Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Crump, Byron C.; Wojahn, John M.; Tomas, Fiona; Mueller, Ryan S.

doi:10.3389/fmicb.2018.00388

Title: Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Journal Article · 15 March 2018 · Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2018.00388 · OSTI ID:1628164

Crump, Byron C. ^[1]; Wojahn, John M. ^[1]; Tomas, Fiona ^[2]; Mueller, Ryan S. ^[3]

Oregon State Univ., Corvallis, OR (United States). College of Earth, Ocean and Atmospheric Sciences
Oregon State Univ., Corvallis, OR (United States). Dept. of Fisheries and Wildlife; Universitat de les Illes Balears (UIB), Esporles (Spain). Instituto Mediterraneo de Estudios Avanzados (IMEDEA). Consejo Superior de Investigaciones Cientificas (CSIC)
Oregon State Univ., Corvallis, OR (United States). Dept. of Mircobiology

Terrestrial plants benefit from many well-understood mutualistic relationships with root and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Oregon State Univ., Corvallis, OR (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1628164

Journal Information:: Frontiers in Microbiology, Vol. 9; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

References (201)

Photosynthetic responses of eelgrass (Zostera marina L.) to light and sediment sulfide in a shallow barrier island lagoon Goodman, Jill L.; Moore, Kenneth A.; Dennison, William C. Aquatic Botany, Vol. 50, Issue 1 https://doi.org/10.1016/0304-3770(94)00444-q	journal	April 1995
Prokaryotic sulfur oxidation Friedrich, Cornelius G.; Bardischewsky, Frank; Rother, Dagmar Current Opinion in Microbiology, Vol. 8, Issue 3 https://doi.org/10.1016/j.mib.2005.04.005	journal	June 2005
Sulfide Intrusion and Detoxification in the Seagrass Zostera marina Hasler-Sheetal, Harald; Holmer, Marianne PLOS ONE, Vol. 10, Issue 6 https://doi.org/10.1371/journal.pone.0129136	journal	June 2015
Competitive Interactions in Mixed-Species Biofilms Containing the Marine Bacterium Pseudoalteromonas tunicata Rao, Dhana; Webb, Jeremy S.; Kjelleberg, Staffan Applied and Environmental Microbiology, Vol. 71, Issue 4 https://doi.org/10.1128/aem.71.4.1729-1736.2005	journal	April 2005
Ecosystem services returned through seagrass restoration: Restoration of ecosystem services Reynolds, Laura K.; Waycott, Michelle; McGlathery, Karen J. Restoration Ecology, Vol. 24, Issue 5 https://doi.org/10.1111/rec.12360	journal	April 2016
Granulosicoccus coccoides sp. nov., isolated from leaves of seagrass (Zostera marina) Kurilenko, Valerie V.; Christen, Richard; Zhukova, Natalia V. International Journal of Systematic and Evolutionary Microbiology, Vol. 60, Issue 4 https://doi.org/10.1099/ijs.0.013516-0	journal	April 2010
Overview of the physiological ecology of carbon metabolism in seagrasses Touchette, Brant W.; Burkholder, JoAnn M. Journal of Experimental Marine Biology and Ecology, Vol. 250, Issue 1-2 https://doi.org/10.1016/s0022-0981(00)00196-9	journal	July 2000
Marine epibiosis. I. Fouling and antifouling: some basic aspects Wahl, M. Marine Ecology Progress Series, Vol. 58 https://doi.org/10.3354/meps058175	journal	January 1989
A native plant growth promoting bacterium, Bacillus sp. B55, rescues growth performance of an ethylene-insensitive plant genotype in nature Meldau, Dorothea G.; Long, Hoang H.; Baldwin, Ian T. Frontiers in Plant Science, Vol. 3 https://doi.org/10.3389/fpls.2012.00112	journal	January 2012
Biosynthesis of Organic Compounds Emitted by Plants Kreuzwieser, J.; Schnitzler, J. -P.; Steinbrecher, R. Plant Biology, Vol. 1, Issue 2 https://doi.org/10.1111/j.1438-8677.1999.tb00238.x	journal	March 1999
Simiduia curdlanivorans sp. nov., a curdlan-degrading bacterium isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Simiduia Park, Sooyeon; Kim, Soo-In; Jung, Yong-Taek International Journal of Systematic and Evolutionary Microbiology, Vol. 64, Issue Pt_11 https://doi.org/10.1099/ijs.0.065334-0	journal	November 2014
Spatial and temporal patterns in abundance of two intertidal seagrasses, Zostera americana den hartog and Zostera marina L. Harrison, Paul Garth Aquatic Botany, Vol. 12 https://doi.org/10.1016/0304-3770(82)90024-9	journal	January 1982
Vanishing Seagrass (Zostera marina, L.) in Swedish Coastal Waters Baden, Susanne; Gullström, Martin; Lundén, Bengt AMBIO: A Journal of the Human Environment, Vol. 32, Issue 5 https://doi.org/10.1579/0044-7447-32.5.374	journal	August 2003
Factors influencing the growth of seagrass seedlings: A case study of Posidonia australis Glasby, Tim M.; Taylor, Skye L.; Housefield, Graham P. Aquatic Botany, Vol. 120 https://doi.org/10.1016/j.aquabot.2014.09.003	journal	January 2015
Habitat-specific distinctions in estuarine denitrification affect both ecosystem function and services Piehler, M. F.; Smyth, A. R. Ecosphere, Vol. 2, Issue 1 https://doi.org/10.1890/es10-00082.1	journal	January 2011
Methanol Emission from Leaves (Enzymatic Detection of Gas-Phase Methanol and Relation of Methanol Fluxes to Stomatal Conductance and Leaf Development) Nemecek-Marshall, M.; MacDonald, R. C.; Franzen, J. J. Plant Physiology, Vol. 108, Issue 4 https://doi.org/10.1104/pp.108.4.1359	journal	August 1995
Methanol:coenzyme M methyltransferase from Methanosarcina barkeri -- substitution of the corrinoid harbouring subunit MtaC by free cob(I)alamin : Substitution of Sauer, Karin; Thauer, Rudolf K. European Journal of Biochemistry, Vol. 261, Issue 3 https://doi.org/10.1046/j.1432-1327.1999.00355.x	journal	May 1999
Epiphytic bacterial communities on two common submerged macrophytes in Taihu Lake: diversity and host-specificity He, Dan; Ren, Lijuan; Wu, Qinglong Chinese Journal of Oceanology and Limnology, Vol. 30, Issue 2 https://doi.org/10.1007/s00343-012-1084-0	journal	March 2012
Bacterial biosynthesis of indole-3-acetic acid Patten, Cheryl L.; Glick, Bernard R. Canadian Journal of Microbiology, Vol. 42, Issue 3 https://doi.org/10.1139/m96-032	journal	March 1996
Complete genome sequence of Arcobacter nitrofigilis type strain (CIT) Pati, Amrita; Gronow, Sabine; Lapidus, Alla Standards in Genomic Sciences, Vol. 2, Issue 3 https://doi.org/10.4056/sigs.912121	journal	June 2010
