Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants
Abstract
:1. Introduction
2. Case Studies to Search the Actively N2-Fixing Diazotrophs in Non-Legumes
2.1. Detection of Expression of nifH Genes in Young Sugarcane Stems
2.2. Detection of Diazotrophic Methanotrophs in Rice Roots by Metaproteomics
3. Molecular Analyses of Diazotrophs in Non-Legumes
3.1. Endophytic Diazotrophs in Maize Plants
3.2. Endophytic Diazotrophs in Sorghum
3.3. Endophytic Diazotrophs in Switchgrass
3.4. Endophytic Diazotrophs in Sugarcane Plants
3.5. Endophytic Diazotrophs in Sweet Potato Plants
3.6. Diazotrophs Associated with Paddy Rice
4. Distribution and Ecophysiological Characteristics of Rhizobia in Non-Leguminous Plants
5. Ecosystem Functioning of Diazotrophic Methanotrophs
6. Research Perspectives
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Site and Sample of Investigation | Detection of nifH Genes | Close Genus Abundance and Bacteria | |
---|---|---|---|
Stem harvested in six regions in Rio Grande do Sul, Brazil [17] | Sequencing of nifH DNA clones | 27% 20% 12.6% 7.4% 5.4% The others restricted to the stem | Ideonella Azospirillum Klebsiella Herbaspirillum Raoultella Methylosinus, Rhizobium |
Root harvested in six regions in Rio Grande do Sul, Brazil [17] | Sequencing of nifH DNA clones | 30% 23.3% 11.9% The other restricted to the root | Bradyrhizobium Azospirillum Klebsiella Dechloromonas |
Rhizosphere soil collected in six regions in Rio Grande do Sul, Brazil [17] | Sequencing of nifH DNA clones | 20.8% 11% 5% 0.2% The others restricted to the rhizosphere soil | Bradyrhizobium Ideonella Azospirillum Klebsiella Methylocystis, Beijerinckia, Geobacter, Rhodovulum, Methylobacterium, Gluconacetobacter, Methylocella, Delftia |
Site and Sample of Investigation | Detection of nifHDK Genes and Their Proteins | Close Genus (Similarity >91%) Abundance and Bacteria | |
---|---|---|---|
Roots harvested from two sorghum lines (KM1, KM2) at late growth stage in a Fukushima field, Japan [20] | Metagenome for nifHDK genes | 68% (KM1), 88% (KM2) 1–3% (KM1, KM2) | Bradyrhizobium spp. (including B. sp. S23321 and B. oligotrophicum S58T) Azorhizobium sp. |
Proteome for NifHDK proteins | 71% (KM1), 69% (KM2) | Bradyrhizobium spp. (including B. sp. S23321 and B. sp. S58T) | |
Rhizosphere of two cultivars (IPA 1011, IS 5322-C) with low (LF) and high fertilizer (HF) in Cerrado soil, Brazil [19] | Sequencing of nifH DNA clones | In IPA-LF 43% 21% 7% 18% In IPA-HF 29% 10% 16% 7% 8% 5% In IS-LF 42% 10% 10% 13% In IS-HF 39% 23% 11% 10% 13% | Bradyrhizobium sp. B. sp. AF484629 Rhizobium etli Azohydromonas australica Bradyrhizobium sp. B. sp. AF484629 Rhizobium etli Azohydromonas australica Ideonella sp. Burkholderia vietnamiensis Bradyrhizobium sp. B. sp. AF484629 Azohydromonas australica Ideonella sp. Bradyrhizobium sp. B. sp. AF484629 Sinorhizobium sp. Azohydromonas australica Ideonella sp. |
Site and Sample of Investigation | Detection of nifH Genes | Close Genus Abundance and Bacteria | |
---|---|---|---|
