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Background: In this study, we aimed to address the low utilization of straw and poor fermentation quality of paper mulberry silage (under natural fermentation conditions). Straw was combined with paper mulberry for ensiling, and the fermentation characteristics, bacterial community, and metabolite composition of the mixed straw and paper mulberry silage were investigated. Four treatment groups were established: corn-straw treatment 2 (3:7 ratio of corn straw to paper mulberry), corn-straw treatment 3 (5:5 ratio of corn straw to paper mulberry), wheat-straw treatment 2 (3:7 ratio of wheat straw to paper mulberry), wheatstraw treatment 3 (5:5 ratio of wheat straw to paper mulberry), and a control group (ensiling of paper mulberry alone). Results: The control group demonstrated the highest pH and ammonia (AN) and acetic acid (AA) content compared with all the treatment groups. Cornstraw treatment 2 had the highest lactic acid content (54.70 g/kg dry weight) compared with the control and other treatment groups. The relative abundance of Enterobacter (7.085%) was the lowest in the control than in the other treatment groups (p < 0.05). The relative abundance of Enterococcus was higher in both the control and wheat-straw treatment 2 (22.03% and 21.29%, respectively) than in other treatment groups. The relative abundance of Lactococcus was highest in wheat-straw treatment 3 (15.83%) compared with the control and other treatment groups. Corn-straw treatments 2 and 3 demonstrated the same metabolite composition but were clearly different from the wheat-straw treatment 2, wheat-straw treatment 3, and the control. Diacetoxyscirpenol (DAS) belongs to the Fusarium metabolite type A trichothecenes, which were not detected in corn or wheat silage. DAS was downregulated in the wheatstraw treatment 3 and both corn-straw treatments compared with the control, which indicates that the addition of straw decreased mycotoxin production. Lactococcus was significantly and positively correlated with gluconic acid content (R2 = 0.5166). Conclusion: Our results suggest that straw treatment can improve the nutritional value of paper mulberry silage by decreasing mycotoxin production, pH value, and AN content and increasing lactic acid production. [ABSTRACT FROM AUTHOR]

The paper deals with the fossil cyanobacterial films from the Lower Proterozoic (Livvian) shungite in Karelia, Russia. The films were previously described as a formal species Cyathotes nigoserica Makarikhin. They were formed by bacteria and possibly by fungi, which inhabited the littoral or supralittoral (the tidal zone). These organisms were adapted to the existence in temporally (possibly, long-lasting) dry conditions, which is proved by the development of dense coatings protecting their bodies from dehydration. This basically bacterial community influenced intensely the mineral substrate, changed its structure, and enriched it with biogenic constituents, thus forming an archaic soil microprofile. The research revealed the following signs of ancient soil formation: surface transformation of the mineral substrate texture by the vital activity of terrestrial organisms (bacteria, fungi) with the formation of a specific cellular topographic pattern,; changes in the internal structure of the substrate and the appearance of wedge-shaped fracture casts in the underlying matrix; redistribution of inorganic compounds during the formation of a paleosurface microprofile (the increasing content of silicon oxide in the upper part with a simultaneous reduction in the amount of iron oxides). [ABSTRACT FROM AUTHOR]

The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell. Viral taxonomic diversity was compared across lakes and ecological function was investigated by characterizing auxiliary metabolic genes (AMGs) and predicting viral hosts. Our data suggest that viral communities differed between the lakes and among sites: these differences were connected to microbial host communities. AMGs were associated with the potential augmentation of multiple biogeochemical processes in host, most notably with phosphorus acquisition, organic nitrogen acquisition, sulfur oxidation, and photosynthesis. Viral genome abundances containing AMGs differed between the lakes and microbial mats, indicating site specialization. Using procrustes analysis, we also identified significant coupling between viral and bacterial communities (p = 0.001). Finally, host predictions indicate viral host preference among the assembled viromes. Collectively, our data show that: (i) viruses are uniquely distributed through the McMurdo Dry Valley lakes, (ii) their AMGs can contribute to overcoming host nutrient limitation and, (iii) viral and bacterial MDV communities are tightly coupled. [ABSTRACT FROM AUTHOR]