Denitrification, nitrogen fixation, community primary productivity and inorganic-N and oxygen fluxes in an intertidal Zostera noltii meadow Welsh, Dt; Bartoli, M.; Nizzoli, D. Marine Ecology Progress Series, Vol. 208 https://doi.org/10.3354/meps208065	journal	January 2000
Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific Cúcio, Catarina; Engelen, Aschwin H.; Costa, Rodrigo Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00440	journal	March 2016
The balance between nitrogen fixation and denitrification on vegetated and non-vegetated intertidal sediments: Nitrogen cycling in intertidal seagrass meadows Russell, Douglas G.; Warry, F. Y.; Cook, Perran L. M. Limnology and Oceanography, Vol. 61, Issue 6 https://doi.org/10.1002/lno.10353	journal	July 2016
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system Chen, I-Min A.; Markowitz, Victor M.; Palaniappan, Krishna BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2629-y	journal	April 2016
Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes Marzano, Shin-Yi Lee; Domier, Leslie L. Virus Research, Vol. 213 https://doi.org/10.1016/j.virusres.2015.11.002	journal	February 2016
Effects of epibiotic bacteria on leaf growth and epiphytes of the seagrass Posidonia oceanica Celdrán, D.; Espinosa, E.; Sánchez-Amat, A. Marine Ecology Progress Series, Vol. 456 https://doi.org/10.3354/meps09672	journal	June 2012
The enhancement of plant growth by free-living bacteria Glick, Bernard R. Canadian Journal of Microbiology, Vol. 41, Issue 2 https://doi.org/10.1139/m95-015	journal	February 1995
The rhizosphere microbiome and plant health Berendsen, Roeland L.; Pieterse, Corné M. J.; Bakker, Peter A. H. M. Trends in Plant Science, Vol. 17, Issue 8 https://doi.org/10.1016/j.tplants.2012.04.001	journal	August 2012
Molecular diversity of diazotrophs in oligotrophic tropical seagrass bed communities Bagwell, Christopher E.; Rocque, Jeannine R.; Smith, Garriett W. FEMS Microbiology Ecology, Vol. 39, Issue 2 https://doi.org/10.1111/j.1574-6941.2002.tb00912.x	journal	February 2002
Ethanol-Induced Injuries to Carrot Cells: The Role of Acetaldehyde Perata, Pierdomenico; Alpi, Amedeo Plant Physiology, Vol. 95, Issue 3 https://doi.org/10.1104/pp.95.3.748	journal	March 1991
Denitrification, N-fixation and nitrogen and phosphorus fluxes in different benthic habitats and their contribution to the nitrogen and phosphorus budgets of a shallow oligotrophic sub-tropical coastal system (southern Moreton Bay, Australia) Eyre, Bradley D.; Ferguson, Angus J. P.; Webb, Arthur Biogeochemistry, Vol. 102, Issue 1-3 https://doi.org/10.1007/s10533-010-9425-6	journal	March 2010
Sedimenticola thiotaurini sp. nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens Jones, Daniel S.; Bailey, Jake V.; Flood, Beverly E. International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 8 https://doi.org/10.1099/ijs.0.000295	journal	August 2015
Indole-3-acetic acid production by pink-pigmented facultative methylotrophic bacteria Omer, Z. S.; Tombolini, R.; Broberg, A. Plant Growth Regulation, Vol. 43, Issue 1 https://doi.org/10.1023/B:GROW.0000038360.09079.ad	journal	May 2004
MONOAMINE OXIDASE: From Genes to Behavior Shih, J. C.; Chen, K.; Ridd, M. J. Annual Review of Neuroscience, Vol. 22, Issue 1 https://doi.org/10.1146/annurev.neuro.22.1.197	journal	March 1999
A novel hydrogen oxidizer amidst the sulfur-oxidizing Thiomicrospira lineage Hansen, Moritz; Perner, Mirjam The ISME Journal, Vol. 9, Issue 3 https://doi.org/10.1038/ismej.2014.173	journal	September 2014
Sulphide intrusion in eelgrass (Zostera marina L.) Pedersen, O.; Binzer, T.; Borum, J. Plant, Cell and Environment, Vol. 27, Issue 5 https://doi.org/10.1111/j.1365-3040.2004.01173.x	journal	May 2004
A Model For the Lowering of Plant Ethylene Concentrations by Plant Growth-promoting Bacteria Glick, Bernard R.; Penrose, Donna M.; Li, Jiping Journal of Theoretical Biology, Vol. 190, Issue 1 https://doi.org/10.1006/jtbi.1997.0532	journal	January 1998
Integrative analysis of environmental sequences using MEGAN4 Huson, D. H.; Mitra, S.; Ruscheweyh, H. -J. Genome Research, Vol. 21, Issue 9 https://doi.org/10.1101/gr.120618.111	journal	June 2011
Phylogenetic Analysis of Bacterial Communities Associated with Leaves of the Seagrass Halophila stipulacea by a Culture-Independent Small-Subunit rRNA Gene Approach Weidner, S.; Arnold, W.; Stackebrandt, E. Microbial Ecology, Vol. 39, Issue 1 https://doi.org/10.1007/s002489900194	journal	January 2000
Science and Management of the Introduced Seagrass Zostera japonica in North America Shafer, Deborah J.; Kaldy, James E.; Gaeckle, Jeffrey L. Environmental Management, Vol. 53, Issue 1 https://doi.org/10.1007/s00267-013-0172-z	journal	October 2013
Generation and possible roles of NO in plant roots and their apoplastic space Stohr, C. Journal of Experimental Botany, Vol. 53, Issue 379 https://doi.org/10.1093/jxb/erf110	journal	December 2002
Algicidal and growth-inhibiting bacteria associated with seagrass and macroalgae beds in Puget Sound, WA, USA Inaba, Nobuharu; Trainer, Vera L.; Onishi, Yuka Harmful Algae, Vol. 62 https://doi.org/10.1016/j.hal.2016.04.004	journal	February 2017
Eutrophication in shallow coastal bays and lagoons: the role of plants in the coastal filter McGlathery, Kj; Sundbäck, K.; Anderson, Ic Marine Ecology Progress Series, Vol. 348 https://doi.org/10.3354/meps07132	journal	October 2007
An Earth-system perspective of the global nitrogen cycle Gruber, Nicolas; Galloway, James N. Nature, Vol. 451, Issue 7176 https://doi.org/10.1038/nature06592	journal	January 2008
Nitrogen fixation in the rhizosphere of marine angiosperms Patriquin, D.; Knowles, R. Marine Biology, Vol. 16, Issue 1 https://doi.org/10.1007/bf00347847	journal	September 1972
Cloning and Characterization of a Novel Agarase from a Newly Isolated Bacterium Simiduia sp. Strain TM-2 Able to Degrade Various Seaweeds Tawara, Mika; Sakatoku, Akihiro; Tiodjio, Rosine E. Applied Biochemistry and Biotechnology, Vol. 177, Issue 3 https://doi.org/10.1007/s12010-015-1765-1	journal	July 2015
Granulosicoccus coccoides sp. nov., isolated from leaves of seagrass (Zostera marina) Kurilenko, Valerie V.; Christen, Richard; Zhukova, Natalia V. International Journal of Systematic and Evolutionary Microbiology, Vol. 60, Issue 4 https://doi.org/10.1099/ijs.0.013516-0	journal	April 2010