Shoots from the tallgrass prairie of northern Oklahoma, USA [21] | Sequencing of nifH DNA clones | 7% 19% 6% 15% 11% 12% 6% 5% 4% 4% 4% | Bradyrhizobium sp. BTAi1 B. sp. MAFF210318 Burkholderia spp. Sphingomonas azotifigens Rhizobium helanshanense Desulfuromonas spp. Azospirillum lipoferum Klebsiella sp. Anaeromyxobacter spp. Geobacter spp. Syntrophobacter fumaroxidans |
Roots from the tallgrass prairie of northern Oklahoma, USA [21] | Sequencing of nifH DNA clones | 9% 12% 18% 17% 21% 13% 14% 6% 1.5% | Bradyrhizobium sp. BTAi1 B. sp. MAFF210318 B. japonicum Burkholderia spp. Sphingomonas azotifigens Anaeromyxobacter spp. Geobacter spp. Methylocystis sp. Methylobacterium nodulans |
RT-PCR amplification of nifH RNA | 10% 36% 13% 7% 9% 15% | Burkholderia spp. Rhizobium helanshanense Desulfuromonas spp. Geobacter spp. Azoarcus sp. BH72 Methylobacterium nodulans |
Site and Sample of Investigation | Detection of nifH Genes | Close Genus Abundance and Bacteria | |
---|---|---|---|
Stems of 8-month-old sugarcane cv. KF92-93, cv. NCo310 and cv. NiF8 grown in Miyako Island, Japan [11] | Sequencing of nifH DNA clones | 100% (KF), 88% (NCo) 73% (NiF) 27% (NiF) | Bradyrhizobium spp. Klebsiella spp. Serratia spp. |
Stems of 50- and 100-day-old sugarcane (cv. NiF8) grown on a commercial soil under high temperature [10] | Sequencing of nifH DNA clones | 22% (50), 19% (100) 17% (50), 16% (100) 19% (50), 19% (100) 15% (50), 13% (100) 22% (50), 13% (100) | Bradyrhizobium sp. BTAi1 B. sp. IRBG230 B. sp. MAFF210318 Azorhizobium caulinodans Rhizobium daejonense |
RT-PCR amplification of nifH RNA | 87% (100) 5% (50), 4% (100) 52% (50) | B sp. IRBG230 B. sp. MAFF210318 Azorhizobium caulinodans | |
Roots of 50- and 100-day-old sugarcane (cv. NiF8) grown on a commercial soil under high temperature [10] | Sequencing of nifH DNA clones | 30% (50), 32% (100) 25% (50), 25% (100) 12% (50), 13% (100) 7% (50), 9% (100) 23% (50), 22% (100) | B. sp. MAFF210318 B. sp. IRBG230, Azorhizobium caulinodans Rhizobium daejonense Beijerinckia derxii |
RT-PCR amplification of nifH RNA | 19% (50) 100% (100) 5% (50) 17% (50) 23% (50) | B. sp. MAFF210318 B. sp. IRBG230, Azorhizobium caulinodans Sinorhizobium fredii Beijerinckia derxii | |
Roots of 59- and 100-day-old sugarcane (cv. NiF8) grown on Ishigaki soil under low temperature [10] | Sequencing of nifH DNA clones | 14% (59), 19% (100) 20% (59), 19% (100) 39% (59), 37% (100) 6% (59), 7% (100) 14% (100) | B. sp. MAFF210318 B. sp. IRBG230, Rhizobium daejonense Methylocystis rosea Methylobacterium sp. |
RT-PCR amplification of nifH RNA | 50% (59), 100%(100) 50% (59) | B. sp. BTAi1 Burkholderia ferrariae | |
Roots of 59- and 100-day-old sugarcane (cv. NiF8) grown on Tanegashima soil under low temperature [10] | Sequencing of nifH DNA clones | 46% (59), 24% (100) 18% (59), 29% (100) 4% (59), 15% (100) 12% (100) 4% (59) 6% (59) | B. sp. MAFF210318 B. sp. IRBG230, B. sp. IRBG228, Methylobacterium nodulans Methylocella silvestris Azonexus caeni |
RT-PCR amplification of nifH RNA | 100% (100) | B. sp. MAFF210318 |
Site and Sample of Investigation | Detection of nifH Genes | Close Genus Abundance and Bacteria | |
