801
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Mueller U, Sachs J. Engineering Microbiomes to Improve Plant and Animal Health. Trends Microbiol 2015; 23:606-617. [DOI: 10.1016/j.tim.2015.07.009] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/08/2015] [Accepted: 07/22/2015] [Indexed: 12/22/2022]
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802
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Knight S, Klaere S, Fedrizzi B, Goddard MR. Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir. Sci Rep 2015; 5:14233. [PMID: 26400688 PMCID: PMC4585847 DOI: 10.1038/srep14233] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/20/2015] [Indexed: 12/31/2022] Open
Abstract
Many crops display differential geographic phenotypes and sensorial signatures, encapsulated by the concept of terroir. The drivers behind these differences remain elusive, and the potential contribution of microbes has been ignored until recently. Significant genetic differentiation between microbial communities and populations from different geographic locations has been demonstrated, but crucially it has not been shown whether this correlates with differential agricultural phenotypes or not. Using wine as a model system, we utilize the regionally genetically differentiated population of Saccharomyces cerevisiae in New Zealand and objectively demonstrate that these populations differentially affect wine phenotype, which is driven by a complex mix of chemicals. These findings reveal the importance of microbial populations for the regional identity of wine, and potentially extend to other important agricultural commodities. Moreover, this suggests that long-term implementation of methods maintaining differential biodiversity may have tangible economic imperatives as well as being desirable in terms of employing agricultural practices that increase responsible environmental stewardship.
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Affiliation(s)
- Sarah Knight
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Steffen Klaere
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Bruno Fedrizzi
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Matthew R. Goddard
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
- The School of Life Sciences, The University of Lincoln, Lincoln, LN6 7DL, United Kingdom
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803
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Smith DL, Subramanian S, Lamont JR, Bywater-Ekegärd M. Signaling in the phytomicrobiome: breadth and potential. FRONTIERS IN PLANT SCIENCE 2015; 6:709. [PMID: 26442023 PMCID: PMC4563166 DOI: 10.3389/fpls.2015.00709] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/24/2015] [Indexed: 05/18/2023]
Abstract
Higher plants have evolved intimate, complex, subtle, and relatively constant relationships with a suite of microbes, the phytomicrobiome. Over the last few decades we have learned that plants and microbes can use molecular signals to communicate. This is well-established for the legume-rhizobia nitrogen-fixing symbiosis, and reasonably elucidated for mycorrhizal associations. Bacteria within the phytomircobiome communicate among themselves through quorum sensing and other mechanisms. Plants also detect materials produced by potential pathogens and activate pathogen-response systems. This intercommunication dictates aspects of plant development, architecture, and productivity. Understanding this signaling via biochemical, genomics, proteomics, and metabolomic studies has added valuable knowledge regarding development of effective, low-cost, eco-friendly crop inputs that reduce fossil fuel intense inputs. This knowledge underpins phytomicrobiome engineering: manipulating the beneficial consortia that manufacture signals/products that improve the ability of the plant-phytomicrobiome community to deal with various soil and climatic conditions, leading to enhanced overall crop plant productivity.
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Affiliation(s)
- Donald L. Smith
- Plant Science Department, McGill University/Macdonald Campus, Sainte-Anne-de-Bellevue, QCCanada
| | | | - John R. Lamont
- Plant Science Department, McGill University/Macdonald Campus, Sainte-Anne-de-Bellevue, QCCanada
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804
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Christian N, Whitaker BK, Clay K. Microbiomes: unifying animal and plant systems through the lens of community ecology theory. Front Microbiol 2015; 6:869. [PMID: 26441846 PMCID: PMC4561359 DOI: 10.3389/fmicb.2015.00869] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/10/2015] [Indexed: 12/20/2022] Open
Abstract
The field of microbiome research is arguably one of the fastest growing in biology. Bacteria feature prominently in studies on animal health, but fungi appear to be the more prominent functional symbionts for plants. Despite the similarities in the ecological organization and evolutionary importance of animal-bacterial and plant-fungal microbiomes, there is a general failure across disciplines to integrate the advances made in each system. Researchers studying bacterial symbionts in animals benefit from greater access to efficient sequencing pipelines and taxonomic reference databases, perhaps due to high medical and veterinary interest. However, researchers studying plant-fungal symbionts benefit from the relative tractability of fungi under laboratory conditions and ease of cultivation. Thus each system has strengths to offer, but both suffer from the lack of a common conceptual framework. We argue that community ecology best illuminates complex species interactions across space and time. In this synthesis we compare and contrast the animal-bacterial and plant-fungal microbiomes using six core theories in community ecology (i.e., succession, community assembly, metacommunities, multi-trophic interactions, disturbance, restoration). The examples and questions raised are meant to spark discussion amongst biologists and lead to the integration of these two systems, as well as more informative, manipulatory experiments on microbiomes research.
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Affiliation(s)
- Natalie Christian
- *Correspondence: Natalie Christian and Briana K. Whitaker, Evolution, Ecology and Behavior Program, Department of Biology, Indiana University, Jordan Hall, 1001 East 3rd Street, Bloomington, IN 47405, USA, ;
| | - Briana K. Whitaker
- *Correspondence: Natalie Christian and Briana K. Whitaker, Evolution, Ecology and Behavior Program, Department of Biology, Indiana University, Jordan Hall, 1001 East 3rd Street, Bloomington, IN 47405, USA, ;
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805
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Xu W, Wang Z, Wu F. The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon. Front Microbiol 2015; 6:899. [PMID: 26388851 PMCID: PMC4555026 DOI: 10.3389/fmicb.2015.00899] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 08/17/2015] [Indexed: 01/15/2023] Open
Abstract
The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system.
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Affiliation(s)
- Weihui Xu
- Department of Horticulture, College of Horticulture, Northeast Agricultural University Harbin, China ; Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University Qiqihar, China ; Heilongjiang Provincial Key University Laboratory of Cold Area Vegetable Biology, Northeast Agricultural University Harbin, China ; Ministry of Agriculture Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in Northeast China, Northeast Agricultural University Harbin, China
| | - Zhigang Wang
- Department of Horticulture, College of Horticulture, Northeast Agricultural University Harbin, China ; Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University Qiqihar, China ; Heilongjiang Provincial Key University Laboratory of Cold Area Vegetable Biology, Northeast Agricultural University Harbin, China ; Ministry of Agriculture Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in Northeast China, Northeast Agricultural University Harbin, China
| | - Fengzhi Wu
- Department of Horticulture, College of Horticulture, Northeast Agricultural University Harbin, China ; Heilongjiang Provincial Key University Laboratory of Cold Area Vegetable Biology, Northeast Agricultural University Harbin, China ; Ministry of Agriculture Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in Northeast China, Northeast Agricultural University Harbin, China
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806
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Liu Z, Dang Y, Li C, Sun D. Inhibitory effect of high NH4(+)-N concentration on anaerobic biotreatment of fresh leachate from a municipal solid waste incineration plant. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 43:188-195. [PMID: 26139135 DOI: 10.1016/j.wasman.2015.06.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 06/22/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
Fresh leachate from municipal solid waste (MSW) incineration plants generally contains extremely high NH4(+)-N concentration which could inhibit the bioactivity of microorganisms. The inhibitory effect of high NH4(+)-N concentration on anaerobic biotreatment of fresh leachate from a MSW incineration plant in China has been investigated in this study. The inhibition processes was studied by both static tests and a laboratory-scale expanded granular sludge bed (EGSB) reactor. The specific methanogenic activity (SMA) of the microorganisms in anaerobic granular sludge was inhibited with the NH4(+)-N concentration increasing to 1000mg/L in static tests. As well the chemical oxygen demand (COD) removal efficiency and the methane yield decreased in the EGSB reactor, while the volatile fatty acids (VFAs) accumulated and extracellular polymeric substances (EPS) of the anaerobic granular sludge increased with NH4(+)-N concentration rising to 1000mg/L, without any rebounding during 30days of operation. Decreasing NH4(+)-N concentration to 500mg/L in influent, the COD removal efficiency recovered to about 85% after 26days. 1000mg/L of NH4(+)-N in leachate was suggested to be the inhibition threshold in EGSB reactor. High-throughput sequencing results showed little changes in microbial communities of the sludge for a high NH4(+)-N concentration, indicating that the survival of most microorganisms was not affected under such a condition. It inhibited the bioactivity of the microorganisms, resulting in decrease of the COD removal efficiency.
