Vadakattu V. S. R. Gupta

Microbiomes associated with both the human gut and plant root rhizosphere are essential for the maintenance of host health and function as holobionts where both the host and microbiome operate as an integrated unit. Though substantial differences exist in both host biology and environment, these systems share functional parallels: both are enriched by host-derived nutrients, undergo successional shifts during development, and maintain core microbiomes that are taxonomically variable yet functionally redundant. Central to both systems is the balance that is maintained where beneficial microbes regulate nutrient cycling, modulate host immune response, and suppress pathogens in the presence of biotic and abiotic influences that may serve to disrupt this equilibrium. When dysbiosis occurs, there is a disruption in the composition and/or function of the associated microbiome and a loss of beneficial functional guilds, which results in a reduction in host fitness. These shared dynamics underscore dysbiosis as a cross-kingdom pathology that may be treated with similar interventions. Probiotics and prebiotics mirror microbial inoculants and organic amendments; synbiotics incorporate both biotic and abiotic factors, while fecal and soil microbiome transplants represent parallel strategies to restore a beneficial microbiome. By framing dysbiosis within a “One Health” perspective and illustrating the connectedness between human and plant health, this review advocates for microbial stewardship as a unifying strategy to mitigate disease, enhance resilience, and ensure sustainable health across both systems.

The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat‐based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro‐organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.

Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome–host relationships, specifically at interfaces critical to One Health—a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.

The wheat (Triticum aestivum) microbiome is essential to its growth and adaptation under the current climatic crisis. Wheat breeding programs are often mainly focused on obtaining more resistant cultivars; thus, plant genotype-by-microbiome interactions have gained attention. In this sense, local wheat cultivars represent a unique opportunity to examine how bacterial communities are recruited and support plant growth under field conditions. In this study, we explored the diversity, community structure, and potential functions of root-associated bacterial communities of four Chilean wheat (Triticum aestivum) cultivars under field conditions through Illumina MiSeq. Analyses showed that Proteobacteria was the most abundant phylum in root endosphere (51.1 to 74.4%) and rhizosphere samples (39.3 to 44.9%) across wheat cultivars. Significant differences (p ≤ 0.05) in alpha and beta diversity were observed in root endosphere and rhizosphere samples, independently of wheat genotypes. Potassium was identified as the main factor driving the rhizosphere microbiomes of wheat. A higher proportion of shared operational taxonomic units (OTUs) were found in rhizosphere (mainly Pseudomonas, Flavobacterium, and Janthinobacterium) compared with root endosphere (dominated by Delftia, Acinetobacter, Stenotrophomonas, Kaistobacter) samples across all cultivars. Analyses of larger predicted functional activities revealed that chemoheterotrophy and aerobic chemoheterotrophy were more observed in the root endosphere environment, whereas among the minor functions, nitrogen cycling was the more predicted trait, related to rhizosphere samples. A co-occurrence analysis revealed complex bacterial interactions in wheat cultivars’ niche microbiomes identifying three (Comamonadaceae, Enterobacteraceae, Micrococcaceae) and four (Corynebacteraceae, Dermabacteraceae, Xanthomonadaceae, Staphylococcaceae) families as keystone taxa for the root endosphere and rhizosphere, respectively. It is suggested that such findings on the differences in root microbiomes associated with wheat cultivars under field conditions would help to develop new cultivars with abilities to recruit specific bacterial communities.

Phosphorus (P) reactions in calcareous soils limit the concentration of P in the soil solution for plant uptake. Calcareous soils with high calcium carbonate content (CaCO₃) and high pH have low P fertiliser efficiency, leading to crop deficiency and limited crop productivity. The aim of this work was to test if soil acidifying amendments could reduce soil pH and improve the solubility of fertiliser P to improve crop P nutrition and biomass. Three calcareous soils with varying CaCO₃ content (14–29% w/w) were used to test acidifying amendments both with and without mono-ammonium phosphate (MAP). Soil was amended with oxalic acid, sulfuric acid, glucose, ammonium sulfate and elemental sulfur (S⁰). Initial titrations demonstrated the ability of oxalic and sulfuric acids to reduce pH and improve P solubility in all three soils. Incubation of the acidifying amendments in the soil with the lowest carbonate content over 14 days (52 days for S⁰) showed increased P solubility and diffusion from MAP granules in soil amended with glucose, sulfuric acid and oxalic acid. There was, however, no improvement in P fertiliser uptake in wheat crops grown in these highly calcareous soils.

Over the past few decades, regulatory RNAs, such as small RNAs (sRNAs), have received increasing attention in the context of host-microbe interactions due to their diverse roles in controlling various biological processes in eukaryotes. In addition, studies have identified an increasing number of sRNAs with novel functions across a wide range of bacteria. What is not well understood is why cells regulate gene expression through post-transcriptional mechanisms rather than at the initiation of transcription. The finding of a multitude of sRNAs and their identified associated targets has allowed further investigation into the role of sRNAs in mediating gene regulation. These foundational data allow for further development of hypotheses concerning how a precise control of gene activity is accomplished through the combination of transcriptional and post-transcriptional regulation. Recently, sRNAs have been reported to participate in interkingdom communication and signalling where sRNAs originating from one kingdom are able to target or control gene expression in another kingdom. For example, small RNAs of fungal pathogens that silence plant genes and vice-versa plant sRNAs that mediate bacterial gene expression. However, there is currently a lack of evidence regarding sRNA-based inter-kingdom signalling across more than two interacting organisms. A habitat that provides an excellent opportunity to investigate interconnectivity is the plant rhizosphere, a multifaceted ecosystem where plants and associated soil microbes are known to interact. In this paper, we discuss how the interconnectivity of bacteria, fungi, and plants within the rhizosphere may be mediated by bacterial sRNAs with a particular focus on disease suppressive and non-suppressive soils. We discuss the potential roles sRNAs may play in the below-ground world and identify potential areas of future research, particularly in reference to the regulation of plant immunity genes by bacterial and fungal communities in disease-suppressive and non-disease-suppressive soils.