---|---|---|---|
Leaf sheath of 6-month-old sugarcane (cv. RB 867515) grown in EMBRAPA without fertilizer and inoculation [41] | Determination of 16S rRNA cDNA sequences | 81% 19% | α-Proteobacteria (mostly Gluconacetobacter) β-Proteobacteria (Burkholderia spp., Herbaspirillum spp.) |
RT-PCR amplification of nifH RNA | 10% 6% 84% | Rhizobium spp. Paraburkholderia tropica Idenella/Herbaspirillum-like bacteria | |
Root of 6-month-old sugarcane (cv. RB 867515) grown in EMBRAPA without fertilizer and inoculation [41] | Determination of 16S rRNA cDNA sequences | 42% 3% 11% 17% 2% 25% | α-Proteobacteria (Rhizobium spp., Bradyrhizobium spp.) β-Proteobacteria δ-Proteobacteria Actinobacteria Acidobacteria, Planctomycetes |
RT-PCR amplification of nifH RNA | 8% 20% 36% 24% 12% | Azospirillum brasilense Bradyrhizobium spp. Methylocapsa spp. Paraburkholderia tropica Idenella/Herbaspirillum-like | |
White shoot roots of 5-month-old sugarcane (cv. RB867515) grown on EMBRAPA field [42] | Trap-plant (siratro) isolates Determination of 16S rRNA and cDNA sequence | 96% 4% | Bradyrhizobium spp. Rhizobium sp. (no nodC) |
Trap-plant (cowpea) isolates Determination of 16S rRNA and cDNA sequence | 23% 3% | Bradyrhizobium spp. Rhizobium spp. | |
Direct plate isolates | 6/9 1/9 1/9 1/9 | Bradyrhizobium spp. (4 no nodC) Rhizobium sp. (no nodC) Methylobacterium Herbaspirillum |
Site and Sampling of Investigation | Detection of nifH Genes | Close Genus (Similarity >91%) Abundance and Bacteria | |
---|---|---|---|
Stem of African sweet potato grown in Uganda and Kenya [47] | Sequencing of nifH DNA clones | 17% (Kenya) 71% (Kenya) 83% (Uganda) | Bradyrhizobium sp. ANU 289 Azoarcus sp. BH72 Clostridium pasteurianum |
Stem harvested in Oct. 2002, Aug. 2004 and Oct. 2004 from cv. Beniazuma grown in Andozol, Japan [48] | Sequencing of nifH DNA clones | 31% (O2) 18% (O4) 18% (O4) 100% (A4), 63% (O4) | Herbaspirillum seropedicae B. sp. MAFF210318 B. sp. IRBG230 Azohydromonas australica |
PCR amplification of nifH RNA | 77% (O2) 22% (O2) 40% (A4) 60% (A4) | Bacillus sp. BT97 B. sp. IRBG228 B. sp. MAFF210318 B. sp. IRBG230 | |
Stem harvested in Oct. 2005 and Aug. 2006 from cv. Ayamurasaki grown on a gray lowland soil, Japan [48] | Sequencing of nifH DNA clones | 100% (O5) 27% (A6) 18% (A6) 18% (A6) 36% (A6) | B. sp. IRBG230 Pelomonas saccharophila Azohydromonas australica Paraburkholderia unamae Tolypothrix sp. PCC7601 |
PCR amplification of nifH RNA | 100% (A6) | Pelomonas saccharophila | |
Tuber of African sweet potato grown in Uganda and Kenya [48] | Sequencing of nifH DNA clones | 28% (Kenya) 71% (Uganda), 14% (Kenya) 71% (Kenya) 29% (Uganda), 28% (Kenya) | Bradyrhizobium japonicum Sinorhizobium meliloti Azoarcus sp. BH72 Paenibacillus odorifer |
Tuber harvested in Oct. 2002, and Oct. 2004 from cv. Beniazuma grown on an Andozol, Japan [48] | Sequencing of nifH DNA clones | 46% (O2) 23% (O2), 30% (O4) 70% (O4) | B. sp. MAFF210318 Bradyrhizobium japonicum Rhizobium leguminosarum |
PCR amplification of nifH RNA | 15% (O2) 85% (O2) | Bradyrhizobium japonicum Bacillus sp. BT97 | |