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system Chen, I-Min A.; Markowitz, Victor M.; Palaniappan, Krishna BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2629-y	journal	April 2016
Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species Cao, Hieu X.; Schmutzer, Thomas; Scholz, Uwe Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00526	journal	July 2015
Differences in Bacterial Community Structure on Hydrilla verticillata and Vallisneria americana in a Freshwater Spring Gordon-Bradley, Nadine; Lymperopoulou, Despoina S.; Williams, Henry Neal Microbes and Environments, Vol. 29, Issue 1 https://doi.org/10.1264/jsme2.ME13064	journal	January 2014
Two Potential Indole-3-Acetaldehyde Dehydrogenases in the Phytopathogenic Fungus Ustilago maydis Basse, Christoph W.; Lottspeich, Friedrich; Steglich, Wolfgang European Journal of Biochemistry, Vol. 242, Issue 3 https://doi.org/10.1111/j.1432-1033.1996.0648r.x	journal	December 1996
Illumina-based analysis the microbial diversity associated with Thalassia hemprichii in Xincun Bay, South China Sea Jiang, Yu-Feng; Ling, Juan; Dong, Jun-De Ecotoxicology, Vol. 24, Issue 7-8 https://doi.org/10.1007/s10646-015-1511-z	journal	June 2015
Ethylene production and decomposition in soils Zechmeister-Boltenstern, S.; Smith, Keith A. Biology and Fertility of Soils, Vol. 26, Issue 4 https://doi.org/10.1007/s003740050388	journal	April 1998
A Three-Stage Symbiosis Forms the Foundation of Seagrass Ecosystems van der Heide, T.; Govers, L. L.; de Fouw, J. Science, Vol. 336, Issue 6087 https://doi.org/10.1126/science.1219973	journal	June 2012
Investigation of the role of a β(1–4) agarase produced by Pseudoalteromonas gracilis B9 in eliciting disease symptoms in the red alga Gracilaria gracilis Schroeder, Declan C.; Jaffer, Mohamed A.; Coyne, Vernon E. Microbiology, Vol. 149, Issue 10 https://doi.org/10.1099/mic.0.26513-0	journal	October 2003
Coastal Ecosystems: A Critical Element of Risk Reduction: Coastal ecosystems and risk reduction Spalding, Mark D.; McIvor, Anna L.; Beck, Michael W. Conservation Letters, Vol. 7, Issue 3 https://doi.org/10.1111/conl.12074	journal	November 2013
Microbial interactions and biocontrol in the rhizosphere Whipps, John M. Journal of Experimental Botany, Vol. 52, Issue suppl_1 https://doi.org/10.1093/jxb/52.suppl_1.487	journal	March 2001
Habitat-specific distinctions in estuarine denitrification affect both ecosystem function and services Piehler, M. F.; Smyth, A. R. Ecosphere, Vol. 2, Issue 1 https://doi.org/10.1890/es10-00082.1	journal	January 2011
Relationship between productivity and N ₂ (C ₂ H ₂ ) fixation in a Thalassia testudinum community1: Productivity and N ₂ fixation Capone, Douglas G.; Penhale, Polly A.; Oremland, Ronald S. Limnology and Oceanography, Vol. 24, Issue 1 https://doi.org/10.4319/lo.1979.24.1.0117	journal	January 1979
Distinct pattern of zeatin distribution in the shoot apical meristem marks stress conditions in Posidonia oceanica (L.) Delile plants Bruno, A.; Petrarulo, M.; Salimonti, A. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, Vol. 143, Issue 1 https://doi.org/10.1080/11263500802633220	journal	March 2009
Ethanol-Induced Injuries to Carrot Cells: The Role of Acetaldehyde Perata, Pierdomenico; Alpi, Amedeo Plant Physiology, Vol. 95, Issue 3 https://doi.org/10.1104/pp.95.3.748	journal	March 1991
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A. The ISME Journal, Vol. 6, Issue 8 https://doi.org/10.1038/ismej.2012.8	journal	March 2012
Marine epibiosis. I. Fouling and antifouling: some basic aspects Wahl, M. Marine Ecology Progress Series, Vol. 58 https://doi.org/10.3354/meps058175	journal	January 1989
Different niches of the Halophila stipulacea seagrass bed harbor distinct populations of nitrogen fixing bacteria Pereg, L. L.; Lipkin, Y.; Sar, N. Marine Biology, Vol. 119, Issue 3 https://doi.org/10.1007/BF00347529	journal	June 1994
Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Weidner, S.; Arnold, W.; Puhler, A. Applied and environmental microbiology, Vol. 62, Issue 3 https://doi.org/10.1128/aem.62.3.766-771.1996	journal	January 1996
Competitive Interactions in Mixed-Species Biofilms Containing the Marine Bacterium Pseudoalteromonas tunicata Rao, Dhana; Webb, Jeremy S.; Kjelleberg, Staffan Applied and Environmental Microbiology, Vol. 71, Issue 4 https://doi.org/10.1128/aem.71.4.1729-1736.2005	journal	April 2005
Photosynthetic responses of eelgrass (Zostera marina L.) to light and sediment sulfide in a shallow barrier island lagoon Goodman, Jill L.; Moore, Kenneth A.; Dennison, William C. Aquatic Botany, Vol. 50, Issue 1 https://doi.org/10.1016/0304-3770(94)00444-q	journal	April 1995
Expansion of seagrass habitat by the exotic Zostera lapontca. and its use by dabbling ducks and brant in Boundary Bay, British Columbia Baldwin, Jr; Loworn, Jr Marine Ecology Progress Series, Vol. 103 https://doi.org/10.3354/meps103119	journal	January 1994
UPARSE: highly accurate OTU sequences from microbial amplicon reads Edgar, Robert C. Nature Methods, Vol. 10, Issue 10 https://doi.org/10.1038/nmeth.2604	journal	August 2013
Temperate Wetland Methanogenesis: The Importance of Vegetation Type and Root Ethanol Production Williams, Christopher J.; Yavitt, Joseph B. Soil Science Society of America Journal, Vol. 74, Issue 1 https://doi.org/10.2136/sssaj2008.0395	journal	January 2010
Molecular cloning in Escherichia coli, expression, and nucleotide sequence of the gene for the ethylene-forming enzyme of Pseudomonas syringae pv. phaseolicola PK2 Fukuda, Hideo; Ogawa, Takahira; Ishihara, Katsuya Biochemical and Biophysical Research Communications, Vol. 188, Issue 2 https://doi.org/10.1016/0006-291x(92)91131-9	journal	October 1992
Impact of light limitation on seagrasses Ralph, P. J.; Durako, M. J.; Enríquez, S. Journal of Experimental Marine Biology and Ecology, Vol. 350, Issue 1-2 https://doi.org/10.1016/j.jembe.2007.06.017	journal	November 2007
Role of Methylotrophy During Symbiosis Between Methylobacterium nodulans and Crotalaria podocarpa Jourand, Philippe; Renier, Adeline; Rapior, Sylvie Molecular Plant-Microbe Interactions®, Vol. 18, Issue 10 https://doi.org/10.1094/mpmi-18-1061	journal	October 2005
