Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates

Mechanistic insights into plant community responses to environmental variables: genome size, cellular nutrient investments, and metabolic tradeoffs

Affecting biodiversity, plants with larger genome sizes (GS) may be restricted in nutrient-poor conditions. This pattern has been attributed to their greater cellular nitrogen (N) and phosphorus (P) investments and hypothesized nutrient-investment tradeoffs between cell synthesis and physiological attributes associated with growth. However, the influence of GS on cell size and functioning may also contribute to GS-dependent growth responses to nutrients. To test whether and how GS is associated with cellular nutrient, stomata, and/or physiological attributes, we examined > 500 forbs and grasses from seven grassland sites conducting a long-term N and P fertilization experiment. Larger GS plants had increased cellular nutrient contents and larger, but fewer stomata than smaller GS plants. Larger GS grasses (but not forbs) also had lower photosynthetic rates and water-use efficiencies. However, nutrients had no direct effect on GS-dependent physiological attributes and GS-dependent physiological changes likely arise from how GS influences cells. At the driest sites, large GS grasses displayed high water-use efficiency mostly because transpiration was reduced relative to photosynthesis in these conditions. We suggest that climatic conditions and GS-associated cell traits that modify physiological responses, rather than resource-investment tradeoffs, largely explain GS-dependent growth responses to nutrients (especially for grasses).

Identification of algal rich microbial blooms in the Sellafield Pile Fuel Storage Pond and the application of ultrasonic treatment to control the formation of blooms

The presence of microorganisms in a range of nuclear facilities has been known for many years. In this study the microbial community inhabiting the Pile Fuel Storage Pond (PFSP), which is a legacy open-aired facility on the Sellafield nuclear site, Cumbria, UK, was determined to help target microbial bloom management strategies in this facility. The PFSP is currently undergoing decommissioning and the development of prolonged dense microbial blooms reduces the visibility within the water. Such impairment in the pond water visibility can lead to delays in pond operations, which also has financial implications. Efforts to control the microbial population within the PFSP are ongoing, with the installation of ultrasonic treatment units. Here next generation sequencing techniques focussing on broad targets for both eukaryotic and prokaryotic organisms were used to identify the microbial community. On-site monitoring of photosynthetic pigments indicated when microbial blooms formed and that eukaryotic algae were most likely to be responsible for these events. The sequencing data suggested that the blooms were dominated by members of the class Chrysophyceae, a group of golden algae, while evidence of cyanobacteria and other photosynthetic bacteria was limited, further supporting eukaryotic organisms causing the blooms. The results of sequencing data from 2018 was used to inform a change in the operational settings of the ultrasonic units, while monitoring of the microbial community and photosynthetic pigments trends was extended. Since the changes were made to the ultrasonic treatment, the visibility in the pond was significantly improved, with an absence of a spring bloom in 2020 and an overall reduction in the number of days lost due to microbial blooms annually. This work extends our knowledge of the diversity of microbes able to colonise nuclear fuel storage ponds, and also suggests that sequencing data can help to optimise the performance of ultrasonic treatments, to control algal proliferation in the PFSP facility and other inhospitable engineered systems.

Top-down structuring of freshwater bacterial communities by mixotrophic flagellates

Mixotrophic and heterotrophic protists hold a key position in aquatic microbial food webs. Whereas they can account for the bulk of bacterivory in pelagic systems, the potential structuring effect of these consumers on bacterial communities is far from clear. We conducted short-term grazing experiments to test for the overall impact on bacterial community structure and possible prey preferences of phagotrophic protists. The protist taxa selected for this study include three mixotrophic flagellates, comprising two obligate- and one facultative mixotroph, and one phagoheterotrophic flagellate lacking phototrophic capacity. Bacterioplankton from seven different lakes were enriched and used to represent semi-natural prey communities. Our study demonstrated protist strain specific impacts on bacterial community composition linked to grazing. The three mixotrophs had variable impacts on bacterial communities where the two obligate mixotrophs exhibited lower grazing rates, while showing a tendency to promote higher bacterial diversity. The phagoheterotroph displayed the highest grazing rates and structured the bacterial communities via apparent selective grazing. Consistent selectivity trends were observed throughout the experiments, such as the apparent avoidance of all flagellates of Actinobacteria, and high grazing on dominant Burkholderiales taxa. However, there was no consistent "fingerprint" of mixotrophic grazing on prey communities, but the structuring impact rather seemed to depend on the trophic mode of the individual protist taxa, i.e. their dependence on phototrophy vs. phagotrophy. Our findings highlight the differential structuring impact of protist taxa on bacterial communities which may have important ecological implications, for example during periodic dominance of obligate mixotrophic bacterivores in changing lake ecosystems.

