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.

The crucifer Arabidopsis thaliana has been used widely as a model organism for the study of plant development. We describe here the development of an efficient insertional mutagenesis system in Arabidopsis

The formation of haploid spores marks the initiation of the gametophytic phase of the life cycle of all vascular plants ranging from ferns to angiosperms. In angiosperms, this process is initiated by the differentiation of a subset of floral cells into sporocytes, which then undergo meiotic divisions to form microspores and megaspores. Currently, there is little information available regarding the genes and proteins that regulate this key step in plant reproduction. We report here the identification of a mutation, SPOROCYTELESS (SPL), which blocks sporocyte formation in Arabidopsis thaliana. Analysis of the SPL mutation suggests that development of the anther walls and the tapetum and microsporocyte formation are tightly coupled, and that nucellar development may be dependent on megasporocyte formation. Molecular cloning of the SPL gene showed that it encodes a novel nuclear protein related to MADS box transcription factors and that it is expressed during microsporogenesis and megasporogenesis. These data suggest that the SPL gene product is a transcriptional regulator of sporocyte development in Arabidopsis.[Key Words: Arabidopsis mutant; sporogenesis; sporocyte; SPL; nuclear protein] Received May 12, 1999; revised version accepted July 1, 1999.The life cycle of plants consists of an alternation between a diploid, sporophytic generation and a haploid, gametophytic generation. The gametophytes of lower plants and nonflowering vascular plants such as ferns are free living organisms that undergo differentiation and development independent of the sporophytes, whereas the gametophytes of flowering plants complete their development within the male and female floral organs of the sporophytes. In flowering plants like Arabidopsis, the transition from the sporophytic phase to the gametophytic phase consists of two sequential processes, sporogenesis and gametogenesis. The latter process mainly involves development of haploid spores into mature gametophytes. Sporogenesis is characterized by the differentiation of hypodermal cells in anthers and in ovule primordia into microsporocytes and megasporocytes, respectively (Maheswari 1950;Misra 1962). The sporocyte, or meiocyte, undergoes meiosis to give rise to the microspores and megaspores. Thus, the differentiation step is marked by the acquisition of a meiotic cell fate by a subset of floral cells. In contrast to the yeasts and fungi, there is relatively little information on the genetic regulation of sporogenesis in the plant kingdom (Dickinson 1994), although several sporophytic mutants that affect sporogenesis have been reported (Robinson-Beers et al. 1992; Lang et al. 1994;Elliott et al. 1996;Klucher et al. 1996;Schneitz et al. 1997;Byzova et al. 1999;Sanders et al. 1999). Here we report the identification and molecular characterization of a gene SPOROCYTELESS (SPL) that is essential for sporogenesis in both male and female organs in Arabidopsis plants. Results Isolation of the sporocyteless mutationThe spl mutation was identified by its complete male and female sterili...

The plant life cycle involves an alternation of generations between sporophyte and gametophyte. Currently, the genes and pathways involved in gametophytic development and function in flowering plants remain largely unknown. A large-scale mutant screen of Ds transposon insertion lines was employed to identify 130 mutants of Arabidopsis thaliana with defects in female gametophyte development and function. A wide variety of mutant phenotypes were observed, ranging from defects in different stages of early embryo sac development to mutants with apparently normal embryo sacs, but exhibiting defects in processes such as pollen tube guidance, fertilization or early embryo development. Unexpectedly, nearly half of the mutants isolated in this study were found to be primarily defective in post-fertilization processes dependent on the maternal allele, suggesting that genes expressed from the female gametophyte or the maternal genome play a major role in the early development of plant embryos. Sequence identification of the genes disrupted in the mutants revealed genes involved in protein degradation, cell death, signal transduction and transcriptional regulation required for embryo sac development, fertilization and early embryogenesis. These results provide a first comprehensive overview of the genes and gene products involved in female gametophyte development and function within a flowering plant.

In flowering plants, penetration of the pollen tube through stigma, style, and transmitting tract is essential for delivery of sperm nuclei to the egg cells embedded deeply within female tissues. Despite its importance in plant reproduction, little is known about the underlying molecular mechanisms that regulate the navigation of the pollen tube through the stigma, style, and transmitting tract. Here, we report the identification and characterization of an Arabidopsis thaliana gene, VANGUARD1 (VGD1) that encodes a pectin methylesterase (PME)-homologous protein of 595 amino acids and is required for enhancing the growth of pollen tubes in the style and transmitting tract tissues. VGD1 was expressed specifically in pollen grain and the pollen tube. The VGD1 protein was distributed throughout the pollen grain and pollen tube, including the plasma membrane and cell wall. Functional interruption of VGD1 reduced PME activity in the pollen to 82% of the wild type and greatly retarded the growth of the pollen tube in the style and transmitting tract, resulting in a significant reduction of male fertility. In addition, the vgd1 pollen tubes were unstable and burst more frequently when germinated and grown on in vitro culture medium, compared with wild-type pollen tubes. Our study suggests that the VGD1 product is required for growth of the pollen tube, possibly via modifying the cell wall and enhancing the interaction of the pollen tube with the female style and transmitting tract tissues