Changes In Microbial Communities Research Articles

The application of shrub willow chip organic amendments impacts soil microbial community dynamics.

Incorporating shrub willow chips into soil may improve the chemical, physical and biological properties of soils with low organic matter but the impact on soil microbial communities and their dynamics is not known. We assessed changes in the soil microbial communities in response to willow chip applied at increasing rates (0, 20, 40 and 60 Mg ha-1) in a potato-barley cropping system. Bacterial and fungal community diversity, relative abundance, and potential functions were assessed using amplicon sequencing of 16S and ITS rRNA genes at six time points. High rates (40 and 60 Mg ha-1) of willow chips had no effect on bacterial alpha diversity but significantly decreased fungal alpha diversity (Shannon) while increasing fungal richness (Chao-1). At rates of 40 Mg ha⁻¹ and higher, the relative abundance of copiotrophic bacterial groups increased, while that of copiotrophic fungal groups decreased. The relative abundance of the most dominant microbial phyla and genera varied over time, with copiotrophic groups declining and oligotrophic groups increasing. High willow chip application rates increased bacterial molecular markers related to carbon fixation and degradation, nitrogen fixation, and phosphorus solubilization, while decreasing markers related to cellobiose transport and denitrification. This study demonstrates the ability of willow chips to influence the microbial community composition and potential function over time.

Study of the Relationship Between Nitrogen, Phosphorus Content, and Microbial Community Changes in Deer Manure Compost with Different Conditioners

Composting is an environmentally friendly method for disposing of solid waste. To enhance the fermentation rate and quality of deer manure composting, we investigated the effects of various conditioners (biochar, zeolite, biochar + zeolite) on the aerobic composting process of deer manure. The results indicated that the combination of biochar and zeolite significantly promoted the degradation of organic matter, resulting in a 34.83% decrease in total organic carbon (TOC) content. The addition of biochar was particularly beneficial for nitrogen retention in the compost, with the total nitrogen content reaching its highest level at 39.55 g/kg. Furthermore, the inclusion of zeolite and biochar altered the phosphorus content of the compost, with zeolite demonstrating a more favorable effect. The addition of a conditioner increased the relative abundance of Ascomycota and Proteobacteria and decreased the relative abundance of Firmicutes; the changes in Corynebacterium, Acinetobacter, and Glutamicibacter were positively correlated with the changes in the carbon-to-nitrogen ratio (C/N ratio) and negatively correlated with total nitrogen (TN) and total phosphorus (TP) levels. The mixed conditioner of biochar + zeolite used in composting exhibited low toxicity and the highest degree of decomposition. In summary, the combination of biochar + zeolite as a mixed conditioner is the optimal choice for reducing the toxicity of compost and promoting its maturation. Further research will be conducted in the future to promote the resource utilization of agricultural wastes such as deer manure.

Study on protein hydrolysis and microbial community changes during the fermentation of pork loin ham mediated by electrical stimulation.

This study explored the effect of electrical stimulation (ES) and Pediococcus pentosaceus LL-07 (P. pentosaceus LL-07) and Staphylococcus simulans QB7 (S. simulans QB7) on the quality and microbial community of loin ham during the ripening. After the ES and starter culture treatments, the Aw and pH were decreased. Surface hydrophobicity, myogenic fiber fragmentation index (MFI), TCA-soluble peptide, amino nitrogen and free amino acids (FAAs) were also significantly higher than the control group (CK) (P < 0.05). This increase was more significant in the E-S group (electrical stimulation followed by inoculation with P. pentosaceus LL-07 and S. simulans QB7) than the rest of the experimental group (E、S、S-E group). Furthermore, the CK and E-S groups were subjected to a bacterial community comparison experiment. The microbial diversity of these two groups was increased. Pediococcus spp. and Staphylococcus spp. became the dominant bacteria in E-S groups during the ripening. Correlation analyses show a strong correlation between protein hydrolysis, microorganisms and FAAs. In conclusion, the combination of ES and starter culture could promote protein hydrolysis, the accumulation of FAAS, and improves the bacterial community of loin ham.

