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The Arctic region is characterized by severe temperatures and a unique ecosystem with largely unexplored microbiomes. Whereas soil microbiomes in temperate regions play key roles in nutrient cycling, organic matter decomposition, greenhouse gas fluxes, and overall ecosystem functioning, Arctic microbiomes remain poorly understood, highlighting the need for a thorough characterization to better predict and manage soil health and resilience. In this study, we compared the microbial profiles of three raised beaches on Devon Island (Nunavut, Canadian Arctic Archipelago), which emerged sequentially between eight and two thousand years ago, to assess their similarities and differences. Samples were collected by genetic horizons along excavations from the top layer to the permafrost. For each horizon, total soil DNA, 16S gene copies dPCR quantification, 16S metabarcoding, and functional prediction were carried out. Total DNA quantification revealed a consistently comparable concentration of genetic material across the three soil beaches (AB2 μ = 2.28 ± 5.44 μg ∙ g -1 , AB1 μ = 4.71 ± 2.35 μg ∙ g -1 , AB3 μ = 5.44 ± 2.91 μg ∙ g -1 ), regardless of site age (AB2 = 2,360 YBP, AB1 = 6,726 YBP, AB3 = 8,410 YBP). Conversely, clear differences emerged by comparing the different horizons at each site. The hierarchical cluster analysis based on the Bray-Curtis dissimilarity matrix revealed a clear separation between surface and deep horizons. The core microbiome analysis highlighted Actinobacteria, Proteobacteria, and Firmicutes as the three predominant phyla accounting for relative abundances of 42%, 22%, and 18%, respectively. Remarkable evidence was the unexpectedly high taxonomic diversity that was recorded in these sites and that surprisingly matched with the commonly observed values in soils of temperate regions. Since these stony shores developed under cold, life-limiting conditions, their apparent microbial richness raises doubts about the potential biases in inferring physiological contexts and active biodiversity directly inferred from culture-independent DNA-based studies. The reason is that such inventories can be possibly inflated, in all environments, by chronically accumulated cells from passive immigration events through atmospheric discharge.

Ecosystems associated with retreating glaciers are undergoing rapid transformation in the context of a changing climate. Invertebrate fauna, including the Chironomidae insect family (non-biting midges), is part of the active biology that characterizes glaciers and their surrounding habitats. The underlying microbiology, present in both the insects’ guts and their physical habitat, represents a critical interface, controlling, on the one hand, the basis of nutrient geochemical cycling and, on the other, the health and nutritional physiology of its hosts. We aimed to assess the extent to which insect-borne bacteria resemble those found in icemelt water and the surrounding wet and terrestrial environments, in order to determine also whether the bacteria found associated with the insects could be interpreted mainly as specific dwellers, putatively involved with active physiological functions, or also as transient cells taken in for other purposes. To this end, we analyzed physical and biological samples from ten different chironomid species in two glacier-fed streams, one proglacial pond, and the surrounding habitats of three glacier systems (Agola, Amola and Mandrone) in the Italian Alps. The samples were analyzed using culture-independent amplified 16S rRNA gene bacterial metabarcoding sequencing. The bacterial diversity in glacial habitats was unexpectedly high, with numbers of sequence variants similar to those recorded in temperate, lowland, productive soils, and almost seven times higher than those found in insects. There was minimal coincidence in sequence variants between insects and habitats, amounting to just 4.9% shared cases, and the few taxa found in both insects and habitats were mostly overrepresented in the former. Additionally, there were no significant differences between insect species or between insect communities from different sites. A number of taxa occurring uniquely in insects or habitats showed peculiarities at all taxonomic levels, including specific phyla. Evidence of microevolutionary distinctness was observed in the form of sequence variants assigned to the same taxonomic name that differed in specific sequence bases and were found to be partitioned either in insect or environmental samples. Interestingly, sequence variants found in both insects and environments scored higher in bioinformatic identification, reaching deeper assigned ranks compared to variants occurring only in insects or the environment. In essence, the compared insect and environmental communities showed a very low level of symmetry and consequently a very high level of specificity to one or the other condition. The data provided limited support about the diet of chironomids in relation to the microbiota of the habitat. This suggests that the food resource for these insects likely consists mostly of dissolved organic matter and detritus of various origins, rather than intact bacteria with sequenceable genomes, as is the case elsewhere with ruminant herbivores or birds.