Bioassays were undertaken in a controlled environment to assess whether the potential for suppression of Rhizoctonia root rot of wheat, in a highly calcareous topsoil, was positively influenced by nutrient (nitrogen (N) or phosphorus (P)) addition and whether any disease suppression response to augmented nutrition was affected by the addition of carbon (C), either as a readily available C source (sucrose) or as wheat stubble. The soil was P deficient, which limited plant growth, populations of putatively beneficial soil microorganisms, and microbial activity and diversity. This ultimately reduced potential for suppression of Rhizoctonia solani AG8. Addition of fertiliser P to the soil increased R. solani AG8 DNA and percent root infection but not the effectiveness of the pathogen. A positive effect of P fertiliser on plant growth partially compensated for the negative effect of increased root infection. Addition of P increased DNA for Microbacterium spp. where labile C had been added and in the presence of plant roots. Stubble addition alone, after 6 weeks of incubation, increased DNA for Pantoea agglomerans, Trichoderma A and Microbacterium spp. although differences in microbial activity and diversity between stubble treatments were only detected after the bioassay had commenced and P was added. Fertiliser P addition to stubble-amended soil resulted in less Rhizoctonia infection compared with that in soil without P or stubble addition. Effectiveness of R. solani AG8 was decreased by 50% with stubble amendment. The application of N alone did not have a marked effect on plant growth or potential for suppression of Rhizoctonia root disease. Agronomic management practices that affect quantity and lability of C input to soil, when combined with strategic P fertiliser decisions, are likely to improve the potential for development of suppression of Rhizoctonia root rot disease in cereal crops on alkaline and highly calcareous soils.

In semiarid sandy soil environments there is a dual challenge of carbon and nitrogen (N) limitation that needs to be managed to ensure timely supply of N to crops. Management of N inputs to soil using combinations of legume stubble addition and fertiliser N in cereal systems is essential to meet crop demand and maintain N in soil organic matter. The aim of this study was to assess soil mineral and biological N pools that influence N supply and N uptake of wheat at early growth stages. The recovery of 15N-labelled fertiliser by wheat was evaluated using a factorial combination of either wheat, lupin or no stubble incorporated with or without 15N fertiliser in a sandy soil system. Soil and plant samples were collected at sowing, tillering, first node and booting to monitor changes in N pools and 15N uptake by the wheat. Crop stubble incorporation one week before sowing increased biological N pools in the surface soil (0–10 cm). Early N immobilisation (sowing–tillering) in all the treatments without 15N fertiliser may have limited N availability for wheat uptake in the subsequent period (tillering–first node), when fertiliser N appeared critical to maximise N supply for plant requirements. Up to 38% of the 15N fertiliser applied at sowing was incorporated into the soil microbial biomass pool, so that fertiliser N was critical to relieve short-term inherent N limitations for both plant and microbial growth, and to supply the longer-term biological pools (microbial biomass) to support subsequent mineralisation potential. Reducing the energy limitation to the microbial pool through inputs of carbon from stubble was also critical to ensure fertiliser N supplied sufficient N to satisfy plant demand later in the growing period. These results have implications for management decisions on semiarid sandy soil systems that aim to synchronise N from inputs of legume stubbles and fertiliser with crop N demand during early growth stages of wheat.

Changed spatial configurations at sowing have been investigated as a strategy to minimize interspecific competition and improve the establishment and persistence of multi-species plantings in pastures, but the impact of this practice on the soil microbiome has received almost no previous research attention. Differences in populations of bacteria and fungi in the surface 10 cm of soil in the third year following pasture establishment were quantified using quantitative polymerase chain reaction and terminal restriction fragment length polymorphism methods. Populations were compared on, and between, drill rows sown to either the perennial grass phalaris (Phalaris aquatica L.), perennial legume lucerne (alfalfa; Medicago sativa L.) or the annual legume subterranean clover (Trifolium subterraneum L.). Results showed that soil microbial abundance and diversity were related to plant distribution across the field at the time of sampling and to soil chemical parameters including total carbon (C), mineral nitrogen (N), pH, and available phosphorus (P), potassium (K) and sulfur (S). Despite the 27-month lag since sowing, pasture species remained concentrated around the original drill row with very little colonization of the inter-row area. The abundance and diversity of bacterial and fungal populations were consistently greater under drill rows associated with higher total C concentrations in the surface soil compared with the inter-row areas. Our results showed that the pH and available nutrients were similar between the subterranean clover drill row and the inter-row, suggesting that soil microbial populations were not impacted directly by these soil fertility parameters, but rather were related to the presence or absence of plants. The abundance of bacteria and fungi were numerically lower under phalaris rows compared to rows sown to legumes. The richness and diversity of fungal populations were lowest between rows where lucerne was planted. Possible explanations for this observation include a lower C:N ratio of lucerne roots and/or a lack of fibrous roots at the soil surface compared to the other species, illustrating the influence of contrasting plant types on the soil microflora community. This study highlights the enduring legacy of the drill row on the spatial distribution of plants well into the pasture phase of a cropping rotation and discusses the opportunity to enhance the microbiome of cropping soils on a large scale during the pasture phase by increasing plant distribution across the landscape.