Agrivoltaics development progresses: From the perspective of photovoltaic impact on crops, soil ecology and climate.

Agrivoltaics, the simultaneous use of land for both agriculture and photovoltaic (PV) energy production, has gained significant attention as a sustainable land-use strategy. This review investigates the progress of agrivoltaics from the perspective of its impacts on crops, soil ecology, and climate. First, the impacts of agrivoltaic systems on solar radiation were assessed, including soil humidity and, temperature dynamics, while considering the potential for changes in soil microbial communities. Second, how PV panels influence crop growth, yield, and quality through the modification of light distribution, temperature regulation, and soil humidity were explored. Lastly, the challenges and propose recommendations for optimizing the integration of agriculture and PV systems were addressed. This review aims to highlight the benefits and trade-offs of agrivoltaics, offering a roadmap for future research and implementation strategies to enhance the synergy between renewable energy production and sustainable agriculture.

Effect of microbial community on the formation of flavor components in cigar tobacco leaves during air-curing

BackgroundThe air-curing process of cigar tobacco leaves is typically conducted in an open environment, involving the participation of various microorganisms. However, the effect of microbial communities during air-curing process on the formation of flavor components remains unclear. Therefore, this study aims to reveal the dynamics of flavor components and microbial community changes, and explore the potential role of microbial communities in flavor formation during the cigar tobacco air-curing process.ResultsHigh-throughput sequencing analysis showed that Pantoea, Sphingomonas and Pseudomonas were the dominant bacterial genera during air-curing process, while Aspergillus was the dominant fungal genus. Subsequently, volatile flavor analysis shows that alkaloids were the most important volatile compounds in cigar leaves, followed by esters, alcohols and aldehydes. Furthermore, 38 characteristic volatile flavor compounds at different periods of air-curing were identified based on PLS-DA in different periods of air-curing. The correlation analysis between microorganisms and flavor components showed that Pantoea and Staphylococcus might promote the flavor formation from browning to post-air-curing and were positively correlated with specific flavor components like phenylacetaldehyde and acetophenone. Phoma, Mycosphaerella, Wallemia, and Cladosporium were identified as key fungal genera influencing flavor formation, as they showed positive correlations with multiple flavor components. These information enrich our understanding of the flavor formation of cigar tobacco during air curing.ConclusionsThere is a complex correlation between the microbial community and the flavor components, which may have a great influence on the flavor formation during the air-curing process of cigar leaves. Bacterial communities have higher species diversity and richness during air-curing, and have more complex correlation characteristics with volatile flavor, which may play more roles in the flavor formation. This study revealed the potential role of microbial community on flavor formation in cigar tobacco air-curing process, and provided guidance for subsequent screening of specific functional microorganisms to improve and stabilize cigar tobacco flavor.

Microbial Communities in Permafrost, Moraine and Deschampsia antarctica Rhizosphere Soils near Ecology Glacier (King George Island, Maritime Antarctic)

While the recession of glaciers in the Antarctic is of global concern under climate change, the impact of deglaciation on soil microbiomes is still limited. Here, soil samples were collected from permafrost (P), moraine (M) and Deschampsia antarctica rhizosphere (R) soils near Ecology Glacier (Antarctic), and their soil physicochemical properties and microbial communities (bacteria, archaea and fungi) were characterized. Our analyses showed that there were significant differences in the soil properties and microbial communities between the R samples and the P and M samples. Specifically, amplicon sequencing of 16S rDNA revealed high bacterial richness and diversity in the studied soils, which were dominated mainly by the phyla Proteobacteria, Actinobacteriota and Bacteroidota. In contrast, lower richness and diversity were observed in the archaeal communities, which were dominated by the phyla Chenarchaeota (M and R) and Thermoplasmadota (M). In addition, fungal community analysis revealed a lower richness and diversity (M and R), dominated by the phylum Ascomycota. Our observations are consistent with previous reports describing the relevant changes in soil microbial communities during glacial recession, including fewer microbial groups studied in soils (archaea and fungi). However, further studies are still needed to elucidate the contributions of microbial communities to soil formation and plant colonization in ice-free soils in Antarctica under global climate change.