Aquilaria sinensis is a significant resin-producing plant worldwide that is crucial for agarwood production. Agarwood has different qualities depending on the method with which it is formed, and the microbial community structures that are present during these methods are also diverse. Furthermore, the microbial communities of plants play crucial roles in determining their health and productivity. While previous studies have investigated the impact of microorganisms on agarwood formation, they lack comprehensiveness, particularly regarding the properties of the microbial community throughout the entire process from seedling to adult to incense formation. We collected roots, stems, leaves, flowers, fruits and other tissues from seedlings, healthy plants and agarwood-producing plants to address this gap and assess the dominant bacterial species in the microbial community structures of A. sinensis at different growth stages and their impacts on growth and agarwood formation. The bacteria and fungi in these tissues were classified and counted from different perspectives. The samples were sequenced using the Illumina sequencing platform, and sequence analyses and species annotations were performed using a range of bioinformatics tools to assess the plant community compositions. An additional comparison of the samples was conducted using diversity analyses to assess their differences. This research revealed that Listeria, Kurtzmanomyces, Ascotaiwania, Acinetobacter, Sphingobium, Fonsecaea, Acrocalymma, Allorhizobium, Bacillus, Pseudomonas, Peethambara, and Debaryomyces are potentially associated with the formation of agarwood. Overall, the data provided in this article help us understand the important roles played by bacteria and fungi in the growth and agarwood formation process of A. sinensis, will support the theoretical basis for the large-scale cultivation of A. sinensis, and provide a basis for further research on microbial community applications in agarwood production and beyond. [ABSTRACT FROM AUTHOR]

Tequila vinasse, a byproduct of the tequila industry, is frequently discharged into water bodies or agricultural fields, posing significant ecological and human health risks. Bacterial communities that inhabit these agricultural fields have developed mechanisms to utilize tequila vinasse as a potential nutrient source and to promote plant growth. In this study, strains from the phyla Actinomycetota and Pseudomonadota were isolated from agricultural fields irrigated with tequila vinasse for 2, 10, and 14 years in Jalisco, Mexico. The results showed that strains of Terrabacter, Azotobacter, Agromyces, Prescottella, and Leifsonia tolerate high concentrations of tequila vinasse and promote maize seedling growth in the presence of tequila vinasse. Additionally, some of the strains solubilize potassium and produce siderophores, cellulase, protease, lipase, and esterase. The strains Terrabacter sp. WCNS1C, Azotobacter sp. WCNS1D, and Azotobacter sp. WCNS2A have potential applications in the bioremediation of tequila vinasse in agricultural fields discharged with tequila vinasse. [ABSTRACT FROM AUTHOR]

Phytoplankton and bacteria form the foundation of marine food webs. While most studies on phytoplankton bloom influence on bacteria dynamics focus on diatom‐dominated blooms due to their global ecological significance, it is unclear if similar patterns extend to other species that compete with diatoms like Phaeocystis spp. This study aimed to contribute to the understanding of associations between phytoplankton and bacteria in a temperate ecosystem. For this, we studied the dynamics of phytoplankton and bacteria, combining 16S metabarcoding, microscopy, and flow cytometry over 4 years (282 samples). Phytoplankton and bacterial communities were studied throughout the year, particularly during contrasting phytoplankton blooms dominated by the Haptophyte Phaeocystis globosa or diatoms. We applied extended local similarity analysis (eLSA) to construct networks during blooming and non‐blooming periods. Overall, the importance of seasonal and species‐specific interactions between phytoplankton and bacteria is highlighted. In winter, mixed diatom communities were interconnected with bacteria, indicating a synergistic degradation of diverse phytoplankton‐derived substrates. In spring, despite the intensity variations of P. globosa blooms, the composition of bacterial communities remained consistent over several years, suggesting establishing a stable‐state environment for bacterial communities. Specific associations between monospecific diatom blooms and bacteria were evidenced in summer. [ABSTRACT FROM AUTHOR]