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Affiliation(s)
- Zhao Liu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, 35 Tsinghua East Road, Beijing 100083, China
| | - Yan Dang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, 35 Tsinghua East Road, Beijing 100083, China
| | - Caihua Li
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, 35 Tsinghua East Road, Beijing 100083, China
| | - Dezhi Sun
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Beijing Forestry University, 35 Tsinghua East Road, Beijing 100083, China.
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807
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Plant-based culture media: Efficiently support culturing rhizobacteria and correctly mirror their in-situ diversity. J Adv Res 2015; 7:305-16. [PMID: 26966571 PMCID: PMC4767806 DOI: 10.1016/j.jare.2015.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/25/2015] [Accepted: 07/28/2015] [Indexed: 11/21/2022] Open
Abstract
Our previous publications and the data presented here provide evidences on the ability of plant-based culture media to optimize the cultivability of rhizobacteria and to support their recovery from plant-soil environments. Compared to the tested chemically-synthetic culture media (e.g. nutrient agar and N-deficient combined-carbon sources media), slurry homogenates, crude saps, juices and powders of cactus (Opuntia ficus-indica) and succulent plants (Aloe vera and Aloe arborescens) were rich enough to support growth of rhizobacteria. Representative isolates of Enterobacter spp., Klebsiella spp., Bacillus spp. and Azospirillum spp. exhibited good growth on agar plates of such plant-based culture media. Cell growth and biomass production in liquid batch cultures were comparable to those reported with the synthetic culture media. In addition, the tested plant-based culture media efficiently recovered populations of rhizobacteria associated to plant roots. Culturable populations of >106–108 cfu g−1 were recovered from the ecto- and endo-rhizospheres of tested host plants. More than 100 endophytic culture-dependent isolates were secured and subjected to morphophysiological identification. Factor and cluster analyses indicated the unique community structure, on species, genera, class and phyla levels, of the culturable population recovered with plant-based culture media, being distinct from that obtained with the chemically-synthetic culture media. Proteobacteria were the dominant (78.8%) on plant-based agar culture medium compared to only 31% on nutrient agar, while Firmicutes prevailed on nutrient agar (69%) compared to the plant-based agar culture media (18.2%). Bacteroidetes, represented by Chryseobacterium indologenes, was only reported (3%) among the culturable rhizobacteria community of the plant-based agar culture medium.
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808
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Nogales A, Nobre T, Valadas V, Ragonezi C, Döring M, Polidoros A, Arnholdt-Schmitt B. Can functional hologenomics aid tackling current challenges in plant breeding? Brief Funct Genomics 2015; 15:288-97. [PMID: 26293603 DOI: 10.1093/bfgp/elv030] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Molecular plant breeding usually overlooks the genetic variability that arises from the association of plants with endophytic microorganisms, when looking at agronomic interesting target traits. This source of variability can have crucial effects on the functionality of the organism considered as a whole (the holobiont), and therefore can be selectable in breeding programs. However, seeing the holobiont as a unit for selection and improvement in breeding programs requires novel approaches for genotyping and phenotyping. These should not focus just at the plant level, but also include the associated endophytes and their functional effects on the plant, to make effective desirable trait screenings. The present review intends to draw attention to a new research field on functional hologenomics that if associated with adequate phenotyping tools could greatly increase the efficiency of breeding programs.
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809
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Yang A, Liu N, Tian Q, Bai W, Williams M, Wang Q, Li L, Zhang WH. Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition. Front Microbiol 2015; 6:789. [PMID: 26322024 PMCID: PMC4533001 DOI: 10.3389/fmicb.2015.00789] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022] Open
Abstract
We evaluated effects of 9-year simulated nitrogen (N) deposition on microbial composition and diversity in the rhizosphere of two dominant temperate grassland species: grass Stipa krylovii and forb Artemisia frigida. Microbiomes in S. krylovii and A. frigida rhizosphere differed, but changed consistently along the N gradient. These changes were correlated to N-induced shifts to plant community. Hence, as plant biomass changed, so did bacterial rhizosphere communities, a result consistent with the role that N fertilizer has been shown to play in altering plant-microbial mutualisms. A total of 23 bacterial phyla were detected in the two rhizospheric soils by pyrosequencing, with Proteobacteria, Acidobacteria, and Bacteroidetes dominating the sequences of all samples. Bacterioidetes and Proteobacteria tended to increase, while Acidobacteria declined with increase in N addition rates. TM7 increased >5-fold in the high N addition rates, especially in S. krylovii rhizosphere. Nitrogen addition also decreased diversity of OTUs (operational taxonomic units), Shannon and Chao1 indices of rhizospheric microbes regardless of plant species. These results suggest that there were both similar but also specific changes in microbial communities of temperate steppes due to N deposition. These findings would contribute to our mechanistic understanding of impacts of N deposition on grassland ecosystem by linking changes in plant traits to their rhizospheric microbes-mediated processes.
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Affiliation(s)
- An Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Nana Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China ; University of Chinese Academy of Sciences Beijing, China
| | - Qiuying Tian
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Wenming Bai
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Mark Williams
- Department of Horticulture, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Qibing Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Linghao Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Wen-Hao Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China ; Research Network of Global Change Biology, Beijing Institutes of Life Science, Chinese Academy of Sciences Beijing, China
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810
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Tremblay J, Singh K, Fern A, Kirton ES, He S, Woyke T, Lee J, Chen F, Dangl JL, Tringe SG. Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol 2015; 6:771. [PMID: 26300854 PMCID: PMC4523815 DOI: 10.3389/fmicb.2015.00771] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/14/2015] [Indexed: 12/24/2022] Open
Abstract
Sequencing of 16S rRNA gene tags is a popular method for profiling and comparing microbial communities. The protocols and methods used, however, vary considerably with regard to amplification primers, sequencing primers, sequencing technologies; as well as quality filtering and clustering. How results are affected by these choices, and whether data produced with different protocols can be meaningfully compared, is often unknown. Here we compare results obtained using three different amplification primer sets (targeting V4, V6–V8, and V7–V8) and two sequencing technologies (454 pyrosequencing and Illumina MiSeq) using DNA from a mock community containing a known number of species as well as complex environmental samples whose PCR-independent profiles were estimated using shotgun sequencing. We find that paired-end MiSeq reads produce higher quality data and enabled the use of more aggressive quality control parameters over 454, resulting in a higher retention rate of high quality reads for downstream data analysis. While primer choice considerably influences quantitative abundance estimations, sequencing platform has relatively minor effects when matched primers are used. Beta diversity metrics are surprisingly robust to both primer and sequencing platform biases.
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Affiliation(s)
- Julien Tremblay
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA ; National Research Council Canada Montreal, QC, Canada
| | - Kanwar Singh
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Alison Fern
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Edward S Kirton
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Shaomei He
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Janey Lee
- Department of Energy Joint Genome Institute Walnut Creek, CA, USA
| | - Feng Chen
- Illumina, Inc. San Francisco, CA, USA
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, Curriculum in Genetics and Molecular Biology, Department of Microbiology and Immunology, Carolina Center for Genome Sciences, University of North Carolina Chapel Hill, NC, USA
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811
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Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie EL, Zhou J, Firestone M. Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons. mBio 2015; 6:e00746. [PMID: 26242625 PMCID: PMC4526712 DOI: 10.1128/mbio.00746-15] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/20/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. IMPORTANCE We document the successional patterns of rhizosphere bacterial communities associated with a "wild" annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address "domesticated" plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable over two growing seasons. There are few studies assessing the reproducibility over multiple seasons. Through the growing season, the rhizosphere community became progressively less diverse, likely reflecting root homogenization of soil microniches. Phylogenetic clustering of the rhizosphere dynamic taxa suggests evolutionary adaptation to Avena roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence.
