Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations

Unravelling the Chloroplast Genome of the Kazakh Apricot (Prunus armeniaca L.) Through MinION Long-Read Sequencing

The study of the genetic diversity and adaptation mechanisms of the Kazakh apricot (Prunus armeniaca L.) is essential for breeding programs and the conservation of plant genetic resources in arid environments. Despite this species' ecological and agricultural significance, its chloroplast genome remains poorly studied due to its complex repetitive structure and secondary metabolites that hinder high-molecular-weight DNA (HMW-DNA) extraction and long-read sequencing. To address this gap, our study aims to develop and optimise sequencing protocols for P. armeniaca under arid conditions using Oxford Nanopore's MinION technology. We successfully extracted HMW-DNA with 50-100 ng/μL concentrations and purity (A260/A280) between 1.8 and 2.0, ensuring high sequencing quality. A total of 10 GB of sequencing data was generated, comprising 155,046 reads, of which 74,733 (48.2%) had a Q-score ≥ 8. The average read length was 1679 bp, with a maximum of 31,144 bp. Chloroplast genome assembly resulted in 33,000 contigs with a total length of 1.1 Gb and a BUSCO completeness score of 97.3%. Functional annotation revealed key genes (nalC, AcrE, and mecC-type BlaZ) associated with stress tolerance and a substantial proportion (≈40%) of hypothetical proteins requiring further investigation. GC content analysis (40.25%) and GC skew data suggest the presence of specific regulatory elements linked to environmental adaptation. This study demonstrates the feasibility of using third-generation sequencing technologies to analyse complex plant genomes and highlights the genetic resilience of P. armeniaca to extreme conditions. The findings provide a foundation for breeding programs to improve drought tolerance and conservation strategies to protect Kazakhstan's unique arid ecosystems.

Gut Microbiota Diversity of Local Egyptian Cattle Managed in Different Ecosystems

The animal gastrointestinal tract contains a complex microbiome whose composition ultimately reflects the co-evolution of microorganisms with their animal host and their host's environment. This study aimed to gain insights into the adaptation of the microbiota of local Egyptian cattle to three different ecosystems (Upper Egypt, Middle Egypt, and Lower Egypt) distributed across 11 governorates (with an average of 12 animals per governorate) using amplicon sequencing. We analyzed the microbiota from 136 fecal samples of local Egyptian cattle through a 16S rRNA gene sequencing approach to better understand the fecal microbial diversity of this breed which developed under different ecosystems. An alpha diversity analysis showed that the fecal microbiota of the Egyptian cattle was not significantly diverse across areas, seasons, sexes, or farm types. Meanwhile, microbiota data revealed significant differences in richness among age groups (p = 0.0018). The microbial community differed significantly in the distribution of its relative abundance rather than in richness across different ecosystems. The taxonomic analysis of the reads identified Firmicutes and Actinobacteriota as the dominant phyla, accounting for over 93% of the total bacterial community in Egyptian cattle. Middle Egypt exhibited a different microbial community composition compared to Upper and Lower Egypt, with a significantly higher abundance of Firmicutes and Euryarchaeota and a lower abundance of Actinobacteriota in this region than the other two ecosystems. Additionally, Middle Egypt had a significantly higher relative abundance of the Methanobacteriaceae family and the Methanobrevibacter genera than Lower and Upper Egypt. These results suggest a difference in the adaptation of the fecal microbial communities of Egyptian cattle raised in Middle Egypt. At the genus level, eleven genera were significantly different among the three ecosystems including Bacillus, DNF00809, Kandleria, Lachnospiraceae_NK3A20_group, Methanobrevibacter, Mogibacterium, Olsenella, Paeniclostridium, Romboutsia, Turicibacter, and UCG-005. These significant differences in microbiota composition may impact the animal's adaptation to varied environments.