This paper continues the studies on the role of bacteria in the environment of summer truffle (Tuber aestivum), focusing on ascomata at three sites in the Nida Basin (southern Poland). Bacterial taxa and the number of OTU sequences identified were determined based on analysis of peridium and gleba collected in 2017 and 2018. The aim of the presented work is to learn the structure of bacterial communities associated with the ascomata of the summer truffle T. aestivum forming in specific stands in south Poland and fine roots of surrounding trees. Sanger DNA sequencing, and next-generation sequencing (NGS) were used. NGS sequencing platforms short-read (300 bases) was selected, using a MiSeq Illumina. The Kruskall-Wallis test was used for alpha diversity analysis and the PERMANOVA test for beta diversity. Alpha and beta biodiversity analyzes were performed using various indices (Chao1, Simpson, Shannon, Faith's phylogenetic, observed OTUs, Heip's evenness measure - alpha diversity; UniFrac, Jaccard, Bray–Curtis - beta diversity). The Sanger method identified six bacterial taxa that were dominant in the community: Bacillus (86.7 %), Pseudomonas (51.5 %), Stenotrophomonas (15.5 %), Paenibacillus (7.9 %), Rhizobium (7.3 %), and Chryseobacterium (8.5 %). In contrast, NGS results showed the dominance (at OTUs >10,000) of taxa: Bradyrhizobiaceae, Sphingobacteriaceae, Micrococcaceae, Yersiniaceae, Sphingomonadaceae, Rhizobiaceae, Flavobacteriaceae, and Comamonadaceae. The PERMANOVA test for the Bray-Curtis and Jaccard indices showed dissimilarities between samples from two of the sites with respect to beta diversity. Significant differences were found in the bacterial communities colonizing the ascomata of T. aestivum and in the root communities with T. aestivum ectomycorrhizae the purpose of this study. The results obtained may be helpful in selecting and monitoring sites suitable for the formation of ascomata of T. aestivum. [ABSTRACT FROM AUTHOR]

Exploring the bacterial community in the S. glauca rhizosphere was of great value for understanding how this species adapted to the salinealkali environment and for the rational development and use of saline-alkali soils. In this study, high-throughput sequencing technology was used to investigate the diversity characteristics and distribution patterns of soil bacterial communities in the rhizosphere of S.glauca-dominated communities in the Hetao Irrigation Distract, Inner Mongolia, China. The relationships among bacterial characteristics, soil physicochemical properties and vegetation in four sampling sites were analyzed. The soil bacterial communities in the rhizosphere of S. glauca-dominated communities were mainly composed of 16 phyla (i.e., Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, Deinococcus-Thermus, Verrucomicrobia, Saccharibacteria, Cyanobacteria, Nitrospirae, JL-ETNP-Z39, Parcubacteria and Chlorobi), and these populations accounted for more than 99% of the total bacterial community. At the genus level, the main bacterial communities comprised Halomonas, Nitriliruptor, Euzebya and Pelagibius, which accounted for 15.70% of the total bacterial community. An alpha diversity analysis indicated that the richness and diversity of rhizosphere soil bacteria differed significantly among the sampling sites, and the bacterial richness and diversity indices of severe saline-alkali land were higher than those of light and moderate saline-alkali land. The principal component analysis (PCA) and linear discriminant analysis effect size (LEfSe) showed significant differences in the species composition of the rhizosphere soil bacterial community among different sampling sites. A correlation analysis showed that the number of bacterial species exhibited the highest correlation with the soil water content (SWC). The richness and evenness indices were significantly correlated with the SWC and SO42-, KC and Mg2+ concentrations. The electrical conductivity (EC), soluble ions (NaC, CO32- + HCO3-, K+, Ca2+, Mg2+, and SO42+), SWC and vegetation coverage (VC) were the main drivers affecting the changes in its community structure. The bacterial community in the rhizosphere of S. glauca enhanced the adaptability of S. glauca to saline-alkali environment by participating in the cycling process of nutrient elements, the decomposition of organic matter and the production of plant growth regulating substances. These results provided a theoretical reference for further study on the relationship among rhizosphere soil microorganisms and salt tolerance in halophytes. [ABSTRACT FROM AUTHOR]

Biological soil crusts, or biocrusts, are microbial communities found in soil surfaces in drylands and in other locations where vascular plant cover is incomplete. They are functionally significant for numerous ecosystem services, most notably in the C fixation and storage due to the ubiquity of photosynthetic microbes. Whereas carbon fixation and storage have been well studied in biocrusts, the composition, function and characteristics of other organisms in the biocrust such as heterotrophic bacteria and especially fungi are considerably less studied and this limits our ability to gain a holistic understanding of biocrust ecology and function. In this research we characterised the fungal community in biocrusts developed on Kalahari Sand soils from a site in southwest Botswana, and combined these data with previously published bacterial community data from the same site. By identifying organisational patterns in the community structure of fungi and bacteria, we found fungi that were either significantly associated with biocrust or the soil beneath biocrusts, leading to the conclusion that they likely perform functions related to the spatial organisation observed. Furthermore, we showed that within biocrusts bacterial and fungal community structures are correlated with each other i.e., a change in the bacterial community is reflected by a corresponding change in the fungal community. Importantly, this correlation but that this correlation does not occur in nearby soils. We propose that different fungi engage in short-range and long-range interactions with dryland soil surface bacteria. We have identified fungi which are candidates for further studies into their potential roles in biocrust ecology at short ranges (e.g., processing of complex compounds for waste management and resource provisioning) and longer ranges (e.g., translocation of resources such as water and the fungal loop model). This research shows that fungi are likely to have a greater contribution to biocrust function and dryland ecology than has generally been recognised. [ABSTRACT FROM AUTHOR]