Shifts in fungal communities drive soil profile nutrient cycling during grassland restoration.

Soil microbial diversity and community life strategies are crucial for nutrient cycling during vegetation restoration. Although the changes in topsoil microbial communities during restoration have been extensively studied, the structure, life strategies, and function of microbial communities in the subsoil remain poorly understood, especially regarding their role in nutrient cycling during vegetation restoration. In this study, we conducted a comprehensive investigation of the changes in the soil microbial community, assembly process, life strategies, and nutrient cycling functional genes in soil profiles (0-100 cm) across a 36 year chronosequence (5, 15, 28, and 36 years) of fenced grassland and one grazing grassland on the Loess Plateau of China. Our results revealed that soil organic carbon increased by 76.0% in topsoil and 91.6% in subsoil after 36 years of restoration. The bacterial communities were influenced primarily by soil depth, while the fungal communities were highly sensitive to the years of restoration. Microbes in the subsoil recovered faster, and the microbial community structure and functional genes in the soil profiles gradually became more consistent following restoration. In addition, we observed a transition in microbial life history strategies from a persistent K-strategy to a rapid r-strategy during restoration. Notably, the fungal community assembly process played an important role in changes in nutrient cycling genes, which were accompanied by increased carbon fixation and nitrogen mineralization function. Overall, our findings provide several novel insights into the impact of changes in the fungal community on soil nutrient cycling in the soil profile during vegetation restoration.IMPORTANCEOur study revealed that microbes in the subsoil recovered faster than those in the topsoil, which contributed to the reduction in differences in microbial community structure and the distribution of functional genes throughout the soil profile during the restoration process. Importantly, the assembly of fungal communities plays a pivotal role in driving changes in nutrient cycling genes, such as increased carbon fixation and nitrogen mineralization, alongside a reduction in carbon degradation gene abundance. These alterations increase soil organic carbon and nutrient availability during restoration. Our results increase the understanding of the critical role of fungal communities in soil nutrient cycling genes, which facilitate nutrient accumulation in soil profiles during grassland restoration. This insight can guide the development of strategies for manipulating fungal communities to increase soil nutrients in grasslands.

Variation and assembly mechanisms of Rhinolophus ferrumequinum skin and cave environmental fungal communities during hibernation periods.

Animal skin acts as the barrier against invasion by pathogens and microbial colonizers. Environmental microbiota plays a significant role in shaping these microbial communities, which, in turn, have profound implications for host health. Previous research has focused on characterizing microorganisms on bats' skin and in their roosting environments, particularly bacterial communities. The emergence of white-nose syndrome, caused by the fungal-pathogen Pseudogymnoascus destructans, highlights the importance of understanding fungal dynamics in cave ecosystems and on bats' skin. In this study, we employed ITS amplicon sequencing to investigate the fungal community associated with the skin of Rhinolophus ferrumequinum and surfaces within hibernacula. In addition, we utilized neutral community and null models to assess the relative importance of stochastic and deterministic processes in fungal community assembly. The infection status of P. destructans did not significantly impact fungal community composition either on bat skin or cave environments. However, fungal diversity was significantly higher in cave environments compared to bat skin. Notably, potentially inhibitory genera of fungal pathogens were present in both bats and cave environments during hibernation. Furthermore, the composition and structure of fungal communities on both bat skin and cave environments varied across hibernation periods. Our findings suggest neutral processes primarily drive the assembly of fungal communities associated with hibernating R. ferrumequinum and cave environments, with dispersal limitation exerting a significant influence. This study provides insights into the fungal communities associated with hibernating R. ferrumequinum and cave environments.IMPORTANCEAnimal habitats provide sources and reservoirs for host microorganisms, making it critical to understand changes in microbial communities between habitats and hosts. While most studies have focused on bacterial microorganisms, research on fungal communities is lacking. This study investigated how community dynamics and assembly processes differ between the skin of hibernating Rhinolophus ferrumequinum and the cave environments under pathogen stress. We found significant differences in the composition and structure of the fungal communities between bat skin and roosting cave environments. Fungal genera with potential inhibitory effects on pathogens were found in all bat skin and cave environments. In addition, dispersal limitations during stochastic processes were a key factor in the formation of environmental fungal communities on bat skin and in caves. These findings offer new insights for exploring pathogen-host-environment-microbe interactions.

