UNASSIGNED: Citrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth.
UNASSIGNED: In a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA and ITS2 amplicon sequencing data to identify predominant prokaryotic and fungal taxa in citrus root samples. Comparative analyses were conducted between root-associated microbial communities and those from the corresponding rhizosphere and bulk soil samples. Additionally, genotype-based group-wise comparisons were performed to assess the impact of citrus genotype on root microbiota composition.
UNASSIGNED: Ten predominant prokaryotic phyla, containing nine bacterial phyla including Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes and one archaeal phylum (Thaumarchaeota), and multiple fungal phyla including Ascomycota and Basidiomycota were identified in the citrus root samples. Compared with the microbial communities from the corresponding rhizosphere and bulk soil samples from the same trees, the prokaryotic and fungal communities in the roots exhibited lower diversity and complexity but greater modularity compared to those in the rhizosphere. In total, 30 root-enriched and 150 root-depleted genera in bacterial community were identified, whereas 21 fungal genera were enriched, and 147 fungal genera were depleted in the root niche compared with the rhizosphere. The citrus genotype significantly affected the root prokaryotic and fungal communities. In addition, we have identified the core root prokaryotic genera comprising Acidibacter, Allorhizobium, Bradyrhizobium, Chitinophaga, Cupriavidus, Devosia, Dongia, Niastella, Pseudomonas, Sphingobium, Steroidobacter and Streptomyces, and the core fungal genera including Acrocalymma, Cladosporium, Fusarium, Gibberella, Mortierella, Neocosmospora and Volutella. The potential functions of these core genera of root microbiota were predicted.
UNASSIGNED: Overall, this study provides new insights into the assembly of microbial communities and identifies core members of citrus root microbiota across a wide geographic range. The findings offer valuable information for manipulating root microbiota to enhance plant growth and health.

An exhaustive analysis was performed on more than 2000 microbiotas from French Protected Designation of Origin (PDO) cheeses, covering most cheese families produced throughout the world. Thanks to a complete and accurate set of associated metadata, we have carried out a deep analysis of the ecological drivers of microbial communities in milk and \"terroir\" cheeses. We show that bacterial and fungal microbiota from milk differed significantly across dairy species while sharing a core microbiome consisting of four microbial species. By contrast, no microbial species were detected in all ripened cheese samples. Our network analysis suggested that the cheese microbiota was organized into independent network modules. These network modules comprised mainly species with an overall relative abundance lower than 1%, showing that the most abundant species were not those with the most interactions. Species assemblages differed depending on human drivers, dairy species, and geographical area, thus demonstrating the contribution of regional know-how to shaping the cheese microbiota. Finally, an extensive analysis at the milk-to-cheese batch level showed that a high proportion of cheese taxa were derived from milk under the influence of the dairy species and protected designation of origin.

UNASSIGNED: Rat models are valuable tools to study the lung microbiota in diseases. Yet the impacts of different lung parts, young and mature adult stages, and the different batches of the same conditions on the healthy rat lung microbiome have not been investigated.
UNASSIGNED: The rat lung microbiome was analyzed to clarify the lung part-dependent and age-dependent differences and to evaluate the effects of several \'batch environmental factors\' on normal rats, after eliminating potential contamination.
UNASSIGNED: The results showed that the contamination could be identified and excluded. The lung microbiome from left and right lung parts was very similar so one representative part could be used in the microbiome study. There were significantly different lung microbial communities between the young and mature adult groups, and also between the different feeding batches groups of the same repetitive feeding conditions, but a common lung microbiota characterized by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria as the most dominant phyla were present in all adult rats. It indicated that the experiment under the same condition of the same rats batch was needed to compare the difference in the lung microbiota and repeated experiments were necessary to confirm the results.
UNASSIGNED: These data represented that the lung bacterial communities were dynamic and rapidly susceptible to environmental influence, clustered strongly by age or different feeding batches but similar in the different lung tissue parts. This study improved the basic understanding of the potential effects on the lung microbiome of healthy rats.

Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance.