The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines Han, Yuchen; Perner, Mirjam Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00989	journal	September 2015
Different bacterial communities associated with the roots and bulk sediment of the seagrass Zostera marina: Zostera marina: root-associated bacteria Jensen, Sheila Ingemann; KÃ¼hl, Michael; PriemÃ©, Anders FEMS Microbiology Ecology, Vol. 62, Issue 1 https://doi.org/10.1111/j.1574-6941.2007.00373.x	journal	October 2007
Effects of anaerobiosis on root metabolism of Zostera marina (eelgrass): implications for survival in reducing sediments Smith, R. D.; Pregnall, A. M.; Alberte, R. S. Marine Biology, Vol. 98, Issue 1 https://doi.org/10.1007/bf00392668	journal	May 1988
In vitro culture of the seagrass Halophila decipiens Bird, Kimon T.; Johnson, Jennifer R.; Jewett-Smith, Jerilyn Aquatic Botany, Vol. 60, Issue 4 https://doi.org/10.1016/S0304-3770(97)00093-4	journal	April 1998
Nitrogen fixation in the rhizosphere of marine angiosperms Patriquin, D.; Knowles, R. Marine Biology, Vol. 16, Issue 1 https://doi.org/10.1007/bf00347847	journal	September 1972
Seagrass landscapes and their effects on associated fauna: A review Boström, Christoffer; Jackson, Emma L.; Simenstad, Charles A. Estuarine, Coastal and Shelf Science, Vol. 68, Issue 3-4 https://doi.org/10.1016/j.ecss.2006.01.026	journal	July 2006
Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes Marzano, Shin-Yi Lee; Domier, Leslie L. Virus Research, Vol. 213 https://doi.org/10.1016/j.virusres.2015.11.002	journal	February 2016
Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria Amin, S. A.; Hmelo, L. R.; van Tol, H. M. Nature, Vol. 522, Issue 7554 https://doi.org/10.1038/nature14488	journal	May 2015
Eutrophication in shallow coastal bays and lagoons: the role of plants in the coastal filter McGlathery, Kj; Sundbäck, K.; Anderson, Ic Marine Ecology Progress Series, Vol. 348 https://doi.org/10.3354/meps07132	journal	October 2007
CHARACTERIZATION AND COMPARISON OF PROKARYOTIC EPIPHYTES ASSOCIATED WITH THREE EAST AFRICAN SEAGRASSES ¹ Uku, Jacqueline; Björk, Mats; Bergman, Birgitta Journal of Phycology, Vol. 43, Issue 4 https://doi.org/10.1111/j.1529-8817.2007.00371.x	journal	August 2007
The plant microbiome Turner, Thomas R.; James, Euan K.; Poole, Philip S. Genome Biology, Vol. 14, Issue 6 https://doi.org/10.1186/gb-2013-14-6-209	journal	June 2013
The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea Olsen, Jeanine L.; Rouzé, Pierre; Verhelst, Bram Nature, Vol. 530, Issue 7590 https://doi.org/10.1038/nature16548	journal	January 2016
C YTOKININ M ETABOLISM AND A CTION Mok, David WS; Mok, Machteld C. Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 52, Issue 1 https://doi.org/10.1146/annurev.arplant.52.1.89	journal	June 2001
Effects of epibiotic bacteria on leaf growth and epiphytes of the seagrass Posidonia oceanica Celdrán, D.; Espinosa, E.; Sánchez-Amat, A. Marine Ecology Progress Series, Vol. 456 https://doi.org/10.3354/meps09672	journal	June 2012
Ribo-Zero Gold Kit: improved RNA-seq results after removal of cytoplasmic and mitochondrial ribosomal RNA Benes, Vladimir; Blake, Jonathon; Doyle, Ken Nature Methods, Vol. 8, Issue 11 https://doi.org/10.1038/nmeth.f.352	journal	October 2011
Sulphide intrusion in eelgrass (Zostera marina L.) Pedersen, O.; Binzer, T.; Borum, J. Plant, Cell and Environment, Vol. 27, Issue 5 https://doi.org/10.1111/j.1365-3040.2004.01173.x	journal	May 2004
Simiduia curdlanivorans sp. nov., a curdlan-degrading bacterium isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Simiduia Park, Sooyeon; Kim, Soo-In; Jung, Yong-Taek International Journal of Systematic and Evolutionary Microbiology, Vol. 64, Issue Pt_11 https://doi.org/10.1099/ijs.0.065334-0	journal	November 2014
High rates of microbial dinitrogen fixation and sulfate reduction associated with the Mediterranean seagrass Posidonia oceanica Lehnen, Nadine; Marchant, Hannah K.; Schwedt, Anne Systematic and Applied Microbiology, Vol. 39, Issue 7 https://doi.org/10.1016/j.syapm.2016.08.004	journal	October 2016
Phylogenetic Analysis of Bacterial Communities Associated with Leaves of the Seagrass Halophila stipulacea by a Culture-Independent Small-Subunit rRNA Gene Approach Weidner, S.; Arnold, W.; Stackebrandt, E. Microbial Ecology, Vol. 39, Issue 1 https://doi.org/10.1007/s002489900194	journal	January 2000
Assessing the ecological status of seagrasses using morphology, biochemical descriptors and microbial community analyses. A study in Halophila stipulacea (Forsk.) Aschers meadows in the northern Red Sea Mejia, Astrid Y.; Rotini, Alice; Lacasella, Federica Ecological Indicators, Vol. 60 https://doi.org/10.1016/j.ecolind.2015.09.014	journal	January 2016
Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis Husnik, Filip; Nikoh, Naruo; Koga, Ryuichi Cell, Vol. 153, Issue 7 https://doi.org/10.1016/j.cell.2013.05.040	journal	June 2013
The human gene for diamine oxidase, an amiloride binding protein. Molecular cloning, sequencing, and characterization of the promoter. Chassande, O.; Renard, S.; Barbry, P. Journal of Biological Chemistry, Vol. 269, Issue 20 https://doi.org/10.1016/s0021-9258(17)36648-6	journal	May 1994
Soil beneficial bacteria and their role in plant growth promotion: a review Hayat, Rifat; Ali, Safdar; Amara, Ummay Annals of Microbiology, Vol. 60, Issue 4 https://doi.org/10.1007/s13213-010-0117-1	journal	August 2010
Reconciling the incompatible: N2 fixation And O2 Gallon, J. R. New Phytologist, Vol. 122, Issue 4 https://doi.org/10.1111/j.1469-8137.1992.tb00087.x	journal	December 1992
Denitrification, N-fixation and nitrogen and phosphorus fluxes in different benthic habitats and their contribution to the nitrogen and phosphorus budgets of a shallow oligotrophic sub-tropical coastal system (southern Moreton Bay, Australia) Eyre, Bradley D.; Ferguson, Angus J. P.; Webb, Arthur Biogeochemistry, Vol. 102, Issue 1-3 https://doi.org/10.1007/s10533-010-9425-6	journal	March 2010
Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics Poretsky, Rachel S.; Gifford, Scott; Rinta-Kanto, Johanna Journal of Visualized Experiments, Issue 0 https://doi.org/10.3791/1086	journal	January 2009
Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient Fortunato, Caroline S.; Crump, Byron C. PLOS ONE, Vol. 10, Issue 11 https://doi.org/10.1371/journal.pone.0140578	journal	November 2015
Distinct pattern of zeatin distribution in the shoot apical meristem marks stress conditions in Posidonia oceanica (L.) Delile plants Bruno, A.; Petrarulo, M.; Salimonti, A. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, Vol. 143, Issue 1 https://doi.org/10.1080/11263500802633220	journal	March 2009
Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis Husnik, Filip; Nikoh, Naruo; Koga, Ryuichi Cell, Vol. 153, Issue 7 https://doi.org/10.1016/j.cell.2013.05.040	journal	June 2013
Promotion of Plant Growth by Bacterial ACC Deaminase Glick, Bernard R.; Todorovic, Biljana; Czarny, Jennifer Critical Reviews in Plant Sciences, Vol. 26, Issue 5-6 https://doi.org/10.1080/07352680701572966	journal	October 2007
Expansion of seagrass habitat by the exotic Zostera lapontca. and its use by dabbling ducks and brant in Boundary Bay, British Columbia Baldwin, Jr; Loworn, Jr Marine Ecology Progress Series, Vol. 103 https://doi.org/10.3354/meps103119	journal	January 1994
Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species Cao, Hieu X.; Schmutzer, Thomas; Scholz, Uwe Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00526	journal	July 2015
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples Wagner, Günter P.; Kin, Koryu; Lynch, Vincent J. Theory in Biosciences, Vol. 131, Issue 4 https://doi.org/10.1007/s12064-012-0162-3	journal	August 2012
Microbial interactions and biocontrol in the rhizosphere Whipps, John M. Journal of Experimental Botany, Vol. 52, Issue suppl_1 https://doi.org/10.1093/jxb/52.suppl_1.487	journal	March 2001
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Li, Dinghua; Liu, Chi-Man; Luo, Ruibang Bioinformatics, Vol. 31, Issue 10 https://doi.org/10.1093/bioinformatics/btv033	journal	January 2015
The effect of flooding on the exchange of the volatile C₂-compounds ethanol, acetaldehyde and acetic acid between leaves of Amazonian floodplain tree species and the atmosphere Rottenberger, S.; Kleiss, B.; Kuhn, U. Biogeosciences, Vol. 5, Issue 4 https://doi.org/10.5194/bg-5-1085-2008	journal	January 2008
Investigation of the role of a β(1–4) agarase produced by Pseudoalteromonas gracilis B9 in eliciting disease symptoms in the red alga Gracilaria gracilis Schroeder, Declan C.; Jaffer, Mohamed A.; Coyne, Vernon E. Microbiology, Vol. 149, Issue 10 https://doi.org/10.1099/mic.0.26513-0	journal	October 2003
Reconciling the incompatible: N2 fixation And O2 Gallon, J. R. New Phytologist, Vol. 122, Issue 4 https://doi.org/10.1111/j.1469-8137.1992.tb00087.x	journal	December 1992
Nitrogen cycling in two temperate Zostera marina beds:seasonal variation Risgaard-Petersen, N.; Ottosen, Ldm Marine Ecology Progress Series, Vol. 198 https://doi.org/10.3354/meps198093	journal	January 2000
Rhizobacterial mediation of plant hormone status Dodd, I. C.; Zinovkina, N. Y.; Safronova, V. I. Annals of Applied Biology, Vol. 157, Issue 3 https://doi.org/10.1111/j.1744-7348.2010.00439.x	journal	October 2010
Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase Watanabe, Tomohiro; Kojima, Hisaya; Fukui, Manabu Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep36262	journal	November 2016
High rates of microbial dinitrogen fixation and sulfate reduction associated with the Mediterranean seagrass Posidonia oceanica Lehnen, Nadine; Marchant, Hannah K.; Schwedt, Anne Systematic and Applied Microbiology, Vol. 39, Issue 7 https://doi.org/10.1016/j.syapm.2016.08.004	journal	October 2016
Overexpression of bacterial ethylene-forming enzyme gene in Trichoderma reesei enhanced the production of ethylene Chen, Xi; Liang, Yong; Hua, Jing International Journal of Biological Sciences https://doi.org/10.7150/ijbs.6.96	journal	January 2010
Illumina-based analysis the microbial diversity associated with Thalassia hemprichii in Xincun Bay, South China Sea Jiang, Yu-Feng; Ling, Juan; Dong, Jun-De Ecotoxicology, Vol. 24, Issue 7-8 https://doi.org/10.1007/s10646-015-1511-z	journal	June 2015
Generation and possible roles of NO in plant roots and their apoplastic space Stohr, C. Journal of Experimental Botany, Vol. 53, Issue 379 https://doi.org/10.1093/jxb/erf110	journal	December 2002
AtIPT3 is a Key Determinant of Nitrate-Dependent Cytokinin Biosynthesis in Arabidopsis Takei, Kentaro; Ueda, Nanae; Aoki, Koh Plant and Cell Physiology, Vol. 45, Issue 8 https://doi.org/10.1093/pcp/pch119	journal	August 2004
Molecular diversity of diazotrophs in oligotrophic tropical seagrass bed communities Bagwell, Christopher E.; Rocque, Jeannine R.; Smith, Garriett W. FEMS Microbiology Ecology, Vol. 39, Issue 2 https://doi.org/10.1111/j.1574-6941.2002.tb00912.x	journal	February 2002
Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge Ettinger, Cassandra L.; Voerman, Sofie E.; Lang, Jenna M. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3246	journal	January 2017
Seagrass landscapes and their effects on associated fauna: A review Boström, Christoffer; Jackson, Emma L.; Simenstad, Charles A. Estuarine, Coastal and Shelf Science, Vol. 68, Issue 3-4 https://doi.org/10.1016/j.ecss.2006.01.026	journal	July 2006
Molecular cloning in Escherichia coli, expression, and nucleotide sequence of the gene for the ethylene-forming enzyme of Pseudomonas syringae pv. phaseolicola PK2 Fukuda, Hideo; Ogawa, Takahira; Ishihara, Katsuya Biochemical and Biophysical Research Communications, Vol. 188, Issue 2 https://doi.org/10.1016/0006-291x(92)91131-9	journal	October 1992
Molecular interaction between Methylobacterium extorquens and seedlings: growth promotion, methanol consumption, and localization of the methanol emission site Abanda-Nkpwatt, D.; Musch, M.; Tschiersch, J. Journal of Experimental Botany, Vol. 57, Issue 15 https://doi.org/10.1093/jxb/erl173	journal	November 2006
Different bacterial communities associated with the roots and bulk sediment of the seagrass Zostera marina: Zostera marina: root-associated bacteria Jensen, Sheila Ingemann; KÃ¼hl, Michael; PriemÃ©, Anders FEMS Microbiology Ecology, Vol. 62, Issue 1 https://doi.org/10.1111/j.1574-6941.2007.00373.x	journal	October 2007