TSST-1 promotes colonization of Staphylococcus aureus within the vaginal tract by activation of CD8+ T cells.

Toxic shock syndrome toxin-1 (TSST-1) is a superantigen produced by Staphylococcus aureus and is the determinant of menstrual toxic shock syndrome (mTSS); however, the impact of TSST-1 on the vaginal environment beyond mTSS is not understood. Herein, we assessed how TSST-1 affects vaginal colonization by S. aureus, host inflammatory responses, and changes in microbial communities within the murine vagina. We demonstrated that TSST-1 induced a CD8+ T-cell-dependent inflammatory response in 24 h that correlated with S. aureus persistence within the vaginal tract. This increase was due to superantigen-dependent T-cell activation that triggered a change in microbial composition within the vaginal tract. Altogether, this study demonstrates that within the vaginal tract, TSST-1 modulates the vaginal microbiota to favor the survival of S. aureus in the absence of mTSS.IMPORTANCEToxic shock syndrome toxin-1 (TSST-1) is a superantigen toxin produced from Staphylococcus aureus that causes the menstrual form of toxic shock syndrome. This research demonstrates that TSST-1 also has a wider function within the vaginal tract than previously expected. We show that TSST-1, by activating CD8+ T cells, induces an inflammatory environment that modifies the vaginal microbiota to favor colonization by S. aureus. These are important findings as S. aureus can colonize the human vaginal tract efficiently and subsequently trigger dysbiosis within the microbial communities leading to several adverse outcomes such as decreased fertility, increased risks for sexually transmitted diseases, and issues related to pregnancy and birth.

Bacterial and fungal diversity and species interactions inversely affect ecosystem functions under drought in a semi-arid grassland.

Extreme climatic events, such as drought, can significantly alter belowground microbial diversity and species interactions, leading to unknown consequences for ecosystem functioning. Here, we simulated a drought gradient by removing 30 %, 50 %, and 70 % of precipitation in a semi-arid grassland over five years. We assessed the effects of drought on bacterial and fungal diversity, as well as on their species interactions. We also evaluated the impact of drought on ecosystem individual functions (e.g., plant biomass and microbial activity), and on multifunctionality (EMF). Finally, we linked the drought-induced changes in microbial communities with the variations in EMF. Drought significantly increased fungal diversity and intensified species interactions, but it decreased bacterial diversity and species interactions. Both plant and microbial biomass significantly decreased with increasing drought severity, while microbial activity showed the opposite trend. Only the -50 % rainfall treatment notably reduced EMF. Bacterial diversity and species interactions positively correlated with most ecosystem functions. However, fungal parameters were negatively associated with these functions. Structural equation modeling indicated that bacterial diversity had a strong direct positive effect on EMF (standardized path coefficient: 0.52), and that bacterial diversity was indirectly suppressed by drought through decreasing soil water content and bacterial phospholipid fatty acids (PLFAs). In contrast, fungal species interactions had a significant direct negative effect on EMF with the highest standardized path coefficient (-0.6) and were directly enhanced by fungal diversity. Drought had indirect positive effects on fungal diversity by decreasing soil water content and stimulating fungal PLFAs. Our results highlight the importance of considering soil microbial species interactions when evaluating the ecological impacts of drought. Furthermore, the divergent regulatory pathways of bacterial and fungal communities to EMF suggest that improving ecosystem functionality may be achieved by enhancing bacterial diversity while mitigating fungal species interactions through reducing fungal diversity.