The biodiversity and activity of microorganisms are crucial for litter decomposition, but how litter traits at different stages of decomposition drive changes in microbial communities has yet to be thoroughly explored. In the typical alpine hilly area of the Qinghai–Tibet Plateau, three types of litter at different decomposition stages were selected under a natural Picea crassifolia (Picea crassifolia Kom.) forest: undecomposed (A-1), partially decomposed (A-2), and fully decomposed (A-3). By measuring physicochemical indicators, microbial diversity, and the composition of the litter at different decomposition stages, this study investigates the community changes and responses of bacteria to litter characteristic changes at different decomposition levels. The results show that with the increase in decomposition level, bacterial diversity increases, community structure changes, and network complexity gradually increases, while the changes in fungal communities are insignificant. Structural equation modeling indicates that the first principal component (PC1) of litter properties is significantly negatively correlated with bacterial diversity and positively correlated with bacterial community composition. There is no significant correlation between fungal diversity and community composition, indicating a closer relationship between bacteria and litter characteristics than fungi. In summary, with an increase in litter decomposition level, the diversity and network complexity of bacterial and fungal communities will significantly increase, which is related to the changes in various litter characteristics. This study provides a scientific basis for the regulatory mechanism of litter decomposition and turnover in the alpine hilly area of the Qinghai–Tibet Plateau, specifically in Picea crassifolia forests. [ABSTRACT FROM AUTHOR]

The rhizosphere and phyllosphere of plants are home to a diverse range of microorganisms that play pivotal roles in ecosystem services. Consequently, plant growth‐promoting bacteria (PGPB) are extensively utilized as inoculants to enhance plant growth and boost productivity. Despite this, the interactions between the rhizosphere and phyllosphere, which are influenced by PGPB inoculation, have not been thoroughly studied to date. In this study, we inoculated Bacillus velezensis SQR9, a PGPB, into the bulk soil, rhizosphere or phyllosphere, and subsequently examined the bacterial communities in the rhizosphere and phyllosphere using amplicon sequencing. Our results revealed that PGPB inoculation increased its abundance in the corresponding compartment, and all treatments demonstrated plant growth promotion effects. Further analysis of the sequencing data indicated that the presence of PGPB exerted a more significant impact on bacterial communities in both the rhizosphere and phyllosphere than in the inoculation compartment. Notably, the PGPB stimulated similar rhizosphere‐beneficial microbes regardless of the inoculation site. We, therefore, conclude that PGPB can promote plant growth both directly and indirectly through the interaction between the rhizosphere and phyllosphere, leading to the enrichment of beneficial microorganisms. [ABSTRACT FROM AUTHOR]

Microbial communities associated with seagrass beds play a crucial role in maintaining the balance of seagrass ecosystems. However, the driving mechanisms behind the structure and functional succession of seagrass microbial communities are still unclear despite the close interaction between seagrass and surrounding microorganisms. To enhance our knowledge of the diversity and functional characteristics of microbial communities in seagrass beds, we employed 16S rRNA gene amplicon sequencing to investigate bacterial communities in seagrass leaves, roots, seawater, and sediments in Caofeidian Zostera marina seagrass beds of Hebei Province, Northern China. Our results highlighted that specific types of bacteria were enriched in different sample compartments, indicating the importance of habitat in influencing microbial diversity and community structure in seagrass bed ecosystems. Notably, the microbial community structure of seagrass leaves and roots showed more similarity to that found in seawater and sediments. Among all the samples, the phylum Pseudomonadota exhibited the highest relative abundance, particularly in sediment samples where they accounted for over 95% of the total bacterial population. In addition, the enrichment of Vibrio, an opportunistic pathogen in several plant samples, alerted us to seagrass and its surrounding marine environments. Finally, functional predictions of microbial communities using PICRUSt2 revealed variations in microbial functions, indicating specific metabolic preferences of microbial communities in different natural environments. The present research sheds light on the mechanisms underlying microbial community succession and their ecological function in seagrass beds. [ABSTRACT FROM AUTHOR]