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Affiliation(s)
- Shengjing Shi
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Erin Nuccio
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Donald J Herman
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ruud Rijkers
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Katerina Estera
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Jiabao Li
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Ulisses Nunes da Rocha
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Jennifer Pett-Ridge
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Eoin L Brodie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Mary Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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812
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Cooper MB, Smith AG. Exploring mutualistic interactions between microalgae and bacteria in the omics age. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:147-53. [PMID: 26318329 DOI: 10.1016/j.pbi.2015.07.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/05/2015] [Accepted: 07/13/2015] [Indexed: 05/27/2023]
Abstract
Microalgae undertake a wide range of mutualistic interactions with bacteria. Here we consider how transcriptomic, metagenomic and metabolomic approaches have been combined with microbiological and biochemical analyses to expand our understanding of algal-bacterial interactions. Identification of the major bacterial species associated with algae indicates that specific bacterial groups, particularly the alpha-Proteobacteria, are found more frequently, suggesting that these may have the means to initiate and maintain symbiotic relationships. Nutrient exchange is frequently the basis of algal-bacterial mutualism, and as the compounds involved are characterised, evidence is accumulating that these are complex and specific molecules, offering opportunities for signalling processes and regulation rather than merely passive diffusion. At the same time, it is clear that the interactions are not static, but can be initiated and broken in response to environmental and developmental cues.
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Affiliation(s)
- Matthew B Cooper
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
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813
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Abstract
Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.
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Affiliation(s)
- Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin R. Theis
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
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814
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Yang Z, Xu X, Guo R, Fan X, Zhao X. Accelerated methanogenesis from effluents of hydrogen-producing stage in anaerobic digestion by mixed cultures enriched with acetate and nano-sized magnetite particles. BIORESOURCE TECHNOLOGY 2015; 190:132-9. [PMID: 25935393 DOI: 10.1016/j.biortech.2015.04.057] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/13/2015] [Accepted: 04/16/2015] [Indexed: 05/16/2023]
Abstract
Potential for paddy soil enrichments obtained in the presence of nano-sized magnetite particles (named as PSEM) to promote methane production from effluents of hydrogen-producing stage in two-stage anaerobic digestion was investigated. The results showed that the addition of magnetite significantly accelerated methane production from acetate in a dose-independent manner. The results from high-throughput sequencing analysis revealed that Rhodocyclaceae-related species were selectively enriched, which were likely the key players for conversion of acetate to methane in PSEM. Compared to the paddy soil enrichments obtained in the absence of magnetite (named as PSEC), the maximum methane production rate in PSEM was significantly higher (1.5-5.5times higher for the artificial medium and 0.2-1.7times higher for the effluents). The accelerated methane production from the effluents indicated remarkably application potential of PSEM for improving performance of anaerobic digestion.
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Affiliation(s)
- Zhiman Yang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Xiaohui Xu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Rongbo Guo
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| | - Xiaolei Fan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Xiaoxian Zhao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; College of Chemical Science and Engineering, Qingdao University, Qingdao 266071, China
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815
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Zachow C, Jahanshah G, de Bruijn I, Song C, Ianni F, Pataj Z, Gerhardt H, Pianet I, Lämmerhofer M, Berg G, Gross H, Raaijmakers JM. The Novel Lipopeptide Poaeamide of the Endophyte Pseudomonas poae RE*1-1-14 Is Involved in Pathogen Suppression and Root Colonization. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:800-10. [PMID: 25761208 DOI: 10.1094/mpmi-12-14-0406-r] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Endophytic Pseudomonas poae strain RE*1-1-14 was originally isolated from internal root tissue of sugar beet plants and shown to suppress growth of the fungal pathogen Rhizoctonia solani both in vitro and in the field. To identify genes involved in its biocontrol activity, RE*1-1-14 random mutagenesis and sequencing led to the identification of a nonribosomal peptide synthetase (NRPS) gene cluster predicted to encode a lipopeptide (LP) with a 10-amino-acid peptide moiety. The two unlinked gene clusters consisted of three NRPS genes, designated poaA (cluster 1) and poaB and poaC (cluster 2), spanning approximately 33.7 kb. In silico analysis followed by chemical analyses revealed that the encoded LP, designated poaeamide, is a structurally new member of the orfamide family. Poaeamide inhibited mycelial growth of R. solani and different oomycetes, including Phytophthora capsici, P. infestans, and Pythium ultimum. The novel LP was shown to be essential for swarming motility of strain RE*1-1-14 and had an impact on root colonization of sugar beet seedlings The poaeamide-deficient mutant colonized the rhizosphere and upper plant cortex at higher densities and with more scattered colonization patterns than the wild type. Collectively, these results indicate that Pseudomonas poae RE*1-1-14 produces a structurally new LP that is relevant for its antagonistic activity against soilborne plant pathogens and for colonization of sugar beet roots.
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Affiliation(s)
- Christin Zachow
- 1 Austrian Centre of Industrial Biotechnology (ACIB GmbH), 8010 Graz, Austria
| | - Ghazaleh Jahanshah
- 2 Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Irene de Bruijn
- 3 Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Chunxu Song
- 3 Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Federica Ianni
- 4 Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen
| | - Zoltán Pataj
- 4 Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen
| | - Heike Gerhardt
- 4 Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen
| | - Isabelle Pianet
- 5 CESAMO-ISM, UMR 5255, CNRS, Université Bordeaux I, 351 Cours de la Libération, F-33405 Talence, France
| | - Michael Lämmerhofer
- 4 Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen
| | - Gabriele Berg
- 6 Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Harald Gross
- 2 Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Jos M Raaijmakers
- 3 Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
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816
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Xu X, Passey T, Wei F, Saville R, Harrison RJ. Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry. HORTICULTURE RESEARCH 2015; 2:15022. [PMID: 26504572 PMCID: PMC4595980 DOI: 10.1038/hortres.2015.22] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 05/25/2023]
Abstract
A phenomenon of yield decline due to weak plant growth in strawberry was recently observed in non-chemo-fumigated soils, which was not associated with the soil fungal pathogen Verticillium dahliae, the main target of fumigation. Amplicon-based metagenomics was used to profile soil microbiota in order to identify microbial organisms that may have caused the yield decline. A total of 36 soil samples were obtained in 2013 and 2014 from four sites for metagenomic studies; two of the four sites had a yield-decline problem, the other two did not. More than 2000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. Relative abundance of individual OTUs was statistically compared for differences between samples from sites with or without yield decline. A total of 721 individual comparisons were statistically significant - involving 366 unique bacterial and 44 unique fungal OTUs. Based on further selection criteria, we focused on 34 bacterial and 17 fungal OTUs and found that yield decline resulted probably from one or more of the following four factors: (1) low abundance of Bacillus and Pseudomonas populations, which are well known for their ability of supressing pathogen development and/or promoting plant growth; (2) lack of the nematophagous fungus (Paecilomyces species); (3) a high level of two non-specific fungal root rot pathogens; and (4) wet soil conditions. This study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes.