Genome-material costs and functional trade-offs in the autopolyploid Solidago gigantea (giant goldenrod) series

PREMISE

Increased genome-material costs of N and P atoms inherent to organisms with larger genomes have been proposed to limit growth under nutrient scarcities and to promote growth under nutrient enrichments. Such responsiveness may reflect a nutrient-dependent diploid versus polyploid advantage that could have vast ecological and evolutionary implications, but direct evidence that material costs increase with ploidy level and/or influence cytotype-dependent growth, metabolic, and/or resource-use trade-offs is limited.

METHODS

We grew diploid, autotetraploid, and autohexaploid Solidago gigantea plants with one of four ambient or enriched N:P ratios and measured traits related to material costs, primary and secondary metabolism, and resource-use.

RESULTS

Relative to diploids, polyploids invested more N and P into cells, and tetraploids grew more with N enrichments, suggesting that material costs increase with ploidy level. Polyploids also generally exhibited strategies that could minimize material-cost constraints over both long (reduced monoploid genome size) and short (more extreme transcriptome downsizing, reduced photosynthesis rates and terpene concentrations, enhanced N-use efficiencies) evolutionary time periods. Furthermore, polyploids had lower transpiration rates but higher water-use efficiencies than diploids, both of which were more pronounced under nutrient-limiting conditions.

CONCLUSIONS

N and P material costs increase with ploidy level, but material-cost constraints might be lessened by resource allocation/investment mechanisms that can also alter ecological dynamics and selection. Our results enhance mechanistic understanding of how global increases in nutrients might provide a release from material-cost constraints in polyploids that could impact ploidy (or genome-size)-specific performances, cytogeographic patterning, and multispecies community structuring.

Unleashing the Potential of EIL Transcription Factors in Enhancing Sweet Orange Resistance to Bacterial Pathologies: Genome-Wide Identification and Expression Profiling

The ETHYLENE INSENSITIVE3-LIKE (EIL) family is one of the most important transcription factor (TF) families in plants and is involved in diverse plant physiological and biochemical processes. In this study, ten EIL transcription factors (CsEILs) in sweet orange were systematically characterized via whole-genome analysis. The CsEIL genes were unevenly distributed across the four sweet orange chromosomes. Putative cis-acting regulatory elements (CREs) associated with CsEIL were found to be involved in plant development, as well as responses to biotic and abiotic stress. Notably, quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed that CsEIL genes were widely expressed in different organs of sweet orange and responded to both high and low temperature, NaCl treatment, and to ethylene-dependent induction of transcription, while eight additionally responded to Xanthomonas citri pv. Citri (Xcc) infection, which causes citrus canker. Among these, CsEIL2, CsEIL5 and CsEIL10 showed pronounced upregulation. Moreover, nine genes exhibited differential expression in response to Candidatus Liberibacter asiaticus (CLas) infection, which causes Citrus Huanglongbing (HLB). The genome-wide characterization and expression profile analysis of CsEIL genes provide insights into the potential functions of the CsEIL family in disease resistance.

Impact of Genome Reduction in Microsporidia

Microsporidia represent an evolutionary outlier in the tree of life and occupy the extreme edge of the eukaryotic domain with some of their biological features. Many of these unicellular fungi-like organisms have reduced their genomic content to potentially the lowest limit. With some of the most compacted eukaryotic genomes, microsporidia are excellent model organisms to study reductive evolution and its functional consequences. While the growing number of sequenced microsporidian genomes have elucidated genome composition and organization, a recent increase in complementary post-genomic studies has started to shed light on the impacts of genome reduction in these unique pathogens. This chapter will discuss the biological framework enabling genome minimization and will use one of the most ancient and essential macromolecular complexes, the ribosome, to illustrate the effects of extreme genome reduction on a structural, molecular, and cellular level. We outline how reductive evolution in microsporidia has shaped DNA organization, the composition and function of the ribosome, and the complexity of the ribosome biogenesis process. Studying compacted mechanisms, processes, or macromolecular machines in microsporidia illuminates their unique lifestyle and provides valuable insights for comparative eukaryotic structural biology.