P1337 High fat diet drives increased dysbiosis in IBD compared to healthy controls

Abstract Background High fat diets (HFD), consisting of low fibre intake and high fat are associated with increased IBD risk. Industrialised diets have known impacts on host health but also impact the gut microbiota1; known to be altered in IBD. Whilst fat is primarily digested in the upper GI tract excess fat travels to the colon, the hub of microbial activity. In this study, microbial community changes in response to HFD were compared in a healthy and IBD patient donor using in vitro continuous culture chemostats. Methods Stool from a healthy donor and a de novo, treatment naive IBD patient were used to seed independent bioreactors. Standard diet was fed until microbial stabilisation followed by 14 days of HFD. Standard diet was then resumed for a 14-day recovery period. Daily sampling was used to assess changes in microbial composition (16S rRNA amplicon sequencing) and function (short chain fatty acids (SCFA) measured by gas-chromatography mass spectrometry). Results Despite comparable bacterial densities at stability the IBD vessel had higher total SCFA output compared to healthy. SCFA profiles were unique between donors with higher acetate and propionate concentration in the IBD vessel (p&amp;lt;0.0086). Butyrate at stability, however, was higher in the healthy vessel (p=0.025). HFD resulted in a depletion of acetate and propionate in both donors and an increase in isobutyrate, isovalerate, heptanoate and octanoate. Following transfer back to standard diet, the healthy vessel remained depleted of propionate (p= 0.0009) and butyrate remained significantly depleted in the IBD vessel (p= 0.0034) and did not recover (stable: recovery; p&amp;lt;0.0001). Healthy only: HFD significantly lowered microbial (alpha) diversity by observed and Shannon metrics (p&amp;lt;0.034) but was unchanged in Chao1 index. By recovery alpha diversity realigned with the stable phase. Beta diversity showed unique composition across each experimental phase (p&amp;lt;0.02). HFD saw a depletion of Faecalibacterium and Blautia in favour of Escherichia-Shigella and Parasutterella genera. Sequence analysis of the IBD vessel is underway. Conclusion HFD affected both HC and IBD microbial communities; isovalerate and isobutyrate levels increased indicating greater amino acid (protein) metabolism by community members. Higher levels of heptanoate and octanoate are indicative of increased fatty acid degradation. The healthy donor had a more robust recovery with only 5 SCFAs remaining altered. In comparison, 8 metabolites remaining altered in IBD with a dramatic impact on butyrate production highlighting the greater fragility in the IBD microbiome. The findings support the need for further mechanistic understanding of the role of diet and microbial changes in IBD.

P1319 Multi-omic modelling of antibiotic perturbed faecal microbial communities demonstrates reduced microbial resilience in IBD