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Affiliation(s)
- Xiangming Xu
- East Malling Research, East Malling, West Malling, Kent, ME19 6BJ, UK
| | - Thomas Passey
- East Malling Research, East Malling, West Malling, Kent, ME19 6BJ, UK
| | - Feng Wei
- East Malling Research, East Malling, West Malling, Kent, ME19 6BJ, UK
| | - Robert Saville
- East Malling Research, East Malling, West Malling, Kent, ME19 6BJ, UK
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817
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Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A. The importance of the microbiome of the plant holobiont. THE NEW PHYTOLOGIST 2015; 206:1196-206. [PMID: 25655016 DOI: 10.1111/nph.13312] [Citation(s) in RCA: 875] [Impact Index Per Article: 97.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/05/2015] [Indexed: 05/18/2023]
Abstract
Plants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses. Hence, the microbiota impact plant growth and survival, two key components of fitness. Plant fitness is therefore a consequence of the plant per se and its microbiota, which collectively form a holobiont. Complementary to the reductionist perception of evolutionary pressures acting on plant or symbiotic compartments, the plant holobiont concept requires a novel perception of evolution. The interlinkages between the plant holobiont components are explored here in the light of current ecological and evolutionary theories. Microbiome complexity and the rules of microbiotic community assemblage are not yet fully understood. It is suggested that the plant can modulate its microbiota to dynamically adjust to its environment. To better understand the level of plant dependence on the microbiotic components, the core microbiota need to be determined at different hierarchical scales of ecology while pan-microbiome analyses would improve characterization of the functions displayed.
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Affiliation(s)
| | - Achim Quaiser
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
| | - Marie Duhamel
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Amandine Le Van
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
| | - Alexis Dufresne
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
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818
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Microbiota Dynamics Associated with Environmental Conditions and Potential Roles of Cellulolytic Communities in Traditional Chinese Cereal Starter Solid-State Fermentation. Appl Environ Microbiol 2015; 81:5144-56. [PMID: 26002897 DOI: 10.1128/aem.01325-15] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/16/2015] [Indexed: 12/25/2022] Open
Abstract
Traditional Chinese solid-state fermented cereal starters contain highly complex microbial communities and enzymes. Very little is known, however, about the microbial dynamics related to environmental conditions, and cellulolytic communities have never been proposed to exist during cereal starter fermentation. In this study, we performed Illumina MiSeq sequencing combined with PCR-denaturing gradient gel electrophoresis to investigate microbiota, coupled with clone library construction to trace cellulolytic communities in both fermentation stages. A succession of microbial assemblages was observed during the fermentation of starters. Lactobacillales and Saccharomycetales dominated the initial stages, with a continuous decline in relative abundance. However, thermotolerant and drought-resistant Bacillales, Eurotiales, and Mucorales were considerably accelerated during the heating stages, and these organisms dominated until the end of fermentation. Enterobacteriales were consistently ubiquitous throughout the process. For the cellulolytic communities, only the genera Sanguibacter, Beutenbergia, Agrobacterium, and Erwinia dominated the initial fermentation stages. In contrast, stages at high incubation temperature induced the appearance and dominance of Bacillus, Aspergillus, and Mucor. The enzymatic dynamics of amylase and glucoamylase also showed a similar trend, with the activities clearly increased in the first 7 days and subsequently decreased until the end of fermentation. Furthermore, β-glucosidase activity continuously and significantly increased during the fermentation process. Evidently, cellulolytic potential can adapt to environmental conditions by changes in the community structure during the fermentation of starters.
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819
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Wang ZG, Hu YL, Xu WH, Liu S, Hu Y, Zhang Y. Impacts of dimethyl phthalate on the bacterial community and functions in black soils. Front Microbiol 2015; 6:405. [PMID: 25999932 PMCID: PMC4419729 DOI: 10.3389/fmicb.2015.00405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/18/2015] [Indexed: 11/13/2022] Open
Abstract
Dimethyl phthalate (DMP), a known endocrine disruptor and one of the phthalate esters (PAEs), is a ubiquitous pollutant. Its impacts on living organisms have aroused great concern. In this study, the impacts of DMP contamination on bacterial communities and functions were tested by using microcosm model in black soils. The results showed that the operational taxonomic unit (OTUs) richness and bacterial diversity were reduced by DMP contamination. The relative percentages of some genera associated with nitrogen metabolism were increased by DMP contamination, while the relative percentages of some other genera that were extremely beneficial to soil health were decreased by DMP contamination. Further, the relative percentages of some genera that possessed the capability to degrade DMP were increased by the DMP treatment at low concentrations (5, 10, and 20 mg/kg), but were decreased by the high concentration DMP treatment (40 mg/kg). Clearly, DMP contamination changed the bacterial community structure and disturbed the metabolic activity and functional diversity of the microbes in black soils. Our results suggest that DMP pollution can alter the metabolism and biodiversity of black soil microorganisms, thereby directly impact fertility and ecosystem functions.
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Affiliation(s)
- Zhi-Gang Wang
- Department of Biotechnology, Institute of Life Science and Agriculture and Forestry, Qiqihar University Qiqihar, China ; Department of Environmental Science and Engineering, Institute of Municipal Environment and Engineering, Harbin Industry University Harbin, China
| | - Yun-Long Hu
- Department of Biotechnology, Institute of Life Science and Agriculture and Forestry, Qiqihar University Qiqihar, China
| | - Wei-Hui Xu
- Department of Biotechnology, Institute of Life Science and Agriculture and Forestry, Qiqihar University Qiqihar, China
| | - Shuai Liu
- Department of Biotechnology, Institute of Life Science and Agriculture and Forestry, Qiqihar University Qiqihar, China
| | - Ying Hu
- Department of Biotechnology, Institute of Life Science and Agriculture and Forestry, Qiqihar University Qiqihar, China
| | - Ying Zhang
- Department of Environmental Science, Institute of Resources and Environment, Northeast Agricultural University Harbin, China
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820
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Hacquard S, Garrido-Oter R, González A, Spaepen S, Ackermann G, Lebeis S, McHardy A, Dangl J, Knight R, Ley R, Schulze-Lefert P. Microbiota and Host Nutrition across Plant and Animal Kingdoms. Cell Host Microbe 2015; 17:603-16. [DOI: 10.1016/j.chom.2015.04.009] [Citation(s) in RCA: 439] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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821
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Lebeis SL. Greater than the sum of their parts: characterizing plant microbiomes at the community-level. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:82-6. [PMID: 25710740 DOI: 10.1016/j.pbi.2015.02.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 05/25/2023]
Abstract
Specific subsets of microbes are capable of assembly into plant-associated communities that influence the fitness of both the host and the microbes. While there is a large spectrum of plant phenotypes cause by microbes, the microbial community members benefit from living in protected and nutrient rich plant-associated environments. Recent advances in '-omics' technologies have provided researchers with the ability to identify and assign functions to even unculturable microbes inhabiting both above-ground and below-ground plant tissues. Thus, we are beginning to unravel the molecular mechanisms of microbiome assembly and activities that contribute to overall plant health, not only for individuals, but also at the community-level.
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Affiliation(s)
- Sarah L Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States.
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822
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Tkacz A, Poole P. Role of root microbiota in plant productivity. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2167-75. [PMID: 25908654 PMCID: PMC4986727 DOI: 10.1093/jxb/erv157] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 05/19/2023]
Abstract
The growing human population requires increasing amounts of food, but modern agriculture has limited possibilities for increasing yields. New crop varieties may be bred to have increased yields and be more resistant to environmental stress and pests. However, they still require fertilization to supplement essential nutrients that are normally limited in the soil. Soil microorganisms present an opportunity to reduce the requirement for inorganic fertilization in agriculture. Microorganisms, due to their enormous genetic pool, are also a potential source of biochemical reactions that recycle essential nutrients for plant growth. Microbes that associate with plants can be considered to be part of the plant's pan-genome. Therefore, it is essential for us to understand microbial community structure and their 'metagenome' and how it is influenced by different soil types and crop varieties. In the future we may be able to modify and better utilize the soil microbiota potential for promoting plant growth.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Philip Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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823
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Selection on soil microbiomes reveals reproducible impacts on plant function. ISME JOURNAL 2015; 9:980-9. [PMID: 25350154 PMCID: PMC4817706 DOI: 10.1038/ismej.2014.196] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/29/2014] [Accepted: 09/03/2014] [Indexed: 02/07/2023]
Abstract
Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early- or late-flowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two- to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools.