Lake Caviahue (37° 50 ‘S and 71° 06’ W; Patagonia, Argentina) is an extreme case of a glacial, naturally acidic, aquatic environment (pH  ~  3). Knowledge of the bacterial communities in the water column of this lake, is incipient, with a basal quantification of the bacterioplankton abundance distribution in the North and South Basins of Lake Caviahue, and the described the presence of sulfur and iron oxidizing bacteria in the lake sediments. The role that bacterioplankton plays in nutrient utilization and recycling in this environment, especially in the phosphorus cycle, has not been studied. In this work, we explore this aspect in further depth by assessing the diversity of pelagic, littoral and sediment bacteria, using state of the art molecular methods and identifying the differences and commonalties in the composition of the cognate communities. Also, we investigate the interactions between the sediments of Lake Caviahue and the microbial communities present in both sediments, pore water and the water column, to comprehend the ecological relationships driving nutrient structure and fluxes, with a special focus on carbon, nitrogen, and phosphorus. Two major environmental patterns were observed: (a) one distinguishing the surface water samples due to temperature, Fe2+, and electrical conductivity, and (b) another distinguishing winter and summer samples due to the high pH and increasing concentrations of N-NH4+, DOC and SO42−, from autumn and spring samples with high soluble reactive phosphorus (SRP) and iron concentrations. The largest bacterial abundance was found in autumn, alongside higher levels of dissolved phosphorus, iron forms, and increased conductivity. The highest values of bacterial biomass were found in the bottom strata of the lake, which is also where the greatest diversity in microbial communities was found. The experiments using continuous flow column microcosms showed that microbial growth over time, in both the test and control columns, was accompanied by a decrease in the concentration of dissolved nutrients (SRP and N-NH4+), providing proof that sediment microorganisms are active and contribute significantly to nutrient utilization/mobilization. [ABSTRACT FROM AUTHOR]

Koumiss, a traditional fermented beverage made from mare's milk, is typically consumed by nomads. Industrialized production of koumiss has been increasingly applied recently due to the increased demand for the beverage and awareness of its potential health benefits. However, it is unknown whether industrial koumiss is comparable to the traditional koumiss in terms of quality. In this study, we compared the microbiological and physicochemical properties in the industrial and traditional koumiss fermentation processes synchronously using culture-dependent and culture-independent approaches. Although Lactobacillus and Kazachstania species were similarly dominant in the bacterial and fungal communities, respectively, in both processes, the microbial counts and diversity in the traditional koumiss were significantly higher than those in the industrial koumiss. Furthermore, the traditional koumiss fermentation consumed more lactose, produced more flavor substances including acetic acid, lactic acid, ethanol, and free amino acids, and reached a lower pH value at the final stage. The physicochemical characters of traditional koumiss were mainly associated with Lactobacillus and Kazachstania species, which, in turn, were positively correlated with each other but negatively correlated with other non-dominant microbes. The starter was the major source of the microbial community of industrial koumiss, whereas both the starter and environment were the major sources of traditional koumiss. Random forest analysis recognized 11 significantly important genera as microbial indicators to distinguish industrial from traditional koumiss. Overall, this study shows that the microbial and physicochemical dynamics during the traditional and industrial fermentation of koumiss differ significantly, and the results obtained are valuable for improving the quality of industrial koumiss. [ABSTRACT FROM AUTHOR]

Summary We present Coracle, an artificial intelligence (AI) framework that can identify associations between bacterial communities and continuous variables. Coracle uses an ensemble approach of prominent feature selection methods and machine learning (ML) models to identify features, i.e. bacteria, associated with a continuous variable, e.g. host thermal tolerance. The results are aggregated into a score that incorporates the performances of the different ML models and the respective feature importance, while also considering the robustness of feature selection. Additionally, regression coefficients provide first insights into the direction of the association. We show the utility of Coracle by analyzing associations between bacterial composition data (i.e. 16S rRNA Amplicon Sequence Variants, ASVs) and coral thermal tolerance (i.e. standardized short-term heat stress-derived diagnostics). This analysis identified high-scoring bacterial taxa that were previously found associated with coral thermal tolerance. Coracle scales with feature number and performs well with hundreds to thousands of features, corresponding to the typical size of current datasets. Coracle performs best if run at a higher taxonomic level first (e.g. order or family) to identify groups of interest that can subsequently be run at the ASV level. Availability and implementation Coracle can be accessed via a dedicated web server that allows free and simple access: http://www.micportal.org/coracle/index. The underlying code is open-source and available via GitHub https://github.com/SebastianStaab/coracle.git. [ABSTRACT FROM AUTHOR]