Soil aggregates are crucial for soil organic carbon (OC) accumulation. This study, utilizing a 32-year fertilization experiment, investigates whether the core microbiome can elucidate variations in carbon content and decomposition across different aggregate sizes more effectively than broader bacterial and fungal community analyses. Employing ensemble learning algorithms that integrate machine learning with network inference, we found that the core microbiome accounts for an average increase of 26 % and 20 % in the explained variance of PCoA and Adonis analyses, respectively, in response to fertilization. Compared to the control, inorganic and organic fertilizers decreased the decomposition index (DDI) by 31 % and 38 %, respectively. The fungal core microbiome predominantly influenced OC content and DDI in larger macroaggregates (>2000 μm), explaining over 35 % of the variance, while the bacterial core microbiome had a lesser impact, explaining <30 %. Conversely, in smaller aggregates (<2000 μm), the bacterial core microbiome significantly influenced DDI (R2 > 0.2), and the fungal core microbiome more strongly affected OC content (R2 > 0.3). Mantel tests showed that pH is the most significant environmental factor affecting core microbiome composition across all aggregate sizes (Mantel\'s r > 0.8, P < 0.01). Linear correlation analysis further confirmed that the core microbiome\'s community structure could accurately predict OC content and DDI in aggregates (R2 > 0.8, P < 0.05). Overall, our findings suggested that the core microbiome provides deeper insights into the variability of aggregate organic carbon content and decomposition, with the bacterial core microbiome playing a particularly pivotal role within the soil aggregates.

Next-generation sequencing (NGS) has revolutionized taxa identification within contaminant-degrading communities. However, uncovering a core degrading microbiome in diverse polluted environments and understanding its associated microbial interactions remains challenging. In this study, we isolated two distinct microbial consortia, namely MA-S and Cl-G, from separate environmental samples using 1,4-dioxane as a target pollutant. Both consortia exhibited a persistent prevalence of the phylum Proteobacteria, especially within the order Rhizobiales. Extensive analysis confirmed that Rhizobiales as the dominant microbial population (> 90 %) across successive degradation cycles, constituting the core degrading microbiome. Co-occurrence network analysis highlighted synergistic interactions within Rhizobiales, especially within the Shinella and Xanthobacter genera, facilitating efficient 1,4-dioxane degradation. The enrichment of Rhizobiales correlated with an increased abundance of essential genes such as PobA, HpaB, ADH, and ALDH. Shinella yambaruensis emerged as a key degrader in both consortia, identified through whole-genome sequencing and RNA-seq analysis, revealing genes implicated in 1,4-dioxane degradation pathways, such as PobA and HpaB. Direct and indirect co-cultivation experiments confirmed synergistic interaction between Shinella sp. and Xanthobacter sp., enhancing the degradation of 1,4-dioxane within the core microbiome Rhizobiales. Our findings advocate for integrating the core microbiome concept into engineered consortia to optimize 1,4-dioxane bioremediation strategies.

BACKGROUND: The holistic characterization of different microbiomes in anaerobic digestion (AD) systems can contribute to a better understanding of these systems and provide starting points for bioengineering. The present study investigates the microbiome of 80 European full-scale AD systems. Operational, chemical and taxonomic data were thoroughly collected, analysed and correlated to identify the main drivers of AD processes.
RESULTS: The present study describes chemical and operational parameters for a broad spectrum of different AD systems. With this data, Spearman correlation and differential abundance analyses were applied to narrow down the role of the individual microorganisms detected. The authors succeeded in further limiting the number of microorganisms in the core microbiome for a broad range of AD systems. Based on 16S rRNA gene amplicon sequencing, MBA03, Proteiniphilum, a member of the family Dethiobacteraceae, the genus Caldicoprobacter and the methanogen Methanosarcina were the most prevalent and abundant organisms identified in all digesters analysed. High ratios for Methanoculleus are often described for agricultural co-digesters. Therefore, it is remarkable that Methanosarcina was surprisingly high in several digesters reaching ratios up to 47.2%. The various statistical analyses revealed that the microorganisms grouped according to different patterns. A purely taxonomic correlation enabled a distinction between an acetoclastic cluster and a hydrogenotrophic one. However, in the multivariate analysis with chemical parameters, the main clusters corresponded to hydrolytic and acidogenic microorganisms, with SAOB bacteria being particularly important in the second group. Including operational parameters resulted in digester-type specific grouping of microbes. Those with separate acidification stood out among the many reactor types due to their unexpected behaviour. Despite maximizing the organic loading rate in the hydrolytic pretreatments, these stages turned into extremely robust methane production units.
CONCLUSIONS: From 80 different AD systems, one of the most holistic data sets is provided. A very distinct formation of microbial clusters was discovered, depending on whether taxonomic, chemical or operational parameters were combined. The microorganisms in the individual clusters were strongly dependent on the respective reference parameters.