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824
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Copeland JK, Yuan L, Layeghifard M, Wang PW, Guttman DS. Seasonal community succession of the phyllosphere microbiome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:274-85. [PMID: 25679538 DOI: 10.1094/mpmi-10-14-0331-fi] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The leaf microbiome is influenced by both biotic and abiotic factors. Currently, we know little about the relative importance of these factors in determining microbiota composition and dynamics. To explore this issue, we collected weekly leaf samples over a 98-day growing season from multiple cultivars of common bean, soybean, and canola planted at three locations in Ontario, Canada, and performed Illumina-based microbiome analysis. We find that the leaf microbiota at the beginning of the season is very strongly influenced by the soil microbiota but, as the season progresses, it differentiates, becomes significantly less diverse, and transitions to having a greater proportion of leaf-specific taxa that are shared among all samples. A phylogenetic investigation of communities by reconstruction of unobserved states imputation of microbiome function inferred from the taxonomic data found significant differences between the soil and leaf microbiome, with a significant enrichment of motility gene categories in the former and metabolic gene categories in the latter. A network co-occurrence analysis identified two highly connected clusters as well as subclusters of putative pathogens and growth-promoting bacteria. These data reveal some of the complex ecological dynamics that occur in microbial communities over the course of a growing season and highlight the importance of community succession.
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825
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Hacquard S, Schadt CW. Towards a holistic understanding of the beneficial interactions across the Populus microbiome. THE NEW PHYTOLOGIST 2015; 205:1424-1430. [PMID: 25422041 DOI: 10.1111/nph.13133] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/24/2014] [Indexed: 05/18/2023]
Abstract
Interactions between trees and microorganisms are tremendously complex and the multispecies networks resulting from these associations have consequences for plant growth and productivity. However, a more holistic view is needed to better understand trees as ecosystems and superorganisms, where many interacting species contribute to the overall stability of the system. While much progress has been made on microbial communities associated with individual tree niches and the molecular interactions between model symbiotic partners, there is still a lack of knowledge of the multi-component interactions necessary for holistic ecosystem-level understanding. We review recent studies in Populus to emphasize the importance of such holistic efforts across the leaf, stem and rooting zones, and discuss prospects for future research in these important ecosystems.
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Affiliation(s)
- Stéphane Hacquard
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37966, USA
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826
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Santhanam R, Baldwin IT, Groten K. In wild tobacco, Nicotiana attenuata, variation among bacterial communities of isogenic plants is mainly shaped by the local soil microbiota independently of the plants' capacity to produce jasmonic acid. Commun Integr Biol 2015; 8:e1017160. [PMID: 26478769 PMCID: PMC4594342 DOI: 10.1080/19420889.2015.1017160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 12/29/2014] [Accepted: 01/05/2015] [Indexed: 02/01/2023] Open
Abstract
The phytohormone jasmonic acid (JA) plays a central role in defense against necrotrophic pathogens and herbivores in Nicotiana attenuata. Recently Santhanam et al.(1) showed that JA does not have a major role in shaping the root- and shoot associated bacterial communities, though a few taxa differed among control (empty vector, EV) plants and plants impaired in their capacity to produce JA (irAOC). In this addendum, we provide additional data showing that the composition of the plant bacterial communities is mainly shaped by tissue type. The qualitative data analysis revealed that at the order level, 5 bacterial OTUs formed a core community found in all tissues irrespective of genotypes, while 9 OTUs were different among roots and shoots. The heterogeneity among individual plants was high masking the potential genotype effect on bacterial communities. Using a culture-dependent approach, 3 of 18 bacterial taxa retrieved either only from one of the genotypes or from both had a growth promoting effect on EV and irAOC seedlings. The data suggest that the local soil niche in which the roots grows is a major driver of the variability in root bacterial communities recruited by different individuals, and the plant growth-promoting effects of some taxa are independent of the genotype.
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Affiliation(s)
- Rakesh Santhanam
- Department of Molecular Ecology; Max Planck Institute for Chemical Ecology; Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology; Max Planck Institute for Chemical Ecology; Jena, Germany
| | - Karin Groten
- Department of Molecular Ecology; Max Planck Institute for Chemical Ecology; Jena, Germany
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827
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Aleklett K, Leff JW, Fierer N, Hart M. Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities. PeerJ 2015; 3:e804. [PMID: 25755932 PMCID: PMC4349149 DOI: 10.7717/peerj.804] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/06/2015] [Indexed: 02/01/2023] Open
Abstract
Plant roots are known to harbor large and diverse communities of bacteria. It has been suggested that plant identity can structure these root-associated communities, but few studies have specifically assessed how the composition of root microbiota varies within and between plant species growing under natural conditions. We assessed the community composition of endophytic and epiphytic bacteria through high throughput sequencing using 16S rDNA derived from root tissues collected from a population of a wild, clonal plant (Orange hawkweed-Pilosella aurantiaca) as well as two neighboring plant species (Oxeye daisy-Leucanthemum vulgare and Alsike clover-Trifolium hybridum). Our first goal was to determine if plant species growing in close proximity, under similar environmental conditions, still hosted unique root microbiota. Our results showed that plants of different species host distinct bacterial communities in their roots. In terms of community composition, Betaproteobacteria (especially the family Oxalobacteraceae) were found to dominate in the root microbiota of L. vulgare and T. hybridum samples, whereas the root microbiota of P. aurantiaca had a more heterogeneous distribution of bacterial abundances where Gammaproteobacteria and Acidobacteria occupied a larger portion of the community. We also explored the extent of individual variance within each plant species investigated, and found that in the plant species thought to have the least genetic variance among individuals (P. aurantiaca) still hosted just as diverse microbial communities. Whether all plant species host their own distinct root microbiota and plants more closely related to each other share more similar bacterial communities still remains to be fully explored, but among the plants examined in this experiment there was no trend that the two species belonging to the same family shared more similarities in terms of bacterial community composition.
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Affiliation(s)
- Kristin Aleklett
- Department of Biology, University of British Columbia-Okanagan , Canada
| | - Jonathan W Leff
- Cooperative Institute for Research in Environmental Sciences and the Department of Ecology and Evolutionary Biology, University of Colorado , Boulder, CO , USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences and the Department of Ecology and Evolutionary Biology, University of Colorado , Boulder, CO , USA
| | - Miranda Hart
- Department of Biology, University of British Columbia-Okanagan , Canada
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828
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Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, McHardy AC, Schulze-Lefert P. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 2015; 17:392-403. [PMID: 25732064 PMCID: PMC4362959 DOI: 10.1016/j.chom.2015.01.011] [Citation(s) in RCA: 624] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/25/2014] [Accepted: 01/06/2015] [Indexed: 11/08/2022]
Abstract
The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface. A small number of bacterial families dominate the root-enriched barley microbiota The host genotype determines the profile of a subset of community members Functions relevant for host interactions are enriched in root-associated taxa Genes mediating host, bacteria, and phage interactions show signs of positive selection
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Affiliation(s)
- Davide Bulgarelli
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Ruben Garrido-Oter
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Philipp C Münch
- Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Aaron Weiman
- Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Johannes Dröge
- Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Yao Pan
- Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Alice C McHardy
- Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany.
