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      Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing

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      Author(s): 1 , 2 , * , 2 , 2 , 1 , *
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      Publication date (Electronic):
      Journal: PLoS ONE
      Publisher: Public Library of Science

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          Abstract

          In this study, we designed a microcosm experiment to explore the composition of the bacterial community in the rhizosphere of maize and bulk soil by sequencing the V3-V4 region of the 16S rRNA gene on the Illumina system. 978–1239 OTUs (cut off level of 3%) were found in rhizosphere and bulk soil samples. Rhizosphere shared features with the bulk soil, such as predominance of Acidobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes and TM7. At genus level, many of the dominant rhizosphere genera ( Chitinophaga, Nitrospira, Flavobacterium, etc.) displayed different patterns of temporal changes in the rhizosphere as opposed to the bulk soil, showing rhizosphere has more impact on soil microorganisms. Besides, we found that significant growth-related dynamic changes in bacterial community structure were mainly associated with phylum Bacteroidetes, Proteobacteria and Actinobacteria (mainly genera Burkholderia, Flavisolibacter and Pseudomonas), indicating that different growth stages affected the bacterial community composition in maize soil. Furthermore, some unique genera in especial Plant-Growth Promoting Rhizobacteria (PGPR) such as Nonomuraea, Thiobacillus and Bradyrhizobium etc., which were beneficial for the plant growth appeared to be more abundant in the rhizosphere than bulk soil, indicating that the selectivity of root to rhizosphere microbial is an important mechanism leading to the differences in the bacteria community structure between rhizosphere and bulk soil.

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          Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

          N Fierer, J W Leff, B. J. Adams … (2012)
          For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.
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            454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity.

            M Buée, M. Reich, C Murat … (2009)
            * Soil fungi play a major role in ecological and biogeochemical processes in forests. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). * Here, we assessed the fungal diversity in six different forest soils using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1). No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units. * Most operational taxonomic units (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant operational taxonomic units showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp. * This study validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.
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              Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

              Katherine Goldfarb, Ulas Karaoz, China A. Hanson … (2011)
              Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin–protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.
              Article 0 comments Cited 191 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Yi Luo: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 25 May 2017
                Publication date Collection: 2017
                Volume: 12
                Issue: 5
                Electronic Location Identifier: e0178425
                Affiliations
                [1 ]School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
                [2 ]Nanjing Institute of Environmental Science, Ministry of Environmental Protection, Nanjing, China
                Nankai University, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: NW YY BY.

                • Data curation: YY.

                • Funding acquisition: NW BY.

                • Investigation: YY XG YZ.

                • Methodology: YY XG.

                • Project administration: YY BY.

                • Resources: NW BP.

                • Software: YY.

                • Supervision: NW BY.

                • Visualization: XG YZ.

                • Writing – original draft: YY.

                • Writing – review & editing: NW BY.

                Author information
                http://orcid.org/0000-0001-9617-0300
                Article
                Publisher ID: PONE-D-17-00044
                DOI: 10.1371/journal.pone.0178425
                PMC ID: 5444823
                PubMed ID: 28542542
                SO-VID: 583b162d-95f3-40ca-b036-aeb49471c202
                License:

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                Date received : 3 January 2017
                Date accepted : 12 May 2017
                Page count
                Figures: 2, Tables: 4, Pages: 11
                Funding
                Funded by: Natural Science Foundation of China
                Award ID: No. 21507037
                Award Recipient :
                ORCID: http://orcid.org/0000-0001-9617-0300
                Funded by: Commonwealth and Environmental Protection Project granted by the MEP
                Award ID: No. 201309031
                Award Recipient :
                ORCID: http://orcid.org/0000-0001-9617-0300
                Funded by: Fundamental Research Funds for NIES in 2016 “Source Apportionment Research of antibiotics pollution in typical drinking water resource
                Award Recipient :
                ORCID: http://orcid.org/0000-0001-9617-0300
                This study was financially support by the Natural Science Foundation of China (No. 21507037), Commonwealth and Environmental Protection Project granted by the MEP (No. 201309031), as well as the Fundamental Research Funds for NIES in 2016 “Source Apportionment Research of antibiotics pollution in typical drinking water resource”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article
                Subject: Biology and Life Sciences
                Subject: Ecology
                Subject: Plant Ecology
                Subject: Plant-Environment Interactions
                Subject: Rhizosphere
                Subject: Ecology and Environmental Sciences
                Subject: Ecology
                Subject: Plant Ecology
                Subject: Plant-Environment Interactions
                Subject: Rhizosphere
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Ecology
                Subject: Plant-Environment Interactions
                Subject: Rhizosphere
                Subject: Research and Analysis Methods
                Subject: Experimental Organism Systems
                Subject: Model Organisms
                Subject: Maize
                Subject: Research and Analysis Methods
                Subject: Model Organisms
                Subject: Maize
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Plants
                Subject: Grasses
                Subject: Maize
                Subject: Research and Analysis Methods
                Subject: Experimental Organism Systems
                Subject: Plant and Algal Models
                Subject: Maize
                Subject: Biology and Life Sciences
                Subject: Microbiology
                Subject: Medical Microbiology
                Subject: Microbial Pathogens
                Subject: Bacterial Pathogens
                Subject: Medicine and Health Sciences
                Subject: Pathology and Laboratory Medicine
                Subject: Pathogens
                Subject: Microbial Pathogens
                Subject: Bacterial Pathogens
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Bacteria
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Bacteria
                Subject: Actinobacteria
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Physiology
                Subject: Nitrogen Fixation
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Bacteria
                Subject: Pseudomonas
                Subject: Biology and Life Sciences
                Subject: Developmental Biology
                Subject: Plant Growth and Development
                Subject: Biology and Life Sciences
                Subject: Plant Science
                Subject: Plant Growth and Development
                Custom metadata
                Data Availability All relevant data are within the paper.

                ScienceOpen disciplines: Uncategorized
                Data availability:
                ScienceOpen disciplines: Uncategorized

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