Biology subjects

Nevo, E.

Publications and source records attributed to Nevo, E..

6 recordsLinked to original sources

bioRxiv2024

Comparative analysis of microbial communities of soils under contrasting microclimates

Understanding how microbiomes influence the life cycle and fitness of crops, and how global change drivers disrupt this network, is pivotal for an understanding of the crop as a holobiont, and of how to provide solutions for Nordic agricultural crop resilience under climate change. Despite decades of use of plant growth-promoting rhizobacteria (PGPR), there is an intrinsic problem with their applications, as it has become evident that their functionality and performance rely on interactions with the environment and with other microorganisms. The synthetic crop-promoting rhizobacterial community strains are being outcompeted by native communities, or their colonisation and active principles are being reduced to ineffective levels. This is the result of the communities being selected on taxonomic criteria rather than qualitative analysis of the microbiome-associated plant phenotypes. In this context there in an urgent need for an approach studying the microbial community and plant complementarity traits from indigenous communities. Here we report the pattern of bacterial distributions at the Evolution Canyon (EC) in Israel to gain insight into microbiomes exposed to contrasting microclimates at the North Facing Slope (NFS) and South Facing Slope (SFS) sun and shade areas using high-throughput sequencing. While the NFS and SFS shaded areas bacterial distribution didnt differ, our results show significant differences between the NFS and the SFS sunny areas. The families Geodermatophilaceae, Beijerinckiaceae, and Pseudonocardiaceae are dominant in the NFS sun area, and the families Rubrobacteriaceae, unclassified Solirubrobacterales bacterium 67-14, unclassified Actinobacteriota, class Gaiellales dominate at the SFS sun area. Likewise, both Shannon and inverse Simpsons diversity indices are higher at the NFS sun area compared to the NFS shaded area. There was no substantial difference between diversity indices in SFS sun and shaded area. Our results advance our understanding of the bacterial distributions at what is in effect a natural laboratory of ecosystems that probably evolved 5-7 million years ago. The data are an important step towards using transcriptomics, metabolomic profiles and selective plating for figuring out key strains and the supporter strains that strengthen the ecological functions of the key strains. Collectively, this will enable us to assemble redundant and stable synthetic PGPR communities consisting of key and supporter strains for promoting plant health and stress tolerance under changing climates.

microbiology↗

bioRxiv2024

Genomic and evolutionary evidence for drought adaptation of grass allopolyploid Brachypodium hybridum

Climate change increases the frequency and severity of drought worldwide, threatening the environmental resilience of cultivated grasses. However, the genetic diversity in many wild grasses could contribute to the development of climate-adapted varieties. Here, we elucidated the impact of polyploidy on drought response using allotetraploid Brachypodium hybridum (Bh) and its progenitor diploid species B. stacei (Bs). Our findings suggest that progenitor species genomic legacies resulting from hybridization and whole-genome duplications conferred greater ecological adaptive advantages to Bh over Bs. Genes related to stomatal regulation and immune response from S-subgenomes were under positive selection during speciation, underscoring their evolutionary importance in adapting to environmental stresses. Biased expression in polyploid subgenomes [B. stacei-type (Bhs) and B. distachyon-type (Bhd)] significantly influenced differential gene expression, with the dominant subgenome exhibiting more differential expression. B. hybridum adapted a drought escape strategy characterized by higher photosynthetic capacity and lower WUEi than Bs, driven by a highly correlated co-expression network involving genes in the circadian rhythm pathway. In summary, our study showed the influence of polyploidy on ecological and environmental adaptation and resilience in model Brachypodium grasses. These insights hold promise for informing the breeding of climate-resilient cereal crops and pasture grasses.

evolutionary biology↗

bioRxiv2023

Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei

Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains one of the most interesting issues in evolutionary biology. However, the patterns of the underlying genetic divergences across the genome vary between different groups. Here we report that Brachypodium stacei, an inbreeding grass species, has been involved in sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses suggest that diploid B. stacei diverged sympatrically in two slopes with contrasting biomes at Evolution Canyon I (ECI), Mount Carmel, Israel, where gene flow has continued freely but reduced with the time. This ecological divergence involved the scattered divergence of many unlinked loci across the total genome that include both coding and non-coding regions. We also identified significantly differential expressions of ABA signaling pathway genes, and contrasting metabolome composition between the arid-vs forest-adapted B. stacei ECI populations. These results suggest that many small loci involved in environmental responses act additively to account for the ecological usages of this species in contrasted environments with gene flow. SignificanceEcological divergence provides evidence for the origin of species through natural selection that has governed evolutionists attention since Darwin. In this study, we present multiple-omics analyses of two plant populations growing sympatrically in contrasted environments and revealed their distinct differentiation across all examined data. These two populations share the most recent ancestor compared with other populations and their divergence started in the early Holocene. We revealed that gene flow had continued but with a progressive reduction over time. The genetic divergences are scattered across the total genome involving many unlinked coding and non-coding regions. These findings highlight the significance of natural selection in the ecological divergence that may finally lead to species formation without geographic isolation.