Effects of some plant growth regulators on the growth of the seagrass Cymodocea nodosa (Ucria) Ascherson Muñoz, Jorge Terrados Aquatic Botany, Vol. 51, Issue 3-4 https://doi.org/10.1016/0304-3770(95)00481-E	journal	August 1995
Temperate Wetland Methanogenesis: The Importance of Vegetation Type and Root Ethanol Production Williams, Christopher J.; Yavitt, Joseph B. Soil Science Society of America Journal, Vol. 74, Issue 1 https://doi.org/10.2136/sssaj2008.0395	journal	January 2010
Role of Methylotrophy During Symbiosis Between Methylobacterium nodulans and Crotalaria podocarpa Jourand, Philippe; Renier, Adeline; Rapior, Sylvie Molecular Plant-Microbe Interactions®, Vol. 18, Issue 10 https://doi.org/10.1094/mpmi-18-1061	journal	October 2005
Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics Stewart, Frank J.; Ottesen, Elizabeth A.; DeLong, Edward F. The ISME Journal, Vol. 4, Issue 7 https://doi.org/10.1038/ismej.2010.18	journal	March 2010
Epiphytic bacterial communities on two common submerged macrophytes in Taihu Lake: diversity and host-specificity He, Dan; Ren, Lijuan; Wu, Qinglong Chinese Journal of Oceanology and Limnology, Vol. 30, Issue 2 https://doi.org/10.1007/s00343-012-1084-0	journal	March 2012
Sedimenticola thiotaurini sp. nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens Jones, Daniel S.; Bailey, Jake V.; Flood, Beverly E. International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 8 https://doi.org/10.1099/ijs.0.000295	journal	August 2015
Soil beneficial bacteria and their role in plant growth promotion: a review Hayat, Rifat; Ali, Safdar; Amara, Ummay Annals of Microbiology, Vol. 60, Issue 4 https://doi.org/10.1007/s13213-010-0117-1	journal	August 2010
Attached Bacterial Populations Shared by Four Species of Aquatic Angiosperms Crump, Byron C.; Koch, Evamaria W. Applied and Environmental Microbiology, Vol. 74, Issue 19 https://doi.org/10.1128/aem.00952-08	journal	August 2008
Denitrification, nitrogen fixation, community primary productivity and inorganic-N and oxygen fluxes in an intertidal Zostera noltii meadow Welsh, Dt; Bartoli, M.; Nizzoli, D. Marine Ecology Progress Series, Vol. 208 https://doi.org/10.3354/meps208065	journal	January 2000
Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics Poretsky, Rachel S.; Gifford, Scott; Rinta-Kanto, Johanna Journal of Visualized Experiments, Issue 0 https://doi.org/10.3791/1086	journal	January 2009
The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines Han, Yuchen; Perner, Mirjam Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00989	journal	September 2015
QIIME allows analysis of high-throughput community sequencing data Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse Nature Methods, Vol. 7, Issue 5 https://doi.org/10.1038/nmeth.f.303	journal	April 2010
Impact of light limitation on seagrasses Ralph, P. J.; Durako, M. J.; Enríquez, S. Journal of Experimental Marine Biology and Ecology, Vol. 350, Issue 1-2 https://doi.org/10.1016/j.jembe.2007.06.017	journal	November 2007
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Li, Dinghua; Liu, Chi-Man; Luo, Ruibang Bioinformatics, Vol. 31, Issue 10 https://doi.org/10.1093/bioinformatics/btv033	journal	January 2015
Biosynthesis of Organic Compounds Emitted by Plants Kreuzwieser, J.; Schnitzler, J. -P.; Steinbrecher, R. Plant Biology, Vol. 1, Issue 2 https://doi.org/10.1111/j.1438-8677.1999.tb00238.x	journal	March 1999
Bacterioplankton Community Shifts in an Arctic Lake Correlate with Seasonal Changes in Organic Matter Source Crump, B. C.; Kling, G. W.; Bahr, M. Applied and Environmental Microbiology, Vol. 69, Issue 4 https://doi.org/10.1128/AEM.69.4.2253-2268.2003	journal	April 2003
Spatial and temporal patterns in abundance of two intertidal seagrasses, Zostera americana den hartog and Zostera marina L. Harrison, Paul Garth Aquatic Botany, Vol. 12 https://doi.org/10.1016/0304-3770(82)90024-9	journal	January 1982
Rhizobacterial mediation of plant hormone status Dodd, I. C.; Zinovkina, N. Y.; Safronova, V. I. Annals of Applied Biology, Vol. 157, Issue 3 https://doi.org/10.1111/j.1744-7348.2010.00439.x	journal	October 2010
Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network Golicz, Agnieszka A.; Schliep, Martin; Lee, Huey Tyng Journal of Experimental Botany, Vol. 66, Issue 5 https://doi.org/10.1093/jxb/eru510	journal	January 2015
Plant host habitat and root exudates shape soil bacterial community structure Haichar, Feth el Zahar; Marol, Christine; Berge, Odile The ISME Journal, Vol. 2, Issue 12 https://doi.org/10.1038/ismej.2008.80	journal	August 2008
Relationship between productivity and N ₂ (C ₂ H ₂ ) fixation in a Thalassia testudinum community1: Productivity and N ₂ fixation Capone, Douglas G.; Penhale, Polly A.; Oremland, Ronald S. Limnology and Oceanography, Vol. 24, Issue 1 https://doi.org/10.4319/lo.1979.24.1.0117	journal	January 1979
Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge Ettinger, Cassandra L.; Voerman, Sofie E.; Lang, Jenna M. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3246	journal	January 2017
Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria Kloepper, Joseph W.; Leong, John; Teintze, Martin Nature, Vol. 286, Issue 5776 https://doi.org/10.1038/286885a0	journal	August 1980
Nitrogen fixation associated with four species of submerged angiosperms in the central Chesapeake bay Lipschultz, Fredric; Cunningham, Jeffrey J.; Court Stevenson, J. Estuarine and Coastal Marine Science, Vol. 9, Issue 6 https://doi.org/10.1016/S0302-3524(79)80014-6	journal	December 1979
Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria Amin, S. A.; Hmelo, L. R.; van Tol, H. M. Nature, Vol. 522, Issue 7554 https://doi.org/10.1038/nature14488	journal	May 2015
Distribution and Evolution of Nitrogen Fixation Genes in the Phylum Bacteroidetes Inoue, Jun-ichi; Oshima, Kenshiro; Suda, Wataru Microbes and environments, Vol. 30, Issue 1 https://doi.org/10.1264/jsme2.ME14142	journal	January 2015
The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea Olsen, Jeanine L.; Rouzé, Pierre; Verhelst, Bram Nature, Vol. 530, Issue 7590 https://doi.org/10.1038/nature16548	journal	January 2016
C YTOKININ M ETABOLISM AND A CTION Mok, David WS; Mok, Machteld C. Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 52, Issue 1 https://doi.org/10.1146/annurev.arplant.52.1.89	journal	June 2001