Tuber harvested in Oct. 2005, Aug. 2006, and Oct. 2006 from cv. Ayamurasaki grown on a gray lowland soil, Japan [48] | Sequencing of nifH DNA clones | 46% (O5) 25% (A6), 28% (O6) 14% (O6) 10% (O5), 33% (A6), 21% (O6) 13% (O5), 17% (A6), 14% (O6) 18% (O5) | Azorhizobium caulinodans B. sp. IRBG230 Sinorhizobium sp. Pelomonas saccharophila Azohydromonas australica Paraburkholderia vietnamiensis |
PCR amplification of nifH RNA | 100% (A6) | B. sp. IRBG230 |
Site and Sample of Investigation | Detection of nifHDK Genes and Their Proteins | Closest Genus Abundance and Bacteria | |
---|---|---|---|
Roots harvested from paddy rice grown on Kyushu University field [58] | Sequencing of nifH DNA clones | γ-Proteobacteria (Klebsiella pneumoniae, Azotobacter) δ-Proteobacteria (Desulfovibrio gigas) | |
Roots harvested from paddy rice (cv. IR55423-01) grown in IRRI field, the Philippines at flowering [59] | Metagenome for nifH DNA | 3/5 1/5 1/5 | Bradyrhizobium sp. BTAi1 Xanthobacter autotrophicus Dickeya dadantii |
RT-PCR amplification of nifH RNA | Geobacter spp. | ||
Roots harvested from cv. Nipponbare rice grown on Tohoku University field at flowering stage [4] | Metaproteome for NifHDK | 29.7% 21.8% 9.3% | Methylocystaceae (Methylosinus sp., Methylocystis sp.) Bradyrhizobiaceae (Bradyrhizobium, Rhodopseudomonas) Burkholderiaceae |
Rhizosphere from paddy rice field of Fujian province, China [60] | RT-PCR amplification of nifH RNA | 4 clones 3 clones 4 clones | α-Proteobacteria (Rhizobium, Methylocystis) β-Proteobacteria (Azoarcus sp., Azospira oryzae, Azotobacter sp.) γ-Proteobacteria (Methylococcus) δ-Proteobacteria (Geobacter) Firmicutes (Helicobacter) |
Rhizosphere collected at IRRI fields, the Philippines 59 to 76 days after rice transplanting [61] | Metagenome 16S rRNA | α-Proteobacteria (Rhizobium, Methylobacterium) Actinobacteria (Microbacterium) | |
Sequencing of nifH DNA clones | Rhizobium, Methylococcus, Dechloromonas, Anaeromyxobacter, Syntrophobacter, some methanogenic archaea | ||
Metaproteome | 33% | α-Proteobacteria (Bradyrhizobium, Rhodopseudomonas, Azospirillum, Methylobacterium, Magnetospirillum, Methylosinus) β-Proteobacteria (Dechloromonas, Acidovorax, Herbaspirillum) δ-Proteobacteria (Anaeromyxobacter, Geobacter, Desulfovibrio) |
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Yoneyama, T.; Terakado-Tonooka, J.; Bao, Z.; Minamisawa, K. Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants. Plants 2019, 8, 408. https://doi.org/10.3390/plants8100408
Yoneyama T, Terakado-Tonooka J, Bao Z, Minamisawa K. Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants. Plants. 2019; 8(10):408. https://doi.org/10.3390/plants8100408
Chicago/Turabian StyleYoneyama, Tadakatsu, Junko Terakado-Tonooka, Zhihua Bao, and Kiwamu Minamisawa. 2019. "Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants" Plants 8, no. 10: 408. https://doi.org/10.3390/plants8100408
APA StyleYoneyama, T., Terakado-Tonooka, J., Bao, Z., & Minamisawa, K. (2019). Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants. Plants, 8(10), 408. https://doi.org/10.3390/plants8100408