The latest Triassic was characterised by protracted biotic extinctions concluding in the End-Triassic Extinction (~ 200 Ma) and a global carbon cycle perturbation. The onset of declining diversity is closely related to reducing conditions that spread globally from upper Sevatian (uppermost Norian) to across the Norian-Rhaetian boundary, likely triggered by unusually high volcanic activity. We correlate significant organic carbon cycle perturbations to an increase of CO 2 in the ocean–atmosphere system, likely outgassed by the Angayucham igneous province, the onset of which is indicated by the initiation of a rapid decline in 87 Sr/ 86 Sr and 188 Os/ 187 Os seawater values. A possible causal mechanism involves elevated CO 2 levels causing global warming and accelerating chemical weathering, which increased nutrient discharge to the oceans and greatly increased biological productivity. Higher export production and oxidation of organic matter led to a global O 2 decrease in marine water across the Norian/Rhaetian boundary (NRB). Biotic consequences of dysoxia/anoxia include worldwide extinctions in some fossil groups, such as bivalves, ammonoids, conodonts, radiolarians.

The worldwide growing consumption of proteins to feed humans and animals has drawn a considerable amount of attention to insect rearing. Insects reared on organic wastes and used as feed for monogastric animals can reduce the environmental impact and increase the sustainability of meat/fish production. In this study, we designed an environmentally closed loop for food supply in which fruit and vegetable waste from markets became rearing substrate for Hermetia illucens (BSF— black soldier fly). A vegetable and fruit-based substrate was compared to a standard diet for Diptera in terms of larval growth, waste reduction index, and overall substrate degradation. Morphological analysis of insect organs was carried out to obtain indications about insect health. Processing steps such as drying and oil extraction from BSF were investigated. Nutritional and microbiological analyses confirmed the good quality of insects and meal. The meal was then used to produce fish feed and its suitability to this purpose was assessed using trout. Earthworms were grown on leftovers of BSF rearing in comparison to a standard substrate. Chemical analyses of vermicompost were performed. The present research demonstrates that insects can be used to reduce organic waste, increasing at the same time the sustainability of aquaculture and creating interesting by-products through the linked bio-system establishment.

A bacterial metabarcoding approach was used to compare the microbiome composition of caecal and faecal samples from fattening Japanese quails ( Coturnix coturnix japonica ) fed three different diet regimes. The tested feedstuffs included (1) a commercial diet for fattening quails, (2) a commercial diet containing 12% full-fat silkworm ( Bombyx mori ) pupae meal, and (3) a commercial diet containing 12% defatted silkworm pupae meal. The aim of the experiment was to verify the relative effect of three variables (diet type, gut tract comparing caecum to rectum, and individual animal) in determining the level of bacterial community dissimilarity to rank the relevance of each of the three factors in affecting and shaping community composition. To infer such ranking, the communities resulting from the high-throughput sequencing from each sample were used to calculate the Bray-Curtis distances in all the pairwise combinations, whereby identical communities would score 0 and totally different ones would yield the maximum distance, equal to 1. The results indicated that the main driver of divergence was the gut tract, as distances between caecal and faecal samples were higher on average, irrespective of diet composition, which scored second in rank, and of whether they had been sampled from the same individual, which was the least effective factor. Simpson’s species diversity indexes was not significantly different when comparing tracts or diets, while community evenness was reduced in full-fat silkworm diet-fed animals. The identities of the differentially displayed taxa that were statistically significant as a function of gut tract and diet regimen are discussed in light of their known physiological and functional traits.

This work aimed to study the effects in tomato ( Solanum lycopersicum L.) of foliar applications of a novel calcium-based biostimulant (SOB01) using an omics approach involving transcriptomics and physiological profiling. A calcium-chloride fertilizer (SOB02) was used as a product reference standard. Plants were grown under well-watered (WW) and water stress (WS) conditions in a growth chamber. We firstly compared the transcriptome profile of treated and untreated tomato plants using the software RStudio. Totally, 968 and 1,657 differentially expressed genes (DEGs) (adj- p -value < 0.1 and |log2(fold change)| ≥ 1) were identified after SOB01 and SOB02 leaf treatments, respectively. Expression patterns of 9 DEGs involved in nutrient metabolism and osmotic stress tolerance were validated by real-time quantitative reverse transcription PCR (RT-qPCR) analysis. Principal component analysis (PCA) on RT-qPCR results highlighted that the gene expression profiles after SOB01 treatment in different water regimes were clustering together, suggesting that the expression pattern of the analyzed genes in well water and water stress plants was similar in the presence of SOB01 treatment. Physiological analyses demonstrated that the biostimulant application increased the photosynthetic rate and the chlorophyll content under water deficiency compared to the standard fertilizer and led to a higher yield in terms of fruit dry matter and a reduction in the number of cracked fruits. In conclusion, transcriptome and physiological profiling provided comprehensive information on the biostimulant effects highlighting that SOB01 applications improved the ability of the tomato plants to mitigate the negative effects of water stress.