Methanol Emission from Leaves (Enzymatic Detection of Gas-Phase Methanol and Relation of Methanol Fluxes to Stomatal Conductance and Leaf Development) Nemecek-Marshall, M.; MacDonald, R. C.; Franzen, J. J. Plant Physiology, Vol. 108, Issue 4 https://doi.org/10.1104/pp.108.4.1359	journal	August 1995
Sulfide Intrusion and Detoxification in the Seagrass Zostera marina Hasler-Sheetal, Harald; Holmer, Marianne PLOS ONE, Vol. 10, Issue 6 https://doi.org/10.1371/journal.pone.0129136	journal	June 2015
Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi Hughes, Riley L.; Arnold, Charles D.; Young, Rebecca R. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-71922-x	journal	September 2020
Microbial Communities and Their Interactions in Soil and Rhizosphere Ecosystems Kent, Angela D.; Triplett, Eric W. Annual Review of Microbiology, Vol. 56, Issue 1 https://doi.org/10.1146/annurev.micro.56.012302.161120	journal	October 2002
Microbial life in the phyllosphere Vorholt, Julia A. Nature Reviews Microbiology, Vol. 10, Issue 12 https://doi.org/10.1038/nrmicro2910	journal	November 2012
T-DNA of Agrobacterium tumefaciens encodes an enzyme of cytokinin biosynthesis. Akiyoshi, D. E.; Klee, H.; Amasino, R. M. Proceedings of the National Academy of Sciences, Vol. 81, Issue 19 https://doi.org/10.1073/pnas.81.19.5994	journal	October 1984
Prokaryotic sulfur oxidation Friedrich, Cornelius G.; Bardischewsky, Frank; Rother, Dagmar Current Opinion in Microbiology, Vol. 8, Issue 3 https://doi.org/10.1016/j.mib.2005.04.005	journal	June 2005
The balance between nitrogen fixation and denitrification on vegetated and non-vegetated intertidal sediments: Nitrogen cycling in intertidal seagrass meadows Russell, Douglas G.; Warry, F. Y.; Cook, Perran L. M. Limnology and Oceanography, Vol. 61, Issue 6 https://doi.org/10.1002/lno.10353	journal	July 2016
Complete genome sequence of Arcobacter nitrofigilis type strain (CIT) Pati, Amrita; Gronow, Sabine; Lapidus, Alla Standards in Genomic Sciences, Vol. 2, Issue 3 https://doi.org/10.4056/sigs.912121	journal	June 2010
Nitrogen Fixation by Epiphytes on sea Grasses1 Goering, J. J.; Parker, P. L. Limnology and Oceanography, Vol. 17, Issue 2 https://doi.org/10.4319/lo.1972.17.2.0320	journal	March 1972
Bacterial biosynthesis of indole-3-acetic acid Patten, Cheryl L.; Glick, Bernard R. Canadian Journal of Microbiology, Vol. 42, Issue 3 https://doi.org/10.1139/m96-032	journal	March 1996
Assessing the ecological status of seagrasses using morphology, biochemical descriptors and microbial community analyses. A study in Halophila stipulacea (Forsk.) Aschers meadows in the northern Red Sea Mejia, Astrid Y.; Rotini, Alice; Lacasella, Federica Ecological Indicators, Vol. 60 https://doi.org/10.1016/j.ecolind.2015.09.014	journal	January 2016
An Earth-system perspective of the global nitrogen cycle Gruber, Nicolas; Galloway, James N. Nature, Vol. 451, Issue 7176 https://doi.org/10.1038/nature06592	journal	January 2008
Indole-3-acetic acid in microbial and microorganism-plant signaling Spaepen, Stijn; Vanderleyden, Jos; Remans, Roseline FEMS Microbiology Reviews, Vol. 31, Issue 4 https://doi.org/10.1111/j.1574-6976.2007.00072.x	journal	July 2007
Microbial Communities and Their Interactions in Soil and Rhizosphere Ecosystems Kent, Angela D.; Triplett, Eric W. Annual Review of Microbiology, Vol. 56, Issue 1 https://doi.org/10.1146/annurev.micro.56.012302.161120	journal	October 2002
Ribo-Zero Gold Kit: improved RNA-seq results after removal of cytoplasmic and mitochondrial ribosomal RNA Benes, Vladimir; Blake, Jonathon; Doyle, Ken Nature Methods, Vol. 8, Issue 11 https://doi.org/10.1038/nmeth.f.352	journal	October 2011
Methanol:coenzyme M methyltransferase from Methanosarcina barkeri -- substitution of the corrinoid harbouring subunit MtaC by free cob(I)alamin : Substitution of Sauer, Karin; Thauer, Rudolf K. European Journal of Biochemistry, Vol. 261, Issue 3 https://doi.org/10.1046/j.1432-1327.1999.00355.x	journal	May 1999
Eelgrass Leaf Surface Microbiomes Are Locally Variable and Highly Correlated with Epibiotic Eukaryotes Bengtsson, Mia M.; Bühler, Anton; Brauer, Anne Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01312	journal	July 2017
Algicidal and growth-inhibiting bacteria associated with seagrass and macroalgae beds in Puget Sound, WA, USA Inaba, Nobuharu; Trainer, Vera L.; Onishi, Yuka Harmful Algae, Vol. 62 https://doi.org/10.1016/j.hal.2016.04.004	journal	February 2017
Plant host habitat and root exudates shape soil bacterial community structure Haichar, Feth el Zahar; Marol, Christine; Berge, Odile The ISME Journal, Vol. 2, Issue 12 https://doi.org/10.1038/ismej.2008.80	journal	August 2008
Methylobacterium-plant interaction genes regulated by plant exudate and quorum sensing molecules Dourado, Manuella Nóbrega; Bogas, Andrea Cristina; Pomini, Armando M. Brazilian Journal of Microbiology, Vol. 44, Issue 4 https://doi.org/10.1590/S1517-83822013000400044	journal	January 2013
The plant microbiome Turner, Thomas R.; James, Euan K.; Poole, Philip S. Genome Biology, Vol. 14, Issue 6 https://doi.org/10.1186/gb-2013-14-6-209	journal	June 2013
Ecosystem services returned through seagrass restoration: Restoration of ecosystem services Reynolds, Laura K.; Waycott, Michelle; McGlathery, Karen J. Restoration Ecology, Vol. 24, Issue 5 https://doi.org/10.1111/rec.12360	journal	April 2016
Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient Fortunato, Caroline S.; Crump, Byron C. PLOS ONE, Vol. 10, Issue 11 https://doi.org/10.1371/journal.pone.0140578	journal	November 2015
Molecular interaction between Methylobacterium extorquens and seedlings: growth promotion, methanol consumption, and localization of the methanol emission site Abanda-Nkpwatt, D.; Musch, M.; Tschiersch, J. Journal of Experimental Botany, Vol. 57, Issue 15 https://doi.org/10.1093/jxb/erl173	journal	November 2006
Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics Stewart, Frank J.; Ottesen, Elizabeth A.; DeLong, Edward F. The ISME Journal, Vol. 4, Issue 7 https://doi.org/10.1038/ismej.2010.18	journal	March 2010
