Microbiol Rev, 37, 793, 10.1111/1574-6976.12024

Steger, 2011, Microorganisms with novel dissimilatory (bi)sulfite reductase genes are widespread and part of the core microbiota in low-sulfate peatlands, Appl Environ Microbiol, 77, 1231, 10.1128/AEM.01352-10

Tardy, 2014, Stability of soil microbial structure and activity depends on microbial diversity, Environ Microbiol Rep, 6, 173, 10.1111/1758-2229.12126

Tedersoo, 2014, Global diversity and geography of soil fungi, Science, 346, 1256688, 10.1126/science.1256688

Van der Gast, 2011, Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities, ISME J, 5, 780, 10.1038/ismej.2010.175

Van Elsas, 2012, Microbial diversity determines the invasion of soil by a bacterial pathogen, Proc Natl Acad Sci USA, 109, 1159, 10.1073/pnas.1109326109

Vivant, 2013, Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil, Plos One, 8, e76991, 10.1371/journal.pone.0076991

Winter, 2010, Trade-offs between competition and defense specialists among unicellular planktonic organisms: the killing the winner hypothesis revisited, Microbiol Mol Biol Rev, 74, 42, 10.1128/MMBR.00034-09

Yachi, 1999, Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis, Proc Natl Acad Sci USA, 96, 1463, 10.1073/pnas.96.4.1463

Yan, 2015, Revisiting the dilution procedure used to manipulate microbial biodiversity in terrestrial systems, Appl Environ Microbiol, 81, 4246, 10.1128/AEM.00958-15

Yenni, 2012, Strong self-limitation promotes the persistence of rare species, Ecology, 93, 456, 10.1890/11-1087.1

Youssef, 2015, Assessing the global phylum level diversity within the bacterial domain: a review, J Adv Res, 6, 269, 10.1016/j.jare.2014.10.005

Zhang, 2009, Quantifying the relative importance of niches and neutrality for coexistence in a model microbial system, Funct Ecol, 23, 1139, 10.1111/j.1365-2435.2009.01579.x