Melatonin promotes the recovery of apple plants after waterlogging by shaping the structure and function of the rhizosphere microbiome

The dynamics of the physiological adaptability of plants and the rhizosphere soil environment after waterlogging remain unclear. Here we investigated the mechanisms regulating plant condition and shaping of the rhizosphere microbiome in a pot experiment. In the experiment, we added melatonin to waterlogged plants, which promoted waterlogging relief. The treatment significantly enhanced photosynthesis and the antioxidant capacity of apple plants, and significantly promoted nitrogen (N) utilization efficiency by upregulating genes related to N transport and metabolism. Multiperiod soil microbiome analysis showed the dynamic effects of melatonin on the diversity of the microbial community during waterlogging recovery. Random forest and linear regression analyses were used to screen for potential beneficial bacteria (e.g., Azoarcus, Pseudomonas and Nocardioides) specifically regulated by melatonin and revealed a positive correlation with soil nutrient levels and plant growth. Furthermore, metagenomic analyses revealed the regulatory effects of melatonin on genes involved in N cycling in soil. Melatonin positively contributed to the accumulation of plant dry weight by upregulating the expression of nifD and nifK (N fixation). In summary, melatonin positively regulates physiological functions in plants and the structure and function of the microbial community; it promoted the recovery of apple plants after waterlogging stress.

Unravelling the genomic and environmental diversity of the ubiquitous Solirubrobacter

Solirubrobacter, though widespread in soils and rhizospheres, has been relatively unexplored despite its ubiquity. Previously acknowledged as a common soil bacterium, our research explores its phylogenomics, pangenomics, environmental diversity, and interactions within bacterial communities. By analysing seven genomic sequences, we have identified a pangenome consisting of 19,645 protein families, of which 2644 are shared across all studied genomes, forming the core genome. Interestingly, despite the non-motility of reported isolates, we discovered genes for flagellin and a partial flagellum assembly pathway. Examining the 16S ribosomal RNA genes of Solirubrobacter revealed substantial diversity, with 3166 operational taxonomic units identified in Mexican soils. Co-occurrence network analysis further demonstrated its significant integration within bacterial communities. Through phylogenomic scrutiny, we conclusively excluded the NCBI's GCA_009993245.1 genome from being classified as a Solirubrobacter. Our research into the metagenomic diversity of Solirubrobacter across various environments confirmed its presence in rhizospheres and certain soils, underscoring its adaptability. The geographical ubiquity of Solirubrobacter in rhizospheres raises intriguing questions regarding its potential interactions with plant hosts and the biotic and abiotic factors influencing its presence in soil. Given its ecological significance and genetic diversity, Solirubrobacter warrants further investigation as a potentially crucial yet underappreciated keystone species.

Co-occurring orchid species associated with different low-abundance mycorrhizal fungi from the soil in a high-diversity conservation area in Denmark

Plant-fungal interactions are ubiquitous across ecosystems and contribute significantly to plant ecology and evolution. All orchids form obligate symbiotic relationships with specific fungi for germination and early growth, and the distribution of terrestrial orchid species has been linked to occurrence and abundance of specific orchid mycorrhizal fungi (OMF) in the soil. The availability of OMF can therefore be a habitat requirement that is relevant to consider when establishing management and conservation strategies for threatened orchid species, but knowledge on the spatial distribution of OMF in soil is limited. We here studied the mycorrhizal associations of three terrestrial orchid species (Anacamptis pyramidalis, Orchis purpurea and Platanthera chlorantha) found in a local orchid diversity hotspot in eastern Denmark, and investigated the abundance of the identified mycorrhizal fungi in the surrounding soil. We applied ITS metabarcoding to samples of orchid roots, rhizosphere soil and bulk soil collected at three localities, supplemented with standard barcoding of root samples with OMF specific primers, and detected 22 Operational Taxonomic Units (OTUs) putatively identified as OMF. The three orchid species displayed different patterns of OMF associations, supporting the theory that association with specific fungi constitutes part of an orchid's ecological niche allowing co-occurrence of many species in orchid-rich habitats. The identified mycorrhizal partners in the basidiomycete families Tulasnellaceae and Ceratobasidiaceae (Cantharallales) were detected in low abundance in rhizosphere soil, and appeared almost absent from bulk soil at the localities. This finding highlights our limited knowledge of the ecology and trophic mode of OMF outside orchid tissues, as well as challenges in the detection of specific OMF with standard methods. Potential implications for management and conservation strategies are discussed.

EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Prieto Maradona M, Querol A, Sijtsma L, Suarez JE, Sundh I, Barizzone F, Correia S, Herman L. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 19: Suitability of taxonomic units notified to EFSA until September 2023

The qualified presumption of safety (QPS) process was developed to provide a safety assessment approach for microorganisms intended for use in food or feed chains. The QPS approach is based on an assessment of published data for each taxonomic unit (TU), with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a TU are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, no new information was found that would change the status of previously recommended QPS TUs. Of 71 microorganisms notified to EFSA between April and September 2023 (30 as feed additives, 22 as food enzymes or additives, 7 as novel foods and 12 from plant protection products [PPP]), 61 were not evaluated because: 26 were filamentous fungi, 1 was Enterococcus faecium, 5 were Escherichia coli, 1 was a bacteriophage (all excluded from the QPS evaluation) and 28 were TUs that already have a QPS status. The other 10 notifications belonged to 9 TUs which were evaluated for a possible QPS status: Ensifer adhaerens and Heyndrickxia faecalis did not get the QPS recommendation due to the limited body of knowledge about their occurrence in the food and/or feed chains and Burkholderia ubonensis also due to its ability to generate biologically active compounds with antimicrobial activity; Klebsiella pneumoniae, Serratia marcescens and Pseudomonas putida due to safety concerns. K. pneumoniae is excluded from future QPS evaluations. Chlamydomonas reinhardtii is recommended for QPS status with the qualification 'for production purposes only'; Clostridium tyrobutyricum is recommended for QPS status with the qualification 'absence of genetic determinants for toxigenic activity'; Candida oleophila has been added as a synonym of Yarrowia lipolytica. The Panel clarifies the extension of the QPS status for genetically modified strains.

A study of microbial diversity in a biofertilizer consortium

Biofertilizers supply living microorganisms to help plants grow and keep their health. This study examines the microbiome composition of a commercial biofertilizer known for its plant growth-promoting activity. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of a biofertilizer, with 163 fungal species and 485 bacterial genera found. The biofertilizer contains a variety of microorganisms previously reported to enhance nutrient uptake, phytohormone production, stress tolerance, and pathogen resistance in plants. Plant roots created a microenvironment that boosted bacterial diversity but filtered fungal communities. Notably, preserving the fungal-inoculated substrate proves critical for keeping fungal diversity in the root fraction. We described that bacteria were more diverse in the rhizosphere than in the substrate. In contrast, root-associated fungi were less diverse than the substrate ones. We propose using plant roots as bioreactors to sustain dynamic environments that promote the proliferation of microorganisms with biofertilizer potential. The study suggests that bacteria grow close to plant roots, while root-associated fungi may be a subset of the substrate fungi. These findings show that the composition of the biofertilizer may be influenced by the selection of microorganisms associated with plant roots, which could have implications for the effectiveness of the biofertilizer in promoting plant growth. In conclusion, our study sheds light on the intricate interplay between plant roots and the biofertilizer's microbial communities. Understanding this relationship can aid in optimizing biofertilizer production and application, contributing to sustainable agricultural practices and improved crop yields.

Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.)

Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico's Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants' growth. The plant microbiome also plays a vital role in establishing invasive plants and host growth and development. However, little is known about the buffelgrass root-associated bacteria and the effects of allelochemicals on the microbiome. We used 16S rRNA gene amplicon sequencing to obtain the microbiome of buffelgrass and compare it between samples treated with root exacknudates and aqueous leachates as allelochemical exposure and samples without allelopathic exposure in two different periods. The Shannon diversity values were between H' = 5.1811-5.5709, with 2,164 reported bacterial Amplicon Sequence Variants (ASVs). A total of 24 phyla were found in the buffelgrass microbiome, predominantly Actinobacteria, Proteobacteria, and Acidobacteria. At the genus level, 30 different genera comprised the buffelgrass core microbiome. Our results show that buffelgrass recruits microorganisms capable of thriving under allelochemical conditions and may be able to metabolize them (e.g., Planctomicrobium, Aurantimonas, and Tellurimicrobium). We also found that the community composition of the microbiome changes depending on the developmental state of buffelgrass (p = 0.0366; ANOSIM). These findings provide new insights into the role of the microbiome in the establishment of invasive plant species and offer potential targets for developing strategies to control buffelgrass invasion.