Cloning and Characterization of a Novel Agarase from a Newly Isolated Bacterium Simiduia sp. Strain TM-2 Able to Degrade Various Seaweeds Tawara, Mika; Sakatoku, Akihiro; Tiodjio, Rosine E. Applied Biochemistry and Biotechnology, Vol. 177, Issue 3 https://doi.org/10.1007/s12010-015-1765-1	journal	July 2015
The enhancement of plant growth by free-living bacteria Glick, Bernard R. Canadian Journal of Microbiology, Vol. 41, Issue 2 https://doi.org/10.1139/m95-015	journal	February 1995
Science and Management of the Introduced Seagrass Zostera japonica in North America Shafer, Deborah J.; Kaldy, James E.; Gaeckle, Jeffrey L. Environmental Management, Vol. 53, Issue 1 https://doi.org/10.1007/s00267-013-0172-z	journal	October 2013
Effects of anaerobiosis on root metabolism of Zostera marina (eelgrass): implications for survival in reducing sediments Smith, R. D.; Pregnall, A. M.; Alberte, R. S. Marine Biology, Vol. 98, Issue 1 https://doi.org/10.1007/bf00392668	journal	May 1988
A Model For the Lowering of Plant Ethylene Concentrations by Plant Growth-promoting Bacteria Glick, Bernard R.; Penrose, Donna M.; Li, Jiping Journal of Theoretical Biology, Vol. 190, Issue 1 https://doi.org/10.1006/jtbi.1997.0532	journal	January 1998
The rhizosphere microbiome and plant health Berendsen, Roeland L.; Pieterse, Corné M. J.; Bakker, Peter A. H. M. Trends in Plant Science, Vol. 17, Issue 8 https://doi.org/10.1016/j.tplants.2012.04.001	journal	August 2012
A Three-Stage Symbiosis Forms the Foundation of Seagrass Ecosystems van der Heide, T.; Govers, L. L.; de Fouw, J. Science, Vol. 336, Issue 6087 https://doi.org/10.1126/science.1219973	journal	June 2012
MONOAMINE OXIDASE: From Genes to Behavior Shih, J. C.; Chen, K.; Ridd, M. J. Annual Review of Neuroscience, Vol. 22, Issue 1 https://doi.org/10.1146/annurev.neuro.22.1.197	journal	March 1999
Integrative analysis of environmental sequences using MEGAN4 Huson, D. H.; Mitra, S.; Ruscheweyh, H. -J. Genome Research, Vol. 21, Issue 9 https://doi.org/10.1101/gr.120618.111	journal	June 2011
Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase Watanabe, Tomohiro; Kojima, Hisaya; Fukui, Manabu Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep36262	journal	November 2016
AtIPT3 is a Key Determinant of Nitrate-Dependent Cytokinin Biosynthesis in Arabidopsis Takei, Kentaro; Ueda, Nanae; Aoki, Koh Plant and Cell Physiology, Vol. 45, Issue 8 https://doi.org/10.1093/pcp/pch119	journal	August 2004
Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network Golicz, Agnieszka A.; Schliep, Martin; Lee, Huey Tyng Journal of Experimental Botany, Vol. 66, Issue 5 https://doi.org/10.1093/jxb/eru510	journal	January 2015
Promotion of Plant Growth by Bacterial ACC Deaminase Glick, Bernard R.; Todorovic, Biljana; Czarny, Jennifer Critical Reviews in Plant Sciences, Vol. 26, Issue 5-6 https://doi.org/10.1080/07352680701572966	journal	October 2007
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A. The ISME Journal, Vol. 6, Issue 8 https://doi.org/10.1038/ismej.2012.8	journal	March 2012
Biological Control in the Phyllosphere Andrews, John H. Annual Review of Phytopathology, Vol. 30, Issue 1 https://doi.org/10.1146/annurev.py.30.090192.003131	journal	September 1992
Two Potential Indole-3-Acetaldehyde Dehydrogenases in the Phytopathogenic Fungus Ustilago maydis Basse, Christoph W.; Lottspeich, Friedrich; Steglich, Wolfgang European Journal of Biochemistry, Vol. 242, Issue 3 https://doi.org/10.1111/j.1432-1033.1996.0648r.x	journal	December 1996
Beyond Light: Physical, Geological, and Geochemical Parameters as Possible Submersed Aquatic Vegetation Habitat Requirements Koch, Evamaria W. Estuaries, Vol. 24, Issue 1 https://doi.org/10.2307/1352808	journal	February 2001
Vanishing Seagrass (Zostera marina, L.) in Swedish Coastal Waters Baden, Susanne; Gullström, Martin; Lundén, Bengt AMBIO: A Journal of the Human Environment, Vol. 32, Issue 5 https://doi.org/10.1579/0044-7447-32.5.374	journal	August 2003
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples Wagner, Günter P.; Kin, Koryu; Lynch, Vincent J. Theory in Biosciences, Vol. 131, Issue 4 https://doi.org/10.1007/s12064-012-0162-3	journal	August 2012
Ethylene production and decomposition in soils Zechmeister-Boltenstern, S.; Smith, Keith A. Biology and Fertility of Soils, Vol. 26, Issue 4 https://doi.org/10.1007/s003740050388	journal	April 1998
Nitric Oxide: A Multitasked Signaling Gas in Plants Domingos, Patricia; Prado, Ana Margarida; Wong, Aloysius Molecular Plant, Vol. 8, Issue 4 https://doi.org/10.1016/j.molp.2014.12.010	journal	April 2015
Coastal Ecosystems: A Critical Element of Risk Reduction: Coastal ecosystems and risk reduction Spalding, Mark D.; McIvor, Anna L.; Beck, Michael W. Conservation Letters, Vol. 7, Issue 3 https://doi.org/10.1111/conl.12074	journal	November 2013

Cited By (7)

Advances and Challenges in Metatranscriptomic Analysis Shakya, Migun; Lo, Chien-Chi; Chain, Patrick S. G. Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00904	journal	September 2019
Advances and Challenges in Metatranscriptomic Analysis Singh, Anushka; Vats, Siddharth; Bhargava, Prachi Microbial Metatranscriptomics Belowground https://doi.org/10.1007/978-981-15-9758-9_21	book	January 2021
Advances and Challenges in Metatranscriptomic Analysis Shakya, Migun; Lo, Chien-Chi; Chain, Patrick S. G. Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00904	journal	September 2019
Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota Chialva, Matteo; Ghignone, Stefano; Novero, Mara Microorganisms, Vol. 8, Issue 1 https://doi.org/10.3390/microorganisms8010038	journal	December 2019
Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome Hurtado-McCormick, Valentina; Kahlke, Tim; Petrou, Katherina Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01011	journal	May 2019
Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota Chialva, Matteo; Ghignone, Stefano; Novero, Mara Microorganisms, Vol. 8, Issue 1 https://doi.org/10.3390/microorganisms8010038	journal	December 2019
Climate Change Impacts on Seagrass Meadows and Macroalgal Forests: An Integrative Perspective on Acclimation and Adaptation Potential Duarte, Bernardo; Martins, Irene; Rosa, Rui Frontiers in Marine Science, Vol. 5 https://doi.org/10.3389/fmars.2018.00190	journal	June 2018