evolutionary biology↗

bioRxiv2023

Evolution of High-Molecular-Mass Hyaluronic Acid is Associated with Subterranean Lifestyle

Hyaluronic acid (HA) is a major component of extracellular matrix (ECM) which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (NMR, Heterocephalus glaber) contains abundant high-molecular-mass HA (HMM-HA) in its tissues, which contributes to this species cancer resistance and possibly longevity. Here we report that abundant HMM-HA is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These species accumulate abundant HMM-HA by regulating the expression of genes involved in HA degradation and synthesis and contain unique mutations in these genes. The abundant high molecular weight HA may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic subterranean environment. HMM-HA may also be coopted to confer cancer resistance and longevity to subterranean mammals. Our work suggests that HMM-HA has evolved with subterranean lifestyle.

evolutionary biology↗

bioRxiv2020

Dampened PI3K/AKT signaling contributes to cancer resistance of the naked mole rat

Mammalian species have a dramatically different susceptibility to cancer. However, how cancer-resistant species resist oncogenic transformation is not fully understood. Here, we performed a comprehensive analysis of oncogene-induced transcriptional changes in the fibroblasts of a cancer-prone species, the mouse, and three cancer-resistant species, the human, the blind mole rat, and the naked mole rat. We report that multiple cellular processes are more refractory to oncogene-induced transcriptional changes in blind mole-rat, naked mole-rat, or human cells compared to mouse cells, such as cell division, cell adhesion, extracellular matrix organization, and metabolism. Strikingly, naked mole rat cells are more resistant to Ras-induced transcriptional changes compared to the other three species. As a mechanism, we found that critical genes in the PI3K pathway including Akt1 and Pik3ca are downregulated in naked mole rat cells. Activating the PI3K/AKT pathway in the naked mole rat cells renders them susceptible to tumorigenic transformation. This study provides multiple new insights into anti-cancer mechanisms in cancer-resistant species of mammals. Significance statementAnimal species differ greatly in their cancer susceptibility. Cancer rates in the mouse range from 50-90%, while two other rodent species, the naked mole rat and the blind mole rat have only a few cancer cases ever reported. Here we examined the mechanisms responsible these differences by comparing changes in transcription patters in response to oncoproteins in the mouse, naked mole rat, blind mole rat and human cells. The most striking finding was that the naked mole rat cells were resistant to transcriptional changes induced by oncogenic Ras. We found that pathways downstream of Ras were naturally attenuated in the naked mole rat. This finding identifies a novel mechanism that evolved to provide tumor resistance to the naked mole rat.

cancer biology↗

bioRxiv2017

The Core Transcriptome Of Mammalian Placentas And The Divergence Of Expression With Placental Shape

IntroductionThe placenta is arguably the most anatomically variable organ in mammals even though its primary function is conserved.\n\nMethodUsing RNA-Seq, we measured the expression profiles of 55 term placentas of 14 species of mammals representing all major eutherian superordinal clades and marsupials, and compared the evolution of expression across clades.\n\nResultsWe identified a set of 115 core genes which is expressed (FPKM[≥] 10) in all eutherian placentas, including genes with immune-modulating properties (ANXA2, ANXA1, S100A11, S100A10, and LGALS1), cell-cell interactions (LAMC1, LUM, and LGALS1), invasion (GRB2 and RALB) and syncytialization (ANXA5 and ANXA1). We also identified multiple pre-eclampsia associated genes which are differentially expressed in Homo sapiens when compared to the other 13 species. Multiple genes are significantly associated with placenta morphology, including EREG and WNT5A which are both associated with placental shape.\n\nDiscussion115 genes are important for the core functions of the placenta in all eutherian species analyzed. The molecular functions and pathways enriched in the core placenta align with the evolutionarily conserved functionality of the placenta.

genomics↗