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
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829
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830
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Porth I, El-Kassaby YA. Using Populus as a lignocellulosic feedstock for bioethanol. Biotechnol J 2015; 10:510-24. [PMID: 25676392 DOI: 10.1002/biot.201400194] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 11/11/2014] [Accepted: 12/30/2014] [Indexed: 11/10/2022]
Abstract
Populus species along with species from the sister genus Salix will provide valuable feedstock resources for advanced second-generation biofuels. Their inherent fast growth characteristics can particularly be exploited for short rotation management, a time and energy saving cultivation alternative for lignocellulosic feedstock supply. Salicaceae possess inherent cell wall characteristics with favorable cellulose to lignin ratios for utilization as bioethanol crop. We review economically important traits relevant for intensively managed biofuel crop plantations, genomic and phenotypic resources available for Populus, breeding strategies for forest trees dedicated to bioenergy provision, and bioprocesses and downstream applications related to opportunities using Salicaceae as a renewable resource. Challenges need to be resolved for every single step of the conversion process chain, i.e., starting from tree domestication for improved performance as a bioenergy crop, bioconversion process, policy development for land use changes associated with advanced biofuels, and harvest and supply logistics associated with industrial-scale biorefinery plants using Populus as feedstock. Significant hurdles towards cost and energy efficiency, environmental friendliness, and yield maximization with regards to biomass pretreatment, saccharification, and fermentation of celluloses and the sustainability of biorefineries as a whole still need to be overcome.
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Affiliation(s)
- Ilga Porth
- Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada.
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831
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Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci U S A 2015; 112:E911-20. [PMID: 25605935 DOI: 10.1073/pnas.1414592112] [Citation(s) in RCA: 1265] [Impact Index Per Article: 140.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput sequencing approaches have provided recent insights into root microbiomes, but our current understanding is still limited relative to animal microbiomes. Here we present a detailed characterization of the root-associated microbiomes of the crop plant rice by deep sequencing, using plants grown under controlled conditions as well as field cultivation at multiple sites. The spatial resolution of the study distinguished three root-associated compartments, the endosphere (root interior), rhizoplane (root surface), and rhizosphere (soil close to the root surface), each of which was found to harbor a distinct microbiome. Under controlled greenhouse conditions, microbiome composition varied with soil source and genotype. In field conditions, geographical location and cultivation practice, namely organic vs. conventional, were factors contributing to microbiome variation. Rice cultivation is a major source of global methane emissions, and methanogenic archaea could be detected in all spatial compartments of field-grown rice. The depth and scale of this study were used to build coabundance networks that revealed potential microbial consortia, some of which were involved in methane cycling. Dynamic changes observed during microbiome acquisition, as well as steady-state compositions of spatial compartments, support a multistep model for root microbiome assembly from soil wherein the rhizoplane plays a selective gating role. Similarities in the distribution of phyla in the root microbiomes of rice and other plants suggest that conclusions derived from this study might be generally applicable to land plants.
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832
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Pyrosequencing reveals fungal communities in the rhizosphere of Xinjiang Jujube. BIOMED RESEARCH INTERNATIONAL 2015; 2015:972481. [PMID: 25685820 PMCID: PMC4313056 DOI: 10.1155/2015/972481] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/26/2014] [Accepted: 11/29/2014] [Indexed: 11/18/2022]
Abstract
Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS) rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA) revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research.
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833
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Quiza L, St-Arnaud M, Yergeau E. Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering. FRONTIERS IN PLANT SCIENCE 2015; 6:507. [PMID: 26236319 PMCID: PMC4500914 DOI: 10.3389/fpls.2015.00507] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/25/2015] [Indexed: 05/18/2023]
Abstract
The goal of microbiome engineering is to manipulate the microbiome toward a certain type of community that will optimize plant functions of interest. For instance, in crop production the goal is to reduce disease susceptibility, increase nutrient availability increase abiotic stress tolerance and increase crop yields. Various approaches can be devised to engineer the plant-microbiome, but one particularly promising approach is to take advantage of naturally evolved plant-microbiome communication channels. This is, however, very challenging as the understanding of the plant-microbiome communication is still mostly rudimentary and plant-microbiome interactions varies between crops species (and even cultivars), between individual members of the microbiome and with environmental conditions. In each individual case, many aspects of the plant-microorganisms relationship should be thoroughly scrutinized. In this article we summarize some of the existing plant-microbiome engineering studies and point out potential avenues for further research.
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Affiliation(s)
- Liliana Quiza
- Energy, Mining and Environment, National Research Council Canada, MontréalQC, Canada
- Institut de Recherche en Biologie Végétale – Jardin Botanique de Montréal and Université de Montréal, MontréalQC, Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale – Jardin Botanique de Montréal and Université de Montréal, MontréalQC, Canada
| | - Etienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, MontréalQC, Canada
- *Correspondence: Etienne Yergeau, National Research Council Canada, 6100 Royalmount Avenue, Montréal, QC H4P 2R2, Canada,
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834
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White LJ, Jothibasu K, Reese RN, Brözel VS, Subramanian S. Spatio Temporal Influence of Isoflavonoids on Bacterial Diversity in the Soybean Rhizosphere. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:22-9. [PMID: 25303334 DOI: 10.1094/mpmi-08-14-0247-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
High bacterial density and diversity near plant roots has been attributed to rhizodeposit compounds that serve as both energy sources and signal molecules. However, it is unclear if and how specific rhizodeposit compounds influence bacterial diversity. We silenced the biosynthesis of isoflavonoids, a major component of soybean rhizodeposits, using RNA interference in hairy-root composite plants, and examined changes in rhizosphere bacteriome diversity. We used successive sonication to isolate soil fractions from different rhizosphere zones at two different time points and analyzed denaturing gradient gel electrophoresis profiles of 16S ribosomal RNA gene amplicons. Extensive diversity analysis of the resulting spatio temporal profiles of soybean bacterial communities indicated that, indeed, isoflavonoids significantly influenced soybean rhizosphere bacterial diversity. Our results also suggested a temporal gradient effect of rhizodeposit isoflavonoids on the rhizosphere. However, the hairy-root transformation process itself significantly altered rhizosphere bacterial diversity, necessitating appropriate additional controls. Gene silencing in hairy-root composite plants combined with successive sonication is a useful tool to determine the spatio temporal effect of specific rhizodeposit compounds on rhizosphere microbial communities.
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835
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Cardinale M, Grube M, Erlacher A, Quehenberger J, Berg G. Bacterial networks and co-occurrence relationships in the lettuce root microbiota. Environ Microbiol 2015; 17:239-52. [PMID: 25367329 DOI: 10.1111/1462-2920.12686] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 10/14/2014] [Accepted: 10/18/2014] [Indexed: 11/29/2022]
Abstract
Lettuce is one of the most common raw foods worldwide, but occasionally also involved in pathogen outbreaks. To understand the correlative structure of the bacterial community as a network, we studied root microbiota of eight ancient and modern Lactuca sativa cultivars and the wild ancestor Lactuca serriola by pyrosequencing of 16S rRNA gene amplicon libraries. The lettuce microbiota was dominated by Proteobacteria and Bacteriodetes, as well as abundant Chloroflexi and Actinobacteria. Cultivar specificity comprised 12.5% of the species. Diversity indices were not different between lettuce cultivar groups but higher than in L. serriola, suggesting that domestication lead to bacterial diversification in lettuce root system. Spearman correlations between operational taxonomic units (OTUs) showed that co-occurrence prevailed over co-exclusion, and complementary fluorescence in situ hybridization-confocal laser scanning microscopy (FISH-CLSM) analyses revealed that this pattern results from both potential interactions and habitat sharing. Predominant taxa, such as Pseudomonas, Flavobacterium and Sphingomonadaceae rather suggested interactions, even though these are not necessarily part of significant modules in the co-occurrence networks. Without any need for complex interactions, single organisms are able to invade into this microbial network and to colonize lettuce plants, a fact that can influence the susceptibility to pathogens. The approach to combine co-occurrence analysis and FISH-CLSM allows reliably reconstructing and interpreting microbial interaction networks.