Herbivore camping reshapes the taxonomy, function and network of pasture soil microbial communities

Although the effects of herbivore camping on soil physicochemical properties have been studied, whether the effects alter the soil microbial communities (e.g., composition, functions, taxonomic and functional diversities, network) remain unknown, especially below the surface. Here, using paired subsoil samples from half month-camping and non-camping, we showed for the first time that camping significantly changed the relative abundance of 21 bacterial phylotypes and five fungal phylotypes. Specifically, we observed significant increases in the relative abundance of putative chitinase and terpenes vanillin-decomposition genes, nitrite reduction function (nirB, nasA), decreases in the relative abundance of putative carbon fixation genes (ackA, PGK, and Pak), starch-decomposition gene (dexB), gene coding nitrogenase (anfG), and tetracycline resistance gene (tetB) for bacterial communities, and significant decreases in the relative abundance of animal endosymbiont and increases in the relative abundance of litter saprotroph and endophyte for fungal communities. However, camping did not significantly impact the taxonomic and functional diversity. The niche restriction was the main driving force of bacterial and fungal community assembly. Compared to no camping, camping increased the stability of bacterial networks but decreased the stability of fungal networks. Camping exerted a positive effect on the network by compressing the niche width and reduced the change in the network by reducing the niche overlap. Our results suggest that camping restructures the soil microbial composition, function, and network, and provides a novel insight into the effect of animal camping on soil microbial communities in grassland.

The response of sugar beet rhizosphere micro-ecological environment to continuous cropping

Continuous cropping can lead to increased soil-borne diseases of sugar beet (Beta vulgaris L.), resulting in a reduction in its yield quality. However, our understanding of the influence of continuous cropping on sugar beet-associated microbial community is limited and their interactions remain unclear. Here, we described and analyzed microbial diversity (N = 30) from three sugar beet belowground compartments (bulk soil, rhizosphere soil, and beetroot) using 16S rRNA and ITS sequencing. The continuous cropping showed lower bacterial alpha diversity in three belowground compartments and higher fungal alpha diversity in roots compared to the non-continuous cropping. There were significant differences in fungal community composition between the two groups. Compared with non-continuous cropping, continuous cropping increased the relative abundance of potentially pathogenic fungi such as Tausonia, Gilbellulopsis, and Fusarium, but decreased the relative abundance of Olpidium. The fungal flora in the three compartments displayed different keystone taxa. Fungi were more closely related to environmental factors than bacteria. Overall, changes in microbial diversity and composition under continuous cropping were more pronounced in the fungal communities, and the results of the study could guide development strategies to mitigate continuous crop adversity.

The Association between Gut Microbiome Diversity and Composition and Heat Tolerance in Cattle

Cattle are raised around the world and are frequently exposed to heat stress, whether in tropical countries or in regions with temperate climates. It is universally acknowledged that compared to those in temperate areas, the cattle breeds developed in tropical and subtropical areas have better heat tolerance. However, the underlying mechanism of heat tolerance has not been fully studied, especially from the perspective of intestinal microbiomics. The present study collected fecal samples of cattle from four representative climatic regions of China, namely, the mesotemperate (HLJ), warm temperate (SD), subtropical (HK), and tropical (SS) regions. Then, the feces were analyzed using high-throughput 16S rRNA sequencing. The results showed that with increasing climatic temperature from HLJ to SS, the abundance of Firmicutes increased, accompanied by an increasing Firmicutes to Bacteroidota ratio. Proteobacteria showed a trend of reduction from HLJ to SS. Patescibacteria, Chloroflexi, and Actinobacteriota were particularly highest in SS for adapting to the tropical environment. The microbial phenotype in the tropics was characterized by an increase in Gram-positive bacteria and a decrease in Gram-negative bacteria, aerobic bacteria, and the forming of_biofilms. Consistently, the functional abundances of organismal systems and metabolism were decreased to reduce the material and energy demands in a hot environment. Genetic information processing and information storage and processing may be how gut flora deals with hot conditions. The present study revealed the differences in the structure and function of gut microbes of cattle from mesotemperate to tropical climates and provided an important reference for future research on the mechanism of heat tolerance regulated by the gut microbiota and a potential microbiota-based target to alleviate heat stress.

All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean (Phaseolus vulgaris) in Its Centre of Domestication

Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.