Abstract Background Excessive antibiotic use is a risk factor in IBD, due to the impact on the gastrointestinal microbiota, but the extent of impact on microbial metabolite production is unknown. Here we investigate the impact of ciprofloxacin (CIP) and metronidazole (MTZ) on gut microbiota structure/function in a healthy donor and a new-onset therapeutic naïve IBD patient. We also investigate the use of autologous faecal microbiota transplant (aFMT) as a microbial therapeutic to assist recovery of the gut ecosystem. Methods Donor faecal specimens (IBD or healthy) were used to inoculate twin chemostat vessels. Following community stabilisation, vessels were dosed daily with CIP or MTZ for 7 days. In the healthy donor vessel, 4 doses of aFMT were administered over 7 days (post antibiotics) followed by a 7-day recovery. In the IBD vessels no FMT was administered. Vessels were sampled daily to monitor microbial profiles (16S rRNA sequencing) and short chain fatty acid (SCFA) profiles (GC-MS). Results CIP in the healthy vessel caused a significant depletion of acetate, butyrate and propionate, remaining significantly depleted during aFMT. CIP dosing also resulted in an enrichment of Escherichia-Shigella and Enterobacter and a loss of Akkermansia, Faecalibacterium and Bacteroides. During recovery acetate and propionate recovered whilst butyrate remained depleted (p=0.004). In the healthy MTZ vessel, acetate increased during antibiotic dosing and was restored following aFMT. Butyrate decreased during MTZ dosing and remained significantly decreased (p&amp;lt;0.031). Propionate levels also reduced following MTZ but were found in highest abundance during aFMT and recovery phases (p&amp;lt;0.038). Parabacteroides increased during MTZ dosing which subsequently decreased to stable abundance. Akkermansia was significantly increased in recovery phase compared to aFMT and stability phases. In the IBD donor, CIP caused a significant reduction in 10 SCFAs and several taxa including Bacteroides and Dialister genera alongside an enrichment of Enterococcus, Lachnospiraceae, Anaerofilum and Eisenbergiella. MTZ treatment resulted in a less dramatic reduction in SCFAs. Microbial community changes included an enrichment of Escherichia-Shigella, Enterococcus and Parasutterella and a depletion of Alistipes and Dialister. Conclusion CIP and MTZ significantly depleted levels of beneficial genera and reduced the abundance of SCFAs. Neither donor community was able to fully restore composition or function. aFMT modulated the healthy donor microbial communities to a "new healthy". Further investigation into long-term antibiotic treatment and the use of microbial therapeutics is needed to fully understand this relationship in the context of IBD.

Characterization of microbial communities in flavors and fragrances during storage

Flavors and fragrances are essential for product quality, yet they are highly susceptible to contamination due to high moisture content and rich nutrients. This study investigates microbial growth, pH changes, volatile compound dynamics, and microbial community changes during the storage of flavors and fragrances. Results indicate that total viable counts (TVC) remained stable for the first three days but increased rapidly afterward, exceeding the acceptable limit of 5 log CFU/mL by day 7. The pH levels initially rose slightly, followed by a steady decline, which indicates spoilage progression. Gas chromatography–mass spectrometry (GC–MS) analysis revealed significant degradation of key aromatic compounds, such as 5-hydroxymethylfurfural (5-HMF), vanillin, and its derivative ethyl vanillin. Whole genome shotgun (WGS) sequencing demonstrated a marked increase in microbial community richness and diversity as storage progressed, with a notable shift in composition. Early storage stages were dominated by fungal species from the Ascomycota phylum, while later stages saw a rise in spoilage-associated bacteria, particularly from the Firmicutes and Proteobacteria phyla. Throughout the storage process, Zygosaccharomyces and its dominant species, Zygosaccharomyces bailii, remained prevalent, though their average relative abundance decreased from 81.26 to 32.29%. In addition, the bacterial species Oceanobacillus sojae and Niallia nealsonii showed significant increases in relative abundance, suggesting that bacteria were one of the key contributors to the spoilage of flavors and fragrances. Functional analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database indicated a shift in metabolic pathways within the microbial community, with heightened metabolic activity correlating with spoilage. These findings provide valuable insights for improving storage methods and quality control of flavors and fragrances.