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Affiliation(s)
- Massimiliano Cardinale
- Institute of Plant Sciences, University of Graz, Graz, Austria; Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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836
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Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T. Roots shaping their microbiome: global hotspots for microbial activity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:403-24. [PMID: 26243728 DOI: 10.1146/annurev-phyto-082712-102342] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Land plants interact with microbes primarily at roots. Despite the importance of root microbial communities for health and nutrient uptake, the current understanding of the complex plant-microbe interactions in the rhizosphere is still in its infancy. Roots provide different microhabitats at the soil-root interface: rhizosphere soil, rhizoplane, and endorhizosphere. We discuss technical aspects of their differentiation that are relevant for the functional analysis of their different microbiomes, and we assess PCR (polymerase chain reaction)-based methods to analyze plant-associated bacterial communities. Development of novel primers will allow a less biased and more quantitative view of these global hotspots of microbial activity. Based on comparison of microbiome data for the different root-soil compartments and on knowledge of bacterial functions, a three-step enrichment model for shifts in community structure from bulk soil toward roots is presented. To unravel how plants shape their microbiome, a major research field is likely to be the coupling of reductionist and molecular ecological approaches, particularly for specific plant genotypes and mutants, to clarify causal relationships in complex root communities.
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Affiliation(s)
- Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, D-28334 Bremen, Germany; , , , ,
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837
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Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems. Appl Microbiol Biotechnol 2014; 99:1337-47. [PMID: 25381908 DOI: 10.1007/s00253-014-6188-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 10/24/2022]
Abstract
So far, the contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation in wastewater treatment processes has not been well understood. In this study, two soil aquifer treatment (SATs) systems were built up to treat synthetic domestic wastewater (column 1) and secondary effluent (column 4), accomplishing an average of 95% ammonia removal during over 550 days of operation. Except at day 322, archaeal amoA genes always outnumbered bacterial amoA genes in both SATs as determined by using quantitative polymerase chain reaction (q-PCR). The ratios of archaeal amoA to 16S rRNA gene averaged at 0.70 ± 0.56 and 0.82 ± 0.62 in column 1 and column 4, respectively, indicating that all the archaea could be AOA carrying amoA gene in the SATs. The results of MiSeq-pyrosequencing targeting on archaeal and bacterial 16S rRNA genes with the primer pair of modified 515R/806R indicated that Nitrososphaera cluster affiliated with thaumarchaeal group I.1b was the dominant AOA species, while Nitrosospira cluster was the dominant ammonia-oxidizing bacteria (AOB). The statistical analysis showed significant relationship between AOA abundance (compared to AOB abundance) and inorganic and total nitrogen concentrations. Based on the mathematical model calculation for microbial growth, AOA had much greater capacity of ammonia oxidation as compared to the specific influent ammonia loading for AOA in the SATs, implying that a small fraction of the total AOA would actively work to oxidize ammonia chemoautotrophically whereas most of AOA would exhibit some level of functional redundancy. These results all pointed that AOA involved in microbial ammonia oxidation in the SATs.
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838
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Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, Vetter MM, Vilhjálmsson BJ, Nordborg M, Gordon JI, Bergelson J. Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nat Commun 2014; 5:5320. [PMID: 25382143 PMCID: PMC4232226 DOI: 10.1038/ncomms6320] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/18/2014] [Indexed: 02/04/2023] Open
Abstract
Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.
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Affiliation(s)
- Matthew W Horton
- 1] Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA [2] Gregor Mendel Institute, Austrian Academy of Sciences, Vienna 1030, Austria
| | - Natacha Bodenhausen
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Kathleen Beilsmith
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Dazhe Meng
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna 1030, Austria
| | - Brian D Muegge
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Sathish Subramanian
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - M Madlen Vetter
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | | | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna 1030, Austria
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
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839
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Youssef NH, Couger MB, McCully AL, Criado AEG, Elshahed MS. Assessing the global phylum level diversity within the bacterial domain: A review. J Adv Res 2014; 6:269-82. [PMID: 26257925 PMCID: PMC4522544 DOI: 10.1016/j.jare.2014.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022] Open
Abstract
Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexandra L McCully
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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840
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Desgarennes D, Garrido E, Torres-Gomez MJ, Peña-Cabriales JJ, Partida-Martinez LP. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species. FEMS Microbiol Ecol 2014; 90:844-57. [PMID: 25314594 DOI: 10.1111/1574-6941.12438] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 01/04/2023] Open
Abstract
Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta.
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Affiliation(s)
- Damaris Desgarennes
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados - Irapuato, Irapuato, México
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841
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Tian Y, Gao L. Bacterial diversity in the rhizosphere of cucumbers grown in soils covering a wide range of cucumber cropping histories and environmental conditions. MICROBIAL ECOLOGY 2014; 68:794-806. [PMID: 25027276 DOI: 10.1007/s00248-014-0461-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/04/2014] [Indexed: 06/03/2023]
Abstract
Rhizosphere microorganisms in soils are important for plant growth. However, the importance of rhizosphere microorganisms is still underestimated since many microorganisms associated with plant roots cannot be cultured and since the microbial diversity in the rhizosphere can be influenced by several factors, such as the cropping history, biogeography, and agricultural practice. Here, we characterized the rhizosphere bacterial diversity of cucumber plants grown in soils covering a wide range of cucumber cropping histories and environmental conditions by using pyrosequencing of bacterial 16S rRNA genes. We also tested the effects of compost addition and/or bacterial inoculation on the bacterial diversity in the rhizosphere. We identified an average of approximately 8,883 reads per sample, corresponding to around 4,993 molecular operational taxonomic units per sample. The Proteobacteria was the most abundant phylum in almost all soils. The abundances of the phyla Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, and Verrucomicrobia varied among the samples, and together with Proteobacteria, these phyla were the six most abundant phyla in almost all analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Flavobacterium, Ohtaekwangia, Opitutus, Gp6, Steroidobacter, and Acidovorax. Overall, compost and microbial amendments increased shoot biomass when compared to untreated soils. However, compost addition decreased the bacterial α-diversity in most soils (but for three soils compost increased diversity), and no statistical effect of microbial amendment on the bacterial α-diversity was found. Moreover, soil amendments did not significantly influence the bacterial β-diversity. Soil organic content appeared more important than compost and microbial amendments in shaping the structure of bacterial communities in the rhizosphere of cucumber.
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Affiliation(s)
- Yongqiang Tian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Agricultural and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China,
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842
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Liu L, Li T, Wei X, Jiang B, Fang P. Effects of a nutrient additive on the density of functional bacteria and the microbial community structure of bioorganic fertilizer. BIORESOURCE TECHNOLOGY 2014; 172:328-334. [PMID: 25280041 DOI: 10.1016/j.biortech.2014.08.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/28/2014] [Accepted: 08/31/2014] [Indexed: 06/03/2023]
Abstract
In this study, a secondary composting experiment was conducted to investigate the effects of concentrated monosodium glutamate wastewater (CMGW) as a nutrient additive on enhancing the density of functional bacteria in bioorganic fertilizer (BOF). The results showed that, as the CMGW was added, the composting mixture temperature rose more quickly and strongly, and the functional bacteria Bacillus subtilis F2 percentage in spores increased significantly. Furthermore, both the highest species richness value (Rs) of a given sample and similarity coefficient value (Cs) between a sample and strain F2 based on DGGE analysis were also observed in the treatment with CMGW. A similar effect of CMGW on the microbial community structure was verified by means of illumine-MiSeq sequencing. It may thus be concluded that CMGW is a recommendable nutrient additive for F2 predominating in the secondary composting process.
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Affiliation(s)
- Li Liu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Tianyu Li
- Zhejiang Provincial Key Laboratory of Subtropical Soil Science and Plant Nutrition, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xinghua Wei
- Zhejiang Provincial Key Laboratory of Subtropical Soil Science and Plant Nutrition, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Bokang Jiang
- Fengyuan Agricultural Science and Technology Co., Ltd., Jinhua 321000, PR China
| | - Ping Fang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Zhejiang Provincial Key Laboratory of Subtropical Soil Science and Plant Nutrition, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China.
