The root tip of a plant is highly sensitive to environmental cues and exerts sensory, chemical and movement responses and has even been likened to an animal’s brain. Yet, the assemblage of microbes at the root tip, the controls governing their diversity, the nature of their recruitment to that particular niche, and their roles in plant phenotypic function, remain poorly understood. This study investigated longitudinal niche differentiation of the root-associated microbiome in chickpeas ( Cicer arietinum L.) and its interactions with both diverse soil types and host plants with genetic variation in phenology, from the exterior to the interior of the root. Compared with late flowering (LF) genotypes, endophyte microbiomes at the apical zone of the early flowering (EF) host were characterised by greater diversity, higher compositional similarity to the basal zone, and closely inhabiting Rhizobacter and Methylotenera across soils. Additionally, EF genotype secreted a specific composition of metabolites from the apical zone, with more carboxylates (benzoic acid) and amino acids (propionic acid) than the LF plant. Our findings demonstrate that longitudinal differentiation within a seedling root is an essential feature shaping the root microbiome and indicative of genetic variation in phenology of host plants.

The root tip of a plant is highly sensitive to environmental cues and exerts sensory, chemical and movement responses and has even been likened to an animal’s brain. Yet, the assemblage of microbes at the root tip, the control of their diversity, the nature of their recruitment to that particular volume, and their roles in plant phenotypic function, remain poorly understood. This study investigated longitudinal niche differentiation of the root-associated microbiome in chickpeas ( Cicer arietinum L.) and its interactions with both diverse soil types and host plants with genetic variation in phenology, from the exterior to the interior of the root. Compared with late flowering (LF) genotypes, endophyte microbiomes at the apical zone of the early flowering (EF) host were characterised by greater diversity, higher compositional similarity to the basal zone, and closely inhabiting Rhizobacter and Methylotenera across soils. Additionally, EF genotypes secreted a specific composition of metabolites from the apical zone, with more carboxylates and amino acids (especially propionic acid and benzoic acid) than the LF plant. Our findings demonstrate that longitudinal differentiation within a seedling root is an essential feature shaping the root microbiome and indicative of genetic variation in phenology of host plants.

Land development is rapidly occurring on sand--dominant soils that cover substantial areas of the Lower Mekong Basin. Sands are at risk of degradation on sloping uplands where agriculture is expanding and on lowland landscapes where intensification of cropping is occurring. Sandstone and granitic geology explain the prevalence of sand-dominant texture in profiles. The sand terrains in uplands of Cambodia and southern Laos mostly have not been comprehensively mapped and their diversity and edaphic properties are poorly understood. On high permeability sands, lowland rainfed rice crops are drought-prone, while nutrient losses from leaching are also a risk. Furthermore, waterlogging, inundation and subsoil hardpans are significant water-related hazards that influence the choice of field crops and forages for lowland soils. Land use change in the lowlands to alternative field crops and forages on sands is contingent on their profitability relative to rice, the amounts and reliability of early wet season rainfall and amounts of stored water available after harvesting rice. Soil acidity, low nutrient status, hard-setting and shallow rooting depth are significant constraints for crops and forages on sands in the lowlands. Low soil fertility and soil acidity are limitations to the productivity of farming systems on the sand profiles in uplands, while erosion, low soil organic matter levels and water balance are concerns for their sustainable use. There is a need for widespread land suitability assessment and the development of sustainable farming systems before uncontrolled expansion of agriculture causes degradation of sandy terrain of the Lower Mekong Basin.