Dynamic changes in the gastrointestinal microbial communities of Gangba sheep and analysis of their functions in plant biomass degradation at high altitude

BackgroundWhile Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestinal tract microbiota plays an important role in host nutrient absorption and metabolism. The identification of dynamic changes in the gastrointestinal microbial communities and their functions is an important step towards improving animal production performance and health.ResultsA comprehensive multi-omics survey of the microbial communities of the Gangba sheep gastrointestinal tract was performed under three distinct feeding strategies: natural grazing, semi-grazing with supplementation, and barn feeding. The dynamic changes, cross-kingdom partnerships and functional potential profiles were analysed and the results revealed that the feeding strategies had a greater impact on the microbial communities than the site of the gastrointestinal tract. The different microbial associations among the groups were revealed by co-occurrence networks based on the amplicon sequence variants (ASVs). Moreover, a Gangba sheep gastrointestinal microbial genomic catalogue was constructed for the first time, including 1146 metagenome-assembled genomes (MAGs) with completeness > 50% and contamination < 10%, among which, 504 bacterial and 15 archaeal MAGs were of high quality with completeness > 80% and contamination < 10%. About 40% of the high-quality MAGs displaying enzyme activity were related to the microbial species that contribute to plant biomass degradation. Most of these enzymes were expressed in rumen metatranscriptome datasets, especially in Prevotella spp. and Ruminococcus spp., suggesting that gastrointestinal microbial communities in ruminants play major roles in the digestion of plant biomass to provide nutrition and energy for the host.ConclusionsThese findings suggest that feeding strategies are the primary cause of changes in the gastrointestinal microbiome. Diversification of livestock feed might be an effective strategy to maintain the diversity and ecological multifunctionality of microbial communities in the gastrointestinal tract. Additionally, the catalogue of microbial genomes and the encoded biomass-degrading enzymes identified here provide insights into the potential microbial functions of the gastrointestinal tract of Gangba sheep at high altitudes. This paves the way for microbial interventions to improve the growth performance, productivity and product quality of ruminant livestock.Eyk4xgS_hcbJW5EurPGBJ5Video

Long-term rice-crab coculturing leads to changes in soil microbial communities

Long-term rice-crab coculturing leads to changes in soil microbial communities

Soil microbes influence the ecology and evolution of plant plasticity.

Stress often induces plant trait plasticity, and microbial communities also alter plant traits. Therefore, it is unclear how much plasticity results from direct plant responses to stress vs indirect responses due to stress-induced changes in soil microbial communities. To test how microbes and microbial community responses to stress affect the ecology and potentially the evolution of plant plasticity, I grew plants in four stress environments (salt, herbicide, herbivory, and no stress) with microbes that had responded to these same environments or with sterile inoculant. Plants delayed flowering under stress only when inoculated with live microbial communities, and this plasticity was maladaptive. However, microbial communities responded to stress in ways that accelerated flowering across all environments. Microbes also affected the expression of genetic variation for plant flowering time and specific leaf area, as well as genetic variation for plasticity of both traits, and disrupted a positive genetic correlation for plasticity in response to herbicide and herbivory stress, suggesting that microbes may affect the pace of plant evolution. Together, these results highlight an important role for soil microbes in plant plastic responses to stress and suggest that microbes may alter the evolution of plant plasticity.

Degradation dynamics of Trifluralin in Qinghai-Tibet Plateau and screening of its degrading strains.

Trifluralin (FLL) is extensively used in rapeseed fields in the Qinghai-Tibet Plateau (QTP) region. However, the degradation kinetics of FLL in this area and its impact on environmental microbial communities are not yet known. To investigate the degradation patterns and ecological benefits of FLL, this study established a comprehensive method for detecting FLL residues and selected efficient degrading bacterial strains. Degradation experiments were conducted in two typical soil types of the QTP, and the dynamic changes in microbial communities were explored. The results indicated that FLL degradation in soils from two different regions of the QTP followed first-order kinetics, with half-lives of 25 and 39 days, respectively. The application of FLL at 173g/ha significantly increased bacterial richness and diversity in the soils of both regions. Three efficient degrading strains were selected from soil samples: FL-3 (Bacillus velezensis) with a degradation rate of 80.81%, FL-5 (Bacillus velezensis) at 51.18%, and FL-6 (Pseudomonas atacamensis) at 49.98%. Moreover, the optimal degradation conditions for these strains were determined, and it was verified that they had no adverse effects on the germination and seedling growth of rapeseed, wheat, and barley. The findings of this study provide important data for the environmental risk assessment of FLL and suggest potential biological resources for the rational use and environmental remediation of this herbicide. These results are significant for developing safe use and environmental management strategies for FLL in the QTP.