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843
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Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE. Conducting a microbiome study. Cell 2014; 158:250-262. [PMID: 25036628 DOI: 10.1016/j.cell.2014.06.037] [Citation(s) in RCA: 459] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/03/2014] [Accepted: 06/27/2014] [Indexed: 12/11/2022]
Abstract
Human microbiome research is an actively developing area of inquiry, with ramifications for our lifestyles, our interactions with microbes, and how we treat disease. Advances depend on carefully executed, controlled, and reproducible studies. Here, we provide a Primer for researchers from diverse disciplines interested in conducting microbiome research. We discuss factors to be considered in the design, execution, and data analysis of microbiome studies. These recommendations should help researchers to enter and contribute to this rapidly developing field.
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Affiliation(s)
- Julia K Goodrich
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Angela C Poole
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Omry Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - William A Walters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - J Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
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844
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Ogawa DMO, Moriya S, Tsuboi Y, Date Y, Prieto-da-Silva ÁRB, Rádis-Baptista G, Yamane T, Kikuchi J. Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses. PLoS One 2014; 9:e110723. [PMID: 25330259 PMCID: PMC4203823 DOI: 10.1371/journal.pone.0110723] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 09/24/2014] [Indexed: 12/11/2022] Open
Abstract
We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems.
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Affiliation(s)
- Diogo M. O. Ogawa
- Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Fortaleza, CE, Brazil
- Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
| | - Shigeharu Moriya
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
- RIKEN Antibiotics Laboratory, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Yuuri Tsuboi
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Álvaro R. B. Prieto-da-Silva
- Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil
- Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil
- Laboratory of Genetics, Butantan Institute, Sao Paulo, SP, Brazil
| | - Gandhi Rádis-Baptista
- Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Fortaleza, CE, Brazil
- Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil
| | - Tetsuo Yamane
- Biotechnology and Natural Resources Program, University of the State of the Amazonas, Manaus, AM, Brazil
- Center for Environment and Biodiversity Studies, University of the State of the Amazonas, Manaus, AM, Brazil
- Center of Biotechnology of Amazon, Manaus, AM, Brazil
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, and Biomass Engineering Corporation Division, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- * E-mail:
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845
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Lakshmanan V, Selvaraj G, Bais HP. Functional soil microbiome: belowground solutions to an aboveground problem. PLANT PHYSIOLOGY 2014; 166:689-700. [PMID: 25059708 PMCID: PMC4213098 DOI: 10.1104/pp.114.245811] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 07/23/2014] [Indexed: 05/07/2023]
Abstract
There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.
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Affiliation(s)
- Venkatachalam Lakshmanan
- Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, Delaware 19711
| | - Gopinath Selvaraj
- Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, Delaware 19711
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, Delaware 19711
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846
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Microbial genome-enabled insights into plant–microorganism interactions. Nat Rev Genet 2014; 15:797-813. [DOI: 10.1038/nrg3748] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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847
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Ofek-Lalzar M, Sela N, Goldman-Voronov M, Green SJ, Hadar Y, Minz D. Niche and host-associated functional signatures of the root surface microbiome. Nat Commun 2014; 5:4950. [PMID: 25232638 DOI: 10.1038/ncomms5950] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/08/2014] [Indexed: 01/20/2023] Open
Abstract
Plant microbiomes are critical to host adaptation and impact plant productivity and health. Root-associated microbiomes vary by soil and host genotype, but the contribution of these factors to community structure and metabolic potential has not been fully addressed. Here we characterize root microbial communities of two disparate agricultural crops grown in the same natural soil in a controlled and replicated experimental system. Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. Root colonization requires multiple functional capabilities, and these capabilities are enriched at the community level. Differences between the root-associated microbial communities from different plants are observed at the genus or species level, and are related to root-zone environmental factors.
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Affiliation(s)
- Maya Ofek-Lalzar
- 1] Department of Soil, Water and Environmental Sciences, Agricultural Research Organization of Israel, Bet Dagan 50250, Israel [2] Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Agricultural Research Organization of Israel, Bet Dagan 50250, Israel
| | - Milana Goldman-Voronov
- Department of Soil, Water and Environmental Sciences, Agricultural Research Organization of Israel, Bet Dagan 50250, Israel
| | - Stefan J Green
- 1] DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois 60612, USA [2] Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, USA
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Dror Minz
- Department of Soil, Water and Environmental Sciences, Agricultural Research Organization of Israel, Bet Dagan 50250, Israel
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848
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Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc Natl Acad Sci U S A 2014; 111:13715-20. [PMID: 25225376 DOI: 10.1073/pnas.1216057111] [Citation(s) in RCA: 273] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phyllosphere--the aerial surfaces of plants, including leaves--is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density-growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant-microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.
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849
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Indoor-air microbiome in an urban subway network: diversity and dynamics. Appl Environ Microbiol 2014; 80:6760-70. [PMID: 25172855 DOI: 10.1128/aem.02244-14] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Subway systems are indispensable for urban societies, but microbiological characteristics of subway aerosols are relatively unknown. Previous studies investigating microbial compositions in subways employed methodologies that underestimated the diversity of microbial exposure for commuters, with little focus on factors governing subway air microbiology, which may have public health implications. Here, a culture-independent approach unraveling the bacterial diversity within the urban subway network in Hong Kong is presented. Aerosol samples from multiple subway lines and outdoor locations were collected. Targeting the 16S rRNA gene V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those associated with skin. Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. Microbial diversities and assemblages also varied depending on the day sampled, as well as the time of day, and changes in microbial communities between peak and nonpeak commuting hours were attributed largely to increases in skin-associated genera in peak samples. Microbial diversities within the subway were influenced by temperature and relative humidity, while carbon dioxide levels showed a positive correlation with abundances of commuter-associated genera. This Hong Kong data set and communities from previous studies conducted in the United States formed distinct community clusters, indicating that additional work is required to unravel the mechanisms that shape subway microbiomes around the globe.
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850
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Zachow C, Müller H, Tilcher R, Berg G. Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima-ancestor of all beet crops-and modern sugar beets. Front Microbiol 2014; 5:415. [PMID: 25206350 PMCID: PMC4144093 DOI: 10.3389/fmicb.2014.00415] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 07/22/2014] [Indexed: 02/01/2023] Open
Abstract
The structure and function of the plant microbiome is driven by plant species and prevailing environmental conditions. Effectuated by breeding efforts, modern crops diverge genetically and phenotypically from their wild relatives but little is known about consequences for the associated microbiota. Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions. Analysis of 16S rRNA gene fingerprints and pyrosequencing-based amplicon libraries revealed plant genotype- and soil-specific microbiomes. Wild beet plants harbor distinct operational taxonomic units (OTUs) and a more diverse bacterial community than the domesticated sugar beet plants. Although the rhizospheres of both plant genotypes were dominated by Proteobacteria and Planctomycetes, 37.5% of dominant OTUs were additionally detected in the wild beet rhizosphere. Analysis of the cultivable fraction confirmed these plant genotype-specific differences at functional level. The proportion of isolates displayed in vitro activity against phytopathogens was lower for wild beet (≤45.8%) than for sugar beet (≤57.5%). Conversely, active isolates from the wild beet exhibited stronger ability to cope with abiotic stresses. From all samples, active isolates of Stenotrophomonas rhizophila were frequently identified. In addition, soil type-specific impacts on the composition of bacterial communities were found: Acidobacteria, Chloroflexi, and Planctomycetes were only detected in plants cultivated in CS; whereas Bacteroidetes and Proteobacteria dominated in PS. Overall, in comparison to modern sugar beets, wild beets were associated with taxonomically and functionally distinct microbiomes.
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Affiliation(s)
- Christin Zachow
- Austrian Center of Industrial Biotechnology (ACIB GmbH) Graz, Austria ; Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
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