Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework.

We have developed a flexible undergraduate curriculum that leverages the place-based research of environmental microbiomes to increase the number of Indigenous researchers in microbiology, data science and scientific computing. Monitoring Environmental Microbiomes (MEM) provides a curriculum and research framework designed to integrate an Indigenous approach when conducting authentic scientific research and to build interest and confidence at the undergraduate level. MEM has been successfully implemented as a short summer workshop to introduce computing practices in microbiome analysis. Based on self-assessed student knowledge of topics and skills, increased scientific confidence and interest in genomics careers were observed. We propose MEM be incorporated in a scalable course-based research experience for undergraduate institutions, including tribal colleges and universities, community colleges and other minority serving institutions. This coupled curricular and research framework explicitly considers cultural perspectives, access and equity to train a diverse future workforce that is more informed to engage in microbiome research and to translate microbiome science to benefit community and environmental health.

Leaf shape and anatomy as indicators of phase change in the grasses: comparison of maize, rice, and bluegrass.

Leaf morphology and anatomy during vegetative phase change was compared in bluegrass, rice, and maize. Maize juvenile leaves are coated with epicuticular wax, lack specialized cells, such as trichomes and bulliform cells, and epidermal cell walls stain a uniform purple color. Adult maize leaves are pubescent, lack epicuticular waxes, and have crenulated epidermal cell walls that stain purple and blue. All bluegrass and rice blades are pubescent, coated with epicuticular waxes, and show purple and blue wall staining. In all three grasses, blade width steadily increases at each node until a threshold size is achieved several nodes before reproductive competence is acquired. Blade-to-sheath length showed a similar trend of continuous change followed by discontinuous change prior to reproduction. Analysis of leaf development demonstrated that maize primordia initiate more rapidly relative to blade and sheath growth than do either bluegrass or rice. We conclude that leaf shape, as defined by blade width and blade-to-sheath ratio, is a reliable indicator of phase, whereas anatomy is not a universal indicator of phase change in the grasses. We speculate that different growth patterns among these grasses may be attributed to changes in the timing of embryonic and postembryonic development.

Division decisions and the spatial regulation of cytokinesis.

Cytokinesis in plant cells in accomplished when a membranous cell plate is guided to a pre-established division site. The orientation of the new wall establishes the starting position of a cell in a growing tissue, but the impact of this position on future development varies. Recently, proteins have been identified that participate in forming, stabilizing and guiding the cell plate to the correct division site. Mutations that affect cytokinesis with varying impacts on plant development are providing information about the mechanics of cytokinesis and also about how the division site is selected.

Balancing division and expansion during maize leaf morphogenesis: analysis of the mutant, warty-1.

Cell division and expansion are growth events that contribute to the developing shape, or morphogenesis, of a plant. Division and expansion are coordinated to the extent that plant organs, such as leaves, generally portray a predictable cellular pattern. To dissect the relationship between division and expansion, and to test for the role of each during morphogenesis, we have identified a recessive mutation warty-1 that produces a primary defect in cell size and shape in mutant leaves. Warty-1 mutant plants are similar to non-mutant siblings in terms of flowering time, overall plant size and leaf shape. Mature adult leaves have raised warts, consisting of excessively enlarged cells, that appear in patchy distribution throughout the blade. Cell wall deposition is abnormal or incomplete, suggesting cytokinesis is also affected, either directly or indirectly. Cells first increase in size at specific positions, which correspond to predictable cell dimensions of a developing 1 cm leaf. Once mutant cells exceed 133% normal size, cytokinesis becomes abnormal. As differentiation progresses, cells that appear normal in the mutant are actually dividing faster and are smaller than comparable cells in non-mutant siblings. These results suggest that (1) cells may compensate for growth defects by altering their cell cycle and that (2) proper execution of cytokinesis may require that cell size ratios are properly maintained.

The tangled-1 mutation alters cell division orientations throughout maize leaf development without altering leaf shape.

It is often assumed that in plants, where the relative positions of cells are fixed by cell walls, division orientations are critical for the generation of organ shapes. However, an alternative perspective is that the generation of shape may be controlled at a regional level independently from the initial orientations of new cell walls. In support of this latter view, we describe here a recessive mutation of maize, tangled-1 (tan-1), that causes cells to divide in abnormal orientations throughout leaf development without altering overall leaf shape. In normal plants, leaf cells divide either transversely or longitudinally relative to the mother cell axis; transverse division are associated with leaf elongation and longitudinal divisions with leaf widening. In tan-l mutant leaves, cells in all tissue layers at a wide range of developmental stages divide transversely at normal frequencies, but longitudinal divisions are largely substituted by a variety of aberrantly oriented divisions in which the new cell wall is crooked or curved. Mutant leaves grow more slowly than normal, but their overall shapes are normal at all stages of their growth. These observations demonstrate that the generation of maize leaf shape does not depend on the precise spatial control of cell division, and support the general view that mechanisms independent from the control of cell division orientations are involved in the generation of shape during plant development.

Acquisition of identity in the developing leaf.