Two decades of bacterial ecology and evolution in a freshwater lake.

Ecology and evolution are considered distinct processes that interact on contemporary time scales in microbiomes. Here, to observe these processes in a natural system, we collected a two-decade, 471-metagenome time series from Lake Mendota (Wisconsin, USA). We assembled 2,855 species-representative genomes and found that genomic change was common and frequent. By tracking strain composition via single nucleotide variants, we identified cyclical seasonal patterns in 80% and decadal shifts in 20% of species. In the dominant freshwater family Nanopelagicaceae, environmental extremes coincided with shifts in strain composition and positive selection of amino acid and nucleic acid metabolism genes. These genes identify organic nitrogen compounds as potential drivers of freshwater responses to global change. Seasonal and long-term strain dynamics could be regarded as ecological processes or, equivalently, as evolutionary change. Rather than as distinct interacting processes, we propose a conceptualization of ecology and evolution as a continuum to better describe change in microbial communities.

Breeding-induced changes in the rhizosphere microbial communities in Lima bean (Phaseolus lunatus)

Lima bean (Phaseolus lunatus L.) breeding aims to select more productive and uniform plant varieties, impacting various plant traits, including root characters. Changes in root traits have repercussions on the rhizosphere, thereby influencing the composition of rhizospheric microbial communities. In this study, we assessed the structure and composition of the microbial community through 16S rRNA sequencing to compare the rhizosphere of different genotypes during lima bean breeding. Specifically, we compared the rhizospheric microbial communities of two parents (P1 - UFPI 628 and P2 – G25276, from Brazil and Argentina, respectively) and their segregation generations (F2 and F7). The microbial richness and diversity remained consistent across all genotypes, while the structure of the microbial community differed between parents (P1 and P2) and the advanced lineage (F7). We observed genotype-specific enrichment of bacterial groups, indicating a nuanced interaction between lima bean genotypes and microbial communities. Moreover, segregating generations exhibited unique enrichment of bacterial families associated with plant growth promotion, such as Pedosphaeraceae (F2) and Xanthobacteraceae (F7). Analysis of microbial interactions revealed an alteration in network complexity, with advanced lineages, particularly F7, displaying a higher number of interactions. Despite taxonomic differences across generations, functional traits remained consistent between parents and advanced lineages. These findings offer valuable insights into optimizing plant-microbe interactions to enhance lima bean yield in breeding programs. By understanding the dynamics of rhizospheric microbial communities in response to breeding efforts, we can harness beneficial interactions to improve plant performance and sustainability in agricultural systems.

Initial abiotic factors as key drivers in core microbe assembly: Regulatory effects on flavor profiles in light-flavor baijiu

Instability in initial abiotic factors of open solid-state fermentation systems can significantly alter Baijiu's flavor profile, but the mechanisms governing microbial interactions and flavor formation remain unclear. This study comprehensively monitored changes in abiotic factors, microbial communities, and flavor profiles across two distinct fermentation processes in a Baijiu distillery, which differed significantly in their management of initial abiotic factors. Our results revealed significant differences in abiotic factors between the two groups, including moisture, ethanol, acidity, glucose, and organic acid levels. The assembly of microbial communities in fermented grains was primarily driven by deterministic processes. The moisture content in the fermentation grains positively affected the growth and metabolism of core microbiota. The rapid proliferation and metabolism of core microbes led to a rapid increase in the acidity of the fermented grains, alongside a significant accumulation of ethyl lactate. This study provides technical support and theoretical guidance for Baijiu production.