A genomic catalog of Earth’s microbiomes
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Nayfach et al. applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla.
Maize brace roots provide stalk anchorage
Reneau et al. use a non‐destructive field‐based mechanical test on plants before and after the removal of brace roots. This precisely determines the contribution of brace roots to establish a rigid base (i.e. stalk anchorage) that limits plant deflection in maize. These measurements demonstrate that the more brace root whorls that contact the soil, the greater their overall contribution to anchorage, but that the contributions of each whorl to anchorage were not equal.
Picture worth a thousand words: Updating repeat photography for 21st century ecologists
While satellite imagery provides a coarse baseline for regional‐scale changes in vegetation, landscape‐scale observations are lacking. Ground‐based repeat photographic points (RPP) can provide this finer baseline. Hammond et al's updated methods can be practically applied to nearly all terrestrial study systems. Landscape changes driven by human (e.g., effects of anthropogenic climate change, land use) and natural activities (e.g., wildfires, phenology, and hydrologic events) are especially well suited to their updated methods.
Ecology and Evolution
Discarded food and resource depletion
Food systems are driven by incentives that often lead to food being discarded before entering the market and to the degradation of natural resources. Vegetable production in the water-scarce province of Almería, Spain, illustrates this and highlights the need for policies ensuring ethical and environmental sustainability standards.
Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea
Min and Kramer have conducted the first in-depth transcriptome profiling of early floral development in Aquilegia at four finely dissected developmental stages, with eight biological replicates per stage. Using differential gene expression analysis and weighted gene co-expression network analysis, they identified both crucial genes whose expression changes mark the transitions between developmental stages and hub genes in co-expression modules. Their results support the potential functional conservation of key genes in early floral development that have been identified in other systems, but also reveal a number of previously unknown or overlooked loci that are worthy of further investigation.
Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy
Sato et al. show that maternal alleles marked by H3K27me3 in the Arabidopsis endosperm were targeted by the H3K27me3 demethylase REF6 and became activated during germination. In contrast, maternal alleles marked by H3K27me3, H3K9me2, and CHGm were protected from REF6 targeting and remained silenced. Our study unveils that combinations of different repressive epigenetic modifications time a key adaptive trait by modulating access of REF6.
Cell wall remodeling and vesicle trafficking mediate the root clock in Arabidopsis
Lateral roots form at regular intervals in the small mustard plant Arabidopsis thaliana. Wachsman et al. have now identified both pectin and subcellular vesicle trafficking as part of the oscillating signaling system that initiates lateral roots. Esterification of pectin regulates its function at the nascent lateral root site, altering the stiffness of cell walls and the strength of cell-cell adhesion. Because lateral root primordia must push through overlying cell layers, reduced cell adhesion at these sites might aid in the formation of lateral roots.
A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming
Han et al. identified a cullin-RING ubiquitin ligase (CRL), containing the substrate adapter ZSWIM8, that mediated TDMD. The ZSWIM8 CRL interacted with AGO proteins, promoted TDMD in a tailing and trimming-independent manner, and regulated miRNA expression in multiple cell types. These findings suggest a model in which the ZSWIM8 ubiquitin ligase mediates TDMD by directing proteasomal decay of miRNA-containing complexes engaged with highly complementary targets.
Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles
Glucke-Thaler et al. show that the hydrolase CbsA acts as a phenotypic switch between vascular and nonvascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the family Xanthomonadaceae and absent in most nonvascular species. CbsA expression allowed nonvascular Xanthomonas to cause vascular blight, while cbsA mutagenesis resulted in reduction of vascular or enhanced nonvascular symptom development.
Efficient simultaneous mutagenesis of multiple genes in specific plant tissues by multiplex CRISPR
Bollier et al. simultaneously mutated six genes either ubiquitously or exclusively in the root cap of Arabidopsis. The mutation frequencies for all target genes were positively correlated and unaffected by the order of gRNAs in the vector, indicating that efficient higher-order mutagenesis in specific plant tissues can be readily achieved.