Leaves are produced repeatedly from the shoot apical meristem of plants. Molecular and cellular evidence show that identity of the leaf and its parts is acquired progressively and that the underlying process changes as the leaf matures. The relative importance of cell lineage compared with a position-dependent model for specifying cell fates is discussed.

Cytoplasmic reorganization accompanies the deposition of a bipolar cell wall in the large-celled red alga Anotrichium tenue.

The filamentous red alga Anotrichium tenue C. Aghard (Naegeli) (formerly Griffithsia tenuis C. Aghard; Baldock, 1976, Aust. T. Bot. 24, 509-593) has large (1-2 mm long), cylindrical, multinucleate cells that exhibit a daily, cyclic redistribution of chloroplasts. Chloroplasts accumulate in the mid-region of each growing cell during the day; consequently, filaments appear banded with a light apical end-band, a dark mid-band and a light basal end-band in each growing cell. Chloroplasts disperse at night so that the bands are no longer visible and the cells appear evenly pigmented. Anotrichium tenue also has a type of cell elongation, known as bipolar band growth, in which new material is added to the microfibrillar part of the wall in bands located at the apical and basal poles of elongating cells. This site of wall growth corresponds to the position of the light-colored end-bands present during the day. Here we examine the structural relationship between the cytoplasmic bands and the wall-growth bands. Our results show that, in addition to the previously described bipolar wall bands, there is a non-microfibrillar wall band in the mid-region of the cell. This wall component apparently branches from near the top of the microfibrillar outer wall and terminates near but not at the bottom of the cell. It contains nodules of sulphated polysaccharide material secreted from a band of vesicles, which co-localize with the chloroplasts in the mid-band. The outer wall appears to enclose the entire cell. Nuclei do not redistribute with the chloroplasts or wall vesicles into the mid-band but remain evenly distributed throughout the cytoplasm. Each wall component grows by a different mechanism. We show that two types of wall growth, diffuse and the bipolar-type of tip growth, occur in the same cell and we propose that the observed segregation of the cytoplasm supports localized growth of the unique inner wall component. Additionally, we show that A. tenue is an excellent model for study of the role and mechanism of cytoplasmic compartmentalization and cell polarity during plant cell growth.

Division and differentiation during normal and liguleless-1 maize leaf development.

The maize leaf is composed of a blade and a sheath, which are separated at the ligular region by a ligule and an auricle. Mutants homozygous for the recessive liguleless-1 (lg1) allele exhibit loss of normal ligule and auricle. The cellular events associated with development of these structures in both normal and liguleless plants are investigated with respect to the timing of cell division and differentiation. A new method is used to assess orientation of anticlinal division planes during development and to determine a division index based on recent epidermal cross-wall deposition. A normal leaf follows three stages of development: first is a preligule stage, in which the primordium is undifferentiated and dividing throughout its length. This stage ends when a row of cells in the preligule region divides more rapidly in both transverse and longitudinal anticlinal planes. During the second stage, ligule and auricle form, blade grows more rapidly than sheath, divisions in the blade become exclusively transverse in orientation, and differentiation begins. The third stage is marked by rapid increase in sheath length. The leaf does not have a distinct basal meristem. Instead, cell divisions are gradually restricted to the base of the leaf with localized sites of increased division at the preligule region. Divisions are not localized to the base of the sheath until near the end of development. The liguleless-1 homozygote shows no alteration in this overall pattern of growth, but does show distinct alteration in the anticlinal division pattern in the preligule region. Two abnormal patterns are observed: either the increase in division rate at the preligule site is absent or it exhibits loss of all longitudinal divisions so that only transverse (or cell-file producing) divisions are present. This pattern is particularly apparent in developing adult leaves on older lg1 plants, in which sporadic ligule vestiges form. From these and results previously published (Becraft et al. (1990) Devl Biol. 14), we conclude that the information carried by the Lg1+ gene product acts earlier in development than formation of the ligule proper. We hypothesize that Lg1+ may be effective at the stage when the blade-sheath boundary is first determined.

The liguleless-1 gene acts tissue specifically in maize leaf development.

The liguleless-1 (lg1) gene affects maize leaf development. In a normal maize leaf, a ligule and auricles separate the blade and sheath. The recessive lg1 mutation prevents formation of ligules and auricles during leaf development. To determine the timing and site of lg1 gene action, we compared development of wild-type and lg1 mutant leaves, and analyzed genetic mosaics composed of wild-type and lg1 mutant cells. In wild-type leaves the first sign of differentiation of the ligular region is a series of specialized anticlinal divisions in the adaxial epidermis. This establishes a distinct band of cells, from which the ligule arises via periclinal divisions. The anticlinal divisions preceding ligule formation are altered in the mutant; therefore, the gene acts early in development, before the periclinal divisions, and possibly during basipetal vascularization. Genetic mosaic analysis indicates that the lg1 gene has at least two functions with different tissue specificities: The Lg1+ wild-type allele acts autonomously in the adaxial epidermis for normal ligule development, and in internal tissues for auricle formation. Wild-type internal tissue in direct contact with lg1 epidermis appears able to induce the mutant epidermis to form a rudimentary ligule. The results indicate that the lg1 gene acts tissue specifically in an early step of ligule and auricle initiation.