Plastics are offering a new niche for microorganisms colonizing their surface, the so-called \"plastisphere,\" in which diversity and community structure remain to be characterized and compared across ocean pelagic regions. Here, we compared the bacterial diversity of microorganisms living on plastic marine debris (PMD) and the surrounding free-living (FL) and organic particle-attached (PA) lifestyles sampled during the Tara expeditions in two of the most plastic polluted zones in the world ocean, i.e., the North Pacific gyre and the Mediterranean Sea. The 16S rRNA gene sequencing analysis confirmed that PMD are a new anthropogenic ocean habitat for marine microbes at the ocean-basin-scale, with clear niche partitioning compared to FL and PA lifestyles. At an ocean-basin-scale, the composition of the plastisphere communities was mainly driven by environmental selection, rather than polymer types or dispersal effect. A plastisphere \"core microbiome\" could be identified, mainly dominated by Rhodobacteraceae and Cyanobacteria. Predicted functions indicated the dominance of carbon, nitrogen and sulfur metabolisms on PMD that open new questions on the role of the plastisphere in a large number of important ecological processes in the marine ecosystem.

Plant epiphytic microorganisms have established a unique symbiotic relationship with plants, which has a significant impact on their growth, immune defense, and environmental adaptation. However, the impact of fertilization methods on the epiphytic microbial community and their correlation with the yield and quality of medicinal plant was still unclear. In current study, we conducted a field fertilization experiment and analyzed the composition of epiphytic bacterial and fungal communities employing high throughput sequencing data in different organs (roots, stems, and leaves) of Salvia miltiorrhiza, as well as their correlation with plant growth. The results showed that fertilization significantly affected the active ingredients and hormone content, soil physicochemical properties, and the composition of epiphytic microbial communities. After fertilization, the plant surface was enriched with a core microbial community mainly composed of bacteria from Firmicutes, Proteobacteria, and Actinobacteria, as well as fungi from Zygomycota and Ascomycota. Additionally, plant growth hormones were the principal factors leading to alterations in the epiphytic microbial community of S. miltiorrhiza. Thus, the most effective method of fertilization involved the application of base fertilizer in combination with foliar fertilizer. This study provides a new perspective for studying the correlation between microbial community function and the quality of S. miltiorrhiza, and also provides a theoretical basis for the cultivation and sustainable development of high-quality medicinal plants.

The gut microbiome is a highly intricate ecosystem that exerts a pivotal influence on the host\'s physiology. Characterizing fish microbiomes is critical to understanding fish physiology and health, but little is known about the ecology and colonization dynamics of microorganisms inhabiting fish species. In this study, we investigated the bacterial communities of two small-bodied fish species, Cyprinella lutrensis (red shiner) and Notropis stramineus (sand shiner), two fish species where gut microbiomes have not been investigated previously and surrounding waters, collected from rivers in Nebraska, USA. Our study focused on evaluating microbial diversity in small-bodied fish and identifying autochthonous microbes present within these species irrespective of location to better understand bacterial community composition and possible roles of such bacterial species. Our results revealed that both red shiner and sand shiner exhibited gut bacterial communities dominated by typical bacterial phyla found in freshwater fish. The phylum Bacteroidota was minimally abundant in both species and significantly lower in relative abundance compared to the surrounding water microbial community. Furthermore, we found that the gut microbiomes of red shiner and sand shiner differed from the microbial community in the surrounding water, suggesting that these fish species contain host-associated bacterial species that may provide benefits to the host such as nutrient digestion and colonization resistance of environmental pathogens. The fish gut bacterial communities were sensitive to environmental conditions such as turbidity, dissolved oxygen, temperature, and total nitrogen. Our findings also show bacterial community differences between fish species; although they shared notable similarities in bacterial taxa at phyla level composition, ASV level analysis of bacterial taxa displayed compositional differences. These findings contribute to a better understanding of the gut bacterial composition of wild, freshwater, small-bodied fish and highlight the influence of intrinsic (host) and environmental factors on shaping the bacterial composition.