(1) Background: Soil nutrient availability in vineyards is shaped by physicochemical and biological processes. However, how baseline edaphic differences are related to soil microbial functional genes and plant elemental composition under biodynamic management remains unclear; (2) Methods: Two biodynamically managed Pinot Noir (Vitis vinifera L.) vineyard sites in Tasmania, hereafter referred to as site 1 (S1) and site 2 (S2), were compared at fruit set, veraison, and ripening. Soil physicochemical properties were measured, soil, leaf, and grape berry elemental compositions were assessed by X-ray fluorescence, and soil microbial taxonomic marker genes and soil microbial functional genes were quantified by qPCR. Because the dataset comprised only six site-by-stage composite samples without independent field-level biological replication, multivariate analyses and partial least squares path modeling were used as exploratory tools; (3) Results: The two sites showed distinct baseline soil physicochemical properties. Soil microbial functional genes varied across sites and phenological stages, with several nitrogen (N)-cycling genes showing higher values at S1 and amoA increasing toward ripening at both sites. AMG, defined here as an arbuscular mycorrhizal fungal (AMF)-related marker, also increased toward ripening and was interpreted separately from the N-cycling genes. Soil elements mainly reflected site-related differences, whereas leaf and berry elements showed clearer variation across phenological stages. The exploratory path model, based on this limited composite dataset, summarized sequential associations among soil physicochemical properties, microbial functional genes, leaf elements, and berry elements, as well as a direct association between soil physicochemical properties and berry elemental composition; (4) Conclusions: These findings describe exploratory soil–microbe–plant association patterns under biodynamic management and should not be interpreted as statistically inferential or causal evidence.

(1) Background: Soil fertility in organic systems depends on interactions between physicochemical properties and biological processes that regulate nutrient availability along the soil profile. However, information on their vertical distribution remains limited, particularly for root crops such as sugar beet. This study evaluated depth-related patterns in soils from three organic farms growing sugar beet. (2) Methods: Soil profiles (0–120 cm) were sampled and analyzed for physicochemical properties, mineral nitrogen (N) forms, and biological indicators, including the QBS-ar index, microbial abundance, and functional genes involved in N and carbon cycling. (3) Results: Nitrate-N and total mineral N were mainly concentrated in the 0–40 cm layer and declined markedly with depth. Microbial abundance and most N-cycling functional genes were similarly enriched in the topsoil, showing clear vertical stratification. Statistical analyses suggested that functional gene composition was associated with mineral N gradients after accounting for soil depth. (4) Conclusions: These findings provide an exploratory indication of relationships between mineral N forms and microbial indicators in an organically managed sugar beet system. Given the limited number of sampling units, results should be interpreted cautiously. However, these results highlight the value of soil profile approaches for understanding N redistribution and improving nutrient management strategies.

The fungus Cercospora beticola causes Cercospora Leaf Spot (CLS) of sugar beet ( Beta vulgaris L.). Despite the global importance of this disease, durable resistance to CLS has still not been obtained. Therefore, the breeding of tolerant hybrids is a major goal for the sugar beet sector. Although recent studies have suggested that the leaf microbiome composition can offer useful predictors to assist plant breeders, this is an untapped resource in sugar beet breeding efforts. Using Ion GeneStudio S5 technology to sequence amplicons from seven 16S rRNA hypervariable regions, the most recurring endophytes discriminating CLS-symptomatic and symptomless sea beets ( Beta vulgaris L.ssp. maritima ) were identified. This allowed the design of taxon-specific primer pairs to quantify the abundance of the most representative endophytic species in large naturally occurring populations of sea beet and subsequently in sugar beet breeding genotypes under either CLS symptomless or infection stages using qPCR. Among the screened bacterial genera, Methylobacterium and Mucilaginibacter were found to be significantly (p < 0.05) more abundant in symptomatic sea beets with respect to symptomless. In cultivated sugar beet material under CLS infection, the comparison between resistant and susceptible genotypes confirmed that the susceptible genotypes hosted higher contents of the above-mentioned bacterial genera. These results suggest that the abundance of these species can be correlated with increased sensitivity to CLS disease. This evidence can further prompt novel protocols to assist plant breeding of sugar beet in the pursuit of improved pathogen resistance.

Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches—marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays—and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge–cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.