Microorganisms represent a substantial portion of the earth’s biodiversity and biomass, and the plant rhizosphere is an innate reservoir teeming with heterogeneous microbes predominated by bacterial communities. Rhiz...Microorganisms represent a substantial portion of the earth’s biodiversity and biomass, and the plant rhizosphere is an innate reservoir teeming with heterogeneous microbes predominated by bacterial communities. Rhizospheric microbial diversity (genetic, phenotypic, and metabolic) has been extensively studied to understand the key ecological roles played by the microbial members, including plant growth promotion. The application of 16S rRNA gene sequencing and next-generation sequencing (NGS) technologies has revolutionized the discovery of novel bacterial groups that have remained undetected by traditional cultivation-based approaches. Such technological advancements have opened new vistas in our current understanding of predominant but concealed and missed bacterial diversity referred to as difficult-to-culture bacterial lineages, especially the predominant phyla Acidobacteria, Verrucomicrobia,Planctomycetes, and Gemmatimonadetes. Regardless of their ubiquity and prevalence, little is known about their ecophysiology because of the non-availability of culturable members. More recently, there has been increased interest in understanding the cosmopolitan distribution and diversity of the difficult-to-culture bacteria, focusing on their role in driving complex plant-microbial interactions and mobilizing nutrients in soil and their potential as sources of novel bioactive metabolites. As an initial step, we review the distribution and significance of such bacterial phyla in soil, their ecophysiological roles, and their hidden plant growth promoting potential. The ability to select and deploy plant probiotic bacteria from the difficult-to-culture fraction of the bacterial community might open new avenues for improving crop health.展开更多
The diversity of Planctomycetes and related bacteria in 3 types of freshwater wetlands with different anthropogenic disturbances were investigated by cloning and sequencing PCR-amplified partial 16S rRNA genes. Three ...The diversity of Planctomycetes and related bacteria in 3 types of freshwater wetlands with different anthropogenic disturbances were investigated by cloning and sequencing PCR-amplified partial 16S rRNA genes. Three clone libraries were constructed using 16S rRNA-targeted forward PCR primer specific for Planctomycetales and general bacterial reverse primer. Phylogenetic analysis of the 16S rRNA gene sequences defined 95 operational taxonomic units (OTUs) with 163 sequences. The clone libraries covered a wide microbial diversity of Proteobacteria and the Planctomycetes-Verrucomicrobia-Chlamydiales (PVC) superphylum. The majority of the OTUs were related to the phylum of Planctomycetes (33 OTUs), Proteobacteria (22 OTUs) and Verrucomicrobia (22 OTUs). Four known genera from the Planctomycetes phylum were all detected. The genus Pirellula (18 OTUs) dominated the Planctomycetes community, but different patterns of distribution were observed in the wetlands. The littoral wetlands of Baiyangdian Lake with the least anthropogenic disturbances covered more species and showed the highest biodiversity. However, the Jiaxing paddy fields with the highest anthropogenic disturbances showed a higher biodiversity than that in the riparian wetlands of the North Canal. Bacteria distantly related to anammox bacteria were also detected with a small proportion (4 OTUs). It showed that wetlands hold a great biodiversity of phyla Planctomycetes and related bacteria; furthermore, there is ample opportunity to discover novel phylotypes of Planctomycetes in the wetland ecosystems.展开更多
文摘Microorganisms represent a substantial portion of the earth’s biodiversity and biomass, and the plant rhizosphere is an innate reservoir teeming with heterogeneous microbes predominated by bacterial communities. Rhizospheric microbial diversity (genetic, phenotypic, and metabolic) has been extensively studied to understand the key ecological roles played by the microbial members, including plant growth promotion. The application of 16S rRNA gene sequencing and next-generation sequencing (NGS) technologies has revolutionized the discovery of novel bacterial groups that have remained undetected by traditional cultivation-based approaches. Such technological advancements have opened new vistas in our current understanding of predominant but concealed and missed bacterial diversity referred to as difficult-to-culture bacterial lineages, especially the predominant phyla Acidobacteria, Verrucomicrobia,Planctomycetes, and Gemmatimonadetes. Regardless of their ubiquity and prevalence, little is known about their ecophysiology because of the non-availability of culturable members. More recently, there has been increased interest in understanding the cosmopolitan distribution and diversity of the difficult-to-culture bacteria, focusing on their role in driving complex plant-microbial interactions and mobilizing nutrients in soil and their potential as sources of novel bioactive metabolites. As an initial step, we review the distribution and significance of such bacterial phyla in soil, their ecophysiological roles, and their hidden plant growth promoting potential. The ability to select and deploy plant probiotic bacteria from the difficult-to-culture fraction of the bacterial community might open new avenues for improving crop health.
基金the projects of National Natural Science Foundation of China(21077119)National Basic Research Program of China(2009CB421103)+2 种基金Special Fund of State Key Joint Laboratory of Environment Simulation and Pollution Control(12L03ESPC)Beijing Nova Program(2011095)K.C.Wong Education Foundation,Hong Kong
文摘The diversity of Planctomycetes and related bacteria in 3 types of freshwater wetlands with different anthropogenic disturbances were investigated by cloning and sequencing PCR-amplified partial 16S rRNA genes. Three clone libraries were constructed using 16S rRNA-targeted forward PCR primer specific for Planctomycetales and general bacterial reverse primer. Phylogenetic analysis of the 16S rRNA gene sequences defined 95 operational taxonomic units (OTUs) with 163 sequences. The clone libraries covered a wide microbial diversity of Proteobacteria and the Planctomycetes-Verrucomicrobia-Chlamydiales (PVC) superphylum. The majority of the OTUs were related to the phylum of Planctomycetes (33 OTUs), Proteobacteria (22 OTUs) and Verrucomicrobia (22 OTUs). Four known genera from the Planctomycetes phylum were all detected. The genus Pirellula (18 OTUs) dominated the Planctomycetes community, but different patterns of distribution were observed in the wetlands. The littoral wetlands of Baiyangdian Lake with the least anthropogenic disturbances covered more species and showed the highest biodiversity. However, the Jiaxing paddy fields with the highest anthropogenic disturbances showed a higher biodiversity than that in the riparian wetlands of the North Canal. Bacteria distantly related to anammox bacteria were also detected with a small proportion (4 OTUs). It showed that wetlands hold a great biodiversity of phyla Planctomycetes and related bacteria; furthermore, there is ample opportunity to discover novel phylotypes of Planctomycetes in the wetland ecosystems.
